Query psy13876
Match_columns 118
No_of_seqs 121 out of 1116
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 22:39:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13876.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13876hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0479|consensus 100.0 6E-31 1.3E-35 215.4 9.1 109 5-118 206-324 (818)
2 KOG0478|consensus 100.0 9.7E-31 2.1E-35 216.6 5.9 113 6-118 323-452 (804)
3 COG1241 MCM2 Predicted ATPase 100.0 1.4E-28 3E-33 205.7 12.7 107 7-118 191-309 (682)
4 KOG0481|consensus 100.0 2.4E-28 5.1E-33 198.2 9.0 113 5-118 228-354 (729)
5 PTZ00111 DNA replication licen 100.0 1.6E-27 3.5E-32 203.6 13.8 106 12-117 346-472 (915)
6 smart00350 MCM minichromosome 99.9 2.2E-26 4.7E-31 188.3 13.8 112 6-117 98-225 (509)
7 KOG0477|consensus 99.9 1.6E-27 3.5E-32 196.3 5.8 110 5-118 351-472 (854)
8 KOG0482|consensus 99.9 4.3E-27 9.4E-32 190.7 6.4 114 5-118 244-365 (721)
9 KOG0480|consensus 99.9 1.6E-26 3.4E-31 190.6 8.5 113 6-118 218-368 (764)
10 PF00493 MCM: MCM2/3/5 family 99.3 7.1E-13 1.5E-17 103.8 0.5 44 74-117 2-46 (331)
11 PF01336 tRNA_anti-codon: OB-f 89.5 2.1 4.6E-05 25.2 5.9 43 13-58 28-74 (75)
12 cd04496 SSB_OBF SSB_OBF: A sub 88.8 1.9 4.2E-05 27.0 5.6 49 9-57 41-98 (100)
13 PF04076 BOF: Bacterial OB fol 86.3 4.3 9.3E-05 26.9 6.2 42 13-58 60-103 (103)
14 PF00436 SSB: Single-strand bi 86.0 2.9 6.4E-05 26.5 5.3 49 10-58 46-103 (104)
15 cd04486 YhcR_OBF_like YhcR_OBF 82.0 3.3 7.2E-05 25.8 4.1 28 13-42 34-61 (78)
16 PF13567 DUF4131: Domain of un 81.9 0.86 1.9E-05 30.7 1.5 50 8-57 111-165 (176)
17 COG2871 NqrF Na+-transporting 79.1 1.1 2.4E-05 35.5 1.4 39 1-40 230-268 (410)
18 cd04482 RPA2_OBF_like RPA2_OBF 78.6 4.9 0.00011 25.7 4.1 22 21-42 43-64 (91)
19 PRK06763 F0F1 ATP synthase sub 78.3 0.55 1.2E-05 34.9 -0.5 40 14-60 65-104 (213)
20 KOG3416|consensus 76.1 3.1 6.6E-05 28.8 2.7 30 12-41 48-77 (134)
21 PF12869 tRNA_anti-like: tRNA_ 74.4 3.2 7E-05 28.1 2.6 29 13-41 99-132 (144)
22 PF11325 DUF3127: Domain of un 74.2 14 0.00031 23.6 5.3 36 7-42 31-69 (84)
23 PRK06752 single-stranded DNA-b 73.9 20 0.00042 23.6 6.2 52 11-62 46-106 (112)
24 TIGR00621 ssb single stranded 73.3 14 0.00031 26.1 5.7 51 11-61 50-109 (164)
25 cd04487 RecJ_OBF2_like RecJ_OB 72.8 19 0.00041 22.0 5.9 29 22-52 40-68 (73)
26 PF08021 FAD_binding_9: Sidero 72.5 3.5 7.6E-05 27.6 2.3 24 13-36 83-112 (117)
27 TIGR00156 conserved hypothetic 72.3 9.2 0.0002 26.3 4.4 41 13-57 83-125 (126)
28 cd04321 ScAspRS_mt_like_N ScAs 71.2 22 0.00048 22.1 6.5 47 13-59 30-84 (86)
29 PRK06863 single-stranded DNA-b 70.4 13 0.00028 26.7 5.0 54 10-63 50-112 (168)
30 PRK07459 single-stranded DNA-b 69.6 25 0.00053 23.7 6.0 52 11-62 43-104 (121)
31 COG4043 Preprotein translocase 69.1 4.4 9.5E-05 27.0 2.1 28 12-39 20-48 (111)
32 PRK00036 primosomal replicatio 66.7 26 0.00055 23.5 5.5 51 10-61 41-98 (107)
33 cd04318 EcAsnRS_like_N EcAsnRS 66.5 27 0.00058 21.3 6.6 45 13-58 30-79 (82)
34 cd04478 RPA2_DBD_D RPA2_DBD_D: 64.8 18 0.00039 22.6 4.4 36 22-61 44-79 (95)
35 PRK10053 hypothetical protein; 63.5 17 0.00038 25.1 4.3 41 13-57 87-129 (130)
36 PRK07274 single-stranded DNA-b 62.4 46 0.001 22.6 6.4 51 11-61 46-104 (131)
37 smart00739 KOW KOW (Kyprides, 59.8 8.2 0.00018 18.5 1.7 11 26-36 2-12 (28)
38 cd04316 ND_PkAspRS_like_N ND_P 59.7 45 0.00097 21.5 6.6 47 14-61 42-96 (108)
39 PRK02801 primosomal replicatio 57.5 42 0.00091 21.7 5.2 44 14-57 50-98 (101)
40 cd04317 EcAspRS_like_N EcAspRS 57.5 55 0.0012 21.9 6.2 49 14-62 44-104 (135)
41 PRK08486 single-stranded DNA-b 56.6 44 0.00095 24.3 5.7 52 11-62 48-108 (182)
42 PRK06958 single-stranded DNA-b 56.5 49 0.0011 24.1 5.9 52 11-62 51-111 (182)
43 PRK08182 single-stranded DNA-b 56.3 56 0.0012 22.8 6.0 52 11-62 53-113 (148)
44 cd03695 CysN_NodQ_II CysN_NodQ 55.5 19 0.00042 22.2 3.2 15 22-36 23-37 (81)
45 PRK07275 single-stranded DNA-b 55.4 55 0.0012 23.3 5.9 53 10-62 45-106 (162)
46 cd04100 Asp_Lys_Asn_RS_N Asp_L 54.8 47 0.001 20.3 7.0 30 13-42 28-64 (85)
47 PRK05853 hypothetical protein; 53.0 40 0.00087 24.0 4.9 46 11-56 42-96 (161)
48 PF02699 YajC: Preprotein tran 50.1 6 0.00013 24.9 0.2 20 20-39 31-51 (82)
49 PF14805 THDPS_N_2: Tetrahydro 49.7 14 0.00031 22.8 1.9 12 100-111 56-67 (70)
50 PRK06293 single-stranded DNA-b 49.6 70 0.0015 22.8 5.7 51 11-61 42-101 (161)
51 PRK08763 single-stranded DNA-b 49.5 91 0.002 22.2 6.3 52 11-62 51-111 (164)
52 PRK07772 single-stranded DNA-b 49.0 50 0.0011 24.1 4.9 31 11-41 52-86 (186)
53 PF02261 Asp_decarbox: Asparta 48.2 20 0.00043 24.4 2.5 24 15-38 68-91 (116)
54 cd06919 Asp_decarbox Aspartate 48.1 15 0.00032 24.8 1.9 25 13-37 65-89 (111)
55 TIGR03635 S17_bact 30S ribosom 47.1 25 0.00054 21.7 2.7 25 12-37 36-60 (71)
56 PF11948 DUF3465: Protein of u 46.6 60 0.0013 22.5 4.7 32 13-44 70-104 (131)
57 cd03696 selB_II selB_II: this 46.4 24 0.00053 21.6 2.6 19 16-34 47-65 (83)
58 cd04323 AsnRS_cyto_like_N AsnR 46.4 67 0.0015 19.6 4.9 20 23-42 44-63 (84)
59 PRK06488 sulfur carrier protei 46.3 26 0.00057 20.5 2.7 26 11-36 28-60 (65)
60 TIGR00739 yajC preprotein tran 45.7 5.1 0.00011 25.5 -0.6 20 20-39 32-52 (84)
61 PRK05159 aspC aspartyl-tRNA sy 44.8 92 0.002 25.5 6.4 49 13-62 45-100 (437)
62 TIGR00223 panD L-aspartate-alp 44.3 18 0.00039 25.0 1.9 24 14-37 67-90 (126)
63 cd06555 ASCH_PF0470_like ASC-1 44.1 30 0.00065 23.1 2.9 26 12-37 18-43 (109)
64 PRK05449 aspartate alpha-decar 44.1 18 0.00039 25.0 1.8 25 13-37 66-90 (126)
65 PF00970 FAD_binding_6: Oxidor 43.0 41 0.00088 20.9 3.3 26 13-38 62-94 (99)
66 PF14427 Pput2613-deam: Pput_2 42.9 18 0.00039 24.5 1.6 25 18-42 55-79 (118)
67 COG2965 PriB Primosomal replic 42.2 86 0.0019 20.8 4.7 38 21-58 63-101 (103)
68 cd04319 PhAsnRS_like_N PhAsnRS 42.0 91 0.002 19.9 6.7 47 14-61 29-82 (103)
69 PF01957 NfeD: NfeD-like C-ter 40.9 40 0.00087 22.3 3.2 21 13-37 113-133 (144)
70 PRK00484 lysS lysyl-tRNA synth 40.7 1.2E+02 0.0027 25.3 6.6 46 13-61 83-136 (491)
71 PRK06751 single-stranded DNA-b 39.6 77 0.0017 22.8 4.7 52 11-62 46-106 (173)
72 PF01455 HupF_HypC: HupF/HypC 39.5 24 0.00052 21.5 1.7 19 18-36 30-48 (68)
73 cd03698 eRF3_II_like eRF3_II_l 39.4 31 0.00068 21.1 2.3 15 19-33 50-64 (83)
74 KOG3411|consensus 38.3 19 0.00042 25.1 1.3 42 77-118 42-85 (143)
75 PF04246 RseC_MucC: Positive r 38.0 38 0.00082 22.8 2.8 15 21-35 47-61 (135)
76 COG1862 YajC Preprotein transl 37.7 9.3 0.0002 25.1 -0.3 20 20-39 38-58 (97)
77 PF00842 Ala_racemase_C: Alani 37.7 38 0.00083 23.0 2.7 17 21-37 79-95 (129)
78 cd03697 EFTU_II EFTU_II: Elong 37.7 39 0.00085 20.9 2.6 17 18-34 51-67 (87)
79 TIGR03630 arch_S17P archaeal r 37.5 51 0.0011 21.9 3.2 26 12-37 62-87 (102)
80 PRK05610 rpsQ 30S ribosomal pr 37.3 41 0.0009 21.4 2.7 25 12-37 41-65 (84)
81 cd03694 GTPBP_II Domain II of 37.2 36 0.00078 21.2 2.4 19 16-34 51-69 (87)
82 PF07107 WI12: Wound-induced p 37.2 42 0.00091 22.6 2.7 34 1-38 1-34 (109)
83 cd04483 hOBFC1_like hOBFC1_lik 37.0 1.1E+02 0.0024 19.4 4.8 21 22-42 59-79 (92)
84 PRK05585 yajC preprotein trans 37.0 10 0.00022 25.2 -0.3 21 20-40 47-68 (106)
85 PF14306 PUA_2: PUA-like domai 36.9 29 0.00062 24.7 2.1 35 1-36 69-103 (160)
86 PF14801 GCD14_N: tRNA methylt 36.8 25 0.00054 20.7 1.4 14 24-37 4-17 (54)
87 PRK13732 single-stranded DNA-b 36.5 1.6E+02 0.0034 21.3 5.9 52 11-62 53-115 (175)
88 PRK08572 rps17p 30S ribosomal 36.1 52 0.0011 22.1 3.1 26 12-37 64-89 (108)
89 PLN02502 lysyl-tRNA synthetase 35.9 1.6E+02 0.0035 25.1 6.7 35 25-62 160-194 (553)
90 TIGR00074 hypC_hupF hydrogenas 35.3 25 0.00055 22.0 1.4 23 10-36 24-46 (76)
91 cd03693 EF1_alpha_II EF1_alpha 35.2 62 0.0013 20.2 3.3 13 23-35 28-40 (91)
92 PF03100 CcmE: CcmE; InterPro 35.0 76 0.0017 21.5 3.9 27 12-38 82-108 (131)
93 PF11604 CusF_Ec: Copper bindi 34.0 49 0.0011 20.0 2.5 25 13-37 29-54 (70)
94 PRK05886 yajC preprotein trans 33.6 14 0.0003 24.8 -0.0 19 20-38 33-52 (109)
95 PF08696 Dna2: DNA replication 33.4 63 0.0014 23.7 3.5 27 12-38 10-37 (209)
96 cd04467 S1_aIF5A S1_aIF5A: Arc 33.2 49 0.0011 19.5 2.3 24 12-35 25-48 (57)
97 COG0853 PanD Aspartate 1-decar 33.1 29 0.00063 23.9 1.5 25 13-37 65-89 (126)
98 TIGR00457 asnS asparaginyl-tRN 32.5 2E+02 0.0043 23.7 6.6 49 12-61 46-101 (453)
99 PF08978 Reoviridae_Vp9: Reovi 31.6 15 0.00031 28.0 -0.2 21 20-40 212-232 (280)
100 COG1571 Predicted DNA-binding 31.5 43 0.00092 27.7 2.5 22 20-41 310-331 (421)
101 PF13742 tRNA_anti_2: OB-fold 31.5 1E+02 0.0022 19.7 3.9 28 24-51 67-94 (99)
102 COG4118 Phd Antitoxin of toxin 31.5 18 0.0004 23.0 0.3 16 21-36 16-31 (84)
103 PRK11507 ribosome-associated p 31.2 26 0.00057 21.6 1.0 14 24-37 51-64 (70)
104 PF01835 A2M_N: MG2 domain; I 30.8 53 0.0012 20.5 2.4 18 25-42 10-27 (99)
105 cd04089 eRF3_II eRF3_II: domai 30.5 70 0.0015 19.5 2.9 17 20-36 20-36 (82)
106 PRK06341 single-stranded DNA-b 30.5 1.6E+02 0.0034 21.1 5.0 46 11-56 52-107 (166)
107 COG0186 RpsQ Ribosomal protein 30.4 73 0.0016 20.5 2.9 16 22-37 52-67 (87)
108 COG2375 ViuB Siderophore-inter 29.8 42 0.00092 26.0 2.1 24 14-37 104-133 (265)
109 PHA03256 BDLF3; Provisional 29.7 97 0.0021 19.4 3.3 45 70-114 15-70 (77)
110 cd04488 RecG_wedge_OBF RecG_we 29.7 1.1E+02 0.0024 17.3 3.6 20 22-41 42-61 (75)
111 TIGR00458 aspS_arch aspartyl-t 29.7 2.4E+02 0.0051 23.1 6.5 48 13-61 41-96 (428)
112 PRK07440 hypothetical protein; 29.6 97 0.0021 18.6 3.3 28 10-37 32-66 (70)
113 CHL00181 cbbX CbbX; Provisiona 29.2 43 0.00093 25.8 2.0 23 85-107 13-35 (287)
114 PF12982 DUF3866: Protein of u 29.1 29 0.00062 27.6 1.1 21 17-37 4-24 (320)
115 TIGR01683 thiS thiamine biosyn 28.7 78 0.0017 18.4 2.7 26 11-36 27-59 (64)
116 smart00357 CSP Cold shock prot 28.7 47 0.001 18.5 1.7 22 15-36 22-47 (64)
117 cd04320 AspRS_cyto_N AspRS_cyt 28.5 1.6E+02 0.0034 18.6 6.5 50 13-62 29-92 (102)
118 PRK14533 groES co-chaperonin G 28.5 46 0.001 21.4 1.8 12 24-35 52-63 (91)
119 TIGR03177 pilus_cpaB Flp pilus 28.2 79 0.0017 23.8 3.3 30 12-41 115-146 (261)
120 cd04322 LysRS_N LysRS_N: N-ter 27.9 1.7E+02 0.0036 18.7 4.8 33 26-61 50-82 (108)
121 PF14485 DUF4431: Domain of un 27.8 1.2E+02 0.0026 17.1 3.3 36 14-49 2-39 (48)
122 PTZ00414 10 kDa heat shock pro 27.5 51 0.0011 21.7 1.9 12 23-34 60-71 (100)
123 PRK06461 single-stranded DNA-b 27.4 1.1E+02 0.0024 20.6 3.7 27 13-39 52-78 (129)
124 PF08206 OB_RNB: Ribonuclease 27.3 45 0.00098 19.2 1.5 25 13-37 19-43 (58)
125 cd00320 cpn10 Chaperonin 10 Kd 27.3 38 0.00082 21.8 1.2 13 23-35 55-67 (93)
126 PRK06531 yajC preprotein trans 27.3 15 0.00033 24.7 -0.6 20 20-39 31-51 (113)
127 CHL00143 rpl3 ribosomal protei 27.2 46 0.001 24.8 1.8 17 23-39 99-115 (207)
128 PTZ00241 40S ribosomal protein 27.1 73 0.0016 22.8 2.8 22 16-37 107-128 (158)
129 PF14444 S1-like: S1-like 27.0 1.2E+02 0.0025 18.1 3.2 15 27-41 35-49 (58)
130 KOG1641|consensus 27.0 50 0.0011 22.0 1.8 15 20-34 60-75 (104)
131 PF14964 DUF4507: Domain of un 27.0 1E+02 0.0022 25.0 3.9 31 84-116 72-102 (362)
132 cd04090 eEF2_II_snRNP Loc2 eEF 26.9 42 0.00092 21.1 1.4 16 22-37 67-82 (94)
133 TIGR00499 lysS_bact lysyl-tRNA 26.8 2.9E+02 0.0063 23.1 6.7 47 13-62 82-137 (496)
134 TIGR00008 infA translation ini 26.7 49 0.0011 20.3 1.6 11 25-35 44-54 (68)
135 PF00337 Gal-bind_lectin: Gala 26.6 54 0.0012 21.7 2.0 20 21-40 5-24 (133)
136 PRK05659 sulfur carrier protei 26.5 1.1E+02 0.0024 17.6 3.2 28 10-37 28-62 (66)
137 PRK12445 lysyl-tRNA synthetase 26.5 2.5E+02 0.0055 23.6 6.3 36 24-62 114-149 (505)
138 PRK13289 bifunctional nitric o 26.4 90 0.002 24.6 3.5 18 21-38 234-251 (399)
139 cd00604 IPT_CGTD IPT domain (d 26.1 52 0.0011 20.5 1.7 12 26-37 11-22 (81)
140 PRK10413 hydrogenase 2 accesso 25.8 1E+02 0.0023 19.4 3.1 26 10-35 27-52 (82)
141 PRK13150 cytochrome c-type bio 25.8 1.3E+02 0.0029 21.4 3.9 28 12-39 89-116 (159)
142 cd04491 SoSSB_OBF SoSSB_OBF: A 25.7 1.6E+02 0.0034 17.7 4.0 29 13-41 35-65 (82)
143 COG2914 Uncharacterized protei 25.7 49 0.0011 21.8 1.5 21 22-42 61-81 (99)
144 PRK12442 translation initiatio 25.6 46 0.001 21.5 1.4 11 25-35 46-56 (87)
145 PRK05305 phosphatidylserine de 25.6 70 0.0015 23.4 2.6 24 12-35 175-198 (206)
146 smart00276 GLECT Galectin. Gal 25.6 70 0.0015 21.3 2.4 21 21-41 4-24 (128)
147 PRK09010 single-stranded DNA-b 25.5 2.6E+02 0.0057 20.1 5.8 31 11-41 53-87 (177)
148 cd06193 siderophore_interactin 25.5 62 0.0013 23.6 2.3 17 22-38 95-111 (235)
149 COG3111 Periplasmic protein wi 24.9 1E+02 0.0022 21.3 3.0 31 25-59 97-127 (128)
150 PF02080 TrkA_C: TrkA-C domain 24.7 53 0.0011 19.0 1.5 15 23-37 45-59 (71)
151 KOG0554|consensus 24.7 4.1E+02 0.0089 22.1 8.3 73 7-80 45-118 (446)
152 PRK06642 single-stranded DNA-b 24.7 1.3E+02 0.0028 21.0 3.7 46 11-56 52-107 (152)
153 COG2374 Predicted extracellula 24.6 1.3E+02 0.0028 26.9 4.3 29 12-41 253-281 (798)
154 PRK08395 fumarate hydratase; P 24.3 38 0.00082 24.3 0.9 21 19-39 8-28 (162)
155 PF08541 ACP_syn_III_C: 3-Oxoa 24.2 56 0.0012 20.0 1.6 13 25-37 65-77 (90)
156 cd06541 ASCH ASC-1 homology or 24.2 89 0.0019 20.2 2.6 23 12-34 17-39 (105)
157 cd06187 O2ase_reductase_like T 24.1 96 0.0021 22.0 3.1 27 12-38 54-88 (224)
158 PRK13165 cytochrome c-type bio 24.0 1.4E+02 0.0031 21.3 3.8 28 12-39 89-116 (160)
159 PF08240 ADH_N: Alcohol dehydr 23.5 1E+02 0.0022 19.5 2.8 21 19-39 46-66 (109)
160 PF14437 MafB19-deam: MafB19-l 23.5 38 0.00082 23.9 0.8 21 7-27 94-115 (146)
161 PRK02983 lysS lysyl-tRNA synth 23.4 3.4E+02 0.0074 25.2 6.9 46 13-61 680-734 (1094)
162 TIGR00164 PS_decarb_rel phosph 23.4 90 0.0019 22.5 2.7 24 12-35 155-178 (189)
163 PRK06944 sulfur carrier protei 23.3 1.1E+02 0.0023 17.6 2.6 23 13-35 30-59 (65)
164 CHL00142 rps17 ribosomal prote 23.2 1.3E+02 0.0029 19.1 3.2 17 21-37 46-62 (84)
165 KOG3141|consensus 23.2 56 0.0012 25.8 1.7 16 23-38 160-175 (310)
166 PF01281 Ribosomal_L9_N: Ribos 22.7 70 0.0015 18.1 1.7 21 14-34 1-21 (48)
167 smart00719 Plus3 Short conserv 22.7 1.6E+02 0.0034 19.3 3.6 12 68-79 92-103 (109)
168 TIGR03595 Obg_CgtA_exten Obg f 22.6 59 0.0013 19.7 1.4 13 25-37 53-65 (69)
169 cd06209 BenDO_FAD_NAD Benzoate 22.1 1.4E+02 0.003 21.4 3.6 27 12-38 59-93 (228)
170 cd04451 S1_IF1 S1_IF1: Transla 21.9 1.3E+02 0.0029 17.4 2.9 23 13-35 25-50 (64)
171 cd06189 flavin_oxioreductase N 21.9 1.4E+02 0.0031 21.3 3.6 27 12-38 54-88 (224)
172 PLN02603 asparaginyl-tRNA synt 21.9 4.7E+02 0.01 22.5 7.0 49 12-61 137-192 (565)
173 cd04088 EFG_mtEFG_II EFG_mtEFG 21.9 53 0.0012 19.8 1.1 18 20-37 55-72 (83)
174 PRK08053 sulfur carrier protei 21.9 1.1E+02 0.0023 18.0 2.5 27 11-37 29-62 (66)
175 TIGR02988 YaaA_near_RecF S4 do 21.6 60 0.0013 18.6 1.3 11 24-34 48-58 (59)
176 PF11302 DUF3104: Protein of u 21.5 59 0.0013 20.4 1.3 15 24-38 4-18 (75)
177 COG2104 ThiS Sulfur transfer p 21.5 1.3E+02 0.0027 18.3 2.7 27 11-37 31-64 (68)
178 PRK10409 hydrogenase assembly 21.5 1.4E+02 0.0031 19.2 3.1 11 25-35 41-51 (90)
179 COG1585 Membrane protein impli 21.3 1.2E+02 0.0027 20.9 3.0 10 28-37 121-130 (140)
180 KOG3606|consensus 21.1 2E+02 0.0044 22.8 4.4 59 2-62 163-231 (358)
181 PRK08228 L(+)-tartrate dehydra 21.1 46 0.001 24.8 0.8 26 14-39 6-31 (204)
182 CHL00141 rpl24 ribosomal prote 21.0 68 0.0015 20.3 1.5 11 25-35 8-18 (83)
183 PF10381 Autophagy_Cterm: Auto 21.0 93 0.002 15.4 1.7 14 85-98 7-20 (25)
184 cd06200 SiR_like1 Cytochrome p 21.0 69 0.0015 23.7 1.8 17 21-37 82-98 (245)
185 PRK00001 rplC 50S ribosomal pr 20.8 76 0.0017 23.7 1.9 16 24-39 98-113 (210)
186 TIGR03625 L3_bact 50S ribosoma 20.6 83 0.0018 23.4 2.1 16 24-39 97-112 (202)
187 PF09932 DUF2164: Uncharacteri 20.6 34 0.00074 21.4 0.0 28 80-107 30-59 (76)
188 cd06213 oxygenase_e_transfer_s 20.4 1.7E+02 0.0037 20.9 3.8 27 12-38 57-91 (227)
189 PF09356 Phage_BR0599: Phage c 20.2 1.4E+02 0.0029 18.6 2.8 21 15-35 30-50 (80)
No 1
>KOG0479|consensus
Probab=99.97 E-value=6e-31 Score=215.43 Aligned_cols=109 Identities=30% Similarity=0.401 Sum_probs=96.7
Q ss_pred cCCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcC---C---CCccceEEEEEEEEEccccccCCCCCCCCCHHHHH
Q psy13876 5 TGASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSS---P---GLLSDTYIEAQRIQCLSKALEDDKPAGTLSEEEMA 78 (118)
Q Consensus 5 ~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~---~---~~~~~~yl~a~~I~~~~~~~~~~~~~~~~~~e~i~ 78 (118)
-+|||+||+++|+|++||||+|+|||||.|.|+||... + ...|++.|-||||+..+++. ...|+.+++.
T Consensus 206 APaGQLPRSVDvilddDLVD~~KPGDRV~ivG~yr~Lp~k~~g~tsg~FRTvliaNni~~l~ke~-----~~~~t~~Di~ 280 (818)
T KOG0479|consen 206 APAGQLPRSVDVILDDDLVDRVKPGDRVNIVGIYRSLPGKSNGNTSGTFRTVLIANNIELLSKEA-----APDFTDEDIR 280 (818)
T ss_pred CCCCCCCcceeEEecccccccCCCCCeeEEEEEEeeccCccCCcccceeEEEEEeccHHhhcccc-----cccCChhhHH
Confidence 46999999999999999999999999999999999884 2 26889999999999887653 3567777755
Q ss_pred ---hhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 79 ---ELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 79 ---~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
.|+ .+|+|+.|++|+|||||||+.||+||+|+|+||+.|+
T Consensus 281 ~i~klsk~kdiFdlLa~SLAPSI~GH~~vKkAillLLlGGvEk~ 324 (818)
T KOG0479|consen 281 NIKKLSKKKDIFDLLARSLAPSIYGHDYVKKAILLLLLGGVEKN 324 (818)
T ss_pred HHHHHHhcCCHHHHHhhccCcccccHHHHHHHHHHHHhccceec
Confidence 567 8999999999999999999999999999999999885
No 2
>KOG0478|consensus
Probab=99.96 E-value=9.7e-31 Score=216.56 Aligned_cols=113 Identities=26% Similarity=0.314 Sum_probs=93.9
Q ss_pred CCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcC--C-------CCccceEEEEEEEEEccccc-c---CCCCCCCC
Q psy13876 6 GASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSS--P-------GLLSDTYIEAQRIQCLSKAL-E---DDKPAGTL 72 (118)
Q Consensus 6 ~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~--~-------~~~~~~yl~a~~I~~~~~~~-~---~~~~~~~~ 72 (118)
..|++|.+|+|+|++||||+|+|||||+|||||++.+ . ..+|++||+++|+.+.+... + +...+..+
T Consensus 323 p~g~tPhtv~v~~~~dLVD~v~pGDrv~VTGi~ra~p~r~np~~r~vkSvyktyldvvh~rk~s~~rl~~~d~~d~~~~~ 402 (804)
T KOG0478|consen 323 PEGSTPHTVSVVLHNDLVDKVRPGDRVEVTGILRATPVRVNPRMRMVKSVYKTYLDVVHIRKASMKRLEGSDERDVDEVR 402 (804)
T ss_pred cCCCCCceEEEEEehhhhhccCCCCeEEEEEEEEeEEeccCcchhhHHHHHHHHhHhhhhhhhhhhhccccccccccccc
Confidence 3789999999999999999999999999999999874 1 26899999999998876531 1 11223334
Q ss_pred CHHHH---Hhhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 73 SEEEM---AELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 73 ~~e~i---~~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
..+++ .+++ +||+|++|++||||+|||||++|||||||||||+.|.
T Consensus 403 ~~~~~e~i~elskrpdiy~lLa~SiAPsIye~edvKkglLLqLfGGt~k~ 452 (804)
T KOG0478|consen 403 RIEDLEKIQELSKRPDIYELLARSIAPSIYELEDVKKGLLLQLFGGTRKE 452 (804)
T ss_pred cHHHHHHHHHHhcCccHHHHHHHhhchhhhcccchhhhHHHHHhcCCccc
Confidence 45554 4556 8999999999999999999999999999999999874
No 3
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=99.96 E-value=1.4e-28 Score=205.74 Aligned_cols=107 Identities=31% Similarity=0.456 Sum_probs=94.0
Q ss_pred CCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcC--------CCCccceEEEEEEEEEccccccCCCCCCCCCHHH--
Q psy13876 7 ASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSS--------PGLLSDTYIEAQRIQCLSKALEDDKPAGTLSEEE-- 76 (118)
Q Consensus 7 ~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~--------~~~~~~~yl~a~~I~~~~~~~~~~~~~~~~~~e~-- 76 (118)
.|++||+++|+|++|||+++.|||+|.||||++..+ .++.|++|++|++|++.+... ...+|+++
T Consensus 191 ~g~~Prs~~vil~~dlv~~~~pGdrV~itGi~~~~~~~~~~~~~~~~~~~~~~~a~~v~~~~~~~-----~~~~t~ed~e 265 (682)
T COG1241 191 GGELPRSIEVILEDDLVDSVRPGDRVKITGVVRIVPSRSLSGRRKGPVFEIYLEANSVEKLDKRE-----EVEITEEDEE 265 (682)
T ss_pred CCCCCceEEEEEecCcccccCCCCEEEEEEEEecccccccccccCCceEEEEEEEEEEEeccchh-----hccCCHHHHH
Confidence 568999999999999999999999999999998664 358999999999999987642 23456544
Q ss_pred -HHhhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 77 -MAELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 77 -i~~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
|.+++ +||+|++|++||||+||||++||+||+||||||++|+
T Consensus 266 ~i~elak~~~i~~~l~~SiaPsIyG~e~VKkAilLqLfgGv~k~ 309 (682)
T COG1241 266 EIKELAKRPDIYDILIKSIAPSIYGHEDVKKAILLQLFGGVKKN 309 (682)
T ss_pred HHHHHhcCCcHHHHHHHHhcccccCcHHHHHHHHHHhcCCCccc
Confidence 66677 8999999999999999999999999999999999984
No 4
>KOG0481|consensus
Probab=99.95 E-value=2.4e-28 Score=198.19 Aligned_cols=113 Identities=28% Similarity=0.426 Sum_probs=95.8
Q ss_pred cCCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcCC----C------CccceEEEEEEEEEccccccCCCCCCCCCH
Q psy13876 5 TGASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSSP----G------LLSDTYIEAQRIQCLSKALEDDKPAGTLSE 74 (118)
Q Consensus 5 ~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~~----~------~~~~~yl~a~~I~~~~~~~~~~~~~~~~~~ 74 (118)
++-|+|||++.+.++++|++++.||.||+|+|||..++. + .+..+|+++.+|+........ .....||+
T Consensus 228 VP~GE~PRhl~L~~dRyL~~kvvPG~RvtI~GIYsI~~~~~~~~s~k~~v~iR~PyirVvGi~~ds~~ss~-~~~~~ft~ 306 (729)
T KOG0481|consen 228 VPVGEMPRHLQLFCDRYLTNKVVPGNRVTIMGIYSIKKFGSTSSSDKSGVGIRTPYIRVVGIQDDSEGSSR-SSATMFTP 306 (729)
T ss_pred CCcCcCcchhhhhhhHHHhccccCCceEEEEEEEEeeeccccCCCCccceeeecceEEEEEEEeccCCccc-cCcccCCh
Confidence 467999999999999999999999999999999987731 1 577899999999887654321 22345664
Q ss_pred ---HHHHhhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 75 ---EEMAELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 75 ---e~i~~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
|+|++|+ .||+|+++++||||+||||+||||||+|+||||++|.
T Consensus 307 eEEEeFk~la~~~d~Ye~is~sIAPSIfG~~DiKkAiaClLFgGsrK~ 354 (729)
T KOG0481|consen 307 EEEEEFKKLAASPDVYERISKSIAPSIFGHEDIKKAIACLLFGGSRKR 354 (729)
T ss_pred hHHHHHHHHhcCccHHHHHhhccCchhcCchhHHHHHHHHhhcCcccc
Confidence 4577888 9999999999999999999999999999999999984
No 5
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=99.95 E-value=1.6e-27 Score=203.58 Aligned_cols=106 Identities=18% Similarity=0.239 Sum_probs=88.5
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEEEEEcC---------CCCccceEEEEEEEEEccccccC--------CCCCCCCCH
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGLFVCSS---------PGLLSDTYIEAQRIQCLSKALED--------DKPAGTLSE 74 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~---------~~~~~~~yl~a~~I~~~~~~~~~--------~~~~~~~~~ 74 (118)
|+++|+|++||||+|+|||+|+|||||++.+ ...+|++|++|+||+..++.... ......|++
T Consensus 346 rsi~v~l~dDLVD~v~PGDrV~VtGIl~~~~~~~~~~~~~~~~~~~~yl~~~~i~~~~~~~~~~~~~~~~~~~~~~~~t~ 425 (915)
T PTZ00111 346 EVINLNLYDDLIDSVKTGDRVTVVGILKVTPIRTSTTRRTLKSLYTYFVNVIHVKVINSTNANQPEKGLKYLGNENDFSD 425 (915)
T ss_pred ceEEEEEecchhccCCCCCEEEEEEEEEeccccccccccccccccceEEEEEEEEEeccccccccccccccccccccCCH
Confidence 9999999999999999999999999999763 12689999999999876532210 012245787
Q ss_pred HH---HHhhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccC
Q psy13876 75 EE---MAELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDR 117 (118)
Q Consensus 75 e~---i~~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k 117 (118)
++ |++|+ +|++|+.|++||||+||||++||+||+||||||++|
T Consensus 426 ed~~~I~~ls~~p~i~~~L~~SiaP~I~G~e~vK~ailL~L~gG~~k 472 (915)
T PTZ00111 426 LQVYKILELSRNPMIYRILLDSFAPSIKARNNVKIGLLCQLFSGNKN 472 (915)
T ss_pred HHHHHHHHHhcCHHHHHHHHHHhCCeEECCHHHHHHHHHHHhcCCcc
Confidence 66 55667 899999999999999999999999999999999975
No 6
>smart00350 MCM minichromosome maintenance proteins.
Probab=99.94 E-value=2.2e-26 Score=188.35 Aligned_cols=112 Identities=34% Similarity=0.479 Sum_probs=91.9
Q ss_pred CCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcC-------CC--CccceEEEEEEEEEcccc--ccCCC-CCCCCC
Q psy13876 6 GASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSS-------PG--LLSDTYIEAQRIQCLSKA--LEDDK-PAGTLS 73 (118)
Q Consensus 6 ~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~-------~~--~~~~~yl~a~~I~~~~~~--~~~~~-~~~~~~ 73 (118)
++|++||+++|+|++||||+|+|||+|+|+|||+..+ .+ +.|.+||+|+||+..+.. ++... ....++
T Consensus 98 p~G~~Prsi~v~l~~dLvd~~~PGD~V~i~Gi~~~~~~~~~~~~~~~~~~~~~~l~a~~i~~~~~~~~~~~~~~~~~~~~ 177 (509)
T smart00350 98 PAGQLPRSVDVILDGDLVDKAKPGDRVEVTGIYRNIPYGFKLNTVKGLPVFATYIEANHVRKLDYKRSFEDCSFSVQSLS 177 (509)
T ss_pred CCCCCCcEEEEEEcccccCcccCCCEEEEEEEEEeeccccccccCCCcceeeEEEEEeEEEEccccccccccccccccCC
Confidence 5799999999999999999999999999999999762 12 347899999999987643 21100 013477
Q ss_pred HHH---HHhhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccC
Q psy13876 74 EEE---MAELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDR 117 (118)
Q Consensus 74 ~e~---i~~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k 117 (118)
+++ |.+|+ +|++|+.|++||||+||||+.+|+|++|+|+||+.+
T Consensus 178 ~~~~~~i~~~~~~~~~~~~l~~si~p~i~G~~~~k~~l~l~l~gg~~~ 225 (509)
T smart00350 178 DEEEEEIRKLSKDPDIYERLSRSLAPSIYGHEDIKKAILLLLFGGVHK 225 (509)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHhhCccccCcHHHHHHHHHHHhCCCcc
Confidence 765 55567 899999999999999999999999999999999754
No 7
>KOG0477|consensus
Probab=99.94 E-value=1.6e-27 Score=196.33 Aligned_cols=110 Identities=27% Similarity=0.388 Sum_probs=96.1
Q ss_pred cCCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcC-------CC-CccceEEEEEEEEEccccccCCCCCCCCCHHH
Q psy13876 5 TGASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSS-------PG-LLSDTYIEAQRIQCLSKALEDDKPAGTLSEEE 76 (118)
Q Consensus 5 ~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~-------~~-~~~~~yl~a~~I~~~~~~~~~~~~~~~~~~e~ 76 (118)
.++|++||+.+|+|..||||.|+|||.|.|||||.... +| ++|.+.++||||.+.+..+ ...++++|+
T Consensus 351 v~~GrlPRsk~vILl~DLvD~~kpGdEievTGIy~nn~d~sLN~kngFpvfatvi~ANhV~~k~~~~----~~~~ltded 426 (854)
T KOG0477|consen 351 VPAGRLPRSKEVILLADLVDSCKPGDEIEVTGIYTNNFDGSLNTKNGFPVFATVIEANHVVKKDGKF----DVDELTDED 426 (854)
T ss_pred CCCCccccchhheehhhhhhhcCCCcceEEeeeecccccccccccCCccccceeheehhhhhhcccc----chhHHhHHH
Confidence 56999999999999999999999999999999998653 23 7899999999998876543 235567777
Q ss_pred HHhh---c-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 77 MAEL---G-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 77 i~~l---~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
+++| + +|++-+++++||||+||||++||+|++|.||||++|+
T Consensus 427 ~k~i~~lskd~~i~~rIiaSiaPsIyGh~~VK~AvAlaLfGGv~kn 472 (854)
T KOG0477|consen 427 FKEIWELSKDPPIKERIIASIAPSIYGHEDVKRAVALALFGGVPKN 472 (854)
T ss_pred HHHHHHHhcCccHHHHHHHhhCchhhchHHHHHHHHHHHhcCCccC
Confidence 6655 5 8999999999999999999999999999999999986
No 8
>KOG0482|consensus
Probab=99.94 E-value=4.3e-27 Score=190.72 Aligned_cols=114 Identities=41% Similarity=0.664 Sum_probs=97.2
Q ss_pred cCCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcC--------CCCccceEEEEEEEEEccccccCCCCCCCCCHHH
Q psy13876 5 TGASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSS--------PGLLSDTYIEAQRIQCLSKALEDDKPAGTLSEEE 76 (118)
Q Consensus 5 ~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~--------~~~~~~~yl~a~~I~~~~~~~~~~~~~~~~~~e~ 76 (118)
++-|.+||+++|.+++.++.+|+|||.|.|+||+-+.. +|.+.++||+|+.|...++.++..+...+.+++.
T Consensus 244 VPvG~IPRsltv~~~ge~tr~~~PGDvV~vsGiFLP~pytGfr~~~aGLladtYLeAh~v~~~nk~~~~~~~~~~~~~~~ 323 (721)
T KOG0482|consen 244 VPVGHIPRSLTVHVYGEMTRKCQPGDVVVVSGIFLPIPYTGFRALKAGLLADTYLEAHRVVQINKKYDNIEKTGELEPEE 323 (721)
T ss_pred CCCCccCceeEEEEecccceecCCCCEEEEeeeecccchhhHHHHHhhhHHHHHHHHhhhhhhccccccccccccccHHH
Confidence 35688999999999999999999999999999987653 5789999999999888877665433344445555
Q ss_pred HHhhcChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 77 MAELGGDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 77 i~~l~~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
.+.++..++|+.|++||||+||||+||||||||+|+||+.|.
T Consensus 324 ~~~~~~~d~yekLa~SiAPEIyGheDVKKaLLLlLVGgvd~~ 365 (721)
T KOG0482|consen 324 LELIAEGDFYEKLAASIAPEIYGHEDVKKALLLLLVGGVDKS 365 (721)
T ss_pred HHHhhcccHHHHHHHhhchhhccchHHHHHHHHHhhCCCCCC
Confidence 555569999999999999999999999999999999999874
No 9
>KOG0480|consensus
Probab=99.93 E-value=1.6e-26 Score=190.64 Aligned_cols=113 Identities=27% Similarity=0.347 Sum_probs=89.4
Q ss_pred CCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcCC-------C-----------CccceEEEEEEEEEcccc--ccC
Q psy13876 6 GASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSSP-------G-----------LLSDTYIEAQRIQCLSKA--LED 65 (118)
Q Consensus 6 ~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~~-------~-----------~~~~~yl~a~~I~~~~~~--~~~ 65 (118)
..|++||+++|+|++|||++|+|||+|++||++...+. | ..+=++++|++|...+.. |..
T Consensus 218 p~GsiPRtvdviLr~dlVe~~~pGD~v~~TGiliVvpdv~~l~~pgsk~~n~r~~~~~~~i~~lkal~Vrdl~yq~aFla 297 (764)
T KOG0480|consen 218 PRGSIPRTVDVILRGDLVETAQPGDKVDITGILIVVPDVSQLGGPGSKAENNRGGETGDGITGLKALGVRDLTYQLAFLA 297 (764)
T ss_pred CCCCCCceeEEEEhhhhHhhcCCCCEEEEEEEEEEecChHHhcCCccccccccCCCcccceeeehhcccccchhhhhHhh
Confidence 37999999999999999999999999999999876541 1 144467899888876543 100
Q ss_pred --------------CCCCCCCCHHHHH---hhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 66 --------------DKPAGTLSEEEMA---ELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 66 --------------~~~~~~~~~e~i~---~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
.....+++.+|+. +++ ++|+|..|++|+||+||||+.||+||+|+||||++|+
T Consensus 298 c~~~~~~~~ee~~~~~~~~~~s~~e~~~~~em~~~~nly~~lv~Sl~PsIyGhe~VK~GilL~LfGGv~K~ 368 (764)
T KOG0480|consen 298 CHVQSTLAVEEDDEEDMLNSMSSEEFAEIREMSKDENLYKNLVNSLFPSIYGHELVKAGILLSLFGGVHKS 368 (764)
T ss_pred hhcccccccchhhhHHHhhhccHHHHHHHHHHhcCchHHHHHHHhhCccccchHHHHhhHHHHHhCCcccc
Confidence 0012235566644 456 8999999999999999999999999999999999985
No 10
>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite.; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.
Probab=99.27 E-value=7.1e-13 Score=103.78 Aligned_cols=44 Identities=55% Similarity=0.968 Sum_probs=38.9
Q ss_pred HHHHHhhc-ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccC
Q psy13876 74 EEEMAELG-GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDR 117 (118)
Q Consensus 74 ~e~i~~l~-~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k 117 (118)
.++|.+|+ +||+|++|++||||+||||+++|+||+||||||+.+
T Consensus 2 ~~~i~~l~~~~~~~~~l~~s~aP~i~g~~~iK~aill~L~~~~~~ 46 (331)
T PF00493_consen 2 EEKIKELSKKPNIFDRLANSIAPSIYGHEDIKKAILLQLFGGVEK 46 (331)
T ss_dssp HHHHHCCCCTTTHHHCCHHHCSSTTTT-HHHHHHHCCCCTT--SC
T ss_pred HHHHHHHhcCCcHHHHHHHHhCCcCcCcHHHHHHHHHHHHhcccc
Confidence 57788999 899999999999999999999999999999999986
No 11
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=89.52 E-value=2.1 Score=25.20 Aligned_cols=43 Identities=7% Similarity=0.066 Sum_probs=31.2
Q ss_pred EEEEEEee----CcccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEE
Q psy13876 13 HWILGLLR----YWQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQC 58 (118)
Q Consensus 13 ~i~v~l~~----dLvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~ 58 (118)
++.+.+-+ ...+.+++||.|.|.|.++..+.+ +..|.+..++.
T Consensus 28 ~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~~~---~~~l~~~~i~~ 74 (75)
T PF01336_consen 28 SIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYNGG---ELELIVPKIEI 74 (75)
T ss_dssp EEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEETTS---SEEEEEEEEEE
T ss_pred cEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEECCc---cEEEEECEEEE
Confidence 45666655 667889999999999999988643 46677666653
No 12
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=88.76 E-value=1.9 Score=27.02 Aligned_cols=49 Identities=14% Similarity=0.015 Sum_probs=35.5
Q ss_pred CCccEEEEEEeeCc----ccceecCCeEEEEEEEEEcC---C-C-CccceEEEEEEEE
Q psy13876 9 MVGKHWILGLLRYW----QNPTMLQNYCILHGLFVCSS---P-G-LLSDTYIEAQRIQ 57 (118)
Q Consensus 9 ~~Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~~---~-~-~~~~~yl~a~~I~ 57 (118)
.-+-.+.|.+-+++ ...+++||.|.|+|.++... + | ..+...+.|.+|.
T Consensus 41 ~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l~~~~~~~~~g~~~~~~~i~~~~i~ 98 (100)
T cd04496 41 EETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEDKDGQKRYGTEVVADRIE 98 (100)
T ss_pred cccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEEEeceeECCCCCEEEEEEEEEEEEE
Confidence 35678899998876 45689999999999998763 1 2 3445556665554
No 13
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=86.34 E-value=4.3 Score=26.89 Aligned_cols=42 Identities=12% Similarity=-0.014 Sum_probs=28.5
Q ss_pred EEEEEEeeCccc--ceecCCeEEEEEEEEEcCCCCccceEEEEEEEEE
Q psy13876 13 HWILGLLRYWQN--PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQC 58 (118)
Q Consensus 13 ~i~v~l~~dLvd--~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~ 58 (118)
+|.|+++++.-. .+.|+|+|+|.|-+-... ..+.|++.+|++
T Consensus 60 ~I~VeId~~~w~g~~vt~~~~Vri~GeVDk~~----~~~~IdV~~I~K 103 (103)
T PF04076_consen 60 EIEVEIDDDVWRGQTVTPDDKVRISGEVDKDW----NKTEIDVDRIEK 103 (103)
T ss_dssp EEEEE--GGGSTT----TTSEEEEEEEEEEET----TEEEEEEEEEEE
T ss_pred cEEEEEChhhcCCcccCCCCEEEEEEEEeCCC----CceEEEEEEEEC
Confidence 588899998554 479999999999987333 357788888864
No 14
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=86.02 E-value=2.9 Score=26.46 Aligned_cols=49 Identities=10% Similarity=-0.062 Sum_probs=33.4
Q ss_pred CccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEE
Q psy13876 10 VGKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQC 58 (118)
Q Consensus 10 ~Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~ 58 (118)
-|-.+.|.+.++++ +.++.||+|.|.|-++... .| ..+...+.|.+|+-
T Consensus 46 ~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~~~G~~~~~~~i~a~~i~f 103 (104)
T PF00436_consen 46 KTDWINVVAWGKLAENVAEYLKKGDRVYVEGRLRTRTYEDKDGQKRYRVEIIADNIEF 103 (104)
T ss_dssp EEEEEEEEEEHHHHHHHHHH--TT-EEEEEEEEEEEEEESTTSSEEEEEEEEEEEEEE
T ss_pred ceEEEEEEeeeecccccceEEcCCCEEEEEEEEEeeEEECCCCCEEEEEEEEEEEEEe
Confidence 45678888888755 4588899999999988763 23 46667788777753
No 15
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=82.00 E-value=3.3 Score=25.81 Aligned_cols=28 Identities=4% Similarity=-0.143 Sum_probs=21.1
Q ss_pred EEEEEEeeCcccceecCCeEEEEEEEEEcC
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~ 42 (118)
-+-|+... ...+++||+|+|+|.+....
T Consensus 34 gifV~~~~--~~~~~~Gd~V~vtG~v~ey~ 61 (78)
T cd04486 34 GIFVYTGS--GADVAVGDLVRVTGTVTEYY 61 (78)
T ss_pred eEEEecCC--CCCCCCCCEEEEEEEEEeeC
Confidence 45555443 67889999999999987654
No 16
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=81.87 E-value=0.86 Score=30.73 Aligned_cols=50 Identities=18% Similarity=0.095 Sum_probs=34.0
Q ss_pred CCCccEEEEEEeeCcccceecCCeEEEEEEEEEcCC-----CCccceEEEEEEEE
Q psy13876 8 SMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSSP-----GLLSDTYIEAQRIQ 57 (118)
Q Consensus 8 g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~~-----~~~~~~yl~a~~I~ 57 (118)
...+..+.+.++.+-...++|||++.++|.+++-+. +--|+.|+...+|.
T Consensus 111 ~~~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~~~~~~Npg~FD~~~yl~~~gI~ 165 (176)
T PF13567_consen 111 IPVSGKILLYLPKDSQPRLQPGDRIRVRGKLKPPSGPTNPGGFDYQRYLRSKGIY 165 (176)
T ss_pred cccceeeEEEeccccccccCCCCEEEEEEEEecCCCCCCCCCcCHHHHHHHCCCE
Confidence 334556777777776667899999999999987631 23445565555553
No 17
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=79.10 E-value=1.1 Score=35.51 Aligned_cols=39 Identities=18% Similarity=0.058 Sum_probs=26.5
Q ss_pred CccccCCCCCccEEEEEEeeCcccceecCCeEEEEEEEEE
Q psy13876 1 MRIATGASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVC 40 (118)
Q Consensus 1 ~~~~~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~ 40 (118)
.||||..-..| .+.=-.....+=+++|||+|+|.|-|-.
T Consensus 230 vRIAtPPp~~~-~~PpG~mSSyi~sLKpGDKvtisGPfGE 268 (410)
T COG2871 230 VRIATPPPRNP-DAPPGQMSSYIWSLKPGDKVTISGPFGE 268 (410)
T ss_pred EEeccCCCCCC-CCCccceeeeEEeecCCCeEEEeccchh
Confidence 48998865443 1222233456678999999999998743
No 18
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=78.64 E-value=4.9 Score=25.70 Aligned_cols=22 Identities=5% Similarity=-0.165 Sum_probs=18.2
Q ss_pred CcccceecCCeEEEEEEEEEcC
Q psy13876 21 YWQNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi~~~~~ 42 (118)
.+...+++||+|.+.|-+....
T Consensus 43 ~~~~~l~~Gd~V~v~G~v~~y~ 64 (91)
T cd04482 43 DVVRLLIPGDEVTVYGSVRPGT 64 (91)
T ss_pred cccCCCCCCCEEEEEEEEecCC
Confidence 5777889999999999987443
No 19
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=78.26 E-value=0.55 Score=34.86 Aligned_cols=40 Identities=8% Similarity=-0.067 Sum_probs=27.4
Q ss_pred EEEEEeeCcccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEcc
Q psy13876 14 WILGLLRYWQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLS 60 (118)
Q Consensus 14 i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~ 60 (118)
+.|+ -|.--.+++||.|.+||.+.. -|..|+.|++|++.+
T Consensus 65 v~i~--~d~~~nvKVGD~VKaTG~m~r-----nf~~ym~A~sVEk~~ 104 (213)
T PRK06763 65 VSVY--IDSLSNVKVGDEVKATGSMMR-----NFTEYMVATAVENTT 104 (213)
T ss_pred eEEE--ecCCCCcccCcEEEEchHHHH-----hhHHhhhhhhheeec
Confidence 5565 456677899999999997421 145577777766654
No 20
>KOG3416|consensus
Probab=76.14 E-value=3.1 Score=28.83 Aligned_cols=30 Identities=7% Similarity=-0.125 Sum_probs=25.8
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEEEEEc
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~ 41 (118)
-+|.+-+-+|..+.++|||.|.+||=|-..
T Consensus 48 gsI~isvW~e~~~~~~PGDIirLt~Gy~Si 77 (134)
T KOG3416|consen 48 GSINISVWDEEGCLIQPGDIIRLTGGYASI 77 (134)
T ss_pred ceEEEEEecCcCcccCCccEEEecccchhh
Confidence 368888999999999999999999977543
No 21
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=74.38 E-value=3.2 Score=28.09 Aligned_cols=29 Identities=3% Similarity=-0.213 Sum_probs=16.9
Q ss_pred EEEEEEeeCc-----ccceecCCeEEEEEEEEEc
Q psy13876 13 HWILGLLRYW-----QNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 13 ~i~v~l~~dL-----vd~~~pGd~V~v~Gi~~~~ 41 (118)
.+.+.+.++- +.++++||+|+|.|++.-.
T Consensus 99 ~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~g~ 132 (144)
T PF12869_consen 99 GVQCYFSNDQEKRASVAKLKKGQKVTIKGICTGY 132 (144)
T ss_dssp S--EEEEEEGGGHHHHHH--TTSEEEEEEE----
T ss_pred eEEEEEccchhhhhhHhcCCCCCEEEEEEEEEee
Confidence 3667777766 4559999999999998644
No 22
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=74.23 E-value=14 Score=23.57 Aligned_cols=36 Identities=0% Similarity=-0.221 Sum_probs=29.9
Q ss_pred CCCCccEEEEEEeeCcc---cceecCCeEEEEEEEEEcC
Q psy13876 7 ASMVGKHWILGLLRYWQ---NPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 7 ~g~~Pr~i~v~l~~dLv---d~~~pGd~V~v~Gi~~~~~ 42 (118)
.++-|+.|.+.+-+|-+ +++++||.|+|.=-++.++
T Consensus 31 ~~qYP~~i~f~~~~dk~~~l~~~~~Gd~V~Vsf~i~~RE 69 (84)
T PF11325_consen 31 EEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGRE 69 (84)
T ss_pred CCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccE
Confidence 46789999999998876 4589999999988777664
No 23
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=73.93 E-value=20 Score=23.62 Aligned_cols=52 Identities=12% Similarity=-0.020 Sum_probs=38.8
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
+..+.|.+-+.+. ..+..||.|.|.|-++..+ .| ..+.+.+.|.+|+.++..
T Consensus 46 t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~~~~G~~~~~~ei~a~~i~~l~~~ 106 (112)
T PRK06752 46 VDFINCVVWRKSAENVTEYCTKGSLVGITGRIHTRNYEDDQGKRIYITEVVIESITFLERR 106 (112)
T ss_pred EEEEEEEEehHHHHHHHHhcCCCCEEEEEEEEEeCccCCCCCcEEEEEEEEEEEEEECCCC
Confidence 4678888887654 4689999999999998773 23 455666888888877654
No 24
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.35 E-value=14 Score=26.12 Aligned_cols=51 Identities=16% Similarity=0.060 Sum_probs=38.5
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEccc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~ 61 (118)
+-.+.|.+-+.+. ..++.|++|.|.|-++... .| ..+.+.|.|.+|..+..
T Consensus 50 t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~L~~~~~~~kdG~~~~~~ev~a~~i~~L~~ 109 (164)
T TIGR00621 50 TEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEDQNGQKRSKTEIIADNVQLLDL 109 (164)
T ss_pred ceEEEEEEehHHHHHHHHhCCCCCEEEEEEEEEeceEECCCCcEEEEEEEEEEEEeeccc
Confidence 4578888887754 4578999999999998773 23 46677888888866543
No 25
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=72.85 E-value=19 Score=22.03 Aligned_cols=29 Identities=7% Similarity=-0.138 Sum_probs=20.8
Q ss_pred cccceecCCeEEEEEEEEEcCCCCccceEEE
Q psy13876 22 WQNPTMLQNYCILHGLFVCSSPGLLSDTYIE 52 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~ 52 (118)
+.-.+++||+|+++|-+.. + ...|+.|++
T Consensus 40 ~~~~l~~Gd~V~v~G~v~~-~-~G~~ql~v~ 68 (73)
T cd04487 40 AYPEVEVGDIVRVTGEVEP-R-DGQLQIEVE 68 (73)
T ss_pred CcCCCCCCCEEEEEEEEec-C-CeEEEEEEe
Confidence 5667899999999999875 3 334555544
No 26
>PF08021 FAD_binding_9: Siderophore-interacting FAD-binding domain; InterPro: IPR013113 Proteins in this entry are siderophore-interacting FAD-binding proteins. This entry includes the vibriobactin utilization protein ViuB, which is involved in the removal of iron from iron-vibriobactin complexes, as well as several hypothetical proteins.; PDB: 2GPJ_A.
Probab=72.46 E-value=3.5 Score=27.57 Aligned_cols=24 Identities=13% Similarity=0.087 Sum_probs=16.1
Q ss_pred EEEEEEeeC------cccceecCCeEEEEE
Q psy13876 13 HWILGLLRY------WQNPTMLQNYCILHG 36 (118)
Q Consensus 13 ~i~v~l~~d------Lvd~~~pGd~V~v~G 36 (118)
.|++.++++ +...++|||+|.|+|
T Consensus 83 ~iDfv~Hg~~Gpas~WA~~A~pGd~v~v~g 112 (117)
T PF08021_consen 83 DIDFVLHGDEGPASRWARSARPGDRVGVTG 112 (117)
T ss_dssp EEEEE--SS--HHHHHHHH--TT-EEEEEE
T ss_pred EEEEEECCCCCchHHHHhhCCCCCEEEEeC
Confidence 577788876 778999999999998
No 27
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=72.27 E-value=9.2 Score=26.33 Aligned_cols=41 Identities=12% Similarity=0.040 Sum_probs=29.9
Q ss_pred EEEEEEeeCccc--ceecCCeEEEEEEEEEcCCCCccceEEEEEEEE
Q psy13876 13 HWILGLLRYWQN--PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQ 57 (118)
Q Consensus 13 ~i~v~l~~dLvd--~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~ 57 (118)
+|.|++++++-. .+.|+|+|+|.|-+-... ..+.+++.+|+
T Consensus 83 ~I~VeId~~~w~G~~v~p~d~V~I~GeVDk~~----~~~~IdV~~I~ 125 (126)
T TIGR00156 83 EINVVIPAAVWNGREVQPKDMVNISGSLDKKS----APAEVDVTHIQ 125 (126)
T ss_pred CEEEEECHHHcCCCcCCCCCEEEEEEEECCCC----CCeEEEEEEEE
Confidence 377888877654 678999999999887332 24677777775
No 28
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=71.21 E-value=22 Score=22.09 Aligned_cols=47 Identities=11% Similarity=-0.055 Sum_probs=29.8
Q ss_pred EEEEEEeeC-----cccceecCCeEEEEEEEEEcCCC---CccceEEEEEEEEEc
Q psy13876 13 HWILGLLRY-----WQNPTMLQNYCILHGLFVCSSPG---LLSDTYIEAQRIQCL 59 (118)
Q Consensus 13 ~i~v~l~~d-----Lvd~~~pGd~V~v~Gi~~~~~~~---~~~~~yl~a~~I~~~ 59 (118)
.+.|.+..+ ...++..|+-|.|+|++...+.. .....-|.+.+++..
T Consensus 30 ~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~~~i~il 84 (86)
T cd04321 30 IIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVVDDIQTL 84 (86)
T ss_pred EEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEEEEEEEe
Confidence 466666543 34578899999999999876531 112334555566544
No 29
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=70.39 E-value=13 Score=26.71 Aligned_cols=54 Identities=15% Similarity=0.024 Sum_probs=41.2
Q ss_pred CccEEEEEEeeCc----ccceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEccccc
Q psy13876 10 VGKHWILGLLRYW----QNPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKAL 63 (118)
Q Consensus 10 ~Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~~ 63 (118)
.+-.+.|.+-+.+ ...++.|++|.|.|-++... .| ..+.+.|.|.+|+.+....
T Consensus 50 ~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeGrL~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~ 112 (168)
T PRK06863 50 VTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRLKTRKWQDQNGQDRYTTEIQGDVLQMLGGRN 112 (168)
T ss_pred cceEEEEEEEhHHHHHHHHHCCCCCEEEEEEEEEeCCccCCCCCEEEEEEEEEeEEEECCCCC
Confidence 4668888888764 45689999999999998773 23 4667789999998776543
No 30
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=69.62 E-value=25 Score=23.69 Aligned_cols=52 Identities=13% Similarity=0.082 Sum_probs=38.9
Q ss_pred ccEEEEEEeeCc----ccceecCCeEEEEEEEEEcC----C-C-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYW----QNPTMLQNYCILHGLFVCSS----P-G-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~~----~-~-~~~~~yl~a~~I~~~~~~ 62 (118)
+..+.|.+-+.+ .+.++.|+.|.|.|-++... . | ..+.+-+.|..|+.++..
T Consensus 43 t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~d~d~G~~r~~~ei~a~~i~~L~~k 104 (121)
T PRK07459 43 PDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRWTDRNTGEDRSKPVIRVDRLELLGSK 104 (121)
T ss_pred ceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecceEcCCCCeEEEEEEEEEeEEEECcCC
Confidence 557888888875 45678899999999998772 2 3 356667888888877643
No 31
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.06 E-value=4.4 Score=27.04 Aligned_cols=28 Identities=14% Similarity=0.042 Sum_probs=24.4
Q ss_pred cEEEEEEeeCcccceecCCeEEEEE-EEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHG-LFV 39 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~G-i~~ 39 (118)
+.+++.|.++---.++|||.+.++| .++
T Consensus 20 K~iEvRl~d~krr~ik~GD~IiF~~~~l~ 48 (111)
T COG4043 20 KKIEVRLADPKRRQIKPGDKIIFNGDKLK 48 (111)
T ss_pred ceEEEEecCHhhcCCCCCCEEEEcCCeeE
Confidence 5799999999999999999999995 444
No 32
>PRK00036 primosomal replication protein N; Reviewed
Probab=66.72 E-value=26 Score=23.47 Aligned_cols=51 Identities=10% Similarity=-0.029 Sum_probs=36.5
Q ss_pred CccEE----EEEEeeCcc---cceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 10 VGKHW----ILGLLRYWQ---NPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 10 ~Pr~i----~v~l~~dLv---d~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
+||.+ .+++-+++. ....+|..+.++|=+-..+ ....+..|++.+|+....
T Consensus 41 ~~Rqv~~~i~ava~G~~a~~~~~l~~Gs~v~v~GFLa~~~-~~~~~LVLHi~~Ie~i~~ 98 (107)
T PRK00036 41 HPRRVELTISAVALGDLALLLADTPLGTEMQVQGFLAPAR-KDSVKVKLHLQQARRIAG 98 (107)
T ss_pred CcceEEEEEEEEEEhhHHHHhcccCCCCEEEEEEEEEECC-CCCCcEEEEhHHeEEccc
Confidence 56764 445556665 4577999999999887643 345688999888887644
No 33
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=66.52 E-value=27 Score=21.28 Aligned_cols=45 Identities=11% Similarity=0.001 Sum_probs=29.7
Q ss_pred EEEEEEeeC-----cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEE
Q psy13876 13 HWILGLLRY-----WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQC 58 (118)
Q Consensus 13 ~i~v~l~~d-----Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~ 58 (118)
++.+.+..+ ...++.+|+-|.|+|++...+.. ..+.-|.+.+++.
T Consensus 30 ~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~-~~~~El~~~~i~i 79 (82)
T cd04318 30 NLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGA-KQPFELQAEKIEV 79 (82)
T ss_pred CEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCC-CCCEEEEEEEEEE
Confidence 466766644 35688999999999999876532 1234455555544
No 34
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=64.78 E-value=18 Score=22.56 Aligned_cols=36 Identities=17% Similarity=0.115 Sum_probs=27.2
Q ss_pred cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 22 WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
..+.+++|+.|.|.|.++..+ .+..|.+..+...+.
T Consensus 44 ~~~~~~~g~~v~v~G~v~~~~----g~~ql~i~~i~~v~d 79 (95)
T cd04478 44 EVEPIEEGTYVRVFGNLKSFQ----GKKSIMAFSIRPVTD 79 (95)
T ss_pred cccccccCCEEEEEEEEcccC----CeeEEEEEEEEEeCC
Confidence 577899999999999998665 245666667766553
No 35
>PRK10053 hypothetical protein; Provisional
Probab=63.48 E-value=17 Score=25.07 Aligned_cols=41 Identities=7% Similarity=-0.016 Sum_probs=30.2
Q ss_pred EEEEEEeeCccc--ceecCCeEEEEEEEEEcCCCCccceEEEEEEEE
Q psy13876 13 HWILGLLRYWQN--PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQ 57 (118)
Q Consensus 13 ~i~v~l~~dLvd--~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~ 57 (118)
+|.|++++++-. .+.|.|+|+|.|-+-... ..+-+++.+|+
T Consensus 87 ~I~VeID~~~w~G~~v~p~~kV~I~GevDk~~----~~~~IdV~~i~ 129 (130)
T PRK10053 87 EINVIIPAAVFDGREVQPDQMININGSLDKKS----APPVVRVTHLQ 129 (130)
T ss_pred cEEEEeCHHHcCCCcCCCCCEEEEEEEECCCC----CCeEEEEEEEe
Confidence 478888887543 689999999999886332 34677777775
No 36
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=62.38 E-value=46 Score=22.56 Aligned_cols=51 Identities=14% Similarity=0.002 Sum_probs=37.8
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC---CC-CccceEEEEEEEEEccc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS---PG-LLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~---~~-~~~~~yl~a~~I~~~~~ 61 (118)
+..+.|.+-+.+. +.++.|+.|.|.|-++..+ .| ..+.+.+.+.+++.++.
T Consensus 46 t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~Grl~~~~y~kdG~~~~~~eviv~~i~~l~~ 104 (131)
T PRK07274 46 ADFINVVLWGKLAETLASYASKGSLISIDGELRTRKYEKDGQTHYVTEVLCQSFQLLES 104 (131)
T ss_pred EEEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEeccCccCCcEEEEEEEEEEEEEECcC
Confidence 5678888887654 4589999999999988763 23 45666788888887654
No 37
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=59.77 E-value=8.2 Score=18.47 Aligned_cols=11 Identities=0% Similarity=-0.161 Sum_probs=9.0
Q ss_pred eecCCeEEEEE
Q psy13876 26 TMLQNYCILHG 36 (118)
Q Consensus 26 ~~pGd~V~v~G 36 (118)
+++||.|.|++
T Consensus 2 ~~~G~~V~I~~ 12 (28)
T smart00739 2 FEVGDTVRVIA 12 (28)
T ss_pred CCCCCEEEEeE
Confidence 57899999876
No 38
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=59.68 E-value=45 Score=21.52 Aligned_cols=47 Identities=11% Similarity=0.008 Sum_probs=31.2
Q ss_pred EEEEEeeC--------cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 14 WILGLLRY--------WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 14 i~v~l~~d--------Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
+.+.+.+. .+..+.+|+.|.|+|++...+... ...-|.+.+++....
T Consensus 42 iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~-~~~Ei~~~~i~il~~ 96 (108)
T cd04316 42 VQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAP-NGVEIIPEEIEVLSE 96 (108)
T ss_pred EEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCC-CCEEEEEeEEEEEeC
Confidence 66666543 345689999999999988765321 234466666766654
No 39
>PRK02801 primosomal replication protein N; Provisional
Probab=57.51 E-value=42 Score=21.75 Aligned_cols=44 Identities=14% Similarity=0.159 Sum_probs=28.7
Q ss_pred EEEEEeeCcc----cceecCCeEEEEEEEEEc-CCCCccceEEEEEEEE
Q psy13876 14 WILGLLRYWQ----NPTMLQNYCILHGLFVCS-SPGLLSDTYIEAQRIQ 57 (118)
Q Consensus 14 i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~-~~~~~~~~yl~a~~I~ 57 (118)
+.|.+-+... +.+..|+.|.|+|-+... .+.......+.+.+|+
T Consensus 50 i~~va~G~~Ae~~~~~l~kGs~v~V~G~L~~~~~~~g~~~~~v~~~~i~ 98 (101)
T PRK02801 50 MPVIVSGNQFQAITQSITVGSKITVQGFISCHQGRNGLSKLVLHAEQIE 98 (101)
T ss_pred EEEEEEcHHHHHHHhhcCCCCEEEEEEEEEEeECCCCCEEEEEEEEEEE
Confidence 7777777655 357789999999999872 2222223336555554
No 40
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=57.51 E-value=55 Score=21.91 Aligned_cols=49 Identities=10% Similarity=-0.005 Sum_probs=30.9
Q ss_pred EEEEEeeC------cccceecCCeEEEEEEEEEcCC-----C-CccceEEEEEEEEEcccc
Q psy13876 14 WILGLLRY------WQNPTMLQNYCILHGLFVCSSP-----G-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 14 i~v~l~~d------Lvd~~~pGd~V~v~Gi~~~~~~-----~-~~~~~yl~a~~I~~~~~~ 62 (118)
+.+.+... .+..+..|+-|.|+|++...+. . ...+.-|.+.+++.....
T Consensus 44 ~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~~~~~~~~El~~~~i~vl~~~ 104 (135)
T cd04317 44 VQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNKA 104 (135)
T ss_pred EEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCCCCCCCcEEEEEeEEEEEECC
Confidence 55666543 3457899999999999886431 1 122344666677666543
No 41
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=56.64 E-value=44 Score=24.26 Aligned_cols=52 Identities=17% Similarity=0.082 Sum_probs=38.5
Q ss_pred ccEEEEEEeeCccc----ceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYWQN----PTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dLvd----~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
+-.+.|.+-+.+++ .++-|++|.|.|-++... .| ..+.+.|.|.+|+.+...
T Consensus 48 t~fi~v~~fg~~AE~~~~~l~KG~~V~VeGrL~~~~y~dkdG~~r~~~eI~a~~v~~L~~~ 108 (182)
T PRK08486 48 VCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESWMDQNGQKRSKHTITAESMQMLDSK 108 (182)
T ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEeCcEECCCCcEEEEEEEEEeEEEECCCC
Confidence 55788888777654 468899999999998763 23 456667888888876543
No 42
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=56.54 E-value=49 Score=24.13 Aligned_cols=52 Identities=13% Similarity=0.047 Sum_probs=39.0
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
+-.+.|.+-+.+. ..++.|+.|.|+|-++... .+ ..+.+-|.|..|+.+...
T Consensus 51 T~w~~V~~fGk~AE~v~~~LkKGs~V~VeGrL~~~~yeDkdG~kr~~~eVvA~~V~fL~sr 111 (182)
T PRK06958 51 TEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIRTRKWQGQDGQDRYSTEIVADQMQMLGGR 111 (182)
T ss_pred ceEEEEEEehHHHHHHHHHhCCCCEEEEEEEEEeCceECCCCcEEEEEEEEEeEEEECCCC
Confidence 5578888887754 5688999999999998773 23 456666888888877643
No 43
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=56.29 E-value=56 Score=22.79 Aligned_cols=52 Identities=13% Similarity=-0.017 Sum_probs=37.6
Q ss_pred ccEEEEEEeeCc----ccceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYW----QNPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
+-.+.|.+-+.+ ...++-|+.|.|+|-++... .| ..+.+-|.|.+|..+...
T Consensus 53 t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~GrL~~~~w~dkdG~~r~~~eI~a~~i~~l~~r 113 (148)
T PRK08182 53 GFWAPVELWHRDAEHWARLYQKGMRVLVEGRMERDEWTDNEDNERVTFKVEARRVGILPYR 113 (148)
T ss_pred cEEEEEEEEhHHHHHHHHhcCCCCEEEEEEEEEecccCCCCCCEEEEEEEEEeEEEEcCCc
Confidence 456888888754 45678899999999998773 23 455666888888776543
No 44
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=55.50 E-value=19 Score=22.19 Aligned_cols=15 Identities=0% Similarity=-0.068 Sum_probs=8.2
Q ss_pred cccceecCCeEEEEE
Q psy13876 22 WQNPTMLQNYCILHG 36 (118)
Q Consensus 22 Lvd~~~pGd~V~v~G 36 (118)
..+.+++||.|.+..
T Consensus 23 ~~G~v~~Gd~v~~~P 37 (81)
T cd03695 23 ASGSIRVGDEVVVLP 37 (81)
T ss_pred ccceEECCCEEEEcC
Confidence 345556666665544
No 45
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=55.38 E-value=55 Score=23.25 Aligned_cols=53 Identities=15% Similarity=-0.006 Sum_probs=39.3
Q ss_pred CccEEEEEEeeCc----ccceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 10 VGKHWILGLLRYW----QNPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 10 ~Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
-+-.+.|.+-+.+ ...++-|+.|.|.|-++.+. .| ..+.+-+.|.+|+.++..
T Consensus 45 ~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeGrl~~r~y~dkdG~k~~~~evva~~i~~l~~~ 106 (162)
T PRK07275 45 EADFINCVIWRQQAENLANWAKKGALIGVTGRIQTRNYENQQGQRVYVTEVVADNFQMLESR 106 (162)
T ss_pred eeeEEEEEEEcHHHHHHHHHcCCCCEEEEEEEEEeceEECCCCCEEEEEEEEEeEEEECCCC
Confidence 3567888888876 45678999999999998763 23 456666888888876543
No 46
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=54.83 E-value=47 Score=20.29 Aligned_cols=30 Identities=7% Similarity=-0.144 Sum_probs=22.1
Q ss_pred EEEEEEeeCc-------ccceecCCeEEEEEEEEEcC
Q psy13876 13 HWILGLLRYW-------QNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 13 ~i~v~l~~dL-------vd~~~pGd~V~v~Gi~~~~~ 42 (118)
.+.+.+..+. ...+..||-|.|+|++...+
T Consensus 28 ~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~ 64 (85)
T cd04100 28 IVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRP 64 (85)
T ss_pred eEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECC
Confidence 4556665442 34789999999999988765
No 47
>PRK05853 hypothetical protein; Validated
Probab=53.00 E-value=40 Score=24.03 Aligned_cols=46 Identities=13% Similarity=-0.011 Sum_probs=32.3
Q ss_pred ccEEEEEEeeCccc----ceecCCeEEEEEEEEEcC----CC-CccceEEEEEEE
Q psy13876 11 GKHWILGLLRYWQN----PTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRI 56 (118)
Q Consensus 11 Pr~i~v~l~~dLvd----~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I 56 (118)
+-.+.|.+-+.+.+ .++-|+.|.|+|-++..+ .| ..+.+-|.|.+|
T Consensus 42 T~wi~V~~wg~lAe~v~~~L~KG~~V~V~GrL~~~~wedkdG~~r~~~eV~a~~V 96 (161)
T PRK05853 42 SLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEDRDGNRRSSLEMRATSV 96 (161)
T ss_pred ccEEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEccceECCCCCEEEEEEEEEEEe
Confidence 44688888887654 478899999999998763 23 344455666655
No 48
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=50.15 E-value=6 Score=24.94 Aligned_cols=20 Identities=5% Similarity=0.013 Sum_probs=3.8
Q ss_pred eCcccceecCCeEEEE-EEEE
Q psy13876 20 RYWQNPTMLQNYCILH-GLFV 39 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~-Gi~~ 39 (118)
.++.++++|||+|..+ |++-
T Consensus 31 ~~m~~~Lk~Gd~VvT~gGi~G 51 (82)
T PF02699_consen 31 QEMLASLKPGDEVVTIGGIYG 51 (82)
T ss_dssp TTGGG----------------
T ss_pred HHHHHcCCCCCEEEECCcEEE
Confidence 5788999999999876 4553
No 49
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=49.70 E-value=14 Score=22.76 Aligned_cols=12 Identities=58% Similarity=0.684 Sum_probs=9.6
Q ss_pred cHHHHHHHHHHH
Q psy13876 100 HEDVKKALLLLL 111 (118)
Q Consensus 100 ~~~vK~ailL~L 111 (118)
|+-||+||||..
T Consensus 56 neWvKkAILL~F 67 (70)
T PF14805_consen 56 NEWVKKAILLYF 67 (70)
T ss_dssp -HHHHHHHHHHH
T ss_pred eHHHHHHHHhcc
Confidence 899999999863
No 50
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=49.56 E-value=70 Score=22.84 Aligned_cols=51 Identities=12% Similarity=-0.041 Sum_probs=37.9
Q ss_pred ccEEEEEEeeCccc----ceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEccc
Q psy13876 11 GKHWILGLLRYWQN----PTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 11 Pr~i~v~l~~dLvd----~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~ 61 (118)
+-.+.|.+-+.+.+ .++-|+.|.|.|-++... .| ..+.+-|.|.+|+.+..
T Consensus 42 T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGrL~~~~y~dkdG~kr~~~eIva~~I~fl~~ 101 (161)
T PRK06293 42 TVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSPESYVDKDGSPQSSLVVSVDTIKFSPF 101 (161)
T ss_pred eEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEEEeCccCCCCCCEEEEEEEEEeEEEECcC
Confidence 45788888777654 478899999999999773 23 45566688888887743
No 51
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=49.48 E-value=91 Score=22.24 Aligned_cols=52 Identities=15% Similarity=0.087 Sum_probs=38.6
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
+..+.|.+-+.+. ..++-|+.|.|.|-++..+ .| ..+.+-|.|..|+.+...
T Consensus 51 t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeGrL~~~~y~dkdG~kr~~~eIva~~i~~L~~~ 111 (164)
T PRK08763 51 TEWHRVKFFGKLGEIAGEYLRKGSQCYIEGSIRYDKFTGQDGQERYVTEIVADEMQMLGGR 111 (164)
T ss_pred ceEEEEEEehHHHHHHHHhcCCCCEEEEEEEEEeceeECCCCCEEEEEEEEEeEEEECCCC
Confidence 4578888888754 4678899999999998762 23 456666888888876654
No 52
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=48.99 E-value=50 Score=24.13 Aligned_cols=31 Identities=10% Similarity=-0.048 Sum_probs=25.2
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~ 41 (118)
+-.+.|.+-+.+. ..++-||+|.|+|-++.+
T Consensus 52 t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL~~r 86 (186)
T PRK07772 52 ALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQR 86 (186)
T ss_pred ceEEEEEEecHHHHHHHHhcCCCCEEEEEEEEEcC
Confidence 4577888888765 467889999999999877
No 53
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=48.17 E-value=20 Score=24.38 Aligned_cols=24 Identities=8% Similarity=-0.002 Sum_probs=18.1
Q ss_pred EEEEeeCcccceecCCeEEEEEEE
Q psy13876 15 ILGLLRYWQNPTMLQNYCILHGLF 38 (118)
Q Consensus 15 ~v~l~~dLvd~~~pGd~V~v~Gi~ 38 (118)
.+.|.+...-.++|||+|.|..--
T Consensus 68 ~I~lNGaAArl~~~GD~vII~sy~ 91 (116)
T PF02261_consen 68 VICLNGAAARLVQVGDRVIIMSYA 91 (116)
T ss_dssp -EEEEGGGGGCS-TT-EEEEEEEE
T ss_pred EEEECCHHHhccCCCCEEEEEEcc
Confidence 567889999999999999998753
No 54
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=48.05 E-value=15 Score=24.83 Aligned_cols=25 Identities=8% Similarity=-0.095 Sum_probs=20.5
Q ss_pred EEEEEEeeCcccceecCCeEEEEEE
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
+=.+.|.+...-.++|||+|+|..-
T Consensus 65 Sg~I~lNGAAAr~~~~GD~vII~sy 89 (111)
T cd06919 65 SGVICLNGAAARLGQPGDRVIIMAY 89 (111)
T ss_pred CCEEEeCCHHHhcCCCCCEEEEEEC
Confidence 3456788888999999999998764
No 55
>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=47.14 E-value=25 Score=21.66 Aligned_cols=25 Identities=4% Similarity=-0.138 Sum_probs=17.2
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
|+-....+++ .+.|+.||.|.|.-.
T Consensus 36 r~kk~~aHD~-~~~~k~GD~V~I~ec 60 (71)
T TIGR03635 36 RTKKYHAHDE-NNECKVGDVVRIIET 60 (71)
T ss_pred ccEEEEEECC-CCCCCCCCEEEEEEc
Confidence 3344445555 457999999998765
No 56
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=46.56 E-value=60 Score=22.52 Aligned_cols=32 Identities=6% Similarity=-0.081 Sum_probs=22.0
Q ss_pred EEEEEEeeCc---ccceecCCeEEEEEEEEEcCCC
Q psy13876 13 HWILGLLRYW---QNPTMLQNYCILHGLFVCSSPG 44 (118)
Q Consensus 13 ~i~v~l~~dL---vd~~~pGd~V~v~Gi~~~~~~~ 44 (118)
++.|.=.=|| +..++.||.|.+.|-|.-.++|
T Consensus 70 tllIahNIDlaprip~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 70 TLLIAHNIDLAPRIPWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred EEEEEeccCccccCcCcCCCCEEEEEEEEEECCCC
Confidence 4455444455 3457789999999999766543
No 57
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=46.44 E-value=24 Score=21.57 Aligned_cols=19 Identities=5% Similarity=-0.122 Sum_probs=11.3
Q ss_pred EEEeeCcccceecCCeEEE
Q psy13876 16 LGLLRYWQNPTMLQNYCIL 34 (118)
Q Consensus 16 v~l~~dLvd~~~pGd~V~v 34 (118)
+...+.-++.+.|||.|.+
T Consensus 47 I~~~~~~~~~a~aGd~v~i 65 (83)
T cd03696 47 IQVHGKDVEEAKAGDRVAL 65 (83)
T ss_pred EEECCcCcCEEcCCCEEEE
Confidence 3445556666666666655
No 58
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=46.39 E-value=67 Score=19.61 Aligned_cols=20 Identities=5% Similarity=-0.046 Sum_probs=16.8
Q ss_pred ccceecCCeEEEEEEEEEcC
Q psy13876 23 QNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 23 vd~~~pGd~V~v~Gi~~~~~ 42 (118)
...+.+|+-|.|+|++...+
T Consensus 44 ~~~l~~es~V~V~G~v~~~~ 63 (84)
T cd04323 44 AKSLTQESSVEVTGEVKEDP 63 (84)
T ss_pred HhcCCCcCEEEEEEEEEECC
Confidence 35788999999999998764
No 59
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=46.27 E-value=26 Score=20.54 Aligned_cols=26 Identities=4% Similarity=-0.134 Sum_probs=20.8
Q ss_pred ccEEEEEEeeCcccc-------eecCCeEEEEE
Q psy13876 11 GKHWILGLLRYWQNP-------TMLQNYCILHG 36 (118)
Q Consensus 11 Pr~i~v~l~~dLvd~-------~~pGd~V~v~G 36 (118)
|+.+-|.+.++.+.+ ++.||+|.|.-
T Consensus 28 ~~~vavavN~~iv~~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 28 GNWLATAVNGELVHKEARAQFVLHEGDRIEILS 60 (65)
T ss_pred CCeEEEEECCEEcCHHHcCccccCCCCEEEEEE
Confidence 456778888888874 89999999864
No 60
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=45.66 E-value=5.1 Score=25.49 Aligned_cols=20 Identities=5% Similarity=0.003 Sum_probs=15.4
Q ss_pred eCcccceecCCeEEEEE-EEE
Q psy13876 20 RYWQNPTMLQNYCILHG-LFV 39 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~G-i~~ 39 (118)
.++.+.++|||+|.-+| ++-
T Consensus 32 ~~m~~~L~~Gd~VvT~gGi~G 52 (84)
T TIGR00739 32 KKLIESLKKGDKVLTIGGIIG 52 (84)
T ss_pred HHHHHhCCCCCEEEECCCeEE
Confidence 46778999999998765 543
No 61
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=44.83 E-value=92 Score=25.48 Aligned_cols=49 Identities=10% Similarity=0.029 Sum_probs=33.0
Q ss_pred EEEEEEeeC-------cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEcccc
Q psy13876 13 HWILGLLRY-------WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 13 ~i~v~l~~d-------Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~~ 62 (118)
.+.+.+..+ .+..+.+||.|.|+|++...+.. ..+.-|.+..++...+.
T Consensus 45 ~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~~~~~-~~~~el~~~~i~vls~a 100 (437)
T PRK05159 45 IIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKANPKA-PGGVEVIPEEIEVLNKA 100 (437)
T ss_pred EEEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEcCCCC-CCCEEEEEeEEEEEeCC
Confidence 477777654 34678899999999999876431 12344666666666543
No 62
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=44.34 E-value=18 Score=24.96 Aligned_cols=24 Identities=8% Similarity=-0.004 Sum_probs=20.2
Q ss_pred EEEEEeeCcccceecCCeEEEEEE
Q psy13876 14 WILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 14 i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
=.+.|.+...-.++|||+|.|..-
T Consensus 67 g~I~lNGAAArl~~~GD~VII~sy 90 (126)
T TIGR00223 67 RIICVNGAAARCVSVGDIVIIASY 90 (126)
T ss_pred CEEEeCCHHHhcCCCCCEEEEEEC
Confidence 356788888999999999999875
No 63
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=44.11 E-value=30 Score=23.12 Aligned_cols=26 Identities=12% Similarity=0.061 Sum_probs=22.8
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
+++++.+.+.=-.++++||.+.++..
T Consensus 18 KtiEiRlnD~kr~~ikvGD~I~f~~~ 43 (109)
T cd06555 18 KTIEIRLNDEKRQQIKVGDKILFNDL 43 (109)
T ss_pred CEEEEEecccchhcCCCCCEEEEEEc
Confidence 68999998888889999999999775
No 64
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=44.05 E-value=18 Score=24.95 Aligned_cols=25 Identities=8% Similarity=0.005 Sum_probs=20.6
Q ss_pred EEEEEEeeCcccceecCCeEEEEEE
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
+=.+.|.+...-.++|||+|+|..-
T Consensus 66 Sg~I~lNGAAAr~~~~GD~vII~ay 90 (126)
T PRK05449 66 SGVICLNGAAARLVQVGDLVIIAAY 90 (126)
T ss_pred CCEEEeCCHHHhcCCCCCEEEEEEC
Confidence 3456778888999999999998864
No 65
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=42.99 E-value=41 Score=20.85 Aligned_cols=26 Identities=12% Similarity=0.222 Sum_probs=18.9
Q ss_pred EEEEEEeeC-------cccceecCCeEEEEEEE
Q psy13876 13 HWILGLLRY-------WQNPTMLQNYCILHGLF 38 (118)
Q Consensus 13 ~i~v~l~~d-------Lvd~~~pGd~V~v~Gi~ 38 (118)
.+++.+... ..+.+++||+|.+.|=+
T Consensus 62 ~~~~~ik~~~~G~~S~~L~~l~~Gd~v~i~gP~ 94 (99)
T PF00970_consen 62 YLEFAIKRYPNGRVSRYLHQLKPGDEVEIRGPY 94 (99)
T ss_dssp EEEEEEEECTTSHHHHHHHTSCTTSEEEEEEEE
T ss_pred cEEEEEEeccCCHHHHHHHhCCCCCEEEEEEcc
Confidence 466665554 44779999999999854
No 66
>PF14427 Pput2613-deam: Pput_2613-like deaminase
Probab=42.93 E-value=18 Score=24.52 Aligned_cols=25 Identities=8% Similarity=0.117 Sum_probs=20.8
Q ss_pred EeeCcccceecCCeEEEEEEEEEcC
Q psy13876 18 LLRYWQNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 18 l~~dLvd~~~pGd~V~v~Gi~~~~~ 42 (118)
.-++|-++.+|||+..|-|+|.+-+
T Consensus 55 i~~~l~~~~~~Gd~m~I~G~ypPC~ 79 (118)
T PF14427_consen 55 ITRDLPLNQVPGDRMLIDGQYPPCN 79 (118)
T ss_pred HHhhcCccccCCceEEEeeecCCCc
Confidence 3467889999999999999997653
No 67
>COG2965 PriB Primosomal replication protein N [DNA replication, recombination, and repair]
Probab=42.20 E-value=86 Score=20.82 Aligned_cols=38 Identities=18% Similarity=0.373 Sum_probs=28.3
Q ss_pred CcccceecCCeEEEEEEEEEc-CCCCccceEEEEEEEEE
Q psy13876 21 YWQNPTMLQNYCILHGLFVCS-SPGLLSDTYIEAQRIQC 58 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi~~~~-~~~~~~~~yl~a~~I~~ 58 (118)
.|.-++.+|..+.|.|-+-.. ..+.+....|.|..|+.
T Consensus 63 ~lt~~i~~Gs~i~v~GFla~~~~~sg~~~lvlha~qi~~ 101 (103)
T COG2965 63 ELTQSITVGSYILVVGFLACHKRRSGLSKLVLHAEQIEF 101 (103)
T ss_pred hhhhccccccEEEEEEEEEeecccCCccEEEEEeeEEEe
Confidence 455668999999999987554 34566678888877764
No 68
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=42.02 E-value=91 Score=19.85 Aligned_cols=47 Identities=4% Similarity=0.068 Sum_probs=29.5
Q ss_pred EEEEEeeC-------cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 14 WILGLLRY-------WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 14 i~v~l~~d-------Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
+.+.+..+ ...++..||-|.|+|++...+.. ....=|.+.+++..++
T Consensus 29 iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~-~~~~Ei~~~~i~vl~~ 82 (103)
T cd04319 29 VQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRA-PGGAEVHGEKLEIIQN 82 (103)
T ss_pred EEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCC-CCCEEEEEEEEEEEec
Confidence 56666543 23467899999999998876422 1233355566666554
No 69
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=40.92 E-value=40 Score=22.33 Aligned_cols=21 Identities=10% Similarity=0.040 Sum_probs=12.8
Q ss_pred EEEEEEeeCcccceecCCeEEEEEE
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
.+++..+++ +++||+|.|+++
T Consensus 113 ~w~A~s~~~----i~~G~~V~Vv~v 133 (144)
T PF01957_consen 113 RWRARSEDE----IPKGDRVRVVGV 133 (144)
T ss_dssp EEEEEESST----B-TT-EEEEEEE
T ss_pred EEEEEeCCC----CCCCCEEEEEEE
Confidence 345555555 778888888886
No 70
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=40.68 E-value=1.2e+02 Score=25.27 Aligned_cols=46 Identities=15% Similarity=0.112 Sum_probs=31.7
Q ss_pred EEEEEEeeCc--------ccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 13 HWILGLLRYW--------QNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 13 ~i~v~l~~dL--------vd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
.+.|++..+. ..++..||.|.|+|++...+.| +.-|.+..++...+
T Consensus 83 ~iQ~v~~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~g---e~el~~~~~~vls~ 136 (491)
T PRK00484 83 RIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKTG---ELSVKATELTLLTK 136 (491)
T ss_pred cEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCCC---cEEEEEeEEEEEec
Confidence 4677776542 2358899999999999876544 45566666666554
No 71
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=39.63 E-value=77 Score=22.80 Aligned_cols=52 Identities=15% Similarity=0.035 Sum_probs=37.0
Q ss_pred ccEEEEEEeeCcc----cceecCCeEEEEEEEEEcC----CC-CccceEEEEEEEEEcccc
Q psy13876 11 GKHWILGLLRYWQ----NPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dLv----d~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I~~~~~~ 62 (118)
+..+.|.+-+.++ ..++-|+.|.|.|-++... .| ..+.+-+.|-+|+.++..
T Consensus 46 tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeGrL~~r~yedkdG~~~~~~eVva~~i~~l~~r 106 (173)
T PRK06751 46 ADFINCVIWRKQAENVANYLKKGSLAGVDGRLQTRNYEGQDGKRVYVTEVLAESVQFLEPR 106 (173)
T ss_pred EEEEEEEEeCcHHHHHHHHcCCCCEEEEEEEEEeCccCCCCCcEEEEEEEEEEEEEeCcCC
Confidence 4578888888754 4578899999999998773 23 344555667778766543
No 72
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=39.55 E-value=24 Score=21.47 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=13.0
Q ss_pred EeeCcccceecCCeEEEEE
Q psy13876 18 LLRYWQNPTMLQNYCILHG 36 (118)
Q Consensus 18 l~~dLvd~~~pGd~V~v~G 36 (118)
+.=+|++.++|||.|.|..
T Consensus 30 V~~~lv~~v~~Gd~VLVHa 48 (68)
T PF01455_consen 30 VSLALVPDVKVGDYVLVHA 48 (68)
T ss_dssp EEGTTCTSB-TT-EEEEET
T ss_pred EEEEEeCCCCCCCEEEEec
Confidence 3447888899999998864
No 73
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=39.41 E-value=31 Score=21.14 Aligned_cols=15 Identities=0% Similarity=-0.365 Sum_probs=7.3
Q ss_pred eeCcccceecCCeEE
Q psy13876 19 LRYWQNPTMLQNYCI 33 (118)
Q Consensus 19 ~~dLvd~~~pGd~V~ 33 (118)
.+.-++.+.|||+|.
T Consensus 50 ~~~~~~~a~aGd~v~ 64 (83)
T cd03698 50 DDEEVDYAVAGENVR 64 (83)
T ss_pred CCeECCEECCCCEEE
Confidence 344445555555544
No 74
>KOG3411|consensus
Probab=38.29 E-value=19 Score=25.10 Aligned_cols=42 Identities=33% Similarity=0.394 Sum_probs=32.6
Q ss_pred HHhhc--ChhHHHHHHHhhcccccCcHHHHHHHHHHHhcCccCC
Q psy13876 77 MAELG--GDQFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118 (118)
Q Consensus 77 i~~l~--~~~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~k~ 118 (118)
.+|++ +||+|..=+.|||..||=.--+=-+-+.-+.||..++
T Consensus 42 ~kElAP~D~dWfytRaASiaRhiylR~~~gvg~~~KiYGg~krr 85 (143)
T KOG3411|consen 42 GKELAPYDPDWYYTRAASIARHIYLRGPVGVGALTKIYGGSKRR 85 (143)
T ss_pred CcccCCCCccHHHHHHHHHHHHHHhccccchhHHHHHhcccccC
Confidence 35777 8999999999999999855555566677788887653
No 75
>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=37.99 E-value=38 Score=22.85 Aligned_cols=15 Identities=0% Similarity=-0.250 Sum_probs=10.7
Q ss_pred CcccceecCCeEEEE
Q psy13876 21 YWQNPTMLQNYCILH 35 (118)
Q Consensus 21 dLvd~~~pGd~V~v~ 35 (118)
.-...+++||+|+|.
T Consensus 47 ~~~~~~~~GD~V~v~ 61 (135)
T PF04246_consen 47 PNPIGAKVGDRVEVE 61 (135)
T ss_pred cCCCCCCCCCEEEEE
Confidence 344478889988875
No 76
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=37.71 E-value=9.3 Score=25.12 Aligned_cols=20 Identities=10% Similarity=0.006 Sum_probs=15.9
Q ss_pred eCcccceecCCeEEEEE-EEE
Q psy13876 20 RYWQNPTMLQNYCILHG-LFV 39 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~G-i~~ 39 (118)
.++.+.+++||+|.-+| ++-
T Consensus 38 ~~ml~sL~kGD~VvT~gGi~G 58 (97)
T COG1862 38 QELLNSLKKGDEVVTIGGIVG 58 (97)
T ss_pred HHHHHhccCCCEEEEcCCeEE
Confidence 46788999999998777 543
No 77
>PF00842 Ala_racemase_C: Alanine racemase, C-terminal domain; InterPro: IPR011079 Alanine racemase (5.1.1.1 from EC) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel.; GO: 0008784 alanine racemase activity, 0006522 alanine metabolic process; PDB: 3HUR_A 4A3Q_B 3S46_A 1RCQ_A 3CO8_A 1VFT_B 1VFH_A 1VFS_B 2DY3_B 4ECL_C ....
Probab=37.67 E-value=38 Score=22.99 Aligned_cols=17 Identities=12% Similarity=0.044 Sum_probs=10.9
Q ss_pred CcccceecCCeEEEEEE
Q psy13876 21 YWQNPTMLQNYCILHGL 37 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi 37 (118)
|.-..+++||+|++.|-
T Consensus 79 ~~~~~v~~GD~V~l~G~ 95 (129)
T PF00842_consen 79 DIEPDVKVGDEVTLFGR 95 (129)
T ss_dssp TSTST--TT-EEEEEEC
T ss_pred CCCCCCCCCCEEEEECC
Confidence 33578999999999993
No 78
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=37.66 E-value=39 Score=20.92 Aligned_cols=17 Identities=6% Similarity=-0.027 Sum_probs=9.9
Q ss_pred EeeCcccceecCCeEEE
Q psy13876 18 LLRYWQNPTMLQNYCIL 34 (118)
Q Consensus 18 l~~dLvd~~~pGd~V~v 34 (118)
.++.-++.+.|||+|.+
T Consensus 51 ~~~~~~~~a~~G~~v~l 67 (87)
T cd03697 51 MFRKTLDEAEAGDNVGV 67 (87)
T ss_pred ECCcCCCEECCCCEEEE
Confidence 34555666666666554
No 79
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=37.51 E-value=51 Score=21.86 Aligned_cols=26 Identities=4% Similarity=-0.226 Sum_probs=18.9
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
|+-....+++-++.++.||.|.|.-.
T Consensus 62 r~kky~aHDe~cn~~kvGD~V~I~E~ 87 (102)
T TIGR03630 62 RRSKIHAHNPPCIDVKEGDIVIIGET 87 (102)
T ss_pred EeeeEEEECCCCCCCCCCCEEEEEEc
Confidence 34445566667778999999998763
No 80
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=37.32 E-value=41 Score=21.37 Aligned_cols=25 Identities=4% Similarity=-0.097 Sum_probs=17.2
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
|+-....+++ -+.|+.||.|.|.-.
T Consensus 41 r~kk~~aHD~-~n~~k~GD~V~I~e~ 65 (84)
T PRK05610 41 RSKKYHAHDE-NNEAKIGDVVRIMET 65 (84)
T ss_pred cceEEEEECC-CCCCCCCCEEEEEEc
Confidence 3444455555 457999999998764
No 81
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=37.22 E-value=36 Score=21.18 Aligned_cols=19 Identities=11% Similarity=-0.197 Sum_probs=12.9
Q ss_pred EEEeeCcccceecCCeEEE
Q psy13876 16 LGLLRYWQNPTMLQNYCIL 34 (118)
Q Consensus 16 v~l~~dLvd~~~pGd~V~v 34 (118)
+...+..++.+.|||+|.+
T Consensus 51 I~~~~~~~~~a~aGd~v~l 69 (87)
T cd03694 51 IHRNRSPVRVVRAGQSASL 69 (87)
T ss_pred EEECCeECCEECCCCEEEE
Confidence 4445677777777777766
No 82
>PF07107 WI12: Wound-induced protein WI12; InterPro: IPR009798 This entry consists of several plant wound-induced protein sequences related to WI12 from Mesembryanthemum crystallinum (Common ice plant) (Q9XES3 from SWISSPROT). Wounding, methyl jasmonate, and pathogen infection is known to induce local WI12 expression. WI12 expression is also thought to be developmentally controlled in the placenta and developing seeds. WI12 preferentially accumulates in the cell wall and it has been suggested that it plays a role in the reinforcement of cell wall composition after wounding and during plant development [].
Probab=37.16 E-value=42 Score=22.56 Aligned_cols=34 Identities=24% Similarity=0.167 Sum_probs=20.4
Q ss_pred CccccCCCCCccEEEEEEeeCcccceecCCeEEEEEEE
Q psy13876 1 MRIATGASMVGKHWILGLLRYWQNPTMLQNYCILHGLF 38 (118)
Q Consensus 1 ~~~~~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~ 38 (118)
||+-||++.- .-...+.-.-++.+ ||.|.+-|..
T Consensus 1 MrlLTG~~~~--~~sF~F~P~sV~af--G~~ViaEG~~ 34 (109)
T PF07107_consen 1 MRLLTGASTS--SSSFRFVPRSVDAF--GSTVIAEGCD 34 (109)
T ss_pred CeeeeCCCCC--cCcEEEeccEEEEE--CCEEEEeccc
Confidence 8999996532 12222333333333 9999999943
No 83
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=37.02 E-value=1.1e+02 Score=19.40 Aligned_cols=21 Identities=5% Similarity=-0.058 Sum_probs=17.9
Q ss_pred cccceecCCeEEEEEEEEEcC
Q psy13876 22 WQNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi~~~~~ 42 (118)
..+.+++|+.|.|.|.++..+
T Consensus 59 ~~~~i~~G~vvrV~G~i~~fr 79 (92)
T cd04483 59 QAKVLEIGDLLRVRGSIRTYR 79 (92)
T ss_pred cccccCCCCEEEEEEEEeccC
Confidence 456799999999999998775
No 84
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=36.96 E-value=10 Score=25.22 Aligned_cols=21 Identities=5% Similarity=-0.108 Sum_probs=15.9
Q ss_pred eCcccceecCCeE-EEEEEEEE
Q psy13876 20 RYWQNPTMLQNYC-ILHGLFVC 40 (118)
Q Consensus 20 ~dLvd~~~pGd~V-~v~Gi~~~ 40 (118)
.++.++++|||+| +..|++-.
T Consensus 47 ~~~~~~Lk~Gd~VvT~gGi~G~ 68 (106)
T PRK05585 47 KKMLSSLAKGDEVVTNGGIIGK 68 (106)
T ss_pred HHHHHhcCCCCEEEECCCeEEE
Confidence 5678999999999 55556643
No 85
>PF14306 PUA_2: PUA-like domain; PDB: 1M8P_C 1I2D_B 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2OFX_B 1J70_B 1G8F_A ....
Probab=36.87 E-value=29 Score=24.67 Aligned_cols=35 Identities=14% Similarity=0.067 Sum_probs=23.2
Q ss_pred CccccCCCCCccEEEEEEeeCcccceecCCeEEEEE
Q psy13876 1 MRIATGASMVGKHWILGLLRYWQNPTMLQNYCILHG 36 (118)
Q Consensus 1 ~~~~~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~G 36 (118)
||++.|.- .|=-|.+-+..+...++++||+|.++.
T Consensus 69 ~rL~~G~~-wpiPI~L~v~~e~~~~l~~G~~v~L~~ 103 (160)
T PF14306_consen 69 MRLPDGTL-WPIPIVLDVSEEEAKSLKEGDKVALRD 103 (160)
T ss_dssp SBETTSSB---S---EEECHHHHTTCTTTSEEEEEE
T ss_pred CCcCCCCE-EeEEEEEECCHHHHHhccCCCEEEEEC
Confidence 78887732 344466666888889999999988764
No 86
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=36.78 E-value=25 Score=20.70 Aligned_cols=14 Identities=14% Similarity=0.048 Sum_probs=8.2
Q ss_pred cceecCCeEEEEEE
Q psy13876 24 NPTMLQNYCILHGL 37 (118)
Q Consensus 24 d~~~pGd~V~v~Gi 37 (118)
+.+++||||.+|.-
T Consensus 4 Gpf~~GdrVQlTD~ 17 (54)
T PF14801_consen 4 GPFRAGDRVQLTDP 17 (54)
T ss_dssp -S--TT-EEEEEET
T ss_pred CCCCCCCEEEEccC
Confidence 45789999999863
No 87
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=36.49 E-value=1.6e+02 Score=21.27 Aligned_cols=52 Identities=17% Similarity=0.054 Sum_probs=35.7
Q ss_pred ccEEEEEEeeCc----ccceecCCeEEEEEEEEEcC---CC-CccceEEEEE---EEEEcccc
Q psy13876 11 GKHWILGLLRYW----QNPTMLQNYCILHGLFVCSS---PG-LLSDTYIEAQ---RIQCLSKA 62 (118)
Q Consensus 11 Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~~---~~-~~~~~yl~a~---~I~~~~~~ 62 (118)
+..+.|.+-+.+ .+.++-|+.|.|.|-++... .| ..+.+-|.|. .++.++..
T Consensus 53 t~w~~Vv~wgk~Ae~v~~~L~KG~~V~VeGrL~~r~ye~dG~kr~~~eIiv~~~g~~~fL~~~ 115 (175)
T PRK13732 53 TEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRTRSWEDNGITRYVTEILVKTTGTMQMLGRA 115 (175)
T ss_pred eeEEEEEEecHHHHHHHHhcCCCCEEEEEEEEEeeeEccCCeEEEEEEEEEeecCeEEEecCC
Confidence 457788888875 45678899999999988762 23 3455556666 56655443
No 88
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=36.14 E-value=52 Score=22.06 Aligned_cols=26 Identities=0% Similarity=-0.254 Sum_probs=18.9
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
|+-....+++-++.|+.||.|.|.-.
T Consensus 64 r~kky~aHDe~cn~~kvGD~V~I~E~ 89 (108)
T PRK08572 64 RRSRIHAHNPPCIDAKVGDKVKIAEC 89 (108)
T ss_pred EeeeEEEECCCCCCCCCCCEEEEEEc
Confidence 33445566666788999999998763
No 89
>PLN02502 lysyl-tRNA synthetase
Probab=35.93 E-value=1.6e+02 Score=25.10 Aligned_cols=35 Identities=14% Similarity=0.046 Sum_probs=26.0
Q ss_pred ceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEcccc
Q psy13876 25 PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 25 ~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~~ 62 (118)
.+..||.|.|+|++...+.| +.-|.+..++...+.
T Consensus 160 ~l~~gdiV~V~G~~~~t~~g---elel~~~~i~vLs~~ 194 (553)
T PLN02502 160 LVDRGDIVGVTGTPGKTKKG---ELSIFPTSFEVLTKC 194 (553)
T ss_pred CCCCCcEEEEEEEEEecCCC---CEEEEEeEEEEEecc
Confidence 47899999999999876654 456667777666543
No 90
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=35.26 E-value=25 Score=21.96 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=15.0
Q ss_pred CccEEEEEEeeCcccceecCCeEEEEE
Q psy13876 10 VGKHWILGLLRYWQNPTMLQNYCILHG 36 (118)
Q Consensus 10 ~Pr~i~v~l~~dLvd~~~pGd~V~v~G 36 (118)
..|.+.+. |++.++|||.|.|.-
T Consensus 24 ~~~~v~l~----lv~~~~vGD~VLVH~ 46 (76)
T TIGR00074 24 IKRDVSLD----LVGEVKVGDYVLVHV 46 (76)
T ss_pred eEEEEEEE----eeCCCCCCCEEEEec
Confidence 44444444 456799999888753
No 91
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=35.23 E-value=62 Score=20.21 Aligned_cols=13 Identities=0% Similarity=-0.256 Sum_probs=6.4
Q ss_pred ccceecCCeEEEE
Q psy13876 23 QNPTMLQNYCILH 35 (118)
Q Consensus 23 vd~~~pGd~V~v~ 35 (118)
.+.++.||.|.+.
T Consensus 28 ~G~i~~gd~v~i~ 40 (91)
T cd03693 28 TGVLKPGMVVTFA 40 (91)
T ss_pred cceeecCCEEEEC
Confidence 3445555555433
No 92
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=35.02 E-value=76 Score=21.50 Aligned_cols=27 Identities=7% Similarity=-0.096 Sum_probs=20.7
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGLF 38 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi~ 38 (118)
..+.|...+.+-|.++.|..|.++|.+
T Consensus 82 ~~i~V~Y~G~~Pd~F~eg~~VVv~G~~ 108 (131)
T PF03100_consen 82 KEIPVVYTGPLPDLFREGQGVVVEGRL 108 (131)
T ss_dssp -EEEEEEES--CTT--TTSEEEEEEEE
T ss_pred cEEEEEECCCCCccccCCCeEEEEEEE
Confidence 568999999999999999999999988
No 93
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=34.03 E-value=49 Score=19.96 Aligned_cols=25 Identities=0% Similarity=-0.388 Sum_probs=15.6
Q ss_pred EEEEEEe-eCcccceecCCeEEEEEE
Q psy13876 13 HWILGLL-RYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 13 ~i~v~l~-~dLvd~~~pGd~V~v~Gi 37 (118)
+|+..+. +-+...+++||+|.++=.
T Consensus 29 TM~F~v~~~~~l~~l~~Gd~V~F~~~ 54 (70)
T PF11604_consen 29 TMDFPVADPVDLAGLKPGDKVRFTFE 54 (70)
T ss_dssp EEEEE--TTSEESS-STT-EEEEEEE
T ss_pred EEEEEcCChhhhhcCCCCCEEEEEEE
Confidence 5666655 556689999999998744
No 94
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=33.57 E-value=14 Score=24.82 Aligned_cols=19 Identities=5% Similarity=-0.183 Sum_probs=14.7
Q ss_pred eCcccceecCCeEEEEE-EE
Q psy13876 20 RYWQNPTMLQNYCILHG-LF 38 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~G-i~ 38 (118)
.++.+.++|||+|.-+| ++
T Consensus 33 ~~m~~~Lk~GD~VvT~gGi~ 52 (109)
T PRK05886 33 IDLHESLQPGDRVHTTSGLQ 52 (109)
T ss_pred HHHHHhcCCCCEEEECCCeE
Confidence 36778999999998665 44
No 95
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=33.41 E-value=63 Score=23.73 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=22.7
Q ss_pred cEEEEEEeeCcccc-eecCCeEEEEEEE
Q psy13876 12 KHWILGLLRYWQNP-TMLQNYCILHGLF 38 (118)
Q Consensus 12 r~i~v~l~~dLvd~-~~pGd~V~v~Gi~ 38 (118)
....|+|++++.+. +++||.|.|.|-+
T Consensus 10 ~~~~v~L~~~W~~t~v~~Gd~I~ii~~~ 37 (209)
T PF08696_consen 10 ETRTVILRDEWCETPVSPGDIIHIIGEF 37 (209)
T ss_pred CeEEEEEeCCcccCCCcCCCEEEEEEEe
Confidence 46789999999974 7899999999943
No 96
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=33.23 E-value=49 Score=19.53 Aligned_cols=24 Identities=0% Similarity=-0.143 Sum_probs=17.4
Q ss_pred cEEEEEEeeCcccceecCCeEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILH 35 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~ 35 (118)
.++++....++.+++.||+.|.+.
T Consensus 25 eT~ev~~p~~~~~~i~~G~eV~y~ 48 (57)
T cd04467 25 ETFEVPIPEEIKDKLEPGKEVEYW 48 (57)
T ss_pred eeEEEecchhhcccCCCCCEEEEE
Confidence 356666555677899999999854
No 97
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=33.12 E-value=29 Score=23.86 Aligned_cols=25 Identities=8% Similarity=-0.003 Sum_probs=20.1
Q ss_pred EEEEEEeeCcccceecCCeEEEEEE
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
+=.+.|.+-..-.++|||+|.|.--
T Consensus 65 Sg~I~lNGAAArl~~~GD~VII~sy 89 (126)
T COG0853 65 SGVICLNGAAARLVQVGDLVIIMSY 89 (126)
T ss_pred CcEEEechHHHhhCCCCCEEEEEEc
Confidence 4456778888889999999998764
No 98
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=32.47 E-value=2e+02 Score=23.74 Aligned_cols=49 Identities=10% Similarity=0.013 Sum_probs=30.3
Q ss_pred cEEEEEEeeC-------cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 12 KHWILGLLRY-------WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 12 r~i~v~l~~d-------Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
-.+.|.+... ....+..||-|.|+|++...+ +...+.-|.+..++....
T Consensus 46 g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~-~~~~~~El~~~~i~vl~~ 101 (453)
T TIGR00457 46 GPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESP-GKGQPVELQVKKIEVVGE 101 (453)
T ss_pred ccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCC-CCCCCEEEEEeEEEEEec
Confidence 3577777654 334689999999999988653 111233345555555543
No 99
>PF08978 Reoviridae_Vp9: Reoviridae VP9; InterPro: IPR015072 This family contains various Reoviridae outer-coat proteins.; PDB: 1W9Z_A.
Probab=31.55 E-value=15 Score=28.01 Aligned_cols=21 Identities=19% Similarity=0.121 Sum_probs=12.8
Q ss_pred eCcccceecCCeEEEEEEEEE
Q psy13876 20 RYWQNPTMLQNYCILHGLFVC 40 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~Gi~~~ 40 (118)
..|++.+.||||+..+|-|--
T Consensus 212 ~nl~nslv~gdr~~~~glyvd 232 (280)
T PF08978_consen 212 TNLVNSLVPGDRARPVGLYVD 232 (280)
T ss_dssp HHHHTTS-GGGB----EEEE-
T ss_pred HHHHhhccCCCccCceeEEEe
Confidence 357899999999999999853
No 100
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.53 E-value=43 Score=27.68 Aligned_cols=22 Identities=9% Similarity=-0.053 Sum_probs=18.9
Q ss_pred eCcccceecCCeEEEEEEEEEc
Q psy13876 20 RYWQNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~Gi~~~~ 41 (118)
++++.++.|||.|++.|.++..
T Consensus 310 r~~a~~L~pGD~i~~~G~~~~~ 331 (421)
T COG1571 310 RELARKLIPGDEITVYGSVKPG 331 (421)
T ss_pred hHHHHhcCCCCEEEEecCcccc
Confidence 5678899999999999998743
No 101
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=31.50 E-value=1e+02 Score=19.72 Aligned_cols=28 Identities=7% Similarity=-0.064 Sum_probs=19.8
Q ss_pred cceecCCeEEEEEEEEEcCCCCccceEE
Q psy13876 24 NPTMLQNYCILHGLFVCSSPGLLSDTYI 51 (118)
Q Consensus 24 d~~~pGd~V~v~Gi~~~~~~~~~~~~yl 51 (118)
...+.|++|.+.|-+....+...++.++
T Consensus 67 ~~l~~G~~V~v~g~~~~y~~~G~~sl~v 94 (99)
T PF13742_consen 67 FDLKDGDKVLVRGRVSFYEPRGSLSLIV 94 (99)
T ss_pred CCCCCCCEEEEEEEEEEECCCcEEEEEE
Confidence 4568899999999988765544444444
No 102
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=31.46 E-value=18 Score=22.99 Aligned_cols=16 Identities=6% Similarity=-0.120 Sum_probs=13.9
Q ss_pred CcccceecCCeEEEEE
Q psy13876 21 YWQNPTMLQNYCILHG 36 (118)
Q Consensus 21 dLvd~~~pGd~V~v~G 36 (118)
+|.+.|++|..|+||=
T Consensus 16 ~lL~rV~aGEev~IT~ 31 (84)
T COG4118 16 ELLRRVRAGEEVIITK 31 (84)
T ss_pred HHHHHHhCCCEEEEee
Confidence 5788999999999983
No 103
>PRK11507 ribosome-associated protein; Provisional
Probab=31.20 E-value=26 Score=21.63 Aligned_cols=14 Identities=7% Similarity=-0.014 Sum_probs=12.2
Q ss_pred cceecCCeEEEEEE
Q psy13876 24 NPTMLQNYCILHGL 37 (118)
Q Consensus 24 d~~~pGd~V~v~Gi 37 (118)
-++.|||.|.+-|.
T Consensus 51 kKl~~GD~V~~~g~ 64 (70)
T PRK11507 51 CKIVAGQTVSFAGH 64 (70)
T ss_pred CCCCCCCEEEECCE
Confidence 47899999999885
No 104
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=30.82 E-value=53 Score=20.47 Aligned_cols=18 Identities=0% Similarity=-0.247 Sum_probs=14.6
Q ss_pred ceecCCeEEEEEEEEEcC
Q psy13876 25 PTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 25 ~~~pGd~V~v~Gi~~~~~ 42 (118)
..+|||.|.+.++++...
T Consensus 10 iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 10 IYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp EE-TTSEEEEEEEEEEEC
T ss_pred CcCCCCEEEEEEEEeccc
Confidence 468999999999988665
No 105
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=30.51 E-value=70 Score=19.52 Aligned_cols=17 Identities=0% Similarity=-0.130 Sum_probs=10.8
Q ss_pred eCcccceecCCeEEEEE
Q psy13876 20 RYWQNPTMLQNYCILHG 36 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~G 36 (118)
.=..+.+++||.|.+..
T Consensus 20 ~v~~G~i~~G~~v~i~P 36 (82)
T cd04089 20 KVESGTIKKGDKLLVMP 36 (82)
T ss_pred EEeeeEEecCCEEEEeC
Confidence 33446677777776666
No 106
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=30.45 E-value=1.6e+02 Score=21.08 Aligned_cols=46 Identities=9% Similarity=-0.034 Sum_probs=31.0
Q ss_pred ccEEEEEEeeC-----cccceecCCeEEEEEEEEEcC----CC-CccceEEEEEEE
Q psy13876 11 GKHWILGLLRY-----WQNPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRI 56 (118)
Q Consensus 11 Pr~i~v~l~~d-----Lvd~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I 56 (118)
+-.+.|.+-++ +...++.|+.|.|.|-++... .| ..+.+.|.+.+|
T Consensus 52 T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~VeGrL~~r~w~dkdG~~r~~~eIiv~~~ 107 (166)
T PRK06341 52 TEWHRVVIFNEGLCKVAEQYLKKGAKVYIEGQLQTRKWTDQSGVERYSTEVVLQGF 107 (166)
T ss_pred ceEEEEEEeChHHHHHHHHhcCCCCEEEEEEEEEeCcEECCCCCEEEEEEEEEEec
Confidence 55778887764 335679999999999998763 23 334455555443
No 107
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=30.39 E-value=73 Score=20.54 Aligned_cols=16 Identities=6% Similarity=-0.089 Sum_probs=13.1
Q ss_pred cccceecCCeEEEEEE
Q psy13876 22 WQNPTMLQNYCILHGL 37 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi 37 (118)
-.+.+++||.|.|.-.
T Consensus 52 e~~~~k~GD~V~I~Et 67 (87)
T COG0186 52 ECNEAKVGDIVRIAET 67 (87)
T ss_pred ccccCCCCCEEEEEEc
Confidence 5778999999998654
No 108
>COG2375 ViuB Siderophore-interacting protein [Inorganic ion transport and metabolism]
Probab=29.83 E-value=42 Score=25.95 Aligned_cols=24 Identities=13% Similarity=0.101 Sum_probs=18.4
Q ss_pred EEEEEe------eCcccceecCCeEEEEEE
Q psy13876 14 WILGLL------RYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 14 i~v~l~------~dLvd~~~pGd~V~v~Gi 37 (118)
|++.++ ..+..+++|||.+.|+|=
T Consensus 104 vDfVlH~~~gpas~WA~~a~~GD~l~i~GP 133 (265)
T COG2375 104 VDFVLHGEGGPASRWARTAQPGDTLTIMGP 133 (265)
T ss_pred EEEEEcCCCCcchhhHhhCCCCCEEEEeCC
Confidence 556666 235688999999999985
No 109
>PHA03256 BDLF3; Provisional
Probab=29.73 E-value=97 Score=19.38 Aligned_cols=45 Identities=27% Similarity=0.244 Sum_probs=27.4
Q ss_pred CCCCHHHHHhhc--ChhHHHHHHHhhcccccC---------cHHHHHHHHHHHhcC
Q psy13876 70 GTLSEEEMAELG--GDQFYSKLAASLAPEIYG---------HEDVKKALLLLLVGG 114 (118)
Q Consensus 70 ~~~~~e~i~~l~--~~~~~~~L~~SiaP~I~G---------~~~vK~ailL~L~GG 114 (118)
.-++|+|+.++. .+-....|+.+++-+.-+ +..-...++|-|+|-
T Consensus 15 ~~IsE~df~~~~~ff~rpLp~lVaevska~~~~~elv~S~~Q~lenI~llLDLvGt 70 (77)
T PHA03256 15 GTIGEREFGELLSWDPTDLPRTVARVYVAVGGLFEQEVSEVQRLENICTLLDLAGV 70 (77)
T ss_pred CccCHHHHHHHHHHcCCcHHHHHHHHHHHhccceeeeechhhhHHHHHHHHHhhcc
Confidence 346899998864 444444455555544433 455566778888773
No 110
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=29.71 E-value=1.1e+02 Score=17.27 Aligned_cols=20 Identities=5% Similarity=-0.160 Sum_probs=16.4
Q ss_pred cccceecCCeEEEEEEEEEc
Q psy13876 22 WQNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi~~~~ 41 (118)
+....++|+.+.+.|.+...
T Consensus 42 ~~~~~~~G~~~~v~Gkv~~~ 61 (75)
T cd04488 42 LKKQLPPGTRVRVSGKVKRF 61 (75)
T ss_pred HHhcCCCCCEEEEEEEEeec
Confidence 56778899999999998754
No 111
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=29.68 E-value=2.4e+02 Score=23.07 Aligned_cols=48 Identities=10% Similarity=0.149 Sum_probs=30.3
Q ss_pred EEEEEEeeC--------cccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 13 HWILGLLRY--------WQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 13 ~i~v~l~~d--------Lvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
.+.+.+... ...++.+||.|.|+|++...+. ...+.-|.+..++....
T Consensus 41 ~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~-~~~~~el~~~~i~vl~~ 96 (428)
T TIGR00458 41 LIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEK-APGGFEIIPTKIEVINE 96 (428)
T ss_pred eEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEecCC-CCCcEEEEEeEEEEEec
Confidence 367766543 2356889999999999986542 11234455555655554
No 112
>PRK07440 hypothetical protein; Provisional
Probab=29.59 E-value=97 Score=18.63 Aligned_cols=28 Identities=0% Similarity=-0.236 Sum_probs=21.6
Q ss_pred CccEEEEEEeeCccc-------ceecCCeEEEEEE
Q psy13876 10 VGKHWILGLLRYWQN-------PTMLQNYCILHGL 37 (118)
Q Consensus 10 ~Pr~i~v~l~~dLvd-------~~~pGd~V~v~Gi 37 (118)
-|+.+-|.+.++++. .++.||+|+|.-.
T Consensus 32 ~~~~vav~~N~~iv~r~~w~~~~L~~gD~IEIv~~ 66 (70)
T PRK07440 32 NPRLVAVEYNGEILHRQFWEQTQVQPGDRLEIVTI 66 (70)
T ss_pred CCCeEEEEECCEEeCHHHcCceecCCCCEEEEEEE
Confidence 477888888877775 4788999998654
No 113
>CHL00181 cbbX CbbX; Provisional
Probab=29.18 E-value=43 Score=25.76 Aligned_cols=23 Identities=22% Similarity=0.263 Sum_probs=19.0
Q ss_pred HHHHHHHhhcccccCcHHHHHHH
Q psy13876 85 FYSKLAASLAPEIYGHEDVKKAL 107 (118)
Q Consensus 85 ~~~~L~~SiaP~I~G~~~vK~ai 107 (118)
..+.+.+++.++++|++.+|+.|
T Consensus 13 ~~~~~~~~l~~~l~Gl~~vK~~i 35 (287)
T CHL00181 13 QIQEVLDILDEELVGLAPVKTRI 35 (287)
T ss_pred CHHHHHHHHHHhcCCcHHHHHHH
Confidence 34567888999999999999866
No 114
>PF12982 DUF3866: Protein of unknown function (DUF3866); InterPro: IPR024479 This family of proteins is currently functionally uncharacterised.
Probab=29.08 E-value=29 Score=27.61 Aligned_cols=21 Identities=5% Similarity=-0.183 Sum_probs=18.0
Q ss_pred EEeeCcccceecCCeEEEEEE
Q psy13876 17 GLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 17 ~l~~dLvd~~~pGd~V~v~Gi 37 (118)
+.+.+|+..+++||+|.+.-.
T Consensus 4 i~Y~~l~G~~~~GD~VllNtT 24 (320)
T PF12982_consen 4 INYPDLTGRVEPGDRVLLNTT 24 (320)
T ss_pred cchHhhCCCCCCCCEEEEecc
Confidence 457899999999999998765
No 115
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=28.71 E-value=78 Score=18.41 Aligned_cols=26 Identities=0% Similarity=-0.270 Sum_probs=19.1
Q ss_pred ccEEEEEEeeCccc-------ceecCCeEEEEE
Q psy13876 11 GKHWILGLLRYWQN-------PTMLQNYCILHG 36 (118)
Q Consensus 11 Pr~i~v~l~~dLvd-------~~~pGd~V~v~G 36 (118)
|..+-|.+.+..+. .++.||+|.|.-
T Consensus 27 ~~~v~v~vN~~iv~~~~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 27 PRRVAVAVNGEIVPRSEWDDTILKEGDRIEIVT 59 (64)
T ss_pred CCeEEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 56777777777663 588999998764
No 116
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=28.68 E-value=47 Score=18.50 Aligned_cols=22 Identities=0% Similarity=-0.358 Sum_probs=16.0
Q ss_pred EEEEeeCc----ccceecCCeEEEEE
Q psy13876 15 ILGLLRYW----QNPTMLQNYCILHG 36 (118)
Q Consensus 15 ~v~l~~dL----vd~~~pGd~V~v~G 36 (118)
++++.... ...+.+||+|.+.=
T Consensus 22 ~i~v~~~~~~~~~~~~~~Gd~V~~~i 47 (64)
T smart00357 22 DVFVHPSQIQGGLKSLREGDEVEFKV 47 (64)
T ss_pred cEEEEhHHhhcCCCcCCCCCEEEEEE
Confidence 55555555 67789999998873
No 117
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=28.50 E-value=1.6e+02 Score=18.58 Aligned_cols=50 Identities=12% Similarity=-0.021 Sum_probs=31.7
Q ss_pred EEEEEEeeCc----------ccceecCCeEEEEEEEEEcCCC----CccceEEEEEEEEEcccc
Q psy13876 13 HWILGLLRYW----------QNPTMLQNYCILHGLFVCSSPG----LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 13 ~i~v~l~~dL----------vd~~~pGd~V~v~Gi~~~~~~~----~~~~~yl~a~~I~~~~~~ 62 (118)
.+.+.+..+. ...+..|+-|.|+|++...+.. .....-|.+..++.....
T Consensus 29 ~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 29 TIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVVSEA 92 (102)
T ss_pred eEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEEecC
Confidence 4666665442 3468899999999999765321 113445666677666543
No 118
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=28.48 E-value=46 Score=21.44 Aligned_cols=12 Identities=8% Similarity=0.027 Sum_probs=9.2
Q ss_pred cceecCCeEEEE
Q psy13876 24 NPTMLQNYCILH 35 (118)
Q Consensus 24 d~~~pGd~V~v~ 35 (118)
-.+++||+|.+.
T Consensus 52 ~~Vk~GD~Vl~~ 63 (91)
T PRK14533 52 FDIKVGDKVIFS 63 (91)
T ss_pred ccccCCCEEEEc
Confidence 458999988754
No 119
>TIGR03177 pilus_cpaB Flp pilus assembly protein CpaB. Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis.
Probab=28.18 E-value=79 Score=23.81 Aligned_cols=30 Identities=0% Similarity=-0.337 Sum_probs=21.7
Q ss_pred cEEEEEEee--CcccceecCCeEEEEEEEEEc
Q psy13876 12 KHWILGLLR--YWQNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 12 r~i~v~l~~--dLvd~~~pGd~V~v~Gi~~~~ 41 (118)
|.+.+.++. -.-+.++|||+|.|.-..+..
T Consensus 115 rav~i~v~~~~~v~g~i~pGD~VDV~~~~~~~ 146 (261)
T TIGR03177 115 RAVAIRVDEVTGVGGFILPGDRVDVLLTRRDD 146 (261)
T ss_pred EEEEEEecccccccccccCCCEEEEEEEeccC
Confidence 345555554 345788999999999988654
No 120
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=27.94 E-value=1.7e+02 Score=18.70 Aligned_cols=33 Identities=21% Similarity=0.085 Sum_probs=22.8
Q ss_pred eecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 26 TMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 26 ~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
+..||-|.|+|.+...+.+. .-|.+..++....
T Consensus 50 l~~g~~V~v~G~v~~~~~g~---~El~~~~~~ils~ 82 (108)
T cd04322 50 LDLGDIIGVTGTPFKTKTGE---LSIFVKEFTLLSK 82 (108)
T ss_pred CCCCCEEEEEEEEEecCCCC---EEEEeCEeEEeec
Confidence 88999999999998776542 2344555555543
No 121
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=27.75 E-value=1.2e+02 Score=17.10 Aligned_cols=36 Identities=14% Similarity=-0.057 Sum_probs=22.4
Q ss_pred EEEEEeeCccccee--cCCeEEEEEEEEEcCCCCccce
Q psy13876 14 WILGLLRYWQNPTM--LQNYCILHGLFVCSSPGLLSDT 49 (118)
Q Consensus 14 i~v~l~~dLvd~~~--pGd~V~v~Gi~~~~~~~~~~~~ 49 (118)
|.+.+.++-.+..+ -|.+|.|+|-+-....+.-+..
T Consensus 2 vQL~l~~~~~~~~~~~~Gk~V~V~G~l~~a~t~hH~Tp 39 (48)
T PF14485_consen 2 VQLILSEEDYSYLKSLLGKRVSVTGKLFHAHTGHHHTP 39 (48)
T ss_pred eEEEeChhhhHHHHHhcCCeEEEEEEEeeccCcccCCc
Confidence 44555555555554 5999999998765544433333
No 122
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=27.46 E-value=51 Score=21.73 Aligned_cols=12 Identities=8% Similarity=0.160 Sum_probs=8.9
Q ss_pred ccceecCCeEEE
Q psy13876 23 QNPTMLQNYCIL 34 (118)
Q Consensus 23 vd~~~pGd~V~v 34 (118)
.-.+++||+|.+
T Consensus 60 ~~~Vk~GD~Vl~ 71 (100)
T PTZ00414 60 TPTVKVGDTVLL 71 (100)
T ss_pred cceecCCCEEEE
Confidence 345899998874
No 123
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=27.43 E-value=1.1e+02 Score=20.58 Aligned_cols=27 Identities=7% Similarity=-0.085 Sum_probs=21.8
Q ss_pred EEEEEEeeCcccceecCCeEEEEEEEE
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGLFV 39 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi~~ 39 (118)
++.+.+=++..+.+++||.|.|.+.+.
T Consensus 52 ~I~~tlW~~~a~~l~~GdvV~I~na~v 78 (129)
T PRK06461 52 RVKLTLWGEQAGSLKEGEVVEIENAWT 78 (129)
T ss_pred EEEEEEeCCccccCCCCCEEEEECcEE
Confidence 366777788888999999999996553
No 124
>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=27.35 E-value=45 Score=19.24 Aligned_cols=25 Identities=8% Similarity=-0.233 Sum_probs=17.1
Q ss_pred EEEEEEeeCcccceecCCeEEEEEE
Q psy13876 13 HWILGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 13 ~i~v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
.-++.+..+-...+..||+|.|.=+
T Consensus 19 ~~DifIp~~~l~~A~~gD~V~v~i~ 43 (58)
T PF08206_consen 19 GEDIFIPPRNLNGAMDGDKVLVRIT 43 (58)
T ss_dssp TEEEEE-HHHHTTS-TT-EEEEEEE
T ss_pred CCCEEECHHHHCCCCCCCEEEEEEe
Confidence 3577778888899999999988643
No 125
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=27.33 E-value=38 Score=21.75 Aligned_cols=13 Identities=0% Similarity=0.013 Sum_probs=9.1
Q ss_pred ccceecCCeEEEE
Q psy13876 23 QNPTMLQNYCILH 35 (118)
Q Consensus 23 vd~~~pGd~V~v~ 35 (118)
...+++||+|.+.
T Consensus 55 ~~~vk~GD~Vl~~ 67 (93)
T cd00320 55 PLSVKVGDKVLFP 67 (93)
T ss_pred cccccCCCEEEEC
Confidence 4468889987643
No 126
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=27.31 E-value=15 Score=24.73 Aligned_cols=20 Identities=15% Similarity=0.114 Sum_probs=14.9
Q ss_pred eCcccceecCCeEEEEE-EEE
Q psy13876 20 RYWQNPTMLQNYCILHG-LFV 39 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~G-i~~ 39 (118)
.++.+++++||+|.-+| ++-
T Consensus 31 ~em~~sLk~GD~VvT~GGi~G 51 (113)
T PRK06531 31 QNQLNAIQKGDEVVTIGGLYG 51 (113)
T ss_pred HHHHHhcCCCCEEEECCCcEE
Confidence 46788999999998444 553
No 127
>CHL00143 rpl3 ribosomal protein L3; Validated
Probab=27.20 E-value=46 Score=24.82 Aligned_cols=17 Identities=6% Similarity=0.051 Sum_probs=14.1
Q ss_pred ccceecCCeEEEEEEEE
Q psy13876 23 QNPTMLQNYCILHGLFV 39 (118)
Q Consensus 23 vd~~~pGd~V~v~Gi~~ 39 (118)
++-+.||+.|+|+|+=+
T Consensus 99 v~~F~~Gq~VDV~g~sK 115 (207)
T CHL00143 99 VDAFSVGQLVNVSGKSI 115 (207)
T ss_pred hhhccCCCEEEEEEEec
Confidence 45689999999999954
No 128
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=27.14 E-value=73 Score=22.80 Aligned_cols=22 Identities=0% Similarity=-0.253 Sum_probs=15.3
Q ss_pred EEEeeCcccceecCCeEEEEEE
Q psy13876 16 LGLLRYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 16 v~l~~dLvd~~~pGd~V~v~Gi 37 (118)
+.++++=+..|+.||.|+|.-.
T Consensus 107 ~~aHd~~~~~~kvGD~V~I~Ec 128 (158)
T PTZ00241 107 IPVHCSPCFDVKEGDIVVVGQC 128 (158)
T ss_pred EEEeCCccCCCCCCCEEEEEEc
Confidence 3444455566999999998654
No 129
>PF14444 S1-like: S1-like
Probab=27.05 E-value=1.2e+02 Score=18.13 Aligned_cols=15 Identities=0% Similarity=0.197 Sum_probs=12.1
Q ss_pred ecCCeEEEEEEEEEc
Q psy13876 27 MLQNYCILHGLFVCS 41 (118)
Q Consensus 27 ~pGd~V~v~Gi~~~~ 41 (118)
+.||+|.+..++...
T Consensus 35 ~vGdrV~v~A~~n~~ 49 (58)
T PF14444_consen 35 KVGDRVLVEAIYNPN 49 (58)
T ss_pred ccCCEEEEEEEeCCC
Confidence 459999999998643
No 130
>KOG1641|consensus
Probab=27.03 E-value=50 Score=22.01 Aligned_cols=15 Identities=7% Similarity=-0.017 Sum_probs=9.6
Q ss_pred eCccc-ceecCCeEEE
Q psy13876 20 RYWQN-PTMLQNYCIL 34 (118)
Q Consensus 20 ~dLvd-~~~pGd~V~v 34 (118)
+.++- .|++||+|-+
T Consensus 60 G~~v~~~Vk~Gd~VLl 75 (104)
T KOG1641|consen 60 GEIVPVSVKVGDRVLL 75 (104)
T ss_pred CCCcCccccCCCEEEe
Confidence 34444 7788888765
No 131
>PF14964 DUF4507: Domain of unknown function (DUF4507)
Probab=26.97 E-value=1e+02 Score=24.96 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=26.9
Q ss_pred hHHHHHHHhhcccccCcHHHHHHHHHHHhcCcc
Q psy13876 84 QFYSKLAASLAPEIYGHEDVKKALLLLLVGGVD 116 (118)
Q Consensus 84 ~~~~~L~~SiaP~I~G~~~vK~ailL~L~GG~~ 116 (118)
.+.+.|++.|--. +.+.++.++...||||..
T Consensus 72 QLleiL~~yF~~~--~~d~~r~~iF~~LF~~~~ 102 (362)
T PF14964_consen 72 QLLEILCDYFQEQ--SDDAVRYAIFDSLFGGQG 102 (362)
T ss_pred HHHHHHHHHHccc--CCHHHHHHHHHHHcCCCC
Confidence 5678899988665 999999999999999865
No 132
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=26.87 E-value=42 Score=21.09 Aligned_cols=16 Identities=19% Similarity=0.356 Sum_probs=13.9
Q ss_pred cccceecCCeEEEEEE
Q psy13876 22 WQNPTMLQNYCILHGL 37 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi 37 (118)
-++.+.+||.|.+.|+
T Consensus 67 ~v~~a~aGdIv~v~gl 82 (94)
T cd04090 67 EVNEAPAGNWVLIKGI 82 (94)
T ss_pred EcceeCCCCEEEEECc
Confidence 3689999999999995
No 133
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=26.84 E-value=2.9e+02 Score=23.13 Aligned_cols=47 Identities=17% Similarity=0.084 Sum_probs=31.4
Q ss_pred EEEEEEeeCcc--------c-ceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEcccc
Q psy13876 13 HWILGLLRYWQ--------N-PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 13 ~i~v~l~~dLv--------d-~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~~ 62 (118)
.+.+++..+-+ . .+..||.|.|+|++...+.| +.-|.+..++...+.
T Consensus 82 ~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~g---elel~~~~i~ilsk~ 137 (496)
T TIGR00499 82 QIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTG---ELSVHVTELQILTKA 137 (496)
T ss_pred cEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCC---cEEEEeeEEEEEecC
Confidence 36677764422 1 36899999999998766543 456667777766553
No 134
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=26.71 E-value=49 Score=20.26 Aligned_cols=11 Identities=0% Similarity=-0.052 Sum_probs=8.9
Q ss_pred ceecCCeEEEE
Q psy13876 25 PTMLQNYCILH 35 (118)
Q Consensus 25 ~~~pGd~V~v~ 35 (118)
.+.|||+|.|.
T Consensus 44 ~I~~GD~V~Ve 54 (68)
T TIGR00008 44 RILPGDKVKVE 54 (68)
T ss_pred EECCCCEEEEE
Confidence 36789999986
No 135
>PF00337 Gal-bind_lectin: Galactoside-binding lectin; InterPro: IPR001079 Galectins (also known as galaptins or S-lectin) are a family of proteins defined by having at least one characteristic carbohydrate recognition domain (CRD) with an affinity for beta-galactosides and sharing certain sequence elements. Members of the galectins family are found in mammals, birds, amphibians, fish, nematodes, sponges, and some fungi. Galectins are known to carry out intra- and extracellular functions through glycoconjugate-mediated recogntion. From the cytosol they may be secreted by non-classical pathways, but they may also be targeted to the nucleus or specific sub-cytosolic sites. Within the same peptide chain some galectins have a CRD with only a few additional amino acids, whereas others have two CRDs joined by a link peptide, and one (galectin-3) has one CRD joined to a different type of domain [, ]. The galectin carbohydrate recognition domain (CRD) is a beta-sandwich of about 135 amino acid. The two sheets are slightly bent with 6 strands forming the concave side and 5 strands forming the convex side. The concave side forms a groove in which carbohydrate is bound, and which is long enough to hold about a linear tetrasaccharide [, ].; GO: 0005529 sugar binding; PDB: 2WSU_B 2WT0_A 2WT1_A 2WT2_B 2WSV_A 1HLC_A 2ZGQ_A 3M3Q_B 1WW5_C 3M3E_A ....
Probab=26.58 E-value=54 Score=21.69 Aligned_cols=20 Identities=10% Similarity=-0.044 Sum_probs=16.9
Q ss_pred CcccceecCCeEEEEEEEEE
Q psy13876 21 YWQNPTMLQNYCILHGLFVC 40 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi~~~ 40 (118)
.|...+.||+.++|.|+...
T Consensus 5 ~l~~~l~~G~~i~i~G~~~~ 24 (133)
T PF00337_consen 5 RLPGGLSPGDSIIIRGTVPP 24 (133)
T ss_dssp EETTEEETTEEEEEEEEEBT
T ss_pred EcCCCCCCCcEEEEEEEECC
Confidence 45678899999999999863
No 136
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=26.54 E-value=1.1e+02 Score=17.64 Aligned_cols=28 Identities=4% Similarity=-0.133 Sum_probs=18.0
Q ss_pred CccEEEEEEeeCccc-------ceecCCeEEEEEE
Q psy13876 10 VGKHWILGLLRYWQN-------PTMLQNYCILHGL 37 (118)
Q Consensus 10 ~Pr~i~v~l~~dLvd-------~~~pGd~V~v~Gi 37 (118)
-++.+-|.+.+..+. .++.||+|.|.-.
T Consensus 28 ~~~~vav~vNg~iv~r~~~~~~~l~~gD~vei~~~ 62 (66)
T PRK05659 28 AGRRVAVEVNGEIVPRSQHASTALREGDVVEIVHA 62 (66)
T ss_pred CCCeEEEEECCeEeCHHHcCcccCCCCCEEEEEEE
Confidence 355666665543333 5888999988654
No 137
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=26.48 E-value=2.5e+02 Score=23.58 Aligned_cols=36 Identities=19% Similarity=0.221 Sum_probs=26.0
Q ss_pred cceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEcccc
Q psy13876 24 NPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 24 d~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~~ 62 (118)
.++..||.|.|+|.+...+.| +.-|.+..++...+.
T Consensus 114 ~~l~~Gd~V~v~G~~~~t~~g---elel~~~~~~llsk~ 149 (505)
T PRK12445 114 KKWDLGDIIGARGTLFKTQTG---ELSIHCTELRLLTKA 149 (505)
T ss_pred hcCCCCCEEEEEEEEEecCCC---cEEEEEeEEEEEecC
Confidence 468899999999998766544 455666677666543
No 138
>PRK13289 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional
Probab=26.36 E-value=90 Score=24.61 Aligned_cols=18 Identities=11% Similarity=0.076 Sum_probs=15.2
Q ss_pred CcccceecCCeEEEEEEE
Q psy13876 21 YWQNPTMLQNYCILHGLF 38 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi~ 38 (118)
.|.+.++|||+|.|.|-+
T Consensus 234 ~L~~~l~~Gd~v~v~gP~ 251 (399)
T PRK13289 234 YLHDHVNVGDVLELAAPA 251 (399)
T ss_pred HHhhcCCCCCEEEEEcCc
Confidence 366789999999999965
No 139
>cd00604 IPT_CGTD IPT domain (domain D) of cyclodextrin glycosyltransferase (CGTase) and similar enzymes. These enzymes are involved in the enzymatic hydrolysis of alpha-1,4 linkages of starch polymers and belong to the glycosyl hydrolase family 13. Most consist of three domains (A,B,C) but CGTase is more complex and has two additional domains (D,E). The function of the IPT/D domain is unknown.
Probab=26.15 E-value=52 Score=20.53 Aligned_cols=12 Identities=17% Similarity=0.055 Sum_probs=10.7
Q ss_pred eecCCeEEEEEE
Q psy13876 26 TMLQNYCILHGL 37 (118)
Q Consensus 26 ~~pGd~V~v~Gi 37 (118)
-+||+.|+|+|.
T Consensus 11 g~pG~~VtI~G~ 22 (81)
T cd00604 11 GKPGNTVTISGE 22 (81)
T ss_pred CCCCCEEEEEEE
Confidence 469999999998
No 140
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=25.82 E-value=1e+02 Score=19.44 Aligned_cols=26 Identities=12% Similarity=0.286 Sum_probs=13.9
Q ss_pred CccEEEEEEeeCcccceecCCeEEEE
Q psy13876 10 VGKHWILGLLRYWQNPTMLQNYCILH 35 (118)
Q Consensus 10 ~Pr~i~v~l~~dLvd~~~pGd~V~v~ 35 (118)
.-|.+.+.|-.+--..+++||.|.|.
T Consensus 27 v~r~V~l~Lv~~~~~~~~vGDyVLVH 52 (82)
T PRK10413 27 IKRDVNIALICEGNPADLLGQWVLVH 52 (82)
T ss_pred eEEEEEeeeeccCCcccccCCEEEEe
Confidence 34555554443322346778877664
No 141
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=25.78 E-value=1.3e+02 Score=21.44 Aligned_cols=28 Identities=4% Similarity=-0.084 Sum_probs=25.2
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGLFV 39 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi~~ 39 (118)
.++.|.-.+.|-|.++.|..|.++|.+.
T Consensus 89 ~~v~V~Y~GilPDlFrEG~gVVveG~~~ 116 (159)
T PRK13150 89 GSVTVSYEGILPDLFREGQGVVVQGTLE 116 (159)
T ss_pred cEEEEEEeccCCccccCCCeEEEEEEEC
Confidence 4688999999999999999999999986
No 142
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=25.73 E-value=1.6e+02 Score=17.70 Aligned_cols=29 Identities=3% Similarity=-0.197 Sum_probs=20.1
Q ss_pred EEEEEEeeCc-ccceecCCeEEEE-EEEEEc
Q psy13876 13 HWILGLLRYW-QNPTMLQNYCILH-GLFVCS 41 (118)
Q Consensus 13 ~i~v~l~~dL-vd~~~pGd~V~v~-Gi~~~~ 41 (118)
++.+.+-++. .+.++|||.|.+. |..+..
T Consensus 35 ~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~ 65 (82)
T cd04491 35 TIRFTLWDEKAADDLEPGDVVRIENAYVREF 65 (82)
T ss_pred EEEEEEECchhcccCCCCCEEEEEeEEEEec
Confidence 4555555554 7789999999999 555433
No 143
>COG2914 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.66 E-value=49 Score=21.81 Aligned_cols=21 Identities=0% Similarity=-0.085 Sum_probs=16.0
Q ss_pred cccceecCCeEEEEEEEEEcC
Q psy13876 22 WQNPTMLQNYCILHGLFVCSS 42 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi~~~~~ 42 (118)
+-+.++.||||+|.+=+.+.+
T Consensus 61 l~~~l~dgDRVEIyRPLlaDP 81 (99)
T COG2914 61 LDDELHDGDRVEIYRPLLADP 81 (99)
T ss_pred ccccccCCCEEEEecccccCh
Confidence 456788899999988766553
No 144
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=25.58 E-value=46 Score=21.47 Aligned_cols=11 Identities=9% Similarity=0.102 Sum_probs=8.8
Q ss_pred ceecCCeEEEE
Q psy13876 25 PTMLQNYCILH 35 (118)
Q Consensus 25 ~~~pGd~V~v~ 35 (118)
.+.|||+|+|.
T Consensus 46 rIl~GD~V~VE 56 (87)
T PRK12442 46 RILAGDRVTLE 56 (87)
T ss_pred EecCCCEEEEE
Confidence 46789999885
No 145
>PRK05305 phosphatidylserine decarboxylase; Provisional
Probab=25.57 E-value=70 Score=23.39 Aligned_cols=24 Identities=4% Similarity=-0.259 Sum_probs=18.9
Q ss_pred cEEEEEEeeCcccceecCCeEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILH 35 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~ 35 (118)
-++++.+..+..-.|++||+|..-
T Consensus 175 StV~l~~p~~~~~~V~~G~kV~~G 198 (206)
T PRK05305 175 SRVDVYLPLGTEPLVSVGQKVVAG 198 (206)
T ss_pred CeEEEEEcCCCcccccCCCEEEcc
Confidence 468888888888888899987653
No 146
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=25.56 E-value=70 Score=21.25 Aligned_cols=21 Identities=5% Similarity=-0.069 Sum_probs=17.0
Q ss_pred CcccceecCCeEEEEEEEEEc
Q psy13876 21 YWQNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi~~~~ 41 (118)
.+-+.++||+.++|+|+....
T Consensus 4 ~lp~~l~~G~~i~i~G~~~~~ 24 (128)
T smart00276 4 PIPGGLKPGQTLTVRGIVLPD 24 (128)
T ss_pred cCCCCCCCCCEEEEEEEECCC
Confidence 445678999999999998654
No 147
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=25.49 E-value=2.6e+02 Score=20.14 Aligned_cols=31 Identities=6% Similarity=-0.067 Sum_probs=25.5
Q ss_pred ccEEEEEEeeCc----ccceecCCeEEEEEEEEEc
Q psy13876 11 GKHWILGLLRYW----QNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 11 Pr~i~v~l~~dL----vd~~~pGd~V~v~Gi~~~~ 41 (118)
+-.+.|.+-+.+ .+.++.|+.|.|.|-++.+
T Consensus 53 t~w~~V~~fgk~Ae~~~~~L~KGs~V~VeGrL~~~ 87 (177)
T PRK09010 53 TEWHRVVLFGKLAEVAGEYLRKGSQVYIEGQLRTR 87 (177)
T ss_pred eEEEEEEEehhHHHHHHHhcCCCCEEEEEEEEEec
Confidence 457788888775 4558999999999999877
No 148
>cd06193 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hy
Probab=25.49 E-value=62 Score=23.64 Aligned_cols=17 Identities=12% Similarity=0.116 Sum_probs=14.6
Q ss_pred cccceecCCeEEEEEEE
Q psy13876 22 WQNPTMLQNYCILHGLF 38 (118)
Q Consensus 22 Lvd~~~pGd~V~v~Gi~ 38 (118)
+..+++|||.|.|.|=+
T Consensus 95 ~l~~l~~Gd~v~v~gP~ 111 (235)
T cd06193 95 WAASAQPGDTLGIAGPG 111 (235)
T ss_pred HHhhCCCCCEEEEECCC
Confidence 45789999999999875
No 149
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=24.87 E-value=1e+02 Score=21.29 Aligned_cols=31 Identities=13% Similarity=0.113 Sum_probs=18.0
Q ss_pred ceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEc
Q psy13876 25 PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCL 59 (118)
Q Consensus 25 ~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~ 59 (118)
+++|-|+|.|.|-+-... ...-+++.+|++.
T Consensus 97 tv~P~dkV~I~GevDk~~----~~~eIdV~~I~k~ 127 (128)
T COG3111 97 TVTPKDKVRIQGEVDKDW----NSVEIDVKHIEKL 127 (128)
T ss_pred ccCcccEEEEEeEEcCCC----ccceeEhhheEec
Confidence 466777777777664332 2444666666553
No 150
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=24.74 E-value=53 Score=18.97 Aligned_cols=15 Identities=13% Similarity=0.036 Sum_probs=10.9
Q ss_pred ccceecCCeEEEEEE
Q psy13876 23 QNPTMLQNYCILHGL 37 (118)
Q Consensus 23 vd~~~pGd~V~v~Gi 37 (118)
-..+++||.+.+.|-
T Consensus 45 ~~~l~~gD~l~v~g~ 59 (71)
T PF02080_consen 45 DTVLQAGDILIVVGD 59 (71)
T ss_dssp T-BE-TTEEEEEEEE
T ss_pred CCEECCCCEEEEEEC
Confidence 457889999999885
No 151
>KOG0554|consensus
Probab=24.72 E-value=4.1e+02 Score=22.13 Aligned_cols=73 Identities=11% Similarity=0.047 Sum_probs=48.2
Q ss_pred CCCCccEEEEEEeeCcccceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccccccC-CCCCCCCCHHHHHhh
Q psy13876 7 ASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSKALED-DKPAGTLSEEEMAEL 80 (118)
Q Consensus 7 ~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~~~~~-~~~~~~~~~e~i~~l 80 (118)
-|+-|..+.|....+....+.+|.-|.++|+++.. +|...+.-+.|..|.......+. ......++.+-++++
T Consensus 45 DGs~~~~lQvVv~~~~~q~la~Gt~i~~~g~l~~~-~~~~q~iel~~eki~~vG~v~~~ypl~Kk~lt~e~LR~~ 118 (446)
T KOG0554|consen 45 DGSCPSPLQVVVDSEQSQLLATGTCISAEGVLKVS-KGAKQQIELNAEKIKVVGTVDESYPLQKKKLTPEMLRDK 118 (446)
T ss_pred CCCCCcceEEEechHHhhhccccceEEEEeeEEec-cchheeeeeeeeEEEEEeecCCCCCCccccCCHHHHhhc
Confidence 45577789999999999999999999999999877 45455555555555443332211 011223556666664
No 152
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=24.65 E-value=1.3e+02 Score=21.03 Aligned_cols=46 Identities=9% Similarity=-0.017 Sum_probs=31.3
Q ss_pred ccEEEEEEeeC-----cccceecCCeEEEEEEEEEcC----CC-CccceEEEEEEE
Q psy13876 11 GKHWILGLLRY-----WQNPTMLQNYCILHGLFVCSS----PG-LLSDTYIEAQRI 56 (118)
Q Consensus 11 Pr~i~v~l~~d-----Lvd~~~pGd~V~v~Gi~~~~~----~~-~~~~~yl~a~~I 56 (118)
+-.+.|.+-+. +...++.|+.|.|.|-++... .| ..+.+-+.|..|
T Consensus 52 T~w~~v~~~g~~~Ae~~~~~l~KG~~V~V~GrL~~~~y~dkdG~~r~~~eVvv~~~ 107 (152)
T PRK06642 52 TEWHRVVIFSEGLVSVVERYVTKGSKLYIEGSLQTRKWNDNSGQEKYTTEVVLQNF 107 (152)
T ss_pred eeEEEEEEeChHHHHHHHHhCCCCCEEEEEEEEEeCeeECCCCCEEEEEEEEEEec
Confidence 56788887774 445689999999999998773 23 333444555544
No 153
>COG2374 Predicted extracellular nuclease [General function prediction only]
Probab=24.64 E-value=1.3e+02 Score=26.89 Aligned_cols=29 Identities=7% Similarity=-0.151 Sum_probs=21.8
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEEEEEc
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGLFVCS 41 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~ 41 (118)
.-|-|+.-+..-+ +.+||+|+|+|.+...
T Consensus 253 eGIFVy~~g~~~~-l~lGd~V~VtG~V~Ey 281 (798)
T COG2374 253 EGIFVYEGGASSD-LSLGDRVTVTGTVSEY 281 (798)
T ss_pred cceEEEeCCCCCC-CCCCCEEEEEEEEEee
Confidence 3455666555556 8999999999998765
No 154
>PRK08395 fumarate hydratase; Provisional
Probab=24.32 E-value=38 Score=24.31 Aligned_cols=21 Identities=10% Similarity=-0.126 Sum_probs=16.7
Q ss_pred eeCcccceecCCeEEEEEEEE
Q psy13876 19 LRYWQNPTMLQNYCILHGLFV 39 (118)
Q Consensus 19 ~~dLvd~~~pGd~V~v~Gi~~ 39 (118)
..+-+.+.+.||+|.++|.+-
T Consensus 8 ~~e~i~~L~~GD~V~LsG~i~ 28 (162)
T PRK08395 8 SWEDVLKLKAGDVVYLSGIIY 28 (162)
T ss_pred CHHHHhhCCCCCEEEEEEEEE
Confidence 344567899999999999753
No 155
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=24.19 E-value=56 Score=20.03 Aligned_cols=13 Identities=15% Similarity=0.197 Sum_probs=11.7
Q ss_pred ceecCCeEEEEEE
Q psy13876 25 PTMLQNYCILHGL 37 (118)
Q Consensus 25 ~~~pGd~V~v~Gi 37 (118)
.++|||+|.+.|.
T Consensus 65 ~~~~Gd~vl~~~~ 77 (90)
T PF08541_consen 65 RIKPGDRVLLVGF 77 (90)
T ss_dssp SSCTTEEEEEEEE
T ss_pred CCCCCCEEEEEEE
Confidence 7889999999886
No 156
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=24.15 E-value=89 Score=20.19 Aligned_cols=23 Identities=17% Similarity=0.249 Sum_probs=18.2
Q ss_pred cEEEEEEeeCcccceecCCeEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCIL 34 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v 34 (118)
+++++.+..+--...+|||.+.|
T Consensus 17 Ktat~r~~~~~~~~~k~Gd~~i~ 39 (105)
T cd06541 17 KTIEIRSLDIYEQLPKAGDYLII 39 (105)
T ss_pred CEEEEEcchhcccCCCCCCEEEE
Confidence 57788776655678899999987
No 157
>cd06187 O2ase_reductase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate, while mono-oxygenases (aka mixed oxygenases) add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=24.14 E-value=96 Score=22.04 Aligned_cols=27 Identities=7% Similarity=0.061 Sum_probs=19.3
Q ss_pred cEEEEEEeeC--------cccceecCCeEEEEEEE
Q psy13876 12 KHWILGLLRY--------WQNPTMLQNYCILHGLF 38 (118)
Q Consensus 12 r~i~v~l~~d--------Lvd~~~pGd~V~v~Gi~ 38 (118)
..+++.+... |.+.++|||.|.|.|-+
T Consensus 54 ~~~~~~i~~~~~G~~s~~l~~~l~~G~~v~i~gP~ 88 (224)
T cd06187 54 GEIEFHVRAVPGGRVSNALHDELKVGDRVRLSGPY 88 (224)
T ss_pred CEEEEEEEeCCCCcchHHHhhcCccCCEEEEeCCc
Confidence 3466655543 55679999999998864
No 158
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=24.04 E-value=1.4e+02 Score=21.28 Aligned_cols=28 Identities=4% Similarity=-0.114 Sum_probs=25.3
Q ss_pred cEEEEEEeeCcccceecCCeEEEEEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILHGLFV 39 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~Gi~~ 39 (118)
.++.|.-.+.|-|.++.|..|.++|.+.
T Consensus 89 ~~v~V~Y~GilPDlFrEG~gVVveG~~~ 116 (160)
T PRK13165 89 GSVTVTYEGILPDLFREGQGIVAQGVLE 116 (160)
T ss_pred eEEEEEEcccCCccccCCCeEEEEEEEC
Confidence 4688999999999999999999999986
No 159
>PF08240 ADH_N: Alcohol dehydrogenase GroES-like domain; InterPro: IPR013154 This is the catalytic domain of alcohol dehydrogenases (1.1.1.1 from EC). Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; a name derived from the superfamily of proteins with a GroES fold. Proteins with a GroES fold structure have a highly conserved hydrophobic core and a glycyl-aspartate dipeptide which is thought to maintain the fold [, ].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1YKF_D 2NVB_A 3FSR_D 1BXZ_B 3FTN_A 3MEQ_D 3UOG_B 3HZZ_B 4DVJ_A 1P0F_A ....
Probab=23.49 E-value=1e+02 Score=19.49 Aligned_cols=21 Identities=0% Similarity=-0.197 Sum_probs=15.6
Q ss_pred eeCcccceecCCeEEEEEEEE
Q psy13876 19 LRYWQNPTMLQNYCILHGLFV 39 (118)
Q Consensus 19 ~~dLvd~~~pGd~V~v~Gi~~ 39 (118)
-+.-+..+++||+|.+.....
T Consensus 46 vG~~v~~~~~Gd~V~~~~~~~ 66 (109)
T PF08240_consen 46 VGPGVTDFKVGDRVVVSPNIG 66 (109)
T ss_dssp ESTTTTSSGTT-EEEEESEEE
T ss_pred eccccccccccceeeeecccC
Confidence 356677799999999977665
No 160
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=23.49 E-value=38 Score=23.93 Aligned_cols=21 Identities=14% Similarity=-0.065 Sum_probs=18.7
Q ss_pred CCCC-ccEEEEEEeeCccccee
Q psy13876 7 ASMV-GKHWILGLLRYWQNPTM 27 (118)
Q Consensus 7 ~g~~-Pr~i~v~l~~dLvd~~~ 27 (118)
+|.+ |+.++++++++.|+.|+
T Consensus 94 ~G~~~g~~~tm~Vdr~vC~~C~ 115 (146)
T PF14437_consen 94 AGKTVGRSMTMYVDRDVCGYCG 115 (146)
T ss_pred hcCccCCeEEEEECcccchHHH
Confidence 4556 99999999999999998
No 161
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=23.44 E-value=3.4e+02 Score=25.25 Aligned_cols=46 Identities=13% Similarity=-0.008 Sum_probs=30.8
Q ss_pred EEEEEEeeCcc---------cceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 13 HWILGLLRYWQ---------NPTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 13 ~i~v~l~~dLv---------d~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
.+.|++..+.+ ..+..||.|.|+|++...+.| +.-+.+..++...+
T Consensus 680 ~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~g---e~ei~~~~i~ll~k 734 (1094)
T PRK02983 680 ELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNG---TLSLLVTSWRLAGK 734 (1094)
T ss_pred eEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCC---CEEEEEeEEEEEec
Confidence 47777776643 247899999999999876554 34455555555543
No 162
>TIGR00164 PS_decarb_rel phosphatidylserine decarboxylase precursor-related protein. It is unclear whether this protein is a form of phosphatidylserine decarboxylase or is a related enzyme. It is found in Neisseria gonorrhoeae, Mycobacterium tuberculosis, and several archaeal species, all of which lack known phosphatidylserine decarboxylase.
Probab=23.38 E-value=90 Score=22.50 Aligned_cols=24 Identities=13% Similarity=-0.155 Sum_probs=18.8
Q ss_pred cEEEEEEeeCcccceecCCeEEEE
Q psy13876 12 KHWILGLLRYWQNPTMLQNYCILH 35 (118)
Q Consensus 12 r~i~v~l~~dLvd~~~pGd~V~v~ 35 (118)
-++++.+..|..-.+++||+|..-
T Consensus 155 Stv~ll~p~~~~~~v~~G~~V~~G 178 (189)
T TIGR00164 155 SRVDLYLPENAQAQVKVGEKVTAG 178 (189)
T ss_pred CeEEEEEcCCCccccCCCCEEEec
Confidence 467888888877788999988753
No 163
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=23.29 E-value=1.1e+02 Score=17.64 Aligned_cols=23 Identities=4% Similarity=-0.084 Sum_probs=15.9
Q ss_pred EEEEEEeeCccc-------ceecCCeEEEE
Q psy13876 13 HWILGLLRYWQN-------PTMLQNYCILH 35 (118)
Q Consensus 13 ~i~v~l~~dLvd-------~~~pGd~V~v~ 35 (118)
.+-+.+.+..+. .++.||+|.|.
T Consensus 30 ~~~v~vN~~~v~~~~~~~~~L~~gD~vei~ 59 (65)
T PRK06944 30 PFAVAVNGDFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred CeEEEECCEEcCchhcccccCCCCCEEEEE
Confidence 455666666664 47889998875
No 164
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=23.20 E-value=1.3e+02 Score=19.09 Aligned_cols=17 Identities=6% Similarity=0.030 Sum_probs=12.6
Q ss_pred CcccceecCCeEEEEEE
Q psy13876 21 YWQNPTMLQNYCILHGL 37 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi 37 (118)
|--+.|+.||.|.|.-.
T Consensus 46 De~n~~~~GD~V~I~e~ 62 (84)
T CHL00142 46 DEENECNIGDQVLIEET 62 (84)
T ss_pred CCCCCCCCCCEEEEEEc
Confidence 34456999999998743
No 165
>KOG3141|consensus
Probab=23.16 E-value=56 Score=25.75 Aligned_cols=16 Identities=13% Similarity=0.015 Sum_probs=13.7
Q ss_pred ccceecCCeEEEEEEE
Q psy13876 23 QNPTMLQNYCILHGLF 38 (118)
Q Consensus 23 vd~~~pGd~V~v~Gi~ 38 (118)
++-++|||.|+|+|+-
T Consensus 160 ~~hFk~GqyVDV~g~T 175 (310)
T KOG3141|consen 160 ARHFKPGQYVDVTGKT 175 (310)
T ss_pred hhhcCCCceEEEEeeE
Confidence 4668999999999984
No 166
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=22.75 E-value=70 Score=18.14 Aligned_cols=21 Identities=10% Similarity=-0.118 Sum_probs=14.3
Q ss_pred EEEEEeeCcccceecCCeEEE
Q psy13876 14 WILGLLRYWQNPTMLQNYCIL 34 (118)
Q Consensus 14 i~v~l~~dLvd~~~pGd~V~v 34 (118)
|.|+|..|.-+-=+.||.|.|
T Consensus 1 m~ViL~~dv~~lG~~Gdiv~V 21 (48)
T PF01281_consen 1 MKVILLKDVPGLGKKGDIVEV 21 (48)
T ss_dssp -EEEESSCCTTSBSTTEEEE-
T ss_pred CEEEEcccccccCCCCCEEEE
Confidence 567787777777677777665
No 167
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=22.74 E-value=1.6e+02 Score=19.26 Aligned_cols=12 Identities=25% Similarity=0.423 Sum_probs=8.5
Q ss_pred CCCCCCHHHHHh
Q psy13876 68 PAGTLSEEEMAE 79 (118)
Q Consensus 68 ~~~~~~~e~i~~ 79 (118)
.+..|+++|+..
T Consensus 92 Sn~~fte~E~~~ 103 (109)
T smart00719 92 SNQDFTEEEFQR 103 (109)
T ss_pred cCCCCCHHHHHH
Confidence 346788888765
No 168
>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=22.58 E-value=59 Score=19.68 Aligned_cols=13 Identities=0% Similarity=-0.151 Sum_probs=10.4
Q ss_pred ceecCCeEEEEEE
Q psy13876 25 PTMLQNYCILHGL 37 (118)
Q Consensus 25 ~~~pGd~V~v~Gi 37 (118)
-+++||.|.|-+.
T Consensus 53 G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 53 GAKDGDTVRIGDF 65 (69)
T ss_pred CCCCCCEEEEccE
Confidence 4789999998764
No 169
>cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.
Probab=22.09 E-value=1.4e+02 Score=21.39 Aligned_cols=27 Identities=7% Similarity=-0.006 Sum_probs=19.3
Q ss_pred cEEEEEEeeC--------cccceecCCeEEEEEEE
Q psy13876 12 KHWILGLLRY--------WQNPTMLQNYCILHGLF 38 (118)
Q Consensus 12 r~i~v~l~~d--------Lvd~~~pGd~V~v~Gi~ 38 (118)
.++++.+... |.+.+++||.|.|.|-+
T Consensus 59 ~~i~~~i~~~~~G~~s~~l~~~l~~G~~v~v~gP~ 93 (228)
T cd06209 59 PRLEFLIRLLPGGAMSSYLRDRAQPGDRLTLTGPL 93 (228)
T ss_pred CeEEEEEEEcCCCcchhhHHhccCCCCEEEEECCc
Confidence 4677766532 34569999999999864
No 170
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=21.91 E-value=1.3e+02 Score=17.39 Aligned_cols=23 Identities=0% Similarity=-0.116 Sum_probs=13.6
Q ss_pred EEEEEEeeCcc---cceecCCeEEEE
Q psy13876 13 HWILGLLRYWQ---NPTMLQNYCILH 35 (118)
Q Consensus 13 ~i~v~l~~dLv---d~~~pGd~V~v~ 35 (118)
.+.+.+.+.|- ..+.+||+|.+.
T Consensus 25 ~~~c~~rGklr~~~~~~~vGD~V~~~ 50 (64)
T cd04451 25 EVLAHISGKMRMNYIRILPGDRVKVE 50 (64)
T ss_pred EEEEEECceeecCCcccCCCCEEEEE
Confidence 45555555553 226678888765
No 171
>cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.
Probab=21.91 E-value=1.4e+02 Score=21.33 Aligned_cols=27 Identities=11% Similarity=0.041 Sum_probs=19.6
Q ss_pred cEEEEEEee--------CcccceecCCeEEEEEEE
Q psy13876 12 KHWILGLLR--------YWQNPTMLQNYCILHGLF 38 (118)
Q Consensus 12 r~i~v~l~~--------dLvd~~~pGd~V~v~Gi~ 38 (118)
..+++.+.. .|.+.++|||.|.|.|-+
T Consensus 54 ~~l~~~vk~~~~G~~s~~l~~~l~~G~~v~i~gP~ 88 (224)
T cd06189 54 GEIELHIRAVPGGSFSDYVFEELKENGLVRIEGPL 88 (224)
T ss_pred CeEEEEEEecCCCccHHHHHHhccCCCEEEEecCC
Confidence 346665543 366789999999999964
No 172
>PLN02603 asparaginyl-tRNA synthetase
Probab=21.88 E-value=4.7e+02 Score=22.49 Aligned_cols=49 Identities=12% Similarity=0.106 Sum_probs=31.3
Q ss_pred cEEEEEEeeCcc-----c--ceecCCeEEEEEEEEEcCCCCccceEEEEEEEEEccc
Q psy13876 12 KHWILGLLRYWQ-----N--PTMLQNYCILHGLFVCSSPGLLSDTYIEAQRIQCLSK 61 (118)
Q Consensus 12 r~i~v~l~~dLv-----d--~~~pGd~V~v~Gi~~~~~~~~~~~~yl~a~~I~~~~~ 61 (118)
..+.|++..+.. . .+..|+-|.|+|++...+.+ ....-|.+..|+....
T Consensus 137 ~~lQ~v~~~~~~~~~~l~~~~l~~gs~V~V~G~v~~~~~~-~~~~EL~v~~i~vlg~ 192 (565)
T PLN02603 137 SNMQCVMTPDAEGYDQVESGLITTGASVLVQGTVVSSQGG-KQKVELKVSKIVVVGK 192 (565)
T ss_pred EeEEEEEECcHHHHHHHhhcCCCCCCEEEEEEEEEecCCC-CccEEEEEeEEEEEEC
Confidence 357777765422 1 37899999999999866433 2234566666665554
No 173
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=21.88 E-value=53 Score=19.82 Aligned_cols=18 Identities=11% Similarity=-0.023 Sum_probs=14.6
Q ss_pred eCcccceecCCeEEEEEE
Q psy13876 20 RYWQNPTMLQNYCILHGL 37 (118)
Q Consensus 20 ~dLvd~~~pGd~V~v~Gi 37 (118)
..-++.+.+||.+.++|+
T Consensus 55 ~~~v~~~~aGdI~~i~g~ 72 (83)
T cd04088 55 QEEVEEAGAGDIGAVAGL 72 (83)
T ss_pred ceECCEeCCCCEEEEECC
Confidence 345689999999999885
No 174
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=21.86 E-value=1.1e+02 Score=17.97 Aligned_cols=27 Identities=7% Similarity=-0.116 Sum_probs=18.7
Q ss_pred ccEEEEEEeeCccc-------ceecCCeEEEEEE
Q psy13876 11 GKHWILGLLRYWQN-------PTMLQNYCILHGL 37 (118)
Q Consensus 11 Pr~i~v~l~~dLvd-------~~~pGd~V~v~Gi 37 (118)
++.+-|.+.++.+. .++.||+|.|.-.
T Consensus 29 ~~~vaVavN~~iv~r~~w~~~~L~~gD~Ieii~~ 62 (66)
T PRK08053 29 QPGAALAINQQIIPREQWAQHIVQDGDQILLFQV 62 (66)
T ss_pred CCcEEEEECCEEeChHHcCccccCCCCEEEEEEE
Confidence 45577777666654 5788999988643
No 175
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=21.62 E-value=60 Score=18.57 Aligned_cols=11 Identities=0% Similarity=-0.133 Sum_probs=8.8
Q ss_pred cceecCCeEEE
Q psy13876 24 NPTMLQNYCIL 34 (118)
Q Consensus 24 d~~~pGd~V~v 34 (118)
.++++||+|.|
T Consensus 48 ~~l~~Gd~v~i 58 (59)
T TIGR02988 48 KKLYPGDVIEI 58 (59)
T ss_pred CCCCCCCEEEe
Confidence 46788999986
No 176
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=21.53 E-value=59 Score=20.38 Aligned_cols=15 Identities=7% Similarity=-0.115 Sum_probs=11.8
Q ss_pred cceecCCeEEEEEEE
Q psy13876 24 NPTMLQNYCILHGLF 38 (118)
Q Consensus 24 d~~~pGd~V~v~Gi~ 38 (118)
=.++|||.|.|..-=
T Consensus 4 L~Vk~Gd~ViV~~~~ 18 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQ 18 (75)
T ss_pred cccCCCCEEEEecCc
Confidence 368999999987654
No 177
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=21.51 E-value=1.3e+02 Score=18.28 Aligned_cols=27 Identities=0% Similarity=-0.291 Sum_probs=20.1
Q ss_pred ccEEEEEEeeCccc-------ceecCCeEEEEEE
Q psy13876 11 GKHWILGLLRYWQN-------PTMLQNYCILHGL 37 (118)
Q Consensus 11 Pr~i~v~l~~dLvd-------~~~pGd~V~v~Gi 37 (118)
|+.+-|.+..+.|- .++-||+|+|.=.
T Consensus 31 ~~~vav~vNg~iVpr~~~~~~~l~~gD~ievv~~ 64 (68)
T COG2104 31 PEGVAVAVNGEIVPRSQWADTILKEGDRIEVVRV 64 (68)
T ss_pred CceEEEEECCEEccchhhhhccccCCCEEEEEEe
Confidence 57777777777776 5778899988643
No 178
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=21.45 E-value=1.4e+02 Score=19.22 Aligned_cols=11 Identities=9% Similarity=0.437 Sum_probs=5.6
Q ss_pred ceecCCeEEEE
Q psy13876 25 PTMLQNYCILH 35 (118)
Q Consensus 25 ~~~pGd~V~v~ 35 (118)
.+++||.|.|.
T Consensus 41 ~~~vGDyVLVH 51 (90)
T PRK10409 41 QPRVGQWVLVH 51 (90)
T ss_pred ccCCCCEEEEe
Confidence 35555555543
No 179
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=21.26 E-value=1.2e+02 Score=20.93 Aligned_cols=10 Identities=10% Similarity=0.125 Sum_probs=7.4
Q ss_pred cCCeEEEEEE
Q psy13876 28 LQNYCILHGL 37 (118)
Q Consensus 28 pGd~V~v~Gi 37 (118)
+||+|.|+++
T Consensus 121 ~G~~V~Vv~v 130 (140)
T COG1585 121 AGDRVEVVGV 130 (140)
T ss_pred CCCEEEEEEe
Confidence 6777777776
No 180
>KOG3606|consensus
Probab=21.11 E-value=2e+02 Score=22.77 Aligned_cols=59 Identities=15% Similarity=0.140 Sum_probs=41.1
Q ss_pred ccccCCCCCccEEEEEEeeCcccceecCCeEEEEEEEEEc--CC------C--CccceEEEEEEEEEcccc
Q psy13876 2 RIATGASMVGKHWILGLLRYWQNPTMLQNYCILHGLFVCS--SP------G--LLSDTYIEAQRIQCLSKA 62 (118)
Q Consensus 2 ~~~~~~g~~Pr~i~v~l~~dLvd~~~pGd~V~v~Gi~~~~--~~------~--~~~~~yl~a~~I~~~~~~ 62 (118)
||-+....=| +-.+.++-.--.|+|-.-..|-||+..+ +. | .+-+-.|++|+|+...+.
T Consensus 163 RL~khG~ekP--LGFYIRDG~SVRVtp~GlekvpGIFISRlVpGGLAeSTGLLaVnDEVlEVNGIEVaGKT 231 (358)
T KOG3606|consen 163 RLHKHGSEKP--LGFYIRDGTSVRVTPHGLEKVPGIFISRLVPGGLAESTGLLAVNDEVLEVNGIEVAGKT 231 (358)
T ss_pred ehhhcCCCCC--ceEEEecCceEEeccccccccCceEEEeecCCccccccceeeecceeEEEcCEEecccc
Confidence 4555554444 5566777777788888888888998655 22 2 466778999999887553
No 181
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=21.10 E-value=46 Score=24.80 Aligned_cols=26 Identities=12% Similarity=-0.008 Sum_probs=19.5
Q ss_pred EEEEEeeCcccceecCCeEEEEEEEE
Q psy13876 14 WILGLLRYWQNPTMLQNYCILHGLFV 39 (118)
Q Consensus 14 i~v~l~~dLvd~~~pGd~V~v~Gi~~ 39 (118)
++.=+..+-+.+++.||+|.++|.+-
T Consensus 6 l~tPl~~e~i~~L~vGD~V~LsG~Iy 31 (204)
T PRK08228 6 LTTPIKDEDLQDIKVGDVIYLTGTLV 31 (204)
T ss_pred ecCCCCHHHHhhCCCCCEEEEEEEEE
Confidence 33334556678999999999999753
No 182
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=21.05 E-value=68 Score=20.26 Aligned_cols=11 Identities=0% Similarity=-0.055 Sum_probs=9.1
Q ss_pred ceecCCeEEEE
Q psy13876 25 PTMLQNYCILH 35 (118)
Q Consensus 25 ~~~pGd~V~v~ 35 (118)
++.+||+|.|.
T Consensus 8 ~I~~GD~V~Vi 18 (83)
T CHL00141 8 HVKIGDTVKII 18 (83)
T ss_pred cccCCCEEEEe
Confidence 67899999874
No 183
>PF10381 Autophagy_Cterm: Autophagocytosis associated protein C-terminal; InterPro: IPR019461 Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex []. It carries a highly characteristic conserved FLKF sequence motif. ; PDB: 2DYT_A.
Probab=21.00 E-value=93 Score=15.37 Aligned_cols=14 Identities=29% Similarity=0.513 Sum_probs=10.6
Q ss_pred HHHHHHHhhccccc
Q psy13876 85 FYSKLAASLAPEIY 98 (118)
Q Consensus 85 ~~~~L~~SiaP~I~ 98 (118)
+|-+.++|+.|+|-
T Consensus 7 iFLKFi~sViPtIe 20 (25)
T PF10381_consen 7 IFLKFISSVIPTIE 20 (25)
T ss_dssp HHHHHHHHHSTTB-
T ss_pred hHHHHHhhcCCcee
Confidence 46677899999883
No 184
>cd06200 SiR_like1 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD
Probab=20.99 E-value=69 Score=23.66 Aligned_cols=17 Identities=6% Similarity=-0.044 Sum_probs=13.5
Q ss_pred CcccceecCCeEEEEEE
Q psy13876 21 YWQNPTMLQNYCILHGL 37 (118)
Q Consensus 21 dLvd~~~pGd~V~v~Gi 37 (118)
.|.+.++|||+|.|.|-
T Consensus 82 ~L~~~~~~Gd~v~i~gp 98 (245)
T cd06200 82 WLTRHAPIGASVALRLR 98 (245)
T ss_pred hhhhCCCCCCEEEEEec
Confidence 34567799999999974
No 185
>PRK00001 rplC 50S ribosomal protein L3; Validated
Probab=20.83 E-value=76 Score=23.72 Aligned_cols=16 Identities=6% Similarity=-0.199 Sum_probs=12.8
Q ss_pred cceecCCeEEEEEEEE
Q psy13876 24 NPTMLQNYCILHGLFV 39 (118)
Q Consensus 24 d~~~pGd~V~v~Gi~~ 39 (118)
+-++||+.|+|+|+=+
T Consensus 98 ~~F~~G~~VDV~g~tK 113 (210)
T PRK00001 98 DIFEAGQKVDVTGTSK 113 (210)
T ss_pred hhccCCCEEEEEEEEc
Confidence 5688899999998854
No 186
>TIGR03625 L3_bact 50S ribosomal protein L3, bacterial. This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to Pfam family pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here.
Probab=20.63 E-value=83 Score=23.39 Aligned_cols=16 Identities=6% Similarity=-0.199 Sum_probs=13.0
Q ss_pred cceecCCeEEEEEEEE
Q psy13876 24 NPTMLQNYCILHGLFV 39 (118)
Q Consensus 24 d~~~pGd~V~v~Gi~~ 39 (118)
+-+.||+.|.|+|+-+
T Consensus 97 ~~F~~G~~VDV~g~sk 112 (202)
T TIGR03625 97 DIFEAGQKVDVTGTSK 112 (202)
T ss_pred eeecCCCEEEEEEEEc
Confidence 6688899999998854
No 187
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.57 E-value=34 Score=21.36 Aligned_cols=28 Identities=21% Similarity=0.477 Sum_probs=20.9
Q ss_pred hcChhHHHHHHHhhccccc--CcHHHHHHH
Q psy13876 80 LGGDQFYSKLAASLAPEIY--GHEDVKKAL 107 (118)
Q Consensus 80 l~~~~~~~~L~~SiaP~I~--G~~~vK~ai 107 (118)
|....+.+.+++-++|.+| |-.|..+-+
T Consensus 30 ~~Ae~LLDF~~~elGp~~YNqgv~DA~~~~ 59 (76)
T PF09932_consen 30 FEAEFLLDFFIEELGPHFYNQGVQDAQAVL 59 (76)
T ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 3356789999999999998 556655443
No 188
>cd06213 oxygenase_e_transfer_subunit The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=20.38 E-value=1.7e+02 Score=20.94 Aligned_cols=27 Identities=7% Similarity=0.058 Sum_probs=19.6
Q ss_pred cEEEEEEeeC--------cccceecCCeEEEEEEE
Q psy13876 12 KHWILGLLRY--------WQNPTMLQNYCILHGLF 38 (118)
Q Consensus 12 r~i~v~l~~d--------Lvd~~~pGd~V~v~Gi~ 38 (118)
..+++.+... |.+.++|||.|.|.|-+
T Consensus 57 ~~l~~~vk~~~~G~~s~~l~~~l~~G~~v~i~gP~ 91 (227)
T cd06213 57 GQLSFHIRKVPGGAFSGWLFGADRTGERLTVRGPF 91 (227)
T ss_pred CEEEEEEEECCCCcchHHHHhcCCCCCEEEEeCCC
Confidence 3566655532 66789999999999864
No 189
>PF09356 Phage_BR0599: Phage conserved hypothetical protein BR0599; InterPro: IPR018964 This entry describes the C-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=20.16 E-value=1.4e+02 Score=18.62 Aligned_cols=21 Identities=19% Similarity=0.077 Sum_probs=15.6
Q ss_pred EEEEeeCcccceecCCeEEEE
Q psy13876 15 ILGLLRYWQNPTMLQNYCILH 35 (118)
Q Consensus 15 ~v~l~~dLvd~~~pGd~V~v~ 35 (118)
.+.|..-+...+.+||.|+|+
T Consensus 30 ~l~L~~p~~~~~~~G~~v~l~ 50 (80)
T PF09356_consen 30 TLTLWRPLPAGLAVGDTVTLY 50 (80)
T ss_pred EEEEeccCcccCCCCCEEEEE
Confidence 355667777788889988876
Done!