Query psy8849
Match_columns 112
No_of_seqs 134 out of 1023
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 20:48:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8849.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8849hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0799 Uncharacterized homolo 100.0 4.5E-48 9.7E-53 267.5 13.0 110 1-110 1-110 (115)
2 PRK11538 ribosome-associated p 100.0 1.3E-46 2.8E-51 257.1 13.4 105 1-105 1-105 (105)
3 TIGR00090 iojap_ybeB iojap-lik 100.0 3.5E-45 7.5E-50 247.4 12.3 98 7-104 2-99 (99)
4 PF02410 Oligomerisation: Olig 100.0 2.6E-43 5.6E-48 238.1 11.1 99 6-104 1-100 (100)
5 KOG3212|consensus 100.0 5E-32 1.1E-36 200.3 11.2 102 6-107 70-174 (208)
6 PRK10678 moaE molybdopterin gu 85.4 10 0.00022 27.4 8.2 75 4-79 61-138 (150)
7 PRK05568 flavodoxin; Provision 84.5 4.3 9.3E-05 27.6 5.9 54 2-56 14-77 (142)
8 COG0314 MoaE Molybdopterin con 81.0 18 0.00039 26.1 8.1 79 3-82 60-141 (149)
9 PRK09271 flavodoxin; Provision 80.7 16 0.00035 25.7 7.8 73 2-77 13-98 (160)
10 cd00756 MoaE MoaE family. Memb 79.2 18 0.0004 25.0 8.2 74 4-78 48-124 (124)
11 PRK03467 hypothetical protein; 75.7 5.9 0.00013 28.5 4.3 53 1-53 1-62 (144)
12 PRK05569 flavodoxin; Provision 75.4 8.9 0.00019 26.0 5.0 53 2-55 14-76 (141)
13 PF06778 Chlor_dismutase: Chlo 74.8 30 0.00066 25.8 8.1 54 5-58 5-62 (193)
14 PF00352 TBP: Transcription fa 71.3 8 0.00017 24.8 3.8 29 35-63 57-86 (86)
15 TIGR01755 flav_wrbA NAD(P)H:qu 69.2 22 0.00048 26.0 6.2 53 3-55 14-94 (197)
16 COG4576 CcmL Carbon dioxide co 68.7 6.6 0.00014 26.1 2.9 31 19-50 38-68 (89)
17 PF14492 EFG_II: Elongation Fa 68.6 5.7 0.00012 24.9 2.6 64 36-101 6-70 (75)
18 PRK11104 hemG protoporphyrinog 67.9 15 0.00034 26.5 5.1 40 2-43 13-56 (177)
19 PRK00394 transcription factor; 67.8 12 0.00025 27.7 4.4 32 35-66 54-86 (179)
20 PRK06756 flavodoxin; Provision 66.9 38 0.00082 23.2 6.7 41 2-43 14-59 (148)
21 PRK14493 putative bifunctional 66.8 51 0.0011 25.7 8.1 73 5-78 195-270 (274)
22 PRK06703 flavodoxin; Provision 66.4 20 0.00042 24.7 5.2 41 2-43 14-58 (151)
23 PRK03767 NAD(P)H:quinone oxido 65.7 16 0.00035 26.6 4.9 53 3-55 15-95 (200)
24 COG3565 Predicted dioxygenase 65.5 6.7 0.00014 27.8 2.6 26 68-93 28-55 (138)
25 TIGR01753 flav_short flavodoxi 65.1 23 0.00049 23.5 5.2 41 2-43 11-55 (140)
26 PRK11921 metallo-beta-lactamas 64.3 23 0.0005 28.6 5.9 42 2-43 260-310 (394)
27 cd07950 Gallate_Doxase_N The N 63.8 27 0.00058 27.3 6.0 97 6-102 36-168 (277)
28 PRK10984 DNA-binding transcrip 63.7 7.4 0.00016 27.5 2.5 43 55-99 12-55 (127)
29 PRK15360 pathogenicity island 63.3 15 0.00032 26.4 4.0 45 35-83 86-130 (137)
30 KOG3348|consensus 63.2 29 0.00063 22.9 5.1 29 16-44 15-44 (85)
31 TIGR01689 EcbF-BcbF capsule bi 63.0 17 0.00038 25.2 4.4 31 36-66 42-80 (126)
32 smart00506 A1pp Appr-1"-p proc 62.9 5.1 0.00011 26.7 1.6 64 34-97 14-85 (133)
33 cd00652 TBP_TLF TATA box bindi 62.8 16 0.00035 26.7 4.4 34 33-66 53-87 (174)
34 PF00258 Flavodoxin_1: Flavodo 62.6 13 0.00027 25.2 3.6 40 2-42 9-54 (143)
35 cd04516 TBP_eukaryotes eukaryo 62.4 17 0.00037 26.7 4.4 31 35-65 55-86 (174)
36 PRK12276 putative heme peroxid 62.3 41 0.00088 26.3 6.7 51 5-57 35-91 (248)
37 PF13277 YmdB: YmdB-like prote 62.2 11 0.00024 29.6 3.5 62 37-98 30-118 (253)
38 PRK09267 flavodoxin FldA; Vali 62.2 17 0.00037 25.5 4.3 39 2-43 14-56 (169)
39 PRK03669 mannosyl-3-phosphogly 60.9 10 0.00022 28.8 3.1 21 35-55 41-61 (271)
40 cd02042 ParA ParA and ParB of 60.3 35 0.00075 21.6 5.2 54 50-103 15-82 (104)
41 PRK08105 flavodoxin; Provision 59.5 26 0.00057 24.6 4.8 42 2-44 14-59 (149)
42 PF02391 MoaE: MoaE protein; 59.3 38 0.00083 23.0 5.5 58 4-61 56-115 (117)
43 COG1066 Sms Predicted ATP-depe 57.7 64 0.0014 27.4 7.4 91 6-100 156-251 (456)
44 PLN02390 molybdopterin synthas 57.6 58 0.0013 22.2 8.3 65 5-70 38-104 (111)
45 cd07366 3MGA_Dioxygenase Subun 57.2 27 0.00059 28.2 5.1 96 7-102 75-223 (328)
46 PF07417 Crl: Transcriptional 57.0 6 0.00013 27.9 1.2 43 55-99 10-53 (125)
47 PRK10513 sugar phosphate phosp 57.0 12 0.00027 27.9 3.0 20 35-54 37-56 (270)
48 PRK07308 flavodoxin; Validated 56.9 46 0.001 22.7 5.7 42 2-44 14-59 (146)
49 PLN00062 TATA-box-binding prot 56.7 24 0.00052 26.1 4.4 31 35-65 55-86 (179)
50 smart00877 BMC Bacterial micro 56.6 40 0.00086 21.1 4.8 43 17-61 21-63 (75)
51 TIGR01487 SPP-like sucrose-pho 55.4 14 0.00029 26.9 2.9 19 35-53 35-53 (215)
52 PF01656 CbiA: CobQ/CobB/MinD/ 55.2 67 0.0015 22.2 8.6 72 6-93 82-161 (195)
53 PF05651 Diacid_rec: Putative 55.1 28 0.00061 24.4 4.4 38 3-47 2-39 (135)
54 PF07801 DUF1647: Protein of u 54.3 27 0.00058 25.1 4.2 46 11-56 34-81 (142)
55 TIGR00254 GGDEF diguanylate cy 54.3 59 0.0013 21.3 7.6 56 3-62 56-111 (165)
56 PF07725 LRR_3: Leucine Rich R 54.2 5.6 0.00012 19.4 0.4 11 97-107 9-19 (20)
57 PRK15031 5-carboxymethyl-2-hyd 54.2 73 0.0016 22.3 6.6 60 3-62 18-91 (126)
58 PF04455 Saccharop_dh_N: LOR/S 53.5 68 0.0015 21.7 6.7 56 6-61 17-74 (103)
59 PRK13363 protocatechuate 4,5-d 53.3 31 0.00068 27.9 4.9 95 7-101 77-226 (335)
60 PRK08367 porA pyruvate ferredo 53.2 66 0.0014 26.5 6.8 42 15-57 244-285 (394)
61 PRK01158 phosphoglycolate phos 53.0 17 0.00037 26.3 3.1 18 35-52 37-54 (230)
62 TIGR03884 sel_bind_Methan sele 52.8 52 0.0011 21.2 4.9 38 2-43 26-63 (74)
63 TIGR01754 flav_RNR ribonucleot 52.5 41 0.00089 22.9 4.8 41 2-43 13-60 (140)
64 PF04430 DUF498: Protein of un 52.4 7.7 0.00017 26.0 1.1 30 33-65 53-82 (110)
65 PRK01964 4-oxalocrotonate taut 52.0 42 0.00091 19.8 4.3 27 39-65 8-35 (64)
66 TIGR00099 Cof-subfamily Cof su 51.3 18 0.00038 26.9 3.0 19 35-53 33-51 (256)
67 PRK10976 putative hydrolase; P 51.1 16 0.00034 27.3 2.7 20 35-54 36-55 (266)
68 PF01820 Dala_Dala_lig_N: D-al 50.9 20 0.00043 24.2 2.9 47 36-82 3-51 (117)
69 PRK05452 anaerobic nitric oxid 50.4 58 0.0013 27.4 6.2 42 2-43 264-314 (479)
70 PRK10530 pyridoxal phosphate ( 50.0 18 0.00039 26.9 2.8 19 35-53 37-55 (272)
71 TIGR01752 flav_long flavodoxin 49.5 41 0.0009 23.8 4.6 39 2-43 12-54 (167)
72 PF14839 DOR: DOR family 49.3 12 0.00026 28.7 1.8 13 72-84 4-16 (216)
73 PF00936 BMC: BMC domain; Int 49.0 28 0.0006 21.8 3.2 44 17-62 22-65 (75)
74 TIGR02461 osmo_MPG_phos mannos 48.7 22 0.00047 26.5 3.1 20 34-53 31-50 (225)
75 TIGR01485 SPP_plant-cyano sucr 48.7 44 0.00095 24.9 4.8 38 36-88 39-76 (249)
76 smart00267 GGDEF diguanylate c 48.4 72 0.0016 20.5 7.4 55 3-61 57-111 (163)
77 COG0561 Cof Predicted hydrolas 48.2 18 0.0004 27.0 2.7 22 34-55 36-57 (264)
78 PRK14481 dihydroxyacetone kina 48.0 1.5E+02 0.0033 24.1 8.3 87 2-104 230-319 (331)
79 COG0716 FldA Flavodoxins [Ener 48.0 28 0.00061 24.2 3.5 68 37-104 4-72 (151)
80 TIGR02463 MPGP_rel mannosyl-3- 47.6 20 0.00044 25.9 2.8 21 35-55 33-53 (221)
81 cd07368 PhnC_Bs_like PhnC is a 47.5 33 0.00071 26.7 4.0 96 7-102 35-167 (277)
82 TIGR01482 SPP-subfamily Sucros 46.7 23 0.0005 25.5 2.9 19 35-53 32-50 (225)
83 cd04887 ACT_MalLac-Enz ACT_Mal 46.3 61 0.0013 19.1 5.7 50 6-56 12-62 (74)
84 cd04518 TBP_archaea archaeal T 46.1 43 0.00093 24.6 4.3 32 35-66 55-87 (174)
85 cd00491 4Oxalocrotonate_Tautom 46.1 48 0.001 18.8 3.8 27 39-65 7-34 (58)
86 PRK15126 thiamin pyrimidine py 45.4 19 0.00042 27.0 2.4 19 35-53 36-54 (272)
87 cd01949 GGDEF Diguanylate-cycl 45.2 80 0.0017 20.1 7.0 55 3-61 54-108 (158)
88 TIGR03371 cellulose_yhjQ cellu 45.0 1.2E+02 0.0026 22.1 7.0 41 20-60 115-163 (246)
89 PRK02289 4-oxalocrotonate taut 44.8 40 0.00087 19.9 3.3 27 39-65 8-35 (60)
90 PF13291 ACT_4: ACT domain; PD 44.6 50 0.0011 20.1 3.9 51 5-56 18-70 (80)
91 PF08282 Hydrolase_3: haloacid 44.2 24 0.00052 25.1 2.7 18 36-53 33-50 (254)
92 COG2199 c-di-GMP synthetase (d 44.0 1.1E+02 0.0023 21.2 7.1 55 4-62 75-129 (181)
93 PF13481 AAA_25: AAA domain; P 44.0 73 0.0016 22.2 5.2 55 5-65 127-181 (193)
94 PF10469 AKAP7_NLS: AKAP7 2'5' 43.7 1.3E+02 0.0027 22.0 7.4 45 21-65 80-132 (209)
95 PF12724 Flavodoxin_5: Flavodo 43.6 36 0.00078 23.4 3.4 48 2-50 10-60 (143)
96 TIGR01486 HAD-SF-IIB-MPGP mann 43.4 25 0.00055 26.2 2.8 18 36-53 34-51 (256)
97 COG2257 Uncharacterized homolo 43.4 39 0.00085 22.6 3.3 25 37-66 24-48 (92)
98 PRK14126 cell division protein 43.2 35 0.00076 22.1 3.1 27 35-62 17-43 (85)
99 PRK09004 FMN-binding protein M 42.5 56 0.0012 22.8 4.3 42 2-44 14-57 (146)
100 TIGR02363 dhaK1 dihydroxyaceto 42.5 1.9E+02 0.004 23.6 8.3 87 2-104 231-320 (329)
101 PRK00745 4-oxalocrotonate taut 42.3 63 0.0014 18.7 3.9 40 40-79 9-53 (62)
102 PRK00907 hypothetical protein; 41.5 1E+02 0.0022 20.3 6.4 53 3-56 27-83 (92)
103 PF05116 S6PP: Sucrose-6F-phos 41.3 64 0.0014 24.4 4.7 38 36-88 37-74 (247)
104 PF07056 DUF1335: Protein of u 41.3 63 0.0014 22.9 4.3 31 34-64 25-61 (131)
105 PRK08366 vorA 2-ketoisovalerat 41.3 1E+02 0.0023 25.3 6.2 25 33-57 259-283 (390)
106 PRK00192 mannosyl-3-phosphogly 41.3 27 0.00058 26.5 2.7 19 36-54 39-57 (273)
107 PRK04998 hypothetical protein; 41.0 98 0.0021 19.9 5.8 53 4-56 26-79 (88)
108 TIGR00013 taut 4-oxalocrotonat 41.0 53 0.0011 19.1 3.5 27 39-65 8-35 (63)
109 cd00248 Mth938-like Mth938-lik 40.6 16 0.00035 24.5 1.2 29 34-65 53-81 (109)
110 cd01983 Fer4_NifH The Fer4_Nif 40.2 66 0.0014 19.0 3.9 49 50-103 14-79 (99)
111 PF10087 DUF2325: Uncharacteri 39.8 1E+02 0.0022 19.8 5.2 62 5-69 10-81 (97)
112 PF00990 GGDEF: GGDEF domain; 39.8 1E+02 0.0023 19.9 7.3 57 4-64 56-112 (161)
113 TIGR01174 ftsA cell division p 39.8 1.9E+02 0.0041 22.9 7.7 43 35-83 149-204 (371)
114 cd06169 BMC Bacterial Micro-Co 39.8 55 0.0012 19.6 3.4 39 17-56 21-59 (62)
115 PRK11477 carbohydrate diacid t 39.5 59 0.0013 26.0 4.5 37 3-46 7-43 (385)
116 PRK12359 flavodoxin FldB; Prov 39.4 82 0.0018 22.9 4.9 38 3-43 14-55 (172)
117 COG1444 Predicted P-loop ATPas 39.4 82 0.0018 28.5 5.6 31 35-65 261-291 (758)
118 PRK02220 4-oxalocrotonate taut 39.3 77 0.0017 18.3 4.3 27 39-65 8-35 (61)
119 PF01250 Ribosomal_S6: Ribosom 39.1 63 0.0014 20.5 3.8 48 35-82 4-64 (92)
120 PRK09627 oorA 2-oxoglutarate-a 38.9 1.1E+02 0.0025 24.9 6.1 25 33-57 274-298 (375)
121 TIGR02471 sucr_syn_bact_C sucr 38.9 34 0.00074 25.2 2.8 19 36-54 32-50 (236)
122 PF02780 Transketolase_C: Tran 37.6 45 0.00098 22.2 3.1 24 34-57 10-33 (124)
123 COG4680 Uncharacterized protei 37.2 32 0.00068 23.2 2.2 24 74-97 53-80 (98)
124 cd01614 EutN_CcmL Ethanolamine 37.1 55 0.0012 21.3 3.3 30 18-48 37-66 (83)
125 COG3027 zapA Cell division pro 37.0 43 0.00094 22.7 2.9 30 35-64 12-41 (105)
126 cd05569 PTS_IIB_fructose PTS_I 36.8 81 0.0018 20.5 4.1 29 37-65 3-31 (96)
127 PRK13365 protocatechuate 4,5-d 36.8 58 0.0012 25.5 3.9 97 6-102 36-168 (279)
128 COG0655 WrbA Multimeric flavod 36.6 1.2E+02 0.0027 22.0 5.5 52 2-54 15-100 (207)
129 PF12641 Flavodoxin_3: Flavodo 36.5 41 0.00089 24.2 2.9 39 2-45 10-51 (160)
130 COG0646 MetH Methionine syntha 36.3 25 0.00054 28.5 1.8 17 40-56 294-310 (311)
131 TIGR03018 pepcterm_TyrKin exop 36.2 1.2E+02 0.0027 21.9 5.4 48 8-55 137-193 (207)
132 PRK06696 uridine kinase; Valid 35.9 1.3E+02 0.0028 22.1 5.5 51 1-64 1-51 (223)
133 COG0489 Mrp ATPases involved i 35.9 2E+02 0.0044 22.1 7.4 59 9-68 154-223 (265)
134 cd07369 PydA_Rs_like PydA is a 35.8 2E+02 0.0044 23.2 7.0 61 6-66 34-117 (329)
135 PF08915 tRNA-Thr_ED: Archaea- 35.7 1.6E+02 0.0036 21.0 5.9 56 4-67 57-112 (138)
136 PRK06242 flavodoxin; Provision 35.2 1E+02 0.0022 20.8 4.6 48 2-55 14-69 (150)
137 PF01121 CoaE: Dephospho-CoA k 35.0 1.1E+02 0.0023 22.3 4.9 45 9-53 93-142 (180)
138 PF10940 DUF2618: Protein of u 34.9 12 0.00025 21.2 -0.2 17 87-103 13-29 (40)
139 PRK15448 ethanolamine cataboli 34.7 56 0.0012 21.9 3.1 30 18-48 37-66 (95)
140 PRK11628 transcriptional regul 34.6 1.3E+02 0.0029 20.2 5.0 12 17-28 15-26 (105)
141 cd08557 PI-PLCc_bacteria_like 34.0 1.9E+02 0.0042 21.3 6.5 50 2-61 80-129 (271)
142 cd04517 TLF TBP-like factors ( 33.8 90 0.002 22.8 4.3 33 34-66 54-87 (174)
143 cd05125 Mth938_2P1-like Mth938 33.5 25 0.00054 24.1 1.3 29 34-65 55-83 (114)
144 PRK13490 chemoreceptor glutami 33.2 1.1E+02 0.0024 22.2 4.7 40 52-91 114-156 (162)
145 cd05006 SIS_GmhA Phosphoheptos 33.0 1.7E+02 0.0038 20.5 6.9 54 8-61 118-173 (177)
146 PRK02047 hypothetical protein; 33.0 1.4E+02 0.0031 19.4 6.6 54 4-57 27-83 (91)
147 PRK00453 rpsF 30S ribosomal pr 33.0 1.2E+02 0.0025 20.1 4.5 48 35-82 5-65 (108)
148 TIGR02704 carboxysome_B carbox 33.0 51 0.0011 21.4 2.6 31 17-48 30-60 (80)
149 PF01713 Smr: Smr domain; Int 32.9 1.1E+02 0.0023 18.9 4.1 45 2-61 7-55 (83)
150 PF13740 ACT_6: ACT domain; PD 32.9 1.2E+02 0.0026 18.5 5.0 59 5-65 14-72 (76)
151 cd05560 Xcc1710_like Xcc1710_l 32.4 31 0.00068 23.2 1.6 29 34-65 53-81 (109)
152 PRK14479 dihydroxyacetone kina 32.2 3.1E+02 0.0068 23.9 7.9 87 2-104 229-318 (568)
153 PRK12337 2-phosphoglycerate ki 32.1 64 0.0014 27.6 3.7 49 20-68 81-133 (475)
154 TIGR01484 HAD-SF-IIB HAD-super 32.0 48 0.0011 23.5 2.7 20 35-54 34-53 (204)
155 PTZ00174 phosphomannomutase; P 31.9 49 0.0011 24.8 2.7 14 35-48 39-52 (247)
156 cd07949 PCA_45_Doxase_B_like_1 31.8 80 0.0017 24.7 4.0 98 5-102 35-167 (276)
157 PRK13487 chemoreceptor glutami 31.8 1.3E+02 0.0027 22.7 4.9 41 52-92 129-172 (201)
158 KOG3782|consensus 31.3 1E+02 0.0022 23.1 4.2 52 13-65 43-94 (189)
159 COG1915 Uncharacterized conser 31.2 2.6E+02 0.0056 23.2 6.8 52 6-57 17-70 (415)
160 cd04886 ACT_ThrD-II-like C-ter 31.1 1E+02 0.0023 17.3 6.6 55 6-65 11-70 (73)
161 PRK05456 ATP-dependent proteas 31.0 62 0.0014 23.5 3.1 33 30-62 35-68 (172)
162 PF02574 S-methyl_trans: Homoc 30.8 26 0.00056 27.2 1.1 18 40-57 288-305 (305)
163 PRK10245 adrA diguanylate cycl 30.5 2.8E+02 0.0061 22.1 7.3 55 4-62 260-314 (366)
164 TIGR00288 conserved hypothetic 30.4 42 0.00091 24.5 2.1 51 32-88 104-154 (160)
165 PF01037 AsnC_trans_reg: AsnC 30.3 1.1E+02 0.0024 17.8 3.7 24 31-54 32-55 (74)
166 TIGR03029 EpsG chain length de 30.1 1.8E+02 0.004 21.8 5.7 48 18-66 211-267 (274)
167 cd04885 ACT_ThrD-I Tandem C-te 29.8 1.3E+02 0.0027 17.9 6.1 52 8-65 13-65 (68)
168 PF08029 HisG_C: HisG, C-termi 29.8 51 0.0011 20.9 2.2 24 6-29 51-74 (75)
169 PRK00341 hypothetical protein; 29.7 1.6E+02 0.0036 19.2 6.0 53 3-57 27-83 (91)
170 COG1692 Calcineurin-like phosp 29.7 27 0.00058 27.6 1.0 77 33-109 29-141 (266)
171 cd08587 PI-PLCXDc_like Catalyt 29.3 2.6E+02 0.0056 21.5 6.5 53 2-62 93-145 (288)
172 TIGR02703 carboxysome_A carbox 29.1 71 0.0015 20.8 2.8 30 18-48 32-61 (81)
173 PRK13488 chemoreceptor glutami 29.0 1.4E+02 0.003 21.5 4.6 42 52-93 109-153 (157)
174 PRK00081 coaE dephospho-CoA ki 28.9 2.2E+02 0.0048 20.4 6.0 44 10-53 96-144 (194)
175 COG1514 LigT 2'-5' RNA ligase 28.7 2.3E+02 0.0051 20.6 6.6 61 5-65 51-115 (180)
176 PF05164 ZapA: Cell division p 28.4 68 0.0015 19.9 2.6 28 35-62 10-37 (89)
177 cd01026 TOPRIM_OLD TOPRIM_OLD: 28.3 47 0.001 21.3 1.9 23 33-55 2-25 (97)
178 PRK13185 chlL protochlorophyll 28.2 2.4E+02 0.0052 21.0 6.0 35 19-53 117-160 (270)
179 COG5440 Uncharacterized conser 27.9 2.5E+02 0.0054 20.7 6.4 52 1-52 1-73 (161)
180 COG4031 Predicted metal-bindin 27.9 1.2E+02 0.0026 23.3 4.1 33 29-61 193-225 (227)
181 TIGR00789 flhB_rel flhB C-term 27.8 98 0.0021 20.0 3.3 26 37-67 19-44 (82)
182 PRK09894 diguanylate cyclase; 27.8 2.6E+02 0.0055 20.8 7.9 55 4-62 182-236 (296)
183 PRK09622 porA pyruvate flavodo 27.7 2.4E+02 0.0052 23.2 6.3 25 33-57 267-291 (407)
184 cd02036 MinD Bacterial cell di 27.5 2E+02 0.0044 19.5 5.3 33 21-53 64-104 (179)
185 KOG3302|consensus 27.4 1.2E+02 0.0027 23.0 4.1 33 33-65 74-107 (200)
186 PF10139 Virul_Fac: Putative b 27.4 1E+02 0.0022 28.2 4.4 40 35-74 375-416 (854)
187 PRK13690 hypothetical protein; 27.4 2.7E+02 0.0059 20.9 6.2 63 1-65 1-69 (184)
188 PF02962 CHMI: 5-carboxymethyl 27.2 78 0.0017 22.0 2.9 60 3-62 17-90 (124)
189 PF03319 EutN_CcmL: Ethanolami 27.0 72 0.0016 20.7 2.5 29 19-48 38-66 (83)
190 PF13614 AAA_31: AAA domain; P 26.7 1.9E+02 0.0041 19.3 4.8 42 5-48 105-155 (157)
191 PRK08006 replicative DNA helic 26.5 2.6E+02 0.0056 23.6 6.4 85 4-92 321-421 (471)
192 PLN02887 hydrolase family prot 26.4 70 0.0015 27.8 3.1 22 34-55 341-362 (580)
193 PRK10645 divalent-cation toler 26.3 1.6E+02 0.0034 20.1 4.2 23 35-57 10-33 (112)
194 TIGR01007 eps_fam capsular exo 26.2 2.4E+02 0.0053 20.0 6.4 46 18-64 126-180 (204)
195 cd04866 LigD_Pol_like_3 LigD_P 26.1 1.8E+02 0.0038 22.5 4.9 33 41-73 104-137 (223)
196 cd07367 CarBb CarBb is the B s 26.0 2.4E+02 0.0053 21.7 5.8 97 6-102 30-157 (268)
197 TIGR01470 cysG_Nterm siroheme 25.8 2.7E+02 0.006 20.5 5.9 53 35-92 71-126 (205)
198 TIGR03190 benz_CoA_bzdN benzoy 25.8 2.9E+02 0.0064 22.3 6.4 56 4-74 299-354 (377)
199 KOG2964|consensus 25.7 18 0.00039 29.5 -0.6 71 18-90 58-134 (361)
200 PRK09966 putative inner membra 25.6 3.3E+02 0.0072 21.4 6.8 54 4-61 302-356 (407)
201 TIGR03328 salvage_mtnB methylt 25.5 2.7E+02 0.0058 20.2 7.1 51 3-61 136-186 (193)
202 PRK07119 2-ketoisovalerate fer 25.5 92 0.002 25.1 3.5 25 33-57 246-270 (352)
203 PF07994 NAD_binding_5: Myo-in 25.5 1.4E+02 0.003 23.8 4.4 33 4-36 132-164 (295)
204 PLN02422 dephospho-CoA kinase 25.0 3.1E+02 0.0068 20.9 6.7 67 18-84 105-180 (232)
205 PF14552 Tautomerase_2: Tautom 25.0 1.2E+02 0.0027 19.3 3.4 27 40-66 36-64 (82)
206 PF03129 HGTP_anticodon: Antic 25.0 1.8E+02 0.0038 18.0 4.3 68 36-103 2-87 (94)
207 COG0492 TrxB Thioredoxin reduc 25.0 42 0.00092 26.6 1.4 30 22-51 92-121 (305)
208 cd03130 GATase1_CobB Type 1 gl 24.8 2.8E+02 0.006 20.2 6.1 50 9-60 15-69 (198)
209 PF01361 Tautomerase: Tautomer 24.8 1.5E+02 0.0032 17.0 4.2 27 39-65 7-34 (60)
210 cd04863 MtLigD_Pol_like MtLigD 24.8 1.9E+02 0.0042 22.3 4.9 33 41-73 113-146 (231)
211 cd06414 GH25_LytC-like The Lyt 24.6 2.7E+02 0.0059 20.0 6.8 54 7-66 76-129 (191)
212 PF12650 DUF3784: Domain of un 24.5 29 0.00062 22.5 0.3 17 88-104 27-43 (97)
213 PF15601 Imm42: Immunity prote 24.5 83 0.0018 22.3 2.7 53 4-58 59-124 (134)
214 KOG0189|consensus 24.2 60 0.0013 25.3 2.0 70 16-109 53-130 (261)
215 PRK13498 chemoreceptor glutami 24.2 1.7E+02 0.0037 21.3 4.4 43 50-92 115-160 (167)
216 COG2848 Uncharacterized conser 24.1 48 0.001 27.9 1.6 96 9-108 57-166 (445)
217 cd00580 CHMI 5-carboxymethyl-2 23.8 1E+02 0.0023 20.4 3.0 62 3-64 17-92 (113)
218 cd07364 PCA_45_Dioxygenase_B S 23.8 1.9E+02 0.0042 22.5 4.9 97 6-102 36-168 (277)
219 COG4840 Uncharacterized protei 23.7 19 0.0004 22.9 -0.7 52 6-57 9-68 (71)
220 COG3835 CdaR Sugar diacid util 23.6 1.3E+02 0.0028 25.0 3.9 37 4-47 5-41 (376)
221 PRK13364 protocatechuate 4,5-d 23.5 2.1E+02 0.0044 22.5 5.0 97 6-102 36-167 (278)
222 PRK12457 2-dehydro-3-deoxyphos 23.5 1.9E+02 0.0042 23.1 4.8 31 35-65 16-49 (281)
223 PF03358 FMN_red: NADPH-depend 23.3 71 0.0015 21.6 2.1 28 37-64 5-32 (152)
224 cd06525 GH25_Lyc-like Lyc mura 23.3 2.8E+02 0.0061 19.7 6.3 52 5-66 68-120 (184)
225 PHA02518 ParA-like protein; Pr 23.1 2.7E+02 0.0059 19.5 5.8 37 18-54 75-119 (211)
226 cd01646 RT_Bac_retron_I RT_Bac 23.0 1.8E+02 0.0038 20.1 4.2 34 31-65 86-119 (158)
227 COG5476 Uncharacterized conser 23.0 5E+02 0.011 22.4 7.8 50 35-84 240-303 (488)
228 PRK08105 flavodoxin; Provision 22.9 2.6E+02 0.0056 19.4 5.0 30 37-66 4-33 (149)
229 PRK06467 dihydrolipoamide dehy 22.9 40 0.00086 27.8 0.9 14 33-46 136-149 (471)
230 cd00304 RT_like RT_like: Rever 22.7 1.4E+02 0.0031 18.3 3.4 31 32-65 45-76 (98)
231 KOG1579|consensus 22.7 62 0.0013 26.3 1.9 19 39-57 296-314 (317)
232 KOG3728|consensus 22.7 1.5E+02 0.0033 23.6 4.0 28 32-59 48-75 (308)
233 cd05565 PTS_IIB_lactose PTS_II 22.5 2.4E+02 0.0052 18.7 5.3 66 1-70 11-79 (99)
234 cd07362 HPCD_like Class III ex 22.5 2.2E+02 0.0047 22.0 4.9 96 6-101 31-157 (272)
235 cd01398 RPI_A RPI_A: Ribose 5- 22.4 1.5E+02 0.0032 22.2 3.8 45 58-102 144-188 (213)
236 PRK06912 acoL dihydrolipoamide 22.4 41 0.00088 27.5 0.9 14 33-46 132-145 (458)
237 PF01330 RuvA_N: RuvA N termin 22.3 92 0.002 18.4 2.3 21 74-94 13-33 (61)
238 PLN02489 homocysteine S-methyl 22.3 41 0.0009 27.0 0.9 18 40-57 316-333 (335)
239 KOG3941|consensus 22.3 2.6E+02 0.0057 23.1 5.4 52 3-54 204-257 (406)
240 COG2509 Uncharacterized FAD-de 22.3 1.9E+02 0.0041 24.9 4.8 44 4-47 173-232 (486)
241 CHL00123 rps6 ribosomal protei 22.3 1.8E+02 0.0039 19.0 3.9 36 35-70 9-45 (97)
242 TIGR00166 S6 ribosomal protein 22.1 2.2E+02 0.0048 18.1 4.6 47 36-82 5-63 (93)
243 PF04025 DUF370: Domain of unk 22.1 2.2E+02 0.0048 18.1 4.3 43 52-94 26-68 (73)
244 PF01941 AdoMet_Synthase: S-ad 22.0 1.6E+02 0.0035 24.7 4.2 52 3-56 169-228 (396)
245 PRK09485 mmuM homocysteine met 22.0 61 0.0013 25.5 1.8 17 40-56 287-303 (304)
246 PRK11359 cyclic-di-GMP phospho 21.9 4E+02 0.0087 22.8 6.8 54 4-61 427-480 (799)
247 cd04862 PaeLigD_Pol_like PaeLi 21.6 2.4E+02 0.0053 21.7 4.9 33 41-73 109-142 (227)
248 PF00408 PGM_PMM_IV: Phosphogl 21.5 2E+02 0.0043 17.3 3.9 25 36-60 49-73 (73)
249 cd04466 S1_YloQ_GTPase S1_YloQ 21.4 1.3E+02 0.0029 17.5 2.9 20 73-92 39-62 (68)
250 cd04876 ACT_RelA-SpoT ACT dom 21.4 1.5E+02 0.0032 15.8 6.0 49 6-55 11-60 (71)
251 TIGR03169 Nterm_to_SelD pyridi 21.3 42 0.00092 26.1 0.7 14 33-46 95-108 (364)
252 PRK01966 ddl D-alanyl-alanine 21.3 94 0.002 24.4 2.7 46 36-81 6-53 (333)
253 PF01583 APS_kinase: Adenylyls 21.2 1.1E+02 0.0024 22.0 2.8 34 36-69 3-36 (156)
254 KOG2972|consensus 21.2 4.3E+02 0.0093 21.0 8.8 78 22-110 111-190 (276)
255 PF13241 NAD_binding_7: Putati 21.2 2.2E+02 0.0047 18.3 4.1 27 35-66 62-88 (103)
256 TIGR02778 ligD_pol DNA polymer 21.1 2.5E+02 0.0053 22.0 4.9 33 41-73 125-158 (245)
257 COG4458 SrfC Uncharacterized p 21.1 1.1E+02 0.0023 27.6 3.1 45 35-79 390-437 (821)
258 PRK14568 vanB D-alanine--D-lac 21.1 1.1E+02 0.0023 24.2 3.0 47 36-82 6-54 (343)
259 cd07187 YvcK_like family of mo 21.0 1.6E+02 0.0034 23.6 3.9 46 6-56 195-240 (308)
260 PF05687 DUF822: Plant protein 21.0 2.5E+02 0.0054 20.4 4.6 44 45-88 19-71 (150)
261 PF03796 DnaB_C: DnaB-like hel 20.9 2.7E+02 0.0058 20.8 5.0 59 3-65 114-172 (259)
262 PRK13512 coenzyme A disulfide 20.8 39 0.00084 27.5 0.4 13 34-46 106-118 (438)
263 cd04893 ACT_GcvR_1 ACT domains 20.7 2.1E+02 0.0046 17.4 5.8 59 5-65 13-71 (77)
264 PF08482 HrpB_C: ATP-dependent 20.7 68 0.0015 22.8 1.6 24 84-107 86-112 (133)
265 cd06592 GH31_glucosidase_KIAA1 20.7 3.7E+02 0.008 20.9 5.9 89 3-98 28-143 (303)
266 PRK06904 replicative DNA helic 20.7 4.3E+02 0.0092 22.2 6.6 58 5-66 320-377 (472)
267 COG2144 Selenophosphate synthe 20.5 1.6E+02 0.0036 23.9 3.9 29 39-67 100-128 (324)
268 PF07992 Pyr_redox_2: Pyridine 20.5 42 0.00092 23.3 0.5 14 33-46 110-123 (201)
269 TIGR03452 mycothione_red mycot 20.4 54 0.0012 26.9 1.2 14 33-46 131-144 (452)
270 KOG1042|consensus 20.4 3.1E+02 0.0067 25.0 5.8 63 31-99 470-549 (845)
271 cd04888 ACT_PheB-BS C-terminal 20.4 2E+02 0.0042 16.8 6.7 51 5-56 12-64 (76)
272 PF01455 HupF_HypC: HupF/HypC 20.4 74 0.0016 19.7 1.6 21 72-93 38-58 (68)
273 COG0010 SpeB Arginase/agmatina 20.3 2.6E+02 0.0055 22.0 5.0 48 2-56 251-298 (305)
274 PF04456 DUF503: Protein of un 20.2 2.6E+02 0.0057 18.1 7.5 43 20-62 35-79 (90)
275 cd00890 Prefoldin Prefoldin is 20.1 95 0.002 20.5 2.2 26 74-99 67-93 (129)
276 PRK13146 hisH imidazole glycer 20.1 3.1E+02 0.0068 20.1 5.2 35 8-43 15-50 (209)
277 PLN02382 probable sucrose-phos 20.1 96 0.0021 25.5 2.6 19 35-53 46-64 (413)
278 cd04861 LigD_Pol_like LigD_Pol 20.1 2.7E+02 0.0059 21.5 4.9 33 41-73 109-142 (227)
No 1
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=100.00 E-value=4.5e-48 Score=267.49 Aligned_cols=110 Identities=36% Similarity=0.709 Sum_probs=107.2
Q ss_pred CCHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEE
Q psy8849 1 MNINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLL 80 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~Wvll 80 (112)
|+..++++.++++|+|+||+||++||++++|++|||||||||+|.||++|+|+++.+.+|+.|..+.++||..+++|+|+
T Consensus 1 ~~~~~l~~~i~~alddkKAeDIv~lDv~~~s~~tDyfVIatg~s~rhv~Aiad~i~~~~k~~g~~~~~~EG~~~~~Wvli 80 (115)
T COG0799 1 MSMEELLEVIVEALDDKKAEDIVVLDVSGKSSLTDYFVIATGNSSRHVKAIADNVKEELKEAGEVPLRIEGLSEGEWVLI 80 (115)
T ss_pred CcHHHHHHHHHHHHHhccCCCeEEEEccCCcccccEEEEEEeCchHHHHHHHHHHHHHHHHcCCCcccccCCCcCCEEEE
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCEEEEeeChhhhhhcchhhhccccccc
Q psy8849 81 DLGDIIIHIMNPYIRNMYNLEEIWGEKEIK 110 (112)
Q Consensus 81 D~g~vvVHif~~e~R~~Y~LE~LW~~~~~~ 110 (112)
|+|+||||||+|+.|+|||||+||+++|..
T Consensus 81 D~GdivVHvf~~e~R~~Y~LEklW~d~~~~ 110 (115)
T COG0799 81 DLGDIVVHVFTPEEREFYNLEKLWGDAPVV 110 (115)
T ss_pred ecCcEEEEecCHHHHHHccHHHHhccCCcc
Confidence 999999999999999999999999999853
No 2
>PRK11538 ribosome-associated protein; Provisional
Probab=100.00 E-value=1.3e-46 Score=257.08 Aligned_cols=105 Identities=30% Similarity=0.589 Sum_probs=102.8
Q ss_pred CCHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEE
Q psy8849 1 MNINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLL 80 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~Wvll 80 (112)
|+++++++.++++|+++||+||+++||++.|+++||||||||+|.||++|+|++|.+.+|+.|.+++++||.++++|+++
T Consensus 1 ~~~~~~~~~i~~~l~dkKa~DI~vlDv~~~~~~~Dy~VIatg~S~rh~~aia~~v~~~~k~~~~~~~~~eG~~~~~Will 80 (105)
T PRK11538 1 MQGKALQDFVIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLPLGVEGENAADWIVV 80 (105)
T ss_pred CCHHHHHHHHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHcCCCCCcccCCCCCCEEEE
Confidence 78889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCEEEEeeChhhhhhcchhhhcc
Q psy8849 81 DLGDIIIHIMNPYIRNMYNLEEIWG 105 (112)
Q Consensus 81 D~g~vvVHif~~e~R~~Y~LE~LW~ 105 (112)
|||+||||||+|+.|+|||||+||+
T Consensus 81 D~g~ivVHif~~e~Re~Y~LE~LW~ 105 (105)
T PRK11538 81 DLGDVIVHVMQEESRRLYELEKLWS 105 (105)
T ss_pred eCCCEEEEcCCHHHHhhcCHHhhhC
Confidence 9999999999999999999999996
No 3
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=100.00 E-value=3.5e-45 Score=247.44 Aligned_cols=98 Identities=35% Similarity=0.713 Sum_probs=96.3
Q ss_pred HHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEE
Q psy8849 7 QIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDII 86 (112)
Q Consensus 7 ~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vv 86 (112)
++.++++|+++||+||+++|+++.++++||||||||+|.||++|+|+++.+.+|+.|.+|+++||.++++|+++|||+|+
T Consensus 2 ~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VI~Tg~S~rh~~aia~~v~~~~k~~~~~~~~~EG~~~~~WillD~g~iv 81 (99)
T TIGR00090 2 LELIVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVEEELKEAGLKPLGVEGLEEGDWVLVDLGDVV 81 (99)
T ss_pred HHHHHHHHHHcCCCCEEEEECCCCCcccCEEEEEEeCCHHHHHHHHHHHHHHHHHcCCCcccccCCCCCCEEEEECCCEE
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeChhhhhhcchhhhc
Q psy8849 87 IHIMNPYIRNMYNLEEIW 104 (112)
Q Consensus 87 VHif~~e~R~~Y~LE~LW 104 (112)
||||+||.|+|||||+||
T Consensus 82 VHif~~e~R~~Y~LE~LW 99 (99)
T TIGR00090 82 VHIFQPEAREFYDLEKLW 99 (99)
T ss_pred EEeCChHHhhhcCHhhcC
Confidence 999999999999999999
No 4
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=100.00 E-value=2.6e-43 Score=238.13 Aligned_cols=99 Identities=36% Similarity=0.664 Sum_probs=90.0
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHH-HhcCCCcccccccCCCCEEEEEcCC
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNI-KNINNNIVNIEGKKSSEWLLLDLGD 84 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~l-k~~~~~~~~~EG~~~~~WvllD~g~ 84 (112)
.++.++++|+++||+||+++|+++.++++||||||||+|+||++|+|+++.+.+ |+.+..++++||.++++|+++|||+
T Consensus 1 ~~~~i~~~l~~~k~~dI~v~dv~~~~~~~dy~II~T~~S~rh~~aia~~v~~~~~k~~~~~~~~~eG~~~~~W~lvD~g~ 80 (100)
T PF02410_consen 1 MLEEIVEALEDKKAEDIVVLDVREKSSWADYFIIATGRSERHVRAIADEVEKALKKEYGERPLRIEGLDESDWVLVDYGD 80 (100)
T ss_dssp -HHHHHHHHHHTT-EEEEEEEGCTTBSS-SEEEEEEESSHHHHHHHHHHHHHHH-HHTT----EEESTTTTSEEEEEESS
T ss_pred CHHHHHHHHHHcCCCCeEEEECCCCCcccCEEEEEEcCCHHHHHHHHHHHHHHHHHHcCCcccccCCCCCCCEEEEcccE
Confidence 368999999999999999999999999999999999999999999999999999 6778889999999999999999999
Q ss_pred EEEEeeChhhhhhcchhhhc
Q psy8849 85 IIIHIMNPYIRNMYNLEEIW 104 (112)
Q Consensus 85 vvVHif~~e~R~~Y~LE~LW 104 (112)
|+||||+||.|+|||||+||
T Consensus 81 ivVHif~~e~R~~Y~LE~LW 100 (100)
T PF02410_consen 81 IVVHIFTPEAREYYDLESLW 100 (100)
T ss_dssp EEEEEEEHHHHHHHCHHHHT
T ss_pred EEEEcCCHHHHhHcCHhhcC
Confidence 99999999999999999999
No 5
>KOG3212|consensus
Probab=99.98 E-value=5e-32 Score=200.32 Aligned_cols=102 Identities=32% Similarity=0.547 Sum_probs=96.1
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc---CCCcccccccCCCCEEEEEc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI---NNNIVNIEGKKSSEWLLLDL 82 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~---~~~~~~~EG~~~~~WvllD~ 82 (112)
.++.++++|.+.+|.||+|+-+.+.+.|+||+|||||+|.||++|+|++|+..+|.. |-+..++||.++++|+++|+
T Consensus 70 ~ve~vv~lLrdenadDVfVi~vpeem~y~dh~VIcSgrs~rhl~aiAe~lv~m~Kik~~kgd~hvriegk~s~dW~v~D~ 149 (208)
T KOG3212|consen 70 TVEEVVKLLRDENADDVFVIPVPEEMFYADHTVICSGRSDRHLRAIAEALVYMAKIKSQKGDKHVRIEGKQSSDWIVIDY 149 (208)
T ss_pred hHHHHHHHHHhcccCceEEEeccccceeeeeEEEEecCchHHHHHHHHHHHHHHHHhhcCCCcccccccccCCCeEEEEe
Confidence 368899999999999999999999999999999999999999999999999998853 55678999999999999999
Q ss_pred CCEEEEeeChhhhhhcchhhhcccc
Q psy8849 83 GDIIIHIMNPYIRNMYNLEEIWGEK 107 (112)
Q Consensus 83 g~vvVHif~~e~R~~Y~LE~LW~~~ 107 (112)
|.++||+|+||+|++||||+||+..
T Consensus 150 g~~vvH~mseeaRe~YdLEsLWa~~ 174 (208)
T KOG3212|consen 150 GKFVVHAMSEEAREYYDLESLWAAE 174 (208)
T ss_pred ceEEEEecCHHHhhhccHHHHhccc
Confidence 9999999999999999999999873
No 6
>PRK10678 moaE molybdopterin guanine dinucleotide biosynthesis protein MoaE; Provisional
Probab=85.35 E-value=10 Score=27.42 Aligned_cols=75 Identities=9% Similarity=-0.039 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCcc--CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCccccccc-CCCCEEE
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLF--DRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGK-KSSEWLL 79 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~--dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~-~~~~Wvl 79 (112)
+++.+...++.......++.+..--+.-... -.+|.+++...+..-..++.+.+.+|.. .|..+.|=. +++.|+-
T Consensus 61 k~l~~I~~ea~~~~~~~~v~i~HR~G~l~~Ge~~v~Vav~s~HR~~Af~A~~~~id~lK~~-vPIWKkE~~~dG~~Wv~ 138 (150)
T PRK10678 61 KALAEIVDEARSRWPLGRVTVIHRVGELWPGDEIVFVGVTSAHRSSAFEAGQFIMDYLKTR-APFWKREATPEGDRWVE 138 (150)
T ss_pred HHHHHHHHHHHHhCCCCcEEEEEeEecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhhc-CCeEEeEEcCCCCEEec
Confidence 3444444455555667888888666544333 3556666666666777888999999874 455555422 2246874
No 7
>PRK05568 flavodoxin; Provisional
Probab=84.51 E-value=4.3 Score=27.60 Aligned_cols=54 Identities=15% Similarity=0.196 Sum_probs=38.5
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEcCCH------HHHHHHHHHHH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASGSSK------RQINALAVSIR 56 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~~S~------rh~~aia~~v~ 56 (112)
+++++++.|++.+.+.+ .++.++|+.... .-+|.+|++|..-. ..+....+.+.
T Consensus 14 nT~~~a~~i~~~~~~~g-~~v~~~~~~~~~~~~~~~~d~iilgsp~y~~~~~~~~~~~~f~~~~~ 77 (142)
T PRK05568 14 NTEAMANLIAEGAKENG-AEVKLLNVSEASVDDVKGADVVALGSPAMGDEVLEEGEMEPFVESIS 77 (142)
T ss_pred hHHHHHHHHHHHHHHCC-CeEEEEECCCCCHHHHHhCCEEEEECCccCcccccchhHHHHHHHhh
Confidence 47889999999886544 589999998754 24699999998643 34555555443
No 8
>COG0314 MoaE Molybdopterin converting factor, large subunit [Coenzyme metabolism]
Probab=81.03 E-value=18 Score=26.10 Aligned_cols=79 Identities=8% Similarity=0.033 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccC--EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccc-cCCCCEEE
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFD--RITIASGSSKRQINALAVSIRKNIKNINNNIVNIEG-KKSSEWLL 79 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~d--y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG-~~~~~Wvl 79 (112)
.+++.+.+.++.+.-...++.++.-.+.-...| ++|.++|...+-.-..++.+.+.+|.. .|..+.|= .++..|+-
T Consensus 60 ~k~l~~I~~e~~~k~~~~~v~i~HriG~l~~Ge~~v~v~v~s~HR~~Af~a~~~~id~lK~~-aPiWKkE~~~dg~~Wv~ 138 (149)
T COG0314 60 EKELEEIAAEAKEKWGLLRVAIIHRIGELKIGEAIVLVGVASAHRKEAFEACEYIIDRLKHR-APIWKKEHTEDGERWVG 138 (149)
T ss_pred HHHHHHHHHHHHHhCCceeEEEEEeeccccCCCcEEEEEEecccHHHHHHHHHHHHHHHHhh-CCceEEEecCCCCeEEe
Confidence 344555555555555678988887777544443 445555555555667788888888874 44444441 23345876
Q ss_pred EEc
Q psy8849 80 LDL 82 (112)
Q Consensus 80 lD~ 82 (112)
-+.
T Consensus 139 ~~~ 141 (149)
T COG0314 139 DRE 141 (149)
T ss_pred ccc
Confidence 544
No 9
>PRK09271 flavodoxin; Provisional
Probab=80.67 E-value=16 Score=25.69 Aligned_cols=73 Identities=11% Similarity=0.202 Sum_probs=42.8
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC------C--ccCEEEEEEcC-----CHHHHHHHHHHHHHHHHhcCCCccc
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT------N--LFDRITIASGS-----SKRQINALAVSIRKNIKNINNNIVN 68 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~------~--~~dy~VIaT~~-----S~rh~~aia~~v~~~lk~~~~~~~~ 68 (112)
+++++++.|++.|...+. ++.+.++.... . -+|.+||+|.+ -+..++...+.+.....+ + ++..
T Consensus 13 nTe~~A~~ia~~l~~~g~-~v~~~~~~~~~~~~~~~~~~~~d~vilgt~T~~~G~~p~~~~~f~~~l~~~~~~-~-k~~a 89 (160)
T PRK09271 13 NTREVAREIEERCEEAGH-EVDWVETDVQTLAEYPLDPEDYDLYLLGTWTDNAGRTPPEMKRFIAELAETIGK-P-PNVA 89 (160)
T ss_pred hHHHHHHHHHHHHHhCCC-eeEEEecccccccccccCcccCCEEEEECcccCCCcCCHHHHHHHHHHHHHhcc-C-CeEE
Confidence 478899999999987554 67667664321 1 24889999942 344566666666543221 1 2233
Q ss_pred ccccCCCCE
Q psy8849 69 IEGKKSSEW 77 (112)
Q Consensus 69 ~EG~~~~~W 77 (112)
+=|..+..|
T Consensus 90 vfgsgd~~~ 98 (160)
T PRK09271 90 VFGTGETQW 98 (160)
T ss_pred EEecCCCCc
Confidence 434444566
No 10
>cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits.
Probab=79.19 E-value=18 Score=25.02 Aligned_cols=74 Identities=9% Similarity=0.044 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccC--EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCccccccc-CCCCEE
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFD--RITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGK-KSSEWL 78 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~d--y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~-~~~~Wv 78 (112)
+++.+.+.++...-...++.+..=-+.-...| .+|.+++...+..-..++.+.+.+|+. .|..+.|=. +++.|+
T Consensus 48 ~~l~~I~~e~~~k~~~~~v~v~HR~G~l~vGe~~v~i~v~a~hR~~af~A~~~~id~lK~~-~PiWKkE~~~~~~~Wv 124 (124)
T cd00756 48 KELEEIAEEARERWGLLRVAIIHRVGRLPPGEAIVLVAVSSPHRKEAFEACEFLIDRLKHR-APIWKKEIFEGGEEWV 124 (124)
T ss_pred HHHHHHHHHHHHhCCCceEEEEEEEcccCCCCEEEEEEEecCCHHHHHHHHHHHHHHHHhh-CCEEEEEEeCCCCEEC
Confidence 34444444555566678888876555443333 445555655566777888888999874 343344322 234574
No 11
>PRK03467 hypothetical protein; Provisional
Probab=75.72 E-value=5.9 Score=28.48 Aligned_cols=53 Identities=11% Similarity=0.048 Sum_probs=40.6
Q ss_pred CCHHHHHHHHHHHHHhcCCCCeEEEecCCC----CCcc-----CEEEEEEcCCHHHHHHHHH
Q psy8849 1 MNINKRQIIVIKILKDIKAQDIKVYDTSNL----TNLF-----DRITIASGSSKRQINALAV 53 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~kka~dI~vldv~~~----~~~~-----dy~VIaT~~S~rh~~aia~ 53 (112)
|+..+-...|.++|.+.+.-..++.+-.+. |.|+ =-++++|..++||++.+..
T Consensus 1 m~~~~~~~~I~~fl~~~hvltLa~~~~~~~w~A~cFY~fd~~~~~l~~~S~~~TrH~~~~~~ 62 (144)
T PRK03467 1 MNNMDTLTAISRWLAKQHVVTLCVGQEGELWCANCFYVFDAQKVAFYLLTEEKTRHGQMMGP 62 (144)
T ss_pred CCChhHHHHHHHHHHhCcEEEEEEEcCCCcceEEEEEEEcCCCeEEEEEcCCCCHHHHHHhh
Confidence 455566779999999999999999876654 2232 2469999999999997644
No 12
>PRK05569 flavodoxin; Provisional
Probab=75.42 E-value=8.9 Score=26.02 Aligned_cols=53 Identities=11% Similarity=0.149 Sum_probs=38.6
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEcC--C----HHHHHHHHHHH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASGS--S----KRQINALAVSI 55 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~~--S----~rh~~aia~~v 55 (112)
+++.+++.|++-+.+.++ ++.++++++.. .-+|.+|++|.. . +.++..+.+.+
T Consensus 14 nT~~iA~~i~~~~~~~g~-~v~~~~~~~~~~~~~~~~d~iilgsPty~~~~~~~~~~~~~~~~l 76 (141)
T PRK05569 14 NVEVLANTIADGAKEAGA-EVTIKHVADAKVEDVLEADAVAFGSPSMDNNNIEQEEMAPFLDQF 76 (141)
T ss_pred HHHHHHHHHHHHHHhCCC-eEEEEECCcCCHHHHhhCCEEEEECCCcCCCcCChHHHHHHHHHh
Confidence 478899999999977654 78999988754 246999999975 1 24566665555
No 13
>PF06778 Chlor_dismutase: Chlorite dismutase; InterPro: IPR010644 This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyses the disproportionation of chlorite into chloride and oxygen [, ]. Note that many family members are hypothetical proteins.; PDB: 2VXH_B 3NN4_A 3NN2_A 3NN3_D 3NN1_E 3QPI_A 3Q08_Q 3Q09_B 1T0T_V 1VDH_E ....
Probab=74.83 E-value=30 Score=25.84 Aligned_cols=54 Identities=13% Similarity=0.056 Sum_probs=41.0
Q ss_pred HHHHHHHHHH---HhcCCC-CeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHH
Q psy8849 5 KRQIIVIKIL---KDIKAQ-DIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKN 58 (112)
Q Consensus 5 ~l~~~i~~~l---~~kka~-dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~ 58 (112)
..++++.+++ .+.+.. -+.++++.+...-+|+|+...+.|..+++.+...+.+.
T Consensus 5 ~~~~e~~~~~~~~~~~~~~~~~~~Y~~~G~radaDl~~w~~~~~~~~lq~~~~~l~~t 62 (193)
T PF06778_consen 5 AAAEEFEAFLEEWEEAGDGVLRGVYSVSGLRADADLMFWWHAPDLEDLQEAERRLRRT 62 (193)
T ss_dssp HHHHHHHHHHHHHHHTTTTEEEEEEEETTTSTT-SEEEEEEESSHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHhccCceEEEEEEeecccCCCcEEEEEeCCCHHHHHHHHHHHHhh
Confidence 4556666666 333333 47899999999999999999999999999988877653
No 14
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=71.27 E-value=8 Score=24.76 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=22.7
Q ss_pred CEEEEEEc-CCHHHHHHHHHHHHHHHHhcC
Q psy8849 35 DRITIASG-SSKRQINALAVSIRKNIKNIN 63 (112)
Q Consensus 35 dy~VIaT~-~S~rh~~aia~~v~~~lk~~~ 63 (112)
.--|++|| +|..+++...+.+.+.|++.|
T Consensus 57 sGki~itGaks~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 57 SGKIVITGAKSEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp TSEEEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 33455565 699999999999999998764
No 15
>TIGR01755 flav_wrbA NAD(P)H:quinone oxidoreductase, type IV. This model represents a protein, WrbA, related to and slightly larger than flavodoxin. It was just shown, in E. coli and Archaeoglobus fulgidus (and previously for some eukaryotic homologs) to act as fourth type of NAD(P)H:quinone oxidoreductase. In E. coli, this protein was earlier reported to be produced during stationary phase, bind to the trp repressor, and make trp operon repression more efficient. WrbA does not interact with the trp operator by itself. Members are found in species in which homologs of the E. coli trp operon repressor TrpR are not detected.
Probab=69.20 E-value=22 Score=26.04 Aligned_cols=53 Identities=11% Similarity=0.155 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCC------------------------CccCEEEEEEcC----CHHHHHHHHHH
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLT------------------------NLFDRITIASGS----SKRQINALAVS 54 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~------------------------~~~dy~VIaT~~----S~rh~~aia~~ 54 (112)
++++++.|++-+++..+-++.++++++.. ..+|.+|++|.. =..+++...+.
T Consensus 14 T~~lA~~ia~g~~~~~g~ev~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~aD~ii~GSPty~g~~~~~lk~fld~ 93 (197)
T TIGR01755 14 IETMARAVAEGAREVDGAEVVVKRVPETVPEEVAEKSHGKTDQTAPVATPQELADYDAIIFGTPTRFGNMASQMRNFLDQ 93 (197)
T ss_pred HHHHHHHHHHHHHhcCCCEEEEEeccccCcHHHHHhccCCcccCCccCCHHHHHHCCEEEEEecccccCccHHHHHHHHh
Confidence 67899999999987656689999986531 246999999965 33344444444
Q ss_pred H
Q psy8849 55 I 55 (112)
Q Consensus 55 v 55 (112)
+
T Consensus 94 ~ 94 (197)
T TIGR01755 94 T 94 (197)
T ss_pred c
Confidence 3
No 16
>COG4576 CcmL Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]
Probab=68.68 E-value=6.6 Score=26.08 Aligned_cols=31 Identities=23% Similarity=0.223 Sum_probs=23.5
Q ss_pred CCCeEEEecCCCCCccCEEEEEEcCCHHHHHH
Q psy8849 19 AQDIKVYDTSNLTNLFDRITIASGSSKRQINA 50 (112)
Q Consensus 19 a~dI~vldv~~~~~~~dy~VIaT~~S~rh~~a 50 (112)
....+.+|.-+ -...+|+++++|+|.||..+
T Consensus 38 ~~~eVA~DsvG-AG~gE~VLvs~GSaAR~~~~ 68 (89)
T COG4576 38 GQCEVAIDSVG-AGTGEWVLLSRGSSARQAHG 68 (89)
T ss_pred cceEEEEeccc-CCcCcEEEEecchHHHHhhc
Confidence 34567777433 45789999999999999764
No 17
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=68.57 E-value=5.7 Score=24.87 Aligned_cols=64 Identities=11% Similarity=0.240 Sum_probs=49.8
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHhc-CCCcccccccCCCCEEEEEcCCEEEEeeChhhhhhcchh
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIKNI-NNNIVNIEGKKSSEWLLLDLGDIIIHIMNPYIRNMYNLE 101 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk~~-~~~~~~~EG~~~~~WvllD~g~vvVHif~~e~R~~Y~LE 101 (112)
+.+-....+...-.++..++.+..++. .+.. ... .+.+.|++-=+|++.+.|....-|+.|++|
T Consensus 6 ~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~-~~d-~et~e~~l~g~Gelhlev~~~~L~~~~~v~ 70 (75)
T PF14492_consen 6 LSVAIEPKNKEDEPKLSEALQKLSEEDPSLRV-ERD-EETGELILSGMGELHLEVLLERLKRRFGVE 70 (75)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHH-TTSEE-EEE-TTTSEEEEEESSHHHHHHHHHHHHHTTCEB
T ss_pred EEEEEEECCHhHHHHHHHHHHHHHhcCCeEEE-EEc-chhceEEEEECCHHHHHHHHHHHHHHHCCe
Confidence 567778899999999999998877763 3332 221 245789999999999999999999999886
No 18
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=67.86 E-value=15 Score=26.48 Aligned_cols=40 Identities=20% Similarity=0.343 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC--Cc--cCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT--NL--FDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~--~~--~dy~VIaT~~ 43 (112)
+++++++.|++.|.. +.++.++++.+.. .+ +|.+||+++.
T Consensus 13 ~T~~iA~~Ia~~l~~--g~~v~~~~~~~~~~~~l~~yD~vIlGspi 56 (177)
T PRK11104 13 QTRKIASYIASELKE--GIQCDVVNLHRIEEPDLSDYDRVVIGASI 56 (177)
T ss_pred hHHHHHHHHHHHhCC--CCeEEEEEhhhcCccCHHHCCEEEEECcc
Confidence 467888888888875 5688888888754 22 6999999875
No 19
>PRK00394 transcription factor; Reviewed
Probab=67.77 E-value=12 Score=27.67 Aligned_cols=32 Identities=16% Similarity=0.285 Sum_probs=26.4
Q ss_pred CEEEEEEc-CCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 35 DRITIASG-SSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 35 dy~VIaT~-~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
.-=++||| +|..+++..++.+.+.+++.|..+
T Consensus 54 sGKiv~tGa~S~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 54 SGKVVCTGAKSVEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred CCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 44467776 999999999999999999988753
No 20
>PRK06756 flavodoxin; Provisional
Probab=66.93 E-value=38 Score=23.20 Aligned_cols=41 Identities=15% Similarity=0.307 Sum_probs=30.1
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC-----CccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT-----NLFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~-----~~~dy~VIaT~~ 43 (112)
+++++++.|++.+.+ .+.++.++|+.+.. .-+|.++++|..
T Consensus 14 nTe~vA~~ia~~l~~-~g~~v~~~~~~~~~~~~~~~~~d~vi~gspt 59 (148)
T PRK06756 14 NTEEMADHIAGVIRE-TENEIEVIDIMDSPEASILEQYDGIILGAYT 59 (148)
T ss_pred hHHHHHHHHHHHHhh-cCCeEEEeehhccCCHHHHhcCCeEEEEeCC
Confidence 478889999998875 45577888886542 235999999844
No 21
>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional
Probab=66.83 E-value=51 Score=25.72 Aligned_cols=73 Identities=11% Similarity=0.053 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCcc-CEEEEEEcCCHHH-HHHHHHHHHHHHHhcCCCcccccccCC-CCEE
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLF-DRITIASGSSKRQ-INALAVSIRKNIKNINNNIVNIEGKKS-SEWL 78 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~-dy~VIaT~~S~rh-~~aia~~v~~~lk~~~~~~~~~EG~~~-~~Wv 78 (112)
++-+.+.++.+.-...++.+..=.+.-... +-++|+.+...|+ .-..++++.+.+|.. .+..+.|=..+ ..|+
T Consensus 195 ~l~~I~~e~~~~~~~~~v~v~Hr~G~l~vge~~v~v~v~a~hR~~af~a~~~~id~lK~~-~piwK~e~~~~g~~Wv 270 (274)
T PRK14493 195 RMAAIREELKQRDGVFEVLLHHRTGVIEAGEDIVFVVVLAGHRQEAFRAVSDGIDRLKDE-VPIFKKEVTVDEEFWV 270 (274)
T ss_pred HHHHHHHHHHHhCCCceEEEEEeeccccCCCeEEEEEEecCCHHHHHHHHHHHHHHHhhc-CCeEEEEEcCCCCEee
Confidence 343444444455566788877655544333 4444444444444 667788888999874 44455543222 3586
No 22
>PRK06703 flavodoxin; Provisional
Probab=66.38 E-value=20 Score=24.74 Aligned_cols=41 Identities=12% Similarity=0.175 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~~ 43 (112)
+++++++.|++.|.+ .+.++.+.++.... .-.|.+||+|..
T Consensus 14 nT~~iA~~ia~~l~~-~g~~v~~~~~~~~~~~~l~~~d~viigspt 58 (151)
T PRK06703 14 NTEDIADLIKVSLDA-FDHEVVLQEMDGMDAEELLAYDGIILGSYT 58 (151)
T ss_pred hHHHHHHHHHHHHHh-cCCceEEEehhhCCHHHHhcCCcEEEEECC
Confidence 478889999998864 45678888887643 235899998843
No 23
>PRK03767 NAD(P)H:quinone oxidoreductase; Provisional
Probab=65.74 E-value=16 Score=26.61 Aligned_cols=53 Identities=9% Similarity=0.152 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCC------------------------CccCEEEEEEcC----CHHHHHHHHHH
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLT------------------------NLFDRITIASGS----SKRQINALAVS 54 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~------------------------~~~dy~VIaT~~----S~rh~~aia~~ 54 (112)
++++++.+++.+.+..+-++.++++++.- ..+|.+|++|.. =+.++++..+.
T Consensus 15 T~~lA~~ia~g~~~~~G~ev~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~aD~ii~gsPty~g~~~~~lk~fld~ 94 (200)
T PRK03767 15 IETMAEAVAEGAREVAGAEVTIKRVPETVPEEVAKKAGGKTDQAAPVATPDELADYDAIIFGTPTRFGNMAGQMRNFLDQ 94 (200)
T ss_pred HHHHHHHHHHHHhhcCCcEEEEEeccccCCHHHHHhcCCCcccCCCccCHHHHHhCCEEEEEecccCCCchHHHHHHHHH
Confidence 67899999999987566789999986421 246999999976 33445555444
Q ss_pred H
Q psy8849 55 I 55 (112)
Q Consensus 55 v 55 (112)
+
T Consensus 95 ~ 95 (200)
T PRK03767 95 T 95 (200)
T ss_pred h
Confidence 4
No 24
>COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]
Probab=65.51 E-value=6.7 Score=27.77 Aligned_cols=26 Identities=23% Similarity=0.623 Sum_probs=21.3
Q ss_pred cccccCCCCEEEEEc-C-CEEEEeeChh
Q psy8849 68 NIEGKKSSEWLLLDL-G-DIIIHIMNPY 93 (112)
Q Consensus 68 ~~EG~~~~~WvllD~-g-~vvVHif~~e 93 (112)
-.||.+.+.|+-+|+ | .++.|+-++-
T Consensus 28 ~~~GRstd~wvdfDfyGHQ~v~Hl~~q~ 55 (138)
T COG3565 28 CKEGRSTDTWVDFDFYGHQVVAHLTPQP 55 (138)
T ss_pred cccccccceEEEeeecccEEEEEecCCc
Confidence 468999999999997 5 8899986654
No 25
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=65.13 E-value=23 Score=23.53 Aligned_cols=41 Identities=12% Similarity=0.303 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~~ 43 (112)
+++++++.+++.+.+. +.++.++++.+.. .-+|.+|++|..
T Consensus 11 nT~~~A~~i~~~~~~~-g~~v~~~~~~~~~~~~l~~~d~iilgspt 55 (140)
T TIGR01753 11 NTEEMANIIAEGLKEA-GAEVDLLEVADADAEDLLSYDAVLLGCST 55 (140)
T ss_pred HHHHHHHHHHHHHHhc-CCeEEEEEcccCCHHHHhcCCEEEEEcCC
Confidence 4788999999998774 4578888887643 236999999866
No 26
>PRK11921 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional
Probab=64.31 E-value=23 Score=28.65 Aligned_cols=42 Identities=14% Similarity=0.232 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHHHh-cCCCCeEEEecCCCC--C------ccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKD-IKAQDIKVYDTSNLT--N------LFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~-kka~dI~vldv~~~~--~------~~dy~VIaT~~ 43 (112)
+++++++.|++-+.+ ..+-++.++|+.... . -+|.+|++|.+
T Consensus 260 nTe~mA~~ia~g~~~~~~g~~v~~~~~~~~~~~~i~~~~~~~d~ii~GspT 310 (394)
T PRK11921 260 STRRMAEAIAEGIKKANKDVTVKLYNSAKSDKNDIITEVFKSKAILVGSST 310 (394)
T ss_pred HHHHHHHHHHHHHhhcCCCCeEEEEECCCCCHHHHHHHHHhCCEEEEECCC
Confidence 378899999999974 455699999998753 1 27899999877
No 27
>cd07950 Gallate_Doxase_N The N-terminal domain of the Class III extradiol dioxygenase, Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. In this subfamily, the subunits A and B are fused to make a single polypeptide chain. The dimer interface for this subfamily may resemble the tetramer interface of classical LigAB en
Probab=63.83 E-value=27 Score=27.32 Aligned_cols=97 Identities=20% Similarity=0.210 Sum_probs=64.5
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCc-cC---EEEEEEcCCHHH---------------HHHHHHHHHHHHHhcCCCc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNL-FD---RITIASGSSKRQ---------------INALAVSIRKNIKNINNNI 66 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~-~d---y~VIaT~~S~rh---------------~~aia~~v~~~lk~~~~~~ 66 (112)
=.+++.+.+.+.+.+=|+++.-.....+ .| .|-|.++.+.+- -..+|+.|.+.+++.|+..
T Consensus 36 a~~~~~~~i~~~~PD~iVvi~~dH~~~f~~d~~p~f~Ig~~~~~~~~d~~~~~~~~~~~~g~~~LA~~i~~~~~~~g~~~ 115 (277)
T cd07950 36 GYEPVKQWLAEQKPDVLFMVYNDHVTSFFFDHYSAFALGVGDSYEVADEGGGPRDLPPIRGHAALAQHIAESLVADEFDL 115 (277)
T ss_pred HHHHHHHHHHHhCCCEEEEEcCcHHHHhccccCCcEEEEecccccccccccCCccCCCCCCCHHHHHHHHHHHHhcCCCe
Confidence 3567778888888888899985555544 67 899999888733 3578999999998887753
Q ss_pred cc--ccccCCCCEEEEEc----CC----EEEEee-------Chhhhhhcchhh
Q psy8849 67 VN--IEGKKSSEWLLLDL----GD----IIIHIM-------NPYIRNMYNLEE 102 (112)
Q Consensus 67 ~~--~EG~~~~~WvllD~----g~----vvVHif-------~~e~R~~Y~LE~ 102 (112)
.. .-|.+-+.|+-+-+ .+ .||+|+ .|..++.|+|=+
T Consensus 116 ~~~~~~~lDHG~~vPL~~l~p~~~~~~~~vVpi~~~~~~~~l~~~~~~~~lG~ 168 (277)
T cd07950 116 TFFQDKPLDHGCFSPLSLLLPHEDGWPVKVVPLQVGVLQFPLPTARRCYKLGQ 168 (277)
T ss_pred eeccCCCCCceeeeeHHHhCcccccCCCceEEEEEEeEecCCCCHHHHHHHHH
Confidence 22 22456677875433 12 245543 235677776643
No 28
>PRK10984 DNA-binding transcriptional regulator Crl; Provisional
Probab=63.67 E-value=7.4 Score=27.54 Aligned_cols=43 Identities=14% Similarity=0.262 Sum_probs=35.3
Q ss_pred HHHHHHhcCCCcccccccCCCCEEEEEcCCEEEEe-eChhhhhhcc
Q psy8849 55 IRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIHI-MNPYIRNMYN 99 (112)
Q Consensus 55 v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHi-f~~e~R~~Y~ 99 (112)
+.+.++..| |+-+|+....+=...||=.|-|++ -.||.|||++
T Consensus 12 Llk~f~alG--PYlRE~qc~e~~ffFDCLaVCVn~k~aPEkREFWG 55 (127)
T PRK10984 12 LIKKFTALG--PYLREGQCEENRFFFDCLAVCVNVKPAPEKREFWG 55 (127)
T ss_pred HHHHHHHhC--chhchhcccCCCEEeeeeeEeccCCCChhhhhhhh
Confidence 555666655 788899888889999999999998 4699999964
No 29
>PRK15360 pathogenicity island 2 effector protein SseE; Provisional
Probab=63.26 E-value=15 Score=26.36 Aligned_cols=45 Identities=11% Similarity=0.299 Sum_probs=30.6
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcC
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLG 83 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g 83 (112)
+-+||. --+.++.+.+-..+.+.|...|-....++| +.|.++|+.
T Consensus 86 rmlii~-~~~~~~l~~~R~rL~~vL~a~GA~~~~idg---~~Wl~~~~~ 130 (137)
T PRK15360 86 KMLIIT-DVLDEKKAMLRRKLLRILTVMGATFTQLDG---DNWTVLSAE 130 (137)
T ss_pred hheeec-cccCHHHHHHHHHHHHHHHHcCCeeeecCC---CeEEEeeHH
Confidence 344444 344566677777788888778877667765 689998853
No 30
>KOG3348|consensus
Probab=63.21 E-value=29 Score=22.92 Aligned_cols=29 Identities=17% Similarity=0.382 Sum_probs=21.0
Q ss_pred hcCCCCeEEEecCCCCC-ccCEEEEEEcCC
Q psy8849 16 DIKAQDIKVYDTSNLTN-LFDRITIASGSS 44 (112)
Q Consensus 16 ~kka~dI~vldv~~~~~-~~dy~VIaT~~S 44 (112)
+.+.+-+.|.|+++-|. .++..|+.-+.+
T Consensus 15 ~l~p~~v~V~D~SgGCG~~F~v~IvS~~Fe 44 (85)
T KOG3348|consen 15 ALEPEHVEVQDVSGGCGSMFDVVIVSAAFE 44 (85)
T ss_pred hcCceEEEEEEcCCCccceEEEEEEccccC
Confidence 34788999999999875 456666665444
No 31
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=63.04 E-value=17 Score=25.23 Aligned_cols=31 Identities=19% Similarity=0.082 Sum_probs=23.4
Q ss_pred EEEEEEcCCHHHHH--------HHHHHHHHHHHhcCCCc
Q psy8849 36 RITIASGSSKRQIN--------ALAVSIRKNIKNINNNI 66 (112)
Q Consensus 36 y~VIaT~~S~rh~~--------aia~~v~~~lk~~~~~~ 66 (112)
.+++||||+.+... ..+..+.+-|++.+++.
T Consensus 42 ~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipY 80 (126)
T TIGR01689 42 EIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPY 80 (126)
T ss_pred EEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCC
Confidence 49999999999876 34456667777888763
No 32
>smart00506 A1pp Appr-1"-p processing enzyme. Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji).
Probab=62.89 E-value=5.1 Score=26.73 Aligned_cols=64 Identities=16% Similarity=0.169 Sum_probs=38.5
Q ss_pred cCEEEEEEcCCHHHHHHHHHHHHHHHHhc--CCCccccc--ccCCCCEEEEEcC----CEEEEeeChhhhhh
Q psy8849 34 FDRITIASGSSKRQINALAVSIRKNIKNI--NNNIVNIE--GKKSSEWLLLDLG----DIIIHIMNPYIRNM 97 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v~~~lk~~--~~~~~~~E--G~~~~~WvllD~g----~vvVHif~~e~R~~ 97 (112)
+|.+|-++-.+..+...++..+.+..-.. ........ -...++|++.+.+ ..|+|+.+|..+.-
T Consensus 14 ~d~IV~~~n~~~~~~~g~a~~i~~~~g~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~Iih~~~p~~~~~ 85 (133)
T smart00506 14 ADAIVNAANSDGAHGGGVAGAIARAAGKALEKEAFRKLAGGECPVGTAVVTEGGNLPAKYVIHAVGPRASGH 85 (133)
T ss_pred CCEEEECCCcccCCCCcHHHHHHHHhChHHHHHHHHHhcCCCcCCccEEEecCCCCCCCEEEEeCCCCCCCC
Confidence 57766666666666556776666544110 00000111 1356889999986 58999999886654
No 33
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=62.80 E-value=16 Score=26.66 Aligned_cols=34 Identities=9% Similarity=0.152 Sum_probs=27.4
Q ss_pred ccCEEEEEEc-CCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 33 LFDRITIASG-SSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 33 ~~dy~VIaT~-~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
|..-=|+||| +|..+++..++.+.+.|++.|...
T Consensus 53 f~sGKivitGaks~~~~~~a~~~~~~~L~~~g~~~ 87 (174)
T cd00652 53 FSSGKMVITGAKSEEDAKLAARKYARILQKLGFPV 87 (174)
T ss_pred ECCCEEEEEecCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 3344577886 899999999999999999988654
No 34
>PF00258 Flavodoxin_1: Flavodoxin; InterPro: IPR008254 This domain is found in a number of proteins including flavodoxin and nitric-oxide synthase. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group [] and are functionally interchangeable with ferredoxins. They have been isolated from prokaryotes, cyanobacteria, and some eukaryotic algae. Nitric oxide synthase (1.14.13.39 from EC) produces nitric oxide from L-arginie and NADPH. Nitric oxide acts as a messenger molecule in the body.; GO: 0010181 FMN binding, 0016491 oxidoreductase activity; PDB: 2WC1_A 2FVX_A 2FOX_A 6NUL_A 1FVX_A 2FAX_A 1FLN_A 1FLA_A 4NLL_A 2FDX_A ....
Probab=62.55 E-value=13 Score=25.15 Aligned_cols=40 Identities=15% Similarity=0.343 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCC------ccCEEEEEEc
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTN------LFDRITIASG 42 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~------~~dy~VIaT~ 42 (112)
+++++++.|++.|.+ ++-++.++|+..... -.+.+|+++.
T Consensus 9 ~te~~A~~ia~~l~~-~g~~~~~~~~~~~~~~~~~~~~~~~~i~~~s 54 (143)
T PF00258_consen 9 NTEKMAEAIAEGLRE-RGVEVRVVDLDDFDDSPSDLSEYDLLIFGVS 54 (143)
T ss_dssp HHHHHHHHHHHHHHH-TTSEEEEEEGGGSCHHHHHHCTTSEEEEEEE
T ss_pred hHHHHHHHHHHHHHH-cCCceeeechhhhhhhhhhhhhhceeeEeec
Confidence 368899999999998 666899999988762 2366666654
No 35
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=62.40 E-value=17 Score=26.70 Aligned_cols=31 Identities=13% Similarity=0.150 Sum_probs=25.5
Q ss_pred CEEEEEEc-CCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 35 DRITIASG-SSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 35 dy~VIaT~-~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
.-=++||| +|...++..++.+.+.|++.|.+
T Consensus 55 SGKiviTGaks~e~a~~a~~~i~~~L~~~g~~ 86 (174)
T cd04516 55 SGKMVCTGAKSEDDSKLAARKYARIIQKLGFP 86 (174)
T ss_pred CCeEEEEecCCHHHHHHHHHHHHHHHHHcCCC
Confidence 44467775 99999999999999999998865
No 36
>PRK12276 putative heme peroxidase; Provisional
Probab=62.26 E-value=41 Score=26.28 Aligned_cols=51 Identities=10% Similarity=0.163 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHhcCCCCe------EEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 5 KRQIIVIKILKDIKAQDI------KVYDTSNLTNLFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI------~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
+.++++..+|++.....+ .++++.+.. +|+|+...+.+...++++-..+++
T Consensus 35 ~~~~e~~~~l~~~~~~~~~~~g~~~~Y~v~G~r--ADlm~w~~~~~~~~lq~~~~~~~~ 91 (248)
T PRK12276 35 AAVDEFLAFLEKWEEVEAAKQGSHAIYSIVGQK--ADLMLMILRPTMEELNEIENELNK 91 (248)
T ss_pred HHHHHHHHHHHHHhhcccccccceeEEEeeccc--ceEEEEEeCCCHHHHHHHHHHHHh
Confidence 455666777766444443 389999866 899999999999999999888875
No 37
>PF13277 YmdB: YmdB-like protein; PDB: 2CV9_B 2Z06_C.
Probab=62.20 E-value=11 Score=29.56 Aligned_cols=62 Identities=11% Similarity=0.181 Sum_probs=39.2
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCCCcc---------------------------cccccCCCCEEEEEcCCEEEEe
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINNNIV---------------------------NIEGKKSSEWLLLDLGDIIIHI 89 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~---------------------------~~EG~~~~~WvllD~g~vvVHi 89 (112)
||||-|.|..|...|.....++|.+.|+..+ ..+|.+...|.+++.++.-|-|
T Consensus 30 fVIaNgENaa~G~Git~~~~~~L~~~GvDviT~GNH~wdkkei~~~i~~~~~ilRPaN~p~~~pG~G~~i~~~~g~kv~V 109 (253)
T PF13277_consen 30 FVIANGENAAGGFGITPKIAEELFKAGVDVITMGNHIWDKKEIFDFIDKEPRILRPANYPPGTPGRGYRIFEKNGKKVAV 109 (253)
T ss_dssp EEEEE-TTTTTTSS--HHHHHHHHHHT-SEEE--TTTTSSTTHHHHHHH-SSEE--TTS-TT-SSBSEEEEEETTEEEEE
T ss_pred EEEECCcccCCCCCCCHHHHHHHHhcCCCEEecCcccccCcHHHHHHhcCCCcEECCCCCCCCCcCcEEEEEECCEEEEE
Confidence 6778888888888888888888777766311 1345677899999999887766
Q ss_pred eChhhhhhc
Q psy8849 90 MNPYIRNMY 98 (112)
Q Consensus 90 f~~e~R~~Y 98 (112)
..=..|-|.
T Consensus 110 iNl~Gr~fm 118 (253)
T PF13277_consen 110 INLMGRVFM 118 (253)
T ss_dssp EEEE--TTS
T ss_pred EECcccccC
Confidence 655555544
No 38
>PRK09267 flavodoxin FldA; Validated
Probab=62.16 E-value=17 Score=25.53 Aligned_cols=39 Identities=15% Similarity=0.217 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCC----ccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTN----LFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~----~~dy~VIaT~~ 43 (112)
+++++++.|++.|.. .++.++|+++... -.|.+||+|..
T Consensus 14 nT~~vA~~Ia~~l~~---~~~~~~~~~~~~~~~l~~~d~vi~g~pt 56 (169)
T PRK09267 14 NTEDIAKMIQKKLGK---DVADVVDIAKASKEDFEAYDLLILGIPT 56 (169)
T ss_pred hHHHHHHHHHHHhCC---CceEEEEhhhCCHhhHhhCCEEEEEecC
Confidence 367788888888853 3678888877532 25888998654
No 39
>PRK03669 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=60.91 E-value=10 Score=28.79 Aligned_cols=21 Identities=10% Similarity=0.213 Sum_probs=16.1
Q ss_pred CEEEEEEcCCHHHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAVSI 55 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v 55 (112)
=.+||||||+...++.+++.+
T Consensus 41 i~~viaTGR~~~~i~~~~~~l 61 (271)
T PRK03669 41 VPVILCSSKTAAEMLPLQQTL 61 (271)
T ss_pred CeEEEEcCCCHHHHHHHHHHh
Confidence 479999999988877665443
No 40
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=60.35 E-value=35 Score=21.59 Aligned_cols=54 Identities=13% Similarity=0.306 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCC--------------EEEEeeChhhhhhcchhhh
Q psy8849 50 ALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGD--------------IIIHIMNPYIRNMYNLEEI 103 (112)
Q Consensus 50 aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~--------------vvVHif~~e~R~~Y~LE~L 103 (112)
.++..+...+.+.|.+..-++.....+|+++|++. .+|=++.++.-....+.++
T Consensus 15 t~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~s~~~~~~~ 82 (104)
T cd02042 15 TTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPLDLDGLEKL 82 (104)
T ss_pred HHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHHHHHHHHHH
Confidence 34555555565567666666666668999999843 3455555555444444433
No 41
>PRK08105 flavodoxin; Provisional
Probab=59.46 E-value=26 Score=24.59 Aligned_cols=42 Identities=10% Similarity=0.197 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCc----cCEEEEEEcCC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNL----FDRITIASGSS 44 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~----~dy~VIaT~~S 44 (112)
+++.+++.+++.|.+. +-++.++++.....+ ++++|++|.+-
T Consensus 14 nte~~A~~l~~~l~~~-g~~~~~~~~~~~~~~~~~~~~~vi~~~sT~ 59 (149)
T PRK08105 14 NALLVAEEAEAILTAQ-GHEVTLFEDPELSDWQPYQDELVLVVTSTT 59 (149)
T ss_pred HHHHHHHHHHHHHHhC-CCceEEechhhCCchhcccCCeEEEEECCC
Confidence 3678889999999864 567888888765433 46777777653
No 42
>PF02391 MoaE: MoaE protein; InterPro: IPR003448 This family contains the MoaE protein that is involved in biosynthesis of molybdopterin []. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulphurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2WP4_B 2OMD_B 1NVJ_E 1FM0_E 3BII_E 1NVI_E 1FMA_E 2QIE_K 2Q5W_E 3RPF_A ....
Probab=59.30 E-value=38 Score=23.01 Aligned_cols=58 Identities=10% Similarity=0.049 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCcc--CEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLF--DRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~--dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
++|.+...++.+.....++.+..--+.-... -.+|.++|...+..-..++.+.+.+|+
T Consensus 56 ~~l~~I~~e~~~~~~~~~v~i~HR~G~l~vGe~~v~V~vsa~hR~eaf~A~~~~id~iK~ 115 (117)
T PF02391_consen 56 KELEEIAEEARERFGIVDVAIVHRVGRLKVGEPIVLVAVSAPHRKEAFEACEYIIDRIKK 115 (117)
T ss_dssp HHHHHHHHHHHHHSTTCEEEEEEEEEEEETTSEEEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCeEEEEEEeeCCCCCCCeEEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 3444445555556667888877644433333 356667777777788888888888886
No 43
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=57.71 E-value=64 Score=27.45 Aligned_cols=91 Identities=20% Similarity=0.208 Sum_probs=59.5
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc-----ccccccCCCCEEEE
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNI-----VNIEGKKSSEWLLL 80 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~-----~~~EG~~~~~Wvll 80 (112)
-++.|.+.+++ +--+++|+|-=+ +-|++ -+=....|-.|+|..+.++.+..|..++.. ...||.=.+-=+|=
T Consensus 156 ~~e~I~~~l~~-~~p~lvVIDSIQ-T~~s~-~~~SapGsVsQVRe~t~~L~~~AK~~~i~~fiVGHVTKeG~IAGPrvLE 232 (456)
T COG1066 156 NLEDIIAELEQ-EKPDLVVIDSIQ-TLYSE-EITSAPGSVSQVREVAAELMRLAKTKNIAIFIVGHVTKEGAIAGPRVLE 232 (456)
T ss_pred CHHHHHHHHHh-cCCCEEEEeccc-eeecc-cccCCCCcHHHHHHHHHHHHHHHHHcCCeEEEEEEEcccccccCchhee
Confidence 35677777777 446888888543 22222 223445789999999999999999988752 34666544555665
Q ss_pred EcCCEEEEeeChhhhhhcch
Q psy8849 81 DLGDIIIHIMNPYIRNMYNL 100 (112)
Q Consensus 81 D~g~vvVHif~~e~R~~Y~L 100 (112)
.+-|.|++ |.-+....|++
T Consensus 233 HmVDtVly-FEGd~~~~~Ri 251 (456)
T COG1066 233 HMVDTVLY-FEGDRHSRYRI 251 (456)
T ss_pred eeeeEEEE-EeccCCCceee
Confidence 66666666 55555555554
No 44
>PLN02390 molybdopterin synthase catalytic subunit
Probab=57.63 E-value=58 Score=22.21 Aligned_cols=65 Identities=11% Similarity=-0.026 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCccC--EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCccccc
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLFD--RITIASGSSKRQINALAVSIRKNIKNINNNIVNIE 70 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~d--y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~E 70 (112)
++-+...++.+.-...++.+..=-+.-...| .+|.+++...+..-..++.+.+.+|.. .|..+.|
T Consensus 38 ~l~~I~~e~~~~~~~~~v~i~HR~G~l~vge~~v~v~v~s~HR~~Af~A~~~~id~lK~~-vPIWKkE 104 (111)
T PLN02390 38 ELRKICDEARSRWSLHKIAVAHRLGPVPVGETSVFVAVSSVHRADALDACKFLIDELKAS-VPIWKKE 104 (111)
T ss_pred HHHHHHHHHHHhCCCceEEEEEeeecccCCCEEEEEEEECCCHHHHHHHHHHHHHHHhhc-CCEEEee
Confidence 3434444445555678888887666544444 455566666666777888899999874 4444444
No 45
>cd07366 3MGA_Dioxygenase Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate. 3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to 3-O-Methylgallate by O-demethylase. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=57.19 E-value=27 Score=28.16 Aligned_cols=96 Identities=9% Similarity=0.097 Sum_probs=63.7
Q ss_pred HHHHHHHHHhcCCCCeEEEecCCCCCccC----EEEEEEcCCHH----H--------------------------HHHHH
Q psy8849 7 QIIVIKILKDIKAQDIKVYDTSNLTNLFD----RITIASGSSKR----Q--------------------------INALA 52 (112)
Q Consensus 7 ~~~i~~~l~~kka~dI~vldv~~~~~~~d----y~VIaT~~S~r----h--------------------------~~aia 52 (112)
.+++.+.+.+.+.+=|+++--.....+.+ .|.|.+|.+-. + -..+|
T Consensus 75 ~~~~~~~i~~~~PDvlVIispDH~~~f~~~~~P~f~I~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~eLA 154 (328)
T cd07366 75 LDRLADFIRAARIDVAVIVGDDQKELFDEALLPAFAIYYGDTITNGPRTREQLDRMPPHEAAAGYAPDEARTYPCHPELA 154 (328)
T ss_pred HHHHHHHHHHhCCCEEEEEcCccHhhhccccCCceEEeecceeecChhhccccccccccccccccCCCCCcCCCCCHHHH
Confidence 46778888888888778776656656666 88888766532 1 25689
Q ss_pred HHHHHHHHhcCCCcccc-----c-ccCCCCEEEEEcC----CE-EEEeeC--------hhhhhhcchhh
Q psy8849 53 VSIRKNIKNINNNIVNI-----E-GKKSSEWLLLDLG----DI-IIHIMN--------PYIRNMYNLEE 102 (112)
Q Consensus 53 ~~v~~~lk~~~~~~~~~-----E-G~~~~~WvllD~g----~v-vVHif~--------~e~R~~Y~LE~ 102 (112)
+.|.+.+.+.|+..... + |.+-+-|+++-+. ++ ||+|+. |..++.|+|=+
T Consensus 155 ~~I~~~l~~~G~dv~~~~~~~~~~~lDHG~~~~l~~~~p~~~iPVVpisin~~~~p~~ps~~r~y~lG~ 223 (328)
T cd07366 155 RHLIKHTVADGFDVAALDHLPDTVGIPHAFGFIYRRIMGDLVIPVVPVLINTFYPPNQPSARRCFEFGR 223 (328)
T ss_pred HHHHHHHHHcCCCeeeecccCcccCCCcchhhHHHHhcCCCCCcEEEEeecCCCCCCCCCHHHHHHHHH
Confidence 99999999888864321 1 3445556665543 44 777753 35577777644
No 46
>PF07417 Crl: Transcriptional regulator Crl; InterPro: IPR009986 This family contains the bacterial transcriptional regulator Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria [].These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. They also stimulate RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.; GO: 0016987 sigma factor activity, 0045893 positive regulation of transcription, DNA-dependent, 0005737 cytoplasm; PDB: 3RPJ_A.
Probab=57.01 E-value=6 Score=27.92 Aligned_cols=43 Identities=14% Similarity=0.281 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCcccccccCCCCEEEEEcCCEEEEe-eChhhhhhcc
Q psy8849 55 IRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIHI-MNPYIRNMYN 99 (112)
Q Consensus 55 v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHi-f~~e~R~~Y~ 99 (112)
+.+.++..| |+-+|+....+=...||=.|.|++ -.||.|+|++
T Consensus 10 Llk~f~alG--PYlRE~qc~e~~ffFDCLaVCVn~k~aPEkREFWG 53 (125)
T PF07417_consen 10 LLKKFAALG--PYLREGQCQEDRFFFDCLAVCVNVKKAPEKREFWG 53 (125)
T ss_dssp HHHHHHTT---TTB-GGG-BTTEEEEEEEEEES-TTS-CCC--EEE
T ss_pred HHHHHHhhC--chhcccccccCcEeeechhhhccCCCChhhhhhhh
Confidence 445565554 788899988999999999999998 4799999964
No 47
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=56.98 E-value=12 Score=27.91 Aligned_cols=20 Identities=5% Similarity=0.160 Sum_probs=15.5
Q ss_pred CEEEEEEcCCHHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAVS 54 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~ 54 (112)
-.|+|||||+...++.+++.
T Consensus 37 ~~~~iaTGR~~~~~~~~~~~ 56 (270)
T PRK10513 37 VNVVLTTGRPYAGVHRYLKE 56 (270)
T ss_pred CEEEEecCCChHHHHHHHHH
Confidence 46999999999877665543
No 48
>PRK07308 flavodoxin; Validated
Probab=56.93 E-value=46 Score=22.74 Aligned_cols=42 Identities=19% Similarity=0.246 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEcCC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASGSS 44 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~~S 44 (112)
+++++++.|++.|.+. +.++.++|+.... .-.|.+|++|.+-
T Consensus 14 nTe~iA~~ia~~l~~~-g~~~~~~~~~~~~~~~l~~~d~vi~g~~t~ 59 (146)
T PRK07308 14 NTEEIADIVADKLREL-GHDVDVDECTTVDASDFEDADIAIVATYTY 59 (146)
T ss_pred hHHHHHHHHHHHHHhC-CCceEEEecccCCHhHhccCCEEEEEeCcc
Confidence 4788999999999754 4467788887642 2347888887653
No 49
>PLN00062 TATA-box-binding protein; Provisional
Probab=56.71 E-value=24 Score=26.06 Aligned_cols=31 Identities=13% Similarity=0.160 Sum_probs=25.0
Q ss_pred CEEEEEEc-CCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 35 DRITIASG-SSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 35 dy~VIaT~-~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
.-=|+||| +|...++..++.+.+.+++.|.+
T Consensus 55 SGKiviTGaks~e~a~~a~~~~~~~L~~lg~~ 86 (179)
T PLN00062 55 SGKMVCTGAKSEHDSKLAARKYARIIQKLGFP 86 (179)
T ss_pred CCeEEEEecCCHHHHHHHHHHHHHHHHHcCCC
Confidence 33467776 79999999999999999998874
No 50
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=56.58 E-value=40 Score=21.15 Aligned_cols=43 Identities=12% Similarity=0.139 Sum_probs=32.0
Q ss_pred cCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 17 IKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 17 kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
.|+-||.++++...++ ..++++.|| +...+++..+...+...+
T Consensus 21 ~KaA~V~l~~~~~~~~-g~~~~~v~G-dvs~V~~Av~a~~~~~~~ 63 (75)
T smart00877 21 LKAANVELVGYESIGG-GKVTVIITG-DVAAVRAAVEAGLEAAER 63 (75)
T ss_pred hhhcCcEEEEEEecCC-CEEEEEEEE-cHHHHHHHHHHHHHHHhh
Confidence 5677999999988776 679999999 666666666666665543
No 51
>TIGR01487 SPP-like sucrose-phosphate phosphatase-like hydrolase, Archaeal. TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases.
Probab=55.39 E-value=14 Score=26.86 Aligned_cols=19 Identities=26% Similarity=0.349 Sum_probs=15.2
Q ss_pred CEEEEEEcCCHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAV 53 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~ 53 (112)
-.++|||||+...++.+++
T Consensus 35 ~~~~~~TGR~~~~~~~~~~ 53 (215)
T TIGR01487 35 IPVSLVTGNTVPFARALAV 53 (215)
T ss_pred CEEEEEcCCcchhHHHHHH
Confidence 4789999999988776654
No 52
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=55.23 E-value=67 Score=22.20 Aligned_cols=72 Identities=14% Similarity=0.141 Sum_probs=49.0
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCC--------CccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCE
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLT--------NLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEW 77 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~--------~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~W 77 (112)
.++.+.+.+.... -|++++|.+... ..+|++|+.+..+..-+.++... .+.+++.+..
T Consensus 82 ~l~~~l~~l~~~~-yD~iiiD~~~~~~~~~~~~l~~ad~viv~~~~~~~~i~~~~~~-~~~l~~~~~~------------ 147 (195)
T PF01656_consen 82 LLREILESLIKSD-YDYIIIDTPPGLSDPVRNALAAADYVIVPIEPDPSSIEGAERL-IELLKRLGKK------------ 147 (195)
T ss_dssp HHHHHHHHHHHTT-SSEEEEEECSSSSHHHHHHHHTSSEEEEEEESSHHHHHHHHHH-HHHHHHHTHT------------
T ss_pred HHHHHHHHhhhcc-ccceeecccccccHHHHHHHHhCceeeeecCCcHHHHHHHHHH-HHHHHHhccc------------
Confidence 3455555544444 999999998752 46799999999999887776654 4566654432
Q ss_pred EEEEcCCEEEEeeChh
Q psy8849 78 LLLDLGDIIIHIMNPY 93 (112)
Q Consensus 78 vllD~g~vvVHif~~e 93 (112)
++...+|++-+.+.
T Consensus 148 --~~~~~vv~N~v~~~ 161 (195)
T PF01656_consen 148 --LKIIGVVINRVDPG 161 (195)
T ss_dssp --EEEEEEEEEEETSC
T ss_pred --cceEEEEEeeeCCC
Confidence 55556777777443
No 53
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=55.08 E-value=28 Score=24.43 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHH
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQ 47 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh 47 (112)
+.++++.|++.+.+.=..+|-++|-. -+||||+...|=
T Consensus 2 ~~~~Aq~Iv~~~~~~i~~~inimd~~-------G~IIAStd~~RI 39 (135)
T PF05651_consen 2 SKELAQKIVDEIMEIIGYNINIMDEN-------GIIIASTDPERI 39 (135)
T ss_pred CHHHHHHHHHHHHHHcCCCEEEECCC-------cEEEecCChhhc
Confidence 46789999999999999999998854 479999999883
No 54
>PF07801 DUF1647: Protein of unknown function (DUF1647); InterPro: IPR012444 This entry consists of hypothetical proteins of unknown function.
Probab=54.35 E-value=27 Score=25.06 Aligned_cols=46 Identities=24% Similarity=0.256 Sum_probs=33.6
Q ss_pred HHHHHhcCCCC--eEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 11 IKILKDIKAQD--IKVYDTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 11 ~~~l~~kka~d--I~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
++.|++.+..| -..+|++....-.+-+|++||.|+-|.......+.
T Consensus 34 l~~Le~l~l~~~~~~~v~l~~~~~n~~~vvfVSa~S~~h~~~~~~~i~ 81 (142)
T PF07801_consen 34 LETLEDLKLLDNPGPFVDLSSSSKNSSDVVFVSATSDNHFNESMKSIS 81 (142)
T ss_pred HHHHhhhhhccCCCcceecccccccCCccEEEEEecchHHHHHHHHHH
Confidence 45566665433 26677877666677899999999999988777654
No 55
>TIGR00254 GGDEF diguanylate cyclase (GGDEF) domain. The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein.
Probab=54.31 E-value=59 Score=21.27 Aligned_cols=56 Identities=16% Similarity=0.032 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
.++++..+++.|.+.-..+..+.-++ -.+|++++++.+......+++.+.+.++..
T Consensus 56 ~~~ll~~~a~~l~~~~~~~~~i~r~~----~~~f~il~~~~~~~~~~~l~~~i~~~~~~~ 111 (165)
T TIGR00254 56 GDEVLREVARILQSSVRGSDVVGRYG----GEEFVVILPGTPLEDALSKAERLRDAINSK 111 (165)
T ss_pred HHHHHHHHHHHHHHhcCcCCEEEEec----CCeEEEEeCCCChHHHHHHHHHHHHHHHhC
Confidence 35677888888877655554444433 247889988888888888888888887654
No 56
>PF07725 LRR_3: Leucine Rich Repeat; InterPro: IPR011713 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by the IPR001611 from INTERPRO model.
Probab=54.22 E-value=5.6 Score=19.38 Aligned_cols=11 Identities=27% Similarity=0.643 Sum_probs=8.6
Q ss_pred hcchhhhcccc
Q psy8849 97 MYNLEEIWGEK 107 (112)
Q Consensus 97 ~Y~LE~LW~~~ 107 (112)
+.+||+||.+-
T Consensus 9 ~S~lekLW~G~ 19 (20)
T PF07725_consen 9 YSKLEKLWEGV 19 (20)
T ss_pred CCChHHhcCcc
Confidence 56899999763
No 57
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=54.18 E-value=73 Score=22.26 Aligned_cols=60 Identities=13% Similarity=-0.002 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCC--------CccC-EEE-----EEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLT--------NLFD-RIT-----IASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~--------~~~d-y~V-----IaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
...|++.+-+++-+-+.-+.--|-++... .-.| -|| |.+|+|..+-+.+++.|-+.+++.
T Consensus 18 ~~~Ll~~l~~~l~~sglF~~~~IK~Ra~~~~~y~vgdg~~~~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l~~~ 91 (126)
T PRK15031 18 LPGLFAKVNQALAATGIFPLGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFALIKAH 91 (126)
T ss_pred HHHHHHHHHHHHHhCCCCCccccEeeeeecCcEEEcCCCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHH
Confidence 45788888888877665554444444321 0111 222 667999999999999999999875
No 58
>PF04455 Saccharop_dh_N: LOR/SDH bifunctional enzyme conserved region ; InterPro: IPR007545 Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to saccharopine dehydrogenase conserved region (IPR005097 from INTERPRO) in eukaryotes [, ].; PDB: 3C2Q_B 3MGJ_A.
Probab=53.54 E-value=68 Score=21.73 Aligned_cols=56 Identities=11% Similarity=0.079 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhcCC-CCeEEEecCCCCC-ccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 6 RQIIVIKILKDIKA-QDIKVYDTSNLTN-LFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 6 l~~~i~~~l~~kka-~dI~vldv~~~~~-~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
++.++.+.+.+.+| -.|.=+++..... .+-.-+..+|.+..|+.+|...|.+.-..
T Consensus 17 il~~vLD~I~d~GG~F~i~~~~vG~~~~d~S~a~l~V~a~d~~~L~~Il~~L~~lga~ 74 (103)
T PF04455_consen 17 ILNRVLDIIMDMGGDFEILEFDVGKSKDDTSYARLQVSAPDEEHLDEILDELHQLGAV 74 (103)
T ss_dssp HHHHHHHHHHHTT-EEEEEEEE--SSTTS-EEEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHhcCCCEEEEEEEeCCCCCCceeEEEEEecCCHHHHHHHHHHHHHHcCC
Confidence 56677787778888 7888899987643 33345668999999999999988865543
No 59
>PRK13363 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=53.29 E-value=31 Score=27.91 Aligned_cols=95 Identities=12% Similarity=0.144 Sum_probs=61.9
Q ss_pred HHHHHHHHHhcCCCCeEEEecCCCCCcc----CEEEEEEcCCHHH--------------------------------HHH
Q psy8849 7 QIIVIKILKDIKAQDIKVYDTSNLTNLF----DRITIASGSSKRQ--------------------------------INA 50 (112)
Q Consensus 7 ~~~i~~~l~~kka~dI~vldv~~~~~~~----dy~VIaT~~S~rh--------------------------------~~a 50 (112)
.+++.+.+.+.+.+=|+++--.....+. ++|.|.+|.+-+= -..
T Consensus 77 ~~~~~~~i~~~~PDvlViispdh~~~F~~~~~p~f~I~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~gd~e 156 (335)
T PRK13363 77 IERMRDAIEAARIDVAVIVGNDQMELFTTDNNPAFAIYYGETIRNNPASREKLPSLPPGVKAAMPGYMPDAETTYPVVPE 156 (335)
T ss_pred HHHHHHHHHHhCCCEEEEEcCCchhhcccccCCceEEeecceeccchhhccccccccccccccccccCCCCCcCCCCCHH
Confidence 4677788888888877887555534443 8899988876651 267
Q ss_pred HHHHHHHHHHhcCCCcccc------cccCCCCEEEEEc----CCE-EEEeeC--------hhhhhhcchh
Q psy8849 51 LAVSIRKNIKNINNNIVNI------EGKKSSEWLLLDL----GDI-IIHIMN--------PYIRNMYNLE 101 (112)
Q Consensus 51 ia~~v~~~lk~~~~~~~~~------EG~~~~~WvllD~----g~v-vVHif~--------~e~R~~Y~LE 101 (112)
+|++|.+.+++.|+..... .|.+-+-|+++-+ .++ ||.|.. +..++.|+|=
T Consensus 157 LA~~I~~~l~~~G~d~~~~~~~~~~~glDHG~~~pl~~l~p~~dipVVpIsl~~~~~P~~~s~~~~~~lG 226 (335)
T PRK13363 157 LARHMIRRLVDDGFDITALDRLPDGEGEGHAFGFVHRQLMKDNVLPTVPVLVNTFYPPNQPTPRRCIALG 226 (335)
T ss_pred HHHHHHHHHHHcCCCeeeecccccccCCCccchhhHHHhcCCCCCcEEEEEeccCCCcCCCCHHHHHHHH
Confidence 9999999999988864321 2345566766633 244 666653 3446666653
No 60
>PRK08367 porA pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed
Probab=53.17 E-value=66 Score=26.50 Aligned_cols=42 Identities=12% Similarity=0.134 Sum_probs=28.6
Q ss_pred HhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 15 KDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 15 ~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
.++-++....++--+ +.-+|++||+.|.+.+.++...+.+++
T Consensus 244 ~~~~grky~~~e~yg-~eDAe~viV~~GS~~~~~keav~~LR~ 285 (394)
T PRK08367 244 EKKFGRKYQKIEEYR-TEDAEIIFVTMGSLAGTLKEFVDKLRE 285 (394)
T ss_pred HHHhCCccceeEEeC-CCCCCEEEEEeCccHHHHHHHHHHHHh
Confidence 333444444444222 234899999999999999988887764
No 61
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=53.00 E-value=17 Score=26.34 Aligned_cols=18 Identities=22% Similarity=0.136 Sum_probs=14.0
Q ss_pred CEEEEEEcCCHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALA 52 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia 52 (112)
-.|+|||||+...++.++
T Consensus 37 ~~~~iaTGR~~~~~~~~~ 54 (230)
T PRK01158 37 IPVILATGNVLCFARAAA 54 (230)
T ss_pred CEEEEEcCCchHHHHHHH
Confidence 478999999988766544
No 62
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=52.83 E-value=52 Score=21.17 Aligned_cols=38 Identities=8% Similarity=0.044 Sum_probs=31.4
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~ 43 (112)
+.++.++.+.+-.++++|.-|+.+++.-. .. +|+|+|+
T Consensus 26 d~d~Al~eM~e~A~~lGAnAVVGvr~d~s---~~-eV~ayGT 63 (74)
T TIGR03884 26 NVDEIVENLREKVKAKGGMGLIAFRITCA---DG-KFLGYGT 63 (74)
T ss_pred CHHHHHHHHHHHHHHcCCCEEEEEEEEcC---CC-EEEEEEE
Confidence 35678889999999999999999988754 22 9999986
No 63
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.
Probab=52.51 E-value=41 Score=22.92 Aligned_cols=41 Identities=10% Similarity=0.254 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHHHHhcCCCCeE-EEecCCCC----Cc--cCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIK-VYDTSNLT----NL--FDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~-vldv~~~~----~~--~dy~VIaT~~ 43 (112)
+++++++.|++.|...+ .++. +.++.+.. .+ +|.+||+|..
T Consensus 13 nTe~iA~~ia~~l~~~g-~~v~~~~~~~~~~~~~~~~~~~d~iilgs~t 60 (140)
T TIGR01754 13 NTEEVAFMIQDYLQKDG-HEVDILHRIGTLADAPLDPENYDLVFLGTWT 60 (140)
T ss_pred hHHHHHHHHHHHHhhCC-eeEEecccccccccCcCChhhCCEEEEEcCe
Confidence 47788899999887544 3454 45555321 22 4778888863
No 64
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=52.37 E-value=7.7 Score=25.96 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=20.8
Q ss_pred ccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 33 LFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
--|++||+||.+. .-+..++.+.+++.|+.
T Consensus 53 ~pe~liiGtG~~~---~~~~~~~~~~l~~~GI~ 82 (110)
T PF04430_consen 53 KPEVLIIGTGKRQ---LFLPPELREYLRKKGIG 82 (110)
T ss_dssp S-SEEEEEETTS----SECTHHHHHHHHTTT-E
T ss_pred CCcEEEEccCCcc---ccCCHHHHHHHHHcCCe
Confidence 4599999999983 33456677888888764
No 65
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=51.96 E-value=42 Score=19.83 Aligned_cols=27 Identities=15% Similarity=0.336 Sum_probs=22.6
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHh-cCCC
Q psy8849 39 IASGSSKRQINALAVSIRKNIKN-INNN 65 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~-~~~~ 65 (112)
+..|+|..|-+++++.|-+.+.+ .|.+
T Consensus 8 l~~grt~eqk~~l~~~it~~l~~~lg~p 35 (64)
T PRK01964 8 LLEGRPEEKIKNLIREVTEAISATLDVP 35 (64)
T ss_pred EeCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 45699999999999999998876 5665
No 66
>TIGR00099 Cof-subfamily Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences.
Probab=51.30 E-value=18 Score=26.95 Aligned_cols=19 Identities=11% Similarity=0.375 Sum_probs=14.7
Q ss_pred CEEEEEEcCCHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAV 53 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~ 53 (112)
-.|+||||++.+.++.+.+
T Consensus 33 ~~~~iaTGR~~~~~~~~~~ 51 (256)
T TIGR00099 33 IKVVLATGRPYKEVKNILK 51 (256)
T ss_pred CeEEEEeCCCHHHHHHHHH
Confidence 5799999999877665544
No 67
>PRK10976 putative hydrolase; Provisional
Probab=51.10 E-value=16 Score=27.33 Aligned_cols=20 Identities=10% Similarity=0.200 Sum_probs=15.3
Q ss_pred CEEEEEEcCCHHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAVS 54 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~ 54 (112)
-.|+|||||+...++.+.+.
T Consensus 36 ~~~~iaTGR~~~~~~~~~~~ 55 (266)
T PRK10976 36 IHFVFATGRHHVDVGQIRDN 55 (266)
T ss_pred CEEEEEcCCChHHHHHHHHh
Confidence 58999999999876655443
No 68
>PF01820 Dala_Dala_lig_N: D-ala D-ala ligase N-terminus; InterPro: IPR011127 This entry represents the N-terminal region of the D-alanine--D-alanine ligase enzyme (6.3.2.4 from EC) which is thought to be involved in substrate binding []. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [].; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005618 cell wall; PDB: 4EG0_B 3E5N_A 3RFC_A 3R5F_A 1IOV_A 1IOW_A 2DLN_A 3Q1K_D 3I12_C 3N8D_B ....
Probab=50.87 E-value=20 Score=24.25 Aligned_cols=47 Identities=17% Similarity=0.236 Sum_probs=31.9
Q ss_pred EEEEEEcCCHHHHHHH--HHHHHHHHHhcCCCcccccccCCCCEEEEEc
Q psy8849 36 RITIASGSSKRQINAL--AVSIRKNIKNINNNIVNIEGKKSSEWLLLDL 82 (112)
Q Consensus 36 y~VIaT~~S~rh~~ai--a~~v~~~lk~~~~~~~~~EG~~~~~WvllD~ 82 (112)
..||+=|+|..|==++ |..|.+.|.+.+..+.-+-=.+++.|.+.+.
T Consensus 3 v~vlfGG~S~EheVSl~Sa~~v~~~L~~~~y~v~~i~i~k~g~~~~~~~ 51 (117)
T PF01820_consen 3 VAVLFGGRSSEHEVSLRSARNVYEALDKEKYEVIPIYIDKDGRWYLGEG 51 (117)
T ss_dssp EEEEEETSSTTHHHHHHHHHHHHHHSHTTTEEEEEEEETTTSCEEEEHH
T ss_pred EEEEeccCchhHHHHHHHHHHHHHHHhhhcceEEEEeecCCCCEEEccc
Confidence 3689999999996654 6678888876655533322134568998874
No 69
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=50.44 E-value=58 Score=27.38 Aligned_cols=42 Identities=7% Similarity=0.177 Sum_probs=33.1
Q ss_pred CHHHHHHHHHHHHHhcC-CCCeEEEecCCCC--C------ccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIK-AQDIKVYDTSNLT--N------LFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kk-a~dI~vldv~~~~--~------~~dy~VIaT~~ 43 (112)
+++++++.|++.+.+.+ +.++.++++.... . -+|.+|++|.+
T Consensus 264 nTe~mA~~ia~gl~~~g~gv~v~~~~v~~~~~~~i~~~~~~ad~vilGspT 314 (479)
T PRK05452 264 NTRMMADAIAQGIAEVDPRVAVKIFNVARSDKNEILTNVFRSKGVLVGSST 314 (479)
T ss_pred HHHHHHHHHHHHHHhhCCCceEEEEECCCCCHHHHHhHHhhCCEEEEECCc
Confidence 47889999999999885 4688999998643 1 26899999866
No 70
>PRK10530 pyridoxal phosphate (PLP) phosphatase; Provisional
Probab=50.02 E-value=18 Score=26.88 Aligned_cols=19 Identities=16% Similarity=0.289 Sum_probs=14.2
Q ss_pred CEEEEEEcCCHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAV 53 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~ 53 (112)
-.|+|||||+...+..+++
T Consensus 37 ~~~~iaTGR~~~~~~~~~~ 55 (272)
T PRK10530 37 YKVIIVTGRHHVAIHPFYQ 55 (272)
T ss_pred CEEEEEcCCChHHHHHHHH
Confidence 4699999999876655443
No 71
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=49.45 E-value=41 Score=23.76 Aligned_cols=39 Identities=18% Similarity=0.398 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEcC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASGS 43 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~~ 43 (112)
+++++++.|++.|.. ..+.++|+.... .-.|.+|++|+.
T Consensus 12 nTe~vA~~Ia~~l~~---~~~~i~~~~~~~~~~l~~~d~ii~gspt 54 (167)
T TIGR01752 12 NTEGIAEKIQKELGE---DDVDVFNIAKASKEDLNAYDKLILGTPT 54 (167)
T ss_pred hHHHHHHHHHHHhCC---CceEEEEcccCCHhHHhhCCEEEEEecC
Confidence 467888888888753 457788887643 234888888865
No 72
>PF14839 DOR: DOR family
Probab=49.26 E-value=12 Score=28.67 Aligned_cols=13 Identities=38% Similarity=0.940 Sum_probs=11.0
Q ss_pred cCCCCEEEEEcCC
Q psy8849 72 KKSSEWLLLDLGD 84 (112)
Q Consensus 72 ~~~~~WvllD~g~ 84 (112)
..+++|+|||+.+
T Consensus 4 ~edD~WilVD~~~ 16 (216)
T PF14839_consen 4 EEDDEWILVDFID 16 (216)
T ss_pred cccCCeEEEEecC
Confidence 4578999999987
No 73
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=49.03 E-value=28 Score=21.84 Aligned_cols=44 Identities=11% Similarity=0.121 Sum_probs=35.7
Q ss_pred cCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 17 IKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 17 kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
.|+-||.++++...+ -.-++++.+| +...+++..+...+.+++.
T Consensus 22 lKaa~V~l~~~~~~~-~g~~~~~i~G-~vs~V~~Av~a~~~~~~~~ 65 (75)
T PF00936_consen 22 LKAANVELVEIELIC-GGKVTVIITG-DVSAVKAAVDAAEEAAGKK 65 (75)
T ss_dssp HHHSSEEEEEEEEES-TTEEEEEEEE-SHHHHHHHHHHHHHHHHHT
T ss_pred hhcCCEEEEEEEecC-CCeEEEEEEE-CHHHHHHHHHHHHHHHhhc
Confidence 467799999988877 5688999999 7888888888888777663
No 74
>TIGR02461 osmo_MPG_phos mannosyl-3-phosphoglycerate phosphatase. Members of this family are mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70). It acts sequentially after mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) in a two-step pathway of biosynthesis of the compatible solute mannosylglycerate, a typical osmolyte of thermophiles.
Probab=48.72 E-value=22 Score=26.52 Aligned_cols=20 Identities=10% Similarity=-0.051 Sum_probs=14.8
Q ss_pred cCEEEEEEcCCHHHHHHHHH
Q psy8849 34 FDRITIASGSSKRQINALAV 53 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~ 53 (112)
.-.+|+|||++.+.+..+.+
T Consensus 31 G~~~vi~TgR~~~~~~~~~~ 50 (225)
T TIGR02461 31 GFPIVFVSSKTRAEQEYYRE 50 (225)
T ss_pred CCEEEEEeCCCHHHHHHHHH
Confidence 34689999999997665443
No 75
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=48.66 E-value=44 Score=24.87 Aligned_cols=38 Identities=13% Similarity=0.139 Sum_probs=24.5
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEE
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIH 88 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVH 88 (112)
-||+||||+...++.+.. +.+.. ..++++.+-|..+.+
T Consensus 39 ~fv~aTGR~~~~~~~~~~-------~~~~~--------~p~~~I~~NGa~I~~ 76 (249)
T TIGR01485 39 LLVYSTGRSPHSYKELQK-------QKPLL--------TPDIWVTSVGSEIYY 76 (249)
T ss_pred eEEEEcCCCHHHHHHHHh-------cCCCC--------CCCEEEEcCCceEEe
Confidence 799999998777664433 22221 234677777877765
No 76
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=48.35 E-value=72 Score=20.48 Aligned_cols=55 Identities=13% Similarity=-0.044 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
..++++.+++.|...-..+-.+.-++ -.+++++..+.+...+..++..+.+.++.
T Consensus 57 ~~~~l~~i~~~l~~~~~~~~~~~r~~----~~~f~ii~~~~~~~~~~~~~~~l~~~~~~ 111 (163)
T smart00267 57 GDELLQEVAQRLSSCLRPGDLLARLG----GDEFALLLPETSLEEAIALAERILQQLRE 111 (163)
T ss_pred HHHHHHHHHHHHHHhcCCCCEEEEec----CceEEEEecCCCHHHHHHHHHHHHHHHhC
Confidence 35677888888877655433343333 34778888888888888888888877764
No 77
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=48.23 E-value=18 Score=26.96 Aligned_cols=22 Identities=9% Similarity=0.199 Sum_probs=17.0
Q ss_pred cCEEEEEEcCCHHHHHHHHHHH
Q psy8849 34 FDRITIASGSSKRQINALAVSI 55 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v 55 (112)
.-+++|||||+.+-++.+.+.+
T Consensus 36 g~~v~iaTGR~~~~~~~~~~~l 57 (264)
T COG0561 36 GVKVVLATGRPLPDVLSILEEL 57 (264)
T ss_pred CCEEEEECCCChHHHHHHHHHc
Confidence 4589999999988777666544
No 78
>PRK14481 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=48.04 E-value=1.5e+02 Score=24.13 Aligned_cols=87 Identities=8% Similarity=0.077 Sum_probs=56.5
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEE---cCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEE
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIAS---GSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWL 78 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT---~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~Wv 78 (112)
+.+++++.+++.|.+ |+ +..+=.++.++.. |.|.--+..+++.+.+.|++.|+.+.+.- -..-=.
T Consensus 230 ~a~~l~~~m~~~ll~---------~~-~~~~gd~v~lLvN~LG~ts~lEl~i~~~~v~~~L~~~gi~i~r~~--vG~~~T 297 (331)
T PRK14481 230 PADEIAEELLEKILE---------DL-KLVAGDEVLVLVNGMGATPLMELYIVYNDVAELLEERGVTVARSL--VGNYMT 297 (331)
T ss_pred CHHHHHHHHHHHHHh---------hc-CCCCCCeEEEEEeCCCCCcHHHHHHHHHHHHHHHHHCCCEEEEEE--eecccc
Confidence 456677777777665 12 1122235666665 45667788999999999999998765542 123345
Q ss_pred EEEcCCEEEEeeChhhhhhcchhhhc
Q psy8849 79 LLDLGDIIIHIMNPYIRNMYNLEEIW 104 (112)
Q Consensus 79 llD~g~vvVHif~~e~R~~Y~LE~LW 104 (112)
-+|...+-|=++.-+. .|+++|
T Consensus 298 Sldm~G~SiTLl~ld~----el~~~l 319 (331)
T PRK14481 298 SLDMAGFSITLLKLDD----ELLELL 319 (331)
T ss_pred cCCCCceEEEEeecCH----HHHHHh
Confidence 5788777777775543 377777
No 79
>COG0716 FldA Flavodoxins [Energy production and conversion]
Probab=47.96 E-value=28 Score=24.16 Aligned_cols=68 Identities=12% Similarity=0.015 Sum_probs=44.4
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEEeeChhhhhhc-chhhhc
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIHIMNPYIRNMY-NLEEIW 104 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHif~~e~R~~Y-~LE~LW 104 (112)
+.|..++.+-+.+.+|+.|.+.+...+.............+.+.++..+++..=+.-..+.= +.+.+|
T Consensus 4 i~Ivy~S~tGnTe~vA~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~~g~~t~~~ge~~~~~~~f~ 72 (151)
T COG0716 4 ILIVYGSRTGNTEKVAEIIAEELGADGFEVDIDIRPGIKDDLLESYDELLLGTPTWGAGELPDDWYDFI 72 (151)
T ss_pred EEEEEEcCCCcHHHHHHHHHHHhccCCceEEEeecCCcchhhhccCCEEEEEeCCCCCCcCCccHHHHH
Confidence 45677777788899999999999988766533343344445555777777776555444433 444444
No 80
>TIGR02463 MPGP_rel mannosyl-3-phosphoglycerate phosphatase-related protein. This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbor-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (TIGR02460). Members of this family are like to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate.
Probab=47.59 E-value=20 Score=25.91 Aligned_cols=21 Identities=5% Similarity=0.210 Sum_probs=17.1
Q ss_pred CEEEEEEcCCHHHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAVSI 55 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v 55 (112)
=.+++|||++..-++.+++.+
T Consensus 33 i~~~i~TgR~~~~~~~~~~~l 53 (221)
T TIGR02463 33 IPVILCTSKTAAEVEYLQKAL 53 (221)
T ss_pred CeEEEEcCCCHHHHHHHHHHc
Confidence 368999999999888777654
No 81
>cd07368 PhnC_Bs_like PhnC is a Class III Extradiol ring-cleavage dioxygenase involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway. This subfamily is composed of Burkholderia sp. PhnC and similar poteins. PhnC is one of nine protein products encoded by the phn locus. These proteins are involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway. PhnC is a member of the class III extradiol dioxygenase family, a group os enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=47.47 E-value=33 Score=26.72 Aligned_cols=96 Identities=13% Similarity=0.035 Sum_probs=60.1
Q ss_pred HHHHHHHHHhcCCCCeEEEecCCCCCccCEE----EEEEcCCH------HH--------HHHHHHHHHHHHHhcCCCccc
Q psy8849 7 QIIVIKILKDIKAQDIKVYDTSNLTNLFDRI----TIASGSSK------RQ--------INALAVSIRKNIKNINNNIVN 68 (112)
Q Consensus 7 ~~~i~~~l~~kka~dI~vldv~~~~~~~dy~----VIaT~~S~------rh--------~~aia~~v~~~lk~~~~~~~~ 68 (112)
.+++.+.+.+.+.+=|+++--.....+.+++ .|.+|... .+ -..+|+.|.+.+++.|++...
T Consensus 35 ~~~~~~~v~~~~pD~ivvi~~dH~~~f~~~~~P~f~i~~~~~~g~~~~~~~~~~~~~~g~~eLA~~i~~~l~~~g~~~~~ 114 (277)
T cd07368 35 YAICAERLAALQVTSVVVIGDDHYTLFGTYCLPMYLIGTGDVDGPYDPLPGLPRAVIENNEPLAHHIMQHGLEYGIDWAV 114 (277)
T ss_pred HHHHHHHHHHcCCCEEEEEcCchHhhhhhccCCceEEecccccCCccccCCCCcccCcCCHHHHHHHHHHHHHcCCCEee
Confidence 4667777888888888888433333344444 66655421 11 246899999999988886432
Q ss_pred --ccccCCCCEEEEEcC--CE--------EEEee-------Chhhhhhcchhh
Q psy8849 69 --IEGKKSSEWLLLDLG--DI--------IIHIM-------NPYIRNMYNLEE 102 (112)
Q Consensus 69 --~EG~~~~~WvllD~g--~v--------vVHif-------~~e~R~~Y~LE~ 102 (112)
.-|.+-+.|+-+-+. +. +|.|+ .+..++.|+|=+
T Consensus 115 ~~~~~lDHG~~vPL~~l~~~~~~~~~~~p~VPV~~n~~~~p~~~~~~~~~lG~ 167 (277)
T cd07368 115 ARSFTVDHAATIPIHLAVRPVRAKGKGMRAIPVYLATGVDPFITSWRAHELGR 167 (277)
T ss_pred ecCcCCCcchhccHHHHhCcccccCCCCCeEEEEEecccCCCCCHHHHHHHHH
Confidence 224577888877762 22 45554 466677777644
No 82
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=46.70 E-value=23 Score=25.49 Aligned_cols=19 Identities=26% Similarity=0.288 Sum_probs=14.7
Q ss_pred CEEEEEEcCCHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAV 53 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~ 53 (112)
-.|+|||||+...++.+++
T Consensus 32 i~~~~aTGR~~~~~~~~~~ 50 (225)
T TIGR01482 32 IPVVLVTGNSVQFARALAK 50 (225)
T ss_pred CEEEEEcCCchHHHHHHHH
Confidence 4799999999887765543
No 83
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=46.33 E-value=61 Score=19.11 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCC-CCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNL-TNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~-~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
++..|+.++.+.++ +|.-++.+.. ...+..-+.....+..|+..+.+.++
T Consensus 12 ~L~~i~~~i~~~~~-nI~~v~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L~ 62 (74)
T cd04887 12 MLGRVTTAIGEAGG-DIGAIDLVEQGRDYTVRDITVDAPSEEHAETIVAAVR 62 (74)
T ss_pred hHHHHHHHHHHcCC-cEEEEEEEEecCCEEEEEEEEEcCCHHHHHHHHHHHh
Confidence 57788899977754 6666665542 34555666788999999998776654
No 84
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=46.11 E-value=43 Score=24.55 Aligned_cols=32 Identities=13% Similarity=0.207 Sum_probs=25.5
Q ss_pred CEEEEEE-cCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 35 DRITIAS-GSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 35 dy~VIaT-~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
.-=++|| ++|..+++..++.+.+.|++.|...
T Consensus 55 SGKiv~tGaks~~~a~~a~~~~~~~L~~~g~~~ 87 (174)
T cd04518 55 SGKMVCTGAKSVEDLHRAVKEIIKKLKDYGIKV 87 (174)
T ss_pred CCeEEEEccCCHHHHHHHHHHHHHHHHhcCCCc
Confidence 3446677 5599999999999999999988653
No 85
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=46.09 E-value=48 Score=18.82 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=21.7
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHh-cCCC
Q psy8849 39 IASGSSKRQINALAVSIRKNIKN-INNN 65 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~-~~~~ 65 (112)
+..|+|..|-+++++.+-+.+.+ .|.+
T Consensus 7 ~~~grt~eqk~~l~~~i~~~l~~~~g~~ 34 (58)
T cd00491 7 ILEGRTDEQKRELIERVTEAVSEILGAP 34 (58)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 34589999999999999998876 4554
No 86
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=45.40 E-value=19 Score=27.02 Aligned_cols=19 Identities=16% Similarity=0.193 Sum_probs=14.8
Q ss_pred CEEEEEEcCCHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAV 53 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~ 53 (112)
-.|+|||||+..-++.+.+
T Consensus 36 ~~~~iaTGR~~~~~~~~~~ 54 (272)
T PRK15126 36 ITLTFATGRHVLEMQHILG 54 (272)
T ss_pred CEEEEECCCCHHHHHHHHH
Confidence 4689999999987665544
No 87
>cd01949 GGDEF Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.
Probab=45.19 E-value=80 Score=20.13 Aligned_cols=55 Identities=16% Similarity=0.075 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
..+++..+++.|.+.-..+-.+.-++ -.+|+++.++.+...+..+...+.+.++.
T Consensus 54 ~~~~l~~~~~~l~~~~~~~~~~~~~~----~~~f~~l~~~~~~~~~~~~~~~l~~~~~~ 108 (158)
T cd01949 54 GDEVLKEVAERLRSSLRESDLVARLG----GDEFAILLPGTDLEEAEALAERLREAIEE 108 (158)
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEEec----CCeEEEEeCCCCHHHHHHHHHHHHHHhcC
Confidence 35677788888876554443333332 35888999888888888888888777654
No 88
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=44.97 E-value=1.2e+02 Score=22.06 Aligned_cols=41 Identities=10% Similarity=0.018 Sum_probs=29.7
Q ss_pred CCeEEEecCCCC--------CccCEEEEEEcCCHHHHHHHHHHHHHHHH
Q psy8849 20 QDIKVYDTSNLT--------NLFDRITIASGSSKRQINALAVSIRKNIK 60 (112)
Q Consensus 20 ~dI~vldv~~~~--------~~~dy~VIaT~~S~rh~~aia~~v~~~lk 60 (112)
.|++++|.+... ..+|++||.+--+..-..++...+.+.++
T Consensus 115 ~D~viiD~pp~~~~~~~~~l~~ad~vii~~~~~~~s~~~~~~~~~~l~~ 163 (246)
T TIGR03371 115 RDWVLIDVPRGPSPITRQALAAADLVLVVVNADAACYATLHQQALALFA 163 (246)
T ss_pred CCEEEEECCCCchHHHHHHHHhCCeEEEEeCCCHHHHHHHHHHHHHHhh
Confidence 399999999842 45799999998887776666654544443
No 89
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=44.82 E-value=40 Score=19.87 Aligned_cols=27 Identities=30% Similarity=0.391 Sum_probs=22.1
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHhc-CCC
Q psy8849 39 IASGSSKRQINALAVSIRKNIKNI-NNN 65 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~~-~~~ 65 (112)
+..|+|..|-+++++.|-+.+.+. |.+
T Consensus 8 ~~~Grs~EqK~~L~~~it~a~~~~~~~p 35 (60)
T PRK02289 8 LFEGRSQEQKNALAREVTEVVSRIAKAP 35 (60)
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 345999999999999999999874 554
No 90
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=44.56 E-value=50 Score=20.09 Aligned_cols=51 Identities=6% Similarity=0.055 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCC--CCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNL--TNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~--~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
-++..|+..+.+. .-+|.-++.... ...+-..+-...++..|+..+.+.|+
T Consensus 18 GlL~dI~~~i~~~-~~nI~~i~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L~ 70 (80)
T PF13291_consen 18 GLLADITSVISEN-GVNIRSINARTNKDDGTARITLTVEVKDLEHLNQIIRKLR 70 (80)
T ss_dssp THHHHHHHHHHCS-SSEEEEEEEEE--ETTEEEEEEEEEESSHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHC-CCCeEEEEeEEeccCCEEEEEEEEEECCHHHHHHHHHHHH
Confidence 4678899999988 557888877764 45667777788899999998877664
No 91
>PF08282 Hydrolase_3: haloacid dehalogenase-like hydrolase; InterPro: IPR013200 The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification []. This HAD domain is found in several distinct enzymes including: Phospholipid-transporting ATPase 1 (3.6.3.1 from EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [] 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (3.1.3.45 from EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [] Mannosyl-3-phosphoglycerate phosphatase (3.1.3.70 from EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [] Phosphoglycolate phopshatase (3.1.3.18 from EC), which catalyses the dephosphorylation of 2-phosphoglycolate [] ; PDB: 2B30_B 3R4C_A 1XVI_B 3IJ5_B 3MMZ_C 3L7Y_A 1XPJ_C 1RLT_B 1RLM_B 2HF2_A ....
Probab=44.24 E-value=24 Score=25.06 Aligned_cols=18 Identities=33% Similarity=0.468 Sum_probs=14.2
Q ss_pred EEEEEEcCCHHHHHHHHH
Q psy8849 36 RITIASGSSKRQINALAV 53 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~ 53 (112)
.++|||||+.+-++.+..
T Consensus 33 ~~~i~TGR~~~~~~~~~~ 50 (254)
T PF08282_consen 33 KLVIATGRSYSSIKRLLK 50 (254)
T ss_dssp EEEEECSSTHHHHHHHHH
T ss_pred EEEEEccCcccccccccc
Confidence 789999999887665554
No 92
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=44.04 E-value=1.1e+02 Score=21.18 Aligned_cols=55 Identities=16% Similarity=0.093 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
++++..+++.|...-...-.+.-+.+ .++.|+..+.+..++..+++.+...++..
T Consensus 75 D~vL~~va~~L~~~~~~~~~~~R~gG----dEF~i~l~~~~~~~~~~~~~~l~~~~~~~ 129 (181)
T COG2199 75 DEVLREVARRLRSNLREGDLVARLGG----DEFAVLLPGTSLEEAARLAERIRAALEEP 129 (181)
T ss_pred HHHHHHHHHHHHHhcCCCCEEEEecc----ceeEEEeCCCCHHHHHHHHHHHHHHHHcc
Confidence 56778888888776655444544444 57899999999999999999997766653
No 93
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=43.97 E-value=73 Score=22.25 Aligned_cols=55 Identities=18% Similarity=0.224 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..++.+.+.+...+.-+++|||--. .+.+- ..++...+..+...+.+..++.|..
T Consensus 127 ~~~~~l~~~~~~~~~~~lvviD~l~--~~~~~----~~~~~~~~~~~~~~l~~la~~~~~~ 181 (193)
T PF13481_consen 127 EDLEELEAALKELYGPDLVVIDPLQ--SLHDG----DENSNSAVAQLMQELKRLAKEYGVA 181 (193)
T ss_dssp HHHHHHHHHHTT----SEEEEE-GG--GG--S-----TT-HHHHHHHHHHHHHHHHHH--E
T ss_pred HHHHHHHHHHhhcCCCcEEEEcCHH--HHhcC----CCCCHHHHHHHHHHHHHHHHHcCCE
Confidence 4567788888886668899998322 22222 5566777778888888877777654
No 94
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=43.69 E-value=1.3e+02 Score=21.95 Aligned_cols=45 Identities=18% Similarity=0.148 Sum_probs=37.5
Q ss_pred CeEEEecCCCCCccC-----EEEEEEcCC---HHHHHHHHHHHHHHHHhcCCC
Q psy8849 21 DIKVYDTSNLTNLFD-----RITIASGSS---KRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 21 dI~vldv~~~~~~~d-----y~VIaT~~S---~rh~~aia~~v~~~lk~~~~~ 65 (112)
.-..+.+++...+.+ -++-|.... ...++.+++.|.+.+++.|+.
T Consensus 80 ~~~~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~ 132 (209)
T PF10469_consen 80 PPLKITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLL 132 (209)
T ss_pred CCceEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCc
Confidence 556788889888888 788776663 689999999999999998875
No 95
>PF12724 Flavodoxin_5: Flavodoxin domain
Probab=43.60 E-value=36 Score=23.35 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecC---CCCCccCEEEEEEcCCHHHHHH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTS---NLTNLFDRITIASGSSKRQINA 50 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~---~~~~~~dy~VIaT~~S~rh~~a 50 (112)
++++.++.|++.|.+. +..+.+-++. ..-.-.|.+|++++-=..++..
T Consensus 10 ~Tk~~A~~ia~~l~~~-~~~v~~~~~~~~~~~~~~yD~vi~gspiy~g~~~~ 60 (143)
T PF12724_consen 10 NTKKIAEWIAEKLGEE-GELVDLEKVEEDEPDLSDYDAVIFGSPIYAGRIPG 60 (143)
T ss_pred hHHHHHHHHHHHHhhh-ccEEEHHhhhhcccccccCCEEEEEEEEECCcCCH
Confidence 4677788888888766 4444444431 1123459999999754444333
No 96
>TIGR01486 HAD-SF-IIB-MPGP mannosyl-3-phosphoglycerate phosphatase family. This small group of proteins is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. Several members of this family from thermophiles (and from Dehalococcoides ethenogenes) are now known to act as mannosyl-3-phosphoglycerate (MPG) phosphatase. In these cases, the enzyme acts after MPG synthase to make the compatible solute mannosylglycerate. We propose that other mesophilic members of this family do not act as mannosyl-3-phosphoglycerate phosphatase. A member of this family is found in Escherichia coli, which appears to lack MPG synthase. Mannosylglycerate is imported in E. coli by phosphoenolpyruvate-dependent transporter (PubMed:14645248), but it appears the phosphorylation is not on the glycerate moiety, that the phosphorylated import is degraded by an alpha-mannosidase from an adjacent gene, and that E. coli would have no pathway to obta
Probab=43.37 E-value=25 Score=26.25 Aligned_cols=18 Identities=6% Similarity=0.135 Sum_probs=13.9
Q ss_pred EEEEEEcCCHHHHHHHHH
Q psy8849 36 RITIASGSSKRQINALAV 53 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~ 53 (112)
.++|||||+...+..+.+
T Consensus 34 ~~~~~TgR~~~~~~~~~~ 51 (256)
T TIGR01486 34 PVIPCTSKTAAEVEYLRK 51 (256)
T ss_pred eEEEEcCCCHHHHHHHHH
Confidence 489999999987665553
No 97
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=43.36 E-value=39 Score=22.62 Aligned_cols=25 Identities=28% Similarity=0.296 Sum_probs=21.5
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
-|+|+|. -.+|+.|.+..|++|++.
T Consensus 24 ~vvA~G~-----G~iAe~II~~Ake~~Vpi 48 (92)
T COG2257 24 KVVASGK-----GEIAEKIIEKAKEHGVPI 48 (92)
T ss_pred EEEeecc-----hHHHHHHHHHHHHcCCCc
Confidence 5899997 568999999999999864
No 98
>PRK14126 cell division protein ZapA; Provisional
Probab=43.17 E-value=35 Score=22.07 Aligned_cols=27 Identities=11% Similarity=0.300 Sum_probs=22.5
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
+|-|.| ..|..|++.+|..|.+.+++.
T Consensus 17 ~Y~i~~-~e~ee~l~~vA~~vd~km~ei 43 (85)
T PRK14126 17 QYTIVG-DESTSHIRMVAAIVDDKMREL 43 (85)
T ss_pred EEEecC-CCcHHHHHHHHHHHHHHHHHH
Confidence 567764 668999999999999998874
No 99
>PRK09004 FMN-binding protein MioC; Provisional
Probab=42.49 E-value=56 Score=22.79 Aligned_cols=42 Identities=7% Similarity=-0.025 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC--CccCEEEEEEcCC
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT--NLFDRITIASGSS 44 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~--~~~dy~VIaT~~S 44 (112)
+++.+++.+++.+.+ .+-++.++|+.... .-.|++||+|.+-
T Consensus 14 nae~~A~~l~~~~~~-~g~~~~~~~~~~~~~l~~~~~li~~~sT~ 57 (146)
T PRK09004 14 GAEYVADHLAEKLEE-AGFSTETLHGPLLDDLSASGLWLIVTSTH 57 (146)
T ss_pred HHHHHHHHHHHHHHH-cCCceEEeccCCHHHhccCCeEEEEECCC
Confidence 367888888888875 45567777766432 1247777777553
No 100
>TIGR02363 dhaK1 dihydroxyacetone kinase, DhaK subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the DhaK subunit of the latter type of dihydroxyacetone kinase, but it specifically excludes the DhaK paralog DhaK2 (TIGR02362) found in the same operon as DhaK and DhaK in the Firmicutes.
Probab=42.47 E-value=1.9e+02 Score=23.59 Aligned_cols=87 Identities=10% Similarity=0.116 Sum_probs=56.3
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEE---cCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEE
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIAS---GSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWL 78 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT---~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~Wv 78 (112)
+.+++++.+++.|.+. +++ ..=.++.++.. |.|.--+..+++.+.+.|++.|+.+.+.- -..-=.
T Consensus 231 ~a~~l~~~l~~~l~~~-------~~~---~~gd~v~vlvN~LG~ts~lEl~i~~~~v~~~L~~~gi~v~r~~--vG~~~T 298 (329)
T TIGR02363 231 SSDEIADELLDKLLDD-------LGL---QSGDRVIVLVNGMGATPLMELYIFYNDVQRLLEQRGVNVARTL--VGNYMT 298 (329)
T ss_pred CHHHHHHHHHHHHHhh-------cCC---CCCCeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE--eecccc
Confidence 3566777777777661 111 12235666665 45666788999999999999998865542 123345
Q ss_pred EEEcCCEEEEeeChhhhhhcchhhhc
Q psy8849 79 LLDLGDIIIHIMNPYIRNMYNLEEIW 104 (112)
Q Consensus 79 llD~g~vvVHif~~e~R~~Y~LE~LW 104 (112)
-+|...+-|=+|.-+. +|+++|
T Consensus 299 Sldm~G~SiTLl~ld~----el~~~l 320 (329)
T TIGR02363 299 SLDMAGFSLTLLKLDD----ELLELW 320 (329)
T ss_pred cCCCCceEEEEeeCCH----HHHHHh
Confidence 5777777777775433 377777
No 101
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=42.34 E-value=63 Score=18.72 Aligned_cols=40 Identities=18% Similarity=0.182 Sum_probs=27.4
Q ss_pred EEcCCHHHHHHHHHHHHHHHHh-cCCCcc----cccccCCCCEEE
Q psy8849 40 ASGSSKRQINALAVSIRKNIKN-INNNIV----NIEGKKSSEWLL 79 (112)
Q Consensus 40 aT~~S~rh~~aia~~v~~~lk~-~~~~~~----~~EG~~~~~Wvl 79 (112)
..|+|..|-+++++.|-+.+.+ .|.++- .++-.+.++|..
T Consensus 9 ~~grs~eqk~~l~~~it~~l~~~~~~p~~~v~V~i~e~~~~~w~~ 53 (62)
T PRK00745 9 FEGRTVEQKRKLVEEITRVTVETLGCPPESVDIIITDVKRENWAT 53 (62)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHcCCChhHEEEEEEEcChHHeeE
Confidence 4589999999999999998876 455431 233344556654
No 102
>PRK00907 hypothetical protein; Provisional
Probab=41.49 E-value=1e+02 Score=20.35 Aligned_cols=53 Identities=11% Similarity=0.068 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHhcCCCCe--EEE--ecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 3 INKRQIIVIKILKDIKAQDI--KVY--DTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI--~vl--dv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
..++.+.|.+++. +++-+. ..+ .-|....|.-.-+-.++.|..|+.++-++|.
T Consensus 27 ~~~l~~~V~~vv~-~h~p~~~~~~i~~r~Ss~GkY~Svtv~i~ats~eQld~iY~~L~ 83 (92)
T PRK00907 27 ERGLETELPRLLA-ATGVELLQERISWKHSSSGKYVSVRIGFRAESREQYDAAHQALR 83 (92)
T ss_pred chhHHHHHHHHHH-HhCCCCCcCcEEeccCCCCEEEEEEEEEEECCHHHHHHHHHHHh
Confidence 3567788888886 445432 222 3344556778889999999999999887765
No 103
>PF05116 S6PP: Sucrose-6F-phosphate phosphohydrolase; InterPro: IPR006380 This family of sequences represent sucrose phosphate phosphohydrolase (SPP) from plants and cyanobacteria []. SPP is a member of the Class IIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.; PDB: 1TJ5_A 2B1Q_A 1TJ4_A 1S2O_A 1U2T_A 2D2V_A 1TJ3_A 1U2S_A 2B1R_A 3GYG_B ....
Probab=41.35 E-value=64 Score=24.39 Aligned_cols=38 Identities=16% Similarity=0.273 Sum_probs=25.4
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEE
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIH 88 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVH 88 (112)
.||++||+|-.+++.+. ++.+.+ ..++++.|.|.-|.|
T Consensus 37 ~~v~~TGRs~~~~~~~~-------~~~~l~--------~Pd~~I~svGt~I~~ 74 (247)
T PF05116_consen 37 LFVYVTGRSLESVLRLL-------REYNLP--------QPDYIITSVGTEIYY 74 (247)
T ss_dssp EEEEE-SS-HHHHHHHH-------HHCT-E--------E-SEEEETTTTEEEE
T ss_pred eEEEECCCCHHHHHHHH-------HhCCCC--------CCCEEEecCCeEEEE
Confidence 68999999987776543 344432 247999999998877
No 104
>PF07056 DUF1335: Protein of unknown function (DUF1335); InterPro: IPR009766 This family represents a conserved region approximately 130 residues long within a number of proteins of unknown function that seem to be specific to the white spot syndrome virus (WSSV).
Probab=41.31 E-value=63 Score=22.90 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=23.7
Q ss_pred cCEEEE------EEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 34 FDRITI------ASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 34 ~dy~VI------aT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
.||||| +-|-|.+++...-..+++.+.+.|.
T Consensus 25 ~~~~IvttDfLiGlG~s~~~v~~~L~~me~~l~~~g~ 61 (131)
T PF07056_consen 25 CDYMIVTTDFLIGLGFSPRNVTKKLKSMEQNLVKHGG 61 (131)
T ss_pred cceEEEehhheeecCCChHHHHHHHHHHHHHHHHccC
Confidence 456555 4599999998888888888877654
No 105
>PRK08366 vorA 2-ketoisovalerate ferredoxin oxidoreductase subunit alpha; Reviewed
Probab=41.31 E-value=1e+02 Score=25.31 Aligned_cols=25 Identities=20% Similarity=0.142 Sum_probs=22.0
Q ss_pred ccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 33 LFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
-+|+.||+.|.+...++...+.+++
T Consensus 259 dAe~~iV~~Gs~~~~~~eav~~lr~ 283 (390)
T PRK08366 259 DADFVFMGMGSLMGTVKEAVDLLRK 283 (390)
T ss_pred CCCEEEEEeCccHHHHHHHHHHHHh
Confidence 4899999999999999988887764
No 106
>PRK00192 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=41.25 E-value=27 Score=26.45 Aligned_cols=19 Identities=5% Similarity=0.172 Sum_probs=15.4
Q ss_pred EEEEEEcCCHHHHHHHHHH
Q psy8849 36 RITIASGSSKRQINALAVS 54 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~ 54 (112)
-++||||++.+.+..+++.
T Consensus 39 ~~~iaTgR~~~~~~~~~~~ 57 (273)
T PRK00192 39 PVIPCTSKTAAEVEVLRKE 57 (273)
T ss_pred EEEEEcCCCHHHHHHHHHH
Confidence 5889999999988876544
No 107
>PRK04998 hypothetical protein; Provisional
Probab=41.04 E-value=98 Score=19.94 Aligned_cols=53 Identities=13% Similarity=0.105 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHhcCCCC-eEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 4 NKRQIIVIKILKDIKAQD-IKVYDTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~d-I~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
.++.+.|.+++.+.-..+ -.-..-+....|.-+-|-+++.|..|+.++-+.+.
T Consensus 26 ~~~~~~v~~v~~~~~~~~~~~~~r~S~~GkY~Svtv~v~v~s~eq~~~iY~~L~ 79 (88)
T PRK04998 26 PELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITITATSIEQVETLYEELA 79 (88)
T ss_pred HhHHHHHHHHHHHhCCCCCCceEccCCCCEEEEEEEEEEECCHHHHHHHHHHHh
Confidence 467778888885542222 11234455567888999999999999999887765
No 108
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=41.03 E-value=53 Score=19.08 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=22.0
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHh-cCCC
Q psy8849 39 IASGSSKRQINALAVSIRKNIKN-INNN 65 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~-~~~~ 65 (112)
...|+|..|-++++..+.+.+.+ .|.+
T Consensus 8 ~~~grt~eqK~~l~~~it~~l~~~lg~~ 35 (63)
T TIGR00013 8 LKEGRTDEQKRQLIEGVTEAMAETLGAN 35 (63)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence 34689999999999999999886 4554
No 109
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=40.58 E-value=16 Score=24.50 Aligned_cols=29 Identities=17% Similarity=0.245 Sum_probs=23.0
Q ss_pred cCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 34 FDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
-|++||+||.+.+. +..++.+.|++.|+.
T Consensus 53 peiliiGTG~~~~~---~~~~~~~~l~~~gI~ 81 (109)
T cd00248 53 PDILLIGTGAEIAF---LPRALRAALRAAGIG 81 (109)
T ss_pred CCEEEEcCCCCCCc---CCHHHHHHHHHcCCe
Confidence 58999999998854 456778888888764
No 110
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=40.17 E-value=66 Score=19.03 Aligned_cols=49 Identities=16% Similarity=0.402 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCCcccccccCCCCEEEEEcC-----------------CEEEEeeChhhhhhcchhhh
Q psy8849 50 ALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLG-----------------DIIIHIMNPYIRNMYNLEEI 103 (112)
Q Consensus 50 aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g-----------------~vvVHif~~e~R~~Y~LE~L 103 (112)
.++..+...+++.|.+..-.. +++++|.+ +.+++++.++.-......++
T Consensus 14 t~~~~l~~~l~~~g~~v~~~~-----d~iivD~~~~~~~~~~~~~~~~~~~~~vi~v~~~~~~~~~~~~~~ 79 (99)
T cd01983 14 TLAANLAAALAKRGKRVLLID-----DYVLIDTPPGLGLLVLLCLLALLAADLVIIVTTPEALAVLGARRL 79 (99)
T ss_pred HHHHHHHHHHHHCCCeEEEEC-----CEEEEeCCCCccchhhhhhhhhhhCCEEEEecCCchhhHHHHHHH
Confidence 456667777777776654443 78888864 34666666666555554443
No 111
>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=39.83 E-value=1e+02 Score=19.77 Aligned_cols=62 Identities=13% Similarity=0.091 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhcCCCCeEE-----Ee-----cCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccc
Q psy8849 5 KRQIIVIKILKDIKAQDIKV-----YD-----TSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNI 69 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~v-----ld-----v~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~ 69 (112)
.....+.+.+++.+++-+.- .. +...-.-+|.+|+.|...+ ++++..+.+..|+.++|....
T Consensus 10 ~~~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~i~~aD~VIv~t~~vs---H~~~~~vk~~akk~~ip~~~~ 81 (97)
T PF10087_consen 10 DRERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSKIKKADLVIVFTDYVS---HNAMWKVKKAAKKYGIPIIYS 81 (97)
T ss_pred ccHHHHHHHHHHcCCEEEEEecCCCCccchhHHHHhcCCCCEEEEEeCCcC---hHHHHHHHHHHHHcCCcEEEE
Confidence 34456677777776665555 01 1122344699999999866 456677788888888875443
No 112
>PF00990 GGDEF: GGDEF domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [,]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [].; PDB: 3IGN_A 3BRE_B 3EZU_A 3ICL_B 3PJX_A 3PJW_A 3HVW_A 3HVA_B 3I5C_B 3I5B_B ....
Probab=39.80 E-value=1e+02 Score=19.90 Aligned_cols=57 Identities=12% Similarity=0.073 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
+++++.+++.|...-..+-.+.-+. -..|+|++...+......+++.+.+.+.....
T Consensus 56 ~~~l~~i~~~L~~~~~~~~~~~r~~----~~~f~il~~~~~~~~~~~~~~~~~~~~~~~~~ 112 (161)
T PF00990_consen 56 DEILRQIAKRLKKQLRESDILARLG----DDEFAILLPDTDSEEAEELAERLERLIDELNE 112 (161)
T ss_dssp HHHHHHHHHHHHHHCCTTSEEEEEE----TTEEEEEEETCTHHHHHHHHHHHHHHHHHHCC
T ss_pred ccccccccccccccccccccccccc----chheeecccccccccchhhhhhhhhhhhhccc
Confidence 4678888999987755544444443 25788999999988777788877777766543
No 113
>TIGR01174 ftsA cell division protein FtsA. This bacterial cell division protein interacts with FtsZ, the bacterial homolog of tubulin. It is an ATP-binding protein and shows structural similarities to actin and heat shock cognate protein 70.
Probab=39.80 E-value=1.9e+02 Score=22.92 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=24.0
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccc-------------cccCCCCEEEEEcC
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNINNNIVNI-------------EGKKSSEWLLLDLG 83 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~-------------EG~~~~~WvllD~g 83 (112)
++.+++.- +.+.+.+.+.++..|..+..+ +......++++|.|
T Consensus 149 ~v~lva~~------~~~v~~~~~~~~~aGl~~~~i~~~~~A~a~a~~~~~~~~~~~~vvDiG 204 (371)
T TIGR01174 149 EVHIITGS------STILRNLVKCVERCGLEVDNIVLSGLASAIAVLTEDEKELGVCLIDIG 204 (371)
T ss_pred EEEEEEEE------HHHHHHHHHHHHHcCCCeeeEEEhhhhhhhhhcCcchhcCCEEEEEeC
Confidence 55555553 233444555666666653221 12235679999997
No 114
>cd06169 BMC Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypo
Probab=39.77 E-value=55 Score=19.57 Aligned_cols=39 Identities=15% Similarity=0.101 Sum_probs=27.9
Q ss_pred cCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 17 IKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 17 kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
.|+-||.++++...++-.-++++.+|.. .-+++-.+...
T Consensus 21 ~KaA~V~l~~~~~~~~~g~~~~~i~G~~-s~V~~A~~a~~ 59 (62)
T cd06169 21 VKAADVELVGIERAGGGGLVTLIIRGDV-SAVKAAVEAAE 59 (62)
T ss_pred hhhcCeEEEEEEecCCCcEEEEEEEECH-HHHHHHHHHHH
Confidence 4677999999998876567888889965 55555444443
No 115
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=39.50 E-value=59 Score=25.99 Aligned_cols=37 Identities=24% Similarity=0.240 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHH
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKR 46 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~r 46 (112)
+.++++.|++-+.+.=..||-++|-.+ .|||||...|
T Consensus 7 ~~~lAq~IV~~~~~ii~~ninimd~~G-------~IIaS~d~~R 43 (385)
T PRK11477 7 DTKMAQDIVARTMRIIDTNINVMDARG-------RIIGSGDRER 43 (385)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEECCCC-------EEEecCChHH
Confidence 578999999999999999999999665 6999998876
No 116
>PRK12359 flavodoxin FldB; Provisional
Probab=39.45 E-value=82 Score=22.88 Aligned_cols=38 Identities=5% Similarity=0.084 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCC----ccCEEEEEEcC
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTN----LFDRITIASGS 43 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~----~~dy~VIaT~~ 43 (112)
++.+++.|++.+ ++..+.++++.+... -.|.+|++|.+
T Consensus 14 Te~vAe~I~~~l---g~~~v~v~~i~~~~~~~l~~yD~iIlG~pT 55 (172)
T PRK12359 14 TEMAAEKIRDII---GEELVDLHNLKDDPPKLMEQYDVLILGIPT 55 (172)
T ss_pred HHHHHHHHHHHh---CCCeEEEEEcccCChhHHccCCEEEEEecc
Confidence 566666666655 233467778876432 25888888876
No 117
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=39.40 E-value=82 Score=28.54 Aligned_cols=31 Identities=10% Similarity=0.107 Sum_probs=27.0
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
-+=||.||-+..-++.+...+.+.|...|.+
T Consensus 261 ~~~iiVTAP~~~nv~~Lf~fa~~~l~~lg~~ 291 (758)
T COG1444 261 SVRIIVTAPTPANVQTLFEFAGKGLEFLGYK 291 (758)
T ss_pred CceEEEeCCCHHHHHHHHHHHHHhHHHhCCc
Confidence 4679999999999999999999998877653
No 118
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=39.35 E-value=77 Score=18.26 Aligned_cols=27 Identities=15% Similarity=0.348 Sum_probs=22.4
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHh-cCCC
Q psy8849 39 IASGSSKRQINALAVSIRKNIKN-INNN 65 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~-~~~~ 65 (112)
+..|+|..|-++++..|.+.+.+ .|.+
T Consensus 8 ~~~Grs~eqk~~l~~~it~~l~~~~~~p 35 (61)
T PRK02220 8 LIEGRTEEQLKALVKDVTAAVSKNTGAP 35 (61)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 45699999999999999999886 4554
No 119
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 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 [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=39.08 E-value=63 Score=20.50 Aligned_cols=48 Identities=19% Similarity=0.332 Sum_probs=33.9
Q ss_pred CEEEEEEcC-CHHHHHHHHHHHHHHHHhcCCCcc------------cccccCCCCEEEEEc
Q psy8849 35 DRITIASGS-SKRQINALAVSIRKNIKNINNNIV------------NIEGKKSSEWLLLDL 82 (112)
Q Consensus 35 dy~VIaT~~-S~rh~~aia~~v~~~lk~~~~~~~------------~~EG~~~~~WvllD~ 82 (112)
+.++|.... +..++.++.+.+.+.+.+.|.... .+.+...|.|+++.+
T Consensus 4 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~~G~Y~~~~f 64 (92)
T PF01250_consen 4 ELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQKEGHYFLFNF 64 (92)
T ss_dssp EEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTECEEEEEEEEE
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCCCEEEEEEEEE
Confidence 457777765 777999999999999998765432 344456677777765
No 120
>PRK09627 oorA 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed
Probab=38.90 E-value=1.1e+02 Score=24.91 Aligned_cols=25 Identities=20% Similarity=0.154 Sum_probs=22.1
Q ss_pred ccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 33 LFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
-+|+.||+.|++.+.++...+.+++
T Consensus 274 dAd~~IV~~GSt~~~~keAv~~lr~ 298 (375)
T PRK09627 274 DAEILIIAYGSVSLSAKEAIKRLRE 298 (375)
T ss_pred CCCEEEEEeCCCHHHHHHHHHHHHh
Confidence 3899999999999999988887764
No 121
>TIGR02471 sucr_syn_bact_C sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial. Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by TIGR02472.
Probab=38.89 E-value=34 Score=25.15 Aligned_cols=19 Identities=21% Similarity=0.198 Sum_probs=15.1
Q ss_pred EEEEEEcCCHHHHHHHHHH
Q psy8849 36 RITIASGSSKRQINALAVS 54 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~ 54 (112)
.|+|||||+...++.+...
T Consensus 32 ~~viaTGR~~~~v~~~~~~ 50 (236)
T TIGR02471 32 GFGIATGRSVESAKSRYAK 50 (236)
T ss_pred eEEEEeCCCHHHHHHHHHh
Confidence 6999999998887766543
No 122
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=37.59 E-value=45 Score=22.16 Aligned_cols=24 Identities=25% Similarity=0.158 Sum_probs=19.8
Q ss_pred cCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 34 FDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
.|..|||+|.....+...++.+.+
T Consensus 10 ~di~iia~G~~~~~al~A~~~L~~ 33 (124)
T PF02780_consen 10 ADITIIAYGSMVEEALEAAEELEE 33 (124)
T ss_dssp SSEEEEEETTHHHHHHHHHHHHHH
T ss_pred CCEEEEeehHHHHHHHHHHHHHHH
Confidence 589999999998888877776654
No 123
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.23 E-value=32 Score=23.25 Aligned_cols=24 Identities=17% Similarity=0.527 Sum_probs=19.1
Q ss_pred CCCEEEEEcC----CEEEEeeChhhhhh
Q psy8849 74 SSEWLLLDLG----DIIIHIMNPYIRNM 97 (112)
Q Consensus 74 ~~~WvllD~g----~vvVHif~~e~R~~ 97 (112)
.+.|+++|.| .+||||+-+-.|=|
T Consensus 53 ~Dnr~Vfdi~GN~yRLIvhv~y~~~ki~ 80 (98)
T COG4680 53 LDNRVVFDIGGNKYRLIVHVAYEFHKIF 80 (98)
T ss_pred ccceEEEEcCCCEEEEEEEEEeecceEE
Confidence 4789999997 69999987766543
No 124
>cd01614 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation,
Probab=37.07 E-value=55 Score=21.29 Aligned_cols=30 Identities=23% Similarity=0.364 Sum_probs=23.6
Q ss_pred CCCCeEEEecCCCCCccCEEEEEEcCCHHHH
Q psy8849 18 KAQDIKVYDTSNLTNLFDRITIASGSSKRQI 48 (112)
Q Consensus 18 ka~dI~vldv~~~~~~~dy~VIaT~~S~rh~ 48 (112)
++.-++++|.=+ ....|++++++|++.|+.
T Consensus 37 ~g~~~VA~D~vG-AG~Ge~Vlv~~Gs~Ar~~ 66 (83)
T cd01614 37 KGEPLVAVDPVG-AGVGEWVLVATGSAARQA 66 (83)
T ss_pred CCCEEEEEECCC-CCCCCEEEEeCChHHhhh
Confidence 556677788776 456899999999888874
No 125
>COG3027 zapA Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]
Probab=37.00 E-value=43 Score=22.68 Aligned_cols=30 Identities=3% Similarity=0.133 Sum_probs=26.3
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
-|-|-|....+.|++.+|..+...+++.+.
T Consensus 12 ~y~v~c~~~qee~L~~~A~~lD~kv~eik~ 41 (105)
T COG3027 12 SYRVNCPEEQEEHLRQAARLLDDKVRELKE 41 (105)
T ss_pred eeEecCCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 588999999999999999999999987543
No 126
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=36.83 E-value=81 Score=20.48 Aligned_cols=29 Identities=14% Similarity=0.087 Sum_probs=26.2
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
+|++.|....|-.-.++.+++.+++.|++
T Consensus 3 ~i~ac~~G~a~s~laa~~L~~aa~~~g~~ 31 (96)
T cd05569 3 AVTACPTGIAHTYMAAEALEKAAKKLGWE 31 (96)
T ss_pred EEEECCCchhHHHHHHHHHHHHHHHCCCe
Confidence 67889999999999999999999999885
No 127
>PRK13365 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=36.82 E-value=58 Score=25.50 Aligned_cols=97 Identities=19% Similarity=0.167 Sum_probs=61.3
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCc-cCE---EEEEEcCCHH------------H---HHHHHHHHHHHHHhcCCCc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNL-FDR---ITIASGSSKR------------Q---INALAVSIRKNIKNINNNI 66 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~-~dy---~VIaT~~S~r------------h---~~aia~~v~~~lk~~~~~~ 66 (112)
=.+++.+.+.+.+.+=|++++-.....+ .|+ |.|.++.+.. . =..+|+.|.+.+.+.|+..
T Consensus 36 a~~~i~~~v~~~~PDviVvi~sdH~~~f~~d~~p~f~Ig~~~~~~~~~~g~~~~~~~~~~g~~eLA~~i~~~~~~~g~~~ 115 (279)
T PRK13365 36 GYEPVAAWLAEQKADVLVFFYNDHCTTFFFDLYPTFALGVGERFPVADEGAGLRPLPPIRGDVQLQAHIAECLVNDEFDL 115 (279)
T ss_pred HHHHHHHHHHHhCCCEEEEEcCchHHHhccccCCceEEEecccccccccccCCCCCCCCCCCHHHHHHHHHHHHHcCCCe
Confidence 3567788888899998999966665554 677 8888877651 0 2358888888888877764
Q ss_pred ccc--cccCCCCEEEEEc--C--C----EEEEee-------Chhhhhhcchhh
Q psy8849 67 VNI--EGKKSSEWLLLDL--G--D----IIIHIM-------NPYIRNMYNLEE 102 (112)
Q Consensus 67 ~~~--EG~~~~~WvllD~--g--~----vvVHif-------~~e~R~~Y~LE~ 102 (112)
... -+.+-+.|+-+-+ . + -||+|+ .+..++.|+|=+
T Consensus 116 ~~~~~~~lDHG~~vPL~~l~~~~~~~~~pvVpi~in~~~~p~~~~~~~~~lG~ 168 (279)
T PRK13365 116 TVFQDKPIDHGCAAPLPLLWPHVPDWPGTVVPIAINVLQYPLPTARRCYRLGQ 168 (279)
T ss_pred eeccCCCCCchhhhHHHHhCCccccCCCCeEEEEEecccCCCCCHHHHHHHHH
Confidence 222 2345566664432 1 1 255554 235677776643
No 128
>COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only]
Probab=36.57 E-value=1.2e+02 Score=22.04 Aligned_cols=52 Identities=15% Similarity=0.111 Sum_probs=39.2
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCC----------CCc--------------------cCEEEEEEcC----CHHH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNL----------TNL--------------------FDRITIASGS----SKRQ 47 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~----------~~~--------------------~dy~VIaT~~----S~rh 47 (112)
++.++++.+++.+++. +-++.++.+++. |.. +|-+|++|.. -+.|
T Consensus 15 ~t~~l~~~~~~g~~~~-G~E~~~i~v~~~~i~~c~~c~~c~~~~~c~~~dD~~~~i~~~l~~aD~iI~gsPvy~g~vsa~ 93 (207)
T COG0655 15 NTAKLAEAVLEGAEEA-GAEVEIIRLPEKNIKPCTGCFACWKKKPCVIKDDDMNEIYEKLLEADGIIFGSPVYFGNVSAQ 93 (207)
T ss_pred cHHHHHHHHHHHHHHc-CCEEEEEEecCCCcccchHHHhhhccCCCCCCcccHHHHHHHHHHCCEEEEeCCeecCCchHH
Confidence 4678999999999999 888899999875 222 5899999954 4555
Q ss_pred HHHHHHH
Q psy8849 48 INALAVS 54 (112)
Q Consensus 48 ~~aia~~ 54 (112)
+++..|.
T Consensus 94 ~K~fiDR 100 (207)
T COG0655 94 MKAFIDR 100 (207)
T ss_pred HHHHHhh
Confidence 6655555
No 129
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=36.53 E-value=41 Score=24.20 Aligned_cols=39 Identities=21% Similarity=0.173 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC---CccCEEEEEEcCCH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT---NLFDRITIASGSSK 45 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~---~~~dy~VIaT~~S~ 45 (112)
+|+++++.|++.|.. .++ +++.+.. .-+|.+.++++.-.
T Consensus 10 NTkkvA~aI~~~l~~---~~~--~~~~~~~~~~~~yD~i~lG~w~d~ 51 (160)
T PF12641_consen 10 NTKKVAEAIAEALGA---KDI--VSVEEPPEDLEDYDLIFLGFWIDK 51 (160)
T ss_pred hHHHHHHHHHHHCCC---cee--EeccccccCCCCCCEEEEEcCccC
Confidence 578888888888877 333 3333322 33577777776433
No 130
>COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
Probab=36.32 E-value=25 Score=28.45 Aligned_cols=17 Identities=24% Similarity=0.552 Sum_probs=0.0
Q ss_pred EEcCCHHHHHHHHHHHH
Q psy8849 40 ASGSSKRQINALAVSIR 56 (112)
Q Consensus 40 aT~~S~rh~~aia~~v~ 56 (112)
|.|+++.|++++++.|.
T Consensus 294 CCGTTPeHIraia~~v~ 310 (311)
T COG0646 294 CCGTTPEHIRAIAEAVK 310 (311)
T ss_pred ccCCCHHHHHHHHHHhc
No 131
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=36.23 E-value=1.2e+02 Score=21.88 Aligned_cols=48 Identities=17% Similarity=0.215 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCCCeEEEecCCCC---------CccCEEEEEEcCCHHHHHHHHHHH
Q psy8849 8 IIVIKILKDIKAQDIKVYDTSNLT---------NLFDRITIASGSSKRQINALAVSI 55 (112)
Q Consensus 8 ~~i~~~l~~kka~dI~vldv~~~~---------~~~dy~VIaT~~S~rh~~aia~~v 55 (112)
+.+.+.+.++-..|++++|.+... ..+|++|+++-.+....+++.+.+
T Consensus 137 ~~~l~~l~~~y~~D~IiiD~pp~~~~~~~~~l~~~aD~viiV~~~~~~~~~~~~~~~ 193 (207)
T TIGR03018 137 RSLLHELARRYPDRIIIIDTPPLLVFSEARALARLVGQIVLVVEEGRTTQEAVKEAL 193 (207)
T ss_pred HHHHHHHHhhCCCCEEEEECCCCcchhHHHHHHHhCCEEEEEEECCCCCHHHHHHHH
Confidence 333444444322399999998542 467999998888776666666544
No 132
>PRK06696 uridine kinase; Validated
Probab=35.91 E-value=1.3e+02 Score=22.12 Aligned_cols=51 Identities=10% Similarity=0.047 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 1 MNINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
|+-+++++.|++.+..+......++=+ +|.|..==..+|..|.+.|+..|.
T Consensus 1 ~~~~~~~~~la~~~~~~~~~~~~iI~I-------------~G~sgsGKSTlA~~L~~~l~~~g~ 51 (223)
T PRK06696 1 MSRKQLIKELAEHILTLNLTRPLRVAI-------------DGITASGKTTFADELAEEIKKRGR 51 (223)
T ss_pred CcHHHHHHHHHHHHHHhCCCCceEEEE-------------ECCCCCCHHHHHHHHHHHHHHcCC
Confidence 677788899998887765444434434 333333323456666666655443
No 133
>COG0489 Mrp ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=35.86 E-value=2e+02 Score=22.09 Aligned_cols=59 Identities=14% Similarity=0.222 Sum_probs=37.2
Q ss_pred HHHHHHHhcCC--CCeEEEecCCC---------CCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCccc
Q psy8849 9 IVIKILKDIKA--QDIKVYDTSNL---------TNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVN 68 (112)
Q Consensus 9 ~i~~~l~~kka--~dI~vldv~~~---------~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~ 68 (112)
.+.++|.+-+- -|..++|.... ..+.|-+||+|--...-...+.. ..+.+++.+.+.++
T Consensus 154 ~~~qll~~~~~~~~D~vIID~PP~~g~~d~~i~~~~~~g~viVt~p~~~~~~~v~k-a~~~~~~~~~~vlG 223 (265)
T COG0489 154 AMLQLLEDVLWGEYDYVIIDTPPGTGDADATVLQRIPDGVVIVTTPGKTALEDVKK-AIDMLEKAGIPVLG 223 (265)
T ss_pred HHHHHHHHHhccCCCEEEEeCCCCchHHHHHHHhccCCeEEEEeCCccchHHHHHH-HHHHHHhcCCceEE
Confidence 34444544444 49999999986 36778888887665555444444 44567776665544
No 134
>cd07369 PydA_Rs_like PydA is a Class III Extradiol ring-cleavage dioxygenase required for the degradation of 3-hydroxy-4-pyridone (HP). This subfamily is composed of Rhizobium sp. PydA and similar proteins. PydA is required for the degradation of 3-hydroxy-4-pyridone (HP), an intermediate in the Leucaena toxin mimosine degradation pathway. It is a member of the class III extradiol dioxygenase family, a group of enzymes that use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=35.84 E-value=2e+02 Score=23.21 Aligned_cols=61 Identities=11% Similarity=0.111 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhcCCCCeEEE-ecCCCCCccC---EEEEEEcCCHH-H------------------HHHHHHHHHHHHHhc
Q psy8849 6 RQIIVIKILKDIKAQDIKVY-DTSNLTNLFD---RITIASGSSKR-Q------------------INALAVSIRKNIKNI 62 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vl-dv~~~~~~~d---y~VIaT~~S~r-h------------------~~aia~~v~~~lk~~ 62 (112)
=.+++.+.+.+.+.+=|+++ +-.-..-+.| .|.|.++.+.+ . =..+|++|.+.+.+.
T Consensus 34 a~~~l~~~v~~~~PD~iVV~~sdH~~~~f~d~~P~f~I~~~~~~~G~~~~~~~~~~~~~~~~~~gd~eLA~~I~~~l~~~ 113 (329)
T cd07369 34 ATLKLGRTLTAARPDVIIAFLDDHFENHFRTNMPTIAIGVAESHSGPADQLMEALRVPKKHYFPGNPEVAEQLLRALVHD 113 (329)
T ss_pred HHHHHHHHHHHhCCCEEEEEcCCchhhhccccCccEEEeecceeeccchhccccCCCCcccCCCCCHHHHHHHHHHHHHC
Confidence 34667777888888777776 6654434556 57776655432 1 256899999999988
Q ss_pred CCCc
Q psy8849 63 NNNI 66 (112)
Q Consensus 63 ~~~~ 66 (112)
|++.
T Consensus 114 G~dv 117 (329)
T cd07369 114 SFDC 117 (329)
T ss_pred CCCe
Confidence 8764
No 135
>PF08915 tRNA-Thr_ED: Archaea-specific editing domain of threonyl-tRNA synthetase; InterPro: IPR015011 Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet []. ; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0005737 cytoplasm; PDB: 3PD4_B 3PD3_A 2HL0_A 2HL1_A 2HKZ_A 3PD5_B 2HL2_A 3PD2_B 1Y2Q_A.
Probab=35.74 E-value=1.6e+02 Score=21.01 Aligned_cols=56 Identities=16% Similarity=0.171 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcc
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIV 67 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~ 67 (112)
++.++.|...+..-|+..|+++--..+++- =.|+.....+...+.+.|+..|++..
T Consensus 57 ~~av~eI~~~a~kv~~~~ivlyPyAHLSs~--------La~P~~A~~iL~~le~~L~~~g~eV~ 112 (138)
T PF08915_consen 57 EKAVEEIKWVAKKVKAKRIVLYPYAHLSSS--------LASPDVAVEILKKLEERLKSRGFEVY 112 (138)
T ss_dssp HHHHHHHHHHHHHTT-SEEEEEE-GGGSSS--------B--HHHHHHHHHHHHHHHHHTT-EEE
T ss_pred HHHHHHHHHHHHhcCCCEEEEeCcccccCC--------cCChHHHHHHHHHHHHHHHhCCCeEE
Confidence 467788999999999999999988887652 24566778899999999988887643
No 136
>PRK06242 flavodoxin; Provisional
Probab=35.20 E-value=1e+02 Score=20.84 Aligned_cols=48 Identities=21% Similarity=0.342 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCC----CccCEEEEEEc----CCHHHHHHHHHHH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLT----NLFDRITIASG----SSKRQINALAVSI 55 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~----~~~dy~VIaT~----~S~rh~~aia~~v 55 (112)
+++++++.|++.|. ..++++.+.. .-+|.+|++|. +=+.+++...+.+
T Consensus 14 nT~~~A~~ia~~l~------~~~~~i~~~~~~~~~~~d~ii~g~pvy~~~~~~~~~~fl~~~ 69 (150)
T PRK06242 14 NTEKIAKAIAEVLD------AEVIDPGDVNPEDLSEYDLIGFGSGIYFGKFHKSLLKLIEKL 69 (150)
T ss_pred CHHHHHHHHHHhcC------cEEecHHHCCcccHhHCCEEEEeCchhcCCcCHHHHHHHHhh
Confidence 46778888887772 3455665432 34589999984 4444555544443
No 137
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=35.05 E-value=1.1e+02 Score=22.25 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=30.5
Q ss_pred HHHHHHHhcCCCCeEEEecCCC-----CCccCEEEEEEcCCHHHHHHHHH
Q psy8849 9 IVIKILKDIKAQDIKVYDTSNL-----TNLFDRITIASGSSKRQINALAV 53 (112)
Q Consensus 9 ~i~~~l~~kka~dI~vldv~~~-----~~~~dy~VIaT~~S~rh~~aia~ 53 (112)
.+.+.+...+...++++|++-. ..++|.+|..++.-..+++.+.+
T Consensus 93 ~~~~~~~~~~~~~~~v~e~pLL~E~~~~~~~D~vi~V~a~~e~ri~Rl~~ 142 (180)
T PF01121_consen 93 EIEKFIKRNKSEKVVVVEIPLLFESGLEKLCDEVIVVYAPEEIRIKRLME 142 (180)
T ss_dssp HHHHHHHHCHSTSEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHH
T ss_pred HHHHHHHhccCCCEEEEEcchhhhhhHhhhhceEEEEECCHHHHHHHHHh
Confidence 3444455555558999999843 56789999999988888777654
No 138
>PF10940 DUF2618: Protein of unknown function (DUF2618); InterPro: IPR021237 This bacterial family of proteins has no known function. The sequences within the family are highly conserved.
Probab=34.93 E-value=12 Score=21.18 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=13.5
Q ss_pred EEeeChhhhhhcchhhh
Q psy8849 87 IHIMNPYIRNMYNLEEI 103 (112)
Q Consensus 87 VHif~~e~R~~Y~LE~L 103 (112)
-|||.|..|.+++.--+
T Consensus 13 rHiMmpshR~~Fd~~~f 29 (40)
T PF10940_consen 13 RHIMMPSHRSCFDFSFF 29 (40)
T ss_pred hhhhchhhhcccchhhh
Confidence 38999999999886433
No 139
>PRK15448 ethanolamine catabolic microcompartment shell protein EutN; Provisional
Probab=34.70 E-value=56 Score=21.87 Aligned_cols=30 Identities=27% Similarity=0.234 Sum_probs=23.5
Q ss_pred CCCCeEEEecCCCCCccCEEEEEEcCCHHHH
Q psy8849 18 KAQDIKVYDTSNLTNLFDRITIASGSSKRQI 48 (112)
Q Consensus 18 ka~dI~vldv~~~~~~~dy~VIaT~~S~rh~ 48 (112)
.+.-++++|.=+ ....|++++++|+|.|+.
T Consensus 37 ~g~~~VAvD~vG-AG~Ge~Vlv~~GssAR~~ 66 (95)
T PRK15448 37 DGQCAVAIDNIG-AGTGEWVLLVSGSSARQA 66 (95)
T ss_pred CCCEEEEEECCC-CCCCCEEEEeCChHHhhh
Confidence 456667788776 567899999999988764
No 140
>PRK11628 transcriptional regulator BolA; Provisional
Probab=34.56 E-value=1.3e+02 Score=20.24 Aligned_cols=12 Identities=25% Similarity=0.277 Sum_probs=9.7
Q ss_pred cCCCCeEEEecC
Q psy8849 17 IKAQDIKVYDTS 28 (112)
Q Consensus 17 kka~dI~vldv~ 28 (112)
.....+.|.|.+
T Consensus 15 l~~~~l~V~d~S 26 (105)
T PRK11628 15 FQPVFLEVVDES 26 (105)
T ss_pred CCCcEEEEEECc
Confidence 456888999988
No 141
>cd08557 PI-PLCc_bacteria_like Catalytic domain of bacterial phosphatidylinositol-specific phospholipase C and similar proteins. This subfamily corresponds to the catalytic domain present in bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and their sequence homologs found in eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Its catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. Eukaryotic homologs in this family are named as phosphatidylinositol-specific phospholipase C X
Probab=33.98 E-value=1.9e+02 Score=21.34 Aligned_cols=50 Identities=10% Similarity=0.087 Sum_probs=34.9
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
+-++.+++|.++|.+.. ..+++|++......... ..-..+.+.+.+.+-.
T Consensus 80 ~~~~vL~~i~~fl~~~p-~E~vil~~~~~~~~~~~---------~~~~~~~~~l~~~~~~ 129 (271)
T cd08557 80 TLEDVLNEVKDFLDAHP-SEVVILDLEHEYGGDNG---------EDHDELDALLRDVLGD 129 (271)
T ss_pred cHHHHHHHHHHHHHHCC-CcEEEEEEEccCCCcch---------hhHHHHHHHHHHHhCc
Confidence 34678899999999987 67999999988765444 2334455555555533
No 142
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=33.76 E-value=90 Score=22.78 Aligned_cols=33 Identities=9% Similarity=0.143 Sum_probs=25.3
Q ss_pred cCEEEEEEc-CCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 34 FDRITIASG-SSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 34 ~dy~VIaT~-~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
..-=++||| +|...++..++.+.+.+++.|.+.
T Consensus 54 ~sGKiviTGaks~~~~~~a~~~~~~~l~~~g~~~ 87 (174)
T cd04517 54 SSGKITITGATSEEEAKQAARRAARLLQKLGFKV 87 (174)
T ss_pred CCCeEEEEccCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 344466775 599999999999999999887653
No 143
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=33.51 E-value=25 Score=24.07 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=21.6
Q ss_pred cCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 34 FDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
-|++||+||.+. +-+..++.+.|++.|+.
T Consensus 55 peiliiGtG~~~---~~~~~~~~~~l~~~gi~ 83 (114)
T cd05125 55 PEILVIGTGRKS---RPLSPELRKYFKKLGIA 83 (114)
T ss_pred CCEEEEccCCCC---CcCCHHHHHHHHHcCCE
Confidence 489999999983 34455677888887764
No 144
>PRK13490 chemoreceptor glutamine deamidase CheD; Provisional
Probab=33.25 E-value=1.1e+02 Score=22.15 Aligned_cols=40 Identities=18% Similarity=0.437 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcCCCccccc-ccCCCCEEEEEc--CCEEEEeeC
Q psy8849 52 AVSIRKNIKNINNNIVNIE-GKKSSEWLLLDL--GDIIIHIMN 91 (112)
Q Consensus 52 a~~v~~~lk~~~~~~~~~E-G~~~~~WvllD~--g~vvVHif~ 91 (112)
++.+.+.|++.|++...-+ |...+..+.+|. |+|.|.-..
T Consensus 114 v~~a~~~L~~~gI~i~a~dvGG~~gR~i~f~~~tG~v~vk~~~ 156 (162)
T PRK13490 114 GKAVKKKLKELSIPILAEDIGGNKGRTMIFDTSDGKVYIKTVG 156 (162)
T ss_pred HHHHHHHHHHcCCcEEEEECCCCCCcEEEEECCCCEEEEEEcC
Confidence 5567788889999865544 667789999987 678777554
No 145
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=33.04 E-value=1.7e+02 Score=20.49 Aligned_cols=54 Identities=13% Similarity=0.141 Sum_probs=38.0
Q ss_pred HHHHHHHHhcCCCCeEEEecC--CCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 8 IIVIKILKDIKAQDIKVYDTS--NLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 8 ~~i~~~l~~kka~dI~vldv~--~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
..+++.+.++++.=|.+-+.. ....++|+.+.+....+.++..+-..+...+.+
T Consensus 118 i~~~~~ak~~Ga~vI~IT~~~~s~La~~aD~~l~~~~~~~~~~~~~~~~~~~~~~~ 173 (177)
T cd05006 118 LKALEAAKERGMKTIALTGRDGGKLLELADIEIHVPSDDTPRIQEVHLLIGHILCE 173 (177)
T ss_pred HHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEEeCCCChHHHHHHHHHHHHHHHH
Confidence 355677777776655555543 346789999999999999888776666655544
No 146
>PRK02047 hypothetical protein; Provisional
Probab=32.99 E-value=1.4e+02 Score=19.42 Aligned_cols=54 Identities=9% Similarity=0.004 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHhcCCC--C-eEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 4 NKRQIIVIKILKDIKAQ--D-IKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~--d-I~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
.++.+.+.+++...-.. + -.-..-|....|.-+-|-.++.|..|+.++-++|.+
T Consensus 27 ~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~GkY~Svtv~v~v~s~eq~~~iY~~L~~ 83 (91)
T PRK02047 27 PEFADTIFKVVSVHDPEFDLEKIEERPSSGGNYTGLTITVRATSREQLDNIYRALTG 83 (91)
T ss_pred HhHHHHHHHHHHHhCCCCccCceEEccCCCCeEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 45667777777655221 1 122344555678899999999999999998887753
No 147
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=32.98 E-value=1.2e+02 Score=20.07 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=33.7
Q ss_pred CEEEEEEcC-CHHHHHHHHHHHHHHHHhcCCCcc------------cccccCCCCEEEEEc
Q psy8849 35 DRITIASGS-SKRQINALAVSIRKNIKNINNNIV------------NIEGKKSSEWLLLDL 82 (112)
Q Consensus 35 dy~VIaT~~-S~rh~~aia~~v~~~lk~~~~~~~------------~~EG~~~~~WvllD~ 82 (112)
+.++|.... +..++.++.+.+.+.+.+.|.... .+.+...|.|+++.+
T Consensus 5 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~I~k~~~G~Y~~~~f 65 (108)
T PRK00453 5 EIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYVLLNF 65 (108)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEecccccccceEcCCCcEEEEEEEEE
Confidence 445555555 899999999999999988655432 344556677777765
No 148
>TIGR02704 carboxysome_B carboxysome peptide B. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to Pfam family pfam03319, participate in other types of shell such as the ethanolamine degradation organelle.
Probab=32.98 E-value=51 Score=21.43 Aligned_cols=31 Identities=23% Similarity=0.073 Sum_probs=23.9
Q ss_pred cCCCCeEEEecCCCCCccCEEEEEEcCCHHHH
Q psy8849 17 IKAQDIKVYDTSNLTNLFDRITIASGSSKRQI 48 (112)
Q Consensus 17 kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~ 48 (112)
..+.-++++|.=+ ....|++++++|+|.|+.
T Consensus 30 ~~g~~~VAvD~vG-AG~Ge~Vlv~~GsaAr~~ 60 (80)
T TIGR02704 30 AKGKISVAVDPVG-APEGKWVFTASGSAARFA 60 (80)
T ss_pred CCCCEEEEEECCC-CCCCCEEEEeCCHHHhcc
Confidence 3566677788776 567899999999877764
No 149
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=32.90 E-value=1.1e+02 Score=18.93 Aligned_cols=45 Identities=13% Similarity=0.309 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCC----HHHHHHHHHHHHHHHHh
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSS----KRQINALAVSIRKNIKN 61 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S----~rh~~aia~~v~~~lk~ 61 (112)
+.++-...+-++|.+-+...+ ..+.|.||+. .-. |-.+|.+.|++
T Consensus 7 ~~~eA~~~l~~~l~~~~~~~~------------~~~~II~G~G~hS~~g~---Lk~~V~~~L~~ 55 (83)
T PF01713_consen 7 TVEEALRALEEFLDEARQRGI------------RELRIITGKGNHSKGGV---LKRAVRRWLEE 55 (83)
T ss_dssp -HHHHHHHHHHHHHHHHHTTH------------SEEEEE--STCTCCTSH---HHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHcCC------------CEEEEEeccCCCCCCCc---HHHHHHHHHHh
Confidence 344444555555555443333 6677777776 332 77778888866
No 150
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=32.85 E-value=1.2e+02 Score=18.50 Aligned_cols=59 Identities=14% Similarity=0.147 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
-++..+.++|.+.++ +|.-+...-.....-.++.+++.. .+...+-.++.+..++.|..
T Consensus 14 Giv~~v~~~l~~~g~-ni~d~~~~~~~~~f~~~~~v~~~~-~~~~~l~~~L~~l~~~~~l~ 72 (76)
T PF13740_consen 14 GIVAAVTGVLAEHGC-NIEDSRQAVLGGRFTLIMLVSIPE-DSLERLESALEELAEELGLD 72 (76)
T ss_dssp THHHHHHHHHHCTT--EEEEEEEEEETTEEEEEEEEEESH-HHHHHHHHHHHHHHHHTT-E
T ss_pred cHHHHHHHHHHHCCC-cEEEEEEEEEcCeEEEEEEEEeCc-ccHHHHHHHHHHHHHHCCcE
Confidence 367788888988864 443333333445556778888884 47777888887777776654
No 151
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=32.37 E-value=31 Score=23.17 Aligned_cols=29 Identities=10% Similarity=0.082 Sum_probs=22.5
Q ss_pred cCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 34 FDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
-|.+||+||.+.+.. ..++.+.|++.|+.
T Consensus 53 peiliiGTG~~~~~~---~~~~~~~l~~~gi~ 81 (109)
T cd05560 53 PEVILLGTGERQRFP---PPALLAPLLARGIG 81 (109)
T ss_pred CCEEEEecCCCCCcC---CHHHHHHHHHcCCe
Confidence 489999999998766 46677788887764
No 152
>PRK14479 dihydroxyacetone kinase; Provisional
Probab=32.22 E-value=3.1e+02 Score=23.91 Aligned_cols=87 Identities=14% Similarity=0.148 Sum_probs=55.7
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEc---CCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEE
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASG---SSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWL 78 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~---~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~Wv 78 (112)
+.+++++.+++.|.+ |+ +...=.++.|+..| .|.--+..++.++.+.|++.|+.+.+.- -..-=.
T Consensus 229 ~a~~~~~~~~~~l~~---------~~-~~~~~d~v~~lvN~lG~t~~~El~i~~~~~~~~l~~~~i~v~~~~--vG~~~T 296 (568)
T PRK14479 229 TADELADRLVDRILA---------DL-PLGAGERVAVLVNGLGATPYEELFVVYGAVARLLAARGITVVRPE--VGEFVT 296 (568)
T ss_pred CHHHHHHHHHHHHHh---------hc-CCCCCCeEEEEecCCCCCcHHHHHHHHHHHHHHHHHCCCEEEEee--eecccc
Confidence 345677777776655 11 11122356666654 5666688899999999999998755442 123345
Q ss_pred EEEcCCEEEEeeChhhhhhcchhhhc
Q psy8849 79 LLDLGDIIIHIMNPYIRNMYNLEEIW 104 (112)
Q Consensus 79 llD~g~vvVHif~~e~R~~Y~LE~LW 104 (112)
-+|...+-|-++.-+. .|+++|
T Consensus 297 sldm~G~SiTl~~~d~----~~~~~l 318 (568)
T PRK14479 297 SLDMAGASLTLMKLDD----ELEELW 318 (568)
T ss_pred cCCCCccEEEeeeCCH----HHHHHh
Confidence 5788877777775543 377777
No 153
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=32.06 E-value=64 Score=27.56 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=33.2
Q ss_pred CCeEEEecCCCCCccCEE----EEEEcCCHHHHHHHHHHHHHHHHhcCCCccc
Q psy8849 20 QDIKVYDTSNLTNLFDRI----TIASGSSKRQINALAVSIRKNIKNINNNIVN 68 (112)
Q Consensus 20 ~dI~vldv~~~~~~~dy~----VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~ 68 (112)
.||.|-+=+...+|..-+ +...|-|.+..+++|..|++.|++.|...+.
T Consensus 81 ~~i~V~~~~~~~PFSkGiLarSL~~aG~~~~~Ay~iA~~Ve~~Lr~~~~~~Is 133 (475)
T PRK12337 81 VDIVVREGRGRRPFSRGVLARSLEDAGFSPREAYELASAVELRLRQEGVREIG 133 (475)
T ss_pred ceEEEecCCCCCCcchhhHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCcccC
Confidence 455555533333333322 2347999999999999999999998876443
No 154
>TIGR01484 HAD-SF-IIB HAD-superfamily hydrolase, subfamily IIB. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing sequences whose relationship to the other groups is unclear.
Probab=32.02 E-value=48 Score=23.53 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=16.3
Q ss_pred CEEEEEEcCCHHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAVS 54 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~ 54 (112)
-.|+||||++...++.+...
T Consensus 34 ~~~~i~TGR~~~~~~~~~~~ 53 (204)
T TIGR01484 34 VKVVLVTGRSLAEIKELLKQ 53 (204)
T ss_pred CEEEEECCCCHHHHHHHHHh
Confidence 37899999999888877654
No 155
>PTZ00174 phosphomannomutase; Provisional
Probab=31.91 E-value=49 Score=24.77 Aligned_cols=14 Identities=29% Similarity=0.394 Sum_probs=11.3
Q ss_pred CEEEEEEcCCHHHH
Q psy8849 35 DRITIASGSSKRQI 48 (112)
Q Consensus 35 dy~VIaT~~S~rh~ 48 (112)
=.|+|||||+...+
T Consensus 39 i~~viaTGR~~~~i 52 (247)
T PTZ00174 39 FKIGVVGGSDYPKI 52 (247)
T ss_pred CEEEEEcCCCHHHH
Confidence 46999999987755
No 156
>cd07949 PCA_45_Doxase_B_like_1 The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase. This subfamily is composed of proteins of unknown function with similarity to the B subunit of Protocatechuate 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=31.82 E-value=80 Score=24.66 Aligned_cols=98 Identities=12% Similarity=0.083 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCC-CccC---EEEEEEcCCHH---------H------HHHHHHHHHHHHHhcCCC
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLT-NLFD---RITIASGSSKR---------Q------INALAVSIRKNIKNINNN 65 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~-~~~d---y~VIaT~~S~r---------h------~~aia~~v~~~lk~~~~~ 65 (112)
+=.+++.+.+.+.+.+=|+++.-.... .+.| +|.|.++.+.. + -..+|++|.+.+++.|++
T Consensus 35 ~a~~~~~~~v~~~~PD~iVvis~dH~~~f~~~~~p~f~i~~~~~~~g~~~~~g~~~~~~~~g~~~LA~~i~~~~~~~g~d 114 (276)
T cd07949 35 DGFPPVHDWLEKAKPDVAVVFYNDHGLNFFLDKMPTFAVGAAPSYRNADEGWGIPALAPFKGDPELSWHLIESLVEDEFD 114 (276)
T ss_pred HHHHHHHHHHHHcCCCEEEEECCcHHhhhccccCCcEEEecCccccCcccccCCCCCCCCCCCHHHHHHHHHHHHHcCCC
Confidence 345677888888888888888753333 2355 78888666322 1 357899999999988885
Q ss_pred ccc--ccccCCCCEEEEEc----CC---EEEEeeCh-------hhhhhcchhh
Q psy8849 66 IVN--IEGKKSSEWLLLDL----GD---IIIHIMNP-------YIRNMYNLEE 102 (112)
Q Consensus 66 ~~~--~EG~~~~~WvllD~----g~---vvVHif~~-------e~R~~Y~LE~ 102 (112)
... .-+.+-+.|+-+-+ ++ -||+|+.. ..++.|+|=+
T Consensus 115 ~~~~~~~~lDHG~~vPL~~l~~~~d~~~pvV~i~~n~~~~p~~~~~~~~~lG~ 167 (276)
T cd07949 115 ITTCQEMLVDHACTLPMQLFWPGAEWPIKVVPVSINTVQHPLPSPKRCFKLGQ 167 (276)
T ss_pred eeccCCCCCCcchhhHHHHhcCccCCCCCEEEEEeccCCCCCCCHHHHHHHHH
Confidence 322 22345566665543 22 26666543 5567776643
No 157
>PRK13487 chemoreceptor glutamine deamidase CheD; Provisional
Probab=31.79 E-value=1.3e+02 Score=22.75 Aligned_cols=41 Identities=12% Similarity=0.115 Sum_probs=31.4
Q ss_pred HHHHHHHHHhcCCCccccc-ccCCCCEEEEEc--CCEEEEeeCh
Q psy8849 52 AVSIRKNIKNINNNIVNIE-GKKSSEWLLLDL--GDIIIHIMNP 92 (112)
Q Consensus 52 a~~v~~~lk~~~~~~~~~E-G~~~~~WvllD~--g~vvVHif~~ 92 (112)
++.+.+.|++.|++....+ |.+.+..+.++. |+|.|.-+..
T Consensus 129 i~~a~~~L~~~gI~iva~DvGG~~gR~v~f~~~tG~v~vk~~~~ 172 (201)
T PRK13487 129 AEFVRDYLQTERIPIVAEDLLDIYPRKVYFFPTTGKVLVKKLKH 172 (201)
T ss_pred HHHHHHHHHHcCCcEEEEECCCCCCcEEEEECCCCEEEEEECCC
Confidence 4557788889999865543 677899999976 8999987644
No 158
>KOG3782|consensus
Probab=31.35 E-value=1e+02 Score=23.06 Aligned_cols=52 Identities=13% Similarity=0.144 Sum_probs=38.5
Q ss_pred HHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 13 ILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 13 ~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..+-||-.++-.+.+....+..- .=|.-++|.-|+.-+.+++-+.+|+++..
T Consensus 43 ~vDPkK~i~vgsFR~~p~G~q~~-~kV~yarSE~hLTEl~E~iCd~mk~Y~~~ 94 (189)
T KOG3782|consen 43 KVDPKKMIDVGSFRLDPQGNQIS-KKVRYARSEMHLTELMEKICDKMKDYLKA 94 (189)
T ss_pred hcCchheeeecceEECCCCCeee-eeeccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 34567777888887776543222 22788999999999999999999987654
No 159
>COG1915 Uncharacterized conserved protein [Function unknown]
Probab=31.16 E-value=2.6e+02 Score=23.18 Aligned_cols=52 Identities=6% Similarity=0.074 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhcCC-CCeEEEecCCCCC-ccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 6 RQIIVIKILKDIKA-QDIKVYDTSNLTN-LFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 6 l~~~i~~~l~~kka-~dI~vldv~~~~~-~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
++....+.+-|..+ ..|.-|++.+..+ -.-.=|+++|.+..|+.-+..++.+
T Consensus 17 il~ralD~I~d~gG~f~vLef~~Gk~k~dpS~A~i~V~~~~~~~leeIl~eL~~ 70 (415)
T COG1915 17 ILNRALDIIVDMGGDFQVLEFNLGKRKTDPSYAEILVSAPDHEHLEEILSELID 70 (415)
T ss_pred hhHHHHHHHhhcCCceEEEEEecccccCCCCceEEEEeCCCHHHHHHHHHHHHH
Confidence 34556666667666 5666677776533 2233478899999999988777664
No 160
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.13 E-value=1e+02 Score=17.33 Aligned_cols=55 Identities=5% Similarity=0.108 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCC-----CCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNL-----TNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~-----~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
.+..+.+++.+.++ +|.-++.... ...+.+.+-..+.+..|+..+.+. +++.|.+
T Consensus 11 ~L~~i~~~i~~~~~-nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~----l~~~g~~ 70 (73)
T cd04886 11 QLAKLLAVIAEAGA-NIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAA----LREAGYD 70 (73)
T ss_pred hHHHHHHHHHHcCC-CEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHH----HHHcCCE
Confidence 45677888876654 5555554432 233445555666777887665554 4555543
No 161
>PRK05456 ATP-dependent protease subunit HslV; Provisional
Probab=31.01 E-value=62 Score=23.52 Aligned_cols=33 Identities=9% Similarity=0.089 Sum_probs=27.8
Q ss_pred CCCc-cCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 30 LTNL-FDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 30 ~~~~-~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
...+ .|++.+|.+-|.-+.+.+++.++..++.+
T Consensus 35 I~~i~~d~i~~~~aG~~aD~q~l~~~l~~~~~~y 68 (172)
T PRK05456 35 VRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEH 68 (172)
T ss_pred EEEeCCCCEEEEEeccHHHHHHHHHHHHHHHHHc
Confidence 3456 89999999999999999999999766643
No 162
>PF02574 S-methyl_trans: Homocysteine S-methyltransferase; InterPro: IPR003726 S-methylmethionine: homocysteine methyltransferase 2.1.1.10 from EC from Escherichia coli accepts selenohomocysteine as a substrate. S-methylmethionine is an abundant plant product that can be utilised for methionine biosynthesis []. Human methionine synthase (5-methyltetrahydrofolate:L-homocysteine S-transmethylase; 2.1.1.13 from EC) shares 53 and 63% identity with the E. coli and the presumptive Caenorhabditis elegans proteins, respectively, and contains all residues implicated in B12 binding to the E. coli protein []. Betaine--homocysteine S-methyltransferase (2.1.1.5 from EC) converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline [].; GO: 0008898 homocysteine S-methyltransferase activity; PDB: 1UMY_A 1LT8_B 1LT7_B 3BOF_B 1Q7Q_B 1Q85_B 1Q7Z_A 1Q7M_A 1Q8A_B 1Q8J_B ....
Probab=30.85 E-value=26 Score=27.24 Aligned_cols=18 Identities=33% Similarity=0.545 Sum_probs=12.2
Q ss_pred EEcCCHHHHHHHHHHHHH
Q psy8849 40 ASGSSKRQINALAVSIRK 57 (112)
Q Consensus 40 aT~~S~rh~~aia~~v~~ 57 (112)
|.|.++.|+++|++.+.+
T Consensus 288 CCGt~P~hI~al~~~l~~ 305 (305)
T PF02574_consen 288 CCGTTPEHIRALAKALDK 305 (305)
T ss_dssp -TT--HHHHHHHHHHTH-
T ss_pred CCCCCHHHHHHHHHHhcC
Confidence 788999999999987753
No 163
>PRK10245 adrA diguanylate cyclase AdrA; Provisional
Probab=30.52 E-value=2.8e+02 Score=22.13 Aligned_cols=55 Identities=7% Similarity=0.060 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
+++++.+++.|.+.-..+-.+.-+.+ .+|.|+..+.+......+++.+.+.+++.
T Consensus 260 D~lL~~vA~~L~~~l~~~d~laRlgg----deFavll~~~~~~~a~~~~~rl~~~l~~~ 314 (366)
T PRK10245 260 DEAIVALTRQLQITLRGSDVIGRFGG----DEFAVIMSGTPAESAITAMSRVHEGLNTL 314 (366)
T ss_pred HHHHHHHHHHHHHhCCCCCEEEEEcC----cEEEEEeCCCCHHHHHHHHHHHHHHHhhc
Confidence 56778888888765443323333332 47788888888888888999998888653
No 164
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=30.38 E-value=42 Score=24.49 Aligned_cols=51 Identities=14% Similarity=0.169 Sum_probs=30.1
Q ss_pred CccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEE
Q psy8849 32 NLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIH 88 (112)
Q Consensus 32 ~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVH 88 (112)
.-.|.||++||.|. ...+...+++.|.....+-.......-|...-|-.|+
T Consensus 104 ~~iD~~vLvSgD~D------F~~Lv~~lre~G~~V~v~g~~~~ts~~L~~acd~FI~ 154 (160)
T TIGR00288 104 PNIDAVALVTRDAD------FLPVINKAKENGKETIVIGAEPGFSTALQNSADIAII 154 (160)
T ss_pred CCCCEEEEEeccHh------HHHHHHHHHHCCCEEEEEeCCCCChHHHHHhcCeEEe
Confidence 45699999999876 4556677888876543332122233344444444443
No 165
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=30.29 E-value=1.1e+02 Score=17.85 Aligned_cols=24 Identities=13% Similarity=0.180 Sum_probs=20.1
Q ss_pred CCccCEEEEEEcCCHHHHHHHHHH
Q psy8849 31 TNLFDRITIASGSSKRQINALAVS 54 (112)
Q Consensus 31 ~~~~dy~VIaT~~S~rh~~aia~~ 54 (112)
+.-.||++.+.++|..++..+...
T Consensus 32 tG~~d~~~~v~~~d~~~l~~~i~~ 55 (74)
T PF01037_consen 32 TGEYDLILKVRARDMEELEEFIRE 55 (74)
T ss_dssp SSSSSEEEEEEESSHHHHHHHHHH
T ss_pred eCCCCEEEEEEECCHHHHHHHHHH
Confidence 345799999999999999887665
No 166
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=30.10 E-value=1.8e+02 Score=21.78 Aligned_cols=48 Identities=15% Similarity=0.271 Sum_probs=28.5
Q ss_pred CCCCeEEEecCCCC---------CccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 18 KAQDIKVYDTSNLT---------NLFDRITIASGSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 18 ka~dI~vldv~~~~---------~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
+.-|++++|.+... ..+|..|+++-........+ ....+.++..|.+.
T Consensus 211 ~~yD~ViiD~pp~~~~~d~~~~~~~~d~vilV~~~~~t~~~~~-~~~~~~l~~~~~~~ 267 (274)
T TIGR03029 211 GDYDVVIVDTPSAEHSSDAQIVATRARGTLIVSRVNETRLHEL-TSLKEHLSGVGVRV 267 (274)
T ss_pred hcCCEEEEeCCCcccccHHHHHHHhCCeEEEEEECCCCCHHHH-HHHHHHHHhCCCCE
Confidence 34799999999742 45677777665443333333 33444555555543
No 167
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.79 E-value=1.3e+02 Score=17.86 Aligned_cols=52 Identities=8% Similarity=0.119 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCCCCeEEEecCCC-CCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 8 IIVIKILKDIKAQDIKVYDTSNL-TNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 8 ~~i~~~l~~kka~dI~vldv~~~-~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..+++.+.+ +-+|+-+.-+.. ...+..+|....++..|+..+.+. |++.|..
T Consensus 13 ~~~~~~i~~--~~nI~~~~~~~~~~~~~~v~v~ie~~~~~~~~~i~~~----L~~~G~~ 65 (68)
T cd04885 13 KKFLELLGP--PRNITEFHYRNQGGDEARVLVGIQVPDREDLAELKER----LEALGYP 65 (68)
T ss_pred HHHHHHhCC--CCcEEEEEEEcCCCCceEEEEEEEeCCHHHHHHHHHH----HHHcCCC
Confidence 455666665 667876655432 346778888888888888776664 4556653
No 168
>PF08029 HisG_C: HisG, C-terminal domain; InterPro: IPR013115 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. This entry represents the C-terminal portion of ATP phosphoribosyltransferase. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates [, ]. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. This domain is not directly involved in catalysis but appears to be responsible for the formation of hexamers induced by the binding of inhibitors to the enzyme, thus regulating activity.; GO: 0000287 magnesium ion binding, 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1Q1K_A 1H3D_A 2VD3_B 1NH7_A 1NH8_A.
Probab=29.78 E-value=51 Score=20.91 Aligned_cols=24 Identities=25% Similarity=0.202 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCC
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSN 29 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~ 29 (112)
.+..++.-|..-+|+||.++++..
T Consensus 51 ~~~~~~~~Lk~~GA~~Ilv~pi~~ 74 (75)
T PF08029_consen 51 QVWDLMDKLKAAGASDILVLPIEK 74 (75)
T ss_dssp CHHHHHHHHHCTT-EEEEEEE-S-
T ss_pred HHHHHHHHHHHcCCCEEEEEeccc
Confidence 456778889999999999999864
No 169
>PRK00341 hypothetical protein; Provisional
Probab=29.72 E-value=1.6e+02 Score=19.17 Aligned_cols=53 Identities=17% Similarity=0.150 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHhcCCCCe--EEE--ecCCCCCccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 3 INKRQIIVIKILKDIKAQDI--KVY--DTSNLTNLFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI--~vl--dv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
..++.+.|.+++. +.+ ++ ..+ .-+....|.-+-|-.++.|..|+.++-++|.+
T Consensus 27 ~~~~~~~V~~iv~-~~~-~~~~~~~~~k~Ss~GkY~S~tv~i~~~s~~q~~~iy~~L~~ 83 (91)
T PRK00341 27 GVGFKDLVIEILQ-KHA-DVDLSTLAERQSSNGKYTTVQLHIVATDEDQLQDINSALRA 83 (91)
T ss_pred chhHHHHHHHHHH-HhC-CCcccceeeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 3467777788876 444 33 222 33444568888899999999999998887753
No 170
>COG1692 Calcineurin-like phosphoesterase [General function prediction only]
Probab=29.70 E-value=27 Score=27.63 Aligned_cols=77 Identities=12% Similarity=0.212 Sum_probs=51.0
Q ss_pred ccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcc---------------------------cccccCCCCEEEEEcCCE
Q psy8849 33 LFDRITIASGSSKRQINALAVSIRKNIKNINNNIV---------------------------NIEGKKSSEWLLLDLGDI 85 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~---------------------------~~EG~~~~~WvllD~g~v 85 (112)
+--=|||+-|.+..|.+.+.+.+.+.+++.|+... -.+|..+..|.+++..+.
T Consensus 29 yk~dfvI~N~ENaa~G~Git~k~y~~l~~~G~dviT~GNH~wd~~ei~~~i~~~~~ilRP~N~p~~~~G~G~~~f~~ng~ 108 (266)
T COG1692 29 YKIDFVIVNGENAAGGFGITEKIYKELLEAGADVITLGNHTWDQKEILDFIDNADRILRPANYPDGTPGKGSRIFKINGK 108 (266)
T ss_pred hcCcEEEEcCccccCCcCCCHHHHHHHHHhCCCEEecccccccchHHHHHhhcccceeccCCCCCCCCcceEEEEEeCCc
Confidence 33348999999999999999999999999877321 134667778899887443
Q ss_pred ---EEEeeC-----h-hhhhhcchhhhcccccc
Q psy8849 86 ---IIHIMN-----P-YIRNMYNLEEIWGEKEI 109 (112)
Q Consensus 86 ---vVHif~-----~-e~R~~Y~LE~LW~~~~~ 109 (112)
|++||- + -.==|+.+++|....+.
T Consensus 109 ki~V~Nl~Grv~m~~~~d~PF~~~d~l~~~~~~ 141 (266)
T COG1692 109 KLAVINLMGRVFMPPALDNPFKAADKLLDEIKL 141 (266)
T ss_pred EEEEEEeeccccCccccCCHHHHHHHHHHhCcc
Confidence 455543 1 12224455666555443
No 171
>cd08587 PI-PLCXDc_like Catalytic domain of phosphatidylinositol-specific phospholipase C X domain containing and similar proteins. This family corresponds to the catalytic domain present in phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD) which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs mainly found in eukaryota. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs and their bacterial homologs contain a single TIM-barrel type catalytic domain, X domain, which is more closely related to that of bacterial PI-PLCs. Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may be
Probab=29.33 E-value=2.6e+02 Score=21.47 Aligned_cols=53 Identities=11% Similarity=0.157 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
..++.+++|.++|.+. -..|++++++......+. +..+-..+...+.+.+...
T Consensus 93 ~~~~~l~~i~~fl~~~-p~Evvil~~~~~~~~~~~-------~~~~~~~l~~~l~~~~~~~ 145 (288)
T cd08587 93 PVDEVLEDVNDFLDEH-PKEVVILDFNHFYGMDDK-------SPEDHEKLVELLEDIFGDK 145 (288)
T ss_pred CHHHHHHHHHHHHHhC-CCcEEEEEEEccccCCcc-------cHHHHHHHHHHHHHHhccc
Confidence 3467889999999986 478999999876554443 5566666666666655443
No 172
>TIGR02703 carboxysome_A carboxysome peptide A. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to Pfam family pfam03319, participate in other types of shell such as the ethanolamine degradation organelle.
Probab=29.09 E-value=71 Score=20.76 Aligned_cols=30 Identities=13% Similarity=0.049 Sum_probs=23.5
Q ss_pred CCCCeEEEecCCCCCccCEEEEEEcCCHHHH
Q psy8849 18 KAQDIKVYDTSNLTNLFDRITIASGSSKRQI 48 (112)
Q Consensus 18 ka~dI~vldv~~~~~~~dy~VIaT~~S~rh~ 48 (112)
.+.-++++|.=+ +...|++++++|+|.|+.
T Consensus 32 ~g~~~VAvD~vG-AG~Ge~Vlv~~Gs~AR~~ 61 (81)
T TIGR02703 32 GGARQVAVDAIG-CKPGDWVLCVGSSAAREA 61 (81)
T ss_pred CCCEEEEEECCC-CCCCCEEEEeCCHHHhhh
Confidence 455667788766 668899999999988874
No 173
>PRK13488 chemoreceptor glutamine deamidase CheD; Provisional
Probab=28.95 E-value=1.4e+02 Score=21.52 Aligned_cols=42 Identities=24% Similarity=0.341 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcCCCccccc-ccCCCCEEEEEc--CCEEEEeeChh
Q psy8849 52 AVSIRKNIKNINNNIVNIE-GKKSSEWLLLDL--GDIIIHIMNPY 93 (112)
Q Consensus 52 a~~v~~~lk~~~~~~~~~E-G~~~~~WvllD~--g~vvVHif~~e 93 (112)
++.+.+.|++.|++...-+ |...+.-+.+|. |++.|.-...+
T Consensus 109 i~~a~~~L~~~gi~i~a~dvGG~~gR~i~f~~~tG~v~vk~~~~~ 153 (157)
T PRK13488 109 IESAKETLKKLGIRIVAEDVGGDYGRTVKFDLKTGKVIVRKANGG 153 (157)
T ss_pred HHHHHHHHHHCCCcEEEEEcCCCCCcEEEEECCCCEEEEEEcCCc
Confidence 5567788889999865433 667789999977 78888766533
No 174
>PRK00081 coaE dephospho-CoA kinase; Reviewed
Probab=28.89 E-value=2.2e+02 Score=20.43 Aligned_cols=44 Identities=20% Similarity=0.396 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCeEEEecCC-----CCCccCEEEEEEcCCHHHHHHHHH
Q psy8849 10 VIKILKDIKAQDIKVYDTSN-----LTNLFDRITIASGSSKRQINALAV 53 (112)
Q Consensus 10 i~~~l~~kka~dI~vldv~~-----~~~~~dy~VIaT~~S~rh~~aia~ 53 (112)
+.+.+...+...++++|++- ...++|++|+.++....+.+.+..
T Consensus 96 ~~~~~~~~~~~~~vv~e~pll~e~~~~~~~D~vi~V~a~~e~~~~Rl~~ 144 (194)
T PRK00081 96 ILEQLQEAESSPYVVLDIPLLFENGLEKLVDRVLVVDAPPETQLERLMA 144 (194)
T ss_pred HHHHHHHcccCCEEEEEehHhhcCCchhhCCeEEEEECCHHHHHHHHHH
Confidence 33344443333689999874 345689999999998888777654
No 175
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=28.74 E-value=2.3e+02 Score=20.64 Aligned_cols=61 Identities=13% Similarity=0.144 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCcc----CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLF----DRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~----dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..++.+++.|.+-....-.-+.+.+..+|. --++-..+....-+.++++.+...+.+.|++
T Consensus 51 ~~~~~l~~~l~~i~~~~~f~i~l~g~g~F~~~~~~rvi~~~v~~~~~L~~L~~~l~~~~~~~g~~ 115 (180)
T COG1514 51 DKADELIEALARIAAPEPFPITLDGAGSFPNPRRPRVIWVGVEETEELRALAEELERALARLGLR 115 (180)
T ss_pred hHHHHHHHHHHHhhcCCceEEEEeeEcccCCCCCCcEEEEcCCCcHHHHHHHHHHHHHHHhcCCC
Confidence 445666677766655423445666666665 4666667777777999999999999887764
No 176
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=28.44 E-value=68 Score=19.90 Aligned_cols=28 Identities=14% Similarity=0.160 Sum_probs=25.3
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
.|-+-|+..+..+++.+|..|.+.+++.
T Consensus 10 ~y~i~~~~~~ee~l~~~a~~i~~~i~~~ 37 (89)
T PF05164_consen 10 EYRIKCPDEDEEYLRKAAELINEKINEI 37 (89)
T ss_dssp EEEECETGCGHHHHHHHHHHHHHHHHHH
T ss_pred EEEeecCCCCHHHHHHHHHHHHHHHHHH
Confidence 5788889999999999999999999874
No 177
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=28.29 E-value=47 Score=21.29 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=15.8
Q ss_pred ccCEEEEEEcCCHHHH-HHHHHHH
Q psy8849 33 LFDRITIASGSSKRQI-NALAVSI 55 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~-~aia~~v 55 (112)
+++.+|++-|.|..-+ +++++.+
T Consensus 2 Fa~~vIlVEG~tE~~~l~~~~~~~ 25 (97)
T cd01026 2 FADKVILVEGDSEEILLPALAKKL 25 (97)
T ss_pred CCCeEEEEecHHHHHHHHHHHHHh
Confidence 5788889999888763 3444443
No 178
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=28.16 E-value=2.4e+02 Score=21.03 Aligned_cols=35 Identities=17% Similarity=0.123 Sum_probs=23.8
Q ss_pred CCCeEEEecCCCC---------CccCEEEEEEcCCHHHHHHHHH
Q psy8849 19 AQDIKVYDTSNLT---------NLFDRITIASGSSKRQINALAV 53 (112)
Q Consensus 19 a~dI~vldv~~~~---------~~~dy~VIaT~~S~rh~~aia~ 53 (112)
.-|++++|..+.. ..+|++||.+..+..=+.++..
T Consensus 117 ~yD~viIDt~g~~~~~~~~~~l~~AD~viip~~~~~~sl~~~~~ 160 (270)
T PRK13185 117 DYDVILFDVLGDVVCGGFAAPLQYADYALIVTANDFDSIFAANR 160 (270)
T ss_pred cCCEEEEecCCCcccCcccchhhhCcEEEEEecCchhhHHHHHH
Confidence 4699999975431 1489999998776554544433
No 179
>COG5440 Uncharacterized conserved protein [Function unknown]
Probab=27.94 E-value=2.5e+02 Score=20.66 Aligned_cols=52 Identities=19% Similarity=0.183 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHHhcCCCCe-------------------EEEecCCCCCccCEEEEEEc--CCHHHHHHHH
Q psy8849 1 MNINKRQIIVIKILKDIKAQDI-------------------KVYDTSNLTNLFDRITIASG--SSKRQINALA 52 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~kka~dI-------------------~vldv~~~~~~~dy~VIaT~--~S~rh~~aia 52 (112)
|+....-+.|-++|.|.+..-. .+++|=....-.||.|||.| -|+.|.+|+.
T Consensus 1 m~~~~~d~~I~~WL~EeG~~~~kv~~~na~fH~~v~~P~~~~~i~VI~p~~~~d~viVA~gi~ls~eH~~al~ 73 (161)
T COG5440 1 MEPLDSDNMILDWLAEEGNVSVKVPDENAPFHFVVKPPTGGKVISVIQPPRGSDMVIVAIGIALSQEHRRALM 73 (161)
T ss_pred CcchhHHHHHHHHHHHhCceeeccCCCCCceeEEecCCCCCceEEEEecCCCCcEEEEEEeeccCHHHHHHHH
Confidence 3334445667777766553222 22333333344588888765 6899999887
No 180
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=27.85 E-value=1.2e+02 Score=23.26 Aligned_cols=33 Identities=3% Similarity=0.112 Sum_probs=28.4
Q ss_pred CCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 29 NLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 29 ~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
+-++.-..+||.|+.|.+-...++..+.+.++.
T Consensus 193 eGss~Qei~vVTTa~s~eeGe~V~~~Ln~~lrd 225 (227)
T COG4031 193 EGSSVQEIRVVTTAGSREEGERVMNLLNEILRD 225 (227)
T ss_pred cCCceeEEEEEEeecchhhHHHHHHHHHHHHhh
Confidence 346778999999999999999999998888765
No 181
>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=27.81 E-value=98 Score=19.97 Aligned_cols=26 Identities=31% Similarity=0.243 Sum_probs=21.3
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCCCcc
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINNNIV 67 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~ 67 (112)
+|+|.|. ..+|..|++..++.|++..
T Consensus 19 ~VvAKG~-----g~~A~~I~~~A~e~~VPi~ 44 (82)
T TIGR00789 19 KVVASGV-----GEVAERIIEIAKKHGIPIV 44 (82)
T ss_pred EEEEEeC-----CHHHHHHHHHHHHcCCCEE
Confidence 6889997 4578999999999998743
No 182
>PRK09894 diguanylate cyclase; Provisional
Probab=27.79 E-value=2.6e+02 Score=20.76 Aligned_cols=55 Identities=15% Similarity=0.065 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
+++++.+++.|...-...-.+.-+.+ .+|+|+..+.+..+...+++.+.+.+...
T Consensus 182 d~~L~~ia~~l~~~~~~~~~~~R~~g----~~F~ill~~~~~~~~~~~~~~l~~~~~~~ 236 (296)
T PRK09894 182 DVVLRTLATYLASWTRDYETVYRYGG----EEFIICLKAATDEEACRAGERIRQLIANH 236 (296)
T ss_pred HHHHHHHHHHHHHhCCCCCEEEEEcC----CeEEEEeCCCCHHHHHHHHHHHHHHHHhC
Confidence 46778888888765444333444433 36777777788888889999998877653
No 183
>PRK09622 porA pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed
Probab=27.72 E-value=2.4e+02 Score=23.17 Aligned_cols=25 Identities=20% Similarity=0.150 Sum_probs=20.2
Q ss_pred ccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 33 LFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
-+|+.||+.|...+.++..++.+++
T Consensus 267 dad~~iV~~Gs~~~~a~ea~~~L~~ 291 (407)
T PRK09622 267 DAEVAIVALGTTYESAIVAAKEMRK 291 (407)
T ss_pred CCCEEEEEEChhHHHHHHHHHHHHh
Confidence 4799999999998888777776643
No 184
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=27.54 E-value=2e+02 Score=19.48 Aligned_cols=33 Identities=9% Similarity=0.038 Sum_probs=21.3
Q ss_pred CeEEEecCCCC--------CccCEEEEEEcCCHHHHHHHHH
Q psy8849 21 DIKVYDTSNLT--------NLFDRITIASGSSKRQINALAV 53 (112)
Q Consensus 21 dI~vldv~~~~--------~~~dy~VIaT~~S~rh~~aia~ 53 (112)
|++++|.++.. ..+|++|+.+..+..-+..+..
T Consensus 64 d~viiD~p~~~~~~~~~~l~~ad~viiv~~~~~~s~~~~~~ 104 (179)
T cd02036 64 DYILIDSPAGIERGFITAIAPADEALLVTTPEISSLRDADR 104 (179)
T ss_pred CEEEEECCCCCcHHHHHHHHhCCcEEEEeCCCcchHHHHHH
Confidence 88888887531 4568888876665555544443
No 185
>KOG3302|consensus
Probab=27.41 E-value=1.2e+02 Score=23.02 Aligned_cols=33 Identities=6% Similarity=0.058 Sum_probs=26.3
Q ss_pred ccCEEEEEE-cCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 33 LFDRITIAS-GSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 33 ~~dy~VIaT-~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
|+--=|+|| |+|....+--|..+.+.+.+.|.+
T Consensus 74 ~ssGKi~ctgA~se~~ar~aark~aRilqkLgf~ 107 (200)
T KOG3302|consen 74 FSSGKIVCTGAKSEDSARLAARKYARILQKLGFP 107 (200)
T ss_pred ecCCcEEEeccCCHHHHHHHHHHHHHHHHHcCCC
Confidence 344458899 889999888888888888888775
No 186
>PF10139 Virul_Fac: Putative bacterial virulence factor; InterPro: IPR017030 This group represents a virulence effector protein, SrfC type.
Probab=27.40 E-value=1e+02 Score=28.24 Aligned_cols=40 Identities=8% Similarity=0.172 Sum_probs=32.6
Q ss_pred CEEEEEEcCCHH-HHHHHHHHHHHHHHh-cCCCcccccccCC
Q psy8849 35 DRITIASGSSKR-QINALAVSIRKNIKN-INNNIVNIEGKKS 74 (112)
Q Consensus 35 dy~VIaT~~S~r-h~~aia~~v~~~lk~-~~~~~~~~EG~~~ 74 (112)
+-+++||+.|.+ .+..++..|..-++. .|..|...++...
T Consensus 375 ~~LlvC~a~~~~~ev~~~~~~l~~Wv~~tqG~tp~~R~~r~p 416 (854)
T PF10139_consen 375 NLLLVCTAASQQSEVKDVGRALDYWVKQTQGETPQVRARRKP 416 (854)
T ss_pred CEEEEeCCCcchhhHHHHHHHHHHHHHHhcCCChHHhccCCC
Confidence 789999999999 899999999998887 4666655555444
No 187
>PRK13690 hypothetical protein; Provisional
Probab=27.38 E-value=2.7e+02 Score=20.92 Aligned_cols=63 Identities=17% Similarity=0.189 Sum_probs=41.3
Q ss_pred CCHHHHHHHHHHHHHh------cCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 1 MNINKRQIIVIKILKD------IKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~------kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
|+.+++.++...++.| .|..||.|+-.|-.. -----|.|..|..=.+++.+.+.+.+++.|+.
T Consensus 1 ~~~~~i~~~~~~~~~El~~~a~l~~g~i~VvGcSTSE--V~G~~IGt~ss~eva~~i~~~l~~~~~~~gi~ 69 (184)
T PRK13690 1 MDLEEIKKQTRQILEELLEQANLKPGQIFVLGCSTSE--VLGERIGTAGSLEVAEAIVEALLEVLKETGIH 69 (184)
T ss_pred CCHHHHHHHHHHHHHHHHHhhCCCCCCEEEEecchHh--hCCcccCCcChHHHHHHHHHHHHHHhhhcCcE
Confidence 4444454444444433 345678887666322 22335788888888999999999888888774
No 188
>PF02962 CHMI: 5-carboxymethyl-2-hydroxymuconate isomerase; InterPro: IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway []. Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria []. 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits []. A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene [].; PDB: 3E6Q_H 1OTG_B.
Probab=27.25 E-value=78 Score=22.02 Aligned_cols=60 Identities=17% Similarity=0.035 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCC---------CCccCEEE-----EEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNL---------TNLFDRIT-----IASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~---------~~~~dy~V-----IaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
...+++.+-+++.+.+.-+.--|-++-. ..-.+-|| |.+|+|..+-+++++.|-+.+++.
T Consensus 17 ~~~ll~~l~~~~~~sglF~~~~IK~Ra~~~~~y~vgdg~~~~~FvHv~l~il~GRs~e~k~~l~~~l~~~l~~~ 90 (124)
T PF02962_consen 17 IPALLRALHDALLASGLFPEGGIKVRAIRCDHYRVGDGQPDDAFVHVTLRILAGRSEEQKKALSEALLAVLKAH 90 (124)
T ss_dssp HHHHHHHHHHHHHCTTSS-GGG-EEEEEEESSEEETTSSS-EEEEEEEEEEETT--HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCcChhceeeeeEecccEEEccCCCCCcEEEEEeeecCCCCHHHHHHHHHHHHHHHHHH
Confidence 4567888888887765433222222211 01112344 778999999999999999999885
No 189
>PF03319 EutN_CcmL: Ethanolamine utilisation protein EutN/carboxysome; InterPro: IPR004992 The ethanolamine utilization protein EutN is involved in the cobalamin-dependent degradation of ethanolamine []. The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB: 2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the centre. This suggests that EutN forms a pore, with an opening of 26 Amstrong in diameter on one face and 14 Amstrong on the other face []. This entry represents a family of related bacterial proteins with roles in ethanolamine and carbon dioxide metabolism.; PDB: 2QW7_F 2RCF_E 2HD3_F 2Z9H_D.
Probab=26.96 E-value=72 Score=20.71 Aligned_cols=29 Identities=31% Similarity=0.381 Sum_probs=19.7
Q ss_pred CCCeEEEecCCCCCccCEEEEEEcCCHHHH
Q psy8849 19 AQDIKVYDTSNLTNLFDRITIASGSSKRQI 48 (112)
Q Consensus 19 a~dI~vldv~~~~~~~dy~VIaT~~S~rh~ 48 (112)
+.-++++|.=+ ....|+++++||++.||.
T Consensus 38 g~~~VA~D~vG-AG~Ge~Vlv~~Gs~Ar~~ 66 (83)
T PF03319_consen 38 GEPIVAVDTVG-AGVGEWVLVTSGSSARQA 66 (83)
T ss_dssp EEEEEEEESS----TT-EEEEEETHHHHHH
T ss_pred CCEEEEEeCCC-CCCCCEEEEECCHHHHHh
Confidence 45567777766 557899999999988875
No 190
>PF13614 AAA_31: AAA domain; PDB: 2VED_B 2PH1_A 3EA0_B 3FKQ_A 3KB1_B 1ION_A 3LA6_H 3BFV_B 3CIO_D.
Probab=26.71 E-value=1.9e+02 Score=19.31 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCC---------CccCEEEEEEcCCHHHH
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLT---------NLFDRITIASGSSKRQI 48 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~---------~~~dy~VIaT~~S~rh~ 48 (112)
+.++.+.+.|.+ .-|++++|+.... ..+|..|+++-.+..-.
T Consensus 105 ~~~~~li~~l~~--~yd~IivD~~~~~~~~~~~~~l~~~D~ii~v~~~~~~s~ 155 (157)
T PF13614_consen 105 EDVEELIDALKE--HYDYIIVDLPSSLSNPDTQAVLELADKIILVVRPDVTSI 155 (157)
T ss_dssp HHHHHHHHHHHH--HSSEEEEEEESTTTHTHHHHHHTTHSEEEEEEETTHHHH
T ss_pred HHHHHHHHHHHH--cCCEEEEECcCCccHHHHHHHHHHCCEEEEEECCCcccc
Confidence 345566666666 6799999999752 46688888887665433
No 191
>PRK08006 replicative DNA helicase; Provisional
Probab=26.50 E-value=2.6e+02 Score=23.57 Aligned_cols=85 Identities=16% Similarity=0.231 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcc-------cccccCCCC
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIV-------NIEGKKSSE 76 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~-------~~EG~~~~~ 76 (112)
.++...+-+...+.++-+++++|==+.-.-.+. +.+....+..++..++...|+.+++.+ ..|+..+..
T Consensus 321 ~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~----~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~r~dkr 396 (471)
T PRK08006 321 TEVRSRARRIFREHGGLSLIMIDYLQLMRVPSL----SDNRTLEIAEISRSLKALAKELQVPVVALSQLNRSLEQRADKR 396 (471)
T ss_pred HHHHHHHHHHHHhcCCCCEEEEccHHHccCCCC----CCCcHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccCCCC
Confidence 344444444444444678888886554221111 222334578889999888888888632 233333322
Q ss_pred EEEEEc---------CCEEEEeeCh
Q psy8849 77 WLLLDL---------GDIIIHIMNP 92 (112)
Q Consensus 77 WvllD~---------g~vvVHif~~ 92 (112)
=.+-|+ -|+|+-+..+
T Consensus 397 P~lsDLreSG~IEqdAD~v~~l~R~ 421 (471)
T PRK08006 397 PVNSDLRESGSIEQDADLIMFIYRD 421 (471)
T ss_pred CchhhhhhcCcccccCCEEEEEecc
Confidence 344454 2788877654
No 192
>PLN02887 hydrolase family protein
Probab=26.40 E-value=70 Score=27.81 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=17.0
Q ss_pred cCEEEEEEcCCHHHHHHHHHHH
Q psy8849 34 FDRITIASGSSKRQINALAVSI 55 (112)
Q Consensus 34 ~dy~VIaT~~S~rh~~aia~~v 55 (112)
.-.|+|||||+...++.+.+.+
T Consensus 341 Gi~~vIATGR~~~~i~~~l~~L 362 (580)
T PLN02887 341 GVKVVIATGKARPAVIDILKMV 362 (580)
T ss_pred CCeEEEEcCCCHHHHHHHHHHh
Confidence 3579999999998877666544
No 193
>PRK10645 divalent-cation tolerance protein CutA; Provisional
Probab=26.31 E-value=1.6e+02 Score=20.13 Aligned_cols=23 Identities=13% Similarity=0.302 Sum_probs=19.4
Q ss_pred CE-EEEEEcCCHHHHHHHHHHHHH
Q psy8849 35 DR-ITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 35 dy-~VIaT~~S~rh~~aia~~v~~ 57 (112)
++ +|.+|..|....+.+|..+.+
T Consensus 10 ~~~lV~tT~p~~e~A~~ia~~Lve 33 (112)
T PRK10645 10 DAVVVLCTAPDEATAQDLAAKVLA 33 (112)
T ss_pred CEEEEEEeCCCHHHHHHHHHHHHH
Confidence 44 799999999999999998764
No 194
>TIGR01007 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.
Probab=26.23 E-value=2.4e+02 Score=20.00 Aligned_cols=46 Identities=11% Similarity=0.192 Sum_probs=29.3
Q ss_pred CCCCeEEEecCCCC---------CccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 18 KAQDIKVYDTSNLT---------NLFDRITIASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 18 ka~dI~vldv~~~~---------~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
+.-|++++|.+... ..+|.+|+.+-.+....+.+... .+.+++.+.
T Consensus 126 ~~yD~ViiD~pp~~~~~~~~~~~~~~D~vilV~~~~~~~~~~~~~~-~~~l~~~~~ 180 (204)
T TIGR01007 126 KYFDYIIIDTPPIGTVTDAAIIARACDASILVTDAGEIKKRDVQKA-KEQLEQTGS 180 (204)
T ss_pred hcCCEEEEeCCCccccchHHHHHHhCCeEEEEEECCCCCHHHHHHH-HHHHHhCCC
Confidence 34699999998642 34798888886665555555443 344555544
No 195
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=26.13 E-value=1.8e+02 Score=22.45 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=26.6
Q ss_pred EcCCHHHHHHHHHHHHHHHHhcCCC-cccccccC
Q psy8849 41 SGSSKRQINALAVSIRKNIKNINNN-IVNIEGKK 73 (112)
Q Consensus 41 T~~S~rh~~aia~~v~~~lk~~~~~-~~~~EG~~ 73 (112)
.|.+-.++...|..+++.|.+.|+. .++..|.+
T Consensus 104 ~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~k 137 (223)
T cd04866 104 SRDHFSLAVEAANLLKEILDALGLTSFVKTSGNK 137 (223)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCccceEccCCC
Confidence 4667789999999999999999986 45566644
No 196
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=26.00 E-value=2.4e+02 Score=21.67 Aligned_cols=97 Identities=13% Similarity=0.172 Sum_probs=58.0
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCC----ccCEEEEEEcCCHH----------H---HHHHHHHHHHHHHhcCCCccc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTN----LFDRITIASGSSKR----------Q---INALAVSIRKNIKNINNNIVN 68 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~----~~dy~VIaT~~S~r----------h---~~aia~~v~~~lk~~~~~~~~ 68 (112)
-++++.+.+.+.|.+=|+|+.-..... ..+.|.|.++..-. . =..+|+.|.+.+++.|++...
T Consensus 30 al~~~~~~l~~~~Pd~ivvis~dH~~~~~~~~~p~~~i~~~~~~~~~~~~g~p~~~~~gd~~LA~~i~~~l~~~g~~~~~ 109 (268)
T cd07367 30 GMAEIGRRVRESRPDVLVVISSDHLFNINLSLQPPFVVGTADSYTPFGDMDIPRELFPGHREFARAFVRQAAEDGFDLAQ 109 (268)
T ss_pred HHHHHHHHHHHcCCCEEEEEeCchhhhcccccCCceEEeeccccccCCcCCCCcccCCCCHHHHHHHHHHHHHcCCCeee
Confidence 345667777777887788887632222 34667776655311 0 246889999999988886422
Q ss_pred cc--ccCCCCEEEEEc----CCE-EEEeeC-------hhhhhhcchhh
Q psy8849 69 IE--GKKSSEWLLLDL----GDI-IIHIMN-------PYIRNMYNLEE 102 (112)
Q Consensus 69 ~E--G~~~~~WvllD~----g~v-vVHif~-------~e~R~~Y~LE~ 102 (112)
.. +.+-+.|+-+-+ .++ ||+|.. +..|+.|+|=+
T Consensus 110 ~~~~~lDHG~~vPL~~l~p~~~iPvV~isin~~~~p~~~~~~~~~lG~ 157 (268)
T cd07367 110 AEELRPDHGVMVPLLFMGPKLDIPVVPLIVNINTDPAPSPRRCWALGK 157 (268)
T ss_pred ecCccCCcchhchHHHhCCCCCCCEEEEEecccCCCCCCHHHHHHHHH
Confidence 21 345566665554 233 666654 24667777644
No 197
>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=25.84 E-value=2.7e+02 Score=20.48 Aligned_cols=53 Identities=8% Similarity=0.182 Sum_probs=29.2
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEE---EEEcCCEEEEeeCh
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWL---LLDLGDIIIHIMNP 92 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~Wv---llD~g~vvVHif~~ 92 (112)
+++|+||+... +...+....++.|+......-...++.+ +++.|+++|=|-|.
T Consensus 71 ~lVi~at~d~~-----ln~~i~~~a~~~~ilvn~~d~~e~~~f~~pa~~~~g~l~iaisT~ 126 (205)
T TIGR01470 71 FLVIAATDDEE-----LNRRVAHAARARGVPVNVVDDPELCSFIFPSIVDRSPVVVAISSG 126 (205)
T ss_pred EEEEECCCCHH-----HHHHHHHHHHHcCCEEEECCCcccCeEEEeeEEEcCCEEEEEECC
Confidence 45555555532 2334555556667653222222334554 37789999988753
No 198
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=25.79 E-value=2.9e+02 Score=22.26 Aligned_cols=56 Identities=9% Similarity=-0.005 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCC
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKS 74 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~ 74 (112)
....+.+.+.+++.++.-|+.+-...-..+ -. -.-.+++.+++.|+|.+.+||..+
T Consensus 299 ~~R~~~i~~lv~~~~~DGVI~~~~kfC~~~----~~-----------e~~~lk~~l~e~GIP~L~iE~D~~ 354 (377)
T TIGR03190 299 HTRYDHVLGLAKEYNVQGAIFLQQKFCDPH----EG-----------DYPDLKRHLEANGIPTLFLEFDIT 354 (377)
T ss_pred HHHHHHHHHHHHHhCCCEEEEecccCCCcc----hh-----------hhHHHHHHHHHCCCCEEEEecCCC
Confidence 557788888889999888877776652221 11 123477788889999999998544
No 199
>KOG2964|consensus
Probab=25.73 E-value=18 Score=29.51 Aligned_cols=71 Identities=25% Similarity=0.354 Sum_probs=42.6
Q ss_pred CCCCeEEEecCCCCCccCEEEE----EEcCCHHHHHHHH-HHHHHHHHhcCCCcccccccCCCCE-EEEEcCCEEEEee
Q psy8849 18 KAQDIKVYDTSNLTNLFDRITI----ASGSSKRQINALA-VSIRKNIKNINNNIVNIEGKKSSEW-LLLDLGDIIIHIM 90 (112)
Q Consensus 18 ka~dI~vldv~~~~~~~dy~VI----aT~~S~rh~~aia-~~v~~~lk~~~~~~~~~EG~~~~~W-vllD~g~vvVHif 90 (112)
|...+.|+-.... -+|...| -||+|.|...+.+ ..|++.......-.+..||.+-.+| .++|||||=|.-.
T Consensus 58 rLp~~~v~~~~~e--~~d~AfiGvPldtgtS~rpGarFgP~~IRE~s~~~~t~n~s~e~~pfksw~~l~D~GDIpV~~y 134 (361)
T KOG2964|consen 58 RLPGVLVLLSGSE--DFDIAFIGVPLDTGTSYRPGARFGPSRIREASRRLNTVNPSLEGNPFKSWAKLVDCGDIPVTSY 134 (361)
T ss_pred cCCceEEEecCCC--ccceEEeccccCCCccCCCccccCCchhhhhhhhhcccCCCcCCccccChhhhcccCCcchhhh
Confidence 4445555544322 2344444 4889988876653 3454444332222357888888898 5789999988643
No 200
>PRK09966 putative inner membrane diguanylate cyclase; Provisional
Probab=25.63 E-value=3.3e+02 Score=21.36 Aligned_cols=54 Identities=9% Similarity=0.134 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCC-HHHHHHHHHHHHHHHHh
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSS-KRQINALAVSIRKNIKN 61 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S-~rh~~aia~~v~~~lk~ 61 (112)
+++++.+++.|.+.-..+-.+.-+.+ .+|.|++.+.+ ...+..+++.+.+.+.+
T Consensus 302 d~~l~~~a~~L~~~~~~~~~~~R~~~----deF~ill~~~~~~~~~~~~~~~i~~~~~~ 356 (407)
T PRK09966 302 DRVLIEIAKRLAEFGGLRHKAYRLGG----DEFAMVLYDVQSESEVQQICSALTQIFNL 356 (407)
T ss_pred HHHHHHHHHHHHHhCCCCCEEEEEcc----ceEEEEEcCCCCHHHHHHHHHHHHHHHhC
Confidence 56788888888776555444444432 46777776654 45788888888777654
No 201
>TIGR03328 salvage_mtnB methylthioribulose-1-phosphate dehydratase. Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine.
Probab=25.53 E-value=2.7e+02 Score=20.20 Aligned_cols=51 Identities=10% Similarity=-0.101 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
+.++.+.+++++++.+..+.+++ ..+=|++.|.|-.+....++.++...+-
T Consensus 136 s~ela~~~~~~l~~~~~~~avll--------~nHGv~~~G~~~~~A~~~~e~lE~~a~~ 186 (193)
T TIGR03328 136 IARLADSVAPYLEAYPDVPGVLI--------RGHGLYAWGRDWEEAKRHLEALEFLFEC 186 (193)
T ss_pred hHHHHHHHHHHHhcCCCCCEEEE--------cCCcceEEcCCHHHHHHHHHHHHHHHHH
Confidence 56788888888876444444443 4555788899999999999988876653
No 202
>PRK07119 2-ketoisovalerate ferredoxin reductase; Validated
Probab=25.52 E-value=92 Score=25.10 Aligned_cols=25 Identities=20% Similarity=0.177 Sum_probs=21.4
Q ss_pred ccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 33 LFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 33 ~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
=+|+.|||+|.....++..++.+++
T Consensus 246 dad~~iva~Gs~~~~a~eA~~~L~~ 270 (352)
T PRK07119 246 DAELVLVAYGTSARIAKSAVDMARE 270 (352)
T ss_pred CCCEEEEEcCccHHHHHHHHHHHHH
Confidence 3799999999999999988887754
No 203
>PF07994 NAD_binding_5: Myo-inositol-1-phosphate synthase; InterPro: IPR002587 1L-myo-Inositol-1-phosphate synthase (5.5.1.4 from EC) catalyzes the conversion of D-glucose 6-phosphate to 1L-myo-inositol-1-phosphate, the first committed step in the production of all inositol-containing compounds, including phospholipids, either directly or by salvage. The enzyme exists in a cytoplasmic form in a wide range of plants, animals, and fungi. It has also been detected in several bacteria and a chloroplast form is observed in alga and higher plants. Inositol phosphates play an important role in signal transduction. In Saccharomyces cerevisiae (Baker's yeast), the transcriptional regulation of the INO1 gene has been studied in detail [] and its expression is sensitive to the availability of phospholipid precursors as well as growth phase. The regulation of the structural gene encoding 1L-myo-inositol-1-phosphate synthase has also been analyzed at the transcriptional level in the aquatic angiosperm, Spirodela polyrrhiza (Giant duckweed) and the halophyte, Mesembryanthemum crystallinum (Common ice plant) [].; GO: 0004512 inositol-3-phosphate synthase activity, 0006021 inositol biosynthetic process, 0008654 phospholipid biosynthetic process; PDB: 1GR0_A 1P1K_B 1LA2_B 1RM0_B 1P1I_B 1JKF_A 1P1F_A 1P1J_B 1JKI_B 1P1H_A ....
Probab=25.50 E-value=1.4e+02 Score=23.78 Aligned_cols=33 Identities=6% Similarity=0.019 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCE
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDR 36 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy 36 (112)
+++.+.|.+++++.+.+.++|+++...-++.+.
T Consensus 132 e~~~~DI~~f~~~~~~d~vVvvn~asTE~~~~~ 164 (295)
T PF07994_consen 132 EQIREDIRDFKKENGLDRVVVVNVASTERYIPV 164 (295)
T ss_dssp HHHHHHHHHHHHHTT-SCEEEEE-SSCC-S---
T ss_pred HHHHHHHHHHHHHhCCCcEEEEECCCCCCCCCC
Confidence 467789999999999999999999987665543
No 204
>PLN02422 dephospho-CoA kinase
Probab=25.01 E-value=3.1e+02 Score=20.87 Aligned_cols=67 Identities=13% Similarity=0.135 Sum_probs=40.0
Q ss_pred CCCCeEEEecCCC-----CCccCEEEEEEcCCHHHHHHHHHH----HHHHHHhcCCCcccccccCCCCEEEEEcCC
Q psy8849 18 KAQDIKVYDTSNL-----TNLFDRITIASGSSKRQINALAVS----IRKNIKNINNNIVNIEGKKSSEWLLLDLGD 84 (112)
Q Consensus 18 ka~dI~vldv~~~-----~~~~dy~VIaT~~S~rh~~aia~~----v~~~lk~~~~~~~~~EG~~~~~WvllD~g~ 84 (112)
+...++++|++-. ..++|++|..++....+++.+... -.+..+....+.+.-+....+++++...|+
T Consensus 105 ~~~~~vv~eipLL~E~~~~~~~D~vI~V~a~~e~ri~RL~~R~g~s~eea~~Ri~~Q~~~eek~~~AD~VI~N~gs 180 (232)
T PLN02422 105 KGCKVIVLDIPLLFETKMDKWTKPVVVVWVDPETQLERLMARDGLSEEQARNRINAQMPLDWKRSKADIVIDNSGS 180 (232)
T ss_pred cCCCEEEEEehhhhhcchhhhCCEEEEEECCHHHHHHHHHHcCCCCHHHHHHHHHHcCChhHHHhhCCEEEECCCC
Confidence 3457999999843 457899999999988888876542 111111111121222333446777766665
No 205
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=25.01 E-value=1.2e+02 Score=19.33 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=17.5
Q ss_pred EE-cCCHHHHHHHHHHHHHHHHh-cCCCc
Q psy8849 40 AS-GSSKRQINALAVSIRKNIKN-INNNI 66 (112)
Q Consensus 40 aT-~~S~rh~~aia~~v~~~lk~-~~~~~ 66 (112)
+. |+|..+=+++-..|.+.|.+ .|++|
T Consensus 36 ~~~gRs~e~K~~ly~~l~~~L~~~~gi~p 64 (82)
T PF14552_consen 36 SGAGRSTEQKKALYRALAERLAEKLGIRP 64 (82)
T ss_dssp ECS---HHHHHHHHHHHHHHHHHHH---G
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHHcCCCH
Confidence 44 89999999999999999976 68765
No 206
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=25.00 E-value=1.8e+02 Score=17.95 Aligned_cols=68 Identities=13% Similarity=0.193 Sum_probs=42.0
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccc-c-----------ccCCCCEEEEEc------CCEEEEeeChhhhhh
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIKNINNNIVNI-E-----------GKKSSEWLLLDL------GDIIIHIMNPYIRNM 97 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~-E-----------G~~~~~WvllD~------g~vvVHif~~e~R~~ 97 (112)
.+||+-+.+..-....|..+...|...|+...-- . -..+..|+++=. |.+.|.-+....+..
T Consensus 2 v~Ii~~~~~~~~~~~~a~~l~~~L~~~gi~v~~d~~~~~~~k~~~~a~~~g~p~~iiiG~~e~~~~~v~vk~~~~~~~~~ 81 (94)
T PF03129_consen 2 VVIIPVGKKDEEIIEYAQELANKLRKAGIRVELDDSDKSLGKQIKYADKLGIPFIIIIGEKELENGTVTVKDRDTGEQET 81 (94)
T ss_dssp EEEEESSCSHHHHHHHHHHHHHHHHHTTSEEEEESSSSTHHHHHHHHHHTTESEEEEEEHHHHHTTEEEEEETTTTEEEE
T ss_pred EEEEEeCCCcHHHHHHHHHHHHHHHHCCCEEEEECCCCchhHHHHHHhhcCCeEEEEECchhHhCCEEEEEECCCCcEEE
Confidence 4677777766677888999999999988631100 0 013345665532 666666666666555
Q ss_pred cchhhh
Q psy8849 98 YNLEEI 103 (112)
Q Consensus 98 Y~LE~L 103 (112)
..+|+|
T Consensus 82 v~~~el 87 (94)
T PF03129_consen 82 VSLEEL 87 (94)
T ss_dssp EECCHH
T ss_pred EEHHHH
Confidence 555554
No 207
>COG0492 TrxB Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]
Probab=24.95 E-value=42 Score=26.57 Aligned_cols=30 Identities=20% Similarity=0.140 Sum_probs=21.5
Q ss_pred eEEEecCCCCCccCEEEEEEcCCHHHHHHH
Q psy8849 22 IKVYDTSNLTNLFDRITIASGSSKRQINAL 51 (112)
Q Consensus 22 I~vldv~~~~~~~dy~VIaT~~S~rh~~ai 51 (112)
...+........++++|||||.+.++.+-.
T Consensus 92 ~F~v~t~~~~~~ak~vIiAtG~~~~~~~~~ 121 (305)
T COG0492 92 PFKVKTDKGTYEAKAVIIATGAGARKLGVP 121 (305)
T ss_pred eEEEEECCCeEEEeEEEECcCCcccCCCCC
Confidence 334444444567899999999999998744
No 208
>cd03130 GATase1_CobB Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. CobB plays a role in cobalamin biosythesis catalyzing the conversion of cobyrinic acid to cobyrinic acid a,c-diamide. CobB belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobB.
Probab=24.82 E-value=2.8e+02 Score=20.16 Aligned_cols=50 Identities=16% Similarity=0.338 Sum_probs=31.3
Q ss_pred HHHHHHHhcCCCCeEEEecC---CCCCccCEEEEEEcCCHHHHHHHHH--HHHHHHH
Q psy8849 9 IVIKILKDIKAQDIKVYDTS---NLTNLFDRITIASGSSKRQINALAV--SIRKNIK 60 (112)
Q Consensus 9 ~i~~~l~~kka~dI~vldv~---~~~~~~dy~VIaT~~S~rh~~aia~--~v~~~lk 60 (112)
+-.++|++ -+-++..++.. .... +|-+||--|.+..++..+.+ .+.+.++
T Consensus 15 e~~~~l~~-~G~~v~~~s~~~~~~l~~-~D~lilPGG~~~~~~~~L~~~~~~~~~i~ 69 (198)
T cd03130 15 ENLELLEA-AGAELVPFSPLKDEELPD-ADGLYLGGGYPELFAEELSANQSMRESIR 69 (198)
T ss_pred HHHHHHHH-CCCEEEEECCCCCCCCCC-CCEEEECCCchHHHHHHHHhhHHHHHHHH
Confidence 33566664 34577777663 3444 79999999988866666644 2444444
No 209
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=24.82 E-value=1.5e+02 Score=17.02 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=20.1
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHh-cCCC
Q psy8849 39 IASGSSKRQINALAVSIRKNIKN-INNN 65 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~-~~~~ 65 (112)
+..|+|..|-+++++.+-+.+.+ .|.+
T Consensus 7 ~~~g~~~e~K~~l~~~it~~~~~~lg~~ 34 (60)
T PF01361_consen 7 IPEGRTAEQKRELAEAITDAVVEVLGIP 34 (60)
T ss_dssp EESTS-HHHHHHHHHHHHHHHHHHHTS-
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 34678999999999999998876 5654
No 210
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=24.78 E-value=1.9e+02 Score=22.33 Aligned_cols=33 Identities=12% Similarity=0.186 Sum_probs=26.2
Q ss_pred EcCCHHHHHHHHHHHHHHHHhcCCC-cccccccC
Q psy8849 41 SGSSKRQINALAVSIRKNIKNINNN-IVNIEGKK 73 (112)
Q Consensus 41 T~~S~rh~~aia~~v~~~lk~~~~~-~~~~EG~~ 73 (112)
.|.+-..+..+|..+++.|.+.|+. .++..|.+
T Consensus 113 ~~~~f~~v~~~A~~~r~~L~~lgL~s~~KTSG~k 146 (231)
T cd04863 113 EPAGLVECARVALWLRDRLAALGLASFPKTSGSK 146 (231)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCccceECCCCC
Confidence 4667789999999999999999986 45566644
No 211
>cd06414 GH25_LytC-like The LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains. LytC is composed of a C-terminal glycosyl hydrolase family 25 (GH25) domain and an N-terminal choline-binding module (CBM) consisting of eleven homologous repeats that specifically recognizes the choline residues of pneumococcal lipoteichoic and teichoic acids. This domain arrangement is the reverse of the major pneumococcal autolysin, LytA, and the CPL-1-like lytic enzymes of the pneumococcal bacteriophages, in which the CBM (consisting of six repeats) is at the C-terminus. This model represents the C-terminal catalytic domain of the LytC-like enzymes.
Probab=24.61 E-value=2.7e+02 Score=19.97 Aligned_cols=54 Identities=24% Similarity=0.230 Sum_probs=33.9
Q ss_pred HHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 7 QIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 7 ~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
++-.++.+...+..-+.++|+....... .+.|..++.+.+....+.+++.|.+|
T Consensus 76 A~~f~~~~~~~~~~~~~~lD~E~~~~~~------~~~~~~~~~~~~~~f~~~v~~~G~~~ 129 (191)
T cd06414 76 AEFVLRLIKGYKLSYPVYYDLEDETQLG------AGLSKDQRTDIANAFCETIEAAGYYP 129 (191)
T ss_pred HHHHHHHhhccCCCCCeEEEeecCCCCC------CCCCHHHHHHHHHHHHHHHHHcCCCe
Confidence 4444555555554446789998643211 14567778888788888888777643
No 212
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=24.54 E-value=29 Score=22.51 Aligned_cols=17 Identities=12% Similarity=0.278 Sum_probs=14.1
Q ss_pred EeeChhhhhhcchhhhc
Q psy8849 88 HIMNPYIRNMYNLEEIW 104 (112)
Q Consensus 88 Hif~~e~R~~Y~LE~LW 104 (112)
|-|++|+|+.||-.+|-
T Consensus 27 ntms~eEk~~~D~~~l~ 43 (97)
T PF12650_consen 27 NTMSKEEKEKYDKKKLC 43 (97)
T ss_pred ccCCHHHHHHhhHHHHH
Confidence 35899999999988773
No 213
>PF15601 Imm42: Immunity protein 42
Probab=24.47 E-value=83 Score=22.34 Aligned_cols=53 Identities=21% Similarity=0.233 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHhcCCCCeE--EEecCC-----------CCCccCEEEEEEcCCHHHHHHHHHHHHHH
Q psy8849 4 NKRQIIVIKILKDIKAQDIK--VYDTSN-----------LTNLFDRITIASGSSKRQINALAVSIRKN 58 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~--vldv~~-----------~~~~~dy~VIaT~~S~rh~~aia~~v~~~ 58 (112)
.+.+++|.+.|......+|+ .-|++. .++++||||-++|+ +-...+++++...
T Consensus 59 ~~eL~~I~~~l~~~~p~~ViWD~~dl~~~ppWg~~i~~~i~~L~~yFvt~dG~--~~f~~l~~a~~~a 124 (134)
T PF15601_consen 59 LKELEEIRKELKKFPPSEVIWDIEDLSKQPPWGDNISPDITSLSDYFVTSDGK--DLFEVLFRALESA 124 (134)
T ss_pred HHHHHHHHHHHhcCChhhheechhhcccCCCCcccCCCCCCcHHHHhcCcchh--hHHHHHHHHHHHH
Confidence 45678888899999988875 223322 25778999988885 2334444444433
No 214
>KOG0189|consensus
Probab=24.19 E-value=60 Score=25.28 Aligned_cols=70 Identities=17% Similarity=0.165 Sum_probs=50.5
Q ss_pred hcCCCCeEEEecCCCCC-ccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEEeeChhh
Q psy8849 16 DIKAQDIKVYDTSNLTN-LFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIHIMNPYI 94 (112)
Q Consensus 16 ~kka~dI~vldv~~~~~-~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHif~~e~ 94 (112)
--+++|++.||+..+++ -...|-|-|++-..+...+.++|++. ||+|-||+|-|+.
T Consensus 53 ~~G~~~lvlid~~~~~~~~~~l~~idT~~~~PeT~~l~d~Vekk-----------------------Y~~i~I~~~~pd~ 109 (261)
T KOG0189|consen 53 ASGLEGLVLIDMLSKTGRPFRLFFIDTLHHFPETLRLFDAVEKK-----------------------YGNIRIHVYFPDA 109 (261)
T ss_pred hccccchHHHHHHHHcCCCceeEEeeccccChHHHHHHHHHHHh-----------------------cCceEEEEEcchh
Confidence 35778888888776543 45788899999999999888888753 3457788887764
Q ss_pred -------hhhcchhhhcccccc
Q psy8849 95 -------RNMYNLEEIWGEKEI 109 (112)
Q Consensus 95 -------R~~Y~LE~LW~~~~~ 109 (112)
|..| +++||.+...
T Consensus 110 ~e~ea~~~~K~-~~~~~E~~~q 130 (261)
T KOG0189|consen 110 VEVEALFASKG-GFSLWEDDHQ 130 (261)
T ss_pred HHHHHHHHhcc-chhheecCch
Confidence 3333 6778877643
No 215
>PRK13498 chemoreceptor glutamine deamidase CheD; Provisional
Probab=24.18 E-value=1.7e+02 Score=21.31 Aligned_cols=43 Identities=9% Similarity=0.116 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhcCCCccccc-ccCCCCEEEEEc--CCEEEEeeCh
Q psy8849 50 ALAVSIRKNIKNINNNIVNIE-GKKSSEWLLLDL--GDIIIHIMNP 92 (112)
Q Consensus 50 aia~~v~~~lk~~~~~~~~~E-G~~~~~WvllD~--g~vvVHif~~ 92 (112)
.=++.+++.|++.|++...-+ |.+.+.-+.+|. |++.|.-...
T Consensus 115 rNi~~a~~~L~~~gi~i~a~DvGG~~gR~i~f~~~tG~v~vk~~~~ 160 (167)
T PRK13498 115 KNIHAALALAEQNGLHLKAQDLGSTGHRSIIFDLWNGNVWVRHQPM 160 (167)
T ss_pred HHHHHHHHHHHHCCCcEEEEeCCCCCCcEEEEECCCCEEEEEECCC
Confidence 335667788899999865433 667789999987 6777765443
No 216
>COG2848 Uncharacterized conserved protein [Function unknown]
Probab=24.07 E-value=48 Score=27.93 Aligned_cols=96 Identities=14% Similarity=0.098 Sum_probs=67.6
Q ss_pred HHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc------ccccccCCCCEEEEEc
Q psy8849 9 IVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNI------VNIEGKKSSEWLLLDL 82 (112)
Q Consensus 9 ~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~------~~~EG~~~~~WvllD~ 82 (112)
..++-+..+.+..|+-..+ +.+..-+++.+....-.-.+|+.+.+..|+.|+.. +...|...++|.+++.
T Consensus 57 e~~~~i~~e~GvpIvnkRi----sVtPisiv~~~~~~~~~v~~a~~Ld~aake~GV~~igG~salv~~g~~~~D~~li~s 132 (445)
T COG2848 57 ETAEELTAELGVPIVNKRI----SVTPISIVAASTADDDLVSLAETLDKAAKEIGVDFIGGFSALVHKGYTKGDEALIRS 132 (445)
T ss_pred HHHHHHHHhhCCceeeeEE----eecchhhhccccccccHHHHHHHHHHHHHhhcchhhhhhHHHHhcccccchHHHHHH
Confidence 3445566666666643332 34445566666666667778999999999977653 3456888899999985
Q ss_pred --------CCEEEEeeChhhhhhcchhhhccccc
Q psy8849 83 --------GDIIIHIMNPYIRNMYNLEEIWGEKE 108 (112)
Q Consensus 83 --------g~vvVHif~~e~R~~Y~LE~LW~~~~ 108 (112)
-.+..|+--.+.|.+-||...-..++
T Consensus 133 Ipeal~~t~rvc~svnV~st~~ginm~av~~~~~ 166 (445)
T COG2848 133 IPEALKSTSRVCSSVNVASTRTGINMDAVLIMGE 166 (445)
T ss_pred HHHHHhhhhhhheeeeehhhhccccHHHHHhccc
Confidence 46778888899999999987765543
No 217
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=23.83 E-value=1e+02 Score=20.38 Aligned_cols=62 Identities=18% Similarity=0.069 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHhcCC---CCeEEEecCCCCCc------cCEEE-----EEEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 3 INKRQIIVIKILKDIKA---QDIKVYDTSNLTNL------FDRIT-----IASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka---~dI~vldv~~~~~~------~dy~V-----IaT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
.+.+++.+-++|.+... .|+.+-=....... .+-|| +..|+|..|-+++++.|.+.+++...
T Consensus 17 ~~~l~~~v~~al~~~~~~p~~dik~r~~~~~~y~~~~~~~~~~fi~i~i~l~~GRs~eqK~~l~~~i~~~l~~~~~ 92 (113)
T cd00580 17 IPELLRALHDALVASGLFPLGGIKVRAIRADHYRVGDGDEDDAFIHVTLRILAGRSEEQKQELSEALLAALRAHLA 92 (113)
T ss_pred HHHHHHHHHHHHHhcCCCChhccEEeeEEcceEEECCCCCCCcEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 35677777777766553 34432111111100 23333 35689999999999999999987543
No 218
>cd07364 PCA_45_Dioxygenase_B Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate. Protocatechuate 4,5-dioxygenase (LigAB) catalyzes the oxidization and subsequent ring-opening of protocatechuate (or 3,4-dihydroxybenzoic acid, PCA), an intermediate in the breakdown of lignin and other compounds. Protocatechuate 4,5-dioxygenase is an aromatic ring opening dioxygenase belonging to the class III extradiol enzyme family, a group of enyzmes that cleaves aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon using a non-heme Fe(II). LigAB is composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. The B subunit (LigB) is the catalytic subunit of LigAB.
Probab=23.76 E-value=1.9e+02 Score=22.51 Aligned_cols=97 Identities=11% Similarity=0.081 Sum_probs=63.6
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCccC----EEEEEEcCCHH---------------HHHHHHHHHHHHHHhcCCCc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNLFD----RITIASGSSKR---------------QINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~~d----y~VIaT~~S~r---------------h~~aia~~v~~~lk~~~~~~ 66 (112)
=.+++.+.+.+.+.+=|+++--.....+.+ .|.|.++.+-+ =-..+|+.|.+.+.+.|+..
T Consensus 36 a~~~~~~~~~~~~pD~vVvi~~dH~~~f~~~~~P~f~i~~~~~~~~~~~~~g~~~~~~~~g~~~LA~~i~~~~~~~g~~~ 115 (277)
T cd07364 36 GYQPARDWIKKNKPDVAIIVYNDHASAFDLDIIPTFAIGTAEEFQPADEGYGPRPVPDVQGHPDLAWHIAQSLILDDFDM 115 (277)
T ss_pred HHHHHHHHHHHhCCCEEEEEcCchHHhhcccCCCceEEeeccccccCccccCCCCCCCCCCCHHHHHHHHHHHHHcCCCE
Confidence 346777888888888788874444566666 89999988433 13568999999999888864
Q ss_pred ccc--cccCCCCEEEEEc--C--C---E-EEEee----C---hhhhhhcchhh
Q psy8849 67 VNI--EGKKSSEWLLLDL--G--D---I-IIHIM----N---PYIRNMYNLEE 102 (112)
Q Consensus 67 ~~~--EG~~~~~WvllD~--g--~---v-vVHif----~---~e~R~~Y~LE~ 102 (112)
... -|.+-+.|+-+-+ . + + ||.++ . +..++.|.|=+
T Consensus 116 ~~~~~~~lDHG~~vPL~~l~p~~~~~p~pVV~vsvn~~~~p~~~~~~~~~lG~ 168 (277)
T cd07364 116 TIVNEMDVDHGLTVPLSIMYGQPEAWPCKVIPLCVNVVQYPQPTGKRCFALGK 168 (277)
T ss_pred EecCCCCCCcchhhhHHHhCCccccCCCCeEEEEeccCCCCCCCHHHHHHHHH
Confidence 321 2556677776643 1 2 2 67763 2 34577777643
No 219
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.68 E-value=19 Score=22.93 Aligned_cols=52 Identities=15% Similarity=0.334 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCC--------CCccCEEEEEEcCCHHHHHHHHHHHHH
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNL--------TNLFDRITIASGSSKRQINALAVSIRK 57 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~--------~~~~dy~VIaT~~S~rh~~aia~~v~~ 57 (112)
+.-.|.++=...+.-++-|+|-.+. +.+.|.+-=-+-.|++-++|+|+++.+
T Consensus 9 l~fmi~eI~~KLnmvN~gvl~~e~~d~~~~edLtdiy~mvkkkenfSpsEmqaiA~eL~r 68 (71)
T COG4840 9 LDFMIEEIREKLNMVNVGVLDPEKYDNANYEDLTDIYDMVKKKENFSPSEMQAIADELGR 68 (71)
T ss_pred HHHHHHHHHHHHhhhhhhccCHHhcccccHHHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence 3334444445556677777766543 234444445567799999999998864
No 220
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=23.60 E-value=1.3e+02 Score=25.00 Aligned_cols=37 Identities=24% Similarity=0.321 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHH
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQ 47 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh 47 (112)
+.+++.|++=.-.-=..+|-|+|- +-+|||||..+|-
T Consensus 5 ~~lAq~IV~r~m~ii~~nInVMd~-------~GvIIgSgd~~Ri 41 (376)
T COG3835 5 KTLAQKIVARTMKIIDYNINVMDA-------DGVIIGSGDPERI 41 (376)
T ss_pred hHHHHHHHHHHHhhccccceEECC-------CCeEEecCChHHh
Confidence 356666666555555678888874 5589999998874
No 221
>PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=23.54 E-value=2.1e+02 Score=22.48 Aligned_cols=97 Identities=18% Similarity=0.178 Sum_probs=60.6
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCC-ccC---EEEEEEcCCHH---------H------HHHHHHHHHHHHHhcCCCc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTN-LFD---RITIASGSSKR---------Q------INALAVSIRKNIKNINNNI 66 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~-~~d---y~VIaT~~S~r---------h------~~aia~~v~~~lk~~~~~~ 66 (112)
-.+++.+.+.+.+.+=|+++--..... +.| .|.|.++.+.+ + -..+|+.|.+.+++.|++.
T Consensus 36 a~~~~~~~v~~~~PDvvVvis~dH~~~ff~d~~p~f~i~~~~~~~g~~~~~g~~~~~~~~~~~~lA~~i~~~l~~~gid~ 115 (278)
T PRK13364 36 GFPPVREWLEKVKPDVAVVFYNDHGLNFFLDKMPTFAVGAAPEYSNADEGWGIPTLAPFKGDTELSWHIIESLVEEEFDI 115 (278)
T ss_pred HHHHHHHHHHHhCCCEEEEECCchHhhhccccCCeEEEeeCceecCChhhcCCCCCCCCCCCHHHHHHHHHHHHHcCCCe
Confidence 346677778888777777775344444 567 89998876543 1 2468899999999988863
Q ss_pred cc--ccccCCCCEEEEEc----CCE---EEEeeC-------hhhhhhcchhh
Q psy8849 67 VN--IEGKKSSEWLLLDL----GDI---IIHIMN-------PYIRNMYNLEE 102 (112)
Q Consensus 67 ~~--~EG~~~~~WvllD~----g~v---vVHif~-------~e~R~~Y~LE~ 102 (112)
.. .-+.+-+-|+-+-+ +++ +|+|+. +..|+.|+|=+
T Consensus 116 ~~~~~~~lDHG~~vPL~~l~~~~d~~~pvVpv~ln~~~~p~~~~~r~~~lG~ 167 (278)
T PRK13364 116 TTCQEMLVDHAFTLPLELFWPGRDYPVKVVPVCINTVQHPLPSARRCYKLGQ 167 (278)
T ss_pred ecccCCCCCcchhhhHHHhCcccCCCCCEEEEEeeccCCCCCCHHHHHHHHH
Confidence 22 22345566665443 222 667764 34666666543
No 222
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=23.52 E-value=1.9e+02 Score=23.09 Aligned_cols=31 Identities=3% Similarity=-0.154 Sum_probs=25.7
Q ss_pred CEEEEE---EcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 35 DRITIA---SGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 35 dy~VIa---T~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..+||| +..|..|+..+|+.+.+..++.|++
T Consensus 16 ~~~~iaGPCsvEs~e~~~~iA~~lk~i~~~~g~~ 49 (281)
T PRK12457 16 PFVLFGGINVLESLDFTLDVCGEYVEVTRKLGIP 49 (281)
T ss_pred ceEEEecCCcccCHHHHHHHHHHHHHHHHHCCCc
Confidence 367776 8999999999999998877777663
No 223
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=23.30 E-value=71 Score=21.59 Aligned_cols=28 Identities=14% Similarity=0.197 Sum_probs=21.7
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCC
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINN 64 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~ 64 (112)
+|.+|.+...+.+.+++.+.+.+++.|.
T Consensus 5 ii~gS~r~~~~t~~l~~~~~~~l~~~g~ 32 (152)
T PF03358_consen 5 IINGSPRKNSNTRKLAEAVAEQLEEAGA 32 (152)
T ss_dssp EEESSSSTTSHHHHHHHHHHHHHHHTTE
T ss_pred EEECcCCCCCHHHHHHHHHHHHHHHcCC
Confidence 3445556678999999999999988654
No 224
>cd06525 GH25_Lyc-like Lyc muramidase is an autolytic lysozyme (autolysin) from Clostridium acetobutylicum encoded by the lyc gene. Lyc has a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
Probab=23.29 E-value=2.8e+02 Score=19.70 Aligned_cols=52 Identities=12% Similarity=0.103 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhc-CCCc
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNI-NNNI 66 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~-~~~~ 66 (112)
+-++..++.+...+..-+.++|+...+. .|...+.+.+....+.+++. |.++
T Consensus 68 ~qA~~f~~~~~~~~~~~~~~lD~E~~~~----------~~~~~~~~~~~~f~~~v~~~~G~~~ 120 (184)
T cd06525 68 EQAENFYNTIKGKKMDLKPALDVEVNFG----------LSKDELNDYVLRFIEEFEKLSGLKV 120 (184)
T ss_pred HHHHHHHHhccccCCCCCeEEEEecCCC----------CCHHHHHHHHHHHHHHHHHHHCCCe
Confidence 3445555666666655678999987542 35566666667777777776 6643
No 225
>PHA02518 ParA-like protein; Provisional
Probab=23.07 E-value=2.7e+02 Score=19.47 Aligned_cols=37 Identities=22% Similarity=0.094 Sum_probs=28.5
Q ss_pred CCCCeEEEecCCCC--------CccCEEEEEEcCCHHHHHHHHHH
Q psy8849 18 KAQDIKVYDTSNLT--------NLFDRITIASGSSKRQINALAVS 54 (112)
Q Consensus 18 ka~dI~vldv~~~~--------~~~dy~VIaT~~S~rh~~aia~~ 54 (112)
..-|++++|.++.. ..+|++||.+-.|..-++++.+.
T Consensus 75 ~~~d~viiD~p~~~~~~~~~~l~~aD~viip~~ps~~~~~~~~~~ 119 (211)
T PHA02518 75 SGYDYVVVDGAPQDSELARAALRIADMVLIPVQPSPFDIWAAPDL 119 (211)
T ss_pred ccCCEEEEeCCCCccHHHHHHHHHCCEEEEEeCCChhhHHHHHHH
Confidence 45799999999752 45799999999888777665553
No 226
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=22.98 E-value=1.8e+02 Score=20.08 Aligned_cols=34 Identities=15% Similarity=0.270 Sum_probs=25.4
Q ss_pred CCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 31 TNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 31 ~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..|+|=++|.+ ++...++.+.+.+.+.+++.|..
T Consensus 86 ~RY~DD~~i~~-~~~~~~~~~~~~i~~~l~~~gL~ 119 (158)
T cd01646 86 VRYVDDIRIFA-DSKEEAEEILEELKEFLAELGLS 119 (158)
T ss_pred EEecCcEEEEc-CCHHHHHHHHHHHHHHHHHCCCE
Confidence 34666666655 67777888888999999987764
No 227
>COG5476 Uncharacterized conserved protein [Function unknown]
Probab=22.95 E-value=5e+02 Score=22.42 Aligned_cols=50 Identities=20% Similarity=0.314 Sum_probs=36.1
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhc----CCCc----------ccccccCCCCEEEEEcCC
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNI----NNNI----------VNIEGKKSSEWLLLDLGD 84 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~----~~~~----------~~~EG~~~~~WvllD~g~ 84 (112)
.-++++|++-.--..++|+++-..+-+. +... +...|....-|++.|.+|
T Consensus 240 g~~lVvt~~D~~~~~a~A~~l~rel~~~r~~~~~~~l~~~~a~~~ala~r~~~g~pvviAD~~D 303 (488)
T COG5476 240 GTILVVTGNDKAAAAALAEELGRELLAARGAFGMAFLDTDEAVDRALATRGRPGKPVVLADVWD 303 (488)
T ss_pred ccEEEEeCCcHHHHHHHHHHHHHHHHhhccccCCCcCCchHHHHHHHHhcCCCCCcEEEecCCC
Confidence 3499999999999999999988776431 2211 122267888999999864
No 228
>PRK08105 flavodoxin; Provisional
Probab=22.93 E-value=2.6e+02 Score=19.42 Aligned_cols=30 Identities=10% Similarity=0.087 Sum_probs=24.0
Q ss_pred EEEEEcCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 37 ITIASGSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 37 ~VIaT~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
+.|.-|+.+-..+.+|+.|.+.+++.|...
T Consensus 4 i~I~YgS~tGnte~~A~~l~~~l~~~g~~~ 33 (149)
T PRK08105 4 VGIFVGTVYGNALLVAEEAEAILTAQGHEV 33 (149)
T ss_pred EEEEEEcCchHHHHHHHHHHHHHHhCCCce
Confidence 456677888888999999999998877653
No 229
>PRK06467 dihydrolipoamide dehydrogenase; Reviewed
Probab=22.87 E-value=40 Score=27.83 Aligned_cols=14 Identities=43% Similarity=0.498 Sum_probs=12.2
Q ss_pred ccCEEEEEEcCCHH
Q psy8849 33 LFDRITIASGSSKR 46 (112)
Q Consensus 33 ~~dy~VIaT~~S~r 46 (112)
-+|++|||||.+++
T Consensus 136 ~~d~lViATGs~p~ 149 (471)
T PRK06467 136 EFDNAIIAAGSRPI 149 (471)
T ss_pred EcCEEEEeCCCCCC
Confidence 46999999999876
No 230
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=22.74 E-value=1.4e+02 Score=18.28 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=20.3
Q ss_pred Ccc-CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 32 NLF-DRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 32 ~~~-dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
.|+ |+++.+... +.+.....+.+.+++.|.+
T Consensus 45 ~Y~DD~~i~~~~~---~~~~~~~~l~~~l~~~gl~ 76 (98)
T cd00304 45 RYVDDLVVIAKSE---QQAVKKRELEEFLARLGLN 76 (98)
T ss_pred EeeCcEEEEeCcH---HHHHHHHHHHHHHHHcCcE
Confidence 344 455444333 7777788888888887764
No 231
>KOG1579|consensus
Probab=22.71 E-value=62 Score=26.29 Aligned_cols=19 Identities=21% Similarity=0.378 Sum_probs=16.5
Q ss_pred EEEcCCHHHHHHHHHHHHH
Q psy8849 39 IASGSSKRQINALAVSIRK 57 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~ 57 (112)
=|.+.+++|+++|+++|..
T Consensus 296 GCCrt~P~~I~aI~e~v~~ 314 (317)
T KOG1579|consen 296 GCCRTTPKHIRAIAEAVKK 314 (317)
T ss_pred cccCCChHHHHHHHHHhhc
Confidence 4789999999999998864
No 232
>KOG3728|consensus
Probab=22.71 E-value=1.5e+02 Score=23.58 Aligned_cols=28 Identities=14% Similarity=0.311 Sum_probs=25.4
Q ss_pred CccCEEEEEEcCCHHHHHHHHHHHHHHH
Q psy8849 32 NLFDRITIASGSSKRQINALAVSIRKNI 59 (112)
Q Consensus 32 ~~~dy~VIaT~~S~rh~~aia~~v~~~l 59 (112)
-+.|.=+||+|.|+.-+++.|..+.+.+
T Consensus 48 ~FGDvkfVC~GGtp~Rmk~~a~~~~~el 75 (308)
T KOG3728|consen 48 RFGDVKFVCMGGTPSRMKQFALYLRDEL 75 (308)
T ss_pred HhCCeEEEEeCCCHHHHHHHHHHHHHHh
Confidence 4789999999999999999999998766
No 233
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=22.53 E-value=2.4e+02 Score=18.65 Aligned_cols=66 Identities=9% Similarity=-0.007 Sum_probs=40.7
Q ss_pred CCHHHHHHHHHHHHHhcCCCCeEEE--ecCCCC-CccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCccccc
Q psy8849 1 MNINKRQIIVIKILKDIKAQDIKVY--DTSNLT-NLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIE 70 (112)
Q Consensus 1 m~~~~l~~~i~~~l~~kka~dI~vl--dv~~~~-~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~E 70 (112)
|+|.-+++.+-+++++++. ++.+. .+++.. ...||=+|.+|. |++-.-+.+.+.+.+.|++...+.
T Consensus 11 aSSs~la~km~~~a~~~gi-~~~i~a~~~~e~~~~~~~~Dvill~P---Qv~~~~~~i~~~~~~~~ipv~~I~ 79 (99)
T cd05565 11 GTSGLLANALNKGAKERGV-PLEAAAGAYGSHYDMIPDYDLVILAP---QMASYYDELKKDTDRLGIKLVTTT 79 (99)
T ss_pred CCHHHHHHHHHHHHHHCCC-cEEEEEeeHHHHHHhccCCCEEEEcC---hHHHHHHHHHHHhhhcCCCEEEeC
Confidence 5777788888888877665 44443 333321 222333666664 566666777777777787754444
No 234
>cd07362 HPCD_like Class III extradiol dioxygenases with similarity to homoprotocatechuate 2,3-dioxygenase, which catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. This subfamily of class III extradiol dioxygenases consists of two types of proteins with known enzymatic activities; 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) and 2-amino-5-chlorophenol 1,6-dioxygenase. HPCD catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield the product alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. 2-amino-5-chlorophenol 1,6-dioxygenase catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. The enzyme is probably a heterotetrame
Probab=22.46 E-value=2.2e+02 Score=22.02 Aligned_cols=96 Identities=13% Similarity=0.092 Sum_probs=53.7
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEE-------EcCCHHH-----------HHHHHHHHHHHHHhcCCCcc
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIA-------SGSSKRQ-----------INALAVSIRKNIKNINNNIV 67 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIa-------T~~S~rh-----------~~aia~~v~~~lk~~~~~~~ 67 (112)
-++++.+.+.+.+-+=|+|+.-.-.+...+.++.+ +.....+ -..+|+.|.+.+++.|+...
T Consensus 31 a~~~l~~~l~~~~Pd~IvvvS~Hw~~~~~~~~~~~~~~~~~~~~~g~p~~~~~~~y~~~g~~~LA~~i~~~l~~~Gi~~~ 110 (272)
T cd07362 31 GMKEIRKRIEELKPDVILVISCHWMSSSFHHFVDATPRHGGLTAVECPDLISDVPYDYPGDPELGRLLVEEGQEAGLRVK 110 (272)
T ss_pred HHHHHHHHhhHcCCCEEEEECCCcccccceeeeccCccccccccCcCCchhhccccCCCCCHHHHHHHHHHHHHcCCcee
Confidence 34556666766677777777664444332222111 1111111 24688999999998888753
Q ss_pred cc----cccCCCCEEEEEc----CCE-EEEee----Chhhhhhcchh
Q psy8849 68 NI----EGKKSSEWLLLDL----GDI-IIHIM----NPYIRNMYNLE 101 (112)
Q Consensus 68 ~~----EG~~~~~WvllD~----g~v-vVHif----~~e~R~~Y~LE 101 (112)
.. -|.+-+.|+-+-+ .++ ||+|. .+..++.|+|=
T Consensus 111 ~~~~~~~~lDHG~~vPL~~l~p~~~iPVV~vs~~~~~~~~~~~~~lG 157 (272)
T cd07362 111 AVNDPTYIWDYGTVVPLRYLNPNKDIPVVSISACWTAASLEESYTWG 157 (272)
T ss_pred eccCCCCCCCcchHHHHHHhCCCCCCcEEEEeccCCCCCHHHHHHHH
Confidence 22 2566677774432 234 77775 35666666553
No 235
>cd01398 RPI_A RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the conversion of phosphosugars into glycolysis intermediates, which are precursors for the synthesis of amino acids, vitamins, nucleotides, and cell wall components. In plants, RPI is part of the Calvin cycle as ribulose 5-phosphate is the carbon dioxide receptor in the first dark reaction of photosynthesis. There are two unrelated types of RPIs (A and B), which catalyze the same reaction, at least one type of RPI is present in an organism. RPI_A is more widely distributed than RPI_B in bacteria, eukaryotes, and archaea.
Probab=22.41 E-value=1.5e+02 Score=22.17 Aligned_cols=45 Identities=20% Similarity=0.253 Sum_probs=26.1
Q ss_pred HHHhcCCCcccccccCCCCEEEEEcCCEEEEeeChhhhhhcchhh
Q psy8849 58 NIKNINNNIVNIEGKKSSEWLLLDLGDIIIHIMNPYIRNMYNLEE 102 (112)
Q Consensus 58 ~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHif~~e~R~~Y~LE~ 102 (112)
.+++.|..+.-+.+...+..++=|-|+.++=+.-++.-+-+.|++
T Consensus 144 ~l~~~g~~~~~R~~~~~~~p~~Td~gn~i~D~~~~~~~~~~~l~~ 188 (213)
T cd01398 144 ELEKLGGKPVLREGSGKGGPVVTDNGNYILDVHFGTIEDPEALEK 188 (213)
T ss_pred HHHHcCCCcEEcccCCCCCcEECCCCCEEEEecCCCCCCHHHHHH
Confidence 333334333233333345688999999999888666544444443
No 236
>PRK06912 acoL dihydrolipoamide dehydrogenase; Validated
Probab=22.40 E-value=41 Score=27.53 Aligned_cols=14 Identities=29% Similarity=0.335 Sum_probs=12.0
Q ss_pred ccCEEEEEEcCCHH
Q psy8849 33 LFDRITIASGSSKR 46 (112)
Q Consensus 33 ~~dy~VIaT~~S~r 46 (112)
-+|++|||||.+++
T Consensus 132 ~~d~lviATGs~p~ 145 (458)
T PRK06912 132 DAEQFIIAAGSEPT 145 (458)
T ss_pred ECCEEEEeCCCCCC
Confidence 46999999998875
No 237
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=22.33 E-value=92 Score=18.42 Aligned_cols=21 Identities=10% Similarity=0.401 Sum_probs=17.0
Q ss_pred CCCEEEEEcCCEEEEeeChhh
Q psy8849 74 SSEWLLLDLGDIIIHIMNPYI 94 (112)
Q Consensus 74 ~~~WvllD~g~vvVHif~~e~ 94 (112)
+.+++++|+|+|-.-|+.|..
T Consensus 13 ~~~~vvi~~~GvGy~v~v~~~ 33 (61)
T PF01330_consen 13 NPDYVVIDVNGVGYEVFVPSN 33 (61)
T ss_dssp ESSEEEEEETTEEEEEEE-HH
T ss_pred cCCEEEEEECCEEEEEEeCCc
Confidence 468999999999998887764
No 238
>PLN02489 homocysteine S-methyltransferase
Probab=22.32 E-value=41 Score=26.95 Aligned_cols=18 Identities=11% Similarity=0.300 Sum_probs=15.7
Q ss_pred EEcCCHHHHHHHHHHHHH
Q psy8849 40 ASGSSKRQINALAVSIRK 57 (112)
Q Consensus 40 aT~~S~rh~~aia~~v~~ 57 (112)
|.|.++.|+++|++.+..
T Consensus 316 CCgt~P~hI~al~~~l~~ 333 (335)
T PLN02489 316 CCRTTPNTIRAISKALSE 333 (335)
T ss_pred CCCCCHHHHHHHHHHHhc
Confidence 789999999999998754
No 239
>KOG3941|consensus
Probab=22.31 E-value=2.6e+02 Score=23.08 Aligned_cols=52 Identities=19% Similarity=0.058 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEE--EEEEcCCHHHHHHHHHH
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRI--TIASGSSKRQINALAVS 54 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~--VIaT~~S~rh~~aia~~ 54 (112)
+.+++....+-+.---+..|+++.++...+-+|-- -|+|+.|+-|-..++++
T Consensus 204 p~ElA~~aL~~M~~Dl~s~it~~~~s~~KDs~d~~q~wiv~~qSP~Qq~ll~eh 257 (406)
T KOG3941|consen 204 PSELAGIALKMMSRDLASSITLLKLSLPKDSSDPQQKWIVTSQSPMQQILLSEH 257 (406)
T ss_pred HHHHHHHHHHHhChhhhhceEEEeccCccccCCcccceeeccCCHhHHHHHHhh
Confidence 34666666666666667889999999766666666 79999999998877764
No 240
>COG2509 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]
Probab=22.30 E-value=1.9e+02 Score=24.90 Aligned_cols=44 Identities=20% Similarity=0.208 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhcCCC---CeEEEecC------------C-CCCccCEEEEEEcCCHHH
Q psy8849 4 NKRQIIVIKILKDIKAQ---DIKVYDTS------------N-LTNLFDRITIASGSSKRQ 47 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~---dI~vldv~------------~-~~~~~dy~VIaT~~S~rh 47 (112)
.+.++.|.+.|++.+++ +-.|.|+- . ..-.+||+|+|.|+|.+-
T Consensus 173 ~~vvkni~~~l~~~G~ei~f~t~VeDi~~~~~~~~~v~~~~g~~i~~~~vvlA~Grsg~d 232 (486)
T COG2509 173 PKVVKNIREYLESLGGEIRFNTEVEDIEIEDNEVLGVKLTKGEEIEADYVVLAPGRSGRD 232 (486)
T ss_pred HHHHHHHHHHHHhcCcEEEeeeEEEEEEecCCceEEEEccCCcEEecCEEEEccCcchHH
Confidence 45667777778777542 22332222 1 134679999999999865
No 241
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=22.27 E-value=1.8e+02 Score=18.99 Aligned_cols=36 Identities=3% Similarity=0.167 Sum_probs=27.0
Q ss_pred CEEEEEEcC-CHHHHHHHHHHHHHHHHhcCCCccccc
Q psy8849 35 DRITIASGS-SKRQINALAVSIRKNIKNINNNIVNIE 70 (112)
Q Consensus 35 dy~VIaT~~-S~rh~~aia~~v~~~lk~~~~~~~~~E 70 (112)
+.++|.... |..++.++.+.+.+.+++.|......+
T Consensus 9 E~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~ 45 (97)
T CHL00123 9 ETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQ 45 (97)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEE
Confidence 455555555 899999999999999999876544433
No 242
>TIGR00166 S6 ribosomal protein S6. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.
Probab=22.11 E-value=2.2e+02 Score=18.11 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=30.1
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCccc------------ccccCCCCEEEEEc
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIKNINNNIVN------------IEGKKSSEWLLLDL 82 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~------------~EG~~~~~WvllD~ 82 (112)
.++|.....+..+.++.+.+.+.+++.|..... +.....|.|+++.+
T Consensus 5 ~~~Il~p~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~k~~~G~Y~~~~f 63 (93)
T TIGR00166 5 IIFLVRPTLSEEVKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVLMNF 63 (93)
T ss_pred EEEEECCCCcHHHHHHHHHHHHHHHhCCCEEEEEEeecceecceEcCCCceEEEEEEEE
Confidence 355555554444888999999999887654322 33445677777665
No 243
>PF04025 DUF370: Domain of unknown function (DUF370); InterPro: IPR007169 This is a bacterial family of unknown function.
Probab=22.08 E-value=2.2e+02 Score=18.10 Aligned_cols=43 Identities=19% Similarity=0.299 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEEeeChhh
Q psy8849 52 AVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIHIMNPYI 94 (112)
Q Consensus 52 a~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHif~~e~ 94 (112)
+..+.+..|+.|.-.-...|.+.-.=++.|.|.|+.-=.+||.
T Consensus 26 ~Krl~~~ak~~~~lIdaT~GrktrsviitdsghviLSa~~~eT 68 (73)
T PF04025_consen 26 IKRLIQEAKEEGKLIDATYGRKTRSVIITDSGHVILSALQPET 68 (73)
T ss_pred HHHHHHHHHHcCcEEEeeCCCceeEEEEEcCCcEEEeeCCHHH
Confidence 4556777777765544567888888999999998876666553
No 244
>PF01941 AdoMet_Synthase: S-adenosylmethionine synthetase (AdoMet synthetase); InterPro: IPR002795 A highly diverged class of S-adenosylmethionine synthetases have been identified in the archaea. S-adenosylmethionine is the primary alkylating agent in all known organisms. ATP:L-methionine S-adenosyltransferase (MAT) catalyses the only known biosynthetic route to this central metabolite. Although the amino acid sequence of MAT is strongly conserved among bacteria and eukarya (see IPR002133 from INTERPRO) no homologues had been recognised in the completed genome sequences of any archaea. The identification of a second major class of MAT emphasises the long evolutionary history of the archaeal lineage and the structural diversity found even in crucial metabolic enzymes []. Three bacterial genomes encode both the archaeal and eukaryotic/bacterial types of MAT [].; GO: 0004478 methionine adenosyltransferase activity, 0005524 ATP binding, 0006730 one-carbon metabolic process
Probab=22.04 E-value=1.6e+02 Score=24.67 Aligned_cols=52 Identities=19% Similarity=0.207 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHhc--------CCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 3 INKRQIIVIKILKDI--------KAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 3 ~~~l~~~i~~~l~~k--------ka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
+++++..+-+.|... =|+||+|+-++....+ -+.||.+.=+|++.++.+++.
T Consensus 169 ~E~~Vl~~Er~lns~~fk~~~p~~GeDiKVMG~R~g~~i--~LTvA~a~v~r~v~~~~~Y~~ 228 (396)
T PF01941_consen 169 TEKLVLETERYLNSPEFKKKFPEVGEDIKVMGLREGDKI--TLTVAMAFVDRYVSSLDEYFE 228 (396)
T ss_pred HHHHHHHHHHHhccccccccCCCcCCCeEEEEEEeCCEE--EEEEEhhhhhhhcCCHHHHHH
Confidence 567777888888664 3799999999987765 477888988888888777654
No 245
>PRK09485 mmuM homocysteine methyltransferase; Provisional
Probab=21.99 E-value=61 Score=25.45 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=14.8
Q ss_pred EEcCCHHHHHHHHHHHH
Q psy8849 40 ASGSSKRQINALAVSIR 56 (112)
Q Consensus 40 aT~~S~rh~~aia~~v~ 56 (112)
|.|.++.|+++|++.+.
T Consensus 287 CCGttP~hI~al~~~l~ 303 (304)
T PRK09485 287 CCRTTPEDIAALAAALK 303 (304)
T ss_pred CCCCCHHHHHHHHHHhh
Confidence 78999999999998763
No 246
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=21.85 E-value=4e+02 Score=22.83 Aligned_cols=54 Identities=9% Similarity=0.136 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHh
Q psy8849 4 NKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKN 61 (112)
Q Consensus 4 ~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~ 61 (112)
+++++.+++.|...-..+-.+--+. -.+|+|++.+.+...+..+++.+.+.+..
T Consensus 427 d~ll~~~a~~l~~~~~~~~~~~r~~----~~eF~il~~~~~~~~~~~~~~~l~~~~~~ 480 (799)
T PRK11359 427 DQALLEVVNRFREKLKPDQYLCRIE----GTQFVLVSLENDVSNITQIADELRNVVSK 480 (799)
T ss_pred HHHHHHHHHHHHHhCCCCCEEEEEc----CCEEEEEEcCCCHHHHHHHHHHHHHHhcC
Confidence 5788888888876554433333333 35788888888877788888888776643
No 247
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=21.61 E-value=2.4e+02 Score=21.70 Aligned_cols=33 Identities=18% Similarity=0.325 Sum_probs=26.2
Q ss_pred EcCCHHHHHHHHHHHHHHHHhcCCC-cccccccC
Q psy8849 41 SGSSKRQINALAVSIRKNIKNINNN-IVNIEGKK 73 (112)
Q Consensus 41 T~~S~rh~~aia~~v~~~lk~~~~~-~~~~EG~~ 73 (112)
.|..-.++..+|..+++.|.+.|+. .+...|.+
T Consensus 109 ~~~~f~~v~~~A~~~r~~L~~lgL~~~~KTSG~k 142 (227)
T cd04862 109 PGVPWKAVVEAALLVRELLDELGLESFVKTSGGK 142 (227)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCccceEccCCC
Confidence 4567789999999999999999986 45566644
No 248
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=21.52 E-value=2e+02 Score=17.33 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=21.5
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHH
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIK 60 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk 60 (112)
.-|.+.|.+...+..+++.+.+.+|
T Consensus 49 iRv~~Ea~~~~~~~~~~~~i~~~ik 73 (73)
T PF00408_consen 49 IRVYVEAPDEEELEEIAEEIAEAIK 73 (73)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 5577888999999999999988775
No 249
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=21.41 E-value=1.3e+02 Score=17.46 Aligned_cols=20 Identities=15% Similarity=0.345 Sum_probs=13.1
Q ss_pred CCCCEEEEEc---CC-EEEEeeCh
Q psy8849 73 KSSEWLLLDL---GD-IIIHIMNP 92 (112)
Q Consensus 73 ~~~~WvllD~---g~-vvVHif~~ 92 (112)
--|+|++++. +. +|..+++.
T Consensus 39 ~VGD~V~~~~~~~~~~~I~~vl~R 62 (68)
T cd04466 39 AVGDRVEFEPEDDGEGVIEEILPR 62 (68)
T ss_pred CCCcEEEEEECCCCcEEEEEEecc
Confidence 4589999984 33 55576643
No 250
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=21.40 E-value=1.5e+02 Score=15.79 Aligned_cols=49 Identities=6% Similarity=-0.023 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCC-CccCEEEEEEcCCHHHHHHHHHHH
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLT-NLFDRITIASGSSKRQINALAVSI 55 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~-~~~dy~VIaT~~S~rh~~aia~~v 55 (112)
.+..+..++.+. .-+|.-+...... .++.+.+.....+..++.++.+.+
T Consensus 11 ~l~~i~~~l~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 60 (71)
T cd04876 11 LLADITTVIAEE-KINILSVNTRTDDDGLATIRLTLEVRDLEHLARIMRKL 60 (71)
T ss_pred HHHHHHHHHHhC-CCCEEEEEeEECCCCEEEEEEEEEECCHHHHHHHHHHH
Confidence 456777888776 4455555444332 344455555556777776555544
No 251
>TIGR03169 Nterm_to_SelD pyridine nucleotide-disulfide oxidoreductase family protein. Members of this protein family include N-terminal sequence regions of (probable) bifunctional proteins whose C-terminal sequences are SelD, or selenide,water dikinase, the selenium donor protein necessary for selenium incorporation into protein (as selenocysteine), tRNA (as 2-selenouridine), or both. However, some members of this family occur in species that do not show selenium incorporation, and the function of this protein family is unknown.
Probab=21.34 E-value=42 Score=26.14 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=11.6
Q ss_pred ccCEEEEEEcCCHH
Q psy8849 33 LFDRITIASGSSKR 46 (112)
Q Consensus 33 ~~dy~VIaT~~S~r 46 (112)
-.||+|||||.+.+
T Consensus 95 ~yD~LviAtG~~~~ 108 (364)
T TIGR03169 95 SYDVLSLDVGSTTP 108 (364)
T ss_pred cccEEEEccCCCCC
Confidence 36999999998764
No 252
>PRK01966 ddl D-alanyl-alanine synthetase A; Reviewed
Probab=21.30 E-value=94 Score=24.42 Aligned_cols=46 Identities=24% Similarity=0.318 Sum_probs=31.4
Q ss_pred EEEEEEcCCHHHHHH--HHHHHHHHHHhcCCCcccccccCCCCEEEEE
Q psy8849 36 RITIASGSSKRQINA--LAVSIRKNIKNINNNIVNIEGKKSSEWLLLD 81 (112)
Q Consensus 36 y~VIaT~~S~rh~~a--ia~~v~~~lk~~~~~~~~~EG~~~~~WvllD 81 (112)
..|++=|.|..|-=+ -+..|.+.|.+.|..+.-+.-.+++.|.+.|
T Consensus 6 i~vl~GG~S~E~~vSl~s~~~v~~~l~~~~~~~~~~~~~~~g~~~~~~ 53 (333)
T PRK01966 6 VALLFGGRSAEHEVSLVSAKSVLKALDKEKYEVVPIGITKDGRWYLID 53 (333)
T ss_pred EEEEeCCCCCcchhhHHHHHHHHHHhcccCCEEEEEEECCCCCEeecc
Confidence 468888888877444 3677888888777765544433456787644
No 253
>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....
Probab=21.22 E-value=1.1e+02 Score=21.99 Aligned_cols=34 Identities=12% Similarity=0.099 Sum_probs=25.2
Q ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccc
Q psy8849 36 RITIASGSSKRQINALAVSIRKNIKNINNNIVNI 69 (112)
Q Consensus 36 y~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~ 69 (112)
++|.-||.|..==..+|.+|.+.|++.|.+....
T Consensus 3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~L 36 (156)
T PF01583_consen 3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLL 36 (156)
T ss_dssp EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEE
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEe
Confidence 4566777777666789999999999988765433
No 254
>KOG2972|consensus
Probab=21.18 E-value=4.3e+02 Score=21.04 Aligned_cols=78 Identities=19% Similarity=0.215 Sum_probs=51.1
Q ss_pred eEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEcCCEEEEeeChhhhh--hcc
Q psy8849 22 IKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDLGDIIIHIMNPYIRN--MYN 99 (112)
Q Consensus 22 I~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~g~vvVHif~~e~R~--~Y~ 99 (112)
-+++++=+. .-.++|+++-.+.--++++ .|+..++++|. +..++.=.+.|.-.+|||| +|+.|+ -.+
T Consensus 111 ~~~ye~~gp---~GV~liVealTdnknr~~~-~iRs~~nk~GG------~s~~~~r~~FdkKG~Vv~V-~~~~~dk~vL~ 179 (276)
T KOG2972|consen 111 FIEYEAMGP---SGVGLIVEALTDNKNRAAS-SIRSIFNKHGG------ASASGVRFLFDKKGVVVNV-PPEKRDKDVLN 179 (276)
T ss_pred EEEEeeecC---CceEEEEEeeeccHhHHHH-HHHHHHHHcCC------cccccceeEEeccceEEec-Chhhcchhhhh
Confidence 355665553 4567888887776666555 48999999875 1223445778886688886 555555 477
Q ss_pred hhhhccccccc
Q psy8849 100 LEEIWGEKEIK 110 (112)
Q Consensus 100 LE~LW~~~~~~ 110 (112)
+|++=..|+.+
T Consensus 180 ie~ie~~A~d~ 190 (276)
T KOG2972|consen 180 IEAIEAGAEDI 190 (276)
T ss_pred HHHHHhccccc
Confidence 77776666543
No 255
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=21.18 E-value=2.2e+02 Score=18.34 Aligned_cols=27 Identities=15% Similarity=0.126 Sum_probs=14.5
Q ss_pred CEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 35 DRITIASGSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
+.+++||+. .++.+.+.+..++.++..
T Consensus 62 ~lV~~at~d-----~~~n~~i~~~a~~~~i~v 88 (103)
T PF13241_consen 62 DLVFAATDD-----PELNEAIYADARARGILV 88 (103)
T ss_dssp SEEEE-SS------HHHHHHHHHHHHHTTSEE
T ss_pred eEEEecCCC-----HHHHHHHHHHHhhCCEEE
Confidence 444444443 345566767777777753
No 256
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=21.13 E-value=2.5e+02 Score=21.95 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=26.1
Q ss_pred EcCCHHHHHHHHHHHHHHHHhcCCC-cccccccC
Q psy8849 41 SGSSKRQINALAVSIRKNIKNINNN-IVNIEGKK 73 (112)
Q Consensus 41 T~~S~rh~~aia~~v~~~lk~~~~~-~~~~EG~~ 73 (112)
.+.+-..+..+|..+++.|.+.|+. .+...|.+
T Consensus 125 ~~~~f~~v~~~A~~~r~~L~~lgL~~f~KTSG~k 158 (245)
T TIGR02778 125 PGVAWKLVVEAAQLIRELLDELGLESFVKTSGGK 158 (245)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCccceEccCCC
Confidence 4567789999999999999999986 44566543
No 257
>COG4458 SrfC Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]
Probab=21.11 E-value=1.1e+02 Score=27.65 Aligned_cols=45 Identities=11% Similarity=0.250 Sum_probs=32.7
Q ss_pred CEEEEEEcCCHH-HHHHHHHHHHHHHHh-cCCCcccccc-cCCCCEEE
Q psy8849 35 DRITIASGSSKR-QINALAVSIRKNIKN-INNNIVNIEG-KKSSEWLL 79 (112)
Q Consensus 35 dy~VIaT~~S~r-h~~aia~~v~~~lk~-~~~~~~~~EG-~~~~~Wvl 79 (112)
+-++|||+.|.| ++.++++++.+-++. .|..|-..+- ..+=-|.+
T Consensus 390 n~LlvCta~~~rSdv~t~~~~Ld~Wv~aTqgEsp~qrarr~pgl~wal 437 (821)
T COG4458 390 NSLLVCTAPSNRSDVATLPDMLDDWVRATQGESPAQRARREPGLFWAL 437 (821)
T ss_pred ceEEEecCCcchhhhccchHHHHHHHHhhCCCCHHHHhhccCceEEEe
Confidence 789999999999 899999999999987 4655433222 23335655
No 258
>PRK14568 vanB D-alanine--D-lactate ligase; Provisional
Probab=21.05 E-value=1.1e+02 Score=24.17 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=31.9
Q ss_pred EEEEEEcCCHHHHHHH--HHHHHHHHHhcCCCcccccccCCCCEEEEEc
Q psy8849 36 RITIASGSSKRQINAL--AVSIRKNIKNINNNIVNIEGKKSSEWLLLDL 82 (112)
Q Consensus 36 y~VIaT~~S~rh~~ai--a~~v~~~lk~~~~~~~~~EG~~~~~WvllD~ 82 (112)
-.|++=|.|..|==++ +..|.+.|.+.|..+..+.=.+++.|.+.|.
T Consensus 6 i~vl~GG~S~E~evSl~s~~~v~~~l~~~~~~v~~i~i~~~g~~~~~~~ 54 (343)
T PRK14568 6 VGILFGGCSEEHPVSVKSAIEVARNLDTEKYEPFYIGITKSGVWKLCDG 54 (343)
T ss_pred EEEEECCCCCchHHHHHhHHHHHHhhcccCCeEEEEEECCCCcEEeCCc
Confidence 5688999999885554 6678888877776654443234468976553
No 259
>cd07187 YvcK_like family of mostly uncharacterized proteins similar to B.subtilis YvcK. One member of this protein family, YvcK from Bacillus subtilis, has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway. In general, this family of mostly uncharacterized proteins is related to the CofD-like protein family. CofD has been characterized as a 2-phospho-L-lactate transferase involved in F420 biosynthesis. This family appears to have the same conserved phosphate binding site as the other family in this hierarchy, but a different substrate binding site.
Probab=21.04 E-value=1.6e+02 Score=23.59 Aligned_cols=46 Identities=11% Similarity=0.048 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 6 RQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 6 l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
++..|.++|.+.+|.-|-+.++.....-++. -+-..|++++++++.
T Consensus 195 lv~gI~eAi~~s~a~kV~v~N~~~~~get~~-----~~~~d~v~~i~~~~~ 240 (308)
T cd07187 195 LVKGIAEAIRASKAPKVYICNLMTQPGETDG-----FTLSDHVRALLRHLG 240 (308)
T ss_pred CchhHHHHHHhCCCCEEEEecCCCCCCCCCC-----CCHHHHHHHHHHHhC
Confidence 4577899999999999999999877655554 244667777777765
No 260
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=21.01 E-value=2.5e+02 Score=20.43 Aligned_cols=44 Identities=16% Similarity=0.250 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHhcCC-Ccccccc--------cCCCCEEEEEcCCEEEE
Q psy8849 45 KRQINALAVSIRKNIKNINN-NIVNIEG--------KKSSEWLLLDLGDIIIH 88 (112)
Q Consensus 45 ~rh~~aia~~v~~~lk~~~~-~~~~~EG--------~~~~~WvllD~g~vvVH 88 (112)
.||-+|||-.|-.-|+..|. ..+..-. -.+.+|++-+=|...=.
T Consensus 19 ERrRRAIaakIfaGLR~~Gny~Lp~~aD~NeVLkALc~eAGw~Ve~DGTtyr~ 71 (150)
T PF05687_consen 19 ERRRRAIAAKIFAGLRAHGNYKLPKHADNNEVLKALCREAGWTVEPDGTTYRK 71 (150)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCcCCHHHHHHHHHHhCCEEEccCCCeecc
Confidence 58899999999999998765 3222111 14578999998876543
No 261
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=20.85 E-value=2.7e+02 Score=20.76 Aligned_cols=59 Identities=17% Similarity=0.241 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 3 INKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
..++...+-..-.+.+..+++++|==+.-...+ ........+..++..++...++.+++
T Consensus 114 ~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~----~~~~~~~~~~~i~~~Lk~lA~~~~i~ 172 (259)
T PF03796_consen 114 IDDIESKIRRLKREGKKVDVVFIDYLQLLKSED----SSDNRRQEIGEISRELKALAKELNIP 172 (259)
T ss_dssp HHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSC----SSSCCHHHHHHHHHHHHHHHHHHTSE
T ss_pred HHHHHHHHHHHHhhccCCCEEEechHHHhcCCC----CCCCHHHHHHHHHHHHHHHHHHcCCe
Confidence 344544444443443666888888555433222 22333445778899999888888875
No 262
>PRK13512 coenzyme A disulfide reductase; Provisional
Probab=20.81 E-value=39 Score=27.53 Aligned_cols=13 Identities=23% Similarity=0.738 Sum_probs=11.3
Q ss_pred cCEEEEEEcCCHH
Q psy8849 34 FDRITIASGSSKR 46 (112)
Q Consensus 34 ~dy~VIaT~~S~r 46 (112)
+||+|||||.+++
T Consensus 106 yd~lviAtGs~~~ 118 (438)
T PRK13512 106 YDKLILSPGASAN 118 (438)
T ss_pred cCEEEECCCCCCC
Confidence 5999999999864
No 263
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=20.75 E-value=2.1e+02 Score=17.39 Aligned_cols=59 Identities=12% Similarity=0.084 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCC
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNN 65 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~ 65 (112)
-++..+.++|.+.++ +|.-++..-.....-+.++.++.. .-..++.+.+....++.|..
T Consensus 13 GiVa~vs~~la~~g~-nI~d~~q~~~~~~F~m~~~~~~~~-~~~~~l~~~l~~~~~~~~l~ 71 (77)
T cd04893 13 GILNELTRAVSESGC-NILDSRMAILGTEFALTMLVEGSW-DAIAKLEAALPGLARRLDLT 71 (77)
T ss_pred hHHHHHHHHHHHcCC-CEEEceeeEEcCEEEEEEEEEecc-ccHHHHHHHHHHHHHHcCCE
Confidence 367888999998865 444443333344444445555542 23445555555555555554
No 264
>PF08482 HrpB_C: ATP-dependent helicase C-terminal; InterPro: IPR013689 This domain is found near the C terminus of bacterial ATP-dependent helicases such as HrpB.
Probab=20.70 E-value=68 Score=22.77 Aligned_cols=24 Identities=17% Similarity=0.466 Sum_probs=20.9
Q ss_pred CEEEEeeChhhhh---hcchhhhcccc
Q psy8849 84 DIIIHIMNPYIRN---MYNLEEIWGEK 107 (112)
Q Consensus 84 ~vvVHif~~e~R~---~Y~LE~LW~~~ 107 (112)
-|.+|+.+|..|- --||.++|.++
T Consensus 86 pl~l~LLSPa~RPiqvT~DL~~FW~~s 112 (133)
T PF08482_consen 86 PLTLELLSPAGRPIQVTQDLASFWQGS 112 (133)
T ss_pred eeEEEEeCCCCCceeeeCCHHHHhccc
Confidence 6899999999995 57999999875
No 265
>cd06592 GH31_glucosidase_KIAA1161 KIAA1161 is an uncharacterized Homo sapiens protein with a glycosyl hydrolase family 31 (GH31) domain that is homologous to the Escherichia coli YihQ glucosidase. Orthologs of KIA1161 are found in eukaryotes and prokaryotes. In bacteria, YihQ (along with YihO) is important for bacterial O-antigen capsule assembly and translocation. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein.
Probab=20.69 E-value=3.7e+02 Score=20.89 Aligned_cols=89 Identities=10% Similarity=0.046 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHhcCC-CCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc-------------cc
Q psy8849 3 INKRQIIVIKILKDIKA-QDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNI-------------VN 68 (112)
Q Consensus 3 ~~~l~~~i~~~l~~kka-~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~-------------~~ 68 (112)
+++.+..+++.+.+.+. -|+.++|..=...+.|+-.=-+- -...+++. +.+++.|++. ..
T Consensus 28 s~~~v~~~~~~~~~~~iP~d~i~iD~~w~~~~g~f~~d~~~--FPdp~~mi----~~l~~~G~k~~l~i~P~i~~~s~~~ 101 (303)
T cd06592 28 NQETVLNYAQEIIDNGFPNGQIEIDDNWETCYGDFDFDPTK--FPDPKGMI----DQLHDLGFRVTLWVHPFINTDSENF 101 (303)
T ss_pred CHHHHHHHHHHHHHcCCCCCeEEeCCCccccCCccccChhh--CCCHHHHH----HHHHHCCCeEEEEECCeeCCCCHHH
Confidence 34556778888888876 79999997644444444221111 12244444 4556666642 11
Q ss_pred ccccCCCCEEEEEc-C------------CEEEEeeChhhhhhc
Q psy8849 69 IEGKKSSEWLLLDL-G------------DIIIHIMNPYIRNMY 98 (112)
Q Consensus 69 ~EG~~~~~WvllD~-g------------~vvVHif~~e~R~~Y 98 (112)
.|+...+ +.+-+. | ..++-.+.|++|++|
T Consensus 102 ~e~~~~g-~~vk~~~g~~~~~~~~w~g~~~~~Dftnp~a~~w~ 143 (303)
T cd06592 102 REAVEKG-YLVSEPSGDIPALTRWWNGTAAVLDFTNPEAVDWF 143 (303)
T ss_pred HhhhhCC-eEEECCCCCCCcccceecCCcceEeCCCHHHHHHH
Confidence 2344333 333332 2 256778889999876
No 266
>PRK06904 replicative DNA helicase; Validated
Probab=20.65 E-value=4.3e+02 Score=22.24 Aligned_cols=58 Identities=9% Similarity=0.096 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCc
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIRKNIKNINNNI 66 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~ 66 (112)
++...+-+....++..+++++|==+.-.-..+ +.+....+..+++.++...|+.+++.
T Consensus 320 ~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~----~~~r~~ei~~isr~LK~lAkel~ipV 377 (472)
T PRK06904 320 ELRSRARRVYRENGGLSLIMVDYLQLMRAPGF----EDNRTLEIAEISRSLKALAKELKVPV 377 (472)
T ss_pred HHHHHHHHHHHhCCCCCEEEEecHHhcCCCCC----CCcHHHHHHHHHHHHHHHHHHhCCeE
Confidence 33333333334444578888884433221111 12223346778888888888888863
No 267
>COG2144 Selenophosphate synthetase-related proteins [General function prediction only]
Probab=20.48 E-value=1.6e+02 Score=23.92 Aligned_cols=29 Identities=24% Similarity=0.302 Sum_probs=25.5
Q ss_pred EEEcCCHHHHHHHHHHHHHHHHhcCCCcc
Q psy8849 39 IASGSSKRQINALAVSIRKNIKNINNNIV 67 (112)
Q Consensus 39 IaT~~S~rh~~aia~~v~~~lk~~~~~~~ 67 (112)
+.+++|+.+++.+.+-+++..++.|++..
T Consensus 100 ~isa~s~d~~~ei~eglr~~a~kfgvpiv 128 (324)
T COG2144 100 AISAKSEDQAREILEGLRKGARKFGVPIV 128 (324)
T ss_pred eeecCCHHHHHHHHHHHHHHHHhcCCcee
Confidence 56899999999999999999999888643
No 268
>PF07992 Pyr_redox_2: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR023753 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes the FAD binding domain which has a nested NADH binding domain and is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3IC9_A 1Q1W_A 3LB8_A 1Q1R_B 3GD4_A 1GV4_A 3GD3_A 2EQ9_E 2EQ6_B 2EQ8_E ....
Probab=20.48 E-value=42 Score=23.32 Aligned_cols=14 Identities=43% Similarity=0.698 Sum_probs=11.2
Q ss_pred ccCEEEEEEcCCHH
Q psy8849 33 LFDRITIASGSSKR 46 (112)
Q Consensus 33 ~~dy~VIaT~~S~r 46 (112)
-+||+|||||..++
T Consensus 110 ~~d~lviAtG~~~~ 123 (201)
T PF07992_consen 110 KYDYLVIATGSRPR 123 (201)
T ss_dssp EEEEEEEESTEEEE
T ss_pred cCCeeeecCccccc
Confidence 46999999996644
No 269
>TIGR03452 mycothione_red mycothione reductase. Mycothiol, a glutathione analog in Mycobacterium tuberculosis and related species, can form a disulfide-linked dimer called mycothione. This enzyme can reduce mycothione to regenerate two mycothiol molecules. The enzyme shows some sequence similarity to glutathione-disulfide reductase, trypanothione-disulfide reductase, and dihydrolipoamide dehydrogenase. The characterized protein from M. tuberculosis, a homodimer, has FAD as a cofactor, one per monomer, and uses NADPH as a substrate.
Probab=20.44 E-value=54 Score=26.89 Aligned_cols=14 Identities=43% Similarity=0.415 Sum_probs=12.0
Q ss_pred ccCEEEEEEcCCHH
Q psy8849 33 LFDRITIASGSSKR 46 (112)
Q Consensus 33 ~~dy~VIaT~~S~r 46 (112)
-+|++|||||.+++
T Consensus 131 ~~d~lIiATGs~p~ 144 (452)
T TIGR03452 131 TGDQIVIAAGSRPY 144 (452)
T ss_pred EeCEEEEEECCCCC
Confidence 46999999998875
No 270
>KOG1042|consensus
Probab=20.40 E-value=3.1e+02 Score=24.99 Aligned_cols=63 Identities=13% Similarity=0.221 Sum_probs=42.7
Q ss_pred CCccCEEEEEEcCCHHHHHHHHHHHHHHHHhcCCCcccccccCCCCEEEEEc-----------------CCEEEEeeChh
Q psy8849 31 TNLFDRITIASGSSKRQINALAVSIRKNIKNINNNIVNIEGKKSSEWLLLDL-----------------GDIIIHIMNPY 93 (112)
Q Consensus 31 ~~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~~~~~~~~EG~~~~~WvllD~-----------------g~vvVHif~~e 93 (112)
+++..+.||+++++....+.+.+.+.+.....|... ...-|+-++- -.+||-|+...
T Consensus 470 ~~l~~W~vi~p~r~~~~a~~fi~~l~r~a~~mgm~i------~~P~~v~i~ddr~~tYvraiqq~v~~D~qmvvcil~~~ 543 (845)
T KOG1042|consen 470 SNLDNWAVIYPGRNNSEAQEFINMLRRVASSMGMQI------REPICVEIKDDRPGTYVRAIQQVVGADIQMVVCILPSD 543 (845)
T ss_pred CCCcceEEEecCccHHHHHHHHHHHHHhccccceec------CCceEEEeCCCChHHHHHHHHHhccCCceEEEEEecCC
Confidence 367789999999999999988888887666655431 1122333221 25677777777
Q ss_pred hhhhcc
Q psy8849 94 IRNMYN 99 (112)
Q Consensus 94 ~R~~Y~ 99 (112)
.-++|+
T Consensus 544 nk~~Y~ 549 (845)
T KOG1042|consen 544 NKTRYD 549 (845)
T ss_pred chhhHH
Confidence 777776
No 271
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.38 E-value=2e+02 Score=16.78 Aligned_cols=51 Identities=12% Similarity=0.169 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCCC-CCccCE-EEEEEcCCHHHHHHHHHHHH
Q psy8849 5 KRQIIVIKILKDIKAQDIKVYDTSNL-TNLFDR-ITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 5 ~l~~~i~~~l~~kka~dI~vldv~~~-~~~~dy-~VIaT~~S~rh~~aia~~v~ 56 (112)
.++..|.+.|.+. .-+|.-+..+.. ...+.. |.+.+....+|+..+.+.++
T Consensus 12 g~l~~I~~~la~~-~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~ 64 (76)
T cd04888 12 GVLSKVLNTIAQV-RGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELR 64 (76)
T ss_pred chHHHHHHHHHHc-CCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHh
Confidence 3667888899776 446666655322 123333 34444444459888877665
No 272
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=20.37 E-value=74 Score=19.74 Aligned_cols=21 Identities=19% Similarity=0.400 Sum_probs=12.8
Q ss_pred cCCCCEEEEEcCCEEEEeeChh
Q psy8849 72 KKSSEWLLLDLGDIIIHIMNPY 93 (112)
Q Consensus 72 ~~~~~WvllD~g~vvVHif~~e 93 (112)
..-|+|+|+..| ..+..++++
T Consensus 38 v~~Gd~VLVHaG-~Ai~~idee 58 (68)
T PF01455_consen 38 VKVGDYVLVHAG-FAIEKIDEE 58 (68)
T ss_dssp B-TT-EEEEETT-EEEEEE-HH
T ss_pred CCCCCEEEEecC-hhheeCCHH
Confidence 456899999999 455555544
No 273
>COG0010 SpeB Arginase/agmatinase/formimionoglutamate hydrolase, arginase family [Amino acid transport and metabolism]
Probab=20.33 E-value=2.6e+02 Score=21.97 Aligned_cols=48 Identities=17% Similarity=0.273 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHHHhcCCCCeEEEecCCCCCccCEEEEEEcCCHHHHHHHHHHHH
Q psy8849 2 NINKRQIIVIKILKDIKAQDIKVYDTSNLTNLFDRITIASGSSKRQINALAVSIR 56 (112)
Q Consensus 2 ~~~~l~~~i~~~l~~kka~dI~vldv~~~~~~~dy~VIaT~~S~rh~~aia~~v~ 56 (112)
+..++...+..+++. .+|+.+||.+.++..| .++.+.+-+..+..++.
T Consensus 251 t~~e~~~~~~~l~~~---~~vvg~DvvEv~P~~D----~~~~Ta~~aa~l~~~ll 298 (305)
T COG0010 251 TFRELLDLLERLLKS---GKVVGFDVVEVNPALD----ISGRTARLAARLIAELL 298 (305)
T ss_pred CHHHHHHHHHHHhcc---CCEEEEEEEEECCCCC----CCccHHHHHHHHHHHHH
Confidence 344555444444444 6899999999998888 45555555555554444
No 274
>PF04456 DUF503: Protein of unknown function (DUF503); InterPro: IPR007546 This is a family of conserved hypothetical bacterial proteins, including TT1725 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), which has a ferredoxin-like alpha+beta-sandwich fold [].; PDB: 1J27_A.
Probab=20.16 E-value=2.6e+02 Score=18.15 Aligned_cols=43 Identities=7% Similarity=0.013 Sum_probs=31.9
Q ss_pred CCeEEEecCCCC--CccCEEEEEEcCCHHHHHHHHHHHHHHHHhc
Q psy8849 20 QDIKVYDTSNLT--NLFDRITIASGSSKRQINALAVSIRKNIKNI 62 (112)
Q Consensus 20 ~dI~vldv~~~~--~~~dy~VIaT~~S~rh~~aia~~v~~~lk~~ 62 (112)
-+|.|-++.... ..+..-+.+-|+|..|+..+.+.+.+.+...
T Consensus 35 fnvSvaEv~~~D~~q~a~lg~a~vs~~~~~~~~~l~~v~~~ie~~ 79 (90)
T PF04456_consen 35 FNVSVAEVGHQDSWQRAVLGFAVVSNSRAHAEQILDKVERFIEEN 79 (90)
T ss_dssp SS-EEEEEE-TT-SSEEEEEEEEEES-HHHHHHHHHHHHHHHHHS
T ss_pred CCeEEEEecCCCcccEEEEEEEEEECCHHHHHHHHHHHHHHHHhC
Confidence 488888887654 4556677788999999999999999998654
No 275
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=20.12 E-value=95 Score=20.53 Aligned_cols=26 Identities=15% Similarity=0.252 Sum_probs=22.2
Q ss_pred CCCEEEEEcC-CEEEEeeChhhhhhcc
Q psy8849 74 SSEWLLLDLG-DIIIHIMNPYIRNMYN 99 (112)
Q Consensus 74 ~~~WvllD~g-~vvVHif~~e~R~~Y~ 99 (112)
+++.++++.| ++.|+.=.+++.+|++
T Consensus 67 ~~~~v~v~iG~~~~ve~~~~eA~~~l~ 93 (129)
T cd00890 67 DDDKVLVDLGTGVYVEKSLEEAIEFLK 93 (129)
T ss_pred CCCEEEEEecCCEEEEecHHHHHHHHH
Confidence 6789999999 9999988888877653
No 276
>PRK13146 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional
Probab=20.11 E-value=3.1e+02 Score=20.08 Aligned_cols=35 Identities=23% Similarity=0.269 Sum_probs=21.1
Q ss_pred HHHHHHHHhcCCC-CeEEEecCCCCCccCEEEEEEcC
Q psy8849 8 IIVIKILKDIKAQ-DIKVYDTSNLTNLFDRITIASGS 43 (112)
Q Consensus 8 ~~i~~~l~~kka~-dI~vldv~~~~~~~dy~VIaT~~ 43 (112)
..++++|++..+. ++.+..-.+.-.-+|-+|| +|.
T Consensus 15 ~s~~~al~~~g~~~~v~~~~~~~~l~~~d~lIl-pG~ 50 (209)
T PRK13146 15 RSAAKALERAGAGADVVVTADPDAVAAADRVVL-PGV 50 (209)
T ss_pred HHHHHHHHHcCCCccEEEECCHHHhcCCCEEEE-CCC
Confidence 5667888877553 6666554332234587777 663
No 277
>PLN02382 probable sucrose-phosphatase
Probab=20.11 E-value=96 Score=25.53 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=14.7
Q ss_pred CEEEEEEcCCHHHHHHHHH
Q psy8849 35 DRITIASGSSKRQINALAV 53 (112)
Q Consensus 35 dy~VIaT~~S~rh~~aia~ 53 (112)
-.||+|||||...++.+.+
T Consensus 46 i~fv~aTGR~~~~~~~l~~ 64 (413)
T PLN02382 46 SLLVFSTGRSPTLYKELRK 64 (413)
T ss_pred eeEEEEcCCCHHHHHHHHH
Confidence 4799999999887765544
No 278
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=20.10 E-value=2.7e+02 Score=21.46 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=26.3
Q ss_pred EcCCHHHHHHHHHHHHHHHHhcCCC-cccccccC
Q psy8849 41 SGSSKRQINALAVSIRKNIKNINNN-IVNIEGKK 73 (112)
Q Consensus 41 T~~S~rh~~aia~~v~~~lk~~~~~-~~~~EG~~ 73 (112)
.|.+-.++..+|..+++.|.+.|+. .+...|.+
T Consensus 109 ~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~k 142 (227)
T cd04861 109 PGVPFEDVVEAALLLRELLDELGLESFPKTSGGK 142 (227)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCccceEccCCC
Confidence 4667789999999999999999986 45566644
Done!