Query psy303
Match_columns 62
No_of_seqs 100 out of 180
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 23:42:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy303.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/303hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04084 ORC2: Origin recognit 99.9 2.6E-28 5.7E-33 176.8 6.2 59 4-62 38-99 (326)
2 KOG2928|consensus 99.9 1.4E-23 3.1E-28 160.7 5.7 58 5-62 234-291 (518)
3 COG5575 ORC2 Origin recognitio 99.8 1.1E-20 2.4E-25 144.1 4.3 58 5-62 241-298 (535)
4 PF14453 ThiS-like: ThiS-like 85.8 0.96 2.1E-05 26.2 2.6 23 35-57 18-40 (57)
5 TIGR01738 bioH putative pimelo 78.1 3.2 6.8E-05 25.6 3.0 29 23-51 8-36 (245)
6 COG1166 SpeA Arginine decarbox 77.5 2.3 5.1E-05 34.7 2.8 27 28-55 145-171 (652)
7 PF13911 AhpC-TSA_2: AhpC/TSA 72.0 16 0.00034 21.9 4.9 33 18-52 11-43 (115)
8 COG2924 Uncharacterized protei 71.8 3.9 8.4E-05 25.9 2.2 28 30-57 61-88 (90)
9 cd00591 HU_IHF Integration hos 69.6 6.6 0.00014 22.6 2.8 28 3-30 21-48 (87)
10 COG0505 CarA Carbamoylphosphat 66.8 5.1 0.00011 30.8 2.3 26 18-43 177-202 (368)
11 PRK11460 putative hydrolase; P 65.0 7.2 0.00016 26.3 2.6 34 23-56 20-56 (232)
12 PF12695 Abhydrolase_5: Alpha/ 64.7 9.1 0.0002 22.4 2.8 29 23-51 3-31 (145)
13 TIGR03695 menH_SHCHC 2-succiny 61.9 14 0.0003 22.5 3.3 30 23-52 5-34 (251)
14 PF12048 DUF3530: Protein of u 61.7 19 0.00041 26.0 4.4 41 19-59 191-233 (310)
15 TIGR00988 hip integration host 60.6 11 0.00024 22.3 2.6 28 3-30 23-50 (94)
16 smart00411 BHL bacterial (prok 57.1 16 0.00034 21.1 2.8 27 4-30 23-49 (90)
17 PLN02771 carbamoyl-phosphate s 56.7 17 0.00036 28.1 3.6 22 21-42 241-262 (415)
18 PF00216 Bac_DNA_binding: Bact 56.3 10 0.00022 21.8 1.9 27 4-30 23-49 (90)
19 PRK05541 adenylylsulfate kinas 56.0 26 0.00056 22.2 3.9 37 17-53 4-43 (176)
20 PF01640 Peptidase_C10: Peptid 56.0 10 0.00022 25.5 2.1 31 13-56 143-173 (192)
21 TIGR02427 protocat_pcaD 3-oxoa 54.0 20 0.00042 22.0 3.0 20 23-42 17-36 (251)
22 PF07985 SRR1: SRR1; InterPro 53.6 9.3 0.0002 21.4 1.4 10 22-31 1-10 (56)
23 TIGR00696 wecB_tagA_cpsF bacte 53.0 48 0.001 22.3 5.0 45 8-54 35-80 (177)
24 PF08157 NUC129: NUC129 domain 51.9 5.2 0.00011 23.9 0.2 17 24-40 26-42 (63)
25 PF05991 NYN_YacP: YacP-like N 51.8 13 0.00029 24.5 2.1 40 18-57 3-56 (166)
26 PF01282 Ribosomal_S24e: Ribos 50.9 18 0.00039 21.8 2.4 29 30-58 14-42 (84)
27 PF12697 Abhydrolase_6: Alpha/ 50.7 15 0.00033 22.0 2.1 30 23-52 2-31 (228)
28 PRK10673 acyl-CoA esterase; Pr 48.7 29 0.00063 22.3 3.3 18 9-26 31-48 (255)
29 cd06533 Glyco_transf_WecG_TagA 47.6 68 0.0015 21.0 5.0 45 7-53 32-77 (171)
30 PF09673 TrbC_Ftype: Type-F co 46.4 28 0.0006 21.8 2.8 26 35-61 13-38 (113)
31 TIGR01201 HU_rel DNA-binding p 46.1 22 0.00049 23.1 2.5 27 4-30 53-79 (145)
32 TIGR00987 himA integration hos 45.6 27 0.00058 20.9 2.6 28 3-30 23-50 (96)
33 cd06559 Endonuclease_V Endonuc 45.4 22 0.00048 24.7 2.5 28 27-54 73-102 (208)
34 PRK10349 carboxylesterase BioH 45.4 35 0.00076 22.2 3.3 30 23-52 17-46 (256)
35 PF03959 FSH1: Serine hydrolas 45.2 33 0.00071 22.8 3.2 14 23-36 8-21 (212)
36 TIGR02240 PHA_depoly_arom poly 44.7 40 0.00086 22.4 3.6 18 9-26 40-57 (276)
37 PF14848 HU-DNA_bdg: DNA-bindi 44.2 23 0.0005 22.4 2.2 25 5-30 53-77 (124)
38 PF02230 Abhydrolase_2: Phosph 44.1 50 0.0011 21.6 3.9 19 23-41 18-36 (216)
39 PRK08116 hypothetical protein; 44.0 97 0.0021 21.8 5.6 33 20-52 114-149 (268)
40 PRK00199 ihfB integration host 43.2 31 0.00066 20.5 2.6 27 4-30 24-50 (94)
41 PF08859 DGC: DGC domain; Int 43.0 24 0.00051 22.1 2.1 31 20-53 29-59 (110)
42 PF07315 DUF1462: Protein of u 42.8 27 0.00059 22.2 2.4 20 34-53 53-75 (93)
43 PF13177 DNA_pol3_delta2: DNA 42.4 90 0.0019 20.1 4.9 25 20-44 19-45 (162)
44 PF07931 CPT: Chloramphenicol 41.8 1.1E+02 0.0023 20.6 6.0 43 9-51 72-114 (174)
45 PRK01178 rps24e 30S ribosomal 41.0 58 0.0013 20.5 3.7 30 29-58 31-60 (99)
46 TIGR03611 RutD pyrimidine util 40.9 48 0.001 20.6 3.3 17 10-26 29-45 (257)
47 PF07728 AAA_5: AAA domain (dy 40.8 45 0.00098 20.1 3.1 30 22-54 1-33 (139)
48 PRK11747 dinG ATP-dependent DN 40.5 1.2E+02 0.0025 24.5 6.1 35 7-43 548-582 (697)
49 COG2969 SspB Stringent starvat 40.2 44 0.00094 23.0 3.2 31 30-60 7-40 (155)
50 PTZ00071 40S ribosomal protein 38.6 53 0.0012 21.9 3.4 30 29-58 36-66 (132)
51 PHA02857 monoglyceride lipase; 38.3 41 0.00088 22.2 2.8 28 24-51 30-58 (276)
52 PRK00285 ihfA integration host 37.2 43 0.00094 20.0 2.6 27 4-30 25-51 (99)
53 PLN02824 hydrolase, alpha/beta 36.6 51 0.0011 22.1 3.1 30 23-52 33-62 (294)
54 PF14577 SEO_C: Sieve element 36.6 69 0.0015 23.2 3.9 37 5-42 17-54 (235)
55 PF02254 TrkA_N: TrkA-N domain 35.8 79 0.0017 18.4 3.6 27 23-52 1-28 (116)
56 KOG2541|consensus 34.9 38 0.00081 25.5 2.4 31 14-47 87-117 (296)
57 COG0776 HimA Bacterial nucleoi 34.9 64 0.0014 20.1 3.2 28 3-30 23-50 (94)
58 PF10707 YrbL-PhoP_reg: PhoP r 33.6 67 0.0015 21.9 3.4 13 31-43 123-135 (199)
59 PF08061 P68HR: P68HR (NUC004) 33.2 15 0.00033 19.4 0.1 8 27-34 20-27 (33)
60 PRK14875 acetoin dehydrogenase 33.0 55 0.0012 22.4 2.9 31 23-53 135-165 (371)
61 PF00004 AAA: ATPase family as 32.7 1E+02 0.0022 17.7 4.0 8 47-54 60-67 (132)
62 PRK11126 2-succinyl-6-hydroxy- 32.5 74 0.0016 20.2 3.3 16 10-26 18-33 (242)
63 PF03808 Glyco_tran_WecB: Glyc 32.2 71 0.0015 20.9 3.2 33 24-56 50-82 (172)
64 PRK03592 haloalkane dehalogena 32.1 71 0.0015 21.4 3.3 30 23-52 31-60 (295)
65 cd05781 DNA_polB_B3_exo DEDDy 31.9 53 0.0011 21.9 2.6 27 28-55 45-71 (188)
66 smart00775 LNS2 LNS2 domain. T 31.8 1.1E+02 0.0023 19.8 4.0 32 22-53 118-150 (157)
67 TIGR01250 pro_imino_pep_2 prol 31.6 80 0.0017 19.9 3.3 30 23-52 29-60 (288)
68 KOG0079|consensus 31.1 46 0.001 23.5 2.3 20 27-47 18-37 (198)
69 cd04955 GT1_like_6 This family 30.9 1.4E+02 0.003 19.9 4.5 42 16-57 217-258 (363)
70 cd05017 SIS_PGI_PMI_1 The memb 30.5 1.3E+02 0.0027 18.1 4.3 32 22-53 1-34 (119)
71 PF08484 Methyltransf_14: C-me 30.2 1.7E+02 0.0036 19.3 4.9 23 18-40 66-88 (160)
72 PF13241 NAD_binding_7: Putati 30.1 1.2E+02 0.0027 17.9 4.5 34 19-57 6-39 (103)
73 PF12146 Hydrolase_4: Putative 29.7 97 0.0021 17.9 3.2 27 22-48 19-45 (79)
74 PF07830 PP2C_C: Protein serin 29.4 44 0.00094 20.4 1.7 13 27-39 67-79 (81)
75 KOG3342|consensus 28.9 79 0.0017 22.2 3.1 13 30-42 15-27 (180)
76 cd00296 SIR2 SIR2 superfamily 28.8 1.3E+02 0.0029 19.8 4.1 45 12-56 162-207 (222)
77 KOG0245|consensus 28.5 32 0.0007 30.2 1.3 12 18-29 84-95 (1221)
78 cd03802 GT1_AviGT4_like This f 27.8 1.5E+02 0.0032 19.6 4.1 39 19-57 196-234 (335)
79 PF01913 FTR: Formylmethanofur 27.8 1.3E+02 0.0028 20.5 3.9 36 19-54 70-108 (144)
80 PRK10753 transcriptional regul 27.7 79 0.0017 18.8 2.6 27 4-30 23-49 (90)
81 cd05006 SIS_GmhA Phosphoheptos 27.7 1.7E+02 0.0037 18.7 5.6 36 8-43 17-56 (177)
82 TIGR00764 lon_rel lon-related 27.6 2.1E+02 0.0046 22.8 5.6 43 14-59 31-78 (608)
83 PF14252 DUF4347: Domain of un 26.8 67 0.0015 21.6 2.4 36 6-41 77-117 (165)
84 PF12165 DUF3594: Domain of un 26.5 32 0.00069 23.3 0.8 10 21-30 37-46 (137)
85 COG0426 FpaA Uncharacterized f 26.3 1.7E+02 0.0037 22.6 4.8 47 6-52 233-282 (388)
86 TIGR00282 metallophosphoestera 26.2 1.2E+02 0.0026 21.8 3.8 36 22-57 2-42 (266)
87 PF02608 Bmp: Basic membrane p 25.7 2.4E+02 0.0052 19.8 5.6 45 13-58 54-98 (306)
88 COG0400 Predicted esterase [Ge 25.3 68 0.0015 22.1 2.3 34 23-56 22-55 (207)
89 cd05784 DNA_polB_II_exo DEDDy 25.1 79 0.0017 21.3 2.5 23 28-50 48-70 (193)
90 PF00462 Glutaredoxin: Glutare 25.1 1.2E+02 0.0025 15.9 4.2 35 19-53 22-57 (60)
91 PRK10985 putative hydrolase; P 25.0 96 0.0021 21.6 3.0 32 21-52 60-94 (324)
92 COG0645 Predicted kinase [Gene 24.8 1.4E+02 0.0031 20.6 3.8 56 3-60 59-117 (170)
93 TIGR01360 aden_kin_iso1 adenyl 24.7 1.1E+02 0.0024 19.1 3.0 22 36-57 72-93 (188)
94 PF02197 RIIa: Regulatory subu 24.5 45 0.00098 17.3 1.0 16 32-47 4-19 (38)
95 PF02086 MethyltransfD12: D12 24.4 41 0.00089 22.4 1.0 28 28-55 2-29 (260)
96 PF00225 Kinesin: Kinesin moto 24.3 1.1E+02 0.0023 21.6 3.2 28 4-31 57-84 (335)
97 PF10915 DUF2709: Protein of u 24.3 39 0.00084 24.6 0.9 24 28-51 165-188 (238)
98 PLN02511 hydrolase 24.3 94 0.002 22.6 3.0 30 23-52 104-136 (388)
99 PF00752 XPG_N: XPG N-terminal 24.2 1.1E+02 0.0024 17.9 2.8 17 41-57 67-85 (101)
100 PF10443 RNA12: RNA12 protein; 24.2 48 0.001 25.9 1.5 12 45-56 148-159 (431)
101 PRK03692 putative UDP-N-acetyl 24.1 2E+02 0.0043 20.3 4.5 35 19-55 104-141 (243)
102 COG1922 WecG Teichoic acid bio 23.9 2.4E+02 0.0053 20.5 5.0 49 8-57 95-147 (253)
103 cd05777 DNA_polB_delta_exo DED 23.8 1.6E+02 0.0034 20.0 3.8 24 26-49 66-89 (230)
104 PLN02578 hydrolase 23.8 1.2E+02 0.0025 21.5 3.3 8 23-30 90-97 (354)
105 PF14639 YqgF: Holliday-juncti 23.6 60 0.0013 21.4 1.7 13 45-57 63-75 (150)
106 PHA02524 43A DNA polymerase su 23.6 1.4E+02 0.0031 23.7 4.0 33 22-55 171-203 (498)
107 PF08235 LNS2: LNS2 (Lipin/Ned 23.4 1.4E+02 0.003 20.1 3.5 35 19-53 116-150 (157)
108 cd05005 SIS_PHI Hexulose-6-pho 23.4 2.1E+02 0.0046 18.3 5.8 45 7-51 20-65 (179)
109 cd04949 GT1_gtfA_like This fam 23.4 2.1E+02 0.0047 19.5 4.5 38 19-57 234-271 (372)
110 PF13529 Peptidase_C39_2: Pept 23.3 1E+02 0.0022 17.8 2.5 47 8-57 87-135 (144)
111 cd05160 DEDDy_DNA_polB_exo DED 23.3 1.6E+02 0.0035 18.9 3.7 25 23-47 55-79 (199)
112 PRK11798 ClpXP protease specif 23.2 1.7E+02 0.0037 19.7 3.8 30 30-59 7-38 (138)
113 PF02399 Herpes_ori_bp: Origin 23.0 2.3E+02 0.0049 24.2 5.2 48 10-59 272-320 (824)
114 TIGR00393 kpsF KpsF/GutQ famil 22.8 1.8E+02 0.004 19.5 4.0 31 22-52 2-33 (268)
115 PRK13768 GTPase; Provisional 22.8 1.4E+02 0.003 20.7 3.5 30 23-52 5-37 (253)
116 cd00027 BRCT Breast Cancer Sup 22.7 1.2E+02 0.0025 15.0 2.8 23 20-42 1-25 (72)
117 cd05783 DNA_polB_B1_exo DEDDy 22.7 93 0.002 21.1 2.5 26 27-55 69-94 (204)
118 COG1213 Predicted sugar nucleo 22.6 30 0.00065 25.2 0.1 25 31-55 30-57 (239)
119 cd00707 Pancreat_lipase_like P 22.5 96 0.0021 21.6 2.6 30 23-52 40-73 (275)
120 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 22.4 91 0.002 18.9 2.3 22 21-42 3-26 (166)
121 TIGR00231 small_GTP small GTP- 22.4 98 0.0021 17.5 2.3 22 21-42 2-25 (161)
122 PF02597 ThiS: ThiS family; I 22.3 90 0.0019 17.0 2.0 24 31-54 24-51 (77)
123 KOG1611|consensus 22.3 1E+02 0.0023 22.7 2.8 37 21-58 164-203 (249)
124 PF13401 AAA_22: AAA domain; P 22.2 98 0.0021 18.0 2.3 14 31-44 17-30 (131)
125 PRK08074 bifunctional ATP-depe 22.1 2E+02 0.0044 24.0 4.7 36 5-40 764-802 (928)
126 PHA02952 EEV maturation protei 22.1 1.2E+02 0.0027 25.0 3.5 34 24-58 247-283 (648)
127 PLN03084 alpha/beta hydrolase 22.1 1.3E+02 0.0028 22.4 3.3 30 23-52 131-160 (383)
128 cd01124 KaiC KaiC is a circadi 22.0 2.1E+02 0.0045 17.7 4.6 29 23-51 2-33 (187)
129 PLN02275 transferase, transfer 22.0 2E+02 0.0043 20.4 4.2 37 19-56 260-296 (371)
130 cd05780 DNA_polB_Kod1_like_exo 21.8 1.6E+02 0.0035 19.4 3.5 30 25-54 50-81 (195)
131 PF02100 ODC_AZ: Ornithine dec 21.8 1.2E+02 0.0025 19.0 2.7 24 27-50 36-61 (108)
132 TIGR03127 RuMP_HxlB 6-phospho 21.6 2.3E+02 0.0049 18.0 5.9 37 8-44 18-54 (179)
133 PRK13938 phosphoheptose isomer 21.5 2.6E+02 0.0056 19.0 4.5 35 9-43 34-68 (196)
134 TIGR01497 kdpB K+-transporting 21.5 45 0.00097 27.2 0.9 9 21-29 650-658 (675)
135 PLN02679 hydrolase, alpha/beta 21.3 1.4E+02 0.0031 21.2 3.3 16 10-25 104-119 (360)
136 TIGR03230 lipo_lipase lipoprot 21.2 1.4E+02 0.003 23.2 3.4 30 23-52 45-80 (442)
137 PRK14010 potassium-transportin 21.1 47 0.001 27.0 0.9 16 21-39 645-660 (673)
138 cd03064 TRX_Fd_NuoE TRX-like [ 20.9 66 0.0014 18.2 1.3 12 43-54 52-63 (80)
139 cd03414 CbiX_SirB_C Sirohydroc 20.9 1.4E+02 0.0029 17.8 2.8 21 23-43 3-27 (117)
140 PF14881 Tubulin_3: Tubulin do 20.9 1.2E+02 0.0025 20.5 2.7 37 18-57 74-116 (180)
141 PF03029 ATP_bind_1: Conserved 20.9 1.4E+02 0.0031 20.7 3.2 32 31-62 9-49 (238)
142 cd05785 DNA_polB_like2_exo Unc 20.8 1.1E+02 0.0024 20.8 2.6 23 28-50 55-77 (207)
143 PRK08763 single-stranded DNA-b 20.8 1.6E+02 0.0035 19.8 3.4 30 19-54 52-81 (164)
144 cd03799 GT1_amsK_like This is 20.7 2.6E+02 0.0057 18.4 5.9 36 20-56 210-245 (355)
145 PRK10566 esterase; Provisional 20.6 1.3E+02 0.0028 19.5 2.8 30 23-52 31-61 (249)
146 PRK01122 potassium-transportin 20.5 48 0.001 27.0 0.9 16 21-39 649-664 (679)
147 KOG2551|consensus 20.4 51 0.0011 23.9 0.9 29 23-51 9-48 (230)
148 cd03081 TRX_Fd_NuoE_FDH_gamma 20.4 70 0.0015 18.5 1.4 10 44-53 53-62 (80)
149 COG0470 HolB ATPase involved i 20.3 2.7E+02 0.0058 18.8 4.4 26 19-44 22-50 (325)
150 TIGR03056 bchO_mg_che_rel puta 20.2 1.7E+02 0.0036 18.7 3.3 18 9-26 43-60 (278)
151 PF13289 SIR2_2: SIR2-like dom 20.2 2.1E+02 0.0045 17.0 4.5 28 16-43 82-109 (143)
152 PF00158 Sigma54_activat: Sigm 20.2 2.6E+02 0.0057 18.2 5.3 50 4-53 6-58 (168)
No 1
>PF04084 ORC2: Origin recognition complex subunit 2 ; InterPro: IPR007220 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 2, which binds the origin of replication. It plays a role in chromosome replication and mating type transcriptional silencing.; GO: 0006260 DNA replication, 0000808 origin recognition complex, 0005634 nucleus
Probab=99.95 E-value=2.6e-28 Score=176.85 Aligned_cols=59 Identities=36% Similarity=0.700 Sum_probs=56.6
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhcC---CcEEEEeccCCCCcccC
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLSN---SKVLVINGFFPDLTLKE 62 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~---~~~lvVnGy~p~~tikd 62 (62)
..+++.||||++||.+||||||||+||||+||++||++++.+ +++||||||+|++|+||
T Consensus 38 ~~~~~~F~qW~~eL~~GFnlL~YG~GSKr~lL~~Fa~~~l~~~~~~~~vvvnGy~p~~~~k~ 99 (326)
T PF04084_consen 38 ELHRKLFPQWMFELSQGFNLLFYGYGSKRKLLNDFAEKYLSDWGDGPVVVVNGYFPSLSIKD 99 (326)
T ss_pred HHHHHHHHHHHHHHhCCCeEEEEecChHHHHHHHHHHHHhhccCCCcEEEEEccCCCCcHHH
Confidence 567889999999999999999999999999999999999999 89999999999999985
No 2
>KOG2928|consensus
Probab=99.89 E-value=1.4e-23 Score=160.72 Aligned_cols=58 Identities=38% Similarity=0.579 Sum_probs=55.6
Q ss_pred hhhhhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCCCcccC
Q psy303 5 ILKDIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPDLTLKE 62 (62)
Q Consensus 5 ~~~~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~~tikd 62 (62)
.++..|+||+++|.+||||||||+||||.||++|+..++.+.+++|||||+|++++|+
T Consensus 234 ~~~~~f~Kw~~~L~~gFNiLfYG~GSKr~lLe~F~~~~L~~~~~~ving~~p~ln~K~ 291 (518)
T KOG2928|consen 234 DYKKMFPKWMFELARGFNILFYGVGSKRALLEEFAPEALYDYTVLVINGYFPSLNVKD 291 (518)
T ss_pred HHHHhhHHHHHHHhccccEEEEecCcHHHHHHHHHHHhcccceEEEEeccCccchHHH
Confidence 4678899999999999999999999999999999999999999999999999999885
No 3
>COG5575 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]
Probab=99.81 E-value=1.1e-20 Score=144.07 Aligned_cols=58 Identities=22% Similarity=0.391 Sum_probs=55.5
Q ss_pred hhhhhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCCCcccC
Q psy303 5 ILKDIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPDLTLKE 62 (62)
Q Consensus 5 ~~~~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~~tikd 62 (62)
++++.||||+|||.+||||||||+|||+.+|++|+..++...||+++|||+|.++.||
T Consensus 241 ~q~k~F~q~~feL~~~FnLLFYG~GSK~~fL~~f~~~~LP~~P~~~lnGY~p~~~~r~ 298 (535)
T COG5575 241 LQCKNFHQELFELARSFNLLFYGYGSKTAFLRKFFPSALPCFPIFYLNGYCPIMSRRE 298 (535)
T ss_pred eeccccHHHHHHHhhhceEEEEecCchHHHHHHHhHHhcCCcceeeecccCccccHHH
Confidence 5788999999999999999999999999999999999999999999999999999875
No 4
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=85.79 E-value=0.96 Score=26.20 Aligned_cols=23 Identities=22% Similarity=0.523 Sum_probs=18.4
Q ss_pred HHHHHHHhhcCCcEEEEeccCCC
Q psy303 35 INEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 35 L~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
|.++++..-.+..++|+|||...
T Consensus 18 l~~lr~~~k~~~DI~I~NGF~~~ 40 (57)
T PF14453_consen 18 LFELRKESKPDADIVILNGFPTK 40 (57)
T ss_pred HHHHHHhhCCCCCEEEEcCcccC
Confidence 56777777778889999999753
No 5
>TIGR01738 bioH putative pimeloyl-BioC--CoA transferase BioH. This CoA-binding enzyme is required for the production of pimeloyl-coenzyme A, the substrate of the BioF protein early in the biosynthesis of biotin. Its exact function is unknown, but is proposed in ref 2. This enzyme belongs to the alpha/beta hydrolase fold family (pfam model pfam00561). Members of this family are restricted to the Proteobacteria.
Probab=78.13 E-value=3.2 Score=25.59 Aligned_cols=29 Identities=17% Similarity=0.492 Sum_probs=14.9
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEE
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVI 51 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvV 51 (62)
|+++|+|+-......+++.+..+.+|+.+
T Consensus 8 v~~HG~~~~~~~~~~~~~~l~~~~~vi~~ 36 (245)
T TIGR01738 8 VLIHGWGMNAEVFRCLDEELSAHFTLHLV 36 (245)
T ss_pred EEEcCCCCchhhHHHHHHhhccCeEEEEe
Confidence 45566666555555555544333344443
No 6
>COG1166 SpeA Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]
Probab=77.52 E-value=2.3 Score=34.66 Aligned_cols=27 Identities=22% Similarity=0.351 Sum_probs=22.6
Q ss_pred ecchHHHHHHHHHHhhcCCcEEEEeccC
Q psy303 28 FGSKYKVINEFHKKMLSNSKVLVINGFF 55 (62)
Q Consensus 28 ~GSKr~lL~~Fa~~~l~~~~~lvVnGy~ 55 (62)
-|||-+|+---|... ..++.||+|||.
T Consensus 145 AGSK~ELm~vLA~~~-~~~~~IvCNGyK 171 (652)
T COG1166 145 AGSKAELMAVLAHAG-NPGSLIVCNGYK 171 (652)
T ss_pred CCCHHHHHHHHHhcC-CCCCeEEecCcc
Confidence 499999999888765 567899999996
No 7
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=71.98 E-value=16 Score=21.89 Aligned_cols=33 Identities=18% Similarity=0.223 Sum_probs=26.4
Q ss_pred HhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 18 IENFNILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 18 ~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
..|-.|++.|.||-.. +++|++..--+.| |.+|
T Consensus 11 ~~gv~lv~I~~g~~~~-~~~f~~~~~~p~~-ly~D 43 (115)
T PF13911_consen 11 AAGVKLVVIGCGSPEG-IEKFCELTGFPFP-LYVD 43 (115)
T ss_pred HcCCeEEEEEcCCHHH-HHHHHhccCCCCc-EEEe
Confidence 5899999999999988 9999987555566 4443
No 8
>COG2924 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.80 E-value=3.9 Score=25.88 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=25.8
Q ss_pred chHHHHHHHHHHhhcCCcEEEEeccCCC
Q psy303 30 SKYKVINEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 30 SKr~lL~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
+-|++|++=.++++.++..+-|.||.|-
T Consensus 61 e~Rk~Leqem~~flf~~~~~~~~GYvpp 88 (90)
T COG2924 61 EHRKLLEQEMVNFLFEGKAVHIEGYVPP 88 (90)
T ss_pred HHHHHHHHHHHHHhhcCccccccccCCC
Confidence 6789999999999999999999999985
No 9
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=69.65 E-value=6.6 Score=22.55 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=24.6
Q ss_pred hhhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 3 KTILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 3 ~~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
+.++..++.....+|.+|-++-+-|+|+
T Consensus 21 ~~vl~~~~~~i~~~L~~g~~V~l~~~G~ 48 (87)
T cd00591 21 EAAVDAFLDVITEALAKGEKVELPGFGT 48 (87)
T ss_pred HHHHHHHHHHHHHHHhCCCeEEEeCCEE
Confidence 3567788899999999999999999995
No 10
>COG0505 CarA Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=66.77 E-value=5.1 Score=30.81 Aligned_cols=26 Identities=19% Similarity=0.324 Sum_probs=23.2
Q ss_pred HhCcceEEEeecchHHHHHHHHHHhh
Q psy303 18 IENFNILLHGFGSKYKVINEFHKKML 43 (62)
Q Consensus 18 ~~gFnlllYG~GSKr~lL~~Fa~~~l 43 (62)
..++.++++=+|.||++|++|+++-+
T Consensus 177 ~~~~~Vv~iD~GvK~nIlr~L~~rg~ 202 (368)
T COG0505 177 EPGKHVVVIDFGVKRNILRELVKRGC 202 (368)
T ss_pred CCCcEEEEEEcCccHHHHHHHHHCCC
Confidence 35899999999999999999998764
No 11
>PRK11460 putative hydrolase; Provisional
Probab=64.96 E-value=7.2 Score=26.32 Aligned_cols=34 Identities=24% Similarity=0.366 Sum_probs=24.4
Q ss_pred eEEEeecchHHHHHHHHHHhhcCC---cEEEEeccCC
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNS---KVLVINGFFP 56 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~---~~lvVnGy~p 56 (62)
|+|+|+|+-.+-+..+++.+-... .++.++|+.|
T Consensus 20 IlLHG~G~~~~~~~~l~~~l~~~~~~~~~i~~~g~~~ 56 (232)
T PRK11460 20 LLFHGVGDNPVAMGEIGSWFAPAFPDALVVSVGGPEP 56 (232)
T ss_pred EEEeCCCCChHHHHHHHHHHHHHCCCCEEECCCCCCC
Confidence 789999999888888777764333 4556677644
No 12
>PF12695 Abhydrolase_5: Alpha/beta hydrolase family; PDB: 3D0K_B 2I3D_B 3DOH_B 3DOI_B 3PFB_A 3S2Z_B 3PFC_A 3QM1_A 3PF8_B 3PF9_A ....
Probab=64.71 E-value=9.1 Score=22.43 Aligned_cols=29 Identities=21% Similarity=0.452 Sum_probs=21.1
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEE
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVI 51 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvV 51 (62)
|+++|.|+.+.-...+++.+.+.+..++.
T Consensus 3 v~~HG~~~~~~~~~~~~~~l~~~G~~v~~ 31 (145)
T PF12695_consen 3 VLLHGWGGSRRDYQPLAEALAEQGYAVVA 31 (145)
T ss_dssp EEECTTTTTTHHHHHHHHHHHHTTEEEEE
T ss_pred EEECCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 57888887777788888888777654333
No 13
>TIGR03695 menH_SHCHC 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase.
Probab=61.86 E-value=14 Score=22.52 Aligned_cols=30 Identities=20% Similarity=0.285 Sum_probs=19.7
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
|+++|.|+-......+++.+-.+..|+.+|
T Consensus 5 v~~hG~~~~~~~~~~~~~~L~~~~~v~~~d 34 (251)
T TIGR03695 5 VFLHGFLGSGADWQALIELLGPHFRCLAID 34 (251)
T ss_pred EEEcCCCCchhhHHHHHHHhcccCeEEEEc
Confidence 567777777666677766655445566665
No 14
>PF12048 DUF3530: Protein of unknown function (DUF3530); InterPro: IPR022529 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.
Probab=61.73 E-value=19 Score=25.98 Aligned_cols=41 Identities=20% Similarity=0.336 Sum_probs=31.8
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCC--cEEEEeccCCCCc
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNS--KVLVINGFFPDLT 59 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~--~~lvVnGy~p~~t 59 (62)
.|+|+++.|.|+==..+.++..+.-... ..|+||.|.|.-.
T Consensus 191 ~~~~ivlIg~G~gA~~~~~~la~~~~~~~daLV~I~a~~p~~~ 233 (310)
T PF12048_consen 191 GGKNIVLIGHGTGAGWAARYLAEKPPPMPDALVLINAYWPQPD 233 (310)
T ss_pred CCceEEEEEeChhHHHHHHHHhcCCCcccCeEEEEeCCCCcch
Confidence 4677999999988888888777664433 3799999999754
No 15
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=60.61 E-value=11 Score=22.32 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=24.2
Q ss_pred hhhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 3 KTILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 3 ~~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
+.++...+......|.+|.++-+-|+|+
T Consensus 23 ~~vv~~~~~~i~~~L~~g~~V~l~gfG~ 50 (94)
T TIGR00988 23 EDAVKTMLEHMASALAQGDRIEIRGFGS 50 (94)
T ss_pred HHHHHHHHHHHHHHHHcCCeEEEcCcEE
Confidence 3567778888999999999999999995
No 16
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=57.12 E-value=16 Score=21.09 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=23.3
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
.++..++.--...|.+|-++-+-|+|+
T Consensus 23 ~vl~~l~~~i~~~L~~g~~V~i~g~G~ 49 (90)
T smart00411 23 AAVDAFLEIITEALKKGEKVELRGFGT 49 (90)
T ss_pred HHHHHHHHHHHHHHhCCCeEEEeCcEE
Confidence 466777888888999999999999995
No 17
>PLN02771 carbamoyl-phosphate synthase (glutamine-hydrolyzing)
Probab=56.72 E-value=17 Score=28.12 Aligned_cols=22 Identities=14% Similarity=0.377 Sum_probs=20.2
Q ss_pred cceEEEeecchHHHHHHHHHHh
Q psy303 21 FNILLHGFGSKYKVINEFHKKM 42 (62)
Q Consensus 21 FnlllYG~GSKr~lL~~Fa~~~ 42 (62)
+.|+++++|.|+.+++.+++.-
T Consensus 241 ~~IvviD~G~K~nIlr~L~~~G 262 (415)
T PLN02771 241 YHVIAYDFGIKHNILRRLASYG 262 (415)
T ss_pred CEEEEECCChHHHHHHHHHHcC
Confidence 7899999999999999999863
No 18
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=56.25 E-value=10 Score=21.82 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=22.2
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
.++..++..-..+|.+|-.+-+-|+|+
T Consensus 23 ~vl~~~~~~i~~~L~~g~~V~l~g~G~ 49 (90)
T PF00216_consen 23 AVLDALFDVIKEALKEGESVKLPGFGT 49 (90)
T ss_dssp HHHHHHHHHHHHHHHTT-EEEETTTEE
T ss_pred HHHHHHHHHHHHHHhcCCeEEeeceeE
Confidence 466778888889999999999999994
No 19
>PRK05541 adenylylsulfate kinase; Provisional
Probab=56.02 E-value=26 Score=22.23 Aligned_cols=37 Identities=19% Similarity=0.444 Sum_probs=26.0
Q ss_pred HHhCcceEEEee-cc-hHHHHHHHHHHhhcCC-cEEEEec
Q psy303 17 EIENFNILLHGF-GS-KYKVINEFHKKMLSNS-KVLVING 53 (62)
Q Consensus 17 L~~gFnlllYG~-GS-Kr~lL~~Fa~~~l~~~-~~lvVnG 53 (62)
...|+.|++.|+ || |..+.+.++..+...+ .+++++|
T Consensus 4 ~~~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~~ 43 (176)
T PRK05541 4 KPNGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDG 43 (176)
T ss_pred CCCCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEec
Confidence 467899999998 55 7778877877775332 3566655
No 20
>PF01640 Peptidase_C10: Peptidase C10 family classification.; InterPro: IPR000200 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C10 (streptopain family, clan CA). Streptopain is a cysteine protease found in Streptococcus pyogenes that shows some structural and functional similarity to papain (family C1) [, ]. The order of the catalytic cysteine/histidine dyad is the same and the surrounding sequences are similar. The two proteins also show similar specificities, both preferring a hydrophobic residue at the P2 site [, ]. Streptopain shows a high degree of sequence similarity to the S. pyogenes exotoxin B, and strong similarity to the prtT gene product of Porphyromonas gingivalis (Bacteroides gingivalis), both of which have been included in the family [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 4D8I_A 4D8E_A 4D8B_A 3BBA_B 3BB7_A 2JTC_A 1PVJ_A 1DKI_D 2UZJ_A.
Probab=55.97 E-value=10 Score=25.48 Aligned_cols=31 Identities=19% Similarity=0.160 Sum_probs=22.4
Q ss_pred HHHHHHhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCC
Q psy303 13 IIQLEIENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFP 56 (62)
Q Consensus 13 W~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p 56 (62)
-..||.+|.-|++.|..... ++..|||||..
T Consensus 143 i~~el~~~rPV~~~g~~~~~-------------GHawViDGy~~ 173 (192)
T PF01640_consen 143 IRNELDNGRPVLYSGNSKSG-------------GHAWVIDGYDS 173 (192)
T ss_dssp HHHHHHTT--EEEEEEETTE-------------EEEEEEEEEES
T ss_pred HHHHHHcCCCEEEEEecCCC-------------CeEEEEcCccC
Confidence 35678889999888887443 88999999954
No 21
>TIGR02427 protocat_pcaD 3-oxoadipate enol-lactonase. Members of this family are 3-oxoadipate enol-lactonase. Note that the substrate is known as 3-oxoadipate enol-lactone, 2-oxo-2,3-dihydrofuran-5-acetate, 4,5-Dihydro-5-oxofuran-2-acetate, and 5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the catalyzes the fourth step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate, and vanillate all can be converted in one step to protocatechuate. This enzyme also acts in catechol degradation. In genomes that catabolize both catechol and protocatechuate, two forms of this enzyme may be found. All members of the seed alignment for this model were chosen from within protocatechuate degradation operons of at least three genes of the pathway, from genomes with the complete pathway through beta-ketoadipate.
Probab=53.97 E-value=20 Score=22.02 Aligned_cols=20 Identities=5% Similarity=0.406 Sum_probs=9.1
Q ss_pred eEEEeecchHHHHHHHHHHh
Q psy303 23 ILLHGFGSKYKVINEFHKKM 42 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~ 42 (62)
|+++|+|+=......+++.+
T Consensus 17 i~~hg~~~~~~~~~~~~~~l 36 (251)
T TIGR02427 17 VFINSLGTDLRMWDPVLPAL 36 (251)
T ss_pred EEEcCcccchhhHHHHHHHh
Confidence 34445554444444444433
No 22
>PF07985 SRR1: SRR1; InterPro: IPR012942 Sensitivity To Red Light Reduced proteins (SRR1) are signalling proteins thought to be involved in regulating the circadian clock input pathway, which is required for normal oscillator function. In Arabidopsis thaliana it regulates the expression of clock-regulated genes such as CCA1 and TOC1. It is also involved in both the phytochrome B (PHYB) and PHYB-independent signaling pathways [].
Probab=53.63 E-value=9.3 Score=21.35 Aligned_cols=10 Identities=40% Similarity=0.577 Sum_probs=8.0
Q ss_pred ceEEEeecch
Q psy303 22 NILLHGFGSK 31 (62)
Q Consensus 22 nlllYG~GSK 31 (62)
+|..||+||=
T Consensus 1 ~ivclGLGsf 10 (56)
T PF07985_consen 1 KIVCLGLGSF 10 (56)
T ss_pred CEEEEEecCc
Confidence 4789999973
No 23
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=53.01 E-value=48 Score=22.28 Aligned_cols=45 Identities=24% Similarity=0.356 Sum_probs=29.2
Q ss_pred hhhHHHHHHH-HhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEecc
Q psy303 8 DIQNGIIQLE-IENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGF 54 (62)
Q Consensus 8 ~~f~qW~~eL-~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy 54 (62)
++++.-..+. ..|..+ |=+||+-+.+++.++.+-.+.|-+.|-|+
T Consensus 35 dl~~~l~~~~~~~~~~v--fllG~~~~v~~~~~~~l~~~yP~l~i~g~ 80 (177)
T TIGR00696 35 DLMEELCQRAGKEKLPI--FLYGGKPDVLQQLKVKLIKEYPKLKIVGA 80 (177)
T ss_pred HHHHHHHHHHHHcCCeE--EEECCCHHHHHHHHHHHHHHCCCCEEEEE
Confidence 3444444333 345454 55699999999999999888874444344
No 24
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=51.92 E-value=5.2 Score=23.86 Aligned_cols=17 Identities=41% Similarity=0.511 Sum_probs=15.4
Q ss_pred EEEeecchHHHHHHHHH
Q psy303 24 LLHGFGSKYKVINEFHK 40 (62)
Q Consensus 24 llYG~GSKr~lL~~Fa~ 40 (62)
++||-||.|.-.++|-.
T Consensus 26 ~LYGpgsnRTT~N~flS 42 (63)
T PF08157_consen 26 RLYGPGSNRTTVNEFLS 42 (63)
T ss_pred hccCCCCCcccHHHHhh
Confidence 69999999999999875
No 25
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=51.85 E-value=13 Score=24.53 Aligned_cols=40 Identities=10% Similarity=0.221 Sum_probs=22.7
Q ss_pred HhCcceEEE-----------eecchHHHHHHHHHHhhcC--C-cEEEEeccCCC
Q psy303 18 IENFNILLH-----------GFGSKYKVINEFHKKMLSN--S-KVLVINGFFPD 57 (62)
Q Consensus 18 ~~gFnlllY-----------G~GSKr~lL~~Fa~~~l~~--~-~~lvVnGy~p~ 57 (62)
-.||||+.- .+..-|+.|-+....+..- . -+||.|||.+.
T Consensus 3 IDGYNli~~~~~l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~~~~ 56 (166)
T PF05991_consen 3 IDGYNLIHAWPELRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAYKVP 56 (166)
T ss_pred EcchhhhCCCHHHHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCCcCC
Confidence 357787655 1233555555555555432 2 27999998654
No 26
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=50.91 E-value=18 Score=21.85 Aligned_cols=29 Identities=10% Similarity=0.291 Sum_probs=24.1
Q ss_pred chHHHHHHHHHHhhcCCcEEEEeccCCCC
Q psy303 30 SKYKVINEFHKKMLSNSKVLVINGFFPDL 58 (62)
Q Consensus 30 SKr~lL~~Fa~~~l~~~~~lvVnGy~p~~ 58 (62)
||.++.++.|..+=.|...|||+|+.+..
T Consensus 14 sr~ei~~klA~~~~~~~~~ivv~~~~t~f 42 (84)
T PF01282_consen 14 SRKEIREKLAAMLNVDPDLIVVFGIKTEF 42 (84)
T ss_dssp -HHHHHHHHHHHHTSTGCCEEEEEEEESS
T ss_pred CHHHHHHHHHHHhCCCCCeEEEeccEecC
Confidence 89999999999997777899999887654
No 27
>PF12697 Abhydrolase_6: Alpha/beta hydrolase family; PDB: 3LLC_A 3A2N_E 3A2M_A 3A2L_A 3AFI_F 3C5V_A 3C5W_P 3E0X_A 2ZJF_A 3QYJ_A ....
Probab=50.69 E-value=15 Score=21.96 Aligned_cols=30 Identities=20% Similarity=0.535 Sum_probs=12.9
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
|+++|+|+=......+++.+-.+..++.+|
T Consensus 2 v~~hG~~~~~~~~~~~~~~l~~~~~v~~~d 31 (228)
T PF12697_consen 2 VFLHGFGGSSESWDPLAEALARGYRVIAFD 31 (228)
T ss_dssp EEE-STTTTGGGGHHHHHHHHTTSEEEEEE
T ss_pred EEECCCCCCHHHHHHHHHHHhCCCEEEEEe
Confidence 345555554444444444442233344443
No 28
>PRK10673 acyl-CoA esterase; Provisional
Probab=48.70 E-value=29 Score=22.27 Aligned_cols=18 Identities=6% Similarity=0.019 Sum_probs=9.8
Q ss_pred hhHHHHHHHHhCcceEEE
Q psy303 9 IQNGIIQLEIENFNILLH 26 (62)
Q Consensus 9 ~f~qW~~eL~~gFnlllY 26 (62)
.|..+...|.++|+++.+
T Consensus 31 ~~~~~~~~l~~~~~vi~~ 48 (255)
T PRK10673 31 NLGVLARDLVNDHDIIQV 48 (255)
T ss_pred HHHHHHHHHhhCCeEEEE
Confidence 344555555566666554
No 29
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=47.61 E-value=68 Score=20.99 Aligned_cols=45 Identities=20% Similarity=0.425 Sum_probs=30.2
Q ss_pred hhhhHHHHHHHHh-CcceEEEeecchHHHHHHHHHHhhcCCcEEEEec
Q psy303 7 KDIQNGIIQLEIE-NFNILLHGFGSKYKVINEFHKKMLSNSKVLVING 53 (62)
Q Consensus 7 ~~~f~qW~~eL~~-gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnG 53 (62)
.++++.-...... +.++-| +|++-+.++++++..-...|-+.|=|
T Consensus 32 ~dl~~~ll~~~~~~~~~v~l--lG~~~~~~~~~~~~l~~~yp~l~i~g 77 (171)
T cd06533 32 SDLMPALLELAAQKGLRVFL--LGAKPEVLEKAAERLRARYPGLKIVG 77 (171)
T ss_pred HHHHHHHHHHHHHcCCeEEE--ECCCHHHHHHHHHHHHHHCCCcEEEE
Confidence 3455555555544 566655 58999999999998887777433333
No 30
>PF09673 TrbC_Ftype: Type-F conjugative transfer system pilin assembly protein; InterPro: IPR019106 This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA [, ]. The N-terminal portion of these proteins is heterogeneous.
Probab=46.38 E-value=28 Score=21.76 Aligned_cols=26 Identities=23% Similarity=0.377 Sum_probs=13.7
Q ss_pred HHHHHHHhhcCCcEEEEeccCCCCccc
Q psy303 35 INEFHKKMLSNSKVLVINGFFPDLTLK 61 (62)
Q Consensus 35 L~~Fa~~~l~~~~~lvVnGy~p~~tik 61 (62)
|.+...+.-.-+-.+|++|+.++ +++
T Consensus 13 L~~l~~~a~~~~~~~V~RG~~~g-~~~ 38 (113)
T PF09673_consen 13 LRNLLKQAERAGVVVVFRGFPDG-SFK 38 (113)
T ss_pred HHHHHHHHHhCCcEEEEECCCCC-CHH
Confidence 33333333333556777777766 543
No 31
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=46.14 E-value=22 Score=23.10 Aligned_cols=27 Identities=11% Similarity=0.121 Sum_probs=23.8
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
..+..+......+|.+|.+|-|=|+|+
T Consensus 53 ~vl~~l~~~i~~~L~~G~~V~L~gfGt 79 (145)
T TIGR01201 53 GIIDRLAYVLRRELANGKTVRLGEIGT 79 (145)
T ss_pred HHHHHHHHHHHHHHhCCCeEEeCCCEE
Confidence 456778888999999999999999996
No 32
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=45.57 E-value=27 Score=20.90 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=23.7
Q ss_pred hhhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 3 KTILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 3 ~~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
+.++..++.-....|..|.+|-|-|+|+
T Consensus 23 ~~vv~~~~~~i~~~L~~g~~V~l~gfG~ 50 (96)
T TIGR00987 23 KELVELFFEEIRRALENGEQVKLSGFGN 50 (96)
T ss_pred HHHHHHHHHHHHHHHHcCCeEEecCCEE
Confidence 3466777888888999999999999994
No 33
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown.
Probab=45.39 E-value=22 Score=24.72 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=23.1
Q ss_pred eecchHHH--HHHHHHHhhcCCcEEEEecc
Q psy303 27 GFGSKYKV--INEFHKKMLSNSKVLVINGF 54 (62)
Q Consensus 27 G~GSKr~l--L~~Fa~~~l~~~~~lvVnGy 54 (62)
|+-|.|++ +.+-.+++.....+|+|||+
T Consensus 73 G~LafRE~p~l~~~~~~l~~~PDlilVDG~ 102 (208)
T cd06559 73 GLLAFREGPPLLEALEKLKTKPDLLLVDGH 102 (208)
T ss_pred hhHHHhhHHHHHHHHHhCCCCCCEEEEeCC
Confidence 78899999 88888877655569999997
No 34
>PRK10349 carboxylesterase BioH; Provisional
Probab=45.38 E-value=35 Score=22.24 Aligned_cols=30 Identities=23% Similarity=0.475 Sum_probs=19.1
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
|+++|+|+=...-..+++.+-.+..|++++
T Consensus 17 vllHG~~~~~~~w~~~~~~L~~~~~vi~~D 46 (256)
T PRK10349 17 VLLHGWGLNAEVWRCIDEELSSHFTLHLVD 46 (256)
T ss_pred EEECCCCCChhHHHHHHHHHhcCCEEEEec
Confidence 477888766666666666665455566554
No 35
>PF03959 FSH1: Serine hydrolase (FSH1); InterPro: IPR005645 This entry represents proteins belonging to the AB hydrolase family. It consists of serine hydrolases of unknown specificity [, ] and includes uncharacterised proteins.; PDB: 1YCD_A.
Probab=45.23 E-value=33 Score=22.84 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=8.2
Q ss_pred eEEEeecchHHHHH
Q psy303 23 ILLHGFGSKYKVIN 36 (62)
Q Consensus 23 lllYG~GSKr~lL~ 36 (62)
|||+|+|+--++++
T Consensus 8 LcLHG~~~na~if~ 21 (212)
T PF03959_consen 8 LCLHGYGQNAEIFR 21 (212)
T ss_dssp EEE--TT--HHHHH
T ss_pred EEeCCCCcCHHHHH
Confidence 79999999877765
No 36
>TIGR02240 PHA_depoly_arom poly(3-hydroxyalkanoate) depolymerase. This family consists of the polyhydroxyalkanoic acid (PHA) depolymerase of Pseudomonas oleovorans, Pseudomonas putida BM01, and related species. This enzyme is part of polyester storage and mobilization system as in many bacteria. However, species containing this enzyme are unusual in their capacity to produce aromatic polyesters when grown on carbon sources such as benzoic acid or phenylacetic acid.
Probab=44.68 E-value=40 Score=22.44 Aligned_cols=18 Identities=6% Similarity=0.089 Sum_probs=9.2
Q ss_pred hhHHHHHHHHhCcceEEE
Q psy303 9 IQNGIIQLEIENFNILLH 26 (62)
Q Consensus 9 ~f~qW~~eL~~gFnlllY 26 (62)
.|..|...|..+|+++.+
T Consensus 40 ~w~~~~~~L~~~~~vi~~ 57 (276)
T TIGR02240 40 LVFPFIEALDPDLEVIAF 57 (276)
T ss_pred HHHHHHHHhccCceEEEE
Confidence 344444455555555554
No 37
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=44.15 E-value=23 Score=22.37 Aligned_cols=25 Identities=20% Similarity=0.596 Sum_probs=20.8
Q ss_pred hhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 5 ILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 5 ~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
++..+......+|.+|+++-+ |+|+
T Consensus 53 vl~~~~~~~~~~l~~G~sV~~-glg~ 77 (124)
T PF14848_consen 53 VLNALKDEMIEALMNGYSVNL-GLGY 77 (124)
T ss_pred HHHHHHHHHHHHHhCCCEEEc-CCEE
Confidence 456678888999999999987 8883
No 38
>PF02230 Abhydrolase_2: Phospholipase/Carboxylesterase; InterPro: IPR003140 This entry represents the alpha/beta hydrolase domain found in phospholipases [], carboxylesterases [] and thioesterases.; GO: 0016787 hydrolase activity; PDB: 3U0V_A 1AUR_A 1AUO_B 1FJ2_B 3CN9_A 3CN7_A.
Probab=44.08 E-value=50 Score=21.63 Aligned_cols=19 Identities=32% Similarity=0.609 Sum_probs=13.1
Q ss_pred eEEEeecchHHHHHHHHHH
Q psy303 23 ILLHGFGSKYKVINEFHKK 41 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~ 41 (62)
|+|+|+|+--+.+....+.
T Consensus 18 i~LHG~G~~~~~~~~~~~~ 36 (216)
T PF02230_consen 18 ILLHGYGDSEDLFALLAEL 36 (216)
T ss_dssp EEE--TTS-HHHHHHHHHH
T ss_pred EEECCCCCCcchhHHHHhh
Confidence 6899999999888877773
No 39
>PRK08116 hypothetical protein; Validated
Probab=43.96 E-value=97 Score=21.79 Aligned_cols=33 Identities=24% Similarity=0.470 Sum_probs=22.6
Q ss_pred CcceEEEe-ecc-hHHHHHHHHHHhhcC-CcEEEEe
Q psy303 20 NFNILLHG-FGS-KYKVINEFHKKMLSN-SKVLVIN 52 (62)
Q Consensus 20 gFnlllYG-~GS-Kr~lL~~Fa~~~l~~-~~~lvVn 52 (62)
+-.++||| .|| |-.|+...+..++.. .+++.++
T Consensus 114 ~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~ 149 (268)
T PRK08116 114 NVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVN 149 (268)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence 34489988 554 788888888887653 4566654
No 40
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=43.24 E-value=31 Score=20.46 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=23.0
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
.++...+......|.+|-++-|-|+|+
T Consensus 24 ~vv~~~~~~i~~~L~~g~~V~l~gfG~ 50 (94)
T PRK00199 24 NAVKEILEEMSDALARGDRIEIRGFGS 50 (94)
T ss_pred HHHHHHHHHHHHHHHcCCeEEEcCCEE
Confidence 456677888888999999999999994
No 41
>PF08859 DGC: DGC domain; InterPro: IPR014958 This protein appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The protein is named after a conserved central motif, the function is unknown.
Probab=43.02 E-value=24 Score=22.11 Aligned_cols=31 Identities=19% Similarity=0.272 Sum_probs=21.5
Q ss_pred CcceEEEeecchHHHHHHHHHHhhcCCcEEEEec
Q psy303 20 NFNILLHGFGSKYKVINEFHKKMLSNSKVLVING 53 (62)
Q Consensus 20 gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnG 53 (62)
+=-+|+-|+|...+-+.+.++ +..|+|+|||
T Consensus 29 ~~~~Cla~v~~~~~~~~~~a~---~~~~iIaIDG 59 (110)
T PF08859_consen 29 GEMSCLAGVGAGVEGLVKSAR---SARPIIAIDG 59 (110)
T ss_pred eeEEechhhhcCcHHHHHHHh---cCCceEEECC
Confidence 345678888887766666654 2348999988
No 42
>PF07315 DUF1462: Protein of unknown function (DUF1462); InterPro: IPR009190 There are currently no experimental data for members of this group of bacterial proteins or their homologues. A crystal structure of Q7A6J8 from SWISSPROT revealed a thioredoxin-like fold, its core consisting of three layers alpha/beta/alpha.; PDB: 1XG8_A.
Probab=42.82 E-value=27 Score=22.21 Aligned_cols=20 Identities=25% Similarity=0.468 Sum_probs=15.8
Q ss_pred HHHHHHHHhhcC---CcEEEEec
Q psy303 34 VINEFHKKMLSN---SKVLVING 53 (62)
Q Consensus 34 lL~~Fa~~~l~~---~~~lvVnG 53 (62)
--++|+++...+ +|+|+|||
T Consensus 53 ~~~~~a~~I~ede~fYPlV~i~~ 75 (93)
T PF07315_consen 53 HDQQFAERILEDELFYPLVVIND 75 (93)
T ss_dssp HHHHHHHHHHTTSS-SSEEEETT
T ss_pred HHHHHHHHHHhcccccceEEECC
Confidence 456888888876 48999987
No 43
>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A ....
Probab=42.43 E-value=90 Score=20.09 Aligned_cols=25 Identities=32% Similarity=0.530 Sum_probs=20.1
Q ss_pred CcceEEEee-cc-hHHHHHHHHHHhhc
Q psy303 20 NFNILLHGF-GS-KYKVINEFHKKMLS 44 (62)
Q Consensus 20 gFnlllYG~-GS-Kr~lL~~Fa~~~l~ 44 (62)
...+||+|- |+ |..+...|+...+.
T Consensus 19 ~ha~L~~G~~g~gk~~~a~~~a~~ll~ 45 (162)
T PF13177_consen 19 PHALLFHGPSGSGKKTLALAFARALLC 45 (162)
T ss_dssp -SEEEEECSTTSSHHHHHHHHHHHHC-
T ss_pred ceeEEEECCCCCCHHHHHHHHHHHHcC
Confidence 467999995 55 99999999999874
No 44
>PF07931 CPT: Chloramphenicol phosphotransferase-like protein; InterPro: IPR012853 The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [, ]. ; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 1QHX_A 1QHN_A 1GRR_A 1QHY_A 1QHS_A 1GRQ_A.
Probab=41.85 E-value=1.1e+02 Score=20.62 Aligned_cols=43 Identities=12% Similarity=0.237 Sum_probs=29.3
Q ss_pred hhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhcCCcEEEE
Q psy303 9 IQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLSNSKVLVI 51 (62)
Q Consensus 9 ~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvV 51 (62)
.+.--......|+||++=++=+.+.-+++..+..|.+.|++.|
T Consensus 72 ~~~~iaa~a~aG~~VIvD~v~~~~~~l~d~l~~~L~~~~vl~V 114 (174)
T PF07931_consen 72 MHAAIAAMARAGNNVIVDDVFLGPRWLQDCLRRLLAGLPVLFV 114 (174)
T ss_dssp HHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHTTS-EEEE
T ss_pred HHHHHHHHHhCCCCEEEecCccCcHHHHHHHHHHhCCCceEEE
Confidence 3444456778999999887755556689999888988887766
No 45
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=40.98 E-value=58 Score=20.46 Aligned_cols=30 Identities=10% Similarity=0.205 Sum_probs=25.5
Q ss_pred cchHHHHHHHHHHhhcCCcEEEEeccCCCC
Q psy303 29 GSKYKVINEFHKKMLSNSKVLVINGFFPDL 58 (62)
Q Consensus 29 GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~~ 58 (62)
=||.++-++.|..+=.+...|||.|+.+..
T Consensus 31 psr~eirekLa~~~~~~~~~vvv~~~~t~f 60 (99)
T PRK01178 31 PSRKDVRKKLAAMLNADKELVVVRKIKTEY 60 (99)
T ss_pred CCHHHHHHHHHHHHCcCCCEEEEEccCccC
Confidence 489999999999887777899999998764
No 46
>TIGR03611 RutD pyrimidine utilization protein D. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the hydrolase, alpha/beta fold family defined by pfam00067.
Probab=40.86 E-value=48 Score=20.64 Aligned_cols=17 Identities=6% Similarity=0.143 Sum_probs=9.7
Q ss_pred hHHHHHHHHhCcceEEE
Q psy303 10 QNGIIQLEIENFNILLH 26 (62)
Q Consensus 10 f~qW~~eL~~gFnlllY 26 (62)
|..+...|.+||+++.+
T Consensus 29 ~~~~~~~l~~~~~vi~~ 45 (257)
T TIGR03611 29 WAPQLDVLTQRFHVVTY 45 (257)
T ss_pred HHHHHHHHHhccEEEEE
Confidence 44444456666666665
No 47
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=40.80 E-value=45 Score=20.09 Aligned_cols=30 Identities=30% Similarity=0.377 Sum_probs=21.7
Q ss_pred ceEEEe---ecchHHHHHHHHHHhhcCCcEEEEecc
Q psy303 22 NILLHG---FGSKYKVINEFHKKMLSNSKVLVINGF 54 (62)
Q Consensus 22 nlllYG---~GSKr~lL~~Fa~~~l~~~~~lvVnGy 54 (62)
|||++| .| |..+++.+++.+ +.+++.|++-
T Consensus 1 ~vlL~G~~G~G-Kt~l~~~la~~~--~~~~~~i~~~ 33 (139)
T PF07728_consen 1 PVLLVGPPGTG-KTTLARELAALL--GRPVIRINCS 33 (139)
T ss_dssp EEEEEESSSSS-HHHHHHHHHHHH--TCEEEEEE-T
T ss_pred CEEEECCCCCC-HHHHHHHHHHHh--hcceEEEEec
Confidence 456665 45 999999999988 7777777654
No 48
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=40.48 E-value=1.2e+02 Score=24.48 Aligned_cols=35 Identities=9% Similarity=0.225 Sum_probs=25.6
Q ss_pred hhhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhh
Q psy303 7 KDIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKML 43 (62)
Q Consensus 7 ~~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l 43 (62)
+.....|... .++.|+.-|-||+.+++++|.+.+-
T Consensus 548 ~~v~~~l~~~--~~~~ll~Q~~~~~~~ll~~f~~~~~ 582 (697)
T PRK11747 548 QKVADLLPRD--LRLMLLVQGDQPRQRLLEKHKKRVD 582 (697)
T ss_pred HHHHHHHHHh--cCCcEEEeCCchHHHHHHHHHHHhc
Confidence 3344444332 4689999999999999999998753
No 49
>COG2969 SspB Stringent starvation protein B [General function prediction only]
Probab=40.22 E-value=44 Score=23.03 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=23.9
Q ss_pred chH-HHHHHHHHHhhcCC--cEEEEeccCCCCcc
Q psy303 30 SKY-KVINEFHKKMLSNS--KVLVINGFFPDLTL 60 (62)
Q Consensus 30 SKr-~lL~~Fa~~~l~~~--~~lvVnGy~p~~ti 60 (62)
|+| -||..|-++++.+. |+|+|+.-.|++++
T Consensus 7 p~RPYLlRA~yeWl~DN~~TPhlvVd~t~~Gv~V 40 (155)
T COG2969 7 PRRPYLLRALYEWLLDNQLTPHLVVDVTLPGVKV 40 (155)
T ss_pred CCcchHHHHHHHHHhcCCCCceEEEEccccCccC
Confidence 444 47889999998765 79999988887653
No 50
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=38.59 E-value=53 Score=21.86 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=25.6
Q ss_pred cchHHHHHHHHHHhh-cCCcEEEEeccCCCC
Q psy303 29 GSKYKVINEFHKKML-SNSKVLVINGFFPDL 58 (62)
Q Consensus 29 GSKr~lL~~Fa~~~l-~~~~~lvVnGy~p~~ 58 (62)
=||.++-+..|.-+= .|...|||.|+.+..
T Consensus 36 pSr~eirekLA~~~~v~d~~~Vvv~~~~T~f 66 (132)
T PTZ00071 36 VSKKDIKEKLAKQYKVADARTIVLFGFKTKF 66 (132)
T ss_pred CCHHHHHHHHHHHhCCCCCCEEEEEccEecC
Confidence 389999999999887 788899999998764
No 51
>PHA02857 monoglyceride lipase; Provisional
Probab=38.29 E-value=41 Score=22.20 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=19.7
Q ss_pred EEEeecchHHHHHHHHHHhhcCC-cEEEE
Q psy303 24 LLHGFGSKYKVINEFHKKMLSNS-KVLVI 51 (62)
Q Consensus 24 llYG~GSKr~lL~~Fa~~~l~~~-~~lvV 51 (62)
+++|+|+-....+.+++.+...+ .|+.+
T Consensus 30 llHG~~~~~~~~~~~~~~l~~~g~~via~ 58 (276)
T PHA02857 30 ISHGAGEHSGRYEELAENISSLGILVFSH 58 (276)
T ss_pred EeCCCccccchHHHHHHHHHhCCCEEEEc
Confidence 34899988888888887775544 45544
No 52
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=37.20 E-value=43 Score=19.99 Aligned_cols=27 Identities=19% Similarity=0.249 Sum_probs=22.0
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
..+..++.....+|.+|-+|-|=|+|+
T Consensus 25 ~vl~~~~~~i~~~L~~g~~V~l~gfG~ 51 (99)
T PRK00285 25 ELVELFFEEIRDALENGEQVKLSGFGN 51 (99)
T ss_pred HHHHHHHHHHHHHHHcCCeEEEcCCEE
Confidence 345666777788899999999999994
No 53
>PLN02824 hydrolase, alpha/beta fold family protein
Probab=36.61 E-value=51 Score=22.07 Aligned_cols=30 Identities=23% Similarity=0.461 Sum_probs=18.6
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
|+++|+|+=.......+..+..++.|+.+|
T Consensus 33 lllHG~~~~~~~w~~~~~~L~~~~~vi~~D 62 (294)
T PLN02824 33 VLVHGFGGNADHWRKNTPVLAKSHRVYAID 62 (294)
T ss_pred EEECCCCCChhHHHHHHHHHHhCCeEEEEc
Confidence 556788865555666666555556666664
No 54
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=36.58 E-value=69 Score=23.20 Aligned_cols=37 Identities=32% Similarity=0.451 Sum_probs=29.1
Q ss_pred hhhh-hhHHHHHHHHhCcceEEEeecchHHHHHHHHHHh
Q psy303 5 ILKD-IQNGIIQLEIENFNILLHGFGSKYKVINEFHKKM 42 (62)
Q Consensus 5 ~~~~-~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~ 42 (62)
++.+ +-|.-..++.+|=.||+|| |.=.+-+++|....
T Consensus 17 lL~d~Idp~i~~wi~e~kyI~iYG-G~D~eWIq~Ft~~a 54 (235)
T PF14577_consen 17 LLVDGIDPTILNWIKEGKYIFIYG-GEDMEWIQEFTKAA 54 (235)
T ss_pred HHHcccCHhHHHHhhCCcEEEEEC-CCCHHHHHHHHHHH
Confidence 3444 6666667789999999999 88889999998655
No 55
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=35.78 E-value=79 Score=18.37 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=14.3
Q ss_pred eEEEeecchHHHHHHHHHHhhcCC-cEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNS-KVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~-~~lvVn 52 (62)
+++.|+| ++-..-++.+..++ ++++|+
T Consensus 1 vvI~G~g---~~~~~i~~~L~~~~~~vvvid 28 (116)
T PF02254_consen 1 VVIIGYG---RIGREIAEQLKEGGIDVVVID 28 (116)
T ss_dssp EEEES-S---HHHHHHHHHHHHTTSEEEEEE
T ss_pred eEEEcCC---HHHHHHHHHHHhCCCEEEEEE
Confidence 4667777 44455555555444 566553
No 56
>KOG2541|consensus
Probab=34.95 E-value=38 Score=25.51 Aligned_cols=31 Identities=13% Similarity=0.140 Sum_probs=23.6
Q ss_pred HHHHHhCcceEEEeecchHHHHHHHHHHhhcCCc
Q psy303 14 IQLEIENFNILLHGFGSKYKVINEFHKKMLSNSK 47 (62)
Q Consensus 14 ~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~ 47 (62)
+-+|++|||++-|--| .|+-+=.-+.+.+.|
T Consensus 87 m~~lsqGynivg~SQG---glv~Raliq~cd~pp 117 (296)
T KOG2541|consen 87 MPELSQGYNIVGYSQG---GLVARALIQFCDNPP 117 (296)
T ss_pred chhccCceEEEEEccc---cHHHHHHHHhCCCCC
Confidence 4589999999999999 666666666666644
No 57
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=34.86 E-value=64 Score=20.12 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=24.2
Q ss_pred hhhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 3 KTILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 3 ~~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
+.+....|......|.+|=.|-|-|+|+
T Consensus 23 ~~~v~~~~~~i~~aL~~G~~V~l~gFG~ 50 (94)
T COG0776 23 EEAVDAFLEEITEALAKGERVELRGFGT 50 (94)
T ss_pred HHHHHHHHHHHHHHHHcCCeEEEeeeee
Confidence 3566777899999999999999999995
No 58
>PF10707 YrbL-PhoP_reg: PhoP regulatory network protein YrbL; InterPro: IPR019647 This entry represents proteins that are activated by the protein PhoP. PhoP controls the expression of a large number of genes that mediate adaptation to low Mg2+ environments and/or virulence in several bacterial species. YbrL is proposed to be acting in a loop activity with PhoP and PrmA analogous to the multi-component loop in Salmonella sp., where the PhoP-dependent PmrD protein activates the regulatory protein PmrA, and the activated PmrA then represses transcription from the PmrD promoter which harbours binding sites for both the PhoP and PmrA proteins. Expression of YrbL is induced in low Mg2+ in a PhoP-dependent fashion and repressed by Fe3+ in a PmrA-dependent manner [].
Probab=33.57 E-value=67 Score=21.93 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=9.8
Q ss_pred hHHHHHHHHHHhh
Q psy303 31 KYKVINEFHKKML 43 (62)
Q Consensus 31 Kr~lL~~Fa~~~l 43 (62)
-+++|++|.+.++
T Consensus 123 ~~~~L~~f~~~l~ 135 (199)
T PF10707_consen 123 LRQALDEFKRYLL 135 (199)
T ss_pred HHHHHHHHHHHHH
Confidence 3577888888875
No 59
>PF08061 P68HR: P68HR (NUC004) repeat; InterPro: IPR012587 This short region is found in two copies in p68-like RNA helicases [].; GO: 0003712 transcription cofactor activity, 0003724 RNA helicase activity, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0005634 nucleus
Probab=33.16 E-value=15 Score=19.38 Aligned_cols=8 Identities=38% Similarity=0.679 Sum_probs=5.6
Q ss_pred eecchHHH
Q psy303 27 GFGSKYKV 34 (62)
Q Consensus 27 G~GSKr~l 34 (62)
||+|||+.
T Consensus 20 GY~skr~~ 27 (33)
T PF08061_consen 20 GYSSKRDF 27 (33)
T ss_pred ccchhhhc
Confidence 77887753
No 60
>PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
Probab=32.99 E-value=55 Score=22.45 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=17.2
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEec
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVING 53 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVnG 53 (62)
|+++|+|+=..-....++.+....+|+.+|.
T Consensus 135 l~~HG~~~~~~~~~~~~~~l~~~~~v~~~d~ 165 (371)
T PRK14875 135 VLIHGFGGDLNNWLFNHAALAAGRPVIALDL 165 (371)
T ss_pred EEECCCCCccchHHHHHHHHhcCCEEEEEcC
Confidence 4556776655555555554444455666653
No 61
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=32.70 E-value=1e+02 Score=17.70 Aligned_cols=8 Identities=38% Similarity=0.463 Sum_probs=3.9
Q ss_pred cEEEEecc
Q psy303 47 KVLVINGF 54 (62)
Q Consensus 47 ~~lvVnGy 54 (62)
++|+++.+
T Consensus 60 ~vl~iDe~ 67 (132)
T PF00004_consen 60 CVLFIDEI 67 (132)
T ss_dssp EEEEEETG
T ss_pred eeeeeccc
Confidence 35555544
No 62
>PRK11126 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; Provisional
Probab=32.51 E-value=74 Score=20.24 Aligned_cols=16 Identities=6% Similarity=-0.039 Sum_probs=8.7
Q ss_pred hHHHHHHHHhCcceEEE
Q psy303 10 QNGIIQLEIENFNILLH 26 (62)
Q Consensus 10 f~qW~~eL~~gFnlllY 26 (62)
|....-.| .+|+++.+
T Consensus 18 w~~~~~~l-~~~~vi~~ 33 (242)
T PRK11126 18 WQPVGEAL-PDYPRLYI 33 (242)
T ss_pred HHHHHHHc-CCCCEEEe
Confidence 44444455 36777764
No 63
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=32.18 E-value=71 Score=20.89 Aligned_cols=33 Identities=15% Similarity=0.189 Sum_probs=25.9
Q ss_pred EEEeecchHHHHHHHHHHhhcCCcEEEEeccCC
Q psy303 24 LLHGFGSKYKVINEFHKKMLSNSKVLVINGFFP 56 (62)
Q Consensus 24 llYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p 56 (62)
=+|=+|++-+.+++.++.+-..+|-+.|-|+.+
T Consensus 50 ~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~~~ 82 (172)
T PF03808_consen 50 RIFLLGGSEEVLEKAAANLRRRYPGLRIVGYHH 82 (172)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence 445578999999999999998888666666554
No 64
>PRK03592 haloalkane dehalogenase; Provisional
Probab=32.13 E-value=71 Score=21.37 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=16.4
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
|+++|+++=...-..++..+..++.|+.++
T Consensus 31 vllHG~~~~~~~w~~~~~~L~~~~~via~D 60 (295)
T PRK03592 31 VFLHGNPTSSYLWRNIIPHLAGLGRCLAPD 60 (295)
T ss_pred EEECCCCCCHHHHHHHHHHHhhCCEEEEEc
Confidence 455666655555555555555555555553
No 65
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=31.87 E-value=53 Score=21.91 Aligned_cols=27 Identities=22% Similarity=0.283 Sum_probs=20.4
Q ss_pred ecchHHHHHHHHHHhhcCCcEEEEeccC
Q psy303 28 FGSKYKVINEFHKKMLSNSKVLVINGFF 55 (62)
Q Consensus 28 ~GSKr~lL~~Fa~~~l~~~~~lvVnGy~ 55 (62)
..|=++||.+|.+..-.-.|-+++ ||+
T Consensus 45 ~~~E~~lL~~F~~~i~~~dPd~i~-gyN 71 (188)
T cd05781 45 GLDDRKIIREFVKYVKEYDPDIIV-GYN 71 (188)
T ss_pred CCCHHHHHHHHHHHHHHcCCCEEE-ecC
Confidence 367899999999988776675554 554
No 66
>smart00775 LNS2 LNS2 domain. This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins. SMP2 is involved in plasmid maintenance and respiration. Lipin proteins are involved in adipose tissue development and insulin resistance.
Probab=31.76 E-value=1.1e+02 Score=19.84 Aligned_cols=32 Identities=19% Similarity=0.367 Sum_probs=26.3
Q ss_pred ceEE-EeecchHHHHHHHHHHhhcCCcEEEEec
Q psy303 22 NILL-HGFGSKYKVINEFHKKMLSNSKVLVING 53 (62)
Q Consensus 22 nlll-YG~GSKr~lL~~Fa~~~l~~~~~lvVnG 53 (62)
++-+ .|+||+-.=.+.+++.-+....+.+||-
T Consensus 118 ~~~f~~~~gn~~~D~~~y~~~gi~~~~i~~i~~ 150 (157)
T smart00775 118 GNPFYAGFGNRITDVISYSAVGIPPSRIFTINP 150 (157)
T ss_pred CCCEEEEeCCCchhHHHHHHcCCChhhEEEECC
Confidence 3444 4899999999999999998888888874
No 67
>TIGR01250 pro_imino_pep_2 proline-specific peptidases, Bacillus coagulans-type subfamily. This model describes a subfamily of the alpha/beta fold family of hydrolases. Characterized members include prolinases (Pro-Xaa dipeptidase, EC 3.4.13.8), prolyl aminopeptidases (EC 3.4.11.5), and a leucyl aminopeptidase
Probab=31.63 E-value=80 Score=19.85 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=17.7
Q ss_pred eEEEe-ecchHHHHHHHHHHhhc-CCcEEEEe
Q psy303 23 ILLHG-FGSKYKVINEFHKKMLS-NSKVLVIN 52 (62)
Q Consensus 23 lllYG-~GSKr~lL~~Fa~~~l~-~~~~lvVn 52 (62)
|+++| .||-+.....++...-. +..|+.+|
T Consensus 29 l~~hG~~g~~~~~~~~~~~~l~~~g~~vi~~d 60 (288)
T TIGR01250 29 LLLHGGPGMSHEYLENLRELLKEEGREVIMYD 60 (288)
T ss_pred EEEcCCCCccHHHHHHHHHHHHhcCCEEEEEc
Confidence 45667 47766665555544433 35677776
No 68
>KOG0079|consensus
Probab=31.07 E-value=46 Score=23.54 Aligned_cols=20 Identities=30% Similarity=0.468 Sum_probs=15.9
Q ss_pred eecchHHHHHHHHHHhhcCCc
Q psy303 27 GFGSKYKVINEFHKKMLSNSK 47 (62)
Q Consensus 27 G~GSKr~lL~~Fa~~~l~~~~ 47 (62)
|+| |..|+.+|++...+...
T Consensus 18 gVG-KssLl~rF~ddtFs~sY 37 (198)
T KOG0079|consen 18 GVG-KSSLLLRFADDTFSGSY 37 (198)
T ss_pred ccc-HHHHHHHHhhcccccce
Confidence 455 99999999999876554
No 69
>cd04955 GT1_like_6 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=30.94 E-value=1.4e+02 Score=19.88 Aligned_cols=42 Identities=10% Similarity=0.101 Sum_probs=25.9
Q ss_pred HHHhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCC
Q psy303 16 LEIENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 16 eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
++...+.+++.|-|+...-+.+...+.+...+.|.+-|+.|.
T Consensus 217 ~l~~~~~l~ivG~~~~~~~~~~~~~~~~~~~~~V~~~g~~~~ 258 (363)
T cd04955 217 KSNSGKKLVIVGNADHNTPYGKLLKEKAAADPRIIFVGPIYD 258 (363)
T ss_pred hhccCceEEEEcCCCCcchHHHHHHHHhCCCCcEEEccccCh
Confidence 455578899999885554444444333344456677787765
No 70
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=30.53 E-value=1.3e+02 Score=18.11 Aligned_cols=32 Identities=22% Similarity=0.295 Sum_probs=20.3
Q ss_pred ceEEEeecchHHHHHHHHHHhhc--CCcEEEEec
Q psy303 22 NILLHGFGSKYKVINEFHKKMLS--NSKVLVING 53 (62)
Q Consensus 22 nlllYG~GSKr~lL~~Fa~~~l~--~~~~lvVnG 53 (62)
+|.++|.|+=....+.|...+.. +.++...+.
T Consensus 1 ~I~i~G~G~S~~~a~~~~~~l~~~~~~~~~~~~~ 34 (119)
T cd05017 1 NIVILGMGGSGIGGDLLESLLLDEAKIPVYVVKD 34 (119)
T ss_pred CEEEEEcCHHHHHHHHHHHHHHhccCCCEEEecC
Confidence 58899999776666655554443 345555544
No 71
>PF08484 Methyltransf_14: C-methyltransferase C-terminal domain; InterPro: IPR013691 This domain is found in bacterial C-methyltransferase proteins, often together with other methyltransferase domains such as IPR013216 from INTERPRO or IPR013217 from INTERPRO. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=30.20 E-value=1.7e+02 Score=19.35 Aligned_cols=23 Identities=22% Similarity=0.190 Sum_probs=13.6
Q ss_pred HhCcceEEEeecchHHHHHHHHH
Q psy303 18 IENFNILLHGFGSKYKVINEFHK 40 (62)
Q Consensus 18 ~~gFnlllYG~GSKr~lL~~Fa~ 40 (62)
.+|-.|..||-|+|=.-+-.++.
T Consensus 66 ~~gk~I~~yGA~~kg~tlln~~g 88 (160)
T PF08484_consen 66 AEGKRIAGYGAGAKGNTLLNYFG 88 (160)
T ss_dssp HTT--EEEE---SHHHHHHHHHT
T ss_pred HcCCEEEEECcchHHHHHHHHhC
Confidence 57888999999999986555543
No 72
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=30.08 E-value=1.2e+02 Score=17.92 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=25.7
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCC
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
+|-++|+.|-| ++-.+=++.++..+..|.| +.|+
T Consensus 6 ~~~~vlVvGgG---~va~~k~~~Ll~~gA~v~v--is~~ 39 (103)
T PF13241_consen 6 KGKRVLVVGGG---PVAARKARLLLEAGAKVTV--ISPE 39 (103)
T ss_dssp TT-EEEEEEES---HHHHHHHHHHCCCTBEEEE--EESS
T ss_pred CCCEEEEECCC---HHHHHHHHHHHhCCCEEEE--ECCc
Confidence 57899999999 8888888888887776665 4444
No 73
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=29.73 E-value=97 Score=17.89 Aligned_cols=27 Identities=15% Similarity=0.333 Sum_probs=21.1
Q ss_pred ceEEEeecchHHHHHHHHHHhhcCCcE
Q psy303 22 NILLHGFGSKYKVINEFHKKMLSNSKV 48 (62)
Q Consensus 22 nlllYG~GSKr~lL~~Fa~~~l~~~~~ 48 (62)
=++++|+|.-..-.+.||+.+...+-.
T Consensus 19 v~i~HG~~eh~~ry~~~a~~L~~~G~~ 45 (79)
T PF12146_consen 19 VVIVHGFGEHSGRYAHLAEFLAEQGYA 45 (79)
T ss_pred EEEeCCcHHHHHHHHHHHHHHHhCCCE
Confidence 367889998888888888888766543
No 74
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=29.40 E-value=44 Score=20.44 Aligned_cols=13 Identities=38% Similarity=0.488 Sum_probs=10.7
Q ss_pred eecchHHHHHHHH
Q psy303 27 GFGSKYKVINEFH 39 (62)
Q Consensus 27 G~GSKr~lL~~Fa 39 (62)
|+-|||.++++.-
T Consensus 67 Gl~sKr~~Ie~vy 79 (81)
T PF07830_consen 67 GLASKRSVIEAVY 79 (81)
T ss_dssp TCGGGHHHHHHHH
T ss_pred CHHHHHHHHHHHh
Confidence 7889999998753
No 75
>KOG3342|consensus
Probab=28.89 E-value=79 Score=22.22 Aligned_cols=13 Identities=0% Similarity=-0.038 Sum_probs=8.3
Q ss_pred chHHHHHHHHHHh
Q psy303 30 SKYKVINEFHKKM 42 (62)
Q Consensus 30 SKr~lL~~Fa~~~ 42 (62)
|+|+++.++..-.
T Consensus 15 n~Rq~l~Q~ln~~ 27 (180)
T KOG3342|consen 15 NIRQLLYQVLNFA 27 (180)
T ss_pred HHHHHHHHHHHHH
Confidence 5677777765543
No 76
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=28.78 E-value=1.3e+02 Score=19.75 Aligned_cols=45 Identities=13% Similarity=0.054 Sum_probs=32.2
Q ss_pred HHHHHHHhCcceEEEeecchHHHHHHHHHHhh-cCCcEEEEeccCC
Q psy303 12 GIIQLEIENFNILLHGFGSKYKVINEFHKKML-SNSKVLVINGFFP 56 (62)
Q Consensus 12 qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l-~~~~~lvVnGy~p 56 (62)
+=..++.+---+|+.|.+-+-.-..++.+... .+.++++||=-.+
T Consensus 162 ~~~~~~~~~d~llviGtSl~v~~~~~l~~~~~~~~~~~~~in~~~~ 207 (222)
T cd00296 162 RALEALLEADLVLVIGTSLTVYPAARLLLRAPERGAPVVIINREPT 207 (222)
T ss_pred HHHHHHhcCCEEEEECCCccccCHHHHHHHHHHCCCcEEEECCCCC
Confidence 33445666788999999988777777777665 4678899885433
No 77
>KOG0245|consensus
Probab=28.47 E-value=32 Score=30.22 Aligned_cols=12 Identities=33% Similarity=0.877 Sum_probs=10.8
Q ss_pred HhCcceEEEeec
Q psy303 18 IENFNILLHGFG 29 (62)
Q Consensus 18 ~~gFnlllYG~G 29 (62)
=+|||+|++.||
T Consensus 84 fEGYN~ClFAYG 95 (1221)
T KOG0245|consen 84 FEGYNVCLFAYG 95 (1221)
T ss_pred hcccceEEEEec
Confidence 479999999998
No 78
>cd03802 GT1_AviGT4_like This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant that accumulated a novel avilamycin derivative lacking the terminal eurekanate residue.
Probab=27.78 E-value=1.5e+02 Score=19.60 Aligned_cols=39 Identities=13% Similarity=-0.055 Sum_probs=27.6
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCC
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
.++.+.+.|-|+..+.+...........+.+.+-|+.|.
T Consensus 196 ~~~~l~i~G~~~~~~~~~~~~~~~~~~~~~v~~~G~~~~ 234 (335)
T cd03802 196 AGIPLKLAGPVSDPDYFYREIAPELLDGPDIEYLGEVGG 234 (335)
T ss_pred cCCeEEEEeCCCCHHHHHHHHHHhcccCCcEEEeCCCCH
Confidence 468899999999887777766655322345677787765
No 79
>PF01913 FTR: Formylmethanofuran-tetrahydromethanopterin formyltransferase; InterPro: IPR022667 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure []. In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].; GO: 0016740 transferase activity, 0006730 one-carbon metabolic process; PDB: 1M5H_E 1M5S_C 1FTR_C 2FHJ_B 2FHK_D.
Probab=27.77 E-value=1.3e+02 Score=20.46 Aligned_cols=36 Identities=17% Similarity=0.362 Sum_probs=25.3
Q ss_pred hCcceEEEeecch---HHHHHHHHHHhhcCCcEEEEecc
Q psy303 19 ENFNILLHGFGSK---YKVINEFHKKMLSNSKVLVINGF 54 (62)
Q Consensus 19 ~gFnlllYG~GSK---r~lL~~Fa~~~l~~~~~lvVnGy 54 (62)
-|.+|++++.+.| ++|+++-.+-.|.....-+.||.
T Consensus 70 PGv~il~f~~~~~~L~~~l~~RigQcVLT~PttA~f~gl 108 (144)
T PF01913_consen 70 PGVSILIFAMSKKKLEKQLLERIGQCVLTCPTTACFNGL 108 (144)
T ss_dssp -EEEEEEEESSHHHHHHHHHHHHHHHTTTSTT-EEEESS
T ss_pred CcEEEEEEeCCHHHHHHHHHHHccCcccCChhHHHhcCC
Confidence 4889999988765 45666666666666667788887
No 80
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=27.74 E-value=79 Score=18.85 Aligned_cols=27 Identities=26% Similarity=0.322 Sum_probs=22.1
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecc
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGS 30 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GS 30 (62)
.++...+......|.+|=.|-+-|+|+
T Consensus 23 ~~v~~~~~~i~~~L~~g~~V~i~gfG~ 49 (90)
T PRK10753 23 AALESTLAAITESLKEGDAVQLVGFGT 49 (90)
T ss_pred HHHHHHHHHHHHHHHcCCeEEEcCCEE
Confidence 455666777888899999999999995
No 81
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=27.69 E-value=1.7e+02 Score=18.70 Aligned_cols=36 Identities=22% Similarity=0.256 Sum_probs=27.8
Q ss_pred hhhHHHHHHHHh----CcceEEEeecchHHHHHHHHHHhh
Q psy303 8 DIQNGIIQLEIE----NFNILLHGFGSKYKVINEFHKKML 43 (62)
Q Consensus 8 ~~f~qW~~eL~~----gFnlllYG~GSKr~lL~~Fa~~~l 43 (62)
+.+.++...+.+ +-+|.+||.|+=..+.+.|+..+.
T Consensus 17 ~~i~~a~~~i~~~i~~~~~I~i~G~G~S~~~A~~~~~~l~ 56 (177)
T cd05006 17 EAIEQAAQLLAEALLNGGKILICGNGGSAADAQHFAAELV 56 (177)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEeCcHHHHHHHHHHHHHh
Confidence 445666666655 779999999988888888887764
No 82
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=27.56 E-value=2.1e+02 Score=22.82 Aligned_cols=43 Identities=21% Similarity=0.272 Sum_probs=28.5
Q ss_pred HHHHHhCcceEEE---eecchHHHHHHHHHHhhcC--CcEEEEeccCCCCc
Q psy303 14 IQLEIENFNILLH---GFGSKYKVINEFHKKMLSN--SKVLVINGFFPDLT 59 (62)
Q Consensus 14 ~~eL~~gFnlllY---G~GSKr~lL~~Fa~~~l~~--~~~lvVnGy~p~~t 59 (62)
..-+.++.|++++ |.| |..+.+.+++.+-.+ ..++.+ .+|+.+
T Consensus 31 ~~a~~~~~~~ll~G~pG~G-KT~la~~la~~l~~~~~~~~~~~--~n~~~~ 78 (608)
T TIGR00764 31 KKAAKQKRNVLLIGEPGVG-KSMLAKAMAELLPDEELEDILVY--PNPEDP 78 (608)
T ss_pred HHHHHcCCCEEEECCCCCC-HHHHHHHHHHHcCchhheeEEEE--eCCCCC
Confidence 3446678899999 555 888999999877544 334444 444443
No 83
>PF14252 DUF4347: Domain of unknown function (DUF4347)
Probab=26.75 E-value=67 Score=21.55 Aligned_cols=36 Identities=17% Similarity=0.128 Sum_probs=28.1
Q ss_pred hhhhhHHHHHHHHhCcceEEEe--ecch---HHHHHHHHHH
Q psy303 6 LKDIQNGIIQLEIENFNILLHG--FGSK---YKVINEFHKK 41 (62)
Q Consensus 6 ~~~~f~qW~~eL~~gFnlllYG--~GSK---r~lL~~Fa~~ 41 (62)
+++...+|...|..+=.|+||| ++.= ++++++.++-
T Consensus 77 ~~~~l~~w~~~L~~~~~IlLyGC~vaag~~G~~fv~~L~~l 117 (165)
T PF14252_consen 77 YADELAQWGQALADDGDILLYGCNVAAGEEGQEFVQRLAQL 117 (165)
T ss_pred HHHHHHHHHHHhCCCCcEEEEcCccCcchhHHHHHHHHHHH
Confidence 3466889999999999999999 4443 6777777763
No 84
>PF12165 DUF3594: Domain of unknown function (DUF3594); InterPro: IPR021998 This presumed domain is functionally uncharacterised.This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00628 from PFAM.
Probab=26.49 E-value=32 Score=23.28 Aligned_cols=10 Identities=30% Similarity=0.281 Sum_probs=7.9
Q ss_pred cceEEEeecc
Q psy303 21 FNILLHGFGS 30 (62)
Q Consensus 21 FnlllYG~GS 30 (62)
=|||+||+-.
T Consensus 37 enLCLYG~p~ 46 (137)
T PF12165_consen 37 ENLCLYGHPD 46 (137)
T ss_pred cceEEecCCC
Confidence 3999999853
No 85
>COG0426 FpaA Uncharacterized flavoproteins [Energy production and conversion]
Probab=26.33 E-value=1.7e+02 Score=22.61 Aligned_cols=47 Identities=15% Similarity=0.176 Sum_probs=37.2
Q ss_pred hhhhhHHHHHHHHhCcceEEEe--ecchHHHHHHHHHHhhcCCc-EEEEe
Q psy303 6 LKDIQNGIIQLEIENFNILLHG--FGSKYKVINEFHKKMLSNSK-VLVIN 52 (62)
Q Consensus 6 ~~~~f~qW~~eL~~gFnlllYG--~GSKr~lL~~Fa~~~l~~~~-~lvVn 52 (62)
+.+.|.+|...+..+-=.++|. |||=+.+.+..++.....+. +.++|
T Consensus 233 i~~~Y~~W~~~~~~~~V~l~Y~smyg~T~~ma~aiaegl~~~gv~v~~~~ 282 (388)
T COG0426 233 IVEAYRDWAEGQPKGKVDLIYDSMYGNTEKMAQAIAEGLMKEGVDVEVIN 282 (388)
T ss_pred HHHHHHHHHccCCcceEEEEEecccCCHHHHHHHHHHHhhhcCCceEEEE
Confidence 4567999999999994456675 89999999999999987775 44443
No 86
>TIGR00282 metallophosphoesterase, MG_246/BB_0505 family. A member of this family from Mycoplasma Pneumoniae has been crystallized and described as a novel phosphatase.
Probab=26.18 E-value=1.2e+02 Score=21.83 Aligned_cols=36 Identities=19% Similarity=0.376 Sum_probs=24.9
Q ss_pred ceEEEe--ecch-HHHHHHHHHHhhcCC--cEEEEeccCCC
Q psy303 22 NILLHG--FGSK-YKVINEFHKKMLSNS--KVLVINGFFPD 57 (62)
Q Consensus 22 nlllYG--~GSK-r~lL~~Fa~~~l~~~--~~lvVnGy~p~ 57 (62)
+|||.| +|+= |+.+.+...++-.+. ..+|+||=+++
T Consensus 2 ~ilfiGDi~G~~Gr~~l~~~L~~lk~~~~~D~vIaNgEn~~ 42 (266)
T TIGR00282 2 KFLFIGDVYGKAGRKIVKNNLPQLKSKYQADLVIANGENTT 42 (266)
T ss_pred eEEEEEecCCHHHHHHHHHHHHHHHHhCCCCEEEEcCcccC
Confidence 466666 5663 888888887776554 48888986553
No 87
>PF02608 Bmp: Basic membrane protein; InterPro: IPR003760 This is a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. All of these proteins are outer membrane proteins and are thus antigenic in nature when possessed by the pathogenic members of the family []. The Bacillus subtilis degR, a positive regulator of the production of degradative enzymes, is also a member of this group [].; GO: 0005886 plasma membrane; PDB: 2HQB_A 3S99_A 2FQW_A 2FQY_A 2FQX_A.
Probab=25.74 E-value=2.4e+02 Score=19.80 Aligned_cols=45 Identities=18% Similarity=0.338 Sum_probs=25.6
Q ss_pred HHHHHHhCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCCC
Q psy303 13 IIQLEIENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPDL 58 (62)
Q Consensus 13 W~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~~ 58 (62)
....-++|++|++-.=..=-+.+.+.|+++ +|...++++|+.+.-
T Consensus 54 ~~~~~~~g~dlIi~~g~~~~~~~~~vA~~y-Pd~~F~~~d~~~~~~ 98 (306)
T PF02608_consen 54 IRQLADQGYDLIIGHGFEYSDALQEVAKEY-PDTKFIIIDGYIDAP 98 (306)
T ss_dssp HHHHHHTT-SEEEEESGGGHHHHHHHHTC--TTSEEEEESS---ST
T ss_pred HHHHHHcCCCEEEEccHHHHHHHHHHHHHC-CCCEEEEEecCcCCC
Confidence 333446999997652222335666777766 666789999987765
No 88
>COG0400 Predicted esterase [General function prediction only]
Probab=25.27 E-value=68 Score=22.15 Aligned_cols=34 Identities=26% Similarity=0.412 Sum_probs=25.7
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEeccCC
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFP 56 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p 56 (62)
|+++|+|.=..-+-.+.+..+.+..++-++|-.+
T Consensus 22 ilLHG~Ggde~~~~~~~~~~~P~~~~is~rG~v~ 55 (207)
T COG0400 22 ILLHGLGGDELDLVPLPELILPNATLVSPRGPVA 55 (207)
T ss_pred EEEecCCCChhhhhhhhhhcCCCCeEEcCCCCcc
Confidence 7899999776666667777777777787777544
No 89
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=25.09 E-value=79 Score=21.34 Aligned_cols=23 Identities=4% Similarity=0.101 Sum_probs=17.8
Q ss_pred ecchHHHHHHHHHHhhcCCcEEE
Q psy303 28 FGSKYKVINEFHKKMLSNSKVLV 50 (62)
Q Consensus 28 ~GSKr~lL~~Fa~~~l~~~~~lv 50 (62)
+-|=++||++|.+....-.|-++
T Consensus 48 ~~~E~~lL~~f~~~i~~~dPDvi 70 (193)
T cd05784 48 FADEKSLLLALIAWFAQYDPDII 70 (193)
T ss_pred ECCHHHHHHHHHHHHHhhCCCEE
Confidence 46889999999999876666433
No 90
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=25.09 E-value=1.2e+02 Score=15.87 Aligned_cols=35 Identities=9% Similarity=0.089 Sum_probs=24.6
Q ss_pred hCcceEEEeecchHHHHHHHHHHh-hcCCcEEEEec
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKM-LSNSKVLVING 53 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~-l~~~~~lvVnG 53 (62)
.|...-.+-+.+-.+..+++.+.. ...-|+|.|||
T Consensus 22 ~~i~y~~~dv~~~~~~~~~l~~~~g~~~~P~v~i~g 57 (60)
T PF00462_consen 22 KGIPYEEVDVDEDEEAREELKELSGVRTVPQVFIDG 57 (60)
T ss_dssp TTBEEEEEEGGGSHHHHHHHHHHHSSSSSSEEEETT
T ss_pred cCCeeeEcccccchhHHHHHHHHcCCCccCEEEECC
Confidence 455556667777667777777763 45669999988
No 91
>PRK10985 putative hydrolase; Provisional
Probab=24.99 E-value=96 Score=21.64 Aligned_cols=32 Identities=13% Similarity=0.177 Sum_probs=20.1
Q ss_pred cceEEEeecc--hHHHHHHHHHHhhcCC-cEEEEe
Q psy303 21 FNILLHGFGS--KYKVINEFHKKMLSNS-KVLVIN 52 (62)
Q Consensus 21 FnlllYG~GS--Kr~lL~~Fa~~~l~~~-~~lvVn 52 (62)
-=|+++|+++ ....+..+++.+...+ .|+++|
T Consensus 60 ~vll~HG~~g~~~~~~~~~~~~~l~~~G~~v~~~d 94 (324)
T PRK10985 60 RLVLFHGLEGSFNSPYAHGLLEAAQKRGWLGVVMH 94 (324)
T ss_pred EEEEeCCCCCCCcCHHHHHHHHHHHHCCCEEEEEe
Confidence 3467889953 3446667777766655 466665
No 92
>COG0645 Predicted kinase [General function prediction only]
Probab=24.84 E-value=1.4e+02 Score=20.56 Aligned_cols=56 Identities=11% Similarity=0.195 Sum_probs=35.1
Q ss_pred hhhhhhhhHHHHHHHHhCcceEEEe-e--cchHHHHHHHHHHhhcCCcEEEEeccCCCCcc
Q psy303 3 KTILKDIQNGIIQLEIENFNILLHG-F--GSKYKVINEFHKKMLSNSKVLVINGFFPDLTL 60 (62)
Q Consensus 3 ~~~~~~~f~qW~~eL~~gFnlllYG-~--GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~~ti 60 (62)
.+-+..+++.|.--|++|+|+.+=+ + ..=|++...-|+.. +-+.+.|+-..|...+
T Consensus 59 ~~vy~~l~~~A~l~l~~G~~VVlDa~~~r~~~R~~~~~~A~~~--gv~~~li~~~ap~~v~ 117 (170)
T COG0645 59 AAVYDELLGRAELLLSSGHSVVLDATFDRPQERALARALARDV--GVAFVLIRLEAPEEVL 117 (170)
T ss_pred HHHHHHHHHHHHHHHhCCCcEEEecccCCHHHHHHHHHHHhcc--CCceEEEEcCCcHHHH
Confidence 4556778999999999999998733 3 33344444444332 2356666666665444
No 93
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=24.68 E-value=1.1e+02 Score=19.07 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=13.5
Q ss_pred HHHHHHhhcCCcEEEEeccCCC
Q psy303 36 NEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 36 ~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
.+.+...+..+..+|++||..+
T Consensus 72 ~~~~~~~~~~~~~~i~dg~~~~ 93 (188)
T TIGR01360 72 KDAMVAALGTSKGFLIDGYPRE 93 (188)
T ss_pred HHHHHcccCcCCeEEEeCCCCC
Confidence 3333334456678899998543
No 94
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=24.53 E-value=45 Score=17.28 Aligned_cols=16 Identities=19% Similarity=0.521 Sum_probs=11.5
Q ss_pred HHHHHHHHHHhhcCCc
Q psy303 32 YKVINEFHKKMLSNSK 47 (62)
Q Consensus 32 r~lL~~Fa~~~l~~~~ 47 (62)
+++|++|....+.+.|
T Consensus 4 ~~lL~~~~~~vl~~qP 19 (38)
T PF02197_consen 4 QELLKEFTREVLREQP 19 (38)
T ss_dssp HHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHCC
Confidence 4789999988886555
No 95
>PF02086 MethyltransfD12: D12 class N6 adenine-specific DNA methyltransferase; InterPro: IPR012327 In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. There are 2 major classes of DNA methyltransferase that differ in the nature of the modifications they effect. The members of one class (C-MTases) methylate a ring carbon and form C5-methylcytosine (see IPR001525 from INTERPRO). Members of the second class (N-MTases) methylate exocyclic nitrogens and form either N4-methylcytosine (N4-MTases) or N6-methyladenine (N6-MTases). Both classes of MTase utilise the cofactor S-adenosyl-L-methionine (SAM) as the methyl donor and are active as monomeric enzymes []. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence. It has been shown [, , , ] that A-Mtases contain a conserved motif Asp/Asn-Pro-Pro-Tyr/Phe in their N-terminal section, this conserved region could be involved in substrate binding or in the catalytic activity. The structure of N6-MTase TaqI (M.TaqI) has been resolved to 2.4 A []. The molecule folds into 2 domains, an N-terminal catalytic domain, which contains the catalytic and cofactor binding sites, and comprises a central 9-stranded beta-sheet, surrounded by 5 helices; and a C-terminal DNA recognition domain, which is formed by 4 small beta-sheets and 8 alpha-helices. The N- and C-terminal domains form a cleft that accommodates the DNA substrate. A classification of N-MTases has been proposed, based on conserved motif (CM) arrangements []. According to this classification, N6-MTases that have a DPPY motif (CM II) occuring after the FxGxG motif (CM I) are designated D12 class N6-adenine MTases.; GO: 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine; PDB: 1Q0T_B 1YFJ_B 1Q0S_A 1YFL_B 1YF3_B 2DPM_A 2ORE_F 2G1P_B.
Probab=24.36 E-value=41 Score=22.36 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=16.0
Q ss_pred ecchHHHHHHHHHHhhcCCcEEEEeccC
Q psy303 28 FGSKYKVINEFHKKMLSNSKVLVINGFF 55 (62)
Q Consensus 28 ~GSKr~lL~~Fa~~~l~~~~~lvVnGy~ 55 (62)
.|||+.|+....+..-...+-.+|+-|.
T Consensus 2 ~G~K~~l~~~I~~~ip~~~~~~~vepF~ 29 (260)
T PF02086_consen 2 PGGKRKLAKWIIELIPKNKHKTYVEPFA 29 (260)
T ss_dssp TT-SGGGHHHHHHHS-S-S-SEEEETT-
T ss_pred CccHHHHHHHHHHHcCCCCCCEEEEEec
Confidence 5999999998777654324445555553
No 96
>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport. The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....
Probab=24.34 E-value=1.1e+02 Score=21.60 Aligned_cols=28 Identities=7% Similarity=0.460 Sum_probs=20.1
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEeecch
Q psy303 4 TILKDIQNGIIQLEIENFNILLHGFGSK 31 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG~GSK 31 (62)
.++......+...+-+|+|.++..||..
T Consensus 57 ~vy~~~~~~~v~~~l~G~n~~i~ayG~t 84 (335)
T PF00225_consen 57 DVYEEVVSPLVDSVLDGYNATIFAYGQT 84 (335)
T ss_dssp HHHHHHTHHHHHHHHTT-EEEEEEEEST
T ss_pred HHHHHHHHHHHHHhhcCCceEEEeeccc
Confidence 3455556677888889999998888753
No 97
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=24.32 E-value=39 Score=24.60 Aligned_cols=24 Identities=33% Similarity=0.506 Sum_probs=19.6
Q ss_pred ecchHHHHHHHHHHhhcCCcEEEE
Q psy303 28 FGSKYKVINEFHKKMLSNSKVLVI 51 (62)
Q Consensus 28 ~GSKr~lL~~Fa~~~l~~~~~lvV 51 (62)
+-||..+|++|..+++...+.+-|
T Consensus 165 f~s~~avieDF~~~ylk~mtL~eV 188 (238)
T PF10915_consen 165 FHSKPAVIEDFEKNYLKPMTLVEV 188 (238)
T ss_pred hcccHHHHHHHHHcccccccHhhc
Confidence 569999999999999987665444
No 98
>PLN02511 hydrolase
Probab=24.27 E-value=94 Score=22.65 Aligned_cols=30 Identities=30% Similarity=0.489 Sum_probs=18.7
Q ss_pred eEEEee-cc-hHHHHHHHHHHhhcCC-cEEEEe
Q psy303 23 ILLHGF-GS-KYKVINEFHKKMLSNS-KVLVIN 52 (62)
Q Consensus 23 lllYG~-GS-Kr~lL~~Fa~~~l~~~-~~lvVn 52 (62)
|+++|+ || ...-+..++...+..+ .|+++|
T Consensus 104 vllHG~~g~s~~~y~~~~~~~~~~~g~~vv~~d 136 (388)
T PLN02511 104 ILLPGLTGGSDDSYVRHMLLRARSKGWRVVVFN 136 (388)
T ss_pred EEECCCCCCCCCHHHHHHHHHHHHCCCEEEEEe
Confidence 677898 33 3345666766666544 577766
No 99
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=24.20 E-value=1.1e+02 Score=17.89 Aligned_cols=17 Identities=24% Similarity=0.565 Sum_probs=10.0
Q ss_pred HhhcCC--cEEEEeccCCC
Q psy303 41 KMLSNS--KVLVINGFFPD 57 (62)
Q Consensus 41 ~~l~~~--~~lvVnGy~p~ 57 (62)
.++..+ |++|.||-.|.
T Consensus 67 ~L~~~gI~PifVFDG~~~~ 85 (101)
T PF00752_consen 67 RLLEHGIKPIFVFDGKPPP 85 (101)
T ss_dssp HHHHTTEEEEEEE--STTG
T ss_pred HHHHCCCEEEEEECCCCch
Confidence 334443 89999998774
No 100
>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]. It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].
Probab=24.19 E-value=48 Score=25.94 Aligned_cols=12 Identities=33% Similarity=0.628 Sum_probs=9.9
Q ss_pred CCcEEEEeccCC
Q psy303 45 NSKVLVINGFFP 56 (62)
Q Consensus 45 ~~~~lvVnGy~p 56 (62)
..||||||+|.-
T Consensus 148 ~~PVVVIdnF~~ 159 (431)
T PF10443_consen 148 RRPVVVIDNFLH 159 (431)
T ss_pred cCCEEEEcchhc
Confidence 368999999964
No 101
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=24.10 E-value=2e+02 Score=20.32 Aligned_cols=35 Identities=23% Similarity=0.337 Sum_probs=23.7
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEE---EEeccC
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVL---VINGFF 55 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~l---vVnGy~ 55 (62)
.|..+ |=+|||.+.+++.++.+-...++- .-+||+
T Consensus 104 ~~~~v--~llG~~~~v~~~a~~~l~~~y~l~i~g~~~Gyf 141 (243)
T PRK03692 104 EGTPV--FLVGGKPEVLAQTEAKLRTQWNVNIVGSQDGYF 141 (243)
T ss_pred cCCeE--EEECCCHHHHHHHHHHHHHHhCCEEEEEeCCCC
Confidence 35555 445999999999988875544322 347887
No 102
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=23.88 E-value=2.4e+02 Score=20.46 Aligned_cols=49 Identities=16% Similarity=0.285 Sum_probs=33.8
Q ss_pred hhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhcCCc---EEEE-eccCCC
Q psy303 8 DIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLSNSK---VLVI-NGFFPD 57 (62)
Q Consensus 8 ~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~~~~---~lvV-nGy~p~ 57 (62)
++++.-+....+. +.=+|=+|+|.+.+++=++++-++.| ++.. +||+..
T Consensus 95 Dl~~~Ll~~a~~~-~~~vfllGgkp~V~~~a~~~l~~~~p~l~ivg~h~GYf~~ 147 (253)
T COG1922 95 DLVEALLKRAAEE-GKRVFLLGGKPGVAEQAAAKLRAKYPGLKIVGSHDGYFDP 147 (253)
T ss_pred HHHHHHHHHhCcc-CceEEEecCCHHHHHHHHHHHHHHCCCceEEEecCCCCCh
Confidence 3444444444444 56677789999999999999999888 3333 377643
No 103
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=23.80 E-value=1.6e+02 Score=20.00 Aligned_cols=24 Identities=4% Similarity=0.120 Sum_probs=18.6
Q ss_pred EeecchHHHHHHHHHHhhcCCcEE
Q psy303 26 HGFGSKYKVINEFHKKMLSNSKVL 49 (62)
Q Consensus 26 YG~GSKr~lL~~Fa~~~l~~~~~l 49 (62)
+-+.|=|+||++|.+....-.|-|
T Consensus 66 ~~~~~E~eLL~~f~~~i~~~DPDi 89 (230)
T cd05777 66 FSFETEEELLLAWRDFVQEVDPDI 89 (230)
T ss_pred EEECCHHHHHHHHHHHHHhcCCCE
Confidence 346899999999999987655533
No 104
>PLN02578 hydrolase
Probab=23.78 E-value=1.2e+02 Score=21.52 Aligned_cols=8 Identities=63% Similarity=1.547 Sum_probs=3.7
Q ss_pred eEEEeecc
Q psy303 23 ILLHGFGS 30 (62)
Q Consensus 23 lllYG~GS 30 (62)
|+++|+|+
T Consensus 90 vliHG~~~ 97 (354)
T PLN02578 90 VLIHGFGA 97 (354)
T ss_pred EEECCCCC
Confidence 34455554
No 105
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=23.61 E-value=60 Score=21.36 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=6.1
Q ss_pred CCcEEEEeccCCC
Q psy303 45 NSKVLVINGFFPD 57 (62)
Q Consensus 45 ~~~~lvVnGy~p~ 57 (62)
...+|+|+|+.++
T Consensus 63 kP~vI~v~g~~~~ 75 (150)
T PF14639_consen 63 KPDVIAVGGNSRE 75 (150)
T ss_dssp --SEEEE--SSTH
T ss_pred CCeEEEEcCCChh
Confidence 3447888887654
No 106
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=23.55 E-value=1.4e+02 Score=23.66 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=25.1
Q ss_pred ceEEEeecchHHHHHHHHHHhhcCCcEEEEeccC
Q psy303 22 NILLHGFGSKYKVINEFHKKMLSNSKVLVINGFF 55 (62)
Q Consensus 22 nlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~ 55 (62)
++.++-+-|=++||.+|.+..-.-.|-|++ ||+
T Consensus 171 ~v~v~~f~sE~eLL~~F~~~i~~~DPDIIt-GYN 203 (498)
T PHA02524 171 NVVYMPFEDEVDLLLNYIQLWKANTPDLVF-GWN 203 (498)
T ss_pred CeEEEEeCCHHHHHHHHHHHHHHhCCCEEE-eCC
Confidence 468999999999999999988765554433 454
No 107
>PF08235 LNS2: LNS2 (Lipin/Ned1/Smp2); InterPro: IPR013209 This domain is found in Saccharomyces cerevisiae (Baker's yeast) protein SMP2, proteins with an N-terminal lipin domain (IPR007651 from INTERPRO) and phosphatidylinositol transfer proteins []. SMP2 is involved in plasmid maintenance and respiration []. Lipin proteins are involved in adipose tissue development and insulin resistance [].
Probab=23.44 E-value=1.4e+02 Score=20.10 Aligned_cols=35 Identities=20% Similarity=0.398 Sum_probs=28.5
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEEEEec
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVLVING 53 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnG 53 (62)
..-|....|||++-.=...++.--+....+.+||-
T Consensus 116 ~~~~pf~agfGN~~tDv~aY~~vGip~~rIF~I~~ 150 (157)
T PF08235_consen 116 PDGNPFYAGFGNRSTDVIAYKAVGIPKSRIFIINP 150 (157)
T ss_pred CCCCeEEEecCCcHHHHHHHHHcCCChhhEEEECC
Confidence 35688999999997777888888888888888874
No 108
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=23.39 E-value=2.1e+02 Score=18.29 Aligned_cols=45 Identities=18% Similarity=0.296 Sum_probs=33.5
Q ss_pred hhhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhc-CCcEEEE
Q psy303 7 KDIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLS-NSKVLVI 51 (62)
Q Consensus 7 ~~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~-~~~~lvV 51 (62)
.+...+....|.+.=+|.++|.|+=..+-+.|+..+.. +.++..+
T Consensus 20 ~~~l~~~~~~i~~a~~I~i~G~G~S~~~A~~~~~~l~~~g~~~~~~ 65 (179)
T cd05005 20 EEELDKLISAILNAKRIFVYGAGRSGLVAKAFAMRLMHLGLNVYVV 65 (179)
T ss_pred HHHHHHHHHHHHhCCeEEEEecChhHHHHHHHHHHHHhCCCeEEEe
Confidence 35577788888888899999999888888888877753 2344444
No 109
>cd04949 GT1_gtfA_like This family is most closely related to the GT1 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltra
Probab=23.36 E-value=2.1e+02 Score=19.53 Aligned_cols=38 Identities=13% Similarity=0.388 Sum_probs=25.5
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCCC
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
....+.++|.|+.+.-+++..+.. .-...|.+-||.+.
T Consensus 234 ~~~~l~i~G~g~~~~~~~~~~~~~-~~~~~v~~~g~~~~ 271 (372)
T cd04949 234 PDATLDIYGYGDEEEKLKELIEEL-GLEDYVFLKGYTRD 271 (372)
T ss_pred CCcEEEEEEeCchHHHHHHHHHHc-CCcceEEEcCCCCC
Confidence 357789999999888777766443 22335666676554
No 110
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=23.31 E-value=1e+02 Score=17.83 Aligned_cols=47 Identities=13% Similarity=-0.059 Sum_probs=25.0
Q ss_pred hhhHHHHHHHHhCcceEEEeecchHHHHHHHHH--HhhcCCcEEEEeccCCC
Q psy303 8 DIQNGIIQLEIENFNILLHGFGSKYKVINEFHK--KMLSNSKVLVINGFFPD 57 (62)
Q Consensus 8 ~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~--~~l~~~~~lvVnGy~p~ 57 (62)
..+.+...+|.+|.-|++..-.+=+.. ... .....++.|||.||..+
T Consensus 87 ~~~~~i~~~i~~G~Pvi~~~~~~~~~~---~~~~~~~~~~~H~vvi~Gy~~~ 135 (144)
T PF13529_consen 87 ASFDDIKQEIDAGRPVIVSVNSGWRPP---NGDGYDGTYGGHYVVIIGYDED 135 (144)
T ss_dssp S-HHHHHHHHHTT--EEEEEETTSS-----TTEEEEE-TTEEEEEEEEE-SS
T ss_pred CcHHHHHHHHHCCCcEEEEEEcccccC---CCCCcCCCcCCEEEEEEEEeCC
Confidence 456778889999988877664221111 000 01235678999999864
No 111
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=23.30 E-value=1.6e+02 Score=18.94 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=19.0
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCc
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSK 47 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~ 47 (62)
.-+..+-|=+++|.+|.+..-.-.|
T Consensus 55 ~~v~~~~~E~~lL~~f~~~i~~~dp 79 (199)
T cd05160 55 IEVEYFADEKELLKRFFDIIREYDP 79 (199)
T ss_pred ceEEEeCCHHHHHHHHHHHHHhcCC
Confidence 4456678999999999998865444
No 112
>PRK11798 ClpXP protease specificity-enhancing factor; Provisional
Probab=23.19 E-value=1.7e+02 Score=19.65 Aligned_cols=30 Identities=10% Similarity=0.355 Sum_probs=23.8
Q ss_pred chHHHHHHHHHHhhcCC--cEEEEeccCCCCc
Q psy303 30 SKYKVINEFHKKMLSNS--KVLVINGFFPDLT 59 (62)
Q Consensus 30 SKr~lL~~Fa~~~l~~~--~~lvVnGy~p~~t 59 (62)
+|--||..+-++++.++ |.|+|+.-.|++.
T Consensus 7 ~rPYLlRA~yeW~~Dn~~TP~l~Vda~~~~v~ 38 (138)
T PRK11798 7 TRPYLLRALYEWIVDNGLTPHLLVDATYPGVQ 38 (138)
T ss_pred CchHHHHHHHHHHhhCCCCcEEEEEcCCCCCc
Confidence 56778999999998764 6899988877654
No 113
>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein. It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication
Probab=22.98 E-value=2.3e+02 Score=24.23 Aligned_cols=48 Identities=19% Similarity=0.116 Sum_probs=33.8
Q ss_pred hHHHHHHHHhCcceEEEe-ecchHHHHHHHHHHhhcCCcEEEEeccCCCCc
Q psy303 10 QNGIIQLEIENFNILLHG-FGSKYKVINEFHKKMLSNSKVLVINGFFPDLT 59 (62)
Q Consensus 10 f~qW~~eL~~gFnlllYG-~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~~t 59 (62)
|..-...|..|=|||++- -.|..+++.+|.... ...|++.||=.|...
T Consensus 272 ~~~L~~~L~~gknIcvfsSt~~~~~~v~~~~~~~--~~~Vl~l~s~~~~~d 320 (824)
T PF02399_consen 272 FSELLARLNAGKNICVFSSTVSFAEIVARFCARF--TKKVLVLNSTDKLED 320 (824)
T ss_pred HHHHHHHHhCCCcEEEEeChHHHHHHHHHHHHhc--CCeEEEEcCCCCccc
Confidence 556667899999999765 334556777777766 556778887666543
No 114
>TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.
Probab=22.85 E-value=1.8e+02 Score=19.49 Aligned_cols=31 Identities=10% Similarity=0.247 Sum_probs=22.3
Q ss_pred ceEEEeecchHHHHHHHHHHhhc-CCcEEEEe
Q psy303 22 NILLHGFGSKYKVINEFHKKMLS-NSKVLVIN 52 (62)
Q Consensus 22 nlllYG~GSKr~lL~~Fa~~~l~-~~~~lvVn 52 (62)
.|.+||.|+=..+-+.|+..+.. +.++..++
T Consensus 2 rI~i~G~G~S~~~a~~~~~~l~~~g~~~~~~~ 33 (268)
T TIGR00393 2 KLVIVGIGKSGLIGKKIVATFASTGTPSFFLH 33 (268)
T ss_pred cEEEEecChHHHHHHHHHHHHHhcCCceEEeC
Confidence 47899999888888888888765 33454443
No 115
>PRK13768 GTPase; Provisional
Probab=22.84 E-value=1.4e+02 Score=20.66 Aligned_cols=30 Identities=13% Similarity=0.298 Sum_probs=19.4
Q ss_pred eEEEeecc--hHHHHHHHHHHhhcCC-cEEEEe
Q psy303 23 ILLHGFGS--KYKVINEFHKKMLSNS-KVLVIN 52 (62)
Q Consensus 23 lllYG~GS--Kr~lL~~Fa~~~l~~~-~~lvVn 52 (62)
+++-|-|. |-.+...++..+...+ ++++||
T Consensus 5 i~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i~ 37 (253)
T PRK13768 5 VFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVN 37 (253)
T ss_pred EEEECCCCccHHHHHHHHHHHHHhcCCceEEEE
Confidence 34444432 7888888888776544 577776
No 116
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=22.71 E-value=1.2e+02 Score=15.03 Aligned_cols=23 Identities=13% Similarity=0.336 Sum_probs=18.1
Q ss_pred CcceEEEee--cchHHHHHHHHHHh
Q psy303 20 NFNILLHGF--GSKYKVINEFHKKM 42 (62)
Q Consensus 20 gFnlllYG~--GSKr~lL~~Fa~~~ 42 (62)
|..+++.|. +.-|+-|.+.+..+
T Consensus 1 ~~~~~i~g~~~~~~~~~l~~~i~~~ 25 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKL 25 (72)
T ss_pred CCEEEEEecCCCcCHHHHHHHHHHc
Confidence 457888887 68888888888776
No 117
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=22.66 E-value=93 Score=21.13 Aligned_cols=26 Identities=23% Similarity=0.272 Sum_probs=18.7
Q ss_pred eecchHHHHHHHHHHhhcCCcEEEEeccC
Q psy303 27 GFGSKYKVINEFHKKMLSNSKVLVINGFF 55 (62)
Q Consensus 27 G~GSKr~lL~~Fa~~~l~~~~~lvVnGy~ 55 (62)
-+-|=+++|++|.+..- +.|++| ||+
T Consensus 69 ~~~~E~~lL~~F~~~i~-~~~~ii--g~N 94 (204)
T cd05783 69 FFDSEKELIREAFKIIS-EYPIVL--TFN 94 (204)
T ss_pred ecCCHHHHHHHHHHHHh-cCCEEE--EeC
Confidence 35789999999999775 446433 454
No 118
>COG1213 Predicted sugar nucleotidyltransferases [Cell envelope biogenesis, outer membrane]
Probab=22.58 E-value=30 Score=25.16 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=11.3
Q ss_pred hHHHHHHHHHHhhcCCc---EEEEeccC
Q psy303 31 KYKVINEFHKKMLSNSK---VLVINGFF 55 (62)
Q Consensus 31 Kr~lL~~Fa~~~l~~~~---~lvVnGy~ 55 (62)
.|++|.+=.+.+...+- ++|+|||.
T Consensus 30 gr~ii~~~i~~L~~~gi~e~vvV~~g~~ 57 (239)
T COG1213 30 GREIIYRTIENLAKAGITEFVVVTNGYR 57 (239)
T ss_pred CeEeHHHHHHHHHHcCCceEEEEeccch
Confidence 34444444444443332 45555554
No 119
>cd00707 Pancreat_lipase_like Pancreatic lipase-like enzymes. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation," the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site.
Probab=22.52 E-value=96 Score=21.65 Aligned_cols=30 Identities=30% Similarity=0.584 Sum_probs=21.1
Q ss_pred eEEEeecchH--HHHHHHHHHhhc--CCcEEEEe
Q psy303 23 ILLHGFGSKY--KVINEFHKKMLS--NSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr--~lL~~Fa~~~l~--~~~~lvVn 52 (62)
|+++|+++-. .....+++.++. +..|++||
T Consensus 40 ilIHG~~~~~~~~~~~~l~~~ll~~~~~nVi~vD 73 (275)
T cd00707 40 FIIHGWTSSGEESWISDLRKAYLSRGDYNVIVVD 73 (275)
T ss_pred EEEcCCCCCCCCcHHHHHHHHHHhcCCCEEEEEE
Confidence 7889987543 556667776664 46788887
No 120
>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t
Probab=22.42 E-value=91 Score=18.88 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=18.4
Q ss_pred cceEEEeecc--hHHHHHHHHHHh
Q psy303 21 FNILLHGFGS--KYKVINEFHKKM 42 (62)
Q Consensus 21 FnlllYG~GS--Kr~lL~~Fa~~~ 42 (62)
|.|++.|-.. |..|+++|...-
T Consensus 3 ~ki~i~G~~~vGKSsli~~~~~~~ 26 (166)
T cd01869 3 FKLLLIGDSGVGKSCLLLRFADDT 26 (166)
T ss_pred EEEEEECCCCCCHHHHHHHHhcCC
Confidence 6789999877 999999998643
No 121
>TIGR00231 small_GTP small GTP-binding protein domain. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.
Probab=22.41 E-value=98 Score=17.50 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=16.8
Q ss_pred cceEEEee-cc-hHHHHHHHHHHh
Q psy303 21 FNILLHGF-GS-KYKVINEFHKKM 42 (62)
Q Consensus 21 FnlllYG~-GS-Kr~lL~~Fa~~~ 42 (62)
++|++.|. || |..|++.+....
T Consensus 2 ~ki~~~G~~~~GKstl~~~l~~~~ 25 (161)
T TIGR00231 2 IKIVIVGDPNVGKSTLLNRLLGNK 25 (161)
T ss_pred eEEEEECCCCCCHHHHHHHHhCCC
Confidence 57888886 33 999999888655
No 122
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=22.34 E-value=90 Score=17.02 Aligned_cols=24 Identities=13% Similarity=0.322 Sum_probs=16.3
Q ss_pred hHHHHHHHHHHh----hcCCcEEEEecc
Q psy303 31 KYKVINEFHKKM----LSNSKVLVINGF 54 (62)
Q Consensus 31 Kr~lL~~Fa~~~----l~~~~~lvVnGy 54 (62)
=++|++...+++ ..+...+.|||=
T Consensus 24 v~~ll~~l~~~~p~~~~~~~~~v~vN~~ 51 (77)
T PF02597_consen 24 VRDLLEALAERYPELALRDRVAVAVNGE 51 (77)
T ss_dssp HHHHHHHHCHHTGGGHTTTTEEEEETTE
T ss_pred HHHHHHHHHhhccccccCccEEEEECCE
Confidence 357777777766 336667888873
No 123
>KOG1611|consensus
Probab=22.26 E-value=1e+02 Score=22.66 Aligned_cols=37 Identities=22% Similarity=0.347 Sum_probs=26.8
Q ss_pred cceEEEeecchHHHHHHHHHHh---hcCCcEEEEeccCCCC
Q psy303 21 FNILLHGFGSKYKVINEFHKKM---LSNSKVLVINGFFPDL 58 (62)
Q Consensus 21 FnlllYG~GSKr~lL~~Fa~~~---l~~~~~lvVnGy~p~~ 58 (62)
++.-++.|+-=+.-|+.|++++ +.+.|++|++ ++|+.
T Consensus 164 ~~~~~~AYrmSKaAlN~f~ksls~dL~~~~ilv~s-ihPGw 203 (249)
T KOG1611|consen 164 RPGGLSAYRMSKAALNMFAKSLSVDLKDDHILVVS-IHPGW 203 (249)
T ss_pred CCcchhhhHhhHHHHHHHHHHhhhhhcCCcEEEEE-ecCCe
Confidence 4555567776678889999988 4567787774 78864
No 124
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=22.15 E-value=98 Score=18.01 Aligned_cols=14 Identities=14% Similarity=0.351 Sum_probs=9.6
Q ss_pred hHHHHHHHHHHhhc
Q psy303 31 KYKVINEFHKKMLS 44 (62)
Q Consensus 31 Kr~lL~~Fa~~~l~ 44 (62)
|-.+++.+++.+..
T Consensus 17 KT~~~~~~~~~~~~ 30 (131)
T PF13401_consen 17 KTTLIKRLARQLNA 30 (131)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHH
Confidence 77777777776654
No 125
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=22.13 E-value=2e+02 Score=23.96 Aligned_cols=36 Identities=25% Similarity=0.484 Sum_probs=25.5
Q ss_pred hhhhhhHHHHHHHH-hCcceEEEee--cchHHHHHHHHH
Q psy303 5 ILKDIQNGIIQLEI-ENFNILLHGF--GSKYKVINEFHK 40 (62)
Q Consensus 5 ~~~~~f~qW~~eL~-~gFnlllYG~--GSKr~lL~~Fa~ 40 (62)
.+++.+..+...+. .++.++.=|. ||+.+++++|.+
T Consensus 764 ~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~ 802 (928)
T PRK08074 764 MLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQ 802 (928)
T ss_pred HHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHh
Confidence 34445555554443 5688888886 899999999986
No 126
>PHA02952 EEV maturation protein; Provisional
Probab=22.13 E-value=1.2e+02 Score=25.03 Aligned_cols=34 Identities=24% Similarity=0.492 Sum_probs=23.9
Q ss_pred EEEeecchHHHHHHHHHHhh---cCCcEEEEeccCCCC
Q psy303 24 LLHGFGSKYKVINEFHKKML---SNSKVLVINGFFPDL 58 (62)
Q Consensus 24 llYG~GSKr~lL~~Fa~~~l---~~~~~lvVnGy~p~~ 58 (62)
+|.+.-| +.|+.+|-++.. .+...+++=||+.++
T Consensus 247 ~f~~~~s-k~li~~FL~Wl~e~~~n~~ti~LvGy~Ss~ 283 (648)
T PHA02952 247 CFINFDS-KKLILDFLKWLKEVMTNTSTIILVGYLSSF 283 (648)
T ss_pred eEecCCH-HHHHHHHHHHHHHHhcCCceEEEEEhhhhh
Confidence 3446667 889999988883 345567777887653
No 127
>PLN03084 alpha/beta hydrolase fold protein; Provisional
Probab=22.08 E-value=1.3e+02 Score=22.36 Aligned_cols=30 Identities=20% Similarity=0.359 Sum_probs=18.6
Q ss_pred eEEEeecchHHHHHHHHHHhhcCCcEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNSKVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~~~lvVn 52 (62)
|+++|+|+=...-+..+..+-.+..|+.++
T Consensus 131 vllHG~~~~~~~w~~~~~~L~~~~~Via~D 160 (383)
T PLN03084 131 LLIHGFPSQAYSYRKVLPVLSKNYHAIAFD 160 (383)
T ss_pred EEECCCCCCHHHHHHHHHHHhcCCEEEEEC
Confidence 677888877666666665554444555553
No 128
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=22.05 E-value=2.1e+02 Score=17.74 Aligned_cols=29 Identities=28% Similarity=0.267 Sum_probs=14.2
Q ss_pred eEEEee-cc-hHHHHHHHHHHhhcCC-cEEEE
Q psy303 23 ILLHGF-GS-KYKVINEFHKKMLSNS-KVLVI 51 (62)
Q Consensus 23 lllYG~-GS-Kr~lL~~Fa~~~l~~~-~~lvV 51 (62)
++++|= || |..+..+|+...+.++ +++.|
T Consensus 2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~ 33 (187)
T cd01124 2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYV 33 (187)
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence 344443 33 5566666665554433 34444
No 129
>PLN02275 transferase, transferring glycosyl groups
Probab=22.02 E-value=2e+02 Score=20.42 Aligned_cols=37 Identities=11% Similarity=0.161 Sum_probs=26.1
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCC
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFP 56 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p 56 (62)
.+..+++.|=|+-|+-|++.+++.--+ .++...||.|
T Consensus 260 ~~i~l~ivG~G~~~~~l~~~~~~~~l~-~v~~~~~~~~ 296 (371)
T PLN02275 260 PRLLFIITGKGPQKAMYEEKISRLNLR-HVAFRTMWLE 296 (371)
T ss_pred CCeEEEEEeCCCCHHHHHHHHHHcCCC-ceEEEcCCCC
Confidence 357899999999999888888765222 2555555554
No 130
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=21.83 E-value=1.6e+02 Score=19.35 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=20.9
Q ss_pred EEeecchHHHHHHHHHHhhcCCc--EEEEecc
Q psy303 25 LHGFGSKYKVINEFHKKMLSNSK--VLVINGF 54 (62)
Q Consensus 25 lYG~GSKr~lL~~Fa~~~l~~~~--~lvVnGy 54 (62)
+..+-|=++||++|.+..-.-.| ++--||.
T Consensus 50 v~~~~~E~~lL~~F~~~i~~~dpdiivgyN~~ 81 (195)
T cd05780 50 VEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGD 81 (195)
T ss_pred EEEeCCHHHHHHHHHHHHHHcCCCEEEecCCC
Confidence 45678899999999998865444 3334443
No 131
>PF02100 ODC_AZ: Ornithine decarboxylase antizyme; InterPro: IPR002993 Ornithine decarboxylase antizyme (ODC-AZ) [] binds to, and destabilises, ornithine decarboxylase (ODC), a key enzyme in polyamine synthesis. ODC is then rapidly degraded. The expression of ODC-AZ requires programmed, ribosomal frameshifting which is modulated according to the cellular concentration of polyamines. High levels of polyamines induce a +1 ribosomal frameshift in the translation of mRNA for the antizyme leading to the expression of a full-length protein. At least two forms of ODC-AZ exist in mammals [] and the protein has been found in Drosophila (protein Gutfeeling).; GO: 0004857 enzyme inhibitor activity, 0008073 ornithine decarboxylase inhibitor activity; PDB: 1ZO0_A.
Probab=21.78 E-value=1.2e+02 Score=19.04 Aligned_cols=24 Identities=33% Similarity=0.522 Sum_probs=13.3
Q ss_pred eecchHHHHH--HHHHHhhcCCcEEE
Q psy303 27 GFGSKYKVIN--EFHKKMLSNSKVLV 50 (62)
Q Consensus 27 G~GSKr~lL~--~Fa~~~l~~~~~lv 50 (62)
+-|||..|+. +||++.+.-..+++
T Consensus 36 ~~~~K~~lvaLLElAee~L~c~~vvi 61 (108)
T PF02100_consen 36 GQGSKESLVALLELAEEKLGCSHVVI 61 (108)
T ss_dssp SS--SHHHHHHHHHHHHHH----EEE
T ss_pred ccccHHHHHHHHHHhcCcCCCCEEEE
Confidence 4689999876 89988775555433
No 132
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=21.63 E-value=2.3e+02 Score=18.03 Aligned_cols=37 Identities=16% Similarity=0.216 Sum_probs=30.0
Q ss_pred hhhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhhc
Q psy303 8 DIQNGIIQLEIENFNILLHGFGSKYKVINEFHKKMLS 44 (62)
Q Consensus 8 ~~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l~ 44 (62)
+.+.+....|.+.=+|.++|.|+=..+.+.|+.++..
T Consensus 18 ~~~~~~~~~l~~a~~I~i~G~G~S~~~A~~~~~~l~~ 54 (179)
T TIGR03127 18 EELDKLADKIIKAKRIFVAGAGRSGLVGKAFAMRLMH 54 (179)
T ss_pred HHHHHHHHHHHhCCEEEEEecCHHHHHHHHHHHHHHh
Confidence 4467777788778899999999888888888887764
No 133
>PRK13938 phosphoheptose isomerase; Provisional
Probab=21.54 E-value=2.6e+02 Score=19.00 Aligned_cols=35 Identities=14% Similarity=0.194 Sum_probs=29.7
Q ss_pred hhHHHHHHHHhCcceEEEeecchHHHHHHHHHHhh
Q psy303 9 IQNGIIQLEIENFNILLHGFGSKYKVINEFHKKML 43 (62)
Q Consensus 9 ~f~qW~~eL~~gFnlllYG~GSKr~lL~~Fa~~~l 43 (62)
.-.+-...+.+|=.|.++|.|+=-.+-+.|+.++.
T Consensus 34 ~a~~~~~~l~~g~rI~i~G~G~S~~~A~~fa~~L~ 68 (196)
T PRK13938 34 IGDRLIAGYRAGARVFMCGNGGSAADAQHFAAELT 68 (196)
T ss_pred HHHHHHHHHHCCCEEEEEeCcHHHHHHHHHHHHcC
Confidence 34455666899999999999999999999999986
No 134
>TIGR01497 kdpB K+-transporting ATPase, B subunit. One sequence is apparently mis-annotated in the primary literature, but properly annotated by TIGR.
Probab=21.51 E-value=45 Score=27.16 Aligned_cols=9 Identities=33% Similarity=0.685 Sum_probs=8.1
Q ss_pred cceEEEeec
Q psy303 21 FNILLHGFG 29 (62)
Q Consensus 21 FnlllYG~G 29 (62)
-|+++||+|
T Consensus 650 ~~~~~~~~~ 658 (675)
T TIGR01497 650 RNLWIYGLG 658 (675)
T ss_pred hceEEecCC
Confidence 499999999
No 135
>PLN02679 hydrolase, alpha/beta fold family protein
Probab=21.35 E-value=1.4e+02 Score=21.25 Aligned_cols=16 Identities=13% Similarity=0.158 Sum_probs=8.8
Q ss_pred hHHHHHHHHhCcceEE
Q psy303 10 QNGIIQLEIENFNILL 25 (62)
Q Consensus 10 f~qW~~eL~~gFnlll 25 (62)
|..|.-.|.++|.++.
T Consensus 104 w~~~~~~L~~~~~via 119 (360)
T PLN02679 104 WRRNIGVLAKNYTVYA 119 (360)
T ss_pred HHHHHHHHhcCCEEEE
Confidence 4444455566666655
No 136
>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=21.16 E-value=1.4e+02 Score=23.19 Aligned_cols=30 Identities=17% Similarity=0.418 Sum_probs=22.2
Q ss_pred eEEEeecc---hHHHHHHHHHHhhc---CCcEEEEe
Q psy303 23 ILLHGFGS---KYKVINEFHKKMLS---NSKVLVIN 52 (62)
Q Consensus 23 lllYG~GS---Kr~lL~~Fa~~~l~---~~~~lvVn 52 (62)
|+++|+++ .+..+.++++.++. +..||+||
T Consensus 45 IlIHG~~~s~~~~~w~~~l~~al~~~~~d~nVI~VD 80 (442)
T TIGR03230 45 IVIHGWTVTGMFESWVPKLVAALYEREPSANVIVVD 80 (442)
T ss_pred EEECCCCcCCcchhhHHHHHHHHHhccCCCEEEEEE
Confidence 89999974 35677778877762 56788887
No 137
>PRK14010 potassium-transporting ATPase subunit B; Provisional
Probab=21.10 E-value=47 Score=27.02 Aligned_cols=16 Identities=38% Similarity=0.592 Sum_probs=11.4
Q ss_pred cceEEEeecchHHHHHHHH
Q psy303 21 FNILLHGFGSKYKVINEFH 39 (62)
Q Consensus 21 FnlllYG~GSKr~lL~~Fa 39 (62)
-|+++||+| -++--|.
T Consensus 645 ~~~~~~~~~---~~~~~~~ 660 (673)
T PRK14010 645 KNMLVYGLG---GMIVPFI 660 (673)
T ss_pred hCeEEeccC---ceeehhh
Confidence 499999999 4544443
No 138
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=20.95 E-value=66 Score=18.23 Aligned_cols=12 Identities=25% Similarity=0.216 Sum_probs=9.1
Q ss_pred hcCCcEEEEecc
Q psy303 43 LSNSKVLVINGF 54 (62)
Q Consensus 43 l~~~~~lvVnGy 54 (62)
+.++|+++|||.
T Consensus 52 C~~gP~v~v~g~ 63 (80)
T cd03064 52 CDLAPVMMINDD 63 (80)
T ss_pred CCCCCEEEECCE
Confidence 357899999873
No 139
>cd03414 CbiX_SirB_C Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both CbiX and SirB are found in a wide range of bacteria.
Probab=20.94 E-value=1.4e+02 Score=17.77 Aligned_cols=21 Identities=19% Similarity=0.282 Sum_probs=15.0
Q ss_pred eEEEeecchHH----HHHHHHHHhh
Q psy303 23 ILLHGFGSKYK----VINEFHKKML 43 (62)
Q Consensus 23 lllYG~GSKr~----lL~~Fa~~~l 43 (62)
+++.|-||.+. -++++++.+-
T Consensus 3 ~llv~HGS~~~~~~~~~~~l~~~l~ 27 (117)
T cd03414 3 VVLVGRGSSDPDANADVAKIARLLE 27 (117)
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHH
Confidence 68889999843 6666776664
No 140
>PF14881 Tubulin_3: Tubulin domain
Probab=20.89 E-value=1.2e+02 Score=20.50 Aligned_cols=37 Identities=16% Similarity=0.435 Sum_probs=22.9
Q ss_pred HhCcceEE------EeecchHHHHHHHHHHhhcCCcEEEEeccCCC
Q psy303 18 IENFNILL------HGFGSKYKVINEFHKKMLSNSKVLVINGFFPD 57 (62)
Q Consensus 18 ~~gFnlll------YG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p~ 57 (62)
.|||+++. =|++| ++|+..++++- +.+++-+-|..+.
T Consensus 74 lQGfQ~~~d~d~gwgGfas--~~Le~L~DEy~-k~~i~~~~~~~~~ 116 (180)
T PF14881_consen 74 LQGFQVLTDVDDGWGGFAS--SLLEHLRDEYP-KKPIIWVWGLRDP 116 (180)
T ss_pred ccceEEEecCCCchHhHHH--HHHHHHHHHcC-CCceEEeecCCCc
Confidence 48999987 25665 57777777773 3344444455443
No 141
>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.
Probab=20.87 E-value=1.4e+02 Score=20.68 Aligned_cols=32 Identities=22% Similarity=0.445 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHhhcC-CcEEEEe--------ccCCCCcccC
Q psy303 31 KYKVINEFHKKMLSN-SKVLVIN--------GFFPDLTLKE 62 (62)
Q Consensus 31 Kr~lL~~Fa~~~l~~-~~~lvVn--------Gy~p~~tikd 62 (62)
|-.+...+.+.+-.. .++.+|| -|.|++.|||
T Consensus 9 KTT~~~~~~~~~~~~~~~~~~vNLDPa~~~~~y~~~iDird 49 (238)
T PF03029_consen 9 KTTFCKGLSEWLESNGRDVYIVNLDPAVENLPYPPDIDIRD 49 (238)
T ss_dssp HHHHHHHHHHHHTTT-S-EEEEE--TT-S--SS--SEEGGG
T ss_pred HHHHHHHHHHHHHhccCCceEEEcchHhcccccCchHHHHh
Confidence 778888888877554 4688888 6777777775
No 142
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=20.84 E-value=1.1e+02 Score=20.78 Aligned_cols=23 Identities=4% Similarity=0.099 Sum_probs=17.9
Q ss_pred ecchHHHHHHHHHHhhcCCcEEE
Q psy303 28 FGSKYKVINEFHKKMLSNSKVLV 50 (62)
Q Consensus 28 ~GSKr~lL~~Fa~~~l~~~~~lv 50 (62)
.-|=+++|++|.+..-.-.|-++
T Consensus 55 ~~~E~~lL~~f~~~i~~~dPdii 77 (207)
T cd05785 55 DAAEKELLEELVAIIRERDPDVI 77 (207)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEE
Confidence 46789999999998876556544
No 143
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.78 E-value=1.6e+02 Score=19.78 Aligned_cols=30 Identities=23% Similarity=0.329 Sum_probs=22.6
Q ss_pred hCcceEEEeecchHHHHHHHHHHhhcCCcEEEEecc
Q psy303 19 ENFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGF 54 (62)
Q Consensus 19 ~gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy 54 (62)
+=|++.++| | +.+++..+|..+..|.|.|=
T Consensus 52 ~w~~Vv~fg---k---~Ae~v~~~L~KGs~V~VeGr 81 (164)
T PRK08763 52 EWHRVKFFG---K---LGEIAGEYLRKGSQCYIEGS 81 (164)
T ss_pred eEEEEEEeh---H---HHHHHHHhcCCCCEEEEEEE
Confidence 347888886 2 45788888999988888774
No 144
>cd03799 GT1_amsK_like This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor.
Probab=20.71 E-value=2.6e+02 Score=18.41 Aligned_cols=36 Identities=11% Similarity=0.179 Sum_probs=27.5
Q ss_pred CcceEEEeecchHHHHHHHHHHhhcCCcEEEEeccCC
Q psy303 20 NFNILLHGFGSKYKVINEFHKKMLSNSKVLVINGFFP 56 (62)
Q Consensus 20 gFnlllYG~GSKr~lL~~Fa~~~l~~~~~lvVnGy~p 56 (62)
++.+.+.|-|..++-+.++++.+ ...+.|.+-|+.|
T Consensus 210 ~~~l~i~G~~~~~~~~~~~~~~~-~~~~~v~~~g~~~ 245 (355)
T cd03799 210 DFRLDIVGDGPLRDELEALIAEL-GLEDRVTLLGAKS 245 (355)
T ss_pred CeEEEEEECCccHHHHHHHHHHc-CCCCeEEECCcCC
Confidence 67888999999888888888876 2334577777765
No 145
>PRK10566 esterase; Provisional
Probab=20.58 E-value=1.3e+02 Score=19.46 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=17.5
Q ss_pred eEEEeecchHHHHHHHHHHhhcCC-cEEEEe
Q psy303 23 ILLHGFGSKYKVINEFHKKMLSNS-KVLVIN 52 (62)
Q Consensus 23 lllYG~GSKr~lL~~Fa~~~l~~~-~~lvVn 52 (62)
|+++|+|+=+.-...+++.+-..+ .++++|
T Consensus 31 v~~HG~~~~~~~~~~~~~~l~~~G~~v~~~d 61 (249)
T PRK10566 31 FFYHGFTSSKLVYSYFAVALAQAGFRVIMPD 61 (249)
T ss_pred EEeCCCCcccchHHHHHHHHHhCCCEEEEec
Confidence 566777776665556666655443 345443
No 146
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=20.53 E-value=48 Score=26.98 Aligned_cols=16 Identities=38% Similarity=0.625 Sum_probs=11.4
Q ss_pred cceEEEeecchHHHHHHHH
Q psy303 21 FNILLHGFGSKYKVINEFH 39 (62)
Q Consensus 21 FnlllYG~GSKr~lL~~Fa 39 (62)
-|+++||+| -++--|.
T Consensus 649 ~~~~~~~~~---~~~~~~~ 664 (679)
T PRK01122 649 RNLLIYGLG---GLIVPFI 664 (679)
T ss_pred hceeEecCC---ceeehhh
Confidence 499999999 4544443
No 147
>KOG2551|consensus
Probab=20.44 E-value=51 Score=23.92 Aligned_cols=29 Identities=24% Similarity=0.472 Sum_probs=22.4
Q ss_pred eEEEee-----------cchHHHHHHHHHHhhcCCcEEEE
Q psy303 23 ILLHGF-----------GSKYKVINEFHKKMLSNSKVLVI 51 (62)
Q Consensus 23 lllYG~-----------GSKr~lL~~Fa~~~l~~~~~lvV 51 (62)
||++|+ ||=|+.|.+-++-++.++|+.+=
T Consensus 9 LcLHGfrQsg~~F~~Ktg~~rK~l~k~~el~f~~aPh~~~ 48 (230)
T KOG2551|consen 9 LCLHGFRQSGKVFSEKTGSLRKLLKKLAELVFPDAPHELP 48 (230)
T ss_pred EEecchhhccHHHHHHhhhHHHHHHhhheEEecCCCccCC
Confidence 577775 88889999888888888886543
No 148
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=20.43 E-value=70 Score=18.48 Aligned_cols=10 Identities=30% Similarity=0.474 Sum_probs=8.0
Q ss_pred cCCcEEEEec
Q psy303 44 SNSKVLVING 53 (62)
Q Consensus 44 ~~~~~lvVnG 53 (62)
..+|+++|||
T Consensus 53 ~~gP~~~v~~ 62 (80)
T cd03081 53 ACSPAAMIDG 62 (80)
T ss_pred CCCCEEEECC
Confidence 4678999987
No 149
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=20.30 E-value=2.7e+02 Score=18.83 Aligned_cols=26 Identities=23% Similarity=0.258 Sum_probs=20.8
Q ss_pred hCcc-eEEEee-cc-hHHHHHHHHHHhhc
Q psy303 19 ENFN-ILLHGF-GS-KYKVINEFHKKMLS 44 (62)
Q Consensus 19 ~gFn-lllYG~-GS-Kr~lL~~Fa~~~l~ 44 (62)
.+-. +||||- |+ |..+...+|+.++.
T Consensus 22 ~~~halL~~Gp~G~Gktt~a~~lA~~l~~ 50 (325)
T COG0470 22 RLPHALLFYGPPGVGKTTAALALAKELLC 50 (325)
T ss_pred CCCceeeeeCCCCCCHHHHHHHHHHHHhC
Confidence 4455 999995 55 99999999998874
No 150
>TIGR03056 bchO_mg_che_rel putative magnesium chelatase accessory protein. Members of this family belong to the alpha/beta fold family hydrolases (PFAM model pfam00561). Members are found in bacterial genomes if and only if they encoded for anoxygenic photosynthetic systems similar to that of Rhodobacter capsulatus and other alpha-Proteobacteria. Members often are encoded in the same operon as subunits of the protoporphyrin IX magnesium chelatase, and were once designated BchO. No literature supports a role as an actual subunit of magnesium chelatase, but an accessory role is possible, as suggested by placement by its probable hydrolase activity.
Probab=20.23 E-value=1.7e+02 Score=18.70 Aligned_cols=18 Identities=6% Similarity=0.119 Sum_probs=11.7
Q ss_pred hhHHHHHHHHhCcceEEE
Q psy303 9 IQNGIIQLEIENFNILLH 26 (62)
Q Consensus 9 ~f~qW~~eL~~gFnlllY 26 (62)
.|..+...|..+|+++.+
T Consensus 43 ~~~~~~~~l~~~~~vi~~ 60 (278)
T TIGR03056 43 SWRDLMPPLARSFRVVAP 60 (278)
T ss_pred HHHHHHHHHhhCcEEEee
Confidence 455666677777777743
No 151
>PF13289 SIR2_2: SIR2-like domain
Probab=20.22 E-value=2.1e+02 Score=16.97 Aligned_cols=28 Identities=14% Similarity=0.228 Sum_probs=19.3
Q ss_pred HHHhCcceEEEeecchHHHHHHHHHHhh
Q psy303 16 LEIENFNILLHGFGSKYKVINEFHKKML 43 (62)
Q Consensus 16 eL~~gFnlllYG~GSKr~lL~~Fa~~~l 43 (62)
++....+++|.|+|---.-++...+...
T Consensus 82 ~~l~~~~~lfiGys~~D~~i~~~l~~~~ 109 (143)
T PF13289_consen 82 SLLRSKTLLFIGYSFNDPDIRQLLRSAL 109 (143)
T ss_pred HHHcCCCEEEEEECCCCHHHHHHHHHHH
Confidence 4447779999999987555555554443
No 152
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=20.15 E-value=2.6e+02 Score=18.21 Aligned_cols=50 Identities=12% Similarity=0.243 Sum_probs=36.4
Q ss_pred hhhhhhhHHHHHHHHhCcceEEEe-ecchHHHHHHHHHHhh--cCCcEEEEec
Q psy303 4 TILKDIQNGIIQLEIENFNILLHG-FGSKYKVINEFHKKML--SNSKVLVING 53 (62)
Q Consensus 4 ~~~~~~f~qW~~eL~~gFnlllYG-~GSKr~lL~~Fa~~~l--~~~~~lvVnG 53 (62)
..++++..+-.......-+|+++| -|+=++++.+...... ++.|.+.||-
T Consensus 6 ~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc 58 (168)
T PF00158_consen 6 PAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNC 58 (168)
T ss_dssp HHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEET
T ss_pred HHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEeh
Confidence 345666666677777788999998 5888888888888765 3678999873
Done!