Query psy16564
Match_columns 157
No_of_seqs 119 out of 1099
Neff 5.6
Searched_HMMs 46136
Date Sat Aug 17 00:24:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3406|consensus 99.9 5.1E-27 1.1E-31 177.1 11.2 108 32-139 15-122 (134)
2 PRK01018 50S ribosomal protein 99.9 3E-26 6.5E-31 167.0 12.7 95 33-143 2-97 (99)
3 TIGR03677 rpl7ae 50S ribosomal 99.9 3.6E-26 7.9E-31 171.1 12.9 108 23-144 1-108 (117)
4 PRK04175 rpl7ae 50S ribosomal 99.9 2.3E-25 5E-30 168.0 13.1 98 35-143 14-111 (122)
5 PTZ00106 60S ribosomal protein 99.9 2.1E-25 4.5E-30 165.2 12.3 93 39-143 13-106 (108)
6 PRK07283 hypothetical protein; 99.9 6E-25 1.3E-29 159.7 12.4 96 33-143 1-96 (98)
7 PRK07714 hypothetical protein; 99.9 3.4E-24 7.3E-29 156.0 12.4 97 33-143 1-97 (100)
8 COG1358 RPL8A Ribosomal protei 99.9 6.4E-24 1.4E-28 159.2 11.5 98 34-143 10-107 (116)
9 PRK05583 ribosomal protein L7A 99.9 8.5E-23 1.8E-27 150.3 12.2 95 36-144 3-97 (104)
10 PF01248 Ribosomal_L7Ae: Ribos 99.9 4.2E-23 9.1E-28 147.2 9.7 94 37-141 1-94 (95)
11 PRK06683 hypothetical protein; 99.9 9.1E-22 2E-26 139.3 10.9 78 44-133 4-81 (82)
12 PRK13602 putative ribosomal pr 99.9 1.1E-21 2.4E-26 138.7 10.9 75 47-133 7-81 (82)
13 COG1911 RPL30 Ribosomal protei 99.8 1.6E-20 3.4E-25 136.3 10.5 95 32-142 4-99 (100)
14 PRK13601 putative L7Ae-like ri 99.8 2.8E-20 6.2E-25 131.8 9.6 73 49-133 6-78 (82)
15 PRK13600 putative ribosomal pr 99.8 5.2E-20 1.1E-24 131.1 9.7 72 50-133 12-83 (84)
16 PRK09190 hypothetical protein; 99.8 1.4E-18 3E-23 142.8 11.3 98 35-145 95-198 (220)
17 PTZ00222 60S ribosomal protein 99.8 8.7E-19 1.9E-23 146.2 7.9 93 52-156 133-225 (263)
18 KOG3167|consensus 99.7 4.6E-18 1E-22 130.6 8.2 104 20-136 30-133 (153)
19 PTZ00365 60S ribosomal protein 99.7 1.1E-16 2.3E-21 134.1 7.0 92 52-155 133-224 (266)
20 KOG3387|consensus 99.7 3.9E-16 8.4E-21 118.2 8.2 91 19-111 4-94 (131)
21 KOG2988|consensus 99.3 3.7E-11 7.9E-16 89.1 8.9 95 41-147 16-111 (112)
22 KOG3166|consensus 97.5 2.3E-05 5E-10 64.3 0.4 79 52-156 110-188 (209)
23 PF08228 RNase_P_pop3: RNase P 97.3 0.0054 1.2E-07 48.5 11.0 81 51-143 55-146 (158)
24 PF03465 eRF1_3: eRF1 domain 3 96.6 0.012 2.6E-07 43.6 7.5 74 37-110 6-98 (113)
25 PF15608 PELOTA_1: PELOTA RNA 95.8 0.053 1.1E-06 40.0 7.1 62 39-102 22-88 (100)
26 PF08032 SpoU_sub_bind: RNA 2' 95.8 0.049 1.1E-06 36.3 6.5 60 52-113 1-61 (76)
27 TIGR00108 eRF peptide chain re 94.5 0.3 6.5E-06 43.7 9.2 65 46-110 287-392 (409)
28 PRK04011 peptide chain release 93.8 0.37 7.9E-06 43.2 8.4 73 38-110 282-396 (411)
29 TIGR03676 aRF1/eRF1 peptide ch 93.8 0.56 1.2E-05 41.9 9.5 64 47-110 284-388 (403)
30 TIGR00111 pelota probable tran 93.7 0.43 9.2E-06 41.8 8.4 73 38-110 263-337 (351)
31 PF10087 DUF2325: Uncharacteri 93.2 0.34 7.3E-06 34.4 5.9 54 57-110 36-93 (97)
32 PRK11181 23S rRNA (guanosine-2 85.9 8.1 0.00018 32.0 9.2 60 51-112 3-64 (244)
33 PRK10864 putative methyltransf 85.8 8.8 0.00019 33.9 9.7 68 43-113 101-170 (346)
34 cd01422 MGS Methylglyoxal synt 85.6 2.8 6.2E-05 30.8 5.7 47 54-100 57-107 (115)
35 TIGR00679 hpr-ser Hpr(Ser) kin 83.0 6.4 0.00014 34.2 7.5 52 58-112 73-125 (304)
36 TIGR00186 rRNA_methyl_3 rRNA m 82.7 13 0.00027 30.6 8.9 57 52-113 3-60 (237)
37 PF02603 Hpr_kinase_N: HPr Ser 80.8 3.8 8.3E-05 30.6 4.8 41 58-101 72-112 (127)
38 COG1537 PelA Predicted RNA-bin 80.5 11 0.00024 33.4 8.3 72 40-111 260-338 (352)
39 cd00532 MGS-like MGS-like doma 80.0 4.6 0.0001 29.2 4.9 46 55-100 55-105 (112)
40 PF02142 MGS: MGS-like domain 78.5 2.8 6.1E-05 29.4 3.3 42 58-99 51-95 (95)
41 PRK05234 mgsA methylglyoxal sy 77.1 6.7 0.00015 30.1 5.2 56 55-110 63-123 (142)
42 PF13727 CoA_binding_3: CoA-bi 75.9 3.6 7.8E-05 30.5 3.4 48 54-101 128-175 (175)
43 COG0159 TrpA Tryptophan syntha 75.8 19 0.00042 30.7 8.1 101 23-133 53-183 (265)
44 KOG4175|consensus 75.1 14 0.00031 31.0 6.9 86 23-112 54-170 (268)
45 PF07997 DUF1694: Protein of u 74.6 11 0.00025 28.2 5.8 47 57-104 52-98 (120)
46 smart00851 MGS MGS-like domain 73.6 7.2 0.00016 26.9 4.3 47 52-98 40-89 (90)
47 TIGR01544 HAD-SF-IE haloacid d 73.1 6.7 0.00015 33.5 4.7 36 21-56 68-104 (277)
48 cd01424 MGS_CPS_II Methylglyox 72.0 12 0.00026 26.6 5.3 45 55-99 55-100 (110)
49 PF13344 Hydrolase_6: Haloacid 72.0 8.8 0.00019 27.3 4.5 47 50-98 13-59 (101)
50 PF07085 DRTGG: DRTGG domain; 71.7 12 0.00026 26.5 5.1 72 31-110 27-102 (105)
51 COG0050 TufB GTPases - transla 67.0 7 0.00015 34.7 3.6 40 64-104 98-138 (394)
52 PF03618 Kinase-PPPase: Kinase 65.6 30 0.00065 29.3 7.1 44 71-115 55-100 (255)
53 PLN02591 tryptophan synthase 65.4 46 0.001 27.9 8.1 88 23-113 38-154 (250)
54 COG1503 eRF1 Peptide chain rel 65.2 38 0.00083 30.8 8.0 64 48-111 292-395 (411)
55 COG0566 SpoU rRNA methylases [ 63.2 74 0.0016 26.6 9.0 59 51-112 22-81 (260)
56 PRK14722 flhF flagellar biosyn 63.2 17 0.00036 32.4 5.3 62 66-138 166-227 (374)
57 cd01483 E1_enzyme_family Super 63.0 15 0.00031 27.2 4.3 35 66-102 88-122 (143)
58 TIGR03025 EPS_sugtrans exopoly 62.4 22 0.00049 31.4 6.0 53 55-107 176-228 (445)
59 PF00009 GTP_EFTU: Elongation 62.3 15 0.00033 28.2 4.4 48 58-105 86-133 (188)
60 COG1168 MalY Bifunctional PLP- 62.0 6.5 0.00014 35.4 2.5 88 9-101 105-198 (388)
61 cd01857 HSR1_MMR1 HSR1/MMR1. 61.2 22 0.00047 26.2 4.9 50 57-106 3-54 (141)
62 PLN02821 1-hydroxy-2-methyl-2- 60.9 20 0.00044 32.9 5.5 50 58-108 353-402 (460)
63 PF07905 PucR: Purine cataboli 59.9 28 0.0006 25.5 5.3 48 60-108 65-113 (123)
64 cd01020 TroA_b Metal binding p 59.9 29 0.00062 28.7 5.9 21 81-101 193-213 (264)
65 TIGR03023 WcaJ_sugtrans Undeca 58.7 28 0.0006 30.9 5.9 55 53-107 177-231 (451)
66 cd03420 SirA_RHOD_Pry_redox Si 58.3 27 0.00059 23.1 4.6 38 60-101 20-57 (69)
67 PF13241 NAD_binding_7: Putati 55.3 15 0.00032 26.1 3.0 34 67-102 60-93 (103)
68 TIGR02342 chap_CCT_delta T-com 54.8 35 0.00076 31.1 6.1 56 57-112 263-321 (517)
69 PRK09590 celB cellobiose phosp 54.7 23 0.00049 25.9 4.0 46 54-101 37-82 (104)
70 PRK06552 keto-hydroxyglutarate 54.1 57 0.0012 26.6 6.6 74 30-111 43-127 (213)
71 PF13611 Peptidase_S76: Serine 53.4 21 0.00044 27.2 3.6 29 73-102 30-58 (121)
72 cd04165 GTPBP1_like GTPBP1-lik 52.9 33 0.00072 27.8 5.1 49 58-106 100-150 (224)
73 PF15632 ATPgrasp_Ter: ATP-gra 52.5 50 0.0011 28.9 6.4 56 52-108 7-81 (329)
74 PF02401 LYTB: LytB protein; 52.3 49 0.0011 28.3 6.2 53 57-111 200-253 (281)
75 PRK13371 4-hydroxy-3-methylbut 52.1 40 0.00086 30.4 5.8 51 57-108 278-328 (387)
76 COG1419 FlhF Flagellar GTP-bin 52.1 42 0.00091 30.4 6.0 50 64-113 230-279 (407)
77 TIGR01182 eda Entner-Doudoroff 51.8 39 0.00085 27.6 5.3 72 32-111 40-119 (204)
78 TIGR03499 FlhF flagellar biosy 51.4 57 0.0012 27.4 6.4 47 66-112 223-269 (282)
79 PF10686 DUF2493: Protein of u 51.2 63 0.0014 21.9 5.5 44 57-101 21-64 (71)
80 PF00205 TPP_enzyme_M: Thiamin 51.1 11 0.00024 27.6 1.8 46 56-101 1-46 (137)
81 KOG4201|consensus 51.1 49 0.0011 28.2 5.8 73 51-137 144-217 (289)
82 cd03017 PRX_BCP Peroxiredoxin 50.7 55 0.0012 23.3 5.5 49 60-113 50-99 (140)
83 PRK06015 keto-hydroxyglutarate 50.6 39 0.00085 27.5 5.1 75 30-111 34-115 (201)
84 PRK05339 PEP synthetase regula 50.4 77 0.0017 27.1 7.0 50 71-121 61-112 (269)
85 cd03338 TCP1_delta TCP-1 (CTT 49.9 49 0.0011 30.0 6.2 56 57-112 262-320 (515)
86 cd00755 YgdL_like Family of ac 49.7 38 0.00082 27.9 5.0 39 61-101 96-134 (231)
87 PRK11018 hypothetical protein; 49.6 44 0.00096 22.8 4.6 38 60-101 29-66 (78)
88 cd01485 E1-1_like Ubiquitin ac 49.2 27 0.00058 27.8 3.9 34 67-102 113-146 (198)
89 TIGR03729 acc_ester putative p 48.9 60 0.0013 26.1 6.0 45 57-101 22-68 (239)
90 COG1493 HprK Serine kinase of 48.7 70 0.0015 28.0 6.6 52 56-110 70-122 (308)
91 PF13407 Peripla_BP_4: Peripla 48.5 53 0.0012 25.7 5.5 42 60-103 48-89 (257)
92 cd03339 TCP1_epsilon TCP-1 (CT 48.4 58 0.0012 29.8 6.4 48 59-111 279-329 (526)
93 PF00899 ThiF: ThiF family; I 47.8 23 0.0005 25.9 3.1 64 34-101 56-124 (135)
94 TIGR02339 thermosome_arch ther 47.1 58 0.0013 29.7 6.2 49 58-111 273-321 (519)
95 PRK05703 flhF flagellar biosyn 46.6 60 0.0013 29.1 6.1 48 65-112 249-296 (424)
96 COG1648 CysG Siroheme synthase 46.4 23 0.00051 28.9 3.2 35 68-104 73-107 (210)
97 TIGR02343 chap_CCT_epsi T-comp 46.4 54 0.0012 30.1 5.9 47 60-111 284-333 (532)
98 cd00757 ThiF_MoeB_HesA_family 46.4 33 0.00071 27.7 4.1 34 67-102 111-144 (228)
99 TIGR00315 cdhB CO dehydrogenas 46.3 57 0.0012 25.7 5.3 46 56-101 17-62 (162)
100 PRK05428 HPr kinase/phosphoryl 46.1 65 0.0014 28.1 6.1 42 57-101 72-113 (308)
101 COG1105 FruK Fructose-1-phosph 44.8 1.2E+02 0.0025 26.6 7.4 49 56-113 148-196 (310)
102 PRK10124 putative UDP-glucose 44.8 61 0.0013 29.3 5.9 53 55-107 191-243 (463)
103 TIGR00789 flhB_rel flhB C-term 44.8 34 0.00074 24.0 3.4 35 72-111 20-54 (82)
104 cd01028 TOPRIM_TopoIA TOPRIM_T 44.4 74 0.0016 23.8 5.5 56 55-110 76-139 (142)
105 PF11823 DUF3343: Protein of u 44.2 36 0.00078 22.7 3.4 31 83-113 14-44 (73)
106 COG2099 CobK Precorrin-6x redu 43.7 53 0.0011 28.1 5.0 59 54-112 53-126 (257)
107 PRK15116 sulfur acceptor prote 43.6 59 0.0013 27.6 5.3 38 62-101 116-153 (268)
108 cd01492 Aos1_SUMO Ubiquitin ac 43.3 41 0.00088 26.8 4.1 34 67-102 110-143 (197)
109 cd04195 GT2_AmsE_like GT2_AmsE 43.1 93 0.002 23.2 6.0 40 71-110 32-72 (201)
110 TIGR02356 adenyl_thiF thiazole 43.1 40 0.00087 26.8 4.1 35 66-102 110-144 (202)
111 KOG2486|consensus 43.1 29 0.00063 30.4 3.4 42 64-105 216-259 (320)
112 PRK08057 cobalt-precorrin-6x r 42.8 70 0.0015 26.7 5.6 47 55-101 53-99 (248)
113 COG0240 GpsA Glycerol-3-phosph 42.7 1.1E+02 0.0023 27.0 6.9 122 16-156 40-177 (329)
114 cd03361 TOPRIM_TopoIA_RevGyr T 42.4 89 0.0019 24.4 5.9 57 54-110 103-167 (170)
115 COG0796 MurI Glutamate racemas 42.3 71 0.0015 27.4 5.6 45 61-111 62-106 (269)
116 PRK13111 trpA tryptophan synth 42.0 2.1E+02 0.0045 24.0 9.0 58 54-113 104-165 (258)
117 cd01879 FeoB Ferrous iron tran 41.5 73 0.0016 22.7 5.0 42 66-107 73-114 (158)
118 PRK00865 glutamate racemase; P 41.2 1.3E+02 0.0028 24.9 7.0 41 58-101 58-98 (261)
119 PF05822 UMPH-1: Pyrimidine 5' 40.5 2.5 5.4E-05 35.7 -3.4 70 23-101 39-113 (246)
120 PRK06512 thiamine-phosphate py 40.2 1.4E+02 0.003 24.4 6.9 53 59-112 32-88 (221)
121 PF02571 CbiJ: Precorrin-6x re 40.1 74 0.0016 26.6 5.4 47 55-101 54-100 (249)
122 PRK12723 flagellar biosynthesi 40.1 76 0.0016 28.3 5.7 46 67-112 206-251 (388)
123 cd01493 APPBP1_RUB Ubiquitin a 39.9 44 0.00095 30.2 4.2 39 67-107 112-150 (425)
124 TIGR01766 tspaseT_teng_C trans 39.8 37 0.0008 22.7 2.9 26 77-102 53-78 (82)
125 TIGR00853 pts-lac PTS system, 39.8 40 0.00087 23.9 3.2 46 53-102 38-83 (95)
126 cd01018 ZntC Metal binding pro 39.7 78 0.0017 26.1 5.4 48 52-101 173-224 (266)
127 cd01491 Ube1_repeat1 Ubiquitin 39.6 40 0.00087 28.9 3.7 41 67-109 105-145 (286)
128 COG1707 ACT domain-containing 39.1 90 0.002 25.6 5.4 74 53-144 123-200 (218)
129 cd03343 cpn60 cpn60 chaperonin 39.1 92 0.002 28.3 6.2 48 58-110 270-317 (517)
130 cd01822 Lysophospholipase_L1_l 39.1 95 0.0021 22.8 5.4 45 56-100 90-141 (177)
131 PRK00945 acetyl-CoA decarbonyl 38.6 89 0.0019 24.9 5.3 46 57-102 25-71 (171)
132 PRK13957 indole-3-glycerol-pho 38.5 1.9E+02 0.0042 24.3 7.6 74 51-138 109-183 (247)
133 COG0420 SbcD DNA repair exonuc 38.5 89 0.0019 27.1 5.8 44 57-101 30-82 (390)
134 PF01297 TroA: Periplasmic sol 38.3 59 0.0013 26.3 4.5 20 82-101 187-206 (256)
135 PF01081 Aldolase: KDPG and KH 38.3 64 0.0014 26.1 4.6 71 33-111 41-119 (196)
136 PF00072 Response_reg: Respons 37.8 84 0.0018 20.9 4.6 67 35-101 10-78 (112)
137 TIGR02355 moeB molybdopterin s 37.7 43 0.00093 27.6 3.5 34 66-101 113-146 (240)
138 COG0352 ThiE Thiamine monophos 37.7 1.1E+02 0.0025 25.0 6.0 57 56-113 24-83 (211)
139 cd01821 Rhamnogalacturan_acety 37.6 86 0.0019 23.9 5.1 22 81-102 133-154 (198)
140 PF08862 DUF1829: Domain of un 37.6 55 0.0012 23.0 3.6 40 61-101 47-86 (88)
141 PRK09437 bcp thioredoxin-depen 37.1 94 0.002 22.8 5.1 51 58-113 55-106 (154)
142 PRK05690 molybdopterin biosynt 37.0 40 0.00086 27.8 3.2 34 67-102 122-155 (245)
143 CHL00073 chlN photochlorophyll 36.9 57 0.0012 29.9 4.5 42 61-102 91-136 (457)
144 cd03018 PRX_AhpE_like Peroxire 36.5 1.3E+02 0.0027 21.7 5.6 50 59-113 54-106 (149)
145 PF00578 AhpC-TSA: AhpC/TSA fa 36.4 1.4E+02 0.0031 20.5 6.2 53 56-113 48-101 (124)
146 PRK12360 4-hydroxy-3-methylbut 36.3 72 0.0016 27.4 4.8 51 58-110 201-252 (281)
147 cd01894 EngA1 EngA1 subfamily. 36.1 96 0.0021 21.9 4.8 22 85-106 96-117 (157)
148 PF00290 Trp_syntA: Tryptophan 36.1 2.7E+02 0.0058 23.5 8.4 87 23-112 46-162 (259)
149 cd02968 SCO SCO (an acronym fo 36.0 1.6E+02 0.0034 20.9 6.1 47 66-113 58-108 (142)
150 cd03770 SR_TndX_transposase Se 35.7 77 0.0017 23.5 4.4 49 54-102 55-107 (140)
151 TIGR03022 WbaP_sugtrans Undeca 35.5 90 0.002 27.6 5.5 55 53-107 174-229 (456)
152 cd01423 MGS_CPS_I_III Methylgl 35.4 49 0.0011 23.7 3.2 42 57-98 61-105 (116)
153 PRK06153 hypothetical protein; 35.3 75 0.0016 28.7 4.9 39 66-106 265-303 (393)
154 COG1436 NtpG Archaeal/vacuolar 35.3 1.4E+02 0.003 21.9 5.6 45 57-102 36-81 (104)
155 TIGR03603 cyclo_dehy_ocin bact 35.3 61 0.0013 28.0 4.2 35 66-100 150-184 (318)
156 TIGR01470 cysG_Nterm siroheme 35.0 57 0.0012 26.2 3.8 36 67-104 69-104 (205)
157 PF00462 Glutaredoxin: Glutare 34.4 1E+02 0.0022 19.1 4.2 40 61-101 17-56 (60)
158 cd01017 AdcA Metal binding pro 34.4 1E+02 0.0022 25.5 5.4 51 50-101 171-227 (282)
159 PRK13010 purU formyltetrahydro 34.3 94 0.002 26.6 5.2 44 52-101 99-148 (289)
160 PRK00124 hypothetical protein; 34.2 63 0.0014 25.4 3.8 30 71-102 3-32 (151)
161 cd03362 TOPRIM_TopoIA_TopoIII 34.0 1.3E+02 0.0028 22.8 5.4 56 55-110 84-148 (151)
162 COG1880 CdhB CO dehydrogenase/ 33.9 1.1E+02 0.0024 24.6 5.1 43 59-101 28-70 (170)
163 COG4148 ModC ABC-type molybdat 33.9 87 0.0019 27.8 4.9 77 34-112 108-198 (352)
164 PF04705 TSNR_N: Thiostrepton- 33.9 44 0.00095 25.0 2.7 65 35-102 15-81 (115)
165 cd03334 Fab1_TCP TCP-1 like do 33.7 1.6E+02 0.0034 24.5 6.4 50 56-110 119-168 (261)
166 PRK05718 keto-hydroxyglutarate 33.1 2E+02 0.0044 23.4 6.7 71 33-111 48-126 (212)
167 cd03363 TOPRIM_TopoIA_TopoI TO 32.9 1.2E+02 0.0027 22.3 5.1 44 66-110 71-120 (123)
168 PF05159 Capsule_synth: Capsul 32.7 70 0.0015 26.1 4.0 30 71-102 3-32 (269)
169 COG0800 Eda 2-keto-3-deoxy-6-p 32.7 77 0.0017 26.3 4.2 72 32-110 45-123 (211)
170 KOG1615|consensus 32.5 1.4E+02 0.003 25.0 5.6 79 29-112 54-148 (227)
171 TIGR00715 precor6x_red precorr 32.4 95 0.0021 26.0 4.8 46 56-101 54-99 (256)
172 cd03769 SR_IS607_transposase_l 32.0 1.1E+02 0.0023 22.8 4.6 47 54-101 49-97 (134)
173 PF02421 FeoB_N: Ferrous iron 31.8 1.2E+02 0.0025 23.7 4.9 53 60-112 71-123 (156)
174 PRK13011 formyltetrahydrofolat 31.4 1.2E+02 0.0026 25.8 5.4 39 57-101 104-144 (286)
175 TIGR00160 MGSA methylglyoxal s 31.3 1E+02 0.0022 24.1 4.4 50 49-101 56-111 (143)
176 PRK11889 flhF flagellar biosyn 31.2 1.5E+02 0.0033 27.2 6.2 45 67-111 269-313 (436)
177 cd03027 GRX_DEP Glutaredoxin ( 31.1 1.5E+02 0.0032 19.1 4.8 31 82-112 13-49 (73)
178 cd04188 DPG_synthase DPG_synth 31.1 85 0.0018 23.9 4.1 41 67-108 30-70 (211)
179 TIGR01295 PedC_BrcD bacterioci 31.0 1.5E+02 0.0032 21.6 5.2 53 50-102 7-61 (122)
180 PRK08328 hypothetical protein; 31.0 80 0.0017 25.7 4.1 34 67-102 118-151 (231)
181 KOG3849|consensus 30.8 79 0.0017 27.9 4.1 34 66-101 298-331 (386)
182 KOG0362|consensus 30.7 96 0.0021 29.1 4.9 57 51-112 262-322 (537)
183 PLN02331 phosphoribosylglycina 30.6 1.2E+02 0.0026 24.6 5.0 42 57-102 14-57 (207)
184 PRK05562 precorrin-2 dehydroge 30.6 58 0.0013 26.9 3.2 35 67-103 85-119 (223)
185 PF00218 IGPS: Indole-3-glycer 30.4 1.8E+02 0.004 24.4 6.2 76 50-139 115-191 (254)
186 PRK00766 hypothetical protein; 30.2 1.2E+02 0.0025 24.7 4.9 48 65-112 69-120 (194)
187 cd06423 CESA_like CESA_like is 30.0 1.3E+02 0.0027 20.8 4.5 41 67-108 26-66 (180)
188 PRK06027 purU formyltetrahydro 29.9 1.2E+02 0.0026 25.8 5.1 39 57-101 104-144 (286)
189 smart00857 Resolvase Resolvase 29.8 1.5E+02 0.0033 21.4 5.1 47 54-101 52-102 (148)
190 TIGR00035 asp_race aspartate r 29.7 97 0.0021 24.9 4.4 51 52-106 60-112 (229)
191 cd01859 MJ1464 MJ1464. This f 29.7 1.5E+02 0.0033 21.6 5.2 14 93-106 40-53 (156)
192 cd01143 YvrC Periplasmic bindi 29.5 1.6E+02 0.0034 22.1 5.3 52 57-113 50-111 (195)
193 cd00338 Ser_Recombinase Serine 29.4 1.8E+02 0.004 20.5 5.4 46 55-101 53-102 (137)
194 cd01537 PBP1_Repressors_Sugar_ 29.3 1.5E+02 0.0033 22.4 5.3 42 57-101 45-86 (264)
195 PF07282 OrfB_Zn_ribbon: Putat 29.1 66 0.0014 20.9 2.8 23 81-103 3-25 (69)
196 TIGR00655 PurU formyltetrahydr 29.1 1.2E+02 0.0026 25.8 4.9 45 52-102 90-140 (280)
197 PRK01045 ispH 4-hydroxy-3-meth 29.1 1.6E+02 0.0035 25.4 5.8 50 57-108 201-250 (298)
198 TIGR03697 NtcA_cyano global ni 29.0 83 0.0018 23.7 3.6 38 75-113 113-156 (193)
199 cd06267 PBP1_LacI_sugar_bindin 28.9 1.7E+02 0.0037 22.2 5.5 41 58-102 46-86 (264)
200 cd01391 Periplasmic_Binding_Pr 28.8 1.6E+02 0.0036 21.8 5.3 42 57-101 48-89 (269)
201 KOG2016|consensus 28.7 56 0.0012 30.4 3.0 34 68-102 119-152 (523)
202 cd02971 PRX_family Peroxiredox 28.6 1.8E+02 0.0039 20.5 5.2 50 59-113 48-99 (140)
203 PLN02721 threonine aldolase 28.3 1.8E+02 0.0038 24.0 5.8 35 67-101 137-178 (353)
204 PRK00299 sulfur transfer prote 28.3 1.3E+02 0.0029 20.5 4.3 41 57-101 27-67 (81)
205 PLN02645 phosphoglycolate phos 28.3 1.2E+02 0.0026 25.6 4.9 47 48-96 41-87 (311)
206 cd07396 MPP_Nbla03831 Homo sap 28.2 1.6E+02 0.0034 24.1 5.4 49 58-106 31-85 (267)
207 COG0541 Ffh Signal recognition 28.2 95 0.0021 28.6 4.4 41 61-101 122-162 (451)
208 cd04196 GT_2_like_d Subfamily 28.2 1.1E+02 0.0025 22.7 4.3 40 68-108 28-67 (214)
209 cd03335 TCP1_alpha TCP-1 (CTT 28.1 1.9E+02 0.004 26.5 6.3 48 60-112 267-317 (527)
210 COG4359 Uncharacterized conser 28.1 2.5E+02 0.0054 23.4 6.4 57 30-102 41-97 (220)
211 PF00448 SRP54: SRP54-type pro 28.1 65 0.0014 25.6 3.0 40 62-102 25-64 (196)
212 cd05017 SIS_PGI_PMI_1 The memb 28.0 1.3E+02 0.0029 21.4 4.4 42 69-111 46-87 (119)
213 COG0425 SirA Predicted redox p 28.0 1.5E+02 0.0034 20.3 4.5 40 58-101 24-64 (78)
214 cd06312 PBP1_ABC_sugar_binding 27.9 1.8E+02 0.004 22.8 5.6 42 58-101 48-89 (271)
215 PRK01889 GTPase RsgA; Reviewed 27.8 82 0.0018 27.5 3.8 38 69-107 116-155 (356)
216 cd01487 E1_ThiF_like E1_ThiF_l 27.7 1E+02 0.0022 23.9 4.0 33 67-101 88-121 (174)
217 TIGR03659 IsdE heme ABC transp 27.7 1.9E+02 0.0041 23.7 5.9 51 58-113 82-141 (289)
218 TIGR01460 HAD-SF-IIA Haloacid 27.7 1.5E+02 0.0033 23.8 5.2 30 50-79 13-42 (236)
219 COG1671 Uncharacterized protei 27.5 98 0.0021 24.4 3.8 31 71-103 4-34 (150)
220 cd01884 EF_Tu EF-Tu subfamily. 27.5 1.4E+02 0.0031 23.5 4.9 44 57-100 80-124 (195)
221 cd06318 PBP1_ABC_sugar_binding 27.4 1.9E+02 0.0041 22.7 5.6 42 58-102 46-88 (282)
222 cd01489 Uba2_SUMO Ubiquitin ac 27.4 88 0.0019 27.1 3.9 35 67-103 90-124 (312)
223 PF08534 Redoxin: Redoxin; In 27.3 1.6E+02 0.0035 21.1 4.9 49 60-113 55-104 (146)
224 cd04164 trmE TrmE (MnmE, ThdF, 27.3 1E+02 0.0023 21.6 3.8 50 59-110 74-123 (157)
225 cd02970 PRX_like2 Peroxiredoxi 27.2 2.3E+02 0.005 20.1 5.7 50 59-113 49-99 (149)
226 PRK12721 secretion system appa 26.9 75 0.0016 28.0 3.4 34 73-111 283-316 (349)
227 TIGR00067 glut_race glutamate 26.9 1.8E+02 0.0039 24.1 5.6 46 59-107 52-100 (251)
228 PRK00087 4-hydroxy-3-methylbut 26.8 1.4E+02 0.003 28.3 5.4 49 58-108 198-246 (647)
229 PF00702 Hydrolase: haloacid d 26.7 2.7E+02 0.006 20.8 6.2 56 52-112 128-193 (215)
230 TIGR01456 CECR5 HAD-superfamil 26.6 1.2E+02 0.0026 25.8 4.6 47 49-96 14-64 (321)
231 PRK06298 type III secretion sy 26.6 76 0.0017 28.1 3.4 34 73-111 284-317 (356)
232 TIGR00216 ispH_lytB (E)-4-hydr 26.4 1.9E+02 0.0042 24.7 5.8 49 58-108 200-248 (280)
233 PLN02775 Probable dihydrodipic 26.4 3.6E+02 0.0077 23.3 7.4 53 58-112 70-125 (286)
234 COG1363 FrvX Cellulase M and r 26.2 87 0.0019 27.8 3.7 29 71-100 257-289 (355)
235 cd04104 p47_IIGP_like p47 (47- 26.2 1.5E+02 0.0033 22.9 4.8 26 81-106 94-119 (197)
236 PRK13109 flhB flagellar biosyn 26.1 78 0.0017 28.0 3.4 34 73-111 292-325 (358)
237 PF13545 HTH_Crp_2: Crp-like h 26.1 76 0.0017 20.5 2.6 33 81-113 2-41 (76)
238 PRK12475 thiamine/molybdopteri 26.1 99 0.0021 26.8 4.0 35 66-102 115-149 (338)
239 TIGR01452 PGP_euk phosphoglyco 26.0 1.4E+02 0.0031 24.6 4.8 30 50-79 17-46 (279)
240 TIGR02181 GRX_bact Glutaredoxi 26.0 1.6E+02 0.0036 19.0 4.3 15 86-100 15-29 (79)
241 TIGR00530 AGP_acyltrn 1-acyl-s 25.9 2.3E+02 0.0049 19.6 5.3 46 56-101 79-128 (130)
242 cd06282 PBP1_GntR_like_2 Ligan 25.9 2E+02 0.0044 22.1 5.5 41 58-101 46-86 (266)
243 TIGR01404 FlhB_rel_III type II 25.8 81 0.0018 27.7 3.4 34 73-111 282-315 (342)
244 PRK05647 purN phosphoribosylgl 25.7 2E+02 0.0043 23.0 5.5 42 56-101 15-58 (200)
245 COG1179 Dinucleotide-utilizing 25.7 1.5E+02 0.0032 25.5 4.8 42 58-101 112-153 (263)
246 cd04168 TetM_like Tet(M)-like 25.7 1.6E+02 0.0035 23.9 5.0 49 58-107 80-129 (237)
247 PRK14723 flhF flagellar biosyn 25.7 1.8E+02 0.004 28.5 6.0 48 65-112 213-260 (767)
248 KOG0460|consensus 25.6 87 0.0019 28.5 3.6 38 66-104 142-180 (449)
249 PF07894 DUF1669: Protein of u 25.5 1.4E+02 0.0031 25.8 4.8 30 77-107 158-187 (284)
250 TIGR01662 HAD-SF-IIIA HAD-supe 25.4 1.9E+02 0.0042 20.5 4.9 50 51-100 25-77 (132)
251 PRK10200 putative racemase; Pr 25.4 1.1E+02 0.0023 25.0 3.9 45 53-101 61-105 (230)
252 CHL00200 trpA tryptophan synth 25.3 4.1E+02 0.0089 22.3 8.7 58 54-113 106-167 (263)
253 TIGR02634 xylF D-xylose ABC tr 25.3 2.1E+02 0.0046 23.4 5.7 41 58-101 45-86 (302)
254 TIGR00619 sbcd exonuclease Sbc 25.3 1.8E+02 0.0039 23.9 5.3 44 58-101 30-82 (253)
255 COG0403 GcvP Glycine cleavage 25.3 2E+02 0.0043 26.6 5.8 63 63-139 159-223 (450)
256 cd03013 PRX5_like Peroxiredoxi 25.2 2.1E+02 0.0045 21.6 5.3 52 57-113 54-109 (155)
257 cd01540 PBP1_arabinose_binding 25.1 2.1E+02 0.0045 22.6 5.5 36 63-101 50-86 (289)
258 PRK12726 flagellar biosynthesi 25.0 2.2E+02 0.0048 25.9 6.1 48 63-111 231-278 (407)
259 PF04609 MCR_C: Methyl-coenzym 24.9 33 0.00072 29.4 0.8 62 41-103 104-165 (268)
260 cd01147 HemV-2 Metal binding p 24.7 2.4E+02 0.0051 22.3 5.7 54 57-113 64-127 (262)
261 PRK10128 2-keto-3-deoxy-L-rham 24.6 1.5E+02 0.0033 25.0 4.8 44 35-79 195-242 (267)
262 KOG3432|consensus 24.6 74 0.0016 24.1 2.5 49 50-101 21-69 (121)
263 cd01539 PBP1_GGBP Periplasmic 24.6 2.3E+02 0.0051 23.0 5.8 41 58-101 48-89 (303)
264 PRK12849 groEL chaperonin GroE 24.5 1.8E+02 0.0038 27.0 5.5 49 60-113 236-298 (542)
265 TIGR03772 anch_rpt_subst ancho 24.4 1.8E+02 0.0039 26.8 5.5 51 50-101 371-427 (479)
266 cd06300 PBP1_ABC_sugar_binding 24.3 2.3E+02 0.005 22.1 5.6 41 58-101 51-92 (272)
267 PRK07377 hypothetical protein; 24.1 1.7E+02 0.0038 23.8 4.8 46 66-112 75-127 (184)
268 PRK07525 sulfoacetaldehyde ace 24.0 1.8E+02 0.0039 26.8 5.5 45 56-100 190-234 (588)
269 PRK10444 UMP phosphatase; Prov 23.9 1.6E+02 0.0035 24.2 4.7 45 50-96 16-60 (248)
270 PRK00278 trpC indole-3-glycero 23.9 4.2E+02 0.0092 22.0 7.6 59 52-111 119-178 (260)
271 PRK08156 type III secretion sy 23.8 94 0.002 27.6 3.5 34 73-111 278-311 (361)
272 PF01206 TusA: Sulfurtransfera 23.7 2.1E+02 0.0045 18.3 4.5 41 58-101 16-58 (70)
273 PRK06995 flhF flagellar biosyn 23.7 2.1E+02 0.0045 26.5 5.8 46 65-110 284-329 (484)
274 KOG2869|consensus 23.7 2.1E+02 0.0044 25.8 5.5 67 45-111 285-361 (379)
275 cd01484 E1-2_like Ubiquitin ac 23.5 1.2E+02 0.0026 25.0 3.9 35 66-102 90-124 (234)
276 cd06378 PBP1_iGluR_NMDA_NR2 N- 23.5 1.3E+02 0.0029 25.9 4.3 43 59-101 54-96 (362)
277 PRK08762 molybdopterin biosynt 23.4 1.1E+02 0.0024 26.7 3.8 34 67-102 225-258 (376)
278 PLN02161 beta-amylase 23.4 1.7E+02 0.0037 27.5 5.2 46 53-98 415-471 (531)
279 TIGR00338 serB phosphoserine p 23.2 3.3E+02 0.0071 20.9 6.2 46 48-98 82-127 (219)
280 TIGR01919 hisA-trpF 1-(5-phosp 23.1 4.3E+02 0.0093 21.7 7.4 60 81-148 61-123 (243)
281 cd06301 PBP1_rhizopine_binding 23.1 2.4E+02 0.0053 21.9 5.5 41 58-101 47-88 (272)
282 cd01482 vWA_collagen_alphaI-XI 23.0 3.2E+02 0.0069 20.2 7.6 47 67-113 103-153 (164)
283 cd03423 SirA SirA (also known 23.0 1.9E+02 0.0042 18.8 4.2 37 61-101 21-57 (69)
284 cd01895 EngA2 EngA2 subfamily. 22.9 2.8E+02 0.006 19.6 5.4 40 68-107 85-126 (174)
285 COG1377 FlhB Flagellar biosynt 22.9 97 0.0021 27.7 3.4 39 67-111 285-323 (363)
286 PLN00197 beta-amylase; Provisi 22.9 1.9E+02 0.0041 27.5 5.3 45 54-98 420-475 (573)
287 PF13519 VWA_2: von Willebrand 22.8 2.2E+02 0.0048 20.3 4.9 50 51-101 81-133 (172)
288 PF04414 tRNA_deacylase: D-ami 22.8 1.7E+02 0.0038 24.1 4.7 45 55-99 169-213 (213)
289 cd06322 PBP1_ABC_sugar_binding 22.8 2.6E+02 0.0056 21.7 5.5 44 57-102 45-88 (267)
290 cd04501 SGNH_hydrolase_like_4 22.6 1.1E+02 0.0025 22.7 3.4 22 81-102 125-146 (183)
291 PRK08322 acetolactate synthase 22.6 2.1E+02 0.0045 25.9 5.6 45 57-101 187-231 (547)
292 cd06313 PBP1_ABC_sugar_binding 22.6 2.7E+02 0.0059 22.1 5.7 42 58-102 46-88 (272)
293 PRK02228 V-type ATP synthase s 22.5 2.8E+02 0.0061 19.7 5.2 35 64-99 41-75 (100)
294 PRK05724 acetyl-CoA carboxylas 22.5 1.2E+02 0.0025 26.7 3.8 33 68-100 108-157 (319)
295 cd06383 PBP1_iGluR_AMPA_Like N 22.5 2.2E+02 0.0049 24.6 5.5 41 59-101 58-98 (368)
296 TIGR03594 GTPase_EngA ribosome 22.4 2E+02 0.0043 25.0 5.2 49 58-106 247-295 (429)
297 PF00118 Cpn60_TCP1: TCP-1/cpn 22.4 81 0.0018 27.7 2.8 52 57-113 235-289 (485)
298 PRK09259 putative oxalyl-CoA d 22.4 1.9E+02 0.0041 26.5 5.3 46 56-101 203-248 (569)
299 PLN02803 beta-amylase 22.2 1.9E+02 0.0042 27.3 5.3 46 53-98 398-454 (548)
300 PRK03244 argD acetylornithine 22.2 2.3E+02 0.005 24.2 5.6 42 66-107 182-230 (398)
301 PF00535 Glycos_transf_2: Glyc 22.2 73 0.0016 22.2 2.1 43 58-101 15-59 (169)
302 TIGR03061 pip_yhgE_Nterm YhgE/ 22.1 3.5E+02 0.0076 20.4 8.4 64 66-143 42-113 (164)
303 CHL00099 ilvB acetohydroxyacid 22.1 2.1E+02 0.0046 26.4 5.6 45 57-101 208-252 (585)
304 PRK02936 argD acetylornithine 22.0 2.2E+02 0.0048 24.0 5.3 35 66-101 166-208 (377)
305 PRK09108 type III secretion sy 22.0 1E+02 0.0023 27.2 3.4 34 73-111 285-318 (353)
306 PF00875 DNA_photolyase: DNA p 22.0 98 0.0021 23.3 2.9 34 68-101 89-124 (165)
307 PRK02842 light-independent pro 22.0 1.3E+02 0.0029 26.7 4.1 37 66-102 96-137 (427)
308 PRK08199 thiamine pyrophosphat 21.9 2.2E+02 0.0048 25.9 5.6 44 57-100 195-238 (557)
309 PF01976 DUF116: Protein of un 21.8 1.6E+02 0.0034 23.0 4.0 31 83-113 75-105 (158)
310 cd00378 SHMT Serine-glycine hy 21.8 2E+02 0.0042 24.5 5.0 46 56-101 150-196 (402)
311 COG1535 EntB Isochorismate hyd 21.8 94 0.002 25.7 2.8 19 83-101 60-78 (218)
312 cd00291 SirA_YedF_YeeD SirA, Y 21.8 2.2E+02 0.0048 18.0 5.1 40 58-101 15-57 (69)
313 PF12687 DUF3801: Protein of u 21.7 2.9E+02 0.0063 22.4 5.7 60 35-102 4-63 (204)
314 cd04169 RF3 RF3 subfamily. Pe 21.7 2.1E+02 0.0045 23.8 5.0 49 58-106 87-135 (267)
315 PLN02801 beta-amylase 21.6 2E+02 0.0044 27.0 5.3 46 53-98 326-382 (517)
316 COG3580 Uncharacterized protei 21.5 1.2E+02 0.0026 27.0 3.5 76 35-111 168-247 (351)
317 COG1861 SpsF Spore coat polysa 21.5 2.3E+02 0.005 24.0 5.1 52 59-113 34-87 (241)
318 PRK03379 vitamin B12-transport 21.5 3.1E+02 0.0068 22.2 6.0 52 58-113 63-123 (260)
319 TIGR00328 flhB flagellar biosy 21.4 1.1E+02 0.0024 26.9 3.4 34 73-111 283-316 (347)
320 cd03422 YedF YedF is a bacteri 21.4 2E+02 0.0043 18.9 4.0 38 60-101 20-57 (69)
321 cd06278 PBP1_LacI_like_2 Ligan 21.4 3E+02 0.0065 21.1 5.6 40 58-102 45-85 (266)
322 cd07402 MPP_GpdQ Enterobacter 21.4 3.4E+02 0.0075 21.1 6.0 46 57-102 28-78 (240)
323 PRK05597 molybdopterin biosynt 21.3 1.3E+02 0.0027 26.3 3.8 33 67-101 118-150 (355)
324 PRK12468 flhB flagellar biosyn 21.2 1.1E+02 0.0024 27.4 3.4 34 73-111 290-323 (386)
325 PF13728 TraF: F plasmid trans 21.2 2.7E+02 0.0059 22.5 5.5 59 55-113 110-182 (215)
326 PRK06965 acetolactate synthase 21.1 2.2E+02 0.0048 26.3 5.5 45 57-101 212-256 (587)
327 cd06320 PBP1_allose_binding Pe 21.1 2.7E+02 0.0059 21.7 5.4 41 60-102 50-90 (275)
328 cd06311 PBP1_ABC_sugar_binding 21.1 3E+02 0.0065 21.5 5.7 41 58-101 51-92 (274)
329 PRK10867 signal recognition pa 21.0 1.7E+02 0.0037 26.6 4.6 35 67-101 129-163 (433)
330 TIGR00513 accA acetyl-CoA carb 21.0 1.3E+02 0.0029 26.3 3.8 33 68-100 108-157 (316)
331 cd01885 EF2 EF2 (for archaea a 21.0 2.2E+02 0.0047 23.1 4.9 50 57-106 88-137 (222)
332 PRK07688 thiamine/molybdopteri 21.0 1.3E+02 0.0027 26.2 3.7 35 67-103 116-150 (339)
333 cd06367 PBP1_iGluR_NMDA N-term 21.0 1.8E+02 0.0039 24.3 4.6 45 56-101 52-97 (362)
334 cd05564 PTS_IIB_chitobiose_lic 20.9 1.3E+02 0.0028 21.1 3.2 46 53-102 34-79 (96)
335 PF01751 Toprim: Toprim domain 20.8 1.7E+02 0.0037 20.2 3.7 29 66-94 58-88 (100)
336 TIGR02346 chap_CCT_theta T-com 20.8 3E+02 0.0064 25.3 6.2 51 57-112 269-322 (531)
337 COG4052 Uncharacterized protei 20.7 49 0.0011 28.4 1.0 66 40-106 105-170 (310)
338 PRK06048 acetolactate synthase 20.7 2.4E+02 0.0051 25.8 5.5 46 56-101 197-242 (561)
339 PRK00098 GTPase RsgA; Reviewed 20.7 1.4E+02 0.003 25.2 3.8 24 84-107 101-124 (298)
340 cd07388 MPP_Tt1561 Thermus the 20.6 3.2E+02 0.0069 22.4 5.8 39 62-101 26-69 (224)
341 cd03418 GRX_GRXb_1_3_like Glut 20.5 2.4E+02 0.0051 17.8 4.8 19 83-101 13-31 (75)
342 PRK07418 acetolactate synthase 20.5 2.3E+02 0.005 26.3 5.5 45 57-101 215-259 (616)
343 COG4087 Soluble P-type ATPase 20.5 2E+02 0.0044 22.6 4.3 51 45-101 24-74 (152)
344 cd06281 PBP1_LacI_like_5 Ligan 20.5 2.8E+02 0.0062 21.6 5.4 61 38-102 17-87 (269)
345 cd06308 PBP1_sensor_kinase_lik 20.5 3E+02 0.0064 21.5 5.5 41 60-102 49-89 (270)
346 cd07035 TPP_PYR_POX_like Pyrim 20.4 3.1E+02 0.0068 20.0 5.3 73 59-143 3-77 (155)
347 TIGR01457 HAD-SF-IIA-hyp2 HAD- 20.4 2.2E+02 0.0047 23.2 4.8 46 50-97 16-61 (249)
348 TIGR01458 HAD-SF-IIA-hyp3 HAD- 20.4 2.3E+02 0.0049 23.2 4.9 28 52-79 22-49 (257)
349 PRK06091 membrane protein FdrA 20.3 2.1E+02 0.0046 27.1 5.2 43 58-102 133-175 (555)
350 PF04244 DPRP: Deoxyribodipyri 20.3 1.5E+02 0.0033 24.4 3.9 53 58-111 82-140 (224)
351 PRK08978 acetolactate synthase 20.2 2.4E+02 0.0052 25.6 5.5 44 58-101 188-231 (548)
352 TIGR02739 TraF type-F conjugat 20.2 2.8E+02 0.0061 23.4 5.5 47 55-101 140-187 (256)
353 cd06295 PBP1_CelR Ligand bindi 20.1 3.4E+02 0.0074 21.2 5.8 40 57-101 54-94 (275)
354 PRK10637 cysG siroheme synthas 20.1 1.3E+02 0.0028 27.1 3.7 36 67-104 72-107 (457)
355 PHA02546 47 endonuclease subun 20.1 2.8E+02 0.0061 23.8 5.6 46 56-101 28-83 (340)
No 1
>KOG3406|consensus
Probab=99.94 E-value=5.1e-27 Score=177.15 Aligned_cols=108 Identities=70% Similarity=1.118 Sum_probs=105.9
Q ss_pred cccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 32 VSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 32 ~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
.||++.+|+.+|+.|+-++.++.|.+++.|+|.+.++.||++|+||++++|.+++++||.+++||++.+.+..+||+|+|
T Consensus 15 ~mdv~~AL~~Vlk~al~~dGlarGi~Ea~KaldkrqA~lcvLaencdep~yvKLVeALcaeh~iplikV~d~k~LGew~G 94 (134)
T KOG3406|consen 15 VMDVNTALQEVLKTALVHDGLARGIHEAAKALDKRQAHLCVLAENCDEPMYVKLVEALCAEHQIPLIKVGDAKELGEWAG 94 (134)
T ss_pred cccHHHHHHHHHHHHHHhchHHhHHHHHHHHHhhCceeEEEEeccCCchHHHHHHHHHHhhcCCCeEEeccchhhhhhhc
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccCCCccceeeeEEEEEecCchhH
Q psy16564 112 LSKLDNMGKARKVVGCSCVVIKVRNWFL 139 (157)
Q Consensus 112 ~~~~~~~gk~rki~~~s~vaI~D~g~~~ 139 (157)
.+++|++|++||+++|||++|.|+|...
T Consensus 95 lckid~eGnarKvvGcs~vvVkd~geet 122 (134)
T KOG3406|consen 95 LCKIDSEGNARKVVGCSCVVVKDYGEET 122 (134)
T ss_pred eeeecCCCCeeEeecceEEEEeeccccc
Confidence 9999999999999999999999999865
No 2
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=99.94 E-value=3e-26 Score=166.96 Aligned_cols=95 Identities=22% Similarity=0.282 Sum_probs=87.1
Q ss_pred ccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEe-CCHHHHHHHhC
Q psy16564 33 SDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKV-DNNKKLGEWAG 111 (157)
Q Consensus 33 m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v-~sk~eLG~a~G 111 (157)
||++++ |++|+++|+++.|.++|+++|++|+++|||||+|+++ ++.++|+.+|++++||++.+ +|++|||+|||
T Consensus 2 ~~~~~~----l~~a~ragkl~~G~~~v~kai~~gkaklViiA~D~~~-~~~~~i~~~c~~~~Ip~~~~~~tk~eLG~a~G 76 (99)
T PRK01018 2 MDFNRE----LRVAVDTGKVILGSKRTIKAIKLGKAKLVIVASNCPK-DIKEDIEYYAKLSGIPVYEYEGSSVELGTLCG 76 (99)
T ss_pred CCHHHH----HHHHHHcCCEEEcHHHHHHHHHcCCceEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEECCCHHHHHHHhC
Confidence 566666 5888999999999999999999999999999999988 89999999999999999887 69999999999
Q ss_pred CCccccCCCccceeeeEEEEEecCchhHHhhh
Q psy16564 112 LSKLDNMGKARKVVGCSCVVIKVRNWFLIICS 143 (157)
Q Consensus 112 ~~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~ 143 (157)
+. +++++++|+|+||+++++.
T Consensus 77 k~-----------~~~~~vaI~D~G~a~~~~~ 97 (99)
T PRK01018 77 KP-----------FTVSALAIVDPGESDILEL 97 (99)
T ss_pred CC-----------CCEEEEEEecCCHHHHHHh
Confidence 76 4579999999999999874
No 3
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=99.94 E-value=3.6e-26 Score=171.07 Aligned_cols=108 Identities=28% Similarity=0.399 Sum_probs=96.4
Q ss_pred CCCCCCCCCcccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 23 NVPSANDEGVSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 23 ~~~~p~~~~~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
|.++|+.+. +.+.+.++|++|+++|+++.|.++|+++|++|+++|||||+|++|.++.++++.+|++++||+++++|
T Consensus 1 ~~~~~~~~~---l~~ki~~lL~la~ragkl~~G~~~v~kaikkgka~LVilA~D~s~~~~~~~i~~lc~~~~Ip~~~~~s 77 (117)
T TIGR03677 1 YVKFEVPEE---LANKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYVYVKK 77 (117)
T ss_pred CCCCcCcHH---HHHHHHHHHHHHHHcCCEeEcHHHHHHHHHcCCccEEEEeCCCCcHHHHHHHHHHHHHcCCCEEEeCC
Confidence 456787766 34455699999999999999999999999999999999999999955889999999999999999999
Q ss_pred HHHHHHHhCCCccccCCCccceeeeEEEEEecCchhHHhhhc
Q psy16564 103 NKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRNWFLIICSR 144 (157)
Q Consensus 103 k~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~~ 144 (157)
+++||++||+. ++|++++|+|+||++.+..+
T Consensus 78 k~eLG~a~Gk~-----------~~~svvaI~d~g~a~~~~~~ 108 (117)
T TIGR03677 78 KEDLGAAAGLE-----------VGAASAAIVDEGKAEELLKE 108 (117)
T ss_pred HHHHHHHhCCC-----------CCeEEEEEEchhhhHHHHHH
Confidence 99999999975 46899999999999976554
No 4
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=99.93 E-value=2.3e-25 Score=167.99 Aligned_cols=98 Identities=29% Similarity=0.433 Sum_probs=90.7
Q ss_pred HHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCc
Q psy16564 35 INKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSK 114 (157)
Q Consensus 35 ~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~ 114 (157)
+++.+.++|+.|+++|+++.|.++|+++|++|+++|||||+|++|.++..+++.+|++++||+++++++++||+|||++
T Consensus 14 l~~ki~~lL~la~ragklv~G~~~v~kaikkgkakLVilA~D~s~~~i~~~~~~lc~~~~Vp~~~~~tk~eLG~a~Gk~- 92 (122)
T PRK04175 14 LAEKALEAVEKARDTGKIKKGTNETTKAVERGIAKLVVIAEDVDPEEIVAHLPLLCEEKKIPYVYVPSKKDLGKAAGLE- 92 (122)
T ss_pred HHHHHHHHHHHHHHcCCEeEcHHHHHHHHHcCCccEEEEeCCCChHHHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCC-
Confidence 6677779999999999999999999999999999999999999996678999999999999999999999999999986
Q ss_pred cccCCCccceeeeEEEEEecCchhHHhhh
Q psy16564 115 LDNMGKARKVVGCSCVVIKVRNWFLIICS 143 (157)
Q Consensus 115 ~~~~gk~rki~~~s~vaI~D~g~~~~~~~ 143 (157)
++++|++|+|+||+..+..
T Consensus 93 ----------~~~svvaI~d~g~a~~~~~ 111 (122)
T PRK04175 93 ----------VGAAAAAIVDAGKAKELVE 111 (122)
T ss_pred ----------CCeEEEEEechhhhHHHHH
Confidence 5689999999999986544
No 5
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=99.93 E-value=2.1e-25 Score=165.25 Aligned_cols=93 Identities=18% Similarity=0.216 Sum_probs=86.3
Q ss_pred HHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEe-CCHHHHHHHhCCCcccc
Q psy16564 39 LQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKV-DNNKKLGEWAGLSKLDN 117 (157)
Q Consensus 39 L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v-~sk~eLG~a~G~~~~~~ 117 (157)
+.++|++|+++|+++.|.++|+++|++|+++|||||+|+++ ++++.|+.+|+.++||++.+ +|++|||+|||++
T Consensus 13 i~~~Lgla~raGKlv~G~~~vlkalk~gkaklViiA~D~~~-~~kkki~~~~~~~~Vpv~~~~~t~~eLG~A~Gk~---- 87 (108)
T PTZ00106 13 INSKLQLVMKSGKYTLGTKSTLKALRNGKAKLVIISNNCPP-IRRSEIEYYAMLSKTGVHHYAGNNNDLGTACGRH---- 87 (108)
T ss_pred HHHHHHHHHHhCCeeecHHHHHHHHHcCCeeEEEEeCCCCH-HHHHHHHHHHhhcCCCEEEeCCCHHHHHHHhCCc----
Confidence 44778999999999999999999999999999999999999 89999999999999999975 8999999999986
Q ss_pred CCCccceeeeEEEEEecCchhHHhhh
Q psy16564 118 MGKARKVVGCSCVVIKVRNWFLIICS 143 (157)
Q Consensus 118 ~gk~rki~~~s~vaI~D~g~~~~~~~ 143 (157)
+++++++|+|+||+++++.
T Consensus 88 -------~r~svvaI~D~G~a~~l~~ 106 (108)
T PTZ00106 88 -------FRVSVMSITDAGDSDILRA 106 (108)
T ss_pred -------cCeEEEEEeCcchHHHHhh
Confidence 4568999999999999863
No 6
>PRK07283 hypothetical protein; Provisional
Probab=99.93 E-value=6e-25 Score=159.74 Aligned_cols=96 Identities=19% Similarity=0.191 Sum_probs=89.0
Q ss_pred ccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 33 SDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 33 m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
|+-++++ ++|++|+++|+++.|.++|+++|++|++++||+|+|+++ ++.+++...|+.++||++.++|++|||++||+
T Consensus 1 ~~~~~~l-~~LglA~raGklv~G~~~v~~aik~gk~~lVi~A~Das~-~~~kk~~~~~~~~~Vp~~~~~t~~eLG~a~Gk 78 (98)
T PRK07283 1 NNKQKIS-NLLGLAQRAGRIISGEELVVKAIQSGQAKLVFLANDAGP-NLTKKVTDKSNYYQVEVSTVFSTLELSAAVGK 78 (98)
T ss_pred CcHHHHH-HHHHHHHHhCCeeEcHHHHHHHHHcCCccEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCC
Confidence 5556777 999999999999999999999999999999999999999 89999999999999999999999999999996
Q ss_pred CccccCCCccceeeeEEEEEecCchhHHhhh
Q psy16564 113 SKLDNMGKARKVVGCSCVVIKVRNWFLIICS 143 (157)
Q Consensus 113 ~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~ 143 (157)
+ | ++++|+|+||++++.+
T Consensus 79 ~--------~-----~vvai~d~g~a~~l~~ 96 (98)
T PRK07283 79 P--------R-----KVLAVTDAGFSKKMRS 96 (98)
T ss_pred C--------c-----eEEEEeChhHHHHHHH
Confidence 4 2 5699999999998764
No 7
>PRK07714 hypothetical protein; Provisional
Probab=99.92 E-value=3.4e-24 Score=156.02 Aligned_cols=97 Identities=19% Similarity=0.245 Sum_probs=88.9
Q ss_pred ccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 33 SDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 33 m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
|+.++.+ ++|++|+++|+++.|.++|+++|++|++++||+|+|+++ ++.+++..+|+.++||+++++|++|||++||+
T Consensus 1 ~~~~~~~-~~Lgla~raGk~v~G~~~v~~al~~g~~~lViiA~D~s~-~~~~ki~~~~~~~~vp~~~~~sk~eLG~a~Gk 78 (100)
T PRK07714 1 MSMSDWK-SFLGLANRARKVISGEELVLKEVRSGKAKLVLLSEDASV-NTTKKITDKCTYYNVPMRKVENRQQLGHAIGK 78 (100)
T ss_pred CCHHHHH-HHHHHHHHhCCeeecHHHHHHHHHhCCceEEEEeCCCCH-HHHHHHHHHHHhcCCCEEEeCCHHHHHHHhCC
Confidence 4556666 999999999999999999999999999999999999999 89999999999999999999999999999998
Q ss_pred CccccCCCccceeeeEEEEEecCchhHHhhh
Q psy16564 113 SKLDNMGKARKVVGCSCVVIKVRNWFLIICS 143 (157)
Q Consensus 113 ~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~ 143 (157)
+ + +++++|+|.||++.+..
T Consensus 79 ~-------~-----~~~vai~d~g~a~~l~~ 97 (100)
T PRK07714 79 D-------E-----RVVVAVLDEGFAKKLRS 97 (100)
T ss_pred C-------c-----ceEEEEeCchhHHHHHH
Confidence 6 2 24799999999998754
No 8
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=6.4e-24 Score=159.20 Aligned_cols=98 Identities=28% Similarity=0.414 Sum_probs=88.0
Q ss_pred cHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 34 DINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 34 ~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
++++.+.++++.|.++|+++.|.++++|+|++|+++|||||+|++|+++..+++.+|++++|||++++|+.+||+|||++
T Consensus 10 ~~~~k~l~~l~~a~~~~ki~~G~~e~~Kai~~g~a~LVviA~Dv~P~~~~~~l~~lc~~~~vpyv~V~sk~~LG~a~g~~ 89 (116)
T COG1358 10 MLEQKALSLLGKASRAGKLKKGTNEVTKAIERGKAKLVVIAEDVSPEELVKHLPALCEEKNVPYVYVGSKKELGKAVGKE 89 (116)
T ss_pred HHHHHHHHHHHHHHhcCCchhhHHHHHHHHHcCCCcEEEEecCCCHHHHHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCC
Confidence 34444449999999999999999999999999999999999999988999999999999999999999999999999986
Q ss_pred ccccCCCccceeeeEEEEEecCchhHHhhh
Q psy16564 114 KLDNMGKARKVVGCSCVVIKVRNWFLIICS 143 (157)
Q Consensus 114 ~~~~~gk~rki~~~s~vaI~D~g~~~~~~~ 143 (157)
+ ..++++.|+||++-+.+
T Consensus 90 -----------~-~~vv~i~~~~~~~~~~~ 107 (116)
T COG1358 90 -----------V-RKVVAIVDKGFAKKLED 107 (116)
T ss_pred -----------c-ceeEEEeehhhhhHHHH
Confidence 1 36789999999965443
No 9
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=99.89 E-value=8.5e-23 Score=150.26 Aligned_cols=95 Identities=20% Similarity=0.324 Sum_probs=88.4
Q ss_pred HHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCcc
Q psy16564 36 NKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKL 115 (157)
Q Consensus 36 ~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~ 115 (157)
++.+ ++|++|+++|+++.|.++|.++|++|+++|||+|+|+++ +.+++|..+|+.++||++.++|++|||.+||++
T Consensus 3 ~k~l-~lLglA~rAGklv~G~~~v~~aik~gk~~lVI~A~D~s~-~~kkki~~~~~~~~vp~~~~~t~~eLg~a~Gk~-- 78 (104)
T PRK05583 3 NKFL-NFLGLTKKAGKLLEGYNKCEEAIKKKKVYLIIISNDISE-NSKNKFKNYCNKYNIPYIEGYSKEELGNAIGRD-- 78 (104)
T ss_pred HHHH-HHHHHHHHhCCeeecHHHHHHHHHcCCceEEEEeCCCCH-hHHHHHHHHHHHcCCCEEEecCHHHHHHHhCCC--
Confidence 5566 999999999999999999999999999999999999999 899999999999999999999999999999975
Q ss_pred ccCCCccceeeeEEEEEecCchhHHhhhc
Q psy16564 116 DNMGKARKVVGCSCVVIKVRNWFLIICSR 144 (157)
Q Consensus 116 ~~~gk~rki~~~s~vaI~D~g~~~~~~~~ 144 (157)
.+++++|+|+||+..+.+.
T Consensus 79 ----------~~~~iai~d~g~a~~l~~~ 97 (104)
T PRK05583 79 ----------EIKILGVKDKNMAKKLLKL 97 (104)
T ss_pred ----------CeEEEEEeChHHHHHHHHH
Confidence 2588999999999977654
No 10
>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=99.89 E-value=4.2e-23 Score=147.20 Aligned_cols=94 Identities=34% Similarity=0.511 Sum_probs=86.8
Q ss_pred HHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccc
Q psy16564 37 KALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLD 116 (157)
Q Consensus 37 k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~ 116 (157)
+.+.++|+.|+++|+++.|.+++.++|++|+++|||+|+|++|.....+++.+|++++||+++++|+.+||++||++
T Consensus 1 ~~i~~~l~~a~~~~~lv~G~~~v~k~l~~~~~~lvilA~d~~~~~~~~~l~~~c~~~~Ip~~~~~s~~eLG~~~g~~--- 77 (95)
T PF01248_consen 1 DKIYKLLKLARKAGRLVKGIKEVLKALKKGKAKLVILAEDCSPDSIKKHLPALCEEKNIPYVFVPSKEELGRACGKK--- 77 (95)
T ss_dssp HHHHHHHHHHHHHSEEEESHHHHHHHHHTTCESEEEEETTSSSGHHHHHHHHHHHHTTEEEEEESHHHHHHHHTTSS---
T ss_pred ChHHHHHHHHHhcCCEEEchHHHHHHHHcCCCcEEEEcCCCChhhhcccchhheeccceeEEEECCHHHHHHHHCCC---
Confidence 35679999999999999999999999999999999999999996666679999999999999999999999999986
Q ss_pred cCCCccceeeeEEEEEecCchhHHh
Q psy16564 117 NMGKARKVVGCSCVVIKVRNWFLII 141 (157)
Q Consensus 117 ~~gk~rki~~~s~vaI~D~g~~~~~ 141 (157)
+.+++++|.|+|++.++
T Consensus 78 --------~~~~~~~i~d~~~a~~l 94 (95)
T PF01248_consen 78 --------RPVSALAIKDAGDAKIL 94 (95)
T ss_dssp --------STSSEEEEEESTTHHHH
T ss_pred --------CcEEEEEEECcccchhh
Confidence 34689999999999876
No 11
>PRK06683 hypothetical protein; Provisional
Probab=99.87 E-value=9.1e-22 Score=139.28 Aligned_cols=78 Identities=24% Similarity=0.427 Sum_probs=73.0
Q ss_pred HHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccc
Q psy16564 44 KTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARK 123 (157)
Q Consensus 44 ~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rk 123 (157)
..+.++|+++.|.++++++|++|+++|||||+|+++ ++.+.|..+|++++||+++++|+.|||++||++
T Consensus 4 ~~~~~agk~v~G~~~v~kaik~gkaklViiA~Da~~-~~~~~i~~~~~~~~Vpv~~~~t~~eLG~A~G~~---------- 72 (82)
T PRK06683 4 QKVSNAENVVVGHKRTLEAIKNGIVKEVVIAEDADM-RLTHVIIRTALQHNIPITKVESVRKLGKVAGIQ---------- 72 (82)
T ss_pred HHHHhCCCEEEcHHHHHHHHHcCCeeEEEEECCCCH-HHHHHHHHHHHhcCCCEEEECCHHHHHHHhCCc----------
Confidence 445578999999999999999999999999999999 899999999999999999999999999999987
Q ss_pred eeeeEEEEEe
Q psy16564 124 VVGCSCVVIK 133 (157)
Q Consensus 124 i~~~s~vaI~ 133 (157)
+++|+++|.
T Consensus 73 -~~~a~~ai~ 81 (82)
T PRK06683 73 -VGASAIGII 81 (82)
T ss_pred -ccEEEEEEe
Confidence 778888886
No 12
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=99.87 E-value=1.1e-21 Score=138.65 Aligned_cols=75 Identities=33% Similarity=0.518 Sum_probs=71.1
Q ss_pred HhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceee
Q psy16564 47 RAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVG 126 (157)
Q Consensus 47 ~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~ 126 (157)
.++|+++.|.++++++|++|+++|||||+|++| ++.++|+.+|++++||+++++|+.|||+|||++ ++
T Consensus 7 ~ragkl~~G~~~v~kai~~gkaklViiA~D~~~-~~~~~i~~~c~~~~Vp~~~~~s~~eLG~a~G~~-----------~~ 74 (82)
T PRK13602 7 SQAKSIVIGTKQTVKALKRGSVKEVVVAEDADP-RLTEKVEALANEKGVPVSKVDSMKKLGKACGIE-----------VG 74 (82)
T ss_pred HhcCCEEEcHHHHHHHHHcCCeeEEEEECCCCH-HHHHHHHHHHHHcCCCEEEECCHHHHHHHHCCC-----------cC
Confidence 478999999999999999999999999999999 899999999999999999999999999999987 67
Q ss_pred eEEEEEe
Q psy16564 127 CSCVVIK 133 (157)
Q Consensus 127 ~s~vaI~ 133 (157)
+++++|.
T Consensus 75 ~a~~ai~ 81 (82)
T PRK13602 75 AAAVAII 81 (82)
T ss_pred EEEEEEe
Confidence 8888885
No 13
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=1.6e-20 Score=136.29 Aligned_cols=95 Identities=22% Similarity=0.310 Sum_probs=86.8
Q ss_pred cccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHh
Q psy16564 32 VSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWA 110 (157)
Q Consensus 32 ~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~ 110 (157)
.|++++.|+.++++ |+++.|.++++|+++.|++++||+|+||++ +.++.|+++++-.+|||+++. +..|||.+|
T Consensus 4 ~~~v~~~L~~avkT----GkvilG~k~tiK~lk~gkaKliiiAsN~P~-~~k~~ieyYAkLs~ipV~~y~Gt~~eLG~~c 78 (100)
T COG1911 4 GDDVEKELKLAVKT----GKVILGSKRTIKSLKLGKAKLIIIASNCPK-ELKEDIEYYAKLSDIPVYVYEGTSVELGTVC 78 (100)
T ss_pred cchHHHHHHHHHhc----CCEEEehHHHHHHHHcCCCcEEEEecCCCH-HHHHHHHHHHHHcCCcEEEecCCceeHHhhh
Confidence 45788888665555 999999999999999999999999999999 899999999999999999999 999999999
Q ss_pred CCCccccCCCccceeeeEEEEEecCchhHHhh
Q psy16564 111 GLSKLDNMGKARKVVGCSCVVIKVRNWFLIIC 142 (157)
Q Consensus 111 G~~~~~~~gk~rki~~~s~vaI~D~g~~~~~~ 142 (157)
|+. ++++|++|+|+|.++|+.
T Consensus 79 gkp-----------f~v~~laIiD~G~S~Il~ 99 (100)
T COG1911 79 GKP-----------FRVAALAIIDEGDSDILA 99 (100)
T ss_pred CCC-----------ceEEEEEEecCchhhhhc
Confidence 975 678999999999999874
No 14
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=99.83 E-value=2.8e-20 Score=131.81 Aligned_cols=73 Identities=23% Similarity=0.393 Sum_probs=68.5
Q ss_pred cCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeE
Q psy16564 49 HDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCS 128 (157)
Q Consensus 49 agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s 128 (157)
-|+++.|.++++++|++|+++|||||+|+++ +++++|..+|++++||+++++|+.+||++||++ ++++
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da~~-~~~k~i~~~c~~~~Vpv~~~~t~~eLG~A~G~~-----------v~aa 73 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDAEE-HVTKKIKELCEEKSIKIVYIDTMKELGVMCGID-----------VGAA 73 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCCCH-HHHHHHHHHHHhCCCCEEEeCCHHHHHHHHCCc-----------cCee
Confidence 4899999999999999999999999999999 999999999999999999999999999999987 6677
Q ss_pred EEEEe
Q psy16564 129 CVVIK 133 (157)
Q Consensus 129 ~vaI~ 133 (157)
+++|.
T Consensus 74 ~~~~~ 78 (82)
T PRK13601 74 AAADI 78 (82)
T ss_pred eEEEe
Confidence 77764
No 15
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=99.82 E-value=5.2e-20 Score=131.08 Aligned_cols=72 Identities=21% Similarity=0.364 Sum_probs=67.7
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeEE
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSC 129 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~ 129 (157)
..++.|.+|++|+|++|++++||||.|++| .+..+|+.+|++++|||++++|+.+||++||++ +++++
T Consensus 12 ~~~vvG~kqt~Kai~kg~~~~v~iA~Da~~-~vv~~l~~lceek~Ip~v~V~s~~~LGkAcgi~-----------V~aa~ 79 (84)
T PRK13600 12 QHFVVGLKETLKALKKDQVTSLIIAEDVEV-YLMTRVLSQINQKNIPVSFFKSKHALGKHVGIN-----------VNATI 79 (84)
T ss_pred cCceeeHHHHHHHHhcCCceEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCC-----------cCeEE
Confidence 356999999999999999999999999999 788999999999999999999999999999997 78888
Q ss_pred EEEe
Q psy16564 130 VVIK 133 (157)
Q Consensus 130 vaI~ 133 (157)
++|.
T Consensus 80 aai~ 83 (84)
T PRK13600 80 VALI 83 (84)
T ss_pred EEEe
Confidence 8875
No 16
>PRK09190 hypothetical protein; Provisional
Probab=99.78 E-value=1.4e-18 Score=142.83 Aligned_cols=98 Identities=17% Similarity=0.168 Sum_probs=89.1
Q ss_pred HHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHh------CCCCEEEeCCHHHHHH
Q psy16564 35 INKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSE------HQIPLIKVDNNKKLGE 108 (157)
Q Consensus 35 ~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~------~~Ipvi~v~sk~eLG~ 108 (157)
+.+.+.++|++|+++|+++.|..+|.++|++|++.|||+|+|+++ +..++|..+|+. ++||++.++++++||.
T Consensus 95 l~~ril~lLGLArRAGklVsG~~~V~~alk~gk~~Lvi~A~DaS~-~t~kKl~~~~~~~~~~~~~~Vp~v~~~tk~eLg~ 173 (220)
T PRK09190 95 LARRALDALGLARKAGQVVSGFEKVDAALRSGEAAALIHASDGAA-DGKRKLDQARRALVHETGREIPVIGLFTAAELGL 173 (220)
T ss_pred HHHHHHHHHHHHhhhCCEeecHHHHHHHHHcCCceEEEEeccCCh-hHHHHHHHHHHhhcccccCCccEEEecCHHHHHH
Confidence 344455999999999999999999999999999999999999999 899999999999 9999999999999999
Q ss_pred HhCCCccccCCCccceeeeEEEEEecCchhHHhhhcc
Q psy16564 109 WAGLSKLDNMGKARKVVGCSCVVIKVRNWFLIICSRK 145 (157)
Q Consensus 109 a~G~~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~~~ 145 (157)
++|++ ..++++|+|.||+..+..+.
T Consensus 174 AlGr~------------~~~~vav~d~gfA~~l~~~~ 198 (220)
T PRK09190 174 AFGRE------------NVIHAALLAGGAAERVVKRA 198 (220)
T ss_pred HhCCC------------ceeEEEEcChHHHHHHHHHH
Confidence 99986 23679999999999877654
No 17
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=99.77 E-value=8.7e-19 Score=146.24 Aligned_cols=93 Identities=23% Similarity=0.400 Sum_probs=84.0
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeEEEE
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSCVV 131 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~va 131 (157)
|+.|.++|+++|++|+++|||||+|++|..++.+|+.+|++++|||++++++.+||+++|+. .|+|++
T Consensus 133 LvsG~n~VtkaIekkKAkLVIIA~DVsPie~vk~LpaLCrk~~VPY~iVktKaeLG~AIGkK------------travVA 200 (263)
T PTZ00222 133 VVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRK------------TATCVA 200 (263)
T ss_pred eccCHHHHHHHHHcCCceEEEEeCCCCHHHHHHHHHHHHHhcCCCEEEECCHHHHHHHHCCC------------CCeEEE
Confidence 88999999999999999999999999997787899999999999999999999999999964 378999
Q ss_pred EecCchhHHhhhccccceeeecccC
Q psy16564 132 IKVRNWFLIICSRKSTQVLSVNYNK 156 (157)
Q Consensus 132 I~D~g~~~~~~~~~~~~~~~~~~~~ 156 (157)
|+|.|..+--.-....+.+..|||.
T Consensus 201 ItD~g~ed~~~l~~lv~~~~~~~nd 225 (263)
T PTZ00222 201 ITDVNAEDEAALKNLIRSVNARFLS 225 (263)
T ss_pred EeeCCcccHHHHHHHHHHHHHhhcc
Confidence 9999987766666677778888874
No 18
>KOG3167|consensus
Probab=99.75 E-value=4.6e-18 Score=130.58 Aligned_cols=104 Identities=25% Similarity=0.455 Sum_probs=94.9
Q ss_pred ccCCCCCCCCCCcccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE
Q psy16564 20 ATDNVPSANDEGVSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK 99 (157)
Q Consensus 20 ~~~~~~~p~~~~~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~ 99 (157)
.++|++.|+++.. +++.+..+++.|.+++.+..|+++|.|.+++|+-.|||||.|.+|.++..||+.+|++++|||++
T Consensus 30 ~~~PIAkPLA~kk--l~kk~~KlvkKa~k~k~lrrGvKevqK~vrkGeKGl~VlAgd~sPiDvi~HlP~lCEd~~vPYvy 107 (153)
T KOG3167|consen 30 AVNPIAKPLASKK--LAKKVYKLVKKAAKQKGLRRGVKEVQKRVRKGEKGLCVLAGDTSPIDVITHLPALCEDRGVPYVY 107 (153)
T ss_pred hhcccccccccHH--HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcceEEEecCCccHHHHhccchhhhccCCCccc
Confidence 4799999999999 88888899999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCHHHHHHHhCCCccccCCCccceeeeEEEEEecCc
Q psy16564 100 VDNNKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRN 136 (157)
Q Consensus 100 v~sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g 136 (157)
++|+.+||.|.|.. | +.+|+.|..-|
T Consensus 108 ~psk~dlg~A~~~k--------r---pt~~v~v~p~~ 133 (153)
T KOG3167|consen 108 TPSKEDLGAAGGTK--------R---PTCCVFVKPGG 133 (153)
T ss_pred cccHHHHHHhcCCC--------C---CceEEEEeeCh
Confidence 99999999999975 2 34566665444
No 19
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=99.67 E-value=1.1e-16 Score=134.06 Aligned_cols=92 Identities=18% Similarity=0.274 Sum_probs=77.4
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeEEEE
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSCVV 131 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~va 131 (157)
+..|++.|+++|++++++|||||+|++|...+.+++.+|++++|||++++++++||+++|+. .++|++
T Consensus 133 vk~Gin~VtklIekkKAkLVIIA~DVsP~t~kk~LP~LC~k~~VPY~iv~sK~eLG~AIGkk------------traVVA 200 (266)
T PTZ00365 133 LKYGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQK------------TAAVVA 200 (266)
T ss_pred HHhhhHHHHHHHHhCCccEEEEeCCCCHHHHHHHHHHHHhccCCCEEEECCHHHHHHHhCCC------------CceEEE
Confidence 77999999999999999999999999997777778999999999999999999999999974 368899
Q ss_pred EecCchhHHhhhccccceeeeccc
Q psy16564 132 IKVRNWFLIICSRKSTQVLSVNYN 155 (157)
Q Consensus 132 I~D~g~~~~~~~~~~~~~~~~~~~ 155 (157)
|+|-...+--.-..-.+.+..|||
T Consensus 201 ItdV~~EDk~~l~~lv~~~~~~~n 224 (266)
T PTZ00365 201 IDNVRKEDQAEFDNLCKNFRAMFN 224 (266)
T ss_pred ecccCHHHHHHHHHHHHHHHHhcc
Confidence 997655554444444455566665
No 20
>KOG3387|consensus
Probab=99.66 E-value=3.9e-16 Score=118.20 Aligned_cols=91 Identities=20% Similarity=0.333 Sum_probs=85.2
Q ss_pred cccCCCCCCCCCCcccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEE
Q psy16564 19 TATDNVPSANDEGVSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 19 ~~~~~~~~p~~~~~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
..++|.++|++++. +.+.+.++.+.|....++..|.++++|++.+|...||++|.||.|-++..|++-+|+..|||++
T Consensus 4 ~~v~~~~~P~ad~~--L~ekildl~Qqa~~~kql~kg~NEaTk~Lnrgi~~~Vv~aaD~kP~eIt~HLp~LcedknVp~v 81 (131)
T KOG3387|consen 4 DGVNPKAYPLADSN--LTEKILDLKQQATGYKQLKKGANEATKTLNRGISEFVVMAADVKPLEITLHLPLLCEDKNVPYV 81 (131)
T ss_pred cccCcccCcccchh--hHHHHHHHHHHHhhHHHHhcccchHhhhhccCceeEEEEEccCCHHHHHHHhHHHhhccCCceE
Confidence 45789999999986 5555559999999999999999999999999999999999999999999999999999999999
Q ss_pred EeCCHHHHHHHhC
Q psy16564 99 KVDNNKKLGEWAG 111 (157)
Q Consensus 99 ~v~sk~eLG~a~G 111 (157)
+|.++..||++||
T Consensus 82 ~Vpsk~alG~~cg 94 (131)
T KOG3387|consen 82 FVPSKQALGLACG 94 (131)
T ss_pred EeeccHHhhhhhh
Confidence 9999999999999
No 21
>KOG2988|consensus
Probab=99.26 E-value=3.7e-11 Score=89.10 Aligned_cols=95 Identities=19% Similarity=0.178 Sum_probs=83.7
Q ss_pred HHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCCccccCC
Q psy16564 41 QVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLSKLDNMG 119 (157)
Q Consensus 41 ~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~~~~~~g 119 (157)
.-|-++.++|+.+.|.+++++.++.|+++|+++|.+|++ --+..|+.++-....+|..+. ...+||.+||+-
T Consensus 16 s~lll~mksgkY~lgyK~T~k~~r~gkakL~~is~n~p~-lrks~ieyyamlak~~v~~~sg~n~~lgt~~g~~------ 88 (112)
T KOG2988|consen 16 SSLLLVMKSGKYILGYKQTLKSLRQGKAKLIIISSNCPP-LRKSEIEYYAMLAKTGVHHYSGNNVELGTACGKT------ 88 (112)
T ss_pred HHHHHHHhhcceeechHHHHHHHHhccceEEEeecCCCC-cchhHHHHHHHHhcCceeeecCCcEeHHHHhcCe------
Confidence 344567788999999999999999999999999999999 677789999988888988877 889999999965
Q ss_pred CccceeeeEEEEEecCchhHHhhhcccc
Q psy16564 120 KARKVVGCSCVVIKVRNWFLIICSRKST 147 (157)
Q Consensus 120 k~rki~~~s~vaI~D~g~~~~~~~~~~~ 147 (157)
++++|+.|+|+|.++++.+-.++
T Consensus 89 -----fRv~v~~ivd~gds~~~~~l~e~ 111 (112)
T KOG2988|consen 89 -----FRVSVLSIVDLGDSDIIAALSER 111 (112)
T ss_pred -----eEeeEEEEEeccchhhhhhcccc
Confidence 67899999999999998876543
No 22
>KOG3166|consensus
Probab=97.53 E-value=2.3e-05 Score=64.28 Aligned_cols=79 Identities=24% Similarity=0.347 Sum_probs=58.1
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeEEEE
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSCVV 131 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~va 131 (157)
+..|++.++..+++.+|+||++|.|.+|.+++.++++||... + +..+ . | ..|++++
T Consensus 110 ~~~gvnTVttLVenKKAQLVV~ahDvDPIELVvFLPaLC~km---i--vk~~--------~---------~--kT~t~~a 165 (209)
T KOG3166|consen 110 LRAGVNTVTTLVENKKAQLVVTAHDVDPIELVVFLPALCRKM---I--VKGK--------H---------R--KTCTTVA 165 (209)
T ss_pred cccCcceEeehhhccccceeEEecccCchhheeecHHhhhhh---c--cccc--------c---------c--ceeeeee
Confidence 678999999999999999999999999999999999999998 1 1211 1 2 3578777
Q ss_pred EecCchhHHhhhccccceeeecccC
Q psy16564 132 IKVRNWFLIICSRKSTQVLSVNYNK 156 (157)
Q Consensus 132 I~D~g~~~~~~~~~~~~~~~~~~~~ 156 (157)
+.+. -+.-.-....+.+..|||.
T Consensus 166 ~v~~--edk~~l~kl~e~i~tn~nd 188 (209)
T KOG3166|consen 166 FVNS--EDKGALAKLVEAIRTNYND 188 (209)
T ss_pred eech--hhHHHHHHHHHHHhccccc
Confidence 7422 2222223345567788874
No 23
>PF08228 RNase_P_pop3: RNase P subunit Pop3; InterPro: IPR013241 This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs. The structure of Pop3 has been assigned the L7Ae/L30e fold []. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologues.
Probab=97.28 E-value=0.0054 Score=48.50 Aligned_cols=81 Identities=12% Similarity=0.272 Sum_probs=63.0
Q ss_pred CceeeHHHHHHHHhcCCe--eEEEEcCCCCchhhHHHHHHHHHhCC--CCEEEeC--CHHHHHHHhCCCccccCCCccce
Q psy16564 51 GLAKGLHEAAKALDRREA--QLCVLADNCDEPAYKKLVQALCSEHQ--IPLIKVD--NNKKLGEWAGLSKLDNMGKARKV 124 (157)
Q Consensus 51 klv~G~~~v~KaL~kgka--kLVIlA~D~s~~~~~~~l~~lc~~~~--Ipvi~v~--sk~eLG~a~G~~~~~~~gk~rki 124 (157)
.+..|.|++.+.|+.... .+||+|..-.|..+..||+.+|.-.+ |..+.++ +...|+.++|..
T Consensus 55 ~v~~GfNsi~~~Le~~~~~~~~vFVcr~D~ps~L~~h~P~Lva~as~~vrLV~Lpkgs~~rLs~aLgi~----------- 123 (158)
T PF08228_consen 55 GVTVGFNSIVRYLECQASDNVYVFVCRSDQPSILTSHFPQLVATASKSVRLVQLPKGSEARLSEALGIP----------- 123 (158)
T ss_pred cEEEehHHHHHHHhcccCCCeEEEEECCCCcHHHHHHHHHHHHhccCcceEEeCChhHHHHHHHHhCCC-----------
Confidence 589999999999994322 47788874356579999999999877 9999988 889999999985
Q ss_pred eeeEEEEEe-----cCchhHHhhh
Q psy16564 125 VGCSCVVIK-----VRNWFLIICS 143 (157)
Q Consensus 125 ~~~s~vaI~-----D~g~~~~~~~ 143 (157)
.+++++|. +.++.+.+.+
T Consensus 124 -r~g~l~v~~~~~~~~~L~~~i~~ 146 (158)
T PF08228_consen 124 -RVGILAVRADAPGAKSLVDLIRS 146 (158)
T ss_pred -CccEEEEecCCcccHHHHHHHHh
Confidence 24788887 3355555554
No 24
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=96.63 E-value=0.012 Score=43.60 Aligned_cols=74 Identities=14% Similarity=0.170 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHhc-CCceeeHHHHHHHHhcCCeeEEEEcCCCCchh------------------hHHHHHHHHHhCCCCE
Q psy16564 37 KALQQVLKTARAH-DGLAKGLHEAAKALDRREAQLCVLADNCDEPA------------------YKKLVQALCSEHQIPL 97 (157)
Q Consensus 37 k~L~~lL~~A~~a-gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~------------------~~~~l~~lc~~~~Ipv 97 (157)
+.+.+++....+. |..+.|.++|.+|++.|.+..++|..|..... +...+...+++.|..+
T Consensus 6 ~~ve~f~~~l~k~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~~~r~~~~~~~~~~~~~~~i~~l~~~a~~~g~~v 85 (113)
T PF03465_consen 6 KLVEEFFEELAKDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRDVERCKCPECGGELEVVELIEELIELAEQSGAKV 85 (113)
T ss_dssp HHHHHHHHHHHTTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESCHHHHHSTTTHSEEEEEEHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhhCCCcEEECHHHHHHHHHhCCCcEEEEecccccccceeccccccccchhhhHHHHHHHHHHHHHcCCEE
Confidence 3455556555555 89999999999999999999999999754322 2577888899999999
Q ss_pred EEeCCHHHHHHHh
Q psy16564 98 IKVDNNKKLGEWA 110 (157)
Q Consensus 98 i~v~sk~eLG~a~ 110 (157)
..+++.-+-|.-+
T Consensus 86 ~iis~~~e~G~~L 98 (113)
T PF03465_consen 86 EIISSEHEEGEQL 98 (113)
T ss_dssp EEE-TTSHHHHHH
T ss_pred EEEcCCCccHHHH
Confidence 9999888877766
No 25
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=95.81 E-value=0.053 Score=39.95 Aligned_cols=62 Identities=21% Similarity=0.203 Sum_probs=49.6
Q ss_pred HHHHHHHHHhcC-----CceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 39 LQQVLKTARAHD-----GLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 39 L~~lL~~A~~ag-----klv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+-..+.+.| .+.-|+-++++.|.+.-...|++-+..+| -..||..||++.||||..+++
T Consensus 22 ~~~v~~i~~~~gI~diN~IKPGIgEaTRvLLRRvP~~vLVr~~~~p--d~~Hl~~LA~ekgVpVe~~~d 88 (100)
T PF15608_consen 22 WAEVERIAERYGISDINLIKPGIGEATRVLLRRVPWKVLVRDPDDP--DLAHLLLLAEEKGVPVEVYPD 88 (100)
T ss_pred HHHHHHHHHHhCCCCcccccCChhHHHHHHHhcCCCEEEECCCCCc--cHHHHHHHHHHcCCcEEEeCC
Confidence 334445555555 57889999999999999888888776666 456999999999999999885
No 26
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=95.81 E-value=0.049 Score=36.35 Aligned_cols=60 Identities=20% Similarity=0.288 Sum_probs=45.5
Q ss_pred ceeeHHHHHHHHhcCC-eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 52 LAKGLHEAAKALDRRE-AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 52 lv~G~~~v~KaL~kgk-akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
++.|.+.+..+|+.+. ..-|++..+... .....+..+|.+.++|+..++ +..|.++++..
T Consensus 1 lieG~~~V~eaL~~~~~i~~l~~~~~~~~-~~~~~i~~~~~~~~i~v~~v~-~~~l~~ls~~~ 61 (76)
T PF08032_consen 1 LIEGRHAVEEALKSGPRIKKLFVTEEKAD-KRIKEILKLAKKKGIPVYEVS-KKVLDKLSDTE 61 (76)
T ss_dssp EEESHHHHHHHHHCTGGEEEEEEETT----CCTHHHHHHHHHCT-EEEEE--HHHHHHCTTTS
T ss_pred CEEEHHHHHHHHcCCCCccEEEEEcCccc-hhHHHHHHHHHHcCCeEEEeC-HHHHHHHcCCC
Confidence 5789999999999975 889999999433 234567889999999999886 66799998743
No 27
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=94.49 E-value=0.3 Score=43.69 Aligned_cols=65 Identities=14% Similarity=0.139 Sum_probs=52.4
Q ss_pred HHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCc-----------------------------------------hhhHH
Q psy16564 46 ARAHDGLAKGLHEAAKALDRREAQLCVLADNCDE-----------------------------------------PAYKK 84 (157)
Q Consensus 46 A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~-----------------------------------------~~~~~ 84 (157)
++..|..+.|.++|.+||+.|.+..++|..|-.- .++..
T Consensus 287 ~~d~G~avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ve 366 (409)
T TIGR00108 287 IQEDGLACYGEDEVLKALDLGAVETLIVSEDLEYIRVTYKCAECGEVIEKTVRELKDKKFAICPACGQEMDVVEERDLIE 366 (409)
T ss_pred hcCCCcEEeCHHHHHHHHHhCCCcEEEEeccccceeEEEEcCCCCceeecccccccccccccCcccCccccchhhhhHHH
Confidence 3447899999999999999999999999997520 12456
Q ss_pred HHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 85 LVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 85 ~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
.|...|+++|..+.++.+.-+=|.-+
T Consensus 367 ~L~e~a~~~Ga~V~iiS~~~eeG~ql 392 (409)
T TIGR00108 367 WLSELAENFGAKLEFISTESEEGAQL 392 (409)
T ss_pred HHHHHHHHcCCEEEEECCCChhHHHH
Confidence 67888999999999999887766443
No 28
>PRK04011 peptide chain release factor 1; Provisional
Probab=93.79 E-value=0.37 Score=43.16 Aligned_cols=73 Identities=15% Similarity=0.198 Sum_probs=54.8
Q ss_pred HHHHHHHH-HHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCC--------------------------------------
Q psy16564 38 ALQQVLKT-ARAHDGLAKGLHEAAKALDRREAQLCVLADNCD-------------------------------------- 78 (157)
Q Consensus 38 ~L~~lL~~-A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s-------------------------------------- 78 (157)
.+..++.. ++..|..+.|.++|.+|++.|.+.-++|.+|-.
T Consensus 282 lle~f~~~l~~d~g~avyG~~~V~~Ale~GAVetLLV~d~l~~~r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~~ 361 (411)
T PRK04011 282 LMEEFFKELAKDGGLAVYGEEEVRKALEMGAVDTLLISEDLRKDRVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSELE 361 (411)
T ss_pred HHHHHHHHHhcCCCcEEEcHHHHHHHHHcCCceEEEEeccccceeEEEEcCCCCcceeeecccccccccccCcccCcccc
Confidence 33344433 334688999999999999999999998876531
Q ss_pred ---chhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 79 ---EPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 79 ---~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
.......|...++++|..+.++.+.-+-|.-+
T Consensus 362 ~~~~~~~v~~l~e~a~~~g~~v~iis~~~e~G~qL 396 (411)
T PRK04011 362 IVEEEDIIEELSELAEQSGTKVEVISTDTEEGEQL 396 (411)
T ss_pred cchhhhHHHHHHHHHHHcCCEEEEECCCChhHHHH
Confidence 11345667888999999999999887777555
No 29
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=93.78 E-value=0.56 Score=41.94 Aligned_cols=64 Identities=17% Similarity=0.179 Sum_probs=51.7
Q ss_pred HhcCCceeeHHHHHHHHhcCCeeEEEEcCCCC-----------------------------------------chhhHHH
Q psy16564 47 RAHDGLAKGLHEAAKALDRREAQLCVLADNCD-----------------------------------------EPAYKKL 85 (157)
Q Consensus 47 ~~agklv~G~~~v~KaL~kgkakLVIlA~D~s-----------------------------------------~~~~~~~ 85 (157)
+..|..+.|.++|.+|++.|.+.-++|..|-. .......
T Consensus 284 ~d~g~avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ve~ 363 (403)
T TIGR03676 284 KDGGLAAYGEEEVRKALEMGAVDTLLISEDLRKIRVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSELEIVEEEDIIEE 363 (403)
T ss_pred cCCCcEEEcHHHHHHHHHhCCCcEEEEEccccceeEEEEcCCCCcceeeecccccccccccCcccCcccccchhhhHHHH
Confidence 34688999999999999999999999987651 1135567
Q ss_pred HHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 86 VQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 86 l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
+...++++|..+.++.+.-+-|.-+
T Consensus 364 L~e~a~~~Ga~V~~iS~~~eeG~ql 388 (403)
T TIGR03676 364 LSELAEESGAKVEIISTDTEEGEQL 388 (403)
T ss_pred HHHHHHHcCCEEEEECCCChhHHHH
Confidence 7888999999999999887777544
No 30
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=93.68 E-value=0.43 Score=41.78 Aligned_cols=73 Identities=12% Similarity=0.130 Sum_probs=55.6
Q ss_pred HHHHHHHHHHh-cCCceeeHHHHHHHHhcCCeeEEEEcCCC-CchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 38 ALQQVLKTARA-HDGLAKGLHEAAKALDRREAQLCVLADNC-DEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 38 ~L~~lL~~A~~-agklv~G~~~v~KaL~kgkakLVIlA~D~-s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
++.+++....+ .|..++|.++|.+|++.|-+.-++|+.+. ....-...+...+++.|..|+.+++.-+-|+-+
T Consensus 263 ~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l~~~r~~~~~l~~~v~~~gg~V~i~Ss~~e~G~qL 337 (351)
T TIGR00111 263 VIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVLVQREEIEKLLDSVESMGGKVVILSTEHELGKQL 337 (351)
T ss_pred HHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEecchhhhHHHHHHHHHHHHHcCCEEEEEcCCCccHHHH
Confidence 44444444433 47999999999999999999999999987 221223456778899999999999887777665
No 31
>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=93.23 E-value=0.34 Score=34.36 Aligned_cols=54 Identities=17% Similarity=0.141 Sum_probs=42.0
Q ss_pred HHHHHHHhc--CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC--CHHHHHHHh
Q psy16564 57 HEAAKALDR--REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD--NNKKLGEWA 110 (157)
Q Consensus 57 ~~v~KaL~k--gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~--sk~eLG~a~ 110 (157)
..-...|.. +++-+||+-.|+-.+.....+...|+++++|+++.. +...|-+++
T Consensus 36 ~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~~akk~~ip~~~~~~~~~~~l~~~l 93 (97)
T PF10087_consen 36 EKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKKAAKKYGIPIIYSRSRGVSSLERAL 93 (97)
T ss_pred ccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHHHHHHcCCcEEEECCCCHHHHHHHH
Confidence 444444554 568999999998888999999999999999999988 444554443
No 32
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=85.90 E-value=8.1 Score=31.97 Aligned_cols=60 Identities=13% Similarity=0.103 Sum_probs=45.9
Q ss_pred CceeeHHHHHHHHhc-C-CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 51 GLAKGLHEAAKALDR-R-EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 51 klv~G~~~v~KaL~k-g-kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
.++.|.+.+..+|+. + ...-+++..+.....+ ..+..+|++.+|++..+. .++|-++++.
T Consensus 3 ~~i~G~~~v~eal~~~~~~~~~l~~~~~~~~~~~-~~~~~~~~~~~i~~~~v~-~~~l~~ls~~ 64 (244)
T PRK11181 3 EIIYGIHAVQALLERAPERFIEVFVLKGREDKRL-LPLINELEAQGIVIQLAN-RQTLDEKAEG 64 (244)
T ss_pred cEEEehHHHHHHHhCCCCceeEEEEECCCcchHH-HHHHHHHHHcCCcEEEeC-HHHHhhhhcC
Confidence 468999999999975 3 5677778777655333 456678888999988775 7889998875
No 33
>PRK10864 putative methyltransferase; Provisional
Probab=85.75 E-value=8.8 Score=33.88 Aligned_cols=68 Identities=12% Similarity=0.137 Sum_probs=50.3
Q ss_pred HHHHHhcCCceeeHHHHHHHHhc--CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 43 LKTARAHDGLAKGLHEAAKALDR--REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 43 L~~A~~agklv~G~~~v~KaL~k--gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
+...+....++.|.+.|..+|+. ..+.-+++.....+ ... .+..++..+++++..+ +.++|-++++..
T Consensus 101 ~~~~~~~~~~I~G~~aV~ealk~~~~~i~~l~~~~~~~~-~~~-~il~~~~~~~~~v~~V-~~~~l~kls~~~ 170 (346)
T PRK10864 101 LRRQRAEETRVYGENACQALFQSRPEAIVRAWFIQSVTP-RFK-EALRWMAANRKAYHVV-DEAELTKASGTE 170 (346)
T ss_pred HhhccCCCcEEEEHHHHHHHHhCCCCceeEEEEecCccH-HHH-HHHHHHHHcCCcEEEe-CHHHHHHHhCCC
Confidence 55666667899999999999986 34666677777665 444 4556667788997766 678899999854
No 34
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=85.55 E-value=2.8 Score=30.82 Aligned_cols=47 Identities=17% Similarity=0.214 Sum_probs=37.3
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCCC--C-c-hhhHHHHHHHHHhCCCCEEEe
Q psy16564 54 KGLHEAAKALDRREAQLCVLADNC--D-E-PAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D~--s-~-~~~~~~l~~lc~~~~Ipvi~v 100 (157)
-|..++...|+.|++.+||--.|- . + ..-...|...|-+++||+++-
T Consensus 57 ~g~~~i~~~i~~g~i~~VInt~~~~~~~~~~~dg~~iRr~a~~~~Ip~~Tt 107 (115)
T cd01422 57 GGDQQIGALIAEGEIDAVIFFRDPLTAQPHEPDVKALLRLCDVYNIPLATN 107 (115)
T ss_pred CchhHHHHHHHcCceeEEEEcCCCCCCCcccccHHHHHHHHHHcCCCEEEc
Confidence 577889999999999999988772 2 1 133567899999999999864
No 35
>TIGR00679 hpr-ser Hpr(Ser) kinase/phosphatase. The hprK gene of Enterococcus faecalis encodes a bifunctional enzyme: the HPr kinase/phosphatase
Probab=82.97 E-value=6.4 Score=34.24 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=40.8
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGL 112 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~ 112 (157)
+.++.+-+.+...+|++.+..++ ..+...|++++||++..+ ...+|+..+..
T Consensus 73 ~~~~~~~~~~~P~iIvt~~~~~p---~~l~~~a~~~~ip~l~t~~~~~~~~~~l~~ 125 (304)
T TIGR00679 73 QIIHNLLTLNPPAIILSKSFTDP---TVLLQVNETYQVPILKTDLFSTELSFRLET 125 (304)
T ss_pred HHHHHHhCCCCCEEEEECcCCCC---HHHHHHHHHhCCcEEEeCCcHHHHHHHHHH
Confidence 35556667889999999998774 457788999999999987 66777776654
No 36
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=82.66 E-value=13 Score=30.60 Aligned_cols=57 Identities=19% Similarity=0.241 Sum_probs=41.2
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCC-CchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNC-DEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~-s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
++.|.+.+..+++.+. ++.+. ... .+ ... .+..+|++.+||++.++ +++|-+++|..
T Consensus 3 ~i~G~~~v~eal~~~~-~~~~~-~~~~~~-~~~-~~~~~~~~~~~~~~~v~-~~~l~~l~~~~ 60 (237)
T TIGR00186 3 YLYGKNAVLEALLNQQ-RVFIL-KGLESK-RLK-KLIQLAKKQGINIQLVD-RQKLDQLTKGG 60 (237)
T ss_pred EEEehHHHHHHHhCCC-EEEEE-ecCcch-HHH-HHHHHHHHcCCcEEEeC-HHHHHHHhCCC
Confidence 5799999999999883 33332 222 23 333 46778888999999985 78899999853
No 37
>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=80.80 E-value=3.8 Score=30.61 Aligned_cols=41 Identities=17% Similarity=0.276 Sum_probs=27.8
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++.|-..+...+|++.|..++ ..+.++|++++||++...
T Consensus 72 ~~l~~l~~~~~P~iIvt~~~~~p---~~l~e~a~~~~ipll~t~ 112 (127)
T PF02603_consen 72 ERLEKLFSYNPPCIIVTRGLEPP---PELIELAEKYNIPLLRTP 112 (127)
T ss_dssp CHHHHHCTTT-S-EEEETTT------HHHHHHHHHCT--EEEES
T ss_pred HHHHHHhCCCCCEEEEECcCCCC---HHHHHHHHHhCCcEEEcC
Confidence 45566667889999999998763 457788999999999877
No 38
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=80.54 E-value=11 Score=33.44 Aligned_cols=72 Identities=19% Similarity=0.225 Sum_probs=54.4
Q ss_pred HHHHH-HHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCC------CchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 40 QQVLK-TARAHDGLAKGLHEAAKALDRREAQLCVLADNC------DEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 40 ~~lL~-~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~------s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
.++|. +|+.-+++.+|.++|.+|++-|.+.-++|+..- ..-.-...+....+..|=+++.+++--+.|.-+-
T Consensus 260 e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~lr~~~~~~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge~Lk 338 (352)
T COG1537 260 EEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRSDDVEEREDVEELLEEVESMGGKVVIVSTEHEPGERLK 338 (352)
T ss_pred HHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhhhcccchhhHHHHHHHHHHHHHcCCeEEEEecCCcchHHHH
Confidence 33443 344467999999999999999999999888742 2213445567778889999999998888887664
No 39
>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=80.04 E-value=4.6 Score=29.20 Aligned_cols=46 Identities=11% Similarity=0.082 Sum_probs=34.7
Q ss_pred eHHHHHHHHhc-CCeeEEEEcCCCC----chhhHHHHHHHHHhCCCCEEEe
Q psy16564 55 GLHEAAKALDR-REAQLCVLADNCD----EPAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 55 G~~~v~KaL~k-gkakLVIlA~D~s----~~~~~~~l~~lc~~~~Ipvi~v 100 (157)
|..++...|+. |++.+||--.|-. ...--..+...|-+++||+++-
T Consensus 55 g~~~i~~~i~~~g~idlVIn~~~~~~~~~~~~dg~~iRR~A~~~~Ip~~T~ 105 (112)
T cd00532 55 GEPTVDAAIAEKGKFDVVINLRDPRRDRCTDEDGTALLRLARLYKIPVTTP 105 (112)
T ss_pred CCcHHHHHHhCCCCEEEEEEcCCCCcccccCCChHHHHHHHHHcCCCEEEC
Confidence 66789999999 9999998866521 1123457889999999999863
No 40
>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=78.55 E-value=2.8 Score=29.40 Aligned_cols=42 Identities=12% Similarity=0.088 Sum_probs=32.1
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhh---HHHHHHHHHhCCCCEEE
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAY---KKLVQALCSEHQIPLIK 99 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~---~~~l~~lc~~~~Ipvi~ 99 (157)
+..+.|+.+++.|||.--+...... --.+..+|.+++||+++
T Consensus 51 ~i~~~i~~~~IdlVIn~~~~~~~~~~~dg~~irr~a~~~~Ip~~T 95 (95)
T PF02142_consen 51 QIMDLIKNGKIDLVINTPYPFSDQEHTDGYKIRRAAVEYNIPLFT 95 (95)
T ss_dssp HHHHHHHTTSEEEEEEE--THHHHHTHHHHHHHHHHHHTTSHEEC
T ss_pred HHHHHHHcCCeEEEEEeCCCCcccccCCcHHHHHHHHHcCCCCcC
Confidence 6899999999999998887655322 35678999999999863
No 41
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=77.05 E-value=6.7 Score=30.11 Aligned_cols=56 Identities=11% Similarity=0.084 Sum_probs=39.8
Q ss_pred eHHHHHHHHhcCCeeEEEEcCC-CCc---hhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHh
Q psy16564 55 GLHEAAKALDRREAQLCVLADN-CDE---PAYKKLVQALCSEHQIPLIKVD-NNKKLGEWA 110 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D-~s~---~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~ 110 (157)
|..+....|+.|++.+||--.| ..+ ..-...|...|-+++||+++-- +-..+-+++
T Consensus 63 g~~~i~~~I~~g~i~lVInt~dp~~~~~~~~D~~~IRR~Av~~~IP~~T~l~tA~a~~~al 123 (142)
T PRK05234 63 GDQQIGALIAEGKIDMLIFFRDPLTAQPHDPDVKALLRLADVWNIPVATNRATADFLISSL 123 (142)
T ss_pred CchhHHHHHHcCceeEEEEecCCCCCCcccchHHHHHHHHHHcCCCEEcCHHHHHHHHHHH
Confidence 6788999999999999988664 222 1224478999999999998743 444444444
No 42
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=75.92 E-value=3.6 Score=30.49 Aligned_cols=48 Identities=13% Similarity=0.117 Sum_probs=33.6
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 54 KGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
...++..+.+++..+.-|++|-+-++......+...|++.++.+..++
T Consensus 128 g~~~~l~~~~~~~~id~v~ial~~~~~~~i~~ii~~~~~~~v~v~~vP 175 (175)
T PF13727_consen 128 GDLDDLPELVREHDIDEVIIALPWSEEEQIKRIIEELENHGVRVRVVP 175 (175)
T ss_dssp --GGGHHHHHHHHT--EEEE--TTS-HHHHHHHHHHHHTTT-EEEE--
T ss_pred cCHHHHHHHHHhCCCCEEEEEcCccCHHHHHHHHHHHHhCCCEEEEeC
Confidence 345888888999999999999887776788899999999999998764
No 43
>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=75.81 E-value=19 Score=30.75 Aligned_cols=101 Identities=12% Similarity=0.134 Sum_probs=70.4
Q ss_pred CCCCCCCCCc-------------ccHHHHHHHHHHHHHhcCC-------------ceeeHHHHHHHHhcCCeeEEEEcCC
Q psy16564 23 NVPSANDEGV-------------SDINKALQQVLKTARAHDG-------------LAKGLHEAAKALDRREAQLCVLADN 76 (157)
Q Consensus 23 ~~~~p~~~~~-------------m~~~k~L~~lL~~A~~agk-------------lv~G~~~v~KaL~kgkakLVIlA~D 76 (157)
|+--|+++++ +++.+.| ++++..+..+. +..|...-++.+++-.+.=+++ -|
T Consensus 53 PfSDPvADGP~Iq~A~~rAL~~g~t~~~~l-el~~~~r~~~~~~Pivlm~Y~Npi~~~Gie~F~~~~~~~GvdGliv-pD 130 (265)
T COG0159 53 PFSDPVADGPTIQAAHLRALAAGVTLEDTL-ELVEEIRAKGVKVPIVLMTYYNPIFNYGIEKFLRRAKEAGVDGLLV-PD 130 (265)
T ss_pred CCCCcCccCHHHHHHHHHHHHCCCCHHHHH-HHHHHHHhcCCCCCEEEEEeccHHHHhhHHHHHHHHHHcCCCEEEe-CC
Confidence 5566777776 6778888 89999886642 5678888777776654555544 58
Q ss_pred CCchhhHHHHHHHHHhCCCCEEEeC----CHHHHHHHhCCCccccCCCccceeeeEEEEEe
Q psy16564 77 CDEPAYKKLVQALCSEHQIPLIKVD----NNKKLGEWAGLSKLDNMGKARKVVGCSCVVIK 133 (157)
Q Consensus 77 ~s~~~~~~~l~~lc~~~~Ipvi~v~----sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~ 133 (157)
.++ +....+...|++++|..+++- +.+.|-+..... +| .+.-.|+.++|
T Consensus 131 LP~-ee~~~~~~~~~~~gi~~I~lvaPtt~~~rl~~i~~~a----~G---FiY~vs~~GvT 183 (265)
T COG0159 131 LPP-EESDELLKAAEKHGIDPIFLVAPTTPDERLKKIAEAA----SG---FIYYVSRMGVT 183 (265)
T ss_pred CCh-HHHHHHHHHHHHcCCcEEEEeCCCCCHHHHHHHHHhC----CC---cEEEEeccccc
Confidence 888 677789999999999777742 557777777654 11 23445666666
No 44
>KOG4175|consensus
Probab=75.11 E-value=14 Score=30.99 Aligned_cols=86 Identities=12% Similarity=0.218 Sum_probs=60.4
Q ss_pred CCCCCCCCCc-------------ccHHHHHHHHHHHHHhcCC-------------ceeeHHHHHHHHhc-CCeeEEEEcC
Q psy16564 23 NVPSANDEGV-------------SDINKALQQVLKTARAHDG-------------LAKGLHEAAKALDR-REAQLCVLAD 75 (157)
Q Consensus 23 ~~~~p~~~~~-------------m~~~k~L~~lL~~A~~agk-------------lv~G~~~v~KaL~k-gkakLVIlA~ 75 (157)
|+--|+++.+ .++++.+ ++++.||.+|- +..|....+...++ |--.|+| -
T Consensus 54 PfSDp~ADGPtIq~~n~~aL~ng~tl~~i~-emvk~ar~~gvt~PIiLmgYYNPIl~yG~e~~iq~ak~aGanGfii--v 130 (268)
T KOG4175|consen 54 PFSDPLADGPTIQAANRRALLNGTTLNSII-EMVKEARPQGVTCPIILMGYYNPILRYGVENYIQVAKNAGANGFII--V 130 (268)
T ss_pred ccCccccCCchhhhhHHHHHHcCCcHHHHH-HHHHHhcccCcccceeeeecccHHHhhhHHHHHHHHHhcCCCceEe--c
Confidence 5566777776 3577788 99999999973 56788877777765 4444443 4
Q ss_pred CCCchhhHHHHHHHHHhCCCCEEEe---C-CHHHHHHHhCC
Q psy16564 76 NCDEPAYKKLVQALCSEHQIPLIKV---D-NNKKLGEWAGL 112 (157)
Q Consensus 76 D~s~~~~~~~l~~lc~~~~Ipvi~v---~-sk~eLG~a~G~ 112 (157)
|.+| +-...+...|++++|..+-. . +.+++-.+...
T Consensus 131 DlPp-EEa~~~Rne~~k~gislvpLvaPsTtdeRmell~~~ 170 (268)
T KOG4175|consen 131 DLPP-EEAETLRNEARKHGISLVPLVAPSTTDERMELLVEA 170 (268)
T ss_pred cCCh-HHHHHHHHHHHhcCceEEEeeCCCChHHHHHHHHHh
Confidence 8888 56667899999999866542 2 55555555543
No 45
>PF07997 DUF1694: Protein of unknown function (DUF1694); InterPro: IPR012543 This family contains many hypothetical proteins.; PDB: 2OHW_A.
Probab=74.56 E-value=11 Score=28.21 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=36.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHH
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNK 104 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~ 104 (157)
.+..++|++.....++|..+.+. .....+..+|+++++|+-.+.+..
T Consensus 52 ~~~~~~l~~~~~~~l~ing~l~~-~~~~~YiklA~~~~~~fTiv~~~~ 98 (120)
T PF07997_consen 52 PEFEQALKDYPNYKLKINGNLDY-SFQSKYIKLANKHGIPFTIVNDPE 98 (120)
T ss_dssp HHHHHHHHC-SSEEEEEETTS-H-HHHHHHHHHHHHTT--EEEE---S
T ss_pred HHHHHHHhhCCCeEEEEcCCCCH-HHHHHHHHHHHHcCCCEEEeCCCC
Confidence 56778888889999999999999 788899999999999999998643
No 46
>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=73.60 E-value=7.2 Score=26.89 Aligned_cols=47 Identities=13% Similarity=0.087 Sum_probs=34.6
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCC-C--chhhHHHHHHHHHhCCCCEE
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNC-D--EPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~-s--~~~~~~~l~~lc~~~~Ipvi 98 (157)
+--|.....+.++.|++.+||--.+- . +..-...+...|.+++||+.
T Consensus 40 i~~~~~~i~~~i~~g~id~VIn~~~~~~~~~~~d~~~iRr~A~~~~Ip~~ 89 (90)
T smart00851 40 VHGGILAILDLIKNGEIDLVINTLYPLGAQPHEDGKALRRAAENIDIPGA 89 (90)
T ss_pred CCCCCHHHHHHhcCCCeEEEEECCCcCcceeccCcHHHHHHHHHcCCCee
Confidence 33455668999999999999986552 2 21224578999999999986
No 47
>TIGR01544 HAD-SF-IE haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.
Probab=73.12 E-value=6.7 Score=33.54 Aligned_cols=36 Identities=8% Similarity=-0.039 Sum_probs=24.6
Q ss_pred cCCCCCCC-CCCcccHHHHHHHHHHHHHhcCCceeeH
Q psy16564 21 TDNVPSAN-DEGVSDINKALQQVLKTARAHDGLAKGL 56 (157)
Q Consensus 21 ~~~~~~p~-~~~~m~~~k~L~~lL~~A~~agklv~G~ 56 (157)
--+.|+|+ +++.|+++..++-+..--.++..+..|.
T Consensus 68 l~~~Y~PiE~d~~~~~~eK~~~m~eWw~k~~~l~~~~ 104 (277)
T TIGR01544 68 LKEKYYPIEVDPVLTVEEKYPYMVEWWTKSHGLLVQQ 104 (277)
T ss_pred HHhhccceecCCCCChHHhhhHHHHHHHHHHHHHhcC
Confidence 34679999 5567888877766666666666665555
No 48
>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=71.99 E-value=12 Score=26.61 Aligned_cols=45 Identities=13% Similarity=0.136 Sum_probs=32.7
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCc-hhhHHHHHHHHHhCCCCEEE
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDE-PAYKKLVQALCSEHQIPLIK 99 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~-~~~~~~l~~lc~~~~Ipvi~ 99 (157)
|..+....|++|++.+||--.+-.. ..---.+...|-+++||++.
T Consensus 55 ~~~~i~~~i~~~~id~vIn~~~~~~~~~~~~~iRR~Av~~~ipl~T 100 (110)
T cd01424 55 GRPNIVDLIKNGEIQLVINTPSGKRAIRDGFSIRRAALEYKVPYFT 100 (110)
T ss_pred CchhHHHHHHcCCeEEEEECCCCCccCccHHHHHHHHHHhCCCEEe
Confidence 5677888888999999988554211 11234688999999999984
No 49
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=71.97 E-value=8.8 Score=27.33 Aligned_cols=47 Identities=23% Similarity=0.318 Sum_probs=33.4
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEE
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
+...-|..++++.|++...+++|+.++.+. ........| +..|+++-
T Consensus 13 ~~~ipga~e~l~~L~~~g~~~~~lTNns~~-s~~~~~~~L-~~~Gi~~~ 59 (101)
T PF13344_consen 13 NEPIPGAVEALDALRERGKPVVFLTNNSSR-SREEYAKKL-KKLGIPVD 59 (101)
T ss_dssp TEE-TTHHHHHHHHHHTTSEEEEEES-SSS--HHHHHHHH-HHTTTT--
T ss_pred CCcCcCHHHHHHHHHHcCCCEEEEeCCCCC-CHHHHHHHH-HhcCcCCC
Confidence 457789999999999988999999999876 334444444 77899864
No 50
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=71.68 E-value=12 Score=26.47 Aligned_cols=72 Identities=19% Similarity=0.231 Sum_probs=38.7
Q ss_pred CcccHHHHHHHHHHHHHhcCCce-e-eH-HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHH
Q psy16564 31 GVSDINKALQQVLKTARAHDGLA-K-GL-HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKL 106 (157)
Q Consensus 31 ~~m~~~k~L~~lL~~A~~agklv-~-G~-~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eL 106 (157)
.-|++...+ +.++. |.++ . |. ..++.......+..+||..+..| ...+..+|++++||++..+ +.-+-
T Consensus 27 ~a~~~~~~~-~~~~~----~~lvIt~gdR~di~~~a~~~~i~~iIltg~~~~---~~~v~~la~~~~i~vi~t~~dtf~t 98 (105)
T PF07085_consen 27 GAMSLSDFL-EYLKP----GDLVITPGDREDIQLAAIEAGIACIILTGGLEP---SEEVLELAKELGIPVISTPYDTFET 98 (105)
T ss_dssp -SS-HHHHH-HCHHT----TEEEEEETT-HHHHHHHCCTTECEEEEETT-------HHHHHHHHHHT-EEEE-SS-HHHH
T ss_pred EECCHHHHH-hhcCC----CeEEEEeCCcHHHHHHHHHhCCCEEEEeCCCCC---CHHHHHHHHHCCCEEEEECCCHHHH
Confidence 345555555 33333 5443 3 43 34444444444888889988766 3457789999999999988 55554
Q ss_pred HHHh
Q psy16564 107 GEWA 110 (157)
Q Consensus 107 G~a~ 110 (157)
.+.+
T Consensus 99 a~~i 102 (105)
T PF07085_consen 99 ARLI 102 (105)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 4443
No 51
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=67.03 E-value=7 Score=34.67 Aligned_cols=40 Identities=25% Similarity=0.264 Sum_probs=32.5
Q ss_pred hcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHH
Q psy16564 64 DRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNK 104 (157)
Q Consensus 64 ~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~ 104 (157)
...-|-||+-|.|-+-+.+.+|+. |+++.++|++.++ +|.
T Consensus 98 qmDgAILVVsA~dGpmPqTrEHiL-larqvGvp~ivvflnK~ 138 (394)
T COG0050 98 QMDGAILVVAATDGPMPQTREHIL-LARQVGVPYIVVFLNKV 138 (394)
T ss_pred hcCccEEEEEcCCCCCCcchhhhh-hhhhcCCcEEEEEEecc
Confidence 445688999999988778999864 8999999999877 553
No 52
>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=65.57 E-value=30 Score=29.33 Aligned_cols=44 Identities=23% Similarity=0.375 Sum_probs=37.5
Q ss_pred EEEcCCCCchhhHHHHHHHHHhCCCCEEEeC--CHHHHHHHhCCCcc
Q psy16564 71 CVLADNCDEPAYKKLVQALCSEHQIPLIKVD--NNKKLGEWAGLSKL 115 (157)
Q Consensus 71 VIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~--sk~eLG~a~G~~~~ 115 (157)
+|+..=+++ ++...+...|++++||++-+. -...|...+|....
T Consensus 55 iV~~Tlv~~-~lr~~l~~~~~~~~i~~~Dll~~~l~~l~~~lg~~p~ 100 (255)
T PF03618_consen 55 IVFYTLVDP-ELREYLEEFCREHGIPCVDLLGPLLSALEEFLGQKPS 100 (255)
T ss_pred EEEEeCCCH-HHHHHHHHHHHhcCCCEEeccHHHHHHHHHHHCcCcc
Confidence 667777888 899999999999999999987 56799999998633
No 53
>PLN02591 tryptophan synthase
Probab=65.37 E-value=46 Score=27.89 Aligned_cols=88 Identities=13% Similarity=0.196 Sum_probs=56.7
Q ss_pred CCCCCCCCCc-------------ccHHHHHHHHHHHHHhcCC------------ceeeHHHHHHHHhcCCeeEEEEcCCC
Q psy16564 23 NVPSANDEGV-------------SDINKALQQVLKTARAHDG------------LAKGLHEAAKALDRREAQLCVLADNC 77 (157)
Q Consensus 23 ~~~~p~~~~~-------------m~~~k~L~~lL~~A~~agk------------lv~G~~~v~KaL~kgkakLVIlA~D~ 77 (157)
|+--|+++++ +++++.+ ++++..|+.-+ +..|.+.-.+.++.--+.=||+. |.
T Consensus 38 PfSDP~aDGpvIq~a~~rAL~~G~~~~~~~-~~~~~~r~~~~~p~ilm~Y~N~i~~~G~~~F~~~~~~aGv~Gviip-DL 115 (250)
T PLN02591 38 PYSDPLADGPVIQAAATRALEKGTTLDSVI-SMLKEVAPQLSCPIVLFTYYNPILKRGIDKFMATIKEAGVHGLVVP-DL 115 (250)
T ss_pred CCCCCcccCHHHHHHHHHHHHcCCCHHHHH-HHHHHHhcCCCCCEEEEecccHHHHhHHHHHHHHHHHcCCCEEEeC-CC
Confidence 4555677766 4555666 66666654321 23477777777776556666555 77
Q ss_pred CchhhHHHHHHHHHhCCCCEEE-e-C--CHHHHHHHhCCC
Q psy16564 78 DEPAYKKLVQALCSEHQIPLIK-V-D--NNKKLGEWAGLS 113 (157)
Q Consensus 78 s~~~~~~~l~~lc~~~~Ipvi~-v-~--sk~eLG~a~G~~ 113 (157)
+. +-...+...|+++++..+. + + +.+++.+++...
T Consensus 116 P~-ee~~~~~~~~~~~gl~~I~lv~Ptt~~~ri~~ia~~~ 154 (250)
T PLN02591 116 PL-EETEALRAEAAKNGIELVLLTTPTTPTERMKAIAEAS 154 (250)
T ss_pred CH-HHHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHHhC
Confidence 76 5566788899999997776 4 2 235577777654
No 54
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=65.17 E-value=38 Score=30.76 Aligned_cols=64 Identities=11% Similarity=0.110 Sum_probs=50.8
Q ss_pred hcCCceeeHHHHHHHHhcCCeeEEEEcCCCCch----------------------------------------hhHHHHH
Q psy16564 48 AHDGLAKGLHEAAKALDRREAQLCVLADNCDEP----------------------------------------AYKKLVQ 87 (157)
Q Consensus 48 ~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~----------------------------------------~~~~~l~ 87 (157)
..|..+.|..++.++|+-|.+..+++..|-... .+...+.
T Consensus 292 ~~Gla~yG~~~vr~aL~~gaVd~llv~Edl~~~r~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~~~v~~~d~vd~l~ 371 (411)
T COG1503 292 DSGLAVYGEEEVREALEMGAVDTLLVSEDLEKERVTYKCPTCGYENLKSKREFEQKRFRCPECGSEMEEVEVSDLVDELA 371 (411)
T ss_pred CcceeecchHHHHHHHHhcccceEEeeccccccceeecCCCcchhhhhcccccccccccCccccccccchhhhhHHHHHH
Confidence 357677999999999999999999999987631 2356777
Q ss_pred HHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 88 ALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 88 ~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
..|++.+..+.++.+..+-|..+=
T Consensus 372 e~a~~~Ga~ve~is~~~~eg~q~~ 395 (411)
T COG1503 372 ELAEESGAKVEIISDDTDEGAQLL 395 (411)
T ss_pred HHHHhcCCeEEEecCchHHHHHHH
Confidence 788888888888887666666554
No 55
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=63.19 E-value=74 Score=26.63 Aligned_cols=59 Identities=20% Similarity=0.257 Sum_probs=47.2
Q ss_pred CceeeHHHHHHHHhcC-CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 51 GLAKGLHEAAKALDRR-EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 51 klv~G~~~v~KaL~kg-kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
.++.|.+.+..+++.+ .+.-+++.++..+ ... .+..+....++|++.+. +..|..+.+.
T Consensus 22 ~~~~G~~~v~~al~~~~~i~~i~~~~~~~~-~~~-~~~~~~~~~~~~~~~v~-~~~l~~~~~~ 81 (260)
T COG0566 22 FLIEGEHAVLEALASGPKIVRILVTEGRLP-RFE-ELLALAAAKGIPVYVVS-EAILDKLSGT 81 (260)
T ss_pred EEEeeHHHHHHHHhcCCCceEEEEecccch-hHH-HHHHHHHhcCCeEEEEC-HHHHHHHhCC
Confidence 6899999999999998 7888888888874 344 56677788899998776 5677777663
No 56
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=63.17 E-value=17 Score=32.39 Aligned_cols=62 Identities=10% Similarity=0.037 Sum_probs=45.0
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeEEEEEecCchh
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRNWF 138 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g~~ 138 (157)
|..+..++..|.....-.+.+..+++..++|+..+.+..+|..++..- ..+.++.|-.+|.+
T Consensus 166 G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l-----------~~~DlVLIDTaG~~ 227 (374)
T PRK14722 166 GASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAEL-----------RNKHMVLIDTIGMS 227 (374)
T ss_pred CCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHh-----------cCCCEEEEcCCCCC
Confidence 555777888887644566788999999999999999888887776532 12345667667765
No 57
>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=62.98 E-value=15 Score=27.18 Aligned_cols=35 Identities=23% Similarity=0.337 Sum_probs=29.8
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
....+||.+.|.. .....+..+|+++++|++...+
T Consensus 88 ~~~diVi~~~d~~--~~~~~l~~~~~~~~i~~i~~~~ 122 (143)
T cd01483 88 DGVDLVIDAIDNI--AVRRALNRACKELGIPVIDAGG 122 (143)
T ss_pred cCCCEEEECCCCH--HHHHHHHHHHHHcCCCEEEEcC
Confidence 4678999999984 4677899999999999998875
No 58
>TIGR03025 EPS_sugtrans exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase. Certain closely related transferase enzymes such as Sinorhizobium ExoY and Lactococcus EpsD lack the N-terminal domain and are not found by this model.
Probab=62.42 E-value=22 Score=31.37 Aligned_cols=53 Identities=9% Similarity=-0.018 Sum_probs=43.2
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
+.++..+.+++..+.-|++|.+..+......+...|++.++++..+++-.++.
T Consensus 176 ~~~~l~~~i~~~~id~ViIa~p~~~~~~~~~ll~~~~~~gv~V~~vP~~~e~~ 228 (445)
T TIGR03025 176 KLDDLVELVRAHRVDEVIIALPLSEEARILELLLQLRDLGVDVRLVPDLFEFL 228 (445)
T ss_pred CHHHHHHHHHhCCCCEEEEecCcccHHHHHHHHHHHHhcCCEEEEeCchhhhc
Confidence 45667788888889999999876664666778899999999999999877753
No 59
>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=62.33 E-value=15 Score=28.18 Aligned_cols=48 Identities=21% Similarity=0.210 Sum_probs=30.3
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKK 105 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~e 105 (157)
++.+++..-.+-++++..+.........+..+|..+++|++.+-+|.+
T Consensus 86 ~~~~~~~~~D~ailvVda~~g~~~~~~~~l~~~~~~~~p~ivvlNK~D 133 (188)
T PF00009_consen 86 EMIRGLRQADIAILVVDANDGIQPQTEEHLKILRELGIPIIVVLNKMD 133 (188)
T ss_dssp HHHHHHTTSSEEEEEEETTTBSTHHHHHHHHHHHHTT-SEEEEEETCT
T ss_pred cccceecccccceeeeecccccccccccccccccccccceEEeeeecc
Confidence 455556655566666665543434555667789999999888765543
No 60
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=62.01 E-value=6.5 Score=35.36 Aligned_cols=88 Identities=17% Similarity=0.201 Sum_probs=55.7
Q ss_pred eeeceEEeeccccCCCCCCCCCCcccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCc------hhh
Q psy16564 9 KTTKIVVVQGTATDNVPSANDEGVSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDE------PAY 82 (157)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~p~~~~~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~------~~~ 82 (157)
|...-|+||+..-.|+|..+-... .+.+.+=| -...|++..-..+..+++..+.+++.|+++==.| .+-
T Consensus 105 ~~gd~Vvi~tPvY~PF~~~i~~n~---R~~i~~pL--~~~~~~y~iD~~~LE~~~~~~~vkl~iLCnPHNP~Grvwt~ee 179 (388)
T COG1168 105 KPGDGVVIQTPVYPPFYNAIKLNG---RKVIENPL--VEDDGRYEIDFDALEKAFVDERVKLFILCNPHNPTGRVWTKEE 179 (388)
T ss_pred cCCCeeEecCCCchHHHHHHhhcC---cEEEeccc--cccCCcEEecHHHHHHHHhcCCccEEEEeCCCCCCCccccHHH
Confidence 445667787744444433332111 01111111 1256888889999999999999999999884333 124
Q ss_pred HHHHHHHHHhCCCCEEEeC
Q psy16564 83 KKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 83 ~~~l~~lc~~~~Ipvi~v~ 101 (157)
...+..+|++|||.|+.=+
T Consensus 180 L~~i~elc~kh~v~VISDE 198 (388)
T COG1168 180 LRKIAELCLRHGVRVISDE 198 (388)
T ss_pred HHHHHHHHHHcCCEEEeec
Confidence 4668899999999998533
No 61
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=61.20 E-value=22 Score=26.17 Aligned_cols=50 Identities=10% Similarity=0.040 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhC--CCCEEEeCCHHHH
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEH--QIPLIKVDNNKKL 106 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~--~Ipvi~v~sk~eL 106 (157)
+++.++|++-.+-++++....+.......+..+..+. +.|++.+.+|.+|
T Consensus 3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~~~l~~~l~~~~~~k~~iivlNK~DL 54 (141)
T cd01857 3 RQLWRVVERSDIVVQIVDARNPLLFRPPDLERYVKEVDPRKKNILLLNKADL 54 (141)
T ss_pred HHHHHHHhhCCEEEEEEEccCCcccCCHHHHHHHHhccCCCcEEEEEechhc
Confidence 5677777776655555544322212333455555554 7888888877776
No 62
>PLN02821 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
Probab=60.92 E-value=20 Score=32.94 Aligned_cols=50 Identities=16% Similarity=0.316 Sum_probs=37.5
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
..+..|...++-++|+-.+-.. .-..+|..+|++.++|.+++++.++|+.
T Consensus 353 dA~~~L~~~~vDlmiVVGG~NS-SNT~~L~eIa~~~g~~sy~Ie~~~eI~~ 402 (460)
T PLN02821 353 DAMYKLVEEKLDLMLVVGGWNS-SNTSHLQEIAEHKGIPSYWIDSEERIGP 402 (460)
T ss_pred HHHHHHhhcCCCEEEEECCCCC-ccHHHHHHHHHHhCCCEEEECCHHHcCc
Confidence 3455554455667766666555 4556789999999999999999999985
No 63
>PF07905 PucR: Purine catabolism regulatory protein-like family; InterPro: IPR012914 This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138 from SWISSPROT). PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression []. The other members of this family are also putative regulatory proteins.
Probab=59.89 E-value=28 Score=25.54 Aligned_cols=48 Identities=17% Similarity=0.259 Sum_probs=33.3
Q ss_pred HHHHh-cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 60 AKALD-RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 60 ~KaL~-kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
++.|. +|-+.|+|--.+.-+ .+-..+.++|+++++|++.++....+..
T Consensus 65 i~~L~~~~~agL~i~~~~~~~-~iP~~~i~~A~~~~lPli~ip~~~~f~~ 113 (123)
T PF07905_consen 65 IRELAEKGAAGLGIKTGRYLD-EIPEEIIELADELGLPLIEIPWEVPFSD 113 (123)
T ss_pred HHHHHHCCCeEEEEeccCccc-cCCHHHHHHHHHcCCCEEEeCCCCCHHH
Confidence 34443 466777775554444 5677889999999999999986544443
No 64
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=59.87 E-value=29 Score=28.69 Aligned_cols=21 Identities=24% Similarity=0.142 Sum_probs=14.4
Q ss_pred hhHHHHHHHHHhCCCCEEEeC
Q psy16564 81 AYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.....+..+.++.+|++++++
T Consensus 193 ~~l~~l~~~ik~~~v~~if~e 213 (264)
T cd01020 193 ADIAAFQNAIKNRQIDALIVN 213 (264)
T ss_pred HHHHHHHHHHHhCCCCEEEeC
Confidence 344566677777788887765
No 65
>TIGR03023 WcaJ_sugtrans Undecaprenyl-phosphate glucose phosphotransferase. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier, knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity.
Probab=58.67 E-value=28 Score=30.86 Aligned_cols=55 Identities=7% Similarity=-0.037 Sum_probs=44.2
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
..+.++..+.+++..+.-|++|....+......+...|+..++++..+++-.++.
T Consensus 177 lg~~~dl~~~i~~~~vd~ViIA~p~~~~~~~~~ll~~~~~~gv~V~vvP~~~e~~ 231 (451)
T TIGR03023 177 LGKLDDLEELIREGEVDEVYIALPLAAEDRILELLDALEDLTVDVRLVPDLFDFA 231 (451)
T ss_pred cCCHHHHHHHHHhcCCCEEEEeeCcccHHHHHHHHHHHHhcCCEEEEeCchhhhc
Confidence 3345778888888999999999876554566778889999999999999877654
No 66
>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=58.28 E-value=27 Score=23.07 Aligned_cols=38 Identities=29% Similarity=0.369 Sum_probs=26.1
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++.+..|+ .|.|++.|.. ....|+.+|++.|-.+..+.
T Consensus 20 l~~l~~G~-~l~V~~d~~~---a~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 20 IDKLQDGE-QLEVKASDPG---FARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred HHcCCCCC-EEEEEECCcc---HHHHHHHHHHHcCCEEEEEE
Confidence 33344455 5677777654 45679999999999988654
No 67
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=55.35 E-value=15 Score=26.08 Aligned_cols=34 Identities=21% Similarity=0.158 Sum_probs=25.9
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+.|||+|.|-. .....+...|++++||+..++.
T Consensus 60 ~~~lV~~at~d~--~~n~~i~~~a~~~~i~vn~~D~ 93 (103)
T PF13241_consen 60 GADLVFAATDDP--ELNEAIYADARARGILVNVVDD 93 (103)
T ss_dssp TESEEEE-SS-H--HHHHHHHHHHHHTTSEEEETT-
T ss_pred hheEEEecCCCH--HHHHHHHHHHhhCCEEEEECCC
Confidence 378999988764 4778899999999999988764
No 68
>TIGR02342 chap_CCT_delta T-complex protein 1, delta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=54.77 E-value=35 Score=31.13 Aligned_cols=56 Identities=11% Similarity=0.122 Sum_probs=40.2
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH---HHHHHHhCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN---KKLGEWAGL 112 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk---~eLG~a~G~ 112 (157)
...++.|....+.+||++.+.+...+-.....++.+++|-++.--++ ++|.+++|-
T Consensus 263 ~~~v~~i~~~g~~lvi~~~~I~~~~l~~l~~~~l~~~~I~av~~v~~~~LerIa~~tGa 321 (517)
T TIGR02342 263 LNIVKKIKKTGCNVLLIQKSILRDAVNDLALHFLAKMKIMVVKDIEREEVEFICKTIGC 321 (517)
T ss_pred HHHHHHHHhcCCCEEEECCCcccccccHHHHHHHhhCCceEEecCCHHHHHHHHHHHCC
Confidence 44566666667899999999865445556777888899999986664 455566663
No 69
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=54.70 E-value=23 Score=25.86 Aligned_cols=46 Identities=17% Similarity=0.242 Sum_probs=36.4
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 54 KGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+..++...+.....-+++++.++.- ....+...|..++||+..++
T Consensus 37 ~~~~e~~~~~~~~~~DvIll~PQi~~--~~~~i~~~~~~~~ipv~~I~ 82 (104)
T PRK09590 37 ITATEGEKAIAAAEYDLYLVSPQTKM--YFKQFEEAGAKVGKPVVQIP 82 (104)
T ss_pred ecHHHHHHhhccCCCCEEEEChHHHH--HHHHHHHHhhhcCCCEEEeC
Confidence 56666666556667889999988864 56778999999999999876
No 70
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=54.13 E-value=57 Score=26.60 Aligned_cols=74 Identities=19% Similarity=0.136 Sum_probs=50.2
Q ss_pred CCcccHHHHHHHHHHHHH-hcC---Cceee------HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE
Q psy16564 30 EGVSDINKALQQVLKTAR-AHD---GLAKG------LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK 99 (157)
Q Consensus 30 ~~~m~~~k~L~~lL~~A~-~ag---klv~G------~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~ 99 (157)
|=+|+...++ +.++..+ +.+ .+..| .+++.++++.| +.|++ +| .+...+..+|++++||++-
T Consensus 43 Eit~~~~~a~-~~i~~l~~~~~~~p~~~vGaGTV~~~~~~~~a~~aG-A~Fiv-----sP-~~~~~v~~~~~~~~i~~iP 114 (213)
T PRK06552 43 EVTYTNPFAS-EVIKELVELYKDDPEVLIGAGTVLDAVTARLAILAG-AQFIV-----SP-SFNRETAKICNLYQIPYLP 114 (213)
T ss_pred EEECCCccHH-HHHHHHHHHcCCCCCeEEeeeeCCCHHHHHHHHHcC-CCEEE-----CC-CCCHHHHHHHHHcCCCEEC
Confidence 3345555566 4444443 332 47777 47788888888 77775 45 4555788899999999987
Q ss_pred -eCCHHHHHHHhC
Q psy16564 100 -VDNNKKLGEWAG 111 (157)
Q Consensus 100 -v~sk~eLG~a~G 111 (157)
+.|-.|+=++..
T Consensus 115 G~~T~~E~~~A~~ 127 (213)
T PRK06552 115 GCMTVTEIVTALE 127 (213)
T ss_pred CcCCHHHHHHHHH
Confidence 448888877764
No 71
>PF13611 Peptidase_S76: Serine peptidase of plant viral polyprotein, P1
Probab=53.45 E-value=21 Score=27.23 Aligned_cols=29 Identities=24% Similarity=0.472 Sum_probs=23.5
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+|+ ++-.++...+.++|.+.|||+.+++.
T Consensus 30 v~~-~~i~dL~~~~~~ic~ergiPIe~I~~ 58 (121)
T PF13611_consen 30 VAN-NEIDDLVREVTEICCERGIPIEIIDK 58 (121)
T ss_pred Eec-CcHHHHHHHHHHHHHHcCCCEEEecC
Confidence 665 33335888899999999999999984
No 72
>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=52.87 E-value=33 Score=27.76 Aligned_cols=49 Identities=20% Similarity=0.157 Sum_probs=29.9
Q ss_pred HHHHHHh--cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 58 EAAKALD--RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 58 ~v~KaL~--kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
.+.+++. .-..-++++..|..+......+..++.+.++|++.+-+|.++
T Consensus 100 ~~~~~~~~~~~D~~llVvda~~g~~~~d~~~l~~l~~~~ip~ivvvNK~D~ 150 (224)
T cd04165 100 TTLFGLTGYAPDYAMLVVAANAGIIGMTKEHLGLALALNIPVFVVVTKIDL 150 (224)
T ss_pred HHHHhhcccCCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEECccc
Confidence 4455554 223444445444333345556677889999999887776654
No 73
>PF15632 ATPgrasp_Ter: ATP-grasp in the biosynthetic pathway with Ter operon
Probab=52.53 E-value=50 Score=28.91 Aligned_cols=56 Identities=18% Similarity=0.305 Sum_probs=42.0
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCc------------------hhhHHHHHHHHHhCCCCEEEeC-CHHHHHH
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDE------------------PAYKKLVQALCSEHQIPLIKVD-NNKKLGE 108 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~------------------~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~ 108 (157)
-..+...++++|+++ ..+-|+|+|.++ .++...+..+|++++|.++.-. +.+.|.+
T Consensus 7 ~~s~~~~~i~~lr~~-~~~~i~~sh~~~~~~~~~~aD~~~~eP~~~~~yv~~~l~~C~~~~Idv~~P~~~~~~l~~ 81 (329)
T PF15632_consen 7 GFSSQRDIIRSLRAN-RDFTIIASHRDPRAPILYAADEAYLEPADGEEYVDWCLDFCKEHGIDVFVPGRNRELLAA 81 (329)
T ss_pred CCccHHHHHHHHHcC-CCeEEEEEeCCCCchHHhcCceeeecCCCHHHHHHHHHHHHHHhCCeEEEcCccHHHHHH
Confidence 356778888888887 777777776543 3678899999999999999877 4444443
No 74
>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=52.32 E-value=49 Score=28.35 Aligned_cols=53 Identities=21% Similarity=0.446 Sum_probs=34.8
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH-HHhC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG-EWAG 111 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG-~a~G 111 (157)
.+..+.|.+ ++-++|+-.+-.. .-..+|-++|++++.|.+.+++..||- .++.
T Consensus 200 Q~a~~~La~-~vD~miVIGg~~S-sNT~kL~eia~~~~~~t~~Ie~~~el~~~~l~ 253 (281)
T PF02401_consen 200 QEAARELAK-EVDAMIVIGGKNS-SNTRKLAEIAKEHGKPTYHIETADELDPEWLK 253 (281)
T ss_dssp HHHHHHHHC-CSSEEEEES-TT--HHHHHHHHHHHHCTTCEEEESSGGG--HHHHT
T ss_pred HHHHHHHHh-hCCEEEEecCCCC-ccHHHHHHHHHHhCCCEEEeCCccccCHhHhC
Confidence 344555544 4666666666555 345567899999999999999999995 4554
No 75
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=52.09 E-value=40 Score=30.39 Aligned_cols=51 Identities=18% Similarity=0.272 Sum_probs=36.9
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
.+.++.|...++-++|+-.+-.. .-..+|-.+|++.+.|.+.+++..+|-.
T Consensus 278 Q~A~~~La~~~vD~miVVGG~nS-SNT~rL~eia~~~g~~ty~Ie~~~eL~~ 328 (387)
T PRK13371 278 QDAMFSLVEEPLDLMVVIGGYNS-SNTTHLQEIAIERGIPSYHIDSPERILS 328 (387)
T ss_pred HHHHHHHhhcCCCEEEEECCCCC-ccHHHHHHHHHhcCCCEEEECCHHHcCC
Confidence 34566665555666666665544 3455678999999999999999999965
No 76
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=52.05 E-value=42 Score=30.44 Aligned_cols=50 Identities=12% Similarity=0.137 Sum_probs=45.3
Q ss_pred hcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 64 DRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 64 ~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
..++-+.-||.-|+--..=.+.|..||+-.|+|+..+.+..+|-.++.--
T Consensus 230 ~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l 279 (407)
T COG1419 230 LKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEAL 279 (407)
T ss_pred hccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHh
Confidence 57788889999999887788999999999999999999999999999853
No 77
>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=51.81 E-value=39 Score=27.56 Aligned_cols=72 Identities=18% Similarity=0.184 Sum_probs=48.2
Q ss_pred cccHHHHHHHHHHHHH-hcCCceee------HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE-eCCH
Q psy16564 32 VSDINKALQQVLKTAR-AHDGLAKG------LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK-VDNN 103 (157)
Q Consensus 32 ~m~~~k~L~~lL~~A~-~agklv~G------~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~-v~sk 103 (157)
+|+...++ +.++..+ ..+.+..| .+++.++++.| ++|+ .+| .+...+...|++++||++- +.|.
T Consensus 40 t~~t~~a~-~~i~~l~~~~~~~~vGAGTVl~~~~a~~a~~aG-A~Fi-----vsP-~~~~~v~~~~~~~~i~~iPG~~Tp 111 (204)
T TIGR01182 40 TLRTPVAL-DAIRLLRKEVPDALIGAGTVLNPEQLRQAVDAG-AQFI-----VSP-GLTPELAKHAQDHGIPIIPGVATP 111 (204)
T ss_pred eCCCccHH-HHHHHHHHHCCCCEEEEEeCCCHHHHHHHHHcC-CCEE-----ECC-CCCHHHHHHHHHcCCcEECCCCCH
Confidence 34555566 4444333 34567777 46777788777 7777 345 4555788899999999987 3477
Q ss_pred HHHHHHhC
Q psy16564 104 KKLGEWAG 111 (157)
Q Consensus 104 ~eLG~a~G 111 (157)
.|+-++..
T Consensus 112 tEi~~A~~ 119 (204)
T TIGR01182 112 SEIMLALE 119 (204)
T ss_pred HHHHHHHH
Confidence 77777764
No 78
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=51.40 E-value=57 Score=27.36 Aligned_cols=47 Identities=6% Similarity=0.086 Sum_probs=35.2
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
|.-+..++..|.....-...+..+++..++|+....+..+|..++..
T Consensus 223 g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~ 269 (282)
T TIGR03499 223 GNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDR 269 (282)
T ss_pred CCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHH
Confidence 44677778877644344567778899999999888888888888764
No 79
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=51.23 E-value=63 Score=21.87 Aligned_cols=44 Identities=11% Similarity=0.308 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
..++..+......++|+-..++. --......+|++++||++.+.
T Consensus 21 ~~~Ld~~~~~~~~~~lvhGga~~-GaD~iA~~wA~~~gv~~~~~~ 64 (71)
T PF10686_consen 21 WAALDKVHARHPDMVLVHGGAPK-GADRIAARWARERGVPVIRFP 64 (71)
T ss_pred HHHHHHHHHhCCCEEEEECCCCC-CHHHHHHHHHHHCCCeeEEeC
Confidence 34455556666778888888855 567778899999999999887
No 80
>PF00205 TPP_enzyme_M: Thiamine pyrophosphate enzyme, central domain; InterPro: IPR012000 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This central domain of TPP enzymes contains a 2-fold Rossman fold. ; GO: 0000287 magnesium ion binding, 0030976 thiamine pyrophosphate binding; PDB: 1OZH_C 1OZF_B 1OZG_B 2Q29_B 2Q28_A 2Q27_B 1OVM_B 1PVD_A 1PYD_B 2VK1_C ....
Probab=51.12 E-value=11 Score=27.64 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++++.+.|.+-+--++++-..+.-......+.+|+++.++|++...
T Consensus 1 i~~~~~~L~~A~rP~il~G~g~~~~~a~~~l~~lae~~~~Pv~~t~ 46 (137)
T PF00205_consen 1 IDEAADLLSSAKRPVILAGRGARRSGAAEELRELAEKLGIPVATTP 46 (137)
T ss_dssp HHHHHHHHHH-SSEEEEE-HHHHHTTCHHHHHHHHHHHTSEEEEEG
T ss_pred CHHHHHHHHhCCCEEEEEcCCcChhhHHHHHHHHHHHHCCCEEecC
Confidence 3577788888777777777666533567789999999999998866
No 81
>KOG4201|consensus
Probab=51.08 E-value=49 Score=28.16 Aligned_cols=73 Identities=12% Similarity=0.190 Sum_probs=51.0
Q ss_pred CceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCC-CEEEeCCHHHHHHHhCCCccccCCCccceeeeEE
Q psy16564 51 GLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQI-PLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSC 129 (157)
Q Consensus 51 klv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~I-pvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~ 129 (157)
.++.---|...+=.+|--..++|+.=-+. ...+.+-.+|+..+. |.+.|.+.+|+++++++ ++-+
T Consensus 144 eFivd~~QI~~aR~~GADaVLLIvamLs~-~~lk~l~k~~K~L~me~LVEVn~~eEm~ralei-------------Gakv 209 (289)
T KOG4201|consen 144 EFIVDPYQIYEARLKGADAVLLIVAMLSD-LLLKELYKISKDLGMEPLVEVNDEEEMQRALEI-------------GAKV 209 (289)
T ss_pred HHccCHHHHHHHHhcCCceeehHHHHcCh-HHHHHHHHHHHHcCCcceeeeccHHHHHHHHHh-------------CcEE
Confidence 45666677777777776444445555444 344566789999776 89999999999999995 3456
Q ss_pred EEEecCch
Q psy16564 130 VVIKVRNW 137 (157)
Q Consensus 130 vaI~D~g~ 137 (157)
++|-+.+.
T Consensus 210 vGvNNRnL 217 (289)
T KOG4201|consen 210 VGVNNRNL 217 (289)
T ss_pred EeecCCcc
Confidence 77765543
No 82
>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w
Probab=50.72 E-value=55 Score=23.32 Aligned_cols=49 Identities=12% Similarity=0.110 Sum_probs=33.8
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~ 113 (157)
.+.+....+.+|.|+.|... .+.++++++++++-.+. ...++++.+|..
T Consensus 50 ~~~~~~~~~~vv~is~d~~~-----~~~~~~~~~~~~~~~l~D~~~~~~~~~gv~ 99 (140)
T cd03017 50 YEEFKALGAVVIGVSPDSVE-----SHAKFAEKYGLPFPLLSDPDGKLAKAYGVW 99 (140)
T ss_pred HHHHHHCCCEEEEEcCCCHH-----HHHHHHHHhCCCceEEECCccHHHHHhCCc
Confidence 34445556888989887433 45667777777666554 567899999975
No 83
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=50.55 E-value=39 Score=27.51 Aligned_cols=75 Identities=13% Similarity=0.139 Sum_probs=49.3
Q ss_pred CCcccHHHHHHHHHHHHHhcCCceee------HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE-eCC
Q psy16564 30 EGVSDINKALQQVLKTARAHDGLAKG------LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK-VDN 102 (157)
Q Consensus 30 ~~~m~~~k~L~~lL~~A~~agklv~G------~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~-v~s 102 (157)
|=+|+...++..+-....+...+..| .+++.++++.| ++|++ +| .+...+..+|++++||++- +.|
T Consensus 34 Eit~~tp~a~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aG-A~Fiv-----SP-~~~~~vi~~a~~~~i~~iPG~~T 106 (201)
T PRK06015 34 EITLRTPAALDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAG-SRFIV-----SP-GTTQELLAAANDSDVPLLPGAAT 106 (201)
T ss_pred EEeCCCccHHHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcC-CCEEE-----CC-CCCHHHHHHHHHcCCCEeCCCCC
Confidence 33455555663333334455677777 46777788877 77774 34 4455688899999999987 447
Q ss_pred HHHHHHHhC
Q psy16564 103 NKKLGEWAG 111 (157)
Q Consensus 103 k~eLG~a~G 111 (157)
-.|+=++..
T Consensus 107 ptEi~~A~~ 115 (201)
T PRK06015 107 PSEVMALRE 115 (201)
T ss_pred HHHHHHHHH
Confidence 777666654
No 84
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=50.44 E-value=77 Score=27.15 Aligned_cols=50 Identities=22% Similarity=0.329 Sum_probs=39.8
Q ss_pred EEEcCCCCchhhHHHHHHHHHhCCCCEEEeC--CHHHHHHHhCCCccccCCCc
Q psy16564 71 CVLADNCDEPAYKKLVQALCSEHQIPLIKVD--NNKKLGEWAGLSKLDNMGKA 121 (157)
Q Consensus 71 VIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~--sk~eLG~a~G~~~~~~~gk~ 121 (157)
+|+..=+++ ++...+...|..++||++-+. --..|...+|......-|..
T Consensus 61 iV~~Tlv~~-elr~~l~~~~~~~~i~~vdll~p~i~~le~~lg~~p~~~pG~~ 112 (269)
T PRK05339 61 IVFYTLVDP-ELREILEERCAEFGIPCIDILGPLIAPLEQELGLKPTPEPGRT 112 (269)
T ss_pred EEEEeCCCH-HHHHHHHHHHHHcCCCEEeccHHHHHHHHHHHCcCCCCCCCcc
Confidence 566677777 899999999999999999977 56799999998744444444
No 85
>cd03338 TCP1_delta TCP-1 (CTT or eukaryotic type II) chaperonin family, delta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=49.89 E-value=49 Score=30.03 Aligned_cols=56 Identities=11% Similarity=0.099 Sum_probs=38.8
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC---HHHHHHHhCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN---NKKLGEWAGL 112 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s---k~eLG~a~G~ 112 (157)
...++.|.+..+.+||++.|.++..+......++.+++|-++.--+ .++|.+++|-
T Consensus 262 ~~~v~~i~~~g~~lvi~~~~i~~~~v~~l~~~~l~~~~I~av~~~~~~~LerIa~~tGa 320 (515)
T cd03338 262 LNMCKKIKKSGCNVLLIQKSILRDAVSDLALHFLAKLKIMVVKDIEREEIEFICKTIGC 320 (515)
T ss_pred HHHHHHHHhcCCCEEEECCCcccccccHHHHHHHHHCCceEEecCCHHHHHHHHHHHCC
Confidence 3344555566689999999986544555667777889999988655 4556666663
No 86
>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=49.70 E-value=38 Score=27.93 Aligned_cols=39 Identities=23% Similarity=0.260 Sum_probs=30.7
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
..+...+..+||.|-|..+ .+..+..+|.+++||++...
T Consensus 96 ~~l~~~~~D~VvdaiD~~~--~k~~L~~~c~~~~ip~I~s~ 134 (231)
T cd00755 96 EDLLGGDPDFVVDAIDSIR--AKVALIAYCRKRKIPVISSM 134 (231)
T ss_pred HHHhcCCCCEEEEcCCCHH--HHHHHHHHHHHhCCCEEEEe
Confidence 3444556889999999765 55678999999999999864
No 87
>PRK11018 hypothetical protein; Provisional
Probab=49.61 E-value=44 Score=22.76 Aligned_cols=38 Identities=16% Similarity=0.206 Sum_probs=25.9
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++.+..|+. |.|++.|... ...|+.+|++.|-.++...
T Consensus 29 l~~l~~G~~-L~V~~d~~~a---~~di~~~~~~~G~~v~~~~ 66 (78)
T PRK11018 29 LPQLKKGEI-LEVVSDCPQS---INNIPLDARNHGYTVLDIQ 66 (78)
T ss_pred HHhCCCCCE-EEEEeCCccH---HHHHHHHHHHcCCEEEEEE
Confidence 344445654 5567776543 4578999999999987654
No 88
>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=27 Score=27.83 Aligned_cols=34 Identities=21% Similarity=0.428 Sum_probs=27.4
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+..+||.+.|. . .....+..+|++++||++...+
T Consensus 113 ~~dvVi~~~d~-~-~~~~~ln~~c~~~~ip~i~~~~ 146 (198)
T cd01485 113 KFTLVIATEEN-Y-ERTAKVNDVCRKHHIPFISCAT 146 (198)
T ss_pred CCCEEEECCCC-H-HHHHHHHHHHHHcCCCEEEEEe
Confidence 46788877665 4 5777899999999999998764
No 89
>TIGR03729 acc_ester putative phosphoesterase. Members of this protein family belong to the larger family pfam00149 (calcineurin-like phosphoesterase), a family largely defined by small motifs of metal-chelating residues. The subfamily in this model shows a good but imperfect co-occurrence in species with domain TIGR03715 that defines a novel class of signal peptide typical of the accessory secretory system.
Probab=48.88 E-value=60 Score=26.07 Aligned_cols=45 Identities=11% Similarity=0.088 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCc--hhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDE--PAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~--~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.+++.+.+.++.+||++.|... ......+..+.+..++|++.+.
T Consensus 22 ~~~~~~~~~~~~d~vv~~GDl~~~~~~~~~~~~~l~~~~~~pv~~v~ 68 (239)
T TIGR03729 22 ETLAQYLKKQKIDHLHIAGDISNDFQRSLPFIEKLQELKGIKVTFNA 68 (239)
T ss_pred HHHHHHHHhcCCCEEEECCccccchhhHHHHHHHHHHhcCCcEEEEC
Confidence 34556666667999999999664 1233445556655679998876
No 90
>COG1493 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]
Probab=48.67 E-value=70 Score=28.03 Aligned_cols=52 Identities=10% Similarity=0.108 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHh
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWA 110 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~ 110 (157)
....++.+-.-+..+||++.+..++ ..+.++|++++||++... +.-+|..-+
T Consensus 70 r~~~i~~~~~~~~P~iI~sk~~~~p---~~l~~~a~~~~~pil~s~~~ts~l~~~l 122 (308)
T COG1493 70 RKKRIGKLFSLDTPALIVSKGLPIP---EELLDAAKKYNIPILTSKLSTSELSFTL 122 (308)
T ss_pred HHHHHHHHhCcCCCEEEEECCCCCC---HHHHHHHHHcCCceEEecchHHHHHHHH
Confidence 4456666667889999999998762 457789999999999987 555554444
No 91
>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=48.48 E-value=53 Score=25.66 Aligned_cols=42 Identities=10% Similarity=0.173 Sum_probs=25.7
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
++.+...++..+|+..--++ .....+ ..|.+.|||++.+.+-
T Consensus 48 i~~~i~~~~d~Iiv~~~~~~-~~~~~l-~~~~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 48 IEQAISQGVDGIIVSPVDPD-SLAPFL-EKAKAAGIPVVTVDSD 89 (257)
T ss_dssp HHHHHHTTESEEEEESSSTT-TTHHHH-HHHHHTTSEEEEESST
T ss_pred HHHHHHhcCCEEEecCCCHH-HHHHHH-HHHhhcCceEEEEecc
Confidence 33333445776666543333 355444 5588889999999855
No 92
>cd03339 TCP1_epsilon TCP-1 (CTT or eukaryotic type II) chaperonin family, epsilon subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=48.37 E-value=58 Score=29.78 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=34.5
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHH---HHHHHhC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNK---KLGEWAG 111 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~---eLG~a~G 111 (157)
.++.|.+-.+.+||++.+.++ ....++.++||.++.-.++. +|.+++|
T Consensus 279 ~v~~i~~~g~~lvi~~~~I~~-----~al~~L~~~~I~av~~v~~~~LerIa~~tG 329 (526)
T cd03339 279 MVEQVKDAGANLVICQWGFDD-----EANHLLLQNGLPAVRWVGGVEIELIAIATG 329 (526)
T ss_pred HHHHHHHCCCCEEEeCCCCCH-----HHHHHHHHCCCEEEEeCCHHHHHHHHHHhC
Confidence 344555556899999999998 35567789999998866555 4555555
No 93
>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=47.76 E-value=23 Score=25.94 Aligned_cols=64 Identities=16% Similarity=0.265 Sum_probs=40.0
Q ss_pred cHHHHHHHHHHHHHhcCCcee-----eHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 34 DINKALQQVLKTARAHDGLAK-----GLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 34 ~~~k~L~~lL~~A~~agklv~-----G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.-.+++++.|......-++.. ........+ ....+||.|.|-. .....+..+|.++++|++...
T Consensus 56 ~Ka~~~~~~l~~~np~~~v~~~~~~~~~~~~~~~~--~~~d~vi~~~d~~--~~~~~l~~~~~~~~~p~i~~~ 124 (135)
T PF00899_consen 56 NKAEAAKERLQEINPDVEVEAIPEKIDEENIEELL--KDYDIVIDCVDSL--AARLLLNEICREYGIPFIDAG 124 (135)
T ss_dssp BHHHHHHHHHHHHSTTSEEEEEESHCSHHHHHHHH--HTSSEEEEESSSH--HHHHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHHHHHHhcCceeeeeeecccccccccccc--cCCCEEEEecCCH--HHHHHHHHHHHHcCCCEEEEE
Confidence 345566666665432222221 223344444 3567999998874 467788999999999999865
No 94
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal. Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacterial), a torroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.
Probab=47.09 E-value=58 Score=29.66 Aligned_cols=49 Identities=14% Similarity=0.185 Sum_probs=34.2
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+.++.|.+-.+.+||.+.+.++ ....++.++||-++.--++.+|.+++-
T Consensus 273 ~~v~~i~~~g~~lvi~~~~I~~-----~al~~L~~~gI~~v~~v~~~~L~rIa~ 321 (519)
T TIGR02339 273 EMVDKIADAGANVVFCQKGIDD-----LAQHYLAKAGILAVRRVKKSDIEKLAR 321 (519)
T ss_pred HHHHHHHhcCCcEEEECCCccH-----HHHHHHHHCCCEEEecCCHHHHHHHHH
Confidence 3445666667899999999998 233455689998877666666555543
No 95
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=46.60 E-value=60 Score=29.13 Aligned_cols=48 Identities=10% Similarity=0.066 Sum_probs=36.1
Q ss_pred cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 65 RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 65 kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
++..+..++..|.........+..+++..++|+....+..+|..++..
T Consensus 249 ~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~ 296 (424)
T PRK05703 249 YGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQ 296 (424)
T ss_pred cCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHH
Confidence 455677778877654234566888899999999888888888888753
No 96
>COG1648 CysG Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]
Probab=46.41 E-value=23 Score=28.87 Aligned_cols=35 Identities=23% Similarity=0.288 Sum_probs=30.3
Q ss_pred eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHH
Q psy16564 68 AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNK 104 (157)
Q Consensus 68 akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~ 104 (157)
+.|||+|.|-++ +-+.+-..|++++|||..++...
T Consensus 73 ~~lviaAt~d~~--ln~~i~~~a~~~~i~vNv~D~p~ 107 (210)
T COG1648 73 AFLVIAATDDEE--LNERIAKAARERRILVNVVDDPE 107 (210)
T ss_pred ceEEEEeCCCHH--HHHHHHHHHHHhCCceeccCCcc
Confidence 899999998755 77889999999999999888654
No 97
>TIGR02343 chap_CCT_epsi T-complex protein 1, epsilon subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT epsilon chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=46.39 E-value=54 Score=30.10 Aligned_cols=47 Identities=11% Similarity=0.200 Sum_probs=33.8
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHH---HHHHHhC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNK---KLGEWAG 111 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~---eLG~a~G 111 (157)
++.|.+..+.+||.+.++++ ....++.+++|.++.-.++. +|.+++|
T Consensus 284 l~~i~~~g~~lvi~~~~I~~-----~al~~L~~~~i~~v~~~~~~~l~~Ia~~tG 333 (532)
T TIGR02343 284 IDDIKKSGANIVICQWGFDD-----EANHLLLQNDLPAVRWVGGHELELIAIATG 333 (532)
T ss_pred HHHHHHcCCCEEEeCCCccH-----HHHHHHHHCCcEEEEcCCHHHHHHHHHHhC
Confidence 44555556899999999998 35567788899988865555 4555555
No 98
>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=46.37 E-value=33 Score=27.71 Aligned_cols=34 Identities=18% Similarity=0.190 Sum_probs=28.5
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+||.|.|-. .....+..+|.++++|++....
T Consensus 111 ~~DvVi~~~d~~--~~r~~l~~~~~~~~ip~i~~g~ 144 (228)
T cd00757 111 GYDLVLDCTDNF--ATRYLINDACVKLGKPLVSGAV 144 (228)
T ss_pred CCCEEEEcCCCH--HHHHHHHHHHHHcCCCEEEEEe
Confidence 488999999954 4677899999999999998764
No 99
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=46.28 E-value=57 Score=25.71 Aligned_cols=46 Identities=15% Similarity=0.244 Sum_probs=34.7
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
-.++.+.|++.+--++++-.-+....-...+.++++..++|++...
T Consensus 17 p~~aa~lLk~AKRPvIivG~ga~~~~a~e~l~~laEklgiPVvtT~ 62 (162)
T TIGR00315 17 PKLVAMMIKRAKRPLLIVGPENLEDEEKELIVKFIEKFDLPVVATA 62 (162)
T ss_pred HHHHHHHHHcCCCcEEEECCCcCcccHHHHHHHHHHHHCCCEEEcC
Confidence 3556667777776677777666533677889999999999999866
No 100
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=46.13 E-value=65 Score=28.07 Aligned_cols=42 Identities=21% Similarity=0.292 Sum_probs=33.3
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+.++.+-+-+...+|++.+..++. .+...|++++||++...
T Consensus 72 ~~~~~~l~~~~~P~iIvt~~~~~p~---~l~~~a~~~~ipll~t~ 113 (308)
T PRK05428 72 KERLKKLFSLEPPCIIVTRGLEPPP---ELLEAAKEAGIPLLRTP 113 (308)
T ss_pred HHHHHHHhCCCCCEEEEECcCCCCH---HHHHHHHHcCCcEEEeC
Confidence 3455566678899999999987742 36789999999999977
No 101
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=44.84 E-value=1.2e+02 Score=26.59 Aligned_cols=49 Identities=16% Similarity=0.242 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
..+.++.+++..+++++ |++...+...|+ .+ |...-++.+||..++|.+
T Consensus 148 y~~li~~~~~~g~~vil---D~Sg~~L~~~L~-----~~-P~lIKPN~~EL~~~~g~~ 196 (310)
T COG1105 148 YAELIRILRQQGAKVIL---DTSGEALLAALE-----AK-PWLIKPNREELEALFGRE 196 (310)
T ss_pred HHHHHHHHHhcCCeEEE---ECChHHHHHHHc-----cC-CcEEecCHHHHHHHhCCC
Confidence 45666666665555543 666643444432 22 888889999999999986
No 102
>PRK10124 putative UDP-glucose lipid carrier transferase; Provisional
Probab=44.80 E-value=61 Score=29.26 Aligned_cols=53 Identities=8% Similarity=0.039 Sum_probs=43.1
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
..++..+.+++.++.-|++|-+..+......+...|+..++++..+++..++.
T Consensus 191 ~~~dL~~~v~~~~IdeViIAip~~~~~~l~ell~~~~~~~v~V~ivP~l~~~~ 243 (463)
T PRK10124 191 NLQQLVEDAKAGKIHNVYIAMSMCDGARVKKLVRQLADTTCSVLLIPDVFTFN 243 (463)
T ss_pred CHHHHHHHHHhCCCCEEEEeCCCcchHHHHHHHHHHHHcCCeEEEecchhhcc
Confidence 44667788888999999999886665667778889999999999999776543
No 103
>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=44.79 E-value=34 Score=24.02 Aligned_cols=35 Identities=20% Similarity=0.349 Sum_probs=25.6
Q ss_pred EEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 72 VLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 72 IlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
|+|.=.+. +...+...+++++||++. ...|.+.+-
T Consensus 20 VvAKG~g~--~A~~I~~~A~e~~VPi~~---~~~LAr~L~ 54 (82)
T TIGR00789 20 VVASGVGE--VAERIIEIAKKHGIPIVE---DPDLVDVLL 54 (82)
T ss_pred EEEEeCCH--HHHHHHHHHHHcCCCEEe---CHHHHHHHH
Confidence 35665554 778899999999999974 345666664
No 104
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=44.42 E-value=74 Score=23.78 Aligned_cols=56 Identities=20% Similarity=0.189 Sum_probs=32.9
Q ss_pred eHHHHHHHHhc--CCeeEEEEcCCCCchh--hHHHHHHHHHhCCCCEEE--eC--CHHHHHHHh
Q psy16564 55 GLHEAAKALDR--REAQLCVLADNCDEPA--YKKLVQALCSEHQIPLIK--VD--NNKKLGEWA 110 (157)
Q Consensus 55 G~~~v~KaL~k--gkakLVIlA~D~s~~~--~~~~l~~lc~~~~Ipvi~--v~--sk~eLG~a~ 110 (157)
+.....+.|++ .++..||+|.|++.+- +..++..+|...+.|+.. +. |..++-+|+
T Consensus 76 ~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~~~v~R~~fsslT~~~I~~A~ 139 (142)
T cd01028 76 DKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFSEITPKAIREAF 139 (142)
T ss_pred cHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCCCCCCeEEEEEccCCHHHHHHHH
Confidence 34444444443 4578999999998732 555666666653455544 33 555555554
No 105
>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=44.17 E-value=36 Score=22.71 Aligned_cols=31 Identities=16% Similarity=0.299 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 83 KKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 83 ~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
.-..+.+++++|+++..+++..+++.-||..
T Consensus 14 a~~~ek~lk~~gi~~~liP~P~~i~~~CG~a 44 (73)
T PF11823_consen 14 AMKAEKLLKKNGIPVRLIPTPREISAGCGLA 44 (73)
T ss_pred HHHHHHHHHHCCCcEEEeCCChhccCCCCEE
Confidence 3456789999999999999999999999954
No 106
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=43.69 E-value=53 Score=28.05 Aligned_cols=59 Identities=17% Similarity=0.146 Sum_probs=44.8
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC---------------CHHHHHHHhCC
Q psy16564 54 KGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD---------------NNKKLGEWAGL 112 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~---------------sk~eLG~a~G~ 112 (157)
.|.++..+.|+...+.+||=|.----.++.......|++.|||++.++ +-+++.++++.
T Consensus 53 l~~e~l~~~l~e~~i~llIDATHPyAa~iS~Na~~aake~gipy~r~eRP~~~~~gd~~~~V~d~~ea~~~~~~ 126 (257)
T COG2099 53 LGAEGLAAFLREEGIDLLIDATHPYAARISQNAARAAKETGIPYLRLERPPWAPNGDNWIEVADIEEAAEAAKQ 126 (257)
T ss_pred CCHHHHHHHHHHcCCCEEEECCChHHHHHHHHHHHHHHHhCCcEEEEECCccccCCCceEEecCHHHHHHHHhc
Confidence 367788888999999999977764444566777889999999997654 45566777664
No 107
>PRK15116 sulfur acceptor protein CsdL; Provisional
Probab=43.62 E-value=59 Score=27.58 Aligned_cols=38 Identities=18% Similarity=0.220 Sum_probs=29.6
Q ss_pred HHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 62 ALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 62 aL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+...+.-+||.|-|... .+..|..+|.+++||++...
T Consensus 116 ~ll~~~~D~VIdaiD~~~--~k~~L~~~c~~~~ip~I~~g 153 (268)
T PRK15116 116 EYMSAGFSYVIDAIDSVR--PKAALIAYCRRNKIPLVTTG 153 (268)
T ss_pred HHhcCCCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEEC
Confidence 344456889999999644 45678999999999999764
No 108
>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=43.29 E-value=41 Score=26.80 Aligned_cols=34 Identities=12% Similarity=0.174 Sum_probs=27.5
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+..+||.+.|- . .....+..+|.+++||++....
T Consensus 110 ~~dvVi~~~~~-~-~~~~~ln~~c~~~~ip~i~~~~ 143 (197)
T cd01492 110 QFDVVVATELS-R-AELVKINELCRKLGVKFYATGV 143 (197)
T ss_pred CCCEEEECCCC-H-HHHHHHHHHHHHcCCCEEEEEe
Confidence 46788888774 4 5777899999999999988764
No 109
>cd04195 GT2_AmsE_like GT2_AmsE_like is involved in exopolysaccharide amylovora biosynthesis. AmsE is a glycosyltransferase involved in exopolysaccharide amylovora biosynthesis in Erwinia amylovora. Amylovara is one of the three exopolysaccharide produced by E. amylovora. Amylovara-deficient mutants are non-pathogenic. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds.
Probab=43.13 E-value=93 Score=23.16 Aligned_cols=40 Identities=13% Similarity=0.317 Sum_probs=22.1
Q ss_pred EEEcCCCC-chhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 71 CVLADNCD-EPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 71 VIlA~D~s-~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
+||..|.+ ...+...+..++.+.++.++..+...-.|.++
T Consensus 32 iiivdd~ss~d~t~~~~~~~~~~~~i~~i~~~~n~G~~~a~ 72 (201)
T cd04195 32 VVLVKDGPVTQSLNEVLEEFKRKLPLKVVPLEKNRGLGKAL 72 (201)
T ss_pred EEEEECCCCchhHHHHHHHHHhcCCeEEEEcCccccHHHHH
Confidence 44444544 54566667777777775555544433334443
No 110
>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=43.11 E-value=40 Score=26.80 Aligned_cols=35 Identities=17% Similarity=0.246 Sum_probs=28.8
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
....+||.|.|..+ ....+..+|.++++|++....
T Consensus 110 ~~~D~Vi~~~d~~~--~r~~l~~~~~~~~ip~i~~~~ 144 (202)
T TIGR02356 110 NNVDLVLDCTDNFA--TRYLINDACVALGTPLISAAV 144 (202)
T ss_pred hCCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEEe
Confidence 35789999988754 677899999999999998763
No 111
>KOG2486|consensus
Probab=43.06 E-value=29 Score=30.43 Aligned_cols=42 Identities=14% Similarity=0.095 Sum_probs=28.8
Q ss_pred hcCCeeEEEEcC--CCCchhhHHHHHHHHHhCCCCEEEeCCHHH
Q psy16564 64 DRREAQLCVLAD--NCDEPAYKKLVQALCSEHQIPLIKVDNNKK 105 (157)
Q Consensus 64 ~kgkakLVIlA~--D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~e 105 (157)
++....-||++- +.+...+.-...++|.+++||+..+.++-+
T Consensus 216 eR~nLv~~FLLvd~sv~i~~~D~~~i~~~ge~~VP~t~vfTK~D 259 (320)
T KOG2486|consen 216 ERENLVRVFLLVDASVPIQPTDNPEIAWLGENNVPMTSVFTKCD 259 (320)
T ss_pred hhhhhheeeeeeeccCCCCCCChHHHHHHhhcCCCeEEeeehhh
Confidence 344444444444 444445666778999999999999997655
No 112
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=42.84 E-value=70 Score=26.72 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=37.4
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.......|+..+..+||=|.=--...+.+.....|++.+|||+.+.
T Consensus 53 ~~~~l~~~l~~~~i~~VIDATHPfA~~is~~a~~ac~~~~ipyiR~e 99 (248)
T PRK08057 53 GAEGLAAYLREEGIDLVIDATHPYAAQISANAAAACRALGIPYLRLE 99 (248)
T ss_pred CHHHHHHHHHHCCCCEEEECCCccHHHHHHHHHHHHHHhCCcEEEEe
Confidence 44555666778889999977765555677888999999999999887
No 113
>COG0240 GpsA Glycerol-3-phosphate dehydrogenase [Energy production and conversion]
Probab=42.74 E-value=1.1e+02 Score=27.04 Aligned_cols=122 Identities=12% Similarity=0.077 Sum_probs=77.2
Q ss_pred eeccccCCCCCCCCCCcc------cHHHHHHHHHHHHHhcCCcee-----eHHHHHHHHh---cCCeeEEEEcCCCCchh
Q psy16564 16 VQGTATDNVPSANDEGVS------DINKALQQVLKTARAHDGLAK-----GLHEAAKALD---RREAQLCVLADNCDEPA 81 (157)
Q Consensus 16 ~~~~~~~~~~~p~~~~~m------~~~k~L~~lL~~A~~agklv~-----G~~~v~KaL~---kgkakLVIlA~D~s~~~ 81 (157)
|..+-+|+.|-|-+.-+- |+.+++ ..+.-++. +.+.+++.+. +..+.+|.++.=..+ .
T Consensus 40 i~~~~~N~~yLp~i~lp~~l~at~Dl~~a~-------~~ad~iv~avPs~~~r~v~~~l~~~l~~~~~iv~~sKGie~-~ 111 (329)
T COG0240 40 INETRENPKYLPGILLPPNLKATTDLAEAL-------DGADIIVIAVPSQALREVLRQLKPLLLKDAIIVSATKGLEP-E 111 (329)
T ss_pred HHhcCcCccccCCccCCcccccccCHHHHH-------hcCCEEEEECChHHHHHHHHHHhhhccCCCeEEEEeccccC-C
Confidence 344457898998654443 444444 22344443 5677888875 577999999998888 5
Q ss_pred hHHHHHHHHHh-CCC-CEEEeCCHHHHHHHhCCCccccCCCccceeeeEEEEEecCchhHHhhhccccceeeecccC
Q psy16564 82 YKKLVQALCSE-HQI-PLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRNWFLIICSRKSTQVLSVNYNK 156 (157)
Q Consensus 82 ~~~~l~~lc~~-~~I-pvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~~~~~~~~~~~~~~ 156 (157)
..+.+.+..++ .+. |+..+. ---+.+=+.+. .| ...+++=.|+.+++.+...|+++++.++.|.
T Consensus 112 t~~l~seii~e~l~~~~~~vLS-GPs~A~EVa~g------~p----ta~~vas~d~~~a~~v~~~f~~~~Frvy~~~ 177 (329)
T COG0240 112 TGRLLSEIIEEELPDNPIAVLS-GPSFAKEVAQG------LP----TAVVVASNDQEAAEKVQALFSSPYFRVYTST 177 (329)
T ss_pred CcchHHHHHHHHcCCCeEEEEE-CccHHHHHhcC------CC----cEEEEecCCHHHHHHHHHHhCCCcEEEEecC
Confidence 66666666665 343 333333 22233333322 12 2335666799999999999999999998775
No 114
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=42.43 E-value=89 Score=24.42 Aligned_cols=57 Identities=14% Similarity=0.036 Sum_probs=35.9
Q ss_pred eeHHHHHHHHhc--CCeeEEEEcCCCCchh--hHHHHHHHHHhCCCCEEE--eC--CHHHHHHHh
Q psy16564 54 KGLHEAAKALDR--REAQLCVLADNCDEPA--YKKLVQALCSEHQIPLIK--VD--NNKKLGEWA 110 (157)
Q Consensus 54 ~G~~~v~KaL~k--gkakLVIlA~D~s~~~--~~~~l~~lc~~~~Ipvi~--v~--sk~eLG~a~ 110 (157)
.+.....+.|++ .++..||+|.|++.+- +..++..++...+.|+.. +. |+.++-+|+
T Consensus 103 ~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~~~~v~R~~fs~it~~~I~~a~ 167 (170)
T cd03361 103 DDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNKNIKRAEFHEVTRRAILEAL 167 (170)
T ss_pred cchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccCCCCeEEEEEecCCHHHHHHHH
Confidence 456666666654 6789999999988632 556677777654445433 33 555555554
No 115
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=42.33 E-value=71 Score=27.40 Aligned_cols=45 Identities=20% Similarity=0.214 Sum_probs=31.7
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+.++++ ++++|||.|... .--++.+=++++||++-+- -..-.|..
T Consensus 62 ~l~~~~-ik~lVIACNTAS---a~al~~LR~~~~iPVvGvi--Paik~A~~ 106 (269)
T COG0796 62 FLLERG-IKALVIACNTAS---AVALEDLREKFDIPVVGVI--PAIKPAVA 106 (269)
T ss_pred HHHHcC-CCEEEEecchHH---HHHHHHHHHhCCCCEEEec--cchHHHHH
Confidence 344455 999999999865 3346777788999999877 33444444
No 116
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=42.01 E-value=2.1e+02 Score=24.00 Aligned_cols=58 Identities=16% Similarity=0.181 Sum_probs=40.2
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE-eC--C-HHHHHHHhCCC
Q psy16564 54 KGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK-VD--N-NKKLGEWAGLS 113 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~-v~--s-k~eLG~a~G~~ 113 (157)
.|.+...+.++.--+.=|++ .|.+. +-...+...|+++++..+. +. + .+++..++...
T Consensus 104 ~G~e~f~~~~~~aGvdGvii-pDLp~-ee~~~~~~~~~~~gl~~I~lvap~t~~eri~~i~~~s 165 (258)
T PRK13111 104 YGVERFAADAAEAGVDGLII-PDLPP-EEAEELRAAAKKHGLDLIFLVAPTTTDERLKKIASHA 165 (258)
T ss_pred cCHHHHHHHHHHcCCcEEEE-CCCCH-HHHHHHHHHHHHcCCcEEEEeCCCCCHHHHHHHHHhC
Confidence 47777777777655555555 58887 5666788899999998877 43 2 46677776654
No 117
>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=41.52 E-value=73 Score=22.68 Aligned_cols=42 Identities=12% Similarity=0.042 Sum_probs=26.7
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
..+.++|+.-|.........+...+.+.++|++.+.+|.+|-
T Consensus 73 ~~~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~iiv~NK~Dl~ 114 (158)
T cd01879 73 EKPDLIVNVVDATNLERNLYLTLQLLELGLPVVVALNMIDEA 114 (158)
T ss_pred CCCcEEEEEeeCCcchhHHHHHHHHHHcCCCEEEEEehhhhc
Confidence 345555555565543332334445567899999999998873
No 118
>PRK00865 glutamate racemase; Provisional
Probab=41.21 E-value=1.3e+02 Score=24.88 Aligned_cols=41 Identities=22% Similarity=0.239 Sum_probs=29.6
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+..+.|++..+.+++||++... .. .+..+-+..++|++-+.
T Consensus 58 ~~~~~L~~~g~d~iVIaCNTa~-~~--~l~~lr~~~~iPvigi~ 98 (261)
T PRK00865 58 EIVEFLLEYGVKMLVIACNTAS-AV--ALPDLRERYDIPVVGIV 98 (261)
T ss_pred HHHHHHHhCCCCEEEEeCchHH-HH--HHHHHHHhCCCCEEeeH
Confidence 4456677777999999999865 22 24455567799999855
No 119
>PF05822 UMPH-1: Pyrimidine 5'-nucleotidase (UMPH-1); InterPro: IPR006434 This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue []. The structure of mouse sequence has been reported []. This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs [] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.; GO: 0000287 magnesium ion binding, 0008253 5'-nucleotidase activity, 0005737 cytoplasm; PDB: 2BDU_B 2G07_A 2G06_A 2G0A_A 2Q4T_A 2G09_A 2G08_A 2VKQ_A 2CN1_A 2JGA_A.
Probab=40.53 E-value=2.5 Score=35.72 Aligned_cols=70 Identities=10% Similarity=0.014 Sum_probs=36.6
Q ss_pred CCCCCC-CCCcccHHHHHHHHHHHHHhcCCceeeHHHHHHHH----hcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCE
Q psy16564 23 NVPSAN-DEGVSDINKALQQVLKTARAHDGLAKGLHEAAKAL----DRREAQLCVLADNCDEPAYKKLVQALCSEHQIPL 97 (157)
Q Consensus 23 ~~~~p~-~~~~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL----~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipv 97 (157)
+.|+|+ .++.|+++..++-+..--+++..+..+..-....| +...+. =.| -...+-.++.+++||+
T Consensus 39 ~kY~PIE~dp~~s~eEK~p~M~EWw~kah~llv~~~l~k~~i~~~V~~s~i~----LRd-----g~~~~f~~L~~~~IP~ 109 (246)
T PF05822_consen 39 EKYYPIEIDPTMSIEEKIPHMEEWWTKAHELLVEQGLTKSEIEEAVKESDIM----LRD-----GVEEFFDKLEEHNIPL 109 (246)
T ss_dssp HHHHHHHT-SSS-HHHHHHHHHHHHHHHHHHHHHHT-BGGGHHHHHHCS-------B-B-----THHHHHHHHHCTT--E
T ss_pred hhccccccCCCCCHHHHHHHHHHHHHHHHHHHHhcCcCHHHHHHHHHhcchh----hhc-----CHHHHHHHHHhcCCCE
Confidence 568888 67789998888777766666666555544333222 222111 111 2234556677777777
Q ss_pred EEeC
Q psy16564 98 IKVD 101 (157)
Q Consensus 98 i~v~ 101 (157)
+.+.
T Consensus 110 lIFS 113 (246)
T PF05822_consen 110 LIFS 113 (246)
T ss_dssp EEEE
T ss_pred EEEe
Confidence 7765
No 120
>PRK06512 thiamine-phosphate pyrophosphorylase; Provisional
Probab=40.25 E-value=1.4e+02 Score=24.37 Aligned_cols=53 Identities=9% Similarity=0.124 Sum_probs=36.5
Q ss_pred HHHHHhcCCee-EEEEcCCCCchh---hHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 59 AAKALDRREAQ-LCVLADNCDEPA---YKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 59 v~KaL~kgkak-LVIlA~D~s~~~---~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
+..++..|.+. +.+=..|.++.. ..+.+..+|+.+++|++ +.+..+|...+|-
T Consensus 32 l~~al~~G~v~~vQlR~K~l~~~~~~~~a~~l~~l~~~~gv~li-INd~~dlA~~~~a 88 (221)
T PRK06512 32 LRAALQGGDVASVILPQYGLDEATFQKQAEKLVPVIQEAGAAAL-IAGDSRIAGRVKA 88 (221)
T ss_pred HHHHHcCCCccEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCEEE-EeCHHHHHHHhCC
Confidence 33455666434 444466766544 35678889999999976 6778899888874
No 121
>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=40.14 E-value=74 Score=26.56 Aligned_cols=47 Identities=15% Similarity=0.156 Sum_probs=37.8
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
|..+....|+...+.+||=|.=--...+.......|++.||||+.+.
T Consensus 54 ~~~~l~~~l~~~~i~~vIDATHPfA~~is~na~~a~~~~~ipylR~e 100 (249)
T PF02571_consen 54 DEEGLAEFLRENGIDAVIDATHPFAAEISQNAIEACRELGIPYLRFE 100 (249)
T ss_pred CHHHHHHHHHhCCCcEEEECCCchHHHHHHHHHHHHhhcCcceEEEE
Confidence 55677777888899999977765555677788899999999999876
No 122
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=40.13 E-value=76 Score=28.34 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=38.6
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
..+..+++.|+....-...+..+|+..++|+....+..+|..++..
T Consensus 206 g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~ 251 (388)
T PRK12723 206 SLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ 251 (388)
T ss_pred CCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH
Confidence 3578889999876567777999999999999999998888887754
No 123
>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=39.90 E-value=44 Score=30.21 Aligned_cols=39 Identities=18% Similarity=0.193 Sum_probs=27.2
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
+..+||.+ +-+. .....+..+|++++||++...+.--.|
T Consensus 112 ~fdiVI~t-~~~~-~~~~~L~~~c~~~~iPlI~~~s~G~~G 150 (425)
T cd01493 112 QFTVVIAT-NLPE-STLLRLADVLWSANIPLLYVRSYGLYG 150 (425)
T ss_pred CCCEEEEC-CCCH-HHHHHHHHHHHHcCCCEEEEecccCEE
Confidence 34566554 4445 455678999999999999988744333
No 124
>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=39.83 E-value=37 Score=22.72 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=21.0
Q ss_pred CCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 77 CDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 77 ~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+-..+...|...|+++||+++.++.
T Consensus 53 ~~~~~~~~~l~yka~~~Gi~v~~v~~ 78 (82)
T TIGR01766 53 WSFRKLISKIKYKAEEYGIEVIEVNP 78 (82)
T ss_pred hhHHHHHHHHHHHHHHcCCeEEEeCc
Confidence 34445778899999999999999873
No 125
>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=39.81 E-value=40 Score=23.91 Aligned_cols=46 Identities=17% Similarity=0.215 Sum_probs=34.4
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
..+..++...+ ...-+|+++..... ....++..+..+|||+..++.
T Consensus 38 a~~~~~~~~~~--~~~Dvill~pqi~~--~~~~i~~~~~~~~ipv~~I~~ 83 (95)
T TIGR00853 38 AGSYGAAGEKL--DDADVVLLAPQVAY--MLPDLKKETDKKGIPVEVING 83 (95)
T ss_pred EecHHHHHhhc--CCCCEEEECchHHH--HHHHHHHHhhhcCCCEEEeCh
Confidence 34555555444 45789999988865 566789999999999998773
No 126
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=39.66 E-value=78 Score=26.07 Aligned_cols=48 Identities=17% Similarity=0.120 Sum_probs=28.9
Q ss_pred ceeeHHHHHHHHhcC-CeeEEEE-cCC--CCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 52 LAKGLHEAAKALDRR-EAQLCVL-ADN--CDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 52 lv~G~~~v~KaL~kg-kakLVIl-A~D--~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++. .+.+...+.+. ....+-+ ..+ .++ .....+..+.++++|++++++
T Consensus 173 ~v~-~H~af~Y~~~~ygl~~~~~~~~~~eps~-~~l~~l~~~ik~~~v~~if~e 224 (266)
T cd01018 173 FMV-YHPAWGYFARDYGLTQIPIEEEGKEPSP-ADLKRLIDLAKEKGVRVVFVQ 224 (266)
T ss_pred EEE-ECchhHHHHHHcCCEEEecCCCCCCCCH-HHHHHHHHHHHHcCCCEEEEc
Confidence 444 44455666542 2333322 233 334 455678888999999999987
No 127
>cd01491 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the first repeat of Ub-E1.
Probab=39.65 E-value=40 Score=28.87 Aligned_cols=41 Identities=22% Similarity=0.344 Sum_probs=30.9
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEW 109 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a 109 (157)
+..+||.+.| +. ....++.++|++++||++...+.--.|.+
T Consensus 105 ~fdvVV~~~~-~~-~~~~~in~~c~~~~ipfI~a~~~G~~G~v 145 (286)
T cd01491 105 KFQVVVLTDA-SL-EDQLKINEFCHSPGIKFISADTRGLFGSI 145 (286)
T ss_pred cCCEEEEecC-CH-HHHHHHHHHHHHcCCEEEEEeccccEEEE
Confidence 3557777766 55 67778999999999999998875555543
No 128
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=39.14 E-value=90 Score=25.56 Aligned_cols=74 Identities=22% Similarity=0.211 Sum_probs=50.4
Q ss_pred eeeHHHHHHHHhc----CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeE
Q psy16564 53 AKGLHEAAKALDR----REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCS 128 (157)
Q Consensus 53 v~G~~~v~KaL~k----gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s 128 (157)
+.|..+..++++. -++..+++|.-.--..+.+.++.+-++++||++... .+|-- | .++
T Consensus 123 lVGEE~laEAVkAV~rLpRv~iLVLAGslMGGkIteaVk~lr~~hgI~VISL~-------M~GSV-------p----dVA 184 (218)
T COG1707 123 LVGEEELAEAVKAVARLPRVGILVLAGSLMGGKITEAVKELREEHGIPVISLN-------MFGSV-------P----DVA 184 (218)
T ss_pred ccChHHHHHHHHHHhccccceeEEEecccccchHHHHHHHHHHhcCCeEEEec-------cCCCC-------c----chh
Confidence 4576666666653 568889999986665788999999999999999764 22311 1 234
Q ss_pred EEEEecCchhHHhhhc
Q psy16564 129 CVVIKVRNWFLIICSR 144 (157)
Q Consensus 129 ~vaI~D~g~~~~~~~~ 144 (157)
=+.|+||-.+-.+.-+
T Consensus 185 DlVvtDPvqAGvlaVM 200 (218)
T COG1707 185 DLVVTDPVQAGVLAVM 200 (218)
T ss_pred heeecCchHhhhhhhh
Confidence 5667787666544433
No 129
>cd03343 cpn60 cpn60 chaperonin family. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. Archaeal cpn60 (thermosome), together with TF55 from thermophilic bacteria and the eukaryotic cytosol chaperonin (CTT), belong to the type II group of chaperonins. Cpn60 consists of two stacked octameric rings, which are composed of one or two different subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis.
Probab=39.12 E-value=92 Score=28.26 Aligned_cols=48 Identities=15% Similarity=0.198 Sum_probs=32.9
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
+.++.|.+-.+.+||.+.+.++ ....++.++||-++.--++.+|.+++
T Consensus 270 ~~v~~i~~~g~~lvi~~~~I~~-----~al~~l~~~gI~~v~~v~~~~l~~Ia 317 (517)
T cd03343 270 EMVDKIADTGANVVFCQKGIDD-----LAQHYLAKAGILAVRRVKKSDMEKLA 317 (517)
T ss_pred HHHHHHHhcCCCEEEeCCCccH-----HHHHHHhHCCcEEEEeCCHHHHHHHH
Confidence 3444666667899999999998 23334567899887766666555544
No 130
>cd01822 Lysophospholipase_L1_like Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.
Probab=39.07 E-value=95 Score=22.79 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=27.6
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCc-------hhhHHHHHHHHHhCCCCEEEe
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDE-------PAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~-------~~~~~~l~~lc~~~~Ipvi~v 100 (157)
..+.++.+++..++++++.--.++ ..+...+..+|++++++++-.
T Consensus 90 l~~li~~~~~~~~~vil~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~d~ 141 (177)
T cd01822 90 LRQMIETAQARGAPVLLVGMQAPPNYGPRYTRRFAAIYPELAEEYGVPLVPF 141 (177)
T ss_pred HHHHHHHHHHCCCeEEEEecCCCCccchHHHHHHHHHHHHHHHHcCCcEech
Confidence 344444555555777766432222 145677888999999998854
No 131
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=38.59 E-value=89 Score=24.90 Aligned_cols=46 Identities=13% Similarity=0.150 Sum_probs=31.9
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCc-hhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDE-PAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~-~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+.+.+.|++-+--++++-.-+.. ......+.+++++.++|++....
T Consensus 25 ~~aa~lI~~AKrPlIivG~ga~~~~ea~e~l~elaEkl~iPVvtT~~ 71 (171)
T PRK00945 25 KIAAMMIKKAKRPLLVVGSLLLDDEELLDRAVKIAKKANIPVAATGG 71 (171)
T ss_pred HHHHHHHHhCCCcEEEECcCccccchHHHHHHHHHHHHCCCEEEccc
Confidence 44555566555556666655533 35777899999999999998664
No 132
>PRK13957 indole-3-glycerol-phosphate synthase; Provisional
Probab=38.54 E-value=1.9e+02 Score=24.33 Aligned_cols=74 Identities=9% Similarity=-0.003 Sum_probs=53.6
Q ss_pred CceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCC-CEEEeCCHHHHHHHhCCCccccCCCccceeeeEE
Q psy16564 51 GLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQI-PLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSC 129 (157)
Q Consensus 51 klv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~I-pvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~ 129 (157)
.++.=..|+..+-.-|---+++++.--++ .....+..+|...|. |++.|.+.+||-+++-.. ...
T Consensus 109 DFIid~~QI~ea~~~GADavLLI~~~L~~-~~l~~l~~~a~~lGle~LVEVh~~~El~~a~~~g-------------a~i 174 (247)
T PRK13957 109 DFILDEIQIREARAFGASAILLIVRILTP-SQIKSFLKHASSLGMDVLVEVHTEDEAKLALDCG-------------AEI 174 (247)
T ss_pred cccCCHHHHHHHHHcCCCEEEeEHhhCCH-HHHHHHHHHHHHcCCceEEEECCHHHHHHHHhCC-------------CCE
Confidence 45666778888888776666777777777 445567889999998 555799999999888632 345
Q ss_pred EEEecCchh
Q psy16564 130 VVIKVRNWF 138 (157)
Q Consensus 130 vaI~D~g~~ 138 (157)
++|-+.+..
T Consensus 175 iGINnRdL~ 183 (247)
T PRK13957 175 IGINTRDLD 183 (247)
T ss_pred EEEeCCCCc
Confidence 777655443
No 133
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=38.51 E-value=89 Score=27.05 Aligned_cols=44 Identities=14% Similarity=0.268 Sum_probs=28.2
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCc-----hhhH----HHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDE-----PAYK----KLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~-----~~~~----~~l~~lc~~~~Ipvi~v~ 101 (157)
.++++.++..++-+||+|.|.-+ .... ..|..+|. .+||++.+.
T Consensus 30 ~~~l~~a~~~~vD~vliAGDlFd~~~Ps~~a~~~~~~~l~~l~~-~~Ipv~~I~ 82 (390)
T COG0420 30 DELLEIAKEEKVDFVLIAGDLFDTNNPSPRALKLFLEALRRLKD-AGIPVVVIA 82 (390)
T ss_pred HHHHHHHHHccCCEEEEccccccCCCCCHHHHHHHHHHHHHhcc-CCCcEEEec
Confidence 45566667778899999999432 1222 33333333 579999987
No 134
>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=38.34 E-value=59 Score=26.31 Aligned_cols=20 Identities=15% Similarity=0.087 Sum_probs=11.6
Q ss_pred hHHHHHHHHHhCCCCEEEeC
Q psy16564 82 YKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 82 ~~~~l~~lc~~~~Ipvi~v~ 101 (157)
....+..++++++|++++.+
T Consensus 187 ~l~~l~~~ik~~~v~~i~~e 206 (256)
T PF01297_consen 187 DLAELIKLIKENKVKCIFTE 206 (256)
T ss_dssp HHHHHHHHHHHTT-SEEEEE
T ss_pred HHHHHHHHhhhcCCcEEEec
Confidence 44455566666777776655
No 135
>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=38.27 E-value=64 Score=26.14 Aligned_cols=71 Identities=21% Similarity=0.220 Sum_probs=46.9
Q ss_pred ccHHHHHHHHHH-HHHhcCCceee------HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE-eCCHH
Q psy16564 33 SDINKALQQVLK-TARAHDGLAKG------LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK-VDNNK 104 (157)
Q Consensus 33 m~~~k~L~~lL~-~A~~agklv~G------~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~-v~sk~ 104 (157)
++-..++ ++++ ...+...+..| .+++.++++.| +.|++- | .....+..+|.++++|++= +.|-.
T Consensus 41 ~~t~~a~-~~I~~l~~~~p~~~vGAGTV~~~e~a~~a~~aG-A~FivS-----P-~~~~~v~~~~~~~~i~~iPG~~Tpt 112 (196)
T PF01081_consen 41 LRTPNAL-EAIEALRKEFPDLLVGAGTVLTAEQAEAAIAAG-AQFIVS-----P-GFDPEVIEYAREYGIPYIPGVMTPT 112 (196)
T ss_dssp TTSTTHH-HHHHHHHHHHTTSEEEEES--SHHHHHHHHHHT--SEEEE-----S-S--HHHHHHHHHHTSEEEEEESSHH
T ss_pred cCCccHH-HHHHHHHHHCCCCeeEEEeccCHHHHHHHHHcC-CCEEEC-----C-CCCHHHHHHHHHcCCcccCCcCCHH
Confidence 3333444 3343 33344677777 57888888888 777753 4 3445688899999999998 66888
Q ss_pred HHHHHhC
Q psy16564 105 KLGEWAG 111 (157)
Q Consensus 105 eLG~a~G 111 (157)
|+-+|..
T Consensus 113 Ei~~A~~ 119 (196)
T PF01081_consen 113 EIMQALE 119 (196)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8866654
No 136
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=37.83 E-value=84 Score=20.94 Aligned_cols=67 Identities=21% Similarity=0.243 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHh-cCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHh-CCCCEEEeC
Q psy16564 35 INKALQQVLKTARA-HDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSE-HQIPLIKVD 101 (157)
Q Consensus 35 ~~k~L~~lL~~A~~-agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~-~~Ipvi~v~ 101 (157)
..+.+..+|+...- .=..+.-..+++..+++....++|+--+.+..+-...+..+... .++|++.+.
T Consensus 10 ~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t 78 (112)
T PF00072_consen 10 IRELLEKLLERAGYEEVTTASSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVT 78 (112)
T ss_dssp HHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEE
T ss_pred HHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccCceEEEEEeeeccccccccccccccccccccEEEec
Confidence 34455555552111 11245567888889999999999998766665555566666555 489999876
No 137
>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=37.73 E-value=43 Score=27.59 Aligned_cols=34 Identities=18% Similarity=0.312 Sum_probs=28.3
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
....+||.|.|..+ ....+..+|.++++|++...
T Consensus 113 ~~~DlVvd~~D~~~--~r~~ln~~~~~~~ip~v~~~ 146 (240)
T TIGR02355 113 AEHDIVVDCTDNVE--VRNQLNRQCFAAKVPLVSGA 146 (240)
T ss_pred hcCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEEE
Confidence 34789999999854 67789999999999999754
No 138
>COG0352 ThiE Thiamine monophosphate synthase [Coenzyme metabolism]
Probab=37.68 E-value=1.1e+02 Score=24.99 Aligned_cols=57 Identities=21% Similarity=0.360 Sum_probs=44.0
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhh---HHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAY---KKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~---~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
.+.+.++|+.|-.-+.+-..|.+.... .+.+..+|.+|++|++ +.+.-+|....|-+
T Consensus 24 ~~~ve~al~~Gv~~vQlR~K~~~~~~~~~~a~~~~~lc~~~~v~li-INd~~dlA~~~~Ad 83 (211)
T COG0352 24 LEWVEAALKGGVTAVQLREKDLSDEEYLALAEKLRALCQKYGVPLI-INDRVDLALAVGAD 83 (211)
T ss_pred HHHHHHHHhCCCeEEEEecCCCChHHHHHHHHHHHHHHHHhCCeEE-ecCcHHHHHhCCCC
Confidence 577888898897888888888877442 3578999999999986 56667777766643
No 139
>cd01821 Rhamnogalacturan_acetylesterase_like Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted by neutral oligosaccharides such as arabinans, galactans and arabinogalactans. Extracellular enzymes participating in the degradation of plant cell wall polymers, such as Rhamnogalacturonan acetylesterase, would typically be found in saprophytic and plant pathogenic fungi and bacteria.
Probab=37.65 E-value=86 Score=23.91 Aligned_cols=22 Identities=27% Similarity=0.605 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHhCCCCEEEeCC
Q psy16564 81 AYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+...+..+|+++++|++-+.+
T Consensus 133 ~~~~~~~~~a~~~~~~~vD~~~ 154 (198)
T cd01821 133 DYPAAMRELAAEEGVPLIDLNA 154 (198)
T ss_pred hHHHHHHHHHHHhCCCEEecHH
Confidence 4678899999999999998764
No 140
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=37.55 E-value=55 Score=23.03 Aligned_cols=40 Identities=8% Similarity=0.150 Sum_probs=32.4
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.-...+..+.++..|... .+...+....++|+|+++-..
T Consensus 47 ~~~~~~~~~~~ii~ND~e~-~i~~~~~~a~~~y~I~~i~wS 86 (88)
T PF08862_consen 47 KRNRKSNSKFYIILNDSEK-PISEDIINALEQYNIKPIPWS 86 (88)
T ss_pred hhccCCCceEEEEECCCCC-ccCHHHHHHHHHCCCceecCC
Confidence 4455677899999999876 688889999999999988654
No 141
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=37.10 E-value=94 Score=22.83 Aligned_cols=51 Identities=6% Similarity=0.160 Sum_probs=34.5
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~ 113 (157)
+..+.+....+.+|-|..|.. ..+..+++++++++-.+. ....+++..|..
T Consensus 55 ~~~~~~~~~~v~vi~Is~d~~-----~~~~~~~~~~~~~~~~l~D~~~~~~~~~gv~ 106 (154)
T PRK09437 55 DNMDELKKAGVVVLGISTDKP-----EKLSRFAEKELLNFTLLSDEDHQVAEQFGVW 106 (154)
T ss_pred HHHHHHHHCCCEEEEEcCCCH-----HHHHHHHHHhCCCCeEEECCCchHHHHhCCC
Confidence 344445555688888877632 345677888888766655 567899999864
No 142
>PRK05690 molybdopterin biosynthesis protein MoeB; Provisional
Probab=37.01 E-value=40 Score=27.79 Aligned_cols=34 Identities=12% Similarity=0.178 Sum_probs=28.0
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+||.|.|... ....+..+|.++++|++....
T Consensus 122 ~~DiVi~~~D~~~--~r~~ln~~~~~~~ip~v~~~~ 155 (245)
T PRK05690 122 GHDLVLDCTDNVA--TRNQLNRACFAAKKPLVSGAA 155 (245)
T ss_pred cCCEEEecCCCHH--HHHHHHHHHHHhCCEEEEeee
Confidence 4779999999654 677899999999999998543
No 143
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=36.93 E-value=57 Score=29.87 Aligned_cols=42 Identities=17% Similarity=0.309 Sum_probs=33.9
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHH----hCCCCEEEeCC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCS----EHQIPLIKVDN 102 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~----~~~Ipvi~v~s 102 (157)
+.+++-..+++|+-+-|.+.-+...|+..|+ +.+|||+.+.+
T Consensus 91 ei~~~~~p~~ifv~~TC~t~iIGdDle~va~~~~~~~gipVV~v~~ 136 (457)
T CHL00073 91 QIKKDRNPSVIVWIGTCTTEIIKMDLEGMAPKLEAEIGIPIVVARA 136 (457)
T ss_pred HHHHhCCCCEEEEEccCcHHhhccCHHHHHHHHHHhhCCCEEEEeC
Confidence 3445567999999999999778888888887 46899999874
No 144
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=36.49 E-value=1.3e+02 Score=21.70 Aligned_cols=50 Identities=8% Similarity=0.098 Sum_probs=33.3
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC-H--HHHHHHhCCC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN-N--KKLGEWAGLS 113 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s-k--~eLG~a~G~~ 113 (157)
..+.+.+..+.++.|..|..+ .+..+.+++++++..+.+ . .++++..|..
T Consensus 54 ~~~~~~~~~v~vi~vs~d~~~-----~~~~~~~~~~~~~~~~~D~~~~~~~~~~~g~~ 106 (149)
T cd03018 54 SLELFEAAGAEVLGISVDSPF-----SLRAWAEENGLTFPLLSDFWPHGEVAKAYGVF 106 (149)
T ss_pred HHHHHHhCCCEEEEecCCCHH-----HHHHHHHhcCCCceEecCCCchhHHHHHhCCc
Confidence 344455556888888877433 345667777787776664 3 6888998864
No 145
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=36.41 E-value=1.4e+02 Score=20.50 Aligned_cols=53 Identities=17% Similarity=0.254 Sum_probs=38.7
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~ 113 (157)
.++..+.++...+.++.|..|..+ .+..+.+++++|+-.+. ...++.+..|..
T Consensus 48 l~~~~~~~~~~~~~vi~is~d~~~-----~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~ 101 (124)
T PF00578_consen 48 LNELYKKYKDKGVQVIGISTDDPE-----EIKQFLEEYGLPFPVLSDPDGELAKAFGIE 101 (124)
T ss_dssp HHHHHHHHHTTTEEEEEEESSSHH-----HHHHHHHHHTCSSEEEEETTSHHHHHTTCE
T ss_pred HHHHhhhhccceEEeeeccccccc-----chhhhhhhhccccccccCcchHHHHHcCCc
Confidence 345556677778999999997755 45666777777666555 577999999975
No 146
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=36.29 E-value=72 Score=27.37 Aligned_cols=51 Identities=16% Similarity=0.322 Sum_probs=34.5
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH-HHh
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG-EWA 110 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG-~a~ 110 (157)
+..+.|. +++-++|+-.+-.. .-..+|-.+|++++.|.+.+++..+|- .++
T Consensus 201 ~a~~~La-~~vD~miVVGg~~S-sNT~rL~eia~~~~~~t~~Ie~~~el~~~~~ 252 (281)
T PRK12360 201 ESAKELS-KEVDVMIVIGGKHS-SNTQKLVKICEKNCPNTFHIETADELDLEML 252 (281)
T ss_pred HHHHHHH-HhCCEEEEecCCCC-ccHHHHHHHHHHHCCCEEEECChHHCCHHHh
Confidence 3345554 44555555555444 234467889999999999999999995 344
No 147
>cd01894 EngA1 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=36.15 E-value=96 Score=21.88 Aligned_cols=22 Identities=18% Similarity=0.163 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCEEEeCCHHHH
Q psy16564 85 LVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 85 ~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
.+..+..+.++|++.+-+|.++
T Consensus 96 ~~~~~~~~~~~piiiv~nK~D~ 117 (157)
T cd01894 96 EIAKYLRKSKKPVILVVNKVDN 117 (157)
T ss_pred HHHHHHHhcCCCEEEEEECccc
Confidence 4555667778999999888765
No 148
>PF00290 Trp_syntA: Tryptophan synthase alpha chain; InterPro: IPR002028 Tryptophan synthase (4.2.1.20 from EC) catalyzes the last step in the biosynthesis of tryptophan [, ]: L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the 2 subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 from INTERPRO is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) [, ]. The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process; PDB: 1TJR_B 1RD5_B 1K8X_A 1QOQ_A 1KFE_A 1KFB_A 2CLO_A 1TTP_A 2RH9_A 1K7F_A ....
Probab=36.14 E-value=2.7e+02 Score=23.54 Aligned_cols=87 Identities=11% Similarity=0.181 Sum_probs=53.0
Q ss_pred CCCCCCCCCc-------------ccHHHHHHHHHHHHH-hcCC------------ceeeHHHHHHHHhcCCeeEEEEcCC
Q psy16564 23 NVPSANDEGV-------------SDINKALQQVLKTAR-AHDG------------LAKGLHEAAKALDRREAQLCVLADN 76 (157)
Q Consensus 23 ~~~~p~~~~~-------------m~~~k~L~~lL~~A~-~agk------------lv~G~~~v~KaL~kgkakLVIlA~D 76 (157)
|+--|+++++ +++.+.+ ++++..+ +.-. +..|.+.-.+.++.-.+.=||| -|
T Consensus 46 PfSDP~ADGpvIq~A~~rAL~~G~~~~~~~-~~~~~ir~~~~~~pivlm~Y~N~i~~~G~e~F~~~~~~aGvdGlIi-pD 123 (259)
T PF00290_consen 46 PFSDPVADGPVIQKASQRALKNGFTLEKIF-ELVKEIRKKEPDIPIVLMTYYNPIFQYGIERFFKEAKEAGVDGLII-PD 123 (259)
T ss_dssp -SSSCTTSSHHHHHHHHHHHHTT--HHHHH-HHHHHHHHHCTSSEEEEEE-HHHHHHH-HHHHHHHHHHHTEEEEEE-TT
T ss_pred CCCCCCCCCHHHHHHHHHHHHCCCCHHHHH-HHHHHHhccCCCCCEEEEeeccHHhccchHHHHHHHHHcCCCEEEE-cC
Confidence 4455666666 5666677 7777777 3222 2357777777776644655544 57
Q ss_pred CCchhhHHHHHHHHHhCCCCEEEeC----CHHHHHHHhCC
Q psy16564 77 CDEPAYKKLVQALCSEHQIPLIKVD----NNKKLGEWAGL 112 (157)
Q Consensus 77 ~s~~~~~~~l~~lc~~~~Ipvi~v~----sk~eLG~a~G~ 112 (157)
.+. +-...+...|+++|++.+.+- +.++|.+++..
T Consensus 124 LP~-ee~~~~~~~~~~~gl~~I~lv~p~t~~~Ri~~i~~~ 162 (259)
T PF00290_consen 124 LPP-EESEELREAAKKHGLDLIPLVAPTTPEERIKKIAKQ 162 (259)
T ss_dssp SBG-GGHHHHHHHHHHTT-EEEEEEETTS-HHHHHHHHHH
T ss_pred CCh-HHHHHHHHHHHHcCCeEEEEECCCCCHHHHHHHHHh
Confidence 777 556678889999999887743 45677776653
No 149
>cd02968 SCO SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properti
Probab=36.02 E-value=1.6e+02 Score=20.91 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=32.2
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC----HHHHHHHhCCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN----NKKLGEWAGLS 113 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s----k~eLG~a~G~~ 113 (157)
+++.+|.|+.|-.. +....+.++.++++.++..+.+ ...|.+.+|..
T Consensus 58 ~~v~~v~vs~d~~~-d~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~g~~ 108 (142)
T cd02968 58 DDVQVVFISVDPER-DTPEVLKAYAKAFGPGWIGLTGTPEEIEALAKAFGVY 108 (142)
T ss_pred CceEEEEEEECCCC-CCHHHHHHHHHHhCCCcEEEECCHHHHHHHHHHhcEE
Confidence 36899999887642 2334567788888766666553 36888888853
No 150
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=35.73 E-value=77 Score=23.55 Aligned_cols=49 Identities=8% Similarity=0.271 Sum_probs=29.4
Q ss_pred eeHHHHHHHHhcCCeeEEEEcC-C---CCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 54 KGLHEAAKALDRREAQLCVLAD-N---CDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~-D---~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
-|.++.++.++.|++..|++.. | -+..+....+..+++.+||.++.+..
T Consensus 55 p~l~~ll~~~~~g~vd~vvv~~ldRl~R~~~d~~~~~~~l~~~~gv~l~~~~~ 107 (140)
T cd03770 55 PGFNRMIEDIEAGKIDIVIVKDMSRLGRNYLKVGLYMEILFPKKGVRFIAIND 107 (140)
T ss_pred HHHHHHHHHHHcCCCCEEEEeccchhccCHHHHHHHHHHHHhhcCcEEEEecC
Confidence 3456667777888877766653 1 01112334455556666999988763
No 151
>TIGR03022 WbaP_sugtrans Undecaprenyl-phosphate galactose phosphotransferase, WbaP. This model includes the enterobacterial enzymes, where the function is presumed to be identical to the S. typhimurium enzyme as well as a somewhat broader group which are likely to catalyze the same or highly similar reactions based on a phylogenetic tree-building analysis of the broader sugar transferase family. Most of these genes are found within large operons dedicated to the production of complex exopolysaccharides such as the enterobacterial O-antigen. The most likely heterogeneity would be in the precise nature of the sugar molecule transferred.
Probab=35.48 E-value=90 Score=27.65 Aligned_cols=55 Identities=11% Similarity=0.035 Sum_probs=42.2
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCC-CEEEeCCHHHHH
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQI-PLIKVDNNKKLG 107 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~I-pvi~v~sk~eLG 107 (157)
+.|..+..+.+++.++.-|++|-+..+......+...|++.++ ++..+++-.++.
T Consensus 174 Vlg~~~l~~~i~~~~id~ViIAip~~~~~~~~~ll~~l~~~~v~~V~~vP~~~e~~ 229 (456)
T TIGR03022 174 VVGADDALRLYARTRYAYVIVAMPGTQAEDMARLVRKLGALHFRNVLIVPSLFGLP 229 (456)
T ss_pred ccChhHHHHHHHhCCCCEEEEecCCccHHHHHHHHHHHHhCCCeEEEEeCcccccc
Confidence 3444667777888889889999875554566777888999999 999999877765
No 152
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=35.39 E-value=49 Score=23.69 Aligned_cols=42 Identities=12% Similarity=0.186 Sum_probs=21.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCch---hhHHHHHHHHHhCCCCEE
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEP---AYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~---~~~~~l~~lc~~~~Ipvi 98 (157)
....+.|+++++.+||-..+-... .---.+...|-+++||++
T Consensus 61 ~~i~~~i~~~~idlVIn~~~~~~~~~~~~~~~iRr~Av~~~ip~i 105 (116)
T cd01423 61 PSLRELLAEGKIDLVINLPSNRGKRVLDNDYVMRRAADDFAVPLI 105 (116)
T ss_pred hhHHHHHHcCCceEEEECCCCCCCccccCcEeeehhhHhhCCccc
Confidence 445556666666666653321110 011235566666666664
No 153
>PRK06153 hypothetical protein; Provisional
Probab=35.32 E-value=75 Score=28.72 Aligned_cols=39 Identities=18% Similarity=0.222 Sum_probs=31.5
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
....+||.|-|..+ .+..+-.+|.+++||++.+.-..++
T Consensus 265 ~~~DiV~dcvDn~~--aR~~ln~~a~~~gIP~Id~G~~l~~ 303 (393)
T PRK06153 265 DGFTFVFVCVDKGS--SRKLIVDYLEALGIPFIDVGMGLEL 303 (393)
T ss_pred cCCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEeeeccee
Confidence 46899999999766 5777889999999999987744433
No 154
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=35.27 E-value=1.4e+02 Score=21.91 Aligned_cols=45 Identities=11% Similarity=0.317 Sum_probs=36.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE-eCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK-VDN 102 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~-v~s 102 (157)
.++++.+.++...++++.+|.-+ ++...+..+-+..-.|.+. +++
T Consensus 36 ~~~~~~l~~~~~~iIiite~~a~-~i~~~i~~~~~~~~~P~iv~IPs 81 (104)
T COG1436 36 RAALRVLAEDDVGIILITEDLAE-KIREEIRRIIRSSVLPAIVEIPS 81 (104)
T ss_pred HHHHHhhccCCceEEEEeHHHHh-hhHHHHHHHhhccCccEEEEeCC
Confidence 46677788889999999999888 7888888777777778765 667
No 155
>TIGR03603 cyclo_dehy_ocin bacteriocin biosynthesis cyclodehydratase, SagC family. Members of this protein family include enzymes related to SagC, a cyclodehydratase involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis.
Probab=35.26 E-value=61 Score=28.00 Aligned_cols=35 Identities=9% Similarity=0.153 Sum_probs=29.2
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEe
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v 100 (157)
....+||.+.|-...++...+.++|.++++|+++.
T Consensus 150 ~~~DlVid~tDn~~~r~L~~iN~ac~~~~~PlV~g 184 (318)
T TIGR03603 150 KDYNYIIICTEHSNISLLRGLNKLSKETKKPNTIA 184 (318)
T ss_pred CCCCEEEECCCCccHhHHHHHHHHHHHHCCCEEEE
Confidence 34789999999887566677999999999999854
No 156
>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=35.02 E-value=57 Score=26.17 Aligned_cols=36 Identities=22% Similarity=0.313 Sum_probs=28.9
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNK 104 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~ 104 (157)
.+.|||+|.|-++ +-..+...|+..+|||..++..+
T Consensus 69 ~~~lVi~at~d~~--ln~~i~~~a~~~~ilvn~~d~~e 104 (205)
T TIGR01470 69 GAFLVIAATDDEE--LNRRVAHAARARGVPVNVVDDPE 104 (205)
T ss_pred CcEEEEECCCCHH--HHHHHHHHHHHcCCEEEECCCcc
Confidence 4889999988764 56678999999999998776543
No 157
>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=34.41 E-value=1e+02 Score=19.05 Aligned_cols=40 Identities=18% Similarity=0.270 Sum_probs=17.6
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.|++..+.+-++==|.++ ...+.+..+.....+|.++++
T Consensus 17 ~~L~~~~i~y~~~dv~~~~-~~~~~l~~~~g~~~~P~v~i~ 56 (60)
T PF00462_consen 17 EFLDEKGIPYEEVDVDEDE-EAREELKELSGVRTVPQVFID 56 (60)
T ss_dssp HHHHHTTBEEEEEEGGGSH-HHHHHHHHHHSSSSSSEEEET
T ss_pred HHHHHcCCeeeEcccccch-hHHHHHHHHcCCCccCEEEEC
Confidence 3344444444444333333 344444444444555555544
No 158
>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=34.40 E-value=1e+02 Score=25.51 Aligned_cols=51 Identities=12% Similarity=0.066 Sum_probs=31.6
Q ss_pred CCceeeHHHHHHHHhcC-CeeEE-EE--cC--CCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 50 DGLAKGLHEAAKALDRR-EAQLC-VL--AD--NCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 50 gklv~G~~~v~KaL~kg-kakLV-Il--A~--D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++.+.-.+.+...+.+. ....+ ++ .. ..++ .....+..+.++++|++++++
T Consensus 171 ~~~~v~~H~af~Y~~~~~gl~~~~~~~~~~~~eps~-~~l~~l~~~ik~~~v~~if~e 227 (282)
T cd01017 171 GKTFVTQHAAFGYLARRYGLKQIAIVGVSPEVEPSP-KQLAELVEFVKKSDVKYIFFE 227 (282)
T ss_pred CCeEEEecccHHHHHHHCCCeEEecccCCCCCCCCH-HHHHHHHHHHHHcCCCEEEEe
Confidence 44455566677777652 23322 22 22 3455 455677888999999999987
No 159
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=34.33 E-value=94 Score=26.58 Aligned_cols=44 Identities=16% Similarity=0.299 Sum_probs=32.1
Q ss_pred ceeeH----HHHHHHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 52 LAKGL----HEAAKALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 52 lv~G~----~~v~KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+++|. ...+.+++.|. +..+++-+|-+. +..+|+++|||++.++
T Consensus 99 l~Sg~g~nl~al~~~~~~~~l~~~i~~visn~~~------~~~~A~~~gIp~~~~~ 148 (289)
T PRK13010 99 MVSKFDHCLNDLLYRWRMGELDMDIVGIISNHPD------LQPLAVQHDIPFHHLP 148 (289)
T ss_pred EEeCCCccHHHHHHHHHCCCCCcEEEEEEECChh------HHHHHHHcCCCEEEeC
Confidence 45664 55566666665 788888888765 2478999999999865
No 160
>PRK00124 hypothetical protein; Validated
Probab=34.17 E-value=63 Score=25.36 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=25.9
Q ss_pred EEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 71 CVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 71 VIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
++|=.|+-| ++..+...|+++++|++.|.|
T Consensus 3 I~VDADACP--Vk~~i~r~a~r~~i~v~~Vas 32 (151)
T PRK00124 3 IYVDADACP--VKDIIIRVAERHGIPVTLVAS 32 (151)
T ss_pred EEEECCCCc--HHHHHHHHHHHHCCeEEEEEe
Confidence 667778878 888899999999999999873
No 161
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=33.98 E-value=1.3e+02 Score=22.78 Aligned_cols=56 Identities=16% Similarity=0.238 Sum_probs=31.3
Q ss_pred eHHHHHHHHhc--CCeeEEEEcCCCCchh--hHHHHHHHHHh-CCCCEEE--eC--CHHHHHHHh
Q psy16564 55 GLHEAAKALDR--REAQLCVLADNCDEPA--YKKLVQALCSE-HQIPLIK--VD--NNKKLGEWA 110 (157)
Q Consensus 55 G~~~v~KaL~k--gkakLVIlA~D~s~~~--~~~~l~~lc~~-~~Ipvi~--v~--sk~eLG~a~ 110 (157)
+.....+.|++ .++..||+|.|++.+- +..++..+|.. .+.|+.. +. |..++-+|+
T Consensus 84 ~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~~~~~v~R~~fsslT~~~I~~A~ 148 (151)
T cd03362 84 GKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKRKPVKRAWFSSLTPKAIRRAF 148 (151)
T ss_pred cHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCCCCCcEEEEEEccCCHHHHHHHH
Confidence 33333444432 3578999999998732 55556666654 2445544 33 455554443
No 162
>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]
Probab=33.91 E-value=1.1e+02 Score=24.62 Aligned_cols=43 Identities=12% Similarity=0.241 Sum_probs=34.3
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+..-|++-+-.|+|+..+.-.++..+++..+.++.+||++...
T Consensus 28 ~ammIkkAkrPLlivGp~~~dee~~E~~vKi~ekfnipivaTa 70 (170)
T COG1880 28 VAMMIKKAKRPLLIVGPLALDEELLELAVKIIEKFNIPIVATA 70 (170)
T ss_pred HHHHHHhcCCceEEecccccCHHHHHHHHHHHHhcCCceEecc
Confidence 3355666667788888887744899999999999999999866
No 163
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=33.89 E-value=87 Score=27.78 Aligned_cols=77 Identities=17% Similarity=0.248 Sum_probs=50.5
Q ss_pred cHHHHHHHHHHH----HHhcCCceeeHHHHH---HHHhcCCeeEEEEcC-----CC-CchhhHHHHHHHHHhCCCCEEEe
Q psy16564 34 DINKALQQVLKT----ARAHDGLAKGLHEAA---KALDRREAQLCVLAD-----NC-DEPAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 34 ~~~k~L~~lL~~----A~~agklv~G~~~v~---KaL~kgkakLVIlA~-----D~-s~~~~~~~l~~lc~~~~Ipvi~v 100 (157)
++++.. .+|+. -|.-..+.-|.+|=. +||.. ...|+++=+ |- -..++.-.++.+..+-+||+++|
T Consensus 108 ~fd~iv-~lLGI~hLL~R~P~~LSGGEkQRVAIGRALLt-~P~LLLmDEPLaSLD~~RK~EilpylERL~~e~~IPIlYV 185 (352)
T COG4148 108 QFDQLV-ALLGIEHLLDRYPGTLSGGEKQRVAIGRALLT-APELLLMDEPLASLDLPRKREILPYLERLRDEINIPILYV 185 (352)
T ss_pred hHHHHH-HHhCcHHHHhhCCCccCcchhhHHHHHHHHhc-CCCeeeecCchhhcccchhhHHHHHHHHHHHhcCCCEEEE
Confidence 355555 66654 233456777887744 34433 355665543 32 22235567788899999999999
Q ss_pred C-CHHHHHHHhCC
Q psy16564 101 D-NNKKLGEWAGL 112 (157)
Q Consensus 101 ~-sk~eLG~a~G~ 112 (157)
. |.+|+-++.-.
T Consensus 186 SHS~~Ev~RLAd~ 198 (352)
T COG4148 186 SHSLDEVLRLADR 198 (352)
T ss_pred ecCHHHHHhhhhe
Confidence 9 99999998864
No 164
>PF04705 TSNR_N: Thiostrepton-resistance methylase, N terminus; InterPro: IPR006795 This region is found in some members of the SpoU-type rRNA methylase family (IPR001537 from INTERPRO).; GO: 0008649 rRNA methyltransferase activity, 0046677 response to antibiotic; PDB: 3GYQ_B 3NK6_A 3NK7_A.
Probab=33.86 E-value=44 Score=25.02 Aligned_cols=65 Identities=17% Similarity=0.250 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHhcCC--ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 35 INKALQQVLKTARAHDG--LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 35 ~~k~L~~lL~~A~~agk--lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+++.+ ++-+..|.+=+ |+--.+..+.+|..|---+=+.+.|..| +--.+.++|++++||+-.+..
T Consensus 15 VqRIi-Dvtk~sRs~ikT~LIED~EPL~~~i~AGvefieVYg~~~~p--~~~~ll~~c~~r~Ipvrlv~~ 81 (115)
T PF04705_consen 15 VQRII-DVTKHSRSNIKTTLIEDPEPLTHSIRAGVEFIEVYGSDGSP--VPPELLAACRQRGIPVRLVDS 81 (115)
T ss_dssp CHHHH-HHHCTSTTTTTEEEEESHHHHHHHHCTT-EEEEEEEETTS-----CCCCHHHHCTT--EEEE-H
T ss_pred hHHHH-hhcccchhhheeeeecCchHHHHHHhcCcEEEEEeeecCCC--CChHHHHHHHhcCCceEEecH
Confidence 45555 66665554433 6677888999999997667778888887 555678999999999988874
No 165
>cd03334 Fab1_TCP TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this domain leads to loss of catalytic activity. However no exact function this domain has been defined. In general, chaperonins are involved in productive folding of proteins.
Probab=33.65 E-value=1.6e+02 Score=24.49 Aligned_cols=50 Identities=14% Similarity=0.148 Sum_probs=36.8
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
..+..+.|..-.+.+||.-..+++ ....++.++||-++.--++.+|.+++
T Consensus 119 l~~~v~kI~~~g~nvIl~~k~I~~-----~a~~~l~k~gI~~v~~v~~~dl~rIa 168 (261)
T cd03334 119 LKNLVSRIVALRPDVILVEKSVSR-----IAQDLLLEAGITLVLNVKPSVLERIS 168 (261)
T ss_pred HHHHHHHHHhcCCCEEEECCccCH-----HHHHHHHHCCCEEEEecCHHHHHHHH
Confidence 455666666667999999888887 34567888999999877666555544
No 166
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=33.11 E-value=2e+02 Score=23.42 Aligned_cols=71 Identities=23% Similarity=0.195 Sum_probs=44.5
Q ss_pred ccHHHHHHHHHHH-HHhcCCceee------HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEE-EeCCHH
Q psy16564 33 SDINKALQQVLKT-ARAHDGLAKG------LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLI-KVDNNK 104 (157)
Q Consensus 33 m~~~k~L~~lL~~-A~~agklv~G------~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi-~v~sk~ 104 (157)
++....+ +.++. ..+...+..| ..++..+++.| +.+++.. ..++ .+...|.+++||++ -+.|..
T Consensus 48 l~~~~~~-~~I~~l~~~~p~~~IGAGTVl~~~~a~~a~~aG-A~FivsP-~~~~-----~vi~~a~~~~i~~iPG~~Tpt 119 (212)
T PRK05718 48 LRTPAAL-EAIRLIAKEVPEALIGAGTVLNPEQLAQAIEAG-AQFIVSP-GLTP-----PLLKAAQEGPIPLIPGVSTPS 119 (212)
T ss_pred cCCccHH-HHHHHHHHHCCCCEEEEeeccCHHHHHHHHHcC-CCEEECC-CCCH-----HHHHHHHHcCCCEeCCCCCHH
Confidence 4444455 33333 2344567677 46666777777 7777533 2333 56778999999999 567777
Q ss_pred HHHHHhC
Q psy16564 105 KLGEWAG 111 (157)
Q Consensus 105 eLG~a~G 111 (157)
|+-++..
T Consensus 120 Ei~~a~~ 126 (212)
T PRK05718 120 ELMLGME 126 (212)
T ss_pred HHHHHHH
Confidence 7766654
No 167
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=32.90 E-value=1.2e+02 Score=22.30 Aligned_cols=44 Identities=14% Similarity=0.113 Sum_probs=26.1
Q ss_pred CCeeEEEEcCCCCchh--hHHHHHHHHHhCCCCEEEe--C--CHHHHHHHh
Q psy16564 66 REAQLCVLADNCDEPA--YKKLVQALCSEHQIPLIKV--D--NNKKLGEWA 110 (157)
Q Consensus 66 gkakLVIlA~D~s~~~--~~~~l~~lc~~~~Ipvi~v--~--sk~eLG~a~ 110 (157)
.++..||+|.|++.+- +..++..++.. +.|+..+ . |..++-+++
T Consensus 71 ~~~~eiiiAtD~drEGe~i~~~i~~~~~~-~~~v~Rl~~sslt~~~I~~A~ 120 (123)
T cd03363 71 KKADEIYLATDPDREGEAIAWHLAEVLKL-KKNVKRVVFNEITKEAIKEAL 120 (123)
T ss_pred hcCCEEEEcCCCCcchHHHHHHHHHHcCC-CCCeEEEEEccCCHHHHHHHH
Confidence 4588999999998732 44455555553 5565543 2 444444443
No 168
>PF05159 Capsule_synth: Capsule polysaccharide biosynthesis protein; InterPro: IPR007833 This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS P42218 from SWISSPROT and LipB P57038 from SWISSPROT. Capsule polysaccharide modification protein lipB/A is involved in the phospholipid modification of the capsular polysaccharide and is a strong requirement for its translocation to the cell surface. The capsule of Neisseria meningitidis serogroup B and of other meningococcal serogroups and other Gram-negative bacterial pathogens, are anchored in the outer membrane through a 1,2-diacylglycerol moiety. The lipA and lipB genes are located on the 3' end of the ctr operon. lipA and lipB do not encode proteins responsible for diacylglycerophosphatidic acid substitution of the meningococcal capsule polymer, but they are required for proper translocation and surface expression of the lipidated polymer []. KpsS is an unusual sulphate-modified form of the capsular polysaccharide in Rhizobium loti (Mesorhizobium loti). Many plants, including R. loti, enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. KpsS functions as a fucosyl sulphotransferase in vitro. The kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases []. Sulphated cell surface polysaccharides are required for optimum nodule formation but limit growth rate and nodule colonisation in M. loti [].; GO: 0000271 polysaccharide biosynthetic process, 0015774 polysaccharide transport
Probab=32.68 E-value=70 Score=26.10 Aligned_cols=30 Identities=20% Similarity=0.341 Sum_probs=23.5
Q ss_pred EEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 71 CVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 71 VIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
||+=+|+.+ .-.....+|+++|||+++++.
T Consensus 3 v~~wg~~~~--~~~~~~~~a~~~~i~~~~~E~ 32 (269)
T PF05159_consen 3 VVVWGDKRP--YHRAAIEVAKELGIPVIFFED 32 (269)
T ss_pred EEEECCCcc--HHHHHHHHHHHhCCCEEEEec
Confidence 566688877 444567889999999999983
No 169
>COG0800 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]
Probab=32.66 E-value=77 Score=26.27 Aligned_cols=72 Identities=19% Similarity=0.173 Sum_probs=46.4
Q ss_pred cccHHHHHHHHHHHHHhcCCceeeH------HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE-eCCHH
Q psy16564 32 VSDINKALQQVLKTARAHDGLAKGL------HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK-VDNNK 104 (157)
Q Consensus 32 ~m~~~k~L~~lL~~A~~agklv~G~------~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~-v~sk~ 104 (157)
+++...++..+=..++..+...+|. .|+..++..| ++|+| +| .+...+...|..+++|++- +.|-.
T Consensus 45 Tl~sp~a~e~I~~l~~~~p~~lIGAGTVL~~~q~~~a~~aG-a~fiV-----sP-~~~~ev~~~a~~~~ip~~PG~~Tpt 117 (211)
T COG0800 45 TLRTPAALEAIRALAKEFPEALIGAGTVLNPEQARQAIAAG-AQFIV-----SP-GLNPEVAKAANRYGIPYIPGVATPT 117 (211)
T ss_pred ecCCCCHHHHHHHHHHhCcccEEccccccCHHHHHHHHHcC-CCEEE-----CC-CCCHHHHHHHHhCCCcccCCCCCHH
Confidence 3444455533334455556777774 6667777777 77774 45 5666788899999999986 44555
Q ss_pred HHHHHh
Q psy16564 105 KLGEWA 110 (157)
Q Consensus 105 eLG~a~ 110 (157)
|+=.++
T Consensus 118 Ei~~Al 123 (211)
T COG0800 118 EIMAAL 123 (211)
T ss_pred HHHHHH
Confidence 544443
No 170
>KOG1615|consensus
Probab=32.54 E-value=1.4e+02 Score=25.01 Aligned_cols=79 Identities=22% Similarity=0.357 Sum_probs=56.9
Q ss_pred CCCcccHHHHHHHHHHHHH------------hcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCC
Q psy16564 29 DEGVSDINKALQQVLKTAR------------AHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIP 96 (157)
Q Consensus 29 ~~~~m~~~k~L~~lL~~A~------------~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ip 96 (157)
|.+.|+++++|+.=|.+-+ +--.++.|+++..+.|.....++.++..--.+ .+...+.+.|||
T Consensus 54 Mng~~~F~eaL~~Rl~llqp~~~qv~~~v~~~k~~lT~Gi~eLv~~L~~~~~~v~liSGGF~~-----~i~~Va~~Lgi~ 128 (227)
T KOG1615|consen 54 MNGEADFQEALAARLSLLQPLQVQVEQFVIKQKPTLTPGIRELVSRLHARGTQVYLISGGFRQ-----LIEPVAEQLGIP 128 (227)
T ss_pred hCCCCcHHHHHHHHHHHhcccHHHHHHHHhcCCCccCCCHHHHHHHHHHcCCeEEEEcCChHH-----HHHHHHHHhCCc
Confidence 7777888888865544332 12368999999999999999999998876555 456667889999
Q ss_pred EEEeC----CHHHHHHHhCC
Q psy16564 97 LIKVD----NNKKLGEWAGL 112 (157)
Q Consensus 97 vi~v~----sk~eLG~a~G~ 112 (157)
.-.++ --...|+..|.
T Consensus 129 ~~n~yAN~l~fd~~Gk~~gf 148 (227)
T KOG1615|consen 129 KSNIYANELLFDKDGKYLGF 148 (227)
T ss_pred HhhhhhheeeeccCCccccc
Confidence 93222 22356777774
No 171
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=32.41 E-value=95 Score=26.02 Aligned_cols=46 Identities=22% Similarity=0.290 Sum_probs=35.3
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.......|...++.+||=|.=--...+.......|++.+|||+.+.
T Consensus 54 ~~~l~~~l~~~~i~~VIDAtHPfA~~is~~a~~a~~~~~ipylR~e 99 (256)
T TIGR00715 54 PQELREFLKRHSIDILVDATHPFAAQITTNATAVCKELGIPYVRFE 99 (256)
T ss_pred HHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHHHhCCcEEEEE
Confidence 3444466677889999988765444677788999999999999885
No 172
>cd03769 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.
Probab=31.99 E-value=1.1e+02 Score=22.77 Aligned_cols=47 Identities=13% Similarity=0.177 Sum_probs=25.3
Q ss_pred eeHHHHHHHHhcCCeeEEEEcC-C-CCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 54 KGLHEAAKALDRREAQLCVLAD-N-CDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~-D-~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
-|..+.++.++.|++..|++.+ | .+- +....+..+|+++||.++.+.
T Consensus 49 p~l~~ll~~i~~g~~d~lvV~~ldRl~R-~~~d~~~~~l~~~gv~l~~~~ 97 (134)
T cd03769 49 KGLLKLLEDVLAGKVERVVITYKDRLAR-FGFELLEELFKAYGVEIVVIN 97 (134)
T ss_pred HHHHHHHHHHHcCCCCEEEEEeccHHHH-hhHHHHHHHHHHCCCEEEEEe
Confidence 4556667777777654444322 2 111 122234456777777777665
No 173
>PF02421 FeoB_N: Ferrous iron transport protein B; InterPro: IPR011619 Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [].; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0016021 integral to membrane; PDB: 3TAH_B 3B1X_A 3SS8_A 3B1W_C 3B1V_A 3LX5_A 3B1Y_A 3LX8_A 3B1Z_A 3K53_B ....
Probab=31.76 E-value=1.2e+02 Score=23.65 Aligned_cols=53 Identities=17% Similarity=0.167 Sum_probs=35.9
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
.+.+..++..+++.--|+...+.--.+...-.+.++|++.+-+|.++.+--|.
T Consensus 71 ~~~l~~~~~D~ii~VvDa~~l~r~l~l~~ql~e~g~P~vvvlN~~D~a~~~g~ 123 (156)
T PF02421_consen 71 RDYLLSEKPDLIIVVVDATNLERNLYLTLQLLELGIPVVVVLNKMDEAERKGI 123 (156)
T ss_dssp HHHHHHTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTE
T ss_pred HHHHhhcCCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEEeCHHHHHHcCC
Confidence 44555778888888888876333233333445689999999888776665554
No 174
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=31.37 E-value=1.2e+02 Score=25.83 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=27.2
Q ss_pred HHHHHHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
...+++++.|+ +..+++-+|-+. +..+|+++|||++.+.
T Consensus 104 ~al~~~~~~~~~~~~i~~visn~~~------~~~lA~~~gIp~~~~~ 144 (286)
T PRK13011 104 NDLLYRWRIGELPMDIVGVVSNHPD------LEPLAAWHGIPFHHFP 144 (286)
T ss_pred HHHHHHHHcCCCCcEEEEEEECCcc------HHHHHHHhCCCEEEeC
Confidence 44555555664 788888777543 4556999999999863
No 175
>TIGR00160 MGSA methylglyoxal synthase. Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer, et al. (MUID:98149311) propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars.
Probab=31.29 E-value=1e+02 Score=24.14 Aligned_cols=50 Identities=14% Similarity=0.199 Sum_probs=37.7
Q ss_pred cCCceeeHHHHHHHHhcCCeeEEEEcCCC------CchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 49 HDGLAKGLHEAAKALDRREAQLCVLADNC------DEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 49 agklv~G~~~v~KaL~kgkakLVIlA~D~------s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+|-+ -|..|.-..|..|++.+||.=.|- +| ++. -|..+|.-||||+-.=.
T Consensus 56 SGpl-GGDqQIga~Ia~g~id~vIFf~DPl~~~phep-Di~-aLlRlc~v~nIP~AtN~ 111 (143)
T TIGR00160 56 SGPM-GGDQQIGALIAEGKIDAVIFFWDPLNAQPHEP-DVK-ALLRLCTVWNIPLATNV 111 (143)
T ss_pred cCCc-cHHHHHHHHHHhCCCCEEEEecCCCCCCCCCc-CHH-HHHHHHHhhCcccccCH
Confidence 4443 678888888899999999988882 23 344 57789999999996533
No 176
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=31.21 E-value=1.5e+02 Score=27.22 Aligned_cols=45 Identities=7% Similarity=0.066 Sum_probs=36.6
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
..+..+++.|.....-...+..+++..++|++...+..+|..++.
T Consensus 269 GkkVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~ 313 (436)
T PRK11889 269 KKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALT 313 (436)
T ss_pred CCcEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHH
Confidence 356778888876545677888899999999998889999988875
No 177
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=31.07 E-value=1.5e+02 Score=19.05 Aligned_cols=31 Identities=19% Similarity=0.335 Sum_probs=18.7
Q ss_pred hHHHHHHHHHhCCCCEEEeC-CH-----HHHHHHhCC
Q psy16564 82 YKKLVQALCSEHQIPLIKVD-NN-----KKLGEWAGL 112 (157)
Q Consensus 82 ~~~~l~~lc~~~~Ipvi~v~-sk-----~eLG~a~G~ 112 (157)
.......+.++++||+..++ .+ .+|-++.|.
T Consensus 13 ~C~ka~~~L~~~gi~~~~~di~~~~~~~~el~~~~g~ 49 (73)
T cd03027 13 DCTAVRLFLREKGLPYVEINIDIFPERKAELEERTGS 49 (73)
T ss_pred hHHHHHHHHHHCCCceEEEECCCCHHHHHHHHHHhCC
Confidence 35556667777888877765 22 245555553
No 178
>cd04188 DPG_synthase DPG_synthase is involved in protein N-linked glycosylation. UDP-glucose:dolichyl-phosphate glucosyltransferase (DPG_synthase) is a transmembrane-bound enzyme of the endoplasmic reticulum involved in protein N-linked glycosylation. This enzyme catalyzes the transfer of glucose from UDP-glucose to dolichyl phosphate.
Probab=31.05 E-value=85 Score=23.91 Aligned_cols=41 Identities=10% Similarity=0.174 Sum_probs=24.7
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
...++ +..|.+.+.+...+..++.+++..+..+.....+|.
T Consensus 30 ~~eii-vvdd~S~D~t~~~~~~~~~~~~~~i~~i~~~~n~G~ 70 (211)
T cd04188 30 SYEII-VVDDGSKDGTAEVARKLARKNPALIRVLTLPKNRGK 70 (211)
T ss_pred CEEEE-EEeCCCCCchHHHHHHHHHhCCCcEEEEEcccCCCc
Confidence 34444 556666657888888888877665444444333443
No 179
>TIGR01295 PedC_BrcD bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris.
Probab=30.98 E-value=1.5e+02 Score=21.63 Aligned_cols=53 Identities=15% Similarity=0.255 Sum_probs=37.6
Q ss_pred CCceeeHHHHHHHHhcCCeeEEE-EcCCCCch-hhHHHHHHHHHhCCCCEEEeCC
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCV-LADNCDEP-AYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVI-lA~D~s~~-~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
|-......+..+.|.+++..+|. =+..|++= ...-.|..+.++.+++++++..
T Consensus 7 ~~~~it~~~~~~~i~~~~~~iv~f~~~~Cp~C~~~~P~l~~~~~~~~~~~y~vdv 61 (122)
T TIGR01295 7 GLEVTTVVRALEALDKKETATFFIGRKTCPYCRKFSGTLSGVVAQTKAPIYYIDS 61 (122)
T ss_pred cceecCHHHHHHHHHcCCcEEEEEECCCChhHHHHhHHHHHHHHhcCCcEEEEEC
Confidence 44566777888889888865554 45556542 2445678888889999999884
No 180
>PRK08328 hypothetical protein; Provisional
Probab=30.97 E-value=80 Score=25.71 Aligned_cols=34 Identities=15% Similarity=0.124 Sum_probs=27.8
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+||-|.|-. .....+..+|.++++|++....
T Consensus 118 ~~D~Vid~~d~~--~~r~~l~~~~~~~~ip~i~g~~ 151 (231)
T PRK08328 118 GVDVIVDCLDNF--ETRYLLDDYAHKKGIPLVHGAV 151 (231)
T ss_pred cCCEEEECCCCH--HHHHHHHHHHHHcCCCEEEEee
Confidence 478999999984 4677888999999999997554
No 181
>KOG3849|consensus
Probab=30.76 E-value=79 Score=27.85 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=28.0
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
|.++-|++|+|.+. +...|...-..++|.+...+
T Consensus 298 ~dakSVfVAsDs~h--mi~Eln~aL~~~~i~vh~l~ 331 (386)
T KOG3849|consen 298 GDAKSVFVASDSDH--MIDELNEALKPYEIEVHRLE 331 (386)
T ss_pred cccceEEEeccchh--hhHHHHHhhcccceeEEecC
Confidence 57999999999976 55667767788999998876
No 182
>KOG0362|consensus
Probab=30.69 E-value=96 Score=29.08 Aligned_cols=57 Identities=14% Similarity=0.243 Sum_probs=41.9
Q ss_pred CceeeHHHHHH----HHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 51 GLAKGLHEAAK----ALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 51 klv~G~~~v~K----aL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
.+..|.+.-++ +|.-..++.||-..-.++ ....||++|+|=++.+.|+-||-++|..
T Consensus 262 ~FSKgEe~lle~~vk~Ia~~gvkViV~~g~V~e-----m~Lhflnky~ImVlqi~Sk~eLrrlcrt 322 (537)
T KOG0362|consen 262 NFSKGEEALLEEQVKAIADAGVKVIVSGGKVDE-----MTLHFLNKYKIMVLQINSKFDLRRLCRT 322 (537)
T ss_pred hhccccHHHHHHHHHHHHhcCCeEEEecCccch-----hhhhhhccccEEEEEeccHhhHHHHHHH
Confidence 34566555444 444456788887777776 3456899999999999999999988854
No 183
>PLN02331 phosphoribosylglycinamide formyltransferase
Probab=30.56 E-value=1.2e+02 Score=24.65 Aligned_cols=42 Identities=14% Similarity=0.085 Sum_probs=26.6
Q ss_pred HHHHHHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 57 HEAAKALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 57 ~~v~KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+++++.|+ +..+++-+|-+. .....+|+++|||++.++.
T Consensus 14 ~al~~~~~~~~l~~~i~~visn~~~----~~~~~~A~~~gIp~~~~~~ 57 (207)
T PLN02331 14 RAIHDACLDGRVNGDVVVVVTNKPG----CGGAEYARENGIPVLVYPK 57 (207)
T ss_pred HHHHHHHHcCCCCeEEEEEEEeCCC----ChHHHHHHHhCCCEEEecc
Confidence 34455666664 555555555433 1245689999999998764
No 184
>PRK05562 precorrin-2 dehydrogenase; Provisional
Probab=30.55 E-value=58 Score=26.93 Aligned_cols=35 Identities=17% Similarity=0.280 Sum_probs=29.2
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
.+.|||.|.|- + .+-..+-..|++.++++..+++.
T Consensus 85 g~~LViaATdD-~-~vN~~I~~~a~~~~~lvn~vd~p 119 (223)
T PRK05562 85 DKHLIVIATDD-E-KLNNKIRKHCDRLYKLYIDCSDY 119 (223)
T ss_pred CCcEEEECCCC-H-HHHHHHHHHHHHcCCeEEEcCCc
Confidence 47899999874 4 58888999999999999988764
No 185
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand []. ; GO: 0004425 indole-3-glycerol-phosphate synthase activity; PDB: 1VC4_A 1PII_A 1JCM_P 1I4N_B 1J5T_A 3TSM_B 4FB7_A 3QJA_A 1JUL_A 2C3Z_A ....
Probab=30.37 E-value=1.8e+02 Score=24.45 Aligned_cols=76 Identities=12% Similarity=0.083 Sum_probs=53.6
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCC-CEEEeCCHHHHHHHhCCCccccCCCccceeeeE
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQI-PLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCS 128 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~I-pvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s 128 (157)
..++.-..|+..+-..|---+++++.=-++ .....+..+|...|. +++.|.+.+||-+++... ..
T Consensus 115 KDFIid~~QI~eA~~~GADaVLLI~~~L~~-~~l~~l~~~a~~lGle~lVEVh~~~El~~al~~~-------------a~ 180 (254)
T PF00218_consen 115 KDFIIDPYQIYEARAAGADAVLLIAAILSD-DQLEELLELAHSLGLEALVEVHNEEELERALEAG-------------AD 180 (254)
T ss_dssp ES---SHHHHHHHHHTT-SEEEEEGGGSGH-HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT--------------S
T ss_pred ccCCCCHHHHHHHHHcCCCEeehhHHhCCH-HHHHHHHHHHHHcCCCeEEEECCHHHHHHHHHcC-------------CC
Confidence 457788889999998897777778887777 566678899999999 566699999999998532 33
Q ss_pred EEEEecCchhH
Q psy16564 129 CVVIKVRNWFL 139 (157)
Q Consensus 129 ~vaI~D~g~~~ 139 (157)
.++|-+.++..
T Consensus 181 iiGINnRdL~t 191 (254)
T PF00218_consen 181 IIGINNRDLKT 191 (254)
T ss_dssp EEEEESBCTTT
T ss_pred EEEEeCccccC
Confidence 57787654433
No 186
>PRK00766 hypothetical protein; Provisional
Probab=30.22 E-value=1.2e+02 Score=24.75 Aligned_cols=48 Identities=13% Similarity=0.085 Sum_probs=35.1
Q ss_pred cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEe----CCHHHHHHHhCC
Q psy16564 65 RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKV----DNNKKLGEWAGL 112 (157)
Q Consensus 65 kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v----~sk~eLG~a~G~ 112 (157)
+.++++|+|..=+---=-.-.+..+.++-++||+.| ++.+.+-.|+-+
T Consensus 69 r~~i~~V~L~Git~agFNvvD~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k 120 (194)
T PRK00766 69 KGQLRVIMLDGITYGGFNVVDIEELYRETGLPVIVVMRKKPDFEAIESALKK 120 (194)
T ss_pred ccceEEEEECCEeeeeeEEecHHHHHHHHCCCEEEEEecCCCHHHHHHHHHH
Confidence 368899999885332112234788899999999999 788888888844
No 187
>cd06423 CESA_like CESA_like is the cellulose synthase superfamily. The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains. The members include cellulose synthase catalytic subunit, chitin synthase, glucan biosynthesis protein and other families of CESA-like proteins. Cellulose synthase catalyzes the polymerization reaction of cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues in plants, most algae, some bacteria and fungi, and even some animals. In bacteria, algae and lower eukaryotes, there is a second unrelated type of cellulose synthase (Type II), which produces acylated cellulose, a derivative of cellulose. Chitin synthase catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin, which is a linear homopolymer of beta-(1,4)-linked GlcNAc residues and Glucan Biosynthesis protein catalyzes the
Probab=30.01 E-value=1.3e+02 Score=20.82 Aligned_cols=41 Identities=12% Similarity=0.203 Sum_probs=21.8
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
...++|+.... .......+..+.......++.+......|.
T Consensus 26 ~~~iivvdd~s-~d~t~~~~~~~~~~~~~~~~~~~~~~~~g~ 66 (180)
T cd06423 26 KLEVIVVDDGS-TDDTLEILEELAALYIRRVLVVRDKENGGK 66 (180)
T ss_pred ceEEEEEeCCC-ccchHHHHHHHhccccceEEEEEecccCCc
Confidence 35555554444 446777777766654344444444444443
No 188
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=29.93 E-value=1.2e+02 Score=25.77 Aligned_cols=39 Identities=18% Similarity=0.304 Sum_probs=25.8
Q ss_pred HHHHHHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
...+++++.|. +..+++-+|-++ +..+|+++|||++.++
T Consensus 104 ~al~~~~~~~~~~~~i~~visn~~~------~~~lA~~~gIp~~~~~ 144 (286)
T PRK06027 104 GDLLWRWRSGELPVEIAAVISNHDD------LRSLVERFGIPFHHVP 144 (286)
T ss_pred HHHHHHHHcCCCCcEEEEEEEcChh------HHHHHHHhCCCEEEec
Confidence 33444445553 677777777643 3456999999999865
No 189
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=29.76 E-value=1.5e+02 Score=21.43 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=28.7
Q ss_pred eeHHHHHHHHhcCCeeEEEEcC-C---CCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 54 KGLHEAAKALDRREAQLCVLAD-N---CDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~-D---~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
-|..+.++.+++|++..|++.. | -++... ..+..+|..+||+++.+.
T Consensus 52 p~l~~ll~~~~~g~~~~ivv~~~~Rl~R~~~~~-~~~~~~l~~~gi~l~~~~ 102 (148)
T smart00857 52 PGLQRLLADLRAGDIDVLVVYKLDRLGRSLRDL-LALLELLEKKGVRLVSVT 102 (148)
T ss_pred HHHHHHHHHHHcCCCCEEEEeccchhhCcHHHH-HHHHHHHHHCCCEEEECc
Confidence 3466677777788776665554 1 122122 334567788888888765
No 190
>TIGR00035 asp_race aspartate racemase.
Probab=29.72 E-value=97 Score=24.94 Aligned_cols=51 Identities=18% Similarity=0.237 Sum_probs=36.6
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC--CHHHH
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD--NNKKL 106 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~--sk~eL 106 (157)
+.--..+..+.|++..+.++++|.+... .. +..+-+..+||++.+- +-..+
T Consensus 60 ~~~~l~~~~~~L~~~g~d~iviaCNTah-~~---~~~l~~~~~iPii~i~~~~~~~~ 112 (229)
T TIGR00035 60 PRPILIDIAVKLENAGADFIIMPCNTAH-KF---AEDIQKAIGIPLISMIEETAEAV 112 (229)
T ss_pred HHHHHHHHHHHHHHcCCCEEEECCccHH-HH---HHHHHHhCCCCEechHHHHHHHH
Confidence 4555667778888888999999999866 33 3455566789999854 34444
No 191
>cd01859 MJ1464 MJ1464. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.
Probab=29.71 E-value=1.5e+02 Score=21.65 Aligned_cols=14 Identities=29% Similarity=0.173 Sum_probs=6.2
Q ss_pred CCCCEEEeCCHHHH
Q psy16564 93 HQIPLIKVDNNKKL 106 (157)
Q Consensus 93 ~~Ipvi~v~sk~eL 106 (157)
.+.|++.+-+|.+|
T Consensus 40 ~~~p~iiv~NK~Dl 53 (156)
T cd01859 40 LGKKLLIVLNKADL 53 (156)
T ss_pred CCCcEEEEEEhHHh
Confidence 34444444444443
No 192
>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=29.47 E-value=1.6e+02 Score=22.10 Aligned_cols=52 Identities=10% Similarity=0.212 Sum_probs=34.4
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC----------HHHHHHHhCCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN----------NKKLGEWAGLS 113 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s----------k~eLG~a~G~~ 113 (157)
.--++.|.+=+.-+||....-.+ . +....++.++|++.+.. -..||+++|++
T Consensus 50 ~~n~E~l~~l~PDlii~~~~~~~-~----~~~~l~~~gi~v~~~~~~~~~~~~~~~~~~lg~~~g~~ 111 (195)
T cd01143 50 NPNVEKIVALKPDLVIVSSSSLA-E----LLEKLKDAGIPVVVLPAASSLDEIYDQIELIGKITGAE 111 (195)
T ss_pred CCCHHHHhccCCCEEEEcCCcCH-H----HHHHHHHcCCcEEEeCCCCCHHHHHHHHHHHHHHhCCh
Confidence 34566677777888877543333 2 23344778999988752 23899999984
No 193
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=29.43 E-value=1.8e+02 Score=20.54 Aligned_cols=46 Identities=11% Similarity=0.157 Sum_probs=31.0
Q ss_pred eHHHHHHHHhcCCeeEEEEcCC----CCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 55 GLHEAAKALDRREAQLCVLADN----CDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D----~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
|.++.++.++.++...|++.+- -++ .-...+...|..+||+++.+.
T Consensus 53 ~~~~ll~~~~~~~~d~ivv~~~~Rl~R~~-~~~~~~~~~l~~~gi~l~~~~ 102 (137)
T cd00338 53 GLQRLLADVKAGKIDVVLVEKLDRLSRNL-VDLLELLELLEAHGVRVVTAD 102 (137)
T ss_pred HHHHHHHHHHcCCCCEEEEEecchhhCCH-HHHHHHHHHHHHCCCEEEEec
Confidence 5677777888777777766552 122 223345667888899998876
No 194
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=29.35 E-value=1.5e+02 Score=22.39 Aligned_cols=42 Identities=24% Similarity=0.219 Sum_probs=24.8
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+.++.+...++..+|+.....+ ... ....+.+.+||++.+.
T Consensus 45 ~~~~~~~~~~~~d~ii~~~~~~~-~~~--~~~~l~~~~ip~v~~~ 86 (264)
T cd01537 45 LSALENLIARGVDGIIIAPSDLT-APT--IVKLARKAGIPVVLVD 86 (264)
T ss_pred HHHHHHHHHcCCCEEEEecCCCc-chh--HHHHhhhcCCCEEEec
Confidence 34444455556666665543333 232 3456688899998875
No 195
>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=29.11 E-value=66 Score=20.88 Aligned_cols=23 Identities=17% Similarity=0.375 Sum_probs=19.4
Q ss_pred hhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 81 AYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
.+...|.+.|+++|++++.++..
T Consensus 3 ~~~~~L~yka~~~G~~v~~v~~~ 25 (69)
T PF07282_consen 3 QFRQRLEYKAEEYGIQVVEVDEA 25 (69)
T ss_pred HHHHHHHHHHHHhCCEEEEECCC
Confidence 36678999999999999999843
No 196
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=29.08 E-value=1.2e+02 Score=25.82 Aligned_cols=45 Identities=16% Similarity=0.247 Sum_probs=30.3
Q ss_pred ceeeHHHHH----HHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 52 LAKGLHEAA----KALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 52 lv~G~~~v~----KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+++|.-..+ .+++.|. +..+++-+|-+. +..+|+++|||++.++.
T Consensus 90 l~Sg~g~nl~~l~~~~~~g~l~~~i~~visn~~~------~~~~A~~~gIp~~~~~~ 140 (280)
T TIGR00655 90 LVSKEDHCLGDLLWRWYSGELDAEIALVISNHED------LRSLVERFGIPFHYIPA 140 (280)
T ss_pred EEcCCChhHHHHHHHHHcCCCCcEEEEEEEcChh------HHHHHHHhCCCEEEcCC
Confidence 456654444 4445564 677777777654 33469999999998774
No 197
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=29.07 E-value=1.6e+02 Score=25.43 Aligned_cols=50 Identities=18% Similarity=0.325 Sum_probs=34.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
.+..+.|.+ ++-++|+-.+-..-++. +|-+.|++++.|.+.+++..+|-.
T Consensus 201 Q~a~~~La~-~vD~miVVGg~~SsNT~-kL~~i~~~~~~~t~~Ie~~~el~~ 250 (298)
T PRK01045 201 QEAVKELAP-QADLVIVVGSKNSSNSN-RLREVAEEAGAPAYLIDDASEIDP 250 (298)
T ss_pred HHHHHHHHh-hCCEEEEECCCCCccHH-HHHHHHHHHCCCEEEECChHHCcH
Confidence 344555554 45555555544331454 678899999999999999999963
No 198
>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=28.96 E-value=83 Score=23.67 Aligned_cols=38 Identities=16% Similarity=0.391 Sum_probs=28.9
Q ss_pred CCCCchhhHHHHHHHHHhCCCC-----EEEeC-CHHHHHHHhCCC
Q psy16564 75 DNCDEPAYKKLVQALCSEHQIP-----LIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 75 ~D~s~~~~~~~l~~lc~~~~Ip-----vi~v~-sk~eLG~a~G~~ 113 (157)
.+..+ .+...|..+|+.++.| .+.++ +..+|+..+|..
T Consensus 113 ~~~~~-Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~t 156 (193)
T TIGR03697 113 RDMGS-RLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGST 156 (193)
T ss_pred CCHHH-HHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCc
Confidence 45656 7888888899987765 23344 999999999975
No 199
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=28.90 E-value=1.7e+02 Score=22.16 Aligned_cols=41 Identities=24% Similarity=0.176 Sum_probs=24.4
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+..+.+..+++..+++....+. ... ...+.+.+||++.+.+
T Consensus 46 ~~~~~~~~~~~d~iii~~~~~~-~~~---~~~~~~~~ipvv~~~~ 86 (264)
T cd06267 46 EALELLLSRRVDGIILAPSRLD-DEL---LEELAALGIPVVLVDR 86 (264)
T ss_pred HHHHHHHHcCcCEEEEecCCcc-hHH---HHHHHHcCCCEEEecc
Confidence 4444555556666666554444 222 3446788999988863
No 200
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=28.76 E-value=1.6e+02 Score=21.81 Aligned_cols=42 Identities=19% Similarity=0.219 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+.++.+....+..+|+...... ... +..++.+.+||++.+.
T Consensus 48 ~~~~~~~~~~~~d~ii~~~~~~~--~~~-~~~~~~~~~ip~v~~~ 89 (269)
T cd01391 48 LEALRDLIQQGVDGIIGPPSSSS--ALA-VVELAAAAGIPVVSLD 89 (269)
T ss_pred HHHHHHHHHcCCCEEEecCCCHH--HHH-HHHHHHHcCCcEEEec
Confidence 34455555556777766655433 222 5667788999999876
No 201
>KOG2016|consensus
Probab=28.74 E-value=56 Score=30.39 Aligned_cols=34 Identities=21% Similarity=0.260 Sum_probs=28.1
Q ss_pred eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 68 AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 68 akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
---|++|.+..+ ...-+|...|++.+||++.+.+
T Consensus 119 qFtvViatnl~E-~~~~kl~~~l~~~~vpll~~rs 152 (523)
T KOG2016|consen 119 QFTVVIATNLNE-QTLLKLAEILREANVPLLLTRS 152 (523)
T ss_pred eeeeeeccccch-hhhhhhHHHHHhcCCceEEEee
Confidence 344778999888 6666799999999999998875
No 202
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=28.62 E-value=1.8e+02 Score=20.53 Aligned_cols=50 Identities=8% Similarity=0.078 Sum_probs=31.6
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhC-CCCEEEeC-CHHHHHHHhCCC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEH-QIPLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~-~Ipvi~v~-sk~eLG~a~G~~ 113 (157)
..+.++.+.+.++.|..|-.+ .+..+.+++ +.++..+. ....+++.+|..
T Consensus 48 ~~~~~~~~~~~~i~is~d~~~-----~~~~~~~~~~~~~~~~l~D~~~~~~~~~g~~ 99 (140)
T cd02971 48 LAEEFAKGGAEVLGVSVDSPF-----SHKAWAEKEGGLNFPLLSDPDGEFAKAYGVL 99 (140)
T ss_pred HHHHHHHCCCEEEEEeCCCHH-----HHHHHHhcccCCCceEEECCChHHHHHcCCc
Confidence 334444566889989887433 244555655 55554444 567899999975
No 203
>PLN02721 threonine aldolase
Probab=28.33 E-value=1.8e+02 Score=23.99 Aligned_cols=35 Identities=23% Similarity=0.338 Sum_probs=24.2
Q ss_pred CeeEEEEcCC-------CCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 67 EAQLCVLADN-------CDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 67 kakLVIlA~D-------~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++|++..- +-+....+.|.++|+++|++++.-+
T Consensus 137 ~~~~v~l~~~~~np~G~~~~~~~l~~l~~l~~~~g~~livD~ 178 (353)
T PLN02721 137 TTRLICLENTHANCGGRCLSVEYTDKVGELAKRHGLKLHIDG 178 (353)
T ss_pred cceEEEEeccccccCCccccHHHHHHHHHHHHHcCCEEEEEc
Confidence 5788888442 1122345678999999999997743
No 204
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=28.33 E-value=1.3e+02 Score=20.51 Aligned_cols=41 Identities=15% Similarity=0.327 Sum_probs=27.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+..++.+..|+. |.|++.|-. ....|+.+|++.|-+++...
T Consensus 27 kk~l~~l~~G~~-l~V~~dd~~---~~~di~~~~~~~G~~~~~~~ 67 (81)
T PRK00299 27 RKTVRNMQPGET-LLIIADDPA---TTRDIPSFCRFMDHELLAQE 67 (81)
T ss_pred HHHHHcCCCCCE-EEEEeCCcc---HHHHHHHHHHHcCCEEEEEE
Confidence 344455555654 444666543 45678999999999997644
No 205
>PLN02645 phosphoglycolate phosphatase
Probab=28.25 E-value=1.2e+02 Score=25.58 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=32.4
Q ss_pred hcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCC
Q psy16564 48 AHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIP 96 (157)
Q Consensus 48 ~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ip 96 (157)
+.+.+.-|..++++.|++...+++|+.++... .....+..| +..|++
T Consensus 41 ~~~~~~~ga~e~l~~lr~~g~~~~~~TN~~~~-~~~~~~~~l-~~lGi~ 87 (311)
T PLN02645 41 KGDKLIEGVPETLDMLRSMGKKLVFVTNNSTK-SRAQYGKKF-ESLGLN 87 (311)
T ss_pred eCCccCcCHHHHHHHHHHCCCEEEEEeCCCCC-CHHHHHHHH-HHCCCC
Confidence 34567889999999999988999999988755 333333333 334544
No 206
>cd07396 MPP_Nbla03831 Homo sapiens Nbla03831 and related proteins, metallophosphatase domain. Nbla03831 (also known as LOC56985) is an uncharacterized Homo sapiens protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.
Probab=28.24 E-value=1.6e+02 Score=24.12 Aligned_cols=49 Identities=20% Similarity=0.195 Sum_probs=32.7
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhh------HHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAY------KKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~------~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
++++.|.+.++.+||++.|...... -..+.......++|++.+...-+.
T Consensus 31 ~~i~~i~~~~~d~vv~~GDlv~~~~~~~~~~~~~~~~~l~~l~~p~~~v~GNHD~ 85 (267)
T cd07396 31 EAVEEWNRESLDFVVQLGDIIDGDNARAEEALDAVLAILDRLKGPVHHVLGNHDL 85 (267)
T ss_pred HHHHHHHcCCCCEEEECCCeecCCCchHHHHHHHHHHHHHhcCCCEEEecCcccc
Confidence 4566666667999999999653121 123345566778999998855444
No 207
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=28.23 E-value=95 Score=28.62 Aligned_cols=41 Identities=17% Similarity=0.327 Sum_probs=34.0
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.+++..-+..++|.|..-+.-.+.|..++++.+||++-..
T Consensus 122 ~~lkk~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~f~~~ 162 (451)
T COG0541 122 KYLKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSG 162 (451)
T ss_pred HHHHHcCCceEEEecccCChHHHHHHHHHHHHcCCceecCC
Confidence 45666667888899998777888899999999999998764
No 208
>cd04196 GT_2_like_d Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=28.22 E-value=1.1e+02 Score=22.67 Aligned_cols=40 Identities=18% Similarity=0.353 Sum_probs=24.9
Q ss_pred eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 68 AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 68 akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
..++| ..|.+++.+...+..++.+++.++..+......|.
T Consensus 28 ~eiiV-vddgS~d~t~~~~~~~~~~~~~~~~~~~~~~~~G~ 67 (214)
T cd04196 28 DELII-SDDGSTDGTVEIIKEYIDKDPFIIILIRNGKNLGV 67 (214)
T ss_pred eEEEE-EeCCCCCCcHHHHHHHHhcCCceEEEEeCCCCccH
Confidence 44554 45666557777888888887655555554444444
No 209
>cd03335 TCP1_alpha TCP-1 (CTT or eukaryotic type II) chaperonin family, alpha subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=28.12 E-value=1.9e+02 Score=26.49 Aligned_cols=48 Identities=10% Similarity=0.134 Sum_probs=33.6
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC---HHHHHHHhCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN---NKKLGEWAGL 112 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s---k~eLG~a~G~ 112 (157)
++.|.+-.+.+||.+.+.++ ....++.+++|-++.--+ .++|.+++|-
T Consensus 267 i~~i~~~g~~lvi~~k~I~d-----~al~~L~~~~I~~v~~v~~~~lerIa~~tGa 317 (527)
T cd03335 267 IKKILAAGANVVLTTGGIDD-----MCLKYFVEAGAMAVRRVKKEDLRRIAKATGA 317 (527)
T ss_pred HHHHHHcCCCEEEeCCCCcH-----HHHHHHHHCCcEEEEeCCHHHHHHHHHHhCC
Confidence 45555555899999999998 344566778888887444 5566667764
No 210
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=28.11 E-value=2.5e+02 Score=23.38 Aligned_cols=57 Identities=19% Similarity=0.222 Sum_probs=0.0
Q ss_pred CCcccHHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 30 EGVSDINKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 30 ~~~m~~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+...++.+.+-.++++ +-.-..++++-|+++-. .+| .-+.+-++|++++||++.+.+
T Consensus 41 s~tiS~rd~~g~mf~~------i~~s~~Eile~llk~i~--------Idp--~fKef~e~ike~di~fiVvSs 97 (220)
T COG4359 41 SKTISFRDGFGRMFGS------IHSSLEEILEFLLKDIK--------IDP--GFKEFVEWIKEHDIPFIVVSS 97 (220)
T ss_pred hCceeHHHHHHHHHHh------cCCCHHHHHHHHHhhcc--------cCc--cHHHHHHHHHHcCCCEEEEeC
No 211
>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=28.06 E-value=65 Score=25.64 Aligned_cols=40 Identities=3% Similarity=0.052 Sum_probs=31.2
Q ss_pred HHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 62 ALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 62 aL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+ ..+..+++.|.....-.+.+..+|+..+||++...+
T Consensus 25 ~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~ 64 (196)
T PF00448_consen 25 LKLK-GKKVALISADTYRIGAVEQLKTYAEILGVPFYVART 64 (196)
T ss_dssp HHHT-T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESST
T ss_pred Hhhc-cccceeecCCCCCccHHHHHHHHHHHhccccchhhc
Confidence 3444 678888899988777888999999999999998764
No 212
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=28.00 E-value=1.3e+02 Score=21.40 Aligned_cols=42 Identities=12% Similarity=0.089 Sum_probs=27.4
Q ss_pred eEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 69 QLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 69 kLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
-+++++..-...++.+ ....|+++++|++.+-+..+|.+++.
T Consensus 46 l~I~iS~SG~t~e~i~-~~~~a~~~g~~iI~IT~~~~l~~~~~ 87 (119)
T cd05017 46 LVIAVSYSGNTEETLS-AVEQAKERGAKIVAITSGGKLLEMAR 87 (119)
T ss_pred EEEEEECCCCCHHHHH-HHHHHHHCCCEEEEEeCCchHHHHHH
Confidence 3444554544434554 45578888999988875567888776
No 213
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=27.98 E-value=1.5e+02 Score=20.27 Aligned_cols=40 Identities=28% Similarity=0.307 Sum_probs=25.6
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCC-CCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQ-IPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~-Ipvi~v~ 101 (157)
.+++.|+.|+ .|-|++.|-.. ...|+.+|++.+ ..++.++
T Consensus 24 k~l~~m~~Ge-~LeV~~ddp~~---~~dIp~~~~~~~~~~ll~~e 64 (78)
T COG0425 24 KALAKLKPGE-ILEVIADDPAA---KEDIPAWAKKEGGHELLEVE 64 (78)
T ss_pred HHHHcCCCCC-EEEEEecCcch---HHHHHHHHHHcCCcEEEEEE
Confidence 3445555564 45557777544 478999999655 6666555
No 214
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=27.91 E-value=1.8e+02 Score=22.82 Aligned_cols=42 Identities=17% Similarity=0.132 Sum_probs=23.6
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++.+...++.-+|+..- ++......+ ..+.+++||++.+.
T Consensus 48 ~~i~~l~~~~vdgiii~~~-~~~~~~~~l-~~~~~~~ipvV~~~ 89 (271)
T cd06312 48 RLIEAAIAAKPDGIVVTIP-DPDALDPAI-KRAVAAGIPVISFN 89 (271)
T ss_pred HHHHHHHHhCCCEEEEeCC-ChHHhHHHH-HHHHHCCCeEEEeC
Confidence 3444455556776666542 221233333 44567899999886
No 215
>PRK01889 GTPase RsgA; Reviewed
Probab=27.76 E-value=82 Score=27.45 Aligned_cols=38 Identities=18% Similarity=-0.008 Sum_probs=26.9
Q ss_pred eEEEEcCC--CCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 69 QLCVLADN--CDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 69 kLVIlA~D--~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
-+++++.| .++ .....+..+|+..++|.+.+-+|.+|.
T Consensus 116 vliV~s~~p~~~~-~~ldr~L~~a~~~~i~piIVLNK~DL~ 155 (356)
T PRK01889 116 VFIVCSLNHDFNL-RRIERYLALAWESGAEPVIVLTKADLC 155 (356)
T ss_pred EEEEEecCCCCCh-hHHHHHHHHHHHcCCCEEEEEEChhcC
Confidence 34444444 333 356677778999999999999999984
No 216
>cd01487 E1_ThiF_like E1_ThiF_like. Member of superfamily of activating enzymes (E1) of the ubiquitin-like proteins. 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=27.74 E-value=1e+02 Score=23.93 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=22.3
Q ss_pred CeeEEEEcCCCCchhhHHHHHHH-HHhCCCCEEEeC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQAL-CSEHQIPLIKVD 101 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~l-c~~~~Ipvi~v~ 101 (157)
...+||.|.|-.. .+..+... |+.+++|++.-.
T Consensus 88 ~~DlVi~~~d~~~--~r~~i~~~~~~~~~ip~i~~~ 121 (174)
T cd01487 88 DCDIVVEAFDNAE--TKAMLAESLLGNKNKPVVCAS 121 (174)
T ss_pred CCCEEEECCCCHH--HHHHHHHHHHHHCCCCEEEEe
Confidence 4789999977654 44444444 555599999864
No 217
>TIGR03659 IsdE heme ABC transporter, heme-binding protein isdE. This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, pfam05031) heme-binding domain. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron.
Probab=27.70 E-value=1.9e+02 Score=23.74 Aligned_cols=51 Identities=10% Similarity=0.091 Sum_probs=35.0
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC---------HHHHHHHhCCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN---------NKKLGEWAGLS 113 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s---------k~eLG~a~G~~ 113 (157)
.-.+.|..=+.-|||.....++ +....+ ++.+||++.+.. -+.||+++|++
T Consensus 82 ~n~E~I~al~PDlIi~~~~~~~-~~~~~l----~~~gi~v~~~~~~~~~~~~~~i~~lg~~~G~~ 141 (289)
T TIGR03659 82 PDMEKIKSLKPTVVLSVTTLEE-DLGPKF----KQLGVEATFLNLTSVDGMKKSITELGEKYGRE 141 (289)
T ss_pred CCHHHHhccCCcEEEEcCcccH-HHHHHH----HHcCCcEEEEcCCCHHHHHHHHHHHHHHhCCH
Confidence 4466677777889987665555 444444 456899987642 35899999975
No 218
>TIGR01460 HAD-SF-IIA Haloacid Dehalogenase Superfamily Class (subfamily) IIA. Many of the genes in this subfamily have been annotated as "pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant.
Probab=27.69 E-value=1.5e+02 Score=23.83 Aligned_cols=30 Identities=20% Similarity=0.258 Sum_probs=24.2
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCc
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDE 79 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~ 79 (157)
+....|..++++.+++....++|+.++...
T Consensus 13 ~~~~~~a~e~i~~l~~~g~~~~~~tN~~~~ 42 (236)
T TIGR01460 13 HKPIPGAAEALNRLRAKGKPVVFLTNNSSR 42 (236)
T ss_pred CccCcCHHHHHHHHHHCCCeEEEEECCCCC
Confidence 456778889999998888889999887744
No 219
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.53 E-value=98 Score=24.41 Aligned_cols=31 Identities=10% Similarity=0.020 Sum_probs=25.6
Q ss_pred EEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 71 CVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 71 VIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
+++=.|+=| ++..+...++++++|+.+|.+.
T Consensus 4 I~VDADACP--Vk~~i~r~A~r~~~~v~~Van~ 34 (150)
T COG1671 4 IWVDADACP--VKDEIYRVAERMGLKVTFVANF 34 (150)
T ss_pred EEEeCCCCc--hHHHHHHHHHHhCCeEEEEeCC
Confidence 456667666 8889999999999999999854
No 220
>cd01884 EF_Tu EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=27.52 E-value=1.4e+02 Score=23.47 Aligned_cols=44 Identities=7% Similarity=0.120 Sum_probs=24.6
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCC-EEEe
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIP-LIKV 100 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ip-vi~v 100 (157)
.++..++..-.+-++++..+-........+..++.+.++| ++.+
T Consensus 80 ~~~~~~~~~~D~~ilVvda~~g~~~~~~~~~~~~~~~~~~~iIvv 124 (195)
T cd01884 80 KNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVF 124 (195)
T ss_pred HHHHHHhhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCcEEEE
Confidence 3445566655555666655433223344455678888898 4443
No 221
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=27.43 E-value=1.9e+02 Score=22.70 Aligned_cols=42 Identities=19% Similarity=0.290 Sum_probs=23.6
Q ss_pred HHHHHHhcCCeeEEEEcC-CCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 58 EAAKALDRREAQLCVLAD-NCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~-D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+.++.+...++.-+|+.. |. + .....+ ..+.+++||++.+..
T Consensus 46 ~~i~~~~~~~~Dgiii~~~~~-~-~~~~~i-~~~~~~~iPvV~~~~ 88 (282)
T cd06318 46 ADVEDLLTRGVNVLIINPVDP-E-GLVPAV-AAAKAAGVPVVVVDS 88 (282)
T ss_pred HHHHHHHHcCCCEEEEecCCc-c-chHHHH-HHHHHCCCCEEEecC
Confidence 345555556665555543 32 2 223333 445678999998873
No 222
>cd01489 Uba2_SUMO Ubiquitin activating enzyme (E1) subunit UBA2. UBA2 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. UBA2 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2.
Probab=27.39 E-value=88 Score=27.12 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=29.1
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
+..+||.|.|..+ ....+..+|..++||++...+.
T Consensus 90 ~~DvVv~a~Dn~~--ar~~in~~c~~~~ip~I~~gt~ 124 (312)
T cd01489 90 QFDLVFNALDNLA--ARRHVNKMCLAADVPLIESGTT 124 (312)
T ss_pred cCCEEEECCCCHH--HHHHHHHHHHHCCCCEEEEecC
Confidence 4778999988654 6778999999999999987753
No 223
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=27.31 E-value=1.6e+02 Score=21.13 Aligned_cols=49 Identities=10% Similarity=0.181 Sum_probs=35.8
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~ 113 (157)
.+....+.+.++.++.|-++ . +..+++++++++..+. ...+|.+.+|..
T Consensus 55 ~~~~~~~~v~~v~v~~~~~~-~----~~~~~~~~~~~~~~~~D~~~~~~~~~~~~ 104 (146)
T PF08534_consen 55 QEKYKDKGVDVVGVSSDDDP-P----VREFLKKYGINFPVLSDPDGALAKALGVT 104 (146)
T ss_dssp HHHHHTTTCEEEEEEESSSH-H----HHHHHHHTTTTSEEEEETTSHHHHHTTCE
T ss_pred hhhhccCceEEEEecccCCH-H----HHHHHHhhCCCceEEechHHHHHHHhCCc
Confidence 33445666999999998888 3 5566677777776665 668999999953
No 224
>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
Probab=27.29 E-value=1e+02 Score=21.60 Aligned_cols=50 Identities=22% Similarity=0.200 Sum_probs=29.5
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
+...+. .+.++++.-|++..........+....++|++.+-+|.+|....
T Consensus 74 ~~~~~~--~~~~~v~v~d~~~~~~~~~~~~~~~~~~~~vi~v~nK~D~~~~~ 123 (157)
T cd04164 74 AREAIE--EADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLLPDS 123 (157)
T ss_pred HHHHHh--hCCEEEEEEECCCCCCHHHHHHHHhhcCCCEEEEEEchhcCCcc
Confidence 334443 34455555565532333333444446789999999999986444
No 225
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=27.23 E-value=2.3e+02 Score=20.05 Aligned_cols=50 Identities=20% Similarity=0.230 Sum_probs=33.4
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~ 113 (157)
..+.+....+.+|.|..|..+ . ...+++++++|+-.+. ...++.+++|..
T Consensus 49 ~~~~~~~~~v~vv~V~~~~~~-~----~~~~~~~~~~~~p~~~D~~~~~~~~~g~~ 99 (149)
T cd02970 49 LLPELDALGVELVAVGPESPE-K----LEAFDKGKFLPFPVYADPDRKLYRALGLV 99 (149)
T ss_pred HHHHHHhcCeEEEEEeCCCHH-H----HHHHHHhcCCCCeEEECCchhHHHHcCce
Confidence 334444556888888877544 2 2367778887766655 567899999974
No 226
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=26.92 E-value=75 Score=28.01 Aligned_cols=34 Identities=18% Similarity=0.148 Sum_probs=23.8
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. +...+.+.|+++|||++.- .-|.|++=
T Consensus 283 vAKG~d~--~A~~Ir~iA~e~~VPiven---~pLARaLY 316 (349)
T PRK12721 283 LEKGKDA--QALHIVKLAERNGIPVVEN---IPLARALF 316 (349)
T ss_pred EEEeCcH--HHHHHHHHHHHcCCCEEeC---HHHHHHHH
Confidence 4444443 6678999999999999853 34566553
No 227
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=26.87 E-value=1.8e+02 Score=24.06 Aligned_cols=46 Identities=24% Similarity=0.222 Sum_probs=31.8
Q ss_pred HHHHHh-cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC--CHHHHH
Q psy16564 59 AAKALD-RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD--NNKKLG 107 (157)
Q Consensus 59 v~KaL~-kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~--sk~eLG 107 (157)
..+.|+ +..+.+++||.|... .+ .+..+-+..+||++.+- .-..+.
T Consensus 52 ~~~~L~~~~g~d~ivIaCNTA~-a~--~~~~l~~~~~iPii~iie~~v~~a~ 100 (251)
T TIGR00067 52 LLTFLKERHNIKLLVVACNTAS-AL--ALEDLQRNFDFPVVGVIEPAIKAAI 100 (251)
T ss_pred HHHHHHHhCCCCEEEEeCchHH-HH--HHHHHHHHCCCCEEeecHHHHHHHH
Confidence 355676 778999999999864 22 35666677899999843 344443
No 228
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=26.84 E-value=1.4e+02 Score=28.28 Aligned_cols=49 Identities=18% Similarity=0.357 Sum_probs=34.5
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
+.++.|. +++-++|+-.+-.. .-..+|-..|++.+.|.+.+++..+|-.
T Consensus 198 ~a~~~la-~~~d~~~vvGg~~S-sNt~~L~~i~~~~~~~~~~ie~~~el~~ 246 (647)
T PRK00087 198 EAAEKLA-KKVDVMIVVGGKNS-SNTTKLYEICKSNCTNTIHIENAGELPE 246 (647)
T ss_pred HHHHHHH-hhCCEEEEECCCCC-ccHHHHHHHHHHHCCCEEEECChHHCCH
Confidence 3344554 45666666555544 2444678899999999999999999965
No 229
>PF00702 Hydrolase: haloacid dehalogenase-like hydrolase; InterPro: IPR005834 This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase). This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1TE2_A 3NAL_A 3NAM_A 3NAN_A 3A1D_B 3J09_A 3J08_A 2B8E_C 3A1E_A 2VOY_J ....
Probab=26.68 E-value=2.7e+02 Score=20.80 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=39.4
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCC-CEEEeCC-------H--HHHHHHhCC
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQI-PLIKVDN-------N--KKLGEWAGL 112 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~I-pvi~v~s-------k--~eLG~a~G~ 112 (157)
+.-|..++++.|++...++.++.+|-.. .....+++.+| +...+.. + .++=+.++.
T Consensus 128 ~~~~~~~~l~~L~~~Gi~~~i~TGD~~~-----~a~~~~~~lgi~~~~v~a~~~~kP~~k~~~~~i~~l~~ 193 (215)
T PF00702_consen 128 LRPGAKEALQELKEAGIKVAILTGDNES-----TASAIAKQLGIFDSIVFARVIGKPEPKIFLRIIKELQV 193 (215)
T ss_dssp BHTTHHHHHHHHHHTTEEEEEEESSEHH-----HHHHHHHHTTSCSEEEEESHETTTHHHHHHHHHHHHTC
T ss_pred chhhhhhhhhhhhccCcceeeeeccccc-----cccccccccccccccccccccccccchhHHHHHHHHhc
Confidence 4568899999999888899999988765 34557788899 4333222 2 566666664
No 230
>TIGR01456 CECR5 HAD-superfamily class IIA hydrolase, TIGR01456, CECR5. The Schizosaccharomyces pombe sequence (EGAD|138276) is annotated as "phosphatidyl synthase," however this is due entirely to a C-terminal region of the protein (outside the region of similarity of this model) which is highly homologous to a family of CDP-alcohol phosphatidyltransferases. (Thus, the annotation of GP|4226073 from C. elegans as similar to phosphatidyl synthase, is a mistake as this gene does not contain the C-terminal portion). The physical connection of the phosphatidyl synthase and the HAD-superfamily hydrolase domain in S. pombe may, however, be an important clue to the substrate for the hydrolases in this equivalog.
Probab=26.62 E-value=1.2e+02 Score=25.77 Aligned_cols=47 Identities=13% Similarity=0.141 Sum_probs=29.9
Q ss_pred cCCceeeHHHHHHHHhcC----CeeEEEEcCCCCchhhHHHHHHHHHhCCCC
Q psy16564 49 HDGLAKGLHEAAKALDRR----EAQLCVLADNCDEPAYKKLVQALCSEHQIP 96 (157)
Q Consensus 49 agklv~G~~~v~KaL~kg----kakLVIlA~D~s~~~~~~~l~~lc~~~~Ip 96 (157)
.+.+.-|..++++.|+.. ...++|+.++... ........+.++.|++
T Consensus 14 g~~~i~ga~eal~~L~~~~~~~g~~~~flTNn~g~-s~~~~~~~l~~~lG~~ 64 (321)
T TIGR01456 14 GKKPIAGASDALRRLNRNQGQLKIPYIFLTNGGGF-SERARAEEISSLLGVD 64 (321)
T ss_pred CccccHHHHHHHHHHhccccccCCCEEEEecCCCC-CHHHHHHHHHHHcCCC
Confidence 356678888888888876 6788888888743 2222233334444443
No 231
>PRK06298 type III secretion system protein; Validated
Probab=26.56 E-value=76 Score=28.07 Aligned_cols=34 Identities=18% Similarity=0.159 Sum_probs=25.3
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. ....+.++|+++|||++. ...|.|++=
T Consensus 284 vAKG~d~--~A~~Ir~iA~e~~VPive---n~pLARaLy 317 (356)
T PRK06298 284 IAMGINL--RAKRIIAEAEKYGVPIMR---NVPLAHQLL 317 (356)
T ss_pred EEeeCcH--HHHHHHHHHHHcCCCEEe---CHHHHHHHH
Confidence 5555544 678899999999999985 346777764
No 232
>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=26.44 E-value=1.9e+02 Score=24.73 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=34.0
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGE 108 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~ 108 (157)
+..+.|.+ ++-++|+-.+-.. .-..+|-+.|++++.|.+.+++..+|..
T Consensus 200 ~a~~~la~-~vD~miVVGg~nS-sNT~rL~ei~~~~~~~t~~Ie~~~el~~ 248 (280)
T TIGR00216 200 DAVKELAP-EVDLMIVIGGKNS-SNTTRLYEIAEEHGPPSYLIETAEELPE 248 (280)
T ss_pred HHHHHHHh-hCCEEEEECCCCC-chHHHHHHHHHHhCCCEEEECChHHCCH
Confidence 34455544 4555555555444 2344678899999999999999999974
No 233
>PLN02775 Probable dihydrodipicolinate reductase
Probab=26.38 E-value=3.6e+02 Score=23.29 Aligned_cols=53 Identities=11% Similarity=0.121 Sum_probs=36.2
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC---CHHHHHHHhCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD---NNKKLGEWAGL 112 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~---sk~eLG~a~G~ 112 (157)
+++..++...+.+|+| |-+.+........+|.++++|++.-- +.++|-+++..
T Consensus 70 ~~l~~~~~~~~~~VvI--DFT~P~a~~~~~~~~~~~g~~~VvGTTG~~~e~l~~~~~~ 125 (286)
T PLN02775 70 AVLSSVKAEYPNLIVV--DYTLPDAVNDNAELYCKNGLPFVMGTTGGDRDRLLKDVEE 125 (286)
T ss_pred HHHHHhhccCCCEEEE--ECCChHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHhc
Confidence 4444444556775555 55544677777889999999999844 77788877763
No 234
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=26.22 E-value=87 Score=27.82 Aligned_cols=29 Identities=14% Similarity=0.285 Sum_probs=22.4
Q ss_pred EEEcCCC----CchhhHHHHHHHHHhCCCCEEEe
Q psy16564 71 CVLADNC----DEPAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 71 VIlA~D~----s~~~~~~~l~~lc~~~~Ipvi~v 100 (157)
+|.+.|. ++ .+.++|.++|+++|||+-..
T Consensus 257 ~i~~~D~~~~~~~-~l~~~L~~~A~~~~Ip~Q~~ 289 (355)
T COG1363 257 VIRVKDASGIYHP-KLRKFLLELAEKNNIPYQVD 289 (355)
T ss_pred EEEEEcCCCCCCH-HHHHHHHHHHHHcCCCeEEE
Confidence 3445554 34 78999999999999999763
No 235
>cd04104 p47_IIGP_like p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=26.18 E-value=1.5e+02 Score=22.95 Aligned_cols=26 Identities=4% Similarity=-0.170 Sum_probs=19.8
Q ss_pred hhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 81 AYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
.....+...+++.+.|++.|.+|.++
T Consensus 94 ~~d~~~~~~l~~~~~~~ilV~nK~D~ 119 (197)
T cd04104 94 SNDVKLAKAIQCMGKKFYFVRTKVDR 119 (197)
T ss_pred HHHHHHHHHHHHhCCCEEEEEecccc
Confidence 45555566777789999999988887
No 236
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=26.12 E-value=78 Score=28.04 Aligned_cols=34 Identities=24% Similarity=0.256 Sum_probs=24.8
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. +...+.+.|+++|||++.- .-|.|++=
T Consensus 292 vAKG~d~--~A~~Ir~~A~e~~VPiven---~pLARaLy 325 (358)
T PRK13109 292 VAKGQDL--IALKIREIAEENGIPVIED---KPLARSLY 325 (358)
T ss_pred EEEeCcH--HHHHHHHHHHHcCCCEEeC---HHHHHHHH
Confidence 4554543 6788999999999999853 45666664
No 237
>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=26.11 E-value=76 Score=20.47 Aligned_cols=33 Identities=9% Similarity=0.153 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHhCCCC-------EEEeCCHHHHHHHhCCC
Q psy16564 81 AYKKLVQALCSEHQIP-------LIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ip-------vi~v~sk~eLG~a~G~~ 113 (157)
.+...|..+|+.++.+ +....+..+|+..+|.+
T Consensus 2 Rla~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~s 41 (76)
T PF13545_consen 2 RLARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVS 41 (76)
T ss_dssp HHHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSC
T ss_pred hHHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCC
Confidence 4566788888887764 33445999999999976
No 238
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=26.06 E-value=99 Score=26.84 Aligned_cols=35 Identities=23% Similarity=0.271 Sum_probs=28.5
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.++-+||.|.|-.+ ....+..+|.++++|+++...
T Consensus 115 ~~~DlVid~~D~~~--~r~~in~~~~~~~ip~i~~~~ 149 (338)
T PRK12475 115 KEVDLIIDATDNFD--TRLLINDLSQKYNIPWIYGGC 149 (338)
T ss_pred cCCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEEEe
Confidence 34789999998654 666799999999999998653
No 239
>TIGR01452 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this alignment have been annotated as pNPPases due to this association.
Probab=26.03 E-value=1.4e+02 Score=24.56 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=23.2
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCc
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDE 79 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~ 79 (157)
+...-|..++++.|+....+++|++++...
T Consensus 17 ~~~~~ga~e~l~~L~~~g~~~~~~Tnns~~ 46 (279)
T TIGR01452 17 ERVVPGAPELLDRLARAGKAALFVTNNSTK 46 (279)
T ss_pred CeeCcCHHHHHHHHHHCCCeEEEEeCCCCC
Confidence 456678888888888877888888887644
No 240
>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=26.01 E-value=1.6e+02 Score=18.98 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=7.7
Q ss_pred HHHHHHhCCCCEEEe
Q psy16564 86 VQALCSEHQIPLIKV 100 (157)
Q Consensus 86 l~~lc~~~~Ipvi~v 100 (157)
...+.++++|++..+
T Consensus 15 a~~~L~~~~i~~~~~ 29 (79)
T TIGR02181 15 AKALLSSKGVTFTEI 29 (79)
T ss_pred HHHHHHHcCCCcEEE
Confidence 344445555555554
No 241
>TIGR00530 AGP_acyltrn 1-acyl-sn-glycerol-3-phosphate acyltransferases. 1-acyl-sn-glycerol-3-phosphate acyltransferase is also called 1-AGP acyltransferase, lysophosphatidic acid acyltransferase, and LPA acyltransferase.
Probab=25.88 E-value=2.3e+02 Score=19.61 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchh----hHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPA----YKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~----~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+++.+++++|..-+++--.+.+... ...-+..++.+.++|++-+.
T Consensus 79 ~~~~~~~l~~g~~v~ifPeG~~~~~~~~~~f~~g~~~la~~~~~pvvpv~ 128 (130)
T TIGR00530 79 LKAAIEVLKQGRSIGVFPEGTRSRGRDILPFKKGAFHIAIKAGVPILPVV 128 (130)
T ss_pred HHHHHHHHhCCCEEEEeCCCCCCCCCCCCCcchhHHHHHHHcCCCEEeEE
Confidence 45667778788654444333333211 23456678888899988654
No 242
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=25.86 E-value=2e+02 Score=22.12 Aligned_cols=41 Identities=15% Similarity=0.180 Sum_probs=25.0
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++.+...++.-+|+...-+. . .. +...+.+.+||++.+.
T Consensus 46 ~~~~~l~~~~vdgiii~~~~~~-~-~~-~~~~~~~~~ipvV~~~ 86 (266)
T cd06282 46 DAVETLLRQRVDGLILTVADAA-T-SP-ALDLLDAERVPYVLAY 86 (266)
T ss_pred HHHHHHHhcCCCEEEEecCCCC-c-hH-HHHHHhhCCCCEEEEe
Confidence 4555666677777777542222 1 12 3456778899988775
No 243
>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=25.79 E-value=81 Score=27.66 Aligned_cols=34 Identities=21% Similarity=0.231 Sum_probs=24.6
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. +...+.+.|+++|||++.- .-|.|++=
T Consensus 282 vAKG~d~--~A~~Ir~iA~e~~VPiven---~pLAR~Ly 315 (342)
T TIGR01404 282 ICKGTDA--QALAVRAYAEEAGIPVVRD---IPLARQLY 315 (342)
T ss_pred EEeeCcH--HHHHHHHHHHHcCCCEeeC---HHHHHHHH
Confidence 5555554 6788999999999999753 45666554
No 244
>PRK05647 purN phosphoribosylglycinamide formyltransferase; Reviewed
Probab=25.75 E-value=2e+02 Score=23.05 Aligned_cols=42 Identities=17% Similarity=0.205 Sum_probs=26.5
Q ss_pred HHHHHHHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
...+++++.++. +..+++-.|-+. . ....+|.++|||++.++
T Consensus 15 ~~~ll~~~~~~~~~~~I~~vvs~~~~-~---~~~~~a~~~gIp~~~~~ 58 (200)
T PRK05647 15 LQAIIDACAAGQLPAEIVAVISDRPD-A---YGLERAEAAGIPTFVLD 58 (200)
T ss_pred HHHHHHHHHcCCCCcEEEEEEecCcc-c---hHHHHHHHcCCCEEEEC
Confidence 456677777764 444443344322 1 25678999999998865
No 245
>COG1179 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]
Probab=25.74 E-value=1.5e+02 Score=25.47 Aligned_cols=42 Identities=21% Similarity=0.233 Sum_probs=33.0
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+....+-.+.--+||=|-|.=+ .+..|..+|.+++||++...
T Consensus 112 en~~~~~~~~~DyvIDaiD~v~--~Kv~Li~~c~~~ki~vIss~ 153 (263)
T COG1179 112 ENLEDLLSKGFDYVIDAIDSVR--AKVALIAYCRRNKIPVISSM 153 (263)
T ss_pred hHHHHHhcCCCCEEEEchhhhH--HHHHHHHHHHHcCCCEEeec
Confidence 3444555567889998888765 78889999999999999764
No 246
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=25.67 E-value=1.6e+02 Score=23.88 Aligned_cols=49 Identities=20% Similarity=0.200 Sum_probs=30.1
Q ss_pred HHHHHHhcCCe-eEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 58 EAAKALDRREA-QLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 58 ~v~KaL~kgka-kLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
++..+++.-.+ -+|+=+.|... .....+..++.++++|++.+-+|.++-
T Consensus 80 ~~~~~l~~aD~~IlVvd~~~g~~-~~~~~~~~~~~~~~~P~iivvNK~D~~ 129 (237)
T cd04168 80 EVERSLSVLDGAILVISAVEGVQ-AQTRILWRLLRKLNIPTIIFVNKIDRA 129 (237)
T ss_pred HHHHHHHHhCeEEEEEeCCCCCC-HHHHHHHHHHHHcCCCEEEEEECcccc
Confidence 45556665554 44444444433 344456667888999998887776653
No 247
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=25.65 E-value=1.8e+02 Score=28.54 Aligned_cols=48 Identities=13% Similarity=0.059 Sum_probs=39.7
Q ss_pred cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCC
Q psy16564 65 RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 65 kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~ 112 (157)
+|..+..+++.|.........+..+++..+||+..+.+..+|-.++..
T Consensus 213 ~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~ 260 (767)
T PRK14723 213 EGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAA 260 (767)
T ss_pred cCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHH
Confidence 455577889999876567788999999999999988898888888764
No 248
>KOG0460|consensus
Probab=25.56 E-value=87 Score=28.50 Aligned_cols=38 Identities=24% Similarity=0.185 Sum_probs=31.0
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHH
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNK 104 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~ 104 (157)
.-+-||+-|.|-.-+.+++|+. ||++-||+-+.++ +|.
T Consensus 142 DGaILVVaatDG~MPQTrEHlL-LArQVGV~~ivvfiNKv 180 (449)
T KOG0460|consen 142 DGAILVVAATDGPMPQTREHLL-LARQVGVKHIVVFINKV 180 (449)
T ss_pred CceEEEEEcCCCCCcchHHHHH-HHHHcCCceEEEEEecc
Confidence 3477899999988878999974 9999999988776 554
No 249
>PF07894 DUF1669: Protein of unknown function (DUF1669); InterPro: IPR012461 This family is composed of sequences derived from hypothetical eukaryotic proteins of unknown function. Some members of this family are annotated as being potential phospholipases but no literature was found to support this.
Probab=25.54 E-value=1.4e+02 Score=25.75 Aligned_cols=30 Identities=10% Similarity=0.088 Sum_probs=22.5
Q ss_pred CCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 77 CDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 77 ~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
.+. ++-..|...|.+.+|||+.+-+...|.
T Consensus 158 TD~-dIf~DLleAa~kR~VpVYiLLD~~~~~ 187 (284)
T PF07894_consen 158 TDV-DIFCDLLEAANKRGVPVYILLDEQNLP 187 (284)
T ss_pred ccH-HHHHHHHHHHHhcCCcEEEEechhcCh
Confidence 444 677778888888899999887766555
No 250
>TIGR01662 HAD-SF-IIIA HAD-superfamily hydrolase, subfamily IIIA. In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme.
Probab=25.44 E-value=1.9e+02 Score=20.46 Aligned_cols=50 Identities=12% Similarity=0.110 Sum_probs=34.3
Q ss_pred CceeeHHHHHHHHhcCCeeEEEEcCCC--Cchh-hHHHHHHHHHhCCCCEEEe
Q psy16564 51 GLAKGLHEAAKALDRREAQLCVLADNC--DEPA-YKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 51 klv~G~~~v~KaL~kgkakLVIlA~D~--s~~~-~~~~l~~lc~~~~Ipvi~v 100 (157)
.+.-|..++++.|++...+++|+++.. .... ....+..+++..+++....
T Consensus 25 ~~~~~v~~~l~~L~~~g~~l~i~Sn~~~~~~~~~~~~~~~~~l~~~~l~~~~~ 77 (132)
T TIGR01662 25 ILYPEVPDALAELKEAGYKVVIVTNQSGIGRGKFSSGRVARRLEELGVPIDVL 77 (132)
T ss_pred eeCCCHHHHHHHHHHCCCEEEEEECCccccccHHHHHHHHHHHHHCCCCEEEE
Confidence 467888999999987778888777754 1101 1445677788888875443
No 251
>PRK10200 putative racemase; Provisional
Probab=25.40 E-value=1.1e+02 Score=25.05 Aligned_cols=45 Identities=29% Similarity=0.325 Sum_probs=32.9
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.-=..+..+.|++..+.++++|.|... .. +..+-+..+||++..-
T Consensus 61 ~~~l~~~~~~L~~~g~~~iviaCNTah-~~---~~~l~~~~~iPii~ii 105 (230)
T PRK10200 61 GDILAEAALGLQRAGAEGIVLCTNTMH-KV---ADAIESRCSLPFLHIA 105 (230)
T ss_pred HHHHHHHHHHHHHcCCCEEEECCchHH-HH---HHHHHHhCCCCEeehH
Confidence 333456677788888999999999976 33 3455567799998844
No 252
>CHL00200 trpA tryptophan synthase alpha subunit; Provisional
Probab=25.35 E-value=4.1e+02 Score=22.31 Aligned_cols=58 Identities=12% Similarity=0.198 Sum_probs=36.5
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC----CHHHHHHHhCCC
Q psy16564 54 KGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD----NNKKLGEWAGLS 113 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~----sk~eLG~a~G~~ 113 (157)
.|.+.-++...+-.+.-|++ -|.++ +-...+...|+++|+..+.+- +.+++.+++...
T Consensus 106 ~G~e~F~~~~~~aGvdgvii-pDLP~-ee~~~~~~~~~~~gi~~I~lv~PtT~~eri~~i~~~a 167 (263)
T CHL00200 106 YGINKFIKKISQAGVKGLII-PDLPY-EESDYLISVCNLYNIELILLIAPTSSKSRIQKIARAA 167 (263)
T ss_pred hCHHHHHHHHHHcCCeEEEe-cCCCH-HHHHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHhC
Confidence 36666666665544555544 46655 345567788999998776632 346777777654
No 253
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=25.34 E-value=2.1e+02 Score=23.36 Aligned_cols=41 Identities=15% Similarity=0.190 Sum_probs=22.6
Q ss_pred HHHHHHhcCCeeEEEEcC-CCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLAD-NCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~-D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++.+...++.-+|++. |.+ .... ....+.+.+||++.+.
T Consensus 45 ~~i~~l~~~~vDgIIi~~~~~~--~~~~-~l~~~~~~~iPvV~~d 86 (302)
T TIGR02634 45 SQIENLIARGVDVLVIIPQNGQ--VLSN-AVQEAKDEGIKVVAYD 86 (302)
T ss_pred HHHHHHHHcCCCEEEEeCCChh--HHHH-HHHHHHHCCCeEEEec
Confidence 444455555665555554 322 1233 3345677889987775
No 254
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.31 E-value=1.8e+02 Score=23.85 Aligned_cols=44 Identities=11% Similarity=0.306 Sum_probs=24.3
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchh---------hHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPA---------YKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~---------~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+..+.+...++.+||++.|.-... ....+..+.....+|++.+.
T Consensus 30 ~l~~~~~~~~~D~lli~GDi~d~~~p~~~~~~~~~~~l~~l~~~~~i~v~~i~ 82 (253)
T TIGR00619 30 DLLEFAKAEQIDALLVAGDVFDTANPPAEAQELFNAFFRNLSDANPIPIVVIS 82 (253)
T ss_pred HHHHHHHHcCCCEEEECCccCCCCCCCHHHHHHHHHHHHHHHhcCCceEEEEc
Confidence 344455566788888888854421 11233333333338888765
No 255
>COG0403 GcvP Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]
Probab=25.27 E-value=2e+02 Score=26.57 Aligned_cols=63 Identities=11% Similarity=0.110 Sum_probs=45.1
Q ss_pred HhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC--CHHHHHHHhCCCccccCCCccceeeeEEEEEecCchhH
Q psy16564 63 LDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD--NNKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRNWFL 139 (157)
Q Consensus 63 L~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~--sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g~~~ 139 (157)
+.+++..-+|++.|+-| .+..-+..+++-.|+.++.++ +-.+|-.+... ..+++.+.-|++.-
T Consensus 159 ~~k~k~~~~~V~~~vhp-qt~~Vl~Tra~~~g~~i~~~~~~d~~~l~~~~~~-------------~~~gv~vQyP~~~G 223 (450)
T COG0403 159 VTKKKRNKFLVPKDVHP-QTLDVLRTRAEGLGIEIEVVDADDLDDLESADDG-------------DVFGVLVQYPNTFG 223 (450)
T ss_pred hhcCcCceEEecCCCCH-HHHHHHHhhcccCceEEEEeccchhhhhhhcccc-------------CeEEEEEecCCCCC
Confidence 34566889999999999 899999999999999999877 33344444111 13556777666554
No 256
>cd03013 PRX5_like Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5 suggests that it may have an important antioxidant role in organelles that are major sources of reactive oxygen species (ROS), as well as a role in the control of signal transduction. PRX5 has been shown to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. As with all other PRXs, the N-terminal peroxidatic cysteine of PRX5 is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Human PRX5 is able to resolve this intermediate by forming an intramolecular disulfide bond with its C-terminal cysteine (the resolving cysteine), which can then be reduced by TRX, just like an atypical 2-cys PRX. This resolving cysteine, however, is not conserved in other members of the subfamily. In such cases
Probab=25.16 E-value=2.1e+02 Score=21.58 Aligned_cols=52 Identities=15% Similarity=0.138 Sum_probs=36.7
Q ss_pred HHHHHHHhcCCe-eEEEEcCCCCchhhHHHHHHHHHhCCC--CEEEeC-CHHHHHHHhCCC
Q psy16564 57 HEAAKALDRREA-QLCVLADNCDEPAYKKLVQALCSEHQI--PLIKVD-NNKKLGEWAGLS 113 (157)
Q Consensus 57 ~~v~KaL~kgka-kLVIlA~D~s~~~~~~~l~~lc~~~~I--pvi~v~-sk~eLG~a~G~~ 113 (157)
.+....+++..+ .++.+..|... ...++|+++++ |+-.+. ...+++++.|.-
T Consensus 54 ~~~~~~f~~~g~~~V~~iS~D~~~-----~~~~~~~~~~~~~~f~lLsD~~~~~~~~ygv~ 109 (155)
T cd03013 54 VENADELKAKGVDEVICVSVNDPF-----VMKAWGKALGAKDKIRFLADGNGEFTKALGLT 109 (155)
T ss_pred HHhHHHHHHCCCCEEEEEECCCHH-----HHHHHHHhhCCCCcEEEEECCCHHHHHHcCCC
Confidence 344556665556 58888888765 24567888887 665555 678999999974
No 257
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=25.07 E-value=2.1e+02 Score=22.65 Aligned_cols=36 Identities=14% Similarity=0.246 Sum_probs=20.3
Q ss_pred HhcCCee-EEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 63 LDRREAQ-LCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 63 L~kgkak-LVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+...++. +++.+.|.+ ....+...+.+++||++.+.
T Consensus 50 ~~~~~~dgiii~~~~~~---~~~~~~~~~~~~~iPvV~~~ 86 (289)
T cd01540 50 LGAQGAKGFVICVPDVK---LGPAIVAKAKAYNMKVVAVD 86 (289)
T ss_pred HHHcCCCEEEEccCchh---hhHHHHHHHHhCCCeEEEec
Confidence 3345554 444444532 22334455678899998876
No 258
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=25.04 E-value=2.2e+02 Score=25.93 Aligned_cols=48 Identities=13% Similarity=0.140 Sum_probs=36.0
Q ss_pred HhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 63 LDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 63 L~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
.++| .+..+++.|.....-...+..+++..++|++...+..+|..++.
T Consensus 231 ~~~g-~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~ 278 (407)
T PRK12726 231 LKQN-RTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQ 278 (407)
T ss_pred HHcC-CeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHH
Confidence 3444 46677888876533466889999999999988888888887664
No 259
>PF04609 MCR_C: Methyl-coenzyme M reductase operon protein C; InterPro: IPR007687 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. Genes encoding the beta (mcrB) and gamma (mcrG) subunits of MCR are separated by two open reading frames coding for two proteins C and D [, ]. The function of proteins C and D is unknown. This entry represents protein C.; GO: 0003824 catalytic activity, 0015948 methanogenesis
Probab=24.95 E-value=33 Score=29.42 Aligned_cols=62 Identities=15% Similarity=0.106 Sum_probs=52.3
Q ss_pred HHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 41 QVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 41 ~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
++|++|+-+|+-..|.++-.+.+-+..--.||.-.+... .+..+...+.+.-+||++.....
T Consensus 104 n~i~L~~G~G~~~~gl~~~E~~~I~~Hd~AV~~~Gn~~~-~I~~K~~~ll~~i~iPiVv~~~P 165 (268)
T PF04609_consen 104 NMIGLARGSGGRIFGLTPKEIEQINEHDLAVFHLGNFKS-CIIYKKRHLLRGIDIPIVVCGGP 165 (268)
T ss_pred ceEEEeccCCCCccCCCHHHHHHHhhcCEEEEEeCCHHH-HHHHHHHHHHhhcCCcEEEecCC
Confidence 788999999999999999988887777777788888877 67777888999999998876654
No 260
>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=24.65 E-value=2.4e+02 Score=22.27 Aligned_cols=54 Identities=15% Similarity=0.252 Sum_probs=36.1
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC----------HHHHHHHhCCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN----------NKKLGEWAGLS 113 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s----------k~eLG~a~G~~ 113 (157)
.--.+.|..=+.-|||......+ . ..+..+.+..+||++.+.. -..||+++|++
T Consensus 64 ~~n~E~i~~l~PDLIi~~~~~~~-~--~~~~~l~~~~gipvv~~~~~~~~~~~~~~i~~lg~~~g~~ 127 (262)
T cd01147 64 TPNYEKIAALKPDVVIDVGSDDP-T--SIADDLQKKTGIPVVVLDGGDSLEDTPEQIRLLGKVLGKE 127 (262)
T ss_pred CCCHHHHHhcCCCEEEEecCCcc-c--hhHHHHHHhhCCCEEEEecCCchHhHHHHHHHHHHHhCCH
Confidence 34566676777888887654333 1 2344455558999988774 35799999975
No 261
>PRK10128 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional
Probab=24.62 E-value=1.5e+02 Score=25.00 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhcCCcee----eHHHHHHHHhcCCeeEEEEcCCCCc
Q psy16564 35 INKALQQVLKTARAHDGLAK----GLHEAAKALDRREAQLCVLADNCDE 79 (157)
Q Consensus 35 ~~k~L~~lL~~A~~agklv~----G~~~v~KaL~kgkakLVIlA~D~s~ 79 (157)
+..++..+++.++++|+..- ....+.+.+++| +.++.++.|..-
T Consensus 195 v~~ai~~v~~a~~~~Gk~~G~~~~~~~~a~~~~~~G-~~~v~~g~D~~~ 242 (267)
T PRK10128 195 VQRIIETSIRRIRAAGKAAGFLAVDPDMAQKCLAWG-ANFVAVGVDTML 242 (267)
T ss_pred HHHHHHHHHHHHHHcCCeEEEcCCCHHHHHHHHHcC-CcEEEEChHHHH
Confidence 77899999999999998532 335667777777 899999999743
No 262
>KOG3432|consensus
Probab=24.60 E-value=74 Score=24.10 Aligned_cols=49 Identities=16% Similarity=0.307 Sum_probs=41.9
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
|-|..|+-++- +.++--+.++.++..+.++...|..|+.+-+|-++-+.
T Consensus 21 GfLlaGvg~v~---~~r~~Nf~vv~~~Tt~~eiedaF~~f~~RdDIaIiLIn 69 (121)
T KOG3432|consen 21 GFLLAGVGEVN---ENREPNFLVVDSKTTVEEIEDAFKSFTARDDIAIILIN 69 (121)
T ss_pred eeeeecccccc---cCCCCCEEEEeccCCHHHHHHHHHhhccccCeEEEEEh
Confidence 66777877776 56778899999999998999999999999999888876
No 263
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=24.56 E-value=2.3e+02 Score=23.01 Aligned_cols=41 Identities=15% Similarity=0.201 Sum_probs=22.8
Q ss_pred HHHHHHhcCCeeEEEE-cCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVL-ADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIl-A~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.+..+...++.-+|+ +.|.+ .....+ ..++..+||++.++
T Consensus 48 ~~i~~l~~~~vdgiii~~~~~~--~~~~~~-~~~~~~giPvV~~~ 89 (303)
T cd01539 48 EQIDTALAKGVDLLAVNLVDPT--AAQTVI-NKAKQKNIPVIFFN 89 (303)
T ss_pred HHHHHHHHcCCCEEEEecCchh--hHHHHH-HHHHHCCCCEEEeC
Confidence 4455544555555555 44432 233333 44577899999875
No 264
>PRK12849 groEL chaperonin GroEL; Reviewed
Probab=24.51 E-value=1.8e+02 Score=27.03 Aligned_cols=49 Identities=10% Similarity=0.168 Sum_probs=30.2
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhC------CCCEEEeCC--------HHHHHHHhCCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEH------QIPLIKVDN--------NKKLGEWAGLS 113 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~------~Ipvi~v~s--------k~eLG~a~G~~ 113 (157)
++.+.+-.+.+||++.++++. -. .++..+ +|-++...+ -++|..++|-.
T Consensus 236 l~~i~~~~~~lvI~~~~I~~~-al----~~l~~~~~~~~~~i~avr~~~~~~~r~~~l~~ia~~tGa~ 298 (542)
T PRK12849 236 LEKVAQSGKPLLIIAEDVEGE-AL----ATLVVNKLRGGLKVAAVKAPGFGDRRKAMLEDIAILTGGT 298 (542)
T ss_pred HHHHHHhCCCEEEECCCCcHH-HH----HHHHHhhhhccccEEEEeCCCccchhHhHHHHHHHHhCCE
Confidence 344444457899999999983 22 222333 666666444 46688888843
No 265
>TIGR03772 anch_rpt_subst anchored repeat ABC transporter, substrate-binding protein. Members of this protein family are ABC transporter permease subunits as identified by pfam00950, but additionally contain the Actinobacterial insert domain described by TIGR03769. Some homologs (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the TIGR03769 insert that occurs just once in this protein family.
Probab=24.40 E-value=1.8e+02 Score=26.84 Aligned_cols=51 Identities=12% Similarity=0.072 Sum_probs=29.4
Q ss_pred CCceeeHHHHHHHHhcC----CeeEEEEcCC--CCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 50 DGLAKGLHEAAKALDRR----EAQLCVLADN--CDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 50 gklv~G~~~v~KaL~kg----kakLVIlA~D--~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++.+.-.+.+...+.+. ...++-+..+ .++ .....+..+.++.+|++++++
T Consensus 371 ~r~vvt~H~af~YLa~~YGL~~~~~~~~~~~~ePS~-~~L~~Li~~IK~~~V~~IF~E 427 (479)
T TIGR03772 371 RRHLITTHDAYSYLGQAYGLNIAGFVTPNPAVEPSL-ADRRRLTRTIENLKVPAVFLE 427 (479)
T ss_pred CCEEEEECCcHHHHHHHCCCeEEeeeccCCCCCCCH-HHHHHHHHHHHHcCCCEEEEe
Confidence 34444455567677653 1222222233 333 345667778888999999986
No 266
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=24.33 E-value=2.3e+02 Score=22.13 Aligned_cols=41 Identities=15% Similarity=0.258 Sum_probs=23.4
Q ss_pred HHHHHHhcCCeeEEEEcC-CCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLAD-NCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~-D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++.+...++.-+|+.. |.+ .....+ ..+.+.+||++.+.
T Consensus 51 ~~~~~~~~~~vdgiIi~~~~~~--~~~~~l-~~~~~~~iPvv~~~ 92 (272)
T cd06300 51 ADIRNLIAQGVDAIIINPASPT--ALNPVI-EEACEAGIPVVSFD 92 (272)
T ss_pred HHHHHHHHcCCCEEEEeCCChh--hhHHHH-HHHHHCCCeEEEEe
Confidence 444444455776666654 322 233333 45567899999865
No 267
>PRK07377 hypothetical protein; Provisional
Probab=24.10 E-value=1.7e+02 Score=23.78 Aligned_cols=46 Identities=11% Similarity=0.040 Sum_probs=35.0
Q ss_pred CCeeEEEEcC-----CCCchhhHHHHHHHHHhCC--CCEEEeCCHHHHHHHhCC
Q psy16564 66 REAQLCVLAD-----NCDEPAYKKLVQALCSEHQ--IPLIKVDNNKKLGEWAGL 112 (157)
Q Consensus 66 gkakLVIlA~-----D~s~~~~~~~l~~lc~~~~--Ipvi~v~sk~eLG~a~G~ 112 (157)
...++-|+.. |... .....+..++++|+ +..+.+++.++|.+++--
T Consensus 75 ~~~Rlgv~~~~~~~~~~~~-~l~~~l~~~~~~y~~rlElv~y~~~~~l~~aL~~ 127 (184)
T PRK07377 75 LVMRLGVLEIETETSSVFD-QLIDQLRTILDKYHLRLELVVYPDLQALEQALRD 127 (184)
T ss_pred cEEEEEEEeccccccccHH-HHHHHHHHHHHHhCceeeEEecCCHHHHHHHHhc
Confidence 5677777773 3222 46677888999988 778888899999999973
No 268
>PRK07525 sulfoacetaldehyde acetyltransferase; Validated
Probab=24.02 E-value=1.8e+02 Score=26.84 Aligned_cols=45 Identities=18% Similarity=0.104 Sum_probs=33.0
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEe
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v 100 (157)
.+++...|.+.+--++++-..+........+.+|+++.++|++..
T Consensus 190 i~~a~~~L~~A~rPvil~G~g~~~~~a~~~l~~lae~~~~pv~tT 234 (588)
T PRK07525 190 LAEAAELLSEAKFPVILSGAGVVLSDAIEECKALAERLDAPVACG 234 (588)
T ss_pred HHHHHHHHHhCCCCEEEECCCccccChHHHHHHHHHHhCCCeEEc
Confidence 345556666667677777777743256778899999999999974
No 269
>PRK10444 UMP phosphatase; Provisional
Probab=23.94 E-value=1.6e+02 Score=24.19 Aligned_cols=45 Identities=11% Similarity=0.132 Sum_probs=31.9
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCC
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIP 96 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ip 96 (157)
+.+.-|..++++.|++....++|+.++... ........+ ...|++
T Consensus 16 ~~~~p~a~~~l~~L~~~g~~~~~~Tn~~~~-~~~~~~~~l-~~~G~~ 60 (248)
T PRK10444 16 NVAVPGAAEFLHRILDKGLPLVLLTNYPSQ-TGQDLANRF-ATAGVD 60 (248)
T ss_pred CeeCccHHHHHHHHHHCCCeEEEEeCCCCC-CHHHHHHHH-HHcCCC
Confidence 466788999999999988999999998875 333333333 445553
No 270
>PRK00278 trpC indole-3-glycerol-phosphate synthase; Reviewed
Probab=23.88 E-value=4.2e+02 Score=21.95 Aligned_cols=59 Identities=10% Similarity=0.088 Sum_probs=43.1
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCC-EEEeCCHHHHHHHhC
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIP-LIKVDNNKKLGEWAG 111 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ip-vi~v~sk~eLG~a~G 111 (157)
++.=..|+..+...|---+.+++.+-++ .....+...|+..|.. ++.+.+.+|+-++.-
T Consensus 119 fi~~~~qi~~a~~~GAD~VlLi~~~l~~-~~l~~li~~a~~lGl~~lvevh~~~E~~~A~~ 178 (260)
T PRK00278 119 FIIDPYQIYEARAAGADAILLIVAALDD-EQLKELLDYAHSLGLDVLVEVHDEEELERALK 178 (260)
T ss_pred ecCCHHHHHHHHHcCCCEEEEEeccCCH-HHHHHHHHHHHHcCCeEEEEeCCHHHHHHHHH
Confidence 4445557777888887777778888666 4556677888888875 455889999988774
No 271
>PRK08156 type III secretion system protein SpaS; Validated
Probab=23.82 E-value=94 Score=27.64 Aligned_cols=34 Identities=15% Similarity=0.221 Sum_probs=25.0
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. +...|.+.+++++||++. ..-|.|++=
T Consensus 278 vAKG~d~--~A~~IreiA~e~~VPive---n~pLARaLY 311 (361)
T PRK08156 278 SVRETNQ--RALAVRAYAEKVGVPVVR---DIKLARRLY 311 (361)
T ss_pred EEecCcH--HHHHHHHHHHHCCCCEee---CHHHHHHHH
Confidence 4554543 778899999999999974 345666664
No 272
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=23.74 E-value=2.1e+02 Score=18.35 Aligned_cols=41 Identities=27% Similarity=0.376 Sum_probs=26.9
Q ss_pred HHHHHHhc--CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDR--REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~k--gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+.++|++ ..-.|.|++.|-.. ...|+.+|+++|-.++.+.
T Consensus 16 ~~~~~l~~l~~G~~l~v~~d~~~~---~~di~~~~~~~g~~~~~~~ 58 (70)
T PF01206_consen 16 KAKKALKELPPGEVLEVLVDDPAA---VEDIPRWCEENGYEVVEVE 58 (70)
T ss_dssp HHHHHHHTSGTT-EEEEEESSTTH---HHHHHHHHHHHTEEEEEEE
T ss_pred HHHHHHHhcCCCCEEEEEECCccH---HHHHHHHHHHCCCEEEEEE
Confidence 34455554 22456677777654 4678999999998877664
No 273
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=23.70 E-value=2.1e+02 Score=26.49 Aligned_cols=46 Identities=9% Similarity=0.083 Sum_probs=34.1
Q ss_pred cCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 65 RREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 65 kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
+|..+..+++.|.....-.+.+..+|+.+++|+....+..++-..+
T Consensus 284 ~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl~~aL 329 (484)
T PRK06995 284 HGASKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVKDAADLRLAL 329 (484)
T ss_pred cCCCeEEEEeCCccchhHHHHHHHHHHHhCCCeeccCCchhHHHHH
Confidence 4555777888898654566778999999999998887666554443
No 274
>KOG2869|consensus
Probab=23.69 E-value=2.1e+02 Score=25.78 Aligned_cols=67 Identities=15% Similarity=0.189 Sum_probs=48.3
Q ss_pred HHHhcCCceeeHHHHHHHHhcCCeeEEEEcCC---CCchhhHHHHHHHHHh---CCCCEEEeCCH----HHHHHHhC
Q psy16564 45 TARAHDGLAKGLHEAAKALDRREAQLCVLADN---CDEPAYKKLVQALCSE---HQIPLIKVDNN----KKLGEWAG 111 (157)
Q Consensus 45 ~A~~agklv~G~~~v~KaL~kgkakLVIlA~D---~s~~~~~~~l~~lc~~---~~Ipvi~v~sk----~eLG~a~G 111 (157)
++....+.-+|.+.|.+|.+.|-..-++|+.. ++.....++...||+. .|=++..+++. ++|.++.|
T Consensus 285 l~~~~drA~yG~khV~~A~e~~AI~tLLitD~lfr~~DV~tRkkyv~lvesVk~~~gkv~Ifss~H~SGEqL~qltG 361 (379)
T KOG2869|consen 285 LSKDPDRACYGPKHVEKANEYGAIETLLITDELFRSQDVATRKKYVRLVESVKENNGKVFIFSSLHVSGEQLAQLTG 361 (379)
T ss_pred hccCccccccCHHHHHHHHhhcchhheehhhhhcccccHHHHHHHHHHHHHHHhcCCcEEEEehhhccHHHHHhhcC
Confidence 34455678899999999999999888877763 2333566677777765 78888888755 55555555
No 275
>cd01484 E1-2_like Ubiquitin activating enzyme (E1), repeat 2-like. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. A set of novel molecules with a structural similarity to Ub, called Ub-like proteins (Ubls), have similar conjugation cascades. In contrast to ubiquitin-E1, which is a single-chain protein with a weakly conserved two-fold repeat, many of the Ubls-E1are a heterodimer where each subunit corresponds to one half of a single-chain E1. This CD represents the family homologou
Probab=23.54 E-value=1.2e+02 Score=25.04 Aligned_cols=35 Identities=17% Similarity=0.140 Sum_probs=29.3
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+..+||.|-|--+ ....+..+|..+++|++...+
T Consensus 90 ~~~DvVi~a~Dn~~--aR~~ln~~c~~~~iplI~~g~ 124 (234)
T cd01484 90 EQFHIIVNALDNII--ARRYVNGMLIFLIVPLIESGT 124 (234)
T ss_pred hCCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEcc
Confidence 45789999988754 677899999999999998775
No 276
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=23.46 E-value=1.3e+02 Score=25.94 Aligned_cols=43 Identities=14% Similarity=0.353 Sum_probs=27.8
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+++.|..+++..+|..-+.+++.....+...|.++.||++.+.
T Consensus 54 vC~ll~~~~V~aiIfgp~~~~~~~a~~~s~~~~~~~vP~is~~ 96 (362)
T cd06378 54 LCDLLSTTKVHGVVFEDDTDQEAVAQILDFISAQTFLPILGIH 96 (362)
T ss_pred HHHHhcccceEEEEecCCCCccccchhhhhhhhceeccEEEec
Confidence 3456677778876666666552233345555666999999875
No 277
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=23.43 E-value=1.1e+02 Score=26.70 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=28.0
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
...+||-|.|..+ ....+..+|.+++||++....
T Consensus 225 ~~D~Vv~~~d~~~--~r~~ln~~~~~~~ip~i~~~~ 258 (376)
T PRK08762 225 DVDVVVDGADNFP--TRYLLNDACVKLGKPLVYGAV 258 (376)
T ss_pred CCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEEe
Confidence 4789999999755 566789999999999998753
No 278
>PLN02161 beta-amylase
Probab=23.42 E-value=1.7e+02 Score=27.53 Aligned_cols=46 Identities=17% Similarity=0.343 Sum_probs=40.6
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCC-----------CCchhhHHHHHHHHHhCCCCEE
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADN-----------CDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D-----------~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
.-|...+.+-+++-.+.|.|-+-+ |+|+.+...+...|++++|++-
T Consensus 415 rDGY~~Ia~m~~rh~~~l~FTClEM~D~eq~~~~~s~Pe~Lv~QV~~aa~~~Gv~~a 471 (531)
T PLN02161 415 RDGYDPVASVLSRHGAALHIPCLDMADSETPEKYLCSPEGLRQQIHDVSKKWTIHVT 471 (531)
T ss_pred ccchHHHHHHHHHcCceEEEEeccccCCCCCccccCCHHHHHHHHHHHHHHcCCcee
Confidence 558899999999999999998874 6787899999999999999985
No 279
>TIGR00338 serB phosphoserine phosphatase SerB. Phosphoserine phosphatase catalyzes the reaction 3-phospho-serine + H2O = L-serine + phosphate. It catalyzes the last of three steps in the biosynthesis of serine from D-3-phosphoglycerate. Note that this enzyme acts on free phosphoserine, not on phosphoserine residues of phosphoproteins.
Probab=23.16 E-value=3.3e+02 Score=20.94 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=30.8
Q ss_pred hcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEE
Q psy16564 48 AHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 48 ~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
+.-.+.-|..++++.+++...+++|+.+...+ .+..+.+..+++-+
T Consensus 82 ~~~~~~~g~~~~l~~l~~~g~~~~IvS~~~~~-----~~~~~l~~~~i~~~ 127 (219)
T TIGR00338 82 ENLPLTEGAEELVKTLKEKGYKVAVISGGFDL-----FAEHVKDKLGLDAA 127 (219)
T ss_pred hcCCcCCCHHHHHHHHHHCCCEEEEECCCcHH-----HHHHHHHHcCCCce
Confidence 34468889999999999876777766654433 33445566666543
No 280
>TIGR01919 hisA-trpF 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase/N-(5'phosphoribosyl)anthranilate isomerase. This model represents a bifunctional protein posessing both hisA (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase) and trpF (N-(5'phosphoribosyl)anthranilate isomerase) activities. Thus, it is involved in both the histidine and tryptophan biosynthetic pathways. Enzymes with this property have been described only in the Actinobacteria (High-GC gram-positive). The enzyme is closely related to the monofunctional HisA proteins (TIGR00007) and in Actinobacteria, the classical monofunctional TrpF is generally absent.
Probab=23.11 E-value=4.3e+02 Score=21.75 Aligned_cols=60 Identities=8% Similarity=0.033 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHhCCCCEEE---eCCHHHHHHHhCCCccccCCCccceeeeEEEEEecCchhHHhhhccccc
Q psy16564 81 AYKKLVQALCSEHQIPLIK---VDNNKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRNWFLIICSRKSTQ 148 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ipvi~---v~sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g~~~~~~~~~~~~ 148 (157)
.....+..+++...+|+.. +.|.+++-+++... -.| +-.+..++.||.+...++..+..|
T Consensus 61 ~n~~~i~~i~~~~~~~v~vgGGIrs~e~~~~~l~~G------a~~--vvigT~a~~~p~~~~~~~~~~g~~ 123 (243)
T TIGR01919 61 NNEMMLEEVVKLLVVVEELSGGRRDDSSLRAALTGG------RAR--VNGGTAALENPWWAAAVIRYGGDI 123 (243)
T ss_pred chHHHHHHHHHHCCCCEEEcCCCCCHHHHHHHHHcC------CCE--EEECchhhCCHHHHHHHHHHcccc
Confidence 3455788888988899877 34888888777642 122 335777889999999999888655
No 281
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=23.06 E-value=2.4e+02 Score=21.93 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=22.4
Q ss_pred HHHHHHhcCCeeEEEE-cCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVL-ADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIl-A~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.++.+...++.-+|+ +.|. + ... .+...+.+.+||++.+.
T Consensus 47 ~~i~~l~~~~vdgiii~~~~~-~-~~~-~~~~~l~~~~iPvv~~~ 88 (272)
T cd06301 47 SQVENFIAQGVDAIIVVPVDT-A-ATA-PIVKAANAAGIPLVYVN 88 (272)
T ss_pred HHHHHHHHcCCCEEEEecCch-h-hhH-HHHHHHHHCCCeEEEec
Confidence 4444444445555554 4443 2 122 33455688899998876
No 282
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=23.05 E-value=3.2e+02 Score=20.24 Aligned_cols=47 Identities=11% Similarity=0.125 Sum_probs=30.8
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC----CHHHHHHHhCCC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD----NNKKLGEWAGLS 113 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~----sk~eLG~a~G~~ 113 (157)
..+.+||-.|-.+..-........++.||.++.+. ...+|.++.+..
T Consensus 103 ~~k~iillTDG~~~~~~~~~a~~lk~~gi~i~~ig~g~~~~~~L~~ia~~~ 153 (164)
T cd01482 103 VPKVVILITDGKSQDDVELPARVLRNLGVNVFAVGVKDADESELKMIASKP 153 (164)
T ss_pred CCEEEEEEcCCCCCchHHHHHHHHHHCCCEEEEEecCcCCHHHHHHHhCCC
Confidence 35566666786553333334455677899998876 466888888853
No 283
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=22.99 E-value=1.9e+02 Score=18.82 Aligned_cols=37 Identities=16% Similarity=0.295 Sum_probs=24.4
Q ss_pred HHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 61 KALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 61 KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+.+..|+ .|.|++.|... ...++.+|++.|-.++...
T Consensus 21 ~~l~~G~-~l~V~~dd~~s---~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 21 RKMKPGD-TLLVLATDPST---TRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred HcCCCCC-EEEEEeCCCch---HHHHHHHHHHcCCEEEEEE
Confidence 3333443 45666666543 5578999999999887654
No 284
>cd01895 EngA2 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=22.90 E-value=2.8e+02 Score=19.62 Aligned_cols=40 Identities=23% Similarity=0.165 Sum_probs=23.4
Q ss_pred eeEEEEcCCCCch--hhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 68 AQLCVLADNCDEP--AYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 68 akLVIlA~D~s~~--~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
+.++++.-|++.. .....+..++...+.|++.+-+|.+|.
T Consensus 85 ~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~~~iiv~nK~Dl~ 126 (174)
T cd01895 85 ADVVLLVIDATEGITEQDLRIAGLILEEGKALVIVVNKWDLV 126 (174)
T ss_pred cCeEEEEEeCCCCcchhHHHHHHHHHhcCCCEEEEEeccccC
Confidence 3444444444321 223345556666789999988887664
No 285
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.90 E-value=97 Score=27.74 Aligned_cols=39 Identities=26% Similarity=0.341 Sum_probs=27.4
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
.|..| +|.-.+. +.-.|.+.|+++|||++. .-.|.|++=
T Consensus 285 ~AP~V-vAKG~d~--~AlkIreiA~e~~Ipi~e---nppLARaLY 323 (363)
T COG1377 285 PAPVV-VAKGVDL--VALKIREIAKEHGIPIIE---NPPLARALY 323 (363)
T ss_pred CCCEE-EEeCCcH--HHHHHHHHHHHcCCceec---ChHHHHHHH
Confidence 34433 6776665 667899999999999974 345666664
No 286
>PLN00197 beta-amylase; Provisional
Probab=22.88 E-value=1.9e+02 Score=27.54 Aligned_cols=45 Identities=22% Similarity=0.299 Sum_probs=39.8
Q ss_pred eeHHHHHHHHhcCCeeEEEEcCC-----------CCchhhHHHHHHHHHhCCCCEE
Q psy16564 54 KGLHEAAKALDRREAQLCVLADN-----------CDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 54 ~G~~~v~KaL~kgkakLVIlA~D-----------~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
-|...+.+.+++-.+.|.|-+-+ |+|+.+...+...|++++|++.
T Consensus 420 DGY~~Ia~mfarh~~~l~FTClEM~D~eqp~~a~s~PE~Lv~QV~~aA~~~Gv~va 475 (573)
T PLN00197 420 DGYLPIAQMLARHGAIFNFTCIEMRDHEQPQDALCAPEKLVRQVALATREAEVPLA 475 (573)
T ss_pred ccHHHHHHHHHHcCCeEEEEecCcccCCCCccccCCHHHHHHHHHHHHHHcCCcEe
Confidence 57889999999999999998874 6787899999999999999985
No 287
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=22.83 E-value=2.2e+02 Score=20.26 Aligned_cols=50 Identities=22% Similarity=0.261 Sum_probs=30.4
Q ss_pred CceeeHHHHHHHHhcC--CeeEEEEcCCCCch-hhHHHHHHHHHhCCCCEEEeC
Q psy16564 51 GLAKGLHEAAKALDRR--EAQLCVLADNCDEP-AYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 51 klv~G~~~v~KaL~kg--kakLVIlA~D~s~~-~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+..|...+.+.+... ..+.+|+-.|..+. .... ....+++.+|+++.+.
T Consensus 81 ~~~~al~~a~~~~~~~~~~~~~iv~iTDG~~~~~~~~-~~~~~~~~~i~i~~v~ 133 (172)
T PF13519_consen 81 NLYDALQEAAKMLASSDNRRRAIVLITDGEDNSSDIE-AAKALKQQGITIYTVG 133 (172)
T ss_dssp -HHHHHHHHHHHHHC-SSEEEEEEEEES-TTHCHHHH-HHHHHHCTTEEEEEEE
T ss_pred cHHHHHHHHHHHHHhCCCCceEEEEecCCCCCcchhH-HHHHHHHcCCeEEEEE
Confidence 4666778888888764 35666666776542 2233 3344568899988865
No 288
>PF04414 tRNA_deacylase: D-aminoacyl-tRNA deacylase; InterPro: IPR007508 D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1YQE_A 2GFQ_B.
Probab=22.82 E-value=1.7e+02 Score=24.06 Aligned_cols=45 Identities=16% Similarity=0.229 Sum_probs=32.1
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK 99 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~ 99 (157)
+.+.+.+++++..+..+++-.+.-.-..+..+..+.++.|||++.
T Consensus 169 ~~~~l~~a~~~s~~~~a~id~K~l~~~~r~~i~~~l~~~gi~v~k 213 (213)
T PF04414_consen 169 DEDVLRQAIEKSGADVAIIDWKSLKSEDRRRIEELLEELGIEVIK 213 (213)
T ss_dssp -HHHHHHHHCHCT-SEEEEETTTS-HHHHHHHHHHHHHHT-EEEE
T ss_pred CHHHHHHHHHhCCCcEEEEecCCCCHHHHHHHHHHHHHcCCeeeC
Confidence 356677788887777788876665557888899999999998863
No 289
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.78 E-value=2.6e+02 Score=21.73 Aligned_cols=44 Identities=18% Similarity=0.272 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+.++.+...++.-+|+..- ++......+.. +.+.+||++.++.
T Consensus 45 ~~~~~~~~~~~vdgiii~~~-~~~~~~~~~~~-~~~~~ipvV~~~~ 88 (267)
T cd06322 45 LSDVEDFITKKVDAIVLSPV-DSKGIRAAIAK-AKKAGIPVITVDI 88 (267)
T ss_pred HHHHHHHHHcCCCEEEEcCC-ChhhhHHHHHH-HHHCCCCEEEEcc
Confidence 34555555666666666432 22123444444 5678999999873
No 290
>cd04501 SGNH_hydrolase_like_4 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=22.61 E-value=1.1e+02 Score=22.71 Aligned_cols=22 Identities=5% Similarity=0.229 Sum_probs=17.6
Q ss_pred hhHHHHHHHHHhCCCCEEEeCC
Q psy16564 81 AYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 81 ~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+...+..+|.+++++++-+.+
T Consensus 125 ~~n~~~~~~a~~~~v~~vd~~~ 146 (183)
T cd04501 125 SLNRWLKDYARENGLLFLDFYS 146 (183)
T ss_pred HHHHHHHHHHHHcCCCEEechh
Confidence 3556788999999999987764
No 291
>PRK08322 acetolactate synthase; Reviewed
Probab=22.58 E-value=2.1e+02 Score=25.93 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=29.9
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+++.+.|.+-+-.++++-..+......+.+.+||+..++||+...
T Consensus 187 ~~~~~~l~~A~rPviv~G~g~~~~~a~~~l~~lae~~~~pv~tt~ 231 (547)
T PRK08322 187 ERAAEAIQAAKNPLILIGAGANRKTASKALTEFVDKTGIPFFTTQ 231 (547)
T ss_pred HHHHHHHHhCCCcEEEECCCcchhcHHHHHHHHHHHhCCCEEEcc
Confidence 344556665555566555555322456788999999999999744
No 292
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.56 E-value=2.7e+02 Score=22.06 Aligned_cols=42 Identities=10% Similarity=0.101 Sum_probs=22.4
Q ss_pred HHHHHHhcCCeeEEEEc-CCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 58 EAAKALDRREAQLCVLA-DNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA-~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+.++.+...++--+|+. .|. + ... .+...+.+.+||++.+.+
T Consensus 46 ~~i~~~~~~~vdgiii~~~~~-~-~~~-~~i~~~~~~~iPvV~~~~ 88 (272)
T cd06313 46 AAIENMASQGWDFIAVDPLGI-G-TLT-EAVQKAIARGIPVIDMGT 88 (272)
T ss_pred HHHHHHHHcCCCEEEEcCCCh-H-HhH-HHHHHHHHCCCcEEEeCC
Confidence 44444445556555554 332 1 122 233455667899888763
No 293
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=22.54 E-value=2.8e+02 Score=19.70 Aligned_cols=35 Identities=14% Similarity=0.196 Sum_probs=26.3
Q ss_pred hcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEE
Q psy16564 64 DRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIK 99 (157)
Q Consensus 64 ~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~ 99 (157)
.++...+|++.++.-+ .+...+..+-++...|.+.
T Consensus 41 ~~~d~gII~Ite~~~~-~i~e~i~~~~~~~~~P~ii 75 (100)
T PRK02228 41 EDDDVGILVMHDDDLE-KLPRRLRRTLEESVEPTVV 75 (100)
T ss_pred hCCCEEEEEEehhHhH-hhHHHHHHHHhcCCCCEEE
Confidence 4677888888888766 5666777766777788776
No 294
>PRK05724 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated
Probab=22.52 E-value=1.2e+02 Score=26.66 Aligned_cols=33 Identities=9% Similarity=0.197 Sum_probs=24.1
Q ss_pred eeEEEEcCCCC---------------chh--hHHHHHHHHHhCCCCEEEe
Q psy16564 68 AQLCVLADNCD---------------EPA--YKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 68 akLVIlA~D~s---------------~~~--~~~~l~~lc~~~~Ipvi~v 100 (157)
-...|+|.|.. |.. ....+..+|.++++|++++
T Consensus 108 rpV~VIa~d~g~~~~e~~~~~~G~~~peg~rKa~R~m~lA~~f~lPIVtl 157 (319)
T PRK05724 108 RPVMVIGHQKGRDTKEKIRRNFGMPRPEGYRKALRLMKMAEKFGLPIITF 157 (319)
T ss_pred EEEEEEEecCCccccccccccCCCCCHHHHHHHHHHHHHHHHcCCCEEEE
Confidence 56778998862 212 2356788999999999986
No 295
>cd06383 PBP1_iGluR_AMPA_Like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current.
Probab=22.45 E-value=2.2e+02 Score=24.57 Aligned_cols=41 Identities=12% Similarity=0.091 Sum_probs=30.1
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++..|.+|.+...|+....+. ....+..+|...+||.+.+.
T Consensus 58 ~C~~~~~gv~~~AIiGp~ss~--~a~~V~si~~~~~IP~Is~s 98 (368)
T cd06383 58 VCDKADSAIVPHLVLDTTTCG--DASEIKSVTGALGIPTFSAS 98 (368)
T ss_pred HHHHHHccCCcEEEECCCcch--hHHHHHHHHhccCCCEEEcc
Confidence 445666777666677776554 55569999999999998764
No 296
>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
Probab=22.45 E-value=2e+02 Score=24.99 Aligned_cols=49 Identities=24% Similarity=0.209 Sum_probs=30.4
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
.+.++++.-.+-++++............+..++.+.++|++.+-+|-+|
T Consensus 247 ~~~~~~~~ad~~ilV~D~~~~~~~~~~~~~~~~~~~~~~iiiv~NK~Dl 295 (429)
T TIGR03594 247 RTLKAIERADVVLLVLDATEGITEQDLRIAGLILEAGKALVIVVNKWDL 295 (429)
T ss_pred HHHHHHHhCCEEEEEEECCCCccHHHHHHHHHHHHcCCcEEEEEECccc
Confidence 4456676666555555433222133445667778889999998877665
No 297
>PF00118 Cpn60_TCP1: TCP-1/cpn60 chaperonin family Chaperonins cpn60 signature Chaperonins TCP-1 signatures 60 kd chaperonin signature; InterPro: IPR002423 Partially folded polypeptide chains, either newly made by ribosomes or emerging from mature proteins unfolded by stress, run the risk of aggregating with one another to the detriment of the organism. Folding of newly synthesised polypeptides in the crowded cellular environment requires the assistance of molecular chaperone proteins, such as the large bacterial chaperonins GroEL and GroES. GroEL and GroES prevent aggregation by encapsulating individual chains within the so-called 'Anfinsen cage' provided by the GroEL-GroES complex, where they can fold in isolation from one another []. GroEL consists of two heptameric rings of identical ATPase subunits stacked back to back, containing a cage in each ring. Each subunit consists of three domains. The equatorial domain contains the nucleotide binding site and is connected by a flexible intermediate domain with the apical domain. The latter presents several hydrophobic amino-acid side chains at the top of the ring, orientated towards the cavity of the cage. These side chains are involved in binding either a partially folded polypeptide chain or a single molecule of GroES. The assembly of proteins has been thought to be the sole result of properties inherent in the primary sequence of polypeptides themselves. In some cases, however, structural information from other protein molecules is required for correct folding and subsequent assembly into oligomers []. These 'helper' molecules are referred to as molecular chaperones, a subfamily of which are the chaperonins [], which include 10 kDa and 60 kDa proteins. These are found in abundance in prokaryotes, chloroplasts and mitochondria. They are required for normal cell growth (as demonstrated by the fact that no temperature sensitive mutants for the chaperonin genes can be found in the temperature range 20 to 43 degrees centigrade []), and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between 6 to 8 identical subunits, whereas the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The cpn10 and cpn60 oligomers also require Mg2+-ATP in order to interact to form a functional complex, although the mechanism of this interaction is as yet unknown []. This chaperonin complex is essential for the correct folding and assembly of polypeptides into oligomeric structures, of which the chaperonins themselves are not a part []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. The 60 kDa form of chaperonin is the immunodominant antigen of patients with Legionnaire's disease [], and is thought to play a role in the protection of the Legionella bacteria from oxygen radicals within macrophages. This hypothesis is based on the finding that the cpn60 gene is upregulated in response to hydrogen peroxide, a source of oxygen radicals. Cpn60 has also been found to display strong antigenicity in many bacterial species [], and has the potential for inducing immune protection against unrelated bacterial infections. The RuBisCO subunit binding protein (which has been implicated in the assembly of RuBisCO) and cpn60 have been found to be evolutionary homologues, the RuBisCO subunit binding protein having the C-terminal Gly-Gly-Met repeat found in all bacterial cpn60 sequences. Although the precise function of this repeat is unknown, it is thought to be important as it is also found in 70 kDa heat-shock proteins []. The crystal structure of Escherichia coli GroEL has been resolved to 2.8A []. The TCP-1 family of proteins act as molecular chaperones for tubulin, actin and probably some other proteins. They are weakly, but significantly, related to the cpn60/groEL chaperonin family. ; GO: 0005524 ATP binding, 0044267 cellular protein metabolic process; PDB: 3IZH_B 3IZI_I 3LOS_I 3IYF_H 3KFK_C 3KFE_E 3RUV_C 3IZK_L 3J02_B 3RUQ_A ....
Probab=22.44 E-value=81 Score=27.73 Aligned_cols=52 Identities=12% Similarity=0.144 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC---CHHHHHHHhCCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD---NNKKLGEWAGLS 113 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~---sk~eLG~a~G~~ 113 (157)
...++.|.+-.+.+|+++.+.++ .+..++.+++|.++.-- .-+.|.+++|-.
T Consensus 235 ~~~~~~i~~~~~~lIi~~~~i~~-----~~l~~l~~~~I~~i~~v~~~~l~~i~~~tg~~ 289 (485)
T PF00118_consen 235 KKILEKIINLGVNLIISQKSIDD-----EALQYLNKNGILVIRRVSKEDLERIARATGAS 289 (485)
T ss_dssp HHHHHHHHTTTSSEEEESSEBTH-----HHHHHHHHCTHEEESSEHHHHHHHHHHHHTSB
T ss_pred ccccceEeeeccceeeeeccccc-----ccchhhhhhhhhccccchHHHHHhhhcccCCc
Confidence 45666777766999999999988 35567789999887633 445777778854
No 298
>PRK09259 putative oxalyl-CoA decarboxylase; Validated
Probab=22.38 E-value=1.9e+02 Score=26.52 Aligned_cols=46 Identities=13% Similarity=0.303 Sum_probs=33.4
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+++...|.+-+--++++-..+........+.+|+++.++||+...
T Consensus 203 l~~~~~~L~~AkrPvIi~G~g~~~~~a~~~l~~lae~l~iPV~tt~ 248 (569)
T PRK09259 203 VDRALDLLKKAKRPLIILGKGAAYAQADEQIREFVEKTGIPFLPMS 248 (569)
T ss_pred HHHHHHHHHhCCCCEEEECcCccccChHHHHHHHHHHHCCCEEecc
Confidence 4455666666666777777676432466789999999999999854
No 299
>PLN02803 beta-amylase
Probab=22.22 E-value=1.9e+02 Score=27.30 Aligned_cols=46 Identities=13% Similarity=0.175 Sum_probs=39.8
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCC-----------CCchhhHHHHHHHHHhCCCCEE
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADN-----------CDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D-----------~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
.-|...+.+.+++-.+.|.|-+-+ |+|+.+...+...|++++|++-
T Consensus 398 rdGY~~Ia~mf~rh~~~l~FTClEM~D~eqp~~~~s~Pe~Lv~Qv~~aa~~~Gv~~a 454 (548)
T PLN02803 398 HDGYLPIARMFSKHGVVLNFTCMEMRDGEQPEHANCSPEGLVRQVKMATRTAGTELA 454 (548)
T ss_pred cccHHHHHHHHHHcCCeEEEEecCcccCCCCccccCCHHHHHHHHHHHHHHcCCcee
Confidence 347889999999999999998874 5777899999999999999984
No 300
>PRK03244 argD acetylornithine aminotransferase; Provisional
Probab=22.22 E-value=2.3e+02 Score=24.15 Aligned_cols=42 Identities=12% Similarity=0.170 Sum_probs=29.1
Q ss_pred CCeeEEEEcCC-------CCchhhHHHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 66 REAQLCVLADN-------CDEPAYKKLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 66 gkakLVIlA~D-------~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
++..+|++-.- .++..+...|.++|+++++.++.=+--..+|
T Consensus 182 ~~~~aviiep~~~~~G~~~~~~~~l~~l~~l~~~~~~llI~DEv~~g~g 230 (398)
T PRK03244 182 DDTAAVFLEPIQGEAGVVPPPAGYLAAAREITDRHGALLVLDEVQTGIG 230 (398)
T ss_pred CCeEEEEEecccCCCCCcCCCHHHHHHHHHHHHHcCCEEEEeccccCCc
Confidence 56777777643 2344567889999999999998755333344
No 301
>PF00535 Glycos_transf_2: Glycosyl transferase family 2; InterPro: IPR001173 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP-N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.; PDB: 2Z87_A 2Z86_B 2D7R_A 2D7I_A 3CKN_A 3CKQ_A 3CKJ_A 3CKV_A 3CKO_A 2FFU_A ....
Probab=22.20 E-value=73 Score=22.17 Aligned_cols=43 Identities=5% Similarity=0.114 Sum_probs=22.5
Q ss_pred HHHHHHhcC--CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRR--EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kg--kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+++.+|.+. ..-=|+|..|.+++.....+..+.+ .+.++..+.
T Consensus 15 ~~l~sl~~q~~~~~eiivvdd~s~d~~~~~~~~~~~-~~~~i~~i~ 59 (169)
T PF00535_consen 15 RTLESLLKQTDPDFEIIVVDDGSTDETEEILEEYAE-SDPNIRYIR 59 (169)
T ss_dssp HHHHHHHHHSGCEEEEEEEECS-SSSHHHHHHHHHC-CSTTEEEEE
T ss_pred HHHHHHhhccCCCEEEEEeccccccccccccccccc-ccccccccc
Confidence 344444432 3333455666655467777666665 455555555
No 302
>TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=22.10 E-value=3.5e+02 Score=20.36 Aligned_cols=64 Identities=13% Similarity=0.055 Sum_probs=46.2
Q ss_pred CCeeEEEEcCCCCchh--------hHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCCccccCCCccceeeeEEEEEecCch
Q psy16564 66 REAQLCVLADNCDEPA--------YKKLVQALCSEHQIPLIKVDNNKKLGEWAGLSKLDNMGKARKVVGCSCVVIKVRNW 137 (157)
Q Consensus 66 gkakLVIlA~D~s~~~--------~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~D~g~ 137 (157)
.++...|+-.|-++ . -...+..+-....+.+..+ +..+.-+++-.. ....+.+.++||
T Consensus 42 ~~lpvaVVd~D~s~-~~~~~~~~~s~~l~~~l~~~~~~~~~~~-~~~ea~~~l~~g------------~~~~~ivIP~~F 107 (164)
T TIGR03061 42 DNLPVAVVNEDKGA-TYDGKTLNAGDDLVKELKKNDDLDWHFV-SAKEAEKGLADG------------KYYMVITIPEDF 107 (164)
T ss_pred CCCeEEEEECCCCC-CcCCcccchHHHHHHHHhcCCCcceEEc-CHHHHHHHhHcC------------cEEEEEEECcch
Confidence 57899999999887 3 4555566655556665544 788888888643 235678899999
Q ss_pred hHHhhh
Q psy16564 138 FLIICS 143 (157)
Q Consensus 138 ~~~~~~ 143 (157)
++-+.+
T Consensus 108 s~~l~~ 113 (164)
T TIGR03061 108 SENATS 113 (164)
T ss_pred hHHHHh
Confidence 998765
No 303
>CHL00099 ilvB acetohydroxyacid synthase large subunit
Probab=22.07 E-value=2.1e+02 Score=26.37 Aligned_cols=45 Identities=16% Similarity=0.131 Sum_probs=31.7
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.++.+.|.+.+--++++-..+....-...+.+|++..++|++...
T Consensus 208 ~~a~~~L~~AkrPvil~G~g~~~~~a~~~l~~lae~lg~PV~tt~ 252 (585)
T CHL00099 208 EQAAKLILQSSQPLLYVGGGAIISDAHQEITELAELYKIPVTTTL 252 (585)
T ss_pred HHHHHHHHcCCCcEEEECCCCchhchHHHHHHHHHHHCCCEEEcc
Confidence 445556666666666666666432467789999999999999744
No 304
>PRK02936 argD acetylornithine aminotransferase; Provisional
Probab=22.05 E-value=2.2e+02 Score=24.04 Aligned_cols=35 Identities=29% Similarity=0.357 Sum_probs=25.2
Q ss_pred CCeeEEEEc--------CCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 66 REAQLCVLA--------DNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 66 gkakLVIlA--------~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+...|++- ...++ .....|..+|++++++++.=+
T Consensus 166 ~~~~~ii~e~i~~~~G~~~~~~-~~l~~l~~l~~~~~~~lI~DE 208 (377)
T PRK02936 166 EEVAAVMLEVVQGEGGVIPADP-AFLQEVQTLCKKFGALLIIDE 208 (377)
T ss_pred CCeEEEEEecccCCCCCccCCH-HHHHHHHHHHHHcCCEEEEec
Confidence 456667662 13344 678889999999999998644
No 305
>PRK09108 type III secretion system protein HrcU; Validated
Probab=22.04 E-value=1e+02 Score=27.15 Aligned_cols=34 Identities=15% Similarity=0.168 Sum_probs=25.0
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. +...+.+.+++++||++. ..-|.|++-
T Consensus 285 vAKG~d~--~A~~Ir~~A~e~~VPvve---n~pLARaLy 318 (353)
T PRK09108 285 IAKGVDD--GALALRRHAHALGIPIVG---NPPVARALY 318 (353)
T ss_pred EEEeCcH--HHHHHHHHHHHcCCCEEe---CHHHHHHHh
Confidence 4554443 678899999999999975 345777765
No 306
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=21.99 E-value=98 Score=23.28 Aligned_cols=34 Identities=15% Similarity=0.149 Sum_probs=13.1
Q ss_pred eeEEEEcCCCCchh--hHHHHHHHHHhCCCCEEEeC
Q psy16564 68 AQLCVLADNCDEPA--YKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 68 akLVIlA~D~s~~~--~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+..|+...|..+.. ....+...|.+++|++..+.
T Consensus 89 ~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~ 124 (165)
T PF00875_consen 89 ATAVYFNEEYTPYERRRDERVRKALKKHGIKVHTFD 124 (165)
T ss_dssp ESEEEEE---SHHHHHHHHHHHHHHHHTTSEEEEE-
T ss_pred cCeeEeccccCHHHHHHHHHHHHHHHhcceEEEEEC
Confidence 55555555544422 11333444444555555444
No 307
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=21.97 E-value=1.3e+02 Score=26.68 Aligned_cols=37 Identities=14% Similarity=0.308 Sum_probs=28.8
Q ss_pred CCeeEEEEcCCCCchhhHHHHHHHHHhC-----CCCEEEeCC
Q psy16564 66 REAQLCVLADNCDEPAYKKLVQALCSEH-----QIPLIKVDN 102 (157)
Q Consensus 66 gkakLVIlA~D~s~~~~~~~l~~lc~~~-----~Ipvi~v~s 102 (157)
.+.++++|..-|.+.-+-..+...|++. ++|++.+.+
T Consensus 96 ~~P~~I~V~tTC~~e~IGDDi~~v~~e~~~~~~~~pvv~v~t 137 (427)
T PRK02842 96 PNISVLFLVGSCPSEVIKLDLEGLAERLSTEFAGVPVLNYSG 137 (427)
T ss_pred CCCCEEEEECCChHHhhcCCHHHHHHHhhcccCCCeEEEeeC
Confidence 4789999999998866667777777652 799998653
No 308
>PRK08199 thiamine pyrophosphate protein; Validated
Probab=21.92 E-value=2.2e+02 Score=25.92 Aligned_cols=44 Identities=20% Similarity=0.199 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEe
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v 100 (157)
.++.+.|.+-+--++|+-..+....-...+.+||+..++||+..
T Consensus 195 ~~~~~~L~~A~rPvi~~G~g~~~~~a~~~l~~lae~~~~pV~tt 238 (557)
T PRK08199 195 ARLAELLARAERPLVILGGSGWTEAAVADLRAFAERWGLPVACA 238 (557)
T ss_pred HHHHHHHHhCCCCEEEECCCcCchhHHHHHHHHHHHhCCCEEEc
Confidence 44556666656666666665543245678999999999999973
No 309
>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=21.84 E-value=1.6e+02 Score=23.03 Aligned_cols=31 Identities=3% Similarity=-0.152 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 83 KKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 83 ~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
...+..+++++|+.++.+....-+-+.+...
T Consensus 75 Ig~l~~lae~~g~~v~i~~Ggt~ar~~ik~~ 105 (158)
T PF01976_consen 75 IGDLKKLAEKYGYKVYIATGGTLARKIIKEY 105 (158)
T ss_pred hhHHHHHHHHcCCEEEEEcChHHHHHHHHHh
Confidence 3578899999999999999888888888754
No 310
>cd00378 SHMT Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers; the mammalian enzyme forms a homotetramer comprising four pyridoxal phosphate-bound active sites.
Probab=21.82 E-value=2e+02 Score=24.50 Aligned_cols=46 Identities=13% Similarity=-0.037 Sum_probs=29.1
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCch-hhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEP-AYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~-~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
..+..+++...+.++|++.....+. .-...|..+|++++++++.=+
T Consensus 150 ~~~l~~~i~~~~~~~v~~~~~~~~~~~~~~~I~~l~~~~~~~li~D~ 196 (402)
T cd00378 150 YDALEKMALEFKPKLIVAGASAYPRPIDFKRFREIADEVGAYLLVDM 196 (402)
T ss_pred HHHHHHHHHhCCCCEEEecCcccCCCcCHHHHHHHHHhcCCEEEEEc
Confidence 4455566655567777775543331 134568889999998876544
No 311
>COG1535 EntB Isochorismate hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.80 E-value=94 Score=25.72 Aligned_cols=19 Identities=16% Similarity=0.401 Sum_probs=15.8
Q ss_pred HHHHHHHHHhCCCCEEEeC
Q psy16564 83 KKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 83 ~~~l~~lc~~~~Ipvi~v~ 101 (157)
...|...|+++||||++.-
T Consensus 60 i~~Lr~~~~~~giPVvyTa 78 (218)
T COG1535 60 IAKLRIWCKQAGIPVVYTA 78 (218)
T ss_pred HHHHHHHHHHcCCcEEEEe
Confidence 3567889999999999854
No 312
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.78 E-value=2.2e+02 Score=17.95 Aligned_cols=40 Identities=25% Similarity=0.293 Sum_probs=26.0
Q ss_pred HHHHHHhc---CCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDR---REAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~k---gkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+.++|++ | -.+.|++.|.. -...++.+|++.|-.+....
T Consensus 15 ~~~~~l~~l~~g-~~l~v~~d~~~---~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 15 KTKKALEKLKSG-EVLEVLLDDPG---AVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred HHHHHHhcCCCC-CEEEEEecCCc---HHHHHHHHHHHcCCEEEEEE
Confidence 34455554 4 44566666653 34578899999999887655
No 313
>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=21.70 E-value=2.9e+02 Score=22.36 Aligned_cols=60 Identities=13% Similarity=0.144 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 35 INKALQQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 35 ~~k~L~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
|..+|..+|+...+.. |-..+-+.++.|.-.-+| ++++ .-.+.|...++.|||.+....+
T Consensus 4 L~~~l~~~lk~~kK~~----Gk~slk~L~k~g~~l~~i---~i~~-~~lk~F~k~AkKyGV~yav~kd 63 (204)
T PF12687_consen 4 LAAALKALLKDYKKTK----GKQSLKKLLKQGKGLKNI---EITD-EDLKEFKKEAKKYGVDYAVKKD 63 (204)
T ss_pred HHHHHHHHHHHHHHhc----CceeHHHHHhcCCCceEE---ecCH-hhHHHHHHHHHHcCCceEEeec
Confidence 4556666665544333 766666667777622222 2333 2344688999999999988874
No 314
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=21.69 E-value=2.1e+02 Score=23.78 Aligned_cols=49 Identities=14% Similarity=0.236 Sum_probs=28.7
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
++..+++.-.+-++++............+..++..+++|++.+-+|.++
T Consensus 87 ~~~~~l~~aD~~IlVvda~~g~~~~~~~i~~~~~~~~~P~iivvNK~D~ 135 (267)
T cd04169 87 DTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDR 135 (267)
T ss_pred HHHHHHHHCCEEEEEEECCCCccHHHHHHHHHHHhcCCCEEEEEECCcc
Confidence 3566666655555555432221123345567788889998887766544
No 315
>PLN02801 beta-amylase
Probab=21.62 E-value=2e+02 Score=26.96 Aligned_cols=46 Identities=15% Similarity=0.086 Sum_probs=40.0
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCC-----------CCchhhHHHHHHHHHhCCCCEE
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADN-----------CDEPAYKKLVQALCSEHQIPLI 98 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D-----------~s~~~~~~~l~~lc~~~~Ipvi 98 (157)
.-|...+.+-+.+-.+.|.|-+-+ |+|+.+...+...|++++|++-
T Consensus 326 rDGY~pIa~m~~rh~~~l~FTClEM~D~eq~~~~~s~PE~Lv~QV~~aa~~~Gv~va 382 (517)
T PLN02801 326 RDGYRPIARMLSRHYGILNFTCLEMRDTEQPAEALSAPQELVQQVLSGAWREGIEVA 382 (517)
T ss_pred ccchHHHHHHHHHcCCeEEEeecccccCCCCcccCCCHHHHHHHHHHHHHHcCCcEe
Confidence 357899999999999999998874 5777899999999999999985
No 316
>COG3580 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.54 E-value=1.2e+02 Score=27.02 Aligned_cols=76 Identities=24% Similarity=0.256 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHhcCC-ceeeHHHHHHHHhcCCeeEEEEcCC---CCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHh
Q psy16564 35 INKALQQVLKTARAHDG-LAKGLHEAAKALDRREAQLCVLADN---CDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWA 110 (157)
Q Consensus 35 ~~k~L~~lL~~A~~agk-lv~G~~~v~KaL~kgkakLVIlA~D---~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~ 110 (157)
.++|++..++....... +..--+++++.+.+..-.-|+||+- .|| .+-.-|+.+-...|+|+++.+|-.-||...
T Consensus 168 ~~~Avqka~~~~~e~r~dir~k~~e~L~~l~~n~~~gVvLaGrPYh~Dp-eiNhgI~e~i~~~g~~IlTedsI~~~~~~~ 246 (351)
T COG3580 168 NEEAVQKAWKEGEEYREDIRKKGEEVLKYLKENGEKGVVLAGRPYHFDP-EINHGIPEKINSRGIPILTEDSIPLLGEIE 246 (351)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCceeEEEeCCccccCc-ccccchHHHHhhcCCeeeecccchhhhccc
Confidence 34444444444333333 2233367778887766666677773 444 455557777789999999999888788777
Q ss_pred C
Q psy16564 111 G 111 (157)
Q Consensus 111 G 111 (157)
|
T Consensus 247 ~ 247 (351)
T COG3580 247 G 247 (351)
T ss_pred c
Confidence 7
No 317
>COG1861 SpsF Spore coat polysaccharide biosynthesis protein F, CMP-KDO synthetase homolog [Cell envelope biogenesis, outer membrane]
Probab=21.53 E-value=2.3e+02 Score=24.04 Aligned_cols=52 Identities=10% Similarity=0.251 Sum_probs=40.0
Q ss_pred HHHHHhcCC--eeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhCCC
Q psy16564 59 AAKALDRRE--AQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAGLS 113 (157)
Q Consensus 59 v~KaL~kgk--akLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G~~ 113 (157)
+++.+++-+ .++|+.++|-.+ ...|+.+|..+|+-++.-...+-|-|.++.-
T Consensus 34 ~lervrks~~~d~ivvATS~~~~---d~~l~~~~~~~G~~vfrGs~~dVL~Rf~~a~ 87 (241)
T COG1861 34 QLERVRKSKDLDKIVVATSDKEE---DDALEEVCRSHGFYVFRGSEEDVLQRFIIAI 87 (241)
T ss_pred HHHHHhccccccceEEEecCCcc---hhHHHHHHHHcCeeEecCCHHHHHHHHHHHH
Confidence 444555444 788888888765 3458899999999999888888899988864
No 318
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=21.50 E-value=3.1e+02 Score=22.17 Aligned_cols=52 Identities=12% Similarity=0.118 Sum_probs=32.9
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC---------HHHHHHHhCCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN---------NKKLGEWAGLS 113 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s---------k~eLG~a~G~~ 113 (157)
--++.|.+=+.-+||...+..+.... ...++.|||++.+.. -..||+++|++
T Consensus 63 ~n~E~il~l~PDlVi~~~~~~~~~~~----~~L~~~gi~v~~~~~~~~~~~~~~i~~lg~~~g~~ 123 (260)
T PRK03379 63 MNLERIVALKPDLVLAWRGGNAERQV----DQLASLGIKVMWVDATSIEQIANALRQLAPWSPQP 123 (260)
T ss_pred CCHHHHHhcCCCEEEEecCCCcHHHH----HHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHcCCH
Confidence 34566666677788765443321222 333678999999852 24789999975
No 319
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=21.42 E-value=1.1e+02 Score=26.93 Aligned_cols=34 Identities=18% Similarity=0.320 Sum_probs=24.3
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. ....+.++|+++|||++.- ..|.+++-
T Consensus 283 vakG~~~--~A~~I~~~A~~~~vPi~~~---~~LAr~Ly 316 (347)
T TIGR00328 283 VAKGVDE--LALKIKEIARENNVPIVEN---PPLARALY 316 (347)
T ss_pred EEeeCcH--HHHHHHHHHHHcCCCEEeC---HHHHHHHH
Confidence 4444443 6778999999999999753 45676664
No 320
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.40 E-value=2e+02 Score=18.85 Aligned_cols=38 Identities=16% Similarity=0.182 Sum_probs=24.4
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++.+..|+. |.|++.|.. -...|+.+|++.|-.+..+.
T Consensus 20 l~~l~~G~~-l~V~~d~~~---s~~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 20 LPSLKPGEI-LEVISDCPQ---SINNIPIDARNHGYKVLAIE 57 (69)
T ss_pred HHcCCCCCE-EEEEecCch---HHHHHHHHHHHcCCEEEEEE
Confidence 333444543 445666543 34578999999999887654
No 321
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.38 E-value=3e+02 Score=21.13 Aligned_cols=40 Identities=13% Similarity=0.309 Sum_probs=21.9
Q ss_pred HHHHHHhcCCeeEEEE-cCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 58 EAAKALDRREAQLCVL-ADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 58 ~v~KaL~kgkakLVIl-A~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
+.++.+.+..+.-+|+ +.|.+. . ....+.+.+||++.++.
T Consensus 45 ~~i~~~~~~~vdgiii~~~~~~~-~----~~~~~~~~~ipvV~~~~ 85 (266)
T cd06278 45 AALRQLLQYRVDGVIVTSGTLSS-E----LAEECRRNGIPVVLINR 85 (266)
T ss_pred HHHHHHHHcCCCEEEEecCCCCH-H----HHHHHhhcCCCEEEECC
Confidence 3444444555554444 444333 1 23445677999998863
No 322
>cd07402 MPP_GpdQ Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain. GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosa
Probab=21.36 E-value=3.4e+02 Score=21.10 Aligned_cols=46 Identities=9% Similarity=0.185 Sum_probs=28.9
Q ss_pred HHHHHHHhcC--CeeEEEEcCCCCchhh---HHHHHHHHHhCCCCEEEeCC
Q psy16564 57 HEAAKALDRR--EAQLCVLADNCDEPAY---KKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 57 ~~v~KaL~kg--kakLVIlA~D~s~~~~---~~~l~~lc~~~~Ipvi~v~s 102 (157)
+++++.+++. ++.+||++.|...... -..+..+-++.++|++.+..
T Consensus 28 ~~~~~~i~~~~~~~d~vi~~GDl~~~~~~~~~~~~~~~l~~~~~p~~~v~G 78 (240)
T cd07402 28 EAVLAHINALHPRPDLVLVTGDLTDDGSPESYERLRELLAALPIPVYLLPG 78 (240)
T ss_pred HHHHHHHHhcCCCCCEEEECccCCCCCCHHHHHHHHHHHhhcCCCEEEeCC
Confidence 3455556554 8999999999554211 12333444556999999873
No 323
>PRK05597 molybdopterin biosynthesis protein MoeB; Validated
Probab=21.26 E-value=1.3e+02 Score=26.26 Aligned_cols=33 Identities=12% Similarity=0.144 Sum_probs=26.7
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
...+||.|.|-.+ ....+..+|.+++||++.-.
T Consensus 118 ~~DvVvd~~d~~~--~r~~~n~~c~~~~ip~v~~~ 150 (355)
T PRK05597 118 DADVILDGSDNFD--TRHLASWAAARLGIPHVWAS 150 (355)
T ss_pred CCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEE
Confidence 4789999998754 66678999999999998753
No 324
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=21.20 E-value=1.1e+02 Score=27.37 Aligned_cols=34 Identities=26% Similarity=0.334 Sum_probs=24.5
Q ss_pred EcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHHHHHhC
Q psy16564 73 LADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKLGEWAG 111 (157)
Q Consensus 73 lA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eLG~a~G 111 (157)
+|.=.+. +...|.+.|+++|||++. ...|.|++=
T Consensus 290 vAKG~d~--~A~~Ir~~A~e~~VPive---n~pLARaLy 323 (386)
T PRK12468 290 LAKGAGA--VALRIRELGAEHRIPLLE---APPLARALF 323 (386)
T ss_pred EEeeCcH--HHHHHHHHHHHcCCcEEe---CHHHHHHHH
Confidence 4555544 678899999999999985 345666654
No 325
>PF13728 TraF: F plasmid transfer operon protein
Probab=21.16 E-value=2.7e+02 Score=22.50 Aligned_cols=59 Identities=14% Similarity=0.223 Sum_probs=42.4
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCch-hhHHHHHHHHHhCCCCEEEeC-C------------HHHHHHHhCCC
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEP-AYKKLVQALCSEHQIPLIKVD-N------------NKKLGEWAGLS 113 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~-~~~~~l~~lc~~~~Ipvi~v~-s------------k~eLG~a~G~~ 113 (157)
-.+++++.|..+-.-++|..+||+-- ...-.+..++.++|++++.|. + ...+.+.+|..
T Consensus 110 ~~~~~l~~la~~~gL~~F~~~~C~~C~~~~pil~~~~~~yg~~v~~vs~DG~~~~~fp~~~~~~g~~~~l~v~ 182 (215)
T PF13728_consen 110 KRDKALKQLAQKYGLFFFYRSDCPYCQQQAPILQQFADKYGFSVIPVSLDGRPIPSFPNPRPDPGQAKRLGVK 182 (215)
T ss_pred HHHHHHHHHhhCeEEEEEEcCCCchhHHHHHHHHHHHHHhCCEEEEEecCCCCCcCCCCCCCCHHHHHHcCCC
Confidence 35678888886666666777888642 244568889999999999988 3 14566677764
No 326
>PRK06965 acetolactate synthase 3 catalytic subunit; Validated
Probab=21.09 E-value=2.2e+02 Score=26.26 Aligned_cols=45 Identities=9% Similarity=-0.006 Sum_probs=32.5
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.++.+.|++-+--++++-..+........+.+|++..++|++...
T Consensus 212 ~~~~~~L~~AkrPvil~G~g~~~~~a~~~l~~lae~~g~pv~tt~ 256 (587)
T PRK06965 212 RKAVSLLLSAKRPYIYTGGGVILANASRELRQLADLLGYPVTNTL 256 (587)
T ss_pred HHHHHHHHhcCCCEEEECCCccccchHHHHHHHHHHhCCCEEEcc
Confidence 445566666666777777777532456778999999999999653
No 327
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=21.08 E-value=2.7e+02 Score=21.73 Aligned_cols=41 Identities=15% Similarity=0.228 Sum_probs=21.6
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
++.+...++.-+|+....++ .....+. .+.+++||++.++.
T Consensus 50 i~~l~~~~vdgiIi~~~~~~-~~~~~~~-~~~~~~iPvV~~~~ 90 (275)
T cd06320 50 AENMINKGYKGLLFSPISDV-NLVPAVE-RAKKKGIPVVNVND 90 (275)
T ss_pred HHHHHHhCCCEEEECCCChH-HhHHHHH-HHHHCCCeEEEECC
Confidence 43444445555545432122 2333343 45678999998864
No 328
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.08 E-value=3e+02 Score=21.54 Aligned_cols=41 Identities=17% Similarity=0.139 Sum_probs=22.6
Q ss_pred HHHHHHhcCCeeEEEE-cCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVL-ADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIl-A~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+..+.+...++.-+|+ +.|.+. ....+. .+.+.+||++.++
T Consensus 51 ~~~~~l~~~~vDgiii~~~~~~~--~~~~i~-~~~~~gIpvV~~d 92 (274)
T cd06311 51 AQQDLLINRKIDALVILPFESAP--LTQPVA-KAKKAGIFVVVVD 92 (274)
T ss_pred HHHHHHHHcCCCEEEEeCCCchh--hHHHHH-HHHHCCCeEEEEc
Confidence 3444444444554444 445432 344444 4567899999876
No 329
>PRK10867 signal recognition particle protein; Provisional
Probab=21.05 E-value=1.7e+02 Score=26.56 Aligned_cols=35 Identities=14% Similarity=0.287 Sum_probs=26.8
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.-+.++++.|.....-...+..++++.+||++...
T Consensus 129 G~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~~~~ 163 (433)
T PRK10867 129 KKKVLLVAADVYRPAAIEQLKTLGEQIGVPVFPSG 163 (433)
T ss_pred CCcEEEEEccccchHHHHHHHHHHhhcCCeEEecC
Confidence 45677788887665566778889999999988753
No 330
>TIGR00513 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the alpha chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.00 E-value=1.3e+02 Score=26.29 Aligned_cols=33 Identities=9% Similarity=0.220 Sum_probs=24.3
Q ss_pred eeEEEEcCCCC---------------chh--hHHHHHHHHHhCCCCEEEe
Q psy16564 68 AQLCVLADNCD---------------EPA--YKKLVQALCSEHQIPLIKV 100 (157)
Q Consensus 68 akLVIlA~D~s---------------~~~--~~~~l~~lc~~~~Ipvi~v 100 (157)
-...|+|.|.. |.. ....+..+|.++++|++++
T Consensus 108 rpV~VIa~d~g~~~~e~~~~~~G~~~p~g~rKa~R~m~lA~~f~iPvVtl 157 (316)
T TIGR00513 108 RPVVVIGHQKGRDTKEKLRRNFGMPAPEGYRKALRLMKMAERFKMPIITF 157 (316)
T ss_pred EEEEEEEecCCccccccccccCCCCCHHHHHHHHHHHHHHHHcCCCEEEE
Confidence 46788999863 212 3356788999999999986
No 331
>cd01885 EF2 EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Seco
Probab=20.98 E-value=2.2e+02 Score=23.11 Aligned_cols=50 Identities=16% Similarity=0.056 Sum_probs=30.0
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
.++..+++.-.+-++++...-......+.+...+...++|++.+-+|.++
T Consensus 88 ~~~~~~l~~aD~~ilVvD~~~g~~~~t~~~l~~~~~~~~p~ilviNKiD~ 137 (222)
T cd01885 88 SEVTAALRLCDGALVVVDAVEGVCVQTETVLRQALKERVKPVLVINKIDR 137 (222)
T ss_pred HHHHHHHHhcCeeEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECCCc
Confidence 35677777666656665444322123334455566778998888766664
No 332
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=20.98 E-value=1.3e+02 Score=26.21 Aligned_cols=35 Identities=17% Similarity=0.072 Sum_probs=28.4
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN 103 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk 103 (157)
..-+||.|.|-. .....+..+|.++++|+++....
T Consensus 116 ~~DlVid~~Dn~--~~r~~ln~~~~~~~iP~i~~~~~ 150 (339)
T PRK07688 116 GVDLIIDATDNF--ETRFIVNDAAQKYGIPWIYGACV 150 (339)
T ss_pred CCCEEEEcCCCH--HHHHHHHHHHHHhCCCEEEEeee
Confidence 478999998864 46778999999999999986543
No 333
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=20.96 E-value=1.8e+02 Score=24.29 Aligned_cols=45 Identities=13% Similarity=0.200 Sum_probs=28.2
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCc-hhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDE-PAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~-~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
...+.+.|..+++..|+ ..-++. ......+..+|..++||++.+.
T Consensus 52 ~~~~~~~l~~~~v~~ii-g~~~s~~~~~~~~~~~v~~~~~iP~Is~~ 97 (362)
T cd06367 52 LLSVCDLLVVQVVAGVV-FSDPTDEEAVAQILDFTSAQTRIPVVGIS 97 (362)
T ss_pred HHHHHHHhcccceEEEE-ecCCCCccchhhhhhhhhhhhcCcEEEee
Confidence 34555666666555554 444444 1134567788999999999864
No 334
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=20.93 E-value=1.3e+02 Score=21.09 Aligned_cols=46 Identities=20% Similarity=0.163 Sum_probs=33.1
Q ss_pred eeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 53 AKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 53 v~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
..+..++... ....-+|+++..... ..+.+...+..+++|+..++.
T Consensus 34 ~~~~~~~~~~--~~~~Diil~~Pqv~~--~~~~i~~~~~~~~~pv~~I~~ 79 (96)
T cd05564 34 AVPESELEEY--IDDADVVLLGPQVRY--MLDEVKKKAAEYGIPVAVIDM 79 (96)
T ss_pred EecHHHHHHh--cCCCCEEEEChhHHH--HHHHHHHHhccCCCcEEEcCh
Confidence 4455555433 356789999988865 455678888889999998774
No 335
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=20.82 E-value=1.7e+02 Score=20.20 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=19.6
Q ss_pred CCeeEEEEcCCCCchh--hHHHHHHHHHhCC
Q psy16564 66 REAQLCVLADNCDEPA--YKKLVQALCSEHQ 94 (157)
Q Consensus 66 gkakLVIlA~D~s~~~--~~~~l~~lc~~~~ 94 (157)
.++.-||+|.|++.+- +..++..++..++
T Consensus 58 ~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~~ 88 (100)
T PF01751_consen 58 KKADEIIIATDPDREGELIAWEIIELLGKNN 88 (100)
T ss_dssp HSCSEEEEEC-SSHHHHHHHHHHHHHHHHHS
T ss_pred hhccEeeecCCCChHHHHHHHHHHHHHhHhC
Confidence 5689999999998732 5566666666544
No 336
>TIGR02346 chap_CCT_theta T-complex protein 1, theta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=20.75 E-value=3e+02 Score=25.32 Aligned_cols=51 Identities=16% Similarity=0.316 Sum_probs=33.9
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCH---HHHHHHhCC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNN---KKLGEWAGL 112 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk---~eLG~a~G~ 112 (157)
...++.|.+-.+.+||...+.++ ....++.+++|-++.-.+. ++|..++|-
T Consensus 269 ~~~l~~i~~~g~~lvi~~~~I~d-----~~~~~l~~~~I~av~~~~~~~l~~Ia~~tGa 322 (531)
T TIGR02346 269 EAYIKAIADSGVNVIVTGGSVGD-----MALHYCEKYNIMVLKIPSKFELRRLCKTVGA 322 (531)
T ss_pred HHHHHHHHHcCCcEEEECCCcCH-----HHHHHHHHCCcEEEecCCHHHHHHHHHHHCC
Confidence 34444555556789988888877 3344667899999886544 456666663
No 337
>COG4052 Uncharacterized protein related to methyl coenzyme M reductase subunit C [General function prediction only]
Probab=20.73 E-value=49 Score=28.43 Aligned_cols=66 Identities=15% Similarity=0.198 Sum_probs=44.8
Q ss_pred HHHHHHHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHHHH
Q psy16564 40 QQVLKTARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNKKL 106 (157)
Q Consensus 40 ~~lL~~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~eL 106 (157)
.|++++||-.|+=+.-..+-.+.|....--.||.-.+-++ =+++.-..|-+.-.||++..++.+++
T Consensus 105 ~NmIGLARG~Gr~is~l~e~ErrLieEHDlavf~~GsF~d-CI~~~K~~Lf~~i~iPvvVtGgPeei 170 (310)
T COG4052 105 TNMIGLARGMGRRISQLREYERRLIEEHDLAVFVFGSFED-CIKKKKPHLFEGIEIPVVVTGGPEEI 170 (310)
T ss_pred cchhhhhhhccchhHHHHHHHHHhhhhcceEEEEecCHHH-HHhhcCCcccccccccEEEeCCcccc
Confidence 4799999999998888888888777665555665554332 23332233445578999999876664
No 338
>PRK06048 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=20.72 E-value=2.4e+02 Score=25.84 Aligned_cols=46 Identities=11% Similarity=0.097 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+++.+.|.+.+-.++++-..+....-...+.+||++.++|++...
T Consensus 197 i~~~a~~L~~AkrPvil~G~g~~~~~a~~~l~~lae~lg~pV~tt~ 242 (561)
T PRK06048 197 IKRAAELIMKAERPIIYAGGGVISSNASEELVELAETIPAPVTTTL 242 (561)
T ss_pred HHHHHHHHHhCCCCEEEECCCcccccHHHHHHHHHHHhCCCEEEcc
Confidence 4455566666666666666666533456778999999999999653
No 339
>PRK00098 GTPase RsgA; Reviewed
Probab=20.71 E-value=1.4e+02 Score=25.19 Aligned_cols=24 Identities=25% Similarity=0.097 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCCEEEeCCHHHHH
Q psy16564 84 KLVQALCSEHQIPLIKVDNNKKLG 107 (157)
Q Consensus 84 ~~l~~lc~~~~Ipvi~v~sk~eLG 107 (157)
..+...++..++|++.+.+|.+|-
T Consensus 101 dr~L~~~~~~~ip~iIVlNK~DL~ 124 (298)
T PRK00098 101 DRFLVLAEANGIKPIIVLNKIDLL 124 (298)
T ss_pred HHHHHHHHHCCCCEEEEEEhHHcC
Confidence 344455778899999999998883
No 340
>cd07388 MPP_Tt1561 Thermus thermophilus Tt1561 and related proteins, metallophosphatase domain. This family includes bacterial proteins related to Tt1561 (also known as Aq1956 in Aquifex aeolicus), an uncharacterized Thermus thermophilus protein. The conserved domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets,
Probab=20.57 E-value=3.2e+02 Score=22.37 Aligned_cols=39 Identities=23% Similarity=0.257 Sum_probs=25.2
Q ss_pred HHhcCCeeEEEEcCCCCc-----hhhHHHHHHHHHhCCCCEEEeC
Q psy16564 62 ALDRREAQLCVLADNCDE-----PAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 62 aL~kgkakLVIlA~D~s~-----~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.++...+.+||++.|... ..+...+..+ ...++|++.+.
T Consensus 26 ~~~~~~~D~vv~~GDl~~~g~~~~~~~~~l~~l-~~l~~pv~~V~ 69 (224)
T cd07388 26 LAPETGADAIVLIGNLLPKAAKSEDYAAFFRIL-GEAHLPTFYVP 69 (224)
T ss_pred HHhhcCCCEEEECCCCCCCCCCHHHHHHHHHHH-HhcCCceEEEc
Confidence 334467899999999744 2234433333 45578999988
No 341
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=20.54 E-value=2.4e+02 Score=17.78 Aligned_cols=19 Identities=16% Similarity=0.174 Sum_probs=11.6
Q ss_pred HHHHHHHHHhCCCCEEEeC
Q psy16564 83 KKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 83 ~~~l~~lc~~~~Ipvi~v~ 101 (157)
......+-++++||+..+.
T Consensus 13 C~~ak~~L~~~~i~~~~i~ 31 (75)
T cd03418 13 CVRAKALLDKKGVDYEEID 31 (75)
T ss_pred HHHHHHHHHHCCCcEEEEE
Confidence 3445555566777777665
No 342
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=20.50 E-value=2.3e+02 Score=26.32 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+++.+.|++.+--++++-.-+....-...|.+||++.++||+...
T Consensus 215 ~~~~~~L~~AkrPvI~~G~g~~~~~a~~~l~~lae~l~~pV~tt~ 259 (616)
T PRK07418 215 NAALKLIEEAERPLLYVGGGAISAGAHAELKELAERFQIPVTTTL 259 (616)
T ss_pred HHHHHHHHhCCCCEEEECCCcCcccHHHHHHHHHHHHCCCEEEcc
Confidence 445556666555566655555422456678999999999999644
No 343
>COG4087 Soluble P-type ATPase [General function prediction only]
Probab=20.50 E-value=2e+02 Score=22.61 Aligned_cols=51 Identities=16% Similarity=0.155 Sum_probs=38.9
Q ss_pred HHHhcCCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 45 TARAHDGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 45 ~A~~agklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
+-...|++..-+.++++.|..- +...|-+.|--- .+.++++.-|||+..++
T Consensus 24 tiatgGklf~ev~e~iqeL~d~-V~i~IASgDr~g-----sl~~lae~~gi~~~rv~ 74 (152)
T COG4087 24 TIATGGKLFSEVSETIQELHDM-VDIYIASGDRKG-----SLVQLAEFVGIPVERVF 74 (152)
T ss_pred EEccCcEEcHhhHHHHHHHHHh-heEEEecCCcch-----HHHHHHHHcCCceeeee
Confidence 3345688888999999999776 776655555443 67889999999999876
No 344
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=20.50 E-value=2.8e+02 Score=21.62 Aligned_cols=61 Identities=11% Similarity=0.112 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhcCCcee----e-----HHHHHHHHhcCCeeEEEEcC-CCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 38 ALQQVLKTARAHDGLAK----G-----LHEAAKALDRREAQLCVLAD-NCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 38 ~L~~lL~~A~~agklv~----G-----~~~v~KaL~kgkakLVIlA~-D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+..+...|+..|.-+. + ....++.+..+++.-+|+.. +.+. ..+...+++.+||++.+++
T Consensus 17 ~~~~i~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~----~~~~~~~~~~~ipvV~i~~ 87 (269)
T cd06281 17 LFSGAEDRLRAAGYSLLIANSLNDPERELEILRSFEQRRMDGIIIAPGDERD----PELVDALASLDLPIVLLDR 87 (269)
T ss_pred HHHHHHHHHHHcCCEEEEEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCCc----HHHHHHHHhCCCCEEEEec
Confidence 34444555555554311 1 33556666666666555543 3221 1234456778999988863
No 345
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=20.48 E-value=3e+02 Score=21.52 Aligned_cols=41 Identities=20% Similarity=0.290 Sum_probs=22.9
Q ss_pred HHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 60 AKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 60 ~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
++.+...++..+|+...... .....+ ..+.+++||++.+++
T Consensus 49 i~~~~~~~vdgiii~~~~~~-~~~~~~-~~~~~~~ipvV~~~~ 89 (270)
T cd06308 49 IENFIRQGVDLLIISPNEAA-PLTPVV-EEAYRAGIPVILLDR 89 (270)
T ss_pred HHHHHHhCCCEEEEecCchh-hchHHH-HHHHHCCCCEEEeCC
Confidence 34444556666666543222 223333 345678999998864
No 346
>cd07035 TPP_PYR_POX_like Pyrimidine (PYR) binding domain of POX and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) and related protiens subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. For glyoxylate carboligase, which belongs to this subfamily, but lacks this conserved glutamate, the rate of the initial TPP activation step is reduced but the ensuing steps of the enzymic reaction proceed efficiently. The PYR and PP domains have a common fold, but do not share strong sequence conservatio
Probab=20.44 E-value=3.1e+02 Score=20.03 Aligned_cols=73 Identities=18% Similarity=0.168 Sum_probs=43.8
Q ss_pred HHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC-CHHHHHHHhCCCccccCCCccceeeeEEEEEe-cCc
Q psy16564 59 AAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD-NNKKLGEWAGLSKLDNMGKARKVVGCSCVVIK-VRN 136 (157)
Q Consensus 59 v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~-sk~eLG~a~G~~~~~~~gk~rki~~~s~vaI~-D~g 136 (157)
+.+.|++..++.||---+.. ....+..+- +.++.++... ...-.+.|.|.. ..+|++ +++.++ .+|
T Consensus 3 i~~~L~~~Gv~~vfg~pg~~---~~~l~~~~~-~~~~~~i~~~~E~~A~~~A~g~~--~~~~~~------~v~~~~~gpG 70 (155)
T cd07035 3 LVEALKAEGVDHVFGVPGGA---ILPLLDALA-RSGIRYILVRHEQGAVGMADGYA--RATGKP------GVVLVTSGPG 70 (155)
T ss_pred HHHHHHHcCCCEEEECCCCc---hHHHHHHhc-cCCCEEEEeCCHHHHHHHHHHHH--HHHCCC------EEEEEcCCCc
Confidence 45677776778887766643 233333333 6778888877 444555666654 122333 455555 999
Q ss_pred hhHHhhh
Q psy16564 137 WFLIICS 143 (157)
Q Consensus 137 ~~~~~~~ 143 (157)
+.+.+..
T Consensus 71 ~~n~~~~ 77 (155)
T cd07035 71 LTNAVTG 77 (155)
T ss_pred HHHHHHH
Confidence 9886643
No 347
>TIGR01457 HAD-SF-IIA-hyp2 HAD-superfamily subfamily IIA hydrolase, TIGR01457. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram positive (low-GC) bacteria. Sequences found in this model are annotated variously as related to NagD or 4-nitrophenyl phosphatase, and this hypothetical equivalog, of all of those within the Class IIA subfamily, is most closely related to the E. coli NagD enzyme and the PGP_euk equivalog (TIGR01452). However, there is presently no evidence that this hypothetical equivalog has the same function of either those.
Probab=20.43 E-value=2.2e+02 Score=23.17 Aligned_cols=46 Identities=13% Similarity=0.204 Sum_probs=30.5
Q ss_pred CCceeeHHHHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCE
Q psy16564 50 DGLAKGLHEAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPL 97 (157)
Q Consensus 50 gklv~G~~~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipv 97 (157)
+..+.|..++++.|++....++|+.++++. ... .+...-+..++++
T Consensus 16 ~~~i~~a~~~l~~l~~~g~~~~~~Tnn~~r-~~~-~~~~~l~~~g~~~ 61 (249)
T TIGR01457 16 KERIPEAETFVHELQKRDIPYLFVTNNSTR-TPE-SVAEMLASFDIPA 61 (249)
T ss_pred CeeCcCHHHHHHHHHHCCCeEEEEeCCCCC-CHH-HHHHHHHHcCCCC
Confidence 456678889999998888889988887754 222 2333334455554
No 348
>TIGR01458 HAD-SF-IIA-hyp3 HAD-superfamily subfamily IIA hydrolase, TIGR01458. This hypothetical equivalog is a member of the IIA subfamily (TIGR01460) of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. One sequence (GP|10716807) has been annotated as a "phospholysine phosphohistidine inorganic pyrophosphatase," probably in reference to studies on similarly described (but unsequenced) enzymes from bovine and rat tissues. However, the supporting information for this annotation has never been published.
Probab=20.42 E-value=2.3e+02 Score=23.20 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=23.7
Q ss_pred ceeeHHHHHHHHhcCCeeEEEEcCCCCc
Q psy16564 52 LAKGLHEAAKALDRREAQLCVLADNCDE 79 (157)
Q Consensus 52 lv~G~~~v~KaL~kgkakLVIlA~D~s~ 79 (157)
..-|..++++.|++...+++|+.++...
T Consensus 22 ~~~~a~~al~~l~~~G~~~~~~Tn~~~~ 49 (257)
T TIGR01458 22 AVPGSQEAVKRLRGASVKVRFVTNTTKE 49 (257)
T ss_pred cCCCHHHHHHHHHHCCCeEEEEECCCCC
Confidence 7789999999999877888888887766
No 349
>PRK06091 membrane protein FdrA; Validated
Probab=20.34 E-value=2.1e+02 Score=27.07 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=31.2
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDN 102 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~s 102 (157)
.+.+++++| ...+|+++..+. .....+.++|+++|+.++=-.+
T Consensus 133 al~ea~~~G-~~viI~S~gfg~-~~E~~L~e~Ar~~GlrvmGPNC 175 (555)
T PRK06091 133 LAEQALDRN-LNVMMFSDNVTL-EDEIRLKTRAREKGLLVMGPDC 175 (555)
T ss_pred HHHHHHHcC-CeEEEEcCCCCH-HHHHHHHHHHHHcCCEEECCCC
Confidence 455666677 567778887865 6777888999999987764444
No 350
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=20.33 E-value=1.5e+02 Score=24.36 Aligned_cols=53 Identities=19% Similarity=0.340 Sum_probs=27.1
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC------CHHHHHHHhC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD------NNKKLGEWAG 111 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~------sk~eLG~a~G 111 (157)
...+.++.....-|.++.=.+- .+...|..+|...+||+..++ +.+++..+++
T Consensus 82 ~L~~~~~~~~~~~~~~~~P~d~-~l~~~l~~~~~~~~i~~~~~~~~~Fl~s~~~f~~~~~ 140 (224)
T PF04244_consen 82 ALARALKQHGIDRLHVMEPGDY-RLEQRLESLAQQLGIPLEVLEDPHFLTSREEFAEWFE 140 (224)
T ss_dssp HHHHHHHHH----EEEE--S-H-HHHHHHHH----SSS-EEEE--TTSSS-HHHHHHHHT
T ss_pred HHHHHHHHcCCCEEEEECCCCH-HHHHHHHhhhcccCCceEEeCCCCccCCHHHHHHHHc
Confidence 3335555555666666655554 788888888888889888765 4567777777
No 351
>PRK08978 acetolactate synthase 2 catalytic subunit; Reviewed
Probab=20.17 E-value=2.4e+02 Score=25.62 Aligned_cols=44 Identities=7% Similarity=0.104 Sum_probs=28.9
Q ss_pred HHHHHHhcCCeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 58 EAAKALDRREAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 58 ~v~KaL~kgkakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
++...|.+.+--++++-..+....-...+.+||+..++|++...
T Consensus 188 ~~~~~L~~AkrPvIl~G~g~~~~~a~~~l~~lae~l~~Pv~tt~ 231 (548)
T PRK08978 188 QARALLAQAKKPVLYVGGGVGMAGAVPALREFLAATGMPAVATL 231 (548)
T ss_pred HHHHHHHcCCCCEEEECCCccccchHHHHHHHHHHHCCCEEEcc
Confidence 34445655555555555545432346678999999999999753
No 352
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.
Probab=20.16 E-value=2.8e+02 Score=23.40 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=36.0
Q ss_pred eHHHHHHHHhcCCeeEEEEcCCCCchh-hHHHHHHHHHhCCCCEEEeC
Q psy16564 55 GLHEAAKALDRREAQLCVLADNCDEPA-YKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 55 G~~~v~KaL~kgkakLVIlA~D~s~~~-~~~~l~~lc~~~~Ipvi~v~ 101 (157)
-..++++.|.+.-.-+.|..+||+--. ..-.|..++.+|||+++-|.
T Consensus 140 ~~~~~i~~la~~~gL~fFy~~~C~~C~~~apil~~fa~~ygi~v~~VS 187 (256)
T TIGR02739 140 QKEKAIQQLSQSYGLFFFYRGKSPISQKMAPVIQAFAKEYGISVIPIS 187 (256)
T ss_pred HHHHHHHHHHhceeEEEEECCCCchhHHHHHHHHHHHHHhCCeEEEEe
Confidence 356778888877778888888886421 34567789999999999986
No 353
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=20.10 E-value=3.4e+02 Score=21.16 Aligned_cols=40 Identities=15% Similarity=0.175 Sum_probs=23.9
Q ss_pred HHHHHHHhcCCeeEEEE-cCCCCchhhHHHHHHHHHhCCCCEEEeC
Q psy16564 57 HEAAKALDRREAQLCVL-ADNCDEPAYKKLVQALCSEHQIPLIKVD 101 (157)
Q Consensus 57 ~~v~KaL~kgkakLVIl-A~D~s~~~~~~~l~~lc~~~~Ipvi~v~ 101 (157)
.+..+.+...++.-+|+ +.+.++ .. ...+...+||++.++
T Consensus 54 ~~~~~~l~~~~~dgiii~~~~~~~-~~----~~~~~~~~ipvV~~~ 94 (275)
T cd06295 54 DWLARYLASGRADGVILIGQHDQD-PL----PERLAETGLPFVVWG 94 (275)
T ss_pred HHHHHHHHhCCCCEEEEeCCCCCh-HH----HHHHHhCCCCEEEEC
Confidence 35566666666665555 434333 22 345578899999875
No 354
>PRK10637 cysG siroheme synthase; Provisional
Probab=20.09 E-value=1.3e+02 Score=27.08 Aligned_cols=36 Identities=22% Similarity=0.175 Sum_probs=28.9
Q ss_pred CeeEEEEcCCCCchhhHHHHHHHHHhCCCCEEEeCCHH
Q psy16564 67 EAQLCVLADNCDEPAYKKLVQALCSEHQIPLIKVDNNK 104 (157)
Q Consensus 67 kakLVIlA~D~s~~~~~~~l~~lc~~~~Ipvi~v~sk~ 104 (157)
.+.|||.|.|-.. +-..+-..|++.+|++..+++..
T Consensus 72 ~~~lv~~at~d~~--~n~~i~~~a~~~~~lvN~~d~~~ 107 (457)
T PRK10637 72 TCWLAIAATDDDA--VNQRVSEAAEARRIFCNVVDAPK 107 (457)
T ss_pred CCEEEEECCCCHH--HhHHHHHHHHHcCcEEEECCCcc
Confidence 3778888877654 77789999999999998877653
No 355
>PHA02546 47 endonuclease subunit; Provisional
Probab=20.08 E-value=2.8e+02 Score=23.78 Aligned_cols=46 Identities=13% Similarity=0.075 Sum_probs=29.1
Q ss_pred HHHHHHHHhcCCeeEEEEcCCCCchh------hHHHHHH----HHHhCCCCEEEeC
Q psy16564 56 LHEAAKALDRREAQLCVLADNCDEPA------YKKLVQA----LCSEHQIPLIKVD 101 (157)
Q Consensus 56 ~~~v~KaL~kgkakLVIlA~D~s~~~------~~~~l~~----lc~~~~Ipvi~v~ 101 (157)
..+++..++..++.+||+|.|.-+.. ....+.. .-.+.+||++.+.
T Consensus 28 l~~ii~~a~~~~vD~VliaGDlfD~~~~~~~~~~~~~~~~l~~~L~~~gi~v~~I~ 83 (340)
T PHA02546 28 IKQAIEYSKAHGITTWIQLGDTFDVRKAITQNTMNFVREKIFDLLKEAGITLHVLV 83 (340)
T ss_pred HHHHHHHHHHcCCCEEEECCcccCCCCCCCHHHHHHHHHHHHHHHHHCCCeEEEEc
Confidence 34455666778899999999965421 1122222 2335689999986
Done!