Query 044269
Match_columns 129
No_of_seqs 111 out of 579
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 13:02:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044269.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044269hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09269 DUF1967: Domain of un 100.0 2.3E-29 5.1E-34 169.4 7.2 69 34-103 1-69 (69)
2 TIGR03595 Obg_CgtA_exten Obg f 100.0 9.4E-29 2E-33 166.6 9.8 69 34-103 1-69 (69)
3 PRK12297 obgE GTPase CgtA; Rev 99.8 1.7E-20 3.6E-25 161.8 10.4 73 32-105 352-424 (424)
4 PRK12296 obgE GTPase CgtA; Rev 99.8 2.2E-19 4.8E-24 158.0 10.7 76 32-108 364-444 (500)
5 COG2012 RPB5 DNA-directed RNA 86.0 0.87 1.9E-05 32.0 2.9 15 83-97 50-64 (80)
6 PF01568 Molydop_binding: Moly 76.9 2.4 5.1E-05 29.0 2.4 17 81-97 37-53 (110)
7 PRK09570 rpoH DNA-directed RNA 71.1 4.6 0.0001 28.1 2.7 44 46-96 17-60 (79)
8 cd02787 MopB_CT_ydeP The MopB_ 69.2 4.7 0.0001 28.0 2.5 17 81-97 38-54 (112)
9 cd02781 MopB_CT_Acetylene-hydr 67.2 5.7 0.00012 28.0 2.6 17 81-97 40-56 (130)
10 COG1497 Predicted transcriptio 66.9 29 0.00062 29.2 7.0 63 36-104 55-124 (260)
11 cd02786 MopB_CT_3 The MopB_CT_ 65.5 6.3 0.00014 27.2 2.5 17 81-97 38-54 (116)
12 PF11213 DUF3006: Protein of u 64.5 4 8.6E-05 27.1 1.3 29 79-107 25-54 (71)
13 TIGR00030 S21p ribosomal prote 63.7 11 0.00023 24.6 3.2 23 64-86 12-34 (58)
14 cd02791 MopB_CT_Nitrate-R-NapA 63.0 7.6 0.00016 26.9 2.5 17 81-97 42-58 (122)
15 cd02790 MopB_CT_Formate-Dh_H F 62.9 7.7 0.00017 26.6 2.5 18 81-98 42-59 (116)
16 cd00508 MopB_CT_Fdh-Nap-like T 62.8 7.7 0.00017 26.6 2.5 18 81-98 42-59 (120)
17 cd02777 MopB_CT_DMSOR-like The 61.5 8.1 0.00018 27.3 2.5 17 81-97 41-57 (127)
18 cd02785 MopB_CT_4 The MopB_CT_ 60.2 8.8 0.00019 27.0 2.5 17 81-97 39-55 (124)
19 cd02789 MopB_CT_FmdC-FwdD The 59.9 9.5 0.00021 26.7 2.6 17 81-97 38-54 (106)
20 cd02794 MopB_CT_DmsA-EC The Mo 59.9 9.1 0.0002 26.9 2.5 17 81-97 37-53 (121)
21 cd02775 MopB_CT Molybdopterin- 59.1 10 0.00022 25.1 2.5 17 81-97 30-46 (101)
22 cd02776 MopB_CT_Nitrate-R-NarG 58.0 10 0.00022 28.1 2.6 17 81-97 38-54 (141)
23 cd02788 MopB_CT_NDH-1_NuoG2-N7 57.6 11 0.00024 25.7 2.6 16 82-97 37-52 (96)
24 cd02792 MopB_CT_Formate-Dh-Na- 57.6 11 0.00024 26.1 2.6 17 81-97 42-58 (122)
25 cd02793 MopB_CT_DMSOR-BSOR-TMA 57.5 11 0.00023 27.0 2.6 18 81-98 40-57 (129)
26 cd02784 MopB_CT_PHLH The MopB_ 57.2 10 0.00022 28.2 2.5 18 80-97 44-61 (137)
27 PRK00270 rpsU 30S ribosomal pr 57.0 16 0.00035 24.2 3.2 23 64-86 13-35 (64)
28 cd02783 MopB_CT_2 The MopB_CT_ 57.0 10 0.00023 28.3 2.6 18 81-98 39-56 (156)
29 PF04014 Antitoxin-MazE: Antid 56.0 14 0.0003 22.3 2.6 15 82-96 15-29 (47)
30 cd02779 MopB_CT_Arsenite-Ox Th 55.7 12 0.00025 26.2 2.5 17 81-97 40-56 (115)
31 cd02778 MopB_CT_Thiosulfate-R- 55.4 12 0.00026 25.9 2.5 16 81-96 37-52 (123)
32 COG1153 FwdD Formylmethanofura 54.0 11 0.00024 28.5 2.3 17 81-97 38-54 (128)
33 PF01191 RNA_pol_Rpb5_C: RNA p 53.9 10 0.00022 26.0 1.8 14 84-97 45-58 (74)
34 cd02782 MopB_CT_1 The MopB_CT_ 52.8 14 0.0003 26.1 2.5 17 81-97 40-56 (129)
35 COG2746 Aminoglycoside N3'-ace 52.6 13 0.00027 31.2 2.5 25 73-97 11-35 (251)
36 PF03990 DUF348: Domain of unk 51.3 16 0.00035 21.9 2.3 19 77-95 18-38 (43)
37 PF10015 DUF2258: Uncharacteri 48.7 19 0.00041 25.0 2.6 34 63-97 29-63 (75)
38 COG2897 SseA Rhodanese-related 47.4 19 0.0004 30.3 2.8 20 80-99 79-98 (285)
39 COG0426 FpaA Uncharacterized f 46.9 19 0.00041 31.7 2.9 22 85-106 121-142 (388)
40 PRK15094 magnesium/cobalt effl 45.4 1E+02 0.0022 25.5 6.9 57 36-104 204-267 (292)
41 PF01628 HrcA: HrcA protein C 45.0 32 0.00069 26.7 3.7 54 43-98 129-183 (224)
42 PRK00082 hrcA heat-inducible t 45.0 82 0.0018 26.7 6.4 51 44-98 232-283 (339)
43 cd01796 DDI1_N DNA damage indu 44.9 21 0.00045 23.2 2.2 16 82-97 55-70 (71)
44 PRK11573 hypothetical protein; 44.5 90 0.0019 27.1 6.7 57 36-104 326-389 (413)
45 PLN02377 3-ketoacyl-CoA syntha 44.1 30 0.00066 31.2 3.8 45 33-79 102-146 (502)
46 cd02780 MopB_CT_Tetrathionate_ 43.4 23 0.0005 25.6 2.5 16 82-97 38-53 (143)
47 COG0186 RpsQ Ribosomal protein 42.8 15 0.00032 26.1 1.3 12 87-98 55-66 (87)
48 PF02938 GAD: GAD domain; Int 41.2 23 0.0005 24.4 2.1 18 80-97 67-84 (95)
49 TIGR03520 GldE gliding motilit 40.2 1.3E+02 0.0029 25.9 7.0 60 36-105 325-394 (408)
50 PF03471 CorC_HlyC: Transporte 39.9 1.1E+02 0.0023 20.1 5.6 53 41-103 4-64 (81)
51 cd01812 BAG1_N Ubiquitin-like 39.6 29 0.00062 21.7 2.2 17 80-96 52-68 (71)
52 PF08845 SymE_toxin: Toxin Sym 38.9 27 0.00058 22.6 2.0 16 81-96 31-46 (57)
53 TIGR03635 S17_bact 30S ribosom 38.4 20 0.00044 24.2 1.4 12 87-98 48-59 (71)
54 COG2015 Alkyl sulfatase and re 37.6 35 0.00077 31.7 3.2 18 89-106 262-279 (655)
55 PF03459 TOBE: TOBE domain; I 37.4 35 0.00076 21.0 2.4 16 81-96 40-55 (64)
56 PF02359 CDC48_N: Cell divisio 37.3 32 0.0007 23.1 2.3 28 81-108 23-54 (87)
57 cd08177 MAR Maleylacetate redu 37.0 25 0.00054 29.2 2.0 44 50-93 266-309 (337)
58 cd06288 PBP1_sucrose_transcrip 37.0 56 0.0012 24.5 3.8 40 60-99 158-212 (269)
59 PF03829 PTSIIA_gutA: PTS syst 36.6 32 0.00069 25.3 2.3 17 87-103 51-67 (117)
60 PF04225 OapA: Opacity-associa 36.0 39 0.00084 23.2 2.6 43 48-96 9-51 (85)
61 TIGR02609 doc_partner putative 35.9 39 0.00085 22.5 2.5 16 81-96 17-32 (74)
62 PF03120 DNA_ligase_OB: NAD-de 35.8 31 0.00068 24.0 2.1 15 83-97 45-59 (82)
63 PRK11507 ribosome-associated p 35.5 27 0.0006 23.7 1.7 26 77-102 42-67 (70)
64 PF08817 YukD: WXG100 protein 35.4 16 0.00035 24.2 0.6 17 80-96 62-78 (79)
65 PLN03111 DNA-directed RNA poly 35.2 37 0.00081 27.5 2.7 13 84-96 177-189 (206)
66 PRK11347 antitoxin ChpS; Provi 35.1 41 0.00088 23.2 2.6 16 81-96 19-34 (83)
67 PF08461 HTH_12: Ribonuclease 35.0 31 0.00066 22.6 1.8 36 47-82 14-50 (66)
68 cd01805 RAD23_N Ubiquitin-like 34.7 38 0.00082 21.6 2.2 16 81-96 56-71 (77)
69 COG0243 BisC Anaerobic dehydro 34.6 32 0.00068 31.8 2.5 17 81-97 678-694 (765)
70 cd00989 PDZ_metalloprotease PD 34.2 37 0.00079 21.3 2.1 20 82-101 24-44 (79)
71 PF12668 DUF3791: Protein of u 34.2 66 0.0014 20.5 3.3 30 51-84 7-36 (62)
72 PRK14990 anaerobic dimethyl su 34.0 28 0.00061 32.4 2.0 21 77-98 726-746 (814)
73 PF04023 FeoA: FeoA domain; I 34.0 39 0.00085 21.5 2.2 18 81-98 26-43 (74)
74 cd01791 Ubl5 UBL5 ubiquitin-li 33.9 38 0.00083 22.4 2.2 16 82-97 56-71 (73)
75 PF02643 DUF192: Uncharacteriz 33.7 27 0.00059 24.7 1.5 14 83-96 93-106 (108)
76 TIGR01439 lp_hng_hel_AbrB loop 33.6 51 0.0011 18.7 2.5 17 81-97 14-30 (43)
77 PRK05282 (alpha)-aspartyl dipe 33.3 35 0.00077 27.6 2.3 31 65-97 88-118 (233)
78 PTZ00061 DNA-directed RNA poly 33.0 42 0.00091 27.2 2.7 13 84-96 176-188 (205)
79 cd06317 PBP1_ABC_sugar_binding 32.9 79 0.0017 23.8 4.1 37 60-97 167-219 (275)
80 KOG2500 Uncharacterized conser 32.7 77 0.0017 26.5 4.2 64 34-97 91-161 (253)
81 cd01804 midnolin_N Ubiquitin-l 32.5 42 0.00091 22.2 2.2 15 82-96 55-69 (78)
82 PF08133 Nuclease_act: Anticod 31.9 27 0.00059 19.6 1.0 23 58-80 1-23 (26)
83 PF08939 DUF1917: Domain of un 31.9 44 0.00095 27.6 2.7 24 58-81 203-226 (243)
84 PF13275 S4_2: S4 domain; PDB: 31.3 29 0.00063 23.1 1.3 26 77-102 38-63 (65)
85 KOG3085 Predicted hydrolase (H 31.3 50 0.0011 27.2 2.9 21 80-100 175-195 (237)
86 PTZ00237 acetyl-CoA synthetase 31.1 44 0.00095 29.9 2.7 18 80-97 106-123 (647)
87 PF13533 Biotin_lipoyl_2: Biot 30.9 35 0.00076 20.8 1.5 21 86-106 16-36 (50)
88 TIGR03479 DMSO_red_II_alp DMSO 30.2 39 0.00085 32.2 2.4 17 81-97 817-833 (912)
89 PF04994 TfoX_C: TfoX C-termin 30.2 62 0.0014 22.0 2.8 36 49-88 12-47 (81)
90 PF08206 OB_RNB: Ribonuclease 30.0 36 0.00079 21.4 1.5 11 86-96 30-40 (58)
91 TIGR02164 torA trimethylamine- 30.0 44 0.00095 31.3 2.6 17 81-97 714-730 (822)
92 PRK05610 rpsQ 30S ribosomal pr 29.9 32 0.0007 23.9 1.4 12 87-98 53-64 (84)
93 PRK11303 DNA-binding transcrip 29.4 73 0.0016 25.1 3.5 39 60-98 219-272 (328)
94 CHL00142 rps17 ribosomal prote 29.3 34 0.00073 23.9 1.4 12 87-98 50-61 (84)
95 PRK11041 DNA-binding transcrip 29.0 83 0.0018 24.4 3.7 39 60-98 194-247 (309)
96 PRK10461 thiamine biosynthesis 29.0 21 0.00046 30.4 0.4 31 65-98 190-220 (350)
97 PRK15102 trimethylamine N-oxid 28.9 47 0.001 31.1 2.6 17 81-97 717-733 (825)
98 cd01799 Hoil1_N Ubiquitin-like 28.6 52 0.0011 21.9 2.2 17 81-97 56-73 (75)
99 COG3127 Predicted ABC-type tra 28.6 48 0.001 32.0 2.6 25 81-105 144-168 (829)
100 COG2179 Predicted hydrolase of 28.4 26 0.00057 27.8 0.8 48 50-102 74-122 (175)
101 PF13180 PDZ_2: PDZ domain; PD 28.2 35 0.00075 22.2 1.2 19 83-101 27-46 (82)
102 COG0828 RpsU Ribosomal protein 28.1 72 0.0016 21.6 2.7 25 64-88 13-37 (67)
103 cd06308 PBP1_sensor_kinase_lik 27.0 95 0.0021 23.5 3.7 20 77-97 195-214 (270)
104 TIGR03089 conserved hypothetic 27.0 61 0.0013 25.3 2.6 17 81-97 42-59 (227)
105 COG0380 OtsA Trehalose-6-phosp 26.9 15 0.00032 33.3 -1.0 41 87-127 144-184 (486)
106 TIGR00638 Mop molybdenum-pteri 26.7 73 0.0016 19.7 2.5 16 81-96 42-57 (69)
107 PTZ00241 40S ribosomal protein 26.7 38 0.00083 26.5 1.4 12 87-98 116-127 (158)
108 cd01808 hPLIC_N Ubiquitin-like 26.6 63 0.0014 20.6 2.2 16 81-96 53-68 (71)
109 PF06253 MTTB: Trimethylamine 26.6 83 0.0018 28.4 3.7 50 48-97 22-85 (505)
110 cd06313 PBP1_ABC_sugar_binding 26.5 1E+02 0.0023 23.7 3.8 36 60-97 164-214 (272)
111 cd00991 PDZ_archaeal_metallopr 26.5 46 0.001 21.6 1.6 21 82-102 22-43 (79)
112 PF14053 DUF4248: Domain of un 26.5 1.9E+02 0.004 19.3 4.6 50 45-94 1-53 (69)
113 PF01982 CTP-dep_RFKase: Domai 26.5 46 0.001 24.8 1.7 11 86-96 109-119 (121)
114 PF12990 DUF3874: Domain of un 26.3 33 0.00072 23.4 0.9 47 41-87 21-68 (73)
115 cd06303 PBP1_LuxPQ_Quorum_Sens 26.2 53 0.0011 25.4 2.1 37 60-97 171-222 (280)
116 cd00990 PDZ_glycyl_aminopeptid 26.1 54 0.0012 20.7 1.9 19 83-101 25-44 (80)
117 PF06300 Tsp45I: Tsp45I type I 25.8 68 0.0015 27.0 2.8 29 62-90 85-113 (261)
118 PF02073 Peptidase_M29: Thermo 25.8 90 0.0019 27.2 3.6 28 63-97 3-30 (398)
119 PRK00285 ihfA integration host 25.6 73 0.0016 21.9 2.5 43 51-100 8-50 (99)
120 PF04724 Glyco_transf_17: Glyc 25.5 73 0.0016 27.5 3.0 21 80-100 168-188 (356)
121 cd06301 PBP1_rhizopine_binding 25.5 52 0.0011 24.9 2.0 21 77-97 196-216 (272)
122 PRK15488 thiosulfate reductase 25.4 58 0.0013 30.0 2.5 18 81-98 673-690 (759)
123 PF10410 DnaB_bind: DnaB-helic 25.3 1E+02 0.0023 18.6 3.0 26 51-76 5-30 (59)
124 TIGR00353 nrfE c-type cytochro 25.3 70 0.0015 29.5 3.0 22 87-108 456-477 (576)
125 PLN02654 acetate-CoA ligase 25.3 64 0.0014 29.0 2.7 19 79-97 133-151 (666)
126 PRK03760 hypothetical protein; 25.0 64 0.0014 23.5 2.3 16 82-97 100-115 (117)
127 cd06293 PBP1_LacI_like_11 Liga 24.8 1.2E+02 0.0027 22.8 3.9 24 77-100 190-213 (269)
128 TIGR00509 bisC_fam molybdopter 24.8 61 0.0013 30.0 2.6 18 81-98 664-681 (770)
129 TIGR01217 ac_ac_CoA_syn acetoa 24.5 68 0.0015 28.7 2.7 19 79-97 127-145 (652)
130 PF13242 Hydrolase_like: HAD-h 24.5 48 0.001 21.2 1.4 21 79-99 10-30 (75)
131 PF12143 PPO1_KFDV: Protein of 24.4 55 0.0012 24.5 1.8 21 75-95 89-109 (130)
132 PF07775 PaRep2b: PaRep2b prot 24.4 4.2E+02 0.0091 24.5 7.6 85 18-105 295-404 (512)
133 PF08922 DUF1905: Domain of un 24.3 65 0.0014 21.7 2.0 20 77-96 58-78 (80)
134 cd04867 TGS_YchF_C TGS_YchF_C: 24.2 85 0.0018 22.1 2.6 9 88-96 73-81 (83)
135 PRK10113 cell division modulat 24.1 47 0.001 23.0 1.3 37 43-79 35-77 (80)
136 cd06274 PBP1_FruR Ligand bindi 24.0 1.3E+02 0.0028 22.7 3.9 23 76-98 190-212 (264)
137 COG2411 Uncharacterized conser 24.0 1.2E+02 0.0025 24.5 3.7 29 79-109 82-112 (188)
138 PRK10050 curli assembly protei 24.0 2.7E+02 0.0059 21.3 5.5 46 61-106 62-107 (138)
139 PRK10377 PTS system glucitol/s 23.9 80 0.0017 23.3 2.6 17 87-103 51-67 (120)
140 PF10431 ClpB_D2-small: C-term 23.9 1.4E+02 0.003 19.4 3.6 20 77-96 62-81 (81)
141 cd01815 BMSC_UbP_N Ubiquitin-l 23.8 74 0.0016 21.7 2.3 17 80-96 56-72 (75)
142 TIGR02166 dmsA_ynfE anaerobic 23.8 52 0.0011 30.4 1.9 18 81-98 712-729 (797)
143 COG0611 ThiL Thiamine monophos 23.8 53 0.0012 28.1 1.9 18 81-98 141-158 (317)
144 cd01809 Scythe_N Ubiquitin-lik 23.6 79 0.0017 19.6 2.2 17 80-96 53-69 (72)
145 TIGR00849 gutA PTS system, glu 23.3 84 0.0018 23.3 2.6 17 87-103 51-67 (121)
146 COG2002 AbrB Regulators of sta 23.3 67 0.0014 22.0 2.0 15 84-98 24-38 (89)
147 TIGR02254 YjjG/YfnB HAD superf 23.2 71 0.0015 23.7 2.3 20 80-99 159-179 (224)
148 PF11302 DUF3104: Protein of u 23.2 58 0.0013 22.6 1.6 14 87-100 5-18 (75)
149 PRK06342 transcription elongat 23.1 89 0.0019 24.0 2.8 16 87-102 140-155 (160)
150 TIGR01509 HAD-SF-IA-v3 haloaci 23.1 87 0.0019 22.3 2.6 21 80-100 147-167 (183)
151 cd01810 ISG15_repeat2 ISG15 ub 23.0 81 0.0018 20.3 2.3 16 81-96 52-67 (74)
152 PF14250 AbrB-like: AbrB-like 23.0 69 0.0015 22.0 1.9 13 84-96 49-61 (71)
153 PF04246 RseC_MucC: Positive r 22.9 54 0.0012 23.7 1.5 14 84-97 48-61 (135)
154 cd06297 PBP1_LacI_like_12 Liga 22.8 1.2E+02 0.0025 23.2 3.5 23 77-99 193-215 (269)
155 TIGR01923 menE O-succinylbenzo 22.8 81 0.0018 25.6 2.7 17 81-97 14-30 (436)
156 cd01803 Ubiquitin Ubiquitin. U 22.7 83 0.0018 19.7 2.2 16 81-96 54-69 (76)
157 PRK14132 riboflavin kinase; Pr 22.7 67 0.0014 24.1 2.0 11 86-96 114-124 (126)
158 TIGR02316 propion_prpE propion 22.6 79 0.0017 27.9 2.8 19 79-97 96-114 (628)
159 cd00591 HU_IHF Integration hos 22.6 1E+02 0.0022 20.1 2.7 43 51-100 5-47 (87)
160 cd08188 Fe-ADH4 Iron-containin 22.4 70 0.0015 27.1 2.3 43 50-92 295-346 (377)
161 PF02424 ApbE: ApbE family; I 22.3 23 0.00051 28.5 -0.6 32 65-99 117-148 (254)
162 COG1021 EntE Peptide arylation 22.3 63 0.0014 29.6 2.1 17 80-96 67-83 (542)
163 cd01540 PBP1_arabinose_binding 22.2 65 0.0014 24.7 1.9 22 76-97 206-227 (289)
164 COG4043 Preprotein translocase 22.2 74 0.0016 23.6 2.1 15 84-98 30-44 (111)
165 TIGR03145 cyt_nit_nrfE cytochr 22.0 95 0.0021 29.0 3.2 44 67-110 481-536 (628)
166 PLN00045 photosystem I reactio 22.0 75 0.0016 23.2 2.0 21 86-106 38-58 (101)
167 cd01807 GDX_N ubiquitin-like d 22.0 88 0.0019 20.1 2.3 17 80-96 53-69 (74)
168 PF00240 ubiquitin: Ubiquitin 21.9 41 0.0009 20.9 0.7 16 81-96 49-64 (69)
169 PRK10369 heme lyase subunit Nr 21.9 86 0.0019 29.0 2.9 44 67-110 417-472 (571)
170 cd06280 PBP1_LacI_like_4 Ligan 21.8 63 0.0014 24.4 1.8 41 60-100 153-208 (263)
171 cd00136 PDZ PDZ domain, also c 21.7 69 0.0015 19.6 1.7 17 85-101 28-45 (70)
172 cd01800 SF3a120_C Ubiquitin-li 21.7 87 0.0019 20.3 2.2 16 81-96 51-66 (76)
173 PF01041 DegT_DnrJ_EryC1: DegT 21.7 1.3E+02 0.0027 25.0 3.7 25 77-101 51-75 (363)
174 TIGR03354 VI_FHA type VI secre 21.6 97 0.0021 27.0 3.1 18 88-105 86-103 (396)
175 TIGR02693 arsenite_ox_L arseni 21.5 77 0.0017 30.0 2.6 17 81-97 732-748 (806)
176 PF13419 HAD_2: Haloacid dehal 21.4 65 0.0014 22.2 1.6 20 80-99 140-159 (176)
177 PRK05609 nusG transcription an 21.4 84 0.0018 23.5 2.4 34 64-98 104-137 (181)
178 PF15007 CEP44: Centrosomal sp 21.3 41 0.00088 25.5 0.6 30 64-93 3-32 (131)
179 PRK03584 acetoacetyl-CoA synth 21.2 88 0.0019 27.7 2.8 19 79-97 127-145 (655)
180 PF05896 NQRA: Na(+)-transloca 21.2 85 0.0018 26.3 2.5 18 85-102 42-59 (257)
181 PRK13532 nitrate reductase cat 21.1 64 0.0014 30.2 2.0 17 81-97 753-769 (830)
182 cd01806 Nedd8 Nebb8-like ubiq 21.1 94 0.002 19.4 2.2 16 81-96 54-69 (76)
183 COG4766 EutQ Ethanolamine util 20.9 68 0.0015 25.5 1.8 13 85-97 137-149 (176)
184 PRK10524 prpE propionyl-CoA sy 20.8 91 0.002 27.3 2.7 18 80-97 98-115 (629)
185 PLN02860 o-succinylbenzoate-Co 20.7 90 0.002 26.9 2.7 19 79-97 45-63 (563)
186 cd06285 PBP1_LacI_like_7 Ligan 20.3 72 0.0016 24.1 1.8 21 77-97 188-208 (265)
187 COG1827 Predicted small molecu 20.3 1.6E+02 0.0035 23.1 3.8 30 45-78 101-130 (168)
188 TIGR02369 trimeth_pyl trimethy 20.3 1E+02 0.0022 28.0 2.9 26 72-97 33-68 (489)
189 cd00987 PDZ_serine_protease PD 20.2 72 0.0016 20.3 1.6 20 83-102 37-57 (90)
190 cd06324 PBP1_ABC_sugar_binding 20.1 65 0.0014 25.4 1.6 23 77-99 215-237 (305)
191 PRK09798 antitoxin MazE; Provi 20.1 95 0.0021 21.3 2.2 15 82-96 21-35 (82)
No 1
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=99.96 E-value=2.3e-29 Score=169.44 Aligned_cols=69 Identities=45% Similarity=0.672 Sum_probs=60.5
Q ss_pred cEEEEcCCCCeEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEEEEE
Q 044269 34 FEIFHDSGSNTWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDMEMVW 103 (129)
Q Consensus 34 f~I~k~~e~g~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~EFey 103 (129)
|+|+++ ++|+|+|+|++||++++||||+++||+.||+++|+++||+++|+++||++||||+||++||+|
T Consensus 1 F~I~~~-~~g~~~V~g~~ie~~~~~~~~~~~e~~~rf~~~L~~~Gv~~~L~~~G~~~GD~V~Ig~~eFe~ 69 (69)
T PF09269_consen 1 FEIERE-DEGVFVVEGPKIERLVAMTNFDDEESLRRFQRKLKKMGVEKALRKAGAKEGDTVRIGDYEFEY 69 (69)
T ss_dssp -EEEEE-ETTEEEEE-HHHHHHHTTEEE-TGGGHHHHHHHHHHTTHHHHHHTTT--TT-EEEETTEEEE-
T ss_pred CEEEEc-CCceEEEEChHHHHHHHhcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEcCEEEEC
Confidence 789997 579999999999999999999999999999999999999999999999999999999999998
No 2
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=99.96 E-value=9.4e-29 Score=166.64 Aligned_cols=69 Identities=39% Similarity=0.658 Sum_probs=66.2
Q ss_pred cEEEEcCCCCeEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEEEEE
Q 044269 34 FEIFHDSGSNTWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDMEMVW 103 (129)
Q Consensus 34 f~I~k~~e~g~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~EFey 103 (129)
|+|++. ++|+|+|+|++|||+++||||+++||+.||+++|+++||+++|+++||++||||+||++||+|
T Consensus 1 f~i~~~-~~~~~~V~g~~ier~~~~~~~~~~e~~~~f~~~L~~~Gv~~~L~~~G~~~GD~V~Ig~~eFe~ 69 (69)
T TIGR03595 1 FEIERD-EDGVFVVSGKKIERWVAKTPFNNDENLRRFARKLKKLGVEDALRKAGAKDGDTVRIGDFEFEW 69 (69)
T ss_pred CEEEEC-CCCeEEEechHHHHHHHHcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEccEEEeC
Confidence 578886 578999999999999999999999999999999999999999999999999999999999997
No 3
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=99.83 E-value=1.7e-20 Score=161.81 Aligned_cols=73 Identities=38% Similarity=0.632 Sum_probs=69.1
Q ss_pred CCcEEEEcCCCCeEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEEEEEEe
Q 044269 32 NDFEIFHDSGSNTWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDMEMVWHD 105 (129)
Q Consensus 32 ~~f~I~k~~e~g~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~EFey~e 105 (129)
++|.|.+. ++|.|+|.|++||++++||||+++|++.||+++|+++||+++|+++||++||+|+||++||+|++
T Consensus 352 ~~~~~~~~-~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~gv~~~l~~~g~~~gd~v~i~~~~f~~~~ 424 (424)
T PRK12297 352 KDFTITRD-EDGVFVVSGEKIERLFKMTNFNRDESLRRFARQLRKMGVDDALREAGAKDGDTVRIGDFEFEFVD 424 (424)
T ss_pred CCcEEEEC-CCCcEEEeChHHHHHHhhccCCCHHHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEECCEEEEEeC
Confidence 46888876 57899999999999999999999999999999999999999999999999999999999999974
No 4
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=99.80 E-value=2.2e-19 Score=157.97 Aligned_cols=76 Identities=25% Similarity=0.488 Sum_probs=71.1
Q ss_pred CCcEEEEcCCC--CeEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEc---CEEEEEEec
Q 044269 32 NDFEIFHDSGS--NTWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVG---DMEMVWHDS 106 (129)
Q Consensus 32 ~~f~I~k~~e~--g~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IG---d~EFey~ed 106 (129)
..|+|.++ ++ |.|+|.|+++|||++||||+++||+.||+++|+++||+++|+++||++||+|+|| +++|+|++.
T Consensus 364 ~~~~i~~~-~~~~~~~~v~g~~~e~~~~~~~~~~~e~~~~~~~~l~~~gv~~~l~~~g~~~gd~v~i~~~~~~~f~~~~~ 442 (500)
T PRK12296 364 AGFTVERD-GDGEGGFRVRGEKPERWVRQTDFDNDEAVGYLADRLARLGVEDELLKAGARPGDAVTIGTGNGVVFDWEPT 442 (500)
T ss_pred CCcEEEeC-CCCCCcEEEeCchHHHHHhccCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEECCCCCEEEEEeec
Confidence 35899886 45 8999999999999999999999999999999999999999999999999999999 999999987
Q ss_pred CC
Q 044269 107 AN 108 (129)
Q Consensus 107 ~~ 108 (129)
..
T Consensus 443 ~~ 444 (500)
T PRK12296 443 TP 444 (500)
T ss_pred cc
Confidence 54
No 5
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=86.03 E-value=0.87 Score=31.97 Aligned_cols=15 Identities=40% Similarity=0.507 Sum_probs=13.1
Q ss_pred HHHcCCCCCCEEEEc
Q 044269 83 LMKLGVKEGDTVIVG 97 (129)
Q Consensus 83 LkkaGakeGDtV~IG 97 (129)
-+..||+.||.|+|=
T Consensus 50 a~~lgak~GdvVkIv 64 (80)
T COG2012 50 AKALGAKPGDVVKIV 64 (80)
T ss_pred HHHccCCCCcEEEEE
Confidence 577899999999984
No 6
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=76.88 E-value=2.4 Score=28.97 Aligned_cols=17 Identities=47% Similarity=0.691 Sum_probs=12.7
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 37 ~dA~~~Gi~~Gd~V~v~ 53 (110)
T PF01568_consen 37 EDAAKLGIKDGDWVRVS 53 (110)
T ss_dssp HHHHHCT--TTCEEEEE
T ss_pred HHHHHhcCcCCCEEEEE
Confidence 55688999999999993
No 7
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=71.10 E-value=4.6 Score=28.12 Aligned_cols=44 Identities=9% Similarity=0.122 Sum_probs=25.1
Q ss_pred EEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEE
Q 044269 46 NVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 46 ~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~I 96 (129)
+++-...+.++++++..... |=+++..== ..+..|++.||.|+|
T Consensus 17 iLs~eE~~~lL~~y~i~~~q----LP~I~~~DP---v~r~~g~k~GdVvkI 60 (79)
T PRK09570 17 ILSEEEAKKLLKEYGIKPEQ----LPKIKASDP---VVKAIGAKPGDVIKI 60 (79)
T ss_pred ECCHHHHHHHHHHcCCCHHH----CCceeccCh---hhhhcCCCCCCEEEE
Confidence 44455666677777655322 222222211 223449999999999
No 8
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=69.24 E-value=4.7 Score=27.98 Aligned_cols=17 Identities=35% Similarity=0.649 Sum_probs=13.8
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.||++||.|+|.
T Consensus 38 ~dA~~lgI~dGd~V~v~ 54 (112)
T cd02787 38 DDIARLGLKAGDRVDLE 54 (112)
T ss_pred HHHHHhCCCCCCEEEEE
Confidence 34567799999999985
No 9
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=67.17 E-value=5.7 Score=27.99 Aligned_cols=17 Identities=41% Similarity=0.628 Sum_probs=14.7
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+...+.|+++||.|+|.
T Consensus 40 ~dA~~~gi~~Gd~V~v~ 56 (130)
T cd02781 40 ETAAKLGIADGDWVWVE 56 (130)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 56788899999999985
No 10
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=66.93 E-value=29 Score=29.21 Aligned_cols=63 Identities=24% Similarity=0.340 Sum_probs=47.2
Q ss_pred EEEcCCCCeEEEEcchHHHHHHhcCCCCHHHHHHHHH----HHHHCChHHHHHHcCCCCCCEEEEc---CEEEEEE
Q 044269 36 IFHDSGSNTWNVVGAGLQRFVQMTNWRYLDSERRFQH----GLEACGVTKSLMKLGVKEGDTVIVG---DMEMVWH 104 (129)
Q Consensus 36 I~k~~e~g~f~V~G~~IEr~v~~tnfd~~es~~rF~r----~Lk~~GV~~aLkkaGakeGDtV~IG---d~EFey~ 104 (129)
|.+. ..|.|+|+=+..|.+.+.++ .+++|.+ .|...-++.|.-+.-|++||+|... ++-+-+.
T Consensus 55 i~~~-gR~~Y~iTkkG~e~l~~~~~-----dlr~f~~ev~~~l~~~~vw~AIA~edI~~Gd~V~L~M~dG~LyA~~ 124 (260)
T COG1497 55 IEKE-GRGEYEITKKGAEWLLEQLS-----DLRRFSEEVELVLDYVMVWTAIAKEDIKEGDTVYLRMKDGYLYASR 124 (260)
T ss_pred eeec-CCeeEEEehhHHHHHHHHHH-----HHHHHHHHHHHHHhhHHHHHHhhHhhhccCCEEEEEecCcEEEEec
Confidence 4443 36689999999999987764 5555554 4577889999999999999999873 5555543
No 11
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=65.54 E-value=6.3 Score=27.20 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=14.1
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 38 ~dA~~lgi~~Gd~V~v~ 54 (116)
T cd02786 38 ADAAARGIADGDLVVVF 54 (116)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45677899999999984
No 12
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=64.50 E-value=4 Score=27.15 Aligned_cols=29 Identities=28% Similarity=0.368 Sum_probs=21.4
Q ss_pred hHHHHHHcCCCCCCEEEE-cCEEEEEEecC
Q 044269 79 VTKSLMKLGVKEGDTVIV-GDMEMVWHDSA 107 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~I-Gd~EFey~ed~ 107 (129)
|...+--.||++||.+.| .+..|...++.
T Consensus 25 vp~~~LP~~~keGDvl~i~~~~~~~~d~ee 54 (71)
T PF11213_consen 25 VPRSRLPEGAKEGDVLEIGEDGSIEIDPEE 54 (71)
T ss_pred EEHHHCCCCCCcccEEEECCCceEEECHHH
Confidence 344455579999999999 78788775543
No 13
>TIGR00030 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.
Probab=63.75 E-value=11 Score=24.57 Aligned_cols=23 Identities=35% Similarity=0.455 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHCChHHHHHHc
Q 044269 64 LDSERRFQHGLEACGVTKSLMKL 86 (129)
Q Consensus 64 ~es~~rF~r~Lk~~GV~~aLkka 86 (129)
+.++.+|.+.+.+-||.+.+++.
T Consensus 12 e~alrrfkr~~~~~gil~e~r~r 34 (58)
T TIGR00030 12 DSALRRFKRKLEKEGILRELKKR 34 (58)
T ss_pred HHHHHHHHHHHHHcchHHHHHHH
Confidence 46889999999999999999864
No 14
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=62.98 E-value=7.6 Score=26.90 Aligned_cols=17 Identities=47% Similarity=0.687 Sum_probs=14.6
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 42 ~dA~~lgi~~Gd~V~v~ 58 (122)
T cd02791 42 EDAARLGLKEGDLVRVT 58 (122)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45788999999999984
No 15
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=62.88 E-value=7.7 Score=26.56 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=14.8
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+-.++.|+++||.|+|..
T Consensus 42 ~dA~~lgi~~Gd~V~v~~ 59 (116)
T cd02790 42 EDAKRLGIEDGEKVRVSS 59 (116)
T ss_pred HHHHHcCCCCCCEEEEEc
Confidence 446788999999999853
No 16
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=62.79 E-value=7.7 Score=26.57 Aligned_cols=18 Identities=39% Similarity=0.693 Sum_probs=14.9
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+..++.|+++||.|+|..
T Consensus 42 ~dA~~lgi~~Gd~V~v~~ 59 (120)
T cd00508 42 EDAARLGIKDGDLVRVSS 59 (120)
T ss_pred HHHHHcCCCCCCEEEEEe
Confidence 456788999999999853
No 17
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=61.46 E-value=8.1 Score=27.34 Aligned_cols=17 Identities=35% Similarity=0.382 Sum_probs=14.6
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 41 ~dA~~lgi~~Gd~V~v~ 57 (127)
T cd02777 41 LDAAARGIKDGDIVRVF 57 (127)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 55778999999999984
No 18
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=60.20 E-value=8.8 Score=27.04 Aligned_cols=17 Identities=29% Similarity=0.270 Sum_probs=14.4
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 39 ~dA~~~gi~~Gd~V~v~ 55 (124)
T cd02785 39 IDAAARGIAHGDLVEVY 55 (124)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45678899999999985
No 19
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=59.93 E-value=9.5 Score=26.69 Aligned_cols=17 Identities=41% Similarity=0.493 Sum_probs=14.4
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 38 ~dA~~lgi~~Gd~V~v~ 54 (106)
T cd02789 38 EDYKLLGKPEGDKVKVT 54 (106)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45788899999999884
No 20
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=59.86 E-value=9.1 Score=26.87 Aligned_cols=17 Identities=35% Similarity=0.491 Sum_probs=14.1
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|-
T Consensus 37 ~~A~~~gi~~Gd~V~v~ 53 (121)
T cd02794 37 LDAAARGIKDGDRVLVF 53 (121)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 34678899999999984
No 21
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=59.13 E-value=10 Score=25.08 Aligned_cols=17 Identities=41% Similarity=0.640 Sum_probs=13.9
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|.|.
T Consensus 30 ~da~~lgl~~Gd~v~v~ 46 (101)
T cd02775 30 EDAAALGIKDGDLVRVE 46 (101)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 34668899999999874
No 22
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.97 E-value=10 Score=28.14 Aligned_cols=17 Identities=41% Similarity=0.454 Sum_probs=14.5
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 38 ~dA~~lgI~dGd~V~v~ 54 (141)
T cd02776 38 KDAAELGIKDNDWVEVF 54 (141)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45788899999999984
No 23
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=57.60 E-value=11 Score=25.72 Aligned_cols=16 Identities=31% Similarity=0.567 Sum_probs=13.4
Q ss_pred HHHHcCCCCCCEEEEc
Q 044269 82 SLMKLGVKEGDTVIVG 97 (129)
Q Consensus 82 aLkkaGakeGDtV~IG 97 (129)
..++.|+++||.|+|.
T Consensus 37 dA~~lGi~~Gd~V~v~ 52 (96)
T cd02788 37 DAARLGLADGDLVEFS 52 (96)
T ss_pred HHHHcCCCCCCEEEEE
Confidence 4677899999999984
No 24
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.59 E-value=11 Score=26.08 Aligned_cols=17 Identities=35% Similarity=0.513 Sum_probs=14.2
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+.-++.|+++||.|+|.
T Consensus 42 ~dA~~lgi~~Gd~V~v~ 58 (122)
T cd02792 42 ELAAERGIKNGDMVWVS 58 (122)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 35678899999999985
No 25
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.53 E-value=11 Score=26.97 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=14.6
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+...+.|+++||.|+|.+
T Consensus 40 ~dA~~~gi~~Gd~V~v~s 57 (129)
T cd02793 40 ADAAARGIADGDIVRVFN 57 (129)
T ss_pred HHHHHcCCCCCCEEEEEc
Confidence 346788999999999853
No 26
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.18 E-value=10 Score=28.23 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.7
Q ss_pred HHHHHHcCCCCCCEEEEc
Q 044269 80 TKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IG 97 (129)
-+...+.||++||.|+|.
T Consensus 44 P~dA~~lGI~dGD~V~V~ 61 (137)
T cd02784 44 PRTAEALGLLQGDVVRIR 61 (137)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 355677799999999995
No 27
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=57.01 E-value=16 Score=24.18 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHCChHHHHHHc
Q 044269 64 LDSERRFQHGLEACGVTKSLMKL 86 (129)
Q Consensus 64 ~es~~rF~r~Lk~~GV~~aLkka 86 (129)
+.|+.+|.+.+.+-||...+++.
T Consensus 13 e~Alrrfkr~~~k~gil~e~r~r 35 (64)
T PRK00270 13 DKALRRFKRKVEKAGILRELRRR 35 (64)
T ss_pred HHHHHHHHHHHHHcchHHHHHHH
Confidence 46889999999999999998863
No 28
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=56.97 E-value=10 Score=28.28 Aligned_cols=18 Identities=44% Similarity=0.656 Sum_probs=15.1
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+..++.||++||.|+|..
T Consensus 39 ~dA~~~GI~dGd~V~v~s 56 (156)
T cd02783 39 KTAKELGIKDGDWVWVES 56 (156)
T ss_pred HHHHHcCCCCCCEEEEEc
Confidence 556788999999999963
No 29
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=55.99 E-value=14 Score=22.28 Aligned_cols=15 Identities=47% Similarity=0.607 Sum_probs=12.0
Q ss_pred HHHHcCCCCCCEEEE
Q 044269 82 SLMKLGVKEGDTVIV 96 (129)
Q Consensus 82 aLkkaGakeGDtV~I 96 (129)
-+++.|+++||.|.|
T Consensus 15 ~~~~l~l~~Gd~v~i 29 (47)
T PF04014_consen 15 IREKLGLKPGDEVEI 29 (47)
T ss_dssp HHHHTTSSTTTEEEE
T ss_pred HHHHcCCCCCCEEEE
Confidence 356679999999875
No 30
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=55.68 E-value=12 Score=26.20 Aligned_cols=17 Identities=35% Similarity=0.425 Sum_probs=14.2
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..++.|+++||.|+|.
T Consensus 40 ~dA~~lgi~~Gd~V~v~ 56 (115)
T cd02779 40 EDAKREGLKNGDLVEVY 56 (115)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45678899999999984
No 31
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=55.42 E-value=12 Score=25.95 Aligned_cols=16 Identities=44% Similarity=0.798 Sum_probs=13.6
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+...+.|+++||.|+|
T Consensus 37 ~dA~~~gi~~Gd~V~v 52 (123)
T cd02778 37 ETAARLGIKDGDRVEV 52 (123)
T ss_pred HHHHHcCCCCCCEEEE
Confidence 3467789999999998
No 32
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=54.00 E-value=11 Score=28.52 Aligned_cols=17 Identities=47% Similarity=0.731 Sum_probs=13.5
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+-|++.|+++||+|++-
T Consensus 38 ~D~~~Lgv~EGD~VkVk 54 (128)
T COG1153 38 EDMKQLGVSEGDKVKVK 54 (128)
T ss_pred HHHHHhCCCcCCeEEEE
Confidence 44666799999999973
No 33
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=53.95 E-value=10 Score=26.05 Aligned_cols=14 Identities=43% Similarity=0.496 Sum_probs=9.5
Q ss_pred HHcCCCCCCEEEEc
Q 044269 84 MKLGVKEGDTVIVG 97 (129)
Q Consensus 84 kkaGakeGDtV~IG 97 (129)
+-.|++.||.|+|-
T Consensus 45 r~~g~k~GdVvkI~ 58 (74)
T PF01191_consen 45 RYLGAKPGDVVKII 58 (74)
T ss_dssp HHTT--TTSEEEEE
T ss_pred hhcCCCCCCEEEEE
Confidence 33499999999994
No 34
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=52.78 E-value=14 Score=26.08 Aligned_cols=17 Identities=35% Similarity=0.552 Sum_probs=14.2
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+...+.|+++||.|+|-
T Consensus 40 ~dA~~~gi~~Gd~V~v~ 56 (129)
T cd02782 40 DDAAALGLADGDKVRVT 56 (129)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45678899999999984
No 35
>COG2746 Aminoglycoside N3'-acetyltransferase [Defense mechanisms]
Probab=52.59 E-value=13 Score=31.15 Aligned_cols=25 Identities=48% Similarity=0.634 Sum_probs=20.0
Q ss_pred HHHHCChHHHHHHcCCCCCCEEEEc
Q 044269 73 GLEACGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 73 ~Lk~~GV~~aLkkaGakeGDtV~IG 97 (129)
..-+.-+.+.|++.|+|+||||.+.
T Consensus 11 ~~s~~~l~~~l~~lG~k~G~~v~vH 35 (251)
T COG2746 11 PRSSQDLKDDLYKLGLKEGDTVIVH 35 (251)
T ss_pred cccHHHHHHHHHHhcCCCCCEEEEe
Confidence 3344557889999999999999875
No 36
>PF03990 DUF348: Domain of unknown function (DUF348) ; InterPro: IPR007137 This domain normally occurs as tandem repeats; however it is found as a single copy in the Saccharomyces cerevisiae (Baker's yeast) DNA-binding nuclear protein YCR593 (P25357 from SWISSPROT).
Probab=51.26 E-value=16 Score=21.86 Aligned_cols=19 Identities=37% Similarity=0.522 Sum_probs=14.3
Q ss_pred CChHHHHHHcCCC--CCCEEE
Q 044269 77 CGVTKSLMKLGVK--EGDTVI 95 (129)
Q Consensus 77 ~GV~~aLkkaGak--eGDtV~ 95 (129)
.-|.++|+++||. +.|.|.
T Consensus 18 ~tV~~~L~~~gI~l~~~D~v~ 38 (43)
T PF03990_consen 18 STVGDALKELGITLGEEDKVS 38 (43)
T ss_pred CCHHHHHHhCCCCCCCCCEEe
Confidence 3477889999988 777764
No 37
>PF10015 DUF2258: Uncharacterized protein conserved in archaea (DUF2258); InterPro: IPR017140 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=48.75 E-value=19 Score=25.00 Aligned_cols=34 Identities=18% Similarity=0.149 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHHHHCChHHHHH-HcCCCCCCEEEEc
Q 044269 63 YLDSERRFQHGLEACGVTKSLM-KLGVKEGDTVIVG 97 (129)
Q Consensus 63 ~~es~~rF~r~Lk~~GV~~aLk-kaGakeGDtV~IG 97 (129)
.++-+.|=.-.|.+. +.+.|. ++|+..||.|+|-
T Consensus 29 ~~~ei~ra~aeLNk~-ly~~lv~~~~i~K~DVVRI~ 63 (75)
T PF10015_consen 29 PPEEIVRAAAELNKK-LYEKLVNKMKIDKLDVVRIR 63 (75)
T ss_pred CHHHHHHHHHHHHHH-HHHHHHHHhCCCcccEEEEE
Confidence 444444444444443 566777 9999999999973
No 38
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=47.36 E-value=19 Score=30.34 Aligned_cols=20 Identities=45% Similarity=0.594 Sum_probs=15.1
Q ss_pred HHHHHHcCCCCCCEEEEcCE
Q 044269 80 TKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IGd~ 99 (129)
.+.|.++||..+|||.++|-
T Consensus 79 a~~~~~~GI~~d~tVVvYdd 98 (285)
T COG2897 79 AKLLGELGIRNDDTVVVYDD 98 (285)
T ss_pred HHHHHHcCCCCCCEEEEECC
Confidence 34556668889999999873
No 39
>COG0426 FpaA Uncharacterized flavoproteins [Energy production and conversion]
Probab=46.92 E-value=19 Score=31.74 Aligned_cols=22 Identities=27% Similarity=0.280 Sum_probs=18.9
Q ss_pred HcCCCCCCEEEEcCEEEEEEec
Q 044269 85 KLGVKEGDTVIVGDMEMVWHDS 106 (129)
Q Consensus 85 kaGakeGDtV~IGd~EFey~ed 106 (129)
-.=++.||++.||+.+++|.+.
T Consensus 121 ~~ivk~Gd~ldlGg~tL~Fi~a 142 (388)
T COG0426 121 FKIVKTGDTLDLGGHTLKFIPA 142 (388)
T ss_pred eeecCCCCEeccCCcEEEEEeC
Confidence 4458999999999999998765
No 40
>PRK15094 magnesium/cobalt efflux protein CorC; Provisional
Probab=45.43 E-value=1e+02 Score=25.46 Aligned_cols=57 Identities=14% Similarity=0.235 Sum_probs=37.6
Q ss_pred EEEcCCCCeEEEEcch-HHHHHHhcCCC----CHHHHHHHHHHHHHCChHHHHHHcCC--CCCCEEEEcCEEEEEE
Q 044269 36 IFHDSGSNTWNVVGAG-LQRFVQMTNWR----YLDSERRFQHGLEACGVTKSLMKLGV--KEGDTVIVGDMEMVWH 104 (129)
Q Consensus 36 I~k~~e~g~f~V~G~~-IEr~v~~tnfd----~~es~~rF~r~Lk~~GV~~aLkkaGa--keGDtV~IGd~EFey~ 104 (129)
|.+. ++|.|.|.|.- |+.+...++++ .++.+.=| + |...|- +.||+|.++++.|+-.
T Consensus 204 i~~~-~~~~~~v~G~~~l~dl~~~l~~~l~~~~~~Tl~G~--i---------~~~l~~iP~~Gd~i~~~~~~f~V~ 267 (292)
T PRK15094 204 FRQL-SRHTWTVRALASIEDFNEAFGTHFSDEEVDTIGGL--V---------MQAFGHLPARGETIDIDGYQFKVA 267 (292)
T ss_pred cEEe-CCCeEEEEeccCHHHHHHHhCCCCCCCCCccHHHH--H---------HHHhCcCCCCCCEEEECCEEEEEE
Confidence 5554 47899999974 66666666654 33344322 1 222243 8999999999999943
No 41
>PF01628 HrcA: HrcA protein C terminal domain; InterPro: IPR021153 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This entry represents the C terminus of HrcA, consisting of the GAF-like domain with the inserted dimerising domain.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1STZ_A.
Probab=45.04 E-value=32 Score=26.73 Aligned_cols=54 Identities=20% Similarity=0.245 Sum_probs=34.5
Q ss_pred CeEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHH-HHHcCCCCCCEEEEcC
Q 044269 43 NTWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKS-LMKLGVKEGDTVIVGD 98 (129)
Q Consensus 43 g~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~a-LkkaGakeGDtV~IGd 98 (129)
..+.+.| +.+++..-+|++.+.++.+.+.|+....... |...--.+|=.|+||.
T Consensus 129 ~~~~~~G--~~~ll~~pef~d~~~l~~ll~llE~~~~l~~ll~~~~~~~~i~V~IG~ 183 (224)
T PF01628_consen 129 ERVYVSG--LSNLLNQPEFSDPEKLRELLELLEDKKILLELLDSLSDDDGISVKIGS 183 (224)
T ss_dssp -SEEEE---HHHHHHSTT---HHHHHHHHHHTT-HHHHHHH-------SSSEEEEGG
T ss_pred ceeEEcC--HHHHcCCccccCHHHHHHHHHHHhCcHHHHHHHhhhccCCceEEEECC
Confidence 4578888 8899999999999999999999998885444 4444434566999984
No 42
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=44.99 E-value=82 Score=26.74 Aligned_cols=51 Identities=20% Similarity=0.201 Sum_probs=39.6
Q ss_pred eEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCC-hHHHHHHcCCCCCCEEEEcC
Q 044269 44 TWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACG-VTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 44 ~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~G-V~~aLkkaGakeGDtV~IGd 98 (129)
.+.+.| ..+++. .|++.+.++.|.+.|+... +.+.|.+....+|=.|+||+
T Consensus 232 ~~~~~G--~~nll~--ef~d~~~l~~ll~~le~~~~l~~ll~~~~~~~~v~V~IG~ 283 (339)
T PRK00082 232 RLIVAG--KANLLN--YLSDLERLRSLLDLLEEKQVLLQLLDESEEAEGVRIFIGS 283 (339)
T ss_pred eEEEeC--HHHHhh--hhccHHHHHHHHHHHhChHHHHHHHHhhccCCCcEEEEcC
Confidence 577888 778888 8999999999999997755 55666455555788899984
No 43
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=44.89 E-value=21 Score=23.20 Aligned_cols=16 Identities=44% Similarity=0.673 Sum_probs=14.1
Q ss_pred HHHHcCCCCCCEEEEc
Q 044269 82 SLMKLGVKEGDTVIVG 97 (129)
Q Consensus 82 aLkkaGakeGDtV~IG 97 (129)
.|...|+++||+|.++
T Consensus 55 ~L~~~gi~~~~~l~l~ 70 (71)
T cd01796 55 LLALYGVKDGDLVVLR 70 (71)
T ss_pred cHHHcCCCCCCEEEEe
Confidence 4888999999999886
No 44
>PRK11573 hypothetical protein; Provisional
Probab=44.54 E-value=90 Score=27.13 Aligned_cols=57 Identities=14% Similarity=0.252 Sum_probs=37.7
Q ss_pred EEEcCCCCeEEEEcc-hHHHHHHhcCCC----CHHHHHHHHHHHHHCChHHHHHHcCC--CCCCEEEEcCEEEEEE
Q 044269 36 IFHDSGSNTWNVVGA-GLQRFVQMTNWR----YLDSERRFQHGLEACGVTKSLMKLGV--KEGDTVIVGDMEMVWH 104 (129)
Q Consensus 36 I~k~~e~g~f~V~G~-~IEr~v~~tnfd----~~es~~rF~r~Lk~~GV~~aLkkaGa--keGDtV~IGd~EFey~ 104 (129)
+.+. ++|.|.|.|. .|+.+-+.++++ +++.+.=| | |...|- +.||++.++++.|+=.
T Consensus 326 i~~~-~~~~~~v~G~~~l~d~~~~l~~~l~~~~~~Tl~G~--------i---~~~lg~iP~~Ge~~~~~~~~f~V~ 389 (413)
T PRK11573 326 VTPQ-NDGSVIIDGTANVREINKAFNWHLPEDDARTVNGV--------I---LEALEEIPVAGTRVRIGEYDIDIL 389 (413)
T ss_pred eEEe-cCCEEEEEeeeEHHHHHHHhCCCCCCCCCeeHHHH--------H---HHHhCcCCCCCCEEEECCEEEEEE
Confidence 5554 4789999996 566666666654 23444333 1 222233 8999999999999843
No 45
>PLN02377 3-ketoacyl-CoA synthase
Probab=44.11 E-value=30 Score=31.25 Aligned_cols=45 Identities=16% Similarity=0.085 Sum_probs=39.5
Q ss_pred CcEEEEcCCCCeEEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCCh
Q 044269 33 DFEIFHDSGSNTWNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACGV 79 (129)
Q Consensus 33 ~f~I~k~~e~g~f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV 79 (129)
+|.-.+. +..++|.-..+-+.+.++..-++++++.+.|+|++.|+
T Consensus 102 d~~c~~p--~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~ri~~~sgi 146 (502)
T PLN02377 102 DYSCYRA--PDHLKAPFARFMEHSRLTGDFDDSSLEFQRKILERSGL 146 (502)
T ss_pred eeeeecC--CccccccHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCC
Confidence 6766674 45699999999999999998999999999999999999
No 46
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=43.43 E-value=23 Score=25.61 Aligned_cols=16 Identities=50% Similarity=0.642 Sum_probs=13.2
Q ss_pred HHHHcCCCCCCEEEEc
Q 044269 82 SLMKLGVKEGDTVIVG 97 (129)
Q Consensus 82 aLkkaGakeGDtV~IG 97 (129)
..++.|+++||.|+|.
T Consensus 38 dA~~lgI~~Gd~V~v~ 53 (143)
T cd02780 38 DAAKLGIKTGDRVRVV 53 (143)
T ss_pred HHHHcCCCCCCEEEEE
Confidence 4567899999999984
No 47
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=42.83 E-value=15 Score=26.13 Aligned_cols=12 Identities=33% Similarity=0.518 Sum_probs=10.5
Q ss_pred CCCCCCEEEEcC
Q 044269 87 GVKEGDTVIVGD 98 (129)
Q Consensus 87 GakeGDtV~IGd 98 (129)
-+++||+|+|..
T Consensus 55 ~~k~GD~V~I~E 66 (87)
T COG0186 55 EAKVGDIVRIAE 66 (87)
T ss_pred cCCCCCEEEEEE
Confidence 589999999975
No 48
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=41.16 E-value=23 Score=24.36 Aligned_cols=18 Identities=28% Similarity=0.481 Sum_probs=11.6
Q ss_pred HHHHHHcCCCCCCEEEEc
Q 044269 80 TKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IG 97 (129)
.+.+.+.|+++||+|.+.
T Consensus 67 ~~l~~~~~a~~GD~ll~~ 84 (95)
T PF02938_consen 67 KALIERLGAKPGDLLLFV 84 (95)
T ss_dssp HHHHHHTT--TTEEEEEE
T ss_pred HHHHHHhCCCCCCEEEEE
Confidence 344566699999999874
No 49
>TIGR03520 GldE gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype.
Probab=40.23 E-value=1.3e+02 Score=25.94 Aligned_cols=60 Identities=13% Similarity=0.170 Sum_probs=37.8
Q ss_pred EEEcCCCCeEEEEcc-hHHHHHHhcCCC---------CHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEEEEEEe
Q 044269 36 IFHDSGSNTWNVVGA-GLQRFVQMTNWR---------YLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDMEMVWHD 105 (129)
Q Consensus 36 I~k~~e~g~f~V~G~-~IEr~v~~tnfd---------~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~EFey~e 105 (129)
+.+. ++|.|.|.|. .|+.+.+.++++ +++.+.=| |.+.| .+=-+.||.|.++++.|+=.+
T Consensus 325 i~~~-~~~~~~v~G~~~l~~l~~~l~~~~~~~~~~~~~~~Tl~G~--------i~~~l-~~iP~~G~~~~~~~~~f~V~~ 394 (408)
T TIGR03520 325 YSKI-DDNNYVFEGKTSLKDFYKILKLEEDMFDEVKGEAETLAGF--------LLEIS-GGFPKKGEKITFENFEFTIEA 394 (408)
T ss_pred eEEe-CCCeEEEEeccCHHHHHHHhCCCccccCCcCCCCccHHHH--------HHHHh-CcCCCCCCEEEECCEEEEEEE
Confidence 5554 4789999964 677777777665 22333322 11222 111389999999999998433
No 50
>PF03471 CorC_HlyC: Transporter associated domain; InterPro: IPR005170 This small domain is found in a family of proteins with the CBS IPR002550 from INTERPRO domain and two CBS domains with this domain found at the C terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.; PDB: 3DED_F 2PLI_C 2R2Z_A 2P4P_A 2O3G_A 2P3H_A 3LLB_A 3LAE_A 2P13_B 2NQW_A ....
Probab=39.86 E-value=1.1e+02 Score=20.09 Aligned_cols=53 Identities=15% Similarity=0.152 Sum_probs=31.1
Q ss_pred CCCeEEEEcc-hHHHHHHhcCCCCHH----HHH-HHHHHHHHCChHHHHHHcCCCCCCEEEEc--CEEEEE
Q 044269 41 GSNTWNVVGA-GLQRFVQMTNWRYLD----SER-RFQHGLEACGVTKSLMKLGVKEGDTVIVG--DMEMVW 103 (129)
Q Consensus 41 e~g~f~V~G~-~IEr~v~~tnfd~~e----s~~-rF~r~Lk~~GV~~aLkkaGakeGDtV~IG--d~EFey 103 (129)
++|.|+|.|. .|+.+.+.++++-++ .+. ++...|. .=-+.||.|.|. +++|+=
T Consensus 4 ~~~~~~v~G~~~l~~l~~~~~~~l~~~~~~Tl~G~i~~~l~----------~iP~~Ge~~~i~~~~~~~~V 64 (81)
T PF03471_consen 4 DDGTYIVSGSTPLDDLNELLGLDLPEEDYDTLGGLILEQLG----------RIPEVGERVEIELENYEFEV 64 (81)
T ss_dssp TTSEEEEETTSBHHHHHHHHTS-TTTTTTSBHHHHHHHHHT----------SS--TTSEEEEEETTEEEEE
T ss_pred cCCEEEEEecCCHHHHHHHHCcCCCccchhhHHHHHHHHcC----------CCCCCCeEEEEEcCCEEEEE
Confidence 4789999996 466666666655322 232 2222222 223479977777 999984
No 51
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=39.63 E-value=29 Score=21.74 Aligned_cols=17 Identities=35% Similarity=0.620 Sum_probs=14.3
Q ss_pred HHHHHHcCCCCCCEEEE
Q 044269 80 TKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~I 96 (129)
.+.|...|+++|++|.+
T Consensus 52 ~~~L~~~~i~~g~~l~v 68 (71)
T cd01812 52 AETLDMSGVKDGSKVML 68 (71)
T ss_pred cCcHHHcCCCCCCEEEE
Confidence 44688999999999976
No 52
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=38.93 E-value=27 Score=22.65 Aligned_cols=16 Identities=44% Similarity=0.461 Sum_probs=13.0
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+-|+++|...||.|.|
T Consensus 31 ~WL~~aGF~~G~~v~V 46 (57)
T PF08845_consen 31 KWLEEAGFTIGDPVKV 46 (57)
T ss_pred hhhHHhCCCCCCEEEE
Confidence 3478889999998886
No 53
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=38.43 E-value=20 Score=24.17 Aligned_cols=12 Identities=33% Similarity=0.393 Sum_probs=10.3
Q ss_pred CCCCCCEEEEcC
Q 044269 87 GVKEGDTVIVGD 98 (129)
Q Consensus 87 GakeGDtV~IGd 98 (129)
.++.||+|.|..
T Consensus 48 ~~k~GD~V~I~e 59 (71)
T TIGR03635 48 ECKVGDVVRIIE 59 (71)
T ss_pred CCCCCCEEEEEE
Confidence 589999999974
No 54
>COG2015 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=37.63 E-value=35 Score=31.72 Aligned_cols=18 Identities=17% Similarity=0.475 Sum_probs=15.2
Q ss_pred CCCCEEEEcCEEEEEEec
Q 044269 89 KEGDTVIVGDMEMVWHDS 106 (129)
Q Consensus 89 keGDtV~IGd~EFey~ed 106 (129)
..|.++.|.+++|+|+-.
T Consensus 262 ~~gE~~~iDGV~~~Fq~t 279 (655)
T COG2015 262 ETGETLTIDGVEFEFQMT 279 (655)
T ss_pred ccCceEEEeceEEEEeeC
Confidence 468899999999999754
No 55
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=37.43 E-value=35 Score=21.04 Aligned_cols=16 Identities=44% Similarity=0.636 Sum_probs=10.8
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+++.+.|+++||.|.+
T Consensus 40 ~~~~~L~L~~G~~V~~ 55 (64)
T PF03459_consen 40 ESAEELGLKPGDEVYA 55 (64)
T ss_dssp HHHHHCT-STT-EEEE
T ss_pred HHHHHcCCCCCCEEEE
Confidence 4566779999999985
No 56
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=37.34 E-value=32 Score=23.14 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=19.5
Q ss_pred HHHHHcCCCCCCEEEEcCEE----EEEEecCC
Q 044269 81 KSLMKLGVKEGDTVIVGDME----MVWHDSAN 108 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd~E----Fey~ed~~ 108 (129)
+.+.+.|+..||+|.|.+-. |.|.....
T Consensus 23 ~~m~~l~l~~gd~v~i~g~~~tv~~v~~~~~~ 54 (87)
T PF02359_consen 23 EDMEELGLFPGDVVLISGKRKTVAFVFPDRPD 54 (87)
T ss_dssp HHHHCTTT-TTEEEEEETTTEEEEEEEEECCS
T ss_pred HHHHHcCCCCccEEEEeCCceEEEEEEECCCC
Confidence 45677899999999997644 66655433
No 57
>cd08177 MAR Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes. Maleylacetate reductases (MAR) play an important role in the degradation of aromatic compounds in aerobic microbes. In fungi and yeasts, the enzymes are involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzymes contribute to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate. Maleylacetate reductases catalyze NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate. In the case of 2-chloromaleylacetate, Maleylacetate reductases initially catalyses the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer. It is inhibited by thiol-blocking reagents such as p-
Probab=37.02 E-value=25 Score=29.24 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=35.5
Q ss_pred chHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCE
Q 044269 50 AGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDT 93 (129)
Q Consensus 50 ~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDt 93 (129)
++..++.+.+..+..+.+.++.+.++++|+-..|++.|+.+.|.
T Consensus 266 ~~~~~~a~~l~~~~~~~~~~i~~l~~~lglp~~l~e~gi~~~~~ 309 (337)
T cd08177 266 EALARLARALGLGAADAADALADLARSLGAPTSLADLGVPRDDI 309 (337)
T ss_pred HHHHHHHHHhCccHHHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 45666777776666677899999999999999999999887664
No 58
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=37.00 E-value=56 Score=24.50 Aligned_cols=40 Identities=20% Similarity=0.280 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHHHHHHH---------------CChHHHHHHcCCCCCCEEEEcCE
Q 044269 60 NWRYLDSERRFQHGLEA---------------CGVTKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk~---------------~GV~~aLkkaGakeGDtV~IGd~ 99 (129)
+++..++...+++.|++ +|+.++|+++|++.+..|.|.++
T Consensus 158 ~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~~~l~~~g~~vp~di~v~g~ 212 (269)
T cd06288 158 DWSADDGYEAAAALLDLDDRPTAIFCGNDRMAMGAYQALLERGLRIPQDVSVVGF 212 (269)
T ss_pred CCChHHHHHHHHHHHhCCCCCCEEEEeCcHHHHHHHHHHHHcCCCCcccceEEee
Confidence 44445566666666654 48999999999986555555433
No 59
>PF03829 PTSIIA_gutA: PTS system glucitol/sorbitol-specific IIA component; InterPro: IPR004716 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2F9H_A.
Probab=36.62 E-value=32 Score=25.26 Aligned_cols=17 Identities=41% Similarity=0.704 Sum_probs=11.5
Q ss_pred CCCCCCEEEEcCEEEEE
Q 044269 87 GVKEGDTVIVGDMEMVW 103 (129)
Q Consensus 87 GakeGDtV~IGd~EFey 103 (129)
-+++||++.||+.+|.=
T Consensus 51 ~i~~Gd~l~i~~~~y~I 67 (117)
T PF03829_consen 51 DIKPGDTLIIGGQEYTI 67 (117)
T ss_dssp ---TT-EEEETTEEEEE
T ss_pred CcCCCCEEEECCeEEEE
Confidence 58999999999998863
No 60
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=35.98 E-value=39 Score=23.19 Aligned_cols=43 Identities=26% Similarity=0.298 Sum_probs=27.7
Q ss_pred EcchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEE
Q 044269 48 VGAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 48 ~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~I 96 (129)
.|.-+..++++.++.. .-+++++..-|-.+.|.. +++||++.+
T Consensus 9 ~GDtLs~iF~~~gls~----~dl~~v~~~~~~~k~L~~--L~pGq~l~f 51 (85)
T PF04225_consen 9 SGDTLSTIFRRAGLSA----SDLYAVLEADGEAKPLTR--LKPGQTLEF 51 (85)
T ss_dssp TT--HHHHHHHTT--H----HHHHHHHHHGGGT--GGG----TT-EEEE
T ss_pred CCCcHHHHHHHcCCCH----HHHHHHHhccCccchHhh--CCCCCEEEE
Confidence 4778999999998765 347788888888888876 999999886
No 61
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=35.89 E-value=39 Score=22.47 Aligned_cols=16 Identities=56% Similarity=0.829 Sum_probs=12.9
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+-|.+.|+++||.|.|
T Consensus 17 ~i~~~lgl~~Gd~v~v 32 (74)
T TIGR02609 17 EVLESLGLKEGDTLYV 32 (74)
T ss_pred HHHHHcCcCCCCEEEE
Confidence 3467889999999964
No 62
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=35.77 E-value=31 Score=23.98 Aligned_cols=15 Identities=40% Similarity=0.713 Sum_probs=10.2
Q ss_pred HHHcCCCCCCEEEEc
Q 044269 83 LMKLGVKEGDTVIVG 97 (129)
Q Consensus 83 LkkaGakeGDtV~IG 97 (129)
+++.|+..||+|.|.
T Consensus 45 i~~~~i~~Gd~V~V~ 59 (82)
T PF03120_consen 45 IKELDIRIGDTVLVT 59 (82)
T ss_dssp HHHTT-BBT-EEEEE
T ss_pred HHHcCCCCCCEEEEE
Confidence 446799999999884
No 63
>PRK11507 ribosome-associated protein; Provisional
Probab=35.45 E-value=27 Score=23.75 Aligned_cols=26 Identities=15% Similarity=0.199 Sum_probs=20.3
Q ss_pred CChHHHHHHcCCCCCCEEEEcCEEEE
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGDMEMV 102 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd~EFe 102 (129)
.|-.+.=|.+-+.+||+|.+.+.++.
T Consensus 42 NGeve~rRgkKl~~GD~V~~~g~~~~ 67 (70)
T PRK11507 42 DGAVETRKRCKIVAGQTVSFAGHSVQ 67 (70)
T ss_pred CCEEecccCCCCCCCCEEEECCEEEE
Confidence 44555566778999999999998765
No 64
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=35.44 E-value=16 Score=24.22 Aligned_cols=17 Identities=29% Similarity=0.765 Sum_probs=10.8
Q ss_pred HHHHHHcCCCCCCEEEE
Q 044269 80 TKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~I 96 (129)
.+-|.++|+.+||+..+
T Consensus 62 ~~tL~~~gV~dGd~L~L 78 (79)
T PF08817_consen 62 DQTLADAGVRDGDVLVL 78 (79)
T ss_dssp TSBCGGGT--TT-EEEE
T ss_pred cCcHhHcCCCCCCEEEe
Confidence 45678889999998875
No 65
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=35.24 E-value=37 Score=27.55 Aligned_cols=13 Identities=31% Similarity=0.516 Sum_probs=11.5
Q ss_pred HHcCCCCCCEEEE
Q 044269 84 MKLGVKEGDTVIV 96 (129)
Q Consensus 84 kkaGakeGDtV~I 96 (129)
+-.|++.||.|+|
T Consensus 177 ry~g~k~G~vvkI 189 (206)
T PLN03111 177 RYYGLKRGQVVKI 189 (206)
T ss_pred HhcCCCCCCEEEE
Confidence 4569999999999
No 66
>PRK11347 antitoxin ChpS; Provisional
Probab=35.10 E-value=41 Score=23.21 Aligned_cols=16 Identities=19% Similarity=0.345 Sum_probs=13.5
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
..|++.|+++||+|.|
T Consensus 19 ~il~~l~l~~G~~v~i 34 (83)
T PRK11347 19 IVMKELNLQPGQSVEA 34 (83)
T ss_pred HHHHHcCCCCCCEEEE
Confidence 3578899999999876
No 67
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=35.05 E-value=31 Score=22.59 Aligned_cols=36 Identities=17% Similarity=0.186 Sum_probs=29.4
Q ss_pred EEcchHHHHHHhcCCCC-HHHHHHHHHHHHHCChHHH
Q 044269 47 VVGAGLQRFVQMTNWRY-LDSERRFQHGLEACGVTKS 82 (129)
Q Consensus 47 V~G~~IEr~v~~tnfd~-~es~~rF~r~Lk~~GV~~a 82 (129)
+....|.+.+...+++- +++++|-.+.|++.|+.+.
T Consensus 14 ~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~ 50 (66)
T PF08461_consen 14 LGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRK 50 (66)
T ss_pred CCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccc
Confidence 34457888888888886 8999999999999996654
No 68
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=34.72 E-value=38 Score=21.64 Aligned_cols=16 Identities=31% Similarity=0.464 Sum_probs=13.1
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
..|.+.|+++|++|.+
T Consensus 56 ~~L~~~~i~~~~~i~~ 71 (77)
T cd01805 56 TTLEEYKIDEKDFVVV 71 (77)
T ss_pred CCHHHcCCCCCCEEEE
Confidence 3578889999999875
No 69
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=34.61 E-value=32 Score=31.78 Aligned_cols=17 Identities=47% Similarity=0.710 Sum_probs=14.7
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+-.++.||++||.|+|.
T Consensus 678 ~DA~~~GI~~GD~V~V~ 694 (765)
T COG0243 678 EDAAKLGIKDGDLVRVE 694 (765)
T ss_pred HHHHHcCCCcCCEEEEE
Confidence 55688899999999995
No 70
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=34.22 E-value=37 Score=21.31 Aligned_cols=20 Identities=25% Similarity=0.591 Sum_probs=14.5
Q ss_pred HHHHcCCCCCCEEE-EcCEEE
Q 044269 82 SLMKLGVKEGDTVI-VGDMEM 101 (129)
Q Consensus 82 aLkkaGakeGDtV~-IGd~EF 101 (129)
...++|+++||+|. |++...
T Consensus 24 ~a~~~gl~~GD~I~~ing~~i 44 (79)
T cd00989 24 PAAKAGLKAGDRILAINGQKI 44 (79)
T ss_pred HHHHcCCCCCCEEEEECCEEC
Confidence 45678999999874 566654
No 71
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=34.20 E-value=66 Score=20.53 Aligned_cols=30 Identities=17% Similarity=0.273 Sum_probs=24.2
Q ss_pred hHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHH
Q 044269 51 GLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLM 84 (129)
Q Consensus 51 ~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLk 84 (129)
-|+.++++.+.+..++.++| ++.|+.+-|.
T Consensus 7 ~Ie~~A~~~~~s~~ea~~~~----~~~~~~~~i~ 36 (62)
T PF12668_consen 7 CIEEFAKKLNISGEEAYNYF----KRSGVIDYII 36 (62)
T ss_pred HHHHHHHHHCcCHHHHHHHH----HHcCcHHHHH
Confidence 48899999999999999888 6777777544
No 72
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=34.01 E-value=28 Score=32.37 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=16.5
Q ss_pred CChHHHHHHcCCCCCCEEEEcC
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd 98 (129)
+.=.+| ++.||++||.|+|.+
T Consensus 726 inp~dA-~~~GI~dGD~V~V~n 746 (814)
T PRK14990 726 INPLDA-QKRGINNGDKVRIFN 746 (814)
T ss_pred EcHHHH-HHcCCCCCCEEEEEc
Confidence 444554 889999999999964
No 73
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=34.00 E-value=39 Score=21.45 Aligned_cols=18 Identities=28% Similarity=0.490 Sum_probs=13.2
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
..|.++|+.+|..|.+-.
T Consensus 26 ~~L~~lGl~~G~~i~v~~ 43 (74)
T PF04023_consen 26 RRLADLGLTPGSEITVIR 43 (74)
T ss_dssp HHHHHCT-STTEEEEEEE
T ss_pred HHHHHCCCCCCCEEEEEE
Confidence 446677899999998864
No 74
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=33.92 E-value=38 Score=22.43 Aligned_cols=16 Identities=19% Similarity=0.206 Sum_probs=13.9
Q ss_pred HHHHcCCCCCCEEEEc
Q 044269 82 SLMKLGVKEGDTVIVG 97 (129)
Q Consensus 82 aLkkaGakeGDtV~IG 97 (129)
.|...|+++|.+|..+
T Consensus 56 tL~~ygi~~~stv~l~ 71 (73)
T cd01791 56 SLGDYEIHDGMNLELY 71 (73)
T ss_pred CHHHcCCCCCCEEEEE
Confidence 5889999999999864
No 75
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=33.72 E-value=27 Score=24.74 Aligned_cols=14 Identities=50% Similarity=0.795 Sum_probs=7.9
Q ss_pred HHHcCCCCCCEEEE
Q 044269 83 LMKLGVKEGDTVIV 96 (129)
Q Consensus 83 LkkaGakeGDtV~I 96 (129)
+.+.|++.||.|.|
T Consensus 93 ~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 93 FEKLGIKVGDRVRI 106 (108)
T ss_dssp HHHHT--TT-EEE-
T ss_pred hhhcCCCCCCEEEe
Confidence 45669999999986
No 76
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=33.64 E-value=51 Score=18.70 Aligned_cols=17 Identities=47% Similarity=0.524 Sum_probs=13.6
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+..+..|+++||.|.|-
T Consensus 14 ~~r~~l~~~~gd~~~i~ 30 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVI 30 (43)
T ss_pred HHHHHcCcCCCCEEEEE
Confidence 34667899999998875
No 77
>PRK05282 (alpha)-aspartyl dipeptidase; Validated
Probab=33.26 E-value=35 Score=27.64 Aligned_cols=31 Identities=23% Similarity=0.327 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEc
Q 044269 65 DSERRFQHGLEACGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 65 es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IG 97 (129)
.+--++.+.|++.|+.+.|+++ ++.| .|.+|
T Consensus 88 Gnt~~l~~~l~~~gl~~~l~~~-~~~G-~~~~G 118 (233)
T PRK05282 88 GNTFQLLKQLYERGLLAPIREA-VKNG-TPYIG 118 (233)
T ss_pred ccHHHHHHHHHHCCcHHHHHHH-HHCC-CEEEE
Confidence 3456889999999999999988 7777 66666
No 78
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=32.98 E-value=42 Score=27.25 Aligned_cols=13 Identities=23% Similarity=0.509 Sum_probs=11.4
Q ss_pred HHcCCCCCCEEEE
Q 044269 84 MKLGVKEGDTVIV 96 (129)
Q Consensus 84 kkaGakeGDtV~I 96 (129)
+-.|++.||.|+|
T Consensus 176 ry~g~k~G~vvkI 188 (205)
T PTZ00061 176 RYFGLSKGQVVKI 188 (205)
T ss_pred HhcCCCCCCEEEE
Confidence 4569999999999
No 79
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=32.86 E-value=79 Score=23.77 Aligned_cols=37 Identities=22% Similarity=0.421 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHHHHHHH----------------CChHHHHHHcCCCCCCEEEEc
Q 044269 60 NWRYLDSERRFQHGLEA----------------CGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk~----------------~GV~~aLkkaGakeGDtV~IG 97 (129)
+++..++...+.+.|.+ +|+.++|+++|++ +|...+|
T Consensus 167 ~~~~~~~~~~~~~~l~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~-~dv~v~g 219 (275)
T cd06317 167 DWDREKAQVAMEALITKFGDDIDGVYAGDDNMARGALNAAKEAGLA-GGIVIVG 219 (275)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccEEEECCCcHHHHHHHHHHhcCCc-CCcEEEE
Confidence 34445555566666654 3788999999999 7776664
No 80
>KOG2500 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.71 E-value=77 Score=26.52 Aligned_cols=64 Identities=22% Similarity=0.332 Sum_probs=31.6
Q ss_pred cEEEEcCCCCeEEEEcchHHHHHHhcCCC--CHHHHHHHHHHHHHCChHHH-----HHHcCCCCCCEEEEc
Q 044269 34 FEIFHDSGSNTWNVVGAGLQRFVQMTNWR--YLDSERRFQHGLEACGVTKS-----LMKLGVKEGDTVIVG 97 (129)
Q Consensus 34 f~I~k~~e~g~f~V~G~~IEr~v~~tnfd--~~es~~rF~r~Lk~~GV~~a-----LkkaGakeGDtV~IG 97 (129)
|-|+.++++|.+---|=..-.--.-+||+ -.|.++|..+.-+.-.-++. =-.+|.|||.||+|.
T Consensus 91 FViRv~dgngr~AFiGlGF~eR~dafDfnvaLqDHfkyv~~~~e~ek~eq~~d~~pslDlgFKEGeTIkin 161 (253)
T KOG2500|consen 91 FVIRVEDGNGRHAFIGLGFGERGDAFDFNVALQDHFKYVKRQKEAEKQEQHYDAGPSLDLGFKEGETIKIN 161 (253)
T ss_pred EEEEEeCCCccEEEEeecccccccccchhhhHHHHHHHHHHHHHHHhhhcccCCCccccccccCCcEEEEE
Confidence 55554434555444443343334445555 34455555443221111000 013699999999985
No 81
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=32.51 E-value=42 Score=22.16 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=13.3
Q ss_pred HHHHcCCCCCCEEEE
Q 044269 82 SLMKLGVKEGDTVIV 96 (129)
Q Consensus 82 aLkkaGakeGDtV~I 96 (129)
.|.+.|+++|++|.+
T Consensus 55 ~L~~~gi~~~~~i~l 69 (78)
T cd01804 55 KLQDLGLGDGSKLTL 69 (78)
T ss_pred cHHHcCCCCCCEEEE
Confidence 589999999999875
No 82
>PF08133 Nuclease_act: Anticodon nuclease activator family; InterPro: IPR012585 This family consists of the anticodon nuclease activator proteins. Pre-existing host tRNAs are reprocessed during Bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5, by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA ligase reactions [].; GO: 0004518 nuclease activity, 0050792 regulation of viral reproduction
Probab=31.92 E-value=27 Score=19.56 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=18.5
Q ss_pred hcCCCCHHHHHHHHHHHHHCChH
Q 044269 58 MTNWRYLDSERRFQHGLEACGVT 80 (129)
Q Consensus 58 ~tnfd~~es~~rF~r~Lk~~GV~ 80 (129)
|.||.++.-+......|+..||.
T Consensus 1 msn~hnehvmqfyr~nlk~~gvf 23 (26)
T PF08133_consen 1 MSNFHNEHVMQFYRHNLKTKGVF 23 (26)
T ss_pred CcchhHHHHHHHHHhhccccccc
Confidence 57888888887778888888874
No 83
>PF08939 DUF1917: Domain of unknown function (DUF1917); InterPro: IPR015034 This family includes various hypothetical proteins.; PDB: 1ZTP_B 2Q4K_C.
Probab=31.91 E-value=44 Score=27.55 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=18.1
Q ss_pred hcCCCCHHHHHHHHHHHHHCChHH
Q 044269 58 MTNWRYLDSERRFQHGLEACGVTK 81 (129)
Q Consensus 58 ~tnfd~~es~~rF~r~Lk~~GV~~ 81 (129)
.-||.+.+.+.|..+.|+++||..
T Consensus 203 T~Df~D~~DV~RVl~~Lr~~gl~~ 226 (243)
T PF08939_consen 203 TPDFRDREDVMRVLRRLRELGLVD 226 (243)
T ss_dssp ES-TT-HHHHHHHHHHHHHTT--S
T ss_pred CCCCCCHHHHHHHHHHHHHcCCcc
Confidence 569999999999999999998854
No 84
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=31.30 E-value=29 Score=23.12 Aligned_cols=26 Identities=19% Similarity=0.208 Sum_probs=14.4
Q ss_pred CChHHHHHHcCCCCCCEEEEcCEEEE
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGDMEMV 102 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd~EFe 102 (129)
.|-.+.=|.+-+++||+|.|++..|.
T Consensus 38 NGe~e~rrg~Kl~~GD~V~~~~~~~~ 63 (65)
T PF13275_consen 38 NGEVETRRGKKLRPGDVVEIDGEEYR 63 (65)
T ss_dssp TTB----SS----SSEEEEETTEEEE
T ss_pred CCEEccccCCcCCCCCEEEECCEEEE
Confidence 34445556677899999999998875
No 85
>KOG3085 consensus Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=31.28 E-value=50 Score=27.16 Aligned_cols=21 Identities=38% Similarity=0.594 Sum_probs=17.7
Q ss_pred HHHHHHcCCCCCCEEEEcCEE
Q 044269 80 TKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IGd~E 100 (129)
..+|..+|+++.|.|.|||--
T Consensus 175 ~~al~~l~v~Pee~vhIgD~l 195 (237)
T KOG3085|consen 175 QLALERLGVKPEECVHIGDLL 195 (237)
T ss_pred HHHHHHhCCChHHeEEecCcc
Confidence 357889999999999999753
No 86
>PTZ00237 acetyl-CoA synthetase; Provisional
Probab=31.13 E-value=44 Score=29.87 Aligned_cols=18 Identities=22% Similarity=0.565 Sum_probs=12.8
Q ss_pred HHHHHHcCCCCCCEEEEc
Q 044269 80 TKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IG 97 (129)
-..|++.|++.||+|.|.
T Consensus 106 A~~L~~~Gv~~GDrV~i~ 123 (647)
T PTZ00237 106 SRVLLNLNISKNDNVLIY 123 (647)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 344555678999999874
No 87
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=30.89 E-value=35 Score=20.84 Aligned_cols=21 Identities=38% Similarity=0.509 Sum_probs=17.0
Q ss_pred cCCCCCCEEEEcCEEEEEEec
Q 044269 86 LGVKEGDTVIVGDMEMVWHDS 106 (129)
Q Consensus 86 aGakeGDtV~IGd~EFey~ed 106 (129)
.-+++||.|+-|+.=|.....
T Consensus 16 v~V~~G~~VkkGd~L~~ld~~ 36 (50)
T PF13533_consen 16 VYVKEGQQVKKGDVLLVLDSP 36 (50)
T ss_pred EEecCCCEEcCCCEEEEECcH
Confidence 357999999999998886543
No 88
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=30.22 E-value=39 Score=32.19 Aligned_cols=17 Identities=35% Similarity=0.524 Sum_probs=15.2
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+-.++.||++||.|+|.
T Consensus 817 ~DA~~~GI~dGD~V~V~ 833 (912)
T TIGR03479 817 KDAAEKGIKDGDQVRIF 833 (912)
T ss_pred HHHHHcCCCcCCEEEEE
Confidence 66789999999999995
No 89
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=30.16 E-value=62 Score=22.03 Aligned_cols=36 Identities=17% Similarity=0.188 Sum_probs=21.8
Q ss_pred cchHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCC
Q 044269 49 GAGLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGV 88 (129)
Q Consensus 49 G~~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGa 88 (129)
|+.+|+++.+.+..+.+.++.. -....+-.|++.|.
T Consensus 12 g~~~e~~L~~vGI~t~~~L~~~----Ga~~a~~~Lk~~~~ 47 (81)
T PF04994_consen 12 GPKSERMLAKVGIHTVEDLREL----GAVEAYLRLKASGP 47 (81)
T ss_dssp -HHHHHHHHHTT--SHHHHHHH----HHHHHHHHHHHH-T
T ss_pred CHHHHHHHHHcCCCCHHHHHHh----CHHHHHHHHHHHCC
Confidence 7899999999999999887554 22233444555543
No 90
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=29.99 E-value=36 Score=21.44 Aligned_cols=11 Identities=45% Similarity=0.788 Sum_probs=7.7
Q ss_pred cCCCCCCEEEE
Q 044269 86 LGVKEGDTVIV 96 (129)
Q Consensus 86 aGakeGDtV~I 96 (129)
.||.+||+|.+
T Consensus 30 ~~A~~gD~V~v 40 (58)
T PF08206_consen 30 NGAMDGDKVLV 40 (58)
T ss_dssp TTS-TT-EEEE
T ss_pred CCCCCCCEEEE
Confidence 48999999985
No 91
>TIGR02164 torA trimethylamine-N-oxide reductase TorA. This very narrowly defined family represents TorA, part of a family of related molybdoenzymes that include biotin sulfoxide reductases, dimethyl sulfoxide reductases, and at least two different subfamilies of trimethylamine-N-oxide reductases. A single enzyme from the larger family may have more than one activity. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon.
Probab=29.97 E-value=44 Score=31.29 Aligned_cols=17 Identities=35% Similarity=0.362 Sum_probs=14.8
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+.-++.||++||.|+|.
T Consensus 714 ~dA~~~GI~dGD~V~V~ 730 (822)
T TIGR02164 714 VDAKARGIKDGDLVRVF 730 (822)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45688999999999995
No 92
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=29.89 E-value=32 Score=23.92 Aligned_cols=12 Identities=33% Similarity=0.401 Sum_probs=10.2
Q ss_pred CCCCCCEEEEcC
Q 044269 87 GVKEGDTVIVGD 98 (129)
Q Consensus 87 GakeGDtV~IGd 98 (129)
-++.||+|.|..
T Consensus 53 ~~k~GD~V~I~e 64 (84)
T PRK05610 53 EAKIGDVVRIME 64 (84)
T ss_pred CCCCCCEEEEEE
Confidence 489999999974
No 93
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=29.35 E-value=73 Score=25.10 Aligned_cols=39 Identities=15% Similarity=0.188 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHHHHHH---------------CChHHHHHHcCCCCCCEEEEcC
Q 044269 60 NWRYLDSERRFQHGLEA---------------CGVTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk~---------------~GV~~aLkkaGakeGDtV~IGd 98 (129)
+++..++...+++.|++ +|+.++|+++|++-.+.|.|.+
T Consensus 219 ~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~g~~~al~~~g~~vP~disv~g 272 (328)
T PRK11303 219 SFEREAGAQLFEKWLETHPMPDALFTTSYTLLQGVLDVLLERPGELPSDLAIAT 272 (328)
T ss_pred CCChHHHHHHHHHHHcCCCCCCEEEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 34445555566666653 5899999999998655566543
No 94
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=29.31 E-value=34 Score=23.93 Aligned_cols=12 Identities=25% Similarity=0.551 Sum_probs=10.4
Q ss_pred CCCCCCEEEEcC
Q 044269 87 GVKEGDTVIVGD 98 (129)
Q Consensus 87 GakeGDtV~IGd 98 (129)
.++.||+|.|..
T Consensus 50 ~~~~GD~V~I~e 61 (84)
T CHL00142 50 ECNIGDQVLIEE 61 (84)
T ss_pred CCCCCCEEEEEE
Confidence 589999999974
No 95
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=29.04 E-value=83 Score=24.40 Aligned_cols=39 Identities=8% Similarity=0.246 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHHHHHHHC---------------ChHHHHHHcCCCCCCEEEEcC
Q 044269 60 NWRYLDSERRFQHGLEAC---------------GVTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk~~---------------GV~~aLkkaGakeGDtV~IGd 98 (129)
+++..++...+.+.|+.. |+.++|+++|++-+|.+.|-+
T Consensus 194 ~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~gv~~al~~~g~~ip~di~vvg 247 (309)
T PRK11041 194 DFTFEAGAKALKQLLDLPQPPTAVFCHSDVMALGALSQAKRMGLRVPQDLSIIG 247 (309)
T ss_pred CCCHHHHHHHHHHHHcCCCCCCEEEEcCcHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 344455566666666532 899999999998665555443
No 96
>PRK10461 thiamine biosynthesis lipoprotein ApbE; Provisional
Probab=28.98 E-value=21 Score=30.35 Aligned_cols=31 Identities=19% Similarity=0.321 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcC
Q 044269 65 DSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 65 es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd 98 (129)
=++.+..+.|++.||..+|.++| ||...+|.
T Consensus 190 yavD~a~~~L~~~Gv~~~lV~~G---Gdi~~~G~ 220 (350)
T PRK10461 190 YAADHLARLMEQEGISRYLVSVG---GALSSRGM 220 (350)
T ss_pred HHHHHHHHHHHHCCCCEEEEEcC---CcEEEECC
Confidence 46888999999999999999999 99888884
No 97
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=28.93 E-value=47 Score=31.13 Aligned_cols=17 Identities=35% Similarity=0.450 Sum_probs=14.7
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+.-++.||++||.|+|.
T Consensus 717 ~DA~~~GI~dGD~V~V~ 733 (825)
T PRK15102 717 QDAKARGIKDGDVVRVF 733 (825)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 45688999999999995
No 98
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=28.58 E-value=52 Score=21.89 Aligned_cols=17 Identities=24% Similarity=0.583 Sum_probs=14.2
Q ss_pred HHHHHcCCC-CCCEEEEc
Q 044269 81 KSLMKLGVK-EGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGak-eGDtV~IG 97 (129)
+.|...|++ +||+|.++
T Consensus 56 ~tL~~ygi~~~g~~~~l~ 73 (75)
T cd01799 56 ETLYSHGIRTNGDSAFLY 73 (75)
T ss_pred CCHHHcCCCCCCCEEEEE
Confidence 468889999 99999874
No 99
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.55 E-value=48 Score=32.01 Aligned_cols=25 Identities=36% Similarity=0.555 Sum_probs=20.6
Q ss_pred HHHHHcCCCCCCEEEEcCEEEEEEe
Q 044269 81 KSLMKLGVKEGDTVIVGDMEMVWHD 105 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd~EFey~e 105 (129)
..|...|+|.||.|.||+..|.-..
T Consensus 144 ~Ll~~LglkvGd~i~vG~~tlri~~ 168 (829)
T COG3127 144 RLLERLGLKVGDRIDVGDATLRIAG 168 (829)
T ss_pred HHHHHhCCCcCceEeecCceEEEEE
Confidence 3466779999999999999998643
No 100
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=28.38 E-value=26 Score=27.84 Aligned_cols=48 Identities=15% Similarity=0.326 Sum_probs=34.3
Q ss_pred chHHHHHHhcCCCCHH-HHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEEEE
Q 044269 50 AGLQRFVQMTNWRYLD-SERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDMEMV 102 (129)
Q Consensus 50 ~~IEr~v~~tnfd~~e-s~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~EFe 102 (129)
+++.+++++.+++..- |..=| ..++.+||+++++..-.+|.|||.=|+
T Consensus 74 ~RV~~~~~~l~v~fi~~A~KP~-----~~~fr~Al~~m~l~~~~vvmVGDqL~T 122 (175)
T COG2179 74 SRVARAAEKLGVPFIYRAKKPF-----GRAFRRALKEMNLPPEEVVMVGDQLFT 122 (175)
T ss_pred HHHHhhhhhcCCceeecccCcc-----HHHHHHHHHHcCCChhHEEEEcchhhh
Confidence 4566677777766422 22222 335678999999999999999999886
No 101
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=28.16 E-value=35 Score=22.15 Aligned_cols=19 Identities=21% Similarity=0.517 Sum_probs=13.3
Q ss_pred HHHcCCCCCCEEE-EcCEEE
Q 044269 83 LMKLGVKEGDTVI-VGDMEM 101 (129)
Q Consensus 83 LkkaGakeGDtV~-IGd~EF 101 (129)
..++|++.||.|. |++..+
T Consensus 27 A~~aGl~~GD~I~~ing~~v 46 (82)
T PF13180_consen 27 AAKAGLQPGDIILAINGKPV 46 (82)
T ss_dssp HHHTTS-TTEEEEEETTEES
T ss_pred HHHCCCCCCcEEEEECCEEc
Confidence 4578999999864 666655
No 102
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=28.08 E-value=72 Score=21.64 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHCChHHHHHHcCC
Q 044269 64 LDSERRFQHGLEACGVTKSLMKLGV 88 (129)
Q Consensus 64 ~es~~rF~r~Lk~~GV~~aLkkaGa 88 (129)
+.|+++|-+.+.+-|+...+++.-.
T Consensus 13 d~ALrrFKr~~~k~gil~e~k~r~~ 37 (67)
T COG0828 13 DKALRRFKRKVEKEGILREMKEREF 37 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4689999999999999999887543
No 103
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=27.03 E-value=95 Score=23.55 Aligned_cols=20 Identities=15% Similarity=0.285 Sum_probs=16.0
Q ss_pred CChHHHHHHcCCCCCCEEEEc
Q 044269 77 CGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IG 97 (129)
.|+.++|+++|++ +|.-.||
T Consensus 195 ~g~~~al~~~g~~-~dv~vvg 214 (270)
T cd06308 195 LGAYLAAKRAGRE-KEIKFIG 214 (270)
T ss_pred HHHHHHHHHcCCC-CCcEEEE
Confidence 5899999999999 7655543
No 104
>TIGR03089 conserved hypothetical protein TIGR03089. This protein family is found, so far, only in the Actinobacteria (Streptomyces, Mycobacterium, Corynebacterium, Nocardia, Propionibacterium, etc.) and never more than one to a genome. Members show twilight-level sequence similarity to family of AMP-binding enzymes described by Pfam model pfam00501.
Probab=27.02 E-value=61 Score=25.30 Aligned_cols=17 Identities=24% Similarity=0.364 Sum_probs=12.2
Q ss_pred HHHHH-cCCCCCCEEEEc
Q 044269 81 KSLMK-LGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkk-aGakeGDtV~IG 97 (129)
..|++ .|+++||.|-|-
T Consensus 42 ~~L~~~~Gv~~GdrV~i~ 59 (227)
T TIGR03089 42 NLLQDELDAEPGSRVALD 59 (227)
T ss_pred HHHHHHhCCCCCCEEEEE
Confidence 34444 489999999874
No 105
>COG0380 OtsA Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]
Probab=26.92 E-value=15 Score=33.30 Aligned_cols=41 Identities=24% Similarity=0.267 Sum_probs=31.7
Q ss_pred CCCCCCEEEEcCEEEEEEecCCCCCCCcccccccccCCCCC
Q 044269 87 GVKEGDTVIVGDMEMVWHDSANNPGPSKAKKGFEDSIKWPQ 127 (129)
Q Consensus 87 GakeGDtV~IGd~EFey~ed~~~~~~~~~~~~~~~~~~~~~ 127 (129)
-+++||+|.|.||.+--.+.+--.-...|+=||--.+-||.
T Consensus 144 ~~~~gDiIWVhDYhL~L~P~mlR~~~~~~~IgfFlHiPfPs 184 (486)
T COG0380 144 IYEPGDIIWVHDYHLLLVPQMLRERIPDAKIGFFLHIPFPS 184 (486)
T ss_pred hcCCCCEEEEEechhhhhHHHHHHhCCCceEEEEEeCCCCC
Confidence 58999999999999877765444444455778888888885
No 106
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=26.74 E-value=73 Score=19.70 Aligned_cols=16 Identities=38% Similarity=0.638 Sum_probs=12.6
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+++.++++++||.|.+
T Consensus 42 ~~~~~l~l~~G~~v~~ 57 (69)
T TIGR00638 42 ESVAELGLKPGKEVYA 57 (69)
T ss_pred HHHhhCCCCCCCEEEE
Confidence 5566778899999875
No 107
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=26.74 E-value=38 Score=26.50 Aligned_cols=12 Identities=67% Similarity=1.066 Sum_probs=10.8
Q ss_pred CCCCCCEEEEcC
Q 044269 87 GVKEGDTVIVGD 98 (129)
Q Consensus 87 GakeGDtV~IGd 98 (129)
.++.||+|.|+.
T Consensus 116 ~~kvGD~V~I~E 127 (158)
T PTZ00241 116 DVKEGDIVVVGQ 127 (158)
T ss_pred CCCCCCEEEEEE
Confidence 599999999995
No 108
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=26.65 E-value=63 Score=20.58 Aligned_cols=16 Identities=31% Similarity=0.470 Sum_probs=13.3
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+.|.+.|+++|++|.+
T Consensus 53 ~tL~~~~i~~~stl~l 68 (71)
T cd01808 53 DTLTQHNIKDGLTVHL 68 (71)
T ss_pred CcHHHcCCCCCCEEEE
Confidence 3588899999999875
No 109
>PF06253 MTTB: Trimethylamine methyltransferase (MTTB); InterPro: IPR010426 This family consists of several trimethylamine methyltransferase (MTTB) proteins from numerous Rhizobium and Methanosarcina species.; GO: 0008168 methyltransferase activity, 0015948 methanogenesis; PDB: 2QNE_A.
Probab=26.58 E-value=83 Score=28.40 Aligned_cols=50 Identities=20% Similarity=0.150 Sum_probs=24.7
Q ss_pred EcchHHHHHHhcCCCCHHHHHHH----HHHHHHCCh-------HHHHHHcCCCC---CCEEEEc
Q 044269 48 VGAGLQRFVQMTNWRYLDSERRF----QHGLEACGV-------TKSLMKLGVKE---GDTVIVG 97 (129)
Q Consensus 48 ~G~~IEr~v~~tnfd~~es~~rF----~r~Lk~~GV-------~~aLkkaGake---GDtV~IG 97 (129)
..+.+.+-..++++=+++.+.+. .++|+..|| .+.|+++|++- |++|+|-
T Consensus 22 ~~~~~~~~~~~~~~ls~~~ie~IHe~sl~ILee~Gv~~~~eeAlei~k~~Ga~V~~eg~~V~ip 85 (505)
T PF06253_consen 22 RSPYIVRNGPPYNFLSEEEIEQIHEASLRILEETGVEFESEEALEIFKKAGARVDEEGGRVRIP 85 (505)
T ss_dssp --------------S-HHHHHHHHHHHHHHHHHT-EEE--HHHHHHHHHTT-EE--ETTEEE--
T ss_pred ccccccccCCCcccCCHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHHcCCEEecCCCeEecC
Confidence 33444455556666666666655 468999997 58899999987 9999986
No 110
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=26.54 E-value=1e+02 Score=23.67 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHHHHHH---------------CChHHHHHHcCCCCCCEEEEc
Q 044269 60 NWRYLDSERRFQHGLEA---------------CGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk~---------------~GV~~aLkkaGakeGDtV~IG 97 (129)
+++...+...+.+.|++ +|+.++|+++|+ +|...||
T Consensus 164 ~~~~~~~~~~~~~~l~~~~~~~ai~~~nd~~a~g~~~al~~~g~--~di~vvg 214 (272)
T cd06313 164 NWDVSKAARIWETWLTKYPQLDGAFCHNDSMALAAYQIMKAAGR--TKIVIGG 214 (272)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCEEEECCCcHHHHHHHHHHHcCC--CceEEEe
Confidence 44445566677777765 489999999998 7765543
No 111
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=26.50 E-value=46 Score=21.56 Aligned_cols=21 Identities=10% Similarity=0.232 Sum_probs=14.8
Q ss_pred HHHHcCCCCCCEEE-EcCEEEE
Q 044269 82 SLMKLGVKEGDTVI-VGDMEMV 102 (129)
Q Consensus 82 aLkkaGakeGDtV~-IGd~EFe 102 (129)
...++|+++||.|. |++....
T Consensus 22 pa~~aGL~~GDiI~~Ing~~v~ 43 (79)
T cd00991 22 PAENAVLHTGDVIYSINGTPIT 43 (79)
T ss_pred hHHhcCCCCCCEEEEECCEEcC
Confidence 34678999999864 6666553
No 112
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=26.49 E-value=1.9e+02 Score=19.32 Aligned_cols=50 Identities=10% Similarity=0.117 Sum_probs=35.2
Q ss_pred EEEEcchHHHHHHhcC--CCCHHHHHHHHHHHHH-CChHHHHHHcCCCCCCEE
Q 044269 45 WNVVGAGLQRFVQMTN--WRYLDSERRFQHGLEA-CGVTKSLMKLGVKEGDTV 94 (129)
Q Consensus 45 f~V~G~~IEr~v~~tn--fd~~es~~rF~r~Lk~-~GV~~aLkkaGakeGDtV 94 (129)
|.|.+-....++.++. ....-|+++|.+-++. -++.++|.+.|-.+++..
T Consensus 1 f~iR~y~k~ELA~lYfP~~~~~sA~r~L~rwI~~~~~L~~~L~~~Gy~~~~r~ 53 (69)
T PF14053_consen 1 FRIRSYGKSELAQLYFPDLTPSSAVRKLRRWIRRNPELLEELEATGYHPRQRS 53 (69)
T ss_pred CccccccHHHHHHHHcCCCCHHHHHHHHHHHHHHCHHHHHHHHHcCCCCCCEe
Confidence 3444444555555543 4456788889888876 479999999999998864
No 113
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=26.49 E-value=46 Score=24.81 Aligned_cols=11 Identities=64% Similarity=1.017 Sum_probs=6.8
Q ss_pred cCCCCCCEEEE
Q 044269 86 LGVKEGDTVIV 96 (129)
Q Consensus 86 aGakeGDtV~I 96 (129)
.|++|||.|.|
T Consensus 109 L~L~DGD~V~v 119 (121)
T PF01982_consen 109 LGLKDGDEVEV 119 (121)
T ss_dssp TT--TT-EEEE
T ss_pred cCCCCCCEEEE
Confidence 58999999987
No 114
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=26.31 E-value=33 Score=23.36 Aligned_cols=47 Identities=13% Similarity=0.216 Sum_probs=28.3
Q ss_pred CCCeEEEEcchHHHHHHhcCCC-CHHHHHHHHHHHHHCChHHHHHHcC
Q 044269 41 GSNTWNVVGAGLQRFVQMTNWR-YLDSERRFQHGLEACGVTKSLMKLG 87 (129)
Q Consensus 41 e~g~f~V~G~~IEr~v~~tnfd-~~es~~rF~r~Lk~~GV~~aLkkaG 87 (129)
++|.|---..-++.+=++.+-. .--++.+|.|+|+++||..+--+.|
T Consensus 21 Ee~e~lsa~~If~~L~k~~~~~l~~~~~~~FGriL~~~gi~~khT~~G 68 (73)
T PF12990_consen 21 EEGEWLSAAEIFERLQKKSPAALRGSNPNHFGRILQKLGIPRKHTRKG 68 (73)
T ss_pred ccceeecHHHHHHHHHHhCccccccCCHHHHHHHHHHcCCCccccCCC
Confidence 4555544444444443333321 1247889999999999987665555
No 115
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=26.22 E-value=53 Score=25.40 Aligned_cols=37 Identities=22% Similarity=0.262 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHHHHHH---------------CChHHHHHHcCCCCCCEEEEc
Q 044269 60 NWRYLDSERRFQHGLEA---------------CGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk~---------------~GV~~aLkkaGakeGDtV~IG 97 (129)
+++..++...+++.|+. +|+.++|+++|+. +|...||
T Consensus 171 ~~~~~~~~~~~~~~l~~~~~~~ai~~~nd~~A~g~l~al~~~G~~-~dv~vvg 222 (280)
T cd06303 171 DATRQKAYQATSDILSNNPDVDFIYACSTDIALGASDALKELGRE-DDILING 222 (280)
T ss_pred CCCHHHHHHHHHHHHHhCCCCcEEEECCcHHHHHHHHHHHHcCCC-CCcEEEe
Confidence 34444555566666543 4899999999996 7766654
No 116
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=26.15 E-value=54 Score=20.68 Aligned_cols=19 Identities=26% Similarity=0.448 Sum_probs=14.0
Q ss_pred HHHcCCCCCCEEE-EcCEEE
Q 044269 83 LMKLGVKEGDTVI-VGDMEM 101 (129)
Q Consensus 83 LkkaGakeGDtV~-IGd~EF 101 (129)
..++|+++||.|. |++..+
T Consensus 25 a~~aGl~~GD~I~~Ing~~v 44 (80)
T cd00990 25 ADKAGLVAGDELVAVNGWRV 44 (80)
T ss_pred HHHhCCCCCCEEEEECCEEh
Confidence 4568999999874 666654
No 117
>PF06300 Tsp45I: Tsp45I type II restriction enzyme; InterPro: IPR010443 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases such as Tsp45I, which recognises the DNA sequence 5' GTSAC, cleaving prior to G-1 [].
Probab=25.85 E-value=68 Score=26.97 Aligned_cols=29 Identities=21% Similarity=0.131 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHHCChHHHHHHcCCCC
Q 044269 62 RYLDSERRFQHGLEACGVTKSLMKLGVKE 90 (129)
Q Consensus 62 d~~es~~rF~r~Lk~~GV~~aLkkaGake 90 (129)
.+|+.+.|++.+|.+||+++.+.+.-...
T Consensus 85 rnP~Ti~ri~g~l~emGl~~i~ek~t~Pk 113 (261)
T PF06300_consen 85 RNPETINRICGRLYEMGLDKIYEKCTEPK 113 (261)
T ss_pred cCcHHHHHHHHHHHHHhHHHHHHHcCCCc
Confidence 58899999999999999999888765443
No 118
>PF02073 Peptidase_M29: Thermophilic metalloprotease (M29); InterPro: IPR000787 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M29 (aminopeptidase T family, clan M-). The protein fold of the peptidase domain and the active site residues are not known for any members of the thermophilic metallo-aminopeptidases family.; GO: 0004177 aminopeptidase activity, 0006508 proteolysis; PDB: 2AYI_D 1ZJC_A.
Probab=25.77 E-value=90 Score=27.19 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=20.5
Q ss_pred CHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEc
Q 044269 63 YLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 63 ~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IG 97 (129)
..+-+.+++++|-+.|| ++|+||+|.|.
T Consensus 3 ~~~~l~kyA~llV~~gl-------nvq~Gq~v~I~ 30 (398)
T PF02073_consen 3 FDERLEKYAELLVKYGL-------NVQPGQKVLIR 30 (398)
T ss_dssp HHHHHHHHHHHHHHTTT----------TT-EEEEE
T ss_pred chHHHHHHHHHHHHhcc-------CCCCCCEEEEE
Confidence 45678889999999998 99999999985
No 119
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=25.59 E-value=73 Score=21.86 Aligned_cols=43 Identities=7% Similarity=0.104 Sum_probs=30.6
Q ss_pred hHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEE
Q 044269 51 GLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 51 ~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~E 100 (129)
-++++.+++.+...++-.-+...++.+. + .+.+|+.|.|+++=
T Consensus 8 l~~~ia~~~~~s~~~v~~vl~~~~~~i~--~-----~L~~g~~V~l~gfG 50 (99)
T PRK00285 8 LAEALFEKVGLSKREAKELVELFFEEIR--D-----ALENGEQVKLSGFG 50 (99)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHHHHHH--H-----HHHcCCeEEEcCCE
Confidence 4677888888887777766666665432 2 45788899998764
No 120
>PF04724 Glyco_transf_17: Glycosyltransferase family 17; InterPro: IPR006813 This family represents beta-1,4-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase (2.4.1.144 from EC). This enzyme transfers the bisecting GlcNAc to the core mannose of complex N-glycans. The addition of this residue is regulated during development and has functional consequences for receptor signalling, cell adhesion, and tumour progression [, ].; GO: 0003830 beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity, 0006487 protein N-linked glycosylation, 0016020 membrane
Probab=25.53 E-value=73 Score=27.50 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=17.5
Q ss_pred HHHHHHcCCCCCCEEEEcCEE
Q 044269 80 TKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IGd~E 100 (129)
...++.+|+++||.|.++|..
T Consensus 168 ~~l~~~~~~~~dDliivSDvD 188 (356)
T PF04724_consen 168 NGLLRLAGIQDDDLIIVSDVD 188 (356)
T ss_pred HHHhhhcCCCCCCEEEEcCcc
Confidence 555678999999999999863
No 121
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=25.51 E-value=52 Score=24.87 Aligned_cols=21 Identities=24% Similarity=0.392 Sum_probs=15.7
Q ss_pred CChHHHHHHcCCCCCCEEEEc
Q 044269 77 CGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IG 97 (129)
+|+.++|+++|++++|.-.||
T Consensus 196 ~~~~~~l~~~g~~~~di~ivg 216 (272)
T cd06301 196 LGAIMALKAAGKSDKDVPVAG 216 (272)
T ss_pred HHHHHHHHHcCCCCCCcEEEe
Confidence 588999999999954644433
No 122
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=25.37 E-value=58 Score=29.98 Aligned_cols=18 Identities=33% Similarity=0.637 Sum_probs=14.7
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+.-++.||++||.|+|.+
T Consensus 673 ~dA~~~GI~dGD~V~v~n 690 (759)
T PRK15488 673 QTAGKLGIKNGDEIRLEN 690 (759)
T ss_pred HHHHHhCCCCCCEEEEEc
Confidence 346788999999999953
No 123
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=25.28 E-value=1e+02 Score=18.55 Aligned_cols=26 Identities=4% Similarity=-0.022 Sum_probs=19.7
Q ss_pred hHHHHHHhcCCCCHHHHHHHHHHHHH
Q 044269 51 GLQRFVQMTNWRYLDSERRFQHGLEA 76 (129)
Q Consensus 51 ~IEr~v~~tnfd~~es~~rF~r~Lk~ 76 (129)
.++++.+..|+++++.-.+|.+.+..
T Consensus 5 ~~~~l~~~~dl~~~egk~~~~~~~~~ 30 (59)
T PF10410_consen 5 LIERLSKGYDLDTPEGKAEAVREAAP 30 (59)
T ss_dssp HHHHHGGGS-TTSHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 46788889999999988888776543
No 124
>TIGR00353 nrfE c-type cytochrome biogenesis protein CcmF. The product of this gene is required for the biogenesis of C-type cytochromes. This gene is thought to have eleven transmembrane helices. Disruption of this gene in Paracoccus denitrificans, encoding a putative transporter, results in formation of an unstable apocytochrome c and deficiency in siderophore production.
Probab=25.28 E-value=70 Score=29.51 Aligned_cols=22 Identities=18% Similarity=0.302 Sum_probs=18.6
Q ss_pred CCCCCCEEEEcCEEEEEEecCC
Q 044269 87 GVKEGDTVIVGDMEMVWHDSAN 108 (129)
Q Consensus 87 GakeGDtV~IGd~EFey~ed~~ 108 (129)
-.++||++.+++++|.|.+-..
T Consensus 456 ~L~pGet~~~~~y~~~y~~~~~ 477 (576)
T TIGR00353 456 RLKPGQSVTLGGYTFRFRCVDL 477 (576)
T ss_pred EECCCCcEEEcCEEEEEeeeee
Confidence 3589999999999999977543
No 125
>PLN02654 acetate-CoA ligase
Probab=25.27 E-value=64 Score=28.97 Aligned_cols=19 Identities=37% Similarity=0.669 Sum_probs=15.2
Q ss_pred hHHHHHHcCCCCCCEEEEc
Q 044269 79 VTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~IG 97 (129)
+-..|++.|++.||.|.|.
T Consensus 133 lA~~L~~~Gv~~GdrV~i~ 151 (666)
T PLN02654 133 LANYLKDVGVKKGDAVVIY 151 (666)
T ss_pred HHHHHHHcCCCCCCEEEEE
Confidence 4466778899999999885
No 126
>PRK03760 hypothetical protein; Provisional
Probab=24.99 E-value=64 Score=23.47 Aligned_cols=16 Identities=25% Similarity=0.202 Sum_probs=12.6
Q ss_pred HHHHcCCCCCCEEEEc
Q 044269 82 SLMKLGVKEGDTVIVG 97 (129)
Q Consensus 82 aLkkaGakeGDtV~IG 97 (129)
...+.|+++||+|.+.
T Consensus 100 ~~~~~gi~~Gd~v~~~ 115 (117)
T PRK03760 100 KIRVLKVEVGDEIEWI 115 (117)
T ss_pred hHHHcCCCCCCEEEEe
Confidence 3567899999999753
No 127
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=24.83 E-value=1.2e+02 Score=22.82 Aligned_cols=24 Identities=13% Similarity=0.203 Sum_probs=18.9
Q ss_pred CChHHHHHHcCCCCCCEEEEcCEE
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd~E 100 (129)
+|+.++|+++|++.++.|.|.++.
T Consensus 190 ~g~~~al~~~g~~vp~di~i~g~d 213 (269)
T cd06293 190 IGLLEVLRERGLSIPGDMSLVGFD 213 (269)
T ss_pred HHHHHHHHHcCCCCccceEEEeec
Confidence 489999999999877767775443
No 128
>TIGR00509 bisC_fam molybdopterin guanine dinucleotide-containing S/N-oxide reductases. This enzyme family shares sequence similarity and a requirement for a molydenum cofactor as the only prosthetic group. The form of the cofactor is a single molybdenum atom coordinated by two molybdopterin guanine dinucleotide molecules. Members of the family include biotin sulfoxide reductase, dimethylsulfoxide reductase, and trimethylamine-N-oxide reductase, although a single member may show all those activities and related activities; it may not be possible to resolve the primary function for members of this family by sequence comparison alone. A number of similar molybdoproteins in which the N-terminal region contains a CXXXC motif and may bind an iron-sulfur cluster are excluded from this set, including formate dehydrogenases and nitrate reductases. Also excluded is the A chain of a heteromeric, anaerobic DMSO reductase, which also contains the CXXXC motif.
Probab=24.80 E-value=61 Score=30.00 Aligned_cols=18 Identities=28% Similarity=0.383 Sum_probs=14.9
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+.-++.||++||.|+|.+
T Consensus 664 ~dA~~~GI~dGD~V~V~s 681 (770)
T TIGR00509 664 DDAAARGIADGDIVRVFN 681 (770)
T ss_pred HHHHHcCCCCCCEEEEEC
Confidence 446788999999999953
No 129
>TIGR01217 ac_ac_CoA_syn acetoacetyl-CoA synthase. This enzyme catalyzes the first step of the mevalonate pathway of IPP biosynthesis. Most bacteria do not use this pathway, but rather the deoxyxylulose pathway.
Probab=24.46 E-value=68 Score=28.66 Aligned_cols=19 Identities=37% Similarity=0.468 Sum_probs=15.2
Q ss_pred hHHHHHHcCCCCCCEEEEc
Q 044269 79 VTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~IG 97 (129)
+-.+|++.|++.||.|.|.
T Consensus 127 lA~~L~~~Gv~~GdrV~i~ 145 (652)
T TIGR01217 127 LAAALRALGVRPGDRVSGY 145 (652)
T ss_pred HHHHHHHcCCCCCCEEEEE
Confidence 3467777889999999984
No 130
>PF13242 Hydrolase_like: HAD-hyrolase-like; PDB: 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A 2HX1_D 2X4D_A 3HLT_C 3L1U_B ....
Probab=24.46 E-value=48 Score=21.23 Aligned_cols=21 Identities=38% Similarity=0.673 Sum_probs=16.4
Q ss_pred hHHHHHHcCCCCCCEEEEcCE
Q 044269 79 VTKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~IGd~ 99 (129)
+..++++.|+...++|.|||-
T Consensus 10 ~~~a~~~~~~~~~~~~~VGD~ 30 (75)
T PF13242_consen 10 LEQALKRLGVDPSRCVMVGDS 30 (75)
T ss_dssp HHHHHHHHTSGGGGEEEEESS
T ss_pred HHHHHHHcCCCHHHEEEEcCC
Confidence 345666678889999999986
No 131
>PF12143 PPO1_KFDV: Protein of unknown function (DUF_B2219); InterPro: IPR022740 This domain represents the C terminus of polyphenol oxidases. This region is primarily found in eukaryotes, although a few bacterial members also exist. It is typically between 138 and 152 amino acids in length and the family is found in association with PF00264 from PFAM and PF12142 from PFAM. Many members are plant or plastid polyphenol oxidases, and there is a highly conserved KFDV sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process
Probab=24.43 E-value=55 Score=24.55 Aligned_cols=21 Identities=29% Similarity=0.561 Sum_probs=17.7
Q ss_pred HHCChHHHHHHcCCCCCCEEE
Q 044269 75 EACGVTKSLMKLGVKEGDTVI 95 (129)
Q Consensus 75 k~~GV~~aLkkaGakeGDtV~ 95 (129)
-++||.+.|+..|+.+-|+|.
T Consensus 89 ~rlgitdlLedLga~~d~sIv 109 (130)
T PF12143_consen 89 LRLGITDLLEDLGAEDDDSIV 109 (130)
T ss_pred EEEEhhHHHHHhCCCCCCEEE
Confidence 468999999999999877654
No 132
>PF07775 PaRep2b: PaRep2b protein; InterPro: IPR011689 This is a group of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional [].
Probab=24.37 E-value=4.2e+02 Score=24.50 Aligned_cols=85 Identities=19% Similarity=0.213 Sum_probs=49.0
Q ss_pred HHHHHHhhcccCCCCCcEEEEcCCCCeEEE--EcchHH---HHHHhcCCCCHHHHHHHHHHHHHC-ChHHHHH-------
Q 044269 18 QVADLVNKQRSASINDFEIFHDSGSNTWNV--VGAGLQ---RFVQMTNWRYLDSERRFQHGLEAC-GVTKSLM------- 84 (129)
Q Consensus 18 ~v~~~L~~~~~~~~~~f~I~k~~e~g~f~V--~G~~IE---r~v~~tnfd~~es~~rF~r~Lk~~-GV~~aLk------- 84 (129)
++.+.|+..--+.-.+|++.. +|.|+| +-+.|- ++...=+-.-+..+++|..++++. |..+.++
T Consensus 295 ~~~~~~k~agl~eg~~~~~~~---~g~y~I~iT~~GLr~i~~lA~~Gd~~Aer~ir~Lee~a~aR~G~~~~~~L~E~lrp 371 (512)
T PF07775_consen 295 AVVNALKAAGLEEGKDFTVKS---SGQYVIRITYDGLREIQRLARQGDEEAERAIRRLEEIAEARHGFYDLKKLIEYLRP 371 (512)
T ss_pred HHHHHHHhcccccCCcceeec---CCeEEEEEcHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHhcChHHHHhHHhhCCc
Confidence 444444433333346888855 344444 344444 444444444556677888888888 9888777
Q ss_pred -------HcCCCCC-----CEEEEcCEEEEEEe
Q 044269 85 -------KLGVKEG-----DTVIVGDMEMVWHD 105 (129)
Q Consensus 85 -------kaGakeG-----DtV~IGd~EFey~e 105 (129)
+.|..-. =+++|-|+..+|.+
T Consensus 372 a~e~gtvd~~l~VeD~er~vkarV~dvk~e~v~ 404 (512)
T PF07775_consen 372 AREAGTVDLPLAVEDEERGVKARVVDVKVEWVE 404 (512)
T ss_pred hhhcccccCCeEEeeCCCceEEEEEEEEEEEee
Confidence 2232222 24677788888843
No 133
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=24.26 E-value=65 Score=21.71 Aligned_cols=20 Identities=35% Similarity=0.461 Sum_probs=11.4
Q ss_pred CChHHHHH-HcCCCCCCEEEE
Q 044269 77 CGVTKSLM-KLGVKEGDTVIV 96 (129)
Q Consensus 77 ~GV~~aLk-kaGakeGDtV~I 96 (129)
++|.++++ +.|+.+||+|.+
T Consensus 58 Lpv~~~vRk~~g~~~Gd~V~v 78 (80)
T PF08922_consen 58 LPVKAAVRKAIGKEAGDTVEV 78 (80)
T ss_dssp EEE-HHHHHHHT--TTSEEEE
T ss_pred EEEcHHHHHHcCCCCCCEEEE
Confidence 34555554 468999999986
No 134
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=24.21 E-value=85 Score=22.11 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=7.0
Q ss_pred CCCCCEEEE
Q 044269 88 VKEGDTVIV 96 (129)
Q Consensus 88 akeGDtV~I 96 (129)
++|||++.+
T Consensus 73 v~DGDi~~f 81 (83)
T cd04867 73 VQDGDIIFF 81 (83)
T ss_pred eeCCeEEEE
Confidence 788998763
No 135
>PRK10113 cell division modulator; Provisional
Probab=24.11 E-value=47 Score=23.03 Aligned_cols=37 Identities=16% Similarity=0.430 Sum_probs=27.0
Q ss_pred CeEEEEcchH------HHHHHhcCCCCHHHHHHHHHHHHHCCh
Q 044269 43 NTWNVVGAGL------QRFVQMTNWRYLDSERRFQHGLEACGV 79 (129)
Q Consensus 43 g~f~V~G~~I------Er~v~~tnfd~~es~~rF~r~Lk~~GV 79 (129)
.+|++.|+++ |++-+.--|..+||..|..+.++.-+.
T Consensus 35 DVW~LrGKYVAFvl~ge~FrRSPaFs~PEsAQRWAnQirQe~~ 77 (80)
T PRK10113 35 DVWMLRGKYVAFVLMGESFLRSPAFSVPESAQRWANQIRQEGE 77 (80)
T ss_pred hhheeccceEEEEEechhhccCCccCCcHHHHHHHHHhhhhhh
Confidence 3677777775 334444559999999999999886554
No 136
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=24.00 E-value=1.3e+02 Score=22.67 Aligned_cols=23 Identities=13% Similarity=0.011 Sum_probs=17.2
Q ss_pred HCChHHHHHHcCCCCCCEEEEcC
Q 044269 76 ACGVTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 76 ~~GV~~aLkkaGakeGDtV~IGd 98 (129)
.+|+.++|+++|++-++-|.|.+
T Consensus 190 A~g~~~al~~~g~~ip~dv~v~g 212 (264)
T cd06274 190 LEGVLRFLRERPGLAPSDLRIAT 212 (264)
T ss_pred HHHHHHHHHHcCCCCCcceEEEE
Confidence 45889999999998655555543
No 137
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=23.99 E-value=1.2e+02 Score=24.50 Aligned_cols=29 Identities=14% Similarity=0.334 Sum_probs=21.0
Q ss_pred hHHHHHHcC--CCCCCEEEEcCEEEEEEecCCC
Q 044269 79 VTKSLMKLG--VKEGDTVIVGDMEMVWHDSANN 109 (129)
Q Consensus 79 V~~aLkkaG--akeGDtV~IGd~EFey~ed~~~ 109 (129)
+.++|++.. ++++|+|.| ++|++.+-.+.
T Consensus 82 Li~~LkriYg~lr~ed~VTI--i~Fe~v~~~d~ 112 (188)
T COG2411 82 LIEELKRIYGELRDEDIVTI--IEFEVVEKLDK 112 (188)
T ss_pred HHHHHHHHcCcCCCCceEEE--EEEEEehhccc
Confidence 356677776 999999999 67777654433
No 138
>PRK10050 curli assembly protein CsgF; Provisional
Probab=23.97 E-value=2.7e+02 Score=21.34 Aligned_cols=46 Identities=7% Similarity=0.061 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEEEEEEec
Q 044269 61 WRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDMEMVWHDS 106 (129)
Q Consensus 61 fd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~EFey~ed 106 (129)
+.+.-++.||.+-|++.=+...++..+..+--++..||++.++.++
T Consensus 62 ~~~~sald~F~~sLqs~Lls~L~~~i~~G~~G~~~tgd~~i~i~~~ 107 (138)
T PRK10050 62 IETPSALDNFTQAIQSQILGGLLSNINTGKPGRMVTNDYIVDIANR 107 (138)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHhhccCCCCceEEECCEEEEEEec
Confidence 4666779999999999888888887776566688889999997644
No 139
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=23.94 E-value=80 Score=23.32 Aligned_cols=17 Identities=12% Similarity=0.141 Sum_probs=14.5
Q ss_pred CCCCCCEEEEcCEEEEE
Q 044269 87 GVKEGDTVIVGDMEMVW 103 (129)
Q Consensus 87 GakeGDtV~IGd~EFey 103 (129)
-++.||++.|++.+|.-
T Consensus 51 ~i~~Gd~l~i~~~~Y~I 67 (120)
T PRK10377 51 ALQPGLQFELGQHRYPV 67 (120)
T ss_pred ccCCCCEEEECCEEEEE
Confidence 48999999999988753
No 140
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=23.86 E-value=1.4e+02 Score=19.39 Aligned_cols=20 Identities=35% Similarity=0.461 Sum_probs=17.1
Q ss_pred CChHHHHHHcCCCCCCEEEE
Q 044269 77 CGVTKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~I 96 (129)
-=+.++|-...+++|++|+|
T Consensus 62 ~~la~~il~~~~~~g~~v~v 81 (81)
T PF10431_consen 62 PPLADAILSGKIKEGDTVRV 81 (81)
T ss_dssp HHHHHHHHHSCSCTTCEEEE
T ss_pred HHHHHHHHcCCCCCcCEeeC
Confidence 35778889999999999987
No 141
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=23.83 E-value=74 Score=21.73 Aligned_cols=17 Identities=24% Similarity=0.505 Sum_probs=14.2
Q ss_pred HHHHHHcCCCCCCEEEE
Q 044269 80 TKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~I 96 (129)
++-|...||++|++|.+
T Consensus 56 ~~TL~dygI~~gstlhL 72 (75)
T cd01815 56 DQTLDFYGIQSGSTIHI 72 (75)
T ss_pred CCcHHHcCCCCCCEEEE
Confidence 35788999999999975
No 142
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.
Probab=23.81 E-value=52 Score=30.39 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=14.8
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
+.-++.||++||.|+|.+
T Consensus 712 ~dA~~lGI~dGD~V~V~s 729 (797)
T TIGR02166 712 IDAQKRGITNGDMVRIFN 729 (797)
T ss_pred HHHHHhCCCcCCEEEEEe
Confidence 345789999999999953
No 143
>COG0611 ThiL Thiamine monophosphate kinase [Coenzyme metabolism]
Probab=23.77 E-value=53 Score=28.10 Aligned_cols=18 Identities=39% Similarity=0.660 Sum_probs=15.0
Q ss_pred HHHHHcCCCCCCEEEEcC
Q 044269 81 KSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IGd 98 (129)
.+|.+.|||+||.|.+-+
T Consensus 141 ~~l~R~gAkpGD~v~vtG 158 (317)
T COG0611 141 RALLRSGAKPGDLVAVTG 158 (317)
T ss_pred chhhccCCCCCCEEEEcC
Confidence 368888999999999854
No 144
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=23.58 E-value=79 Score=19.58 Aligned_cols=17 Identities=24% Similarity=0.489 Sum_probs=13.7
Q ss_pred HHHHHHcCCCCCCEEEE
Q 044269 80 TKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~I 96 (129)
..-|...|+++|++|.+
T Consensus 53 ~~~L~~~~i~~~~~l~l 69 (72)
T cd01809 53 DETLSEYKVEDGHTIHL 69 (72)
T ss_pred cCcHHHCCCCCCCEEEE
Confidence 34677889999999875
No 145
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=23.34 E-value=84 Score=23.27 Aligned_cols=17 Identities=18% Similarity=0.417 Sum_probs=14.4
Q ss_pred CCCCCCEEEEcCEEEEE
Q 044269 87 GVKEGDTVIVGDMEMVW 103 (129)
Q Consensus 87 GakeGDtV~IGd~EFey 103 (129)
-++.||++.||+.+|.-
T Consensus 51 ~i~~Gd~l~i~~~~Y~I 67 (121)
T TIGR00849 51 TLKPGQVFMIGGIAYPV 67 (121)
T ss_pred CcCCCCEEEECCEEEEE
Confidence 48999999999988753
No 146
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=23.32 E-value=67 Score=21.95 Aligned_cols=15 Identities=40% Similarity=0.539 Sum_probs=11.9
Q ss_pred HHcCCCCCCEEEEcC
Q 044269 84 MKLGVKEGDTVIVGD 98 (129)
Q Consensus 84 kkaGakeGDtV~IGd 98 (129)
+..|+++||.|.|..
T Consensus 24 ~~lgi~~Gd~lei~~ 38 (89)
T COG2002 24 EALGIKEGDVLEIIV 38 (89)
T ss_pred HHhCCCCCCEEEEEE
Confidence 456999999988753
No 147
>TIGR02254 YjjG/YfnB HAD superfamily (subfamily IA) hydrolase, TIGR02254. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). Most likely, these enzymes are phosphatases.
Probab=23.25 E-value=71 Score=23.70 Aligned_cols=20 Identities=15% Similarity=0.443 Sum_probs=16.5
Q ss_pred HHHHHHc-CCCCCCEEEEcCE
Q 044269 80 TKSLMKL-GVKEGDTVIVGDM 99 (129)
Q Consensus 80 ~~aLkka-GakeGDtV~IGd~ 99 (129)
..+|++. |+++.++|.|||-
T Consensus 159 ~~~~~~~~~~~~~~~v~igD~ 179 (224)
T TIGR02254 159 NYALERMPKFSKEEVLMIGDS 179 (224)
T ss_pred HHHHHHhcCCCchheEEECCC
Confidence 4567777 9999999999985
No 148
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=23.16 E-value=58 Score=22.56 Aligned_cols=14 Identities=64% Similarity=0.821 Sum_probs=11.6
Q ss_pred CCCCCCEEEEcCEE
Q 044269 87 GVKEGDTVIVGDME 100 (129)
Q Consensus 87 GakeGDtV~IGd~E 100 (129)
++|+||+|.+.+-.
T Consensus 5 ~Vk~Gd~ViV~~~~ 18 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQ 18 (75)
T ss_pred ccCCCCEEEEecCc
Confidence 68999999987654
No 149
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=23.12 E-value=89 Score=23.99 Aligned_cols=16 Identities=44% Similarity=0.607 Sum_probs=13.4
Q ss_pred CCCCCCEEEEcCEEEE
Q 044269 87 GVKEGDTVIVGDMEMV 102 (129)
Q Consensus 87 GakeGDtV~IGd~EFe 102 (129)
|-+.||+|.++.+.|+
T Consensus 140 Gk~vGD~V~v~~~~~e 155 (160)
T PRK06342 140 GKAVGDVVSVGGQELE 155 (160)
T ss_pred CCCCCCEEEECCEEEE
Confidence 9999999999866654
No 150
>TIGR01509 HAD-SF-IA-v3 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED. HAD subfamilies caused by an overly broad single model.
Probab=23.10 E-value=87 Score=22.29 Aligned_cols=21 Identities=33% Similarity=0.463 Sum_probs=16.2
Q ss_pred HHHHHHcCCCCCCEEEEcCEE
Q 044269 80 TKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IGd~E 100 (129)
..++++.|+.++++|.|||-.
T Consensus 147 ~~~~~~~~~~~~~~~~vgD~~ 167 (183)
T TIGR01509 147 LLALKKLGLKPEECLFVDDSP 167 (183)
T ss_pred HHHHHHcCCCcceEEEEcCCH
Confidence 445666788999999999854
No 151
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=23.01 E-value=81 Score=20.29 Aligned_cols=16 Identities=38% Similarity=0.536 Sum_probs=13.4
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
+.|...|+++|+++.+
T Consensus 52 ~tL~~~~i~~~~tl~l 67 (74)
T cd01810 52 HPLGEYGLKPGCTVFM 67 (74)
T ss_pred CCHHHcCCCCCCEEEE
Confidence 4678889999999875
No 152
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=23.01 E-value=69 Score=22.05 Aligned_cols=13 Identities=31% Similarity=0.659 Sum_probs=9.6
Q ss_pred HHcCCCCCCEEEE
Q 044269 84 MKLGVKEGDTVIV 96 (129)
Q Consensus 84 kkaGakeGDtV~I 96 (129)
+++|.++||...|
T Consensus 49 ~~m~L~PGdEFeI 61 (71)
T PF14250_consen 49 KQMGLKPGDEFEI 61 (71)
T ss_pred HHhCCCCCCEEEE
Confidence 3458899998665
No 153
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=22.93 E-value=54 Score=23.71 Aligned_cols=14 Identities=43% Similarity=0.534 Sum_probs=11.5
Q ss_pred HHcCCCCCCEEEEc
Q 044269 84 MKLGVKEGDTVIVG 97 (129)
Q Consensus 84 kkaGakeGDtV~IG 97 (129)
...|+++||.|.|+
T Consensus 48 ~~~~~~~GD~V~v~ 61 (135)
T PF04246_consen 48 NPIGAKVGDRVEVE 61 (135)
T ss_pred CCCCCCCCCEEEEE
Confidence 35699999999975
No 154
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=22.84 E-value=1.2e+02 Score=23.25 Aligned_cols=23 Identities=26% Similarity=0.434 Sum_probs=17.9
Q ss_pred CChHHHHHHcCCCCCCEEEEcCE
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd~ 99 (129)
+|+.++|+++|++-.|-+.|-++
T Consensus 193 ~g~~~~l~~~g~~vP~di~vvg~ 215 (269)
T cd06297 193 LGALQEAVELGLTVGEDVRVVGF 215 (269)
T ss_pred HHHHHHHHHcCCCCCCceEEEEE
Confidence 68999999999986666665444
No 155
>TIGR01923 menE O-succinylbenzoate-CoA ligase. This model represents an enzyme, O-succinylbenzoate-CoA ligase, which is involved in the fourth step of the menaquinone biosynthesis pathway. O-succinylbenzoate-CoA ligase, together with menB - naphtoate synthase, take 2-succinylbenzoate and convert it into 1,4-di-hydroxy-2- naphtoate.
Probab=22.82 E-value=81 Score=25.60 Aligned_cols=17 Identities=29% Similarity=0.501 Sum_probs=13.0
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
..|+++|++.||.|.|.
T Consensus 14 ~~l~~~g~~~gd~v~i~ 30 (436)
T TIGR01923 14 KALKAQGIRSGSRVALV 30 (436)
T ss_pred HHHHHhCCCCCCEEEEE
Confidence 34566788999999883
No 156
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=22.71 E-value=83 Score=19.71 Aligned_cols=16 Identities=13% Similarity=0.358 Sum_probs=12.9
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
..|.+.|+++|++|.+
T Consensus 54 ~~L~~~~i~~~~~i~l 69 (76)
T cd01803 54 RTLSDYNIQKESTLHL 69 (76)
T ss_pred CcHHHcCCCCCCEEEE
Confidence 3577789999999875
No 157
>PRK14132 riboflavin kinase; Provisional
Probab=22.70 E-value=67 Score=24.15 Aligned_cols=11 Identities=45% Similarity=0.842 Sum_probs=9.8
Q ss_pred cCCCCCCEEEE
Q 044269 86 LGVKEGDTVIV 96 (129)
Q Consensus 86 aGakeGDtV~I 96 (129)
.+.+|||.|.|
T Consensus 114 L~LkDGD~V~I 124 (126)
T PRK14132 114 LNLKDGDVVKI 124 (126)
T ss_pred cCCCCCCEEEE
Confidence 59999999987
No 158
>TIGR02316 propion_prpE propionate--CoA ligase. This family contains one of three readily separable clades of proteins in the group of acetate and propionate--CoA ligases. Characterized members of this family act on propionate. From propionyl-CoA, there is a cyclic degradation pathway: it is ligated by PrpC to the TCA cycle intermediate oxaloacetate, acted upon further by PrpD and an aconitase, then cleaved by PrpB to pyruvate and the TCA cycle intermediate succinate.
Probab=22.64 E-value=79 Score=27.86 Aligned_cols=19 Identities=37% Similarity=0.588 Sum_probs=14.5
Q ss_pred hHHHHHHcCCCCCCEEEEc
Q 044269 79 VTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~IG 97 (129)
+-..|++.|++.||.|.|.
T Consensus 96 lA~~L~~~Gv~~Gd~V~i~ 114 (628)
T TIGR02316 96 FASALRALGVGRGDRVLIY 114 (628)
T ss_pred HHHHHHHcCCCCCCEEEEE
Confidence 3456677788999999874
No 159
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=22.63 E-value=1e+02 Score=20.10 Aligned_cols=43 Identities=14% Similarity=0.173 Sum_probs=29.6
Q ss_pred hHHHHHHhcCCCCHHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCEE
Q 044269 51 GLQRFVQMTNWRYLDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 51 ~IEr~v~~tnfd~~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~E 100 (129)
-++++..++++...++..-+...+..+. + -+.+|+.|.|+++=
T Consensus 5 l~~~ia~~~~~~~~~v~~vl~~~~~~i~--~-----~L~~g~~V~l~~~G 47 (87)
T cd00591 5 LIEAIAEKTGLSKKDAEAAVDAFLDVIT--E-----ALAKGEKVELPGFG 47 (87)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHHHHHH--H-----HHhCCCeEEEeCCE
Confidence 4677888888887777766665555432 2 34588899997653
No 160
>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=22.36 E-value=70 Score=27.08 Aligned_cols=43 Identities=26% Similarity=0.267 Sum_probs=32.6
Q ss_pred chHHHHHHhcCCCC---------HHHHHHHHHHHHHCChHHHHHHcCCCCCC
Q 044269 50 AGLQRFVQMTNWRY---------LDSERRFQHGLEACGVTKSLMKLGVKEGD 92 (129)
Q Consensus 50 ~~IEr~v~~tnfd~---------~es~~rF~r~Lk~~GV~~aLkkaGakeGD 92 (129)
+++.++.+.++.+. .+.+.++.+.++++|+-..|.+.|+.+.|
T Consensus 295 ~~~~~la~~~g~~~~~~~~~~~~~~~~~~i~~l~~~lglp~~L~e~gv~~~~ 346 (377)
T cd08188 295 ERYARIAEALGLDVRGLTTEEAALAVIEAVRRLRAALGVPETLGDLGVKRED 346 (377)
T ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHcCCCHHH
Confidence 45666666666543 34578888999999999999999987755
No 161
>PF02424 ApbE: ApbE family; InterPro: IPR003374 This prokaryotic family of lipoproteins are related to ApbE, from Salmonella typhimurium. ApbE is involved in thiamine synthesis []. More specifically is may be involved in the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) during the biosynthesis of the pyrimidine moiety of thiamine.; PDB: 2O34_B 2O18_C 1VRM_A 3PND_D.
Probab=22.32 E-value=23 Score=28.49 Aligned_cols=32 Identities=28% Similarity=0.436 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcCE
Q 044269 65 DSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 65 es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd~ 99 (129)
-++.+..+.|++.|+..+|.++| ||...+|..
T Consensus 117 yavD~~~~~L~~~gi~~~lVn~G---Gdi~~~G~~ 148 (254)
T PF02424_consen 117 YAVDRAAELLREAGITNALVNAG---GDIRAIGSK 148 (254)
T ss_dssp HHHHHHHHHHHHTTTSCEEEEET---TEEEEESBC
T ss_pred HHHHHHHHHHHHcCCCeEEEeCC---CcEEEeccC
Confidence 46788888999999999999999 999998865
No 162
>COG1021 EntE Peptide arylation enzymes [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.31 E-value=63 Score=29.58 Aligned_cols=17 Identities=53% Similarity=0.890 Sum_probs=14.8
Q ss_pred HHHHHHcCCCCCCEEEE
Q 044269 80 TKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~I 96 (129)
-..|+++||+.||+|.+
T Consensus 67 Aa~l~~lGi~~Gd~vlv 83 (542)
T COG1021 67 AAGLRRLGIKPGDTVLV 83 (542)
T ss_pred HHHHHhcCCCCCCEEEE
Confidence 45788999999999986
No 163
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=22.19 E-value=65 Score=24.65 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=16.9
Q ss_pred HCChHHHHHHcCCCCCCEEEEc
Q 044269 76 ACGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 76 ~~GV~~aLkkaGakeGDtV~IG 97 (129)
.+|+.++|+++|+++.|...||
T Consensus 206 a~g~~~al~~~g~~~~di~vig 227 (289)
T cd01540 206 VLGAVRATEQSGIAAADVIGVG 227 (289)
T ss_pred HHHHHHHHHHcCCCCcceEEEe
Confidence 4578899999999965665554
No 164
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.17 E-value=74 Score=23.57 Aligned_cols=15 Identities=27% Similarity=0.512 Sum_probs=12.1
Q ss_pred HHcCCCCCCEEEEcC
Q 044269 84 MKLGVKEGDTVIVGD 98 (129)
Q Consensus 84 kkaGakeGDtV~IGd 98 (129)
+.+|+++||++...+
T Consensus 30 krr~ik~GD~IiF~~ 44 (111)
T COG4043 30 KRRQIKPGDKIIFNG 44 (111)
T ss_pred hhcCCCCCCEEEEcC
Confidence 457999999998763
No 165
>TIGR03145 cyt_nit_nrfE cytochrome c nitrate reductase biogenesis protein NrfE. Members of this protein family closely resemble the CcmF protein of the CcmABCDEFGH system, or system I, for c-type cytochrome biogenesis (GenProp0678). Members are found, as a rule, next to closely related paralogs of CcmG and CcmH and always located near other genes associated with the cytochrome c nitrite reductase enzyme complex. As a rule, members are found in species that also encode bona fide members of the CcmF, CcmG, and CcmH families.
Probab=22.03 E-value=95 Score=29.01 Aligned_cols=44 Identities=18% Similarity=0.172 Sum_probs=29.6
Q ss_pred HHHHHHHHHHCChH------------HHHHHcCCCCCCEEEEcCEEEEEEecCCCC
Q 044269 67 ERRFQHGLEACGVT------------KSLMKLGVKEGDTVIVGDMEMVWHDSANNP 110 (129)
Q Consensus 67 ~~rF~r~Lk~~GV~------------~aLkkaGakeGDtV~IGd~EFey~ed~~~~ 110 (129)
.++.-..+-+.||- +.=++.-.++||++.++++++.|.+-....
T Consensus 481 ~~~~G~~laH~Gval~~~Gi~~ss~~~~e~~~~l~~Ge~~~~~~y~~~~~~~~~~~ 536 (628)
T TIGR03145 481 LRQLGMVLAHLGVAICAIGAIMVSYFGSEIGVRLAPQQQQPLGGYEFRYQGFENVI 536 (628)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccceeEEEECCCCeEEEcCEEEEEeeceecC
Confidence 35566666666642 222344568999999999999997754433
No 166
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=21.99 E-value=75 Score=23.18 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=18.7
Q ss_pred cCCCCCCEEEEcCEEEEEEec
Q 044269 86 LGVKEGDTVIVGDMEMVWHDS 106 (129)
Q Consensus 86 aGakeGDtV~IGd~EFey~ed 106 (129)
-|++-|+.|+|-.-|=.|+.+
T Consensus 38 ig~~RGskVrIlR~ESYWyn~ 58 (101)
T PLN00045 38 IGPKRGSKVKILRPESYWFND 58 (101)
T ss_pred cccCCCCEEEEccccceeecC
Confidence 489999999999999888766
No 167
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=21.97 E-value=88 Score=20.05 Aligned_cols=17 Identities=12% Similarity=0.178 Sum_probs=14.2
Q ss_pred HHHHHHcCCCCCCEEEE
Q 044269 80 TKSLMKLGVKEGDTVIV 96 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~I 96 (129)
+.-|...|+++|++|.+
T Consensus 53 ~~~L~~~~i~~~~~l~l 69 (74)
T cd01807 53 DKRLSDYSIGPNAKLNL 69 (74)
T ss_pred CCCHHHCCCCCCCEEEE
Confidence 45688999999999975
No 168
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=21.93 E-value=41 Score=20.92 Aligned_cols=16 Identities=38% Similarity=0.744 Sum_probs=11.6
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
..|.+.|+++|++|.+
T Consensus 49 ~tL~~~~i~~~~~I~l 64 (69)
T PF00240_consen 49 KTLSDYGIKDGSTIHL 64 (69)
T ss_dssp SBTGGGTTSTTEEEEE
T ss_pred CcHHHcCCCCCCEEEE
Confidence 4566778888888764
No 169
>PRK10369 heme lyase subunit NrfE; Provisional
Probab=21.93 E-value=86 Score=29.02 Aligned_cols=44 Identities=14% Similarity=0.171 Sum_probs=28.8
Q ss_pred HHHHHHHHHHCChHHH------------HHHcCCCCCCEEEEcCEEEEEEecCCCC
Q 044269 67 ERRFQHGLEACGVTKS------------LMKLGVKEGDTVIVGDMEMVWHDSANNP 110 (129)
Q Consensus 67 ~~rF~r~Lk~~GV~~a------------LkkaGakeGDtV~IGd~EFey~ed~~~~ 110 (129)
.++.--.+-+.|+-=. =++.-.++||++.+++++|.|.+-....
T Consensus 417 ~~~~g~~laH~Gval~~~Gi~~ss~~~~e~~~~l~~G~~~~~~~y~~~~~~~~~~~ 472 (571)
T PRK10369 417 RVQLPALLAHAGVLLFAAGIVVSSVSRQEISLNLQPGQQVTLAGYTFRFERLDLQA 472 (571)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccceeEEEEECCCCcEEEecEEEEEeeeeecc
Confidence 4555666666664221 1233348999999999999997754433
No 170
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.81 E-value=63 Score=24.44 Aligned_cols=41 Identities=10% Similarity=0.117 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHHHHHH---------------HCChHHHHHHcCCCCCCEEEEcCEE
Q 044269 60 NWRYLDSERRFQHGLE---------------ACGVTKSLMKLGVKEGDTVIVGDME 100 (129)
Q Consensus 60 nfd~~es~~rF~r~Lk---------------~~GV~~aLkkaGakeGDtV~IGd~E 100 (129)
+++...+...+.+.|+ .+|+.++|+++|++.++.|.|-++.
T Consensus 153 ~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~~p~di~iig~d 208 (263)
T cd06280 153 APTAEAAEAALAAWLAAPERPEALVASNGLLLLGALRAVRAAGLRIPQDLALAGFD 208 (263)
T ss_pred ccCHHHHHHHHHHHhcCCCCCcEEEECCcHHHHHHHHHHHHcCCCCCCcEEEEEeC
Confidence 3444555666677775 3488999999999988888775443
No 171
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=21.71 E-value=69 Score=19.56 Aligned_cols=17 Identities=24% Similarity=0.710 Sum_probs=13.2
Q ss_pred HcCCCCCCEEE-EcCEEE
Q 044269 85 KLGVKEGDTVI-VGDMEM 101 (129)
Q Consensus 85 kaGakeGDtV~-IGd~EF 101 (129)
++|++.||.|. |++...
T Consensus 28 ~~gl~~GD~I~~Ing~~v 45 (70)
T cd00136 28 RAGLQAGDVILAVNGTDV 45 (70)
T ss_pred HcCCCCCCEEEEECCEEC
Confidence 47999999886 666654
No 172
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=21.71 E-value=87 Score=20.34 Aligned_cols=16 Identities=19% Similarity=0.326 Sum_probs=13.4
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
.-|...|+++|++|.+
T Consensus 51 ~tL~~~~i~~g~~l~v 66 (76)
T cd01800 51 NSLAYYNLANGTIIHL 66 (76)
T ss_pred CcHHHcCCCCCCEEEE
Confidence 4677889999999976
No 173
>PF01041 DegT_DnrJ_EryC1: DegT/DnrJ/EryC1/StrS aminotransferase family; InterPro: IPR000653 This entry represents a family that are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA P72454 from SWISSPROT, StsC P77952 from SWISSPROT and StsS []. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase 2.6.1.50 from EC, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin [].; PDB: 2FNI_A 2FNU_A 2FN6_A 2PO3_A 3UWC_A 1O61_B 1O62_B 1O69_B 1B9I_A 1B9H_A ....
Probab=21.70 E-value=1.3e+02 Score=24.96 Aligned_cols=25 Identities=32% Similarity=0.470 Sum_probs=19.8
Q ss_pred CChHHHHHHcCCCCCCEEEEcCEEE
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGDMEM 101 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd~EF 101 (129)
.++.-+|+..|+++||.|.+-.+.|
T Consensus 51 ~Al~~al~~l~~~~gdeVi~p~~t~ 75 (363)
T PF01041_consen 51 SALHLALRALGLGPGDEVIVPAYTF 75 (363)
T ss_dssp HHHHHHHHHTTGGTTSEEEEESSS-
T ss_pred HHHHHHHHhcCCCcCceEecCCCcc
Confidence 3577889999999999999875443
No 174
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=21.57 E-value=97 Score=27.00 Aligned_cols=18 Identities=28% Similarity=0.471 Sum_probs=16.4
Q ss_pred CCCCCEEEEcCEEEEEEe
Q 044269 88 VKEGDTVIVGDMEMVWHD 105 (129)
Q Consensus 88 akeGDtV~IGd~EFey~e 105 (129)
+++||+|.||++++.+.-
T Consensus 86 L~~GD~I~iG~~~lrv~~ 103 (396)
T TIGR03354 86 LEQGDRLRLGDYEIRVSL 103 (396)
T ss_pred cCCCCEEEECCEEEEEEe
Confidence 889999999999998865
No 175
>TIGR02693 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export.
Probab=21.46 E-value=77 Score=29.98 Aligned_cols=17 Identities=41% Similarity=0.544 Sum_probs=14.7
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+.-++.||++||.|+|.
T Consensus 732 ~DA~~lGI~dGD~V~V~ 748 (806)
T TIGR02693 732 EDAKRLGLKSGDLVEVY 748 (806)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 55678999999999995
No 176
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=21.39 E-value=65 Score=22.22 Aligned_cols=20 Identities=35% Similarity=0.647 Sum_probs=15.4
Q ss_pred HHHHHHcCCCCCCEEEEcCE
Q 044269 80 TKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IGd~ 99 (129)
..++++.|+++.++|.|||-
T Consensus 140 ~~~~~~~~~~p~~~~~vgD~ 159 (176)
T PF13419_consen 140 RRALEKLGIPPEEILFVGDS 159 (176)
T ss_dssp HHHHHHHTSSGGGEEEEESS
T ss_pred HHHHHHcCCCcceEEEEeCC
Confidence 44555569999999999974
No 177
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=21.39 E-value=84 Score=23.46 Aligned_cols=34 Identities=26% Similarity=0.302 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHCChHHHHHHcCCCCCCEEEEcC
Q 044269 64 LDSERRFQHGLEACGVTKSLMKLGVKEGDTVIVGD 98 (129)
Q Consensus 64 ~es~~rF~r~Lk~~GV~~aLkkaGakeGDtV~IGd 98 (129)
.+-+..|.+.+.. +....-...+++.||.|+|-+
T Consensus 104 ~~ei~~l~~~~~~-~~~~~~~~~~~~~Gd~VrI~~ 137 (181)
T PRK05609 104 EKEVEKILKQLQE-GVEKPKPKVDFEVGEMVRVID 137 (181)
T ss_pred HHHHHHHHHHhhc-ccccCccccCCCCCCEEEEec
Confidence 3446666554433 322222357899999999954
No 178
>PF15007 CEP44: Centrosomal spindle body, CEP44
Probab=21.26 E-value=41 Score=25.46 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHCChHHHHHHcCCCCCCE
Q 044269 64 LDSERRFQHGLEACGVTKSLMKLGVKEGDT 93 (129)
Q Consensus 64 ~es~~rF~r~Lk~~GV~~aLkkaGakeGDt 93 (129)
..++.+|++.|++++-...+-..|+..||.
T Consensus 3 ~~~l~~L~~~Lr~~~yp~~vd~~~l~~G~p 32 (131)
T PF15007_consen 3 KGNLRRLEQELRSLKYPDEVDYQGLYKGDP 32 (131)
T ss_pred hhHHHHHHHHHHHCCCCCccCHHHHhcCCH
Confidence 357889999999999888888888888875
No 179
>PRK03584 acetoacetyl-CoA synthetase; Provisional
Probab=21.18 E-value=88 Score=27.67 Aligned_cols=19 Identities=37% Similarity=0.478 Sum_probs=15.0
Q ss_pred hHHHHHHcCCCCCCEEEEc
Q 044269 79 VTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~IG 97 (129)
+-..|++.|++.||+|.|.
T Consensus 127 lA~~L~~~Gv~~gd~V~i~ 145 (655)
T PRK03584 127 LAAALRALGVGPGDRVAAY 145 (655)
T ss_pred HHHHHHHcCCCCCCEEEEE
Confidence 4456778889999999874
No 180
>PF05896 NQRA: Na(+)-translocating NADH-quinone reductase subunit A (NQRA); InterPro: IPR008703 This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+ potential driven by aerobic respiration [].; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0006814 sodium ion transport, 0055114 oxidation-reduction process
Probab=21.16 E-value=85 Score=26.25 Aligned_cols=18 Identities=44% Similarity=0.488 Sum_probs=15.6
Q ss_pred HcCCCCCCEEEEcCEEEE
Q 044269 85 KLGVKEGDTVIVGDMEMV 102 (129)
Q Consensus 85 kaGakeGDtV~IGd~EFe 102 (129)
++=+|+||.|+.|+--|+
T Consensus 42 km~VkeGD~Vk~Gq~LF~ 59 (257)
T PF05896_consen 42 KMLVKEGDRVKAGQPLFE 59 (257)
T ss_pred cEEeccCCEEeCCCeeEe
Confidence 345899999999999997
No 181
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=21.12 E-value=64 Score=30.25 Aligned_cols=17 Identities=29% Similarity=0.405 Sum_probs=14.1
Q ss_pred HHHHHcCCCCCCEEEEc
Q 044269 81 KSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 81 ~aLkkaGakeGDtV~IG 97 (129)
+.-++.||++||.|+|.
T Consensus 753 ~DA~~~GI~dGD~V~V~ 769 (830)
T PRK13532 753 EDAKARGLRRGDEVKVV 769 (830)
T ss_pred HHHHHcCCCCCCEEEEE
Confidence 34468899999999995
No 182
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=21.12 E-value=94 Score=19.44 Aligned_cols=16 Identities=13% Similarity=0.270 Sum_probs=13.0
Q ss_pred HHHHHcCCCCCCEEEE
Q 044269 81 KSLMKLGVKEGDTVIV 96 (129)
Q Consensus 81 ~aLkkaGakeGDtV~I 96 (129)
.-|...|+++|++|.+
T Consensus 54 ~tl~~~~i~~g~~i~l 69 (76)
T cd01806 54 KTAADYKLEGGSVLHL 69 (76)
T ss_pred CCHHHcCCCCCCEEEE
Confidence 3577789999999875
No 183
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=20.87 E-value=68 Score=25.46 Aligned_cols=13 Identities=15% Similarity=0.342 Sum_probs=9.4
Q ss_pred HcCCCCCCEEEEc
Q 044269 85 KLGVKEGDTVIVG 97 (129)
Q Consensus 85 kaGakeGDtV~IG 97 (129)
..=+++||.|.|=
T Consensus 137 tv~a~aGDvifiP 149 (176)
T COG4766 137 TVIAGAGDVIFIP 149 (176)
T ss_pred eEecCCCcEEEec
Confidence 3457888888883
No 184
>PRK10524 prpE propionyl-CoA synthetase; Provisional
Probab=20.79 E-value=91 Score=27.31 Aligned_cols=18 Identities=39% Similarity=0.621 Sum_probs=14.2
Q ss_pred HHHHHHcCCCCCCEEEEc
Q 044269 80 TKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 80 ~~aLkkaGakeGDtV~IG 97 (129)
-..|++.|++.||.|.|.
T Consensus 98 A~~L~~~Gv~~gd~V~i~ 115 (629)
T PRK10524 98 AAMLRSLGVQRGDRVLIY 115 (629)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 356677788999999885
No 185
>PLN02860 o-succinylbenzoate-CoA ligase
Probab=20.74 E-value=90 Score=26.90 Aligned_cols=19 Identities=32% Similarity=0.796 Sum_probs=14.5
Q ss_pred hHHHHHHcCCCCCCEEEEc
Q 044269 79 VTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 79 V~~aLkkaGakeGDtV~IG 97 (129)
+-.+|.++|+++||+|-|.
T Consensus 45 la~~L~~~Gv~~gd~V~v~ 63 (563)
T PLN02860 45 LAAGLLRLGLRNGDVVAIA 63 (563)
T ss_pred HHHHHHHhCCCCCCEEEEE
Confidence 4445677788999999874
No 186
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=20.30 E-value=72 Score=24.06 Aligned_cols=21 Identities=24% Similarity=0.273 Sum_probs=15.9
Q ss_pred CChHHHHHHcCCCCCCEEEEc
Q 044269 77 CGVTKSLMKLGVKEGDTVIVG 97 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IG 97 (129)
+|+.++|+++|++.++.|.|-
T Consensus 188 ~g~~~~l~~~g~~~p~di~ii 208 (265)
T cd06285 188 IGVMGAARDRGLRVPDDVALV 208 (265)
T ss_pred HHHHHHHHHcCCCCCcceEEE
Confidence 589999999999855445543
No 187
>COG1827 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]
Probab=20.28 E-value=1.6e+02 Score=23.14 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=23.3
Q ss_pred EEEEcchHHHHHHhcCCCCHHHHHHHHHHHHHCC
Q 044269 45 WNVVGAGLQRFVQMTNWRYLDSERRFQHGLEACG 78 (129)
Q Consensus 45 f~V~G~~IEr~v~~tnfd~~es~~rF~r~Lk~~G 78 (129)
..|.|+ +-+..+..+++.+.+|.+.|+..|
T Consensus 101 H~IyG~----i~~~l~v~~~edve~fv~~Le~s~ 130 (168)
T COG1827 101 HPIYGE----ITASLDVKDREDVERFVEKLEESG 130 (168)
T ss_pred eeeecc----cccccccCCHHHHHHHHHHHHHcC
Confidence 445553 345667889999999999999998
No 188
>TIGR02369 trimeth_pyl trimethylamine:corrinoid methyltransferase. This model represents a distinct subfamily of pfam06253. All members here are trimethylamine:corrinoid methyltransferases that contain a critical pyrrolysine residue incorporated during translation via a special tRNA for a TAG (amber) codon. Known members so far are from the genus Methanosarcina. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with dimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates trimethylamine, leaving dimethylamine, and methylates the prosthetic group of its small cognate corrinoid protein, MttC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence.
Probab=20.26 E-value=1e+02 Score=28.03 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=19.4
Q ss_pred HHHHHCChHH-------HHHHcCCC---CCCEEEEc
Q 044269 72 HGLEACGVTK-------SLMKLGVK---EGDTVIVG 97 (129)
Q Consensus 72 r~Lk~~GV~~-------aLkkaGak---eGDtV~IG 97 (129)
++|+..||.- .++++|++ +|..|+|.
T Consensus 33 ~iLee~Gi~~~~~eale~~~~aGa~V~~~~~rV~~p 68 (489)
T TIGR02369 33 DVLMNPGVQVSDPEARQIFKENGCEVDEKTNVVKIP 68 (489)
T ss_pred HHHHHcCCccCCHHHHHHHHHcCCEEcCCCCEEEeC
Confidence 3677777654 67899999 56778876
No 189
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=20.16 E-value=72 Score=20.30 Aligned_cols=20 Identities=30% Similarity=0.446 Sum_probs=15.3
Q ss_pred HHHcCCCCCCEE-EEcCEEEE
Q 044269 83 LMKLGVKEGDTV-IVGDMEMV 102 (129)
Q Consensus 83 LkkaGakeGDtV-~IGd~EFe 102 (129)
..++|+++||.| .|++....
T Consensus 37 a~~~gl~~GD~I~~Ing~~i~ 57 (90)
T cd00987 37 AAKAGLKPGDVILAVNGKPVK 57 (90)
T ss_pred HHHcCCCcCCEEEEECCEECC
Confidence 456899999965 78888764
No 190
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.14 E-value=65 Score=25.43 Aligned_cols=23 Identities=26% Similarity=0.494 Sum_probs=17.7
Q ss_pred CChHHHHHHcCCCCCCEEEEcCE
Q 044269 77 CGVTKSLMKLGVKEGDTVIVGDM 99 (129)
Q Consensus 77 ~GV~~aLkkaGakeGDtV~IGd~ 99 (129)
+|+.++|+++|++-++.|.|-++
T Consensus 215 ~g~~~al~~~g~~vp~di~vig~ 237 (305)
T cd06324 215 FGALRAAKEAGRKPGRDVLFGGV 237 (305)
T ss_pred HHHHHHHHHcCCCcCCCEEEEec
Confidence 68999999999997655555444
No 191
>PRK09798 antitoxin MazE; Provisional
Probab=20.13 E-value=95 Score=21.33 Aligned_cols=15 Identities=20% Similarity=0.284 Sum_probs=12.5
Q ss_pred HHHHcCCCCCCEEEE
Q 044269 82 SLMKLGVKEGDTVIV 96 (129)
Q Consensus 82 aLkkaGakeGDtV~I 96 (129)
.|+++|+.+||+|.|
T Consensus 21 ~l~~l~l~~g~~vei 35 (82)
T PRK09798 21 LMQALNLNIDDEVKI 35 (82)
T ss_pred HHHHcCCCCCCEEEE
Confidence 477889999999865
Done!