Query psy13938
Match_columns 245
No_of_seqs 216 out of 1233
Neff 7.2
Searched_HMMs 46136
Date Sat Aug 17 00:17:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00115 CASc Caspase, inter 100.0 1E-48 2.2E-53 341.4 13.6 212 17-233 1-241 (241)
2 cd00032 CASc Caspase, interleu 100.0 4E-45 8.7E-50 319.1 13.1 213 16-232 1-243 (243)
3 KOG3573|consensus 100.0 2.8E-29 6.1E-34 225.5 6.7 180 7-190 53-244 (300)
4 PF00656 Peptidase_C14: Caspas 99.8 6.4E-20 1.4E-24 158.4 15.1 203 25-231 1-248 (248)
5 KOG3573|consensus 98.8 1.1E-09 2.3E-14 98.7 2.3 72 160-245 168-241 (300)
6 smart00115 CASc Caspase, inter 98.4 2E-07 4.4E-12 81.4 4.0 67 167-245 112-182 (241)
7 cd00032 CASc Caspase, interleu 98.2 1.4E-06 2.9E-11 76.2 4.1 69 165-245 111-186 (243)
8 COG4249 Uncharacterized protei 98.0 3.8E-06 8.3E-11 77.9 3.6 146 23-178 2-167 (380)
9 KOG1546|consensus 96.1 0.068 1.5E-06 48.5 10.4 78 23-103 62-151 (362)
10 PF12770 CHAT: CHAT domain 92.3 1 2.2E-05 39.4 9.0 99 28-135 82-202 (287)
11 PF14538 Raptor_N: Raptor N-te 91.2 4.6 0.0001 32.9 11.0 72 50-132 50-145 (154)
12 cd02012 TPP_TK Thiamine pyroph 78.1 13 0.00027 32.5 8.0 55 25-82 158-212 (255)
13 PF01650 Peptidase_C13: Peptid 76.5 3.4 7.4E-05 36.5 3.9 64 68-136 78-163 (256)
14 PRK11104 hemG protoporphyrinog 74.6 4.8 0.0001 33.3 4.2 76 42-128 9-85 (177)
15 PF00763 THF_DHG_CYH: Tetrahyd 69.2 17 0.00036 28.0 5.9 55 22-85 28-85 (117)
16 KOG2862|consensus 69.1 11 0.00023 34.7 5.2 66 51-130 105-180 (385)
17 TIGR02964 xanthine_xdhC xanthi 68.1 9 0.0002 33.5 4.6 27 44-70 106-132 (246)
18 PF13478 XdhC_C: XdhC Rossmann 65.8 12 0.00026 29.7 4.6 26 45-70 5-30 (136)
19 PLN02204 diacylglycerol kinase 65.3 43 0.00094 33.3 9.1 78 21-109 157-236 (601)
20 PF09827 CRISPR_Cas2: CRISPR a 64.5 45 0.00098 23.3 6.9 52 47-98 13-67 (78)
21 PRK14188 bifunctional 5,10-met 64.1 42 0.00091 30.3 8.2 71 22-103 31-106 (296)
22 PRK14569 D-alanyl-alanine synt 63.8 45 0.00097 29.7 8.4 66 23-103 3-68 (296)
23 PF03698 UPF0180: Uncharacteri 62.9 9.5 0.00021 27.7 3.1 39 43-95 3-41 (80)
24 PRK11914 diacylglycerol kinase 62.7 70 0.0015 28.4 9.4 54 24-84 9-62 (306)
25 PRK14189 bifunctional 5,10-met 60.5 56 0.0012 29.4 8.2 71 22-103 31-106 (285)
26 PRK14179 bifunctional 5,10-met 58.9 60 0.0013 29.2 8.1 64 22-96 31-97 (284)
27 PRK14176 bifunctional 5,10-met 58.5 69 0.0015 28.9 8.5 55 22-85 37-94 (287)
28 PRK14171 bifunctional 5,10-met 58.2 68 0.0015 28.9 8.4 55 22-85 31-88 (288)
29 PF04577 DUF563: Protein of un 57.2 21 0.00045 29.3 4.7 44 49-103 120-163 (206)
30 PF02016 Peptidase_S66: LD-car 57.1 24 0.00053 31.4 5.4 74 48-127 14-95 (284)
31 cd01240 PH_beta-ARK Beta adren 56.4 4.7 0.0001 31.1 0.6 16 225-240 21-36 (116)
32 PRK14184 bifunctional 5,10-met 56.3 75 0.0016 28.6 8.3 55 22-85 30-87 (286)
33 PRK14168 bifunctional 5,10-met 55.6 64 0.0014 29.2 7.8 71 22-103 32-107 (297)
34 cd07062 Peptidase_S66_mccF_lik 55.0 48 0.001 29.9 7.0 76 47-127 17-99 (308)
35 PLN02616 tetrahydrofolate dehy 54.9 74 0.0016 29.7 8.2 62 23-95 103-167 (364)
36 COG0513 SrmB Superfamily II DN 54.6 61 0.0013 31.4 8.1 49 24-85 273-322 (513)
37 PRK14167 bifunctional 5,10-met 53.8 72 0.0016 28.9 7.9 55 22-85 30-87 (297)
38 PRK14169 bifunctional 5,10-met 53.5 77 0.0017 28.5 7.9 63 22-95 29-94 (282)
39 PRK14180 bifunctional 5,10-met 53.3 69 0.0015 28.8 7.6 55 22-85 30-87 (282)
40 PRK14174 bifunctional 5,10-met 53.0 79 0.0017 28.6 8.0 63 22-95 30-95 (295)
41 PRK14193 bifunctional 5,10-met 51.6 81 0.0018 28.4 7.8 55 22-85 31-88 (284)
42 PF01471 PG_binding_1: Putativ 51.3 11 0.00024 24.6 1.7 39 47-85 2-40 (57)
43 PF03484 B5: tRNA synthetase B 51.3 19 0.00041 25.0 3.0 25 43-67 14-38 (70)
44 cd07025 Peptidase_S66 LD-Carbo 50.9 48 0.001 29.4 6.3 75 48-127 14-95 (282)
45 PLN02897 tetrahydrofolate dehy 50.8 85 0.0018 29.1 7.9 71 22-103 85-160 (345)
46 PLN02516 methylenetetrahydrofo 50.6 98 0.0021 28.1 8.2 71 22-103 38-113 (299)
47 PRK14173 bifunctional 5,10-met 49.9 79 0.0017 28.5 7.4 70 23-103 29-103 (287)
48 PRK14177 bifunctional 5,10-met 49.7 87 0.0019 28.2 7.6 54 23-85 33-89 (284)
49 cd02067 B12-binding B12 bindin 49.1 71 0.0015 24.0 6.2 31 51-81 17-48 (119)
50 PRK14183 bifunctional 5,10-met 48.7 96 0.0021 27.9 7.7 55 22-85 30-87 (281)
51 PRK14187 bifunctional 5,10-met 47.8 1.2E+02 0.0026 27.4 8.3 55 22-85 31-88 (294)
52 PRK14190 bifunctional 5,10-met 47.7 1.1E+02 0.0023 27.6 7.9 55 22-85 31-88 (284)
53 PF10137 TIR-like: Predicted n 47.7 33 0.00071 26.9 4.1 48 50-100 13-60 (125)
54 PRK14178 bifunctional 5,10-met 47.4 1.1E+02 0.0024 27.4 8.0 55 22-85 25-82 (279)
55 PRK09004 FMN-binding protein M 46.7 1E+02 0.0022 24.5 7.0 48 44-103 12-60 (146)
56 PRK14185 bifunctional 5,10-met 46.6 1.1E+02 0.0023 27.7 7.8 55 22-85 30-87 (293)
57 PLN02958 diacylglycerol kinase 46.3 1.2E+02 0.0027 29.2 8.7 103 22-135 110-212 (481)
58 PRK14181 bifunctional 5,10-met 45.8 1.1E+02 0.0023 27.7 7.6 63 22-95 25-90 (287)
59 PRK14182 bifunctional 5,10-met 45.8 1E+02 0.0022 27.8 7.4 63 22-95 29-94 (282)
60 PRK14166 bifunctional 5,10-met 45.8 1.1E+02 0.0024 27.5 7.7 63 22-95 29-94 (282)
61 PRK14191 bifunctional 5,10-met 45.0 1.3E+02 0.0028 27.1 8.0 55 22-85 30-87 (285)
62 cd02017 TPP_E1_EcPDC_like Thia 44.2 66 0.0014 30.3 6.2 41 25-68 178-219 (386)
63 PRK10792 bifunctional 5,10-met 43.4 85 0.0018 28.3 6.6 54 23-85 33-89 (285)
64 PF08538 DUF1749: Protein of u 43.3 68 0.0015 29.2 6.0 97 39-135 41-150 (303)
65 PRK13012 2-oxoacid dehydrogena 43.3 67 0.0015 33.6 6.6 41 25-67 263-303 (896)
66 PF03193 DUF258: Protein of un 43.3 66 0.0014 26.4 5.4 43 51-101 2-44 (161)
67 COG0075 Serine-pyruvate aminot 43.2 57 0.0012 30.6 5.7 79 22-130 78-168 (383)
68 COG2945 Predicted hydrolase of 42.6 56 0.0012 28.0 5.0 61 1-68 4-67 (210)
69 PRK14172 bifunctional 5,10-met 42.3 1.3E+02 0.0029 26.9 7.6 54 23-85 32-88 (278)
70 PF00919 UPF0004: Uncharacteri 42.2 83 0.0018 23.4 5.4 21 47-67 13-33 (98)
71 smart00874 B5 tRNA synthetase 42.2 23 0.0005 24.2 2.3 27 40-66 11-37 (71)
72 PRK14175 bifunctional 5,10-met 41.7 1.5E+02 0.0032 26.7 7.9 55 22-85 31-88 (286)
73 PRK14194 bifunctional 5,10-met 40.6 1.6E+02 0.0034 26.8 7.9 71 22-103 32-107 (301)
74 PRK14170 bifunctional 5,10-met 40.4 1.5E+02 0.0033 26.6 7.8 63 22-95 30-95 (284)
75 cd02004 TPP_BZL_OCoD_HPCL Thia 40.4 1.2E+02 0.0027 24.3 6.7 59 24-84 94-160 (172)
76 PRK14186 bifunctional 5,10-met 40.3 1.5E+02 0.0032 26.9 7.6 70 23-103 32-106 (297)
77 PF10087 DUF2325: Uncharacteri 38.4 95 0.0021 22.6 5.3 48 47-102 9-63 (97)
78 PRK13337 putative lipid kinase 38.3 1.6E+02 0.0035 26.1 7.7 38 47-84 18-55 (304)
79 PRK10953 cysJ sulfite reductas 37.1 84 0.0018 31.3 6.1 70 44-123 72-147 (600)
80 cd00578 L-fuc_L-ara-isomerases 36.9 1.6E+02 0.0035 27.8 7.8 55 46-103 21-77 (452)
81 TIGR01931 cysJ sulfite reducta 36.2 96 0.0021 30.8 6.3 70 44-123 69-144 (597)
82 PRK05899 transketolase; Review 36.0 1.3E+02 0.0029 29.8 7.4 56 26-85 182-237 (624)
83 PRK14192 bifunctional 5,10-met 35.9 2.3E+02 0.0049 25.3 8.2 55 22-85 32-89 (283)
84 PF08901 DUF1847: Protein of u 35.3 48 0.001 27.2 3.4 36 18-67 52-87 (157)
85 PLN02790 transketolase 35.3 1.8E+02 0.0038 29.3 8.1 55 26-84 169-225 (654)
86 TIGR02370 pyl_corrinoid methyl 35.0 99 0.0021 25.9 5.5 69 50-127 101-172 (197)
87 cd02001 TPP_ComE_PpyrDC Thiami 34.8 1.7E+02 0.0037 23.4 6.7 55 25-84 89-143 (157)
88 KOG0331|consensus 34.5 1.1E+02 0.0023 30.1 6.1 66 21-103 338-406 (519)
89 COG3959 Transketolase, N-termi 34.0 1.5E+02 0.0032 26.0 6.3 35 49-83 193-227 (243)
90 PRK06774 para-aminobenzoate sy 33.9 83 0.0018 25.9 4.8 26 50-75 12-39 (191)
91 PRK12571 1-deoxy-D-xylulose-5- 33.2 2.1E+02 0.0046 28.7 8.2 31 54-84 239-270 (641)
92 cd02011 TPP_PK Thiamine pyroph 33.1 1.6E+02 0.0034 25.6 6.4 35 50-84 137-171 (227)
93 PF03575 Peptidase_S51: Peptid 32.8 81 0.0018 25.1 4.4 43 50-103 2-46 (154)
94 PF02878 PGM_PMM_I: Phosphoglu 32.8 2.2E+02 0.0048 22.0 6.8 56 39-100 46-101 (137)
95 PRK11776 ATP-dependent RNA hel 32.6 1.5E+02 0.0032 28.0 6.8 49 24-85 242-291 (460)
96 PRK05723 flavodoxin; Provision 32.6 2.2E+02 0.0047 22.8 6.9 50 44-103 11-61 (151)
97 TIGR00147 lipid kinase, YegS/R 32.2 2.7E+02 0.0058 24.4 8.0 78 46-135 17-96 (293)
98 PRK08105 flavodoxin; Provision 31.6 1E+02 0.0022 24.5 4.8 50 44-103 12-62 (149)
99 cd03372 TPP_ComE Thiamine pyro 31.6 2.8E+02 0.0061 22.6 7.6 54 26-83 90-144 (179)
100 cd00568 TPP_enzymes Thiamine p 31.6 46 0.00099 26.3 2.8 58 24-83 92-156 (168)
101 PRK11253 ldcA L,D-carboxypepti 31.4 1.6E+02 0.0036 26.5 6.6 56 46-101 15-78 (305)
102 KOG0461|consensus 31.1 1.2E+02 0.0025 28.6 5.5 59 24-84 123-189 (522)
103 PF00456 Transketolase_N: Tran 30.9 1.2E+02 0.0026 27.8 5.7 54 25-82 174-228 (332)
104 PRK11702 hypothetical protein; 30.7 60 0.0013 25.0 3.0 30 55-84 16-47 (108)
105 PF08002 DUF1697: Protein of u 30.7 2E+02 0.0044 22.6 6.3 81 47-135 18-111 (137)
106 COG1691 NCAIR mutase (PurE)-re 30.6 1.2E+02 0.0026 26.6 5.2 80 15-96 92-179 (254)
107 COG1619 LdcA Uncharacterized p 30.5 2E+02 0.0044 26.2 7.0 77 46-127 24-107 (313)
108 PRK13054 lipid kinase; Reviewe 30.0 3E+02 0.0066 24.3 8.1 38 46-83 16-53 (300)
109 COG3023 ampD N-acetyl-anhydrom 29.9 43 0.00094 29.6 2.4 39 43-85 195-233 (257)
110 cd04907 ACT_ThrD-I_2 Second of 29.8 75 0.0016 22.7 3.3 39 17-67 33-71 (81)
111 KOG1349|consensus 28.8 76 0.0016 28.3 3.7 47 90-136 138-195 (309)
112 PF00781 DAGK_cat: Diacylglyce 28.8 2.6E+02 0.0057 21.2 9.9 77 50-136 17-96 (130)
113 PF00462 Glutaredoxin: Glutare 28.8 1.6E+02 0.0034 19.0 4.6 36 48-83 10-45 (60)
114 COG1163 DRG Predicted GTPase [ 28.7 90 0.002 28.9 4.3 78 47-137 198-278 (365)
115 TIGR03702 lip_kinase_YegS lipi 28.5 2.9E+02 0.0062 24.4 7.6 36 48-83 14-49 (293)
116 PRK04537 ATP-dependent RNA hel 28.4 2.1E+02 0.0046 28.1 7.3 47 25-84 258-305 (572)
117 COG2247 LytB Putative cell wal 28.3 1.1E+02 0.0025 28.0 4.9 89 17-118 69-158 (337)
118 COG4004 Uncharacterized protei 28.2 54 0.0012 24.4 2.3 28 42-69 6-33 (96)
119 PF03568 Peptidase_C50: Peptid 28.2 82 0.0018 29.3 4.2 43 51-103 277-320 (383)
120 PRK10590 ATP-dependent RNA hel 27.8 1.6E+02 0.0035 27.8 6.2 56 46-104 254-311 (456)
121 cd03371 TPP_PpyrDC Thiamine py 27.7 2.1E+02 0.0046 23.6 6.3 55 25-84 96-151 (188)
122 PF13439 Glyco_transf_4: Glyco 27.6 1.1E+02 0.0023 23.4 4.2 30 40-69 8-37 (177)
123 COG3797 Uncharacterized protei 26.9 2.3E+02 0.0049 23.8 6.0 48 47-94 18-75 (178)
124 PRK14333 (dimethylallyl)adenos 26.8 2.8E+02 0.006 26.3 7.6 56 19-84 2-71 (448)
125 PRK08007 para-aminobenzoate sy 26.6 1.4E+02 0.003 24.7 4.9 21 50-70 12-32 (187)
126 TIGR00706 SppA_dom signal pept 26.5 1.8E+02 0.0039 24.3 5.7 55 70-130 13-70 (207)
127 PRK12315 1-deoxy-D-xylulose-5- 26.4 4.6E+02 0.01 25.9 9.2 31 53-83 199-230 (581)
128 TIGR01573 cas2 CRISPR-associat 26.3 2.6E+02 0.0057 20.4 6.8 52 47-99 15-71 (95)
129 PRK12753 transketolase; Review 26.2 3.3E+02 0.0071 27.5 8.2 55 26-84 178-233 (663)
130 PF01927 Mut7-C: Mut7-C RNAse 26.1 87 0.0019 24.9 3.5 32 48-79 7-38 (147)
131 PF00656 Peptidase_C14: Caspas 25.9 83 0.0018 26.4 3.5 25 204-240 162-186 (248)
132 PHA02627 hypothetical protein; 25.9 91 0.002 21.5 2.9 25 47-71 34-58 (73)
133 PF04320 DUF469: Protein with 25.8 86 0.0019 23.8 3.1 29 56-84 11-41 (101)
134 PF14164 YqzH: YqzH-like prote 25.7 1.3E+02 0.0028 20.9 3.7 34 51-85 8-41 (64)
135 PLN02234 1-deoxy-D-xylulose-5- 25.5 2.7E+02 0.0058 28.1 7.4 32 52-83 274-306 (641)
136 PRK13055 putative lipid kinase 25.3 3.6E+02 0.0077 24.4 7.8 21 47-67 19-39 (334)
137 PRK06756 flavodoxin; Provision 25.2 2.1E+02 0.0046 22.2 5.6 73 46-127 15-89 (148)
138 TIGR00177 molyb_syn molybdenum 24.9 3.4E+02 0.0074 21.2 6.9 41 44-84 21-65 (144)
139 COG3959 Transketolase, N-termi 24.8 1.1E+02 0.0024 26.8 4.0 15 88-102 138-152 (243)
140 cd06353 PBP1_BmpA_Med_like Per 24.7 2.2E+02 0.0048 24.6 6.1 49 51-106 21-70 (258)
141 COG3286 Uncharacterized protei 24.6 1.6E+02 0.0035 25.1 4.8 54 48-101 89-154 (204)
142 COG5206 GPI8 Glycosylphosphati 24.4 98 0.0021 27.8 3.6 99 70-179 110-237 (382)
143 PRK14571 D-alanyl-alanine synt 24.1 2.3E+02 0.0049 25.0 6.1 30 40-69 11-40 (299)
144 PRK13059 putative lipid kinase 24.1 4.5E+02 0.0098 23.2 8.1 28 48-75 19-46 (295)
145 COG3171 Uncharacterized protei 23.7 99 0.0022 24.0 3.1 30 56-85 25-56 (119)
146 TIGR00232 tktlase_bact transke 23.6 2.6E+02 0.0057 28.1 7.0 54 26-83 174-228 (653)
147 PF09840 DUF2067: Uncharacteri 23.6 1.8E+02 0.0039 24.5 5.1 39 47-85 85-128 (190)
148 cd04518 TBP_archaea archaeal T 23.6 45 0.00099 27.7 1.4 49 16-65 40-88 (174)
149 TIGR03186 AKGDH_not_PDH alpha- 23.5 2.2E+02 0.0047 30.0 6.4 41 25-67 249-289 (889)
150 PRK09405 aceE pyruvate dehydro 23.5 1.9E+02 0.0042 30.3 6.1 41 25-67 255-295 (891)
151 PF03668 ATP_bind_2: P-loop AT 23.4 3.3E+02 0.0071 24.6 6.9 76 51-131 15-91 (284)
152 PF10150 RNase_E_G: Ribonuclea 23.3 2.1E+02 0.0045 25.4 5.7 47 39-85 17-69 (271)
153 cd02064 FAD_synthetase_N FAD s 22.8 1.3E+02 0.0029 24.6 4.1 34 48-81 117-157 (180)
154 PF07927 YcfA: YcfA-like prote 22.7 89 0.0019 20.1 2.5 16 51-66 2-17 (56)
155 COG1660 Predicted P-loop-conta 22.6 2.9E+02 0.0062 24.9 6.2 83 43-134 9-95 (286)
156 PF01364 Peptidase_C25: Peptid 22.6 1.2E+02 0.0027 27.8 4.2 61 70-139 226-288 (378)
157 TIGR00759 aceE pyruvate dehydr 22.5 2.4E+02 0.0052 29.6 6.5 41 25-67 249-289 (885)
158 PRK03094 hypothetical protein; 22.4 64 0.0014 23.4 1.8 27 43-69 3-29 (80)
159 PF10865 DUF2703: Domain of un 22.3 1.3E+02 0.0028 23.5 3.7 28 50-77 29-57 (120)
160 smart00490 HELICc helicase sup 22.2 2.4E+02 0.0052 18.4 5.3 34 52-85 2-36 (82)
161 PTZ00089 transketolase; Provis 21.9 4.4E+02 0.0096 26.5 8.2 55 26-84 180-236 (661)
162 cd00316 Oxidoreductase_nitroge 21.7 2.6E+02 0.0056 25.5 6.2 31 48-78 166-198 (399)
163 PRK06703 flavodoxin; Provision 21.6 2.5E+02 0.0055 21.8 5.4 65 46-123 15-84 (151)
164 PRK05261 putative phosphoketol 21.2 4E+02 0.0088 27.6 7.8 35 49-83 216-250 (785)
165 PRK04837 ATP-dependent RNA hel 21.0 2.4E+02 0.0052 26.2 5.9 15 49-63 267-281 (423)
166 PRK11712 ribonuclease G; Provi 20.9 3.5E+02 0.0075 26.3 7.0 47 39-85 140-192 (489)
167 PRK11192 ATP-dependent RNA hel 20.9 2.9E+02 0.0063 25.7 6.4 65 23-103 244-310 (434)
168 PF06866 DUF1256: Protein of u 20.8 4.8E+02 0.01 21.5 7.7 46 120-168 84-131 (163)
169 PF06076 Orthopox_F14: Orthopo 20.8 1.3E+02 0.0028 20.7 2.9 25 47-71 34-58 (73)
170 TIGR01753 flav_short flavodoxi 20.8 2.2E+02 0.0049 21.4 4.8 47 46-102 12-58 (140)
171 PRK02261 methylaspartate mutas 20.7 1.6E+02 0.0035 23.2 4.0 36 48-83 99-134 (137)
172 PRK09401 reverse gyrase; Revie 20.6 2.5E+02 0.0055 30.4 6.5 54 48-109 342-401 (1176)
173 PRK14763 coenzyme PQQ biosynth 20.4 56 0.0012 18.4 0.9 10 59-68 11-20 (26)
174 cd04906 ACT_ThrD-I_1 First of 20.3 1.6E+02 0.0035 20.8 3.6 23 47-69 52-74 (85)
175 COG2185 Sbm Methylmalonyl-CoA 20.3 3.2E+02 0.0069 22.0 5.6 61 45-111 24-87 (143)
176 PRK14976 5'-3' exonuclease; Pr 20.1 6.2E+02 0.013 22.5 8.5 62 22-83 54-125 (281)
177 cd02014 TPP_POX Thiamine pyrop 20.0 1.8E+02 0.0038 23.6 4.2 58 25-84 98-161 (178)
178 cd04516 TBP_eukaryotes eukaryo 20.0 74 0.0016 26.4 2.0 48 16-64 40-87 (174)
No 1
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=100.00 E-value=1e-48 Score=341.43 Aligned_cols=212 Identities=36% Similarity=0.557 Sum_probs=167.8
Q ss_pred ccCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh-hcCCCCceEEE
Q psy13938 17 YNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ-EDHSDADCLVI 95 (245)
Q Consensus 17 Y~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~-~~~~~~d~~vv 95 (245)
|+|+++|+|+||||||..|. .+.+|.|+++|+++|+++|++|||+|+++.|+|.+||.+.|++|++ .+|..+||++|
T Consensus 1 Y~m~~~p~g~alII~n~~f~--~~~~r~g~~~D~~~l~~~f~~lgF~V~~~~dlt~~em~~~l~~~~~~~~~~~~d~~v~ 78 (241)
T smart00115 1 YRMNSKPRGLALIINNENFH--SLPRRNGTDVDAENLTELFQSLGYEVHVKNNLTAEEMLEELKEFAERPEHSDSDSFVC 78 (241)
T ss_pred CCCCCCCCcEEEEEECccCC--CCcCCCCcHHHHHHHHHHHHHCCCEEEEecCCCHHHHHHHHHHHHhccccCCCCEEEE
Confidence 99999999999999999998 6899999999999999999999999999999999999999999998 48999999999
Q ss_pred EeccCCcc------------hhhhhhccccccccccCCCceEEEEecccCcccCCCeeeecCC-Cc--ccccCCCCcCCC
Q psy13938 96 TVLTHGLG------------EQKLWLPFTADKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRA-NT--ETDAGVNAYKIP 160 (245)
Q Consensus 96 ~ilSHG~~------------i~~I~~~f~~~~c~~L~~KPKlf~iQACRG~~~~~gv~~~d~~-~~--e~~~~~~~~~ip 160 (245)
||||||.+ +++|++.|++.+||+|+|||||||||||||++.+.|+...+.. .. +.+ ......+|
T Consensus 79 ~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~c~~L~~kPKlffiqACRg~~~~~g~~~~~~~~~~~~~~~-~~~~~~~p 157 (241)
T smart00115 79 VLLSHGEEGGIYGTDHSPLPLDEIFSLFNGDNCPSLAGKPKLFFIQACRGDELDGGVPVEDDVDDPPTEFE-DDAIYKIP 157 (241)
T ss_pred EEcCCCCCCeEEEecCCEEEHHHHHHhccccCChhhcCCCcEEEEeCCCCCCCCCCeeccccccccccccc-ccccccCC
Confidence 99999987 8999999999999999999999999999999999888653221 11 111 22355799
Q ss_pred CCCCeEEEecccCCchhhccCccccCcEEEee---ccCc---cccCCCc----cccCCCc---cceeeeeccccCccccc
Q psy13938 161 SYADFLIAYSTVEDSLLACRGTKLDGGVRLVS---RANT---ETDAGVN----AYKIPSY---ADFLIAYSTVEDCKLCL 227 (245)
Q Consensus 161 ~~~D~li~ysT~pg~~~~~~g~~~d~gv~l~~---~~~~---e~d~~~~----~~~iP~~---aDfL~~~sTve~~tl~~ 227 (245)
..+|+|++|||.||+++|+... .++|.+.+ .... ..+.... ...+-.. ..---|+|.+..+||+|
T Consensus 158 ~~~D~li~ysT~pG~va~r~~~--~gS~fi~~L~~~l~~~~~~~~l~~ilt~V~~~V~~~~~~~~~~kQ~p~~~st~L~k 235 (241)
T smart00115 158 VEADFLAAYSTTPGYVSWRNPT--RGSWFIQSLCQVLKEYARSLDLLDILTEVNRKVAVKFESVHAKKQMPTIESMTLTK 235 (241)
T ss_pred CcCcEEEEEeCCCCeEeecCCC--CCchHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhcccCCcEeCCccEeecCcc
Confidence 9999999999999999996543 35564311 1111 0010000 0011110 12246888777777999
Q ss_pred ccccCC
Q psy13938 228 YPFIFP 233 (245)
Q Consensus 228 ~~~~~p 233 (245)
+|||+|
T Consensus 236 ~~yf~p 241 (241)
T smart00115 236 KLYFFP 241 (241)
T ss_pred eeeCCC
Confidence 999998
No 2
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=100.00 E-value=4e-45 Score=319.10 Aligned_cols=213 Identities=36% Similarity=0.508 Sum_probs=165.7
Q ss_pred cccCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 16 EYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 16 ~Y~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
.|+|++.++|+||||||.+|.. .+..|.|+++|++.|+++|++|||+|.++.|+|.+||.+.|++|++.+|..+||++|
T Consensus 1 ~y~m~~~~~g~aLII~n~~f~~-~~~~r~g~~~D~~~l~~~f~~lgF~V~~~~nlt~~~~~~~l~~f~~~~~~~~d~~v~ 79 (243)
T cd00032 1 IYKMNSKRRGLALIINNENFDK-GLKDRDGTDVDAENLTKLFESLGYEVEVKNNLTAEEILEELKEFASPDHSDSDSFVC 79 (243)
T ss_pred CcCCCCCCCCEEEEEechhcCC-CCCCCCChHHHHHHHHHHHHHCCCEEEEeCCCCHHHHHHHHHHHHhccCCCCCeeEE
Confidence 4999999999999999999983 388999999999999999999999999999999999999999999877999999999
Q ss_pred EeccCCcc------------hhhhhhccccccccccCCCceEEEEecccCcccCCCeeeecCCCc----ccc-cCCCCcC
Q psy13938 96 TVLTHGLG------------EQKLWLPFTADKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRANT----ETD-AGVNAYK 158 (245)
Q Consensus 96 ~ilSHG~~------------i~~I~~~f~~~~c~~L~~KPKlf~iQACRG~~~~~gv~~~d~~~~----e~~-~~~~~~~ 158 (245)
||||||.+ +++|+++|++.+||+|.+||||||||||||++.+.|+........ +.. .......
T Consensus 80 ~~~sHG~~~~l~~~D~~~v~l~~i~~~f~~~~~~sl~~kPKl~~iqACRg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (243)
T cd00032 80 VILSHGEEGGIYGTDGDVVPIDEITSLFNGDNCPSLAGKPKLFFIQACRGDELDLGVEVDSGADEPPDVETEAEDDAVQT 159 (243)
T ss_pred EECCCCCCCEEEEecCcEEEHHHHHHhhccCCCccccCCCcEEEEECCCCCcCCCceeccCccccccccccccccccccC
Confidence 99999987 899999999999999999999999999999999988755211100 000 0123567
Q ss_pred CCCCCCeEEEecccCCchhhccCccccCcEEEee--c-cCcc---ccCCC----ccccCCCcc---ceeeeeccccCccc
Q psy13938 159 IPSYADFLIAYSTVEDSLLACRGTKLDGGVRLVS--R-ANTE---TDAGV----NAYKIPSYA---DFLIAYSTVEDCKL 225 (245)
Q Consensus 159 ip~~~D~li~ysT~pg~~~~~~g~~~d~gv~l~~--~-~~~e---~d~~~----~~~~iP~~a---DfL~~~sTve~~tl 225 (245)
+|..+|+|++|||.||+++++... .++|.+.+ . .... .+... ....+-... +---|+|.+ .+||
T Consensus 160 ~p~~~d~lv~ysT~pG~~a~r~~~--~gS~fi~~l~~~l~~~~~~~~l~~il~~V~~~V~~~~~~~~~~kQ~P~~-~stL 236 (243)
T cd00032 160 IPVEADFLVAYSTVPGYVSWRNTK--KGSWFIQSLCQVLRKYAHSLDLLDILTKVNRKVAEKFESVNGKKQMPCF-RSTL 236 (243)
T ss_pred CCCcccEEEEecCCCCeEeecCCC--CCCEeHHHHHHHHHHhCCCCcHHHHHHHHHHHHhhhhccCCCceeCCcc-cccc
Confidence 999999999999999999997543 36665411 1 1110 01000 001111111 123567755 8999
Q ss_pred ccccccC
Q psy13938 226 CLYPFIF 232 (245)
Q Consensus 226 ~~~~~~~ 232 (245)
+|+||||
T Consensus 237 ~k~~yf~ 243 (243)
T cd00032 237 TKKLYFF 243 (243)
T ss_pred ceeEeCC
Confidence 9999997
No 3
>KOG3573|consensus
Probab=99.95 E-value=2.8e-29 Score=225.54 Aligned_cols=180 Identities=32% Similarity=0.508 Sum_probs=157.4
Q ss_pred CCCCCCCCCcccCCCCCceEEEEEeCCCCCCC-CCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhh
Q psy13938 7 PMPVAKDSAEYNMSHPRRGRALVFNHDEFQMD-NMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 7 ~~~~~~~~~~Y~m~~~~~G~aLIInn~~F~~~-~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~ 85 (245)
..|....+..|+|.+..++.++|+++.+|..- .+..|.|++.|+..|.+.+..++|.|...++.+..+|...+++++..
T Consensus 53 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~r~~~~~l~~~l~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 132 (300)
T KOG3573|consen 53 RKPKRSSASTYDMALLELEKLLILGKQNLDLLIDLKSRVGTELLATILESYERDLGFEVTTANDDIPGEMQSLLKEVSYL 132 (300)
T ss_pred ccCCCccccccccchhhhHHhhhcChhhcchhhccccccChHHHHHHHHHhhhccCCCccccCccccHHHHHHHHHhhhh
Confidence 44555566779999999999999999999852 57889999999999999999999999999999999999999999999
Q ss_pred cCCCCceEEEEeccCCcc-----------hhhhhhccccccccccCCCceEEEEecccCcccCCCeeeecCCCcccccCC
Q psy13938 86 DHSDADCLVITVLTHGLG-----------EQKLWLPFTADKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGV 154 (245)
Q Consensus 86 ~~~~~d~~vv~ilSHG~~-----------i~~I~~~f~~~~c~~L~~KPKlf~iQACRG~~~~~gv~~~d~~~~e~~~~~ 154 (245)
+|.+.+|+.+..+|||+. +++|+.+|++.+||+|.+|||+||||||||++.+.|+.. ++.....+ .+
T Consensus 133 ~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~i~~~f~~~~c~~L~~kPK~~~iqac~g~~~~~~~~~-~~~~~~~~-~~ 210 (300)
T KOG3573|consen 133 DDSDNNCTACSMLSHGEEKHIYAKDDVLPLEDIFHGFNGANCPSLKGKPKVFFIQACRGDQLDLGVFP-DVDTEKLD-DD 210 (300)
T ss_pred cccccchhhhhhhcccccceeccCCCeeeHHHHHHHhhhccChhhhcCCcEEEehhccCCCCCCCccc-cccccccc-cc
Confidence 999999999999999943 899999999999999999999999999999999988876 33212222 44
Q ss_pred CCcCCCCCCCeEEEecccCCchhhccCccccCcEEE
Q psy13938 155 NAYKIPSYADFLIAYSTVEDSLLACRGTKLDGGVRL 190 (245)
Q Consensus 155 ~~~~ip~~~D~li~ysT~pg~~~~~~g~~~d~gv~l 190 (245)
..+++|+++|||++|||+|||++||+.+. |+|++
T Consensus 211 ~~~~ips~aD~L~~~st~~g~~s~R~~~~--gsw~I 244 (300)
T KOG3573|consen 211 ATYKIPSEADFLVSYSTTPGYVSWRDPTK--GSWFI 244 (300)
T ss_pred hhccCccccceeEeeecCCCceeeecCCC--ceeeH
Confidence 57889999999999999999999987644 56654
No 4
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 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 sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=99.84 E-value=6.4e-20 Score=158.36 Aligned_cols=203 Identities=21% Similarity=0.279 Sum_probs=143.4
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEE--EeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCc
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSV--YTNPEFREITEILSNLSQEDHSDADCLVITVLTHGL 102 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~--~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~ 102 (245)
++||||+|.+|. ...+|.|+.+|++.|+++|+++||.|.. ..|+|.++|.+.|+++.+... ..|+++|+|++||.
T Consensus 1 ~~AliIg~~~y~--~~~~L~~~~~D~~~~~~~L~~~gf~~~~~l~~~~t~~~i~~~l~~l~~~~~-~~D~~~~yfsGHG~ 77 (248)
T PF00656_consen 1 KRALIIGVNYYQ--NPPPLPGAVNDAEAMAEALEKLGFDVENILIDNATRANILKALRELLQRAQ-PGDSVVFYFSGHGI 77 (248)
T ss_dssp EEEEEEEESSTS--STCHCTTHHHHHHHHHHHHHHTTEEEEEEEEESSSHHHHHHHHHHHHTSGG-TCSEEEEEEESEEE
T ss_pred CEEEEEEeeCCC--CCCCCCCHHHHHHHHHHHHHHcCCceeeccccchHHHHHHHHHhhhhccCC-CCCeeEEEEecccc
Confidence 689999999998 4589999999999999999999999999 999999999999999997644 78999999999995
Q ss_pred c------------------hhh---hhhccccccccccCCCceEEEEecccCcccCCCeeeecCC--Cc--------ccc
Q psy13938 103 G------------------EQK---LWLPFTADKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRA--NT--------ETD 151 (245)
Q Consensus 103 ~------------------i~~---I~~~f~~~~c~~L~~KPKlf~iQACRG~~~~~gv~~~d~~--~~--------e~~ 151 (245)
. ++. +.+.|+...|+.+..|||+||+||||+.....+....... .. ...
T Consensus 78 ~~~~~~~~~~~~~d~~~~~~d~~~~~~~~l~~~~~~~~~~~~k~~ilD~C~sg~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (248)
T PF00656_consen 78 QVDGEGGDEDSGYDGYLLPLDANLILDDELRDLLCKSLPKKPKLFILDCCRSGGFIDGLSSSSGESSKREERKLSSSIPP 157 (248)
T ss_dssp TETTCCSTEEEETSSEEEEHHHHEEHHHHTSTTTTGGGTTS-EEEEEESESSSBTBCEEEEEESSSTSS-EECHCCCCCC
T ss_pred ccCCccCcccccccceeeecchhhhHHHHHhhhhhhhccCCccEEeeccccCCccCCccccccccccccccccccccccc
Confidence 4 344 6678888888889999999999999999876554332110 00 001
Q ss_pred cCCCCcCCCCCCCeEEEecccCCchhhccCccccCcEE---EeeccCccc-c-----CCCccccCCCcc--ce-eeeecc
Q psy13938 152 AGVNAYKIPSYADFLIAYSTVEDSLLACRGTKLDGGVR---LVSRANTET-D-----AGVNAYKIPSYA--DF-LIAYST 219 (245)
Q Consensus 152 ~~~~~~~ip~~~D~li~ysT~pg~~~~~~g~~~d~gv~---l~~~~~~e~-d-----~~~~~~~iP~~a--Df-L~~~sT 219 (245)
........+...++++++||.++..++..+. ..+|+. +........ + .......+-... .+ -.|.|.
T Consensus 158 ~~~~~~~~~~~~~~~~~~as~~~~~s~e~~~-~~~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~~~~v~~~~~~~Q~P~ 236 (248)
T PF00656_consen 158 EDPNRSDVPSPSGFIVLSASRPGQTSYEDSP-GSGGLFTYALLEALKGNAADDPNQSWDELLEELLTEVNQKVAREQTPQ 236 (248)
T ss_dssp SSCCSEEEETTTSEEEEESSSTTBCEEEECT-TTEEHHHHHHHHHHHHHTTTSTTCCTTSBHHHHHHHHHHHHHSBEEEE
T ss_pred cccccccccCCCCcEEEEeccccceeecccC-ccCHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHhHCCCceeCe
Confidence 0222445667799999999999999986622 233432 111110000 0 001111111000 11 368888
Q ss_pred ccCccccccccc
Q psy13938 220 VEDCKLCLYPFI 231 (245)
Q Consensus 220 ve~~tl~~~~~~ 231 (245)
+..+++++.|||
T Consensus 237 ~~~s~~~~~~~f 248 (248)
T PF00656_consen 237 FSCSTLTKDLYF 248 (248)
T ss_dssp EEEEESSSBEBS
T ss_pred eeeECCccccCC
Confidence 888999999997
No 5
>KOG3573|consensus
Probab=98.85 E-value=1.1e-09 Score=98.72 Aligned_cols=72 Identities=36% Similarity=0.431 Sum_probs=55.8
Q ss_pred CCCCCeEEEecccCC--chhhccCccccCcEEEeeccCccccCCCccccCCCccceeeeeccccCcccccccccCCCccc
Q psy13938 160 PSYADFLIAYSTVED--SLLACRGTKLDGGVRLVSRANTETDAGVNAYKIPSYADFLIAYSTVEDCKLCLYPFIFPNPLS 237 (245)
Q Consensus 160 p~~~D~li~ysT~pg--~~~~~~g~~~d~gv~l~~~~~~e~d~~~~~~~iP~~aDfL~~~sTve~~tl~~~~~~~pg~~s 237 (245)
...++-+-..+-.|+ |+|||||++++.|+.. ....+.-.....+.||+.||||++|||+ |||+|
T Consensus 168 ~f~~~~c~~L~~kPK~~~iqac~g~~~~~~~~~--~~~~~~~~~~~~~~ips~aD~L~~~st~------------~g~~s 233 (300)
T KOG3573|consen 168 GFNGANCPSLKGKPKVFFIQACRGDQLDLGVFP--DVDTEKLDDDATYKIPSEADFLVSYSTT------------PGYVS 233 (300)
T ss_pred HhhhccChhhhcCCcEEEehhccCCCCCCCccc--cccccccccchhccCccccceeEeeecC------------CCcee
Confidence 344666667777787 9999999999999875 1111111223567899999999999999 99999
Q ss_pred cccCCCCC
Q psy13938 238 SRVTDNGE 245 (245)
Q Consensus 238 ~r~~~~g~ 245 (245)
||++..||
T Consensus 234 ~R~~~~gs 241 (300)
T KOG3573|consen 234 WRDPTKGS 241 (300)
T ss_pred eecCCCce
Confidence 99999997
No 6
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=98.42 E-value=2e-07 Score=81.42 Aligned_cols=67 Identities=37% Similarity=0.528 Sum_probs=48.3
Q ss_pred EEecccCC--chhhccCccccCcEEEeecc-Ccc-ccCCCccccCCCccceeeeeccccCcccccccccCCCccccccCC
Q psy13938 167 IAYSTVED--SLLACRGTKLDGGVRLVSRA-NTE-TDAGVNAYKIPSYADFLIAYSTVEDCKLCLYPFIFPNPLSSRVTD 242 (245)
Q Consensus 167 i~ysT~pg--~~~~~~g~~~d~gv~l~~~~-~~e-~d~~~~~~~iP~~aDfL~~~sTve~~tl~~~~~~~pg~~s~r~~~ 242 (245)
-.....|. |+|||||...+.|+...... ..+ .........+|..+|+|++|||+ |||+|||++.
T Consensus 112 ~~L~~kPKlffiqACRg~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~D~li~ysT~------------pG~va~r~~~ 179 (241)
T smart00115 112 PSLAGKPKLFFIQACRGDELDGGVPVEDDVDDPPTEFEDDAIYKIPVEADFLAAYSTT------------PGYVSWRNPT 179 (241)
T ss_pred hhhcCCCcEEEEeCCCCCCCCCCeecccccccccccccccccccCCCcCcEEEEEeCC------------CCeEeecCCC
Confidence 34455666 99999999999887542211 000 01122345799999999999999 9999999998
Q ss_pred CCC
Q psy13938 243 NGE 245 (245)
Q Consensus 243 ~g~ 245 (245)
.||
T Consensus 180 ~gS 182 (241)
T smart00115 180 RGS 182 (241)
T ss_pred CCc
Confidence 886
No 7
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=98.19 E-value=1.4e-06 Score=76.24 Aligned_cols=69 Identities=38% Similarity=0.469 Sum_probs=49.3
Q ss_pred eEEEecccCC--chhhccCccccCcEEEeeccCcc-----ccCCCccccCCCccceeeeeccccCcccccccccCCCccc
Q psy13938 165 FLIAYSTVED--SLLACRGTKLDGGVRLVSRANTE-----TDAGVNAYKIPSYADFLIAYSTVEDCKLCLYPFIFPNPLS 237 (245)
Q Consensus 165 ~li~ysT~pg--~~~~~~g~~~d~gv~l~~~~~~e-----~d~~~~~~~iP~~aDfL~~~sTve~~tl~~~~~~~pg~~s 237 (245)
.+-.+...|. ++|||||...+.|+......... .........+|..+|+|++|||+ |||++
T Consensus 111 ~~~sl~~kPKl~~iqACRg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~d~lv~ysT~------------pG~~a 178 (243)
T cd00032 111 NCPSLAGKPKLFFIQACRGDELDLGVEVDSGADEPPDVETEAEDDAVQTIPVEADFLVAYSTV------------PGYVS 178 (243)
T ss_pred CCccccCCCcEEEEECCCCCcCCCceeccCccccccccccccccccccCCCCcccEEEEecCC------------CCeEe
Confidence 3334555676 89999999998886543211100 01122446789999999999999 99999
Q ss_pred cccCCCCC
Q psy13938 238 SRVTDNGE 245 (245)
Q Consensus 238 ~r~~~~g~ 245 (245)
||++..||
T Consensus 179 ~r~~~~gS 186 (243)
T cd00032 179 WRNTKKGS 186 (243)
T ss_pred ecCCCCCC
Confidence 99998886
No 8
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=98.02 E-value=3.8e-06 Score=77.93 Aligned_cols=146 Identities=20% Similarity=0.246 Sum_probs=99.4
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCc
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGL 102 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~ 102 (245)
.++.||||.|..+. .-..+.+..+|...++.++..+||+|....|+....|+..|..|+.. ....+-+++...+||.
T Consensus 2 ~~r~alvigns~~~--~aa~l~np~~da~~~a~~L~~iGfdvy~~~d~~~~~~~~~L~~f~~d-a~ga~~al~~~aGhg~ 78 (380)
T COG4249 2 ERRVALVIGNSTYY--VAAPLANPANDAGAMALWLTAIGFDVYLDTDLPKSGLRRALRYFAED-AEGADVALIYYAGHGL 78 (380)
T ss_pred CcceEEEeecCccc--ccccCCCchhhHHHHHHHHHHcCceeecccccchHHHHhHHHHHHHH-HHHHhHHHhhhccccc
Confidence 36899999998776 45567788999999999999999999999999999999999999865 3556788899999998
Q ss_pred c---------hh-hh-hhcccc-----ccc----cccCCCceEEEEecccCcccCCCeeeecCCCcccccCCCCcCCCCC
Q psy13938 103 G---------EQ-KL-WLPFTA-----DKC----RTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNAYKIPSY 162 (245)
Q Consensus 103 ~---------i~-~I-~~~f~~-----~~c----~~L~~KPKlf~iQACRG~~~~~gv~~~d~~~~e~~~~~~~~~ip~~ 162 (245)
+ ++ ++ ..-+-. ..| .....+-+++|.++||...........-+ +-....-...
T Consensus 79 Q~~~~~~~~pv~~~~~~~~~~~~~~v~~~~~~~~~p~~~~V~~~~lD~~~~~~~~d~~~~~fs-------G~g~~~~~d~ 151 (380)
T COG4249 79 QVDGTNYLLPVDADDVSPTFAVTEAVLIDCRLIPLPARTKVRRVLLDAARDNPPADTILFFFS-------GHGATPGADG 151 (380)
T ss_pred cccCccccccchhhhccccchhhhhhhhhhhcccCCchhHHHHHHHHHhhcCchhhhhhheee-------ccccccCCCC
Confidence 7 10 00 000000 011 11234557889999998876321111001 1111111333
Q ss_pred CCeEEEecccCCchhh
Q psy13938 163 ADFLIAYSTVEDSLLA 178 (245)
Q Consensus 163 ~D~li~ysT~pg~~~~ 178 (245)
.++|+.+.|.|+-++.
T Consensus 152 ~~~lia~~t~p~~~a~ 167 (380)
T COG4249 152 RAYLIAFDTRPGAVAY 167 (380)
T ss_pred ceeEEeecCChhhhcc
Confidence 4499999999987764
No 9
>KOG1546|consensus
Probab=96.08 E-value=0.068 Score=48.51 Aligned_cols=78 Identities=21% Similarity=0.282 Sum_probs=57.8
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHh-CCcEE---EEE--------eCCCHHHHHHHHHHHhhhcCCCC
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYA-LGFEV---SVY--------TNPEFREITEILSNLSQEDHSDA 90 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~-LgF~V---~~~--------~nlt~~em~~~l~~~~~~~~~~~ 90 (245)
.+.+||||.- +|.+ ......|.-+|+.+|+++|-+ +||.- .+. .-.|.+-|+.+|..+.+.. ...
T Consensus 62 gkrrAvLiGI-NY~g-Tk~ELrGCINDv~~M~~~Lv~rfGFs~ddI~~LtDt~~s~~~~PT~~Nir~Al~wLV~~a-q~g 138 (362)
T KOG1546|consen 62 GKRRAVLIGI-NYPG-TKNELRGCINDVHRMRKLLVERFGFSEDDILMLTDTDESPVRIPTGKNIRRALRWLVESA-QPG 138 (362)
T ss_pred ccceEEEEee-cCCC-cHHHHhhhHHHHHHHHHHHHHhhCCChhheEEEecCCCcccccCcHHHHHHHHHHHHhcC-CCC
Confidence 4456888764 3432 344678999999999998865 89962 211 2358899999999988763 445
Q ss_pred ceEEEEeccCCcc
Q psy13938 91 DCLVITVLTHGLG 103 (245)
Q Consensus 91 d~~vv~ilSHG~~ 103 (245)
|++|+=+.+||.+
T Consensus 139 D~LvfHYSGHGtr 151 (362)
T KOG1546|consen 139 DSLVFHYSGHGTR 151 (362)
T ss_pred CEEEEEecCCCCc
Confidence 9999999999976
No 10
>PF12770 CHAT: CHAT domain
Probab=92.27 E-value=1 Score=39.43 Aligned_cols=99 Identities=21% Similarity=0.318 Sum_probs=67.0
Q ss_pred EEEeCCCCCCC-----CCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCc
Q psy13938 28 LVFNHDEFQMD-----NMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGL 102 (245)
Q Consensus 28 LIInn~~F~~~-----~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~ 102 (245)
|+|.+-.+... ......++....+.|.+.+..-+-.+....+.|.+++.+.+ ....+=++-|.+||.
T Consensus 82 l~i~~p~~~~~~~~~~~~~~l~~~~~e~~~l~~~~~~~~~~~~~~~~at~~~l~~~l--------~~~~~~ilH~a~Hg~ 153 (287)
T PF12770_consen 82 LVIGNPDFGGSLIRGAALSPLPGAQREADALAELLGAGGLRVLVGPEATKDALLEAL--------ERRGPDILHFAGHGT 153 (287)
T ss_pred EEEecCCCcccccccccccCchHHHHHHHHHHHHhcccceeEeeccCCCHHHHHhhh--------ccCCCCEEEEEcccc
Confidence 88888776521 34677889999999999998877788999999999999998 112333778888885
Q ss_pred c-----------hhh----hhhcccccc-cc-ccCCCceEEEEecccCcc
Q psy13938 103 G-----------EQK----LWLPFTADK-CR-TLAGKPKIFFIQACRGTK 135 (245)
Q Consensus 103 ~-----------i~~----I~~~f~~~~-c~-~L~~KPKlf~iQACRG~~ 135 (245)
. +.+ --..+.... .. .|.+ |+++|+.||.+..
T Consensus 154 ~~~~~~~~~~l~l~~~~~~~~~~l~~~~l~~l~l~~-~~lVvLsaC~s~~ 202 (287)
T PF12770_consen 154 FDPDPPDQSGLVLSDESGQEDGLLSAEELAQLDLRG-PRLVVLSACESAS 202 (287)
T ss_pred cCCCCCCCCEEEEeccCCCCCcccCHHHHHhhcCCC-CCEEEecCcCCcC
Confidence 4 110 011111111 11 1333 9999999998873
No 11
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=91.18 E-value=4.6 Score=32.94 Aligned_cols=72 Identities=15% Similarity=0.286 Sum_probs=53.8
Q ss_pred HHHHHHHHHhCC--cEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc----------------------hh
Q psy13938 50 VKNLEAAFYALG--FEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG----------------------EQ 105 (245)
Q Consensus 50 ~~~l~~~f~~Lg--F~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~----------------------i~ 105 (245)
.+.|+.-++++- -.+....|.|.+++++.+.++.+... .+-+++-+.+||.. +.
T Consensus 50 ~~~l~~qY~~~~~~~~~~~~~dpt~e~~~~~~~~~R~~a~--~~RvLFHYnGhGvP~Pt~~GeIw~f~~~~tqyip~si~ 127 (154)
T PF14538_consen 50 GKNLQSQYESWQPRARYKQSLDPTVEDLKRLCQSLRRNAK--DERVLFHYNGHGVPRPTENGEIWVFNKNYTQYIPLSIY 127 (154)
T ss_pred HHHHHHHHHHhCccCcEEEecCCCHHHHHHHHHHHHhhCC--CceEEEEECCCCCCCCCCCCeEEEEcCCCCcceEEEHH
Confidence 555666666663 45778889999999999999987632 27789999999975 33
Q ss_pred hhhhccccccccccCCCceEEEEeccc
Q psy13938 106 KLWLPFTADKCRTLAGKPKIFFIQACR 132 (245)
Q Consensus 106 ~I~~~f~~~~c~~L~~KPKlf~iQACR 132 (245)
+|++ ..|.|-+||+++..
T Consensus 128 dL~~---------~lg~Psi~V~DC~~ 145 (154)
T PF14538_consen 128 DLQS---------WLGSPSIYVFDCSN 145 (154)
T ss_pred HHHH---------hcCCCEEEEEECCc
Confidence 4433 46889999998753
No 12
>cd02012 TPP_TK Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. In addition, the enzyme plays a central role in the Calvin cycle in plants. Typically, TKs are homodimers. They require TPP and divalent cations, such as magnesium ions, for activity.
Probab=78.09 E-value=13 Score=32.52 Aligned_cols=55 Identities=16% Similarity=0.215 Sum_probs=36.0
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHH
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNL 82 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~ 82 (245)
-+.+|+||..+.. ..+........++.+.|+.+|+++.....-+.+++.+.+++.
T Consensus 158 ~li~vvdnN~~~~---~~~~~~~~~~~~~~~~~~a~G~~~~~v~G~d~~~l~~al~~a 212 (255)
T cd02012 158 NLIAIVDSNRIQI---DGPTDDILFTEDLAKKFEAFGWNVIEVDGHDVEEILAALEEA 212 (255)
T ss_pred cEEEEEECCCccc---cCcHhhccCchhHHHHHHHcCCeEEEECCCCHHHHHHHHHHH
Confidence 3788888876642 222223334578899999999998876644566666665443
No 13
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 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 the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=76.52 E-value=3.4 Score=36.50 Aligned_cols=64 Identities=16% Similarity=0.290 Sum_probs=38.2
Q ss_pred eCCCHHHHHHHHHHHh----hh--cCCCCceEEEEeccCCcc------------hhhhhhccccccccccCCCce----E
Q psy13938 68 TNPEFREITEILSNLS----QE--DHSDADCLVITVLTHGLG------------EQKLWLPFTADKCRTLAGKPK----I 125 (245)
Q Consensus 68 ~nlt~~em~~~l~~~~----~~--~~~~~d~~vv~ilSHG~~------------i~~I~~~f~~~~c~~L~~KPK----l 125 (245)
.++|.+.+...|+-=. .+ ....-|-++|++.+||+. -.+|.+.+.. +..+-+ +
T Consensus 78 ~~v~~~~fl~vL~G~~~~~~~kvl~s~~~D~vfiy~~~HG~~~~l~~~~~~~l~~~~L~~~L~~-----m~~~~~y~~lv 152 (256)
T PF01650_consen 78 EDVTPENFLNVLTGDKSVPSGKVLNSTENDNVFIYFTGHGGPGFLKFPDGEELTADDLADALDK-----MHEKKRYKKLV 152 (256)
T ss_pred cccCHHHHHHHhcCCCCCCccccccCCCCCeEEEEEeccCCCCcccCCCcccccHHHHHHHHHH-----HHhhCCcceEE
Confidence 3566666666554111 01 224578899999999987 2344444332 333444 8
Q ss_pred EEEecccCccc
Q psy13938 126 FFIQACRGTKL 136 (245)
Q Consensus 126 f~iQACRG~~~ 136 (245)
|++.||..+..
T Consensus 153 ~~veaC~SGs~ 163 (256)
T PF01650_consen 153 FVVEACYSGSF 163 (256)
T ss_pred EEEecccccch
Confidence 99999987654
No 14
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=74.60 E-value=4.8 Score=33.28 Aligned_cols=76 Identities=20% Similarity=0.248 Sum_probs=48.8
Q ss_pred CCCCcHHH-HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcchhhhhhccccccccccC
Q psy13938 42 PRPGSGAD-VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQKLWLPFTADKCRTLA 120 (245)
Q Consensus 42 ~R~Gs~~D-~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c~~L~ 120 (245)
.+.|+-.. ++.|.+.+.. |.+|.+.+- .+....+...||.+++..-.|.+.+...+..|-..+-..|.
T Consensus 9 S~~G~T~~iA~~Ia~~l~~-g~~v~~~~~----------~~~~~~~l~~yD~vIlGspi~~G~~~~~~~~fl~~~~~~l~ 77 (177)
T PRK11104 9 SRDGQTRKIASYIASELKE-GIQCDVVNL----------HRIEEPDLSDYDRVVIGASIRYGHFHSALYKFVKKHATQLN 77 (177)
T ss_pred CCCChHHHHHHHHHHHhCC-CCeEEEEEh----------hhcCccCHHHCCEEEEECccccCCcCHHHHHHHHHHHHHhC
Confidence 36777777 7779999998 998877641 12222345678998888877866633222222222345689
Q ss_pred CCceEEEE
Q psy13938 121 GKPKIFFI 128 (245)
Q Consensus 121 ~KPKlf~i 128 (245)
+||-++|.
T Consensus 78 ~K~v~~F~ 85 (177)
T PRK11104 78 QMPSAFFS 85 (177)
T ss_pred CCeEEEEE
Confidence 99977775
No 15
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=69.25 E-value=17 Score=28.02 Aligned_cols=55 Identities=20% Similarity=0.265 Sum_probs=39.9
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
...++|+|.-+ ++.+|..=++...+..+++|..++.+ .+.|.+++.+.++++...
T Consensus 28 ~~P~Laii~vg---------~d~~S~~Y~~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~i~~lN~D 85 (117)
T PF00763_consen 28 ITPKLAIILVG---------DDPASISYVRSKQKAAEKLGIEFELIELPEDISEEELLELIEKLNED 85 (117)
T ss_dssp ---EEEEEEES-----------HHHHHHHHHHHHHHHHHT-EEEEEEE-TTSSHHHHHHHHHHHHH-
T ss_pred CCcEEEEEecC---------CChhHHHHHHHHHHHHHHcCCceEEEECCCCcCHHHHHHHHHHHhCC
Confidence 45688888543 34567777889999999999987655 579999999999999765
No 16
>KOG2862|consensus
Probab=69.05 E-value=11 Score=34.70 Aligned_cols=66 Identities=26% Similarity=0.289 Sum_probs=44.4
Q ss_pred HHHHHHHHhCCcEEEEEe-----CCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc----hhhhhhccccccccccCC
Q psy13938 51 KNLEAAFYALGFEVSVYT-----NPEFREITEILSNLSQEDHSDADCLVITVLTHGLG----EQKLWLPFTADKCRTLAG 121 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~~~-----nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~----i~~I~~~f~~~~c~~L~~ 121 (245)
.+..+..+++|++|.+.+ -.+.++|.+.|.+- + -..+++.||+. ++++...+. .-|.
T Consensus 105 ~ra~D~~~r~ga~V~~v~~~~G~~~~le~i~~~lsqh-----~----p~~vfv~hgdsSTgV~q~~~~~~g-~lc~---- 170 (385)
T KOG2862|consen 105 QRAADCARRYGAEVDVVEADIGQAVPLEEITEKLSQH-----K----PKAVFVTHGDSSTGVLQDLLAISG-ELCH---- 170 (385)
T ss_pred HHHHHHHHhhCceeeEEecCcccCccHHHHHHHHHhc-----C----CceEEEEecCccccccchHHHHHH-HHhh----
Confidence 345677889999997663 47888888887652 2 23678899998 677776664 3343
Q ss_pred Cc-eEEEEec
Q psy13938 122 KP-KIFFIQA 130 (245)
Q Consensus 122 KP-Klf~iQA 130 (245)
|+ -+|++++
T Consensus 171 k~~~lllVD~ 180 (385)
T KOG2862|consen 171 KHEALLLVDT 180 (385)
T ss_pred cCCeEEEEec
Confidence 54 4555553
No 17
>TIGR02964 xanthine_xdhC xanthine dehydrogenase accessory protein XdhC. Members of this protein family are the accessory protein XdhC for insertion of the molybdenum cofactor into the xanthine dehydrogenase large chain, XdhB, in bacteria. This protein is not part of the mature xanthine dehydrogenase. Xanthine dehydrogenase is an enzyme for purine catabolism, from other purines to xanthine to urate to further breakdown products.
Probab=68.08 E-value=9 Score=33.54 Aligned_cols=27 Identities=22% Similarity=0.164 Sum_probs=24.2
Q ss_pred CCcHHHHHHHHHHHHhCCcEEEEEeCC
Q psy13938 44 PGSGADVKNLEAAFYALGFEVSVYTNP 70 (245)
Q Consensus 44 ~Gs~~D~~~l~~~f~~LgF~V~~~~nl 70 (245)
.|+-.++..|.++...|||+|.+..+-
T Consensus 106 fGaG~va~~la~la~~lGf~V~v~D~R 132 (246)
T TIGR02964 106 FGAGHVGRALVRALAPLPCRVTWVDSR 132 (246)
T ss_pred ECCcHHHHHHHHHHhcCCCEEEEEeCC
Confidence 588899999999999999999997654
No 18
>PF13478 XdhC_C: XdhC Rossmann domain; PDB: 3ON5_A 2WE8_B 2WE7_A.
Probab=65.79 E-value=12 Score=29.67 Aligned_cols=26 Identities=31% Similarity=0.424 Sum_probs=22.0
Q ss_pred CcHHHHHHHHHHHHhCCcEEEEEeCC
Q psy13938 45 GSGADVKNLEAAFYALGFEVSVYTNP 70 (245)
Q Consensus 45 Gs~~D~~~l~~~f~~LgF~V~~~~nl 70 (245)
|+-.++..|.++...|||.|.+..+-
T Consensus 5 GaG~va~al~~la~~lg~~v~v~d~r 30 (136)
T PF13478_consen 5 GAGHVARALARLAALLGFRVTVVDPR 30 (136)
T ss_dssp S-STCHHHHHHHHHHCTEEEEEEES-
T ss_pred eCcHHHHHHHHHHHhCCCEEEEEcCC
Confidence 56678999999999999999998875
No 19
>PLN02204 diacylglycerol kinase
Probab=65.28 E-value=43 Score=33.30 Aligned_cols=78 Identities=6% Similarity=0.124 Sum_probs=50.2
Q ss_pred CCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccC
Q psy13938 21 HPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTH 100 (245)
Q Consensus 21 ~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSH 100 (245)
.+++.+.+|||- ...+..+..-.+.+..+|+..|+++.+..--.+.+-.+.+++.++.+...+|.+|+|
T Consensus 157 ~r~k~llVivNP-------~sGkg~~~~~~~~V~p~f~~a~i~~~v~~T~~aghA~d~~~~~~~~~l~~~D~VVaV---- 225 (601)
T PLN02204 157 GRPKNLLVFVHP-------LSGKGSGSRTWETVSPIFIRAKVKTKVIVTERAGHAFDVMASISNKELKSYDGVIAV---- 225 (601)
T ss_pred CCCceEEEEECC-------CCCCcchHHHHHHHHHHHHHcCCeEEEEEecCcchHHHHHHHHhhhhccCCCEEEEE----
Confidence 345566777764 222222334566899999999998777666556667777777765555667866654
Q ss_pred Ccc--hhhhhh
Q psy13938 101 GLG--EQKLWL 109 (245)
Q Consensus 101 G~~--i~~I~~ 109 (245)
|++ +.+|+.
T Consensus 226 GGDGt~nEVlN 236 (601)
T PLN02204 226 GGDGFFNEILN 236 (601)
T ss_pred cCccHHHHHHH
Confidence 555 555554
No 20
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=64.46 E-value=45 Score=23.30 Aligned_cols=52 Identities=15% Similarity=0.165 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHhCCcEE---EEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEec
Q psy13938 47 GADVKNLEAAFYALGFEV---SVYTNPEFREITEILSNLSQEDHSDADCLVITVL 98 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V---~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~il 98 (245)
++...++.+.++++|..+ ...-+++..+..+.++++.+.-....|++.++=+
T Consensus 13 ~k~~~kv~k~L~~~g~~iQ~SVf~~~~~~~~~~~l~~~l~~~i~~~~d~i~i~~l 67 (78)
T PF09827_consen 13 NKRRNKVRKILKSYGTRIQYSVFEGNLTNAELRKLRRELEKLIDPDEDSIRIYPL 67 (78)
T ss_dssp HHHHHHHHHHHHHTTEEEETTEEEEEE-HHHHHHHHHHHHHHSCTTTCEEEEEEE
T ss_pred cHHHHHHHHHHHHhCccccceEEEEEcCHHHHHHHHHHHHhhCCCCCCEEEEEEe
Confidence 467889999999999655 2344899999998888887753344477666544
No 21
>PRK14188 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=64.07 E-value=42 Score=30.34 Aligned_cols=71 Identities=14% Similarity=0.162 Sum_probs=51.6
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEe-
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITV- 97 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~i- 97 (245)
.+.++|+|.-+ ++.++..=++.-.+..+++|++++.+ .+.|.+|+.+.|+++.+. .+.+.++|-+
T Consensus 31 ~~p~La~i~vg---------~~~~s~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~i~~lN~d--~~V~GIlvq~P 99 (296)
T PRK14188 31 VTPGLAVVLVG---------EDPASQVYVRSKGKQTKEAGMASFEHKLPADTSQAELLALIARLNAD--PAIHGILVQLP 99 (296)
T ss_pred CCCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCcEEEEeCC
Confidence 35688888643 45567788899999999999998877 589999999999888654 3344454442
Q ss_pred -ccCCcc
Q psy13938 98 -LTHGLG 103 (245)
Q Consensus 98 -lSHG~~ 103 (245)
=.|-.+
T Consensus 100 lp~~~~~ 106 (296)
T PRK14188 100 LPKHLDS 106 (296)
T ss_pred CCCCCCH
Confidence 246543
No 22
>PRK14569 D-alanyl-alanine synthetase A; Provisional
Probab=63.78 E-value=45 Score=29.65 Aligned_cols=66 Identities=14% Similarity=0.185 Sum_probs=42.9
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCc
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGL 102 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~ 102 (245)
+..++|+.+= .-..|.-|-+-++.+.+.|+++||+|... |.+..++...| .. ...|.++.++ ||.
T Consensus 3 ~~~i~vl~gg------~s~e~~vsl~s~~~v~~aL~~~g~~~~~~-~~~~~~~~~~l---~~---~~~d~vf~~l--hG~ 67 (296)
T PRK14569 3 NEKIVVLYGG------DSPEREVSLKSGKAVLDSLISQGYDAVGV-DASGKELVAKL---LE---LKPDKCFVAL--HGE 67 (296)
T ss_pred CcEEEEEeCC------CCCchHhHHHHHHHHHHHHHHcCCEEEEE-cCCchhHHHHh---hc---cCCCEEEEeC--CCC
Confidence 3456777541 45678889999999999999999998665 44433433222 21 2466555544 885
Q ss_pred c
Q psy13938 103 G 103 (245)
Q Consensus 103 ~ 103 (245)
.
T Consensus 68 ~ 68 (296)
T PRK14569 68 D 68 (296)
T ss_pred C
Confidence 4
No 23
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=62.92 E-value=9.5 Score=27.72 Aligned_cols=39 Identities=23% Similarity=0.408 Sum_probs=29.0
Q ss_pred CCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 43 RPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 43 R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
|.|-+....++++.|++-||+|....+-. +...+||+|+
T Consensus 3 kIAVE~~Ls~v~~~L~~~GyeVv~l~~~~--------------~~~~~daiVv 41 (80)
T PF03698_consen 3 KIAVEEGLSNVKEALREKGYEVVDLENEQ--------------DLQNVDAIVV 41 (80)
T ss_pred eEEecCCchHHHHHHHHCCCEEEecCCcc--------------ccCCcCEEEE
Confidence 45566778899999999999998776422 3456777765
No 24
>PRK11914 diacylglycerol kinase; Reviewed
Probab=62.75 E-value=70 Score=28.44 Aligned_cols=54 Identities=7% Similarity=0.078 Sum_probs=36.2
Q ss_pred ceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh
Q psy13938 24 RGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 24 ~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~ 84 (245)
+.++||+|- ...+-.+.+..+.+.+.|++.|+++.++.--...+..+..++...
T Consensus 9 ~~~~iI~NP-------~sG~g~~~~~~~~~~~~l~~~g~~~~~~~t~~~~~~~~~a~~~~~ 62 (306)
T PRK11914 9 GKVTVLTNP-------LSGHGAAPHAAERAIARLHHRGVDVVEIVGTDAHDARHLVAAALA 62 (306)
T ss_pred ceEEEEECC-------CCCCCcHHHHHHHHHHHHHHcCCeEEEEEeCCHHHHHHHHHHHHh
Confidence 456666653 222222456677888999999999887766667777777777653
No 25
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=60.45 E-value=56 Score=29.42 Aligned_cols=71 Identities=17% Similarity=0.182 Sum_probs=50.7
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhhcCCCCceEEEEec
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQEDHSDADCLVITVL 98 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~~~~~~d~~vv~il 98 (245)
.+.++|+|.-+ ++.++..=++...+.++++|++++.++ |.|.+|+.+.++++-+. .+.+.++|-+=
T Consensus 31 ~~p~Laii~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d--~~V~GIlvq~P 99 (285)
T PRK14189 31 HQPGLAVILVG---------DNPASQVYVRNKVKACEDNGFHSLKDRYPADLSEAELLARIDELNRD--PKIHGILVQLP 99 (285)
T ss_pred CCCeEEEEEeC---------CCchHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCC--CCCCeEEEeCC
Confidence 35689888643 455688889999999999999987764 78999999999987653 33344444322
Q ss_pred --cCCcc
Q psy13938 99 --THGLG 103 (245)
Q Consensus 99 --SHG~~ 103 (245)
.|-.+
T Consensus 100 lp~~i~~ 106 (285)
T PRK14189 100 LPKHIDS 106 (285)
T ss_pred CCCCCCH
Confidence 35544
No 26
>PRK14179 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=58.91 E-value=60 Score=29.22 Aligned_cols=64 Identities=19% Similarity=0.285 Sum_probs=47.3
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVIT 96 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~ 96 (245)
.+.++|+|.-+ ++..+..=++...+..+++|++++.+ +|.|.+|+.+.|+++-+. ...+.++|-
T Consensus 31 ~~P~Laii~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d--~~V~GIivq 97 (284)
T PRK14179 31 IVPGLVVILVG---------DNPASQVYVRNKERSALAAGFKSEVVRLPETISQEELLDLIERYNQD--PTWHGILVQ 97 (284)
T ss_pred CCceEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEEc
Confidence 34689888543 45567777888999999999998665 578899999999888754 334444443
No 27
>PRK14176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=58.53 E-value=69 Score=28.88 Aligned_cols=55 Identities=18% Similarity=0.219 Sum_probs=43.7
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-+ ++..|..=++.-.+..+++|++++.+ .+.|.+|+.+.++++.+.
T Consensus 37 ~~P~Laii~vg---------~d~aS~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~LN~D 94 (287)
T PRK14176 37 ITPGLATILVG---------DDPASKMYVRLKHKACERVGIRAEDQFLPADTTQEELLELIDSLNKR 94 (287)
T ss_pred CCCeEEEEEEC---------CCcchHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 34689988643 45567888999999999999998665 578899999999888753
No 28
>PRK14171 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=58.20 E-value=68 Score=28.91 Aligned_cols=55 Identities=16% Similarity=0.165 Sum_probs=43.7
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-. ++.+|..=++.-.+..+++|++++.++ +.|.+|+.+.++++.+.
T Consensus 31 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~~l~~~I~~LN~D 88 (288)
T PRK14171 31 ASPKLAIVLVG---------DNPASIIYVKNKIKNAHKIGIDTLLVNLSTTIHTNDLISKINELNLD 88 (288)
T ss_pred CCCeEEEEEeC---------CCccHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCC
Confidence 34588888643 456688888999999999999987764 78999999999887654
No 29
>PF04577 DUF563: Protein of unknown function (DUF563); InterPro: IPR007657 This is a family of uncharacterised glycosyltransferases belonging to glycosyltransferase family 61. Sequences are further processed into a mature form.; GO: 0016757 transferase activity, transferring glycosyl groups
Probab=57.20 E-value=21 Score=29.33 Aligned_cols=44 Identities=20% Similarity=0.299 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 49 DVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 49 D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
..+.|.+.|++.||++...++++..|. ++-+++.+ ++|..||..
T Consensus 120 Ne~el~~~l~~~~~~~v~~~~~s~~eq---v~~~~~a~--------viig~hGs~ 163 (206)
T PF04577_consen 120 NEDELLEILKKYGFEVVDPEDLSFEEQ---VKLFASAK--------VIIGPHGSA 163 (206)
T ss_pred CHHHHHHHHhhCCeEEEeCCCCCHHHH---HHHhcCCC--------EEEecCchH
Confidence 344666999999999888888885444 44444433 788999987
No 30
>PF02016 Peptidase_S66: LD-carboxypeptidase; InterPro: IPR003507 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature is found in the Escherichia coli microcin C7 self-immunity protein mccF and in muramoyltetrapeptide carboxypeptidase (3.4.17.13 from EC, LD-carboxypeptidase A). LD-carboxypeptidase A belongs to MEROPS peptidase family S66 (clan SS). The entry also contains uncharacterised proteins including hypothetical proteins from various bacteria archaea.; PDB: 1ZRS_A 1ZL0_B 2AUM_B 2AUN_B 3TLG_A 3TLC_A 3TLZ_B 3TLY_B 3TLE_A 3TLB_B ....
Probab=57.06 E-value=24 Score=31.43 Aligned_cols=74 Identities=19% Similarity=0.208 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHH------HHHHHHHHHhhh-cCCCCceEEEEeccCCcc-hhhhhhcccccccccc
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFR------EITEILSNLSQE-DHSDADCLVITVLTHGLG-EQKLWLPFTADKCRTL 119 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~------em~~~l~~~~~~-~~~~~d~~vv~ilSHG~~-i~~I~~~f~~~~c~~L 119 (245)
...++-.+.|+++||+|.+..++... .-++..+++.+. ...+.+.++| .-|+. ..+|..++.- ..+
T Consensus 14 ~~l~~~~~~L~~~G~~v~~~~~~~~~~~~~ags~~~Ra~dL~~a~~d~~i~aI~~---~rGGyg~~rlL~~ld~---~~i 87 (284)
T PF02016_consen 14 ERLERGIKRLESWGFKVVVGPHVFKRDGYLAGSDEERAEDLNEAFADPEIDAIWC---ARGGYGANRLLPYLDY---DAI 87 (284)
T ss_dssp HHHHHHHHHHHHTTEEEEE-TTTTS-BTTBSS-HHHHHHHHHHHHHSTTEEEEEE---S--SS-GGGGGGGCHH---HHH
T ss_pred HHHHHHHHHHHhCCCEEEECCcccccCCCcCCCHHHHHHHHHHHhcCCCCCEEEE---eeccccHHHHHhcccc---ccc
Confidence 45677888999999999999886665 444555555432 1233334433 33333 3444444331 124
Q ss_pred CCCceEEE
Q psy13938 120 AGKPKIFF 127 (245)
Q Consensus 120 ~~KPKlf~ 127 (245)
+..||+|+
T Consensus 88 ~~~pK~~i 95 (284)
T PF02016_consen 88 RKNPKIFI 95 (284)
T ss_dssp HHSG-EEE
T ss_pred ccCCCEEE
Confidence 45688887
No 31
>cd01240 PH_beta-ARK Beta adrenergic receptor kinase 1(beta ARK1)(GRK2) pleckstrin homology (PH) domain. Beta adrenergic receptor kinase 1(beta ARK1)(GRK2) pleckstrin homology (PH) domain. Beta ARK1 is a G protein-coupled receptor kinase (GRK). It phosphorylates activated G-protein coupled receptors leading to the release of the previously bound heterotrimeric G protein agonist and thus signal termination. It consists of a domain found in regulators of G-protein signaling (RGS)(RH), a serine/threonine kinase domain and a C-terminal PH domain. The Beta-Ark 1 PH domain has an extended C-terminal helix, which mediates interactions with G beta gamma subunits. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or
Probab=56.41 E-value=4.7 Score=31.08 Aligned_cols=16 Identities=25% Similarity=0.247 Sum_probs=14.0
Q ss_pred cccccccCCCcccccc
Q psy13938 225 LCLYPFIFPNPLSSRV 240 (245)
Q Consensus 225 l~~~~~~~pg~~s~r~ 240 (245)
.+|||+|||+=++|+.
T Consensus 21 Q~Ry~~LfPNRLE~~~ 36 (116)
T cd01240 21 QTRYFKLYPNRLELYG 36 (116)
T ss_pred HHHHheeCcceeeecc
Confidence 4799999999999963
No 32
>PRK14184 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=56.31 E-value=75 Score=28.61 Aligned_cols=55 Identities=20% Similarity=0.326 Sum_probs=44.0
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.- .++.+|..=++.-.+..+++|++++.+. |.|.+|+.+.++++-+.
T Consensus 30 ~~P~Laii~v---------g~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d 87 (286)
T PRK14184 30 RAPGLAVILV---------GEDPASQVYVRNKERACEDAGIVSEAFRLPADTTQEELEDLIAELNAR 87 (286)
T ss_pred CCCEEEEEEe---------CCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 3468888853 3456677888899999999999987764 78999999999988643
No 33
>PRK14168 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=55.63 E-value=64 Score=29.23 Aligned_cols=71 Identities=13% Similarity=0.103 Sum_probs=51.1
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEec
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITVL 98 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~il 98 (245)
...++++|.-+ ++..+..=++...+..+++|++++.+ .+.|.+|+.+.|+++.+. .+.+.++|-+=
T Consensus 32 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~D--~~V~GIivqlP 100 (297)
T PRK14168 32 KVPGLVTILVG---------ESPASLSYVTLKIKTAHRLGFHEIQDNQSVDITEEELLALIDKYNND--DSIHGILVQLP 100 (297)
T ss_pred CCCeEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEEeCC
Confidence 34689988644 34567777889999999999999887 589999999999988754 33444444322
Q ss_pred --cCCcc
Q psy13938 99 --THGLG 103 (245)
Q Consensus 99 --SHG~~ 103 (245)
.|-.+
T Consensus 101 lP~~i~~ 107 (297)
T PRK14168 101 LPKHINE 107 (297)
T ss_pred CCCCCCH
Confidence 45544
No 34
>cd07062 Peptidase_S66_mccF_like Microcin C7 self-immunity protein determines resistance to exogenous microcin C7. Microcin C7 self-immunity protein (mccF): MccF, a homolog of the LD-carboxypeptidase family, mediates resistance against exogenously added microcin C7 (MccC7), a ribosomally-encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. The plasmid-encoded mccF gene is transcribed in the opposite direction to the other five genes (mccA-E) and is required for the full expression of immunity but not for production. The catalytic triad residues (Ser, His, Glu) of LD-carboxypeptidase are also conserved in MccF, strongly suggesting that MccF shares the hydrolytic activity with LD-carboxypeptidases. Substrates of MccF have not been deduced, but could likely be microcin C7 precursors. The possible role of MccF is to defend producer cells against exogenous microcin from re-entering after having been exported. It is suggested that M
Probab=55.05 E-value=48 Score=29.85 Aligned_cols=76 Identities=18% Similarity=0.203 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHhCCcEEEEEeCCCHHH------HHHHHHHHhhh-cCCCCceEEEEeccCCcchhhhhhcccccccccc
Q psy13938 47 GADVKNLEAAFYALGFEVSVYTNPEFRE------ITEILSNLSQE-DHSDADCLVITVLTHGLGEQKLWLPFTADKCRTL 119 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~~nlt~~e------m~~~l~~~~~~-~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c~~L 119 (245)
....++-.+.|+++||+|.+..++.... -++...++.+. .-...++++++.=+.| -.+|..++.- ..+
T Consensus 17 ~~~~~~~~~~L~~~G~~v~~~~~~~~~~~~~ag~~~~Ra~dL~~a~~Dp~i~aI~~~rGG~g--~~rlL~~lD~---~~i 91 (308)
T cd07062 17 PHRLERAKKRLENLGFEVVEGPNALKGDKYLSASPEERAEELMAAFADPSIKAIIPTIGGDD--SNELLPYLDY---ELI 91 (308)
T ss_pred HHHHHHHHHHHHhCCCEEEEecccccccccccCCHHHHHHHHHHHhcCCCCCEEEECCcccC--HhhhhhhcCH---HHH
Confidence 4567778889999999999988864432 44455555443 1234566666554444 3344444321 125
Q ss_pred CCCceEEE
Q psy13938 120 AGKPKIFF 127 (245)
Q Consensus 120 ~~KPKlf~ 127 (245)
+..||+|+
T Consensus 92 ~~~PK~fi 99 (308)
T cd07062 92 KKNPKIFI 99 (308)
T ss_pred hhCCCEEE
Confidence 67788876
No 35
>PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=54.87 E-value=74 Score=29.68 Aligned_cols=62 Identities=16% Similarity=0.269 Sum_probs=46.2
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
..++|+|.- .++..+..=++.-.+..+++|++++.++ +.|.+|+.+.++++-+. .+.+.++|
T Consensus 103 ~P~LaiIlv---------G~dpaS~~Yv~~k~K~~e~~GI~~~~~~lpe~~te~ell~~I~~LN~D--~~V~GIlV 167 (364)
T PLN02616 103 VPGLAVILV---------GDRKDSATYVRNKKKACDSVGINSFEVRLPEDSTEQEVLKFISGFNND--PSVHGILV 167 (364)
T ss_pred CCeEEEEEe---------CCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCC--CCCCEEEE
Confidence 458888853 3456677788999999999999987764 88999999999888643 33344443
No 36
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=54.62 E-value=61 Score=31.43 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=42.0
Q ss_pred ceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEE-EEEeCCCHHHHHHHHHHHhhh
Q psy13938 24 RGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEV-SVYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 24 ~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V-~~~~nlt~~em~~~l~~~~~~ 85 (245)
.+.+|||.| |...++.|...+...||.| .+|-+++.++=.+.|++|...
T Consensus 273 ~~~~IVF~~-------------tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g 322 (513)
T COG0513 273 EGRVIVFVR-------------TKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDG 322 (513)
T ss_pred CCeEEEEeC-------------cHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcC
Confidence 446999877 5678889999999999997 577799999999999999843
No 37
>PRK14167 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=53.79 E-value=72 Score=28.88 Aligned_cols=55 Identities=18% Similarity=0.218 Sum_probs=43.5
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.- .++.+|..=++...+..+++|++++.++ +.|.+|+.+.|+++.+.
T Consensus 30 ~~P~LaiI~v---------g~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 87 (297)
T PRK14167 30 VTPGLATVLM---------SDDPASETYVSMKQRDCEEVGIEAIDVEIDPDAPAEELYDTIDELNAD 87 (297)
T ss_pred CCceEEEEEe---------CCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 3458888853 3456677888999999999999987664 78899999999888653
No 38
>PRK14169 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=53.55 E-value=77 Score=28.47 Aligned_cols=63 Identities=16% Similarity=0.279 Sum_probs=46.7
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
.+.++++|.-. ++..|..=++.-.+..+++|++++.+ .+.|.+|+.+.|+++.+. .+.+.++|
T Consensus 29 ~~P~Laii~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D--~~V~GIlv 94 (282)
T PRK14169 29 VTPTLAVVLVG---------SDPASEVYVRNKQRRAEDIGVRSLMFRLPEATTQADLLAKVAELNHD--PDVDAILV 94 (282)
T ss_pred CCCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEE
Confidence 34588888643 44567777889999999999998776 578999999999887653 33344444
No 39
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=53.27 E-value=69 Score=28.80 Aligned_cols=55 Identities=18% Similarity=0.246 Sum_probs=43.7
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-+. ...+..=++...+..+++|++++.+ .+.|.+|+.+.|+++.+.
T Consensus 30 ~~P~La~I~vg~---------d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 87 (282)
T PRK14180 30 ITPKLVAIIVGN---------DPASKTYVASKEKACAQVGIDSQVITLPEHTTESELLELIDQLNND 87 (282)
T ss_pred CCCeEEEEEeCC---------CHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 346888886442 3456777888999999999999887 789999999999888643
No 40
>PRK14174 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=52.98 E-value=79 Score=28.58 Aligned_cols=63 Identities=14% Similarity=0.295 Sum_probs=46.8
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
.+.++|+|.-+ ++..+..=++.-.+..+++|++++.+ .+.|.+|+.+.|+++.+. .+.+.++|
T Consensus 30 ~~P~Laii~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D--~~V~GIlv 95 (295)
T PRK14174 30 KVPGLTVIIVG---------EDPASQVYVRNKAKSCKEIGMNSTVIELPADTTEEHLLKKIEDLNND--PDVHGILV 95 (295)
T ss_pred CCCeEEEEEeC---------CChHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEE
Confidence 35688888543 45567777889999999999998766 478899999999888653 33344444
No 41
>PRK14193 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=51.59 E-value=81 Score=28.37 Aligned_cols=55 Identities=18% Similarity=0.254 Sum_probs=43.3
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-+ ++.++..=++...+..+++|++++.+ .|.|.+|+.+.++++-+.
T Consensus 31 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~D 88 (284)
T PRK14193 31 ITPGLGTVLVG---------DDPGSQAYVRGKHRDCAEVGITSIRRDLPADATQEELNAVIDELNAD 88 (284)
T ss_pred CCceEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 35689988643 34567777888999999999998766 479999999999888654
No 42
>PF01471 PG_binding_1: Putative peptidoglycan binding domain; InterPro: IPR002477 This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [, , ]. Examples are: Muramoyl-pentapeptide carboxypeptidase (3.4.17.8 from EC) N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, 3.5.1.28 from EC) Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, 3.2.1.17 from EC) Membrane-bound lytic murein transglycosylase B Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX []. Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [, ], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism []. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [].; GO: 0008152 metabolic process; PDB: 1L6J_A 3BKH_A 3BKV_A 1GXD_A 1EAK_D 1CK7_A 1SLM_A 1LBU_A 1SU3_B.
Probab=51.28 E-value=11 Score=24.63 Aligned_cols=39 Identities=23% Similarity=0.252 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhh
Q psy13938 47 GADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~ 85 (245)
..|+..|+..|..+||........-..++.+.|+.|.+.
T Consensus 2 ~~~v~~lq~~L~~~gy~~~~~~g~~~~~t~~Av~~fQ~~ 40 (57)
T PF01471_consen 2 GPDVKALQQYLNRLGYYPGPVDGIFDPETREAVKAFQKA 40 (57)
T ss_dssp SHHHHHHHHHHHHTTTT-SSTTSBSHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHcCCCCCCCCCCcCHHHHHHHHHHHHH
Confidence 368999999999999985545567789999999999864
No 43
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=51.28 E-value=19 Score=24.96 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=16.6
Q ss_pred CCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 43 RPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 43 R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
..|.+...+.+.+.|++|||++...
T Consensus 14 ~lG~~i~~~~i~~~L~~lg~~~~~~ 38 (70)
T PF03484_consen 14 LLGIDISPEEIIKILKRLGFKVEKI 38 (70)
T ss_dssp HHTS---HHHHHHHHHHTT-EEEE-
T ss_pred HhCCCCCHHHHHHHHHHCCCEEEEC
Confidence 4577778888999999999988764
No 44
>cd07025 Peptidase_S66 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein. LD-carboxypeptidase (Muramoyltetrapeptide carboxypeptidase; EC 3.4.17.13; Merops family S66; initially described as Carboxypeptidase II) family also includes the microcin c7 self-immunity protein (MccF) as well as uncharacterized proteins including hypothetical proteins. LD-carboxypeptidase hydrolyzes the amide bond that links the dibasic amino acids to C-terminal D-amino acids. The physiological substrates of LD-carboxypeptidase are tetrapeptide fragments (such as UDP-MurNAc-tetrapeptides) that are produced when bacterial cell walls are degraded; they contain an L-configured residue (L-lysine or meso-diaminopimelic acid residue) as the penultimate residue and D-alanine as the ultimate residue. A possible role of LD-carboxypeptidase is in peptidoglycan recycling whereby the resulting tripeptide (precursor for murein synthesis) can be reconverted into peptidoglycan by attachment o
Probab=50.93 E-value=48 Score=29.43 Aligned_cols=75 Identities=20% Similarity=0.212 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHH------HHHHHHHHHhhh-cCCCCceEEEEeccCCcchhhhhhccccccccccC
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFR------EITEILSNLSQE-DHSDADCLVITVLTHGLGEQKLWLPFTADKCRTLA 120 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~------em~~~l~~~~~~-~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c~~L~ 120 (245)
...+...+.|++.||+|....++... .-++..+++.+. .-.+.+.++++.=+.| -.+|..++.- ..++
T Consensus 14 ~~~~~~~~~L~~~G~~v~~~~~~~~~~~~~a~s~~~Ra~dL~~a~~d~~i~aI~~~rGG~g--a~rlL~~ld~---~~~~ 88 (282)
T cd07025 14 ERLERAIARLESLGLEVVVGPHVLARDGYLAGTDEERAADLNAAFADPEIKAIWCARGGYG--ANRLLPYLDY---DLIR 88 (282)
T ss_pred HHHHHHHHHHHhCCCEEEeccchhhhcCccCCCHHHHHHHHHHHhhCCCCCEEEEcCCcCC--HHHhhhhCCH---HHHh
Confidence 67888899999999999988875542 334444555432 1234555555444343 3344443321 2245
Q ss_pred CCceEEE
Q psy13938 121 GKPKIFF 127 (245)
Q Consensus 121 ~KPKlf~ 127 (245)
..||+|+
T Consensus 89 ~~pK~~i 95 (282)
T cd07025 89 ANPKIFV 95 (282)
T ss_pred hCCeEEE
Confidence 7788876
No 45
>PLN02897 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=50.81 E-value=85 Score=29.08 Aligned_cols=71 Identities=15% Similarity=0.132 Sum_probs=51.1
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEe-
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITV- 97 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~i- 97 (245)
.+.++|+|.- ..+..+..=++.-.+..+++|++++.+ .|.|.+|+.+.|+++-+. .+.+.++|-+
T Consensus 85 ~~P~LaiIlv---------GddpaS~~Yv~~k~K~a~~~GI~~~~~~l~~~~te~ell~~I~~lN~D--~~V~GIlVQlP 153 (345)
T PLN02897 85 KVPGLAVVLV---------GQQRDSQTYVRNKIKACEETGIKSLLAELPEDCTEGQILSALRKFNED--TSIHGILVQLP 153 (345)
T ss_pred CCCeEEEEEe---------CCChHHHHHHHHHHHHHHhcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEEeCC
Confidence 3458888853 445667788899999999999998776 578999999999888654 3344454442
Q ss_pred -ccCCcc
Q psy13938 98 -LTHGLG 103 (245)
Q Consensus 98 -lSHG~~ 103 (245)
=.|-.+
T Consensus 154 LP~hid~ 160 (345)
T PLN02897 154 LPQHLDE 160 (345)
T ss_pred CCCCCCH
Confidence 246554
No 46
>PLN02516 methylenetetrahydrofolate dehydrogenase (NADP+)
Probab=50.62 E-value=98 Score=28.07 Aligned_cols=71 Identities=18% Similarity=0.138 Sum_probs=49.6
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEec
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITVL 98 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~il 98 (245)
...++|+|.-+ ++..+..=++.-.+..+++|++++.+ .+.|.+|+.+.|.++.+. .+.+.++|-+=
T Consensus 38 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~s~~el~~~I~~lN~D--~~V~GIlvq~P 106 (299)
T PLN02516 38 KVPGLAVVIVG---------SRKDSQTYVNMKRKACAEVGIKSFDVDLPENISEAELISKVHELNAN--PDVHGILVQLP 106 (299)
T ss_pred CCCeEEEEEEC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCeEEEecC
Confidence 34588888644 34557777888999999999997666 688999999999988654 23344444322
Q ss_pred --cCCcc
Q psy13938 99 --THGLG 103 (245)
Q Consensus 99 --SHG~~ 103 (245)
.|-.+
T Consensus 107 lP~~id~ 113 (299)
T PLN02516 107 LPKHINE 113 (299)
T ss_pred CCCCcCH
Confidence 46554
No 47
>PRK14173 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=49.93 E-value=79 Score=28.49 Aligned_cols=70 Identities=19% Similarity=0.175 Sum_probs=49.3
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEec-
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITVL- 98 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~il- 98 (245)
+.++|+|.-+ ++.+|..=++...+..+++|++++.+ .+.|.+|+.+.++++-+. ...+.++|-+=
T Consensus 29 ~P~Laii~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D--~~V~GIlvqlPL 97 (287)
T PRK14173 29 VPHLRVVRLG---------EDPASVSYVRLKDRQAKALGLRSQVEVLPESTSQEELLELIARLNAD--PEVDGILVQLPL 97 (287)
T ss_pred CCcEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEEeCCC
Confidence 4588888643 45567777889999999999998766 478899999999888653 23344443322
Q ss_pred -cCCcc
Q psy13938 99 -THGLG 103 (245)
Q Consensus 99 -SHG~~ 103 (245)
.|-.+
T Consensus 98 P~~i~~ 103 (287)
T PRK14173 98 PPHIDF 103 (287)
T ss_pred CCCCCH
Confidence 46554
No 48
>PRK14177 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=49.66 E-value=87 Score=28.18 Aligned_cols=54 Identities=15% Similarity=0.151 Sum_probs=42.9
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
..++|+|.-+ ++..|..=++...+..+++|++++.+ .+.|.+|+.+.|+++.+.
T Consensus 33 ~P~Laii~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~s~~el~~~I~~lN~D 89 (284)
T PRK14177 33 IPKLATILVG---------NNPASETYVSMKVKACHKVGMGSEMIRLKEQTTTEELLGVIDKLNLD 89 (284)
T ss_pred CCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 4588888644 34557777889999999999998775 578999999999888653
No 49
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=49.08 E-value=71 Score=23.99 Aligned_cols=31 Identities=26% Similarity=0.205 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCcEEEE-EeCCCHHHHHHHHHH
Q psy13938 51 KNLEAAFYALGFEVSV-YTNPEFREITEILSN 81 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~-~~nlt~~em~~~l~~ 81 (245)
.-+...|+.-||+|.. ..+++.+++.+.+.+
T Consensus 17 ~~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~ 48 (119)
T cd02067 17 NIVARALRDAGFEVIDLGVDVPPEEIVEAAKE 48 (119)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHH
Confidence 4578899999999955 467888887777643
No 50
>PRK14183 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=48.70 E-value=96 Score=27.88 Aligned_cols=55 Identities=20% Similarity=0.163 Sum_probs=43.1
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-+ ++..+..=++...+..+++|+.++.++ +.|.+++.+.++++.+.
T Consensus 30 ~~P~Laii~vg---------dd~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~D 87 (281)
T PRK14183 30 IVPGLAVILVG---------DDPASHTYVKMKAKACDRVGIYSITHEMPSTISQKEILETIAMMNNN 87 (281)
T ss_pred CCCeEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 35688888543 455677778889999999999987764 78899999999888643
No 51
>PRK14187 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=47.80 E-value=1.2e+02 Score=27.42 Aligned_cols=55 Identities=15% Similarity=0.140 Sum_probs=43.3
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-+ ++..+..=++...+..+++|++++.+ .+.|.+|+.+.|+++.+.
T Consensus 31 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~e~~l~~~I~~lN~d 88 (294)
T PRK14187 31 LFPCLIVILVG---------DDPASQLYVRNKQRKAEMLGLRSETILLPSTISESSLIEKINELNND 88 (294)
T ss_pred CCCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 35688888643 45667788889999999999998766 467889999999888754
No 52
>PRK14190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=47.73 E-value=1.1e+02 Score=27.63 Aligned_cols=55 Identities=18% Similarity=0.266 Sum_probs=42.9
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.- .++.++..=++...+..+++|++++.++ +.|.+|+.+.++++-+.
T Consensus 31 ~~P~Laii~v---------g~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 88 (284)
T PRK14190 31 IVPGLAVILV---------GDDPASHSYVRGKKKAAEKVGIYSELYEFPADITEEELLALIDRLNAD 88 (284)
T ss_pred CCCeEEEEEe---------CCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 3458888853 3455677778889999999999987764 78899999999887654
No 53
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=47.72 E-value=33 Score=26.94 Aligned_cols=48 Identities=19% Similarity=0.291 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccC
Q psy13938 50 VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTH 100 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSH 100 (245)
.+.+++.++++|+++.+..+..... ...+.++.+. .+..+|++++|+-
T Consensus 13 ~~~v~~~L~~~~~ep~i~~~~~~~g-~tiie~le~~--~~~~~faIvl~Tp 60 (125)
T PF10137_consen 13 AEAVERFLEKLGLEPIIWHEQPNLG-QTIIEKLEEA--ADSVDFAIVLFTP 60 (125)
T ss_pred HHHHHHHHHhCCCceEEeecCCCCC-CchHHHHHHH--hccCCEEEEEEcc
Confidence 4458899999999998876543211 2233444322 2225677777774
No 54
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=47.38 E-value=1.1e+02 Score=27.41 Aligned_cols=55 Identities=18% Similarity=0.123 Sum_probs=43.3
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.-+ ++.+|..=++.-.+..+++|++++.+ .|.|.+|+.+.++++-+.
T Consensus 25 ~~P~Laii~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 82 (279)
T PRK14178 25 LYPRLATVIVG---------DDPASQMYVRMKHRACERVGIGSVGIELPGDATTRTVLERIRRLNED 82 (279)
T ss_pred CCCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 34688888543 45567777888999999999998665 588999999999888654
No 55
>PRK09004 FMN-binding protein MioC; Provisional
Probab=46.68 E-value=1e+02 Score=24.51 Aligned_cols=48 Identities=25% Similarity=0.365 Sum_probs=32.6
Q ss_pred CCcH-HHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 44 PGSG-ADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 44 ~Gs~-~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
.|+- .=++.|.+.++++|++|.+..... +.+ ...++-++++..++|.-
T Consensus 12 tGnae~~A~~l~~~~~~~g~~~~~~~~~~-------~~~-----l~~~~~li~~~sT~G~G 60 (146)
T PRK09004 12 LGGAEYVADHLAEKLEEAGFSTETLHGPL-------LDD-----LSASGLWLIVTSTHGAG 60 (146)
T ss_pred chHHHHHHHHHHHHHHHcCCceEEeccCC-------HHH-----hccCCeEEEEECCCCCC
Confidence 4444 446679999999999998864322 111 23457788888888764
No 56
>PRK14185 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=46.62 E-value=1.1e+02 Score=27.75 Aligned_cols=55 Identities=24% Similarity=0.222 Sum_probs=43.0
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++|+|.- .++..+..=++.-.+..+++|.+++.+ .+.|.+|+.+.++++.+.
T Consensus 30 ~~P~LaiI~v---------g~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 87 (293)
T PRK14185 30 KRPHLAAILV---------GHDGGSETYVANKVKACEECGFKSSLIRYESDVTEEELLAKVRELNQD 87 (293)
T ss_pred CCCeEEEEEe---------CCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 3568888853 445667777888999999999998665 478889999999888643
No 57
>PLN02958 diacylglycerol kinase/D-erythro-sphingosine kinase
Probab=46.25 E-value=1.2e+02 Score=29.17 Aligned_cols=103 Identities=13% Similarity=0.041 Sum_probs=53.0
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCC
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHG 101 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG 101 (245)
+++.+.+|+|-. -.+..+...=.+.++.+|+..|+++.+..--.+.+..+.++++. ...+|.+|+ +-+=|
T Consensus 110 ~~kr~lvIvNP~------SGkg~a~k~~~~~v~~~L~~~gi~~~v~~T~~~ghA~~la~~~~---~~~~D~VV~-vGGDG 179 (481)
T PLN02958 110 RPKRLLVFVNPF------GGKKSASKIFFDVVKPLLEDADIQLTIQETKYQLHAKEVVRTMD---LSKYDGIVC-VSGDG 179 (481)
T ss_pred CCcEEEEEEcCC------CCCcchhHHHHHHHHHHHHHcCCeEEEEeccCccHHHHHHHHhh---hcCCCEEEE-EcCCC
Confidence 456667777642 11222222223468889999999988776655566666665553 234665544 32222
Q ss_pred cchhhhhhccccccccccCCCceEEEEecccCcc
Q psy13938 102 LGEQKLWLPFTADKCRTLAGKPKIFFIQACRGTK 135 (245)
Q Consensus 102 ~~i~~I~~~f~~~~c~~L~~KPKlf~iQACRG~~ 135 (245)
. +.++..-+....=..-..++.|=+|.|=-|+.
T Consensus 180 T-lnEVvNGL~~~~~~~~~~~~pLGiIPaGTgNd 212 (481)
T PLN02958 180 I-LVEVVNGLLEREDWKTAIKLPIGMVPAGTGNG 212 (481)
T ss_pred H-HHHHHHHHhhCccccccccCceEEecCcCcch
Confidence 2 56655543211000001135566666644444
No 58
>PRK14181 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=45.81 E-value=1.1e+02 Score=27.71 Aligned_cols=63 Identities=16% Similarity=0.247 Sum_probs=46.8
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
.+.++|+|.-+ ++.++..=++.-.+..+++|++++.+ .+.|.+|+.+.++++.+. .+.+.++|
T Consensus 25 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~d--~~V~GIlv 90 (287)
T PRK14181 25 TAPGLAVVLIG---------NDPASEVYVGMKVKKATDLGMVSKAHRLPSDATLSDILKLIHRLNND--PNIHGILV 90 (287)
T ss_pred CCCcEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCeEEE
Confidence 35688888543 45567777889999999999998766 478999999999988753 33344444
No 59
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=45.80 E-value=1e+02 Score=27.76 Aligned_cols=63 Identities=13% Similarity=0.191 Sum_probs=46.6
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
.+.++|+|.-+ ++.+|..=++.-.+..+++|++++.++ |.|.+|+.+.++++.+. .+.+.++|
T Consensus 29 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~d--~~V~GIiv 94 (282)
T PRK14182 29 VQTGLTVVRVG---------DDPASAIYVRGKRKDCEEVGITSVEHHLPATTTQAELLALIARLNAD--PAVHGILV 94 (282)
T ss_pred CCCeEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEE
Confidence 35688888543 445677778899999999999987764 78999999999888654 33344444
No 60
>PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=45.78 E-value=1.1e+02 Score=27.47 Aligned_cols=63 Identities=19% Similarity=0.290 Sum_probs=46.3
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
...++++|.-+ ++..|..=++...+..+++|++++.+ .+.|.+|+.+.++++.+. .+.+.++|
T Consensus 29 ~~P~Laii~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~D--~~V~GIiv 94 (282)
T PRK14166 29 IESCLAVILVG---------DNPASQTYVKSKAKACEECGIKSLVYHLNENTTQNELLALINTLNHD--DSVHGILV 94 (282)
T ss_pred CCceEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEE
Confidence 34688888543 44567777889999999999997666 578999999999888643 33344443
No 61
>PRK14191 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=44.97 E-value=1.3e+02 Score=27.09 Aligned_cols=55 Identities=18% Similarity=0.236 Sum_probs=42.9
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++++|.-. ++..|..=++...+..+++|++++.+ .+.|.+|+.+.|+++.+.
T Consensus 30 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 87 (285)
T PRK14191 30 KRPKLAVILVG---------KDPASQTYVNMKIKACERVGMDSDLHTLQENTTEAELLSLIKDLNTD 87 (285)
T ss_pred CCCeEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 34588888543 34567777889999999999998766 468889999999888654
No 62
>cd02017 TPP_E1_EcPDC_like Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative decarboxylation of pyruvate and the subsequent acetylation of coenzyme A to acetyl-CoA. The E1 component of PDC catalyzes the first step of the multistep process, using TPP and a divalent cation as cofactors. E. coli PDC is a homodimeric enzyme.
Probab=44.19 E-value=66 Score=30.25 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=25.6
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcH-HHHHHHHHHHHhCCcEEEEEe
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSG-ADVKNLEAAFYALGFEVSVYT 68 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~-~D~~~l~~~f~~LgF~V~~~~ 68 (245)
-+++|+++.....++ ..... ...+.|++.|+.+|++|....
T Consensus 178 NLivIvD~N~~qidG---~t~~v~~~~e~l~~kf~AfGW~vi~V~ 219 (386)
T cd02017 178 NLIFVVNCNLQRLDG---PVRGNGKIIQELEGIFRGAGWNVIKVI 219 (386)
T ss_pred CEEEEEECCCCccCC---cccccccCchhHHHHHHhcCCEEEEEe
Confidence 367777654443211 11111 245799999999999998764
No 63
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=43.44 E-value=85 Score=28.26 Aligned_cols=54 Identities=22% Similarity=0.319 Sum_probs=42.6
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
+.++++|.- .++..|..=++.-.+..+++|++++.+ .+.|.+|+.+.|+++-+.
T Consensus 33 ~P~Laii~v---------g~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~s~~el~~~I~~lN~d 89 (285)
T PRK10792 33 APGLAVVLV---------GSDPASQVYVASKRKACEEVGFVSRSYDLPETTSEAELLALIDELNAD 89 (285)
T ss_pred CceEEEEEe---------CCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 458888853 345567777889999999999997666 478999999999888653
No 64
>PF08538 DUF1749: Protein of unknown function (DUF1749); InterPro: IPR013744 This is a plant and fungal family of unknown function. This family contains many hypothetical proteins. ; PDB: 2Q0X_B.
Probab=43.34 E-value=68 Score=29.18 Aligned_cols=97 Identities=14% Similarity=0.122 Sum_probs=56.2
Q ss_pred CCCCCCCcHHHHHHHHHHHHhCCcEEEEEe-------------CCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcchh
Q psy13938 39 NMTPRPGSGADVKNLEAAFYALGFEVSVYT-------------NPEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQ 105 (245)
Q Consensus 39 ~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~-------------nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~i~ 105 (245)
++..-..|--=...|.+.+++.||.|.... +-..+||.+.++-+....-....-==||+|+|..--+
T Consensus 41 GLtDGl~tvpY~~~La~aL~~~~wsl~q~~LsSSy~G~G~~SL~~D~~eI~~~v~ylr~~~~g~~~~~kIVLmGHSTGcQ 120 (303)
T PF08538_consen 41 GLTDGLLTVPYLPDLAEALEETGWSLFQVQLSSSYSGWGTSSLDRDVEEIAQLVEYLRSEKGGHFGREKIVLMGHSTGCQ 120 (303)
T ss_dssp -TT--TT-STCHHHHHHHHT-TT-EEEEE--GGGBTTS-S--HHHHHHHHHHHHHHHHHHS------S-EEEEEECCHHH
T ss_pred CCCCCCCCCchHHHHHHHhccCCeEEEEEEecCccCCcCcchhhhHHHHHHHHHHHHHHhhccccCCccEEEEecCCCcH
Confidence 455444454447789999999999986542 3347899999888875521111111388999998888
Q ss_pred hhhhccccccccccCCCceEEEEecccCcc
Q psy13938 106 KLWLPFTADKCRTLAGKPKIFFIQACRGTK 135 (245)
Q Consensus 106 ~I~~~f~~~~c~~L~~KPKlf~iQACRG~~ 135 (245)
+++.++...+...-..+-+-+|+||--.+.
T Consensus 121 dvl~Yl~~~~~~~~~~~VdG~ILQApVSDR 150 (303)
T PF08538_consen 121 DVLHYLSSPNPSPSRPPVDGAILQAPVSDR 150 (303)
T ss_dssp HHHHHHHH-TT---CCCEEEEEEEEE---T
T ss_pred HHHHHHhccCccccccceEEEEEeCCCCCh
Confidence 999988754431224455679999975544
No 65
>PRK13012 2-oxoacid dehydrogenase subunit E1; Provisional
Probab=43.30 E-value=67 Score=33.59 Aligned_cols=41 Identities=29% Similarity=0.460 Sum_probs=25.7
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
-+.+|||+-...-++ .=.|..+..+.|+..|+..|+.|...
T Consensus 263 NLi~ivD~N~~~lDG--~v~~~~~~~~~l~~~f~a~GW~Vi~v 303 (896)
T PRK13012 263 NLVFVINCNLQRLDG--PVRGNGRIIQELEALFRGAGWNVIKV 303 (896)
T ss_pred cEEEEEECCCccccC--ccccccccchHHHHHHHhCCCEEEEE
Confidence 367777664332111 11122334689999999999999866
No 66
>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis. RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.
Probab=43.25 E-value=66 Score=26.40 Aligned_cols=43 Identities=19% Similarity=0.230 Sum_probs=33.8
Q ss_pred HHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCC
Q psy13938 51 KNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHG 101 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG 101 (245)
+++.+.++++||+|......+.+.+.++.+.+..+ +++++++-
T Consensus 2 ~~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k--------~~vl~G~S 44 (161)
T PF03193_consen 2 EELLEQYEKLGYPVFFISAKTGEGIEELKELLKGK--------TSVLLGQS 44 (161)
T ss_dssp HHHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTS--------EEEEECST
T ss_pred HHHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCC--------EEEEECCC
Confidence 57888999999999999988888888877666654 57777773
No 67
>COG0075 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]
Probab=43.22 E-value=57 Score=30.64 Aligned_cols=79 Identities=16% Similarity=0.209 Sum_probs=54.6
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe-----CCCHHHHHHHHHHHhhhcCCCCceEEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT-----NPEFREITEILSNLSQEDHSDADCLVIT 96 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~-----nlt~~em~~~l~~~~~~~~~~~d~~vv~ 96 (245)
.|-..+|++.|..|- +++.++.+.+|-+|++.+ -.+-+++.+.|++ ..++ =.+
T Consensus 78 ~pgdkVLv~~nG~FG--------------~R~~~ia~~~g~~v~~~~~~wg~~v~p~~v~~~L~~-----~~~~---~~V 135 (383)
T COG0075 78 EPGDKVLVVVNGKFG--------------ERFAEIAERYGAEVVVLEVEWGEAVDPEEVEEALDK-----DPDI---KAV 135 (383)
T ss_pred CCCCeEEEEeCChHH--------------HHHHHHHHHhCCceEEEeCCCCCCCCHHHHHHHHhc-----CCCc---cEE
Confidence 356789999999996 578889999999987764 3677888888761 1222 256
Q ss_pred eccCCcc-------hhhhhhccccccccccCCCceEEEEec
Q psy13938 97 VLTHGLG-------EQKLWLPFTADKCRTLAGKPKIFFIQA 130 (245)
Q Consensus 97 ilSHG~~-------i~~I~~~f~~~~c~~L~~KPKlf~iQA 130 (245)
.+.|++. +++|-+. .+..-+++|++|
T Consensus 136 ~~vH~ETSTGvlnpl~~I~~~--------~k~~g~l~iVDa 168 (383)
T COG0075 136 AVVHNETSTGVLNPLKEIAKA--------AKEHGALLIVDA 168 (383)
T ss_pred EEEeccCcccccCcHHHHHHH--------HHHcCCEEEEEe
Confidence 7778876 4444332 334467888886
No 68
>COG2945 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]
Probab=42.59 E-value=56 Score=27.99 Aligned_cols=61 Identities=20% Similarity=0.292 Sum_probs=40.8
Q ss_pred CCCcccCCCCCCCCCcccCCC-CCceEEEEEeCCCCCCCCCCCCCCcHHH--HHHHHHHHHhCCcEEEEEe
Q psy13938 1 MEDIEVPMPVAKDSAEYNMSH-PRRGRALVFNHDEFQMDNMTPRPGSGAD--VKNLEAAFYALGFEVSVYT 68 (245)
Q Consensus 1 ~~~~~~~~~~~~~~~~Y~m~~-~~~G~aLIInn~~F~~~~~~~R~Gs~~D--~~~l~~~f~~LgF~V~~~~ 68 (245)
|.++-..=|..+-+..|.-.. ..+|+|||-. ..+.--|+..| +..|.+.|.++||.+...+
T Consensus 4 ~~~v~i~Gp~G~le~~~~~~~~~~~~iAli~H-------PHPl~gGtm~nkvv~~la~~l~~~G~atlRfN 67 (210)
T COG2945 4 MPTVIINGPAGRLEGRYEPAKTPAAPIALICH-------PHPLFGGTMNNKVVQTLARALVKRGFATLRFN 67 (210)
T ss_pred CCcEEecCCcccceeccCCCCCCCCceEEecC-------CCccccCccCCHHHHHHHHHHHhCCceEEeec
Confidence 344444555666556666655 7889999842 33444556544 7789999999999987654
No 69
>PRK14172 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=42.26 E-value=1.3e+02 Score=26.95 Aligned_cols=54 Identities=15% Similarity=0.125 Sum_probs=42.2
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
+.++++|.-+ ++..|..=++...+..+++|.+++.+ .+.|.+|+.+.++++-+.
T Consensus 32 ~P~Laii~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~d 88 (278)
T PRK14172 32 IPKIASILVG---------NDGGSIYYMNNQEKVANSLGIDFKKIKLDESISEEDLINEIEELNKD 88 (278)
T ss_pred CceEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 3588888644 34557777888899999999998766 478999999999888653
No 70
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=42.23 E-value=83 Score=23.41 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhCCcEEEEE
Q psy13938 47 GADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~ 67 (245)
..|.+.|...|...||++...
T Consensus 13 ~~Dse~i~~~l~~~G~~~~~~ 33 (98)
T PF00919_consen 13 QYDSERIASILQAAGYEIVDD 33 (98)
T ss_pred HHHHHHHHHHHHhcCCeeecc
Confidence 589999999999999976543
No 71
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=42.19 E-value=23 Score=24.22 Aligned_cols=27 Identities=30% Similarity=0.455 Sum_probs=21.2
Q ss_pred CCCCCCcHHHHHHHHHHHHhCCcEEEE
Q psy13938 40 MTPRPGSGADVKNLEAAFYALGFEVSV 66 (245)
Q Consensus 40 ~~~R~Gs~~D~~~l~~~f~~LgF~V~~ 66 (245)
.....|.+.+.+.+.++|++|||++..
T Consensus 11 i~~llG~~i~~~ei~~~L~~lg~~~~~ 37 (71)
T smart00874 11 INRLLGLDLSAEEIEEILKRLGFEVEV 37 (71)
T ss_pred HHHHHCCCCCHHHHHHHHHHCCCeEEe
Confidence 344567777888899999999998854
No 72
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=41.74 E-value=1.5e+02 Score=26.72 Aligned_cols=55 Identities=13% Similarity=0.122 Sum_probs=43.0
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
.+.++++|.-+ ++..+..=++.-.+..+++|++++.+ .|.|.+|+.+.++++.+.
T Consensus 31 ~~p~Laii~vg---------~~~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d 88 (286)
T PRK14175 31 FTPKLSVILVG---------NDGASQSYVRSKKKAAEKIGMISEIVHLEETATEEEVLNELNRLNND 88 (286)
T ss_pred CCCeEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 45688888543 45567777888999999999998766 478899999999888643
No 73
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=40.59 E-value=1.6e+02 Score=26.81 Aligned_cols=71 Identities=11% Similarity=0.126 Sum_probs=50.1
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEec
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITVL 98 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~il 98 (245)
.+.++|+|.-+ ++..+..=++.-.+..+++|.+++.+ .|.|.+|+.+.++++-+. ...+.++|-+=
T Consensus 32 ~~P~LaiI~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~D--~~V~GIlvqlP 100 (301)
T PRK14194 32 IEPALAVILVG---------NDPASQVYVRNKILRAEEAGIRSLEHRLPADTSQARLLALIAELNAD--PSVNGILLQLP 100 (301)
T ss_pred CCCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCC--CCCCeEEEeCC
Confidence 35689988643 45567777888999999999998665 478999999999887654 33444544322
Q ss_pred --cCCcc
Q psy13938 99 --THGLG 103 (245)
Q Consensus 99 --SHG~~ 103 (245)
.|-.+
T Consensus 101 LP~~i~~ 107 (301)
T PRK14194 101 LPAHIDE 107 (301)
T ss_pred CCCCCCH
Confidence 46554
No 74
>PRK14170 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=40.44 E-value=1.5e+02 Score=26.61 Aligned_cols=63 Identities=14% Similarity=0.231 Sum_probs=46.1
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEE
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVI 95 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv 95 (245)
.+.++|+|.-+ ++..+..=++.-.+..+++|++++.+ .|.|.+|+.+.++++.+. ...+.++|
T Consensus 30 ~~P~Laii~vg---------~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D--~~V~GIiv 95 (284)
T PRK14170 30 KKPGLAVVLVG---------DNQASRTYVRNKQKRTEEAGMKSVLIELPENVTEEKLLSVVEELNED--KTIHGILV 95 (284)
T ss_pred CCCeEEEEEeC---------CCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCeEEE
Confidence 34688888644 34567777888999999999998765 578899999999888654 33344444
No 75
>cd02004 TPP_BZL_OCoD_HPCL Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules of benzaldehyde and enabling the Pseudomonas to grow on benzoin as the sole carbon and energy source. OCoD has a role in the detoxification of oxalate, catalyzing the decarboxylation of oxalyl-CoA to formate. 2-HPCL is a peroxisomal enzyme which plays a role in the alpha-oxidation of 3-methyl-branched fatty acids, catalyzing the cleavage of 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde. All these enzymes depend on Mg2+ and TPP for activity.
Probab=40.40 E-value=1.2e+02 Score=24.28 Aligned_cols=59 Identities=12% Similarity=-0.053 Sum_probs=36.6
Q ss_pred ceEEEEEeCCCCCCCC--------CCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh
Q psy13938 24 RGRALVFNHDEFQMDN--------MTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 24 ~G~aLIInn~~F~~~~--------~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~ 84 (245)
+=+.+|+||..+.... .....+++...-++.++.+.+|+......+ .+|+.+.|++...
T Consensus 94 pv~ivv~NN~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~la~a~G~~~~~v~~--~~el~~al~~a~~ 160 (172)
T cd02004 94 PIVVVVGNNGGWYQGLDGQQLSYGLGLPVTTLLPDTRYDLVAEAFGGKGELVTT--PEELKPALKRALA 160 (172)
T ss_pred CEEEEEEECcccccchhhhhhhccCCCceeccCCCCCHHHHHHHCCCeEEEECC--HHHHHHHHHHHHH
Confidence 3467788997764210 011112222234578888888998766664 7889999988754
No 76
>PRK14186 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=40.26 E-value=1.5e+02 Score=26.93 Aligned_cols=70 Identities=20% Similarity=0.238 Sum_probs=49.2
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE---eCCCHHHHHHHHHHHhhhcCCCCceEEEEec-
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY---TNPEFREITEILSNLSQEDHSDADCLVITVL- 98 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~---~nlt~~em~~~l~~~~~~~~~~~d~~vv~il- 98 (245)
+.++|+|.-+ ++.++..=++.-.+..+++|++++.+ .+.|.+|+.+.|+++-+. .+.+.++|-+=
T Consensus 32 ~p~LaiI~vg---------dd~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D--~~V~GIivq~PL 100 (297)
T PRK14186 32 PPGLAVLRVG---------DDPASAVYVRNKEKACARVGIASFGKHLPADTSQAEVEALIAQLNQD--ERVDGILLQLPL 100 (297)
T ss_pred CceEEEEEeC---------CChHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC--CCCCEEEEeCCC
Confidence 4588888643 34567777889999999999998655 578999999999888654 33344444322
Q ss_pred -cCCcc
Q psy13938 99 -THGLG 103 (245)
Q Consensus 99 -SHG~~ 103 (245)
.|-.+
T Consensus 101 P~~i~~ 106 (297)
T PRK14186 101 PKHLDE 106 (297)
T ss_pred CCCCCH
Confidence 46544
No 77
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=38.37 E-value=95 Score=22.65 Aligned_cols=48 Identities=10% Similarity=0.160 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCcEEEEE---eCCCHHH--HHHHHHHHhhhcCCCCceEEEEe--ccCCc
Q psy13938 47 GADVKNLEAAFYALGFEVSVY---TNPEFRE--ITEILSNLSQEDHSDADCLVITV--LTHGL 102 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~---~nlt~~e--m~~~l~~~~~~~~~~~d~~vv~i--lSHG~ 102 (245)
+.....+++.+++.|++...+ ...+..+ +.+.+ .+.|+++|+. .||+.
T Consensus 9 ~~~~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~i--------~~aD~VIv~t~~vsH~~ 63 (97)
T PF10087_consen 9 EDRERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSKI--------KKADLVIVFTDYVSHNA 63 (97)
T ss_pred cccHHHHHHHHHHcCCEEEEEecCCCCccchhHHHHhc--------CCCCEEEEEeCCcChHH
Confidence 345678999999999999988 2222222 33332 5567766653 45654
No 78
>PRK13337 putative lipid kinase; Reviewed
Probab=38.29 E-value=1.6e+02 Score=26.13 Aligned_cols=38 Identities=11% Similarity=0.099 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh
Q psy13938 47 GADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~ 84 (245)
.+....+.+.+++.|+++.++.=-...+..+..++...
T Consensus 18 ~~~~~~~~~~l~~~~~~~~~~~t~~~~~a~~~a~~~~~ 55 (304)
T PRK13337 18 KKNLPDVLQKLEQAGYETSAHATTGPGDATLAAERAVE 55 (304)
T ss_pred HHHHHHHHHHHHHcCCEEEEEEecCCCCHHHHHHHHHh
Confidence 45667788899999999877665566777777776653
No 79
>PRK10953 cysJ sulfite reductase subunit alpha; Provisional
Probab=37.13 E-value=84 Score=31.25 Aligned_cols=70 Identities=16% Similarity=0.247 Sum_probs=44.1
Q ss_pred CCcHHH-HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc-----hhhhhhcccccccc
Q psy13938 44 PGSGAD-VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG-----EQKLWLPFTADKCR 117 (245)
Q Consensus 44 ~Gs~~D-~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~-----i~~I~~~f~~~~c~ 117 (245)
.|+-.+ ++.|.+.++..||.|.+.. + .++...+....+.++++..+||+- ...+++.+....-|
T Consensus 72 TGnae~lA~~la~~l~~~g~~~~v~~-~---------~d~~~~~L~~~~~vl~v~ST~G~Ge~Pdna~~F~~~L~~~~~~ 141 (600)
T PRK10953 72 TGNARRVAEQLRDDLLAAKLNVNLVN-A---------GDYKFKQIAQEKLLIVVTSTQGEGEPPEEAVALHKFLFSKKAP 141 (600)
T ss_pred chHHHHHHHHHHHHHHhCCCCcEEec-h---------HhCCHhHhccCCeEEEEECCCCCCCCChhHHHHHHHHhhCcCc
Confidence 455444 6678899999999987653 1 122222234567889999999864 45556666444445
Q ss_pred ccCCCc
Q psy13938 118 TLAGKP 123 (245)
Q Consensus 118 ~L~~KP 123 (245)
.|.++.
T Consensus 142 ~L~~~~ 147 (600)
T PRK10953 142 KLENTA 147 (600)
T ss_pred CCCCCE
Confidence 566554
No 80
>cd00578 L-fuc_L-ara-isomerases L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute.
Probab=36.88 E-value=1.6e+02 Score=27.84 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=41.0
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCC--CHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNP--EFREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nl--t~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
.+...+.+.+.++++|++|.....+ |.+++++..++|.+. +.|.+++++.+-|.+
T Consensus 21 ~~~~~~~~~~~l~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~---~~d~ii~~~~tf~~~ 77 (452)
T cd00578 21 VEEYAREVADLLNELPVEVVDKPEVTGTPDEARKAAEEFNEA---NCDGLIVWMHTFGPA 77 (452)
T ss_pred HHHHHHHHHHHHhcCCceEEecCcccCCHHHHHHHHHHHhhc---CCcEEEEcccccccH
Confidence 4567888999999999999777653 677788887777653 577777666666655
No 81
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component. This model describes an NADPH-dependent sulfite reductase flavoprotein subunit. Most members of this family are found in Cys biosynthesis gene clusters. The closest homologs below the trusted cutoff are designated as subunits nitrate reductase.
Probab=36.16 E-value=96 Score=30.75 Aligned_cols=70 Identities=19% Similarity=0.269 Sum_probs=44.0
Q ss_pred CCcHHH-HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc-----hhhhhhcccccccc
Q psy13938 44 PGSGAD-VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG-----EQKLWLPFTADKCR 117 (245)
Q Consensus 44 ~Gs~~D-~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~-----i~~I~~~f~~~~c~ 117 (245)
.|+-.+ ++.|.+-++..||.|.+.. +.++...+....+-++++..+||+- ...+++.+...+-|
T Consensus 69 TGnae~~A~~l~~~l~~~g~~~~v~~----------~~d~~~~~l~~~~~li~v~ST~GeGe~Pdna~~F~~~L~~~~~~ 138 (597)
T TIGR01931 69 TGNARRLAKRLAEKLEAAGFSVRLSS----------ADDYKFKQLKKERLLLLVISTQGEGEPPEEAISFHKFLHSKKAP 138 (597)
T ss_pred chHHHHHHHHHHHHHHhCCCccEEec----------hHHCCHhhcccCceEEEEeCCCCCCcCCHHHHHHHHHHHhCCCc
Confidence 444444 6679999999999987753 2223223345567788899999864 44555555443345
Q ss_pred ccCCCc
Q psy13938 118 TLAGKP 123 (245)
Q Consensus 118 ~L~~KP 123 (245)
.|.++.
T Consensus 139 ~L~~~~ 144 (597)
T TIGR01931 139 KLENLR 144 (597)
T ss_pred ccCCCe
Confidence 565553
No 82
>PRK05899 transketolase; Reviewed
Probab=36.00 E-value=1.3e+02 Score=29.81 Aligned_cols=56 Identities=11% Similarity=0.246 Sum_probs=39.7
Q ss_pred EEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhh
Q psy13938 26 RALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 26 ~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~ 85 (245)
+.+|+||..+.. ..+.. ......+.+.|+.+|+.+...+--+.+++...+++..+.
T Consensus 182 li~v~dnN~~~~---~~~~~-~~~~~~~~~~~~a~G~~~~~VdG~d~~~l~~al~~a~~~ 237 (624)
T PRK05899 182 LIVIYDDNRISI---DGPTE-GWFTEDVKKRFEAYGWHVIEVDGHDVEAIDAAIEEAKAS 237 (624)
T ss_pred EEEEEECCCCcc---ccccc-ccccccHHHHhccCCCeEEEECCCCHHHHHHHHHHHHhc
Confidence 788888877753 22222 122367889999999999887656788999999886543
No 83
>PRK14192 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=35.91 E-value=2.3e+02 Score=25.34 Aligned_cols=55 Identities=13% Similarity=0.110 Sum_probs=42.9
Q ss_pred CCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEe---CCCHHHHHHHHHHHhhh
Q psy13938 22 PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT---NPEFREITEILSNLSQE 85 (245)
Q Consensus 22 ~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~---nlt~~em~~~l~~~~~~ 85 (245)
.+.++++|.-. ++.+|..=+..-.+.|+++|.+.+... +.+.+++.+.++++.+.
T Consensus 32 ~~p~L~~i~vg---------~~~~s~~Y~~~~~~~~~~~Gi~~~~~~l~~~~~~~~l~~~i~~Ln~d 89 (283)
T PRK14192 32 RTPILATILVG---------DDPASATYVRMKGNACRRVGMDSLKVELPQETTTEQLLAKIEELNAN 89 (283)
T ss_pred CCCeEEEEEeC---------CChhHHHHHHHHHHHHHHcCCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 35689888643 456677778889999999999986553 68899999999888643
No 84
>PF08901 DUF1847: Protein of unknown function (DUF1847); InterPro: IPR014997 This group of proteins are functionally uncharacterised. They contain 4 N-terminal cysteines that may form a zinc-binding domain.
Probab=35.31 E-value=48 Score=27.17 Aligned_cols=36 Identities=28% Similarity=0.335 Sum_probs=29.6
Q ss_pred cCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 18 NMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 18 ~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
.|..++.|+|..| |-.+.++.+.+.|+.-||+|...
T Consensus 52 ~mgykkiGiAfCi--------------GL~~EA~~~~~iL~~~gFev~sV 87 (157)
T PF08901_consen 52 RMGYKKIGIAFCI--------------GLRKEARILAKILEANGFEVYSV 87 (157)
T ss_pred HcCCCeeeehhhH--------------hHHHHHHHHHHHHHHCCCEEEEE
Confidence 5777888888886 34578999999999999998654
No 85
>PLN02790 transketolase
Probab=35.26 E-value=1.8e+02 Score=29.32 Aligned_cols=55 Identities=15% Similarity=0.314 Sum_probs=38.1
Q ss_pred EEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeC--CCHHHHHHHHHHHhh
Q psy13938 26 RALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTN--PEFREITEILSNLSQ 84 (245)
Q Consensus 26 ~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~n--lt~~em~~~l~~~~~ 84 (245)
+.+|++|-.+.-+ ...+ ..-.+.+.+.|+.+|+++..-.+ -..++|.+.+++..+
T Consensus 169 li~i~d~N~~~i~---~~~~-~~~~~~~~~~f~a~G~~~~~vdgg~hd~~~l~~a~~~a~~ 225 (654)
T PLN02790 169 LIVLYDDNHISID---GDTE-IAFTEDVDKRYEALGWHTIWVKNGNTDYDEIRAAIKEAKA 225 (654)
T ss_pred EEEEEecCCcccc---CCcc-cccchhHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHHh
Confidence 6777877666432 1111 12246778999999999988877 578888888877654
No 86
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=35.04 E-value=99 Score=25.88 Aligned_cols=69 Identities=12% Similarity=0.093 Sum_probs=42.4
Q ss_pred HHHHHHHHHhCCcEEE-EEeCCCHHHHHHHHHHHhhhcCCCCceEEEEecc-CCcc-hhhhhhccccccccccCCCceEE
Q psy13938 50 VKNLEAAFYALGFEVS-VYTNPEFREITEILSNLSQEDHSDADCLVITVLT-HGLG-EQKLWLPFTADKCRTLAGKPKIF 126 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilS-HG~~-i~~I~~~f~~~~c~~L~~KPKlf 126 (245)
..-+..+|+..||+|. .-.|++.+++.+.+++..- |.+.+-.+. +-.. +.++.+.++.. .+.+++|++
T Consensus 101 ~~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~~p------d~v~lS~~~~~~~~~~~~~i~~l~~~---~~~~~v~i~ 171 (197)
T TIGR02370 101 KNIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKP------LMLTGSALMTTTMYGQKDINDKLKEE---GYRDSVKFM 171 (197)
T ss_pred HHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCC------CEEEEccccccCHHHHHHHHHHHHHc---CCCCCCEEE
Confidence 3457889999999998 6689999999998865432 222222221 1111 56666655432 234567766
Q ss_pred E
Q psy13938 127 F 127 (245)
Q Consensus 127 ~ 127 (245)
+
T Consensus 172 v 172 (197)
T TIGR02370 172 V 172 (197)
T ss_pred E
Confidence 5
No 87
>cd02001 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors.
Probab=34.80 E-value=1.7e+02 Score=23.37 Aligned_cols=55 Identities=20% Similarity=0.207 Sum_probs=32.1
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~ 84 (245)
=+.+|+||..+..-....-..+..| +.++-+.+|+...... +.+|+.+.|++...
T Consensus 89 i~~vV~nN~~~g~~~~~~~~~~~~d---~~~lA~a~G~~~~~v~--~~~el~~al~~a~~ 143 (157)
T cd02001 89 LILVVLDNRAYGSTGGQPTPSSNVN---LEAWAAACGYLVLSAP--LLGGLGSEFAGLLA 143 (157)
T ss_pred EEEEEEeCccccccCCcCCCCCCCC---HHHHHHHCCCceEEcC--CHHHHHHHHHHHHh
Confidence 4567779988763111111112344 4555555677754443 58999999988764
No 88
>KOG0331|consensus
Probab=34.46 E-value=1.1e+02 Score=30.07 Aligned_cols=66 Identities=14% Similarity=0.292 Sum_probs=48.1
Q ss_pred CCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEE-EEEeCCCHHHHHHHHHHHhhhcCCCCceEEEE--e
Q psy13938 21 HPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEV-SVYTNPEFREITEILSNLSQEDHSDADCLVIT--V 97 (245)
Q Consensus 21 ~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V-~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~--i 97 (245)
..+.|.+|||+| |.+.+++|...|+..||.+ -+|-|.+.+|=...|++|...+. .++|+ +
T Consensus 338 ~~~~~KvIIFc~-------------tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~----~vLVATdV 400 (519)
T KOG0331|consen 338 SDSEGKVIIFCE-------------TKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKS----PVLVATDV 400 (519)
T ss_pred ccCCCcEEEEec-------------chhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCc----ceEEEccc
Confidence 456788999887 5678999999999999876 46678999999999988765421 12221 4
Q ss_pred ccCCcc
Q psy13938 98 LTHGLG 103 (245)
Q Consensus 98 lSHG~~ 103 (245)
.+||-+
T Consensus 401 AaRGLD 406 (519)
T KOG0331|consen 401 AARGLD 406 (519)
T ss_pred ccccCC
Confidence 567766
No 89
>COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]
Probab=33.95 E-value=1.5e+02 Score=26.00 Aligned_cols=35 Identities=26% Similarity=0.350 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 49 DVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 49 D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
..+-|.+-|+.+||+|...+--..++|.+.+.+..
T Consensus 193 ~~~pL~~k~eAFGw~V~evdG~d~~~i~~a~~~~~ 227 (243)
T COG3959 193 PKEPLADKWEAFGWEVIEVDGHDIEEIVEALEKAK 227 (243)
T ss_pred CcchhHHHHHhcCceEEEEcCcCHHHHHHHHHhhh
Confidence 35669999999999998887666666666665443
No 90
>PRK06774 para-aminobenzoate synthase component II; Provisional
Probab=33.86 E-value=83 Score=25.94 Aligned_cols=26 Identities=38% Similarity=0.436 Sum_probs=20.5
Q ss_pred HHHHHHHHHhCCcEEEEEeC--CCHHHH
Q psy13938 50 VKNLEAAFYALGFEVSVYTN--PEFREI 75 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~n--lt~~em 75 (245)
..+|.+.|+++|.+|.+..| .+.+++
T Consensus 12 ~~nl~~~l~~~~~~~~v~~~~~~~~~~~ 39 (191)
T PRK06774 12 TYNLYQYFCELGTEVMVKRNDELQLTDI 39 (191)
T ss_pred HHHHHHHHHHCCCcEEEEeCCCCCHHHH
Confidence 46899999999999998885 455554
No 91
>PRK12571 1-deoxy-D-xylulose-5-phosphate synthase; Provisional
Probab=33.16 E-value=2.1e+02 Score=28.67 Aligned_cols=31 Identities=16% Similarity=0.287 Sum_probs=23.4
Q ss_pred HHHHHhCCcEEE-EEeCCCHHHHHHHHHHHhh
Q psy13938 54 EAAFYALGFEVS-VYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 54 ~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~~ 84 (245)
...|+.+||++. ..+-=..++|.+.|++..+
T Consensus 239 ~~~f~a~G~~~~~~vdGhd~~~l~~al~~ak~ 270 (641)
T PRK12571 239 GTLFEELGFTYVGPIDGHDMEALLSVLRAARA 270 (641)
T ss_pred hhHHHHcCCEEECccCCCCHHHHHHHHHHHHh
Confidence 478999999998 4554567888888876543
No 92
>cd02011 TPP_PK Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent magnesium ions and TPP for activity.
Probab=33.10 E-value=1.6e+02 Score=25.64 Aligned_cols=35 Identities=17% Similarity=0.270 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh
Q psy13938 50 VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~ 84 (245)
.+.|.+.|+.+||.+...+--..++|.+.+.+..+
T Consensus 137 ~e~l~~~~~~yG~~~~~VDG~D~~av~~~~a~a~~ 171 (227)
T cd02011 137 HEELEALFRGYGYEPYFVEGDDPETMHQAMAATLD 171 (227)
T ss_pred chhHHHHHHhCCCceEEECCCCHHHHHHHHHHHHH
Confidence 56899999999999987765666777777776654
No 93
>PF03575 Peptidase_S51: Peptidase family S51; InterPro: IPR005320 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S51 (clan PC(S)). The type example being dipeptidase E (alpha-aspartyl dipeptidase) from Escherichia coli. The family contains alpha-aspartyl dipeptidases (dipeptidase E) and cyanophycinases. The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E has been determine at 1.2-A resolution. The structure of this 25kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organisation of the catalytic triad differ from those of the known serine proteases. This enzyme appears to represent a new example of convergent evolution of peptidase activity []. Alpha-aspartyl dipeptidase hydrolyses dipeptides containing N-terminal aspartate residues, asp-|-xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides. In the cyanobacteria, cyanophycinase is an exopeptidase that catalyses the hydrolytic cleavage of multi-l-arginyl-poly-l-aspartic acid (cyanophycin; a water- insoluble reserve polymer) into aspartate-arginine dipeptides.; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis; PDB: 3EN0_B 1FYE_A 1FY2_A 3L4E_A.
Probab=32.83 E-value=81 Score=25.06 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCcEEEEEeCCC--HHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 50 VKNLEAAFYALGFEVSVYTNPE--FREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~nlt--~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
.++.++.|+++|++|....-.+ .+++.+.| ...+ +++++=|+.
T Consensus 2 ~~~~~~~f~~~g~~v~~l~~~~~~~~~~~~~i---~~ad--------~I~~~GG~~ 46 (154)
T PF03575_consen 2 VEKFRKAFRKLGFEVDQLDLSDRNDADILEAI---READ--------AIFLGGGDT 46 (154)
T ss_dssp HHHHHHHHHHCT-EEEECCCTSCGHHHHHHHH---HHSS--------EEEE--S-H
T ss_pred HHHHHHHHHHCCCEEEEEeccCCChHHHHHHH---HhCC--------EEEECCCCH
Confidence 3678999999999976555433 33444333 3332 566677766
No 94
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=32.77 E-value=2.2e+02 Score=21.98 Aligned_cols=56 Identities=23% Similarity=0.208 Sum_probs=41.0
Q ss_pred CCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccC
Q psy13938 39 NMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTH 100 (245)
Q Consensus 39 ~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSH 100 (245)
+.+.|..+..=.+.+.+.|...|.+|....-.+...+.-.++++. +++-+++=.||
T Consensus 46 g~D~R~~s~~~~~~~~~~l~~~G~~V~~~g~~~tP~~~~~~~~~~------~~ggi~iTaSh 101 (137)
T PF02878_consen 46 GRDTRPSSPMLAKALAAGLRANGVDVIDIGLVPTPALSFAIRQLN------ADGGIMITASH 101 (137)
T ss_dssp EE-SSTTHHHHHHHHHHHHHHTTEEEEEEEEB-HHHHHHHHHHHT------ESEEEEE--TT
T ss_pred EEcccCCHHHHHHHHHHHHhhcccccccccccCcHHhhhhccccc------cceeeEEEecC
Confidence 566889999999999999999999999888788888777776642 34555555555
No 95
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=32.62 E-value=1.5e+02 Score=28.00 Aligned_cols=49 Identities=18% Similarity=0.335 Sum_probs=39.7
Q ss_pred ceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEE-EEeCCCHHHHHHHHHHHhhh
Q psy13938 24 RGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVS-VYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 24 ~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~~~ 85 (245)
.+.+||+.| +..+++.+.+.|...|+.|. .|.+++..+-...++.|...
T Consensus 242 ~~~~lVF~~-------------t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g 291 (460)
T PRK11776 242 PESCVVFCN-------------TKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANR 291 (460)
T ss_pred CCceEEEEC-------------CHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence 356777766 56789999999999999985 45689999999999988754
No 96
>PRK05723 flavodoxin; Provisional
Probab=32.62 E-value=2.2e+02 Score=22.81 Aligned_cols=50 Identities=20% Similarity=0.415 Sum_probs=33.7
Q ss_pred CCcHHH-HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 44 PGSGAD-VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 44 ~Gs~~D-~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
.|+-.+ ++.|.+.+...|++|......+..++. ++ ..+-++++..++|.-
T Consensus 11 tG~ae~~A~~la~~l~~~g~~~~~~~~~~~~~~~----~~------~~~~li~~~sT~G~G 61 (151)
T PRK05723 11 YGTAEEVARHAESLLKAAGFEAWHNPRASLQDLQ----AF------APEALLAVTSTTGMG 61 (151)
T ss_pred chHHHHHHHHHHHHHHHCCCceeecCcCCHhHHH----hC------CCCeEEEEECCCCCC
Confidence 444444 667889999999999876554444442 11 236788899999864
No 97
>TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Probab=32.17 E-value=2.7e+02 Score=24.40 Aligned_cols=78 Identities=12% Similarity=0.131 Sum_probs=41.8
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc--hhhhhhccccccccccCCCc
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG--EQKLWLPFTADKCRTLAGKP 123 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~--i~~I~~~f~~~~c~~L~~KP 123 (245)
+....+.+.+.|++.|+++.+..--...+..+.+++... ..+|++ ++ .|++ +.++...+.. ...+|
T Consensus 17 ~~~~~~~i~~~l~~~~~~~~~~~t~~~~~~~~~~~~~~~---~~~d~i-vv---~GGDGTl~~v~~~l~~-----~~~~~ 84 (293)
T TIGR00147 17 DNKPLREVIMLLREEGMEIHVRVTWEKGDAARYVEEARK---FGVDTV-IA---GGGDGTINEVVNALIQ-----LDDIP 84 (293)
T ss_pred hHHHHHHHHHHHHHCCCEEEEEEecCcccHHHHHHHHHh---cCCCEE-EE---ECCCChHHHHHHHHhc-----CCCCC
Confidence 345577899999999999877654444344444433222 234433 22 4555 5555543322 12345
Q ss_pred eEEEEecccCcc
Q psy13938 124 KIFFIQACRGTK 135 (245)
Q Consensus 124 Klf~iQACRG~~ 135 (245)
.|-+|.+=.|+.
T Consensus 85 ~lgiiP~Gt~N~ 96 (293)
T TIGR00147 85 ALGILPLGTAND 96 (293)
T ss_pred cEEEEcCcCHHH
Confidence 566666644443
No 98
>PRK08105 flavodoxin; Provisional
Probab=31.61 E-value=1e+02 Score=24.51 Aligned_cols=50 Identities=26% Similarity=0.410 Sum_probs=32.8
Q ss_pred CCcH-HHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 44 PGSG-ADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 44 ~Gs~-~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
.|+- .=+++|.+.+.+.|++|.+...- ++......+.+.++++..++|.-
T Consensus 12 tGnte~~A~~l~~~l~~~g~~~~~~~~~----------~~~~~~~~~~~~vi~~~sT~G~G 62 (149)
T PRK08105 12 YGNALLVAEEAEAILTAQGHEVTLFEDP----------ELSDWQPYQDELVLVVTSTTGQG 62 (149)
T ss_pred chHHHHHHHHHHHHHHhCCCceEEechh----------hCCchhcccCCeEEEEECCCCCC
Confidence 3444 44677999999999999876521 11111123457889999999854
No 99
>cd03372 TPP_ComE Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors.
Probab=31.58 E-value=2.8e+02 Score=22.63 Aligned_cols=54 Identities=15% Similarity=0.189 Sum_probs=31.2
Q ss_pred EEEEEeCCCCCCCCCC-CCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 26 RALVFNHDEFQMDNMT-PRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 26 ~aLIInn~~F~~~~~~-~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
+.+|+||..+..-... .......| +.++-+.+|+....... +.+++.+.|++..
T Consensus 90 ~vvV~NN~~~~~~~~~~~~~~~~~d---~~~lA~a~G~~~~~v~~-~~~el~~al~~a~ 144 (179)
T cd03372 90 IIVVLDNGAYGSTGNQPTHAGKKTD---LEAVAKACGLDNVATVA-SEEAFEKAVEQAL 144 (179)
T ss_pred EEEEEcCccccccCCCCCCCCCCCC---HHHHHHHcCCCeEEecC-CHHHHHHHHHHhc
Confidence 6778899887632111 11111234 44555677877654443 6788888877664
No 100
>cd00568 TPP_enzymes Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes.
Probab=31.56 E-value=46 Score=26.29 Aligned_cols=58 Identities=14% Similarity=0.084 Sum_probs=35.2
Q ss_pred ceEEEEEeCCCCCCC-CC------CCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 24 RGRALVFNHDEFQMD-NM------TPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 24 ~G~aLIInn~~F~~~-~~------~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
.=+.+|+||..+..- .. ..+.+......++.++++.+|++.....+ .+++.+.+++..
T Consensus 92 ~~~~iv~nN~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~a~~~G~~~~~v~~--~~~l~~a~~~a~ 156 (168)
T cd00568 92 PVIVVVFNNGGYGTIRMHQEAFYGGRVSGTDLSNPDFAALAEAYGAKGVRVED--PEDLEAALAEAL 156 (168)
T ss_pred CcEEEEEECCccHHHHHHHHHHcCCCcccccCCCCCHHHHHHHCCCeEEEECC--HHHHHHHHHHHH
Confidence 346777788766421 00 11122222234578888889998765543 778888888765
No 101
>PRK11253 ldcA L,D-carboxypeptidase A; Provisional
Probab=31.35 E-value=1.6e+02 Score=26.49 Aligned_cols=56 Identities=13% Similarity=-0.032 Sum_probs=33.2
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCH------HHHHHHHHHHhhhc-CCC-CceEEEEeccCC
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEF------REITEILSNLSQED-HSD-ADCLVITVLTHG 101 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~------~em~~~l~~~~~~~-~~~-~d~~vv~ilSHG 101 (245)
.+.+.++..+.|+++||+|....++.. ..-++..+++.+.- ..+ .++++|+.=+.|
T Consensus 15 ~~~~~~~~i~~L~~~G~~v~~~~~~~~~~~~~agtd~~Ra~dL~~a~a~~dpi~aI~~~rGGyg 78 (305)
T PRK11253 15 DQAAALRGVQRLTDAGHQVENVEVIARRYQRFAGTDGERLADLNSLADLTTPNTIVLAVRGGYG 78 (305)
T ss_pred CHHHHHHHHHHHHhCCCEEeeccccccccCccCCCHHHHHHHHHHHHhcCCCccEEEEecccCC
Confidence 556788888899999999988776432 22344444443320 122 666655544444
No 102
>KOG0461|consensus
Probab=31.12 E-value=1.2e+02 Score=28.63 Aligned_cols=59 Identities=17% Similarity=0.183 Sum_probs=39.8
Q ss_pred ceEEEEEeCCCCCCCCCCCCCCc-HHHHHHHHHHHHhCCcE-------EEEEeCCCHHHHHHHHHHHhh
Q psy13938 24 RGRALVFNHDEFQMDNMTPRPGS-GADVKNLEAAFYALGFE-------VSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 24 ~G~aLIInn~~F~~~~~~~R~Gs-~~D~~~l~~~f~~LgF~-------V~~~~nlt~~em~~~l~~~~~ 84 (245)
+-+++||||..-.+ ...|... ++-..+++++++..||+ |-...-.-+++|.+.|+++-.
T Consensus 123 ~klvvvinkid~lp--E~qr~ski~k~~kk~~KtLe~t~f~g~~PI~~vsa~~G~~~~~~i~eL~e~l~ 189 (522)
T KOG0461|consen 123 KKLVVVINKIDVLP--ENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVSAADGYFKEEMIQELKEALE 189 (522)
T ss_pred cceEEEEecccccc--chhhhhHHHHHHHHHHHHHHhcCcCCCCceeEEecCCCccchhHHHHHHHHHH
Confidence 35788889876552 2233332 45577899999999996 233344667788888888754
No 103
>PF00456 Transketolase_N: Transketolase, thiamine diphosphate binding domain; InterPro: IPR005474 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; PDB: 3M49_B 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 3HYL_A 3RIM_A ....
Probab=30.92 E-value=1.2e+02 Score=27.82 Aligned_cols=54 Identities=11% Similarity=0.221 Sum_probs=33.1
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE-eCCCHHHHHHHHHHH
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY-TNPEFREITEILSNL 82 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~-~nlt~~em~~~l~~~ 82 (245)
-+++||.+-...- ..+. .....+.+.+.|+.+||+|... ..-..++|.+.|++.
T Consensus 174 nLi~i~D~N~~q~---dg~~-~~~~~~~~~~k~~a~Gw~v~~v~dGhd~~~i~~A~~~a 228 (332)
T PF00456_consen 174 NLIVIYDSNGIQI---DGPT-DIVFSEDIAKKFEAFGWNVIEVCDGHDVEAIYAAIEEA 228 (332)
T ss_dssp TEEEEEEEESEET---TEEG-GGTHHSHHHHHHHHTT-EEEEEEETTBHHHHHHHHHHH
T ss_pred CEEEEEecCCccc---CCCc-ccccchHHHHHHHHhhhhhcccccCcHHHHHHHHHHHH
Confidence 4778885544331 1111 1233567899999999999876 556666777666554
No 104
>PRK11702 hypothetical protein; Provisional
Probab=30.75 E-value=60 Score=24.96 Aligned_cols=30 Identities=20% Similarity=0.313 Sum_probs=23.7
Q ss_pred HHHHhCCcEEEEE--eCCCHHHHHHHHHHHhh
Q psy13938 55 AAFYALGFEVSVY--TNPEFREITEILSNLSQ 84 (245)
Q Consensus 55 ~~f~~LgF~V~~~--~nlt~~em~~~l~~~~~ 84 (245)
.=|+.|||.|... ++++.+++...+.+|..
T Consensus 16 ~EFqeLGF~v~~~~~~~~~~e~~D~~vD~fId 47 (108)
T PRK11702 16 DEFQELGFSVNWRFPEGTSEEQIDATVDAFID 47 (108)
T ss_pred HhhHhheeEEEEEECCCCCHHHHHHHHHHHHH
Confidence 4589999999665 45888888888888864
No 105
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=30.68 E-value=2e+02 Score=22.63 Aligned_cols=81 Identities=21% Similarity=0.292 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHhCCcE-EEEE---------eCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcchhhhhhccccccc
Q psy13938 47 GADVKNLEAAFYALGFE-VSVY---------TNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQKLWLPFTADKC 116 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~-V~~~---------~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c 116 (245)
..-...|+++|+++||. |.+| .+.+.+++...|.+.-..... ++.-++ +.| .+++-.... .|
T Consensus 18 ki~MaeLr~~l~~~Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG-~~v~v~-vrs----~~el~~i~~--~n 89 (137)
T PF08002_consen 18 KIKMAELREALEDLGFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFG-FDVPVI-VRS----AEELRAIIA--AN 89 (137)
T ss_dssp ---HHHHHHHHHHCT-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-T-T---EE-EEE----HHHHHHHHT--T-
T ss_pred cccHHHHHHHHHHcCCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcC-CCeEEE-Eee----HHHHHHHHH--HC
Confidence 35688999999999996 4433 688999999999887665333 222222 222 344444443 35
Q ss_pred cccC---CCceEEEEecccCcc
Q psy13938 117 RTLA---GKPKIFFIQACRGTK 135 (245)
Q Consensus 117 ~~L~---~KPKlf~iQACRG~~ 135 (245)
|-.. ..|+-+.+=-|.+..
T Consensus 90 Pf~~~~~~~~~~~~v~fl~~~~ 111 (137)
T PF08002_consen 90 PFPWEAEADPKRLYVTFLSGPP 111 (137)
T ss_dssp -GGGGS----SEEEEEEE-TT-
T ss_pred CCcccccCCcceEEEEEeCCCC
Confidence 6552 467766666665554
No 106
>COG1691 NCAIR mutase (PurE)-related proteins [General function prediction only]
Probab=30.57 E-value=1.2e+02 Score=26.58 Aligned_cols=80 Identities=20% Similarity=0.279 Sum_probs=56.4
Q ss_pred CcccCCCCCceEEEEEeCCCCCCCCCCCCC-----CcHHH---HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhc
Q psy13938 15 AEYNMSHPRRGRALVFNHDEFQMDNMTPRP-----GSGAD---VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQED 86 (245)
Q Consensus 15 ~~Y~m~~~~~G~aLIInn~~F~~~~~~~R~-----Gs~~D---~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~ 86 (245)
..++......|..|+|.+.++.. ....+- || .| ++.-..+.+.||++|...-|.--..|..++..+.+..
T Consensus 92 ~~~d~~y~e~ar~~~i~~~~~~~-~~~g~vgvlsAGT-SDlPvAeEa~~tae~lG~ev~~~~DvGVAGiHRLl~~l~r~~ 169 (254)
T COG1691 92 RFADVEYNEAARTLAIKDPNYEP-KKGGKVGVLSAGT-SDLPVAEEAAVTAEELGVEVQKVYDVGVAGIHRLLSALKRLK 169 (254)
T ss_pred cccceEEcccCcEEEecCCCCCc-ccCceEEEEecCC-CCcchHHHHHHHHHHhCceEEEEEeeccchHHhhhhHHHHHH
Confidence 34555556778888888876642 111221 22 34 6677889999999999999999999999998777654
Q ss_pred CCCCceEEEE
Q psy13938 87 HSDADCLVIT 96 (245)
Q Consensus 87 ~~~~d~~vv~ 96 (245)
..+.++++|+
T Consensus 170 ~~~~~~lIVv 179 (254)
T COG1691 170 IEDADVLIVV 179 (254)
T ss_pred hhCCCeEEEE
Confidence 4566666553
No 107
>COG1619 LdcA Uncharacterized proteins, homologs of microcin C7 resistance protein MccF [Defense mechanisms]
Probab=30.46 E-value=2e+02 Score=26.22 Aligned_cols=77 Identities=21% Similarity=0.221 Sum_probs=46.9
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCHH------HHHHHHHHHhhh-cCCCCceEEEEeccCCcchhhhhhccccccccc
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEFR------EITEILSNLSQE-DHSDADCLVITVLTHGLGEQKLWLPFTADKCRT 118 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~~------em~~~l~~~~~~-~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c~~ 118 (245)
.....++-.+.|+.+||+|..-+..... ..++.+.++.+. .-.+.+++++++=+-| -..|..++.. ..
T Consensus 24 ~~~~~~~a~~~L~~~G~~v~~~~~i~~~~~~~a~s~~~R~~dL~~af~d~~vk~Il~~rGGyg--s~rlLp~ld~---~~ 98 (313)
T COG1619 24 ATDALKRAIQRLENLGFEVVFGEHILRRDQYFAGSDEERAEDLMSAFSDPDVKAILCVRGGYG--SNRLLPYLDY---DL 98 (313)
T ss_pred hHHHHHHHHHHHHHcCCEEEechhhhhccccccCCHHHHHHHHHHHhcCCCCeEEEEcccCCC--hhhhhhhcch---HH
Confidence 5678888999999999999877653322 224555555442 2245566666554444 3334433331 23
Q ss_pred cCCCceEEE
Q psy13938 119 LAGKPKIFF 127 (245)
Q Consensus 119 L~~KPKlf~ 127 (245)
.+..||+|+
T Consensus 99 i~~~pKifi 107 (313)
T COG1619 99 IRNHPKIFI 107 (313)
T ss_pred HhcCCceEE
Confidence 677899997
No 108
>PRK13054 lipid kinase; Reviewed
Probab=29.96 E-value=3e+02 Score=24.30 Aligned_cols=38 Identities=8% Similarity=0.079 Sum_probs=26.1
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
..+....+.+.|++-|+++.+..-....+..+..++..
T Consensus 16 ~~~~~~~~~~~l~~~g~~~~v~~t~~~~~a~~~a~~~~ 53 (300)
T PRK13054 16 GNEELREAVGLLREEGHTLHVRVTWEKGDAARYVEEAL 53 (300)
T ss_pred chHHHHHHHHHHHHcCCEEEEEEecCCCcHHHHHHHHH
Confidence 34677778889999999877665544555555555554
No 109
>COG3023 ampD N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]
Probab=29.92 E-value=43 Score=29.63 Aligned_cols=39 Identities=18% Similarity=0.304 Sum_probs=34.3
Q ss_pred CCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhh
Q psy13938 43 RPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 43 R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~ 85 (245)
+.| .|++.|++.|..+||.|.. ....++.++.++.|...
T Consensus 195 ~~~--~~v~~lq~~L~~YGY~v~~--~~~d~~t~~vv~aFQ~h 233 (257)
T COG3023 195 LKG--EDVAALQEMLARYGYGVEI--GVFDQETQQVVRAFQMH 233 (257)
T ss_pred hcc--CCHHHHHHHHHHhCcCCCc--chhhHHHHHHHHHHHHH
Confidence 445 7999999999999999999 88899999999998753
No 110
>cd04907 ACT_ThrD-I_2 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.79 E-value=75 Score=22.73 Aligned_cols=39 Identities=26% Similarity=0.358 Sum_probs=27.9
Q ss_pred ccCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 17 YNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 17 Y~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
|.......|.+||--. ++ +. |...|.+.++++||.+.-.
T Consensus 33 YR~~~~~~a~vlvGi~-------~~---~~--~~~~l~~~l~~~g~~~~dl 71 (81)
T cd04907 33 YRNQGSDYGRVLVGIQ-------VP---DA--DLDELKERLDALGYPYQEE 71 (81)
T ss_pred EecCCCCceeEEEEEE-------eC---hH--HHHHHHHHHHHcCCCeEEC
Confidence 8887777787777322 11 22 9999999999999986543
No 111
>KOG1349|consensus
Probab=28.78 E-value=76 Score=28.35 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=24.3
Q ss_pred CceEEEEeccCCcc-------hhhhhhccccccccccCC----CceEEEEecccCccc
Q psy13938 90 ADCLVITVLTHGLG-------EQKLWLPFTADKCRTLAG----KPKIFFIQACRGTKL 136 (245)
Q Consensus 90 ~d~~vv~ilSHG~~-------i~~I~~~f~~~~c~~L~~----KPKlf~iQACRG~~~ 136 (245)
.+-+++++-+||++ .++|.+.=-......|.. +-=+|+|+.||+...
T Consensus 138 ~SNIlIYmtGHGgd~FlKFqd~eelts~dLadai~qm~e~~Ryneil~miDTCQaasl 195 (309)
T KOG1349|consen 138 GSNILIYLTGHGGDGFLKFQDAEELTSDDLADAIQQMWEKKRYNEILFMIDTCQAASL 195 (309)
T ss_pred CCcEEEEEccCCCccceecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccchHHH
Confidence 45577788889987 222211000000111211 224789999998853
No 112
>PF00781 DAGK_cat: Diacylglycerol kinase catalytic domain; InterPro: IPR001206 The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [, ]. Eukaryotic DAG-kinase (2.7.1.107 from EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PDOC00018 from PROSITEDOC), PH (see PDOC50003 from PROSITEDOC), SAM (see PDOC50105 from PROSITEDOC) , DAG/PE-binding C1 domain (see PDOC00379 from PROSITEDOC) and ankyrin repeats (see PDOC50088 from PROSITEDOC) []. In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PDOC00820 from PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold []. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [, ]. This domain is usually associated with an accessory domain (see IPR000756 from INTERPRO).; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway; PDB: 2JGR_A 2BON_A 3T5P_D 3S40_A 2P1R_A 2QV7_A 2QVL_A.
Probab=28.78 E-value=2.6e+02 Score=21.19 Aligned_cols=77 Identities=23% Similarity=0.287 Sum_probs=44.1
Q ss_pred HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCC-ceEEEEeccCCcc--hhhhhhccccccccccCCCceEE
Q psy13938 50 VKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDA-DCLVITVLTHGLG--EQKLWLPFTADKCRTLAGKPKIF 126 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~-d~~vv~ilSHG~~--i~~I~~~f~~~~c~~L~~KPKlf 126 (245)
.+.+...|+..+.++.++.=.. ++..+.+...... ..+ +.+++ + |++ +.++...+.....+ .+|.+-
T Consensus 17 ~~~v~~~l~~~~~~~~~~~t~~-~~~~~~~~~~~~~--~~~~~~ivv-~---GGDGTl~~vv~~l~~~~~~---~~~~l~ 86 (130)
T PF00781_consen 17 WKKVEPALRAAGIDYEVIETES-AGHAEALARILAL--DDYPDVIVV-V---GGDGTLNEVVNGLMGSDRE---DKPPLG 86 (130)
T ss_dssp HHHHHHHHHHTTCEEEEEEESS-TTHHHHHHHHHHH--TTS-SEEEE-E---ESHHHHHHHHHHHCTSTSS---S--EEE
T ss_pred HHHHHHHHHHcCCceEEEEEec-cchHHHHHHHHhh--ccCccEEEE-E---cCccHHHHHHHHHhhcCCC---ccceEE
Confidence 5889999999999887766544 5555555543332 222 33322 2 444 67776665443222 288899
Q ss_pred EEecccCccc
Q psy13938 127 FIQACRGTKL 136 (245)
Q Consensus 127 ~iQACRG~~~ 136 (245)
+|.+.-|+.+
T Consensus 87 iiP~GT~N~~ 96 (130)
T PF00781_consen 87 IIPAGTGNDF 96 (130)
T ss_dssp EEE-SSS-HH
T ss_pred EecCCChhHH
Confidence 9998766654
No 113
>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=28.75 E-value=1.6e+02 Score=18.97 Aligned_cols=36 Identities=22% Similarity=0.102 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
-++.+.+++|+++|...+..+=-+.++..+.|++.+
T Consensus 10 ~~C~~~~~~L~~~~i~y~~~dv~~~~~~~~~l~~~~ 45 (60)
T PF00462_consen 10 PYCKKAKEFLDEKGIPYEEVDVDEDEEAREELKELS 45 (60)
T ss_dssp HHHHHHHHHHHHTTBEEEEEEGGGSHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHcCCeeeEcccccchhHHHHHHHHc
Confidence 488999999999999875544333336666666665
No 114
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=28.67 E-value=90 Score=28.93 Aligned_cols=78 Identities=18% Similarity=0.197 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHhCCc---EEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcchhhhhhccccccccccCCCc
Q psy13938 47 GADVKNLEAAFYALGF---EVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQKLWLPFTADKCRTLAGKP 123 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF---~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c~~L~~KP 123 (245)
.-|.+.++.++++.|. +|.+..|.|-+++.+.|..-. ....|++| ++-.+.+. .+.-..|..+|
T Consensus 198 ~~d~~~ir~iL~Ey~I~nA~V~Ir~dvTlDd~id~l~~nr----vY~p~l~v--~NKiD~~~-------~e~~~~l~~~~ 264 (365)
T COG1163 198 HLDEDTVRAILREYRIHNADVLIREDVTLDDLIDALEGNR----VYKPALYV--VNKIDLPG-------LEELERLARKP 264 (365)
T ss_pred cCCHHHHHHHHHHhCcccceEEEecCCcHHHHHHHHhhcc----eeeeeEEE--EecccccC-------HHHHHHHHhcc
Confidence 4677788888888776 699999999999999985431 22345544 33332211 12233477899
Q ss_pred eEEEEecccCcccC
Q psy13938 124 KIFFIQACRGTKLD 137 (245)
Q Consensus 124 Klf~iQACRG~~~~ 137 (245)
+.++|.|=+|-+.+
T Consensus 265 ~~v~isa~~~~nld 278 (365)
T COG1163 265 NSVPISAKKGINLD 278 (365)
T ss_pred ceEEEecccCCCHH
Confidence 99999998876655
No 115
>TIGR03702 lip_kinase_YegS lipid kinase YegS. Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. Bakali, et al. report phosphatidylglycerol kinase activity for the member from Escherichia coli, but refrain from calling that activity synonymous with its biological role. Note that a broader, subfamily-type model (TIGR00147), includes this family but also multiple paralogs in some species and varied functions.
Probab=28.54 E-value=2.9e+02 Score=24.37 Aligned_cols=36 Identities=14% Similarity=0.144 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
.....+.+.|++-|+++.++.=-...+-.+..++..
T Consensus 14 ~~~~~~~~~l~~~g~~~~v~~t~~~~~a~~~a~~~~ 49 (293)
T TIGR03702 14 EDVREAVGDLRDEGIQLHVRVTWEKGDAQRYVAEAL 49 (293)
T ss_pred hHHHHHHHHHHHCCCeEEEEEecCCCCHHHHHHHHH
Confidence 356677888999999877664333334444444443
No 116
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=28.35 E-value=2.1e+02 Score=28.11 Aligned_cols=47 Identities=19% Similarity=0.333 Sum_probs=38.0
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEE-EeCCCHHHHHHHHHHHhh
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSV-YTNPEFREITEILSNLSQ 84 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~-~~nlt~~em~~~l~~~~~ 84 (245)
..+|||.| +...++.|.+.|.+.|+.|.. +-+++..+=...+++|..
T Consensus 258 ~k~LVF~n-------------t~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~ 305 (572)
T PRK04537 258 ARTMVFVN-------------TKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQK 305 (572)
T ss_pred CcEEEEeC-------------CHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHc
Confidence 45777765 457899999999999998854 458999999999999975
No 117
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=28.27 E-value=1.1e+02 Score=28.02 Aligned_cols=89 Identities=18% Similarity=0.104 Sum_probs=55.2
Q ss_pred ccCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEE
Q psy13938 17 YNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVIT 96 (245)
Q Consensus 17 Y~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ 96 (245)
|.+-..++-.+|||.+-.= =..+-++-|+.+|+.|...---+.-|.-+.+-++-++++...-.=+-+
T Consensus 69 ~eI~~lnpd~VLIIGGp~A-------------Vs~~yE~~Lks~GitV~RigG~nR~ETa~~v~~~~~~~yp~af~n~kv 135 (337)
T COG2247 69 DEIIELNPDLVLIIGGPIA-------------VSPNYENALKSLGITVKRIGGANRYETAEKVAKFFREDYPNAFKNVKV 135 (337)
T ss_pred HHHHhhCCceEEEECCCCc-------------CChhHHHHHHhCCcEEEEecCcchHHHHHHHHHHHHhhchhhhcCeEE
Confidence 4555566788999976321 223456677899999988888888888877777766554432221455
Q ss_pred eccCCcc-hhhhhhccccccccc
Q psy13938 97 VLTHGLG-EQKLWLPFTADKCRT 118 (245)
Q Consensus 97 ilSHG~~-i~~I~~~f~~~~c~~ 118 (245)
++-||-+ .+.+++.....-||-
T Consensus 136 vvv~GwDy~~~~~e~~k~~~~p~ 158 (337)
T COG2247 136 VVVYGWDYADALMELMKEGIVPV 158 (337)
T ss_pred EEEeccccHHHHHHHHhcCccee
Confidence 5667766 334444444444553
No 118
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.19 E-value=54 Score=24.44 Aligned_cols=28 Identities=21% Similarity=0.284 Sum_probs=22.5
Q ss_pred CCCCcHHHHHHHHHHHHhCCcEEEEEeC
Q psy13938 42 PRPGSGADVKNLEAAFYALGFEVSVYTN 69 (245)
Q Consensus 42 ~R~Gs~~D~~~l~~~f~~LgF~V~~~~n 69 (245)
-..|=..|.++|.+.+++|||+|...-|
T Consensus 6 ~krGf~~~~dri~~~l~e~g~~v~~eGD 33 (96)
T COG4004 6 VKRGFKPDPDRIMRGLSELGWTVSEEGD 33 (96)
T ss_pred cccCCCCCHHHHHHHHHHhCeeEeeccc
Confidence 3456667999999999999999876544
No 119
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 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 C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=28.16 E-value=82 Score=29.34 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=34.2
Q ss_pred HHHHHHHHhCC-cEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc
Q psy13938 51 KNLEAAFYALG-FEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG 103 (245)
Q Consensus 51 ~~l~~~f~~Lg-F~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~ 103 (245)
+++...|++.+ ++-.+..-+|.+||.+.|. ..| ++++.+||+-
T Consensus 277 ~~~~~~~~~~~~w~g~~g~~P~~~e~~~~l~--------~~d--lf~Y~GHG~G 320 (383)
T PF03568_consen 277 KRFEPFFKSWKGWKGIIGRAPTEEEFLQALT--------SSD--LFLYCGHGSG 320 (383)
T ss_pred HHHHHHHhcccCCCceECCCCCHHHHHHHHH--------hCC--eEEEecCCcH
Confidence 46777888877 9999999999999998883 223 5679999975
No 120
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=27.83 E-value=1.6e+02 Score=27.81 Aligned_cols=56 Identities=18% Similarity=0.236 Sum_probs=40.5
Q ss_pred cHHHHHHHHHHHHhCCcEEE-EEeCCCHHHHHHHHHHHhhhcCCCCceEEE-EeccCCcch
Q psy13938 46 SGADVKNLEAAFYALGFEVS-VYTNPEFREITEILSNLSQEDHSDADCLVI-TVLTHGLGE 104 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~~~~~~~~d~~vv-~ilSHG~~i 104 (245)
+..+++.|.+.|.+.|+.+. .|.+++.++-.+.+.+|... ....+|+ -+++-|.++
T Consensus 254 t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g---~~~iLVaTdv~~rGiDi 311 (456)
T PRK10590 254 TKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSG---DIRVLVATDIAARGLDI 311 (456)
T ss_pred cHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcC---CCcEEEEccHHhcCCCc
Confidence 45788999999999999864 56689999999999999753 2233332 245567663
No 121
>cd03371 TPP_PpyrDC Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. These proteins require TPP and divalent metal cation cofactors.
Probab=27.72 E-value=2.1e+02 Score=23.61 Aligned_cols=55 Identities=16% Similarity=0.141 Sum_probs=31.8
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEE-EEEeCCCHHHHHHHHHHHhh
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEV-SVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V-~~~~nlt~~em~~~l~~~~~ 84 (245)
=+.+|+||..+..-....-.+... ++.++.+.+|+.. .... +.+|+.+.|++..+
T Consensus 96 i~ivV~NN~~yg~~~~~~~~~~~~---d~~~~A~a~G~~~~~~v~--~~~el~~al~~a~~ 151 (188)
T cd03371 96 LIHIVLNNGAHDSVGGQPTVSFDV---SLPAIAKACGYRAVYEVP--SLEELVAALAKALA 151 (188)
T ss_pred cEEEEEeCchhhccCCcCCCCCCC---CHHHHHHHcCCceEEecC--CHHHHHHHHHHHHh
Confidence 478888998774211001112223 4566667778764 2222 78899888887653
No 122
>PF13439 Glyco_transf_4: Glycosyltransferase Family 4; PDB: 2JJM_E 3MBO_C 2GEJ_A 2GEK_A.
Probab=27.61 E-value=1.1e+02 Score=23.44 Aligned_cols=30 Identities=30% Similarity=0.306 Sum_probs=25.3
Q ss_pred CCCCCCcHHHHHHHHHHHHhCCcEEEEEeC
Q psy13938 40 MTPRPGSGADVKNLEAAFYALGFEVSVYTN 69 (245)
Q Consensus 40 ~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~n 69 (245)
....-|++.=+.+|.+.|.+.|++|.+...
T Consensus 8 ~~~~GG~e~~~~~l~~~l~~~G~~v~v~~~ 37 (177)
T PF13439_consen 8 LPNIGGAERVVLNLARALAKRGHEVTVVSP 37 (177)
T ss_dssp TTSSSHHHHHHHHHHHHHHHTT-EEEEEES
T ss_pred CCCCChHHHHHHHHHHHHHHCCCEEEEEEc
Confidence 345789999999999999999999998854
No 123
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.94 E-value=2.3e+02 Score=23.76 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHhCCcE----------EEEEeCCCHHHHHHHHHHHhhhcCCCCceEE
Q psy13938 47 GADVKNLEAAFYALGFE----------VSVYTNPEFREITEILSNLSQEDHSDADCLV 94 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~----------V~~~~nlt~~em~~~l~~~~~~~~~~~d~~v 94 (245)
..=...|+..++.|||+ +.-..+....|+.+.|+.+-.+....+..++
T Consensus 18 kV~MAdLka~~~dlGf~~v~T~iaSGNlvf~s~~~~~el~~klE~afe~~fg~~~dil 75 (178)
T COG3797 18 KVVMADLKAALTDLGFANVRTYIASGNLVFESEAGAAELEAKLEAAFEKRFGRHVDIL 75 (178)
T ss_pred eEeHHHHHHHHHHcCcchhhHhhhcCCEEEEcCCChHHHHHHHHHHHHHHcCCCccEE
Confidence 34567899999999996 3444567799999999987655444433333
No 124
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=26.78 E-value=2.8e+02 Score=26.30 Aligned_cols=56 Identities=14% Similarity=0.269 Sum_probs=36.4
Q ss_pred CCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEE---------E-----eCCCHHHHHHHHHHHhh
Q psy13938 19 MSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSV---------Y-----TNPEFREITEILSNLSQ 84 (245)
Q Consensus 19 m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~---------~-----~nlt~~em~~~l~~~~~ 84 (245)
|++.++.++++ .+..+.. ..|.+.|...|++.||++.- . .+-+.+++.+.|.++..
T Consensus 2 ~~~~~~~~~i~---------t~GC~~N-~~ds~~~~~~l~~~G~~~~~~~~~ADiiiiNTC~v~~~a~~~~~~~i~~~~~ 71 (448)
T PRK14333 2 MNSSRRSYWIT---------TFGCQMN-KADSERMAGILEDMGYQWAEDELQADLVLYNTCTIRDNAEQKVYSYLGRQAK 71 (448)
T ss_pred cCCCCcEEEEE---------EcCCCCc-HHHHHHHHHHHHHCcCEECCCcccCCEEEEEeeeeeehHHHHHHHHHHHHHH
Confidence 56655555554 2333332 48999999999999996532 1 34566777777777643
No 125
>PRK08007 para-aminobenzoate synthase component II; Provisional
Probab=26.63 E-value=1.4e+02 Score=24.68 Aligned_cols=21 Identities=38% Similarity=0.354 Sum_probs=17.6
Q ss_pred HHHHHHHHHhCCcEEEEEeCC
Q psy13938 50 VKNLEAAFYALGFEVSVYTNP 70 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~nl 70 (245)
..+|.+.|+++|.+|.+..+-
T Consensus 12 t~nl~~~l~~~g~~v~v~~~~ 32 (187)
T PRK08007 12 TWNLYQYFCELGADVLVKRND 32 (187)
T ss_pred HHHHHHHHHHCCCcEEEEeCC
Confidence 357999999999999888763
No 126
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=26.46 E-value=1.8e+02 Score=24.35 Aligned_cols=55 Identities=9% Similarity=0.233 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc---hhhhhhccccccccccCCCceEEEEec
Q psy13938 70 PEFREITEILSNLSQEDHSDADCLVITVLTHGLG---EQKLWLPFTADKCRTLAGKPKIFFIQA 130 (245)
Q Consensus 70 lt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~---i~~I~~~f~~~~c~~L~~KPKlf~iQA 130 (245)
.+..++.+.|+++.+. .+...+++.+-|.|+. .++|.+.+.. ++ .+||-+-+++.
T Consensus 13 ~s~~~l~~~l~~a~~d--~~i~~vvl~~~s~Gg~~~~~~~l~~~i~~--~~--~~kpvia~v~g 70 (207)
T TIGR00706 13 VSPEDFDKKIKRIKDD--KSIKALLLRINSPGGTVVASEEIYEKLKK--LK--AKKPVVASMGG 70 (207)
T ss_pred cCHHHHHHHHHHHhhC--CCccEEEEEecCCCCCHHHHHHHHHHHHH--hc--CCCCEEEEECC
Confidence 5678888888877743 4567888888888887 5667666642 44 48998888864
No 127
>PRK12315 1-deoxy-D-xylulose-5-phosphate synthase; Provisional
Probab=26.38 E-value=4.6e+02 Score=25.89 Aligned_cols=31 Identities=13% Similarity=0.305 Sum_probs=24.6
Q ss_pred HHHHHHhCCcEEEEE-eCCCHHHHHHHHHHHh
Q psy13938 53 LEAAFYALGFEVSVY-TNPEFREITEILSNLS 83 (245)
Q Consensus 53 l~~~f~~LgF~V~~~-~nlt~~em~~~l~~~~ 83 (245)
+.+.|+.+||.+... +--..+++.+.+++..
T Consensus 199 ~~~~~~a~G~~~~~v~DG~D~~~l~~a~~~a~ 230 (581)
T PRK12315 199 ENNLFKAMGLDYRYVEDGNDIESLIEAFKEVK 230 (581)
T ss_pred HHHHHHhcCCeEEEeeCCCCHHHHHHHHHHHH
Confidence 457899999998766 5577888988888754
No 128
>TIGR01573 cas2 CRISPR-associated endoribonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead.
Probab=26.32 E-value=2.6e+02 Score=20.41 Aligned_cols=52 Identities=17% Similarity=0.167 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHhCCcE-E---EEEeCCCHHHHHH-HHHHHhhhcCCCCceEEEEecc
Q psy13938 47 GADVKNLEAAFYALGFE-V---SVYTNPEFREITE-ILSNLSQEDHSDADCLVITVLT 99 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~-V---~~~~nlt~~em~~-~l~~~~~~~~~~~d~~vv~ilS 99 (245)
.+...++.+++++.||. | .-..++|..+..+ ..+.+.+.- ...|++.++-++
T Consensus 15 ~k~r~kv~k~L~~~G~~rvQ~SVf~~~~~~~~~~~~l~~~l~~~i-~~~dsv~i~~l~ 71 (95)
T TIGR01573 15 RKRRRKLRKLLEKYGLQRVQYSVFEGILEPNQLARKLIERLKRII-PDEGDIRIYPLT 71 (95)
T ss_pred HHHHHHHHHHHHHcchhheeccEEEEEcCHHHHHHHHHHHHHHhC-CCCCeEEEEEeC
Confidence 56788899999999943 3 2335788888884 444444432 235666555543
No 129
>PRK12753 transketolase; Reviewed
Probab=26.23 E-value=3.3e+02 Score=27.51 Aligned_cols=55 Identities=13% Similarity=0.137 Sum_probs=35.4
Q ss_pred EEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEE-EeCCCHHHHHHHHHHHhh
Q psy13938 26 RALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSV-YTNPEFREITEILSNLSQ 84 (245)
Q Consensus 26 ~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~-~~nlt~~em~~~l~~~~~ 84 (245)
+.+|++|-.+.-+ ...+. .-.+++.+.|+.+|+.|.. ..--..++|.+.+++...
T Consensus 178 Li~ivd~N~~~i~---~~~~~-~~~~~~~~~f~a~Gw~~~~~vDGhD~~~i~~a~~~a~~ 233 (663)
T PRK12753 178 LIGFYDHNGISID---GETEG-WFTDDTAKRFEAYHWHVIHEIDGHDPQAIKEAILEAQS 233 (663)
T ss_pred EEEEEECCCCcCC---CChhh-hcChhHHHHHHHcCCeEEceeCCCCHHHHHHHHHHHHH
Confidence 5667776555422 11111 1136889999999999984 544567888888876543
No 130
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=26.14 E-value=87 Score=24.95 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHH
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFREITEIL 79 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l 79 (245)
.....|.+.|+.+||++....+.+-.+|...-
T Consensus 7 ~~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A 38 (147)
T PF01927_consen 7 AMLGRLARWLRLLGYDTLYSRDIDDDEILELA 38 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHh
Confidence 34568999999999999999999888888764
No 131
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 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 sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=25.93 E-value=83 Score=26.37 Aligned_cols=25 Identities=20% Similarity=0.317 Sum_probs=21.0
Q ss_pred cccCCCccceeeeeccccCcccccccccCCCcccccc
Q psy13938 204 AYKIPSYADFLIAYSTVEDCKLCLYPFIFPNPLSSRV 240 (245)
Q Consensus 204 ~~~iP~~aDfL~~~sTve~~tl~~~~~~~pg~~s~r~ 240 (245)
....+...++++.+|+. +|..||+.
T Consensus 162 ~~~~~~~~~~~~~~as~------------~~~~s~e~ 186 (248)
T PF00656_consen 162 RSDVPSPSGFIVLSASR------------PGQTSYED 186 (248)
T ss_dssp SEEEETTTSEEEEESSS------------TTBCEEEE
T ss_pred cccccCCCCcEEEEecc------------ccceeecc
Confidence 34567778999999999 89999988
No 132
>PHA02627 hypothetical protein; Provisional
Probab=25.90 E-value=91 Score=21.47 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHhCCcEEEEEeCCC
Q psy13938 47 GADVKNLEAAFYALGFEVSVYTNPE 71 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~~nlt 71 (245)
+.|...|-..+.+||.+|..-+|.+
T Consensus 34 ed~i~ellniltelgcdvdfde~fs 58 (73)
T PHA02627 34 EDDITELLNILTELGCDVDFDEDFS 58 (73)
T ss_pred HHHHHHHHHHHHHhCCCcccccchH
Confidence 5677788889999999998887754
No 133
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=25.83 E-value=86 Score=23.78 Aligned_cols=29 Identities=28% Similarity=0.397 Sum_probs=22.8
Q ss_pred HHHhCCcEEEEEeC--CCHHHHHHHHHHHhh
Q psy13938 56 AFYALGFEVSVYTN--PEFREITEILSNLSQ 84 (245)
Q Consensus 56 ~f~~LgF~V~~~~n--lt~~em~~~l~~~~~ 84 (245)
=|+.|||.|...-+ .+.+++...+.+|..
T Consensus 11 EFqelGF~v~~~~~~~~~~e~~D~~~D~fId 41 (101)
T PF04320_consen 11 EFQELGFEVSCRFAEGTSEEQIDAFVDAFID 41 (101)
T ss_pred hhheeEEEEEEEECCCCCHHHHHHHHHHHHH
Confidence 48899999976643 688888888888764
No 134
>PF14164 YqzH: YqzH-like protein
Probab=25.73 E-value=1.3e+02 Score=20.92 Aligned_cols=34 Identities=15% Similarity=0.243 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhh
Q psy13938 51 KNLEAAFYALGFEVSVYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~ 85 (245)
+-+++.|+..|+++.+ .-++..|.+.+.+.+...
T Consensus 8 Kmi~~~l~QYg~d~~~-~pls~~E~~~L~~~i~~~ 41 (64)
T PF14164_consen 8 KMIINCLRQYGYDVEC-MPLSDEEWEELCKHIQER 41 (64)
T ss_pred HHHHHHHHHhCCcccC-CCCCHHHHHHHHHHHHHH
Confidence 4578999999999865 357888888888877654
No 135
>PLN02234 1-deoxy-D-xylulose-5-phosphate synthase
Probab=25.52 E-value=2.7e+02 Score=28.10 Aligned_cols=32 Identities=22% Similarity=0.363 Sum_probs=26.1
Q ss_pred HHHHHHHhCCcEEE-EEeCCCHHHHHHHHHHHh
Q psy13938 52 NLEAAFYALGFEVS-VYTNPEFREITEILSNLS 83 (245)
Q Consensus 52 ~l~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~ 83 (245)
.+...|+.+||++. ...-=..++|.+.|++..
T Consensus 274 ~~~~~fe~fG~~~~g~vDGHd~~~l~~al~~~k 306 (641)
T PLN02234 274 TSSTLFEELGFHYVGPVDGHNIDDLVSILETLK 306 (641)
T ss_pred CHHHHHHHcCCEEEeeECCCCHHHHHHHHHHHH
Confidence 45789999999998 666678888888887754
No 136
>PRK13055 putative lipid kinase; Reviewed
Probab=25.29 E-value=3.6e+02 Score=24.38 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHhCCcEEEEE
Q psy13938 47 GADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~ 67 (245)
......+++.|++.|+++.++
T Consensus 19 ~~~~~~i~~~l~~~g~~~~i~ 39 (334)
T PRK13055 19 KKNVADILDILEQAGYETSAF 39 (334)
T ss_pred HHHHHHHHHHHHHcCCeEEEE
Confidence 455678899999999887654
No 137
>PRK06756 flavodoxin; Provisional
Probab=25.23 E-value=2.1e+02 Score=22.20 Aligned_cols=73 Identities=15% Similarity=0.121 Sum_probs=42.0
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCC-cch-hhhhhccccccccccCCCc
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHG-LGE-QKLWLPFTADKCRTLAGKP 123 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG-~~i-~~I~~~f~~~~c~~L~~KP 123 (245)
|+.=++.|.+.+++.|.+|.+.+=.+... ..+..++|.+++..-+|| +.+ +.+.+.+..-.-..|.+||
T Consensus 15 Te~vA~~ia~~l~~~g~~v~~~~~~~~~~---------~~~~~~~d~vi~gspt~~~g~~p~~~~~fl~~l~~~~l~~k~ 85 (148)
T PRK06756 15 TEEMADHIAGVIRETENEIEVIDIMDSPE---------ASILEQYDGIILGAYTWGDGDLPDDFLDFYDAMDSIDLTGKK 85 (148)
T ss_pred HHHHHHHHHHHHhhcCCeEEEeehhccCC---------HHHHhcCCeEEEEeCCCCCCCCcHHHHHHHHHHhcCCCCCCE
Confidence 44557779999999999987663211111 122356788888888987 332 2233333211112477887
Q ss_pred eEEE
Q psy13938 124 KIFF 127 (245)
Q Consensus 124 Klf~ 127 (245)
-.+|
T Consensus 86 ~~~f 89 (148)
T PRK06756 86 AAVF 89 (148)
T ss_pred EEEE
Confidence 4443
No 138
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=24.92 E-value=3.4e+02 Score=21.23 Aligned_cols=41 Identities=34% Similarity=0.317 Sum_probs=29.2
Q ss_pred CCcHHH--HHHHHHHHHhCCcEEEEEeCC--CHHHHHHHHHHHhh
Q psy13938 44 PGSGAD--VKNLEAAFYALGFEVSVYTNP--EFREITEILSNLSQ 84 (245)
Q Consensus 44 ~Gs~~D--~~~l~~~f~~LgF~V~~~~nl--t~~em~~~l~~~~~ 84 (245)
.|.-.| ...|+++++++|++|..+.=+ ..++|.+.|++..+
T Consensus 21 ~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~l~~~~~ 65 (144)
T TIGR00177 21 PGQIYDSNGPLLAALLEEAGFNVSRLGIVPDDPEEIREILRKAVD 65 (144)
T ss_pred CCeEEeCcHHHHHHHHHHCCCeEEEEeecCCCHHHHHHHHHHHHh
Confidence 455444 456999999999999766533 46778888877654
No 139
>COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]
Probab=24.75 E-value=1.1e+02 Score=26.78 Aligned_cols=15 Identities=20% Similarity=0.242 Sum_probs=9.2
Q ss_pred CCCceEEEEeccCCc
Q psy13938 88 SDADCLVITVLTHGL 102 (245)
Q Consensus 88 ~~~d~~vv~ilSHG~ 102 (245)
...++.|.|||+-|+
T Consensus 138 ~~~~~~VyvilGDGE 152 (243)
T COG3959 138 KGSPYRVYVILGDGE 152 (243)
T ss_pred cCCCceEEEEecCcc
Confidence 344566667777765
No 140
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=24.67 E-value=2.2e+02 Score=24.60 Aligned_cols=49 Identities=27% Similarity=0.266 Sum_probs=36.1
Q ss_pred HHHHHHHHhCCcEEEEEeCC-CHHHHHHHHHHHhhhcCCCCceEEEEeccCCcchhh
Q psy13938 51 KNLEAAFYALGFEVSVYTNP-EFREITEILSNLSQEDHSDADCLVITVLTHGLGEQK 106 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~~~nl-t~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~i~~ 106 (245)
+.++++=+++|.++...++. +.+++.+.|+++++.. +|-+++ ||.+..+
T Consensus 21 ~G~~~~~~~~gv~~~~~e~~~~~~~~~~~i~~~~~~g---~dlIi~----~g~~~~~ 70 (258)
T cd06353 21 EGRKAAEKALGVEVTYVENVPEGADAERVLRELAAQG---YDLIFG----TSFGFMD 70 (258)
T ss_pred HHHHHHHHhcCCeEEEEecCCchHhHHHHHHHHHHcC---CCEEEE----CchhhhH
Confidence 56777777799999999988 8889999999998652 333333 7776333
No 141
>COG3286 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.58 E-value=1.6e+02 Score=25.07 Aligned_cols=54 Identities=22% Similarity=0.297 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHhCCcEEEEE-----eCCCHHHHHHHHHHHhhh--c-----CCCCceEEEEeccCC
Q psy13938 48 ADVKNLEAAFYALGFEVSVY-----TNPEFREITEILSNLSQE--D-----HSDADCLVITVLTHG 101 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~-----~nlt~~em~~~l~~~~~~--~-----~~~~d~~vv~ilSHG 101 (245)
+-.+-|.++++.+||.|++. .|....++.+.++++++. + .+...==+|+..||=
T Consensus 89 Vp~~vl~daLk~~GyrVevr~~~l~T~ap~~ev~E~vreLse~~~E~~~~~lt~~vrklVv~~S~~ 154 (204)
T COG3286 89 VPPDVLIDALKLLGYRVEVRGGELKTNAPWSEVVELVRELSEVYREARFQPLTRQVRKLVVAVSIV 154 (204)
T ss_pred CCHHHHHHHHHhCCceEEeeCceeecCCCHHHHHHHHHHHHHHHHHHHhccccchhhhhhhhhhhH
Confidence 66788999999999999755 678899999999888753 1 111222356677773
No 142
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=24.38 E-value=98 Score=27.82 Aligned_cols=99 Identities=21% Similarity=0.306 Sum_probs=53.7
Q ss_pred CCHHHHHHHHHHHhhhcC--------CCCceEEEEeccCCcc------------hhhhhhccccccccccCCC----ceE
Q psy13938 70 PEFREITEILSNLSQEDH--------SDADCLVITVLTHGLG------------EQKLWLPFTADKCRTLAGK----PKI 125 (245)
Q Consensus 70 lt~~em~~~l~~~~~~~~--------~~~d~~vv~ilSHG~~------------i~~I~~~f~~~~c~~L~~K----PKl 125 (245)
.|.+-+.++|.+-+-++| ...+-++++.-+||++ -++|..-+. .|..| --+
T Consensus 110 vTve~firLLt~r~~en~p~sKrlltdE~SNIfIYmtGHGgd~FlKFqdaeemtseDladai~-----ql~~~kRyNeIl 184 (382)
T COG5206 110 VTVEVFIRLLTARSGENHPKSKRLLTDESSNIFIYMTGHGGDAFLKFQDAEEMTSEDLADAIS-----QLAAKKRYNEIL 184 (382)
T ss_pred chHHHHHHHHHhhccCCChhhhhhcccccCcEEEEEccCCCccceecccHHHhhhHHHHHHHH-----HHHHhhhhceEE
Confidence 455666777766543332 2355677888899997 234443332 12222 136
Q ss_pred EEEecccCcccCC-----CeeeecCCCcccccCCCCcCCCCCCCeEEEecccCCchhhc
Q psy13938 126 FFIQACRGTKLDG-----GVRLVSRANTETDAGVNAYKIPSYADFLIAYSTVEDSLLAC 179 (245)
Q Consensus 126 f~iQACRG~~~~~-----gv~~~d~~~~e~~~~~~~~~ip~~~D~li~ysT~pg~~~~~ 179 (245)
|.|+.|+.+..-. .|....+ .| ........++|.+|+-+-...|.-+|
T Consensus 185 fmiDTCQAnaly~k~ysPNvLavgs--Se----ig~ssyShhsd~~IgvaVIDrFty~~ 237 (382)
T COG5206 185 FMIDTCQANALYDKSYSPNVLAVGS--SE----IGQSSYSHHSDSLIGVAVIDRFTYFF 237 (382)
T ss_pred EEeeccccchhhhhccCCceEEEec--cc----cCCccccccchhhhhHHHhhcchHHH
Confidence 8899999876421 1111111 11 11223556678888777776654444
No 143
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=24.10 E-value=2.3e+02 Score=24.97 Aligned_cols=30 Identities=27% Similarity=0.311 Sum_probs=25.6
Q ss_pred CCCCCCcHHHHHHHHHHHHhCCcEEEEEeC
Q psy13938 40 MTPRPGSGADVKNLEAAFYALGFEVSVYTN 69 (245)
Q Consensus 40 ~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~n 69 (245)
-..|.-|-+=++.+.+.|+++|++|.....
T Consensus 11 s~e~~~sl~s~~~i~~al~~~g~~~~~i~~ 40 (299)
T PRK14571 11 SREREISLRSGERVKKALEKLGYEVTVFDV 40 (299)
T ss_pred CCCccchHHHHHHHHHHHHHcCCeEEEEcc
Confidence 356788889999999999999999988753
No 144
>PRK13059 putative lipid kinase; Reviewed
Probab=24.09 E-value=4.5e+02 Score=23.16 Aligned_cols=28 Identities=11% Similarity=0.150 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHHHH
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFREI 75 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~em 75 (245)
...+.+++.+++.|+++.++.-....+.
T Consensus 19 ~~~~~i~~~l~~~g~~~~~~~~~~~~~~ 46 (295)
T PRK13059 19 SELDKVIRIHQEKGYLVVPYRISLEYDL 46 (295)
T ss_pred HHHHHHHHHHHHCCcEEEEEEccCcchH
Confidence 4567788999999999877654444443
No 145
>COG3171 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.67 E-value=99 Score=23.98 Aligned_cols=30 Identities=23% Similarity=0.437 Sum_probs=24.0
Q ss_pred HHHhCCcEEE--EEeCCCHHHHHHHHHHHhhh
Q psy13938 56 AFYALGFEVS--VYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 56 ~f~~LgF~V~--~~~nlt~~em~~~l~~~~~~ 85 (245)
-|++|||.|. .+++.+++++-+.+..|..+
T Consensus 25 EFQeLgF~v~~~~~eg~~ae~~dea~drFide 56 (119)
T COG3171 25 EFQELGFSVQWSFHEGTSAEDVDEAVDRFIDE 56 (119)
T ss_pred HHHhhheeeEEEecCCccHHHHHHHHHHHHHH
Confidence 4889999994 55778899999888887654
No 146
>TIGR00232 tktlase_bact transketolase, bacterial and yeast. This model is designed to capture orthologs of bacterial transketolases. The group includes two from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous.
Probab=23.65 E-value=2.6e+02 Score=28.07 Aligned_cols=54 Identities=17% Similarity=0.351 Sum_probs=35.8
Q ss_pred EEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE-eCCCHHHHHHHHHHHh
Q psy13938 26 RALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY-TNPEFREITEILSNLS 83 (245)
Q Consensus 26 ~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~-~nlt~~em~~~l~~~~ 83 (245)
+.+|++|-.+.-++... .. . .+.+.+.|+.+|+.|... .--..++|.+.+++..
T Consensus 174 Li~ivd~N~~~i~~~~~--~~-~-~~~~~~~~~a~Gw~~~~v~DG~D~~ai~~A~~~a~ 228 (653)
T TIGR00232 174 LIVLYDSNRISIDGAVD--GS-F-TEDVAKRFEAYGWEVLEVEDGHDLAAIDAAIEEAK 228 (653)
T ss_pred EEEEEeCCCeeeccccc--cc-c-CccHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHH
Confidence 67777766664321111 11 1 367999999999999887 4456778888877654
No 147
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=23.63 E-value=1.8e+02 Score=24.50 Aligned_cols=39 Identities=23% Similarity=0.336 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhCCcEEE-----EEeCCCHHHHHHHHHHHhhh
Q psy13938 47 GADVKNLEAAFYALGFEVS-----VYTNPEFREITEILSNLSQE 85 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~-----~~~nlt~~em~~~l~~~~~~ 85 (245)
..-.+-|.++++-+||.++ ++.|.+.+++.+.+++++..
T Consensus 85 ~vp~d~L~~~L~~~G~~ae~~~~~i~T~a~~eev~~l~~~Lse~ 128 (190)
T PF09840_consen 85 PVPPDLLVDALKLLGYKAEYREDVIKTDAPLEEVVELAERLSEI 128 (190)
T ss_pred CCCHHHHHHHHHhCCCeeEEeCCeEEecCCHHHHHHHHHHHHHH
Confidence 3445679999999999986 45689999999999988763
No 148
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=23.62 E-value=45 Score=27.67 Aligned_cols=49 Identities=16% Similarity=0.223 Sum_probs=31.8
Q ss_pred cccCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEE
Q psy13938 16 EYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVS 65 (245)
Q Consensus 16 ~Y~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~ 65 (245)
.|++. .|+..+||+.+.+..--+-.....+..=.+++.+.++++||.+.
T Consensus 40 i~Rl~-~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L~~~g~~~~ 88 (174)
T cd04518 40 VYRLE-DPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKLKDYGIKVI 88 (174)
T ss_pred EEEcc-CCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHHhcCCCcc
Confidence 36675 57899999888766421222233334446678888999998753
No 149
>TIGR03186 AKGDH_not_PDH alpha-ketoglutarate dehydrogenase. Several bacterial species have a paralog to homodimeric form of the pyruvate dehydrogenase E1 component (see model TIGR00759), often encoded next to L-methionine gamma-lyase gene (mdeA). The member from a strain of Pseudomonas putida was shown to act on alpha-ketobutyrate, which is produced by MdeA.This model serves as an exception model to TIGR00759, as other proteins hitting TIGR00759 should be identified as the pyruvate dehydrogenase E1 component.
Probab=23.54 E-value=2.2e+02 Score=29.96 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=24.9
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
-+.+||++....-++ +. .+.....+.|++.|+..|++|...
T Consensus 249 NLi~IvD~N~~qlDG-~t-~~~~~~~e~l~~kf~a~GW~vi~v 289 (889)
T TIGR03186 249 NLVFVINCNLQRLDG-PV-RGNGRIIDELESQFAGAGWNVIKV 289 (889)
T ss_pred CEEEEEeCCCCccCC-cc-ccccccchHHHHHHHhCCCEEEEE
Confidence 467777654332111 11 111233588999999999999865
No 150
>PRK09405 aceE pyruvate dehydrogenase subunit E1; Reviewed
Probab=23.53 E-value=1.9e+02 Score=30.30 Aligned_cols=41 Identities=24% Similarity=0.383 Sum_probs=24.9
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
-+.+|||.-...-++ +. .|..+..+.|++.|+..|+.|...
T Consensus 255 NLi~ivD~N~q~lDG-~v-~~~~~~~~~l~~~f~a~GW~Vi~v 295 (891)
T PRK09405 255 NLIFVINCNLQRLDG-PV-RGNGKIIQELEGIFRGAGWNVIKV 295 (891)
T ss_pred CEEEEEECCCcccCC-cc-ccccccchhHHHHHhhCCCEEEEE
Confidence 366777653332111 11 112234689999999999999876
No 151
>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins. This is a family of putative P-loop ATPases [], as they contain an ATP-binding site and display ATPase and GTPase activities.; GO: 0005524 ATP binding
Probab=23.45 E-value=3.3e+02 Score=24.55 Aligned_cols=76 Identities=17% Similarity=0.207 Sum_probs=51.5
Q ss_pred HHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc-hhhhhhccccccccccCCCceEEEEe
Q psy13938 51 KNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG-EQKLWLPFTADKCRTLAGKPKIFFIQ 129 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~-i~~I~~~f~~~~c~~L~~KPKlf~iQ 129 (245)
...-++|+.+|| .+..|+...=+.+.++...+.. ...+-+++++=..+.. ..++.+.+..- ....-..+++|++
T Consensus 15 s~Al~~lED~Gy--~cvDNlP~~Ll~~l~~~~~~~~-~~~~~~Ai~iD~R~~~~~~~~~~~~~~l--~~~~~~~~ilFLd 89 (284)
T PF03668_consen 15 STALRALEDLGY--YCVDNLPPSLLPQLIELLAQSN-SKIEKVAIVIDIRSREFFEDLFEALDEL--RKKGIDVRILFLD 89 (284)
T ss_pred HHHHHHHHhcCe--eEEcCCcHHHHHHHHHHHHhcC-CCCceEEEEEeCCChHHHHHHHHHHHHH--HhcCCceEEEEEE
Confidence 345689999999 4568999988888887766543 4567788888888766 44444333210 0123468999999
Q ss_pred cc
Q psy13938 130 AC 131 (245)
Q Consensus 130 AC 131 (245)
|=
T Consensus 90 A~ 91 (284)
T PF03668_consen 90 AS 91 (284)
T ss_pred CC
Confidence 83
No 152
>PF10150 RNase_E_G: Ribonuclease E/G family; InterPro: IPR019307 Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs []. RNA-binding protein AU-1 binds to RNA loop regions that are with AU-rich sequences [].; PDB: 2BX2_L 2VRT_D 2VMK_D 2C4R_L 1SMX_B 1SLJ_A 2C0B_L 1SN8_B.
Probab=23.25 E-value=2.1e+02 Score=25.36 Aligned_cols=47 Identities=15% Similarity=0.234 Sum_probs=32.4
Q ss_pred CCCCCCCcHHHHHHHHHHHHhC---CcEEEEE---eCCCHHHHHHHHHHHhhh
Q psy13938 39 NMTPRPGSGADVKNLEAAFYAL---GFEVSVY---TNPEFREITEILSNLSQE 85 (245)
Q Consensus 39 ~~~~R~Gs~~D~~~l~~~f~~L---gF~V~~~---~nlt~~em~~~l~~~~~~ 85 (245)
+.+.+...+...++|+++++.+ |+-+.+. .+.+.+++.+.++.+.+.
T Consensus 17 ~vSrKI~d~~~R~~Lk~i~~~~~~~~~GvIiRT~A~~a~~e~L~~El~~L~~~ 69 (271)
T PF10150_consen 17 GVSRKISDEEERERLKKILESLLPEGEGVIIRTAAAGASEEELEKELEELREK 69 (271)
T ss_dssp EE-TTS-TH-HHHHHHHHHHTS--TT-EEEE-GGGGGS-HHHHHHHHHHHHHH
T ss_pred eecCCCCCchhHHHHHHHHHHhCCCCCeEEEecCcCCCCHHHHHHHHHHHHHH
Confidence 5677888888999999999876 6666555 468888888888887765
No 153
>cd02064 FAD_synthetase_N FAD synthetase, N-terminal domain of the bifunctional enzyme. FAD synthetase_N. N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities. The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain is thought to have kinase activity. FAD synthetase is present among all kingdoms of life. However, the bifunctional enzyme is not found in mammals, which use separate enzymes for FMN and FAD formation.
Probab=22.84 E-value=1.3e+02 Score=24.59 Aligned_cols=34 Identities=29% Similarity=0.325 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhCCcEEEEEe-------CCCHHHHHHHHHH
Q psy13938 48 ADVKNLEAAFYALGFEVSVYT-------NPEFREITEILSN 81 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~-------nlt~~em~~~l~~ 81 (245)
.|.+.|++.++++||+|.+.. ..+...|++.|++
T Consensus 117 g~~~~L~~~~~~~g~~v~~v~~~~~~~~~iSST~IR~~i~~ 157 (180)
T cd02064 117 GDAELLKELGKKYGFEVTVVPPVTLDGERVSSTRIREALAE 157 (180)
T ss_pred CCHHHHHHhhhhcCcEEEEeCcEecCCcEEcHHHHHHHHHh
Confidence 467778899999999987643 4788999998865
No 154
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=22.66 E-value=89 Score=20.15 Aligned_cols=16 Identities=25% Similarity=0.279 Sum_probs=12.3
Q ss_pred HHHHHHHHhCCcEEEE
Q psy13938 51 KNLEAAFYALGFEVSV 66 (245)
Q Consensus 51 ~~l~~~f~~LgF~V~~ 66 (245)
+.|.++|+++||.+..
T Consensus 2 ~el~k~L~~~G~~~~r 17 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVR 17 (56)
T ss_dssp HHHHHHHHHTT-EEEE
T ss_pred hHHHHHHHHCCCEEec
Confidence 4688999999998763
No 155
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=22.62 E-value=2.9e+02 Score=24.89 Aligned_cols=83 Identities=14% Similarity=0.186 Sum_probs=48.9
Q ss_pred CCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc----hhhhhhccccccccc
Q psy13938 43 RPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLG----EQKLWLPFTADKCRT 118 (245)
Q Consensus 43 R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~----i~~I~~~f~~~~c~~ 118 (245)
+.||-+-+ -.++|+.||| .+..||..+=+-+.+. +........+-+.|++=-.+.+ +++..+.+...+ +
T Consensus 9 lSGAGKsv--Al~~lEDlGy--ycvDNLPp~Llp~~~~-~~~~~~~~~~kvAv~iDiRs~~~~~~l~~~l~~l~~~~-~- 81 (286)
T COG1660 9 LSGAGKSV--ALRVLEDLGY--YCVDNLPPQLLPKLAD-LMLTLESRITKVAVVIDVRSREFFGDLEEVLDELKDNG-D- 81 (286)
T ss_pred CCCCcHHH--HHHHHHhcCe--eeecCCCHHHHHHHHH-HHhhcccCCceEEEEEecccchhHHHHHHHHHHHHhcC-C-
Confidence 45664433 4688999999 5567888765555544 2223234456666666555555 444444443221 1
Q ss_pred cCCCceEEEEecccCc
Q psy13938 119 LAGKPKIFFIQACRGT 134 (245)
Q Consensus 119 L~~KPKlf~iQACRG~ 134 (245)
=+|+|+|+.|-+..
T Consensus 82 --~~~~iLFLeA~~~~ 95 (286)
T COG1660 82 --IDPRVLFLEADDET 95 (286)
T ss_pred --CCceEEEEECchhH
Confidence 26999999996443
No 156
>PF01364 Peptidase_C25: Peptidase family C25 This family belongs to family C25 of the peptidase classification.; InterPro: IPR001769 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 C25 (gingipain, clan CD). The protein fold of the peptidase domain for members of this entry resembles that of caspase 1, the type example for clan CD. This is a protein family found only in the bacteria. Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=22.55 E-value=1.2e+02 Score=27.77 Aligned_cols=61 Identities=18% Similarity=0.192 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcchhhhhhccccccccccCCCc--eEEEEecccCcccCCC
Q psy13938 70 PEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQKLWLPFTADKCRTLAGKP--KIFFIQACRGTKLDGG 139 (245)
Q Consensus 70 lt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~i~~I~~~f~~~~c~~L~~KP--Klf~iQACRG~~~~~g 139 (245)
.+.+.|.+.|.+ .+.++.+.+||....---..|.......|.+++ =+++..+|--..+|.+
T Consensus 226 ~~~~~i~~~ln~---------G~~~v~y~GHG~~~~w~~~~~~~~d~~~l~N~~~~p~~~s~~C~~g~fd~~ 288 (378)
T PF01364_consen 226 GTRDNIINALNQ---------GAGFVNYFGHGSPTSWADEDFTSSDISNLNNKNKLPVVISAACYTGNFDDP 288 (378)
T ss_dssp --HHHHHHHHHH-----------SEEEEES-B-SSBBTTT--BTTTGGG---TT---EEEEESSSTT-TTSS
T ss_pred chHHHHHHHHhC---------CCeEEEEecCCchhhcccCcccHhHHHHhcCCCCceEEEEeECCCcCCCCC
Confidence 667777777754 456789999998711000012334455666655 4566679998887644
No 157
>TIGR00759 aceE pyruvate dehydrogenase E1 component, homodimeric type. WARNING: This family is classified as subfamily rather than equivalog because it includes a counterexample from Pseudomonas putida, MdeB, that is active as an E1 component of an alpha-ketoglutarate dehydrogenase complex rather than a pyruvate dehydrogase complex. The second pyruvate dehydrogenase complex E1 protein from Alcaligenes eutrophus, PdhE, complements an aceE mutant of E. coli but is not part of a pyruvate dehydrogenase complex operon, is more similar to the Pseudomonas putida MdeB than to E. coli AceE, and may have also have a different primary specificity.
Probab=22.52 E-value=2.4e+02 Score=29.57 Aligned_cols=41 Identities=27% Similarity=0.421 Sum_probs=24.6
Q ss_pred eEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEE
Q psy13938 25 GRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67 (245)
Q Consensus 25 G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~ 67 (245)
-+.+|||+....-++. .| |..+-.+.|++.|+..|++|...
T Consensus 249 NLi~IVD~N~~qlDG~-v~-~~~~i~e~le~~F~a~GW~Vi~V 289 (885)
T TIGR00759 249 NLTFVINCNLQRLDGP-VR-GNGKIIQELESLFRGAGWNVIKV 289 (885)
T ss_pred CEEEEEeCCCCccCCc-cc-cccccchhHHHHHHhcCCEEEEE
Confidence 4677776644332111 11 11112478999999999999765
No 158
>PRK03094 hypothetical protein; Provisional
Probab=22.37 E-value=64 Score=23.41 Aligned_cols=27 Identities=19% Similarity=0.366 Sum_probs=21.9
Q ss_pred CCCcHHHHHHHHHHHHhCCcEEEEEeC
Q psy13938 43 RPGSGADVKNLEAAFYALGFEVSVYTN 69 (245)
Q Consensus 43 R~Gs~~D~~~l~~~f~~LgF~V~~~~n 69 (245)
|.|-+....++++.|++-||+|.-.++
T Consensus 3 kIaVE~~Ls~i~~~L~~~GYeVv~l~~ 29 (80)
T PRK03094 3 KIGVEQSLTDVQQALKQKGYEVVQLRS 29 (80)
T ss_pred eEEeecCcHHHHHHHHHCCCEEEecCc
Confidence 456677788999999999999986653
No 159
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=22.28 E-value=1.3e+02 Score=23.46 Aligned_cols=28 Identities=29% Similarity=0.392 Sum_probs=21.2
Q ss_pred HHHHHHHHHhCCcEEEEEe-CCCHHHHHH
Q psy13938 50 VKNLEAAFYALGFEVSVYT-NPEFREITE 77 (245)
Q Consensus 50 ~~~l~~~f~~LgF~V~~~~-nlt~~em~~ 77 (245)
++.|+..|+.+||+|...+ .++.+++..
T Consensus 29 v~~l~~~L~~~Giev~l~~~~l~~~~~~~ 57 (120)
T PF10865_consen 29 VKELAPVLAPLGIEVRLEEIELDEEEFAR 57 (120)
T ss_pred HHHHHHHHHhCCcEEEEEEEECChHHHhh
Confidence 6778999999999997765 566655443
No 160
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=22.17 E-value=2.4e+02 Score=18.45 Aligned_cols=34 Identities=24% Similarity=0.300 Sum_probs=25.1
Q ss_pred HHHHHHHhCCcEEEEE-eCCCHHHHHHHHHHHhhh
Q psy13938 52 NLEAAFYALGFEVSVY-TNPEFREITEILSNLSQE 85 (245)
Q Consensus 52 ~l~~~f~~LgF~V~~~-~nlt~~em~~~l~~~~~~ 85 (245)
.|.+.|+..|+.+... .+++.++-.+.++.|...
T Consensus 2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~ 36 (82)
T smart00490 2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNG 36 (82)
T ss_pred HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcC
Confidence 5678888889987655 467777777777777654
No 161
>PTZ00089 transketolase; Provisional
Probab=21.95 E-value=4.4e+02 Score=26.53 Aligned_cols=55 Identities=15% Similarity=0.322 Sum_probs=35.3
Q ss_pred EEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEEEEeC-C-CHHHHHHHHHHHhh
Q psy13938 26 RALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTN-P-EFREITEILSNLSQ 84 (245)
Q Consensus 26 ~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~n-l-t~~em~~~l~~~~~ 84 (245)
+.+|++|-.+.-++... ....+.+.+.|+.+|++|..-.| - ..+++.+.+++...
T Consensus 180 Li~i~d~N~~~i~~~~~----~~~~~~~~~~f~a~G~~~i~v~dG~~D~~~l~~a~~~a~~ 236 (661)
T PTZ00089 180 LIVLYDDNKITIDGNTD----LSFTEDVEKKYEAYGWHVIEVDNGNTDFDGLRKAIEEAKK 236 (661)
T ss_pred EEEEEECCCcccccCcc----cccCccHHHHHHhcCCcEEEeCCCCCCHHHHHHHHHHHHh
Confidence 66777765554221111 11236788999999999988744 3 57788888776543
No 162
>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molec
Probab=21.72 E-value=2.6e+02 Score=25.51 Aligned_cols=31 Identities=19% Similarity=0.448 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhCCcEEEEEeC--CCHHHHHHH
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTN--PEFREITEI 78 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~n--lt~~em~~~ 78 (245)
.|...|+++|+++|++|...-+ .|.+||.+.
T Consensus 166 ~d~~el~~ll~~~G~~v~~~~~~~~s~~~i~~~ 198 (399)
T cd00316 166 GDLRELKRLLEEMGIRVNALFDGGTTVEELREL 198 (399)
T ss_pred hhHHHHHHHHHHcCCcEEEEcCCCCCHHHHHhh
Confidence 6999999999999999977654 688888763
No 163
>PRK06703 flavodoxin; Provisional
Probab=21.60 E-value=2.5e+02 Score=21.85 Aligned_cols=65 Identities=15% Similarity=0.166 Sum_probs=39.8
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCc-c----hhhhhhccccccccccC
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGL-G----EQKLWLPFTADKCRTLA 120 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~-~----i~~I~~~f~~~~c~~L~ 120 (245)
|+.=++.|.+.++..|.+|.+..- ...+ ..+..+++.++++.-++|. . +..+++.+.. ..|.
T Consensus 15 T~~iA~~ia~~l~~~g~~v~~~~~-~~~~---------~~~l~~~d~viigspt~~~g~~p~~~~~f~~~l~~---~~l~ 81 (151)
T PRK06703 15 TEDIADLIKVSLDAFDHEVVLQEM-DGMD---------AEELLAYDGIILGSYTWGDGDLPYEAEDFHEDLEN---IDLS 81 (151)
T ss_pred HHHHHHHHHHHHHhcCCceEEEeh-hhCC---------HHHHhcCCcEEEEECCCCCCcCcHHHHHHHHHHhc---CCCC
Confidence 566677899999999999887642 1111 1123567778887777763 2 4444444432 2366
Q ss_pred CCc
Q psy13938 121 GKP 123 (245)
Q Consensus 121 ~KP 123 (245)
+|+
T Consensus 82 ~k~ 84 (151)
T PRK06703 82 GKK 84 (151)
T ss_pred CCE
Confidence 776
No 164
>PRK05261 putative phosphoketolase; Provisional
Probab=21.20 E-value=4e+02 Score=27.58 Aligned_cols=35 Identities=17% Similarity=0.258 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 49 DVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 49 D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
..+.|.+.|+.+||++...+--..++|.+.+.+..
T Consensus 216 ~~e~l~~rf~g~Gw~~i~VDG~D~~av~~a~a~al 250 (785)
T PRK05261 216 SDEELEALFRGYGYEPYFVEGDDPADMHQEMAAAL 250 (785)
T ss_pred CcHhHHHHHHHCCCeeEEECCCCHHHHHHHHHHHH
Confidence 45789999999999998665345566666655443
No 165
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=21.03 E-value=2.4e+02 Score=26.21 Aligned_cols=15 Identities=13% Similarity=0.116 Sum_probs=6.2
Q ss_pred HHHHHHHHHHhCCcE
Q psy13938 49 DVKNLEAAFYALGFE 63 (245)
Q Consensus 49 D~~~l~~~f~~LgF~ 63 (245)
.++.|.+.|...|+.
T Consensus 267 ~~~~l~~~L~~~g~~ 281 (423)
T PRK04837 267 RCEEIWGHLAADGHR 281 (423)
T ss_pred HHHHHHHHHHhCCCc
Confidence 334444444444444
No 166
>PRK11712 ribonuclease G; Provisional
Probab=20.95 E-value=3.5e+02 Score=26.34 Aligned_cols=47 Identities=15% Similarity=0.149 Sum_probs=37.8
Q ss_pred CCCCCCCcHHHHHHHHHHHHhC-----CcEEEEE-eCCCHHHHHHHHHHHhhh
Q psy13938 39 NMTPRPGSGADVKNLEAAFYAL-----GFEVSVY-TNPEFREITEILSNLSQE 85 (245)
Q Consensus 39 ~~~~R~Gs~~D~~~l~~~f~~L-----gF~V~~~-~nlt~~em~~~l~~~~~~ 85 (245)
+.+.|...+.+..+|+++...+ |+-+++. .+.+.+++.+.+..+.+.
T Consensus 140 giSrKI~de~~R~rLk~i~~~~~~~~~GvIiRT~A~~a~~eel~~dl~~L~~~ 192 (489)
T PRK11712 140 GVSQRIESEEERERLKKIVAPYCDEQGGFIIRTAAEGVGEEELAQDAAFLKRL 192 (489)
T ss_pred eEecCCCChHHHHHHHHHHHhhCCCCceEEEEccCCCCCHHHHHHHHHHHHHH
Confidence 6677888888999999998874 7777554 689999999999887654
No 167
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=20.92 E-value=2.9e+02 Score=25.68 Aligned_cols=65 Identities=18% Similarity=0.267 Sum_probs=42.3
Q ss_pred CceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEEE-EEeCCCHHHHHHHHHHHhhhcCCCCceEEE-EeccC
Q psy13938 23 RRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVS-VYTNPEFREITEILSNLSQEDHSDADCLVI-TVLTH 100 (245)
Q Consensus 23 ~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~~~~~~~~d~~vv-~ilSH 100 (245)
..+.+|||.| +..+++.|.+.|+..|+.+. .+.+++.++-.+.++.|.... ...+|+ =+++.
T Consensus 244 ~~~~~lVF~~-------------s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~---~~vLVaTd~~~~ 307 (434)
T PRK11192 244 EVTRSIVFVR-------------TRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGR---VNVLVATDVAAR 307 (434)
T ss_pred CCCeEEEEeC-------------ChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCC---CcEEEEcccccc
Confidence 3466777766 34678888888888888764 445788888888888886532 222221 15566
Q ss_pred Ccc
Q psy13938 101 GLG 103 (245)
Q Consensus 101 G~~ 103 (245)
|.+
T Consensus 308 GiD 310 (434)
T PRK11192 308 GID 310 (434)
T ss_pred Ccc
Confidence 665
No 168
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=20.83 E-value=4.8e+02 Score=21.49 Aligned_cols=46 Identities=28% Similarity=0.391 Sum_probs=29.0
Q ss_pred CCCceEEEEecccCcccCCCee-eecCCCcccccCCC-CcCCCCCCCeEEE
Q psy13938 120 AGKPKIFFIQACRGTKLDGGVR-LVSRANTETDAGVN-AYKIPSYADFLIA 168 (245)
Q Consensus 120 ~~KPKlf~iQACRG~~~~~gv~-~~d~~~~e~~~~~~-~~~ip~~~D~li~ 168 (245)
-..|-++-|+||=|....-|.. +..++ ... +.+ ...+|.-+|+-|.
T Consensus 84 ~~~~~IIAIDAcLG~~~~vG~I~~~~gp-l~P--G~gv~K~LP~VGd~sIt 131 (163)
T PF06866_consen 84 HPNPFIIAIDACLGRPDNVGYITLGNGP-LKP--GAGVGKKLPPVGDISIT 131 (163)
T ss_pred CCCCeEEEEECCCCCcccceEEEEcCCC-CCC--chhhCCCCCCCcCEEEE
Confidence 3578999999999998766643 33331 111 222 4568888886554
No 169
>PF06076 Orthopox_F14: Orthopoxvirus F14 protein; InterPro: IPR009280 This family consists of several short Orthopoxvirus F14 proteins. The function of this protein is unknown.
Probab=20.81 E-value=1.3e+02 Score=20.71 Aligned_cols=25 Identities=24% Similarity=0.271 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhCCcEEEEEeCCC
Q psy13938 47 GADVKNLEAAFYALGFEVSVYTNPE 71 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~~nlt 71 (245)
+.|...|-..+.+||.+|..-+|.+
T Consensus 34 ed~i~ellniltelgcdvdfde~fs 58 (73)
T PF06076_consen 34 EDDIMELLNILTELGCDVDFDENFS 58 (73)
T ss_pred HHHHHHHHHHHHHhCCCcccccchh
Confidence 4566778888999999998877743
No 170
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=20.77 E-value=2.2e+02 Score=21.40 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=31.7
Q ss_pred cHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCc
Q psy13938 46 SGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGL 102 (245)
Q Consensus 46 s~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~ 102 (245)
|+.=++.|.+.+...|++|.+.. ++..+. .+...+|.+++..-+||.
T Consensus 12 T~~~A~~i~~~~~~~g~~v~~~~-~~~~~~---------~~l~~~d~iilgspty~~ 58 (140)
T TIGR01753 12 TEEMANIIAEGLKEAGAEVDLLE-VADADA---------EDLLSYDAVLLGCSTWGD 58 (140)
T ss_pred HHHHHHHHHHHHHhcCCeEEEEE-cccCCH---------HHHhcCCEEEEEcCCCCC
Confidence 45557789999999999987764 221111 122457888888888874
No 171
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=20.68 E-value=1.6e+02 Score=23.22 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 48 ADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
.|.+...+.++++||+.....+-+.+++-..|++..
T Consensus 99 ~~~~~~~~~l~~~G~~~vf~~~~~~~~i~~~l~~~~ 134 (137)
T PRK02261 99 HDFEEVEKKFKEMGFDRVFPPGTDPEEAIDDLKKDL 134 (137)
T ss_pred cChHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHh
Confidence 355556666667777666666667777777666654
No 172
>PRK09401 reverse gyrase; Reviewed
Probab=20.58 E-value=2.5e+02 Score=30.43 Aligned_cols=54 Identities=17% Similarity=0.216 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhCCcEEE-EEeCCCHHHHHHHHHHHhhhcCCCCceEEEE-----eccCCcchhhhhh
Q psy13938 48 ADVKNLEAAFYALGFEVS-VYTNPEFREITEILSNLSQEDHSDADCLVIT-----VLTHGLGEQKLWL 109 (245)
Q Consensus 48 ~D~~~l~~~f~~LgF~V~-~~~nlt~~em~~~l~~~~~~~~~~~d~~vv~-----ilSHG~~i~~I~~ 109 (245)
..++.|.+.|+..||.|. .|.++ .+.+++|.+. ..+.+|.. +++-|.++.+++.
T Consensus 342 ~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G---~~~VLVatas~tdv~aRGIDiP~~Ir 401 (1176)
T PRK09401 342 EYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEG---EVDVLVGVASYYGVLVRGIDLPERIR 401 (1176)
T ss_pred HHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCC---CCCEEEEecCCCCceeecCCCCccee
Confidence 448899999999999976 66666 4455667643 23444432 4566766666444
No 173
>PRK14763 coenzyme PQQ biosynthesis protein A; Provisional
Probab=20.38 E-value=56 Score=18.42 Aligned_cols=10 Identities=50% Similarity=1.095 Sum_probs=8.1
Q ss_pred hCCcEEEEEe
Q psy13938 59 ALGFEVSVYT 68 (245)
Q Consensus 59 ~LgF~V~~~~ 68 (245)
+|||+|..|-
T Consensus 11 R~GfEvTmYi 20 (26)
T PRK14763 11 RFGFEVTMYV 20 (26)
T ss_pred eeeeEEEEEE
Confidence 5899998874
No 174
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.30 E-value=1.6e+02 Score=20.83 Aligned_cols=23 Identities=17% Similarity=0.359 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHhCCcEEEEEeC
Q psy13938 47 GADVKNLEAAFYALGFEVSVYTN 69 (245)
Q Consensus 47 ~~D~~~l~~~f~~LgF~V~~~~n 69 (245)
..+.+.+.+.|++.||.+....+
T Consensus 52 ~~~~~~i~~~L~~~G~~~~~~~~ 74 (85)
T cd04906 52 AEELAELLEDLKSAGYEVVDLSD 74 (85)
T ss_pred HHHHHHHHHHHHHCCCCeEECCC
Confidence 56889999999999998876443
No 175
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=20.26 E-value=3.2e+02 Score=22.04 Aligned_cols=61 Identities=21% Similarity=0.188 Sum_probs=37.9
Q ss_pred CcHHHHHHHHHHHHhCCcEEEEEe-CCCHHHHHHHHHHHhhhcCCCCceEEEEeccCCcc--hhhhhhcc
Q psy13938 45 GSGADVKNLEAAFYALGFEVSVYT-NPEFREITEILSNLSQEDHSDADCLVITVLTHGLG--EQKLWLPF 111 (245)
Q Consensus 45 Gs~~D~~~l~~~f~~LgF~V~~~~-nlt~~em~~~l~~~~~~~~~~~d~~vv~ilSHG~~--i~~I~~~f 111 (245)
|=+.=.+-+.++|+..||+|..-- .-|.+|+-... .+ .+.+.++++.++=|.. +..+.+.+
T Consensus 24 gHd~gakvia~~l~d~GfeVi~~g~~~tp~e~v~aA---~~---~dv~vIgvSsl~g~h~~l~~~lve~l 87 (143)
T COG2185 24 GHDRGAKVIARALADAGFEVINLGLFQTPEEAVRAA---VE---EDVDVIGVSSLDGGHLTLVPGLVEAL 87 (143)
T ss_pred ccccchHHHHHHHHhCCceEEecCCcCCHHHHHHHH---Hh---cCCCEEEEEeccchHHHHHHHHHHHH
Confidence 334456789999999999997664 55554443332 22 4456666666665554 55555544
No 176
>PRK14976 5'-3' exonuclease; Provisional
Probab=20.10 E-value=6.2e+02 Score=22.48 Aligned_cols=62 Identities=11% Similarity=0.083 Sum_probs=47.2
Q ss_pred CCceEEEEEeCC--CCCCC----CCCCCCCcHHH----HHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHh
Q psy13938 22 PRRGRALVFNHD--EFQMD----NMTPRPGSGAD----VKNLEAAFYALGFEVSVYTNPEFREITEILSNLS 83 (245)
Q Consensus 22 ~~~G~aLIInn~--~F~~~----~~~~R~Gs~~D----~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~ 83 (245)
++.-+++++.-. +|... .-.+|..+..+ ...++++++.+|+.+......-++++.-.|..-.
T Consensus 54 ~p~~~~v~fD~~~~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~ 125 (281)
T PRK14976 54 NPSYILIAFDAGRKTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKL 125 (281)
T ss_pred CCCEEEEEEECCCCcccccccHHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHH
Confidence 566778888753 45443 44578777766 6668889999999999999999999999885543
No 177
>cd02014 TPP_POX Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. It requires FAD in addition to TPP and a divalent cation as cofactors.
Probab=20.04 E-value=1.8e+02 Score=23.62 Aligned_cols=58 Identities=16% Similarity=0.133 Sum_probs=32.9
Q ss_pred eEEEEEeCCCCCCC------CCCCCCCcHHHHHHHHHHHHhCCcEEEEEeCCCHHHHHHHHHHHhh
Q psy13938 25 GRALVFNHDEFQMD------NMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQ 84 (245)
Q Consensus 25 G~aLIInn~~F~~~------~~~~R~Gs~~D~~~l~~~f~~LgF~V~~~~nlt~~em~~~l~~~~~ 84 (245)
=+.+|+||..+..- ......++....-++.++.+.+|++..... +.+|+.+.|++..+
T Consensus 98 ~~~iv~NN~~~~~~~~~~~~~~~~~~~~~~~~~d~~~la~a~G~~~~~v~--~~~el~~~l~~a~~ 161 (178)
T cd02014 98 VIVVVFNNSDLGFIKWEQEVMGQPEFGVDLPNPDFAKIAEAMGIKGIRVE--DPDELEAALDEALA 161 (178)
T ss_pred cEEEEEECCchhHHHHHHHHhcCCceeccCCCCCHHHHHHHCCCeEEEeC--CHHHHHHHHHHHHh
Confidence 46788899766310 001112222112245667777788766554 46788888877654
No 178
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=20.01 E-value=74 Score=26.39 Aligned_cols=48 Identities=15% Similarity=0.247 Sum_probs=30.4
Q ss_pred cccCCCCCceEEEEEeCCCCCCCCCCCCCCcHHHHHHHHHHHHhCCcEE
Q psy13938 16 EYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEV 64 (245)
Q Consensus 16 ~Y~m~~~~~G~aLIInn~~F~~~~~~~R~Gs~~D~~~l~~~f~~LgF~V 64 (245)
.|++. .|+..+||+.+.+..--+-.....+..=.+++.+.++++||++
T Consensus 40 i~Rl~-~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L~~~g~~~ 87 (174)
T cd04516 40 IMRIR-EPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARIIQKLGFPA 87 (174)
T ss_pred EEEeC-CCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHHHcCCCC
Confidence 37775 5778899988876541112222223333567888899999975
Done!