Query 046259
Match_columns 62
No_of_seqs 136 out of 1010
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 10:16:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046259.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046259hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4442 Clathrin coat binding 99.9 4E-23 8.7E-28 140.9 5.5 58 1-61 202-259 (729)
2 KOG1080 Histone H3 (Lys4) meth 99.9 7.6E-23 1.7E-27 144.3 5.8 58 1-62 948-1005(1005)
3 KOG1141 Predicted histone meth 99.7 2.6E-17 5.7E-22 114.9 3.5 61 1-61 1198-1261(1262)
4 KOG1082 Histone H3 (Lys9) meth 99.4 2.1E-13 4.5E-18 88.8 3.2 61 1-61 281-353 (364)
5 KOG1079 Transcriptional repres 99.4 5.4E-13 1.2E-17 91.7 4.6 41 1-42 674-714 (739)
6 smart00317 SET SET (Su(var)3-9 99.2 3.5E-11 7.6E-16 65.5 5.6 35 1-36 82-116 (116)
7 KOG1083 Putative transcription 99.1 3.3E-11 7.2E-16 86.2 3.7 41 1-42 1259-1299(1306)
8 COG2940 Proteins containing SE 99.1 5.4E-11 1.2E-15 79.6 2.1 61 1-62 414-480 (480)
9 KOG1085 Predicted methyltransf 99.0 2.8E-10 6E-15 73.1 2.9 38 2-40 343-380 (392)
10 PF00856 SET: SET domain; Int 98.9 4.4E-09 9.6E-14 59.2 5.5 36 1-37 127-162 (162)
11 smart00508 PostSET Cysteine-ri 98.7 1.1E-08 2.4E-13 44.1 1.3 16 47-62 2-17 (26)
12 KOG1081 Transcription factor N 98.6 1.5E-08 3.2E-13 68.2 2.1 57 1-61 380-436 (463)
13 KOG2589 Histone tail methylase 98.3 1.1E-06 2.3E-11 58.2 4.1 47 1-53 205-251 (453)
14 KOG2461 Transcription factor B 96.3 0.0049 1.1E-07 41.3 3.0 26 15-40 121-146 (396)
15 PF08666 SAF: SAF domain; Int 94.4 0.028 6.1E-07 27.6 1.5 15 19-33 3-17 (63)
16 PF00856 SET: SET domain; Int 93.5 0.053 1.1E-06 30.0 1.6 16 18-33 2-17 (162)
17 KOG1337 N-methyltransferase [G 90.8 0.3 6.5E-06 33.1 3.0 24 15-38 255-278 (472)
18 smart00858 SAF This domain fam 88.9 0.33 7.1E-06 23.6 1.6 17 19-35 3-19 (64)
19 KOG2084 Predicted histone tail 86.5 1.7 3.7E-05 28.6 4.2 36 2-42 215-251 (482)
20 TIGR03569 NeuB_NnaB N-acetylne 86.1 0.45 9.8E-06 31.3 1.4 20 17-36 277-296 (329)
21 TIGR02059 swm_rep_I cyanobacte 85.9 4.3 9.4E-05 22.6 5.1 31 9-39 68-98 (101)
22 TIGR03586 PseI pseudaminic aci 82.5 0.89 1.9E-05 29.9 1.6 21 16-36 274-294 (327)
23 COG1188 Ribosome-associated he 80.3 3.6 7.7E-05 22.9 3.3 28 8-39 35-62 (100)
24 PF06718 DUF1203: Protein of u 79.1 2.4 5.3E-05 24.1 2.4 18 21-38 6-24 (117)
25 TIGR03170 flgA_cterm flagella 76.9 1.3 2.7E-05 24.6 0.8 16 20-35 2-17 (122)
26 COG2089 SpsE Sialic acid synth 72.3 1.9 4.2E-05 28.7 0.9 20 16-35 288-307 (347)
27 PF12690 BsuPI: Intracellular 68.0 4.5 9.8E-05 21.3 1.7 21 20-40 50-70 (82)
28 PF13121 DUF3976: Domain of un 66.2 5.7 0.00012 18.2 1.6 15 19-33 2-16 (41)
29 PF11720 Inhibitor_I78: Peptid 64.8 2.4 5.1E-05 21.1 0.2 18 22-39 25-42 (60)
30 COG4495 Uncharacterized protei 63.6 16 0.00034 20.6 3.3 33 8-40 14-46 (109)
31 PF04225 OapA: Opacity-associa 63.1 4.4 9.6E-05 21.5 1.0 17 22-38 39-55 (85)
32 KOG4115 Dynein-associated prot 61.2 4.6 9.9E-05 22.3 0.9 13 23-35 58-70 (97)
33 PF14169 YdjO: Cold-inducible 60.6 5 0.00011 20.2 0.9 11 51-61 20-30 (59)
34 PF04014 Antitoxin-MazE: Antid 60.0 9.4 0.0002 17.7 1.8 15 25-39 20-34 (47)
35 COG4118 Phd Antitoxin of toxin 59.0 3.1 6.7E-05 22.3 -0.0 15 23-37 18-32 (84)
36 PF06211 BAMBI: BMP and activi 57.7 6.4 0.00014 22.1 1.1 13 46-58 23-35 (107)
37 PRK06005 flgA flagellar basal 57.5 7 0.00015 23.2 1.3 20 16-35 32-51 (160)
38 TIGR03248 galactar-dH20 galact 56.6 8.3 0.00018 27.1 1.7 17 21-38 42-58 (507)
39 PF03896 TRAP_alpha: Transloco 54.8 8.6 0.00019 25.0 1.5 19 23-41 143-161 (285)
40 PRK12618 flgA flagellar basal 54.0 9.1 0.0002 22.2 1.4 19 17-35 19-37 (141)
41 KOG1631 Translocon-associated 53.9 8.4 0.00018 24.7 1.3 20 23-42 120-139 (261)
42 PF13780 DUF4176: Domain of un 53.8 29 0.00063 18.1 3.2 33 8-40 7-40 (76)
43 TIGR03177 pilus_cpaB Flp pilus 53.6 8.4 0.00018 24.2 1.3 21 15-35 34-54 (261)
44 PF12969 DUF3857: Domain of Un 53.1 24 0.00051 20.2 3.1 24 15-38 79-102 (177)
45 PF10989 DUF2808: Protein of u 52.2 44 0.00096 19.2 4.6 28 9-36 82-109 (146)
46 COG3831 Uncharacterized conser 52.1 37 0.00081 18.3 3.8 20 15-38 14-33 (85)
47 cd01758 PLAT_LPL PLAT/ LH2 dom 50.3 44 0.00094 19.3 3.8 9 3-11 97-105 (137)
48 KOG2155 Tubulin-tyrosine ligas 50.3 9.8 0.00021 26.8 1.3 39 1-39 213-252 (631)
49 TIGR02988 YaaA_near_RecF S4 do 48.6 27 0.00059 16.8 2.5 15 21-35 45-59 (59)
50 PF09478 CBM49: Carbohydrate b 48.4 18 0.00038 18.7 1.9 14 24-37 65-78 (80)
51 PF07177 Neuralized: Neuralize 46.8 25 0.00054 17.9 2.2 22 15-36 28-49 (69)
52 PRK07018 flgA flagellar basal 46.2 13 0.00028 23.1 1.3 17 17-33 110-126 (235)
53 cd03420 SirA_RHOD_Pry_redox Si 46.1 11 0.00023 18.9 0.8 16 22-37 19-34 (69)
54 PF09544 DUF2381: Protein of u 45.1 83 0.0018 20.4 4.9 25 15-39 73-99 (289)
55 TIGR00049 Iron-sulfur cluster 44.9 25 0.00055 18.7 2.2 35 21-55 62-102 (105)
56 PF13144 SAF_2: SAF-like 44.8 13 0.00029 22.1 1.1 21 17-37 114-134 (196)
57 PLN02311 chalcone isomerase 44.3 14 0.00031 23.9 1.3 20 19-38 195-214 (271)
58 COG4091 Predicted homoserine d 43.4 14 0.00031 25.3 1.2 17 21-37 395-411 (438)
59 PF02810 SEC-C: SEC-C motif; 42.5 6.4 0.00014 15.7 -0.3 9 48-56 3-11 (21)
60 PF12791 RsgI_N: Anti-sigma fa 41.9 42 0.0009 15.9 4.3 25 15-39 15-39 (56)
61 PRK08515 flgA flagellar basal 41.9 17 0.00037 22.6 1.3 18 17-34 100-117 (222)
62 PF13715 DUF4480: Domain of un 41.0 29 0.00062 17.6 2.0 21 17-38 33-54 (88)
63 cd08759 Type_III_cohesin_like 41.0 40 0.00088 20.2 2.8 17 23-39 9-26 (160)
64 PRK13623 iron-sulfur cluster i 40.5 19 0.0004 19.8 1.2 26 30-55 81-112 (115)
65 PF06483 ChiC: Chitinase C; I 39.5 24 0.00053 21.6 1.7 25 16-40 56-82 (180)
66 TIGR02268 Myxococcus xanthus p 39.4 1.1E+02 0.0023 20.2 4.7 27 14-40 76-104 (295)
67 PF02599 CsrA: Global regulato 39.3 50 0.0011 16.1 3.1 25 3-27 17-41 (54)
68 PRK10348 ribosome-associated h 38.5 31 0.00068 20.0 2.0 20 20-39 43-62 (133)
69 TIGR02011 IscA iron-sulfur clu 37.5 24 0.00051 19.1 1.3 27 29-55 70-102 (105)
70 PRK00568 carbon storage regula 36.8 68 0.0015 16.9 3.5 26 3-28 17-42 (76)
71 KOG2943 Predicted glyoxalase [ 36.8 21 0.00046 23.2 1.2 12 31-42 82-93 (299)
72 KOG1338 Uncharacterized conser 36.7 29 0.00062 24.1 1.8 23 16-38 238-260 (466)
73 cd06555 ASCH_PF0470_like ASC-1 36.4 32 0.00069 19.2 1.8 12 24-35 30-41 (109)
74 PF03173 CHB_HEX: Putative car 36.0 55 0.0012 19.5 2.8 34 8-41 71-105 (164)
75 PF04314 DUF461: Protein of un 34.9 75 0.0016 17.3 3.1 25 14-38 76-101 (110)
76 COG3848 Phosphohistidine swive 34.9 27 0.00058 19.8 1.3 19 20-38 82-100 (111)
77 PRK09504 sufA iron-sulfur clus 34.9 27 0.0006 19.6 1.4 9 47-55 111-119 (122)
78 PF03534 SpvB: Salmonella viru 34.4 1.1E+02 0.0023 20.0 4.1 36 5-40 207-247 (293)
79 cd00404 Aconitase_swivel Aconi 34.1 29 0.00062 18.7 1.3 12 24-35 76-87 (88)
80 TIGR03230 lipo_lipase lipoprot 34.0 83 0.0018 21.8 3.7 9 26-34 423-431 (442)
81 COG3884 FatA Acyl-ACP thioeste 34.0 67 0.0015 20.7 3.1 25 15-39 193-217 (250)
82 PF00313 CSD: 'Cold-shock' DNA 33.3 42 0.0009 16.3 1.8 15 24-38 39-53 (66)
83 PF14250 AbrB-like: AbrB-like 33.1 44 0.00096 17.5 1.8 16 23-38 50-65 (71)
84 COG0425 SirA Predicted redox p 33.0 22 0.00048 18.5 0.7 16 22-37 25-40 (78)
85 PHA00198 nonstructural protein 32.9 28 0.00061 18.6 1.1 14 17-30 2-15 (86)
86 PF08040 NADH_oxidored: MNLL s 32.8 11 0.00025 19.0 -0.4 18 17-34 41-58 (59)
87 PF11604 CusF_Ec: Copper bindi 31.2 44 0.00095 16.9 1.7 16 23-38 40-55 (70)
88 COG0603 Predicted PP-loop supe 31.2 28 0.0006 22.0 1.0 25 16-40 16-40 (222)
89 PF14100 PmoA: Methane oxygena 30.6 37 0.00079 21.6 1.5 20 21-40 235-254 (271)
90 COG3012 Uncharacterized protei 30.6 40 0.00087 20.1 1.6 9 48-56 135-143 (151)
91 TIGR01451 B_ant_repeat conserv 30.5 47 0.001 15.8 1.6 14 23-36 5-18 (53)
92 PF11325 DUF3127: Domain of un 30.3 46 0.00099 17.8 1.7 17 24-40 51-67 (84)
93 PF09956 DUF2190: Uncharacteri 30.3 1E+02 0.0022 17.0 3.7 19 18-36 30-48 (106)
94 cd00918 Der-p2_like Several gr 30.2 37 0.00081 19.1 1.4 18 23-40 72-89 (120)
95 smart00659 RPOLCX RNA polymera 30.1 40 0.00088 15.7 1.3 10 46-55 18-28 (44)
96 KOG3851 Sulfide:quinone oxidor 30.0 31 0.00068 23.6 1.2 11 27-37 127-137 (446)
97 PF01476 LysM: LysM domain; I 29.8 25 0.00055 15.4 0.6 10 25-34 34-43 (44)
98 cd04467 S1_aIF5A S1_aIF5A: Arc 29.8 48 0.0011 16.4 1.6 11 24-34 37-47 (57)
99 cd01579 AcnA_Bact_Swivel Bacte 29.4 34 0.00073 19.4 1.1 11 25-35 110-120 (121)
100 COG1261 FlgA Flagellar basal b 29.3 35 0.00077 21.4 1.3 19 16-34 94-112 (220)
101 PF10442 FIST_C: FIST C domain 28.9 1.1E+02 0.0023 16.8 4.3 22 15-38 47-68 (136)
102 PF09044 Kp4: Kp4; InterPro: 28.6 35 0.00076 19.8 1.1 14 24-38 113-126 (128)
103 COG5216 Uncharacterized conser 28.5 28 0.0006 17.7 0.6 8 47-54 22-29 (67)
104 PF07081 DUF1349: Protein of u 28.3 88 0.0019 18.6 2.9 23 15-37 151-173 (183)
105 PRK06804 flgA flagellar basal 28.2 40 0.00086 21.6 1.4 19 17-35 136-154 (261)
106 COG0261 RplU Ribosomal protein 28.2 55 0.0012 18.3 1.8 20 18-37 19-38 (103)
107 PRK14998 cold shock-like prote 28.1 65 0.0014 16.5 2.0 18 23-40 39-56 (73)
108 cd03422 YedF YedF is a bacteri 28.0 31 0.00067 17.2 0.7 15 22-36 19-33 (69)
109 PF00254 FKBP_C: FKBP-type pep 28.0 52 0.0011 16.8 1.7 17 24-40 3-19 (94)
110 PF01206 TusA: Sulfurtransfera 27.6 21 0.00046 17.5 0.1 17 22-38 20-36 (70)
111 PF13598 DUF4139: Domain of un 27.4 1.7E+02 0.0037 18.6 4.5 25 16-40 194-218 (317)
112 PF08756 YfkB: YfkB-like domai 27.3 25 0.00055 20.9 0.4 35 25-59 79-131 (153)
113 PRK01712 carbon storage regula 27.3 98 0.0021 15.8 3.4 26 3-28 17-42 (64)
114 COG4918 Uncharacterized protei 27.3 40 0.00087 19.0 1.1 16 25-40 71-86 (114)
115 PF07610 DUF1573: Protein of u 27.1 76 0.0016 14.5 3.7 19 17-35 24-42 (45)
116 PF01345 DUF11: Domain of unkn 26.9 50 0.0011 16.4 1.4 19 20-38 31-49 (76)
117 KOG1728 40S ribosomal protein 26.7 42 0.0009 19.9 1.2 19 22-40 114-132 (156)
118 COG3480 SdrC Predicted secrete 26.7 46 0.001 22.4 1.5 15 24-38 172-186 (342)
119 PF08487 VIT: Vault protein in 26.5 56 0.0012 17.9 1.7 17 20-37 99-115 (118)
120 PRK09502 iscA iron-sulfur clus 26.5 42 0.00092 18.2 1.2 9 47-55 96-104 (107)
121 PF08669 GCV_T_C: Glycine clea 26.3 93 0.002 16.1 2.5 21 18-38 65-85 (95)
122 PF05938 Self-incomp_S1: Plant 26.1 1.1E+02 0.0024 16.4 2.8 25 25-51 30-54 (110)
123 smart00609 VIT Vault protein I 25.8 57 0.0012 18.6 1.6 18 17-35 108-125 (130)
124 COG0787 Alr Alanine racemase [ 25.7 51 0.0011 22.2 1.6 22 17-40 239-260 (360)
125 COG0316 sufA Fe-S cluster asse 25.7 47 0.001 18.6 1.2 11 45-55 97-107 (110)
126 cd00912 ML The ML (MD-2-relate 25.3 58 0.0013 18.0 1.6 19 22-40 78-96 (127)
127 cd00118 LysM Lysin domain, fou 25.3 53 0.0011 13.3 1.2 13 22-34 33-45 (46)
128 PRK09890 cold shock protein Cs 25.3 81 0.0018 15.9 2.0 18 23-40 42-59 (70)
129 cd04458 CSP_CDS Cold-Shock Pro 25.2 81 0.0018 15.2 2.0 17 23-39 38-54 (65)
130 PRK10354 RNA chaperone/anti-te 24.7 82 0.0018 15.8 2.0 17 24-40 43-59 (70)
131 PRK02625 rpoC1 DNA-directed RN 24.5 27 0.00059 25.3 0.2 39 15-53 11-74 (627)
132 TIGR01997 sufA_proteo FeS asse 23.9 45 0.00097 18.1 0.9 9 47-55 96-104 (107)
133 PF10907 DUF2749: Protein of u 23.9 42 0.00091 17.3 0.8 10 23-32 53-62 (66)
134 PRK15463 cold shock-like prote 23.8 90 0.002 15.8 2.0 17 23-39 42-58 (70)
135 PF04797 Herpes_ORF11: Herpesv 23.7 81 0.0018 21.1 2.3 20 23-42 272-291 (379)
136 PF07703 A2M_N_2: Alpha-2-macr 23.5 1.4E+02 0.003 16.2 3.0 23 16-38 95-118 (136)
137 cd05829 Sortase_E Sortase E (S 23.5 63 0.0014 18.5 1.6 19 18-36 65-83 (144)
138 PF02298 Cu_bind_like: Plastoc 23.3 44 0.00095 17.5 0.8 18 22-39 15-32 (85)
139 TIGR02084 leud 3-isopropylmala 23.2 64 0.0014 19.1 1.6 14 25-38 107-120 (156)
140 PF01835 A2M_N: MG2 domain; I 23.2 1.2E+02 0.0027 15.6 2.6 7 28-34 13-19 (99)
141 PF06205 GT36_AF: Glycosyltran 23.2 75 0.0016 16.8 1.7 24 15-38 59-82 (90)
142 PF06200 tify: tify domain; I 23.2 80 0.0017 14.2 1.6 12 28-39 4-15 (36)
143 TIGR02231 conserved hypothetic 23.1 2.1E+02 0.0045 19.8 4.2 25 16-40 393-417 (525)
144 smart00588 NEUZ domain in neur 23.0 1E+02 0.0022 17.3 2.4 21 16-36 30-50 (123)
145 PF08290 Hep_core_N: Hepatitis 22.9 36 0.00078 14.4 0.3 14 48-61 10-27 (27)
146 PF10077 DUF2314: Uncharacteri 22.6 71 0.0015 18.3 1.6 17 22-38 76-92 (133)
147 COG3738 Uncharacterized protei 22.3 2E+02 0.0044 17.7 4.6 29 7-35 147-175 (200)
148 TIGR02308 RNA_lig_T4_1 RNA lig 22.1 61 0.0013 22.1 1.5 21 15-35 172-192 (374)
149 PRK12617 flgA flagellar basal 22.1 56 0.0012 20.3 1.2 19 16-34 88-106 (214)
150 cd00915 MD-1_MD-2 MD-1 and MD- 22.1 90 0.002 18.0 2.0 19 21-39 80-100 (130)
151 PF09227 DUF1962: Domain of un 22.0 44 0.00094 16.8 0.6 10 51-60 48-57 (64)
152 PF03459 TOBE: TOBE domain; I 21.9 71 0.0015 15.2 1.4 13 25-37 46-58 (64)
153 cd03423 SirA SirA (also known 21.7 49 0.0011 16.4 0.8 16 22-37 19-34 (69)
154 PF03423 CBM_25: Carbohydrate 21.7 1.2E+02 0.0027 15.8 2.4 10 30-39 19-28 (87)
155 TIGR02657 amicyanin amicyanin. 21.4 60 0.0013 16.6 1.1 12 25-36 14-25 (83)
156 PRK09937 stationary phase/star 21.2 1.1E+02 0.0023 15.8 2.0 18 23-40 39-56 (74)
157 TIGR00202 csrA carbon storage 21.1 1.4E+02 0.0031 15.4 3.4 25 3-27 17-41 (69)
158 PRK10943 cold shock-like prote 21.1 1.1E+02 0.0024 15.3 2.0 17 23-39 41-57 (69)
159 TIGR02381 cspD cold shock doma 20.9 1.1E+02 0.0024 15.2 2.0 18 23-40 39-56 (68)
160 TIGR02087 LEUD_arch 3-isopropy 20.8 82 0.0018 18.6 1.7 16 24-39 104-119 (154)
161 PF11113 Phage_head_chap: Head 20.8 1.3E+02 0.0029 15.0 3.5 29 13-42 11-39 (56)
162 PF08348 PAS_6: YheO-like PAS 20.5 1.8E+02 0.0038 16.3 4.0 20 2-21 18-37 (118)
163 COG3369 Zinc finger domain con 20.4 53 0.0012 17.5 0.7 11 46-56 30-40 (78)
164 PF05207 zf-CSL: CSL zinc fing 20.3 46 0.001 16.1 0.5 10 46-55 17-26 (55)
165 PRK03760 hypothetical protein; 20.1 50 0.0011 18.5 0.7 16 20-35 100-115 (117)
166 KOG2540 Cytochrome oxidase ass 20.0 2.6E+02 0.0056 18.1 4.8 45 9-53 157-204 (269)
No 1
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.88 E-value=4e-23 Score=140.89 Aligned_cols=58 Identities=36% Similarity=0.688 Sum_probs=54.0
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCCCCCceEEEecCCCCCceec
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDEPEEFKVPCLCKAPNCRKFM 61 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~~~~~~~~C~Cgs~~Crg~l 61 (62)
+|||+++.|.|.+ ..||||||.|.|++||||||||++..+. ....+|+||+++|||||
T Consensus 202 ~PNa~~~KWtV~~-~lRvGiFakk~I~~GEEITFDYqf~rYG--r~AQ~CyCgeanC~G~I 259 (729)
T KOG4442|consen 202 DPNAEVQKWTVPD-ELRVGIFAKKVIKPGEEITFDYQFDRYG--RDAQPCYCGEANCRGWI 259 (729)
T ss_pred CCCceeeeeeeCC-eeEEEEeEecccCCCceeeEeccccccc--ccccccccCCccccccc
Confidence 6999999999986 8999999999999999999999998764 46799999999999998
No 2
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=99.87 E-value=7.6e-23 Score=144.27 Aligned_cols=58 Identities=53% Similarity=1.151 Sum_probs=54.3
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCCCCCceEEEecCCCCCceecC
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDEPEEFKVPCLCKAPNCRKFMN 62 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~~~~~~~~C~Cgs~~Crg~l~ 62 (62)
+|||+++++.|++ ..+|+|||.|+|++||||||||.+..++ .+++|+|||++|||+||
T Consensus 948 ~PNCyakvi~V~g-~~~IvIyakr~I~~~EElTYDYkF~~e~---~kipClCgap~Crg~~n 1005 (1005)
T KOG1080|consen 948 NPNCYAKVITVEG-DKRIVIYSKRDIAAGEELTYDYKFPTED---DKIPCLCGAPNCRGFLN 1005 (1005)
T ss_pred CCCceeeEEEecC-eeEEEEEEecccccCceeeeeccccccc---cccccccCCCccccccC
Confidence 6999999999997 7899999999999999999999998765 38999999999999986
No 3
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=99.67 E-value=2.6e-17 Score=114.93 Aligned_cols=61 Identities=28% Similarity=0.518 Sum_probs=56.8
Q ss_pred CCceEEEEEEeCCC---ccEEEEEEcCCCCCCCeEEEEcCCCCCCCCCceEEEecCCCCCceec
Q 046259 1 MPNCYARIMSVGDD---ESRIVLIAKTNVSAGDELTYDYLFDPDEPEEFKVPCLCKAPNCRKFM 61 (62)
Q Consensus 1 ~PNc~~~~v~~~~~---~~~i~i~A~rdI~~GeELt~dY~~~~~~~~~~~~~C~Cgs~~Crg~l 61 (62)
+||+.++.|.|+.+ .|+++|||.|.|++|+||||||+++-.....+...|+||+.+|||+|
T Consensus 1198 ~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~~keL~C~CGa~~CrgrL 1261 (1262)
T KOG1141|consen 1198 DPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVATKELTCHCGAENCRGRL 1261 (1262)
T ss_pred CccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccccceEEEecChhhhhccc
Confidence 59999999999766 68999999999999999999999998888888999999999999986
No 4
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=99.39 E-value=2.1e-13 Score=88.76 Aligned_cols=61 Identities=28% Similarity=0.398 Sum_probs=50.4
Q ss_pred CCceEEEEEEeCCC---ccEEEEEEcCCCCCCCeEEEEcCCCCC-----CC----CCceEEEecCCCCCceec
Q 046259 1 MPNCYARIMSVGDD---ESRIVLIAKTNVSAGDELTYDYLFDPD-----EP----EEFKVPCLCKAPNCRKFM 61 (62)
Q Consensus 1 ~PNc~~~~v~~~~~---~~~i~i~A~rdI~~GeELt~dY~~~~~-----~~----~~~~~~C~Cgs~~Crg~l 61 (62)
+||+.+..|..+.. .++++|||+++|.||+||||||+.... .. ...+..|.||+.+||+.+
T Consensus 281 ~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~~~~~~~~~~~~~~~~~~~c~c~~~~cr~~~ 353 (364)
T KOG1082|consen 281 SPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAYKLLVQDGANIYTPVMKKNCNCGLEKCRGLL 353 (364)
T ss_pred CccceeeeeeecCCccchheeeeeeccccCCCcccchhhcccccccccccccccccccchhhcCCCHHhCccc
Confidence 59999999987633 689999999999999999999997632 10 235688999999999976
No 5
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=99.38 E-value=5.4e-13 Score=91.74 Aligned_cols=41 Identities=44% Similarity=0.914 Sum_probs=37.8
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCC
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDE 42 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~ 42 (62)
+|||++.++.|.+ .+||+|||+|+|.+||||+|||.+..+.
T Consensus 674 nPNCYAkvm~V~G-dhRIGifAkRaIeagEELffDYrYs~~~ 714 (739)
T KOG1079|consen 674 NPNCYAKVMMVAG-DHRIGIFAKRAIEAGEELFFDYRYSPEH 714 (739)
T ss_pred CCCcEEEEEEecC-CcceeeeehhhcccCceeeeeeccCccc
Confidence 6999999999986 8999999999999999999999987654
No 6
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.23 E-value=3.5e-11 Score=65.51 Aligned_cols=35 Identities=43% Similarity=0.755 Sum_probs=31.5
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEc
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY 36 (62)
.||+.+..+..++ ..++.|+|+|||++|||||+||
T Consensus 82 ~pN~~~~~~~~~~-~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 82 EPNCELLFVEVNG-DSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CCCEEEEEEEECC-CcEEEEEECCCcCCCCEEeecC
Confidence 5999999888754 5589999999999999999999
No 7
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=99.15 E-value=3.3e-11 Score=86.17 Aligned_cols=41 Identities=41% Similarity=0.642 Sum_probs=37.7
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCC
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDE 42 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~ 42 (62)
.|||..+.|.+++ .+|+++||+|||.+||||||||++....
T Consensus 1259 KPNc~~qkwSVNG-~~Rv~L~A~rDi~kGEELtYDYN~ks~~ 1299 (1306)
T KOG1083|consen 1259 KPNCEMQKWSVNG-EYRVGLFALRDLPKGEELTYDYNFKSFN 1299 (1306)
T ss_pred CCCCccccccccc-eeeeeeeecCCCCCCceEEEeccccccC
Confidence 5999999999997 9999999999999999999999986544
No 8
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=99.07 E-value=5.4e-11 Score=79.63 Aligned_cols=61 Identities=33% Similarity=0.572 Sum_probs=52.2
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCCCC------CceEEEecCCCCCceecC
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDEPE------EFKVPCLCKAPNCRKFMN 62 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~~~------~~~~~C~Cgs~~Crg~l~ 62 (62)
+|||.+....+.+ ..++.++|+|||++|||||+||+...+... ...+.|.||+..|+++|+
T Consensus 414 ~pN~~~~~~~~~g-~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 480 (480)
T COG2940 414 TPNCEASPIEVNG-IFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHTMS 480 (480)
T ss_pred CCCcceecccccc-cceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCCCC
Confidence 5999999887764 689999999999999999999998876632 245899999999999874
No 9
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=99.00 E-value=2.8e-10 Score=73.12 Aligned_cols=38 Identities=24% Similarity=0.549 Sum_probs=35.6
Q ss_pred CceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 2 PNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 2 PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
+||.+++|.+++ .++++++|.|||++||||+|||++..
T Consensus 343 gNl~TKvv~Idg-~pHLiLvA~rdIa~GEELlYDYGDRS 380 (392)
T KOG1085|consen 343 GNLKTKVVEIDG-SPHLILVARRDIAQGEELLYDYGDRS 380 (392)
T ss_pred CcceeeEEEecC-CceEEEEeccccccchhhhhhccccc
Confidence 799999999986 89999999999999999999999864
No 10
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=98.91 E-value=4.4e-09 Score=59.17 Aligned_cols=36 Identities=28% Similarity=0.443 Sum_probs=29.7
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcC
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYL 37 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~ 37 (62)
+|||.+...... ....+.|.|.|+|++||||+++||
T Consensus 127 ~pn~~~~~~~~~-~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 127 DPNCEVSFDFDG-DGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp STSEEEEEEEET-TTTEEEEEESS-B-TTSBEEEEST
T ss_pred ccccceeeEeec-ccceEEEEECCccCCCCEEEEEEC
Confidence 589999987654 378999999999999999999997
No 11
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=98.66 E-value=1.1e-08 Score=44.05 Aligned_cols=16 Identities=69% Similarity=1.545 Sum_probs=14.3
Q ss_pred eEEEecCCCCCceecC
Q 046259 47 KVPCLCKAPNCRKFMN 62 (62)
Q Consensus 47 ~~~C~Cgs~~Crg~l~ 62 (62)
.++|+|||++|||+|+
T Consensus 2 ~~~C~CGs~~CRG~l~ 17 (26)
T smart00508 2 KQPCLCGAPNCRGFLG 17 (26)
T ss_pred CeeeeCCCccccceec
Confidence 4799999999999983
No 12
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=98.64 E-value=1.5e-08 Score=68.19 Aligned_cols=57 Identities=30% Similarity=0.491 Sum_probs=49.1
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCCCCCceEEEecCCCCCceec
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDEPEEFKVPCLCKAPNCRKFM 61 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~~~~~~~~C~Cgs~~Crg~l 61 (62)
+|||....+.+.+ ..+++++|.+.|++|+||||+|+..- ......|.||+.+|.+.+
T Consensus 380 ~~~v~~~k~~~~~-~t~~~~~a~~~i~~g~e~t~~~n~~~---~~~~~~~~~~~e~~~~~~ 436 (463)
T KOG1081|consen 380 QPNVETEKWQVIG-DTRVGLFAPRQIEAGEELTFNYNGNC---EGNEKRCCCGSENCTETK 436 (463)
T ss_pred CCceeechhheec-ccccccccccccccchhhhheeeccc---cCCcceEeecccccccCC
Confidence 5788888887765 79999999999999999999999874 346789999999999876
No 13
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=98.29 E-value=1.1e-06 Score=58.22 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=36.3
Q ss_pred CCceEEEEEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCCCCCCCceEEEecC
Q 046259 1 MPNCYARIMSVGDDESRIVLIAKTNVSAGDELTYDYLFDPDEPEEFKVPCLCK 53 (62)
Q Consensus 1 ~PNc~~~~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~~~~~~~~~~C~Cg 53 (62)
.|||.... .+..++.+-++|||+||||||--|+..+.. .....|.|-
T Consensus 205 rpnCkFvs----~g~~tacvkvlRDIePGeEITcFYgs~fFG--~~N~~CeC~ 251 (453)
T KOG2589|consen 205 RPNCKFVS----TGRDTACVKVLRDIEPGEEITCFYGSGFFG--ENNEECECV 251 (453)
T ss_pred CCCceeec----CCCceeeeehhhcCCCCceeEEeecccccC--CCCceeEEe
Confidence 37887653 235789999999999999999999988743 456667773
No 14
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=96.26 E-value=0.0049 Score=41.28 Aligned_cols=26 Identities=15% Similarity=0.110 Sum_probs=22.8
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
...|.+.|+|+|.+||||-+.|+.++
T Consensus 121 ~~~Ifyrt~r~I~p~eELlVWY~~e~ 146 (396)
T KOG2461|consen 121 GENIFYRTIRDIRPNEELLVWYGSEY 146 (396)
T ss_pred cCceEEEecccCCCCCeEEEEeccch
Confidence 35799999999999999999998653
No 15
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=94.39 E-value=0.028 Score=27.63 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=11.4
Q ss_pred EEEEcCCCCCCCeEE
Q 046259 19 VLIAKTNVSAGDELT 33 (62)
Q Consensus 19 ~i~A~rdI~~GeELt 33 (62)
.++|.|||++|+.|+
T Consensus 3 vvVA~~di~~G~~i~ 17 (63)
T PF08666_consen 3 VVVAARDIPAGTVIT 17 (63)
T ss_dssp EEEESSTB-TT-BEC
T ss_pred EEEEeCccCCCCEEc
Confidence 478999999999985
No 16
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=93.48 E-value=0.053 Score=30.01 Aligned_cols=16 Identities=25% Similarity=0.383 Sum_probs=12.3
Q ss_pred EEEEEcCCCCCCCeEE
Q 046259 18 IVLIAKTNVSAGDELT 33 (62)
Q Consensus 18 i~i~A~rdI~~GeELt 33 (62)
.++||.|||++||-|-
T Consensus 2 rGl~At~dI~~Ge~I~ 17 (162)
T PF00856_consen 2 RGLFATRDIKAGEVIL 17 (162)
T ss_dssp EEEEESS-B-TTEEEE
T ss_pred EEEEECccCCCCCEEE
Confidence 4799999999999876
No 17
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=90.80 E-value=0.3 Score=33.14 Aligned_cols=24 Identities=33% Similarity=0.526 Sum_probs=22.0
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~ 38 (62)
...+-+++.++|++|||+.++||.
T Consensus 255 d~~~~l~~~~~v~~geevfi~YG~ 278 (472)
T KOG1337|consen 255 DEAVELVAERDVSAGEEVFINYGP 278 (472)
T ss_pred CCcEEEEEeeeecCCCeEEEecCC
Confidence 458999999999999999999985
No 18
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=88.87 E-value=0.33 Score=23.62 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=14.4
Q ss_pred EEEEcCCCCCCCeEEEE
Q 046259 19 VLIAKTNVSAGDELTYD 35 (62)
Q Consensus 19 ~i~A~rdI~~GeELt~d 35 (62)
.++|.++|++|+.|+-+
T Consensus 3 v~va~~~i~~G~~i~~~ 19 (64)
T smart00858 3 VVVAARDLPAGEVITAE 19 (64)
T ss_pred EEEEeCccCCCCCcchh
Confidence 46889999999998863
No 19
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=86.46 E-value=1.7 Score=28.56 Aligned_cols=36 Identities=25% Similarity=0.330 Sum_probs=25.7
Q ss_pred CceEEEEEEeCCCccEEEEEEcCCCCCCC-eEEEEcCCCCCC
Q 046259 2 PNCYARIMSVGDDESRIVLIAKTNVSAGD-ELTYDYLFDPDE 42 (62)
Q Consensus 2 PNc~~~~v~~~~~~~~i~i~A~rdI~~Ge-ELt~dY~~~~~~ 42 (62)
||+.+ ..+ .....+.+.+++.+++ ||+..|......
T Consensus 215 pn~~~---~~~--~~~~~~~~~~~~~~~~~~l~~~y~~~~~~ 251 (482)
T KOG2084|consen 215 PNISV---IFD--GRGLALLVPAGIDAGEEELTISYTDPLLS 251 (482)
T ss_pred CCeEE---EEC--CceeEEEeecccCCCCCEEEEeecccccC
Confidence 77772 222 4567778888888887 999999876544
No 20
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=86.07 E-value=0.45 Score=31.27 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=17.7
Q ss_pred EEEEEEcCCCCCCCeEEEEc
Q 046259 17 RIVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~dY 36 (62)
|-.++|.+||++||.||.+=
T Consensus 277 rrsl~a~~di~~G~~lt~~~ 296 (329)
T TIGR03569 277 RKSLVAAKDIKKGEIFTEDN 296 (329)
T ss_pred ceEEEEccCcCCCCEecHHh
Confidence 66899999999999999763
No 21
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=85.91 E-value=4.3 Score=22.60 Aligned_cols=31 Identities=32% Similarity=0.506 Sum_probs=24.7
Q ss_pred EEeCCCccEEEEEEcCCCCCCCeEEEEcCCC
Q 046259 9 MSVGDDESRIVLIAKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 9 v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~ 39 (62)
|.+++.-..+-+--.+.|..||++|+.|..+
T Consensus 68 VsV~~s~ktVTLTL~~~V~~Gq~VTVsYt~p 98 (101)
T TIGR02059 68 VSLGGSNTTITLTLAQVVEDGDEVTLSYTKN 98 (101)
T ss_pred EEEcCcccEEEEEecccccCCCEEEEEeeCC
Confidence 4454434578888899999999999999765
No 22
>TIGR03586 PseI pseudaminic acid synthase.
Probab=82.52 E-value=0.89 Score=29.90 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=18.0
Q ss_pred cEEEEEEcCCCCCCCeEEEEc
Q 046259 16 SRIVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~dY 36 (62)
.|-.++|.|||++||-||.+-
T Consensus 274 ~rrsl~a~~di~~G~~it~~~ 294 (327)
T TIGR03586 274 FRRSLYVVKDIKKGETFTEEN 294 (327)
T ss_pred eeEEEEEccCcCCCCEecHHh
Confidence 366899999999999999763
No 23
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=80.31 E-value=3.6 Score=22.89 Aligned_cols=28 Identities=21% Similarity=0.159 Sum_probs=21.2
Q ss_pred EEEeCCCccEEEEEEcCCCCCCCeEEEEcCCC
Q 046259 8 IMSVGDDESRIVLIAKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 8 ~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~ 39 (62)
.|.+++ ...=+.++++.|++|++.|+..
T Consensus 35 rV~vNG----~~aKpS~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 35 RVKVNG----QRAKPSKEVKVGDILTIRFGNK 62 (100)
T ss_pred eEEECC----EEcccccccCCCCEEEEEeCCc
Confidence 455554 2237899999999999999864
No 24
>PF06718 DUF1203: Protein of unknown function (DUF1203); InterPro: IPR009593 This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species.
Probab=79.11 E-value=2.4 Score=24.07 Aligned_cols=18 Identities=22% Similarity=0.311 Sum_probs=14.7
Q ss_pred EEcCCCCCCCe-EEEEcCC
Q 046259 21 IAKTNVSAGDE-LTYDYLF 38 (62)
Q Consensus 21 ~A~rdI~~GeE-Lt~dY~~ 38 (62)
.++|||++||+ |-++|..
T Consensus 6 ~cL~~~~~Ge~~lLlsy~p 24 (117)
T PF06718_consen 6 HCLRDAEPGEELLLLSYRP 24 (117)
T ss_pred EecccCCCCCeEEEEecCC
Confidence 57999999998 5677864
No 25
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=76.86 E-value=1.3 Score=24.58 Aligned_cols=16 Identities=19% Similarity=0.459 Sum_probs=13.6
Q ss_pred EEEcCCCCCCCeEEEE
Q 046259 20 LIAKTNVSAGDELTYD 35 (62)
Q Consensus 20 i~A~rdI~~GeELt~d 35 (62)
++|.|+|++||-|+-+
T Consensus 2 ~Va~r~I~~G~~i~~~ 17 (122)
T TIGR03170 2 VVAKRPLKRGEVISPE 17 (122)
T ss_pred EEECcccCCCCCcCHH
Confidence 6899999999987753
No 26
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=72.26 E-value=1.9 Score=28.73 Aligned_cols=20 Identities=30% Similarity=0.521 Sum_probs=16.7
Q ss_pred cEEEEEEcCCCCCCCeEEEE
Q 046259 16 SRIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~d 35 (62)
.+-.+|+.+||++||-|+-+
T Consensus 288 ~~Rsl~~~kdikkGe~ls~~ 307 (347)
T COG2089 288 ARRSLVATKDIKKGEILSED 307 (347)
T ss_pred HhhheeeecccccCcccccc
Confidence 34569999999999998865
No 27
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=68.01 E-value=4.5 Score=21.32 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=13.2
Q ss_pred EEEcCCCCCCCeEEEEcCCCC
Q 046259 20 LIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 20 i~A~rdI~~GeELt~dY~~~~ 40 (62)
......|+|||+++|.-..+.
T Consensus 50 al~~~~l~pGe~~~~~~~~~~ 70 (82)
T PF12690_consen 50 ALQEETLEPGESLTYEETWDL 70 (82)
T ss_dssp --EEEEE-TT-EEEEEEEESS
T ss_pred eeeEEEECCCCEEEEEEEECC
Confidence 444667899999999876654
No 28
>PF13121 DUF3976: Domain of unknown function (DUF3976)
Probab=66.24 E-value=5.7 Score=18.25 Aligned_cols=15 Identities=13% Similarity=0.443 Sum_probs=12.8
Q ss_pred EEEEcCCCCCCCeEE
Q 046259 19 VLIAKTNVSAGDELT 33 (62)
Q Consensus 19 ~i~A~rdI~~GeELt 33 (62)
.+|..+||..|..||
T Consensus 2 y~fvrkdit~~ntlt 16 (41)
T PF13121_consen 2 YFFVRKDITKDNTLT 16 (41)
T ss_pred EEEEEeeccCCCeee
Confidence 578899999998887
No 29
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=64.76 E-value=2.4 Score=21.10 Aligned_cols=18 Identities=33% Similarity=0.488 Sum_probs=14.9
Q ss_pred EcCCCCCCCeEEEEcCCC
Q 046259 22 AKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~~ 39 (62)
..|=|.||+.+|.||..+
T Consensus 25 ~~Rvi~Pg~~vTmDyr~d 42 (60)
T PF11720_consen 25 TVRVIRPGDAVTMDYRPD 42 (60)
T ss_pred ceEEeCCCCcCcccCCCC
Confidence 356688999999999864
No 30
>COG4495 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.61 E-value=16 Score=20.62 Aligned_cols=33 Identities=21% Similarity=0.545 Sum_probs=27.0
Q ss_pred EEEeCCCccEEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 8 IMSVGDDESRIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 8 ~v~~~~~~~~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
+|.+.++...+-|+....|+.++|=-|||..-.
T Consensus 14 iV~lk~~~~klMIi~R~~~k~~~~~~fDY~a~~ 46 (109)
T COG4495 14 IVRLKGGDSKLMIISRGQIKVDEETMFDYSACP 46 (109)
T ss_pred EEEEcCCCeEEEEEeccceeecceeeecccccc
Confidence 455655678899999999999999999997543
No 31
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=63.10 E-value=4.4 Score=21.50 Aligned_cols=17 Identities=18% Similarity=0.249 Sum_probs=10.2
Q ss_pred EcCCCCCCCeEEEEcCC
Q 046259 22 AKTNVSAGDELTYDYLF 38 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~ 38 (62)
.+..|+||++|.|.-..
T Consensus 39 ~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 39 PLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp -GGG--TT-EEEEEE-T
T ss_pred hHhhCCCCCEEEEEECC
Confidence 56789999999998764
No 32
>KOG4115 consensus Dynein-associated protein Roadblock [Cell cycle control, cell division, chromosome partitioning; Cell motility]
Probab=61.21 E-value=4.6 Score=22.35 Aligned_cols=13 Identities=15% Similarity=0.406 Sum_probs=11.5
Q ss_pred cCCCCCCCeEEEE
Q 046259 23 KTNVSAGDELTYD 35 (62)
Q Consensus 23 ~rdI~~GeELt~d 35 (62)
.||+.|+++|||=
T Consensus 58 VrdlDpsn~Ltfl 70 (97)
T KOG4115|consen 58 VRDLDPSNDLTFL 70 (97)
T ss_pred HHccCCcCceEEE
Confidence 6899999999984
No 33
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=60.56 E-value=5 Score=20.25 Aligned_cols=11 Identities=27% Similarity=0.915 Sum_probs=9.5
Q ss_pred ecCCCCCceec
Q 046259 51 LCKAPNCRKFM 61 (62)
Q Consensus 51 ~Cgs~~Crg~l 61 (62)
.|-+..|+|||
T Consensus 20 ~Ct~e~C~gWm 30 (59)
T PF14169_consen 20 ECTSEDCNGWM 30 (59)
T ss_pred EeCCCCCCccc
Confidence 47799999997
No 34
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=60.05 E-value=9.4 Score=17.70 Aligned_cols=15 Identities=27% Similarity=0.375 Sum_probs=12.8
Q ss_pred CCCCCCeEEEEcCCC
Q 046259 25 NVSAGDELTYDYLFD 39 (62)
Q Consensus 25 dI~~GeELt~dY~~~ 39 (62)
.|++|+||.+.+...
T Consensus 20 ~l~~Gd~v~i~~~~~ 34 (47)
T PF04014_consen 20 GLKPGDEVEIEVEGD 34 (47)
T ss_dssp TSSTTTEEEEEEETT
T ss_pred CCCCCCEEEEEEeCC
Confidence 699999999998654
No 35
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=58.98 E-value=3.1 Score=22.28 Aligned_cols=15 Identities=27% Similarity=0.284 Sum_probs=11.8
Q ss_pred cCCCCCCCeEEEEcC
Q 046259 23 KTNVSAGDELTYDYL 37 (62)
Q Consensus 23 ~rdI~~GeELt~dY~ 37 (62)
++.+++|||+++-=.
T Consensus 18 L~rV~aGEev~IT~~ 32 (84)
T COG4118 18 LRRVRAGEEVIITKR 32 (84)
T ss_pred HHHHhCCCEEEEeeC
Confidence 456889999998754
No 36
>PF06211 BAMBI: BMP and activin membrane-bound inhibitor (BAMBI) N-terminal domain; InterPro: IPR009345 This family consists of several eukaryotic BMP and activin membrane-bound inhibitor (BAMBI) proteins. Members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-beta, bone morphogenetic proteins (BMPs), activins and nodals, are vital for regulating growth and differentiation. BAMBI is related to TGF-beta-family type I receptors but lacks an intracellular kinase domain. BAMBI is co-expressed with the ventralising morphogen BMP4 during Xenopus embryogenesis and requires BMP signalling for its expression. The protein stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling [].
Probab=57.74 E-value=6.4 Score=22.12 Aligned_cols=13 Identities=38% Similarity=1.094 Sum_probs=11.2
Q ss_pred ceEEEecCCCCCc
Q 046259 46 FKVPCLCKAPNCR 58 (62)
Q Consensus 46 ~~~~C~Cgs~~Cr 58 (62)
..++|+|.++.|.
T Consensus 23 GEIRCYCn~P~CV 35 (107)
T PF06211_consen 23 GEIRCYCNAPHCV 35 (107)
T ss_pred CceEEecCCccee
Confidence 3499999999996
No 37
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=57.49 E-value=7 Score=23.16 Aligned_cols=20 Identities=10% Similarity=0.297 Sum_probs=16.0
Q ss_pred cEEEEEEcCCCCCCCeEEEE
Q 046259 16 SRIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~d 35 (62)
..-.++|.|+|.+||-|+=+
T Consensus 32 ~v~vvVa~r~I~rGevIt~~ 51 (160)
T PRK06005 32 RIAFVVPSTTIYPGETISDS 51 (160)
T ss_pred cEEEEEEccCcCCCCCcCHH
Confidence 34478999999999987754
No 38
>TIGR03248 galactar-dH20 galactarate dehydratase. Galactarate dehydratase converts D-galactarate to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (, GenProp0714).
Probab=56.62 E-value=8.3 Score=27.09 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=13.5
Q ss_pred EEcCCCCCCCeEEEEcCC
Q 046259 21 IAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 21 ~A~rdI~~GeELt~dY~~ 38 (62)
||++||++||.+ +.|+.
T Consensus 42 iAl~dI~~Ge~V-iKYG~ 58 (507)
T TIGR03248 42 VALVDLAKGTAI-IRYGE 58 (507)
T ss_pred EEecccCCCCee-EECCc
Confidence 788999999887 46764
No 39
>PF03896 TRAP_alpha: Translocon-associated protein (TRAP), alpha subunit; InterPro: IPR005595 The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane [].; GO: 0005783 endoplasmic reticulum
Probab=54.75 E-value=8.6 Score=24.99 Aligned_cols=19 Identities=37% Similarity=0.789 Sum_probs=16.3
Q ss_pred cCCCCCCCeEEEEcCCCCC
Q 046259 23 KTNVSAGDELTYDYLFDPD 41 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~~ 41 (62)
.+.|+||+|.||.|.+...
T Consensus 143 ~~~V~pg~~aT~~YsF~~~ 161 (285)
T PF03896_consen 143 NREVPPGEEATFPYSFTPS 161 (285)
T ss_pred CcccCCCCeEEEEEEEecc
Confidence 4689999999999998653
No 40
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=53.98 E-value=9.1 Score=22.22 Aligned_cols=19 Identities=11% Similarity=0.092 Sum_probs=14.7
Q ss_pred EEEEEEcCCCCCCCeEEEE
Q 046259 17 RIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~d 35 (62)
.=.++|.|+|.+||-|+=+
T Consensus 19 ~~VvVA~r~L~rGevIt~~ 37 (141)
T PRK12618 19 AETVVAARTIRALTVIGAE 37 (141)
T ss_pred eEEEEEccCcCCCCCcCHH
Confidence 3457899999999987643
No 41
>KOG1631 consensus Translocon-associated complex TRAP, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.92 E-value=8.4 Score=24.65 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=16.5
Q ss_pred cCCCCCCCeEEEEcCCCCCC
Q 046259 23 KTNVSAGDELTYDYLFDPDE 42 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~~~ 42 (62)
.|.|++++|.|++|++-..+
T Consensus 120 N~~Vpp~~qaT~~Y~F~~se 139 (261)
T KOG1631|consen 120 NRSVPPSEQATLPYGFAVSE 139 (261)
T ss_pred cccCCCcceeeeeeeeeehh
Confidence 48899999999999975433
No 42
>PF13780 DUF4176: Domain of unknown function (DUF4176)
Probab=53.81 E-value=29 Score=18.10 Aligned_cols=33 Identities=15% Similarity=0.483 Sum_probs=23.8
Q ss_pred EEEeCCCccEEEEEEcCCCC-CCCeEEEEcCCCC
Q 046259 8 IMSVGDDESRIVLIAKTNVS-AGDELTYDYLFDP 40 (62)
Q Consensus 8 ~v~~~~~~~~i~i~A~rdI~-~GeELt~dY~~~~ 40 (62)
+|.+.+....+.|+..+-+. .+++-.|||..-.
T Consensus 7 VV~L~~~~~~~mI~gR~~~~~~~~~~~~DY~g~~ 40 (76)
T PF13780_consen 7 VVELKGGTKKVMIIGRKQIIEEGTKKYFDYVGCP 40 (76)
T ss_pred EEEECCCCccEEEEEEEEeeecCCcEEEeeeEEe
Confidence 45555556667777777777 8999999997543
No 43
>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=53.63 E-value=8.4 Score=24.18 Aligned_cols=21 Identities=24% Similarity=0.401 Sum_probs=17.3
Q ss_pred ccEEEEEEcCCCCCCCeEEEE
Q 046259 15 ESRIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~d 35 (62)
...-.++|.|||.+|+.|+=+
T Consensus 34 ~~~~V~VA~~~I~~G~~I~~~ 54 (261)
T TIGR03177 34 PTVPVVVAARDLPAGTPITAE 54 (261)
T ss_pred CceeEEEEcccCCCCCCCCHH
Confidence 455678999999999998844
No 44
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=53.07 E-value=24 Score=20.16 Aligned_cols=24 Identities=33% Similarity=0.582 Sum_probs=14.8
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~ 38 (62)
..+...+++.++++|+.|-+.|..
T Consensus 79 ~~~~~~~~~p~v~~GdiIe~~y~~ 102 (177)
T PF12969_consen 79 DSRTKVFAFPDVRVGDIIEYSYTI 102 (177)
T ss_dssp T-EEEEEE--S--TT-EEEEEEEE
T ss_pred CcEEEEEEcCCCCCCcEEEEEEEE
Confidence 356677999999999999999865
No 45
>PF10989 DUF2808: Protein of unknown function (DUF2808); InterPro: IPR021256 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=52.22 E-value=44 Score=19.21 Aligned_cols=28 Identities=18% Similarity=0.238 Sum_probs=23.3
Q ss_pred EEeCCCccEEEEEEcCCCCCCCeEEEEc
Q 046259 9 MSVGDDESRIVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 9 v~~~~~~~~i~i~A~rdI~~GeELt~dY 36 (62)
+.++.....|.|+--..|.||+.+|+.-
T Consensus 82 v~~~~~~~~i~I~f~~PV~pG~tv~V~l 109 (146)
T PF10989_consen 82 VEWDEDGRTITITFDEPVPPGTTVTVVL 109 (146)
T ss_pred EEEcCCCCEEEEEeCCCCCCCCEEEEEE
Confidence 4455457889999999999999999987
No 46
>COG3831 Uncharacterized conserved protein [Function unknown]
Probab=52.12 E-value=37 Score=18.32 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=15.1
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~ 38 (62)
..+....++. |.||+.+||-
T Consensus 14 ~~kFy~~~i~----g~~L~~~wGR 33 (85)
T COG3831 14 MAKFYAVEIE----GAELTRNWGR 33 (85)
T ss_pred ccceEEEEEe----cceeEEeecc
Confidence 5565566665 9999999984
No 47
>cd01758 PLAT_LPL PLAT/ LH2 domain present in lipoprotein lipase (LPL). LPL is a key enzyme in catabolism of plasma lipoprotein triglycerides (TGs) and has therefeore has a profound influence on triglyceride and high-density lipoprotein (HDL) cholesterol levels in the blood. In general, PLAT/LH2 domain's proposed function is to mediate interaction with lipids or membrane bound proteins.
Probab=50.29 E-value=44 Score=19.32 Aligned_cols=9 Identities=22% Similarity=0.169 Sum_probs=3.8
Q ss_pred ceEEEEEEe
Q 046259 3 NCYARIMSV 11 (62)
Q Consensus 3 Nc~~~~v~~ 11 (62)
...++.+.|
T Consensus 97 ~l~~~~I~V 105 (137)
T cd01758 97 GLTIRKIRV 105 (137)
T ss_pred eEEEEEEEE
Confidence 334444444
No 48
>KOG2155 consensus Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=50.26 E-value=9.8 Score=26.81 Aligned_cols=39 Identities=18% Similarity=0.227 Sum_probs=26.9
Q ss_pred CCceEEEEEEeCCC-ccEEEEEEcCCCCCCCeEEEEcCCC
Q 046259 1 MPNCYARIMSVGDD-ESRIVLIAKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 1 ~PNc~~~~v~~~~~-~~~i~i~A~rdI~~GeELt~dY~~~ 39 (62)
+||-.+.....-.. ...-.++-+|+...|||+|-|+...
T Consensus 213 ePnf~~aPf~fmPq~vaYsimwp~k~~~tgeE~trDfasg 252 (631)
T KOG2155|consen 213 EPNFRIAPFMFMPQNVAYSIMWPTKPVNTGEEITRDFASG 252 (631)
T ss_pred CCcceeeeheecchhcceeEEeeccCCCCchHHHHHHhhc
Confidence 46666554443221 3345589999999999999997654
No 49
>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=48.58 E-value=27 Score=16.78 Aligned_cols=15 Identities=13% Similarity=0.173 Sum_probs=11.9
Q ss_pred EEcCCCCCCCeEEEE
Q 046259 21 IAKTNVSAGDELTYD 35 (62)
Q Consensus 21 ~A~rdI~~GeELt~d 35 (62)
....-+++|++|+++
T Consensus 45 ~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 45 RRGKKLYPGDVIEIP 59 (59)
T ss_pred CCCCCCCCCCEEEeC
Confidence 446788999999875
No 50
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=48.42 E-value=18 Score=18.69 Aligned_cols=14 Identities=21% Similarity=0.764 Sum_probs=11.8
Q ss_pred CCCCCCCeEEEEcC
Q 046259 24 TNVSAGDELTYDYL 37 (62)
Q Consensus 24 rdI~~GeELt~dY~ 37 (62)
..|+||+..+|-|-
T Consensus 65 ~~i~pg~s~~FGYI 78 (80)
T PF09478_consen 65 PTIKPGQSFTFGYI 78 (80)
T ss_pred cccCCCCEEEEEEE
Confidence 48999999999884
No 51
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=46.80 E-value=25 Score=17.90 Aligned_cols=22 Identities=5% Similarity=0.152 Sum_probs=13.7
Q ss_pred ccEEEEEEcCCCCCCCeEEEEc
Q 046259 15 ESRIVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY 36 (62)
...=.+|+.|.|+.||.+.+--
T Consensus 28 f~~giVFS~rPl~~~E~~~v~I 49 (69)
T PF07177_consen 28 FNNGIVFSSRPLRIGEKFEVRI 49 (69)
T ss_dssp SSS-EEEESS-B-TT-EEEEEE
T ss_pred CCceEEEecCCccCCCEEEEEE
Confidence 3445689999999999877753
No 52
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=46.18 E-value=13 Score=23.12 Aligned_cols=17 Identities=18% Similarity=0.382 Sum_probs=14.3
Q ss_pred EEEEEEcCCCCCCCeEE
Q 046259 17 RIVLIAKTNVSAGDELT 33 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt 33 (62)
.-+++|.|+|++|+.|+
T Consensus 110 ~~VvVA~r~I~rG~~I~ 126 (235)
T PRK07018 110 GPYVVAARPLARGEKLS 126 (235)
T ss_pred EEEEEEccccCCCCCcC
Confidence 34578999999999987
No 53
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=46.10 E-value=11 Score=18.94 Aligned_cols=16 Identities=13% Similarity=0.219 Sum_probs=11.8
Q ss_pred EcCCCCCCCeEEEEcC
Q 046259 22 AKTNVSAGDELTYDYL 37 (62)
Q Consensus 22 A~rdI~~GeELt~dY~ 37 (62)
|++.+++|++|.+-=.
T Consensus 19 al~~l~~G~~l~V~~d 34 (69)
T cd03420 19 EIDKLQDGEQLEVKAS 34 (69)
T ss_pred HHHcCCCCCEEEEEEC
Confidence 5788999998776443
No 54
>PF09544 DUF2381: Protein of unknown function (DUF2381); InterPro: IPR011754 This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.
Probab=45.13 E-value=83 Score=20.42 Aligned_cols=25 Identities=20% Similarity=0.458 Sum_probs=21.8
Q ss_pred ccEEEEEEcCCCCCCC--eEEEEcCCC
Q 046259 15 ESRIVLIAKTNVSAGD--ELTYDYLFD 39 (62)
Q Consensus 15 ~~~i~i~A~rdI~~Ge--ELt~dY~~~ 39 (62)
...+.+....|+.+|| +|++-|.+.
T Consensus 73 ~~~l~L~P~~~l~~ger~~L~V~f~dg 99 (289)
T PF09544_consen 73 ERSLILVPSEDLPEGERLPLTVRFADG 99 (289)
T ss_pred CCEEEEEECccCCCCCceEEEEEECCC
Confidence 5789999999999999 888888764
No 55
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=44.86 E-value=25 Score=18.74 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=19.7
Q ss_pred EEcCCCCCCCeEEEEcCCCCCCC------CCceEEEecCCC
Q 046259 21 IAKTNVSAGDELTYDYLFDPDEP------EEFKVPCLCKAP 55 (62)
Q Consensus 21 ~A~rdI~~GeELt~dY~~~~~~~------~~~~~~C~Cgs~ 55 (62)
+..+++.-=+.+|+||....... ......|-||+.
T Consensus 62 id~~~~~~l~~~~IDy~~~~~~~~f~i~nPn~~~~c~cg~s 102 (105)
T TIGR00049 62 VDPKSLPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKS 102 (105)
T ss_pred EeHHHHhhhCCCEEEEeecCCcceEEEECCCCCccCCCCcC
Confidence 33444444456888886643221 223467999974
No 56
>PF13144 SAF_2: SAF-like
Probab=44.75 E-value=13 Score=22.07 Aligned_cols=21 Identities=38% Similarity=0.396 Sum_probs=15.3
Q ss_pred EEEEEEcCCCCCCCeEEEEcC
Q 046259 17 RIVLIAKTNVSAGDELTYDYL 37 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~dY~ 37 (62)
-++..|.|+|.+|+-||-++-
T Consensus 114 ~~G~~a~r~i~~G~~i~~~~l 134 (196)
T PF13144_consen 114 LIGKVAKRNIRAGQPITPSDL 134 (196)
T ss_pred hCCeEEEEEcCCCCEeeeccc
Confidence 456777777888877777764
No 57
>PLN02311 chalcone isomerase
Probab=44.31 E-value=14 Score=23.89 Aligned_cols=20 Identities=5% Similarity=0.260 Sum_probs=16.9
Q ss_pred EEEEcCCCCCCCeEEEEcCC
Q 046259 19 VLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 19 ~i~A~rdI~~GeELt~dY~~ 38 (62)
.+|.-++|++|++|+|+|..
T Consensus 195 ~~F~~~~l~kGd~I~~~~~p 214 (271)
T PLN02311 195 SIFQNRSLNKGTVIFLTWIN 214 (271)
T ss_pred HHhcCCCCCCCCEEEEEEeC
Confidence 46777899999999999964
No 58
>COG4091 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=43.41 E-value=14 Score=25.27 Aligned_cols=17 Identities=29% Similarity=0.515 Sum_probs=14.0
Q ss_pred EEcCCCCCCCeEEEEcC
Q 046259 21 IAKTNVSAGDELTYDYL 37 (62)
Q Consensus 21 ~A~rdI~~GeELt~dY~ 37 (62)
.-.|+|++||-||||=-
T Consensus 395 ~v~rpIkKge~iTyddv 411 (438)
T COG4091 395 KVKRPIKKGELITYDDV 411 (438)
T ss_pred eEecccCCCcEEecccc
Confidence 34679999999999853
No 59
>PF02810 SEC-C: SEC-C motif; InterPro: IPR004027 The SEC-C motif found in the C terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain.; PDB: 1OZB_J 1TM6_A 2I9W_A 2JQ5_A.
Probab=42.52 E-value=6.4 Score=15.72 Aligned_cols=9 Identities=33% Similarity=0.910 Sum_probs=6.4
Q ss_pred EEEecCCCC
Q 046259 48 VPCLCKAPN 56 (62)
Q Consensus 48 ~~C~Cgs~~ 56 (62)
..|-|||.+
T Consensus 3 ~~CpCgSg~ 11 (21)
T PF02810_consen 3 DPCPCGSGK 11 (21)
T ss_dssp SBTTTSCSS
T ss_pred CcCcCCCCc
Confidence 358899864
No 60
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=41.89 E-value=42 Score=15.93 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=19.6
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~~ 39 (62)
.--+-+-...+.+.|||+.|+-...
T Consensus 15 GeF~~ik~~~~~~vG~eI~~~~~~~ 39 (56)
T PF12791_consen 15 GEFIKIKRKPGMEVGQEIEFDEKDI 39 (56)
T ss_pred CcEEEEeCCCCCcccCEEEEechhh
Confidence 4566677788899999999987543
No 61
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=41.88 E-value=17 Score=22.56 Aligned_cols=18 Identities=28% Similarity=0.218 Sum_probs=15.0
Q ss_pred EEEEEEcCCCCCCCeEEE
Q 046259 17 RIVLIAKTNVSAGDELTY 34 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~ 34 (62)
.=+++|.|.|.+||-|+-
T Consensus 100 ~~v~Va~r~i~rG~~I~~ 117 (222)
T PRK08515 100 LEVLKSIRAIKKDDNLTA 117 (222)
T ss_pred EEEEEEccccCCCCCCCH
Confidence 345899999999999874
No 62
>PF13715 DUF4480: Domain of unknown function (DUF4480)
Probab=41.05 E-value=29 Score=17.62 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=16.6
Q ss_pred EEEEEEcCCCCCCC-eEEEEcCC
Q 046259 17 RIVLIAKTNVSAGD-ELTYDYLF 38 (62)
Q Consensus 17 ~i~i~A~rdI~~Ge-ELt~dY~~ 38 (62)
.-|.|.+. +++|+ .|.|.|-.
T Consensus 33 ~~G~F~i~-~~~g~~~l~is~~G 54 (88)
T PF13715_consen 33 ENGRFSIK-LPEGDYTLKISYIG 54 (88)
T ss_pred CCeEEEEE-EcCCCeEEEEEEeC
Confidence 35678888 88998 99999743
No 63
>cd08759 Type_III_cohesin_like Cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents type III cohesins and closely related domains.
Probab=40.97 E-value=40 Score=20.18 Aligned_cols=17 Identities=47% Similarity=0.618 Sum_probs=13.2
Q ss_pred cCCCCCCCeEEEE-cCCC
Q 046259 23 KTNVSAGDELTYD-YLFD 39 (62)
Q Consensus 23 ~rdI~~GeELt~d-Y~~~ 39 (62)
..++++||.+|++ |+..
T Consensus 9 k~~~~aGetvti~vkg~~ 26 (160)
T cd08759 9 KTTVKAGETITIDLYGQG 26 (160)
T ss_pred ccccCCCCEEEEEEEecc
Confidence 4458999999999 5544
No 64
>PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional
Probab=40.51 E-value=19 Score=19.85 Aligned_cols=26 Identities=19% Similarity=0.280 Sum_probs=14.3
Q ss_pred CeEEEEcCCCCCCC------CCceEEEecCCC
Q 046259 30 DELTYDYLFDPDEP------EEFKVPCLCKAP 55 (62)
Q Consensus 30 eELt~dY~~~~~~~------~~~~~~C~Cgs~ 55 (62)
+.+|+||....... ......|-||+.
T Consensus 81 ~g~~IDy~~~~~~~~F~f~NPn~~~~CgCg~S 112 (115)
T PRK13623 81 VGAEVDYTEGLEGSRFVIKNPNAKTTCGCGSS 112 (115)
T ss_pred CCCEEEeecCCCcceEEEECCCCCcCCCCCcC
Confidence 34677776543221 123466999863
No 65
>PF06483 ChiC: Chitinase C; InterPro: IPR009470 This ~170 aa region is found at the C-terminal to the catalytic domain (IPR001223 from INTERPRO) found in members of glycoside hydrolase family 18.
Probab=39.49 E-value=24 Score=21.60 Aligned_cols=25 Identities=16% Similarity=0.486 Sum_probs=19.2
Q ss_pred cEEEE--EEcCCCCCCCeEEEEcCCCC
Q 046259 16 SRIVL--IAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 16 ~~i~i--~A~rdI~~GeELt~dY~~~~ 40 (62)
+.|.| -+-++|.-|.|+.|||....
T Consensus 56 Pkl~iTNns~~~iPGGt~~~FD~ptSa 82 (180)
T PF06483_consen 56 PKLTITNNSGQTIPGGTEFEFDYPTSA 82 (180)
T ss_pred CcEEEEcCCCcccCCccEEEEccccCC
Confidence 44544 35789999999999998654
No 66
>TIGR02268 Myxococcus xanthus paralogous family TIGR02268. This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.
Probab=39.39 E-value=1.1e+02 Score=20.24 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=22.8
Q ss_pred CccEEEEEEcCCCCCCC--eEEEEcCCCC
Q 046259 14 DESRIVLIAKTNVSAGD--ELTYDYLFDP 40 (62)
Q Consensus 14 ~~~~i~i~A~rdI~~Ge--ELt~dY~~~~ 40 (62)
+..++.+....++.+|| +|++-|.+..
T Consensus 76 g~~~l~L~P~~~L~~gERl~L~V~F~DGa 104 (295)
T TIGR02268 76 TETHLILVPSEALPEGERLPLTVRFADGA 104 (295)
T ss_pred CCcEEEEEEccccCCCCceEEEEEEcCCC
Confidence 35789999999999999 8888887643
No 67
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=39.33 E-value=50 Score=16.15 Aligned_cols=25 Identities=8% Similarity=0.211 Sum_probs=18.8
Q ss_pred ceEEEEEEeCCCccEEEEEEcCCCC
Q 046259 3 NCYARIMSVGDDESRIVLIAKTNVS 27 (62)
Q Consensus 3 Nc~~~~v~~~~~~~~i~i~A~rdI~ 27 (62)
|-.+.++.+.++.-+++|-|-++++
T Consensus 17 ~I~I~Vl~i~~~~VklgI~AP~~v~ 41 (54)
T PF02599_consen 17 DIEITVLEISGGQVKLGIDAPKEVP 41 (54)
T ss_dssp TEEEEEEEEETTEEEEEEEECTTSE
T ss_pred CEEEEEEEEcCCEEEEEEECCCCCE
Confidence 4456666676667899999998875
No 68
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=38.53 E-value=31 Score=20.01 Aligned_cols=20 Identities=20% Similarity=-0.037 Sum_probs=17.5
Q ss_pred EEEcCCCCCCCeEEEEcCCC
Q 046259 20 LIAKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 20 i~A~rdI~~GeELt~dY~~~ 39 (62)
.-+.+.+++|++|++.++..
T Consensus 43 ~Kps~~V~~gd~l~v~~~~~ 62 (133)
T PRK10348 43 SKPSKIVELNATLTLRQGND 62 (133)
T ss_pred CCCCCccCCCCEEEEEECCE
Confidence 57889999999999999864
No 69
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=37.47 E-value=24 Score=19.13 Aligned_cols=27 Identities=19% Similarity=0.276 Sum_probs=13.6
Q ss_pred CCeEEEEcCCCCCCC------CCceEEEecCCC
Q 046259 29 GDELTYDYLFDPDEP------EEFKVPCLCKAP 55 (62)
Q Consensus 29 GeELt~dY~~~~~~~------~~~~~~C~Cgs~ 55 (62)
=+..|+||..+.... ......|-||+.
T Consensus 70 l~g~~IDy~~~~~~~~F~~~nPna~~~CgCg~S 102 (105)
T TIGR02011 70 LDGTQLDFVKEGLNEGFKFTNPNVKDECGCGES 102 (105)
T ss_pred hCCCEEEEecCCCcceEEEECCCCCccCCCCCC
Confidence 344566775432110 122356999853
No 70
>PRK00568 carbon storage regulator; Provisional
Probab=36.85 E-value=68 Score=16.93 Aligned_cols=26 Identities=15% Similarity=0.202 Sum_probs=20.2
Q ss_pred ceEEEEEEeCCCccEEEEEEcCCCCC
Q 046259 3 NCYARIMSVGDDESRIVLIAKTNVSA 28 (62)
Q Consensus 3 Nc~~~~v~~~~~~~~i~i~A~rdI~~ 28 (62)
|-.+.++.+.++.-+++|-|-+++.-
T Consensus 17 ~I~I~Vl~i~g~~VrlGI~AP~~v~I 42 (76)
T PRK00568 17 NIHIKVISIDRGSVRLGFEAPESTLI 42 (76)
T ss_pred CeEEEEEEEcCCEEEEEEECCCCCeE
Confidence 45567777777788999999998863
No 71
>KOG2943 consensus Predicted glyoxalase [Carbohydrate transport and metabolism]
Probab=36.80 E-value=21 Score=23.19 Aligned_cols=12 Identities=50% Similarity=0.675 Sum_probs=9.3
Q ss_pred eEEEEcCCCCCC
Q 046259 31 ELTYDYLFDPDE 42 (62)
Q Consensus 31 ELt~dY~~~~~~ 42 (62)
||||+|+-..++
T Consensus 82 ELTYNYgV~~Ye 93 (299)
T KOG2943|consen 82 ELTYNYGVSKYE 93 (299)
T ss_pred EEEeccCcccee
Confidence 899999876544
No 72
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.68 E-value=29 Score=24.11 Aligned_cols=23 Identities=22% Similarity=0.371 Sum_probs=19.9
Q ss_pred cEEEEEEcCCCCCCCeEEEEcCC
Q 046259 16 SRIVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~dY~~ 38 (62)
.-+-++|.|+|++|+|+--.|+.
T Consensus 238 NcL~mva~r~iekgdev~n~dg~ 260 (466)
T KOG1338|consen 238 NCLEMVADRNIEKGDEVDNSDGL 260 (466)
T ss_pred cceeeeecCCCCCcccccccccc
Confidence 45678999999999999988974
No 73
>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=36.41 E-value=32 Score=19.25 Aligned_cols=12 Identities=17% Similarity=0.703 Sum_probs=10.7
Q ss_pred CCCCCCCeEEEE
Q 046259 24 TNVSAGDELTYD 35 (62)
Q Consensus 24 rdI~~GeELt~d 35 (62)
++|++|+.|.|.
T Consensus 30 ~~ikvGD~I~f~ 41 (109)
T cd06555 30 QQIKVGDKILFN 41 (109)
T ss_pred hcCCCCCEEEEE
Confidence 579999999995
No 74
>PF03173 CHB_HEX: Putative carbohydrate binding domain; InterPro: IPR004866 This domain represents the N-terminal domain in chitobiases and beta-hexosaminidases 3.2.1.52 from EC. Chitobiases degrade chitin, which forms the exoskeleton in insects and crustaceans, and which is one of the most abundant polysaccharides on earth []. Beta-hexosaminidases are composed of either a HexA/HexB heterodimer or a HexB homodimer, and can hydrolyse diverse substrates, including GM(2)-gangliosides; mutations in this enzyme are associated with Tay-Sachs disease []. HexB is structurally similar to chitobiase, consisting of a beta sandwich structure; this structure is similar to that found in the cellulose-binding domain of cellulase from Cellulomonas fimi (IPR001919 from INTERPRO), suggesting that it may function as a carbohydrate-binding domain.; GO: 0030246 carbohydrate binding; PDB: 1C7T_A 1QBA_A 1QBB_A 1C7S_A.
Probab=35.95 E-value=55 Score=19.54 Aligned_cols=34 Identities=15% Similarity=0.239 Sum_probs=20.0
Q ss_pred EEEeCCCccEEEEEEc-CCCCCCCeEEEEcCCCCC
Q 046259 8 IMSVGDDESRIVLIAK-TNVSAGDELTYDYLFDPD 41 (62)
Q Consensus 8 ~v~~~~~~~~i~i~A~-rdI~~GeELt~dY~~~~~ 41 (62)
+-.++++.++|.--+. +-|+|||.+++.|-...+
T Consensus 71 i~hinGDl~kl~Pt~~F~gl~~Ges~~I~~~~~~w 105 (164)
T PF03173_consen 71 ITHINGDLHKLTPTAGFKGLAPGESLEIPFVGEYW 105 (164)
T ss_dssp EEE-STTEEEEEE-TT---B-TTEEEEEEEEEES-
T ss_pred EEEEcCeEEEEeECCCCCccCCCCEEEEEEEcccc
Confidence 3445666777766664 679999999999865443
No 75
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=34.95 E-value=75 Score=17.29 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=16.1
Q ss_pred CccEEEEEEc-CCCCCCCeEEEEcCC
Q 046259 14 DESRIVLIAK-TNVSAGDELTYDYLF 38 (62)
Q Consensus 14 ~~~~i~i~A~-rdI~~GeELt~dY~~ 38 (62)
+.+++-|+-+ +.+++||.+.+.-.+
T Consensus 76 gg~HlmL~g~~~~l~~G~~v~ltL~f 101 (110)
T PF04314_consen 76 GGYHLMLMGLKRPLKPGDTVPLTLTF 101 (110)
T ss_dssp CCCEEEEECESS-B-TTEEEEEEEEE
T ss_pred CCEEEEEeCCcccCCCCCEEEEEEEE
Confidence 3578877774 778889887666544
No 76
>COG3848 Phosphohistidine swiveling domain [Signal transduction mechanisms]
Probab=34.91 E-value=27 Score=19.76 Aligned_cols=19 Identities=21% Similarity=0.044 Sum_probs=15.4
Q ss_pred EEEcCCCCCCCeEEEEcCC
Q 046259 20 LIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 20 i~A~rdI~~GeELt~dY~~ 38 (62)
=-|...|+.|+.+|+|=..
T Consensus 82 ~~at~~i~dG~~vTvD~~r 100 (111)
T COG3848 82 KKATQLIRDGAIVTVDAQR 100 (111)
T ss_pred cchhhhccCCCEEEEeccc
Confidence 3578899999999999543
No 77
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=34.87 E-value=27 Score=19.58 Aligned_cols=9 Identities=22% Similarity=0.619 Sum_probs=6.4
Q ss_pred eEEEecCCC
Q 046259 47 KVPCLCKAP 55 (62)
Q Consensus 47 ~~~C~Cgs~ 55 (62)
...|-||+.
T Consensus 111 ~~~CgCG~S 119 (122)
T PRK09504 111 QNECGCGES 119 (122)
T ss_pred CCCcCCCCC
Confidence 367999863
No 78
>PF03534 SpvB: Salmonella virulence plasmid 65kDa B protein
Probab=34.40 E-value=1.1e+02 Score=19.99 Aligned_cols=36 Identities=19% Similarity=0.244 Sum_probs=22.5
Q ss_pred EEEEEEeCCCccEEEEEEcCCCCCCC-----eEEEEcCCCC
Q 046259 5 YARIMSVGDDESRIVLIAKTNVSAGD-----ELTYDYLFDP 40 (62)
Q Consensus 5 ~~~~v~~~~~~~~i~i~A~rdI~~Ge-----ELt~dY~~~~ 40 (62)
+.+.|..++..+...+++...-.+.+ ||-|||+...
T Consensus 207 YL~~v~YGN~~~~~~l~~~~~~~~~~~~wlf~lvfDYGe~~ 247 (293)
T PF03534_consen 207 YLKRVRYGNRTPSADLYLWDSPDPSPEDWLFELVFDYGERD 247 (293)
T ss_pred EEEEEEECCCCccccceeeccCCCcccCeEEEEEEEcCCCC
Confidence 45566665545555666666644443 5999998643
No 79
>cd00404 Aconitase_swivel Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid.
Probab=34.11 E-value=29 Score=18.74 Aligned_cols=12 Identities=33% Similarity=0.476 Sum_probs=10.1
Q ss_pred CCCCCCCeEEEE
Q 046259 24 TNVSAGDELTYD 35 (62)
Q Consensus 24 rdI~~GeELt~d 35 (62)
..|+.|+||++|
T Consensus 76 ~~i~~gd~l~id 87 (88)
T cd00404 76 LKLHTGDELDIY 87 (88)
T ss_pred hhcCCCCEEEeC
Confidence 448999999986
No 80
>TIGR03230 lipo_lipase lipoprotein lipase. Members of this protein family are lipoprotein lipase (EC 3.1.1.34), a eukaryotic triacylglycerol lipase active in plasma and similar to pancreatic and hepatic triacylglycerol lipases (EC 3.1.1.3). It is also called clearing factor. It cleaves chylomicron and VLDL triacylglycerols; it also has phospholipase A-1 activity.
Probab=33.98 E-value=83 Score=21.75 Aligned_cols=9 Identities=11% Similarity=0.446 Sum_probs=4.1
Q ss_pred CCCCCeEEE
Q 046259 26 VSAGDELTY 34 (62)
Q Consensus 26 I~~GeELt~ 34 (62)
|++|||++|
T Consensus 423 ~~~~~~~~~ 431 (442)
T TIGR03230 423 QRGGEAAVF 431 (442)
T ss_pred ccCCcceeE
Confidence 344444444
No 81
>COG3884 FatA Acyl-ACP thioesterase [Lipid metabolism]
Probab=33.97 E-value=67 Score=20.70 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=21.9
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~~ 39 (62)
..++.+-=.+.+++|+-||+-|-..
T Consensus 193 p~r~~l~y~keva~G~~iti~~e~~ 217 (250)
T COG3884 193 PLRLTLEYVKEVAPGEKITIVYEVH 217 (250)
T ss_pred cceeEEEEEcccCCCCeEEEEEEEc
Confidence 5688889999999999999999654
No 82
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=33.26 E-value=42 Score=16.31 Aligned_cols=15 Identities=13% Similarity=0.357 Sum_probs=11.3
Q ss_pred CCCCCCCeEEEEcCC
Q 046259 24 TNVSAGDELTYDYLF 38 (62)
Q Consensus 24 rdI~~GeELt~dY~~ 38 (62)
+.+..|++++|....
T Consensus 39 ~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 39 RSLKEGDRVEFEVEE 53 (66)
T ss_dssp TS--TTSEEEEEEEE
T ss_pred ccCCCCCEEEEEEEE
Confidence 678899999999876
No 83
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=33.13 E-value=44 Score=17.45 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=12.6
Q ss_pred cCCCCCCCeEEEEcCC
Q 046259 23 KTNVSAGDELTYDYLF 38 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~ 38 (62)
.=+.+||+|..+.-+.
T Consensus 50 ~m~L~PGdEFeI~Lgr 65 (71)
T PF14250_consen 50 QMGLKPGDEFEIKLGR 65 (71)
T ss_pred HhCCCCCCEEEEEeCc
Confidence 4578999999887654
No 84
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=33.00 E-value=22 Score=18.53 Aligned_cols=16 Identities=19% Similarity=0.071 Sum_probs=12.6
Q ss_pred EcCCCCCCCeEEEEcC
Q 046259 22 AKTNVSAGDELTYDYL 37 (62)
Q Consensus 22 A~rdI~~GeELt~dY~ 37 (62)
|++++++||.|.+-=.
T Consensus 25 ~l~~m~~Ge~LeV~~d 40 (78)
T COG0425 25 ALAKLKPGEILEVIAD 40 (78)
T ss_pred HHHcCCCCCEEEEEec
Confidence 6789999999887543
No 85
>PHA00198 nonstructural protein
Probab=32.87 E-value=28 Score=18.64 Aligned_cols=14 Identities=0% Similarity=0.059 Sum_probs=11.2
Q ss_pred EEEEEEcCCCCCCC
Q 046259 17 RIVLIAKTNVSAGD 30 (62)
Q Consensus 17 ~i~i~A~rdI~~Ge 30 (62)
++-+|+++|++.+-
T Consensus 2 hmkvfSI~D~Kt~~ 15 (86)
T PHA00198 2 HMKVFSIFDIKTEI 15 (86)
T ss_pred ceEEEEEEeccccc
Confidence 46789999999873
No 86
>PF08040 NADH_oxidored: MNLL subunit; InterPro: IPR012575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the MNLL subunits of NADH:ubiquinone oxidoreductase complex []. MNLL subunit is one of the many subunits found in the complex and it contains a mitochondrial import sequence. However, the role of MNLL subunit is unclear [].; GO: 0003954 NADH dehydrogenase activity, 0005739 mitochondrion
Probab=32.79 E-value=11 Score=18.96 Aligned_cols=18 Identities=17% Similarity=0.493 Sum_probs=14.1
Q ss_pred EEEEEEcCCCCCCCeEEE
Q 046259 17 RIVLIAKTNVSAGDELTY 34 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~ 34 (62)
+-++|.-|..++|||.++
T Consensus 41 KSaLygrRelkpge~psW 58 (59)
T PF08040_consen 41 KSALYGRRELKPGEEPSW 58 (59)
T ss_pred hhhhccCCCCCCCCCCCC
Confidence 456777789999999765
No 87
>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=31.24 E-value=44 Score=16.89 Aligned_cols=16 Identities=13% Similarity=0.405 Sum_probs=11.7
Q ss_pred cCCCCCCCeEEEEcCC
Q 046259 23 KTNVSAGDELTYDYLF 38 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~ 38 (62)
+..+++|+.+.|....
T Consensus 40 l~~l~~Gd~V~F~~~~ 55 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFER 55 (70)
T ss_dssp ESS-STT-EEEEEEEE
T ss_pred hhcCCCCCEEEEEEEE
Confidence 5789999999998754
No 88
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=31.17 E-value=28 Score=21.97 Aligned_cols=25 Identities=24% Similarity=0.178 Sum_probs=15.2
Q ss_pred cEEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 16 SRIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
..+..+|+++=..=.-|||||++..
T Consensus 16 tt~l~~a~~~~~ev~alsfdYGQrh 40 (222)
T COG0603 16 TTCLAWAKKEGYEVHALTFDYGQRH 40 (222)
T ss_pred HHHHHHHHhcCCEEEEEEeeCCCCc
Confidence 4444555555433344899999864
No 89
>PF14100 PmoA: Methane oxygenase PmoA
Probab=30.61 E-value=37 Score=21.64 Aligned_cols=20 Identities=20% Similarity=0.238 Sum_probs=16.0
Q ss_pred EEcCCCCCCCeEEEEcCCCC
Q 046259 21 IAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 21 ~A~rdI~~GeELt~dY~~~~ 40 (62)
..-..|++|+.|++.|..-.
T Consensus 235 ~~~~~l~~G~~l~~rYr~~v 254 (271)
T PF14100_consen 235 DGPLTLPPGETLTLRYRVVV 254 (271)
T ss_pred cCceecCCCCeEEEEEEEEE
Confidence 44567999999999998643
No 90
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.56 E-value=40 Score=20.08 Aligned_cols=9 Identities=33% Similarity=0.910 Sum_probs=7.5
Q ss_pred EEEecCCCC
Q 046259 48 VPCLCKAPN 56 (62)
Q Consensus 48 ~~C~Cgs~~ 56 (62)
.+|.|||-+
T Consensus 135 dpC~CGsgk 143 (151)
T COG3012 135 DPCPCGSGK 143 (151)
T ss_pred CCccCCCCc
Confidence 899999853
No 91
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=30.55 E-value=47 Score=15.79 Aligned_cols=14 Identities=43% Similarity=0.665 Sum_probs=10.7
Q ss_pred cCCCCCCCeEEEEc
Q 046259 23 KTNVSAGDELTYDY 36 (62)
Q Consensus 23 ~rdI~~GeELt~dY 36 (62)
...+.+|+.|+|-=
T Consensus 5 ~~~~~~Gd~v~Yti 18 (53)
T TIGR01451 5 KTVATIGDTITYTI 18 (53)
T ss_pred ccccCCCCEEEEEE
Confidence 35678999998864
No 92
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=30.30 E-value=46 Score=17.83 Aligned_cols=17 Identities=24% Similarity=0.483 Sum_probs=13.8
Q ss_pred CCCCCCCeEEEEcCCCC
Q 046259 24 TNVSAGDELTYDYLFDP 40 (62)
Q Consensus 24 rdI~~GeELt~dY~~~~ 40 (62)
-+++.|+++++++....
T Consensus 51 ~~~~~Gd~V~Vsf~i~~ 67 (84)
T PF11325_consen 51 DNFQVGDEVKVSFNIEG 67 (84)
T ss_pred ccCCCCCEEEEEEEeec
Confidence 57899999999887643
No 93
>PF09956 DUF2190: Uncharacterized conserved protein (DUF2190); InterPro: IPR011231 This entry is represented by Bacteriophage VT1-Sakai, H0018. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised conserved proteins.
Probab=30.27 E-value=1e+02 Score=17.02 Aligned_cols=19 Identities=21% Similarity=0.237 Sum_probs=14.3
Q ss_pred EEEEEcCCCCCCCeEEEEc
Q 046259 18 IVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 18 i~i~A~rdI~~GeELt~dY 36 (62)
+.=+|..||++||+.+..=
T Consensus 30 ~~GVA~~~~~~Ge~g~~~~ 48 (106)
T PF09956_consen 30 LFGVALTDAAAGETGELHT 48 (106)
T ss_pred EEEEEeeccCCCCeEEEEE
Confidence 4557888999999877653
No 94
>cd00918 Der-p2_like Several group 2 allergen proteins belong to the ML domain family. They include Dermatophagoides pteronyssinus, group 2 (Der p 2) and D. farinae, group 2 (Der f 2) allergens. These house dust mites cause heavy atopic diseases such as asthma and dermatitis. Although the allergenic properties of these proteins have been well characterized, their biological function in mites is unknown.
Probab=30.17 E-value=37 Score=19.09 Aligned_cols=18 Identities=17% Similarity=0.423 Sum_probs=15.3
Q ss_pred cCCCCCCCeEEEEcCCCC
Q 046259 23 KTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~ 40 (62)
...|++||..+|.|....
T Consensus 72 ~CPl~~G~~~~y~~~~~V 89 (120)
T cd00918 72 KCPIKKGQHYDIKYTWNV 89 (120)
T ss_pred eCCCcCCcEEEEEEeeec
Confidence 788999999999997643
No 95
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.13 E-value=40 Score=15.69 Aligned_cols=10 Identities=30% Similarity=0.411 Sum_probs=6.3
Q ss_pred ceEEE-ecCCC
Q 046259 46 FKVPC-LCKAP 55 (62)
Q Consensus 46 ~~~~C-~Cgs~ 55 (62)
..+.| .||+.
T Consensus 18 ~~irC~~CG~r 28 (44)
T smart00659 18 DVVRCRECGYR 28 (44)
T ss_pred CceECCCCCce
Confidence 45777 57764
No 96
>KOG3851 consensus Sulfide:quinone oxidoreductase/flavo-binding protein [Energy production and conversion]
Probab=30.00 E-value=31 Score=23.60 Aligned_cols=11 Identities=55% Similarity=1.265 Sum_probs=9.3
Q ss_pred CCCCeEEEEcC
Q 046259 27 SAGDELTYDYL 37 (62)
Q Consensus 27 ~~GeELt~dY~ 37 (62)
.-||||+|||-
T Consensus 127 ~gg~eIsYdyl 137 (446)
T KOG3851|consen 127 RGGEEISYDYL 137 (446)
T ss_pred cCCcEEeeeeE
Confidence 46999999994
No 97
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=29.84 E-value=25 Score=15.40 Aligned_cols=10 Identities=30% Similarity=0.587 Sum_probs=7.5
Q ss_pred CCCCCCeEEE
Q 046259 25 NVSAGDELTY 34 (62)
Q Consensus 25 dI~~GeELt~ 34 (62)
+|.+|++|.+
T Consensus 34 ~l~~G~~l~i 43 (44)
T PF01476_consen 34 NLQPGQKLCI 43 (44)
T ss_dssp CGGTTEEEEE
T ss_pred cCCCCCEEEe
Confidence 3788888875
No 98
>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=29.76 E-value=48 Score=16.43 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=9.0
Q ss_pred CCCCCCCeEEE
Q 046259 24 TNVSAGDELTY 34 (62)
Q Consensus 24 rdI~~GeELt~ 34 (62)
-+|++|+|+.+
T Consensus 37 ~~i~~G~eV~y 47 (57)
T cd04467 37 DKLEPGKEVEY 47 (57)
T ss_pred ccCCCCCEEEE
Confidence 47999999873
No 99
>cd01579 AcnA_Bact_Swivel Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. This distinct subfamily is found only in bacteria and archea. Its exact characteristics are not known.
Probab=29.38 E-value=34 Score=19.43 Aligned_cols=11 Identities=27% Similarity=0.504 Sum_probs=9.7
Q ss_pred CCCCCCeEEEE
Q 046259 25 NVSAGDELTYD 35 (62)
Q Consensus 25 dI~~GeELt~d 35 (62)
.++.|+||++|
T Consensus 110 ~~~~gd~i~id 120 (121)
T cd01579 110 RFEQGDQLELP 120 (121)
T ss_pred hcCCCCEEEcC
Confidence 48999999987
No 100
>COG1261 FlgA Flagellar basal body P-ring biosynthesis protein [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=29.28 E-value=35 Score=21.41 Aligned_cols=19 Identities=16% Similarity=0.361 Sum_probs=15.8
Q ss_pred cEEEEEEcCCCCCCCeEEE
Q 046259 16 SRIVLIAKTNVSAGDELTY 34 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~ 34 (62)
+.-.+.|.|.|++||-|+.
T Consensus 94 ~~~~~va~r~I~~Ge~i~a 112 (220)
T COG1261 94 PGEVVVAARTIYRGEKISA 112 (220)
T ss_pred cceEEEEecccCCCCccCh
Confidence 4467899999999998873
No 101
>PF10442 FIST_C: FIST C domain; InterPro: IPR019494 This entry represents a novel sensory domain, designated FIST C (short for F-box and intracellular signal transduction, C-terminal), which is present in signal transduction proteins from bacteria, archaea and eukaryotes. The chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [].
Probab=28.92 E-value=1.1e+02 Score=16.79 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=16.7
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~ 38 (62)
...|.++ .+|+.|++|.+-+..
T Consensus 47 ~gsl~~~--~~v~eG~~v~l~~~~ 68 (136)
T PF10442_consen 47 DGSLTFA--GDVPEGSEVQLMEGD 68 (136)
T ss_pred CCEEEEe--eecCCCCEEEEEcCC
Confidence 4556444 489999999998865
No 102
>PF09044 Kp4: Kp4; InterPro: IPR015131 Killer toxins are polypeptides secreted by some fungal species that kill sensitive cells of the same or related species, often functioning by creating pores in target cell membranes. The fungal killer toxin KP4 from the corn smut fungus, Ustilago maydis (Smut fungus), is encoded by a resident symbiotic double-stranded RNA virus, Ustilago maydis P4 virus (UmV4), within fungal cells. Unlike most killer toxins, KP4 is a single polypeptide []. KP4 inhibits voltage-gated calcium channels in mammalian cells, which in turn inhibits cell growth and division by blocking calcium import. KP4 adopts a structure consisting of a two-layer alpha/beta sandwich with a left-handed crossover []. ; PDB: 1KPT_B.
Probab=28.57 E-value=35 Score=19.76 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=7.0
Q ss_pred CCCCCCCeEEEEcCC
Q 046259 24 TNVSAGDELTYDYLF 38 (62)
Q Consensus 24 rdI~~GeELt~dY~~ 38 (62)
.|+..| |||+||-.
T Consensus 113 NdV~~G-eLTvN~V~ 126 (128)
T PF09044_consen 113 NDVSNG-ELTVNYVD 126 (128)
T ss_dssp --GGG--EEEEEEE-
T ss_pred CcccCC-eEEEEEec
Confidence 344444 68998853
No 103
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=28.47 E-value=28 Score=17.73 Aligned_cols=8 Identities=38% Similarity=1.078 Sum_probs=5.3
Q ss_pred eEEEecCC
Q 046259 47 KVPCLCKA 54 (62)
Q Consensus 47 ~~~C~Cgs 54 (62)
-++|-||.
T Consensus 22 tyPCPCGD 29 (67)
T COG5216 22 TYPCPCGD 29 (67)
T ss_pred EecCCCCC
Confidence 46777774
No 104
>PF07081 DUF1349: Protein of unknown function (DUF1349); InterPro: IPR009784 This family consists of several hypothetical bacterial proteins but contains one sequence (P40893 from SWISSPROT) from Saccharomyces cerevisiae. Members of this family are typically around 200 residues in length. The function of this family is unknown.; PDB: 3MEP_B 3O12_A.
Probab=28.34 E-value=88 Score=18.64 Aligned_cols=23 Identities=22% Similarity=0.299 Sum_probs=16.3
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYL 37 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~ 37 (62)
..++|++|.+....|-+..|++-
T Consensus 151 ~~~VG~~A~sP~~~g~~~~F~~f 173 (183)
T PF07081_consen 151 EVQVGVYACSPQGEGFEVEFDDF 173 (183)
T ss_dssp -EEEEEEEE-SSSS--EEEEEEE
T ss_pred cEEEEEEEeCCCCCcEEEEEeEE
Confidence 67899999999988888888863
No 105
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.16 E-value=40 Score=21.62 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=14.7
Q ss_pred EEEEEEcCCCCCCCeEEEE
Q 046259 17 RIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~d 35 (62)
.=+++|.|+|.+||-|+-+
T Consensus 136 ~~VvVA~r~L~rG~~I~~~ 154 (261)
T PRK06804 136 LPVWVAKQTLERGRKVQAD 154 (261)
T ss_pred EEEEEEccCcCCCCCcCHH
Confidence 3457899999999987643
No 106
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=28.16 E-value=55 Score=18.29 Aligned_cols=20 Identities=20% Similarity=0.584 Sum_probs=15.6
Q ss_pred EEEEEcCCCCCCCeEEEEcC
Q 046259 18 IVLIAKTNVSAGDELTYDYL 37 (62)
Q Consensus 18 i~i~A~rdI~~GeELt~dY~ 37 (62)
+...=.=|.++|++++||=-
T Consensus 19 ~i~vEkl~~e~g~~v~f~~V 38 (103)
T COG0261 19 VIKVEKLDAEPGDKVEFDEV 38 (103)
T ss_pred EEEEEEcCCCCCCEEEEEEE
Confidence 44566778999999999854
No 107
>PRK14998 cold shock-like protein CspD; Provisional
Probab=28.13 E-value=65 Score=16.52 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=14.9
Q ss_pred cCCCCCCCeEEEEcCCCC
Q 046259 23 KTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~ 40 (62)
.+.+.+|+.++|+.....
T Consensus 39 ~~~l~~G~~V~f~~~~~~ 56 (73)
T PRK14998 39 YRTLKAGQSVRFDVHQGP 56 (73)
T ss_pred CCCCCCCCEEEEEEEECC
Confidence 378999999999987653
No 108
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=27.98 E-value=31 Score=17.23 Aligned_cols=15 Identities=20% Similarity=0.162 Sum_probs=10.9
Q ss_pred EcCCCCCCCeEEEEc
Q 046259 22 AKTNVSAGDELTYDY 36 (62)
Q Consensus 22 A~rdI~~GeELt~dY 36 (62)
|++.+++||.|.+--
T Consensus 19 al~~l~~G~~l~V~~ 33 (69)
T cd03422 19 ALPSLKPGEILEVIS 33 (69)
T ss_pred HHHcCCCCCEEEEEe
Confidence 577889999766543
No 109
>PF00254 FKBP_C: FKBP-type peptidyl-prolyl cis-trans isomerase; InterPro: IPR001179 Synonym(s): Peptidylprolyl cis-trans isomerase FKBP-type peptidylprolyl isomerases (5.2.1.8 from EC) in vertebrates, are receptors for the two immunosuppressants, FK506 and rapamycin. The drugs inhibit T cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. Peptidylprolyl isomerases accelerate protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides. These proteins are found in a variety of organisms.; GO: 0006457 protein folding; PDB: 1IX5_A 3JXV_A 3JYM_A 1T11_A 1PBK_A 1FD9_A 2VCD_A 3B7X_A 1Q6H_B 1Q6I_B ....
Probab=27.97 E-value=52 Score=16.82 Aligned_cols=17 Identities=24% Similarity=0.247 Sum_probs=13.1
Q ss_pred CCCCCCCeEEEEcCCCC
Q 046259 24 TNVSAGDELTYDYLFDP 40 (62)
Q Consensus 24 rdI~~GeELt~dY~~~~ 40 (62)
+-++.|+.++++|....
T Consensus 3 ~~~~~gd~V~i~y~~~~ 19 (94)
T PF00254_consen 3 RTPKEGDTVTIHYTGRL 19 (94)
T ss_dssp SSBSTTSEEEEEEEEEE
T ss_pred ccCCCCCEEEEEEEEEE
Confidence 45788999999997543
No 110
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=27.58 E-value=21 Score=17.55 Aligned_cols=17 Identities=18% Similarity=0.010 Sum_probs=11.9
Q ss_pred EcCCCCCCCeEEEEcCC
Q 046259 22 AKTNVSAGDELTYDYLF 38 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~ 38 (62)
|++.+++|++|.+--..
T Consensus 20 ~l~~l~~G~~l~v~~d~ 36 (70)
T PF01206_consen 20 ALKELPPGEVLEVLVDD 36 (70)
T ss_dssp HHHTSGTT-EEEEEESS
T ss_pred HHHhcCCCCEEEEEECC
Confidence 56788999998876544
No 111
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=27.36 E-value=1.7e+02 Score=18.57 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=21.1
Q ss_pred cEEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 16 SRIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
..++=-.+..+.+||++.+.+|.+.
T Consensus 194 ~~vG~~~l~~~~~ge~~~l~~G~d~ 218 (317)
T PF13598_consen 194 TFVGESRLPHTAPGEEFELSFGVDP 218 (317)
T ss_pred EEEEeeecCCCCCCCEEEEEcccCC
Confidence 5677778999999999999998753
No 112
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 YfkB is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=27.30 E-value=25 Score=20.88 Aligned_cols=35 Identities=29% Similarity=0.556 Sum_probs=22.7
Q ss_pred CCCCCCeEEEEcCCCCC------------------CCCCceEEEecCCCCCce
Q 046259 25 NVSAGDELTYDYLFDPD------------------EPEEFKVPCLCKAPNCRK 59 (62)
Q Consensus 25 dI~~GeELt~dY~~~~~------------------~~~~~~~~C~Cgs~~Crg 59 (62)
+|-.|+-+--|++...- ....+...|+|.+.+|-|
T Consensus 79 NiFtGdviVTDFgD~~~lgNI~~d~L~~~f~~W~~~~l~~slnCHCp~v~ClG 131 (153)
T PF08756_consen 79 NIFTGDVIVTDFGDEPPLGNIQTDSLTDAFDRWLDSPLAKSLNCHCPAVKCLG 131 (153)
T ss_pred eEecCCEEEecCCCCCCccccccCcHHHHHHHHhcCcccccccCcCCcccccC
Confidence 44457777777765310 112345889999999987
No 113
>PRK01712 carbon storage regulator; Provisional
Probab=27.29 E-value=98 Score=15.79 Aligned_cols=26 Identities=23% Similarity=0.307 Sum_probs=19.1
Q ss_pred ceEEEEEEeCCCccEEEEEEcCCCCC
Q 046259 3 NCYARIMSVGDDESRIVLIAKTNVSA 28 (62)
Q Consensus 3 Nc~~~~v~~~~~~~~i~i~A~rdI~~ 28 (62)
|-.+.++.+.++.-+++|-|-+++..
T Consensus 17 ~I~I~V~~i~~~~VrlGI~AP~~v~I 42 (64)
T PRK01712 17 DIEVTVLGVKGNQVRIGINAPKEVSV 42 (64)
T ss_pred CEEEEEEEEeCCEEEEEEECCCCceE
Confidence 34566666766678999999888764
No 114
>COG4918 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.28 E-value=40 Score=18.98 Aligned_cols=16 Identities=31% Similarity=0.204 Sum_probs=11.6
Q ss_pred CCCCCCeEEEEcCCCC
Q 046259 25 NVSAGDELTYDYLFDP 40 (62)
Q Consensus 25 dI~~GeELt~dY~~~~ 40 (62)
.+---+|+|+||+..+
T Consensus 71 ~~Ff~D~mtidyN~~~ 86 (114)
T COG4918 71 SYFFQDEMTIDYNPSY 86 (114)
T ss_pred eeEecceeeeecCCcc
Confidence 3444689999998764
No 115
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=27.09 E-value=76 Score=14.46 Aligned_cols=19 Identities=11% Similarity=0.156 Sum_probs=13.5
Q ss_pred EEEEEEcCCCCCCCeEEEE
Q 046259 17 RIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~d 35 (62)
..+-+..+.|+|||...+.
T Consensus 24 t~~~~~~~~i~PGes~~i~ 42 (45)
T PF07610_consen 24 TTAEYSKKPIAPGESGKIK 42 (45)
T ss_pred EEeeCCcceECCCCEEEEE
Confidence 3445666789999987664
No 116
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=26.90 E-value=50 Score=16.45 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=14.8
Q ss_pred EEEcCCCCCCCeEEEEcCC
Q 046259 20 LIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 20 i~A~rdI~~GeELt~dY~~ 38 (62)
-.....+.+||+|+|-...
T Consensus 31 ~~~~~~~~~Gd~v~ytitv 49 (76)
T PF01345_consen 31 TVNPSTANPGDTVTYTITV 49 (76)
T ss_pred ecCCCcccCCCEEEEEEEE
Confidence 4557789999999998643
No 117
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=26.74 E-value=42 Score=19.94 Aligned_cols=19 Identities=16% Similarity=0.072 Sum_probs=14.7
Q ss_pred EcCCCCCCCeEEEEcCCCC
Q 046259 22 AKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~~~ 40 (62)
+.|||+.|+-+|+-=-.+.
T Consensus 114 cFrdi~~gDiVtvGecrPL 132 (156)
T KOG1728|consen 114 CFRDIQEGDIVTVGECRPL 132 (156)
T ss_pred hhhccccCCEEEEeecccc
Confidence 5689999999998755443
No 118
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=26.68 E-value=46 Score=22.36 Aligned_cols=15 Identities=40% Similarity=0.581 Sum_probs=12.2
Q ss_pred CCCCCCCeEEEEcCC
Q 046259 24 TNVSAGDELTYDYLF 38 (62)
Q Consensus 24 rdI~~GeELt~dY~~ 38 (62)
+.=++|+|+|++|.-
T Consensus 172 ~~~k~Gd~VtI~~~r 186 (342)
T COG3480 172 SSKKPGDEVTIDYER 186 (342)
T ss_pred hccCCCCeEEEEEEe
Confidence 445799999999983
No 119
>PF08487 VIT: Vault protein inter-alpha-trypsin domain; InterPro: IPR013694 Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition []. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N terminus of a von Willebrand factor type A domain (IPR002035 from INTERPRO) in ITI heavy chains (ITIHs) and their precursors.
Probab=26.49 E-value=56 Score=17.94 Aligned_cols=17 Identities=18% Similarity=0.403 Sum_probs=12.6
Q ss_pred EEEcCCCCCCCeEEEEcC
Q 046259 20 LIAKTNVSAGDELTYDYL 37 (62)
Q Consensus 20 i~A~rdI~~GeELt~dY~ 37 (62)
-..+ +|.||++++|...
T Consensus 99 ~~~v-ni~p~~~v~i~l~ 115 (118)
T PF08487_consen 99 TVSV-NIPPNEEVTIELT 115 (118)
T ss_pred EEEE-EeCCCCEEEEEEE
Confidence 3445 9999999888643
No 120
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=26.46 E-value=42 Score=18.20 Aligned_cols=9 Identities=33% Similarity=0.656 Sum_probs=6.3
Q ss_pred eEEEecCCC
Q 046259 47 KVPCLCKAP 55 (62)
Q Consensus 47 ~~~C~Cgs~ 55 (62)
...|-||+.
T Consensus 96 ~~~CgCG~S 104 (107)
T PRK09502 96 KDECGCGES 104 (107)
T ss_pred CCccCCCCC
Confidence 367999864
No 121
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=26.30 E-value=93 Score=16.07 Aligned_cols=21 Identities=14% Similarity=0.241 Sum_probs=15.8
Q ss_pred EEEEEcCCCCCCCeEEEEcCC
Q 046259 18 IVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 18 i~i~A~rdI~~GeELt~dY~~ 38 (62)
+++.......+|++|+++...
T Consensus 65 la~v~~~~~~~g~~l~v~~~g 85 (95)
T PF08669_consen 65 LAYVDREYAEPGTELEVEIRG 85 (95)
T ss_dssp EEEEEGGGGSTTSEEEEEETT
T ss_pred EEEECHHHcCCCCEEEEEECC
Confidence 455556789999999998643
No 122
>PF05938 Self-incomp_S1: Plant self-incompatibility protein S1; InterPro: IPR010264 This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self-incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties [].
Probab=26.12 E-value=1.1e+02 Score=16.40 Aligned_cols=25 Identities=8% Similarity=0.090 Sum_probs=16.1
Q ss_pred CCCCCCeEEEEcCCCCCCCCCceEEEe
Q 046259 25 NVSAGDELTYDYLFDPDEPEEFKVPCL 51 (62)
Q Consensus 25 dI~~GeELt~dY~~~~~~~~~~~~~C~ 51 (62)
.+++|++..|.+..... ....+-|.
T Consensus 30 ~l~~g~~~~~~F~~~~~--~~t~f~C~ 54 (110)
T PF05938_consen 30 VLKPGQSYSFSFRDNFF--GTTLFWCH 54 (110)
T ss_pred ECCCCCEEEEEEecCcC--CceeEEEE
Confidence 47789999999876542 23445553
No 123
>smart00609 VIT Vault protein Inter-alpha-Trypsin domain.
Probab=25.85 E-value=57 Score=18.57 Aligned_cols=18 Identities=22% Similarity=0.534 Sum_probs=13.3
Q ss_pred EEEEEEcCCCCCCCeEEEE
Q 046259 17 RIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~d 35 (62)
-+.-..+ +|.||+++++.
T Consensus 108 ~~F~~~V-NIppg~~v~v~ 125 (130)
T smart00609 108 EQFTVSV-NVAPGSKVTFE 125 (130)
T ss_pred CcEEEEE-EeCCCCEEEEE
Confidence 3444557 99999998875
No 124
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane]
Probab=25.68 E-value=51 Score=22.21 Aligned_cols=22 Identities=27% Similarity=0.295 Sum_probs=17.6
Q ss_pred EEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 17 RIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 17 ~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
+.-+..+|.|++|| ++.|+.++
T Consensus 239 ~a~ii~vr~v~~Ge--~VgYG~t~ 260 (360)
T COG0787 239 KARIIQVRTVPAGE--TVGYGATF 260 (360)
T ss_pred EEEEEEEEEeCCCC--cccCCcEE
Confidence 44578899999999 78888654
No 125
>COG0316 sufA Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]
Probab=25.68 E-value=47 Score=18.62 Aligned_cols=11 Identities=27% Similarity=0.579 Sum_probs=8.0
Q ss_pred CceEEEecCCC
Q 046259 45 EFKVPCLCKAP 55 (62)
Q Consensus 45 ~~~~~C~Cgs~ 55 (62)
..+..|.||+.
T Consensus 97 NA~~~CgCg~S 107 (110)
T COG0316 97 NAKSSCGCGES 107 (110)
T ss_pred CCCccccCCCC
Confidence 34588999964
No 126
>cd00912 ML The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids.
Probab=25.32 E-value=58 Score=17.96 Aligned_cols=19 Identities=11% Similarity=0.228 Sum_probs=15.7
Q ss_pred EcCCCCCCCeEEEEcCCCC
Q 046259 22 AKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~~~ 40 (62)
....|++||+++|.+....
T Consensus 78 ~~CPl~~G~~~~~~~~~~v 96 (127)
T cd00912 78 SFCPLRKGQQYSYAKTVNV 96 (127)
T ss_pred ccCCcCCCCEEEEEEEEec
Confidence 5688999999999996654
No 127
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=25.31 E-value=53 Score=13.33 Aligned_cols=13 Identities=23% Similarity=0.440 Sum_probs=8.9
Q ss_pred EcCCCCCCCeEEE
Q 046259 22 AKTNVSAGDELTY 34 (62)
Q Consensus 22 A~rdI~~GeELt~ 34 (62)
..+.|.+|+.|++
T Consensus 33 ~~~~~~~g~~l~i 45 (46)
T cd00118 33 DPDNLQVGQKLKI 45 (46)
T ss_pred CccccCCCCEEec
Confidence 3456788888764
No 128
>PRK09890 cold shock protein CspG; Provisional
Probab=25.26 E-value=81 Score=15.90 Aligned_cols=18 Identities=0% Similarity=0.064 Sum_probs=14.3
Q ss_pred cCCCCCCCeEEEEcCCCC
Q 046259 23 KTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~ 40 (62)
.+.+++|+.++|+.....
T Consensus 42 ~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK09890 42 FRTLNENQKVEFSIEQGQ 59 (70)
T ss_pred CCCCCCCCEEEEEEEECC
Confidence 367899999999986543
No 129
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=25.19 E-value=81 Score=15.17 Aligned_cols=17 Identities=12% Similarity=0.276 Sum_probs=14.4
Q ss_pred cCCCCCCCeEEEEcCCC
Q 046259 23 KTNVSAGDELTYDYLFD 39 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~ 39 (62)
.+.+++|+.++|+....
T Consensus 38 ~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 38 FRSLEEGDRVEFELEEG 54 (65)
T ss_pred CCcCCCCCEEEEEEEEC
Confidence 46789999999998775
No 130
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=24.74 E-value=82 Score=15.82 Aligned_cols=17 Identities=6% Similarity=0.286 Sum_probs=14.0
Q ss_pred CCCCCCCeEEEEcCCCC
Q 046259 24 TNVSAGDELTYDYLFDP 40 (62)
Q Consensus 24 rdI~~GeELt~dY~~~~ 40 (62)
+.+++|+.++|......
T Consensus 43 ~~l~~G~~V~f~~~~~~ 59 (70)
T PRK10354 43 KSLDEGQKVSFTIESGA 59 (70)
T ss_pred CCCCCCCEEEEEEEECC
Confidence 67899999999987643
No 131
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=24.54 E-value=27 Score=25.29 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=25.4
Q ss_pred ccEEEEEEcCCCCCCC-----------eE----EEEcCCCCCCC----------CCceEEEecC
Q 046259 15 ESRIVLIAKTNVSAGD-----------EL----TYDYLFDPDEP----------EEFKVPCLCK 53 (62)
Q Consensus 15 ~~~i~i~A~rdI~~Ge-----------EL----t~dY~~~~~~~----------~~~~~~C~Cg 53 (62)
.-+|.+.+-..|.... |+ |++|....-+. ..+...|.||
T Consensus 11 ~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kpeTinyrT~KPE~dGLFCerIFGP~k~~eC~CG 74 (627)
T PRK02625 11 YVKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCG 74 (627)
T ss_pred eEEEEecCHHHHHHHHHhhcCCCceeeEECCCcccccCCCCCCCCCEeechhcCCccCcEEeCC
Confidence 4567776666666655 66 89997542221 2356899999
No 132
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=23.90 E-value=45 Score=18.09 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=6.3
Q ss_pred eEEEecCCC
Q 046259 47 KVPCLCKAP 55 (62)
Q Consensus 47 ~~~C~Cgs~ 55 (62)
...|-||+.
T Consensus 96 ~~~CgCG~S 104 (107)
T TIGR01997 96 TSACGCGES 104 (107)
T ss_pred CCccCCCCC
Confidence 356999864
No 133
>PF10907 DUF2749: Protein of unknown function (DUF2749); InterPro: IPR024475 This bacterial family of proteins represent the TrbJ and TrbK genes of the Ti plasmid conjugative transfer operon [].
Probab=23.86 E-value=42 Score=17.27 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=7.9
Q ss_pred cCCCCCCCeE
Q 046259 23 KTNVSAGDEL 32 (62)
Q Consensus 23 ~rdI~~GeEL 32 (62)
++||+-|+|.
T Consensus 53 l~~i~~gqem 62 (66)
T PF10907_consen 53 LRDIRGGQEM 62 (66)
T ss_pred CCCCCCCccc
Confidence 4789999885
No 134
>PRK15463 cold shock-like protein CspF; Provisional
Probab=23.82 E-value=90 Score=15.81 Aligned_cols=17 Identities=6% Similarity=0.176 Sum_probs=14.2
Q ss_pred cCCCCCCCeEEEEcCCC
Q 046259 23 KTNVSAGDELTYDYLFD 39 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~ 39 (62)
.+.+++|+.++|+....
T Consensus 42 ~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 42 AEELTTGLRVEFCRING 58 (70)
T ss_pred CCCCCCCCEEEEEEEEC
Confidence 56799999999998654
No 135
>PF04797 Herpes_ORF11: Herpesvirus dUTPase protein; InterPro: IPR006882 This family of proteins are found in Herpesvirus. This family includes proteins called ORF10 and ORF11 amongst others.
Probab=23.66 E-value=81 Score=21.10 Aligned_cols=20 Identities=10% Similarity=0.223 Sum_probs=15.7
Q ss_pred cCCCCCCCeEEEEcCCCCCC
Q 046259 23 KTNVSAGDELTYDYLFDPDE 42 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~~~ 42 (62)
-+-|+|||++.+.|+..+..
T Consensus 272 ~~~IpP~es~~v~~~~~y~~ 291 (379)
T PF04797_consen 272 EKTIPPGESTKVKYNNMYEQ 291 (379)
T ss_pred ceEECCCCEEEEEEccEEEe
Confidence 45689999999999876544
No 136
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=23.49 E-value=1.4e+02 Score=16.22 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=16.0
Q ss_pred cEEEEEE-cCCCCCCCeEEEEcCC
Q 046259 16 SRIVLIA-KTNVSAGDELTYDYLF 38 (62)
Q Consensus 16 ~~i~i~A-~rdI~~GeELt~dY~~ 38 (62)
..+-+-+ ....+||++++++-..
T Consensus 95 ~~v~l~~~~~~~~Pg~~~~~~i~~ 118 (136)
T PF07703_consen 95 LKVELTASPDEYKPGEEVTLRIKA 118 (136)
T ss_dssp SSEEEEESSSSBTTTSEEEEEEEE
T ss_pred ceEEEEEecceeCCCCEEEEEEEe
Confidence 3455666 5688899998887544
No 137
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=23.48 E-value=63 Score=18.50 Aligned_cols=19 Identities=16% Similarity=0.291 Sum_probs=16.2
Q ss_pred EEEEEcCCCCCCCeEEEEc
Q 046259 18 IVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 18 i~i~A~rdI~~GeELt~dY 36 (62)
..|.-+.++++|++|++..
T Consensus 65 ~~F~~L~~l~~GD~I~v~~ 83 (144)
T cd05829 65 AVFFRLGDLRKGDKVEVTR 83 (144)
T ss_pred hhhcchhcCCCCCEEEEEE
Confidence 4477789999999999887
No 138
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=23.31 E-value=44 Score=17.53 Aligned_cols=18 Identities=22% Similarity=0.449 Sum_probs=11.9
Q ss_pred EcCCCCCCCeEEEEcCCC
Q 046259 22 AKTNVSAGDELTYDYLFD 39 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~~ 39 (62)
+.+....|+-|.|.|...
T Consensus 15 ~~~~F~vGD~LvF~y~~~ 32 (85)
T PF02298_consen 15 SGKTFRVGDTLVFNYDSG 32 (85)
T ss_dssp CTS-BETTEEEEEE--TT
T ss_pred cCCcEeCCCEEEEEecCC
Confidence 346678999999999764
No 139
>TIGR02084 leud 3-isopropylmalate dehydratase, small subunit. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The members of the seed for this model are those sequences which are gene clustered with other genes involved in leucine biosynthesis and include some archaea.
Probab=23.23 E-value=64 Score=19.14 Aligned_cols=14 Identities=29% Similarity=0.437 Sum_probs=11.7
Q ss_pred CCCCCCeEEEEcCC
Q 046259 25 NVSAGDELTYDYLF 38 (62)
Q Consensus 25 dI~~GeELt~dY~~ 38 (62)
.+++|+||++|...
T Consensus 107 ~l~~gd~i~idl~~ 120 (156)
T TIGR02084 107 EIEEGDEVEVDLEK 120 (156)
T ss_pred HhCCCCEEEEECCC
Confidence 37899999999754
No 140
>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=23.23 E-value=1.2e+02 Score=15.59 Aligned_cols=7 Identities=14% Similarity=0.767 Sum_probs=3.2
Q ss_pred CCCeEEE
Q 046259 28 AGDELTY 34 (62)
Q Consensus 28 ~GeELt~ 34 (62)
|||.+.|
T Consensus 13 PGetV~~ 19 (99)
T PF01835_consen 13 PGETVHF 19 (99)
T ss_dssp TTSEEEE
T ss_pred CCCEEEE
Confidence 4444444
No 141
>PF06205 GT36_AF: Glycosyltransferase 36 associated family ; InterPro: IPR010403 This domain is found in the NvdB protein (P20471 from SWISSPROT), which is involved in the production of beta-(1-->2)-glucan.; PDB: 1V7V_A 1V7W_A 1V7X_A 3ACT_B 2CQT_A 3QFY_B 3QFZ_A 2CQS_A 3QG0_B 3AFJ_A ....
Probab=23.19 E-value=75 Score=16.78 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=15.7
Q ss_pred ccEEEEEEcCCCCCCCeEEEEcCC
Q 046259 15 ESRIVLIAKTNVSAGDELTYDYLF 38 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~dY~~ 38 (62)
.+-.+|-..=.|+|||+..+-|-.
T Consensus 59 Dpc~al~~~v~L~PGe~~~v~f~l 82 (90)
T PF06205_consen 59 DPCAALQVRVTLEPGEEKEVVFLL 82 (90)
T ss_dssp -EEEEEEEEEEE-TT-EEEEEEEE
T ss_pred CeEEEEEEEEEECCCCEEEEEEEE
Confidence 466666666689999998887743
No 142
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=23.15 E-value=80 Score=14.18 Aligned_cols=12 Identities=25% Similarity=0.022 Sum_probs=8.8
Q ss_pred CCCeEEEEcCCC
Q 046259 28 AGDELTYDYLFD 39 (62)
Q Consensus 28 ~GeELt~dY~~~ 39 (62)
....||+.|+..
T Consensus 4 ~~~qLTIfY~G~ 15 (36)
T PF06200_consen 4 ETAQLTIFYGGQ 15 (36)
T ss_pred CCCcEEEEECCE
Confidence 346799999864
No 143
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=23.06 E-value=2.1e+02 Score=19.82 Aligned_cols=25 Identities=16% Similarity=0.143 Sum_probs=20.2
Q ss_pred cEEEEEEcCCCCCCCeEEEEcCCCC
Q 046259 16 SRIVLIAKTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~dY~~~~ 40 (62)
..++--.+..+.+|||+.+.+|.+.
T Consensus 393 ~fvG~~~l~~~~~ge~~~l~~G~D~ 417 (525)
T TIGR02231 393 GFVGRSHLENVAPGERFELSLGVDE 417 (525)
T ss_pred EeEEeeecCCCCCCCeEEEeccCCC
Confidence 4566667888999999999998653
No 144
>smart00588 NEUZ domain in neuralized proteins.
Probab=22.97 E-value=1e+02 Score=17.31 Aligned_cols=21 Identities=0% Similarity=0.089 Sum_probs=16.5
Q ss_pred cEEEEEEcCCCCCCCeEEEEc
Q 046259 16 SRIVLIAKTNVSAGDELTYDY 36 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~dY 36 (62)
..-.+|+.|.|+.||-+.+--
T Consensus 30 ~~givFS~rPl~~~E~~~v~i 50 (123)
T smart00588 30 CNALVFSARPLRINELFEVKI 50 (123)
T ss_pred CceEEecCCCCcCCCEEEEEE
Confidence 345689999999999876654
No 145
>PF08290 Hep_core_N: Hepatitis core protein, putative zinc finger; InterPro: IPR013195 This entry represent a short region found at the N terminus of some viral capsid (HBcAg) proteins from various Hepatitis B virus (HBV), which is a major human pathogen. The conservation of four Cys residues suggests that this region acts as a zinc binding domain. Hepatitis virus is composed of an outer envelope of host-derived lipid containing the surface proteins, and an inner protein capsid that contains genomic DNA. The capsid is composed of a single polypeptide, HBcAg, also known as the core antigen. The capsid has a 5-helical fold, where two long helices form a hairpin that dimerises into a 4-helical bundle []; this fold is unusual for icosahedral viruses. The monomer fold is stabilised by a hydrophobic core that is highly conserved among human viral variants. The capsid is assembled from dimers via interactions involving a highly conserved arginine-rich region near the C terminus. This viral capsid acts as a core antigen, the major immunodominant region lying at the tips of the alpha-helical hairpins that form spikes on the capsid surface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005198 structural molecule activity, 0009405 pathogenesis
Probab=22.89 E-value=36 Score=14.41 Aligned_cols=14 Identities=21% Similarity=0.854 Sum_probs=7.9
Q ss_pred EEEecC----CCCCceec
Q 046259 48 VPCLCK----APNCRKFM 61 (62)
Q Consensus 48 ~~C~Cg----s~~Crg~l 61 (62)
+.|.|. |+-|-||+
T Consensus 10 iscscpt~qasklclgwL 27 (27)
T PF08290_consen 10 ISCSCPTVQASKLCLGWL 27 (27)
T ss_pred eeccCCcchhhhhhcccC
Confidence 455554 55566664
No 146
>PF10077 DUF2314: Uncharacterized protein conserved in bacteria (DUF2314); InterPro: IPR018756 This domain of unkown function is found in various bacterial hypothetical proteins, as well as putative ankyrin repeat proteins.
Probab=22.60 E-value=71 Score=18.28 Aligned_cols=17 Identities=29% Similarity=0.333 Sum_probs=13.9
Q ss_pred EcCCCCCCCeEEEEcCC
Q 046259 22 AKTNVSAGDELTYDYLF 38 (62)
Q Consensus 22 A~rdI~~GeELt~dY~~ 38 (62)
-+.+++.|++++|+-..
T Consensus 76 ~i~~v~~Gd~v~~~~~~ 92 (133)
T PF10077_consen 76 YITNVKEGDRVSFPIED 92 (133)
T ss_pred ccCCCCCCCEEEEChHH
Confidence 46789999999998654
No 147
>COG3738 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.25 E-value=2e+02 Score=17.72 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=20.6
Q ss_pred EEEEeCCCccEEEEEEcCCCCCCCeEEEE
Q 046259 7 RIMSVGDDESRIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 7 ~~v~~~~~~~~i~i~A~rdI~~GeELt~d 35 (62)
..|..+++.++|++.+.+--.+|..|-+.
T Consensus 147 vsWRLdngl~HiGv~sd~~~~~g~plViH 175 (200)
T COG3738 147 VSWRLDNGLAHIGVVSDGFTRDGTPLVIH 175 (200)
T ss_pred EEEEcCCCCceeEEEecCCCCCCCeEEEe
Confidence 45667777899999998766666555544
No 148
>TIGR02308 RNA_lig_T4_1 RNA ligase, T4 RnlA family. Members of this family are phage proteins with ATP-dependent RNA ligase activity. Host defense to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL.
Probab=22.14 E-value=61 Score=22.07 Aligned_cols=21 Identities=24% Similarity=0.626 Sum_probs=18.9
Q ss_pred ccEEEEEEcCCCCCCCeEEEE
Q 046259 15 ESRIVLIAKTNVSAGDELTYD 35 (62)
Q Consensus 15 ~~~i~i~A~rdI~~GeELt~d 35 (62)
.+++.+-++|+..-|++|+++
T Consensus 172 ~~~LvLL~iR~N~TG~Yl~~~ 192 (374)
T TIGR02308 172 EPKLILLNVRHNETGEYVSYD 192 (374)
T ss_pred CCCEEEEEEEEcCCCCeeeHH
Confidence 588999999999999999765
No 149
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.12 E-value=56 Score=20.32 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=14.8
Q ss_pred cEEEEEEcCCCCCCCeEEE
Q 046259 16 SRIVLIAKTNVSAGDELTY 34 (62)
Q Consensus 16 ~~i~i~A~rdI~~GeELt~ 34 (62)
..-.++|.|.|.+||-|+-
T Consensus 88 ~~~vvVa~r~l~rG~~I~~ 106 (214)
T PRK12617 88 NQDVLVLRRGITAGETISL 106 (214)
T ss_pred EEEEEEEeeecCCCCCcCH
Confidence 3446789999999998753
No 150
>cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family.
Probab=22.12 E-value=90 Score=18.02 Aligned_cols=19 Identities=16% Similarity=0.336 Sum_probs=15.4
Q ss_pred EEcCCCCCCCeEEEE--cCCC
Q 046259 21 IAKTNVSAGDELTYD--YLFD 39 (62)
Q Consensus 21 ~A~rdI~~GeELt~d--Y~~~ 39 (62)
|+...+++||+.+|. +...
T Consensus 80 ~s~CP~~kGet~~Y~~p~slp 100 (130)
T cd00915 80 YSFCGALKGETVYYVGPFSFK 100 (130)
T ss_pred cccCCccCCceEEEeeeeccc
Confidence 467889999999999 7654
No 151
>PF09227 DUF1962: Domain of unknown function (DUF1962); InterPro: IPR015308 Members of this family of fungal proteins are functionally uncharacterised []. ; PDB: 1UOY_A.
Probab=22.03 E-value=44 Score=16.82 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=5.0
Q ss_pred ecCCCCCcee
Q 046259 51 LCKAPNCRKF 60 (62)
Q Consensus 51 ~Cgs~~Crg~ 60 (62)
-|++..|+|.
T Consensus 48 dc~~stc~g~ 57 (64)
T PF09227_consen 48 DCGASTCHGT 57 (64)
T ss_dssp E-SSS--EEE
T ss_pred ecCccccccc
Confidence 3788888875
No 152
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=21.93 E-value=71 Score=15.15 Aligned_cols=13 Identities=23% Similarity=0.332 Sum_probs=7.4
Q ss_pred CCCCCCeEEEEcC
Q 046259 25 NVSAGDELTYDYL 37 (62)
Q Consensus 25 dI~~GeELt~dY~ 37 (62)
++++|+++.+-..
T Consensus 46 ~L~~G~~V~~~ik 58 (64)
T PF03459_consen 46 GLKPGDEVYASIK 58 (64)
T ss_dssp T-STT-EEEEEE-
T ss_pred CCCCCCEEEEEEe
Confidence 3668999887654
No 153
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.72 E-value=49 Score=16.40 Aligned_cols=16 Identities=19% Similarity=0.123 Sum_probs=11.4
Q ss_pred EcCCCCCCCeEEEEcC
Q 046259 22 AKTNVSAGDELTYDYL 37 (62)
Q Consensus 22 A~rdI~~GeELt~dY~ 37 (62)
|++.+++|+.|.+=-.
T Consensus 19 ~l~~l~~G~~l~V~~d 34 (69)
T cd03423 19 KVRKMKPGDTLLVLAT 34 (69)
T ss_pred HHHcCCCCCEEEEEeC
Confidence 5678899997766443
No 154
>PF03423 CBM_25: Carbohydrate binding domain (family 25); InterPro: IPR005085 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM25 from CAZY which has a starch-binding function as has been demonstrated in one case.; PDB: 2LAB_A 2C3X_B 2C3V_A 2C3W_C 2LAA_A.
Probab=21.67 E-value=1.2e+02 Score=15.81 Aligned_cols=10 Identities=10% Similarity=0.099 Sum_probs=4.8
Q ss_pred CeEEEEcCCC
Q 046259 30 DELTYDYLFD 39 (62)
Q Consensus 30 eELt~dY~~~ 39 (62)
.+|.+.+++.
T Consensus 19 ~~v~~~~G~n 28 (87)
T PF03423_consen 19 PNVHLHGGFN 28 (87)
T ss_dssp -EEEEEETTS
T ss_pred CcEEEEecCC
Confidence 4555555544
No 155
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=21.42 E-value=60 Score=16.60 Aligned_cols=12 Identities=33% Similarity=0.534 Sum_probs=8.9
Q ss_pred CCCCCCeEEEEc
Q 046259 25 NVSAGDELTYDY 36 (62)
Q Consensus 25 dI~~GeELt~dY 36 (62)
.|.+|+.+||.=
T Consensus 14 ~v~~GdtVt~~N 25 (83)
T TIGR02657 14 HVKVGDTVTWIN 25 (83)
T ss_pred EECCCCEEEEEE
Confidence 367888888853
No 156
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=21.19 E-value=1.1e+02 Score=15.76 Aligned_cols=18 Identities=22% Similarity=0.444 Sum_probs=14.7
Q ss_pred cCCCCCCCeEEEEcCCCC
Q 046259 23 KTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~ 40 (62)
.+.+.+|+.++|+.....
T Consensus 39 ~~~l~~G~~V~f~~~~~~ 56 (74)
T PRK09937 39 YRTLKAGQSVQFDVHQGP 56 (74)
T ss_pred CCCCCCCCEEEEEEEECC
Confidence 478999999999986653
No 157
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=21.07 E-value=1.4e+02 Score=15.42 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=18.2
Q ss_pred ceEEEEEEeCCCccEEEEEEcCCCC
Q 046259 3 NCYARIMSVGDDESRIVLIAKTNVS 27 (62)
Q Consensus 3 Nc~~~~v~~~~~~~~i~i~A~rdI~ 27 (62)
+..+.++.+.++.-+++|-|-+++.
T Consensus 17 ~I~I~Vl~i~g~~VrlGI~AP~~v~ 41 (69)
T TIGR00202 17 DIEVKVLSVKGDQVKLGIEAPKEIS 41 (69)
T ss_pred CEEEEEEEEcCCeEEEEEECCCCCe
Confidence 3455666666667899999988875
No 158
>PRK10943 cold shock-like protein CspC; Provisional
Probab=21.06 E-value=1.1e+02 Score=15.35 Aligned_cols=17 Identities=6% Similarity=0.225 Sum_probs=13.7
Q ss_pred cCCCCCCCeEEEEcCCC
Q 046259 23 KTNVSAGDELTYDYLFD 39 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~ 39 (62)
.+.+.+|+.++|.-...
T Consensus 41 ~~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 41 FKTLAEGQNVEFEIQDG 57 (69)
T ss_pred CCCCCCCCEEEEEEEEC
Confidence 36789999999987664
No 159
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=20.88 E-value=1.1e+02 Score=15.22 Aligned_cols=18 Identities=17% Similarity=0.494 Sum_probs=14.6
Q ss_pred cCCCCCCCeEEEEcCCCC
Q 046259 23 KTNVSAGDELTYDYLFDP 40 (62)
Q Consensus 23 ~rdI~~GeELt~dY~~~~ 40 (62)
.+.+++|+.++|+.....
T Consensus 39 ~~~l~~G~~V~f~~~~~~ 56 (68)
T TIGR02381 39 YRTLKAGQKVQFEVVQGP 56 (68)
T ss_pred CCCCCCCCEEEEEEEECC
Confidence 477899999999987654
No 160
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit. This subfamily is most closely related to the 3-isopropylmalate dehydratase, small subunits which form TIGR00171. This subfamily includes the members of TIGR02084 which are gene clustered with other genes of leucine biosynthesis. The rest of the subfamily includes mainly archaeal species which exhibit two hits to this model. In these cases it is possible that one or the other of the hits does not have a 3-isopropylmalate dehydratase activity but rather one of the other related aconitase-like activities.
Probab=20.82 E-value=82 Score=18.61 Aligned_cols=16 Identities=31% Similarity=0.441 Sum_probs=12.7
Q ss_pred CCCCCCCeEEEEcCCC
Q 046259 24 TNVSAGDELTYDYLFD 39 (62)
Q Consensus 24 rdI~~GeELt~dY~~~ 39 (62)
..|++|+||++|....
T Consensus 104 ~~i~~gd~i~vdl~~~ 119 (154)
T TIGR02087 104 EGIKDGDEVTVDLETG 119 (154)
T ss_pred HHCCCCCEEEEECCCC
Confidence 4589999999996543
No 161
>PF11113 Phage_head_chap: Head assembly gene product; InterPro: IPR021049 This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex [].
Probab=20.75 E-value=1.3e+02 Score=14.95 Aligned_cols=29 Identities=28% Similarity=0.446 Sum_probs=22.6
Q ss_pred CCccEEEEEEcCCCCCCCeEEEEcCCCCCC
Q 046259 13 DDESRIVLIAKTNVSAGDELTYDYLFDPDE 42 (62)
Q Consensus 13 ~~~~~i~i~A~rdI~~GeELt~dY~~~~~~ 42 (62)
++..+|+.+..-.+. +-+|++||+...++
T Consensus 11 dG~~hiVYi~~~~~~-~G~l~vdfsT~~e~ 39 (56)
T PF11113_consen 11 DGESHIVYITELHYD-DGKLKVDFSTPSED 39 (56)
T ss_pred CCCEEEEEEEEEEEc-CCeEEEEEeCCCcc
Confidence 447888888887888 66899999987653
No 162
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=20.49 E-value=1.8e+02 Score=16.27 Aligned_cols=20 Identities=40% Similarity=0.665 Sum_probs=12.3
Q ss_pred CceEEEEEEeCCCccEEEEE
Q 046259 2 PNCYARIMSVGDDESRIVLI 21 (62)
Q Consensus 2 PNc~~~~v~~~~~~~~i~i~ 21 (62)
|||++..-.+.+....|.-.
T Consensus 18 ~~~EVVLHDl~~~~~sIv~I 37 (118)
T PF08348_consen 18 PNCEVVLHDLSDPEHSIVAI 37 (118)
T ss_pred CCeEEEEEECCCCCCEEEEE
Confidence 78888877775434444333
No 163
>COG3369 Zinc finger domain containing protein (CDGSH-type) [Function unknown]
Probab=20.40 E-value=53 Score=17.46 Aligned_cols=11 Identities=18% Similarity=0.456 Sum_probs=8.1
Q ss_pred ceEEEecCCCC
Q 046259 46 FKVPCLCKAPN 56 (62)
Q Consensus 46 ~~~~C~Cgs~~ 56 (62)
+...|+||...
T Consensus 30 ~~~LCrCG~S~ 40 (78)
T COG3369 30 QAALCRCGHSE 40 (78)
T ss_pred EEEEEeccCcC
Confidence 45789999654
No 164
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=20.26 E-value=46 Score=16.14 Aligned_cols=10 Identities=30% Similarity=1.045 Sum_probs=7.5
Q ss_pred ceEEEecCCC
Q 046259 46 FKVPCLCKAP 55 (62)
Q Consensus 46 ~~~~C~Cgs~ 55 (62)
-..+|+||..
T Consensus 17 ~~y~CRCG~~ 26 (55)
T PF05207_consen 17 YSYPCRCGGE 26 (55)
T ss_dssp EEEEETTSSE
T ss_pred EEEcCCCCCE
Confidence 4588999964
No 165
>PRK03760 hypothetical protein; Provisional
Probab=20.10 E-value=50 Score=18.51 Aligned_cols=16 Identities=31% Similarity=0.432 Sum_probs=11.6
Q ss_pred EEEcCCCCCCCeEEEE
Q 046259 20 LIAKTNVSAGDELTYD 35 (62)
Q Consensus 20 i~A~rdI~~GeELt~d 35 (62)
.++...|++|+.|.|.
T Consensus 100 ~~~~~gi~~Gd~v~~~ 115 (117)
T PRK03760 100 KIRVLKVEVGDEIEWI 115 (117)
T ss_pred hHHHcCCCCCCEEEEe
Confidence 4556678888888764
No 166
>KOG2540 consensus Cytochrome oxidase assembly factor COX11 [Posttranslational modification, protein turnover, chaperones]
Probab=20.02 E-value=2.6e+02 Score=18.05 Aligned_cols=45 Identities=20% Similarity=0.332 Sum_probs=27.3
Q ss_pred EEeCCCccEEEEEEcCCCCCCCeEEEE-cCCCCCCCC--CceEEEecC
Q 046259 9 MSVGDDESRIVLIAKTNVSAGDELTYD-YLFDPDEPE--EFKVPCLCK 53 (62)
Q Consensus 9 v~~~~~~~~i~i~A~rdI~~GeELt~d-Y~~~~~~~~--~~~~~C~Cg 53 (62)
+.|-.+...++|++.++-.--.-+-+. |+....+.. -.++.|.|=
T Consensus 157 iyV~PGEtALaFYta~N~sdkpIiGvstYni~P~~Aa~YFnKiqCFCF 204 (269)
T KOG2540|consen 157 IYVLPGETALAFYTAENPSDKPIIGVSTYNITPGQAAVYFNKIQCFCF 204 (269)
T ss_pred EEEcCCcceeeeEeccCCCCCCceeeEeeccCccHhhhheeceeEEee
Confidence 344445677888888877666666665 665432211 235788884
Done!