Query 030509
Match_columns 176
No_of_seqs 159 out of 1045
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 14:48:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030509.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030509hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03652 UPF0081: Uncharacteri 100.0 3.5E-46 7.5E-51 287.8 5.5 134 22-159 1-135 (135)
2 PRK00109 Holliday junction res 100.0 2.4E-44 5.3E-49 278.4 15.8 135 20-159 2-137 (138)
3 COG0816 Predicted endonuclease 100.0 4.5E-44 9.7E-49 277.6 14.2 137 21-161 1-138 (141)
4 TIGR00250 RNAse_H_YqgF RNAse H 100.0 1.8E-43 4E-48 271.1 14.1 129 25-158 1-130 (130)
5 smart00732 YqgFc Likely ribonu 99.6 4.8E-15 1E-19 106.3 10.6 98 22-126 1-99 (99)
6 PRK00039 ruvC Holliday junctio 98.3 2.5E-05 5.4E-10 62.2 12.4 103 21-130 1-112 (164)
7 cd00529 RuvC_resolvase Hollida 97.7 0.00047 1E-08 54.0 10.0 94 23-119 1-103 (154)
8 PF02075 RuvC: Crossover junct 97.7 0.00029 6.3E-09 55.1 8.5 101 24-131 1-110 (149)
9 TIGR00228 ruvC crossover junct 97.6 0.00049 1.1E-08 54.5 8.7 101 24-131 1-109 (156)
10 COG2183 Tex Transcriptional ac 97.4 0.002 4.3E-08 62.0 11.5 93 22-121 330-424 (780)
11 PF04312 DUF460: Protein of un 97.2 0.0047 1E-07 48.0 9.8 109 20-150 30-138 (138)
12 PF14639 YqgF: Holliday-juncti 97.1 0.0095 2.1E-07 46.8 10.6 96 21-122 4-109 (150)
13 COG0817 RuvC Holliday junction 96.8 0.0021 4.5E-08 51.1 4.7 99 25-130 1-108 (160)
14 COG2433 Uncharacterized conser 96.8 0.013 2.7E-07 55.2 10.4 109 22-152 244-352 (652)
15 PRK05082 N-acetylmannosamine k 95.5 0.098 2.1E-06 44.1 8.6 102 23-129 2-115 (291)
16 COG1940 NagC Transcriptional r 95.0 0.12 2.7E-06 44.0 7.9 109 19-131 3-127 (314)
17 COG1548 Predicted transcriptio 95.0 0.083 1.8E-06 45.6 6.5 102 21-129 2-108 (330)
18 PRK09557 fructokinase; Reviewe 94.8 0.15 3.1E-06 43.4 7.9 102 24-130 2-116 (301)
19 PF04848 Pox_A22: Poxvirus A22 93.6 2.2 4.8E-05 33.3 11.5 119 22-151 1-133 (143)
20 PRK13310 N-acetyl-D-glucosamin 93.5 0.39 8.5E-06 40.7 7.8 102 24-130 2-116 (303)
21 PF07318 DUF1464: Protein of u 93.0 1 2.3E-05 40.0 9.9 114 26-152 1-138 (343)
22 PRK13311 N-acetyl-D-glucosamin 92.9 0.73 1.6E-05 38.3 8.4 102 24-130 2-116 (256)
23 PRK13321 pantothenate kinase; 92.2 2.1 4.6E-05 35.9 10.4 56 24-81 2-63 (256)
24 TIGR00744 ROK_glcA_fam ROK fam 91.4 0.88 1.9E-05 38.6 7.3 100 25-130 1-117 (318)
25 PF00480 ROK: ROK family; Int 90.0 0.46 9.9E-06 36.8 4.0 100 26-131 1-112 (179)
26 COG1214 Inactive homolog of me 89.9 1.4 3.1E-05 36.4 7.0 88 22-117 1-95 (220)
27 TIGR01766 tspaseT_teng_C trans 89.7 0.99 2.1E-05 31.0 5.1 60 63-123 13-82 (82)
28 PRK12408 glucokinase; Provisio 89.2 1.1 2.4E-05 39.0 6.2 96 18-119 12-118 (336)
29 PRK00292 glk glucokinase; Prov 88.7 2.1 4.6E-05 36.6 7.5 94 23-127 3-108 (316)
30 TIGR03725 bact_YeaZ universal 88.2 4 8.6E-05 33.0 8.4 87 24-118 1-92 (202)
31 PRK13318 pantothenate kinase; 88.0 2.6 5.6E-05 35.3 7.5 57 24-82 2-64 (258)
32 PF01548 DEDD_Tnp_IS110: Trans 88.0 2.5 5.5E-05 31.6 6.8 85 24-126 1-85 (144)
33 PF14239 RRXRR: RRXRR protein 86.5 0.65 1.4E-05 37.6 2.8 22 22-43 51-72 (176)
34 PRK09698 D-allose kinase; Prov 85.1 4.9 0.00011 33.9 7.7 103 22-128 4-122 (302)
35 PRK14101 bifunctional glucokin 84.9 2.6 5.6E-05 39.9 6.5 65 21-88 17-85 (638)
36 PRK15080 ethanolamine utilizat 82.3 24 0.00052 29.7 10.7 94 19-125 21-130 (267)
37 PRK09472 ftsA cell division pr 77.2 13 0.00028 33.4 7.9 62 22-83 8-84 (420)
38 PRK09982 universal stress prot 75.7 12 0.00027 27.8 6.4 46 63-117 92-137 (142)
39 TIGR01865 cas_Csn1 CRISPR-asso 72.7 3.3 7.1E-05 40.7 3.1 23 23-45 2-24 (805)
40 PF07282 OrfB_Zn_ribbon: Putat 71.9 2.5 5.3E-05 28.2 1.5 45 110-154 15-68 (69)
41 COG1646 Predicted phosphate-bi 71.7 12 0.00027 31.7 5.9 48 63-118 30-77 (240)
42 PF03932 CutC: CutC family; I 71.1 11 0.00025 30.9 5.5 60 68-136 79-142 (201)
43 smart00842 FtsA Cell division 69.4 23 0.00051 27.8 6.9 60 24-83 1-75 (187)
44 PF11104 PilM_2: Type IV pilus 68.8 19 0.0004 31.2 6.7 60 26-85 1-72 (340)
45 PRK00047 glpK glycerol kinase; 68.6 15 0.00032 33.5 6.3 23 23-45 6-28 (498)
46 TIGR00749 glk glucokinase, pro 68.1 18 0.00038 31.0 6.3 61 25-87 1-68 (316)
47 TIGR03723 bact_gcp putative gl 68.0 28 0.00061 30.1 7.6 88 24-118 1-108 (314)
48 PRK09604 UGMP family protein; 67.7 55 0.0012 28.5 9.4 91 22-119 1-111 (332)
49 PRK15027 xylulokinase; Provisi 66.6 15 0.00032 33.4 5.8 24 23-46 1-24 (484)
50 PRK09605 bifunctional UGMP fam 66.5 30 0.00064 31.9 7.9 94 22-121 1-110 (535)
51 PRK03011 butyrate kinase; Prov 66.3 39 0.00084 30.1 8.3 128 22-156 2-165 (358)
52 TIGR01312 XylB D-xylulose kina 66.0 15 0.00032 33.0 5.6 22 25-46 1-22 (481)
53 PRK13928 rod shape-determining 65.4 64 0.0014 27.8 9.3 99 25-125 6-110 (336)
54 PF03309 Pan_kinase: Type III 65.3 36 0.00079 27.4 7.3 58 24-81 1-60 (206)
55 PF00370 FGGY_N: FGGY family o 64.7 21 0.00047 29.0 6.0 49 24-72 2-58 (245)
56 PRK13320 pantothenate kinase; 64.6 29 0.00062 29.1 6.8 53 22-81 2-55 (244)
57 PF03464 eRF1_2: eRF1 domain 2 64.2 16 0.00035 27.4 4.8 95 24-127 4-118 (133)
58 TIGR01769 GGGP geranylgeranylg 64.1 23 0.00051 29.1 6.0 47 63-117 13-59 (205)
59 PF02844 GARS_N: Phosphoribosy 64.0 13 0.00029 27.2 4.1 40 63-115 51-90 (100)
60 TIGR01174 ftsA cell division p 63.2 32 0.00068 30.1 7.1 61 24-84 2-77 (371)
61 PF05378 Hydant_A_N: Hydantoin 62.7 22 0.00048 28.2 5.5 56 25-81 2-63 (176)
62 COG0418 PyrC Dihydroorotase [N 62.5 9.7 0.00021 33.7 3.6 51 80-134 130-189 (344)
63 PRK15118 universal stress glob 62.5 35 0.00076 25.0 6.3 47 63-118 92-138 (144)
64 COG1070 XylB Sugar (pentulose 61.8 25 0.00054 32.3 6.4 23 20-42 2-24 (502)
65 PF05188 MutS_II: MutS domain 61.1 60 0.0013 23.4 12.8 119 24-162 3-129 (137)
66 TIGR01175 pilM type IV pilus a 60.5 54 0.0012 28.1 8.0 64 22-85 3-78 (348)
67 PRK13322 pantothenate kinase; 60.5 92 0.002 26.1 9.1 52 24-81 2-54 (246)
68 PHA02942 putative transposase; 59.6 13 0.00028 33.3 4.0 87 71-161 263-371 (383)
69 COG4012 Uncharacterized protei 59.0 82 0.0018 27.7 8.5 98 22-135 1-99 (342)
70 PRK13324 pantothenate kinase; 59.0 48 0.001 28.1 7.2 56 24-81 2-64 (258)
71 cd05785 DNA_polB_like2_exo Unc 58.9 49 0.0011 26.9 7.0 22 60-82 59-80 (207)
72 PRK10966 exonuclease subunit S 58.6 56 0.0012 29.4 8.0 71 61-135 26-102 (407)
73 PF02579 Nitro_FeMo-Co: Dinitr 58.6 45 0.00098 22.6 6.0 50 64-130 43-92 (94)
74 TIGR00555 panK_eukar pantothen 58.5 75 0.0016 27.4 8.4 90 24-131 2-92 (279)
75 PRK10116 universal stress prot 57.8 47 0.001 24.1 6.3 47 63-117 91-137 (142)
76 cd03409 Chelatase_Class_II Cla 57.1 54 0.0012 22.6 6.2 52 78-135 3-59 (101)
77 TIGR03192 benz_CoA_bzdQ benzoy 56.8 41 0.00088 29.3 6.5 52 20-74 30-82 (293)
78 PTZ00294 glycerol kinase-like 56.4 30 0.00065 31.7 5.9 23 23-45 3-25 (504)
79 cd03416 CbiX_SirB_N Sirohydroc 56.4 57 0.0012 22.8 6.3 56 77-136 2-59 (101)
80 PF00532 Peripla_BP_1: Peripla 56.1 71 0.0015 26.7 7.8 121 31-162 1-147 (279)
81 PLN02295 glycerol kinase 55.7 32 0.0007 31.6 6.0 47 24-70 2-56 (512)
82 PRK00923 sirohydrochlorin coba 54.9 50 0.0011 24.2 6.0 54 77-136 4-61 (126)
83 PF03237 Terminase_6: Terminas 54.8 57 0.0012 27.1 7.0 61 20-81 224-290 (384)
84 TIGR00241 CoA_E_activ CoA-subs 54.3 41 0.00089 27.7 6.0 46 24-73 2-48 (248)
85 cd02067 B12-binding B12 bindin 54.2 57 0.0012 23.5 6.1 53 63-122 39-92 (119)
86 TIGR01315 5C_CHO_kinase FGGY-f 54.2 33 0.00072 31.8 5.9 48 24-71 2-57 (541)
87 PF07355 GRDB: Glycine/sarcosi 54.2 40 0.00086 30.2 6.1 58 58-121 64-123 (349)
88 PRK13317 pantothenate kinase; 53.9 95 0.0021 26.6 8.3 85 22-130 2-87 (277)
89 TIGR01314 gntK_FGGY gluconate 53.9 29 0.00063 31.7 5.4 23 24-46 2-24 (505)
90 cd05781 DNA_polB_B3_exo DEDDy 53.8 84 0.0018 25.0 7.5 24 58-82 47-70 (188)
91 COG3513 Predicted CRISPR-assoc 53.4 12 0.00026 37.2 2.9 24 20-43 2-25 (1088)
92 TIGR01768 GGGP-family geranylg 53.2 42 0.00091 28.1 5.8 45 64-117 17-61 (223)
93 PF13727 CoA_binding_3: CoA-bi 52.5 48 0.001 24.7 5.7 45 63-117 130-174 (175)
94 PF14331 ImcF-related_N: ImcF- 52.2 42 0.00091 28.3 5.8 55 62-117 9-75 (266)
95 PRK10939 autoinducer-2 (AI-2) 52.1 45 0.00097 30.7 6.4 24 22-45 3-26 (520)
96 PF00012 HSP70: Hsp70 protein; 52.1 13 0.00028 34.3 2.9 18 24-41 1-18 (602)
97 PTZ00340 O-sialoglycoprotein e 51.5 81 0.0018 28.1 7.6 90 22-118 1-108 (345)
98 PRK10331 L-fuculokinase; Provi 51.3 37 0.00081 30.7 5.7 23 23-45 3-25 (470)
99 PRK11572 copper homeostasis pr 51.3 57 0.0012 27.8 6.4 61 68-137 80-144 (248)
100 KOG4013 Predicted Cu2+ homeost 50.7 35 0.00076 28.6 4.8 58 67-134 87-150 (255)
101 PF02310 B12-binding: B12 bind 50.5 83 0.0018 22.3 6.5 48 64-118 41-88 (121)
102 TIGR00619 sbcd exonuclease Sbc 50.3 79 0.0017 26.3 7.1 53 62-117 27-81 (253)
103 PF07066 DUF3882: Lactococcus 49.7 46 0.001 26.4 5.1 64 21-85 1-75 (159)
104 TIGR01311 glycerol_kin glycero 48.8 43 0.00094 30.5 5.7 24 23-46 2-25 (493)
105 PRK09545 znuA high-affinity zi 48.0 61 0.0013 28.0 6.3 43 90-136 235-277 (311)
106 PRK14046 malate--CoA ligase su 47.6 1E+02 0.0022 27.6 7.8 86 44-136 282-367 (392)
107 cd02812 PcrB_like PcrB_like pr 47.6 58 0.0013 27.1 5.8 47 64-118 15-61 (219)
108 cd01018 ZntC Metal binding pro 47.1 59 0.0013 27.1 5.9 57 90-159 200-256 (266)
109 PRK13326 pantothenate kinase; 47.0 1.7E+02 0.0036 24.8 8.7 22 22-43 6-27 (262)
110 PRK15005 universal stress prot 45.9 41 0.00088 24.5 4.3 19 63-81 96-114 (144)
111 cd03413 CbiK_C Anaerobic cobal 45.7 94 0.002 22.5 6.1 55 77-136 3-57 (103)
112 cd06294 PBP1_ycjW_transcriptio 45.6 1.1E+02 0.0024 24.2 7.1 19 63-81 49-67 (270)
113 PRK13927 rod shape-determining 45.4 1.9E+02 0.0041 24.6 9.0 27 22-48 5-31 (334)
114 TIGR01016 sucCoAbeta succinyl- 45.3 1.1E+02 0.0024 27.0 7.7 84 44-134 282-365 (386)
115 cd01989 STK_N The N-terminal d 44.7 38 0.00083 24.7 4.0 19 63-81 92-110 (146)
116 cd01988 Na_H_Antiporter_C The 43.6 38 0.00082 23.9 3.7 21 63-83 83-103 (132)
117 cd01017 AdcA Metal binding pro 43.4 86 0.0019 26.3 6.4 44 89-136 202-245 (282)
118 KOG3289 Uncharacterized conser 43.3 67 0.0014 26.4 5.3 103 67-171 64-179 (199)
119 PRK04169 geranylgeranylglycery 42.9 74 0.0016 26.7 5.8 41 68-117 26-66 (232)
120 PF06180 CbiK: Cobalt chelatas 42.2 47 0.001 28.3 4.6 64 45-117 76-147 (262)
121 TIGR00671 baf pantothenate kin 42.1 99 0.0021 25.8 6.5 55 24-81 1-56 (243)
122 TIGR02628 fuculo_kin_coli L-fu 41.9 68 0.0015 29.0 5.8 22 24-45 3-24 (465)
123 PHA02533 17 large terminase pr 41.8 1.2E+02 0.0027 28.4 7.6 62 17-81 310-378 (534)
124 PLN02757 sirohydrochlorine fer 41.4 1.1E+02 0.0024 23.8 6.3 52 75-130 14-67 (154)
125 PF00072 Response_reg: Respons 41.3 1.1E+02 0.0024 20.6 6.8 62 64-135 33-94 (112)
126 PF13167 GTP-bdg_N: GTP-bindin 41.2 1.4E+02 0.0029 21.6 7.3 71 61-135 8-81 (95)
127 COG1924 Activator of 2-hydroxy 41.1 1.2E+02 0.0027 27.5 7.1 52 20-74 133-184 (396)
128 PRK13929 rod-share determining 41.0 1.1E+02 0.0025 26.3 6.9 68 23-91 5-73 (335)
129 PRK13410 molecular chaperone D 40.5 29 0.00063 33.4 3.3 21 22-42 2-22 (668)
130 PF03709 OKR_DC_1_N: Orn/Lys/A 40.4 1.4E+02 0.003 21.8 6.3 55 63-125 26-81 (115)
131 TIGR01234 L-ribulokinase L-rib 40.2 66 0.0014 29.7 5.5 23 23-45 2-25 (536)
132 PF00582 Usp: Universal stress 40.2 1.2E+02 0.0026 20.8 6.3 49 63-117 91-139 (140)
133 TIGR02260 benz_CoA_red_B benzo 40.2 1.5E+02 0.0032 26.9 7.7 60 63-129 339-405 (413)
134 PRK04123 ribulokinase; Provisi 40.1 73 0.0016 29.4 5.8 23 22-44 3-26 (548)
135 cd02064 FAD_synthetase_N FAD s 39.8 1.1E+02 0.0023 24.0 6.1 64 64-135 89-160 (180)
136 cd03414 CbiX_SirB_C Sirohydroc 39.4 1.2E+02 0.0025 21.7 5.8 55 77-135 3-59 (117)
137 cd03412 CbiK_N Anaerobic cobal 39.4 46 0.001 24.9 3.7 49 77-134 3-52 (127)
138 cd01829 SGNH_hydrolase_peri2 S 39.2 86 0.0019 24.1 5.4 50 64-118 98-148 (200)
139 COG0420 SbcD DNA repair exonuc 39.1 1.1E+02 0.0025 26.8 6.7 53 62-117 28-81 (390)
140 PF13407 Peripla_BP_4: Peripla 38.8 1.4E+02 0.0031 23.5 6.8 50 58-120 40-89 (257)
141 PRK10606 btuE putative glutath 38.6 50 0.0011 26.5 4.0 39 63-101 43-84 (183)
142 cd06297 PBP1_LacI_like_12 Liga 38.5 1.5E+02 0.0033 23.7 7.0 18 64-81 45-62 (269)
143 PRK00994 F420-dependent methyl 38.4 1.8E+02 0.0039 25.0 7.4 66 59-135 45-110 (277)
144 PRK00290 dnaK molecular chaper 38.1 30 0.00066 32.7 3.0 20 22-41 2-21 (627)
145 COG3703 ChaC Uncharacterized p 37.8 40 0.00087 27.6 3.3 25 17-41 53-77 (190)
146 TIGR02026 BchE magnesium-proto 37.6 1.4E+02 0.0031 27.4 7.3 71 58-135 223-298 (497)
147 TIGR00290 MJ0570_dom MJ0570-re 37.5 1.1E+02 0.0024 25.5 6.0 38 63-104 74-111 (223)
148 cd00851 MTH1175 This uncharact 37.2 1.4E+02 0.0029 20.6 5.7 48 64-128 53-100 (103)
149 PF13911 AhpC-TSA_2: AhpC/TSA 37.2 87 0.0019 22.3 4.8 46 65-124 4-49 (115)
150 PF00155 Aminotran_1_2: Aminot 37.1 1.5E+02 0.0032 25.0 7.0 55 63-123 132-192 (363)
151 TIGR00289 conserved hypothetic 37.1 1.2E+02 0.0025 25.3 6.1 38 63-104 74-111 (222)
152 COG1521 Pantothenate kinase ty 36.8 91 0.002 26.6 5.4 24 23-47 1-24 (251)
153 cd06547 GH85_ENGase Endo-beta- 36.7 1.7E+02 0.0038 25.7 7.4 58 61-119 90-149 (339)
154 PF03358 FMN_red: NADPH-depend 36.6 1.7E+02 0.0037 21.6 6.5 49 63-117 61-112 (152)
155 PF14450 FtsA: Cell division p 36.0 35 0.00077 25.0 2.6 19 24-42 1-19 (120)
156 COG0443 DnaK Molecular chapero 36.0 56 0.0012 30.9 4.4 22 21-42 4-25 (579)
157 CHL00094 dnaK heat shock prote 35.9 34 0.00074 32.4 3.0 21 22-42 2-22 (621)
158 TIGR02717 AcCoA-syn-alpha acet 35.8 3.4E+02 0.0073 24.7 9.8 73 58-136 354-428 (447)
159 cd00984 DnaB_C DnaB helicase C 35.8 1.8E+02 0.0038 23.3 6.9 61 58-119 107-171 (242)
160 PLN02669 xylulokinase 35.7 99 0.0021 29.0 6.0 27 19-45 5-31 (556)
161 cd01844 SGNH_hydrolase_like_6 35.7 1.5E+02 0.0033 22.5 6.2 52 66-119 49-101 (177)
162 cd00950 DHDPS Dihydrodipicolin 35.7 83 0.0018 26.3 5.1 62 63-131 84-152 (284)
163 cd02071 MM_CoA_mut_B12_BD meth 35.6 1.7E+02 0.0038 21.3 7.7 67 63-137 39-105 (122)
164 cd01019 ZnuA Zinc binding prot 35.5 1.4E+02 0.003 25.3 6.4 43 89-135 210-252 (286)
165 PRK13411 molecular chaperone D 35.2 40 0.00086 32.3 3.3 21 22-42 2-22 (653)
166 PRK14878 UGMP family protein; 34.9 1.5E+02 0.0032 25.7 6.6 90 25-120 1-105 (323)
167 cd01137 PsaA Metal binding pro 34.5 1.3E+02 0.0029 25.4 6.2 45 88-136 207-251 (287)
168 TIGR02529 EutJ ethanolamine ut 34.4 1.9E+02 0.0041 23.8 7.0 90 26-125 1-103 (239)
169 PRK15456 universal stress prot 34.4 42 0.0009 24.6 2.7 20 63-82 94-113 (142)
170 PF01884 PcrB: PcrB family; I 34.2 1.3E+02 0.0028 25.3 5.9 44 64-118 22-66 (230)
171 TIGR00329 gcp_kae1 metallohydr 34.0 3E+02 0.0065 23.5 9.4 89 25-119 1-108 (305)
172 KOG0237 Glycinamide ribonucleo 33.6 1.1E+02 0.0024 29.7 5.9 70 63-135 57-144 (788)
173 PF01026 TatD_DNase: TatD rela 33.6 1.1E+02 0.0024 25.3 5.4 93 62-158 73-169 (255)
174 PF04412 DUF521: Protein of un 33.4 2.4E+02 0.0052 25.7 7.9 89 20-128 243-337 (400)
175 PF01182 Glucosamine_iso: Gluc 33.1 1E+02 0.0022 24.6 5.0 54 62-121 9-62 (199)
176 PRK14457 ribosomal RNA large s 33.0 2.4E+02 0.0053 24.9 7.7 90 61-153 240-339 (345)
177 PRK11678 putative chaperone; P 32.6 42 0.0009 30.7 2.9 18 24-41 2-19 (450)
178 TIGR01918 various_sel_PB selen 32.4 1.4E+02 0.003 27.5 6.2 56 59-120 61-118 (431)
179 PRK13930 rod shape-determining 32.3 48 0.001 28.2 3.1 18 23-40 9-26 (335)
180 TIGR01917 gly_red_sel_B glycin 32.3 1.4E+02 0.0031 27.5 6.2 57 58-120 60-118 (431)
181 PRK13331 pantothenate kinase; 32.1 1.7E+02 0.0036 24.9 6.3 25 20-44 5-29 (251)
182 PTZ00009 heat shock 70 kDa pro 31.8 50 0.0011 31.6 3.4 22 20-41 2-23 (653)
183 cd06271 PBP1_AglR_RafR_like Li 31.8 2.5E+02 0.0054 22.0 7.1 19 63-81 48-66 (268)
184 KOG1856 Transcription elongati 31.7 2.2E+02 0.0048 29.7 7.9 58 62-121 654-711 (1299)
185 COG4020 Uncharacterized protei 31.7 98 0.0021 27.0 4.8 61 22-82 3-65 (332)
186 cd00338 Ser_Recombinase Serine 31.4 1.9E+02 0.0041 20.7 5.9 53 63-123 54-107 (137)
187 COG0151 PurD Phosphoribosylami 31.3 1.2E+02 0.0027 27.8 5.7 70 63-135 52-139 (428)
188 cd01124 KaiC KaiC is a circadi 31.2 2.2E+02 0.0048 21.5 6.5 58 62-123 83-142 (187)
189 PF06723 MreB_Mbl: MreB/Mbl pr 31.2 1.1E+02 0.0024 26.8 5.3 105 23-129 2-112 (326)
190 cd01828 sialate_O-acetylestera 30.8 2.3E+02 0.0049 21.1 6.7 54 62-118 37-94 (169)
191 COG2102 Predicted ATPases of P 30.6 1.4E+02 0.003 25.1 5.5 39 63-105 75-113 (223)
192 cd06300 PBP1_ABC_sugar_binding 30.2 2.8E+02 0.006 22.0 7.2 44 63-119 50-93 (272)
193 PTZ00400 DnaK-type molecular c 30.2 48 0.001 31.8 3.0 20 22-41 41-60 (663)
194 TIGR03190 benz_CoA_bzdN benzoy 30.2 1.5E+02 0.0033 26.2 6.0 53 62-122 301-354 (377)
195 COG0079 HisC Histidinol-phosph 30.0 1.4E+02 0.003 26.4 5.7 51 63-121 135-186 (356)
196 PTZ00186 heat shock 70 kDa pre 29.9 58 0.0013 31.3 3.5 22 21-42 26-47 (657)
197 cd00248 Mth938-like Mth938-lik 29.8 2.1E+02 0.0046 20.8 5.8 55 63-131 41-95 (109)
198 TIGR03471 HpnJ hopanoid biosyn 29.3 2.9E+02 0.0063 25.0 7.8 44 58-105 228-272 (472)
199 PRK12359 flavodoxin FldB; Prov 29.2 60 0.0013 25.8 3.0 28 78-105 138-166 (172)
200 cd08165 MPP_MPPE1 human MPPE1 29.2 2.5E+02 0.0054 21.4 6.5 52 63-117 27-82 (156)
201 COG4126 Hydantoin racemase [Am 29.1 86 0.0019 26.5 3.9 41 61-115 161-201 (230)
202 COG1831 Predicted metal-depend 28.7 1.6E+02 0.0034 25.7 5.6 71 63-136 110-186 (285)
203 PF14606 Lipase_GDSL_3: GDSL-l 28.5 1.8E+02 0.004 23.4 5.7 52 64-118 49-100 (178)
204 PF12641 Flavodoxin_3: Flavodo 28.5 2.7E+02 0.0058 21.8 6.6 30 73-105 38-67 (160)
205 PRK00696 sucC succinyl-CoA syn 28.3 3E+02 0.0065 24.3 7.6 84 44-134 282-365 (388)
206 PF01869 BcrAD_BadFG: BadF/Bad 28.2 1.8E+02 0.0039 23.9 5.9 22 25-46 1-22 (271)
207 COG0363 NagB 6-phosphogluconol 28.2 1.5E+02 0.0033 24.8 5.4 51 64-122 18-74 (238)
208 PRK04147 N-acetylneuraminate l 28.1 3.7E+02 0.008 22.7 8.2 59 63-131 26-93 (293)
209 PF00701 DHDPS: Dihydrodipicol 28.1 1.7E+02 0.0037 24.6 5.7 61 64-131 86-153 (289)
210 KOG0968 DNA polymerase zeta, c 27.4 1.5E+02 0.0032 31.0 5.8 71 31-104 701-781 (1488)
211 TIGR00674 dapA dihydrodipicoli 27.3 1.4E+02 0.003 25.1 5.1 50 63-119 82-132 (285)
212 cd00562 NifX_NifB This CD repr 27.3 2.1E+02 0.0045 19.5 5.8 51 64-130 51-101 (102)
213 COG0655 WrbA Multimeric flavod 27.2 1E+02 0.0022 24.6 4.1 35 63-102 66-100 (207)
214 cd00458 SugarP_isomerase Sugar 27.1 2.1E+02 0.0047 22.1 5.8 52 63-121 9-60 (169)
215 PRK08769 DNA polymerase III su 26.9 2.2E+02 0.0049 24.8 6.4 63 69-131 67-135 (319)
216 PRK01433 hscA chaperone protei 26.8 67 0.0015 30.5 3.3 19 22-40 19-37 (595)
217 TIGR02350 prok_dnaK chaperone 26.8 56 0.0012 30.6 2.8 18 24-41 2-19 (595)
218 PLN03226 serine hydroxymethylt 26.7 2.6E+02 0.0056 25.7 7.1 19 63-81 172-190 (475)
219 PRK03170 dihydrodipicolinate s 26.7 1.4E+02 0.0031 25.1 5.1 61 63-130 85-152 (292)
220 TIGR03123 one_C_unchar_1 proba 26.6 3.6E+02 0.0078 23.7 7.6 87 25-118 1-93 (318)
221 KOG4184 Predicted sugar kinase 26.6 96 0.0021 28.3 4.0 68 62-131 226-300 (478)
222 PRK11175 universal stress prot 26.6 1.7E+02 0.0037 24.2 5.5 20 63-82 96-115 (305)
223 PF13177 DNA_pol3_delta2: DNA 26.6 3E+02 0.0064 21.1 6.6 62 68-131 61-124 (162)
224 KOG0104 Molecular chaperones G 26.6 1.1E+02 0.0023 30.6 4.6 32 18-53 18-49 (902)
225 PF10035 DUF2179: Uncharacteri 26.4 82 0.0018 19.7 2.8 19 63-81 29-47 (55)
226 PF08608 Wyosine_form: Wyosine 26.4 87 0.0019 20.9 2.9 28 89-121 26-53 (62)
227 cd01400 6PGL 6PGL: 6-Phosphogl 26.4 1.8E+02 0.0039 23.6 5.5 49 63-121 12-62 (219)
228 TIGR00615 recR recombination p 26.4 1.1E+02 0.0025 25.0 4.2 28 63-90 123-151 (195)
229 PRK13790 phosphoribosylamine-- 26.4 2.1E+02 0.0046 25.2 6.2 19 63-81 16-34 (379)
230 COG0145 HyuA N-methylhydantoin 26.3 2.5E+02 0.0055 27.3 7.1 58 22-81 2-64 (674)
231 TIGR00696 wecB_tagA_cpsF bacte 26.3 3.3E+02 0.0072 21.6 7.3 56 62-128 36-91 (177)
232 TIGR00683 nanA N-acetylneurami 26.3 1.8E+02 0.0038 24.8 5.6 52 63-120 85-137 (290)
233 cd01833 XynB_like SGNH_hydrola 26.2 2.6E+02 0.0057 20.4 6.2 56 63-118 66-124 (157)
234 TIGR03191 benz_CoA_bzdO benzoy 26.2 1.8E+02 0.0039 26.4 5.9 48 63-118 350-398 (430)
235 PRK07667 uridine kinase; Provi 26.1 2.3E+02 0.0051 22.2 6.0 53 63-121 3-57 (193)
236 TIGR00111 pelota probable tran 25.9 2.1E+02 0.0046 25.2 6.1 130 22-162 136-273 (351)
237 TIGR03566 FMN_reduc_MsuE FMN r 25.7 1.5E+02 0.0033 22.9 4.7 49 63-117 59-107 (174)
238 PF03644 Glyco_hydro_85: Glyco 25.7 1.5E+02 0.0033 25.8 5.1 57 61-119 86-144 (311)
239 cd01987 USP_OKCHK USP domain i 25.6 75 0.0016 22.4 2.7 21 63-83 74-94 (124)
240 PF06490 FleQ: Flagellar regul 25.6 2.6E+02 0.0057 20.2 5.8 47 67-123 35-81 (109)
241 PRK05183 hscA chaperone protei 25.6 70 0.0015 30.4 3.2 20 22-41 19-38 (616)
242 TIGR01198 pgl 6-phosphoglucono 25.4 2E+02 0.0044 23.6 5.6 37 77-121 29-66 (233)
243 PF01902 ATP_bind_4: ATP-bindi 25.4 1.2E+02 0.0026 25.1 4.3 37 63-103 74-110 (218)
244 cd06311 PBP1_ABC_sugar_binding 25.3 3.5E+02 0.0076 21.5 7.1 45 63-119 49-93 (274)
245 PRK10854 exopolyphosphatase; P 25.3 2.2E+02 0.0048 26.3 6.4 93 17-118 6-117 (513)
246 PRK10355 xylF D-xylose transpo 25.3 4.2E+02 0.0092 22.5 8.7 44 65-120 72-115 (330)
247 PF00349 Hexokinase_1: Hexokin 25.3 42 0.0009 27.4 1.5 67 19-85 60-144 (206)
248 TIGR02313 HpaI-NOT-DapA 2,4-di 25.2 4.3E+02 0.0092 22.5 8.0 59 63-131 23-89 (294)
249 cd01545 PBP1_SalR Ligand-bindi 25.1 3.3E+02 0.0071 21.4 6.7 18 63-80 45-62 (270)
250 PLN03184 chloroplast Hsp70; Pr 25.1 69 0.0015 30.8 3.1 21 22-42 39-59 (673)
251 TIGR03858 LLM_2I7G probable ox 24.9 1.4E+02 0.003 25.8 4.8 26 58-83 287-312 (337)
252 cd00598 GH18_chitinase-like Th 24.9 2.8E+02 0.0061 21.4 6.2 46 60-105 90-135 (210)
253 COG0386 BtuE Glutathione perox 24.8 1.4E+02 0.0031 23.8 4.3 40 63-102 43-85 (162)
254 COG2205 KdpD Osmosensitive K+ 24.6 3.4E+02 0.0074 27.4 7.6 54 62-121 322-376 (890)
255 PRK10569 NAD(P)H-dependent FMN 24.5 1.6E+02 0.0035 23.5 4.8 49 63-117 57-105 (191)
256 COG2248 Predicted hydrolase (m 24.5 1.3E+02 0.0029 26.2 4.3 46 33-85 167-212 (304)
257 PRK07179 hypothetical protein; 24.3 2.4E+02 0.0051 24.7 6.2 51 63-122 170-221 (407)
258 TIGR03286 methan_mark_15 putat 24.3 3.1E+02 0.0067 25.1 6.9 25 20-44 142-166 (404)
259 PF00464 SHMT: Serine hydroxym 24.2 2.1E+02 0.0046 26.0 5.9 34 63-101 158-191 (399)
260 TIGR03729 acc_ester putative p 24.1 2.3E+02 0.005 22.9 5.7 47 63-117 21-67 (239)
261 PRK13329 pantothenate kinase; 24.1 4.3E+02 0.0093 22.1 8.5 18 23-40 2-19 (249)
262 cd06282 PBP1_GntR_like_2 Ligan 24.0 3.5E+02 0.0076 21.1 7.0 12 70-81 51-62 (266)
263 PF01297 TroA: Periplasmic sol 24.0 2.7E+02 0.0058 22.7 6.1 43 89-135 181-223 (256)
264 PF00875 DNA_photolyase: DNA p 23.9 3.2E+02 0.007 20.6 6.3 18 64-81 78-95 (165)
265 TIGR01753 flav_short flavodoxi 23.7 1.9E+02 0.0042 20.7 4.7 40 75-117 46-86 (140)
266 PRK03459 rnpA ribonuclease P; 23.7 3.2E+02 0.0068 20.4 6.4 59 29-98 45-110 (122)
267 PF03088 Str_synth: Strictosid 23.7 2E+02 0.0043 20.5 4.5 26 7-34 24-49 (89)
268 KOG1220 Phosphoglucomutase/pho 23.5 1.8E+02 0.004 27.9 5.4 49 67-123 91-142 (607)
269 cd07019 S49_SppA_1 Signal pept 23.4 3.9E+02 0.0085 21.4 7.0 52 60-117 24-76 (211)
270 PF09298 FAA_hydrolase_N: Fuma 23.4 38 0.00083 24.9 0.8 12 30-41 14-25 (107)
271 PRK05627 bifunctional riboflav 23.3 3E+02 0.0064 23.9 6.5 64 64-135 103-175 (305)
272 COG1433 Uncharacterized conser 23.3 3.3E+02 0.0072 20.5 6.6 54 64-134 55-108 (121)
273 PRK09112 DNA polymerase III su 23.3 2.8E+02 0.0061 24.4 6.4 65 67-131 93-163 (351)
274 cd01541 PBP1_AraR Ligand-bindi 23.2 2.9E+02 0.0064 21.9 6.1 18 63-81 45-62 (273)
275 TIGR02313 HpaI-NOT-DapA 2,4-di 22.8 2.2E+02 0.0047 24.3 5.5 51 64-120 85-136 (294)
276 cd06305 PBP1_methylthioribose_ 22.7 3.9E+02 0.0084 21.1 7.2 18 63-81 45-62 (273)
277 cd05784 DNA_polB_II_exo DEDDy 22.7 1.9E+02 0.0041 23.2 4.8 21 61-82 53-73 (193)
278 PF02833 DHHA2: DHHA2 domain; 22.7 1.1E+02 0.0023 22.3 3.2 49 25-81 25-73 (127)
279 COG0329 DapA Dihydrodipicolina 22.6 3.2E+02 0.0069 23.5 6.5 49 63-118 88-137 (299)
280 KOG4245 Predicted metal-depend 22.6 1.4E+02 0.003 25.3 4.0 73 47-121 68-141 (297)
281 COG3643 Glutamate formiminotra 22.4 1E+02 0.0022 26.6 3.3 46 76-124 88-133 (302)
282 PF01993 MTD: methylene-5,6,7, 22.4 2.8E+02 0.0061 23.9 5.9 86 64-160 49-159 (276)
283 TIGR00683 nanA N-acetylneurami 22.3 4.8E+02 0.01 22.1 8.3 58 64-131 24-90 (290)
284 PRK10812 putative DNAse; Provi 22.3 4E+02 0.0088 22.3 7.0 69 63-135 77-147 (265)
285 PLN02721 threonine aldolase 22.2 2.6E+02 0.0057 23.4 5.8 54 63-121 120-180 (353)
286 cd00293 USP_Like Usp: Universa 22.2 1E+02 0.0022 21.0 2.8 21 63-83 82-102 (130)
287 COG0675 Transposase and inacti 22.1 99 0.0021 25.6 3.2 46 111-160 297-350 (364)
288 PRK00304 hypothetical protein; 21.8 2.9E+02 0.0063 19.3 5.5 34 86-124 28-61 (75)
289 TIGR03567 FMN_reduc_SsuE FMN r 21.8 1.9E+02 0.0042 22.3 4.6 49 63-117 56-104 (171)
290 cd06324 PBP1_ABC_sugar_binding 21.7 4.6E+02 0.0099 21.6 7.3 46 64-122 47-93 (305)
291 cd06316 PBP1_ABC_sugar_binding 21.5 3.4E+02 0.0073 22.0 6.3 43 63-119 46-89 (294)
292 TIGR02263 benz_CoA_red_C benzo 21.5 2E+02 0.0043 25.5 5.1 48 63-118 310-358 (380)
293 PF08288 PIGA: PIGA (GPI ancho 21.4 3.3E+02 0.0071 19.7 6.6 80 29-121 3-85 (90)
294 cd00615 Orn_deC_like Ornithine 21.3 2.8E+02 0.0061 23.1 5.8 50 63-122 142-193 (294)
295 PF11215 DUF3010: Protein of u 21.2 4E+02 0.0087 20.7 10.0 61 61-131 48-110 (138)
296 COG1693 Repressor of nif and g 21.1 83 0.0018 27.7 2.5 26 21-46 271-296 (325)
297 TIGR00315 cdhB CO dehydrogenas 21.1 2.8E+02 0.006 21.9 5.4 37 64-104 18-55 (162)
298 PRK06242 flavodoxin; Provision 21.1 1.8E+02 0.0039 21.4 4.2 38 74-117 43-80 (150)
299 cd06301 PBP1_rhizopine_binding 21.0 4.2E+02 0.0091 20.9 7.3 17 64-81 47-63 (272)
300 cd06309 PBP1_YtfQ_like Peripla 21.0 4.3E+02 0.0093 21.0 6.7 42 64-118 46-87 (273)
301 TIGR00083 ribF riboflavin kina 20.9 1.2E+02 0.0025 26.3 3.4 69 64-135 87-158 (288)
302 cd08180 PDD 1,3-propanediol de 20.9 1.9E+02 0.0041 24.9 4.8 53 62-121 66-119 (332)
303 cd06317 PBP1_ABC_sugar_binding 20.8 4.2E+02 0.0092 20.8 6.9 43 64-119 47-89 (275)
304 COG1504 Uncharacterized conser 20.8 1.6E+02 0.0035 22.3 3.7 54 63-132 51-106 (121)
305 TIGR03275 methan_mark_8 putati 20.8 1.8E+02 0.0038 25.0 4.4 57 24-100 156-212 (259)
306 COG0329 DapA Dihydrodipicolina 20.6 5.5E+02 0.012 22.0 8.9 79 43-131 7-93 (299)
307 PF14871 GHL6: Hypothetical gl 20.5 1.5E+02 0.0033 22.5 3.6 21 60-80 110-130 (132)
308 cd06307 PBP1_uncharacterized_s 20.4 4.4E+02 0.0096 20.9 7.8 43 64-120 50-92 (275)
309 cd01016 TroA Metal binding pro 20.3 2.5E+02 0.0055 23.5 5.3 41 89-133 192-232 (276)
310 PRK02724 hypothetical protein; 20.3 3.3E+02 0.0071 20.3 5.1 48 23-72 9-56 (104)
311 cd06267 PBP1_LacI_sugar_bindin 20.3 4.1E+02 0.0088 20.4 6.9 17 64-81 46-62 (264)
312 PF09547 Spore_IV_A: Stage IV 20.1 3.7E+02 0.0081 25.2 6.6 50 73-131 180-230 (492)
313 cd00954 NAL N-Acetylneuraminic 20.1 5.3E+02 0.011 21.7 8.2 77 43-129 3-88 (288)
No 1
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=100.00 E-value=3.5e-46 Score=287.81 Aligned_cols=134 Identities=34% Similarity=0.555 Sum_probs=123.2
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFI 100 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa 100 (176)
|++||||||++|||||+||+.+.+|+|+.++.+.+.. .++++|.+++++|+|+.||||+|++ ||+++++++.+++|+
T Consensus 1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~--~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~ 78 (135)
T PF03652_consen 1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNRE--KDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFA 78 (135)
T ss_dssp -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCC--CCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHH
T ss_pred CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCc--hHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHH
Confidence 6899999999999999999999999999999976554 3489999999999999999999999 999999999999999
Q ss_pred HHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030509 101 DDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN 159 (176)
Q Consensus 101 ~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~ 159 (176)
++|++. ++++||++|||||||++|++.|++.|.+++++|+.+|++||++|||+||++
T Consensus 79 ~~L~~~--~~~ipV~~~DEr~TT~~A~~~l~~~g~~~~k~k~~iD~~AA~iILq~yLd~ 135 (135)
T PF03652_consen 79 EELKKR--FPGIPVILVDERLTTKEAERRLRESGLSRKKRKKKIDSIAAAIILQSYLDS 135 (135)
T ss_dssp HHHHHH--H-TSEEEEEECSCSHHCCHCCHHHTT-SHHHHCHHHCCCHHHHHHHHHHCC
T ss_pred HHHHHh--cCCCcEEEECCChhHHHHHHHHHHcCCChhhcCccccHHHHHHHHHHHHhC
Confidence 999984 579999999999999999999999999999999999999999999999984
No 2
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=100.00 E-value=2.4e-44 Score=278.45 Aligned_cols=135 Identities=31% Similarity=0.509 Sum_probs=125.8
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHH
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKL 98 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~ 98 (176)
..|++||||||++|||||+||+.+.+|+|+.++.+++... .+++|.+++++|+++.||||+|++ ||++++++..+++
T Consensus 2 ~~~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~--~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~ 79 (138)
T PRK00109 2 PSGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTP--DWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARK 79 (138)
T ss_pred CCCcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCch--HHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHH
Confidence 3578999999999999999999999999999998876443 379999999999999999999999 9999999999999
Q ss_pred HHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030509 99 FIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN 159 (176)
Q Consensus 99 Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~ 159 (176)
|+++|++. + ++||++|||||||++|+++|++.|.+++++|+.+|++||++|||+||++
T Consensus 80 f~~~L~~~--~-~~~v~~~DEr~TT~~A~~~l~~~~~~~~~~k~~vD~~AA~iILq~yL~~ 137 (138)
T PRK00109 80 FANRLEGR--F-GLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLDS 137 (138)
T ss_pred HHHHHHHH--h-CCCEEEEcCCcCHHHHHHHHHHcCCChhhcccchhHHHHHHHHHHHHhc
Confidence 99999974 5 8999999999999999999999998888888999999999999999985
No 3
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.5e-44 Score=277.62 Aligned_cols=137 Identities=28% Similarity=0.483 Sum_probs=128.8
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHH
Q 030509 21 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLF 99 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~F 99 (176)
++++||||||+||||||+||+.+.+|+|+++|.+.+..+ ..|+.|.+++++|+++.||||+|+| +|++++.++.+++|
T Consensus 1 ~~~ilalD~G~KrIGvA~sd~~~~~A~pl~~i~~~~~~~-~~~~~l~~li~~~~~~~vVVGlP~~m~g~~~~~~~~~~~f 79 (141)
T COG0816 1 GMRILALDVGTKRIGVAVSDILGSLASPLETIKRKNGKP-QDFNALLKLVKEYQVDTVVVGLPLNMDGTEGPRAELARKF 79 (141)
T ss_pred CceEEEEecCCceEEEEEecCCCccccchhhheeccccH-hhHHHHHHHHHHhCCCEEEEecCcCCCCCcchhHHHHHHH
Confidence 378999999999999999999999999999999887764 2389999999999999999999999 99999999999999
Q ss_pred HHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhhhh
Q 030509 100 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNAN 161 (176)
Q Consensus 100 a~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~~~ 161 (176)
+++|+++ | ++||++||||+||++|++.|.++|++++++|+.+|++||++|||+||+...
T Consensus 80 ~~~L~~r--~-~lpv~l~DERltTv~A~~~L~~~~~~~~~rk~~iD~~AA~~ILq~~ld~~~ 138 (141)
T COG0816 80 AERLKKR--F-NLPVVLWDERLSTVEAERMLIEAGVSRKKRKGVIDSLAAVLILESYLDRNH 138 (141)
T ss_pred HHHHHHh--c-CCCEEEEcCccCHHHHHHHHHHcCCchhhhcchhHHHHHHHHHHHHHHhhh
Confidence 9999984 6 899999999999999999999999999999999999999999999999754
No 4
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=100.00 E-value=1.8e-43 Score=271.07 Aligned_cols=129 Identities=26% Similarity=0.345 Sum_probs=121.4
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHH
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDL 103 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L 103 (176)
||||||++|||||+||+.+.+|+|+.++..++.. ..++.|.+++++|+++.||||+|++ ||++|+++++|++|+++|
T Consensus 1 laiD~G~kriGvA~~d~~~~~a~pl~~i~~~~~~--~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L 78 (130)
T TIGR00250 1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGE--PDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRL 78 (130)
T ss_pred CeEccCCCeEEEEEECCCCCEEeceEEEEecCCc--HHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHH
Confidence 6999999999999999999999999999876543 3479999999999999999999999 999999999999999999
Q ss_pred HhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHh
Q 030509 104 SATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLD 158 (176)
Q Consensus 104 ~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~ 158 (176)
++. + ++||++|||||||.+|++.|++.|++++++|..+|++||++|||+||+
T Consensus 79 ~~~--~-~~~v~~~DEr~TT~~A~~~l~~~g~~~~~~k~~vD~~AA~iILq~yLd 130 (130)
T TIGR00250 79 EGR--F-GVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYLD 130 (130)
T ss_pred HHH--h-CCCEEEEcCCcCHHHHHHHHHHcCCChhhccccHhHHHHHHHHHHHhC
Confidence 874 5 899999999999999999999999999889999999999999999995
No 5
>smart00732 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.
Probab=99.62 E-value=4.8e-15 Score=106.25 Aligned_cols=98 Identities=24% Similarity=0.456 Sum_probs=83.3
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFI 100 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa 100 (176)
+++||||+|..+||+|+.|+.+.+..++.+....+ .+.+++.|.+++.++++++|+||.|-. +|..+.... ..|.
T Consensus 1 ~~ilgiD~Ggt~i~~a~~d~~g~~~~~~~~~~~~~--~~~~~~~l~~~i~~~~~~~i~Ig~pg~v~g~~~~~~~--~~l~ 76 (99)
T smart00732 1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTN--KEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETE--EAFA 76 (99)
T ss_pred CcEEEEccCCCeEEEEEECCCCCEecCEEEEEecC--cchHHHHHHHHHHHhCCCEEEEeCCcCCCCCcCHHHH--HHHH
Confidence 35899999999999999999999998877655322 234579999999999999999999999 998776654 7899
Q ss_pred HHHHhccCCCCCcEEEecCcccHHHH
Q 030509 101 DDLSATKKLEDMKYAYWNEGFTSKGV 126 (176)
Q Consensus 101 ~~L~~~~~~~~lpV~~~DEr~TT~~A 126 (176)
+.|++. + ++||+++||+.||.+|
T Consensus 77 ~~l~~~--~-~~pv~~~nDa~st~~a 99 (99)
T smart00732 77 ELLKER--F-NLPVVLVDERLATVYA 99 (99)
T ss_pred HHHHHh--h-CCcEEEEeCCcccccC
Confidence 999874 4 8999999999999865
No 6
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=98.26 E-value=2.5e-05 Score=62.16 Aligned_cols=103 Identities=18% Similarity=0.203 Sum_probs=67.7
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceec--cceeeeCCCCC-----hhhHHHHHHHHHHhcCCCEEEEeccCC--CCCCch
Q 030509 21 RGRFLGLDVGDKYVGLSISDPKNKIAS--PLSVLLRKKNT-----IDLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAA 91 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~~~~a~--Pl~~i~~~~~~-----~~~~~~~L~~li~e~~~~~iVVGlPl~--dG~~s~ 91 (176)
+++|||||+|..++|+|+-+..+...+ -.++|..+... .....+.|.+++++|+|+.++|=-|.- |.+.+-
T Consensus 1 ~m~iLGIDPgl~~tG~avi~~~~~~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~~Pd~vaiE~~f~~~n~~sa~ 80 (164)
T PRK00039 1 MMRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEYQPDEVAIEEVFFNKNPQSAL 80 (164)
T ss_pred CCEEEEEccccCceeEEEEEecCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEehhhhccChHHHH
Confidence 379999999999999999886654222 22355543221 123468899999999999999988876 344333
Q ss_pred HHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 92 DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 92 ~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
...+++--+...... . ++||+.+ |..+.+...
T Consensus 81 ~l~~arGvi~la~~~--~-~ipv~ey----~P~~VKk~v 112 (164)
T PRK00039 81 KLGQARGVAILAAAQ--R-GLPVAEY----TPLQVKKAV 112 (164)
T ss_pred HHHHHHHHHHHHHHH--c-CCCEEEE----CHHHhhhhh
Confidence 333455544444432 3 8999865 566665554
No 7
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=97.70 E-value=0.00047 Score=53.98 Aligned_cols=94 Identities=14% Similarity=0.233 Sum_probs=58.0
Q ss_pred eEEEEecCCCeEEEEEecCCCceecc--ceeeeCCCC-C----hhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCch-HH
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIASP--LSVLLRKKN-T----IDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAA-DA 93 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a~P--l~~i~~~~~-~----~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~-~~ 93 (176)
+|||||+|..++|+|+.+..+....- ..++..... . .....+.|.+++.+++|+.++|=-+.- .+..+. ..
T Consensus 1 rILGIDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~~Pd~vaiE~~~~~~n~~s~~~l 80 (154)
T cd00529 1 RILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQFQPDVVAIERVFFAKNPDSALKL 80 (154)
T ss_pred CEEEEccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEEEhhcccChHHHHHH
Confidence 68999999999999998765433222 345654422 1 124578899999999999999987665 332221 11
Q ss_pred HHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 94 VQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 94 ~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
..++.-+-..... .++||+.++-
T Consensus 81 ~~~~Gvi~~~~~~---~~i~v~e~~P 103 (154)
T cd00529 81 GQARGALILALAN---RNLPVFEYTP 103 (154)
T ss_pred HHHHHHHHHHHHH---cCCCEEEEcc
Confidence 2223333222221 2788887753
No 8
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=97.68 E-value=0.00029 Score=55.05 Aligned_cols=101 Identities=17% Similarity=0.209 Sum_probs=57.3
Q ss_pred EEEEecCCCeEEEEEecCCCceecc--ceeeeCCCC-C----hhhHHHHHHHHHHhcCCCEEEEeccCC--CCCCchHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASP--LSVLLRKKN-T----IDLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAV 94 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~P--l~~i~~~~~-~----~~~~~~~L~~li~e~~~~~iVVGlPl~--dG~~s~~~~ 94 (176)
|||||+|..++|.|+-+..+.-... ..+|..... + .....+.|.+++++|+|+.+++=-|.. |-+..-...
T Consensus 1 ILGIDPgl~~tG~avi~~~~~~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~~P~~vaiE~~f~~~n~~s~~~l~ 80 (149)
T PF02075_consen 1 ILGIDPGLSNTGYAVIEEDGGKLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEYNPDEVAIEEIFFGKNPKSALKLG 80 (149)
T ss_dssp EEEEE--SSEEEEEEEEEETTEEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEEE-S----HHHHHHHH
T ss_pred CEEECCCCCCeeEEEEEeeCCEEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhhCCCEEEeehhhhccCHHHHHHHH
Confidence 7999999999999998875432222 245654332 1 123468899999999999999998877 222223334
Q ss_pred HHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 95 QVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 95 ~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
+++-.+...... .++||..+ |..+.+..+-
T Consensus 81 ~arGvi~l~~~~---~~i~v~~y----~P~~vKk~vt 110 (149)
T PF02075_consen 81 QARGVILLAAAQ---RGIPVFEY----TPSEVKKAVT 110 (149)
T ss_dssp HHHHHHHHHHHT---TT--EEEE----EHHHHHHHHT
T ss_pred HHHHHHHHHHHH---cCCeEEEE----CHHHHHHHhh
Confidence 555555554432 38887754 7777776654
No 9
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=97.59 E-value=0.00049 Score=54.54 Aligned_cols=101 Identities=15% Similarity=0.234 Sum_probs=65.4
Q ss_pred EEEEecCCCeEEEEEecCCCceec--cceeeeCCCCCh----hhHHHHHHHHHHhcCCCEEEEeccCC--CCCCchHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIAS--PLSVLLRKKNTI----DLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQ 95 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~--Pl~~i~~~~~~~----~~~~~~L~~li~e~~~~~iVVGlPl~--dG~~s~~~~~ 95 (176)
|||||+|+.++|.|+-+..+.-.+ -.++|..++.+. ....+.|.+++++|+|+.+.|=-++. |.+.+-...+
T Consensus 1 ILGIDPGl~~tG~gvi~~~~~~~~~v~~G~I~t~~~~~~~RL~~I~~~l~~~i~~y~P~~~aiE~~F~~~N~~sa~~lg~ 80 (156)
T TIGR00228 1 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPNYFAIEQVFMAKNADSALKLGQ 80 (156)
T ss_pred CEeECcccccccEEEEEecCCeEEEEEeeEEECCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEeHHhhccCHHHHHHHHH
Confidence 699999999999999875443322 234565433221 13468899999999999999987766 4444444445
Q ss_pred HHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 96 VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 96 v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
+|-.+-..... .++||+ -||..+.+..+-
T Consensus 81 arGvilla~~~---~~ipv~----Ey~P~~vKkavt 109 (156)
T TIGR00228 81 ARGVAIVAAVN---QELPVF----EYAARQVKQTVV 109 (156)
T ss_pred HHHHHHHHHHH---cCCCEE----EECHHHHHHHhc
Confidence 55554433332 389998 356666655543
No 10
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.39 E-value=0.002 Score=61.98 Aligned_cols=93 Identities=18% Similarity=0.258 Sum_probs=66.5
Q ss_pred CeEEEEecCCCe-EEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHH
Q 030509 22 GRFLGLDVGDKY-VGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLF 99 (176)
Q Consensus 22 ~~iLglD~G~kr-iGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~F 99 (176)
..+||||+|-+. |=+|+.|..|.+..-..+++... ...+...+.|..++..|+|+.|.|| +||.|..+. +|
T Consensus 330 ~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIG----ngTaSrete---~f 402 (780)
T COG2183 330 KATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIG----NGTASRETE---KF 402 (780)
T ss_pred cceeecCCccccccEEEEEcCCCceeceeEEEcCCCccchHHHHHHHHHHHHHhCceEEEEe----cCCcchhHH---HH
Confidence 379999999665 66899999887765444444332 1123446788999999999999999 999997665 46
Q ss_pred HHHHHhccCCCCCcEEEecCcc
Q 030509 100 IDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 100 a~~L~~~~~~~~lpV~~~DEr~ 121 (176)
+..+-+.....++..+.+.|..
T Consensus 403 v~~vl~~~~~~~~~~viVsEag 424 (780)
T COG2183 403 VADVLKELPKEKVLKVIVSEAG 424 (780)
T ss_pred HHHHHHhccCCCCcEEEEcccc
Confidence 5566543223578888888854
No 11
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=97.21 E-value=0.0047 Score=47.98 Aligned_cols=109 Identities=17% Similarity=0.167 Sum_probs=71.0
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHH
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLF 99 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~F 99 (176)
+..-|+|||+|+ .+|+|+-|-.|. ++.+...++.+ ..++.++|.++.-=.||-= |=+.- -..|+++
T Consensus 30 ~~~lIVGiDPG~-ttgiAildL~G~---~l~l~S~R~~~----~~evi~~I~~~G~PviVAt----DV~p~--P~~V~Ki 95 (138)
T PF04312_consen 30 RRYLIVGIDPGT-TTGIAILDLDGE---LLDLKSSRNMS----RSEVIEWISEYGKPVIVAT----DVSPP--PETVKKI 95 (138)
T ss_pred CCCEEEEECCCc-eeEEEEEecCCc---EEEEEeecCCC----HHHHHHHHHHcCCEEEEEe----cCCCC--cHHHHHH
Confidence 456799999998 589999998875 44455555443 4778888888865544443 33333 3444444
Q ss_pred HHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHH
Q 030509 100 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAV 150 (176)
Q Consensus 100 a~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~ 150 (176)
+..+ +-..+.=++.+|..+=.++..+.+.+- .....=|++||+
T Consensus 96 a~~f-------~A~ly~P~~dlsveeK~~l~~~~~~~~-~n~HeRDALAAA 138 (138)
T PF04312_consen 96 ARSF-------NAVLYTPERDLSVEEKQELAREYSERY-ENDHERDALAAA 138 (138)
T ss_pred HHHh-------CCcccCCCCcCCHHHHHHHHHhhCCCC-CCchHHhHhhcC
Confidence 4444 344555589999998888887766421 223345888885
No 12
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=97.08 E-value=0.0095 Score=46.77 Aligned_cols=96 Identities=14% Similarity=0.209 Sum_probs=45.7
Q ss_pred CCeEEEEecCCCe----EEEEEecCCCceeccceeeeC--CCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHH
Q 030509 21 RGRFLGLDVGDKY----VGLSISDPKNKIASPLSVLLR--KKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAV 94 (176)
Q Consensus 21 ~~~iLglD~G~kr----iGvAvsd~~~~~a~Pl~~i~~--~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~ 94 (176)
..++|||-+|..+ +-.|+-|..|.+.-=+..... .........+.|.+++.+++|+.|+|| | .+..+.
T Consensus 4 ~~rVla~~~g~g~~~~~~~~v~ld~~G~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~kP~vI~v~-----g-~~~~s~ 77 (150)
T PF14639_consen 4 GPRVLALSWGSGDGDDAVFCVVLDENGEVLDHLKLVYNERDRERKEEDMERLKKFIEKHKPDVIAVG-----G-NSRESR 77 (150)
T ss_dssp ---EEEEE-TT--TTS-EEEEEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--------SSTHHH
T ss_pred CCEEEEEEcCCCCCCCCEEEEEECCCCcEEEEEEEcCCccchHHHHHHHHHHHHHHHHcCCeEEEEc-----C-CChhHH
Confidence 3589999999766 556777888876553322111 111223446889999999999999997 4 233444
Q ss_pred HHHHHHHHHH-h---ccCCCCCcEEEecCccc
Q 030509 95 QVKLFIDDLS-A---TKKLEDMKYAYWNEGFT 122 (176)
Q Consensus 95 ~v~~Fa~~L~-~---~~~~~~lpV~~~DEr~T 122 (176)
+..++.+.+- + ....+.++|+++||...
T Consensus 78 ~l~~~v~~~v~~~~~~~~~~~i~V~~v~~~~A 109 (150)
T PF14639_consen 78 KLYDDVRDIVEELDEDEQMPPIPVVIVDDEVA 109 (150)
T ss_dssp HHHHHHHHHHHHTTB-TTS-B--EEE---TTH
T ss_pred HHHHHHHHHHHHhhhcccCCCceEEEECcHHH
Confidence 4433333332 2 11235799999999764
No 13
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=96.81 E-value=0.0021 Score=51.10 Aligned_cols=99 Identities=15% Similarity=0.223 Sum_probs=64.3
Q ss_pred EEEecCCCeEEEEEecCCCceeccc--eeeeCCCCC-----hhhHHHHHHHHHHhcCCCEEEEeccCC--CCCCchHHHH
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPL--SVLLRKKNT-----IDLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQ 95 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl--~~i~~~~~~-----~~~~~~~L~~li~e~~~~~iVVGlPl~--dG~~s~~~~~ 95 (176)
||||+|+.+||.++-+..+.-.+++ .+|...+.. ...+.+.|.+++++|+|+.+.|=-.+- |-+..-...+
T Consensus 1 lGIDPGl~~~G~gvI~~~~~~l~~v~~G~I~t~~~~~l~~RL~~l~~~l~~vl~~~~P~~~AIE~~F~~kN~~s~lklgQ 80 (160)
T COG0817 1 LGIDPGLRRTGYGVIEVEGRQLSYLASGVIRTSSDAPLAERLKQLYDGLSEVLDEYQPDEVAIEQVFVNKNADSALKLGQ 80 (160)
T ss_pred CCcCCCccccceEEEEccCCeEEEEeeeEEecCCCccHHHHHHHHHHHHHHHHHHhCCCeeehhHHHHhcChHHHHHHHH
Confidence 6899999999999999887765554 466554221 123467888999999999999998766 3333333444
Q ss_pred HHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 96 VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 96 v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
+|-.+-....+ .++||.. ||..+.+...
T Consensus 81 ARGv~~la~~~---~~l~v~e----Y~p~~VKkav 108 (160)
T COG0817 81 ARGVALLAAAR---RGLPVFE----YTPNQVKKAV 108 (160)
T ss_pred HHHHHHHHHHH---cCCChhh----ccHHHHHHHh
Confidence 44444333221 2788764 4555555444
No 14
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=96.79 E-value=0.013 Score=55.20 Aligned_cols=109 Identities=15% Similarity=0.177 Sum_probs=77.9
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 101 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~ 101 (176)
.-|.|||+|. .+|+|+-|-+|.+. .+..+++.+ ..++.++|.+|.-=.||-= |=++-+ .|++
T Consensus 244 ~lIVGIDPGi-TtgiAvldldGevl---~~~S~r~~~----~~eVve~I~~lG~PvvVAt----DVtp~P------~~V~ 305 (652)
T COG2433 244 SLIVGIDPGI-TTGIAVLDLDGEVL---DLESRRGID----RSEVVEFISELGKPVVVAT----DVTPAP------ETVK 305 (652)
T ss_pred ceEEEeCCCc-eeeEEEEecCCcEE---eeeccccCC----HHHHHHHHHHcCCceEEEc----cCCCCh------HHHH
Confidence 3689999998 68999999988643 344455443 4788999999976656555 555555 4667
Q ss_pred HHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHH
Q 030509 102 DLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGI 152 (176)
Q Consensus 102 ~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iI 152 (176)
+|+.. | +-+.+.=|+.+|+.+=+..++..+++-.. ...=|++||++-
T Consensus 306 KiAas--f-~A~ly~P~~dLsveEK~~~~r~~~~~~~d-dH~RDALAAA~k 352 (652)
T COG2433 306 KIAAS--F-NAVLYTPDRDLSVEEKQEALRTLKISVSD-DHERDALAAAYK 352 (652)
T ss_pred HHHHH--c-CCcccCCcccCCHHHHHHHHhhcCCCCCC-chHHHHHHHHHH
Confidence 77763 5 66666779999999998877766665432 234599999864
No 15
>PRK05082 N-acetylmannosamine kinase; Provisional
Probab=95.45 E-value=0.098 Score=44.12 Aligned_cols=102 Identities=12% Similarity=0.140 Sum_probs=67.0
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhc--CCCEEEEeccCC-C-CCC---ch---
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEF--NLEGFIVGYPFN-R-QQN---AA--- 91 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~--~~~~iVVGlPl~-d-G~~---s~--- 91 (176)
.++|+|+|..++-+++.|..+.+-.. ..++... .+++.+.+.|.+++++. ++.+|.||.|=. | +.. ++
T Consensus 2 ~~lgvdig~~~i~~~l~dl~g~i~~~-~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~igi~~pG~vd~~~~~~~~~~~~ 80 (291)
T PRK05082 2 TTLAIDIGGTKIAAALVGEDGQIRQR-RQIPTPASQTPEALRQALSALVSPLQAQADRVAVASTGIINDGILTALNPHNL 80 (291)
T ss_pred cEEEEEECCCEEEEEEEcCCCcEEEE-EEecCCCCCCHHHHHHHHHHHHHHhhhcCcEEEEeCcccccCCeeEEecCCCC
Confidence 58999999999999999987655432 2333321 23444667788877764 678999999844 3 211 10
Q ss_pred -HHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHH
Q 030509 92 -DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELL 129 (176)
Q Consensus 92 -~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~ 129 (176)
..+. ..+.+.|++. + ++||++.++--+..-|+..
T Consensus 81 ~~w~~-~~l~~~l~~~--~-~~pv~v~NDa~a~a~aE~~ 115 (291)
T PRK05082 81 GGLLH-FPLVQTLEQL--T-DLPTIALNDAQAAAWAEYQ 115 (291)
T ss_pred ccccC-CChHHHHHHH--h-CCCEEEECcHHHHHHHHHH
Confidence 1111 2466677763 5 8999999888777777654
No 16
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=95.01 E-value=0.12 Score=43.95 Aligned_cols=109 Identities=14% Similarity=0.149 Sum_probs=67.6
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCC-----hhhHHHHHHHHHHhc----CCCEEEEeccCC-CCC
Q 030509 19 SKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNT-----IDLMAEDFRSLISEF----NLEGFIVGYPFN-RQQ 88 (176)
Q Consensus 19 ~~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~-----~~~~~~~L~~li~e~----~~~~iVVGlPl~-dG~ 88 (176)
+.++.++|||+|..+|=+|+.|..+.+-.- ..++....+ .+.+.+.+.+++.++ .+.+|.++.|.. +..
T Consensus 3 ~~~~~~lgidIggt~i~~~l~d~~g~~l~~-~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~iGIgi~~pg~~~~~ 81 (314)
T COG1940 3 PEAMTVLGIDIGGTKIKVALVDLDGEILLR-ERIPTPTPDPEEAILEAILALVAELLKQAQGRVAIIGIGIPGPGDVDNG 81 (314)
T ss_pred ccCcEEEEEEecCCEEEEEEECCCCcEEEE-EEEecCCCCchhHHHHHHHHHHHHHHHhcCCcCceEEEEeccceeccCC
Confidence 456889999999999999999998765321 222222111 123344455555543 466666776766 432
Q ss_pred C----chHHHH--HHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 89 N----AADAVQ--VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 89 ~----s~~~~~--v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
. .+.... --.|++.|++. + ++||...++--.-.-|+..+-
T Consensus 82 ~~~~~~~~~~~~~~~~l~~~L~~~--~-~~Pv~veNDan~aalaE~~~g 127 (314)
T COG1940 82 TVIVPAPNLGWWNGVDLAEELEAR--L-GLPVFVENDANAAALAEAWFG 127 (314)
T ss_pred cEEeecCCCCccccccHHHHHHHH--H-CCCEEEecHHHHHHHHHHHhC
Confidence 1 111111 12478889874 5 899999998888877777654
No 17
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=94.96 E-value=0.083 Score=45.59 Aligned_cols=102 Identities=19% Similarity=0.200 Sum_probs=61.8
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceeccceeeeC-CCCChhhHHHHHHHHHHhcCCCEE--EEeccCCCCCCchHHHHHH
Q 030509 21 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLR-KKNTIDLMAEDFRSLISEFNLEGF--IVGYPFNRQQNAADAVQVK 97 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~-~~~~~~~~~~~L~~li~e~~~~~i--VVGlPl~dG~~s~~~~~v~ 97 (176)
.+++||||+|...+-+|.+|..... .-+--+|. ++ .+.+-+.|++++..++++.+ |+---|-| -....++-|+
T Consensus 2 ~~kilGiDIGGAntk~a~~DG~~~~-~d~~YlPMWk~--k~rL~~~Lkei~~k~~~~~vgvvMTaELaD-~f~tk~eGVe 77 (330)
T COG1548 2 KMKILGIDIGGANTKIASSDGDNYK-IDHIYLPMWKK--KDRLEETLKEIVHKDNVDYVGVVMTAELAD-AFKTKAEGVE 77 (330)
T ss_pred CceEEEeeccCccchhhhccCCeee-eeEEEeccccc--hhHHHHHHHHHhccCCcceeEEEeeHHHHH-HhhhHHhHHH
Confidence 4789999999999999999976522 11111221 11 13445778888877777743 33211112 2333455666
Q ss_pred HHHHHHHhccCCCCCcEEEecCc--ccHHHHHHH
Q 030509 98 LFIDDLSATKKLEDMKYAYWNEG--FTSKGVELL 129 (176)
Q Consensus 98 ~Fa~~L~~~~~~~~lpV~~~DEr--~TT~~A~~~ 129 (176)
..++...+. | +.||+++|=. +-|.+|.+.
T Consensus 78 ~Ii~~v~~A--f-~~pv~~v~~~G~~~ssEa~~~ 108 (330)
T COG1548 78 DIIDTVEKA--F-NCPVYVVDVNGNFLSSEALKN 108 (330)
T ss_pred HHHHHHHHh--c-CCceEEEeccCcCcChhHhcC
Confidence 777778763 6 8899988843 333366553
No 18
>PRK09557 fructokinase; Reviewed
Probab=94.85 E-value=0.15 Score=43.37 Aligned_cols=102 Identities=17% Similarity=0.087 Sum_probs=64.0
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc-----CCCEEEEeccCC----CCCCc----
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFN----RQQNA---- 90 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~~~~iVVGlPl~----dG~~s---- 90 (176)
++|+|+|..++-+++.|..+.+-.- ..++....+.+.+.+.|.+++++. .+.+|.||.|=. +|...
T Consensus 2 ~lgidig~t~~~~~l~d~~g~i~~~-~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgi~~pG~vd~~~g~i~~~~~ 80 (301)
T PRK09557 2 RIGIDLGGTKIEVIALDDAGEELFR-KRLPTPRDDYQQTIEAIATLVDMAEQATGQRGTVGVGIPGSISPYTGLVKNANS 80 (301)
T ss_pred EEEEEECCCcEEEEEECCCCCEEEE-EEecCCCCCHHHHHHHHHHHHHHHHhhcCCceEEEecCcccCcCCCCeEEecCC
Confidence 7999999999999999977654322 333333223345567777766654 357799999732 23211
Q ss_pred hHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 91 ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 91 ~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
.+. .--.+.+.|++. + ++||++.+.--...-|+.++
T Consensus 81 ~~~-~~~~l~~~l~~~--~-~~pv~~~NDa~aaA~aE~~~ 116 (301)
T PRK09557 81 TWL-NGQPLDKDLSAR--L-NREVRLANDANCLAVSEAVD 116 (301)
T ss_pred ccc-cCCCHHHHHHHH--H-CCCEEEccchhHHHHHHHHh
Confidence 110 112355667663 5 78999888877777776554
No 19
>PF04848 Pox_A22: Poxvirus A22 protein; InterPro: IPR006932 This family, representing the Poxvirus A22 protein, is a Holliday junction resolvase, it specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products. ; GO: 0000287 magnesium ion binding, 0000400 four-way junction DNA binding, 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination
Probab=93.58 E-value=2.2 Score=33.34 Aligned_cols=119 Identities=13% Similarity=0.138 Sum_probs=65.5
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeee--CCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLL--RKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLF 99 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~--~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~F 99 (176)
|.+++||+|.+..|..+-+..+.. +..+. ..+.+.+....-+..+++ ++++.|+|=- ....++ ..++..|
T Consensus 1 mii~sIDiGikNlA~~iie~~~~~---i~~~~i~~~~~~~~~~~~~~~dl~~-~~~d~VlIEr---Q~~r~~-~~~i~~f 72 (143)
T PF04848_consen 1 MIILSIDIGIKNLAYCIIEFEGNK---IRVIDISKVDWSRDWEYRILKDLLK-YEADTVLIER---QPPRNP-NVKIVHF 72 (143)
T ss_pred CeEEEEecCCCceeEEEEEcCCCe---EEEEEeccCCcccchHHHHHHHHhh-ccCCEEEEec---CCCCCc-chhHHHH
Confidence 468999999999999999975533 22222 111122222233444444 8899999873 223333 3345567
Q ss_pred HHHHHhccCCCCCcEEEecCc-----------ccHHHHHHHhccCCCCCCCCC-CCCcHHHHHH
Q 030509 100 IDDLSATKKLEDMKYAYWNEG-----------FTSKGVELLLNPLDLHPVEYK-TILDKFAAVG 151 (176)
Q Consensus 100 a~~L~~~~~~~~lpV~~~DEr-----------~TT~~A~~~l~~~g~~~~~~k-~~iD~~AA~i 151 (176)
.+..-.. ++..|..+|=. .|-..++..+.+.+...--.+ +.+|++|=++
T Consensus 73 I~~~f~~---~~~kv~~v~p~~~~~~Y~~RKk~SVe~~~~~~~~~~~~~~i~~~kK~DDlADa~ 133 (143)
T PF04848_consen 73 IHGYFYI---KNTKVICVSPKMKGWSYRERKKRSVEVFKNWIKEFGIDDFIPKSKKKDDLADAF 133 (143)
T ss_pred HHHHhcc---CCceEEEECcccccCCHHHHHHHHHHHHHHHHHhCCchhhchhhccchHHHHHH
Confidence 6655431 36678888754 233444455554443211111 3456666555
No 20
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional
Probab=93.52 E-value=0.39 Score=40.69 Aligned_cols=102 Identities=20% Similarity=0.180 Sum_probs=63.8
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcC-----CCEEEEeccCC-C---CCCch---
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN-----LEGFIVGYPFN-R---QQNAA--- 91 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~-----~~~iVVGlPl~-d---G~~s~--- 91 (176)
++|||+|..+|-+++.|..+.+..- ..++....+.+.+++.|.+++++.. +.+|-||.|=. | |....
T Consensus 2 ~lgidig~t~i~~~l~d~~g~i~~~-~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~igia~pG~vd~~~g~~~~~~~ 80 (303)
T PRK13310 2 YYGFDIGGTKIELGVFNEKLELQWE-ERVPTPRDSYDAFLDAVCELVAEADQRFGCKGSVGIGIPGMPETEDGTLYAANV 80 (303)
T ss_pred eEEEEeCCCcEEEEEECCCCcEEEE-EEecCCCcCHHHHHHHHHHHHHHHHhhcCCcceEEEeCCCcccCCCCEEeccCc
Confidence 6999999999999999977644432 2333322334556677777775532 34788998844 3 32111
Q ss_pred -HHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 92 -DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 92 -~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
.... -.+.+.|++. + ++||++.+.--.-.-|+.++
T Consensus 81 ~~w~~-~~l~~~l~~~--~-~~pV~ieNDa~aaalaE~~~ 116 (303)
T PRK13310 81 PAASG-KPLRADLSAR--L-GRDVRLDNDANCFALSEAWD 116 (303)
T ss_pred ccccC-CcHHHHHHHH--H-CCCeEEeccHhHHHHHHhhh
Confidence 0111 2466778763 5 89999988877666665443
No 21
>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown.
Probab=93.04 E-value=1 Score=39.95 Aligned_cols=114 Identities=13% Similarity=0.181 Sum_probs=70.4
Q ss_pred EEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc-CCCEEEE----eccCC-CCCCch--------
Q 030509 26 GLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIV----GYPFN-RQQNAA-------- 91 (176)
Q Consensus 26 glD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~~~~iVV----GlPl~-dG~~s~-------- 91 (176)
|+|+||+-+-+++-|..+.+.. ...+++.....+ -..|.+.++++ +++.|+. |+|+. -...++
T Consensus 1 GIDpGT~s~dv~~~dd~g~v~~-~~~ipt~~v~~~--p~~iv~~l~~~~~~dlIa~psGyG~pl~~~~ei~d~e~~l~tl 77 (343)
T PF07318_consen 1 GIDPGTKSFDVCGLDDDGKVIF-YFSIPTEEVAKN--PSIIVEELEEFGDIDLIAGPSGYGLPLKRIREITDREIFLLTL 77 (343)
T ss_pred CCCCCCCcEEEEEEccCCcEEE-EeeccHHHhhhC--HHHHHHHHHhccCCCEEEeCCcCCcccccccccchhhhhceEe
Confidence 6899999999999998666554 244544332222 24577777887 9999886 67876 222111
Q ss_pred ----HHHH----HHHHHHHHHhccCCCCCcEEEec--CcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHH
Q 030509 92 ----DAVQ----VKLFIDDLSATKKLEDMKYAYWN--EGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGI 152 (176)
Q Consensus 92 ----~~~~----v~~Fa~~L~~~~~~~~lpV~~~D--Er~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iI 152 (176)
.... .++|.+.|++. ++|++++- -.+.|+-+++.+.. ..-+.-|.+|-+.+
T Consensus 78 ~~~~~~g~~~~Glr~~~~~l~~~----~l~~~~iPgVi~LptVP~~RK~N~------IDmGTaDKva~a~l 138 (343)
T PF07318_consen 78 IEESEVGRRIGGLRKLVRELAES----NLPAYFIPGVIHLPTVPAWRKINR------IDMGTADKVASAAL 138 (343)
T ss_pred ecccccccccccHHHHHHHHHhC----CCCEEEeCceeccCCCchHhhhcc------cccCcHhHHHHHHH
Confidence 1111 56677777652 67877766 47778877665431 11234467766554
No 22
>PRK13311 N-acetyl-D-glucosamine kinase; Provisional
Probab=92.92 E-value=0.73 Score=38.31 Aligned_cols=102 Identities=16% Similarity=0.114 Sum_probs=65.6
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcC-----CCEEEEeccCC---C-CCCc----
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN-----LEGFIVGYPFN---R-QQNA---- 90 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~-----~~~iVVGlPl~---d-G~~s---- 90 (176)
++|+|+|..++-+++.|..+.+-. ...++....+.+.+++.+.+++++.. +.+|-||.|=- + |...
T Consensus 2 ~lgidiggt~i~~~l~d~~g~i~~-~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgv~~pG~vd~~~g~i~~~~~ 80 (256)
T PRK13311 2 YYGFDMGGTKIELGVFDENLQRIW-HKRVPTPREDYPQLLQILRDLTEEADTYCGVQGSVGIGIPGLPNADDGTVFTANV 80 (256)
T ss_pred EEEEEECCCcEEEEEECCCCCEEE-EEEecCCCcCHHHHHHHHHHHHHHHHhhcCCCceEEEEecCcEECCCCEEEccCC
Confidence 699999999999999997764332 13333333334456777777776542 34788888843 2 3211
Q ss_pred hHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 91 ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 91 ~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
+.... ..+++.|+++ + ++||.+-++--+...|+...
T Consensus 81 ~~w~~-~~l~~~l~~~--~-~~pV~leNDanaaAlaE~~~ 116 (256)
T PRK13311 81 PSAMG-QPLQADLSRL--I-QREVRIDNDANCFALSEAWD 116 (256)
T ss_pred CcccC-CChHHHHHHH--H-CCCEEEEchhhHHHHHHHHh
Confidence 11111 3677778763 4 78999988887777776654
No 23
>PRK13321 pantothenate kinase; Reviewed
Probab=92.22 E-value=2.1 Score=35.86 Aligned_cols=56 Identities=23% Similarity=0.301 Sum_probs=39.3
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhc-----CCCEEEEe
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEF-----NLEGFIVG 81 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~-----~~~~iVVG 81 (176)
+|+||+|..+|=+|+-|......+ ..++... ...+.+...+.++++++ +++.++|+
T Consensus 2 iL~IDIGnT~ik~gl~~~~~i~~~--~~~~T~~~~~~~~~~~~l~~l~~~~~~~~~~i~~i~vs 63 (256)
T PRK13321 2 LLLIDVGNTNIKLGVFDGDRLLRS--FRLPTDKSRTSDELGILLLSLFRHAGLDPEDIRAVVIS 63 (256)
T ss_pred EEEEEECCCeEEEEEEECCEEEEE--EEEecCCCCCHHHHHHHHHHHHHHcCCChhhCCeEEEE
Confidence 799999999999999985432222 2333322 22345678888888876 48999999
No 24
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase). This alignment models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution.
Probab=91.39 E-value=0.88 Score=38.62 Aligned_cols=100 Identities=17% Similarity=0.222 Sum_probs=61.2
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh----c-----CCCEEEEeccCC-CCCCc----
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE----F-----NLEGFIVGYPFN-RQQNA---- 90 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e----~-----~~~~iVVGlPl~-dG~~s---- 90 (176)
+|+|+|..++-+++.|..+.+-.- ...+.. .+.+.+++.|.+++++ . ++.+|.||.|=. |...+
T Consensus 1 lgidig~t~~~~~l~d~~g~i~~~-~~~~~~-~~~~~~~~~l~~~i~~~~~~~~~~~~~i~gIgva~pG~vd~~~g~~~~ 78 (318)
T TIGR00744 1 IGVDIGGTTIKLGVVDEEGNILSK-WKVPTD-TTPETIVDAIASAVDSFIQHIAKVGHEIVAIGIGAPGPVNRQRGTVYF 78 (318)
T ss_pred CEEEeCCCEEEEEEECCCCCEEEE-EEeCCC-CCHHHHHHHHHHHHHHHHHhcCCCccceEEEEEeccccccCCCCEEEe
Confidence 589999999999999977644321 233322 2233445555555433 2 578899999843 32111
Q ss_pred ---hHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 91 ---ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 91 ---~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
..... ..+.+.|++. + ++||++.+.--+..-|+.++
T Consensus 79 ~~~~~w~~-~~l~~~l~~~--~-~~pv~v~NDa~~~alaE~~~ 117 (318)
T TIGR00744 79 AVNLDWKQ-EPLKEKVEAR--V-GLPVVVENDANAAALGEYKK 117 (318)
T ss_pred cCCCCCCC-CCHHHHHHHH--H-CCCEEEechHHHHHHHHHHh
Confidence 00111 1366677763 4 79999998888777776654
No 25
>PF00480 ROK: ROK family; InterPro: IPR000600 A family of bacterial proteins has been described which groups transcriptional repressors, sugar kinases and yet uncharacterised open reading frames []. This family, known as ROK (Repressor, ORF, Kinase) includes the xylose operon repressor, xylR, from Bacillus subtilis, Lactobacillus pentosus and Staphylococcus xylosus; N-acetylglucosamine repressor, nagC, from Escherichia coli; glucokinase 2.7.1.2 from EC from Streptomyces coelicolor; fructokinase 2.7.1.4 from EC from Pediococcus pentosaceus, Streptococcus mutans and Zymomonas mobilis; allokinase 2.7.1.55 from EC and mlc from E. coli; and E. coli hypothetical proteins yajF and yhcI and the corresponding Haemophilus influenzae proteins. The repressor proteins (xylR and nagC) from this family possess an N-terminal region not present in the sugar kinases and which contains an helix-turn-helix DNA-binding motif.; PDB: 2GUP_A 3LM2_B 3EO3_A 2YHY_A 2YHW_A 2YI1_A 3MCP_A 1Z05_A 3HTV_A 3OHR_A ....
Probab=89.95 E-value=0.46 Score=36.80 Aligned_cols=100 Identities=12% Similarity=0.208 Sum_probs=64.1
Q ss_pred EEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh----cCCCEEEEeccCC-C-CC------CchHH
Q 030509 26 GLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE----FNLEGFIVGYPFN-R-QQ------NAADA 93 (176)
Q Consensus 26 glD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e----~~~~~iVVGlPl~-d-G~------~s~~~ 93 (176)
|||+|..++=+++.|..+.+..- ..++.. .+.+.+++.|.+++++ +...+|-|+.|=. + ++ .....
T Consensus 1 gidig~~~i~~~l~d~~g~ii~~-~~~~~~-~~~~~~~~~l~~~i~~~~~~~~~~gIgi~~pG~v~~~~g~i~~~~~~~~ 78 (179)
T PF00480_consen 1 GIDIGGTSIRIALVDLDGEIIYS-ESIPTP-TSPEELLDALAELIERLLADYGRSGIGISVPGIVDSEKGRIISSPNPGW 78 (179)
T ss_dssp EEEEESSEEEEEEEETTSCEEEE-EEEEHH-SSHHHHHHHHHHHHHHHHHHHTCEEEEEEESSEEETTTTEEEECSSGTG
T ss_pred CEEECCCEEEEEEECCCCCEEEE-EEEECC-CCHHHHHHHHHHHHHHHHhhcccccEEEeccccCcCCCCeEEecCCCCc
Confidence 79999999999999988766542 445443 3334445555555544 4434899998854 2 22 11222
Q ss_pred HHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 94 VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 94 ~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
.. ..+.+.|++. | ++||.+.+.--....|+..+.
T Consensus 79 ~~-~~l~~~l~~~--~-~~pv~i~Nd~~~~a~ae~~~~ 112 (179)
T PF00480_consen 79 EN-IPLKEELEER--F-GVPVIIENDANAAALAEYWFG 112 (179)
T ss_dssp TT-CEHHHHHHHH--H-TSEEEEEEHHHHHHHHHHHHS
T ss_pred cc-CCHHHHhhcc--c-ceEEEEecCCCcceeehhhcC
Confidence 22 3567778764 5 899999988777667766543
No 26
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=89.91 E-value=1.4 Score=36.43 Aligned_cols=88 Identities=14% Similarity=0.126 Sum_probs=56.9
Q ss_pred CeEEEEecCCCeEEEEEecC--CCceeccceeeeCCCCChhhHHHHHHHHHHhc-----CCCEEEEeccCCCCCCchHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDP--KNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFNRQQNAADAV 94 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~--~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~~~~iVVGlPl~dG~~s~~~~ 94 (176)
|++|+||--++.+++|+-+. ...++.=.....+ ...+.+...+.+++.+- +++.|+||. --|+.+. .+
T Consensus 1 m~iLaiDTs~~~~s~ai~~~~~~~vl~~~~~~~~r--~hse~l~~~i~~ll~~~~~~~~dld~iav~~--GPGSFTG-lR 75 (220)
T COG1214 1 MKILAIDTSTSALSVALYLADDGKVLAEHTEKLKR--NHAERLMPMIDELLKEAGLSLQDLDAIAVAK--GPGSFTG-LR 75 (220)
T ss_pred CcEEEEEcChhhhhhheeecCCCcEEEEEEEeccc--cHHHHHHHHHHHHHHHcCCCHHHCCEEEEcc--CCCcccc-hh
Confidence 57999999999999998776 5554553333322 22234567778887776 688899992 0344443 22
Q ss_pred HHHHHHHHHHhccCCCCCcEEEe
Q 030509 95 QVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 95 ~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
---.||+-|.-. .++|++=+
T Consensus 76 IG~~~AkgLA~~---l~iplvgv 95 (220)
T COG1214 76 IGVAFAKGLALA---LNIPLVGV 95 (220)
T ss_pred hHHHHHHHHHHH---cCCCEEEe
Confidence 335788888753 27787754
No 27
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam model pfam01385, and other proteins.
Probab=89.70 E-value=0.99 Score=30.97 Aligned_cols=60 Identities=12% Similarity=0.092 Sum_probs=34.6
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCC---ch-HHHHH-----HHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQN---AA-DAVQV-----KLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~---s~-~~~~v-----~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
...|.+...+ .++.||||..-+ .+.. +. ..+.+ ..|.+.|+......|++|+.+||.+||
T Consensus 13 a~~iv~~~~~-~~~~Ivie~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~yka~~~Gi~v~~v~~~yTS 82 (82)
T TIGR01766 13 VKQIVEYAKE-NNGTIVLEDLKNIKEMVDKKSKYLRRKLHQWSFRKLISKIKYKAEEYGIEVIEVNPAYTS 82 (82)
T ss_pred HHHHHHHHHH-cCCEEEECCccchhhhcchhhHHHHHHHHhhhHHHHHHHHHHHHHHcCCeEEEeCccccc
Confidence 3555555555 679999997653 2221 11 11111 234444443211249999999999997
No 28
>PRK12408 glucokinase; Provisional
Probab=89.21 E-value=1.1 Score=39.04 Aligned_cols=96 Identities=15% Similarity=0.123 Sum_probs=56.3
Q ss_pred cCCCCeEEEEecCCCeEEEEEecCCCcee-----ccceeeeCCCCChhhHHHHHHHHHHh-cCCCEEEEeccC--C-CCC
Q 030509 18 VSKRGRFLGLDVGDKYVGLSISDPKNKIA-----SPLSVLLRKKNTIDLMAEDFRSLISE-FNLEGFIVGYPF--N-RQQ 88 (176)
Q Consensus 18 ~~~~~~iLglD~G~kriGvAvsd~~~~~a-----~Pl~~i~~~~~~~~~~~~~L~~li~e-~~~~~iVVGlPl--~-dG~ 88 (176)
++++-++|++|+|.-+|=+|+.|..+.++ ......+... .+.+.+.+.+++++ .++.++.||.|= . +|.
T Consensus 12 ~~~~~~~L~~DIGGT~i~~al~d~~g~~~~~~~~~~~~~~~t~~--~~~~~~~i~~~~~~~~~~~~igIg~pG~~~~~g~ 89 (336)
T PRK12408 12 VPRPESFVAADVGGTHVRVALVCASPDAAKPVELLDYRTYRCAD--YPSLAAILADFLAECAPVRRGVIASAGYALDDGR 89 (336)
T ss_pred CcccccEEEEEcChhhhheeEEeccCCccccccccceeEecCCC--ccCHHHHHHHHHhcCCCcCEEEEEecCCceECCE
Confidence 45666799999999999999998655421 1112332221 12334556666653 458899999974 3 554
Q ss_pred CchHHH-HHHHHHHHHHhccCCCCCc-EEEecC
Q 030509 89 NAADAV-QVKLFIDDLSATKKLEDMK-YAYWNE 119 (176)
Q Consensus 89 ~s~~~~-~v~~Fa~~L~~~~~~~~lp-V~~~DE 119 (176)
.. .+. .-..+.+.|++. + ++| |++.+.
T Consensus 90 v~-~~nl~w~~~~~~l~~~--~-~~~~V~l~ND 118 (336)
T PRK12408 90 VI-TANLPWTLSPEQIRAQ--L-GLQAVHLVND 118 (336)
T ss_pred EE-ecCCCCccCHHHHHHH--c-CCCeEEEeec
Confidence 32 100 011245677763 4 775 877653
No 29
>PRK00292 glk glucokinase; Provisional
Probab=88.65 E-value=2.1 Score=36.58 Aligned_cols=94 Identities=10% Similarity=0.047 Sum_probs=56.5
Q ss_pred eEEEEecCCCeEEEEEecC-CCc-eeccceeeeCCCCChhhHHHHHHHHHHh---cCCCEEEEeccCC-CC-CC----ch
Q 030509 23 RFLGLDVGDKYVGLSISDP-KNK-IASPLSVLLRKKNTIDLMAEDFRSLISE---FNLEGFIVGYPFN-RQ-QN----AA 91 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~-~~~-~a~Pl~~i~~~~~~~~~~~~~L~~li~e---~~~~~iVVGlPl~-dG-~~----s~ 91 (176)
.+||+|+|..+|=+++.|. .+. +.+ ..++... .+.+.+.|.+++++ .++.+|.||.|=- |. +. ..
T Consensus 3 ~~lgiDIGgT~i~~~l~~~~~~~~~~~--~~~~~~~--~~~~~~~l~~~l~~~~~~~~~gigIg~pG~vd~~~i~~~n~~ 78 (316)
T PRK00292 3 PALVGDIGGTNARFALCDWANGEIEQI--KTYATAD--YPSLEDAIRAYLADEHGVQVRSACFAIAGPVDGDEVRMTNHH 78 (316)
T ss_pred eEEEEEcCccceEEEEEecCCCceeee--EEEecCC--CCCHHHHHHHHHHhccCCCCceEEEEEeCcccCCEEEecCCC
Confidence 5899999999999999983 443 322 3333322 12345677777765 3588999999854 32 21 11
Q ss_pred HHHHHHHHHHHHHhccCCCCCc-EEEecCcccHHHHH
Q 030509 92 DAVQVKLFIDDLSATKKLEDMK-YAYWNEGFTSKGVE 127 (176)
Q Consensus 92 ~~~~v~~Fa~~L~~~~~~~~lp-V~~~DEr~TT~~A~ 127 (176)
+. ...+.|++. + ++| |++.+.--.-.-|+
T Consensus 79 w~----~~~~~l~~~--~-~~p~v~l~ND~~aaalgE 108 (316)
T PRK00292 79 WA----FSIAAMKQE--L-GLDHLLLINDFTAQALAI 108 (316)
T ss_pred cc----cCHHHHHHH--h-CCCeEEEEecHHHHHccc
Confidence 11 124667663 4 786 88777654433333
No 30
>TIGR03725 bact_YeaZ universal bacterial protein YeaZ. This family describes a protein family, YeaZ, that appears to be universal in bacteria, but whose function is unknown. This family is related to the gcp (glycoprotease) protein family, also universal in bacteria and unknown in function. In Gram-positive lineages, members of these two related families often belong to the same operon, along with the ribosomal-protein-alanine acetyltransferase gene. Members of this family may occur as fusions with gcp or the ribosomal protein N-acetyltransferase rimI, and is frequently encoded next to rimI.
Probab=88.24 E-value=4 Score=32.97 Aligned_cols=87 Identities=14% Similarity=0.155 Sum_probs=56.3
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc-----CCCEEEEeccCCCCCCchHHHHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFNRQQNAADAVQVKL 98 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~~~~iVVGlPl~dG~~s~~~~~v~~ 98 (176)
+|+||--+..++||+.+....++.-. ........+.+...|.+++++. +++.|+||. --|+.+. .+-.-.
T Consensus 1 iLaidTs~~~~sval~~~~~~~~~~~--~~~~~~h~~~l~~~i~~~l~~~~~~~~~i~~iav~~--GPGSfTG-lRig~~ 75 (202)
T TIGR03725 1 ILAIDTSTEALSVALLDDGEILAERS--EEAGRNHSEILLPMIEELLAEAGLSLQDLDAIAVGV--GPGSFTG-LRIGLA 75 (202)
T ss_pred CEEEECCCcceEEEEEECCEEEEEEe--ehhhHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEec--CCChHHh-HHHHHH
Confidence 58999999999999998654444321 1111122234567777777765 688888881 0345544 445578
Q ss_pred HHHHHHhccCCCCCcEEEec
Q 030509 99 FIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 99 Fa~~L~~~~~~~~lpV~~~D 118 (176)
+|+-|... . ++|++-++
T Consensus 76 ~akgla~~--~-~~p~~~vs 92 (202)
T TIGR03725 76 TAKGLALA--L-GIPLVGVS 92 (202)
T ss_pred HHHHHHHH--h-CCCEEecC
Confidence 88888863 3 78887654
No 31
>PRK13318 pantothenate kinase; Reviewed
Probab=88.03 E-value=2.6 Score=35.28 Aligned_cols=57 Identities=18% Similarity=0.283 Sum_probs=38.0
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhcC-----CCEEEEec
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEFN-----LEGFIVGY 82 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~-----~~~iVVGl 82 (176)
+|+||+|-.+|=+|+.|. +.+... ..++... ...+.+.+.+.++++.++ +++|+||-
T Consensus 2 iL~IDIGnT~iK~al~d~-g~i~~~-~~~~t~~~~~~~~~~~~l~~l~~~~~~~~~~i~~I~iss 64 (258)
T PRK13318 2 LLAIDVGNTNTVFGLYEG-GKLVAH-WRISTDSRRTADEYGVWLKQLLGLSGLDPEDITGIIISS 64 (258)
T ss_pred EEEEEECCCcEEEEEEEC-CEEEEE-EEEeCCCCCCHHHHHHHHHHHHHHcCCCcccCceEEEEE
Confidence 799999999999999984 433321 2333221 122345677788877654 78999994
No 32
>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition. This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=87.97 E-value=2.5 Score=31.59 Aligned_cols=85 Identities=13% Similarity=0.088 Sum_probs=54.0
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDL 103 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L 103 (176)
++|||+|....=+++.++.+..... ..+..... . +.++.+.+.++. .++||+=- -|..+. .++..|
T Consensus 1 ~vGiDv~k~~~~v~v~~~~~~~~~~-~~~~~~~~---~-~~~l~~~l~~~~--~~~v~~E~-tg~y~~------~l~~~L 66 (144)
T PF01548_consen 1 FVGIDVSKDTHDVCVIDPNGEKLRR-FKFENDPA---G-LEKLLDWLASLG--PVLVVMEA-TGGYWR------PLADFL 66 (144)
T ss_pred eEEEEcccCeEEEEEEcCCCcEEEE-EEEecccc---c-hhHHhhhhcccc--cccccccc-ccccch------hhhhhe
Confidence 5899999999999999998843333 45544322 2 577788888775 56666311 243332 344456
Q ss_pred HhccCCCCCcEEEecCcccHHHH
Q 030509 104 SATKKLEDMKYAYWNEGFTSKGV 126 (176)
Q Consensus 104 ~~~~~~~~lpV~~~DEr~TT~~A 126 (176)
... +++|++++=+.....+
T Consensus 67 ~~~----g~~v~~vnp~~~~~~~ 85 (144)
T PF01548_consen 67 QDA----GIEVVVVNPLQVKRFR 85 (144)
T ss_pred ecc----cccccccccccccccc
Confidence 542 7899998766554433
No 33
>PF14239 RRXRR: RRXRR protein
Probab=86.46 E-value=0.65 Score=37.60 Aligned_cols=22 Identities=32% Similarity=0.517 Sum_probs=19.2
Q ss_pred CeEEEEecCCCeEEEEEecCCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPKN 43 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~ 43 (176)
.-.+|||+|++.+|+|+.+...
T Consensus 51 pi~lgiDpGsk~tGiav~~~~~ 72 (176)
T PF14239_consen 51 PIRLGIDPGSKTTGIAVVSEKK 72 (176)
T ss_pred CEEEEECCCCCeEEEEEEeCCE
Confidence 4579999999999999988763
No 34
>PRK09698 D-allose kinase; Provisional
Probab=85.11 E-value=4.9 Score=33.86 Aligned_cols=103 Identities=15% Similarity=0.255 Sum_probs=61.3
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCC-C---hhhHHHHHHHHHHhc--CCCEEEEeccCC-CCCC-----
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKN-T---IDLMAEDFRSLISEF--NLEGFIVGYPFN-RQQN----- 89 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~-~---~~~~~~~L~~li~e~--~~~~iVVGlPl~-dG~~----- 89 (176)
..++|+|+|..++-+++.|..+.+-.- ..++.... . .+.+.+.+.+++++. ++.+|-||.|=. |...
T Consensus 4 ~~~lgidig~t~i~~~l~d~~g~i~~~-~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~i~gigia~pG~vd~~~g~i~~ 82 (302)
T PRK09698 4 NVVLGIDMGGTHIRFCLVDAEGEILHC-EKKRTAEVIAPDLVSGLGEMIDEYLRRFNARCHGIVMGFPALVSKDRRTVIS 82 (302)
T ss_pred cEEEEEEcCCcEEEEEEEcCCCCEEEE-EEeCCccccchHHHHHHHHHHHHHHHHcCCCeeEEEEeCCcceeCCCCEEEe
Confidence 568999999999999999977644321 22322211 1 223345566666654 678999999843 3211
Q ss_pred chHH----HHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHH
Q 030509 90 AADA----VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 128 (176)
Q Consensus 90 s~~~----~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 128 (176)
++.. -.-..+.+.|++. + ++||++.+.--....|+.
T Consensus 83 ~~~~~~~~~~~~~l~~~l~~~--~-~~pv~v~NDa~aaa~~E~ 122 (302)
T PRK09698 83 TPNLPLTALDLYDLADKLENT--L-NCPVFFSRDVNLQLLWDV 122 (302)
T ss_pred cCCCCccccccCCHHHHHHHH--h-CCCEEEcchHhHHHHHHH
Confidence 1100 0112466777763 4 899998887655444443
No 35
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=84.87 E-value=2.6 Score=39.92 Aligned_cols=65 Identities=12% Similarity=0.194 Sum_probs=46.3
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc---CCCEEEEeccCC-CCC
Q 030509 21 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF---NLEGFIVGYPFN-RQQ 88 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~---~~~~iVVGlPl~-dG~ 88 (176)
.+++||+|+|.-+|=+|+.|..+.+.. ...++.... +.+.+.|.+++++. .+.++.||.|=- |+.
T Consensus 17 ~~~~L~iDIGGT~ir~al~~~~g~i~~-~~~~~t~~~--~~~~~~i~~~l~~~~~~~~~~igig~pGpVd~~ 85 (638)
T PRK14101 17 DGPRLLADVGGTNARFALETGPGEITQ-IRVYPGADY--PTLTDAIRKYLKDVKIGRVNHAAIAIANPVDGD 85 (638)
T ss_pred CCCEEEEEcCchhheeeeecCCCcccc-eeEEecCCC--CCHHHHHHHHHHhcCCCCcceEEEEEecCccCC
Confidence 367999999999999999987765533 245554332 34567777777665 488999999866 553
No 36
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=82.25 E-value=24 Score=29.71 Aligned_cols=94 Identities=15% Similarity=0.180 Sum_probs=52.9
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCC--------CChhhHHHHHHHHHH---hc---CCCEEEEeccC
Q 030509 19 SKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK--------NTIDLMAEDFRSLIS---EF---NLEGFIVGYPF 84 (176)
Q Consensus 19 ~~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~--------~~~~~~~~~L~~li~---e~---~~~~iVVGlPl 84 (176)
.....++|||+|+.+|=+.+.+.... ++.+..... .+.+.....|.++++ ++ ++..+++..|-
T Consensus 21 ~~~~~~~~iDiGSssi~~vv~~~~~~---~~~~~~~~~~~vr~G~i~di~~a~~~i~~~~~~ae~~~g~~i~~v~~~vp~ 97 (267)
T PRK15080 21 TESPLKVGVDLGTANIVLAVLDEDGQ---PVAGALEWADVVRDGIVVDFIGAVTIVRRLKATLEEKLGRELTHAATAIPP 97 (267)
T ss_pred CCCCEEEEEEccCceEEEEEEcCCCC---EEEEEeccccccCCCEEeeHHHHHHHHHHHHHHHHHHhCCCcCeEEEEeCC
Confidence 34678999999999999888765442 222222111 122223334444433 33 47889999997
Q ss_pred C-CCCCchHHHHHHHHHHHHHhccCCCCCcEE-EecCcccHHH
Q 030509 85 N-RQQNAADAVQVKLFIDDLSATKKLEDMKYA-YWNEGFTSKG 125 (176)
Q Consensus 85 ~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~-~~DEr~TT~~ 125 (176)
+ +-.. -+.+.+-++.. ++++. +++|.+....
T Consensus 98 ~~~~~~------~~~~~~~~~~a----Gl~~~~ii~e~~A~a~ 130 (267)
T PRK15080 98 GTSEGD------PRAIINVVESA----GLEVTHVLDEPTAAAA 130 (267)
T ss_pred CCCchh------HHHHHHHHHHc----CCceEEEechHHHHHH
Confidence 7 4211 12344444442 66766 7777764443
No 37
>PRK09472 ftsA cell division protein FtsA; Reviewed
Probab=77.18 E-value=13 Score=33.40 Aligned_cols=62 Identities=11% Similarity=0.234 Sum_probs=39.8
Q ss_pred CeEEEEecCCCeEEEEEec--CCC-ceeccceeeeCCC------CChhhHHHHHHHHHHh------cCCCEEEEecc
Q 030509 22 GRFLGLDVGDKYVGLSISD--PKN-KIASPLSVLLRKK------NTIDLMAEDFRSLISE------FNLEGFIVGYP 83 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd--~~~-~~a~Pl~~i~~~~------~~~~~~~~~L~~li~e------~~~~~iVVGlP 83 (176)
..+.|||+|+.+|=+.+++ +.+ .-.......+... .+.+.+.+.|++.+++ .++..+++|.|
T Consensus 8 ~~i~~lDIGsskv~~vv~~~~~~~~~~i~g~~~~~s~gi~~G~I~d~~~~~~aI~~av~~ae~~~g~~i~~v~v~i~ 84 (420)
T PRK09472 8 KLVVGLEIGTAKVAALVGEVLPDGMVNIIGVGSCPSRGMDKGGVNDLESVVKCVQRAIDQAELMADCQISSVYLALS 84 (420)
T ss_pred CEEEEEEcccceEEEEEEEEcCCCCEEEEEEEEccCCCccCCEEEcHHHHHHHHHHHHHHHHHHhCCcccEEEEEec
Confidence 4688999999999887776 222 1112222222211 1334556778888776 57999999987
No 38
>PRK09982 universal stress protein UspD; Provisional
Probab=75.70 E-value=12 Score=27.82 Aligned_cols=46 Identities=4% Similarity=0.008 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.|.+.++++++|.||+| .+ .+...+.. ..++++-+. ..+||..+
T Consensus 92 ~~~I~~~A~~~~aDLIVmG----~~-~~~~~~~~-~va~~V~~~---s~~pVLvv 137 (142)
T PRK09982 92 PETLLEIMQKEQCDLLVCG----HH-HSFINRLM-PAYRGMINK---MSADLLIV 137 (142)
T ss_pred HHHHHHHHHHcCCCEEEEe----CC-hhHHHHHH-HHHHHHHhc---CCCCEEEe
Confidence 5889999999999999999 55 34433333 366666653 37887654
No 39
>TIGR01865 cas_Csn1 CRISPR-associated protein, Csn1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.
Probab=72.69 E-value=3.3 Score=40.72 Aligned_cols=23 Identities=39% Similarity=0.622 Sum_probs=20.1
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~ 45 (176)
.+||||.|+.-||.||.|.+...
T Consensus 2 y~LGLDiGt~SvGWAVv~~d~~~ 24 (805)
T TIGR01865 2 YILGLDIGIASVGWAIVEDDYKV 24 (805)
T ss_pred ceeEEeecccceeEEEEeccccc
Confidence 58999999999999999977543
No 40
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=71.85 E-value=2.5 Score=28.16 Aligned_cols=45 Identities=20% Similarity=0.087 Sum_probs=26.4
Q ss_pred CCCcEEEecCcccHHHHHHH--hccCCCCCC-------CCCCCCcHHHHHHHHH
Q 030509 110 EDMKYAYWNEGFTSKGVELL--LNPLDLHPV-------EYKTILDKFAAVGILQ 154 (176)
Q Consensus 110 ~~lpV~~~DEr~TT~~A~~~--l~~~g~~~~-------~~k~~iD~~AA~iILq 154 (176)
.+++|+.+||.+||..--.= ......+.+ -..-.=|-.||.-|++
T Consensus 15 ~G~~v~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~naA~NI~~ 68 (69)
T PF07282_consen 15 YGIQVVEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDVNAARNILR 68 (69)
T ss_pred hCCEEEEECCCCCccCccCcccccccccccceEEcCCCCCEECcHHHHHHHHhc
Confidence 38999999999998854211 000000000 0123468899988885
No 41
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=71.65 E-value=12 Score=31.67 Aligned_cols=48 Identities=10% Similarity=0.293 Sum_probs=40.8
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.+++.+.+.+...|+|.|| ||.+-....+.++.++++++ +++||++.-
T Consensus 30 ~~ei~~~~~~~GTDaImIG-----GS~gvt~~~~~~~v~~ik~~---~~lPvilfP 77 (240)
T COG1646 30 ADEIAEAAAEAGTDAIMIG-----GSDGVTEENVDNVVEAIKER---TDLPVILFP 77 (240)
T ss_pred cHHHHHHHHHcCCCEEEEC-----CcccccHHHHHHHHHHHHhh---cCCCEEEec
Confidence 4778888888999999999 88888888899999999963 389998874
No 42
>PF03932 CutC: CutC family; InterPro: IPR005627 Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are between 200 and 300 amino acids in length and are found in both eukaryotes and bacteria.; GO: 0005507 copper ion binding, 0055070 copper ion homeostasis; PDB: 2BDQ_A 3IWP_I 1X8C_B 1X7I_A 1TWD_B.
Probab=71.13 E-value=11 Score=30.92 Aligned_cols=60 Identities=15% Similarity=0.268 Sum_probs=38.4
Q ss_pred HHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe---cCcccHHHHHHHhccCCCC
Q 030509 68 SLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW---NEGFTSKGVELLLNPLDLH 136 (176)
Q Consensus 68 ~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~---DEr~TT~~A~~~l~~~g~~ 136 (176)
+.+++..+++||+| .|+ ||+... ..++++.+.. .++|++|. |+-....+|-+.|.+.|++
T Consensus 79 ~~~~~~GadG~VfG-~L~~dg~iD~--~~~~~Li~~a------~~~~~tFHRAfD~~~d~~~al~~L~~lG~~ 142 (201)
T PF03932_consen 79 RMLRELGADGFVFG-ALTEDGEIDE--EALEELIEAA------GGMPVTFHRAFDEVPDPEEALEQLIELGFD 142 (201)
T ss_dssp HHHHHTT-SEEEE---BETTSSB-H--HHHHHHHHHH------TTSEEEE-GGGGGSSTHHHHHHHHHHHT-S
T ss_pred HHHHHcCCCeeEEE-eECCCCCcCH--HHHHHHHHhc------CCCeEEEeCcHHHhCCHHHHHHHHHhcCCC
Confidence 34566789999999 577 888764 2333443332 27899885 8888899999888876664
No 43
>smart00842 FtsA Cell division protein FtsA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains PUBMED:9352931.
Probab=69.41 E-value=23 Score=27.85 Aligned_cols=60 Identities=17% Similarity=0.300 Sum_probs=36.2
Q ss_pred EEEEecCCCeEEEEEecCC--C-ceeccceeeeCCC------CChhhHHHHHHHHHHhc------CCCEEEEecc
Q 030509 24 FLGLDVGDKYVGLSISDPK--N-KIASPLSVLLRKK------NTIDLMAEDFRSLISEF------NLEGFIVGYP 83 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~--~-~~a~Pl~~i~~~~------~~~~~~~~~L~~li~e~------~~~~iVVGlP 83 (176)
+.|||+|+.+|=+.++... + .-.-.....+... .+.+.+.+.|++.+++- +++.++++.|
T Consensus 1 ~~~lDIGs~~ik~vv~~~~~~~~~~i~g~~~~~s~gi~~G~I~d~~~~~~~I~~ai~~ae~~~~~~i~~V~v~i~ 75 (187)
T smart00842 1 IVGLDIGTSKIKALVAEVDEDGEINVIGVGEVPSRGIRKGVIVDIEAAARAIREAVEEAERMAGVKIDSVYVGIS 75 (187)
T ss_pred CEEEEeccceEEEEEEEEcCCCCEEEEEEEEecCCCccCcEEECHHHHHHHHHHHHHHHHHHhCCcccEEEEEEc
Confidence 4799999999998888532 2 1111122222211 12344566677777654 5789999987
No 44
>PF11104 PilM_2: Type IV pilus assembly protein PilM;; PDB: 2YCH_A.
Probab=68.76 E-value=19 Score=31.22 Aligned_cols=60 Identities=18% Similarity=0.333 Sum_probs=36.4
Q ss_pred EEecCCCeEEEEEecCCCc---------eeccceeeeCCC-CChhhHHHHHHHHHHhcCC--CEEEEeccCC
Q 030509 26 GLDVGDKYVGLSISDPKNK---------IASPLSVLLRKK-NTIDLMAEDFRSLISEFNL--EGFIVGYPFN 85 (176)
Q Consensus 26 glD~G~kriGvAvsd~~~~---------~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~~--~~iVVGlPl~ 85 (176)
|||+|+..|-++-....+. ...|-..+.... .+.+.+.+.|+++++++++ ..+++++|-+
T Consensus 1 GiDiG~~siK~v~l~~~~~~~~l~~~~~~~~p~~~i~~g~i~d~~~l~~~L~~~~~~~~~~~k~v~~aip~~ 72 (340)
T PF11104_consen 1 GIDIGSSSIKAVELSKKGNRFQLEAFASIPLPPGAISDGEIVDPEALAEALKELLKENKIKGKKVVLAIPGS 72 (340)
T ss_dssp EEEE-SSEEEEEEEETTTT--EEEEEEEEE--TTSEETTEES-HHHHHHHHHHHHHHHT----EEEEEE-GG
T ss_pred CeecCCCeEEEEEEEEcCCccEEEEEEEEECCCCCccCCCcCCHHHHHHHHHHHHHHcCCCCCeEEEEeCCC
Confidence 8999999999997665421 113333332221 2345667899999998866 6799999854
No 45
>PRK00047 glpK glycerol kinase; Provisional
Probab=68.62 E-value=15 Score=33.55 Aligned_cols=23 Identities=30% Similarity=0.309 Sum_probs=19.7
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~ 45 (176)
.+||||+|+..+=+++-|..+.+
T Consensus 6 ~~lgiD~GTts~Ka~l~d~~g~~ 28 (498)
T PRK00047 6 YILALDQGTTSSRAIIFDHDGNI 28 (498)
T ss_pred EEEEEecCCCceEEEEECCCCCE
Confidence 58999999999999999987543
No 46
>TIGR00749 glk glucokinase, proteobacterial type. This model represents glucokinase of E. coli and close homologs, mostly from other proteobacteria, presumed to have equivalent function. This glucokinase is more closely related to a number of uncharacterized paralogs than to the glucokinase glcK (fromerly yqgR) of Bacillus subtilis and its closest homologs, so the two sets are represented by separate models.
Probab=68.13 E-value=18 Score=31.03 Aligned_cols=61 Identities=11% Similarity=0.048 Sum_probs=38.9
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcC------CCEEEEeccCC-CC
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN------LEGFIVGYPFN-RQ 87 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~------~~~iVVGlPl~-dG 87 (176)
|++|+|.-+|=+|+.|..+.......+.+.. ..+.+.+.|.+++.+.+ +..+.||.|-- +|
T Consensus 1 l~~DIGGT~i~~glvd~~g~~l~~~~~~~~~--~~~~l~~~i~~~l~~~~~~~~~~~~~~~Igi~Gpv~~ 68 (316)
T TIGR00749 1 LVGDIGGTNARLALCEIAPGEISQAKTYSGL--DFPSLEAVVRVYLEEHKVELKDPIAKGCFAIACPITG 68 (316)
T ss_pred CeEecCcceeeEEEEecCCCceeeeEEEecC--CCCCHHHHHHHHHHhcccccCCCcCeEEEEEeCcccC
Confidence 5799999999999988754322223443222 22345677888877642 55677887755 44
No 47
>TIGR03723 bact_gcp putative glycoprotease GCP. This model represents bacterial members of a protein family that is widely distributed. In a few pathogenic species, the protein is exported in a way that may represent an exceptional secondary function. This model plus companion (archaeal) model TIGR03722 together span the prokaryotic member sequences of TIGR00329, a protein family that appears universal in life, and whose broad function is unknown. A member of TIGR03722 has been characterized as a DNA-binding protein with apurinic endopeptidase activity. In contrast, the rare characterized members of the present family show O-sialoglycoprotein endopeptidase (EC. 3.4.24.57) activity after export. These include glycoprotease (gcp) from Pasteurella haemolytica A1 and a cohemolysin from Riemerella anatipestifer (GB|AAG39646.1). The member from Staphylococcus aureus is essential and is related to cell wall dynamics and the modulation of autolysis, but members are also found in the Mycoplasmas
Probab=67.99 E-value=28 Score=30.13 Aligned_cols=88 Identities=11% Similarity=0.172 Sum_probs=52.4
Q ss_pred EEEEecCCCeEEEEEecCCC-ceecccee-----------eeC--CCCChhhHHHHHHHHHHh-----cCCCEEEEeccC
Q 030509 24 FLGLDVGDKYVGLSISDPKN-KIASPLSV-----------LLR--KKNTIDLMAEDFRSLISE-----FNLEGFIVGYPF 84 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~-~~a~Pl~~-----------i~~--~~~~~~~~~~~L~~li~e-----~~~~~iVVGlPl 84 (176)
+||||-=+..++||+.|... .++.-... .|. .....+.+...|.+++++ .+++.|.|+
T Consensus 1 iLaIdTs~~~~sval~~~~~~il~~~~~~~~~~~~~~gGi~p~~~~~~H~~~l~~~i~~~l~~~~~~~~~id~iav~--- 77 (314)
T TIGR03723 1 ILGIETSCDETAVAIVDDGKGLLSNIVASQIELHARYGGVVPELASRAHLEAIPPLIEEALAEAGLTLSDIDAIAVT--- 77 (314)
T ss_pred CEEEECcccceEEEEEECCceEEEEEEeehhhhccCcCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEe---
Confidence 68999999999999998654 33321100 000 001112334556666665 368999998
Q ss_pred CCCCCchH-HHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 85 NRQQNAAD-AVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 85 ~dG~~s~~-~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.|=-+-. .+-...+|+.|... + ++|++.++
T Consensus 78 -~GPGsftglrig~~~Ak~la~~--~-~~p~~~v~ 108 (314)
T TIGR03723 78 -AGPGLIGALLVGVSFAKALALA--L-NKPLIGVN 108 (314)
T ss_pred -cCCChHHhHHHHHHHHHHHHHH--h-CCCEEecc
Confidence 3322222 23346788888763 3 78988885
No 48
>PRK09604 UGMP family protein; Validated
Probab=67.67 E-value=55 Score=28.53 Aligned_cols=91 Identities=13% Similarity=0.145 Sum_probs=54.0
Q ss_pred CeEEEEecCCCeEEEEEecCC-Cceecc-cee----------eeCC--CCChhhHHHHHHHHHHhc-----CCCEEEEec
Q 030509 22 GRFLGLDVGDKYVGLSISDPK-NKIASP-LSV----------LLRK--KNTIDLMAEDFRSLISEF-----NLEGFIVGY 82 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~-~~~a~P-l~~----------i~~~--~~~~~~~~~~L~~li~e~-----~~~~iVVGl 82 (176)
|.+||||--...+++|+.|.. ..++.- ... +|.. ....+.+...+.+++++. +++.|+|+.
T Consensus 1 m~iLgIdTS~~~~sval~~~~~~il~~~~~~~~~~~~~~~Gi~P~~a~~~H~~~l~~~i~~~L~~~~~~~~did~iavt~ 80 (332)
T PRK09604 1 MLILGIETSCDETSVAVVDDGRGLLSNVVASQIDLHARYGGVVPELASRAHVENIVPLIEEALKEAGLTLEDIDAIAVTA 80 (332)
T ss_pred CeEEEEEccccceEEEEEECCCcEEEEEEecchhcccccCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEec
Confidence 579999999999999999865 333321 010 1100 000112234466666654 579999994
Q ss_pred -cCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 83 -PFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 83 -Pl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
| |+.+. -+....+|+.|... + ++|++.++.
T Consensus 81 GP---G~~tg-lrvg~~~Ak~La~~--~-~ipl~~v~h 111 (332)
T PRK09604 81 GP---GLVGA-LLVGVSFAKALALA--L-NKPLIGVNH 111 (332)
T ss_pred CC---CcHHh-HHHHHHHHHHHHHH--h-CCCEEeecC
Confidence 2 33222 34446788888863 3 789888853
No 49
>PRK15027 xylulokinase; Provisional
Probab=66.62 E-value=15 Score=33.43 Aligned_cols=24 Identities=17% Similarity=0.498 Sum_probs=20.5
Q ss_pred eEEEEecCCCeEEEEEecCCCcee
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIA 46 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a 46 (176)
.+||||+|+..+=.++-|..+.+.
T Consensus 1 ~~lgID~GTts~Ka~l~d~~G~vv 24 (484)
T PRK15027 1 MYIGIDLGTSGVKVILLNEQGEVV 24 (484)
T ss_pred CEEEEEecccceEEEEEcCCCCEE
Confidence 379999999999999999877554
No 50
>PRK09605 bifunctional UGMP family protein/serine/threonine protein kinase; Validated
Probab=66.55 E-value=30 Score=31.90 Aligned_cols=94 Identities=11% Similarity=0.041 Sum_probs=55.0
Q ss_pred CeEEEEecCCCeEEEEEecCCC-ceeccceeeeCC----------CCChhhHHHHHHHHHHh-----cCCCEEEEeccCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPKN-KIASPLSVLLRK----------KNTIDLMAEDFRSLISE-----FNLEGFIVGYPFN 85 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~-~~a~Pl~~i~~~----------~~~~~~~~~~L~~li~e-----~~~~~iVVGlPl~ 85 (176)
|.+||||-=..-+.+|+.+..+ .++.-..++... ......+...+.+++++ .+++.|.|+.-
T Consensus 1 m~il~iets~~~~s~a~~~~~~~~~~~~~~~~~~~~gg~~p~~~~~~H~~~l~~~i~~~l~~~~~~~~~id~iav~~g-- 78 (535)
T PRK09605 1 MIVLGIEGTAWKTSAGIVDSDGDVLFNESDPYKPPSGGIHPREAAEHHAEAIPKVIKEALEEAGLKPEDIDLVAFSQG-- 78 (535)
T ss_pred CEEEEEEccccceEEEEEeCCCcEEEEEEeeccCCcCCCChHHHHHHHHHHHHHHHHHHHHHcCCCHhhCCEEEECCC--
Confidence 5799999999999999998543 333321211100 00111233445556555 45799999831
Q ss_pred CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 86 RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 86 dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
-|..+. -.....||+.|+.. + ++|++.++.-.
T Consensus 79 Pg~~~~-l~vg~~~ak~la~~--~-~~~~~~v~h~~ 110 (535)
T PRK09605 79 PGLGPC-LRVVATAARALALS--L-DVPLIGVNHCV 110 (535)
T ss_pred CCcHhh-HHHHHHHHHHHHHH--h-CCCeecccHHH
Confidence 232222 23446788888864 4 78888875433
No 51
>PRK03011 butyrate kinase; Provisional
Probab=66.32 E-value=39 Score=30.05 Aligned_cols=128 Identities=12% Similarity=0.170 Sum_probs=67.9
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCC----------CChhhHHHHHHHHHHhc-----CCCEEEEec----
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK----------NTIDLMAEDFRSLISEF-----NLEGFIVGY---- 82 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~----------~~~~~~~~~L~~li~e~-----~~~~iVVGl---- 82 (176)
++||.|.+|+--+=+|+-+....+.. +++.... ...+.-.+.+.+++++. ++++| +|-
T Consensus 2 ~~il~inpgststk~a~~~~~~~~~~--~~~~h~~~~~~~~~~~~~q~~~r~~~i~~~l~~~g~~~~~l~av-~~RgG~~ 78 (358)
T PRK03011 2 MRILVINPGSTSTKIAVFEDEKPIFE--ETLRHSAEELEKFKTIIDQYEFRKQAILDFLKEHGIDLSELDAV-VGRGGLL 78 (358)
T ss_pred CEEEEEcCCCchheEEEEcCCceeee--eccccCHHHHhcCCCccchHHHHHHHHHHHHHHcCCChhcceEE-EEcCCCC
Confidence 68999999999999999986654443 2332210 11122235677777766 45555 888
Q ss_pred -cCCCCCC----------------chHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCc
Q 030509 83 -PFNRQQN----------------AADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILD 145 (176)
Q Consensus 83 -Pl~dG~~----------------s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD 145 (176)
|.+.|+. ...+.-.--.+.++.+. + ++|++.+|=-+....-... +-.|+..-+||---+
T Consensus 79 ~~v~gG~~~v~~~~~~~l~~~~~~~~~~nl~~~~a~~~~~~--~-~~p~~v~D~~~~~~~~~~a-~~~~lp~i~R~~gfH 154 (358)
T PRK03011 79 KPIPGGTYRVNEAMLEDLKNGKYGEHASNLGAIIAYEIAKE--L-GIPAFIVDPVVVDEMEPVA-RISGLPEIERKSIFH 154 (358)
T ss_pred cccCCCCEEcCHHHHHHHHhcCCCCCCCCHHHHHHHHHHHh--c-CCCEEEECCcccccCCHHH-HHcCCCCcceeecch
Confidence 8777775 22222222233344432 3 7888777753332211111 012333333344455
Q ss_pred HHHHHHHHHHH
Q 030509 146 KFAAVGILQEY 156 (176)
Q Consensus 146 ~~AA~iILq~y 156 (176)
.++-..+.++|
T Consensus 155 gln~~~va~~~ 165 (358)
T PRK03011 155 ALNQKAVARRV 165 (358)
T ss_pred HHhHHHHHHHH
Confidence 55555555555
No 52
>TIGR01312 XylB D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization.
Probab=65.98 E-value=15 Score=33.05 Aligned_cols=22 Identities=27% Similarity=0.501 Sum_probs=19.1
Q ss_pred EEEecCCCeEEEEEecCCCcee
Q 030509 25 LGLDVGDKYVGLSISDPKNKIA 46 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a 46 (176)
||||+|+..+=+++.|..+.+.
T Consensus 1 lgIDiGtt~ik~~l~d~~g~i~ 22 (481)
T TIGR01312 1 LGIDLGTSGVKALLVDEQGEVI 22 (481)
T ss_pred CceeecCcceEEEEECCCCCEE
Confidence 5899999999999999877543
No 53
>PRK13928 rod shape-determining protein Mbl; Provisional
Probab=65.37 E-value=64 Score=27.75 Aligned_cols=99 Identities=17% Similarity=0.237 Sum_probs=50.7
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCC-ChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCch---HHHHHHHHH
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKN-TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAA---DAVQVKLFI 100 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~-~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~---~~~~v~~Fa 100 (176)
+|||+|+.++=|+..+....+..|=-+-...+. ..-.+-++-.+.+. ..+..+.+..|+.+|.... .....+.+.
T Consensus 6 ~gIDlGt~~~~i~~~~~~~v~~~psvv~~~~~~~~i~~vG~~A~~~~~-~~p~~~~~~~pi~~G~i~d~~~~~~~l~~~~ 84 (336)
T PRK13928 6 IGIDLGTANVLVYVKGKGIVLNEPSVVAIDKNTNKVLAVGEEARRMVG-RTPGNIVAIRPLRDGVIADYDVTEKMLKYFI 84 (336)
T ss_pred eEEEcccccEEEEECCCCEEEccCCEEEEECCCCeEEEecHHHHHhhh-cCCCCEEEEccCCCCeEecHHHHHHHHHHHH
Confidence 899999999999997655555555222222111 11001122222222 2367788889988776544 233445555
Q ss_pred HHHHhccCCCCCc--EEEecCcccHHH
Q 030509 101 DDLSATKKLEDMK--YAYWNEGFTSKG 125 (176)
Q Consensus 101 ~~L~~~~~~~~lp--V~~~DEr~TT~~ 125 (176)
+++... ....-| ++.+-..+|..+
T Consensus 85 ~~~~~~-~~~~~p~~vitvP~~~~~~~ 110 (336)
T PRK13928 85 NKACGK-RFFSKPRIMICIPTGITSVE 110 (336)
T ss_pred HHHhcc-CCCCCCeEEEEeCCCCCHHH
Confidence 554322 111345 334445555443
No 54
>PF03309 Pan_kinase: Type III pantothenate kinase; InterPro: IPR004619 Pantothenate kinase (PanK or CoaA) catalyses the first step of the universal five step coenzyme A (CoA) biosynthesis pathway. CoA is a ubiquitous and essential cofactor in all living organsims. Pantothenate kinase catalyses the first and rate limiting step in the CoA biosynthetic pathway, which involves transferring a phosphoryl group from ATP to pantothenate, also known as vitamin B5. Three distinct types of pantothenate kinase enzymes have been identified: type I PanK enzymes are typified by the E. coli CoaA protein, type II enzymes are primarily found in eukaryotic organisms whilst type III enzymes have a wider phylogenic distribution and are not feedback inhibited by CoA []. This entry represents the type III pantothenate kinase family, such as that found in Helicobacter pylori. PanK III enzymes have a much wider phylogenic distribution than PanK I, and differs significantly in biochemical activity. PanK III enzymes are are not feedback inhibited by CoA concentration (which is also the case for PanK II enzymes), and PanK III enzymes have an unusually high Km for ATP []. ; GO: 0045893 positive regulation of transcription, DNA-dependent; PDB: 2GTD_E 3BF1_F 3BEX_D 3BF3_F 2NRH_B 2H3G_X 3DJC_J 2F9T_A 2F9W_A.
Probab=65.32 E-value=36 Score=27.37 Aligned_cols=58 Identities=17% Similarity=0.279 Sum_probs=39.4
Q ss_pred EEEEecCCCeEEEEEecCCCceecccee--eeCCCCChhhHHHHHHHHHHhcCCCEEEEe
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSV--LLRKKNTIDLMAEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~--i~~~~~~~~~~~~~L~~li~e~~~~~iVVG 81 (176)
+|.||.|-.+|=+|+.+..........+ ........+.+...+.+++...+.+.+++.
T Consensus 1 ~L~iDiGNT~ik~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~is 60 (206)
T PF03309_consen 1 ILLIDIGNTRIKWALFDGDKLIDPSGRISHSTALDSSSDELLELLESLLPQPKIDAVIIS 60 (206)
T ss_dssp EEEEEE-SSEEEEEEEETTEEEE-EEEE-EEECTTSSHHHHHHHHHHHHHCTTCGEEEEE
T ss_pred CEEEEECCCeEEEEEEECCEEEeeeeEEEecccccccHHHHHHHHHHHhccccCCcEEEE
Confidence 6899999999999999977555411112 112222234556788888998888888888
No 55
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=64.74 E-value=21 Score=28.98 Aligned_cols=49 Identities=24% Similarity=0.389 Sum_probs=30.0
Q ss_pred EEEEecCCCeEEEEEecCCCcee----ccceeeeCC----CCChhhHHHHHHHHHHh
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIA----SPLSVLLRK----KNTIDLMAEDFRSLISE 72 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a----~Pl~~i~~~----~~~~~~~~~~L~~li~e 72 (176)
+||||+|+-.+=+++-|..+.+. .|+...... ..+++.+++.+.+.+++
T Consensus 2 ~lgiDiGTts~K~~l~d~~g~iv~~~~~~~~~~~~~~g~~e~d~~~~~~~~~~~~~~ 58 (245)
T PF00370_consen 2 YLGIDIGTTSVKAVLFDEDGKIVASASRPYPYYTPEPGWAEQDPDEIWEAICEALKE 58 (245)
T ss_dssp EEEEEECSSEEEEEEEETTSCEEEEEEEEETEBCSSTTEEEE-HHHHHHHHHHHHHH
T ss_pred EEEEEEcccceEEEEEeCCCCEEEEEEEeeeeccccccccccChHHHHHHHHHHHHH
Confidence 79999999999999999776443 222222111 12455566665555544
No 56
>PRK13320 pantothenate kinase; Reviewed
Probab=64.64 E-value=29 Score=29.09 Aligned_cols=53 Identities=17% Similarity=0.312 Sum_probs=35.6
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc-CCCEEEEe
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIVG 81 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~~~~iVVG 81 (176)
+++|.||.|-.+|=+|+.+....+.+ ..++ .+++...+.++++.+ +++.++|.
T Consensus 2 ~M~L~iDiGNT~ik~~~~~~~~~~~~--~~~~-----~~~~~~~l~~~~~~~~~i~~i~vs 55 (244)
T PRK13320 2 SMNLVIDIGNTTTKLAVFEGDELLEV--FVVS-----TEGVEESLEKLLAKYPAIRDAIVS 55 (244)
T ss_pred ceEEEEEeCCCcEEEEEEECCEEEEE--EEEc-----cHHHHHHHHHHHHHCCCCCEEEEE
Confidence 46999999999999999986443322 1222 123345666666665 58888887
No 57
>PF03464 eRF1_2: eRF1 domain 2; InterPro: IPR005141 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination ; PDB: 3AGK_A 2VGN_A 2VGM_A 3J16_A 3IZQ 3IR9_A 3OBW_A 3MCA_B 2QI2_A 3E1Y_D ....
Probab=64.19 E-value=16 Score=27.44 Aligned_cols=95 Identities=12% Similarity=0.123 Sum_probs=50.0
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCC----C---------hhhHHHHHHHHHHhc------CCCEEEEeccC
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKN----T---------IDLMAEDFRSLISEF------NLEGFIVGYPF 84 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~----~---------~~~~~~~L~~li~e~------~~~~iVVGlPl 84 (176)
++.+|-|...||+.-+.......+=-..++.+.. + ...++.++.+-+.++ .++.|||+-
T Consensus 4 ~v~id~g~A~i~~l~~~~~~~~~~i~~~ip~K~~~Gg~s~~rf~r~~~~~~f~~~i~~~l~~~f~~~~~~~~~iIiaG-- 81 (133)
T PF03464_consen 4 IVVIDEGEANICLLRGYGTEILQRIESNIPGKHKKGGQSQRRFEREKALEKFFKEIAEALKKYFLVNFDDVKCIIIAG-- 81 (133)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHHHHHHHHHHHHHHHHHHHHHHHHHCCCHTTTCSEEEEEE--
T ss_pred EEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEEC--
Confidence 6889999999999865533222221112233221 0 123455555555554 899999993
Q ss_pred CCCCCchHHHHHHHHHHHHHhccCCCC-CcEEEecCcccHHHHH
Q 030509 85 NRQQNAADAVQVKLFIDDLSATKKLED-MKYAYWNEGFTSKGVE 127 (176)
Q Consensus 85 ~dG~~s~~~~~v~~Fa~~L~~~~~~~~-lpV~~~DEr~TT~~A~ 127 (176)
++.... .|.+.+.......+ ..+..+|=+.+...+-
T Consensus 82 ----PGf~k~---~f~~~l~~~~~~~~~~~i~~~~~s~~~~~gl 118 (133)
T PF03464_consen 82 ----PGFTKE---EFYKYLKAEARRKDKKKIVVVDTSSGGESGL 118 (133)
T ss_dssp ----STTHHH---HHHHHHHHHHHHHTCCEEEEEE-SSSCHHHH
T ss_pred ----CHHHHH---HHHHHHHHhhHhhcCCEEEEEECCCCCHHHH
Confidence 333322 45555544211112 3466666555555553
No 58
>TIGR01769 GGGP geranylgeranylglyceryl phosphate synthase. This model represents geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The active enzyme is reported to be a homopentamer in Methanobacterium thermoautotrophicum but is reported to be a homodimer in Thermoplasma acidophilum.
Probab=64.08 E-value=23 Score=29.11 Aligned_cols=47 Identities=6% Similarity=0.140 Sum_probs=37.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
+.++.+.+.+...+.|.|| ||.+-....+.+..+.+++. .++||++.
T Consensus 13 ~~~ia~~v~~~gtDaI~VG-----GS~gvt~~~~~~~v~~ik~~---~~lPvilf 59 (205)
T TIGR01769 13 IEKIAKNAKDAGTDAIMVG-----GSLGIVESNLDQTVKKIKKI---TNLPVILF 59 (205)
T ss_pred HHHHHHHHHhcCCCEEEEc-----CcCCCCHHHHHHHHHHHHhh---cCCCEEEE
Confidence 4556677788889999999 88766667778888888863 38999876
No 59
>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR020562 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ....
Probab=63.99 E-value=13 Score=27.24 Aligned_cols=40 Identities=23% Similarity=0.288 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEE
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA 115 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~ 115 (176)
.+.|.+++++++++.+||| .+.+. +.-.++.|.+. ++|++
T Consensus 51 ~~~l~~~a~~~~idlvvvG------PE~pL---~~Gl~D~l~~~----gi~vf 90 (100)
T PF02844_consen 51 PEELADFAKENKIDLVVVG------PEAPL---VAGLADALRAA----GIPVF 90 (100)
T ss_dssp HHHHHHHHHHTTESEEEES------SHHHH---HTTHHHHHHHT----T-CEE
T ss_pred HHHHHHHHHHcCCCEEEEC------ChHHH---HHHHHHHHHHC----CCcEE
Confidence 6899999999999999999 44443 34567778763 67765
No 60
>TIGR01174 ftsA cell division protein FtsA. This bacterial cell division protein interacts with FtsZ, the bacterial homolog of tubulin. It is an ATP-binding protein and shows structural similarities to actin and heat shock cognate protein 70.
Probab=63.17 E-value=32 Score=30.09 Aligned_cols=61 Identities=16% Similarity=0.230 Sum_probs=37.7
Q ss_pred EEEEecCCCeEEEEEecCC--C-ceeccceeeeCC---C---CChhhHHHHHHHHHHh------cCCCEEEEeccC
Q 030509 24 FLGLDVGDKYVGLSISDPK--N-KIASPLSVLLRK---K---NTIDLMAEDFRSLISE------FNLEGFIVGYPF 84 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~--~-~~a~Pl~~i~~~---~---~~~~~~~~~L~~li~e------~~~~~iVVGlPl 84 (176)
++|||+|+.+|=+++.... + .-.......+.. + .+.+.+.+.|++.+++ .++..++++.|=
T Consensus 2 ~~~lDIGs~~ik~vv~~~~~~~~~~i~~~~~~~~~gi~~G~I~d~~~~~~~i~~al~~~e~~~~~~i~~v~~~v~g 77 (371)
T TIGR01174 2 IVGLDIGTSKICAIVAEVLEDGELNIIGVGTHPSRGIKKGVINDIEAAVGSIQRAIEAAELMAGCEIRSVIVSISG 77 (371)
T ss_pred EEEEEeccceEEEEEEEEcCCCCEEEEEEEEecCCCccCcEEEcHHHHHHHHHHHHHHHHHHhCCcccEEEEEEcc
Confidence 6899999999998887532 2 111111122211 1 1234556778888876 478899999873
No 61
>PF05378 Hydant_A_N: Hydantoinase/oxoprolinase N-terminal region; InterPro: IPR008040 This domain is found at the N terminus of the hydantoinase/oxoprolinase IPR002821 from INTERPRO family.
Probab=62.69 E-value=22 Score=28.22 Aligned_cols=56 Identities=20% Similarity=0.380 Sum_probs=38.5
Q ss_pred EEEecCCCeEEEEEecCC-CceeccceeeeCCCCChhhHHHHHHHHHHhc-----CCCEEEEe
Q 030509 25 LGLDVGDKYVGLSISDPK-NKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVG 81 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~-~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~~~~iVVG 81 (176)
+|||+|.-.+=..+.|+. +.+++ .++......-..-+.+.|.++..++ +++.|++|
T Consensus 2 igIDvGGT~TD~v~~d~~~~~~~~-~K~~Tt~~d~~~gi~~al~~l~~~~~~~~~~i~~v~~g 63 (176)
T PF05378_consen 2 IGIDVGGTFTDAVLLDEDTGVVAT-AKVPTTPDDPAEGILEALDALLEESGIDPSDIDRVRHG 63 (176)
T ss_pred eeEecCCCcEEEEEEeCCCCEEEE-EEeCCCCcCHHHHHHHHHHhhhcccCCChhhCcEEEec
Confidence 799999999988888887 44554 3444332222223457788887765 67899998
No 62
>COG0418 PyrC Dihydroorotase [Nucleotide transport and metabolism]
Probab=62.52 E-value=9.7 Score=33.68 Aligned_cols=51 Identities=14% Similarity=0.278 Sum_probs=34.7
Q ss_pred EeccCC-CCCCchHH--------HHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCC
Q 030509 80 VGYPFN-RQQNAADA--------VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD 134 (176)
Q Consensus 80 VGlPl~-dG~~s~~~--------~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g 134 (176)
+|+||. .|...... ..+...-+.|.+ +||++.|++ |..||+.|-+..++.+
T Consensus 130 ~gmpLlvHGEvt~~~vDifdrE~~Fi~~vl~pl~~--~fP~LKIV~--EHiTT~dav~~v~~~~ 189 (344)
T COG0418 130 IGMPLLVHGEVTDAEVDIFDREAAFIESVLEPLRQ--RFPKLKIVL--EHITTKDAVEYVKDAN 189 (344)
T ss_pred cCCeEEEecccCCccccchhhHHHHHHHHHHHHHh--hCCcceEEE--EEeccHHHHHHHHhcC
Confidence 578887 77654332 223333345555 588988887 9999999998887654
No 63
>PRK15118 universal stress global response regulator UspA; Provisional
Probab=62.52 E-value=35 Score=25.00 Aligned_cols=47 Identities=9% Similarity=0.077 Sum_probs=31.7
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.+.|.+.++++++|.||+| .- +......-..++++-+. .++||..+-
T Consensus 92 ~~~I~~~a~~~~~DLIV~G----s~--~~~~~~lgSva~~v~~~---a~~pVLvv~ 138 (144)
T PRK15118 92 GQVLVDAIKKYDMDLVVCG----HH--QDFWSKLMSSARQLINT---VHVDMLIVP 138 (144)
T ss_pred HHHHHHHHHHhCCCEEEEe----Cc--ccHHHHHHHHHHHHHhh---CCCCEEEec
Confidence 5889999999999999999 22 11222233566666553 378888774
No 64
>COG1070 XylB Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]
Probab=61.82 E-value=25 Score=32.34 Aligned_cols=23 Identities=26% Similarity=0.362 Sum_probs=20.3
Q ss_pred CCCeEEEEecCCCeEEEEEecCC
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~ 42 (176)
.+..+||||.|+..+=.++-|..
T Consensus 2 ~~~~~lgIDiGTt~~Kavl~d~~ 24 (502)
T COG1070 2 MMKYVLGIDIGTTSVKAVLFDED 24 (502)
T ss_pred CccEEEEEEcCCCcEEEEEEeCC
Confidence 45789999999999988888887
No 65
>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....
Probab=61.06 E-value=60 Score=23.39 Aligned_cols=119 Identities=13% Similarity=0.140 Sum_probs=70.2
Q ss_pred EEEEec--CCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHH
Q 030509 24 FLGLDV--GDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 101 (176)
Q Consensus 24 iLglD~--G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~ 101 (176)
+++|-. ....+|+|..|..+.-.. +..+.. ..+|...+..++|..||+. ++..+.... ....
T Consensus 3 l~aI~~~~~~~~~gla~~D~sTGe~~-~~~~~d--------~~~L~~~L~~~~P~EIi~~----~~~~~~~~~---~~~~ 66 (137)
T PF05188_consen 3 LAAIYEKNDEDSYGLAYIDLSTGEFY-VTEFED--------YSELKSELARLSPREIIIP----EGFSSSDIS---ALLS 66 (137)
T ss_dssp EEEEEEETCSSEEEEEEEETTTTEEE-EEEEEC--------HHHHHHHHHHH-ESEEEEE----TTCSHHHHH---HHHH
T ss_pred EEEEEEecCCCEEEEEEEECCCCEEE-EEEeCC--------HHHHHHHHHhcCCeEEEEc----CCCcccccc---hhhh
Confidence 566666 677799999997654433 222321 4788999999999999999 777665431 1111
Q ss_pred HHHhccCCCCCcE-EEecCcccHHHHHHHhcc-CCCCCCCC----CCCCcHHHHHHHHHHHHhhhhh
Q 030509 102 DLSATKKLEDMKY-AYWNEGFTSKGVELLLNP-LDLHPVEY----KTILDKFAAVGILQEYLDNANR 162 (176)
Q Consensus 102 ~L~~~~~~~~lpV-~~~DEr~TT~~A~~~l~~-~g~~~~~~----k~~iD~~AA~iILq~yL~~~~~ 162 (176)
.+.. ....+ ...+..+.+..+.+.+.+ .+...-+. ...-..++|.--|=.||.....
T Consensus 67 ~~~~----~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~Al~all~Yl~~t~~ 129 (137)
T PF05188_consen 67 SLKN----SFFKVTETPSWYFDSEFASEDIEEQFGVADLDGFGLEEDKELALSALGALLKYLEETQK 129 (137)
T ss_dssp CCTT----TCCEEEEETCGGGSHHHHHHHHHHHCTSSSTCCCTTGGGGHHHHHHHHHHHHHHHHTTT
T ss_pred hhcc----ccceeeecchhhhhhHHHHHHHHHhhccccccccCccCCCHHHHHHHHHHHHHHHHHCc
Confidence 1221 12233 334556666666655542 22211111 3345678888888899987644
No 66
>TIGR01175 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.
Probab=60.50 E-value=54 Score=28.06 Aligned_cols=64 Identities=17% Similarity=0.310 Sum_probs=40.9
Q ss_pred CeEEEEecCCCeEEEEEecCCCc--e-------eccceeeeCCC-CChhhHHHHHHHHHHhcCC--CEEEEeccCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNK--I-------ASPLSVLLRKK-NTIDLMAEDFRSLISEFNL--EGFIVGYPFN 85 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~--~-------a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~~--~~iVVGlPl~ 85 (176)
..++|||+|+..|=++.....+. . ..|-..+.... .+.+.+...|.+++++.+. ..+++++|-+
T Consensus 3 ~~~vgiDIg~~~Ik~v~~~~~~~~~~v~~~~~~~~p~~~i~~g~i~d~~~~~~~l~~~~~~~~~~~k~v~~alp~~ 78 (348)
T TIGR01175 3 SLLVGIDIGSTSVKVAQLKRSGDRYKLEHYAVEPLPAGIFTEGHIVEYQAVAEALKELLSELGINTKKAATAVPGS 78 (348)
T ss_pred CcEEEEEeccCeEEEEEEEecCCceEEEEEEEEECCCCcccCCCccCHHHHHHHHHHHHHHcCCCcceEEEEecCC
Confidence 46899999999999888874221 1 12222222111 1334567888888888754 5799999854
No 67
>PRK13322 pantothenate kinase; Reviewed
Probab=60.48 E-value=92 Score=26.06 Aligned_cols=52 Identities=13% Similarity=0.135 Sum_probs=31.8
Q ss_pred EEEEecCCCeEEEEEecC-CCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEe
Q 030509 24 FLGLDVGDKYVGLSISDP-KNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~-~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVG 81 (176)
+|.||.|-.+|=+++.+. ...+.+ .. .....+.+...+..+ ....++.++|.
T Consensus 2 ~L~IDiGNT~iK~~l~~~~~~~~~~-~~----~~~t~~~~~~~l~~~-~~~~i~~v~vs 54 (246)
T PRK13322 2 ILELDCGNSRLKWRVIDNGGQIIEH-GA----HLDSPAELLLGLANL-ASLAPTRCRIV 54 (246)
T ss_pred EEEEEeCCCcEEEEEEcCCCchhhh-cc----ccCCHHHHHHHHHhC-CccCCCEEEEE
Confidence 899999999999999985 332221 11 111222333445433 34468999998
No 68
>PHA02942 putative transposase; Provisional
Probab=59.59 E-value=13 Score=33.33 Aligned_cols=87 Identities=9% Similarity=-0.049 Sum_probs=47.6
Q ss_pred HhcCCCEEEEeccCC-CCCCchHHHHH---------HHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCC----
Q 030509 71 SEFNLEGFIVGYPFN-RQQNAADAVQV---------KLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH---- 136 (176)
Q Consensus 71 ~e~~~~~iVVGlPl~-dG~~s~~~~~v---------~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~---- 136 (176)
.+++.+.|||+...+ ........+.+ .+|...|+-.....|++|+.+|+++||..--. .|-.
T Consensus 263 ~~~~~~~IviEdL~gm~k~~~~l~k~~~~~~~~~~~~~l~~~LeYKA~~~G~~Vv~V~p~yTSq~Cs~----CG~~~~~l 338 (383)
T PHA02942 263 EDLGANVIKLEDLKNLIKDVNKLPAEFRDKLYLMQYHRIQYWIEWQAKKHGMIVEFVNPSYSSVSCPK----CGHKMVEI 338 (383)
T ss_pred HhCCCCEEEEccHHHHHhcccccchHHHHHhhhhhHHHHHHHHHHHHHHhCCEEEEECCCCCCccCCC----CCCccCcC
Confidence 355678999997643 22111111111 22333343221124899999999999864321 2211
Q ss_pred -CCC-------CCCCCcHHHHHHHHHHHHhhhh
Q 030509 137 -PVE-------YKTILDKFAAVGILQEYLDNAN 161 (176)
Q Consensus 137 -~~~-------~k~~iD~~AA~iILq~yL~~~~ 161 (176)
.+. -...-|-.||.-|+...+....
T Consensus 339 ~~r~f~C~~CG~~~drD~nAA~NI~~rg~~~~~ 371 (383)
T PHA02942 339 AHRYFHCPSCGYENDRDVIAIMNLNGRGSLTLS 371 (383)
T ss_pred CCCEEECCCCCCEeCcHHHHHHHHHHHHHHHhc
Confidence 110 1245689999999987765543
No 69
>COG4012 Uncharacterized protein conserved in archaea [Function unknown]
Probab=59.05 E-value=82 Score=27.65 Aligned_cols=98 Identities=14% Similarity=0.145 Sum_probs=57.6
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 101 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~ 101 (176)
+++|++|+|.-..-|-.-|. ..--|+.-+.+..- . .+.++|+.+.++ .+..+++|-|.- |..+. ++|-+
T Consensus 1 mkila~DvG~GTqDi~~~d~-~~EnSl~mVmPspt-~--~~A~R~R~~~~~-g~~l~l~G~~MG-GGp~t-----ravrr 69 (342)
T COG4012 1 MKILAIDVGVGTQDIVAYDG-DPENSLRMVMPSPT-S--TLAQRLRFMLRE-GPYLALIGVPMG-GGPTT-----RAVRR 69 (342)
T ss_pred CceEEEEecCCceeEEEecC-CcccceeEeecCch-H--HHHHHHHHHhcc-CCcEEEEeeecC-CChhh-----HHHHH
Confidence 47999999998887777665 23335444554432 1 235677766654 458899998876 43332 34555
Q ss_pred HHHhccCCCCCcEEEe-cCcccHHHHHHHhccCCC
Q 030509 102 DLSATKKLEDMKYAYW-NEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 102 ~L~~~~~~~~lpV~~~-DEr~TT~~A~~~l~~~g~ 135 (176)
.|++ +.+|+.- |-.+|-..--+++.++|+
T Consensus 70 hlk~-----G~rVyatedAAlT~hddleRv~emgi 99 (342)
T COG4012 70 HLKK-----GTRVYATEDAALTLHDDLERVEEMGI 99 (342)
T ss_pred HHhc-----CCeeEechhhhhhhhcCHHHHHhhCe
Confidence 6664 5666543 333444433455555654
No 70
>PRK13324 pantothenate kinase; Reviewed
Probab=58.96 E-value=48 Score=28.13 Aligned_cols=56 Identities=18% Similarity=0.306 Sum_probs=36.0
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeC--CCCChhhHHHHHHHHHHhc-----CCCEEEEe
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLR--KKNTIDLMAEDFRSLISEF-----NLEGFIVG 81 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~--~~~~~~~~~~~L~~li~e~-----~~~~iVVG 81 (176)
+|+||.|-.+|=+++.|......+ . .+.. .....|++...|..++... .++.+++.
T Consensus 2 iL~iDiGNT~ik~gl~~~~~~~~~-~-r~~t~~~~~t~de~~~~l~~~~~~~~~~~~~i~~viis 64 (258)
T PRK13324 2 LLVMDMGNSHIHIGVFDGDRIVSQ-I-RYATSSVDSTSDQMGVFLRQALRENSVDLGKIDGCGIS 64 (258)
T ss_pred EEEEEeCCCceEEEEEECCEEEEE-E-EEecCccccchHHHHHHHHHHHHhcCCCccCCCeEEEE
Confidence 899999999999999985443222 1 2222 1112344556677777653 57888888
No 71
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=58.92 E-value=49 Score=26.90 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHHhcCCCEEEEec
Q 030509 60 DLMAEDFRSLISEFNLEGFIVGY 82 (176)
Q Consensus 60 ~~~~~~L~~li~e~~~~~iVVGl 82 (176)
..++.++.+++.+++|+ ||+|+
T Consensus 59 ~~lL~~f~~~i~~~dPd-ii~g~ 80 (207)
T cd05785 59 KELLEELVAIIRERDPD-VIEGH 80 (207)
T ss_pred HHHHHHHHHHHHHhCCC-EEecc
Confidence 45789999999999998 88896
No 72
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=58.60 E-value=56 Score=29.44 Aligned_cols=71 Identities=15% Similarity=0.091 Sum_probs=45.4
Q ss_pred hHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHH-HHHHHHHHHHhccCCCCCcEEEe----cCcccHHHHHHHhccCC
Q 030509 61 LMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAV-QVKLFIDDLSATKKLEDMKYAYW----NEGFTSKGVELLLNPLD 134 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~-~v~~Fa~~L~~~~~~~~lpV~~~----DEr~TT~~A~~~l~~~g 134 (176)
.+++.|.+++.+++|+.|||.-=+- .+..+..+. ...+|..+|.+. ++||+++ |-.-.......+|...|
T Consensus 26 ~~l~~l~~~i~~~~~D~viIaGDifD~~~p~~~a~~~~~~~l~~L~~~----~~~v~~I~GNHD~~~~l~~~~~~l~~~g 101 (407)
T PRK10966 26 AFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQT----GCQLVVLAGNHDSVATLNESRDLLAFLN 101 (407)
T ss_pred HHHHHHHHHHHhcCCCEEEECCccccCCCCcHHHHHHHHHHHHHHHhc----CCcEEEEcCCCCChhhhhhHHHHHHHCC
Confidence 3467888889999999999975555 444444443 345677777752 6788876 43333334556666655
Q ss_pred C
Q 030509 135 L 135 (176)
Q Consensus 135 ~ 135 (176)
+
T Consensus 102 i 102 (407)
T PRK10966 102 T 102 (407)
T ss_pred c
Confidence 4
No 73
>PF02579 Nitro_FeMo-Co: Dinitrogenase iron-molybdenum cofactor; InterPro: IPR003731 This entry represents several Nif (B, X and Y) proteins, which are involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing bacteria. The nitrogenase complex catalyses the reduction of atmospheric dinitrogen to ammonia, and is composed of an iron metalloprotein (dinitrogenase reductase; homodimer of NifH; IPR000392 from INTERPRO) and a Fe-Mo metalloprotein (dinitrogenase; heterotetramer of NifD and NifK; IPR000318 from INTERPRO). The pathway for the synthesis of the Fe-Mo cofactor involves several proteins, including NifB, NifE, NifH, NifN, NifQ, NifV and NifX. NifB appears to be an iron-sulphur source for FeMo-co biosynthesis, while NifX may be associated with the mature FeMo-co, in particular with the addition of homocitrate during the last step of biosynthesis []. The NifX protein shows sequence similarity with the C terminus of NifB [], as well as to the conserved protein MTH1175 from the archaeon Methanobacterium thermoautotrophicum, which displays a ribonuclease H-like motif of three layers, alpha/beta/alpha, with a single mixed beta-sheet [].; PDB: 2QTD_A 2KLA_A 1EO1_A 1P90_A 1RDU_A 2YX6_D 1O13_A 1T3V_A 2RE2_B 2WFB_A.
Probab=58.56 E-value=45 Score=22.65 Aligned_cols=50 Identities=12% Similarity=0.060 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
..+.+++.+++++.+|+| ..++ .....|++. ++.|+.. ...+-.+|-+.|
T Consensus 43 ~~~~~~l~~~~v~~li~~------~iG~------~~~~~L~~~----gI~v~~~-~~~~i~~~l~~~ 92 (94)
T PF02579_consen 43 DKIAKFLAEEGVDVLICG------GIGE------GAFRALKEA----GIKVYQG-AGGDIEEALEAY 92 (94)
T ss_dssp THHHHHHHHTTESEEEES------CSCH------HHHHHHHHT----TSEEEES-TSSBHHHHHHHH
T ss_pred hhHHHHHHHcCCCEEEEe------CCCH------HHHHHHHHC----CCEEEEc-CCCCHHHHHHHH
Confidence 567777777999999999 4565 344567763 7899888 777777776554
No 74
>TIGR00555 panK_eukar pantothenate kinase, eukaryotic/staphyloccocal type. This model describes a eukaryotic form of pantothenate kinase, characterized from the fungus Aspergillus nidulans and with similar forms known in several other eukaryotes. It also includes forms from several Gram-positive bacteria suggested to have originated from the eukaryotic form by lateral transfer. It differs in a number of biochemical properties (such as inhibition by acetyl-CoA) from most bacterial CoaA and lacks sequence similarity. This enzyme is the key regulatory step in the biosynthesis of coenzyme A (CoA).
Probab=58.52 E-value=75 Score=27.41 Aligned_cols=90 Identities=13% Similarity=0.137 Sum_probs=54.8
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc-CCCEEEEeccCCCCCCchHHHHHHHHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIVGYPFNRQQNAADAVQVKLFIDD 102 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~ 102 (176)
.+|||.|...+=+++.|..+.+-. ..+++++. +.+++.|.+..... .+..|.+ -|.-+ .+|++.
T Consensus 2 ~iGiDiGgT~~Kiv~~~~~~~~~f--~~~~~~~~--~~~~~~l~~~~~~~~~~~~i~~-----TGgGa------~k~~~~ 66 (279)
T TIGR00555 2 RIGIDIGGTLIKVVYEEPKGRRKF--KTFETTNI--DKFIEWLKNQIHRHSRITTLCA-----TGGGA------FKFAEL 66 (279)
T ss_pred eEEEEeCcceEEEEEEcCCCcEEE--EEeecccH--HHHHHHHHHHHHhhcCceEEEE-----ECCcH------HHHHHH
Confidence 689999999999999987766553 56666542 23334443333211 1222222 13322 357777
Q ss_pred HHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 103 LSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 103 L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
+... + ++++...||=-+...+-+.+.
T Consensus 67 ~~~~--~-~v~~~k~dE~~a~~~g~~~ll 92 (279)
T TIGR00555 67 IYES--A-GIQLHKFDEFDALIQGLNYLL 92 (279)
T ss_pred hccc--c-CCcccchhHHHHHHHHHHHHh
Confidence 7752 3 678888999888777776663
No 75
>PRK10116 universal stress protein UspC; Provisional
Probab=57.79 E-value=47 Score=24.11 Aligned_cols=47 Identities=9% Similarity=0.080 Sum_probs=29.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.|.+.++++++|.||+|- -..+...... ..++++-.. .+.||..+
T Consensus 91 ~~~I~~~a~~~~~DLiV~g~----~~~~~~~~~~-s~a~~v~~~---~~~pVLvv 137 (142)
T PRK10116 91 SEHILEVCRKHHFDLVICGN----HNHSFFSRAS-CSAKRVIAS---SEVDVLLV 137 (142)
T ss_pred HHHHHHHHHHhCCCEEEEcC----CcchHHHHHH-HHHHHHHhc---CCCCEEEE
Confidence 47888899999999999993 2222222222 345566542 36787765
No 76
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=57.12 E-value=54 Score=22.57 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=29.5
Q ss_pred EEEeccCCCCCCc--hHHHHHHHHHHHHHhccCCCCCc--EEEecC-cccHHHHHHHhccCCC
Q 030509 78 FIVGYPFNRQQNA--ADAVQVKLFIDDLSATKKLEDMK--YAYWNE-GFTSKGVELLLNPLDL 135 (176)
Q Consensus 78 iVVGlPl~dG~~s--~~~~~v~~Fa~~L~~~~~~~~lp--V~~~DE-r~TT~~A~~~l~~~g~ 135 (176)
++|| .|+.. +....+.++++.|++. ++..+ +.|... .-+..++-+.|...|.
T Consensus 3 llv~----HGs~~~s~~~~~~~~~~~~l~~~--~~~~~v~~a~~~~~~P~i~~~l~~l~~~g~ 59 (101)
T cd03409 3 LVVG----HGSPYKDPYKKDIEAQAHNLAES--LPDFPYYVGFQSGLGPDTEEAIRELAEEGY 59 (101)
T ss_pred EEEE----CCCCCCccHHHHHHHHHHHHHHH--CCCCCEEEEEECCCCCCHHHHHHHHHHcCC
Confidence 5666 66665 4555667777777663 22233 334554 4566666666655554
No 77
>TIGR03192 benz_CoA_bzdQ benzoyl-CoA reductase, bzd-type, Q subunit. Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=56.75 E-value=41 Score=29.33 Aligned_cols=52 Identities=12% Similarity=0.155 Sum_probs=31.1
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCCh-hhHHHHHHHHHHhcC
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTI-DLMAEDFRSLISEFN 74 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~-~~~~~~L~~li~e~~ 74 (176)
..|..+|||+|+..+=+++-|.. .+.. ...++ ...++ +...+-|.++.++..
T Consensus 30 ~~m~~~GIDiGStt~K~Vlld~~-~i~~-~~~~~-tg~~~~~~a~~~l~~~l~~~g 82 (293)
T TIGR03192 30 AKIITCGIDVGSVSSQAVLVCDG-ELYG-YNSMR-TGNNSPDSAKNALQGIMDKIG 82 (293)
T ss_pred cccEEEEEEeCchhEEEEEEeCC-EEEE-EEeec-CCCCHHHHHHHHHHHHHHHcC
Confidence 33678999999999999999853 3332 23333 33332 222345556656553
No 78
>PTZ00294 glycerol kinase-like protein; Provisional
Probab=56.40 E-value=30 Score=31.66 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=20.6
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~ 45 (176)
.+||||+|+..|=+++-|..+.+
T Consensus 3 ~~lgiDiGTts~Ka~l~d~~G~~ 25 (504)
T PTZ00294 3 YIGSIDQGTTSTRFIIFDEKGNV 25 (504)
T ss_pred EEEEEecCCCceEEEEECCCCCE
Confidence 58999999999999999988765
No 79
>cd03416 CbiX_SirB_N Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both are found in a wide range of bacteria. This subgroup also contains single domain proteins from archaea and bacteria which may represent the ancestral form of class II chelatases before domain duplication occurred.
Probab=56.37 E-value=57 Score=22.76 Aligned_cols=56 Identities=11% Similarity=0.065 Sum_probs=37.1
Q ss_pred EEEEeccCCCCCCchHH-HHHHHHHHHHHhccCCCCCcEEEecC-cccHHHHHHHhccCCCC
Q 030509 77 GFIVGYPFNRQQNAADA-VQVKLFIDDLSATKKLEDMKYAYWNE-GFTSKGVELLLNPLDLH 136 (176)
Q Consensus 77 ~iVVGlPl~dG~~s~~~-~~v~~Fa~~L~~~~~~~~lpV~~~DE-r~TT~~A~~~l~~~g~~ 136 (176)
.++|| .|+.++.+ ..+..+++.+++...+..+.+-|.+. .-|-.++-+.+...|.+
T Consensus 2 ivlv~----hGS~~~~~~~~~~~l~~~l~~~~~~~~v~~afle~~~p~~~~~l~~l~~~g~~ 59 (101)
T cd03416 2 LLLVG----HGSRDPRAAEALEALAERLRERLPGDEVELAFLELAEPSLAEALDELAAQGAT 59 (101)
T ss_pred EEEEE----cCCCCHHHHHHHHHHHHHHHhhCCCCcEEEEEEEcCCCCHHHHHHHHHHcCCC
Confidence 46788 89988644 46788999998742122344556665 66677777777766654
No 80
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=56.07 E-value=71 Score=26.66 Aligned_cols=121 Identities=14% Similarity=0.136 Sum_probs=63.0
Q ss_pred CCeEEEEEecCCCcee-------------ccceeee-CCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHH
Q 030509 31 DKYVGLSISDPKNKIA-------------SPLSVLL-RKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQV 96 (176)
Q Consensus 31 ~kriGvAvsd~~~~~a-------------~Pl~~i~-~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v 96 (176)
|+.|||-+.+....+. ..+.++- ..+.+.+. ++..+.+.++++++||+- +.. .. .+ .
T Consensus 1 t~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~~~~~--e~~i~~l~~~~vDGiI~~-s~~-~~-~~---~- 71 (279)
T PF00532_consen 1 TKTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGDDEEK--EEYIELLLQRRVDGIILA-SSE-ND-DE---E- 71 (279)
T ss_dssp -CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETTTHHH--HHHHHHHHHTTSSEEEEE-SSS-CT-CH---H-
T ss_pred CCEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCCchHH--HHHHHHHHhcCCCEEEEe-ccc-CC-hH---H-
Confidence 4678888877643221 2222221 22233332 355667788999999998 222 11 11 1
Q ss_pred HHHHHHHHhcc------C---CC-CCcEEEecCcccHHHHHHHhccCCCCC--CCCCCCCcHHHHHHHHHHHHhhhhh
Q 030509 97 KLFIDDLSATK------K---LE-DMKYAYWNEGFTSKGVELLLNPLDLHP--VEYKTILDKFAAVGILQEYLDNANR 162 (176)
Q Consensus 97 ~~Fa~~L~~~~------~---~~-~lpV~~~DEr~TT~~A~~~l~~~g~~~--~~~k~~iD~~AA~iILq~yL~~~~~ 162 (176)
+...++... + .+ ++|.+..|.+-...+|-+.|.+.|-++ ---....+...+.-=++.|.+....
T Consensus 72 --l~~~~~~~iPvV~~~~~~~~~~~~~~V~~D~~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~ 147 (279)
T PF00532_consen 72 --LRRLIKSGIPVVLIDRYIDNPEGVPSVYIDNYEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKE 147 (279)
T ss_dssp --HHHHHHTTSEEEEESS-SCTTCTSCEEEEEHHHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHH
T ss_pred --HHHHHHcCCCEEEEEeccCCcccCCEEEEcchHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHH
Confidence 111222100 0 12 455566666666677778887777544 1112344555666677777766543
No 81
>PLN02295 glycerol kinase
Probab=55.66 E-value=32 Score=31.57 Aligned_cols=47 Identities=13% Similarity=0.128 Sum_probs=30.9
Q ss_pred EEEEecCCCeEEEEEecCCCcee----ccceeeeCC----CCChhhHHHHHHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIA----SPLSVLLRK----KNTIDLMAEDFRSLI 70 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a----~Pl~~i~~~----~~~~~~~~~~L~~li 70 (176)
+||||.|+..+=.++-|..+.+. .++.+.... +.+++.+|+.+.+.+
T Consensus 2 vlgID~GTts~Ka~l~d~~G~~~~~~~~~~~~~~~~~G~~Eqdp~~~w~~~~~~i 56 (512)
T PLN02295 2 VGAIDQGTTSTRFIIYDRDARPVASHQVEFTQIYPQAGWVEHDPMEILESVLTCI 56 (512)
T ss_pred EEEEecCCCceEEEEECCCCCEEEEEeecccccCCCCCcEeeCHHHHHHHHHHHH
Confidence 79999999999999999887663 444332221 124556676655543
No 82
>PRK00923 sirohydrochlorin cobaltochelatase; Reviewed
Probab=54.95 E-value=50 Score=24.21 Aligned_cols=54 Identities=9% Similarity=-0.044 Sum_probs=33.9
Q ss_pred EEEEeccCCCCCCchHH-HHHHHHHHHHHhccCCCCCcE--EEec-CcccHHHHHHHhccCCCC
Q 030509 77 GFIVGYPFNRQQNAADA-VQVKLFIDDLSATKKLEDMKY--AYWN-EGFTSKGVELLLNPLDLH 136 (176)
Q Consensus 77 ~iVVGlPl~dG~~s~~~-~~v~~Fa~~L~~~~~~~~lpV--~~~D-Er~TT~~A~~~l~~~g~~ 136 (176)
.|+|| .||..+.+ ..+..|++.++++ .+..+| -|.+ ..-|-.++-+.+...|.+
T Consensus 4 lvlv~----hGS~~~~~~~~~~~~~~~l~~~--~~~~~v~~afle~~~P~l~~~l~~l~~~g~~ 61 (126)
T PRK00923 4 LLLVG----HGSRLPYNKEVVTKIAEKIKEK--HPFYIVEVGFMEFNEPTIPEALKKLIGTGAD 61 (126)
T ss_pred EEEEe----CCCCChHHHHHHHHHHHHHHHh--CCCCeEEEEEEEcCCCCHHHHHHHHHHcCCC
Confidence 57888 88887655 6778888888764 233344 4454 345556666666555543
No 83
>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []. The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.
Probab=54.81 E-value=57 Score=27.12 Aligned_cols=61 Identities=13% Similarity=0.185 Sum_probs=30.9
Q ss_pred CCCeEEEEecC----CCeEEEEEe--cCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEe
Q 030509 20 KRGRFLGLDVG----DKYVGLSIS--DPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 20 ~~~~iLglD~G----~kriGvAvs--d~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVG 81 (176)
....++|+|+| ...+++.+. ......-. +........+...+.+.|.++...+.+..|++=
T Consensus 224 ~~~~~~g~D~a~~~~~d~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~d 290 (384)
T PF03237_consen 224 DWPIIIGVDPAGGKGGDYTAIVVWEIVDDDGFYV-VDDEYERGMSPEEWAERIRELYKKYNPIKIYID 290 (384)
T ss_dssp T--EEEEEE--SSCTTB-EEEEEE-E-SSSSEEE-EEEEEESSS-TTTHHHHHHHHHHHTTS--EEEE
T ss_pred CceEEEEEECCCCCccCCEEEEEEccccccceEE-eeehhhcCCCHHHHHHHHHHHHhhcCceEEEEc
Confidence 34568999999 455555555 22222211 222222223334567889999999999999885
No 84
>TIGR00241 CoA_E_activ CoA-substrate-specific enzyme activase, putative. This domain may be involved in generating or regenerating the active sites of enzymes related to (R)-2-hydroxyglutaryl-CoA dehydratase and benzoyl-CoA reductase.
Probab=54.25 E-value=41 Score=27.75 Aligned_cols=46 Identities=20% Similarity=0.249 Sum_probs=27.5
Q ss_pred EEEEecCCCeEEEEEecCCCce-eccceeeeCCCCChhhHHHHHHHHHHhc
Q 030509 24 FLGLDVGDKYVGLSISDPKNKI-ASPLSVLLRKKNTIDLMAEDFRSLISEF 73 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~-a~Pl~~i~~~~~~~~~~~~~L~~li~e~ 73 (176)
++|||.|+..+=.++-| .+.+ ++- ..+ .....+.+.+.|.+++++.
T Consensus 2 ~lGIDiGtts~K~vl~d-~g~il~~~--~~~-~~~~~~~~~~~l~~~~~~~ 48 (248)
T TIGR00241 2 SLGIDSGSTTTKMVLME-DGKVIGYK--WLD-TTPVIEETARAILEALKEA 48 (248)
T ss_pred EEEEEcChhheEEEEEc-CCEEEEEE--Eec-CCCCHHHHHHHHHHHHHHc
Confidence 78999999999999988 4433 321 121 2222223345566776554
No 85
>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=54.25 E-value=57 Score=23.46 Aligned_cols=53 Identities=13% Similarity=0.046 Sum_probs=37.9
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCC-CCcEEEecCccc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLE-DMKYAYWNEGFT 122 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~-~lpV~~~DEr~T 122 (176)
.+++.+.+.+++++.|++. .+.+.....+.++++.+++. .+ +++|++--=-.+
T Consensus 39 ~~~l~~~~~~~~pdvV~iS-----~~~~~~~~~~~~~i~~l~~~--~~~~~~i~vGG~~~~ 92 (119)
T cd02067 39 PEEIVEAAKEEDADAIGLS-----GLLTTHMTLMKEVIEELKEA--GLDDIPVLVGGAIVT 92 (119)
T ss_pred HHHHHHHHHHcCCCEEEEe-----ccccccHHHHHHHHHHHHHc--CCCCCeEEEECCCCC
Confidence 4678888899999987776 45556667888999999874 44 666665544333
No 86
>TIGR01315 5C_CHO_kinase FGGY-family pentulose kinase. This model represents a subfamily of the FGGY family of carbohydrate kinases. This subfamily is closely related to a set of ribulose kinases, and many members are designated ribitol kinase. However, the member from Klebsiella pneumoniae, from a ribitol catabolism operon, accepts D-ribulose and to a lesser extent D-arabinitol and ribitol (PubMed:9639934 and JW Lengeler, personal communication); its annotation in GenBank as ribitol kinase is imprecise and may have affected public annotation of related proteins.
Probab=54.24 E-value=33 Score=31.78 Aligned_cols=48 Identities=15% Similarity=0.250 Sum_probs=30.1
Q ss_pred EEEEecCCCeEEEEEecCCCcee----ccceeeeC----CCCChhhHHHHHHHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIA----SPLSVLLR----KKNTIDLMAEDFRSLIS 71 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a----~Pl~~i~~----~~~~~~~~~~~L~~li~ 71 (176)
+||||+|+..|=+++-|..+.+. .|+.+... .+.+++.+|+.+.+.++
T Consensus 2 ~lgID~GTts~Ka~l~d~~G~i~~~~~~~~~~~~~~~g~~eqdp~~~~~~~~~~i~ 57 (541)
T TIGR01315 2 YIGVDVGTGSARACIIDSTGDILALAAQNIKTWTPSSGLEGQSSVYIWQAICNCVK 57 (541)
T ss_pred EEEEEecCcCEEEEEEcCCCCEEEEEEeeeeeccCCCCcccCCHHHHHHHHHHHHH
Confidence 79999999999999999886543 33332211 12344555666544444
No 87
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=54.16 E-value=40 Score=30.18 Aligned_cols=58 Identities=12% Similarity=0.209 Sum_probs=42.9
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEE--EecCcc
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA--YWNEGF 121 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~--~~DEr~ 121 (176)
+.++..++|.+++++.++|.+|.|=-+|-|.++..|..+- +.+.+. + ++|++ +..|.-
T Consensus 64 n~eea~~~i~~mv~~~~pD~viaGPaFnagrYG~acg~v~---~aV~e~--~-~IP~vtaM~~ENp 123 (349)
T PF07355_consen 64 NKEEALKKILEMVKKLKPDVVIAGPAFNAGRYGVACGEVA---KAVQEK--L-GIPVVTAMYEENP 123 (349)
T ss_pred CHHHHHHHHHHHHHhcCCCEEEEcCCcCCchHHHHHHHHH---HHHHHh--h-CCCEEEEecccCh
Confidence 3456689999999999999999995566899998887654 444442 3 78865 566764
No 88
>PRK13317 pantothenate kinase; Provisional
Probab=53.95 E-value=95 Score=26.55 Aligned_cols=85 Identities=12% Similarity=0.049 Sum_probs=48.8
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh-cCCCEEEEeccCCCCCCchHHHHHHHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE-FNLEGFIVGYPFNRQQNAADAVQVKLFI 100 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e-~~~~~iVVGlPl~dG~~s~~~~~v~~Fa 100 (176)
+..+|||.|...+=+++-|....+.. .+..++ ..+.+.+++.+ .++..|++= |+-+. .|+
T Consensus 2 ~~~iGIDiGstt~K~v~~~~~~~~~~--~~~~~~------~~~~~~~~l~~~~~~~~i~~T-----G~g~~------~~~ 62 (277)
T PRK13317 2 EMKIGIDAGGTLTKIVYLEEKKQRTF--KTEYSA------EGKKVIDWLINLQDIEKICLT-----GGKAG------YLQ 62 (277)
T ss_pred CceEEEEeCcccEEEEEEcCCCeEEE--EeeccH------HHHHHHHHhhccCCceEEEEE-----Ccchh------hhh
Confidence 56789999999999999887665442 222222 13455555543 345544442 33221 233
Q ss_pred HHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 101 DDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 101 ~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
+.+. . ++|++.+||=-.+..+-+.+
T Consensus 63 ~~~~----~-~~~~~~v~E~~a~~~g~~~l 87 (277)
T PRK13317 63 QLLN----Y-GYPIAEFVEFEATGLGVRYL 87 (277)
T ss_pred HHHh----c-CCCeeeeHHHHHHHHHHHHH
Confidence 2222 2 67877788866666655554
No 89
>TIGR01314 gntK_FGGY gluconate kinase, FGGY type. Gluconate is derived from glucose in two steps. This model describes one form of gluconate kinase, belonging to the FGGY family of carbohydrate kinases. Gluconate kinase phosphoryates gluconate for entry into the Entner-Douderoff pathway.
Probab=53.88 E-value=29 Score=31.70 Aligned_cols=23 Identities=22% Similarity=0.476 Sum_probs=20.0
Q ss_pred EEEEecCCCeEEEEEecCCCcee
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIA 46 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a 46 (176)
+||||+|+..+=+++-|..+.+.
T Consensus 2 ~lgiDiGtt~~K~~l~d~~g~i~ 24 (505)
T TIGR01314 2 MIGVDIGTTSTKAVLFEENGKIV 24 (505)
T ss_pred EEEEeccccceEEEEEcCCCCEE
Confidence 79999999999999999887553
No 90
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=53.84 E-value=84 Score=25.03 Aligned_cols=24 Identities=25% Similarity=0.570 Sum_probs=19.1
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEec
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGY 82 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGl 82 (176)
+...++.++.+++++++|+ +++|+
T Consensus 47 ~E~~lL~~F~~~i~~~dPd-~i~gy 70 (188)
T cd05781 47 DDRKIIREFVKYVKEYDPD-IIVGY 70 (188)
T ss_pred CHHHHHHHHHHHHHHcCCC-EEEec
Confidence 3346789999999999999 55596
No 91
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=53.40 E-value=12 Score=37.23 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=20.5
Q ss_pred CCCeEEEEecCCCeEEEEEecCCC
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKN 43 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~ 43 (176)
....+||+|.|..-||.|++..+.
T Consensus 2 ~~~yilglDIGi~SVGWAvve~de 25 (1088)
T COG3513 2 KKAYILGLDIGINSVGWAVVEDDE 25 (1088)
T ss_pred CcceEEEeeccccceeeEEeeccc
Confidence 456899999999999999987543
No 92
>TIGR01768 GGGP-family geranylgeranylglyceryl phosphate synthase family protein. This model represents a family of sequences including geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The clade of bacterial sequences may have the same function or a closely related function. This model supercedes TIGR00265, which has been retired.
Probab=53.21 E-value=42 Score=28.07 Aligned_cols=45 Identities=9% Similarity=0.259 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.++.+-+.+...+.|+|| ||.+-....+.+..+.+++ + .+||++.
T Consensus 17 ~~~~~~~~~~gtdai~vG-----GS~~vt~~~~~~~v~~ik~---~-~lPvilf 61 (223)
T TIGR01768 17 DEIAKAAAESGTDAILIG-----GSQGVTYEKTDTLIEALRR---Y-GLPIILF 61 (223)
T ss_pred HHHHHHHHhcCCCEEEEc-----CCCcccHHHHHHHHHHHhc---c-CCCEEEe
Confidence 445566677789999999 8888777888889999986 4 5998875
No 93
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=52.54 E-value=48 Score=24.69 Aligned_cols=45 Identities=20% Similarity=0.467 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.+.+++++++++.|+|=+|..+ .+.+.++.+.+++. ++.|.++
T Consensus 130 ~~~l~~~~~~~~id~v~ial~~~~------~~~i~~ii~~~~~~----~v~v~~v 174 (175)
T PF13727_consen 130 LDDLPELVREHDIDEVIIALPWSE------EEQIKRIIEELENH----GVRVRVV 174 (175)
T ss_dssp GGGHHHHHHHHT--EEEE--TTS-------HHHHHHHHHHHHTT----T-EEEE-
T ss_pred HHHHHHHHHhCCCCEEEEEcCccC------HHHHHHHHHHHHhC----CCEEEEe
Confidence 367899999999999999987761 24567788888863 6676654
No 94
>PF14331 ImcF-related_N: ImcF-related N-terminal domain
Probab=52.22 E-value=42 Score=28.33 Aligned_cols=55 Identities=16% Similarity=0.187 Sum_probs=35.9
Q ss_pred HHHHHHHHHHhcC----CCEEEEeccCC---CCCC-----chHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 62 MAEDFRSLISEFN----LEGFIVGYPFN---RQQN-----AADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 62 ~~~~L~~li~e~~----~~~iVVGlPl~---dG~~-----s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.|..+.+++++++ +++|||=+|.. +++. ...+..+++-.+.|.+... ..+|||++
T Consensus 9 ~W~~~L~lL~~~R~r~PlnGvil~vs~~~Ll~~~~~~r~l~~~a~~lR~rL~el~~~lg-~~~PVYvv 75 (266)
T PF14331_consen 9 EWQAFLDLLRRHRPRQPLNGVILTVSVDDLLNADEAERELEALARALRQRLEELQRTLG-VRLPVYVV 75 (266)
T ss_pred HHHHHHHHHHhcCCCCCCCEEEEEEEHHHHhcCChhhhHHHHHHHHHHHHHHHHHHHhC-CCCCeEee
Confidence 4788888888774 79999999966 3333 3335555555555554322 37898865
No 95
>PRK10939 autoinducer-2 (AI-2) kinase; Provisional
Probab=52.06 E-value=45 Score=30.66 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=20.6
Q ss_pred CeEEEEecCCCeEEEEEecCCCce
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~ 45 (176)
..+||||+|+.-+=+++-|..+.+
T Consensus 3 ~~~lgID~GTts~Ka~l~d~~G~~ 26 (520)
T PRK10939 3 SYLMALDAGTGSIRAVIFDLNGNQ 26 (520)
T ss_pred cEEEEEecCCCceEEEEECCCCCE
Confidence 369999999999999999988643
No 96
>PF00012 HSP70: Hsp70 protein; InterPro: IPR013126 Heat shock proteins, Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region []. Hsp70 proteins have an average molecular weight of 70 kDa [, , ]. In most species,there are many proteins that belong to the hsp70 family. Some of these are only expressed under stress conditions (strictly inducible), while some are present in cells under normal growth conditions and are not heat-inducible (constitutive or cognate) [, ]. Hsp70 proteins can be found in different cellular compartments(nuclear, cytosolic, mitochondrial, endoplasmic reticulum, for example).; PDB: 2P32_D 3D2F_A 2QXL_A 3D2E_C 3C7N_A 3FE1_C 4ANI_C 2V7Y_A 2KHO_A 3DPQ_B ....
Probab=52.05 E-value=13 Score=34.32 Aligned_cols=18 Identities=17% Similarity=0.460 Sum_probs=15.2
Q ss_pred EEEEecCCCeEEEEEecC
Q 030509 24 FLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~ 41 (176)
++|||+|+..+.||+.+.
T Consensus 1 viGID~Gt~~~~va~~~~ 18 (602)
T PF00012_consen 1 VIGIDLGTTNSKVAVFKN 18 (602)
T ss_dssp EEEEEE-SSEEEEEEEET
T ss_pred CEEEEeccCCEEEEEEEe
Confidence 689999999999998764
No 97
>PTZ00340 O-sialoglycoprotein endopeptidase-like protein; Provisional
Probab=51.47 E-value=81 Score=28.07 Aligned_cols=90 Identities=11% Similarity=0.073 Sum_probs=52.7
Q ss_pred CeEEEEecCCCeEEEEEecCCC-ceeccc---------eeeeCC--CCChhhHHHHHHHHHHh-----cCCCEEEEeccC
Q 030509 22 GRFLGLDVGDKYVGLSISDPKN-KIASPL---------SVLLRK--KNTIDLMAEDFRSLISE-----FNLEGFIVGYPF 84 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~-~~a~Pl---------~~i~~~--~~~~~~~~~~L~~li~e-----~~~~~iVVGlPl 84 (176)
|.+||||==...+++|+.|..+ .++.-. ++++.. ....+.+..-+.+++++ .+++.|.|.
T Consensus 1 ~~iLgIETScd~tsvAl~~~~~~il~~~~~sq~~~~G~GvvP~~a~r~H~~~l~~~i~~~l~~a~~~~~did~Iavt--- 77 (345)
T PTZ00340 1 FLALGIEGSANKLGVGIVTSDGEILSNVRETYITPPGTGFLPRETAQHHREHILSLVKEALEEAKITPSDISLICYT--- 77 (345)
T ss_pred CeEEEEEccchhhEEEEEECCCcEEEEEEeeccccCCCCcCchHHHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEe---
Confidence 4799999999999999998543 333211 222211 00111223444555554 368999998
Q ss_pred CCCCCchH-HHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 85 NRQQNAAD-AVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 85 ~dG~~s~~-~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.|=-... -.-...||+.|+.. + ++|++-++
T Consensus 78 -~GPGl~~~LrVG~~~Ak~LA~a--~-~~PligV~ 108 (345)
T PTZ00340 78 -KGPGMGAPLSVGAVVARTLSLL--W-GKPLVGVN 108 (345)
T ss_pred -cCCCcHhhHHHHHHHHHHHHHH--c-CCCEeecc
Confidence 4432312 23336788888863 3 78888665
No 98
>PRK10331 L-fuculokinase; Provisional
Probab=51.35 E-value=37 Score=30.69 Aligned_cols=23 Identities=35% Similarity=0.348 Sum_probs=20.0
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~ 45 (176)
.+||||+|+..+=+++-|.++.+
T Consensus 3 ~~lgID~GTt~~Ka~l~d~~G~~ 25 (470)
T PRK10331 3 VILVLDCGATNVRAIAVDRQGKI 25 (470)
T ss_pred eEEEEecCCCceEEEEEcCCCcE
Confidence 48999999999999999887754
No 99
>PRK11572 copper homeostasis protein CutC; Provisional
Probab=51.34 E-value=57 Score=27.78 Aligned_cols=61 Identities=10% Similarity=0.191 Sum_probs=41.6
Q ss_pred HHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEE---ecCcccHHHHHHHhccCCCCC
Q 030509 68 SLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAY---WNEGFTSKGVELLLNPLDLHP 137 (176)
Q Consensus 68 ~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~---~DEr~TT~~A~~~l~~~g~~~ 137 (176)
+.+++..+++||+| -|+ ||+.... ..++|-+. ..++|++| +|+--...+|-+.|.+.|+.+
T Consensus 80 ~~~~~~GadGvV~G-~L~~dg~vD~~------~~~~Li~~--a~~~~vTFHRAfD~~~d~~~al~~l~~lG~~r 144 (248)
T PRK11572 80 ATVRELGFPGLVTG-VLDVDGHVDMP------RMRKIMAA--AGPLAVTFHRAFDMCANPLNALKQLADLGVAR 144 (248)
T ss_pred HHHHHcCCCEEEEe-eECCCCCcCHH------HHHHHHHH--hcCCceEEechhhccCCHHHHHHHHHHcCCCE
Confidence 44567789999999 466 8886642 22223221 12788887 488878888988888878743
No 100
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=50.72 E-value=35 Score=28.55 Aligned_cols=58 Identities=14% Similarity=0.221 Sum_probs=35.2
Q ss_pred HHHHHhcCCCEEEEeccCC-CCCCch-HHHHHHHHHHHHHhccCCCCCcEEEe---cCcccHHHHHH-HhccCC
Q 030509 67 RSLISEFNLEGFIVGYPFN-RQQNAA-DAVQVKLFIDDLSATKKLEDMKYAYW---NEGFTSKGVEL-LLNPLD 134 (176)
Q Consensus 67 ~~li~e~~~~~iVVGlPl~-dG~~s~-~~~~v~~Fa~~L~~~~~~~~lpV~~~---DEr~TT~~A~~-~l~~~g 134 (176)
.++++++..+++|+| .++ ||+... +|+. +-... -++||.|. |=.+--+.+.+ .|.+.|
T Consensus 87 v~llk~~GAdGfVFG-aLt~dgsid~~~C~s-------i~~~~--rplPVTFHRAfD~~~D~k~~lE~~l~~lG 150 (255)
T KOG4013|consen 87 VELLKKAGADGFVFG-ALTSDGSIDRTSCQS-------IIETA--RPLPVTFHRAFDVAYDWKTCLEDALLDLG 150 (255)
T ss_pred HHHHHHcCCCceEEe-ecCCCCCcCHHHHHH-------HHHhc--CCCceeeeeehhhhcCHHHHHHHHHHHhh
Confidence 467899999999999 577 888763 2222 22211 26898875 44444444443 443433
No 101
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=50.46 E-value=83 Score=22.29 Aligned_cols=48 Identities=4% Similarity=-0.008 Sum_probs=33.4
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
+++.+.+.+++++.|.+. ...+.....+.++++.+++. .|+++|+.=-
T Consensus 41 ~~l~~~~~~~~pd~V~iS-----~~~~~~~~~~~~l~~~~k~~--~p~~~iv~GG 88 (121)
T PF02310_consen 41 EELVEALRAERPDVVGIS-----VSMTPNLPEAKRLARAIKER--NPNIPIVVGG 88 (121)
T ss_dssp HHHHHHHHHTTCSEEEEE-----ESSSTHHHHHHHHHHHHHTT--CTTSEEEEEE
T ss_pred HHHHHHHhcCCCcEEEEE-----ccCcCcHHHHHHHHHHHHhc--CCCCEEEEEC
Confidence 677888888899988777 33555566677888887763 4566665543
No 102
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.32 E-value=79 Score=26.32 Aligned_cols=53 Identities=13% Similarity=0.174 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCC-CCCCchHH-HHHHHHHHHHHhccCCCCCcEEEe
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFN-RQQNAADA-VQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~-~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.++++.+++.+++++.+|++-=+. +...+..+ ....+|.++|.+. . .+||+++
T Consensus 27 ~l~~l~~~~~~~~~D~lli~GDi~d~~~p~~~~~~~~~~~l~~l~~~--~-~i~v~~i 81 (253)
T TIGR00619 27 FLDDLLEFAKAEQIDALLVAGDVFDTANPPAEAQELFNAFFRNLSDA--N-PIPIVVI 81 (253)
T ss_pred HHHHHHHHHHHcCCCEEEECCccCCCCCCCHHHHHHHHHHHHHHHhc--C-CceEEEE
Confidence 468888888999999988875555 44444433 3345666777652 1 2888876
No 103
>PF07066 DUF3882: Lactococcus phage M3 protein; InterPro: IPR009773 This family consists of several Lactococcus bacteriophage 712, middle-3 (M3) proteins of around 160 residues in length. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The function of this family is unknown.
Probab=49.66 E-value=46 Score=26.40 Aligned_cols=64 Identities=14% Similarity=0.321 Sum_probs=39.4
Q ss_pred CCeEEEEecCCCe-----EEEEEecCCCceeccceeeeCCCCCh----hhHHHHHHHHHHhcCC--CEEEEeccCC
Q 030509 21 RGRFLGLDVGDKY-----VGLSISDPKNKIASPLSVLLRKKNTI----DLMAEDFRSLISEFNL--EGFIVGYPFN 85 (176)
Q Consensus 21 ~~~iLglD~G~kr-----iGvAvsd~~~~~a~Pl~~i~~~~~~~----~~~~~~L~~li~e~~~--~~iVVGlPl~ 85 (176)
|..+|+||+-+.- +|.|+-+....+.+... ...+..++ ...+++|+.++++++. .-|||=-|.-
T Consensus 1 ~~~~LslD~STs~~~~~gTG~A~~~~~~~~~~si~-~~~k~Ks~~ER~k~ias~Lk~ii~~~d~~~y~i~IE~~vm 75 (159)
T PF07066_consen 1 MKKVLSLDFSTSSKKGEGTGWAFFKGSDLVVGSIK-AKHKSKSFFERAKSIASELKTIIQKYDLKFYIIVIEKPVM 75 (159)
T ss_pred CCeeEEEEEecccCCCCCceeEEecCCeEEEeeee-ecCcccCHHHHHHHHHHHHHHHHHHhCCCcceEEEecccc
Confidence 3579999999998 99999975444344321 11111110 1235788888988853 4466665543
No 104
>TIGR01311 glycerol_kin glycerol kinase. This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases.
Probab=48.83 E-value=43 Score=30.48 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=20.2
Q ss_pred eEEEEecCCCeEEEEEecCCCcee
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIA 46 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a 46 (176)
.+||||+|+..|=+++-|..+.+.
T Consensus 2 ~~lgiDiGtt~iKa~l~d~~g~~l 25 (493)
T TIGR01311 2 YILAIDQGTTSSRAIVFDKDGNIV 25 (493)
T ss_pred eEEEEecCCCceEEEEECCCCCEE
Confidence 379999999999999999776444
No 105
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=47.99 E-value=61 Score=27.96 Aligned_cols=43 Identities=9% Similarity=0.115 Sum_probs=36.3
Q ss_pred chHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCC
Q 030509 90 AADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 136 (176)
Q Consensus 90 s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 136 (176)
.+..+.+.++++.+++. +++++|++..+++..++.+-.+.|.+
T Consensus 235 eps~~~l~~l~~~ik~~----~v~~If~e~~~~~~~~~~la~e~g~~ 277 (311)
T PRK09545 235 QPGAQRLHEIRTQLVEQ----KATCVFAEPQFRPAVIESVAKGTSVR 277 (311)
T ss_pred CCCHHHHHHHHHHHHHc----CCCEEEecCCCChHHHHHHHHhcCCe
Confidence 35678888999999874 89999999999999999888877753
No 106
>PRK14046 malate--CoA ligase subunit beta; Provisional
Probab=47.64 E-value=1e+02 Score=27.63 Aligned_cols=86 Identities=15% Similarity=0.079 Sum_probs=49.5
Q ss_pred ceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 44 KIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 44 ~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
..+.|+.+- . ..+++.+.+.|..++++-+++.|+|-.+ . |. ......++.+++.+++. . ++.|++.+-..-..
T Consensus 282 ~paNPlDlg-g-~a~~e~~~~aL~~ll~Dp~VdaVlv~i~-g-gi-~~~~~vA~~Ii~a~~~~-~-~~kPvvv~l~G~~~ 354 (392)
T PRK14046 282 EPANFLDVG-G-GASPERVAKAFRLVLSDRNVKAILVNIF-A-GI-NRCDWVAEGVVQAAREV-G-IDVPLVVRLAGTNV 354 (392)
T ss_pred CCcCCEEec-C-CCCHHHHHHHHHHHHcCCCCCEEEEEcC-C-CC-CCHHHHHHHHHHHHHhc-C-CCCcEEEEcCCCCH
Confidence 445677662 2 2344555566777777889999998766 2 21 11123344445444431 1 25677554433466
Q ss_pred HHHHHHhccCCCC
Q 030509 124 KGVELLLNPLDLH 136 (176)
Q Consensus 124 ~~A~~~l~~~g~~ 136 (176)
.++++.|.+.|+.
T Consensus 355 e~~~~iL~~~Gip 367 (392)
T PRK14046 355 EEGRKILAESGLP 367 (392)
T ss_pred HHHHHHHHHcCCC
Confidence 7778878887753
No 107
>cd02812 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.
Probab=47.61 E-value=58 Score=27.10 Aligned_cols=47 Identities=11% Similarity=0.248 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
..|.+++.+...+.|+|| ||.+-. ....+..+.+++..+ .+||++.-
T Consensus 15 ~~~~~~~~~~gtdai~vG-----GS~~v~-~~~~~~~~~ik~~~~--~~Pvilfp 61 (219)
T cd02812 15 EEIAKLAEESGTDAIMVG-----GSDGVS-STLDNVVRLIKRIRR--PVPVILFP 61 (219)
T ss_pred HHHHHHHHhcCCCEEEEC-----Cccchh-hhHHHHHHHHHHhcC--CCCEEEeC
Confidence 668888888889999999 888765 566667777775311 38888664
No 108
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=47.07 E-value=59 Score=27.14 Aligned_cols=57 Identities=16% Similarity=0.322 Sum_probs=43.0
Q ss_pred chHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030509 90 AADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN 159 (176)
Q Consensus 90 s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~ 159 (176)
.+..+.+.++.+.+++. +++++|++...++..++.+-++.|++ -..+|.++ .+|++.
T Consensus 200 eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~la~~~g~~----v~~ld~~~-----~~y~~~ 256 (266)
T cd01018 200 EPSPADLKRLIDLAKEK----GVRVVFVQPQFSTKSAEAIAREIGAK----VVTIDPLA-----ADWEEN 256 (266)
T ss_pred CCCHHHHHHHHHHHHHc----CCCEEEEcCCCCcHHHHHHHHHcCCe----EEEeCCcH-----HHHHHH
Confidence 35678888999999874 78999999999999999887777763 23456554 356654
No 109
>PRK13326 pantothenate kinase; Reviewed
Probab=46.97 E-value=1.7e+02 Score=24.84 Aligned_cols=22 Identities=14% Similarity=0.359 Sum_probs=19.1
Q ss_pred CeEEEEecCCCeEEEEEecCCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPKN 43 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~ 43 (176)
..+|+||+|-.+|=+++-+...
T Consensus 6 ~~~L~IDiGNT~ik~glf~~~~ 27 (262)
T PRK13326 6 SSQLIIDIGNTSISFALYKDNK 27 (262)
T ss_pred cEEEEEEeCCCeEEEEEEECCE
Confidence 4689999999999999998654
No 110
>PRK15005 universal stress protein F; Provisional
Probab=45.87 E-value=41 Score=24.47 Aligned_cols=19 Identities=11% Similarity=0.216 Sum_probs=17.0
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.|.+.++++++|.||+|
T Consensus 96 ~~~I~~~a~~~~~DLIV~G 114 (144)
T PRK15005 96 KDRILELAKKIPADMIIIA 114 (144)
T ss_pred HHHHHHHHHHcCCCEEEEe
Confidence 5788889999999999999
No 111
>cd03413 CbiK_C Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases, and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=45.66 E-value=94 Score=22.47 Aligned_cols=55 Identities=7% Similarity=-0.071 Sum_probs=32.8
Q ss_pred EEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCC
Q 030509 77 GFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 136 (176)
Q Consensus 77 ~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 136 (176)
.++|| .|+..+.....+.|++.+++.. .+++.+-+..=.-|-.++-+.+...|.+
T Consensus 3 illvg----HGSr~~~~~~~~~l~~~l~~~~-~~~v~~~~lE~~P~i~~~l~~l~~~G~~ 57 (103)
T cd03413 3 VVFMG----HGTDHPSNAVYAALEYVLREED-PANVFVGTVEGYPGLDDVLAKLKKAGIK 57 (103)
T ss_pred EEEEE----CCCCchhhhHHHHHHHHHHhcC-CCcEEEEEEcCCCCHHHHHHHHHHcCCC
Confidence 46788 8888876777788888887632 1234455665333444455555555543
No 112
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=45.55 E-value=1.1e+02 Score=24.17 Aligned_cols=19 Identities=26% Similarity=0.583 Sum_probs=15.5
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.+..++..+++++||+-
T Consensus 49 ~~~~~~~~~~~~~dgiii~ 67 (270)
T cd06294 49 LEEVKKMIQQKRVDGFILL 67 (270)
T ss_pred HHHHHHHHHHcCcCEEEEe
Confidence 4677788888889999986
No 113
>PRK13927 rod shape-determining protein MreB; Provisional
Probab=45.43 E-value=1.9e+02 Score=24.57 Aligned_cols=27 Identities=19% Similarity=0.295 Sum_probs=18.2
Q ss_pred CeEEEEecCCCeEEEEEecCCCceecc
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASP 48 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~P 48 (176)
.+.+|||+|+.++=+...+....+..|
T Consensus 5 ~~~igIDlGt~~~~i~~~~~~~~~~~p 31 (334)
T PRK13927 5 SNDLGIDLGTANTLVYVKGKGIVLNEP 31 (334)
T ss_pred cceeEEEcCcceEEEEECCCcEEEecC
Confidence 357899999998877665544333344
No 114
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit. This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G
Probab=45.35 E-value=1.1e+02 Score=26.98 Aligned_cols=84 Identities=12% Similarity=0.073 Sum_probs=48.4
Q ss_pred ceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 44 KIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 44 ~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
..+.|+.+- ...+.+.+.+.|..+.++-+++.|+|-++ |........++.+++.+++. . ++.||+.+-.....
T Consensus 282 ~~aNplDlg--g~a~~~~~~~al~~l~~dp~vd~ilv~i~---gg~~~~~~va~~i~~a~~~~-~-~~kPvvv~~~g~~~ 354 (386)
T TIGR01016 282 EPANFLDVG--GGASAERVREALKLVLSDKSVKVVFINIF---GGITRCDLVAKGLVEALKEV-G-VNVPVVVRLEGTNV 354 (386)
T ss_pred CCCCcEEec--CCCCHHHHHHHHHHHHcCCCCCEEEEECC---CCCCCHHHHHHHHHHHHHhc-C-CCCcEEEEeCCccH
Confidence 345666652 22344455566777777889999998655 22222233445555555542 1 13677555444455
Q ss_pred HHHHHHhccCC
Q 030509 124 KGVELLLNPLD 134 (176)
Q Consensus 124 ~~A~~~l~~~g 134 (176)
.+++++|.+.|
T Consensus 355 ~~~~~~L~~~G 365 (386)
T TIGR01016 355 EEGKKILAESG 365 (386)
T ss_pred HHHHHHHHHcC
Confidence 67788888877
No 115
>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine kinases. The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding.
Probab=44.69 E-value=38 Score=24.72 Aligned_cols=19 Identities=11% Similarity=0.433 Sum_probs=16.9
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.|.+.+++++++.||+|
T Consensus 92 ~~~I~~~a~~~~~dlIV~G 110 (146)
T cd01989 92 AKAIVEYVADHGITKLVMG 110 (146)
T ss_pred HHHHHHHHHHcCCCEEEEe
Confidence 4778899999999999999
No 116
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=43.59 E-value=38 Score=23.93 Aligned_cols=21 Identities=19% Similarity=0.219 Sum_probs=18.6
Q ss_pred HHHHHHHHHhcCCCEEEEecc
Q 030509 63 AEDFRSLISEFNLEGFIVGYP 83 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlP 83 (176)
.+.|.+++++++++.||+|..
T Consensus 83 ~~~I~~~a~~~~~dlIV~G~~ 103 (132)
T cd01988 83 ASGILRTAKERQADLIIMGWH 103 (132)
T ss_pred HHHHHHHHHhcCCCEEEEecC
Confidence 588999999999999999954
No 117
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=43.41 E-value=86 Score=26.35 Aligned_cols=44 Identities=20% Similarity=0.295 Sum_probs=36.1
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCC
Q 030509 89 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 136 (176)
Q Consensus 89 ~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 136 (176)
..+..+.+.++.+.+++. +++++|++..+++..++.+-++.|.+
T Consensus 202 ~eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~la~~~g~~ 245 (282)
T cd01017 202 VEPSPKQLAELVEFVKKS----DVKYIFFEENASSKIAETLAKETGAK 245 (282)
T ss_pred CCCCHHHHHHHHHHHHHc----CCCEEEEeCCCChHHHHHHHHHcCCc
Confidence 345678889999999874 89999999999999998887776653
No 118
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=43.30 E-value=67 Score=26.35 Aligned_cols=103 Identities=15% Similarity=0.090 Sum_probs=62.7
Q ss_pred HHHHHhc--CCCEEEEeccCCCCCC--chHHHHHHHHHHHHHhccCCCCCcEEEec-CcccHHHHHHH---hccCCCCCC
Q 030509 67 RSLISEF--NLEGFIVGYPFNRQQN--AADAVQVKLFIDDLSATKKLEDMKYAYWN-EGFTSKGVELL---LNPLDLHPV 138 (176)
Q Consensus 67 ~~li~e~--~~~~iVVGlPl~dG~~--s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D-Er~TT~~A~~~---l~~~g~~~~ 138 (176)
..+|+.| +...+|+|+=-.+-+. .....-+.+.|.++++. |++-++.++| -++|..--+.. |...|.+.+
T Consensus 64 l~lId~~~~~~GlviaGyy~Ane~~~D~s~~~~A~kiadrIse~--f~~A~ilv~dn~~l~~~~e~~~v~v~e~~g~rW~ 141 (199)
T KOG3289|consen 64 LNLIDVWGAQAGLVIAGYYHANERVNDQSLNPVALKIADRISEF--FPDAAILVLDNKKLVPQCERPPVIVLEDQGLRWR 141 (199)
T ss_pred HHHHHHHHHhcCeEEEEEeecCCCccccCccHHHHHHHHHHHhh--CCCCeEEEEeccccccccCCCCEEEeeccCccee
Confidence 3455554 5678899983222221 22334556788999874 7888988887 45554322222 224554444
Q ss_pred CCCC----CCcHHHHHHHHHHHHhhhhhhcccc-cccc
Q 030509 139 EYKT----ILDKFAAVGILQEYLDNANRKVNLK-ANVL 171 (176)
Q Consensus 139 ~~k~----~iD~~AA~iILq~yL~~~~~~~~~~-~~~~ 171 (176)
.+++ .-|-..|-.+|+.+|+++.-..-.+ ||-|
T Consensus 142 ~~d~~~~~~~d~~e~~~~ls~ll~~~~~r~LvDfDnHL 179 (199)
T KOG3289|consen 142 PKDKTLVQWSDWLEGRQMLSALLESRAYRDLVDFDNHL 179 (199)
T ss_pred ecCCchhhhhcchhHHHHHHHHHhhhhhhhhcchhhcc
Confidence 4332 3578889999999999877655554 4444
No 119
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=42.88 E-value=74 Score=26.70 Aligned_cols=41 Identities=17% Similarity=0.326 Sum_probs=33.1
Q ss_pred HHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 68 SLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 68 ~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
+.+.+...+.|+|| ||.+-....+.++.+.+++ + ++||++.
T Consensus 26 ~~~~~~gtdai~vG-----GS~~vt~~~~~~~v~~ik~---~-~lPvilf 66 (232)
T PRK04169 26 EAICESGTDAIIVG-----GSDGVTEENVDELVKAIKE---Y-DLPVILF 66 (232)
T ss_pred HHHHhcCCCEEEEc-----CCCccchHHHHHHHHHHhc---C-CCCEEEe
Confidence 55666789999999 8887777788888899985 3 7898875
No 120
>PF06180 CbiK: Cobalt chelatase (CbiK); InterPro: IPR010388 This group, typified by Salmonella typhimurium CbiK, contains anaerobic cobalt chelatases that act in the anaerobic cobalamin biosynthesis pathway [, ]. Cobalamin (vitamin B12) can be complexed with metal via ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in S. typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. This group belongs to the class of ATP-independent, single-subunit chelatases that also includes distantly related protoporphyrin IX (PPIX) ferrochelatase (HemH) (Class II chelatases) []. The structure of S. typhimurium CbiK shows that it has a remarkably similar topology to Bacillus subtilis ferrochelatase despite only weak sequence conservation []. Both enzymes contain a histidine residue identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase []. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency []. It should be noted that CysG and Met8p, which are multifunctional proteins associated with siroheme biosynthesis, include chelatase activity and can therefore be considered as the third class of chelatases []. As with the class II chelatases, they do not require ATP for activity. However, they are not structurally similar to HemH or CbiK, and it is likely that they have arisen by the acquisition of a chelatase function within a dehydrogenase catalytic framework [, ].; GO: 0016852 sirohydrochlorin cobaltochelatase activity; PDB: 1QGO_A 2XWP_A 2XVZ_A 2XVX_A 2XVY_A.
Probab=42.18 E-value=47 Score=28.34 Aligned_cols=64 Identities=14% Similarity=0.325 Sum_probs=39.6
Q ss_pred eeccceeeeCCCCChhhHHHHHHHHHHhcC--CCEEEEeccCC-C-CCCchHHHHHHHHHHHHHhccCCC----CCcEEE
Q 030509 45 IASPLSVLLRKKNTIDLMAEDFRSLISEFN--LEGFIVGYPFN-R-QQNAADAVQVKLFIDDLSATKKLE----DMKYAY 116 (176)
Q Consensus 45 ~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~--~~~iVVGlPl~-d-G~~s~~~~~v~~Fa~~L~~~~~~~----~lpV~~ 116 (176)
..+|+.+++-. + ++.|.+.++.+. .+.|+||.|+- . |.. +....++.+++.|... ++ +-.++|
T Consensus 76 ~VQplhiipG~-----E-y~~l~~~v~~~~~~F~~i~~g~PLL~~~g~~-~~~~D~~~va~aL~~~--~~~~~~~~a~vl 146 (262)
T PF06180_consen 76 VVQPLHIIPGE-----E-YEKLRATVEAYKHDFKKIVLGRPLLYTMGQE-NSPEDYEAVAEALAEE--FPKKRKDEAVVL 146 (262)
T ss_dssp EEEE--SCSSH-----H-HHHHHHHHHHHCCCSSEEEEE--SCSS------SHHHHHHHHHHHHCC--S-TT-TTEEEEE
T ss_pred EEeecceeCcH-----h-HHHHHHHHHHhhccCCeEEeccccccccccc-CChHHHHHHHHHHHHh--ccccCCCCEEEE
Confidence 44777777643 2 678888888764 68999999998 3 555 6677888899999863 32 344666
Q ss_pred e
Q 030509 117 W 117 (176)
Q Consensus 117 ~ 117 (176)
+
T Consensus 147 m 147 (262)
T PF06180_consen 147 M 147 (262)
T ss_dssp E
T ss_pred E
Confidence 5
No 121
>TIGR00671 baf pantothenate kinase, type III. This model describes a family of proteins found in a single copy in at least ten different early completed bacterial genomes. The only characterized member of the family is Bvg accessory factor (Baf), a protein required, in addition to the regulatory operon bvgAS, for heterologous transcription of the Bordetella pertussis toxin operon (ptx) in E. coli.
Probab=42.11 E-value=99 Score=25.77 Aligned_cols=55 Identities=18% Similarity=0.259 Sum_probs=33.6
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCC-CCChhhHHHHHHHHHHhcCCCEEEEe
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRK-KNTIDLMAEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~-~~~~~~~~~~L~~li~e~~~~~iVVG 81 (176)
+|++|+|-.+|=+|+-+... +... -.++.. ....+++...|..++.+ +++.+++.
T Consensus 1 ~L~iDiGNT~i~~g~~~~~~-~~~~-~r~~t~~~~t~de~~~~l~~~~~~-~i~~v~vs 56 (243)
T TIGR00671 1 LLLIDVGNTRIVFALNSGNK-VYQF-WRLATNLMKTYDEHSEFLKELFGK-SLNKAFIS 56 (243)
T ss_pred CEEEEECCCcEEEEEEECCE-EEEE-EEecCCCccChHHHHHHHHHHHHh-hCCEEEEE
Confidence 47899999999999988643 2221 122211 12233444556666655 48888888
No 122
>TIGR02628 fuculo_kin_coli L-fuculokinase. Members of this family are L-fuculokinase, from the clade that includes the L-fuculokinase of Escherichia coli. This enzyme catalyzes the second step in fucose catabolism. This family belongs to FGGY family of carbohydrate kinases (pfam02782, pfam00370). It is encoded by the kinase (K) gene of the fucose (fuc) operon.
Probab=41.86 E-value=68 Score=29.01 Aligned_cols=22 Identities=27% Similarity=0.320 Sum_probs=19.3
Q ss_pred EEEEecCCCeEEEEEecCCCce
Q 030509 24 FLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~ 45 (176)
+||||+|+.-+=+++-|..+.+
T Consensus 3 ilgiD~GTss~K~~l~d~~g~~ 24 (465)
T TIGR02628 3 ILVLDCGATNLRAIAINRQGKI 24 (465)
T ss_pred EEEEecCCCcEEEEEEcCCCCE
Confidence 7999999999999999987643
No 123
>PHA02533 17 large terminase protein; Provisional
Probab=41.79 E-value=1.2e+02 Score=28.41 Aligned_cols=62 Identities=18% Similarity=0.229 Sum_probs=42.0
Q ss_pred ccCCCCeEEEEecC----CCeEEEEEecCCCceeccceeee---CCCCChhhHHHHHHHHHHhcCCCEEEEe
Q 030509 17 KVSKRGRFLGLDVG----DKYVGLSISDPKNKIASPLSVLL---RKKNTIDLMAEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 17 ~~~~~~~iLglD~G----~kriGvAvsd~~~~~a~Pl~~i~---~~~~~~~~~~~~L~~li~e~~~~~iVVG 81 (176)
+.+....++|+|++ ...-++.|-|+.. .|..++. .+..++....+.|.++.+.|++..|.|=
T Consensus 310 P~~~~~y~ig~D~a~G~~~D~s~~~V~~~~~---~~~r~v~~~~~~~~~~~~~a~~I~~l~~~Yn~a~i~id 378 (534)
T PHA02533 310 PVEGHKYIATLDVSEGRGQDYSALHIIDITE---YPYKQVAVYHNNTISPLILPDIIVDYLMEYNEAPVYIE 378 (534)
T ss_pred CCCCceEEEEEECCCCCCCceeEEEEEccCC---CCcEEEEEEecCCCCHHHHHHHHHHHHHHhCceEEEEe
Confidence 34555679999998 4567777777642 2344443 3334555567899999999998877764
No 124
>PLN02757 sirohydrochlorine ferrochelatase
Probab=41.42 E-value=1.1e+02 Score=23.82 Aligned_cols=52 Identities=10% Similarity=-0.066 Sum_probs=26.6
Q ss_pred CCEEEEeccCCCCCCchHH-HHHHHHHHHHHhccCCCCCcEEEec-CcccHHHHHHHh
Q 030509 75 LEGFIVGYPFNRQQNAADA-VQVKLFIDDLSATKKLEDMKYAYWN-EGFTSKGVELLL 130 (176)
Q Consensus 75 ~~~iVVGlPl~dG~~s~~~-~~v~~Fa~~L~~~~~~~~lpV~~~D-Er~TT~~A~~~l 130 (176)
...++|| .||..+.+ ..+.+|++.|++...++.+.+.|.. ..-|-.+|-+.+
T Consensus 14 ~~lllvg----HGSrd~~a~~~~~~la~~l~~~~~~~~V~~aFle~~~Psl~eal~~l 67 (154)
T PLN02757 14 DGVVIVD----HGSRRKESNLMLEEFVAMYKQKTGHPIVEPAHMELAEPSIKDAFGRC 67 (154)
T ss_pred cEEEEEe----CCCCCHHHHHHHHHHHHHHHhhCCCCcEEEEEEecCCCCHHHHHHHH
Confidence 3557777 77766654 4557777777653222223344444 233444443333
No 125
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=41.27 E-value=1.1e+02 Score=20.64 Aligned_cols=62 Identities=10% Similarity=0.088 Sum_probs=42.8
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
++..+.+.+..++.+++++-+.++ .+ .++++.|++. .++.|++++=..-++....+.+ +.|.
T Consensus 33 ~~~~~~~~~~~~d~iiid~~~~~~-~~------~~~~~~i~~~--~~~~~ii~~t~~~~~~~~~~~~-~~g~ 94 (112)
T PF00072_consen 33 EEALELLKKHPPDLIIIDLELPDG-DG------LELLEQIRQI--NPSIPIIVVTDEDDSDEVQEAL-RAGA 94 (112)
T ss_dssp HHHHHHHHHSTESEEEEESSSSSS-BH------HHHHHHHHHH--TTTSEEEEEESSTSHHHHHHHH-HTTE
T ss_pred HHHHHHhcccCceEEEEEeeeccc-cc------cccccccccc--cccccEEEecCCCCHHHHHHHH-HCCC
Confidence 566677788899999999655532 22 3567777764 3588998887777766666666 4444
No 126
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=41.20 E-value=1.4e+02 Score=21.65 Aligned_cols=71 Identities=11% Similarity=0.112 Sum_probs=39.3
Q ss_pred hHHHHHHHHHHhcC--CCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 61 LMAEDFRSLISEFN--LEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 61 ~~~~~L~~li~e~~--~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
.-++++..+++.-+ +.+-|+-.... |...--...++.+.++.++. .++.++.+|..+|..+.+.+-...|.
T Consensus 8 ~~l~El~~L~~t~g~~vv~~~~q~~~~~~p~~~iG~GK~eei~~~~~~----~~~d~vvfd~~Lsp~Q~rNLe~~~~~ 81 (95)
T PF13167_consen 8 ESLEELEELAETAGYEVVGTVVQKRRKPDPKTYIGSGKVEEIKELIEE----LDADLVVFDNELSPSQQRNLEKALGV 81 (95)
T ss_pred HHHHHHHHHHHHCCCeEEEEEEecCCCCCcceeechhHHHHHHHHHhh----cCCCEEEECCCCCHHHHHHHHHHHCC
Confidence 34688888887643 33323332222 22221122334444444443 26788889988999998877554443
No 127
>COG1924 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]
Probab=41.06 E-value=1.2e+02 Score=27.55 Aligned_cols=52 Identities=13% Similarity=0.178 Sum_probs=34.3
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcC
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN 74 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~ 74 (176)
..+..||||.|+..+=+++-+....+... .+......+. ..+.|.+.+++-+
T Consensus 133 ~~~~~LGID~GSTtTK~VLm~d~~~I~~~--~~~~t~g~p~-~~~~l~~~le~l~ 184 (396)
T COG1924 133 QGMYTLGIDSGSTTTKAVLMEDGKEILYG--FYVSTKGRPI-AEKALKEALEELG 184 (396)
T ss_pred cCcEEEEEecCCcceeEEEEeCCCeEEEE--EEEcCCCChh-HHHHHHHHHHHcc
Confidence 56889999999999999988877756653 3333333332 2355555555543
No 128
>PRK13929 rod-share determining protein MreBH; Provisional
Probab=41.04 E-value=1.1e+02 Score=26.31 Aligned_cols=68 Identities=12% Similarity=0.156 Sum_probs=34.1
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCCh-hhHHHHHHHHHHhcCCCEEEEeccCCCCCCch
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTI-DLMAEDFRSLISEFNLEGFIVGYPFNRQQNAA 91 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~-~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~ 91 (176)
+.+|||+|+..+=+........+-.|--+....+... -.+-++-.+... ..++.+++-.|+.+|....
T Consensus 5 ~~~giDlGt~~~~i~~~~~~~~~~~ps~va~~~~~~~~~~vG~~A~~~~~-~~p~~~~~~~pi~~G~I~d 73 (335)
T PRK13929 5 TEIGIDLGTANILVYSKNKGIILNEPSVVAVDTETKAVLAIGTEAKNMIG-KTPGKIVAVRPMKDGVIAD 73 (335)
T ss_pred CeEEEEcccccEEEEECCCcEEecCCcEEEEECCCCeEEEeCHHHHHhhh-cCCCcEEEEecCCCCccCC
Confidence 4699999999997654332222224422221111110 000122222222 3467777779999877544
No 129
>PRK13410 molecular chaperone DnaK; Provisional
Probab=40.54 E-value=29 Score=33.37 Aligned_cols=21 Identities=24% Similarity=0.566 Sum_probs=18.2
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~ 42 (176)
+.++|||+|+..+-||+.++.
T Consensus 2 ~~viGIDlGTt~s~va~~~~g 22 (668)
T PRK13410 2 GRIVGIDLGTTNSVVAVMEGG 22 (668)
T ss_pred CcEEEEEeCCCcEEEEEEECC
Confidence 579999999999999998653
No 130
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=40.37 E-value=1.4e+02 Score=21.79 Aligned_cols=55 Identities=9% Similarity=0.260 Sum_probs=38.3
Q ss_pred HHHHHHHHHh-cCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHH
Q 030509 63 AEDFRSLISE-FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKG 125 (176)
Q Consensus 63 ~~~L~~li~e-~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~ 125 (176)
.+....+++. -.+.++||-+ + .........+.+.+..+ .+ ++||++.=|+.++..
T Consensus 26 ~dd~~~~i~~~~~i~avvi~~---d---~~~~~~~~~ll~~i~~~-~~-~iPVFl~~~~~~~~~ 81 (115)
T PF03709_consen 26 TDDALAIIESFTDIAAVVISW---D---GEEEDEAQELLDKIRER-NF-GIPVFLLAERDTTED 81 (115)
T ss_dssp HHHHHHHHHCTTTEEEEEEEC---H---HHHHHHHHHHHHHHHHH-ST-T-EEEEEESCCHHHC
T ss_pred hHHHHHHHHhCCCeeEEEEEc---c---cccchhHHHHHHHHHHh-CC-CCCEEEEecCCCccc
Confidence 3566677766 4789999985 3 55556667888888875 34 999999888765443
No 131
>TIGR01234 L-ribulokinase L-ribulokinase. This enzyme catalyzes the second step in arabinose catabolism. The most closely related protein subfamily outside the scope of this model includes ribitol kinase from E. coli.
Probab=40.22 E-value=66 Score=29.72 Aligned_cols=23 Identities=17% Similarity=0.134 Sum_probs=19.1
Q ss_pred eEEEEecCCCeEEEEEec-CCCce
Q 030509 23 RFLGLDVGDKYVGLSISD-PKNKI 45 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd-~~~~~ 45 (176)
.+||||.||.-+=+++-| ..+.+
T Consensus 2 ~~lgiD~GTss~Ka~l~d~~~G~~ 25 (536)
T TIGR01234 2 YAIGVDFGTLSGRALAVDVATGEE 25 (536)
T ss_pred eEEEEecCCCceEEEEEECCCCcE
Confidence 389999999999999999 65533
No 132
>PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F ....
Probab=40.20 E-value=1.2e+02 Score=20.76 Aligned_cols=49 Identities=10% Similarity=0.021 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.|.+++++++++.||+|-.-..+... ...-.++++|.+. . +.||..+
T Consensus 91 ~~~i~~~~~~~~~dliv~G~~~~~~~~~---~~~gs~~~~l~~~--~-~~pVlvv 139 (140)
T PF00582_consen 91 ADAIIEFAEEHNADLIVMGSRGRSGLER---LLFGSVAEKLLRH--A-PCPVLVV 139 (140)
T ss_dssp HHHHHHHHHHTTCSEEEEESSSTTSTTT---SSSHHHHHHHHHH--T-SSEEEEE
T ss_pred chhhhhccccccceeEEEeccCCCCccC---CCcCCHHHHHHHc--C-CCCEEEe
Confidence 5889999999999999999655311111 0112345555543 2 6787654
No 133
>TIGR02260 benz_CoA_red_B benzoyl-CoA reductase, bcr type, subunit B. This model describes B, or beta, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA.
Probab=40.17 E-value=1.5e+02 Score=26.89 Aligned_cols=60 Identities=10% Similarity=0.254 Sum_probs=38.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe-----cCcc-cHHHHHHH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW-----NEGF-TSKGVELL 129 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~-----DEr~-TT~~A~~~ 129 (176)
.+.|.++++++++|+||.=.-.. +....+... ..+.+.+. . ++|+..+ |+|. +..+.+.+
T Consensus 339 ~~~l~~l~ke~~aDGVI~~~~~~C~~~~~e~~~----~~~~l~e~--~-GIP~L~iE~D~~d~r~~d~gQ~~TR 405 (413)
T TIGR02260 339 VDLLEKYINEYEADGLLINSIKSCNSFSAGQLL----MMREIEKR--T-GKPAAFIETDLVDPRYFSAANVKNR 405 (413)
T ss_pred HHHHHHHHHHhCCCEEEEeccCCCCcchhhhHH----HHHHHHHH--c-CCCEEEEEcCCCCcccCCHHHHHHH
Confidence 68899999999999999987666 665554332 22334431 1 7886655 4555 44444443
No 134
>PRK04123 ribulokinase; Provisional
Probab=40.13 E-value=73 Score=29.43 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=19.3
Q ss_pred CeEEEEecCCCeEEEEEecC-CCc
Q 030509 22 GRFLGLDVGDKYVGLSISDP-KNK 44 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~-~~~ 44 (176)
..+||||.|+.-+=+++-|. .+.
T Consensus 3 ~~~lgiD~GTts~Ka~l~d~~~g~ 26 (548)
T PRK04123 3 AYVIGLDFGTDSVRALLVDCATGE 26 (548)
T ss_pred cEEEEEecCCCceEEEEEECCCCc
Confidence 35899999999999999994 654
No 135
>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=39.76 E-value=1.1e+02 Score=24.05 Aligned_cols=64 Identities=19% Similarity=0.216 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCC--CchHHHHHHHHHHHHHhccCCCCCcEEEec------CcccHHHHHHHhccCCC
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQ--NAADAVQVKLFIDDLSATKKLEDMKYAYWN------EGFTSKGVELLLNPLDL 135 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~--~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D------Er~TT~~A~~~l~~~g~ 135 (176)
+.+..++...+++.+|||.-..-|. .+. ....++++ ++ . ++.++.++ +..||..-++.+.+..+
T Consensus 89 ~Fi~~il~~~~~~~ivvG~Df~FG~~~~g~-~~~L~~~~---~~---~-g~~v~~v~~~~~~~~~iSST~IR~~i~~G~i 160 (180)
T cd02064 89 EFVEDLLVKLNAKHVVVGFDFRFGKGRSGD-AELLKELG---KK---Y-GFEVTVVPPVTLDGERVSSTRIREALAEGDV 160 (180)
T ss_pred HHHHHHHhhcCCeEEEEccCCCCCCCCCCC-HHHHHHhh---hh---c-CcEEEEeCcEecCCcEEcHHHHHHHHHhCCH
Confidence 3455566555899999997554121 121 11122222 22 1 55666655 46899988888875443
No 136
>cd03414 CbiX_SirB_C Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both CbiX and SirB are found in a wide range of bacteria.
Probab=39.38 E-value=1.2e+02 Score=21.73 Aligned_cols=55 Identities=15% Similarity=0.080 Sum_probs=32.7
Q ss_pred EEEEeccCCCCCCch-HHHHHHHHHHHHHhccCCCCCcEEEecC-cccHHHHHHHhccCCC
Q 030509 77 GFIVGYPFNRQQNAA-DAVQVKLFIDDLSATKKLEDMKYAYWNE-GFTSKGVELLLNPLDL 135 (176)
Q Consensus 77 ~iVVGlPl~dG~~s~-~~~~v~~Fa~~L~~~~~~~~lpV~~~DE-r~TT~~A~~~l~~~g~ 135 (176)
.++|| .||..+ ....+.++++.+++...+..+.+-|.+. .-|-.+|-+.+.+.|.
T Consensus 3 ~llv~----HGS~~~~~~~~~~~l~~~l~~~~~~~~v~~afle~~~P~~~~~l~~l~~~g~ 59 (117)
T cd03414 3 VVLVG----RGSSDPDANADVAKIARLLEEGTGFARVETAFAAATRPSLPEALERLRALGA 59 (117)
T ss_pred EEEEc----CCCCCHHHHHHHHHHHHHHHHhcCCCeEEEEEecCCCCCHHHHHHHHHHcCC
Confidence 46777 788755 3457788888887642111233456664 5556666666654443
No 137
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=39.35 E-value=46 Score=24.86 Aligned_cols=49 Identities=18% Similarity=0.221 Sum_probs=32.0
Q ss_pred EEEEeccCCCCCCchHHH-HHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCC
Q 030509 77 GFIVGYPFNRQQNAADAV-QVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD 134 (176)
Q Consensus 77 ~iVVGlPl~dG~~s~~~~-~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g 134 (176)
-++|| -||..+.++ .+..+++.+++. +|+.+|.+ -|||...++.|...|
T Consensus 3 illv~----fGS~~~~~~~~~~~i~~~l~~~--~p~~~V~~---afts~~i~~~l~~~~ 52 (127)
T cd03412 3 ILLVS----FGTSYPTAEKTIDAIEDKVRAA--FPDYEVRW---AFTSRMIRKKLKKRG 52 (127)
T ss_pred EEEEe----CCCCCHHHHHHHHHHHHHHHHH--CCCCeEEE---EecHHHHHHHHHhcC
Confidence 46788 888887553 568888889863 66666643 466655555554433
No 138
>cd01829 SGNH_hydrolase_peri2 SGNH_peri2; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=39.15 E-value=86 Score=24.10 Aligned_cols=50 Identities=14% Similarity=0.158 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 64 EDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
+.+.+.+++..+..|+++.|.. ....++......+..+.+.+. ..+.|+|
T Consensus 98 ~~lv~~~~~~~~~vili~~pp~~~~~~~~~~~~~~~~~~~~a~~-----~~~~~id 148 (200)
T cd01829 98 DELLNVARAKGVPVIWVGLPAMRSPKLSADMVYLNSLYREEVAK-----AGGEFVD 148 (200)
T ss_pred HHHHHHHHhCCCcEEEEcCCCCCChhHhHHHHHHHHHHHHHHHH-----cCCEEEE
Confidence 3444445567888899998766 433333333344444444432 2356666
No 139
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=39.14 E-value=1.1e+02 Score=26.77 Aligned_cols=53 Identities=11% Similarity=0.169 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.++.+++.+.++|.||++-=+- .+..+.. .+..|.+.|.+-. ..++||+.+
T Consensus 28 ~f~~~l~~a~~~~vD~vliAGDlFd~~~Ps~~--a~~~~~~~l~~l~-~~~Ipv~~I 81 (390)
T COG0420 28 AFDELLEIAKEEKVDFVLIAGDLFDTNNPSPR--ALKLFLEALRRLK-DAGIPVVVI 81 (390)
T ss_pred HHHHHHHHHHHccCCEEEEccccccCCCCCHH--HHHHHHHHHHHhc-cCCCcEEEe
Confidence 468888999999999999996666 5555543 3445666665421 137999877
No 140
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=38.78 E-value=1.4e+02 Score=23.53 Aligned_cols=50 Identities=18% Similarity=0.190 Sum_probs=29.9
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr 120 (176)
+.+...+.|.+++.+ ++++||+.-+-.+. .. .+.+++.+. ++||+++|-.
T Consensus 40 d~~~q~~~i~~~i~~-~~d~Iiv~~~~~~~----~~----~~l~~~~~~----gIpvv~~d~~ 89 (257)
T PF13407_consen 40 DPEEQIEQIEQAISQ-GVDGIIVSPVDPDS----LA----PFLEKAKAA----GIPVVTVDSD 89 (257)
T ss_dssp THHHHHHHHHHHHHT-TESEEEEESSSTTT----TH----HHHHHHHHT----TSEEEEESST
T ss_pred CHHHHHHHHHHHHHh-cCCEEEecCCCHHH----HH----HHHHHHhhc----CceEEEEecc
Confidence 334445677777754 59999998322211 11 344556652 7888888755
No 141
>PRK10606 btuE putative glutathione peroxidase; Provisional
Probab=38.65 E-value=50 Score=26.47 Aligned_cols=39 Identities=15% Similarity=0.319 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcCC-CEEEEeccCC--CCCCchHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNL-EGFIVGYPFN--RQQNAADAVQVKLFID 101 (176)
Q Consensus 63 ~~~L~~li~e~~~-~~iVVGlPl~--dG~~s~~~~~v~~Fa~ 101 (176)
...|.++.++++- +..|+|.|.+ .+.+......+++|++
T Consensus 43 ~~~L~~L~~~y~~~gl~Vlg~p~nqf~~qe~~~~~ei~~f~~ 84 (183)
T PRK10606 43 YEQLENIQKAWADQGFVVLGFPCNQFLGQEPGSDEEIKTYCR 84 (183)
T ss_pred HHHHHHHHHHHhhCCeEEEEeeccccccCCCCCHHHHHHHHH
Confidence 5778888888865 4668899998 3455455677888876
No 142
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=38.52 E-value=1.5e+02 Score=23.73 Aligned_cols=18 Identities=11% Similarity=0.287 Sum_probs=12.6
Q ss_pred HHHHHHHHhcCCCEEEEe
Q 030509 64 EDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVG 81 (176)
+.+.+.+..+++++||+-
T Consensus 45 ~~~~~~l~~~~vdgvi~~ 62 (269)
T cd06297 45 RYLESTTLAYLTDGLLLA 62 (269)
T ss_pred HHHHHHHHhcCCCEEEEe
Confidence 444455667888888886
No 143
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=38.36 E-value=1.8e+02 Score=25.03 Aligned_cols=66 Identities=14% Similarity=0.103 Sum_probs=44.2
Q ss_pred hhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 59 IDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 59 ~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
++..-+....++++|+++-+|+.-|-. +..++... | +.|+.. ++|.+.+-..-|++.. +.|.+.|+
T Consensus 45 pe~~~~~~~~~~~~~~pDf~i~isPN~-a~PGP~~A--R---E~l~~~----~iP~IvI~D~p~~K~~-d~l~~~g~ 110 (277)
T PRK00994 45 PEEVEEVVKKMLEEWKPDFVIVISPNP-AAPGPKKA--R---EILKAA----GIPCIVIGDAPGKKVK-DAMEEQGL 110 (277)
T ss_pred HHHHHHHHHHHHHhhCCCEEEEECCCC-CCCCchHH--H---HHHHhc----CCCEEEEcCCCccchH-HHHHhcCC
Confidence 344334566777999999999997754 34444322 2 235542 8899988888888755 77777665
No 144
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=38.11 E-value=30 Score=32.70 Aligned_cols=20 Identities=20% Similarity=0.617 Sum_probs=17.4
Q ss_pred CeEEEEecCCCeEEEEEecC
Q 030509 22 GRFLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~ 41 (176)
+.++|||+|+..+-+|+.++
T Consensus 2 ~~viGIDlGTt~s~va~~~~ 21 (627)
T PRK00290 2 GKIIGIDLGTTNSCVAVMEG 21 (627)
T ss_pred CcEEEEEeCcccEEEEEEEC
Confidence 46899999999999999864
No 145
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=37.81 E-value=40 Score=27.64 Aligned_cols=25 Identities=32% Similarity=0.529 Sum_probs=21.3
Q ss_pred ccCCCCeEEEEecCCCeEEEEEecC
Q 030509 17 KVSKRGRFLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 17 ~~~~~~~iLglD~G~kriGvAvsd~ 41 (176)
+...+|.+||+|.|..-+|||.-=|
T Consensus 53 T~~~PGlvl~L~~GGsc~GvafRip 77 (190)
T COG3703 53 TAEQPGLVLGLDRGGSCEGVAYRIP 77 (190)
T ss_pred CcCCCceEEEeeCCCcEEEEEEEcC
Confidence 4456799999999999999998655
No 146
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase. This model respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase.
Probab=37.58 E-value=1.4e+02 Score=27.37 Aligned_cols=71 Identities=13% Similarity=0.220 Sum_probs=45.7
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe-cCccc----HHHHHHHhcc
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW-NEGFT----SKGVELLLNP 132 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~-DEr~T----T~~A~~~l~~ 132 (176)
+++.++++|..+++++++..|.+. |++..--.+.+.+|++.|.++. .+.+.+. .-|.+ +.+--+.|.+
T Consensus 223 s~e~Vv~Ei~~l~~~~gv~~~~~~----Dd~f~~~~~~~~~l~~~l~~~~---~l~i~w~~~~r~~~i~~d~ell~~l~~ 295 (497)
T TIGR02026 223 DPKKFVDEIEWLVRTHGVGFFILA----DEEPTINRKKFQEFCEEIIARN---PISVTWGINTRVTDIVRDADILHLYRR 295 (497)
T ss_pred CHHHHHHHHHHHHHHcCCCEEEEE----ecccccCHHHHHHHHHHHHhcC---CCCeEEEEecccccccCCHHHHHHHHH
Confidence 456678999999999999998887 6655444567788999987641 1444332 22322 2333455666
Q ss_pred CCC
Q 030509 133 LDL 135 (176)
Q Consensus 133 ~g~ 135 (176)
+|.
T Consensus 296 aG~ 298 (497)
T TIGR02026 296 AGL 298 (497)
T ss_pred hCC
Confidence 665
No 147
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=37.46 E-value=1.1e+02 Score=25.47 Aligned_cols=38 Identities=11% Similarity=0.363 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLS 104 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~ 104 (176)
.+.|.+.+++.+++++|.| |=....|...+++.++++.
T Consensus 74 ~e~l~~~l~~~gv~~vv~G----dI~s~~qr~~~e~v~~~lg 111 (223)
T TIGR00290 74 VEELKGILHTLDVEAVVFG----AIYSEYQKTRIERVCRELG 111 (223)
T ss_pred HHHHHHHHHHcCCCEEEEC----CcccHHHHHHHHHHHHhcC
Confidence 6888898999899999999 6555556666666655553
No 148
>cd00851 MTH1175 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).
Probab=37.21 E-value=1.4e+02 Score=20.56 Aligned_cols=48 Identities=15% Similarity=0.075 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHH
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 128 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 128 (176)
..+.+++.+++++.+|+| ..++ .....|++. ++.++..++ .+-.+|-.
T Consensus 53 ~~~~~~l~~~~v~~vi~~------~iG~------~~~~~l~~~----gI~v~~~~~-~~i~~vl~ 100 (103)
T cd00851 53 GKAAEFLADEGVDVVIVG------GIGP------RALNKLRNA----GIKVYKGAE-GTVEEAIE 100 (103)
T ss_pred hHHHHHHHHcCCCEEEeC------CCCc------CHHHHHHHC----CCEEEEcCC-CCHHHHHH
Confidence 567777788999999998 3443 233457653 788988887 45555543
No 149
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=37.18 E-value=87 Score=22.30 Aligned_cols=46 Identities=7% Similarity=0.077 Sum_probs=29.9
Q ss_pred HHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHH
Q 030509 65 DFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 124 (176)
Q Consensus 65 ~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~ 124 (176)
+...-+++-.++.|||| -|+... +++|++.. .+ +.| ++.|+....-
T Consensus 4 ~~~~~l~~~gv~lv~I~----~g~~~~----~~~f~~~~----~~-p~~-ly~D~~~~lY 49 (115)
T PF13911_consen 4 RRKPELEAAGVKLVVIG----CGSPEG----IEKFCELT----GF-PFP-LYVDPERKLY 49 (115)
T ss_pred HhHHHHHHcCCeEEEEE----cCCHHH----HHHHHhcc----CC-CCc-EEEeCcHHHH
Confidence 34555666889999999 566522 56787552 25 568 7888854333
No 150
>PF00155 Aminotran_1_2: Aminotransferase class I and II 1-aminocyclopropane-1-carboxylate synthase signature aspartate aminotransferase signature; InterPro: IPR004839 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into class I and class II. This entry includes proteins from both subfamilies.; GO: 0016769 transferase activity, transferring nitrogenous groups, 0030170 pyridoxal phosphate binding, 0009058 biosynthetic process; PDB: 3NRA_B 3P6K_B 3OP7_A 3ASB_A 3ASA_A 1W7M_A 3FVX_A 1W7N_A 3FVU_B 3FVS_A ....
Probab=37.13 E-value=1.5e+02 Score=25.01 Aligned_cols=55 Identities=9% Similarity=0.192 Sum_probs=37.8
Q ss_pred HHHHHHHHHhc-----CCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 63 AEDFRSLISEF-----NLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 63 ~~~L~~li~e~-----~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
.+.|.+.++++ ++..+++--|-| .|..=+ ....+++++.+++. ++ ++++||.|..
T Consensus 132 ~~~l~~~l~~~~~~~~~~~~v~~~~p~nPtG~~~~-~~~l~~l~~~~~~~----~~-~ii~De~y~~ 192 (363)
T PF00155_consen 132 PEALEEALDELPSKGPRPKAVLICNPNNPTGSVLS-LEELRELAELAREY----NI-IIIVDEAYSD 192 (363)
T ss_dssp HHHHHHHHHTSHTTTETEEEEEEESSBTTTTBB---HHHHHHHHHHHHHT----TS-EEEEEETTTT
T ss_pred ccccccccccccccccccceeeecccccccccccc-cccccchhhhhccc----cc-ceeeeeceec
Confidence 58888888886 578899999999 887432 34456677766652 43 4557887754
No 151
>TIGR00289 conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.
Probab=37.05 E-value=1.2e+02 Score=25.26 Aligned_cols=38 Identities=16% Similarity=0.370 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLS 104 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~ 104 (176)
.+.+.+.+++..+++||.| +=....|...+++.++++.
T Consensus 74 ~~~l~~~l~~~gv~~vv~G----dI~s~~qr~~~e~vc~~~g 111 (222)
T TIGR00289 74 VEDLAGQLGELDVEALCIG----AIESNYQKSRIDKVCRELG 111 (222)
T ss_pred HHHHHHHHHHcCCCEEEEC----ccccHHHHHHHHHHHHHcC
Confidence 6788888888899999999 6666666666666666654
No 152
>COG1521 Pantothenate kinase type III (Bvg accessory factor family protein) [Transcription]
Probab=36.82 E-value=91 Score=26.55 Aligned_cols=24 Identities=17% Similarity=0.418 Sum_probs=19.1
Q ss_pred eEEEEecCCCeEEEEEecCCCceec
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIAS 47 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a~ 47 (176)
++|.||.|-.++=+|+.+ .+.+..
T Consensus 1 ~~L~iDiGNT~~~~a~~~-~~~~~~ 24 (251)
T COG1521 1 MLLLIDIGNTRIVFALYE-GGKVVQ 24 (251)
T ss_pred CeEEEEeCCCeEEEEEec-CCeEEE
Confidence 479999999999999998 344443
No 153
>cd06547 GH85_ENGase Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins. The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the protein and N-acetylglucosamine 2 forms the reducing end of the released glycan. ENGase is a key enzyme in the processing of free oligosaccharides in the cytosol of eukaryotes. Oligosaccharides formed in the lumen of the endoplasmic reticulum are transported into the cytosol where they are catabolized by cytosolic ENGases and other enzymes, possibly to maximize the reutilization of the component sugars. ENGases have an eight-stranded alpha/beta barrel topology and are classified as a family 85 glycosyl hydrolase (GH85) domain. The GH85 ENGases are sequence-similar to the family 18 glycosyl hydrolases, also known as GH18 chitinases. An ENGase-like protein is also found in bacteria and is included in this alignment mod
Probab=36.72 E-value=1.7e+02 Score=25.74 Aligned_cols=58 Identities=12% Similarity=0.286 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhcc--CCCCCcEEEecC
Q 030509 61 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATK--KLEDMKYAYWNE 119 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~--~~~~lpV~~~DE 119 (176)
.++++|.++++.+..+++.|-.=.. +...+.+.....|.+.|.+.. ..++..|++.|=
T Consensus 90 ~~a~kLv~lak~yGfDGw~iN~E~~-~~~~~~~~~l~~F~~~L~~~~~~~~~~~~v~WYDs 149 (339)
T cd06547 90 PVADKLVEVAKYYGFDGWLINIETE-LGDAEKAKRLIAFLRYLKAKLHENVPGSLVIWYDS 149 (339)
T ss_pred HHHHHHHHHHHHhCCCceEeeeecc-CCcHHHHHHHHHHHHHHHHHHhhcCCCcEEEEEec
Confidence 4679999999999999988873222 223456777788888887642 235778888884
No 154
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=36.57 E-value=1.7e+02 Score=21.55 Aligned_cols=49 Identities=18% Similarity=0.270 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHH---hccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLS---ATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~---~~~~~~~lpV~~~ 117 (176)
++++.+.+. +.|+||+|-|...|+.+...+ .|.+++. .. .+.+-++.++
T Consensus 61 ~~~~~~~l~--~aD~iI~~sP~y~~~~s~~lK---~~lD~~~~~~~~-~~~~K~~~~i 112 (152)
T PF03358_consen 61 VQELYDKLK--EADGIIFASPVYNGSVSGQLK---NFLDRLSCWFRR-ALRGKPVAII 112 (152)
T ss_dssp HHHHHHHHH--HSSEEEEEEEEBTTBE-HHHH---HHHHTHHHTHTT-TTTTSEEEEE
T ss_pred HHHHHhcee--cCCeEEEeecEEcCcCChhhh---HHHHHhcccccc-ccCCCEEEEE
Confidence 456666554 589999999999777776544 6777774 22 2446666655
No 155
>PF14450 FtsA: Cell division protein FtsA; PDB: 1E4F_T 4A2B_A 4A2A_A 1E4G_T.
Probab=35.99 E-value=35 Score=24.99 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=16.0
Q ss_pred EEEEecCCCeEEEEEecCC
Q 030509 24 FLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~ 42 (176)
+.+||+|+.+|.+++....
T Consensus 1 i~~iDiGs~~~~~~i~~~~ 19 (120)
T PF14450_consen 1 IVVIDIGSSKTKVAIAEDG 19 (120)
T ss_dssp EEEEEE-SSSEEEEEEETT
T ss_pred CEEEEcCCCcEEEEEEEeC
Confidence 5789999999999999873
No 156
>COG0443 DnaK Molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=35.98 E-value=56 Score=30.95 Aligned_cols=22 Identities=14% Similarity=0.305 Sum_probs=19.8
Q ss_pred CCeEEEEecCCCeEEEEEecCC
Q 030509 21 RGRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~ 42 (176)
+..++|||+|+-.+=||+.++.
T Consensus 4 ~~~~iGIDlGTTNS~vA~~~~~ 25 (579)
T COG0443 4 AKKAIGIDLGTTNSVVAVMRGG 25 (579)
T ss_pred CceEEEEEcCCCcEEEEEEeCC
Confidence 3579999999999999999976
No 157
>CHL00094 dnaK heat shock protein 70
Probab=35.92 E-value=34 Score=32.40 Aligned_cols=21 Identities=19% Similarity=0.520 Sum_probs=18.0
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~ 42 (176)
+.++|||+|+..+-+|+.++.
T Consensus 2 ~~viGIDlGTt~s~va~~~~g 22 (621)
T CHL00094 2 GKVVGIDLGTTNSVVAVMEGG 22 (621)
T ss_pred CceEEEEeCcccEEEEEEECC
Confidence 469999999999999998653
No 158
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=35.85 E-value=3.4e+02 Score=24.66 Aligned_cols=73 Identities=14% Similarity=0.155 Sum_probs=40.5
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcE-EEecCcccHHHHHHHhccCCC
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKY-AYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV-~~~DEr~TT~~A~~~l~~~g~ 135 (176)
+++.+.+.|..+.++-+++.++|.+... .... ...++.+++..++. .+.|+ ..+.+-....++++.|.+.|+
T Consensus 354 ~~~~~~~al~~l~~dp~vd~Vlv~~~~~~~~~~---~~~a~~l~~~~~~~---~~KPvv~~~~gg~~~~~~~~~L~~~Gi 427 (447)
T TIGR02717 354 TPERYAKALKTVAEDENVDGVVVVLTPTAMTDP---EEVAKGIIEGAKKS---NEKPVVAGFMGGKSVDPAKRILEENGI 427 (447)
T ss_pred CHHHHHHHHHHHHcCCCCCEEEEEccCCccCCH---HHHHHHHHHHHHhc---CCCcEEEEecCCccHHHHHHHHHhCCC
Confidence 3445456666677777899999887532 1111 23334455544431 13354 344444455667777777665
Q ss_pred C
Q 030509 136 H 136 (176)
Q Consensus 136 ~ 136 (176)
.
T Consensus 428 p 428 (447)
T TIGR02717 428 P 428 (447)
T ss_pred C
Confidence 3
No 159
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=35.81 E-value=1.8e+02 Score=23.27 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=37.0
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEeccCC---CCC-CchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYPFN---RQQ-NAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlPl~---dG~-~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
+.+.+.+.+..++.+++++.|||=. ++ .+. .......+.++.+.|+...+-.+++++++-+
T Consensus 107 ~~~~l~~~i~~~~~~~~~~~vvID~-l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q 171 (242)
T cd00984 107 TVSDIRSRARRLKKEHGLGLIVIDY-LQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQ 171 (242)
T ss_pred CHHHHHHHHHHHHHhcCCCEEEEcC-chhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecc
Confidence 3445567778888888999999873 43 222 2334445566666665321113888888764
No 160
>PLN02669 xylulokinase
Probab=35.74 E-value=99 Score=28.98 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=22.8
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCce
Q 030509 19 SKRGRFLGLDVGDKYVGLSISDPKNKI 45 (176)
Q Consensus 19 ~~~~~iLglD~G~kriGvAvsd~~~~~ 45 (176)
|....+||||+||..+=.++-|..+.+
T Consensus 5 ~~~~~~LGiD~GT~s~Ka~l~d~~g~v 31 (556)
T PLN02669 5 PEDSLFLGFDSSTQSLKATVLDSNLRI 31 (556)
T ss_pred CCCCeEEEEecccCCeEEEEEcCCCCE
Confidence 555679999999999999998988765
No 161
>cd01844 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=35.70 E-value=1.5e+02 Score=22.51 Aligned_cols=52 Identities=13% Similarity=0.117 Sum_probs=35.5
Q ss_pred HHHHHHhcCCCEEEEeccCCC-CCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 66 FRSLISEFNLEGFIVGYPFNR-QQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 66 L~~li~e~~~~~iVVGlPl~d-G~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
+.+++..++++.|||-+=-|| +...+..+..+.+.+.+.+. .|+.||+++.=
T Consensus 49 ~~~~~~~~~pd~vii~~G~ND~~~~~~~~~~~~~~i~~i~~~--~p~~~iil~~~ 101 (177)
T cd01844 49 VAELLRDVPADLYIIDCGPNIVGAEAMVRERLGPLVKGLRET--HPDTPILLVSP 101 (177)
T ss_pred HHHHHHhcCCCEEEEEeccCCCccHHHHHHHHHHHHHHHHHH--CcCCCEEEEec
Confidence 456677789999998655552 22224667778888888863 46778887653
No 162
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=35.65 E-value=83 Score=26.32 Aligned_cols=62 Identities=11% Similarity=0.164 Sum_probs=42.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc------ccHHHHHHHhc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG------FTSKGVELLLN 131 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr------~TT~~A~~~l~ 131 (176)
.-++.+.+.+..++++++.-|.. .-+. ..+.+|-+.+.+. .++||+++|-- +|...-+++..
T Consensus 84 ~~~~a~~a~~~G~d~v~~~~P~~~~~~~----~~l~~~~~~ia~~---~~~pi~lYn~P~~~g~~ls~~~~~~L~~ 152 (284)
T cd00950 84 AIELTKRAEKAGADAALVVTPYYNKPSQ----EGLYAHFKAIAEA---TDLPVILYNVPGRTGVNIEPETVLRLAE 152 (284)
T ss_pred HHHHHHHHHHcCCCEEEEcccccCCCCH----HHHHHHHHHHHhc---CCCCEEEEEChhHhCCCCCHHHHHHHhc
Confidence 45677778889999999999977 5443 3345666666653 37999999853 45555555543
No 163
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=35.64 E-value=1.7e+02 Score=21.28 Aligned_cols=67 Identities=9% Similarity=0.014 Sum_probs=44.8
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCC
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHP 137 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~ 137 (176)
.+++.+.+.+++++.|++. ++.......++++++.|++.. ++++++ ++-=+..+.+ ...|.+.|+..
T Consensus 39 ~e~~~~~a~~~~~d~V~iS-----~~~~~~~~~~~~~~~~L~~~~-~~~i~i-~~GG~~~~~~-~~~~~~~G~d~ 105 (122)
T cd02071 39 PEEIVEAAIQEDVDVIGLS-----SLSGGHMTLFPEVIELLRELG-AGDILV-VGGGIIPPED-YELLKEMGVAE 105 (122)
T ss_pred HHHHHHHHHHcCCCEEEEc-----ccchhhHHHHHHHHHHHHhcC-CCCCEE-EEECCCCHHH-HHHHHHCCCCE
Confidence 4788888999999998886 566677778899999998852 224444 4443333333 34556677643
No 164
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=35.54 E-value=1.4e+02 Score=25.33 Aligned_cols=43 Identities=12% Similarity=0.091 Sum_probs=35.8
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 89 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 89 ~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
..+..+.+.++.+.+++. +++++|.+...++..++.+-++.|.
T Consensus 210 ~eps~~~l~~l~~~ik~~----~v~~If~e~~~~~~~~~~ia~~~g~ 252 (286)
T cd01019 210 IDPGAKRLAKIRKEIKEK----GATCVFAEPQFHPKIAETLAEGTGA 252 (286)
T ss_pred CCCCHHHHHHHHHHHHHc----CCcEEEecCCCChHHHHHHHHhcCc
Confidence 445678888899988873 8999999999999999988877775
No 165
>PRK13411 molecular chaperone DnaK; Provisional
Probab=35.21 E-value=40 Score=32.26 Aligned_cols=21 Identities=19% Similarity=0.545 Sum_probs=17.9
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~ 42 (176)
+.++|||+|+..+=||+.++.
T Consensus 2 ~~viGIDlGTt~s~va~~~~g 22 (653)
T PRK13411 2 GKVIGIDLGTTNSCVAVLEGG 22 (653)
T ss_pred CcEEEEEeCcccEEEEEEECC
Confidence 469999999999999997653
No 166
>PRK14878 UGMP family protein; Provisional
Probab=34.85 E-value=1.5e+02 Score=25.74 Aligned_cols=90 Identities=12% Similarity=0.134 Sum_probs=50.7
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCC----------CChhhHHHHHHHHHHh-----cCCCEEEEeccCCCCCC
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKK----------NTIDLMAEDFRSLISE-----FNLEGFIVGYPFNRQQN 89 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~----------~~~~~~~~~L~~li~e-----~~~~~iVVGlPl~dG~~ 89 (176)
||||-=..-+++|+.+....++.-..+..+.. ...+.+...+.+++++ .+++.|.|+.- -|..
T Consensus 1 l~iets~~~~s~al~~~~~i~~~~~~~~~~~~gg~~p~~~~~~h~~~l~~~i~~~l~~a~~~~~did~Iavt~g--PG~~ 78 (323)
T PRK14878 1 LGIESTAHTLGVGIVKEDKVLANVRDTYVPEKGGIHPREAAQHHAEVAPELLRKALEKAGISIEDIDAVAVSQG--PGLG 78 (323)
T ss_pred CEEecCCcccEEEEEECCEEEEEEEEecccCcCCcCccHHHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecC--CCcc
Confidence 57777778889999875444443322221100 0011233556666666 46799999931 1333
Q ss_pred chHHHHHHHHHHHHHhccCCCCCcEEEecCc
Q 030509 90 AADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120 (176)
Q Consensus 90 s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr 120 (176)
+ .-+-...||+.|+.. + ++|++.++.-
T Consensus 79 ~-~lrvg~~~Ak~la~~--~-~~p~~~v~h~ 105 (323)
T PRK14878 79 P-ALRVGATAARALALK--Y-NKPLVPVNHC 105 (323)
T ss_pred c-chHHHHHHHHHHHHH--h-CCCccccchH
Confidence 2 223336678888763 3 7788887653
No 167
>cd01137 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=34.48 E-value=1.3e+02 Score=25.44 Aligned_cols=45 Identities=7% Similarity=0.141 Sum_probs=37.1
Q ss_pred CCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCC
Q 030509 88 QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 136 (176)
Q Consensus 88 ~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 136 (176)
...+..+.+.++.+.+++. +++++|++..+++..++.+-++.|.+
T Consensus 207 ~~eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~ia~~~gv~ 251 (287)
T cd01137 207 EEEGTPKQVATLIEQVKKE----KVPAVFVESTVNDRLMKQVAKETGAK 251 (287)
T ss_pred CCCCCHHHHHHHHHHHHHh----CCCEEEEeCCCChHHHHHHHHHhCCc
Confidence 3446688889999999873 89999999999999998887777764
No 168
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=34.41 E-value=1.9e+02 Score=23.80 Aligned_cols=90 Identities=11% Similarity=0.200 Sum_probs=45.5
Q ss_pred EEecCCCeEEEEEecCCC-cee---ccceeeeCCC-CChhh---HHHHHHHHHHh---cCCCEEEEeccCC-CCCCchHH
Q 030509 26 GLDVGDKYVGLSISDPKN-KIA---SPLSVLLRKK-NTIDL---MAEDFRSLISE---FNLEGFIVGYPFN-RQQNAADA 93 (176)
Q Consensus 26 glD~G~kriGvAvsd~~~-~~a---~Pl~~i~~~~-~~~~~---~~~~L~~li~e---~~~~~iVVGlPl~-dG~~s~~~ 93 (176)
|||+|+..|=+.+.+... ..| .|-..+.... .+.+. ++.++.+.+++ ..+..+|++.|-+ +...-
T Consensus 1 g~dig~~~ik~v~~~~~~~~~~~~~~~~~~~~~g~I~d~~~~~~~l~~l~~~a~~~~g~~~~~vvisVP~~~~~~~r--- 77 (239)
T TIGR02529 1 GVDLGTANIVIVVLDEDGQPVAGVMQFADVVRDGIVVDFLGAVEIVRRLKDTLEQKLGIELTHAATAIPPGTIEGDP--- 77 (239)
T ss_pred CCCcccceEEEEEEecCCCEEEEEecccccccCCeEEEhHHHHHHHHHHHHHHHHHhCCCcCcEEEEECCCCCcccH---
Confidence 689999999877755443 222 1111111100 11222 23444433322 3578999999988 54432
Q ss_pred HHHHHHHHHHHhccCCCCCc-EEEecCcccHHH
Q 030509 94 VQVKLFIDDLSATKKLEDMK-YAYWNEGFTSKG 125 (176)
Q Consensus 94 ~~v~~Fa~~L~~~~~~~~lp-V~~~DEr~TT~~ 125 (176)
+...+.++.. ++. +.+++|.+....
T Consensus 78 ---~a~~~a~~~a----Gl~~~~li~ep~Aaa~ 103 (239)
T TIGR02529 78 ---KVIVNVIESA----GIEVLHVLDEPTAAAA 103 (239)
T ss_pred ---HHHHHHHHHc----CCceEEEeehHHHHHH
Confidence 1233334432 454 456667654443
No 169
>PRK15456 universal stress protein UspG; Provisional
Probab=34.38 E-value=42 Score=24.63 Aligned_cols=20 Identities=15% Similarity=0.401 Sum_probs=18.1
Q ss_pred HHHHHHHHHhcCCCEEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGY 82 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGl 82 (176)
.+.|.+.+++++++.||+|-
T Consensus 94 ~~~I~~~a~~~~~DLIVmG~ 113 (142)
T PRK15456 94 RDEVNELAEELGADVVVIGS 113 (142)
T ss_pred HHHHHHHHhhcCCCEEEEcC
Confidence 57899999999999999993
No 170
>PF01884 PcrB: PcrB family; InterPro: IPR008205 This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase, which is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) []. Some of the prokaryotic proteins in this family are related to pcrB. The Staphylococcus aureus chromosomal gene pcrA encodes a protein with significant similarity (40% identity) to two Escherichia coli helicases: the helicase II encoded by the uvrD gene and the Rep helicase. PcrB gene seems to belong to an operon containing at least one other gene, pcrBA, downstream from pcrB []. The PcrB proteins often contain an FMN binding site although the function of these proteins is still unknown.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 1VIZ_A 2F6X_B 2F6U_B 3VKD_A 3VKA_A 3VK5_B 3VKC_B 3VKB_B.
Probab=34.15 E-value=1.3e+02 Score=25.27 Aligned_cols=44 Identities=14% Similarity=0.196 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCC-chHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQN-AADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~-s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
+.+.+.+.+...|.|+|| ||. +..... ....+++. +++||++.-
T Consensus 22 ~~~~~~~~~~gtDai~VG-----GS~~~~~~d~---vv~~ik~~---~~lPvilfP 66 (230)
T PF01884_consen 22 EEALEAACESGTDAIIVG-----GSDTGVTLDN---VVALIKRV---TDLPVILFP 66 (230)
T ss_dssp HHHHHHHHCTT-SEEEEE------STHCHHHHH---HHHHHHHH---SSS-EEEET
T ss_pred HHHHHHHHhcCCCEEEEC-----CCCCccchHH---HHHHHHhc---CCCCEEEeC
Confidence 444555577889999999 888 444444 44555542 389998874
No 171
>TIGR00329 gcp_kae1 metallohydrolase, glycoprotease/Kae1 family. This subfamily includes the well-studied secreted O-sialoglycoprotein endopeptidase (glycoprotease, EC 3.4.24.57) of Pasteurella haemolytica, a pathogen. A member from Riemerella anatipestifer, associated with cohemolysin activity, likewise is exported without benefit of a classical signal peptide and shows glycoprotease activity on the test substrate glycophorin. However, archaeal members of this subfamily show unrelated activities as demonstrated in Pyrococcus abyssi: DNA binding, iron binding, apurinic endonuclease activity, genomic association with a kinase domain, and no glycoprotease activity. This family thus pulls together a set of proteins as a homology group that appears to be near-universal in life, yet heterogeneous in assayed function between bacteria and archaea.
Probab=33.98 E-value=3e+02 Score=23.52 Aligned_cols=89 Identities=15% Similarity=0.117 Sum_probs=51.4
Q ss_pred EEEecCCCeEEEEEecCC-Cceeccceee-----------eC--CCCChhhHHHHHHHHHHhc-----CCCEEEEeccCC
Q 030509 25 LGLDVGDKYVGLSISDPK-NKIASPLSVL-----------LR--KKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFN 85 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~-~~~a~Pl~~i-----------~~--~~~~~~~~~~~L~~li~e~-----~~~~iVVGlPl~ 85 (176)
||||--...+++|+.|.. ..++.-..+. +. .....+.+...+.+++++- +++.|+|+.=
T Consensus 1 LaidTs~~~~sval~~~~~~il~~~~~~~~~~~~~~gGi~p~~~~~~H~~~l~~~i~~~l~~~~~~~~did~iav~~G-- 78 (305)
T TIGR00329 1 LGIETSCDDTGVAIVDEEGNVLANIKISQIPLHAKYGGVVPEEASRHHAENIPPLLERALIESNVDKSEIDLIAYTQG-- 78 (305)
T ss_pred CEEecCccceEEEEEECCCcEEEEEEecccccccccCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecC--
Confidence 689999999999999862 3343211110 10 0001123345566666553 5799999830
Q ss_pred CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 86 RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 86 dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
-|+.+. .+....+|+.|... + ++|++.++.
T Consensus 79 PG~~tg-lrvg~~~Ak~la~~--~-~~p~~~v~h 108 (305)
T TIGR00329 79 PGLGGS-LRVGATFARSLALS--L-DKPLIGVNH 108 (305)
T ss_pred CCchhh-HHHHHHHHHHHHHH--h-CCCEeeccc
Confidence 233332 34446788888863 3 889988853
No 172
>KOG0237 consensus Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism]
Probab=33.62 E-value=1.1e+02 Score=29.71 Aligned_cols=70 Identities=19% Similarity=0.206 Sum_probs=49.1
Q ss_pred HHHHHHHHHhcCCCEEEEec--cCCCC----------------CCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHH
Q 030509 63 AEDFRSLISEFNLEGFIVGY--PFNRQ----------------QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 124 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGl--Pl~dG----------------~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~ 124 (176)
++.|.++..+|+|..+|+|= ||-+| ....|.+--+.|++.+-.+ .++|-.-|+-=--+.
T Consensus 57 ~~ala~f~~e~~I~lVvvGPE~PL~~Gl~~~l~~~gi~~FGPs~~aAqlE~sK~fsK~fm~r---~~IPTA~y~~ft~~e 133 (788)
T KOG0237|consen 57 FEALASFCKEHNINLVVVGPELPLVAGLADVLRSAGIPCFGPSKQAAQLEASKNFSKDFMHR---HNIPTAKYKTFTDPE 133 (788)
T ss_pred HHHHHHHHHHcceeEEEECCchhhhhhhhhhhhccCcceeCchHHHHHhhhhHHHHHHHHHh---cCCCcceeeeeCCHH
Confidence 68999999999999999983 44333 2345555668899888764 388865554333347
Q ss_pred HHHHHhccCCC
Q 030509 125 GVELLLNPLDL 135 (176)
Q Consensus 125 ~A~~~l~~~g~ 135 (176)
+|...+....+
T Consensus 134 ~a~sfi~~~~~ 144 (788)
T KOG0237|consen 134 EAKSFIQSATD 144 (788)
T ss_pred HHHHHHHhCCC
Confidence 88888776554
No 173
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=33.62 E-value=1.1e+02 Score=25.25 Aligned_cols=93 Identities=15% Similarity=0.260 Sum_probs=50.7
Q ss_pred HHHHHHHH--HHhcCCCEE-EEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCC
Q 030509 62 MAEDFRSL--ISEFNLEGF-IVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPV 138 (176)
Q Consensus 62 ~~~~L~~l--i~e~~~~~i-VVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~ 138 (176)
..+.|.++ +...++.+| =|||++..........+.+-|.+.|+-.... ++||.+...+ +..+.-+.+.+.+...
T Consensus 73 ~~~~l~~l~~~~~~~~~aIGEiGLD~~~~~~~~~~~Q~~vF~~ql~lA~~~-~~pv~iH~r~-a~~~~l~il~~~~~~~- 149 (255)
T PF01026_consen 73 DLEELEELINLNRPKVVAIGEIGLDYYWRNEEDKEVQEEVFERQLELAKEL-NLPVSIHCRK-AHEELLEILKEYGPPN- 149 (255)
T ss_dssp HHHHHHHHHHHTSTTEEEEEEEEEETTTTSSSGHHHHHHHHHHHHHHHHHH-TCEEEEEEES-HHHHHHHHHHHTTGGT-
T ss_pred HHHHHHHHHHhccccceeeeeeccCcccccCCcHHHHHHHHHHHHHHHHHh-CCcEEEecCC-cHHHHHHHHHhccccc-
Confidence 35677777 665666656 6899984112222333444555555421123 7898888777 5666667776655221
Q ss_pred CCCCCCcHHHHHH-HHHHHHh
Q 030509 139 EYKTILDKFAAVG-ILQEYLD 158 (176)
Q Consensus 139 ~~k~~iD~~AA~i-ILq~yL~ 158 (176)
.+..++.+.+.. .++.+++
T Consensus 150 -~~~i~H~f~g~~~~~~~~~~ 169 (255)
T PF01026_consen 150 -LRVIFHCFSGSPEEAKKFLD 169 (255)
T ss_dssp -SEEEETT--S-HHHHHHHHH
T ss_pred -eeEEEecCCCCHHHHHHHHh
Confidence 145555555444 5555553
No 174
>PF04412 DUF521: Protein of unknown function (DUF521); InterPro: IPR007506 This is a group of hypothetical proteins.
Probab=33.37 E-value=2.4e+02 Score=25.67 Aligned_cols=89 Identities=9% Similarity=0.063 Sum_probs=56.9
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc------CCCEEEEeccCCCCCCchHH
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF------NLEGFIVGYPFNRQQNAADA 93 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~------~~~~iVVGlPl~dG~~s~~~ 93 (176)
.+-.+.|+-+--....-|+... .+++.-. .+.|.+..++. ++|.+++|-|-- ..
T Consensus 243 ~m~Hi~GvTPEa~~~~~a~~~~-------~e~i~i~-------~~dl~~~~~~l~~~~~~~~D~V~lGcPH~------S~ 302 (400)
T PF04412_consen 243 AMFHIVGVTPEAPTLEAAFGGK-------AERITIT-------DADLEEVYEELNTAGDEKVDLVALGCPHL------SL 302 (400)
T ss_pred eeEEEeCCCCCCCcchhhhcCC-------ceEEEeC-------HHHHHHHHHHhccCCCCCCCEEEECCCCC------CH
Confidence 3456777777777666666543 2333322 13344444444 899999995544 45
Q ss_pred HHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHH
Q 030509 94 VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 128 (176)
Q Consensus 94 ~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 128 (176)
++++++++.|+.+..-++.+++.+=-|.+-..|++
T Consensus 303 ~El~~ia~ll~gr~~~~~~~~~i~t~~~v~~~a~~ 337 (400)
T PF04412_consen 303 EELREIAELLEGRKVHPNVPLWITTSRAVYELAER 337 (400)
T ss_pred HHHHHHHHHHhCCCCCCCceEEEECCHHHHHHHHh
Confidence 56778888898753235888888877777777765
No 175
>PF01182 Glucosamine_iso: Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase; InterPro: IPR006148 This domain is characteristic of the enzymes 6-phosphogluconolactonase (3.1.1.31 from EC), Glucosamine-6-phosphate isomerase (3.5.99.6 from EC), and Galactosamine-6-phosphate isomerase. 6-Phosphogluconolactonase is the enzyme responsible for the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconate, the second step in the pentose phosphate pathway. Glucosamine-6-phosphate isomerase (or Glucosamine 6-phosphate deaminase) is the enzyme responsible for the conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate []. It is the last specific step in the pathway for N-acetylglucosamine (GlcNAC) utilization in bacteria such as Escherichia coli (gene nagB) or in fungi such as Candida albicans (gene NAG1).; GO: 0005975 carbohydrate metabolic process; PDB: 3CSS_A 3CH7_A 1Y89_B 3TX2_A 2BKX_B 2BKV_B 3E15_B 1HOR_B 1JT9_A 1HOT_A ....
Probab=33.13 E-value=1e+02 Score=24.65 Aligned_cols=54 Identities=9% Similarity=0.065 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
+.+.|.+.+++.+. ++||+ .|..++. ...+.+++.-+....+.++-+++.|||+
T Consensus 9 i~~~i~~~i~~~~~--~~i~L---sgGstp~-~~y~~L~~~~~~~i~w~~v~~~~~DEr~ 62 (199)
T PF01182_consen 9 IAEAIEEAIAERGR--AVIAL---SGGSTPK-PLYQELAKLHKERIDWSRVHFFNVDERV 62 (199)
T ss_dssp HHHHHHHHHHHCSS--EEEEE-----SCTHH-HHHHHHHHHHHTCSCGGGEEEEESEEES
T ss_pred HHHHHHHHHHHCCC--EEEEE---cCCHHHH-HHHHHHhhhccccCChhHeEEEeCcccc
Confidence 45667777776644 66665 3444443 2234455444221123467799999998
No 176
>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=33.03 E-value=2.4e+02 Score=24.91 Aligned_cols=90 Identities=16% Similarity=0.097 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhcc-CCCC-CcEEEec----CcccHHH---HHHHhc
Q 030509 61 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATK-KLED-MKYAYWN----EGFTSKG---VELLLN 131 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~-~~~~-lpV~~~D----Er~TT~~---A~~~l~ 131 (176)
.+++.+.+...+.+. .|.+=+|+=.| .+...+.++++++.|+... .. + +|+.-+. ++.|..+ ..+.|.
T Consensus 240 ~l~~~~~~y~~~~gr-~I~iey~LIpG-vNDs~e~a~~La~~l~~l~~~V-nLIPynp~~~~~~~~ps~e~i~~f~~~L~ 316 (345)
T PRK14457 240 NLLEDCRHYVAITGR-RVSFEYILLGG-VNDLPEHAEELANLLRGFQSHV-NLIPYNPIDEVEFQRPSPKRIQAFQRVLE 316 (345)
T ss_pred HHHHHHHHHHHHhCC-EEEEEEEEECC-cCCCHHHHHHHHHHHhcCCCeE-EEecCCCCCCCCCCCCCHHHHHHHHHHHH
Confidence 445666666665432 47777776523 2222334445555554310 00 1 2221111 2333332 234555
Q ss_pred cCCCCCCCCC-CCCcHHHHHHHH
Q 030509 132 PLDLHPVEYK-TILDKFAAVGIL 153 (176)
Q Consensus 132 ~~g~~~~~~k-~~iD~~AA~iIL 153 (176)
..|+.-..++ .=.|-.|||--|
T Consensus 317 ~~Gi~vtvR~~~G~di~aaCGqL 339 (345)
T PRK14457 317 QRGVAVSVRASRGLDANAACGQL 339 (345)
T ss_pred HCCCeEEEeCCCCCchhhccccc
Confidence 6676433222 335777787655
No 177
>PRK11678 putative chaperone; Provisional
Probab=32.64 E-value=42 Score=30.73 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=16.1
Q ss_pred EEEEecCCCeEEEEEecC
Q 030509 24 FLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~ 41 (176)
++|||+||..+=||+.+.
T Consensus 2 ~iGID~GTtNs~va~~~~ 19 (450)
T PRK11678 2 FIGFDYGTANCSVAVMRD 19 (450)
T ss_pred eEEEecCccceeeEEeeC
Confidence 689999999999999863
No 178
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=32.44 E-value=1.4e+02 Score=27.55 Aligned_cols=56 Identities=13% Similarity=0.199 Sum_probs=41.5
Q ss_pred hhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEE--EecCc
Q 030509 59 IDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA--YWNEG 120 (176)
Q Consensus 59 ~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~--~~DEr 120 (176)
.++..++|.++++++++|.+|.|=-+|-|.++..|..+-+ .++++ + ++|++ ++-|.
T Consensus 61 ~eea~~~i~~mv~k~~pDv~iaGPaFNagrYG~acg~va~---aV~e~--~-~IP~vt~My~EN 118 (431)
T TIGR01918 61 LEEAVARVLEMLKDKEPDIFIAGPAFNAGRYGVACGEICK---VVQDK--L-NVPAVTSMYVEN 118 (431)
T ss_pred HHHHHHHHHHHHHhcCCCEEEEcCccCCccHHHHHHHHHH---HHHHh--h-CCCeEEEecccC
Confidence 4566799999999999999999955668999988876544 34442 3 77865 55675
No 179
>PRK13930 rod shape-determining protein MreB; Provisional
Probab=32.26 E-value=48 Score=28.24 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=14.3
Q ss_pred eEEEEecCCCeEEEEEec
Q 030509 23 RFLGLDVGDKYVGLSISD 40 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd 40 (176)
+.+|||+|+..+-+++.+
T Consensus 9 ~~vgiDlGt~~t~i~~~~ 26 (335)
T PRK13930 9 KDIGIDLGTANTLVYVKG 26 (335)
T ss_pred cceEEEcCCCcEEEEECC
Confidence 469999999988777653
No 180
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=32.26 E-value=1.4e+02 Score=27.50 Aligned_cols=57 Identities=19% Similarity=0.255 Sum_probs=41.9
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEE--EecCc
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA--YWNEG 120 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~--~~DEr 120 (176)
+.++..++|.++++++++|.+|.|=-+|-|.++..|..+-+ .++++ + ++|++ ++-|.
T Consensus 60 n~eea~~~i~~mv~k~~pDv~iaGPaFNagrYG~acg~va~---aV~e~--~-~IP~vtaMy~EN 118 (431)
T TIGR01917 60 NLEEAKAKVLEMIKGANPDIFIAGPAFNAGRYGMAAGAITK---AVQDE--L-GIKAFTAMYEEN 118 (431)
T ss_pred CHHHHHHHHHHHHHhcCCCEEEEcCccCCccHHHHHHHHHH---HHHHh--h-CCCeEEEecccC
Confidence 34566799999999999999999955668999988876544 34442 3 77865 55675
No 181
>PRK13331 pantothenate kinase; Reviewed
Probab=32.12 E-value=1.7e+02 Score=24.85 Aligned_cols=25 Identities=12% Similarity=0.203 Sum_probs=21.0
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCc
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNK 44 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~ 44 (176)
..+++|+||+|-.+|=+++-+....
T Consensus 5 ~~~~~L~iDiGNT~~~~g~f~~~~~ 29 (251)
T PRK13331 5 TSNEWLALMIGNSRLHWGYFSGETL 29 (251)
T ss_pred CCCcEEEEEeCCCcEEEEEEECCEE
Confidence 3478999999999999999986543
No 182
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=31.83 E-value=50 Score=31.56 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=18.3
Q ss_pred CCCeEEEEecCCCeEEEEEecC
Q 030509 20 KRGRFLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~ 41 (176)
..+.++|||+|+..+=||+.++
T Consensus 2 ~~~~~iGIDlGTt~s~va~~~~ 23 (653)
T PTZ00009 2 TKGPAIGIDLGTTYSCVGVWKN 23 (653)
T ss_pred CcccEEEEEeCcccEEEEEEeC
Confidence 3467999999999998998754
No 183
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=31.78 E-value=2.5e+02 Score=22.01 Aligned_cols=19 Identities=26% Similarity=0.476 Sum_probs=15.2
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.+.+++.++++++||+.
T Consensus 48 ~~~~~~~~~~~~vdgiii~ 66 (268)
T cd06271 48 LEVYRRLVESGLVDGVIIS 66 (268)
T ss_pred HHHHHHHHHcCCCCEEEEe
Confidence 4667778888889999985
No 184
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=31.72 E-value=2.2e+02 Score=29.69 Aligned_cols=58 Identities=9% Similarity=0.088 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
+.+.+.++|+..+|..|.|+-+-. ........++.....|.-...++.+||+++|+-+
T Consensus 654 ~~d~f~kFI~~~kP~vi~v~g~~r--~~q~~~~~I~~~v~el~~~~~~~~ipv~~vd~el 711 (1299)
T KOG1856|consen 654 FQDLFKKFIEKKKPHVIGVSGENR--LKQKIYEAIRQLVHELLISDQGHPIPVIYVDNEL 711 (1299)
T ss_pred HHHHHHHHHHhcCCCEEEeeCCCc--hhHHHHHHHHHHHHhccccccCCCcceeecccHH
Confidence 346788899999999999984411 1234455555555555432224689999999754
No 185
>COG4020 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.72 E-value=98 Score=27.02 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=39.4
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHH--HHhcCCCEEEEec
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSL--ISEFNLEGFIVGY 82 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~l--i~e~~~~~iVVGl 82 (176)
+..+|+|.|+.=|-+|+-|.+...-+.|.--+.........+++|.+- +.-++++.|-+-+
T Consensus 3 m~fVGiDHGTsgi~~ai~d~e~~~~Fklgrae~~~~~ek~~L~~l~de~~i~l~eidlialtY 65 (332)
T COG4020 3 MMFVGIDHGTSGIKFAIYDGEKDPEFKLGRAELRKVAEKSLLRELEDEARIALEEIDLIALTY 65 (332)
T ss_pred eEEEeecCCCcceEEEEEcCCCCceEEechhhhhhhhHHHHHHHhhHhhCCccccceEEEEee
Confidence 568999999999999999977765554443333322222334555555 4445788777654
No 186
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=31.37 E-value=1.9e+02 Score=20.74 Aligned_cols=53 Identities=8% Similarity=0.029 Sum_probs=37.2
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
+.++.+.+++..++.|||--+-. .-+ ...+..|.+.|... +++++.+++.+.+
T Consensus 54 ~~~ll~~~~~~~~d~ivv~~~~Rl~R~----~~~~~~~~~~l~~~----gi~l~~~~~~~~~ 107 (137)
T cd00338 54 LQRLLADVKAGKIDVVLVEKLDRLSRN----LVDLLELLELLEAH----GVRVVTADGEIDL 107 (137)
T ss_pred HHHHHHHHHcCCCCEEEEEecchhhCC----HHHHHHHHHHHHHC----CCEEEEecCCccc
Confidence 67888888888899999985544 222 22445667777752 8999999976654
No 187
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=31.30 E-value=1.2e+02 Score=27.83 Aligned_cols=70 Identities=17% Similarity=0.184 Sum_probs=48.1
Q ss_pred HHHHHHHHHhcCCCEEEEec--cCCCC----------------CCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHH
Q 030509 63 AEDFRSLISEFNLEGFIVGY--PFNRQ----------------QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 124 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGl--Pl~dG----------------~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~ 124 (176)
.+.|.++.++++++.+|||= ||-.| ....+-+--+.|++.+-++ . ++|...+..=.+..
T Consensus 52 ~~~lv~fA~~~~idl~vVGPE~pL~~GvvD~l~~~Gi~vFGPsk~AA~lE~SK~faK~fm~k--~-~IPta~y~~f~~~e 128 (428)
T COG0151 52 HEALVAFAKEKNVDLVVVGPEAPLVAGVVDALRAAGIPVFGPTKAAAQLEGSKAFAKDFMKK--Y-GIPTAEYEVFTDPE 128 (428)
T ss_pred HHHHHHHHHHcCCCEEEECCcHHHhhhhHHHHHHCCCceeCcCHHHHHHHhhHHHHHHHHHH--c-CCCcccccccCCHH
Confidence 58999999999999999983 22222 2334445557899999875 3 78844444444677
Q ss_pred HHHHHhccCCC
Q 030509 125 GVELLLNPLDL 135 (176)
Q Consensus 125 ~A~~~l~~~g~ 135 (176)
+|+..+.+.|.
T Consensus 129 ~a~ayi~~~g~ 139 (428)
T COG0151 129 EAKAYIDEKGA 139 (428)
T ss_pred HHHHHHHHcCC
Confidence 78888876554
No 188
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=31.24 E-value=2.2e+02 Score=21.47 Aligned_cols=58 Identities=9% Similarity=0.137 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCC--CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~--dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
+...+...+.+++++.+||=-|-. +.........+.++...|++. +..++++.+....
T Consensus 83 ~~~~i~~~~~~~~~~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~----g~tvi~v~~~~~~ 142 (187)
T cd01124 83 LIQRLKDAIEEFKAKRVVIDSVSGLLLMEQSTARLEIRRLLFALKRF----GVTTLLTSEQSGL 142 (187)
T ss_pred HHHHHHHHHHHhCCCEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHC----CCEEEEEeccccC
Confidence 357788888889999999997765 333344455566777777652 7788888766543
No 189
>PF06723 MreB_Mbl: MreB/Mbl protein; InterPro: IPR004753 Bacterial cell shape varies greatly between species, and characteristic morphologies are used for identification purposes. In addition to individual cell shape, the way in which groups of cells are arranged is also typical of some bacterial species, especially Gram-positive coccoids. For many years, it was believed that micro-organisms with other than spheroidal cell shapes maintained morphology by means of their external cell walls. Recently, however, studies of the Gram-positive rod Bacillus subtilis have revealed two related genes that are essential for the integrity of cell morphogenesis []. Termed mreB and mbl, the gene products localise close to the cell surface, forming filamentous helical structures. Many homologues have been found in diverse bacterial groups, suggesting a common ancestor []. The crystal structure of MreB from Thermotoga maritima has been resolved using X-ray crystallography []. It consists of 19 beta-strands and 15 alpha- helices, and shows remarkable structural similarity to eukaryotic actin. MreB crystals also contain proto-filaments, with individual proteins assembling into polymers like F-actin, in the same orientation. It is hypothesised therefore, that MreB was the forerunner of actin in early eukaryotes [].; GO: 0000902 cell morphogenesis; PDB: 1JCF_A 1JCE_A 2WUS_A 1JCG_A.
Probab=31.24 E-value=1.1e+02 Score=26.84 Aligned_cols=105 Identities=13% Similarity=0.182 Sum_probs=52.3
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceee-eCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCc---hHHHHHHH
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIASPLSVL-LRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNA---ADAVQVKL 98 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a~Pl~~i-~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s---~~~~~v~~ 98 (176)
+-+|||+||.++=|.+.+....+-.|=-+- .......-.+-++-.+++. ..++.|.+=.|+.+|-.+ .....++.
T Consensus 2 ~~igIDLGT~~t~i~~~~~Giv~~epSvVA~~~~~~~i~avG~~A~~m~g-ktp~~i~~~~Pl~~GvI~D~~~~~~~l~~ 80 (326)
T PF06723_consen 2 KDIGIDLGTSNTRIYVKGKGIVLNEPSVVAYDKDTGKILAVGDEAKAMLG-KTPDNIEVVRPLKDGVIADYEAAEEMLRY 80 (326)
T ss_dssp SEEEEEE-SSEEEEEETTTEEEEEEES-EEEETTT--EEEESHHHHTTTT-S-GTTEEEE-SEETTEESSHHHHHHHHHH
T ss_pred CceEEecCcccEEEEECCCCEEEecCcEEEEECCCCeEEEEhHHHHHHhh-cCCCccEEEccccCCcccCHHHHHHHHHH
Confidence 358999999999887776544555553222 2211110000111122222 347788888898888654 34446677
Q ss_pred HHHHHHhccCCCCCc--EEEecCcccHHHHHHH
Q 030509 99 FIDDLSATKKLEDMK--YAYWNEGFTSKGVELL 129 (176)
Q Consensus 99 Fa~~L~~~~~~~~lp--V~~~DEr~TT~~A~~~ 129 (176)
|.++......+ .-| ++=+--..|.+|-+..
T Consensus 81 ~l~k~~~~~~~-~~p~vvi~vP~~~T~verrA~ 112 (326)
T PF06723_consen 81 FLKKALGRRSF-FRPRVVICVPSGITEVERRAL 112 (326)
T ss_dssp HHHHHHTSS-S-S--EEEEEE-SS--HHHHHHH
T ss_pred HHHHhccCCCC-CCCeEEEEeCCCCCHHHHHHH
Confidence 77777653122 223 3445677777665544
No 190
>cd01828 sialate_O-acetylesterase_like2 sialate_O-acetylesterase_like subfamily of the SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=30.80 E-value=2.3e+02 Score=21.11 Aligned_cols=54 Identities=7% Similarity=0.140 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCC-CCCC---chHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFN-RQQN---AADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~-dG~~---s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
+.+.|.+++ ..+++.+|+-+-.| -+.. ....+..+++.+.+.+. .++.+|+++.
T Consensus 37 ~~~~l~~~~-~~~pd~vvl~~G~ND~~~~~~~~~~~~~l~~li~~~~~~--~~~~~vi~~~ 94 (169)
T cd01828 37 LLARLDEDV-ALQPKAIFIMIGINDLAQGTSDEDIVANYRTILEKLRKH--FPNIKIVVQS 94 (169)
T ss_pred HHHHHHHHh-ccCCCEEEEEeeccCCCCCCCHHHHHHHHHHHHHHHHHH--CCCCeEEEEe
Confidence 356677777 67899999998888 3322 34445556666666652 3577887764
No 191
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=30.63 E-value=1.4e+02 Score=25.10 Aligned_cols=39 Identities=13% Similarity=0.393 Sum_probs=33.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHh
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 105 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~ 105 (176)
.+.|.+.++.-++++||.| +=-...|..++++.|+++.-
T Consensus 75 ve~L~~~l~~l~~d~iv~G----aI~s~yqk~rve~lc~~lGl 113 (223)
T COG2102 75 VEELKEALRRLKVDGIVAG----AIASEYQKERVERLCEELGL 113 (223)
T ss_pred HHHHHHHHHhCcccEEEEc----hhhhHHHHHHHHHHHHHhCC
Confidence 6889999999999999999 66667788888888888763
No 192
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=30.24 E-value=2.8e+02 Score=22.04 Aligned_cols=44 Identities=16% Similarity=0.280 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
.+.+..++. +++++||+. ....... . ...+.+.+. ++|++++|-
T Consensus 50 ~~~~~~~~~-~~vdgiIi~----~~~~~~~-~---~~l~~~~~~----~iPvv~~~~ 93 (272)
T cd06300 50 IADIRNLIA-QGVDAIIIN----PASPTAL-N---PVIEEACEA----GIPVVSFDG 93 (272)
T ss_pred HHHHHHHHH-cCCCEEEEe----CCChhhh-H---HHHHHHHHC----CCeEEEEec
Confidence 455666555 599999997 2221111 1 122345442 788888873
No 193
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=30.20 E-value=48 Score=31.80 Aligned_cols=20 Identities=25% Similarity=0.566 Sum_probs=17.4
Q ss_pred CeEEEEecCCCeEEEEEecC
Q 030509 22 GRFLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~ 41 (176)
+.++|||+|+..+-+|+.+.
T Consensus 41 ~~viGIDlGTt~s~va~~~~ 60 (663)
T PTZ00400 41 GDIVGIDLGTTNSCVAIMEG 60 (663)
T ss_pred CcEEEEEECcccEEEEEEeC
Confidence 57999999999999998753
No 194
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=30.20 E-value=1.5e+02 Score=26.22 Aligned_cols=53 Identities=17% Similarity=0.159 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCccc
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 122 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~T 122 (176)
-.+.|.++++++++|+||.=.... +-...+... ++ +.|++. ++|+..+|=-++
T Consensus 301 R~~~i~~lv~~~~~DGVI~~~~kfC~~~~~e~~~-lk---~~l~e~----GIP~L~iE~D~~ 354 (377)
T TIGR03190 301 RYDHVLGLAKEYNVQGAIFLQQKFCDPHEGDYPD-LK---RHLEAN----GIPTLFLEFDIT 354 (377)
T ss_pred HHHHHHHHHHHhCCCEEEEecccCCCcchhhhHH-HH---HHHHHC----CCCEEEEecCCC
Confidence 368899999999999999988777 655554322 22 345542 899888864444
No 195
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=29.97 E-value=1.4e+02 Score=26.37 Aligned_cols=51 Identities=10% Similarity=0.156 Sum_probs=37.7
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
++.+...+.+ +++.|++..|-| .|+.-. ...+++|++.+.. --++.+||.|
T Consensus 135 ~~~~~~~~~~-~~~lv~i~nPNNPTG~~~~-~~~l~~l~~~~~~------~~~vVvDEAY 186 (356)
T COG0079 135 LDAILAAIRD-KTKLVFLCNPNNPTGTLLP-REELRALLEALPE------GGLVVIDEAY 186 (356)
T ss_pred HHHHHHhhhc-CCCEEEEeCCCCCCCCCCC-HHHHHHHHHhCCC------CcEEEEeCch
Confidence 4777777777 899999999999 998765 3445666665542 2378889876
No 196
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=29.91 E-value=58 Score=31.31 Aligned_cols=22 Identities=27% Similarity=0.631 Sum_probs=18.8
Q ss_pred CCeEEEEecCCCeEEEEEecCC
Q 030509 21 RGRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~ 42 (176)
++.++|||+|+..+-||+.+..
T Consensus 26 ~~~viGIDLGTTnS~vA~~~~~ 47 (657)
T PTZ00186 26 QGDVIGVDLGTTYSCVATMDGD 47 (657)
T ss_pred cceEEEEEeCcCeEEEEEEeCC
Confidence 4579999999999999998653
No 197
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=29.78 E-value=2.1e+02 Score=20.75 Aligned_cols=55 Identities=15% Similarity=0.120 Sum_probs=34.5
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
.+.|..++....|+.+||| -|..... --.+..+.|.+. ++.+...| |.+|=+.|.
T Consensus 41 ~~~l~~~~~~~~peiliiG----TG~~~~~--~~~~~~~~l~~~----gI~vE~m~----T~aAcrTyN 95 (109)
T cd00248 41 PEALLPLLAEDRPDILLIG----TGAEIAF--LPRALRAALRAA----GIGVEVMS----TGAACRTYN 95 (109)
T ss_pred HHHHHHHHhhCCCCEEEEc----CCCCCCc--CCHHHHHHHHHc----CCeEEEeC----cHHHHHHHH
Confidence 4667777665469999999 6765521 113344556653 67776654 777766654
No 198
>TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
Probab=29.32 E-value=2.9e+02 Score=25.01 Aligned_cols=44 Identities=11% Similarity=0.266 Sum_probs=34.5
Q ss_pred ChhhHHHHHHHHHHhc-CCCEEEEeccCCCCCCchHHHHHHHHHHHHHh
Q 030509 58 TIDLMAEDFRSLISEF-NLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 105 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~-~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~ 105 (176)
+.+.++++|+.+.+.+ .+..|.++ |++.+...+.+.++++.|.+
T Consensus 228 s~e~V~~Ei~~~~~~~~~~~~i~f~----Dd~f~~~~~~~~~l~~~l~~ 272 (472)
T TIGR03471 228 SAESVIEEVKYALENFPEVREFFFD----DDTFTDDKPRAEEIARKLGP 272 (472)
T ss_pred CHHHHHHHHHHHHHhcCCCcEEEEe----CCCCCCCHHHHHHHHHHHhh
Confidence 4566789999988877 68888888 77766666778888888876
No 199
>PRK12359 flavodoxin FldB; Provisional
Probab=29.24 E-value=60 Score=25.79 Aligned_cols=28 Identities=11% Similarity=0.292 Sum_probs=23.8
Q ss_pred EEEeccCC-CCCCchHHHHHHHHHHHHHh
Q 030509 78 FIVGYPFN-RQQNAADAVQVKLFIDDLSA 105 (176)
Q Consensus 78 iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~ 105 (176)
-.||||+. +......-+++.+|++.|+.
T Consensus 138 ~f~gl~lD~~nq~~~t~~ri~~W~~~~~~ 166 (172)
T PRK12359 138 LFVGLALDEVNQYDLSDERIQQWCEQILL 166 (172)
T ss_pred EEEEEEEcCCCchhhhHHHHHHHHHHHHH
Confidence 47899999 88777788999999998874
No 200
>cd08165 MPP_MPPE1 human MPPE1 and related proteins, metallophosphatase domain. MPPE1 is a functionally uncharacterized metallophosphatase domain-containing protein. The MPPE1 gene is located on chromosome 18 and is a candidate susceptibility gene for Bipolar disorder. MPPE1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to
Probab=29.17 E-value=2.5e+02 Score=21.42 Aligned_cols=52 Identities=10% Similarity=-0.031 Sum_probs=31.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCch---HHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAA---DAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~---~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.+.+++++.+|+.||+.-=+. ++.... ....+.+|.+.+.. .++.|++++
T Consensus 27 ~~~~~~~i~~~~pd~vv~~GDl~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~i~~v 82 (156)
T cd08165 27 ERSFQTSLWLLQPDVVFVLGDLFDEGKWSTDEEWEDYVERFKKMFGH---PPDLPLHVV 82 (156)
T ss_pred HHHHHHHHHhcCCCEEEECCCCCCCCccCCHHHHHHHHHHHHHHhcc---CCCCeEEEE
Confidence 35778889999999999875444 443211 22334555555442 236788775
No 201
>COG4126 Hydantoin racemase [Amino acid transport and metabolism]
Probab=29.09 E-value=86 Score=26.48 Aligned_cols=41 Identities=17% Similarity=0.240 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEE
Q 030509 61 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA 115 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~ 115 (176)
.++.+..+-++|-..+.||+| =+..+. .+.+|++. | ++||+
T Consensus 161 ~l~~~~~~a~~edgAeaIiLG----CAGms~-------la~~Lq~~--~-gvPVI 201 (230)
T COG4126 161 LLVIEAAEALKEDGAEAIILG----CAGMSD-------LADQLQKA--F-GVPVI 201 (230)
T ss_pred HHHHHHHHHhhhcCCCEEEEc----CccHHH-------HHHHHHHH--h-CCCcc
Confidence 346777888888899999999 454553 35678773 5 78864
No 202
>COG1831 Predicted metal-dependent hydrolase (urease superfamily) [General function prediction only]
Probab=28.71 E-value=1.6e+02 Score=25.67 Aligned_cols=71 Identities=15% Similarity=0.147 Sum_probs=54.7
Q ss_pred HHHHHHHHHhcCCCEE-EEeccCC--CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHH---hccCCCC
Q 030509 63 AEDFRSLISEFNLEGF-IVGYPFN--RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELL---LNPLDLH 136 (176)
Q Consensus 63 ~~~L~~li~e~~~~~i-VVGlPl~--dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~---l~~~g~~ 136 (176)
++-..+++.+..+++| =||-|-. +-..=+.+..+...|-.|++. . +.||.+.-|+++..+-++. .++.|++
T Consensus 110 lelA~k~v~eg~avaiGEvGrPHypVs~~v~~~~n~vl~~a~elA~d--v-dc~vqLHtes~~~~~~~~i~~~ak~~G~~ 186 (285)
T COG1831 110 LELAAKLVEEGKAVAIGEVGRPHYPVSEEVWEASNEVLEYAMELAKD--V-DCAVQLHTESLDEETYEEIAEMAKEAGIK 186 (285)
T ss_pred HHHHHHHHhccceeeeeccCCCCCCCCHHHHHHHHHHHHHHHHHhhc--C-CCcEEEecCCCChHHHHHHHHHHHHhCCC
Confidence 5667888999999998 8998866 555556777787888888863 3 8999999999999665544 5567764
No 203
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=28.48 E-value=1.8e+02 Score=23.39 Aligned_cols=52 Identities=12% Similarity=0.137 Sum_probs=39.4
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.++.+++.+-..+.+|+-.=.| .+.....+.+..|.+.|.+. .|+.||+++.
T Consensus 49 ~~~a~~ia~~~a~~~~ld~~~N-~~~~~~~~~~~~fv~~iR~~--hP~tPIllv~ 100 (178)
T PF14606_consen 49 PEVADLIAEIDADLIVLDCGPN-MSPEEFRERLDGFVKTIREA--HPDTPILLVS 100 (178)
T ss_dssp HHHHHHHHHS--SEEEEEESHH-CCTTTHHHHHHHHHHHHHTT---SSS-EEEEE
T ss_pred HHHHHHHhcCCCCEEEEEeecC-CCHHHHHHHHHHHHHHHHHh--CCCCCEEEEe
Confidence 5678888888889999875444 66778889999999999985 5799999886
No 204
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=28.46 E-value=2.7e+02 Score=21.77 Aligned_cols=30 Identities=13% Similarity=0.320 Sum_probs=22.7
Q ss_pred cCCCEEEEeccCCCCCCchHHHHHHHHHHHHHh
Q 030509 73 FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 105 (176)
Q Consensus 73 ~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~ 105 (176)
.+.|.|.+|.+...|+..+ .+++|.+.|+.
T Consensus 38 ~~yD~i~lG~w~d~G~~d~---~~~~fl~~l~~ 67 (160)
T PF12641_consen 38 EDYDLIFLGFWIDKGTPDK---DMKEFLKKLKG 67 (160)
T ss_pred CCCCEEEEEcCccCCCCCH---HHHHHHHHccC
Confidence 4678999999888777765 45678887764
No 205
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=28.29 E-value=3e+02 Score=24.28 Aligned_cols=84 Identities=18% Similarity=0.108 Sum_probs=46.0
Q ss_pred ceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 44 KIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 44 ~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
..+.|+.+. .. .+.+.+.+.|..+.+.-+++.++|-++ |........++.+++..++. . ++.||+.+-=.-..
T Consensus 282 ~~~NPvDl~-g~-~~~e~~~~aL~~l~~d~~vd~vlv~~~---~~~~~~~~va~~i~~~~~~~-~-~~kPvv~~~~g~~~ 354 (388)
T PRK00696 282 EPANFLDVG-GG-ATAERVAEAFKIILSDPNVKAILVNIF---GGITRCDVIAEGIIAAVKEV-G-VTVPLVVRLEGTNV 354 (388)
T ss_pred CcCCeEEec-CC-CCHHHHHHHHHHHhcCCCCCEEEEEeC---CCCCCHHHHHHHHHHHHHhc-C-CCCcEEEEeCCCCH
Confidence 445676662 22 344455566777777788999998644 22222233344444444431 1 25676544322355
Q ss_pred HHHHHHhccCC
Q 030509 124 KGVELLLNPLD 134 (176)
Q Consensus 124 ~~A~~~l~~~g 134 (176)
.+++++|.+.|
T Consensus 355 ~~~~~~L~~~G 365 (388)
T PRK00696 355 ELGKKILAESG 365 (388)
T ss_pred HHHHHHHHHCC
Confidence 67777788776
No 206
>PF01869 BcrAD_BadFG: BadF/BadG/BcrA/BcrD ATPase family; InterPro: IPR002731 This domain is found in the BadF (O07462 from SWISSPROT) and BadG (O07463 from SWISSPROT) proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase (P11568 from SWISSPROT). The hypothetical protein AQ_278 from Aquifex aeolicus O66634 from SWISSPROT contains two copies of this region suggesting that the family may structurally dimerise.; PDB: 2E2N_B 2E2Q_A 2E2P_B 2E2O_A 1ZBS_A 2CH6_A 2CH5_D 1ZC6_A 1HUX_A.
Probab=28.23 E-value=1.8e+02 Score=23.94 Aligned_cols=22 Identities=27% Similarity=0.410 Sum_probs=19.2
Q ss_pred EEEecCCCeEEEEEecCCCcee
Q 030509 25 LGLDVGDKYVGLSISDPKNKIA 46 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a 46 (176)
||||-|.-++=+.+.|..+.+.
T Consensus 1 lGIDgGgTkt~~vl~d~~g~il 22 (271)
T PF01869_consen 1 LGIDGGGTKTKAVLVDENGNIL 22 (271)
T ss_dssp EEEEECSSEEEEEEEETTSEEE
T ss_pred CEEeeChheeeeEEEeCCCCEE
Confidence 7999999999999999887643
No 207
>COG0363 NagB 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]
Probab=28.16 E-value=1.5e+02 Score=24.77 Aligned_cols=51 Identities=8% Similarity=0.028 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCCC--EEEEeccCCCCCCchHHHHHHHHHHHHHhc----cCCCCCcEEEecCccc
Q 030509 64 EDFRSLISEFNLE--GFIVGYPFNRQQNAADAVQVKLFIDDLSAT----KKLEDMKYAYWNEGFT 122 (176)
Q Consensus 64 ~~L~~li~e~~~~--~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~----~~~~~lpV~~~DEr~T 122 (176)
+.|...+.+-... .+++|+ .|..++. .|-+.|.+. ..+.++-+++.|||+=
T Consensus 18 ~~i~~~~~~~~~~~~~~~l~L---sgGsTP~-----~~ye~L~~~~~~~~~w~~v~~f~~DEr~v 74 (238)
T COG0363 18 EIIADKLQAAKAERGRAVLAL---SGGSTPL-----ALYEALVKLPQGQLDWSKVTIFNLDERVV 74 (238)
T ss_pred HHHHHHHHhhhhccCcEEEEE---CCCCCHH-----HHHHHHHhhhccCCCchheEEEecccccc
Confidence 3444444433322 578887 5666663 333444332 2356778999999974
No 208
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=28.13 E-value=3.7e+02 Score=22.69 Aligned_cols=59 Identities=10% Similarity=0.156 Sum_probs=35.9
Q ss_pred HHHHHHHHHh-cCCCEEEEeccCCCCCCch--------HHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 63 AEDFRSLISE-FNLEGFIVGYPFNRQQNAA--------DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 63 ~~~L~~li~e-~~~~~iVVGlPl~dG~~s~--------~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
++++.+.+-+ ..+++|+++ |+.++ ..+.++..++... ..+||+.-=-..||.+|.++.+
T Consensus 26 ~~~li~~l~~~~Gv~gi~v~-----GstGE~~~Ls~eEr~~~~~~~~~~~~-----~~~~viagvg~~~t~~ai~~a~ 93 (293)
T PRK04147 26 LRRLVRFNIEKQGIDGLYVG-----GSTGEAFLLSTEEKKQVLEIVAEEAK-----GKVKLIAQVGSVNTAEAQELAK 93 (293)
T ss_pred HHHHHHHHHhcCCCCEEEEC-----CCccccccCCHHHHHHHHHHHHHHhC-----CCCCEEecCCCCCHHHHHHHHH
Confidence 4555556666 889999987 65544 2222233333322 1578777666788888877654
No 209
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=28.10 E-value=1.7e+02 Score=24.56 Aligned_cols=61 Identities=8% Similarity=0.226 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC------cccHHHHHHHhc
Q 030509 64 EDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE------GFTSKGVELLLN 131 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE------r~TT~~A~~~l~ 131 (176)
-++.+.+++..+++++|.-|.. ..+..+ +.+|-+.+.+. +++||+++|. .+|.....++..
T Consensus 86 i~~a~~a~~~Gad~v~v~~P~~~~~s~~~----l~~y~~~ia~~---~~~pi~iYn~P~~tg~~ls~~~l~~L~~ 153 (289)
T PF00701_consen 86 IELARHAQDAGADAVLVIPPYYFKPSQEE----LIDYFRAIADA---TDLPIIIYNNPARTGNDLSPETLARLAK 153 (289)
T ss_dssp HHHHHHHHHTT-SEEEEEESTSSSCCHHH----HHHHHHHHHHH---SSSEEEEEEBHHHHSSTSHHHHHHHHHT
T ss_pred HHHHHHHhhcCceEEEEeccccccchhhH----HHHHHHHHHhh---cCCCEEEEECCCccccCCCHHHHHHHhc
Confidence 4556667888999999999988 554333 44555556553 4899999885 345555555544
No 210
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=27.36 E-value=1.5e+02 Score=31.02 Aligned_cols=71 Identities=18% Similarity=0.263 Sum_probs=48.0
Q ss_pred CCeEEEEEecCC---Cceeccc-------eeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHH
Q 030509 31 DKYVGLSISDPK---NKIASPL-------SVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFI 100 (176)
Q Consensus 31 ~kriGvAvsd~~---~~~a~Pl-------~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa 100 (176)
...+||+|.|.. ...-+++ .++.. +.. -++++++.+++..|.|+ |++|+-.++++-|-..+++..|.
T Consensus 701 i~~~gv~Vv~~~~~ds~~~t~~~~~~~~~~V~~~-~sE-~elf~ev~~~i~q~DPD-Il~GyEi~~~SWGyl~eR~~~l~ 777 (1488)
T KOG0968|consen 701 IVSVGVIVVDKVCPDSHVQTTTLGGIYGCRVVVM-ESE-LELFEEVAKLIVQYDPD-ILLGYEIHNLSWGYLIERAKLLG 777 (1488)
T ss_pred eeeeeEEEEeccCccccccccccCCcCCceEEEe-hhH-HHHHHHHHHHHHhcCcc-eeeeeeecccchHHHHHHHHHhc
Confidence 778999999933 2222221 22211 112 25689999999999999 89999988888887777766654
Q ss_pred HHHH
Q 030509 101 DDLS 104 (176)
Q Consensus 101 ~~L~ 104 (176)
-.|-
T Consensus 778 ~di~ 781 (1488)
T KOG0968|consen 778 IDIS 781 (1488)
T ss_pred chHH
Confidence 4443
No 211
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=27.32 E-value=1.4e+02 Score=25.12 Aligned_cols=50 Identities=14% Similarity=0.339 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
.-++.+..++..++++++.-|.. ..+. ..+.+|-+.+.+. . ++||+++|-
T Consensus 82 ~i~~a~~a~~~Gad~v~v~pP~y~~~~~----~~i~~~~~~i~~~--~-~~pi~lYn~ 132 (285)
T TIGR00674 82 AISLTKFAEDVGADGFLVVTPYYNKPTQ----EGLYQHFKAIAEE--V-DLPIILYNV 132 (285)
T ss_pred HHHHHHHHHHcCCCEEEEcCCcCCCCCH----HHHHHHHHHHHhc--C-CCCEEEEEC
Confidence 35566777889999999999988 5443 3444555556542 3 789998884
No 212
>cd00562 NifX_NifB This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).
Probab=27.30 E-value=2.1e+02 Score=19.51 Aligned_cols=51 Identities=20% Similarity=0.070 Sum_probs=35.3
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHh
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 130 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 130 (176)
..+.+++...+++.+|+| ..++. ....|++. ++.++..++..|-.+|-+.|
T Consensus 51 ~~~~~~l~~~~v~~vi~~------~iG~~------a~~~l~~~----gI~v~~~~~~~~v~eal~~~ 101 (102)
T cd00562 51 KLAARLLALEGCDAVLVG------GIGGP------AAAKLEAA----GIKPIKAAEGGTIEEALEAL 101 (102)
T ss_pred hHHHHHHHHCCCcEEEEc------ccCcc------HHHHHHHc----CCEEEEcCCCCcHHHHHHhh
Confidence 356677778899999999 35542 33467653 78998888766767665543
No 213
>COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only]
Probab=27.20 E-value=1e+02 Score=24.65 Aligned_cols=35 Identities=26% Similarity=0.395 Sum_probs=25.2
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDD 102 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~ 102 (176)
++.|.+.+. +.|+||+|-|...|+.|.+. +.|.++
T Consensus 66 ~~~i~~~l~--~aD~iI~gsPvy~g~vsa~~---K~fiDR 100 (207)
T COG0655 66 MNEIYEKLL--EADGIIFGSPVYFGNVSAQM---KAFIDR 100 (207)
T ss_pred HHHHHHHHH--HCCEEEEeCCeecCCchHHH---HHHHhh
Confidence 456666555 57999999999977766654 467776
No 214
>cd00458 SugarP_isomerase SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway.
Probab=27.06 E-value=2.1e+02 Score=22.12 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
.+.+.+.+++.+.-.|.++ |..++. ...+.+++..... .+.++-+++.|||+
T Consensus 9 ~~~i~~~~~~~~~~~i~ls-----gGsTp~-~~y~~L~~~~~~~-~w~~v~~f~~DEr~ 60 (169)
T cd00458 9 EDKXEKLLEEKDDMVIGLG-----TGSTPA-YFYKLLGEKLKRG-EISDIVGFPTDERY 60 (169)
T ss_pred HHHHHHHHHhCCCEEEEEC-----CCccHH-HHHHHHHhhhhhC-CccceEEEECcccc
Confidence 4556666655554444444 443431 2223333332221 14467789999985
No 215
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=26.86 E-value=2.2e+02 Score=24.83 Aligned_cols=63 Identities=13% Similarity=0.110 Sum_probs=42.5
Q ss_pred HHHhcCCCEEEEe-ccCCCCC---CchHHHHHHHHHHHHHhccCCCCCcEEEec--CcccHHHHHHHhc
Q 030509 69 LISEFNLEGFIVG-YPFNRQQ---NAADAVQVKLFIDDLSATKKLEDMKYAYWN--EGFTSKGVELLLN 131 (176)
Q Consensus 69 li~e~~~~~iVVG-lPl~dG~---~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D--Er~TT~~A~~~l~ 131 (176)
+.....||-.+|. .|-..|. .+-...+||++.+.+......-+..|+++| |++|..+|..+|+
T Consensus 67 ~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLK 135 (319)
T PRK08769 67 IAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLK 135 (319)
T ss_pred HhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHH
Confidence 3455679999996 4533232 223466788888877753211245788888 9999999999987
No 216
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=26.83 E-value=67 Score=30.47 Aligned_cols=19 Identities=21% Similarity=0.338 Sum_probs=16.8
Q ss_pred CeEEEEecCCCeEEEEEec
Q 030509 22 GRFLGLDVGDKYVGLSISD 40 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd 40 (176)
..++|||+|+....||+..
T Consensus 19 ~~viGIDlGTT~S~va~~~ 37 (595)
T PRK01433 19 QIAVGIDFGTTNSLIAIAT 37 (595)
T ss_pred ceEEEEEcCcccEEEEEEe
Confidence 4589999999999999974
No 217
>TIGR02350 prok_dnaK chaperone protein DnaK. Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.
Probab=26.79 E-value=56 Score=30.62 Aligned_cols=18 Identities=17% Similarity=0.514 Sum_probs=16.1
Q ss_pred EEEEecCCCeEEEEEecC
Q 030509 24 FLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~ 41 (176)
++|||+|+..+=+|+.++
T Consensus 2 viGIDlGtt~s~va~~~~ 19 (595)
T TIGR02350 2 IIGIDLGTTNSCVAVMEG 19 (595)
T ss_pred EEEEEeCcccEEEEEEEC
Confidence 799999999999998765
No 218
>PLN03226 serine hydroxymethyltransferase; Provisional
Probab=26.74 E-value=2.6e+02 Score=25.68 Aligned_cols=19 Identities=16% Similarity=0.176 Sum_probs=16.8
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.|.+++.++++..||+|
T Consensus 172 ~d~Le~~l~~~~pklIv~~ 190 (475)
T PLN03226 172 YDKLEKKAMLFRPKLIIAG 190 (475)
T ss_pred HHHHHHHHhhcCCeEEEEe
Confidence 6889999988889999997
No 219
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=26.66 E-value=1.4e+02 Score=25.08 Aligned_cols=61 Identities=13% Similarity=0.219 Sum_probs=40.3
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc------ccHHHHHHHh
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG------FTSKGVELLL 130 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr------~TT~~A~~~l 130 (176)
.-++.+.+++..++++++--|.. .-+. +.+.+|-+.+.+. . ++||+++|-- +|.....++.
T Consensus 85 ~i~~a~~a~~~G~d~v~~~pP~~~~~~~----~~i~~~~~~ia~~--~-~~pv~lYn~P~~~g~~l~~~~~~~L~ 152 (292)
T PRK03170 85 AIELTKFAEKAGADGALVVTPYYNKPTQ----EGLYQHFKAIAEA--T-DLPIILYNVPGRTGVDILPETVARLA 152 (292)
T ss_pred HHHHHHHHHHcCCCEEEECCCcCCCCCH----HHHHHHHHHHHhc--C-CCCEEEEECccccCCCCCHHHHHHHH
Confidence 35666777889999999999987 5432 3344555666553 3 7899988742 5555555553
No 220
>TIGR03123 one_C_unchar_1 probable H4MPT-linked C1 transfer pathway protein. This protein family was identified, by the method of partial phylogenetic profiling, as related to the use of tetrahydromethanopterin (H4MPT) as a C-1 carrier. Characteristic markers of the H4MPT-linked C1 transfer pathway include formylmethanofuran dehydrogenase subunits, methenyltetrahydromethanopterin cyclohydrolase, etc. Tetrahydromethanopterin, a tetrahydrofolate analog, occurs in methanogenic archaea, bacterial methanotrophs, planctomycetes, and a few other lineages.
Probab=26.64 E-value=3.6e+02 Score=23.69 Aligned_cols=87 Identities=17% Similarity=0.248 Sum_probs=47.1
Q ss_pred EEEecCCCeEEEEEecCCCceec----cceeeeCCCCChhhHHHHHHHHHHhcCC-CEEEEeccCC-CCCCchHHHHHHH
Q 030509 25 LGLDVGDKYVGLSISDPKNKIAS----PLSVLLRKKNTIDLMAEDFRSLISEFNL-EGFIVGYPFN-RQQNAADAVQVKL 98 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~----Pl~~i~~~~~~~~~~~~~L~~li~e~~~-~~iVVGlPl~-dG~~s~~~~~v~~ 98 (176)
+|+|+|...+=+|..|+++.... |+ .+ .++. +.+-+.|.+++++.++ +...|=+-=. -.-.....+=|+.
T Consensus 1 ~G~DiGGA~~K~a~~~~~g~~~~v~~~~~-pl-W~~~--~~L~~~l~~~~~~~~~~~~~avtMTgELaD~f~~r~~GV~~ 76 (318)
T TIGR03123 1 LGIDIGGANTKAAELDEDGRIKEVHQLYC-PL-WKGN--DKLAETLKEISQDLSSADNVAVTMTGELADCFEDKAEGVEF 76 (318)
T ss_pred CccccccceeeeEEecCCCceeEEEEecC-cc-cCCc--hHHHHHHHHHHHhcCccceEEEEeehhhhhhhcCHHHHHHH
Confidence 58999999999998886663331 11 11 1221 2334667777766665 4444432111 1112244555666
Q ss_pred HHHHHHhccCCCCCcEEEec
Q 030509 99 FIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 99 Fa~~L~~~~~~~~lpV~~~D 118 (176)
.++.+++. |+ -|+.++.
T Consensus 77 i~~~~~~~--~~-~~~~i~~ 93 (318)
T TIGR03123 77 ILAAVESA--FG-SPVSVFA 93 (318)
T ss_pred HHHHHHHh--cC-CCeEEEe
Confidence 67777763 63 3655443
No 221
>KOG4184 consensus Predicted sugar kinase [Carbohydrate transport and metabolism; General function prediction only]
Probab=26.61 E-value=96 Score=28.29 Aligned_cols=68 Identities=15% Similarity=0.177 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhcCCCEEEEe-ccCCCC-CCchHHHHHHHHHHHHHhccCCCCCcEE-----EecCcccHHHHHHHhc
Q 030509 62 MAEDFRSLISEFNLEGFIVG-YPFNRQ-QNAADAVQVKLFIDDLSATKKLEDMKYA-----YWNEGFTSKGVELLLN 131 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVG-lPl~dG-~~s~~~~~v~~Fa~~L~~~~~~~~lpV~-----~~DEr~TT~~A~~~l~ 131 (176)
..+.+-+-+++++|+.+||- +-+-++ +..++-++.+...+.|... .+++|++ +.||-++|.--+..|-
T Consensus 226 ~~E~f~~Al~~fqPdLvVvsGlhmme~qske~r~~rl~~V~r~L~~i--P~gip~HlElaS~~~~~l~~~i~h~VlP 300 (478)
T KOG4184|consen 226 AVEQFTDALKMFQPDLVVVSGLHMMEMQSKEEREARLQQVVRSLSDI--PTGIPVHLELASMTNRELMSSIVHQVLP 300 (478)
T ss_pred HHHHHHHHHHHhCCCEEEEechhHHhhhhHHHHHHHHHHHHHHHhcC--CCCCchhhhHhHHHHHHHHHHHHHHhhh
Confidence 45778888999999999884 333332 3335555666677777652 4689987 5788888887776654
No 222
>PRK11175 universal stress protein UspE; Provisional
Probab=26.60 E-value=1.7e+02 Score=24.19 Aligned_cols=20 Identities=5% Similarity=-0.230 Sum_probs=18.1
Q ss_pred HHHHHHHHHhcCCCEEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGY 82 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGl 82 (176)
.+.|.+.++++++|.||+|.
T Consensus 96 ~~~i~~~a~~~~~DLiV~G~ 115 (305)
T PRK11175 96 FEAIIQEVIAGGHDLVVKMT 115 (305)
T ss_pred HHHHHHHHHhcCCCEEEEeC
Confidence 57899999999999999993
No 223
>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A ....
Probab=26.60 E-value=3e+02 Score=21.11 Aligned_cols=62 Identities=15% Similarity=0.117 Sum_probs=36.9
Q ss_pred HHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec--CcccHHHHHHHhc
Q 030509 68 SLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN--EGFTSKGVELLLN 131 (176)
Q Consensus 68 ~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D--Er~TT~~A~~~l~ 131 (176)
.+.....+|..++.- -. ...+-....++++.+.+.......+..|+.+| |++|..++..+|+
T Consensus 61 ~~~~~~~~d~~~~~~-~~-~~~~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK 124 (162)
T PF13177_consen 61 RIEEGNHPDFIIIKP-DK-KKKSIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLK 124 (162)
T ss_dssp HHHTT-CTTEEEEET-TT-SSSSBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHH
T ss_pred HHHhccCcceEEEec-cc-ccchhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHH
Confidence 444456789888862 11 11133457777777777653111245677776 8898888888876
No 224
>KOG0104 consensus Molecular chaperones GRP170/SIL1, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=26.58 E-value=1.1e+02 Score=30.55 Aligned_cols=32 Identities=19% Similarity=0.589 Sum_probs=26.0
Q ss_pred cCCCCeEEEEecCCCeEEEEEecCCCceeccceeee
Q 030509 18 VSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLL 53 (176)
Q Consensus 18 ~~~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~ 53 (176)
++...-+|+||+|+..|=+|+..| | .|+.++-
T Consensus 18 ~~~~~AvmsVDlGse~~Kv~vVkP-G---vPmeIvL 49 (902)
T KOG0104|consen 18 LSSALAVMSVDLGSEWIKVAVVKP-G---VPMEIVL 49 (902)
T ss_pred ccchhhheeeecccceeEEEEecC-C---CCeEEee
Confidence 456678999999999999999998 3 5666653
No 225
>PF10035 DUF2179: Uncharacterized protein conserved in bacteria (DUF2179); InterPro: IPR019264 This entry, found mostly in hypothetical bacterial proteins, has no known function. ; PDB: 3HLU_B.
Probab=26.43 E-value=82 Score=19.74 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=15.3
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
+.+|.+++++.+|++||+=
T Consensus 29 ~~~l~~~I~~~Dp~AFi~v 47 (55)
T PF10035_consen 29 LPKLKKIIKEIDPKAFISV 47 (55)
T ss_dssp HHHHHHHHHCC-TT-EEEE
T ss_pred HHHHHHHHHHhCCCEEEEE
Confidence 6899999999999999874
No 226
>PF08608 Wyosine_form: Wyosine base formation; InterPro: IPR013917 The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW []. ; PDB: 2YX0_A 2Z2U_A.
Probab=26.42 E-value=87 Score=20.87 Aligned_cols=28 Identities=21% Similarity=0.189 Sum_probs=18.8
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 89 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 89 ~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
.-+..++|.+|+++|.+. ++....||+-
T Consensus 26 nmp~h~eV~~F~~~l~~~-----~~y~i~~e~~ 53 (62)
T PF08608_consen 26 NMPWHEEVLDFAEELAEL-----LGYEITDEHE 53 (62)
T ss_dssp GS--HHHHHHHHHHHHTT-----STEEEEEEEC
T ss_pred CCCcHHHHHHHHHHHHhh-----cCCEEEeccc
Confidence 346788999999999972 3466666653
No 227
>cd01400 6PGL 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard against the accumulation of the delta form of the lactone, which may be toxic through its reaction with endogenous cellular nucleophiles.
Probab=26.40 E-value=1.8e+02 Score=23.57 Aligned_cols=49 Identities=14% Similarity=0.139 Sum_probs=27.9
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhc--cCCCCCcEEEecCcc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSAT--KKLEDMKYAYWNEGF 121 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~--~~~~~lpV~~~DEr~ 121 (176)
.+.+.+.+++.. .+++|+ .|..++. .+-+.|.+. ..+.++-++++|||+
T Consensus 12 ~~~i~~~i~~~~--~~~l~l---sGGstp~-----~~y~~L~~~~~i~w~~v~~f~~DEr~ 62 (219)
T cd01400 12 AEALAAAIAKRG--RFSLAL---SGGSTPK-----PLYELLAAAPALDWSKVHVFLGDERC 62 (219)
T ss_pred HHHHHHHHHhcC--eEEEEE---CCCccHH-----HHHHHhccccCCCCceEEEEEeeccc
Confidence 344555454443 466665 4655653 344445432 134577789999997
No 228
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.39 E-value=1.1e+02 Score=25.04 Aligned_cols=28 Identities=7% Similarity=0.051 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNA 90 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s 90 (176)
++.|.+.+++.++..||+.+..+ .|..+
T Consensus 123 i~~L~~Ri~~~~v~EVIlAt~~tvEGe~T 151 (195)
T TIGR00615 123 IAALLKRLQEESVKEVILATNPTVEGEAT 151 (195)
T ss_pred HHHHHHHHhcCCCcEEEEeCCCCchHHHH
Confidence 68888889888999999998877 77544
No 229
>PRK13790 phosphoribosylamine--glycine ligase; Provisional
Probab=26.38 E-value=2.1e+02 Score=25.19 Aligned_cols=19 Identities=11% Similarity=0.309 Sum_probs=17.1
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.|.+++++++++.+|+|
T Consensus 16 ~~~l~~~~~~~~id~vi~g 34 (379)
T PRK13790 16 HQAILDFAKQQNVDWVVIG 34 (379)
T ss_pred HHHHHHHHHHhCCCEEEEC
Confidence 5889999999999999988
No 230
>COG0145 HyuA N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=26.35 E-value=2.5e+02 Score=27.33 Aligned_cols=58 Identities=19% Similarity=0.263 Sum_probs=37.7
Q ss_pred CeEEEEecCCCeEEEEEecCCC-ceeccceeeeCCCCChhhHHHHHHHHHHhc----CCCEEEEe
Q 030509 22 GRFLGLDVGDKYVGLSISDPKN-KIASPLSVLLRKKNTIDLMAEDFRSLISEF----NLEGFIVG 81 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~-~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~----~~~~iVVG 81 (176)
+..+|||.|.-.+=+.+-|..+ .+.. .+++.. ..........+.+++..+ +++.+++|
T Consensus 2 ~~~iGID~GGTfTDaV~~~~~~g~~~~-~K~lTt-P~~~~~~~~~~~~~~~~~~~~~~i~~v~~g 64 (674)
T COG0145 2 MLRIGIDVGGTFTDAVLLDEDGGVLAT-IKVLTT-PDLPSGIVNAGIRLALELLEGSEVDLVVHG 64 (674)
T ss_pred ceEEEEEcCCCcEeEEEEeCCCCEEEE-EEccCC-CCchhhHHHHHHHHHhhccccccccEEEEe
Confidence 5689999999999888877765 2332 333333 222223345666666664 69999999
No 231
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=26.35 E-value=3.3e+02 Score=21.59 Aligned_cols=56 Identities=11% Similarity=0.069 Sum_probs=39.7
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHH
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 128 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 128 (176)
++..|.+...+.+...+++| |++. .+.+.++.|++ ++|++.|...+=.++..+...
T Consensus 36 l~~~l~~~~~~~~~~vfllG-----~~~~----v~~~~~~~l~~--~yP~l~i~g~~g~f~~~~~~~ 91 (177)
T TIGR00696 36 LMEELCQRAGKEKLPIFLYG-----GKPD----VLQQLKVKLIK--EYPKLKIVGAFGPLEPEERKA 91 (177)
T ss_pred HHHHHHHHHHHcCCeEEEEC-----CCHH----HHHHHHHHHHH--HCCCCEEEEECCCCChHHHHH
Confidence 46777777777788889999 5544 34567778877 378999887777776554433
No 232
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=26.28 E-value=1.8e+02 Score=24.76 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=35.8
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr 120 (176)
.-++.+..++..++++++.-|.. ..+. +.+.+|-+.+.+. .+++|++++|--
T Consensus 85 ~i~la~~a~~~Gad~v~v~~P~y~~~~~----~~i~~yf~~v~~~--~~~lpv~lYn~P 137 (290)
T TIGR00683 85 AVELGKYATELGYDCLSAVTPFYYKFSF----PEIKHYYDTIIAE--TGGLNMIVYSIP 137 (290)
T ss_pred HHHHHHHHHHhCCCEEEEeCCcCCCCCH----HHHHHHHHHHHhh--CCCCCEEEEeCc
Confidence 35666778889999999988877 5543 3444555555432 236999988864
No 233
>cd01833 XynB_like SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=26.19 E-value=2.6e+02 Score=20.39 Aligned_cols=56 Identities=7% Similarity=-0.006 Sum_probs=23.6
Q ss_pred HHHHHHHHHhcC--CCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 63 AEDFRSLISEFN--LEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 63 ~~~L~~li~e~~--~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
++++.+.+++.. +.-+++++|.. +....+......+..+++.+.....+..+.++|
T Consensus 66 ~~~~i~~i~~~~p~~~ii~~~~~p~~~~~~~~~~~~~n~~l~~~~~~~~~~~~~v~~vd 124 (157)
T cd01833 66 LRALIDQMRAANPDVKIIVATLIPTTDASGNARIAEYNAAIPGVVADLRTAGSPVVLVD 124 (157)
T ss_pred HHHHHHHHHHhCCCeEEEEEeCCCCCCcchhHHHHHHHHHHHHHHHHHhcCCCCEEEEe
Confidence 345555555553 34455665444 333233333333333333321001124566666
No 234
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=26.15 E-value=1.8e+02 Score=26.45 Aligned_cols=48 Identities=10% Similarity=0.208 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.+.|.++++++++|+||.=.=.. +....++. .++++. ++. ++|+..+|
T Consensus 350 ~~~l~~li~e~~vDGVI~~~~~~C~~~s~e~~-~ik~~l---~~~----GIP~L~ie 398 (430)
T TIGR03191 350 SEMMLNIARDWNVDGCMLHLNRGCEGLSIGIM-ENRLAI---AKA----GIPIMTFE 398 (430)
T ss_pred HHHHHHHHHHHCCCEEEEcCCCCCccchHhHH-HHHHHH---HHc----CCCEEEEE
Confidence 68899999999999999864333 44433333 345544 331 78876553
No 235
>PRK07667 uridine kinase; Provisional
Probab=26.10 E-value=2.3e+02 Score=22.21 Aligned_cols=53 Identities=8% Similarity=0.160 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCc--EEEecCcc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMK--YAYWNEGF 121 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lp--V~~~DEr~ 121 (176)
.++|.+.+.+++...+|||+== ++-+..+..++.+++.|.+. +++ ++-.|..+
T Consensus 3 ~~~~~~~~~~~~~~~~iIgI~G--~~gsGKStla~~L~~~l~~~----~~~~~~i~~Dd~~ 57 (193)
T PRK07667 3 TNELINIMKKHKENRFILGIDG--LSRSGKTTFVANLKENMKQE----GIPFHIFHIDDYI 57 (193)
T ss_pred HHHHHHHHHhcCCCCEEEEEEC--CCCCCHHHHHHHHHHHHHhC----CCcEEEEEcCccc
Confidence 4677788899999999999731 12234455567777777652 455 55555544
No 236
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=25.94 E-value=2.1e+02 Score=25.23 Aligned_cols=130 Identities=15% Similarity=0.043 Sum_probs=64.7
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCC------CChhhHHHHHHHHHHhc-CCCEEEEeccCCCCCCchHHH
Q 030509 22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK------NTIDLMAEDFRSLISEF-NLEGFIVGYPFNRQQNAADAV 94 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~------~~~~~~~~~L~~li~e~-~~~~iVVGlPl~dG~~s~~~~ 94 (176)
--++.+|-|...||+--+......++=-..+|.+. .....++.++.+-+.++ .+++|||+ +++....
T Consensus 136 ~~~vv~d~g~A~i~ll~~~~~~~~~~i~~~iP~K~~~~~~e~~~~~Ff~~v~~~l~~~~~v~~iIia------GPGf~k~ 209 (351)
T TIGR00111 136 TAAVVMEEGIAHVGLVRQYSVEEIQKIEYHMPGKKRTLKFGELRKEFYKEIAKKLLNFDDLKTIIVA------GPGFYKN 209 (351)
T ss_pred EEEEEEeCCcEEEEEEcCCEEEEEEEEEEeCCCCcccchhHHHHHHHHHHHHHHHhhhcccCEEEEE------CCHHHHH
Confidence 45788999999999887765433333111232221 11234566666666665 79999999 4444444
Q ss_pred HHHHHHHHHHhccCCCCCcEEEecCcccHHHHH-HHhccCCCCCCCCCCCCcHHHHHHHHHHHHhhhhh
Q 030509 95 QVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVE-LLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANR 162 (176)
Q Consensus 95 ~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~-~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~~~~ 162 (176)
.|.+.|.+...-.....+..|=+++...+- +.|....+.+ .-...-..-..-++++|++....
T Consensus 210 ---~f~~~l~~~~~~~~~k~ii~~~s~g~~~gl~EvL~~~~v~~--~l~d~k~~~E~~~l~~f~~~l~k 273 (351)
T TIGR00111 210 ---DFYDFIFERYPEEANKAVLENCSTGGRAGINEVLKRGLVAR--ILQETRYAKEIMVIDEFLEHLAK 273 (351)
T ss_pred ---HHHHHHHHHhhhhhCCcEEEecCCCchhHHHHHHhChHHHH--HHhhhhHHHHHHHHHHHHHHHhc
Confidence 344444432100012334445233223332 2232111111 01122333456789999987644
No 237
>TIGR03566 FMN_reduc_MsuE FMN reductase, MsuE subfamily. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. The NADP-dependent enzyme from E. coli is outside the scope of this model.
Probab=25.72 E-value=1.5e+02 Score=22.86 Aligned_cols=49 Identities=18% Similarity=0.151 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
+.++.+-+. +.|+||+|-|..+|+.+.+.+. |.+.+... .+.+-|+.++
T Consensus 59 ~~~~~~~i~--~AD~iIi~tP~Y~~s~~~~LKn---~lD~~~~~-~l~~K~~~~v 107 (174)
T TIGR03566 59 AERILQAIE--SADLLVVGSPVYRGSYTGLFKH---LFDLVDPN-ALIGKPVLLA 107 (174)
T ss_pred HHHHHHHHH--HCCEEEEECCcCcCcCcHHHHH---HHHhcCHh-HhCCCEEEEE
Confidence 456666555 5899999999998888876664 44444321 1335565554
No 238
>PF03644 Glyco_hydro_85: Glycosyl hydrolase family 85 ; InterPro: IPR005201 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This group of endo-beta-N-acetylglucosaminidases belong to the glycoside hydrolase family 85 (GH85 from CAZY). These enzymes work on a broad spectrum of substrates.; GO: 0033925 mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity, 0005737 cytoplasm; PDB: 2W92_A 2W91_A 2VTF_B 3FHQ_B 3FHA_D 3GDB_A.
Probab=25.65 E-value=1.5e+02 Score=25.79 Aligned_cols=57 Identities=11% Similarity=0.244 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccC-CCCCcEEEecC
Q 030509 61 LMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKK-LEDMKYAYWNE 119 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~-~~~lpV~~~DE 119 (176)
..+++|.++++-+..|+..|-.--. .+ ...+...+.|.+.|.+... .++..|.+.|=
T Consensus 86 ~~A~kLi~ia~~yGFDGw~iN~E~~~~~--~~~~~~l~~F~~~l~~~~~~~~~~~v~WYDs 144 (311)
T PF03644_consen 86 PYADKLIEIAKYYGFDGWLINIETPLSG--PEDAENLIDFLKYLRKEAHENPGSEVIWYDS 144 (311)
T ss_dssp HHHHHHHHHHHHHT--EEEEEEEESSTT--GGGHHHHHHHHHHHHHHHHHT-T-EEEEES-
T ss_pred HHHHHHHHHHHHcCCCceEEEecccCCc--hhHHHHHHHHHHHHHHHhhcCCCcEEEEeec
Confidence 3579999999999999999885443 22 2567788888888876422 34567888886
No 239
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=25.60 E-value=75 Score=22.40 Aligned_cols=21 Identities=29% Similarity=0.419 Sum_probs=18.7
Q ss_pred HHHHHHHHHhcCCCEEEEecc
Q 030509 63 AEDFRSLISEFNLEGFIVGYP 83 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlP 83 (176)
.+.|.+.+++++++.||+|..
T Consensus 74 ~~~I~~~~~~~~~dllviG~~ 94 (124)
T cd01987 74 AEAIVEFAREHNVTQIVVGKS 94 (124)
T ss_pred HHHHHHHHHHcCCCEEEeCCC
Confidence 588999999999999999953
No 240
>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).
Probab=25.60 E-value=2.6e+02 Score=20.15 Aligned_cols=47 Identities=9% Similarity=-0.076 Sum_probs=30.5
Q ss_pred HHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 67 RSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 67 ~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
.....+..-..++|| .|+.+ ....+.+.|.+. ++.+||.+..|..+.
T Consensus 35 ~~~~~~~~~~~~~v~----~g~~~----~~~~~l~~l~~~--~~~~Pvlllg~~~~~ 81 (109)
T PF06490_consen 35 SQADWSSPWEACAVI----LGSCS----KLAELLKELLKW--APHIPVLLLGEHDSP 81 (109)
T ss_pred HHhhhhcCCcEEEEE----ecCch----hHHHHHHHHHhh--CCCCCEEEECCCCcc
Confidence 444555566777777 56655 223444555543 578999999988877
No 241
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=25.56 E-value=70 Score=30.37 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=17.4
Q ss_pred CeEEEEecCCCeEEEEEecC
Q 030509 22 GRFLGLDVGDKYVGLSISDP 41 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~ 41 (176)
..++|||+|+..+-||+.+.
T Consensus 19 ~~~iGIDlGTt~s~va~~~~ 38 (616)
T PRK05183 19 RLAVGIDLGTTNSLVATVRS 38 (616)
T ss_pred CeEEEEEeccccEEEEEEEC
Confidence 46899999999999999754
No 242
>TIGR01198 pgl 6-phosphogluconolactonase. This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with
Probab=25.37 E-value=2e+02 Score=23.57 Aligned_cols=37 Identities=11% Similarity=0.183 Sum_probs=21.8
Q ss_pred EEEEeccCCCCCCchHHHHHHHHHHHHHh-ccCCCCCcEEEecCcc
Q 030509 77 GFIVGYPFNRQQNAADAVQVKLFIDDLSA-TKKLEDMKYAYWNEGF 121 (176)
Q Consensus 77 ~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~-~~~~~~lpV~~~DEr~ 121 (176)
.+++++ .|..++. .+-+.|.+ ...+.++-+++.|||+
T Consensus 29 ~~~lal---sGGstp~-----~~y~~L~~~~i~w~~v~~f~~DER~ 66 (233)
T TIGR01198 29 QFSLAL---SGGRSPI-----ALLEALAAQPLDWSRIHLFLGDERY 66 (233)
T ss_pred cEEEEE---CCCccHH-----HHHHHHhhCCCCcceEEEEEecccc
Confidence 356665 4555552 33344443 1234577899999997
No 243
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from SWISSPROT from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins.; PDB: 3RK0_A 3RK1_A 3RJZ_A 2D13_D.
Probab=25.37 E-value=1.2e+02 Score=25.05 Aligned_cols=37 Identities=19% Similarity=0.342 Sum_probs=21.9
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDL 103 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L 103 (176)
.+.+.+.+++.+++++|.| |=....+...+++.++++
T Consensus 74 ~~~l~~~l~~~~v~~vv~G----dI~~~~~r~~~e~vc~~l 110 (218)
T PF01902_consen 74 VEDLKEALKELKVEAVVFG----DIDSEYQRNWVERVCERL 110 (218)
T ss_dssp HHHHHHHHCTC--SEEE------TTS-HHHHHHHHHHHHHC
T ss_pred hHHHHHHHHHcCCCEEEEC----cCCcHHHHHHHHHHHHHc
Confidence 5888999999999999999 655455544444444443
No 244
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=25.35 E-value=3.5e+02 Score=21.51 Aligned_cols=45 Identities=9% Similarity=0.169 Sum_probs=25.6
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
...+.+.+..+++++||+. |.+ .... ....+++.+. ++||+++|-
T Consensus 49 ~~~~~~~l~~~~vDgiii~-~~~---~~~~----~~~i~~~~~~----gIpvV~~d~ 93 (274)
T cd06311 49 QNAQQDLLINRKIDALVIL-PFE---SAPL----TQPVAKAKKA----GIFVVVVDR 93 (274)
T ss_pred HHHHHHHHHHcCCCEEEEe-CCC---chhh----HHHHHHHHHC----CCeEEEEcC
Confidence 3455665666789999996 333 1111 1222344432 788888874
No 245
>PRK10854 exopolyphosphatase; Provisional
Probab=25.34 E-value=2.2e+02 Score=26.34 Aligned_cols=93 Identities=15% Similarity=0.166 Sum_probs=56.8
Q ss_pred ccCCCCeEEEEecCCCeEEEEEecCCCceeccceeee----C-----CCC--Ch------hhHHHHHHHHHHhcCCCE-E
Q 030509 17 KVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLL----R-----KKN--TI------DLMAEDFRSLISEFNLEG-F 78 (176)
Q Consensus 17 ~~~~~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~----~-----~~~--~~------~~~~~~L~~li~e~~~~~-i 78 (176)
+-|+++.+-+||.|+--|=+.|.+....-...+.... - .++ ++ -..+....+++++++++. .
T Consensus 6 ~~~~~~~~A~IDIGSNSirL~I~e~~~~~~~~i~~~k~~vrLg~g~~~~g~Ls~e~~~r~~~~L~~F~~~~~~~~v~~v~ 85 (513)
T PRK10854 6 KSPRPQEFAAVDLGSNSFHMVIARVVDGAMQIIGRLKQRVHLADGLDSDNMLSEEAMERGLNCLSLFAERLQGFSPANVC 85 (513)
T ss_pred CCCCCCEEEEEEeccchheEEEEEecCCcEEEeeeeeEEEECCCCcCCCCCcCHHHHHHHHHHHHHHHHHHHhCCCCeEE
Confidence 3467788999999999999998875422112221110 0 011 11 123566778888999864 4
Q ss_pred EEeccCCCCCCc-hHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 79 IVGYPFNRQQNA-ADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 79 VVGlPl~dG~~s-~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
+|| |.. ..+.....|.+++++. ++++|...+
T Consensus 86 ~vA------TsAlReA~N~~~fl~~i~~~---tGl~i~vIs 117 (513)
T PRK10854 86 IVG------THTLRQALNATDFLKRAEKV---IPYPIEIIS 117 (513)
T ss_pred EEe------hHHHHcCcCHHHHHHHHHHH---HCCCeEEeC
Confidence 555 321 2233446899999874 388888887
No 246
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=25.30 E-value=4.2e+02 Score=22.46 Aligned_cols=44 Identities=9% Similarity=0.129 Sum_probs=23.8
Q ss_pred HHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc
Q 030509 65 DFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120 (176)
Q Consensus 65 ~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr 120 (176)
++.+.+..+++++||+- |.+ .+.. ....+.+.+. ++||+++|..
T Consensus 72 ~~i~~l~~~~vDGiIi~-~~~---~~~~----~~~l~~~~~~----~iPvV~id~~ 115 (330)
T PRK10355 72 SQIENMINRGVDVLVII-PYN---GQVL----SNVIKEAKQE----GIKVLAYDRM 115 (330)
T ss_pred HHHHHHHHcCCCEEEEe-CCC---hhhH----HHHHHHHHHC----CCeEEEECCC
Confidence 33334456799999996 221 1111 1233445442 6788888753
No 247
>PF00349 Hexokinase_1: Hexokinase; InterPro: IPR022672 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways []. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains []. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. Hexokinase (2.7.1.1 from EC), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and PF03727 from PFAM. Some hexokinases have two copies of each of these domains. This entry represents the N-terminal domain.; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3O1W_A 3O6W_A 3O4W_B 3O08_B 3O80_A 3O5B_A 3O8M_A 3O1B_A 1BG3_A 4DHY_A ....
Probab=25.28 E-value=42 Score=27.45 Aligned_cols=67 Identities=21% Similarity=0.455 Sum_probs=37.3
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCce--ec--cceeeeCC--CCC----hhhHHHHHHHHHHhcCC--------CEEEE
Q 030509 19 SKRGRFLGLDVGDKYVGLSISDPKNKI--AS--PLSVLLRK--KNT----IDLMAEDFRSLISEFNL--------EGFIV 80 (176)
Q Consensus 19 ~~~~~iLglD~G~kriGvAvsd~~~~~--a~--Pl~~i~~~--~~~----~~~~~~~L~~li~e~~~--------~~iVV 80 (176)
...|.+||||+|....=|+...-.+.- .. --..++.. ... .+...+.|.+++.++.. -++..
T Consensus 60 ~E~G~~LalDlGGTnlRv~~V~L~g~~~~~~~~~~~~ip~~~~~~~~~~lFd~ia~~i~~f~~~~~~~~~~~~l~lGfTF 139 (206)
T PF00349_consen 60 NEKGDFLALDLGGTNLRVALVELSGNGKVEIEQEKYKIPEELMNGSGEELFDFIADCIAEFLKEHNLESRDEKLPLGFTF 139 (206)
T ss_dssp TTEEEEEEEEESSSSEEEEEEEEESSSEEEEEEEEEE--HHHHTSBHHHHHHHHHHHHHHHHHHTTTTSTTSEEEEEEEE
T ss_pred CCCceEEEEeecCcEEEEEEEEEcCCCCceeeeccccCChHHhcCCcccHHHHHHHHHHHHHHHhcccccccccceEEEE
Confidence 355789999999998888877644331 10 00011110 111 23334556667776655 45555
Q ss_pred eccCC
Q 030509 81 GYPFN 85 (176)
Q Consensus 81 GlPl~ 85 (176)
-.|.+
T Consensus 140 SFP~~ 144 (206)
T PF00349_consen 140 SFPVE 144 (206)
T ss_dssp ESSEE
T ss_pred EEEEE
Confidence 56877
No 248
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=25.20 E-value=4.3e+02 Score=22.45 Aligned_cols=59 Identities=12% Similarity=0.107 Sum_probs=36.5
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCch--------HHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAA--------DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~--------~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
++++.+.+-+..+++|+++ |+.++ +.+.++.+++... .++||+.-=-..||.+|-++.+
T Consensus 23 l~~lv~~~~~~Gv~gi~v~-----GstGE~~~Ls~~Er~~l~~~~~~~~~-----g~~pvi~gv~~~~t~~ai~~a~ 89 (294)
T TIGR02313 23 LRELIEFQIEGGSHAISVG-----GTSGEPGSLTLEERKQAIENAIDQIA-----GRIPFAPGTGALNHDETLELTK 89 (294)
T ss_pred HHHHHHHHHHcCCCEEEEC-----ccCcccccCCHHHHHHHHHHHHHHhC-----CCCcEEEECCcchHHHHHHHHH
Confidence 4566666666789999987 65543 3333333333332 1578876666688888866654
No 249
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=25.13 E-value=3.3e+02 Score=21.40 Aligned_cols=18 Identities=33% Similarity=0.621 Sum_probs=12.5
Q ss_pred HHHHHHHHHhcCCCEEEE
Q 030509 63 AEDFRSLISEFNLEGFIV 80 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVV 80 (176)
...+.+.+..+++++||+
T Consensus 45 ~~~~~~~l~~~~vdgiii 62 (270)
T cd01545 45 AERVRALLQRSRVDGVIL 62 (270)
T ss_pred HHHHHHHHHHCCCCEEEE
Confidence 456666666777888776
No 250
>PLN03184 chloroplast Hsp70; Provisional
Probab=25.13 E-value=69 Score=30.83 Aligned_cols=21 Identities=14% Similarity=0.401 Sum_probs=17.6
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030509 22 GRFLGLDVGDKYVGLSISDPK 42 (176)
Q Consensus 22 ~~iLglD~G~kriGvAvsd~~ 42 (176)
..++|||+|+..+-+|+.++.
T Consensus 39 ~~viGIDlGTt~s~va~~~~g 59 (673)
T PLN03184 39 EKVVGIDLGTTNSAVAAMEGG 59 (673)
T ss_pred CCEEEEEeCcCcEEEEEEECC
Confidence 359999999999999987543
No 251
>TIGR03858 LLM_2I7G probable oxidoreductase, LLM family. This model describes a highly conserved, somewhat broadly distributed family withing the luciferase-like monooxygenase (LLM) superfamily. Most members are from species incapable of synthesizing coenzyme F420, bound by some members of the LLM superfamily. Members, therefore, are more likely to use FMN as a cofactor.
Probab=24.89 E-value=1.4e+02 Score=25.79 Aligned_cols=26 Identities=23% Similarity=0.492 Sum_probs=16.2
Q ss_pred ChhhHHHHHHHHHHhcCCCEEEEecc
Q 030509 58 TIDLMAEDFRSLISEFNLEGFIVGYP 83 (176)
Q Consensus 58 ~~~~~~~~L~~li~e~~~~~iVVGlP 83 (176)
+++++.++|.++.++..++.|++..|
T Consensus 287 tPe~V~e~i~~~~~~~G~d~~~l~~~ 312 (337)
T TIGR03858 287 SPETVAEKIADTIETLGLDRFMLHYS 312 (337)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEEec
Confidence 34555666666666666777776643
No 252
>cd00598 GH18_chitinase-like The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel. The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins. The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are inclu
Probab=24.87 E-value=2.8e+02 Score=21.41 Aligned_cols=46 Identities=11% Similarity=0.351 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHh
Q 030509 60 DLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 105 (176)
Q Consensus 60 ~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~ 105 (176)
..+++.+.+++++++.++|.+=+-......++.......|.+.|++
T Consensus 90 ~~f~~~~~~~v~~~~~DGidiD~E~~~~~~~~~~~~~~~ll~~lr~ 135 (210)
T cd00598 90 AAFANSLVSFLKTYGFDGVDIDWEYPGAADNSDRENFITLLRELRS 135 (210)
T ss_pred HHHHHHHHHHHHHcCCCceEEeeeCCCCcCccHHHHHHHHHHHHHH
Confidence 4568999999999999999997654411110123344456666655
No 253
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=24.79 E-value=1.4e+02 Score=23.83 Aligned_cols=40 Identities=18% Similarity=0.306 Sum_probs=33.0
Q ss_pred HHHHHHHHHhcCCC-EEEEeccCC--CCCCchHHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNLE-GFIVGYPFN--RQQNAADAVQVKLFIDD 102 (176)
Q Consensus 63 ~~~L~~li~e~~~~-~iVVGlPl~--dG~~s~~~~~v~~Fa~~ 102 (176)
.+.|..|.+.|+-. -.|+|.|-| .|.+-...++|.+|++.
T Consensus 43 YegLe~Ly~ky~~~Gf~VLgFPcNQF~~QEPg~~eEI~~fC~~ 85 (162)
T COG0386 43 YEGLEALYKKYKDKGFEVLGFPCNQFGGQEPGSDEEIAKFCQL 85 (162)
T ss_pred HHHHHHHHHHHhhCCcEEEeccccccccCCCCCHHHHHHHHHh
Confidence 68889999888654 467899999 77888888999999874
No 254
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=24.59 E-value=3.4e+02 Score=27.39 Aligned_cols=54 Identities=11% Similarity=0.037 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHH-HHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 62 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQ-VKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~-v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
..+.|.++.+++++..||||-|. .+.+... -..|+++|... .+++.|+.+....
T Consensus 322 v~~~i~~ya~~~~~TkiViG~~~----~~rw~~~~~~~l~~~L~~~--~~~idv~ii~~~~ 376 (890)
T COG2205 322 VAKAIARYAREHNATKIVIGRSR----RSRWRRLFKGSLADRLARE--APGIDVHIVALDA 376 (890)
T ss_pred HHHHHHHHHHHcCCeeEEeCCCc----chHHHHHhcccHHHHHHhc--CCCceEEEeeCCC
Confidence 46899999999999999999443 3333222 15788888763 4578888776433
No 255
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=24.51 E-value=1.6e+02 Score=23.50 Aligned_cols=49 Identities=18% Similarity=0.264 Sum_probs=31.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
+.++.+.+. +.|+||||-|..+|+.+...+. |.+.+... .+.+-|+..+
T Consensus 57 ~~~~~~~i~--~AD~iIi~tP~Y~~s~pg~LKn---~iD~l~~~-~l~~K~v~ii 105 (191)
T PRK10569 57 LKTFTEQLA--QADGLIVATPVYKASFSGALKT---LLDLLPER-ALEHKVVLPL 105 (191)
T ss_pred HHHHHHHHH--HCCEEEEECCccCCCCCHHHHH---HHHhCChh-hhCCCEEEEE
Confidence 456666555 5899999999998888886664 44444321 1334455544
No 256
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=24.45 E-value=1.3e+02 Score=26.18 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=29.0
Q ss_pred eEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC
Q 030509 33 YVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN 85 (176)
Q Consensus 33 riGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~ 85 (176)
-++++|.|....+.+.-.+ +. +. -++-.+++.|++|+.+++|-|.+
T Consensus 167 Vl~v~V~dg~~~i~faSDv-qG----p~--~~~~l~~i~e~~P~v~ii~GPpt 212 (304)
T COG2248 167 VLMVAVTDGKSSIVFASDV-QG----PI--NDEALEFILEKRPDVLIIGGPPT 212 (304)
T ss_pred EEEEEEecCCeEEEEcccc-cC----CC--ccHHHHHHHhcCCCEEEecCCch
Confidence 3567777766554432111 10 11 24567788889999999999877
No 257
>PRK07179 hypothetical protein; Provisional
Probab=24.30 E-value=2.4e+02 Score=24.66 Aligned_cols=51 Identities=12% Similarity=0.087 Sum_probs=33.7
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCccc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 122 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~T 122 (176)
.+.|.+.+++..+..|++--|.+ .|...+. + +.++..++ . ++ ++.+||.++
T Consensus 170 ~~~l~~~l~~~~~~lV~v~~v~n~tG~i~pl-~---~I~~l~~~---~-~~-~livDea~~ 221 (407)
T PRK07179 170 VDHLRRQIERHGPGIIVVDSVYSTTGTIAPL-A---DIVDIAEE---F-GC-VLVVDESHS 221 (407)
T ss_pred HHHHHHHHHhcCCeEEEECCCCCCCCccccH-H---HHHHHHHH---c-CC-EEEEECccc
Confidence 47788888766677777877778 8888773 2 33333333 1 43 677888876
No 258
>TIGR03286 methan_mark_15 putative methanogenesis marker protein 15. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. Related proteins include the BadF/BadG/BcrA/BcrD ATPase family (pfam01869), which includes an activator for (R)-2-hydroxyglutaryl-CoA dehydratase.
Probab=24.29 E-value=3.1e+02 Score=25.11 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=20.0
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCc
Q 030509 20 KRGRFLGLDVGDKYVGLSISDPKNK 44 (176)
Q Consensus 20 ~~~~iLglD~G~kriGvAvsd~~~~ 44 (176)
..+..+|||.|+..+=+++-|....
T Consensus 142 ~~g~~lGIDiGSTttK~Vl~dd~~I 166 (404)
T TIGR03286 142 QEGLTLGIDSGSTTTKAVVMEDNEV 166 (404)
T ss_pred cCCEEEEEEcChhheeeEEEcCCeE
Confidence 4467899999999999998885433
No 259
>PF00464 SHMT: Serine hydroxymethyltransferase; InterPro: IPR001085 Synonym(s): Serine hydroxymethyltransferase, Serine aldolase, Threonine aldolase Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme and belongs to the aspartate aminotransferase superfamily (fold type I) []. The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme []. The enzyme carries out interconversion of serine and glycine using PLP as the cofactor. SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer [, ]. PLP dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalysed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V) [, ]. In vertebrates, glycine hydroxymethyltransferase exists in a cytoplasmic and a mitochondrial form whereas only one form is found in prokaryotes.; GO: 0004372 glycine hydroxymethyltransferase activity, 0006544 glycine metabolic process, 0006563 L-serine metabolic process; PDB: 3GBX_B 3H7F_A 1YJS_A 2VMW_A 2W7H_A 2W7E_A 2VMY_B 2W7L_A 2VMZ_A 2VMS_A ....
Probab=24.24 E-value=2.1e+02 Score=25.96 Aligned_cols=34 Identities=18% Similarity=0.303 Sum_probs=21.4
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHH
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 101 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~ 101 (176)
++++.+++++++|+.||+| ++.-...-..++|.+
T Consensus 158 ~d~l~~~a~~~kPklIi~G-----~S~y~~~~d~~~~re 191 (399)
T PF00464_consen 158 YDELEKLAKEHKPKLIICG-----ASSYPRPIDFKRFRE 191 (399)
T ss_dssp HHHHHHHHHHH--SEEEEE------SSTSS---HHHHHH
T ss_pred HHHHHHHHhhcCCCEEEEC-----chhccCccCHHHHHH
Confidence 7999999999999999999 444444444445544
No 260
>TIGR03729 acc_ester putative phosphoesterase. Members of this protein family belong to the larger family pfam00149 (calcineurin-like phosphoesterase), a family largely defined by small motifs of metal-chelating residues. The subfamily in this model shows a good but imperfect co-occurrence in species with domain TIGR03715 that defines a novel class of signal peptide typical of the accessory secretory system.
Probab=24.13 E-value=2.3e+02 Score=22.88 Aligned_cols=47 Identities=13% Similarity=0.241 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
++.+.+.+.+.+++.||+. |...........+.+.|.+. .+.||+++
T Consensus 21 l~~~~~~~~~~~~d~vv~~-----GDl~~~~~~~~~~~~~l~~~---~~~pv~~v 67 (239)
T TIGR03729 21 LETLAQYLKKQKIDHLHIA-----GDISNDFQRSLPFIEKLQEL---KGIKVTFN 67 (239)
T ss_pred HHHHHHHHHhcCCCEEEEC-----CccccchhhHHHHHHHHHHh---cCCcEEEE
Confidence 4667777777889999887 54433233445666666642 25788776
No 261
>PRK13329 pantothenate kinase; Reviewed
Probab=24.09 E-value=4.3e+02 Score=22.10 Aligned_cols=18 Identities=33% Similarity=0.654 Sum_probs=16.6
Q ss_pred eEEEEecCCCeEEEEEec
Q 030509 23 RFLGLDVGDKYVGLSISD 40 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd 40 (176)
++|-||.|-.||=.|+.|
T Consensus 2 m~LliD~GNTriKw~~~~ 19 (249)
T PRK13329 2 TFLAIDVGNTRLKWGLYD 19 (249)
T ss_pred CEEEEEcCcchheeeEec
Confidence 488899999999999998
No 262
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=24.02 E-value=3.5e+02 Score=21.10 Aligned_cols=12 Identities=17% Similarity=0.462 Sum_probs=8.2
Q ss_pred HHhcCCCEEEEe
Q 030509 70 ISEFNLEGFIVG 81 (176)
Q Consensus 70 i~e~~~~~iVVG 81 (176)
+..+++++||+.
T Consensus 51 l~~~~vdgiii~ 62 (266)
T cd06282 51 LLRQRVDGLILT 62 (266)
T ss_pred HHhcCCCEEEEe
Confidence 334678888875
No 263
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=23.99 E-value=2.7e+02 Score=22.72 Aligned_cols=43 Identities=16% Similarity=0.207 Sum_probs=25.3
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 89 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 89 ~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
..+..+.+.++.+.+++. ++++++.+...++..++.+-.+.|+
T Consensus 181 ~~ps~~~l~~l~~~ik~~----~v~~i~~e~~~~~~~~~~la~~~g~ 223 (256)
T PF01297_consen 181 EEPSPKDLAELIKLIKEN----KVKCIFTEPQFSSKLAEALAKETGV 223 (256)
T ss_dssp SSS-HHHHHHHHHHHHHT----T-SEEEEETTS-THHHHHHHHCCT-
T ss_pred cCCCHHHHHHHHHHhhhc----CCcEEEecCCCChHHHHHHHHHcCC
Confidence 344556666777777663 6677777777777767666555554
No 264
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=23.92 E-value=3.2e+02 Score=20.63 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=9.0
Q ss_pred HHHHHHHHhcCCCEEEEe
Q 030509 64 EDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVG 81 (176)
+.|.+++++++++.|+.-
T Consensus 78 ~~l~~l~~~~~~~~V~~~ 95 (165)
T PF00875_consen 78 EVLPELAKEYGATAVYFN 95 (165)
T ss_dssp HHHHHHHHHHTESEEEEE
T ss_pred HHHHHHHHhcCcCeeEec
Confidence 444455555555555544
No 265
>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=23.69 E-value=1.9e+02 Score=20.75 Aligned_cols=40 Identities=15% Similarity=0.268 Sum_probs=25.0
Q ss_pred CCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 75 LEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 75 ~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
.+.||+|-|.. .|... ...++.|.+.|... .+.+.++..+
T Consensus 46 ~d~iilgspty~~g~~p--~~~~~~f~~~l~~~-~~~gk~~~vf 86 (140)
T TIGR01753 46 YDAVLLGCSTWGDEDLE--QDDFEPFFEELEDI-DLGGKKVALF 86 (140)
T ss_pred CCEEEEEcCCCCCCCCC--cchHHHHHHHhhhC-CCCCCEEEEE
Confidence 68999999998 66543 13455677777642 2345565544
No 266
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=23.69 E-value=3.2e+02 Score=20.41 Aligned_cols=59 Identities=19% Similarity=0.307 Sum_probs=32.5
Q ss_pred cCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhc------CCCEEEEeccCC-CCCCchHHHHHHH
Q 030509 29 VGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF------NLEGFIVGYPFN-RQQNAADAVQVKL 98 (176)
Q Consensus 29 ~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~------~~~~iVVGlPl~-dG~~s~~~~~v~~ 98 (176)
.|..|+|+++|-..+. .+. ++. .=..|.++.+.. ..|.|||+.|-- +-+..+..+.+..
T Consensus 45 ~~~~R~G~~VsKKvG~-----AV~-RNR-----iKR~lRe~~R~~~~~l~~g~D~Viiar~~~~~~~~~~l~~~l~~ 110 (122)
T PRK03459 45 FGGPRFGLVVSKAVGN-----AVI-RHR-----VSRRLRHICADIVDQVPETHHVVIRALPGAATASSAELERDVRA 110 (122)
T ss_pred CCCCEEEEEEeeeccc-----hhH-HHH-----HHHHHHHHHHHhhhccCCCcEEEEEECcccccCCHHHHHHHHHH
Confidence 4668999999975432 222 221 113333433322 468899998766 5454544444433
No 267
>PF03088 Str_synth: Strictosidine synthase; InterPro: IPR018119 This entry represents a conserved region found in strictosidine synthase (4.3.3.2 from EC), a key enzyme in alkaloid biosynthesis. It catalyses the Pictet-Spengler stereospecific condensation of tryptamine with secologanin to form strictosidine []. The structure of the native enzyme from the Indian medicinal plant Rauvolfia serpentina (Serpentwood) (Devilpepper) represents the first example of a six-bladed four-stranded beta-propeller fold from the plant kingdom [].; GO: 0016844 strictosidine synthase activity, 0009058 biosynthetic process; PDB: 2FPB_A 2V91_B 2FP8_A 3V1S_B 2FPC_A 2VAQ_A 2FP9_B.
Probab=23.67 E-value=2e+02 Score=20.47 Aligned_cols=26 Identities=23% Similarity=0.311 Sum_probs=18.7
Q ss_pred hhHHHHHhhhccCCCCeEEEEecCCCeE
Q 030509 7 LRLFEQMLKRKVSKRGRFLGLDVGDKYV 34 (176)
Q Consensus 7 ~~~~~~~~~~~~~~~~~iLglD~G~kri 34 (176)
.+.+..++++. ..||++-.|+-++.+
T Consensus 24 ~~~~~~~le~~--~~GRll~ydp~t~~~ 49 (89)
T PF03088_consen 24 RDWVYDLLEGR--PTGRLLRYDPSTKET 49 (89)
T ss_dssp TGHHHHHHHT-----EEEEEEETTTTEE
T ss_pred cceeeeeecCC--CCcCEEEEECCCCeE
Confidence 45556666664 669999999999998
No 268
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=23.46 E-value=1.8e+02 Score=27.90 Aligned_cols=49 Identities=16% Similarity=0.219 Sum_probs=30.9
Q ss_pred HHHHHhcCCC---EEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccH
Q 030509 67 RSLISEFNLE---GFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 123 (176)
Q Consensus 67 ~~li~e~~~~---~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT 123 (176)
.+.+.+.-++ +||||. ||..+. ++||+..+......+++|++++|--+|
T Consensus 91 a~yl~~~~~~~~~giviG~---D~R~~S-----~~fA~l~a~vf~~~g~~v~lf~~~v~T 142 (607)
T KOG1220|consen 91 AAYLKNQFPSKNLGIVIGH---DGRYNS-----KRFAELVAAVFLLNGFKVYLFSELVPT 142 (607)
T ss_pred HHHHHHhCCcccceEEEec---CCccch-----HHHHHHHHHHHHhCCceEEEeccccCC
Confidence 3344444453 999996 888774 567766654321248999999954433
No 269
>cd07019 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-te
Probab=23.43 E-value=3.9e+02 Score=21.40 Aligned_cols=52 Identities=10% Similarity=0.067 Sum_probs=31.1
Q ss_pred hhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 60 DLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 60 ~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
..+.+.|.++..+.++.+||+- .+ .|..-.....+.+..+.+++ . +.||+-+
T Consensus 24 ~~l~~~l~~a~~d~~v~~ivL~--~~s~Gg~~~~~~~~~~~l~~~~~---~-~kpVia~ 76 (211)
T cd07019 24 DTTAAQIRDARLDPKVKAIVLR--VNSPGGSVTASEVIRAELAAARA---A-GKPVVVS 76 (211)
T ss_pred HHHHHHHHHHhhCCCceEEEEE--EcCCCcCHHHHHHHHHHHHHHHh---C-CCCEEEE
Confidence 3456777888888899999996 34 44333334444454455554 2 4576543
No 270
>PF09298 FAA_hydrolase_N: Fumarylacetoacetase N-terminal; InterPro: IPR015377 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation []. This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders [, ]. The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole []. FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures []. This entry represents the N-terminal domain of fumarylacetoacetase.; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process; PDB: 1QCN_B 1QCO_B 2HZY_A 1QQJ_B 1HYO_A.
Probab=23.39 E-value=38 Score=24.90 Aligned_cols=12 Identities=33% Similarity=0.509 Sum_probs=10.3
Q ss_pred CCCeEEEEEecC
Q 030509 30 GDKYVGLSISDP 41 (176)
Q Consensus 30 G~kriGvAvsd~ 41 (176)
+..|+||||+|.
T Consensus 14 ~~pR~gvaIGd~ 25 (107)
T PF09298_consen 14 PSPRVGVAIGDQ 25 (107)
T ss_dssp ESEEEEEEETTE
T ss_pred CCCeeEEEECCE
Confidence 668999999985
No 271
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=23.33 E-value=3e+02 Score=23.89 Aligned_cols=64 Identities=19% Similarity=0.214 Sum_probs=36.2
Q ss_pred HHHHHH-HHhcCCCEEEEeccCCCCC--CchHHHHHHHHHHHHHhccCCCCCcEEEe------cCcccHHHHHHHhccCC
Q 030509 64 EDFRSL-ISEFNLEGFIVGYPFNRQQ--NAADAVQVKLFIDDLSATKKLEDMKYAYW------NEGFTSKGVELLLNPLD 134 (176)
Q Consensus 64 ~~L~~l-i~e~~~~~iVVGlPl~dG~--~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~------DEr~TT~~A~~~l~~~g 134 (176)
+.+.++ ++..+++.||||.=..-|. .+. ....+++++ + + +..|+.+ +++.||..-++.+.++.
T Consensus 103 ~Fi~~~l~~~l~~~~iVvG~Df~FG~~~~G~-~~~L~~~~~---~---~-g~~v~~v~~~~~~~~~ISST~IR~~I~~G~ 174 (305)
T PRK05627 103 EFIEDLLVKGLNAKHVVVGFDFRFGKKRAGD-FELLKEAGK---E---F-GFEVTIVPEVKEDGERVSSTAIRQALAEGD 174 (305)
T ss_pred HHHHHHHHhccCCCEEEECCCCCCCCCCCCC-HHHHHHHHH---H---c-CcEEEEeccEecCCCcCchHHHHHHHHcCC
Confidence 345554 4568999999996443121 121 222222222 2 1 4555544 47899999998887544
Q ss_pred C
Q 030509 135 L 135 (176)
Q Consensus 135 ~ 135 (176)
+
T Consensus 175 i 175 (305)
T PRK05627 175 L 175 (305)
T ss_pred H
Confidence 3
No 272
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=23.32 E-value=3.3e+02 Score=20.53 Aligned_cols=54 Identities=13% Similarity=0.014 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCC
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD 134 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g 134 (176)
-.+.+++.++.++.+|++ ..++.+.. .|+.. ++.|+..++ .|..+|-..+....
T Consensus 55 ~~~a~~l~~~gvdvvi~~------~iG~~a~~------~l~~~----GIkv~~~~~-~~V~e~i~~~~~g~ 108 (121)
T COG1433 55 IRIAELLVDEGVDVVIAS------NIGPNAYN------ALKAA----GIKVYVAPG-GTVEEAIKAFLEGE 108 (121)
T ss_pred HHHHHHHHHcCCCEEEEC------ccCHHHHH------HHHHc----CcEEEecCC-CCHHHHHHHHhcCC
Confidence 458899999999999999 55554332 46652 788998888 77888877766433
No 273
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=23.30 E-value=2.8e+02 Score=24.43 Aligned_cols=65 Identities=12% Similarity=0.172 Sum_probs=40.2
Q ss_pred HHHHHhcCCCEEEEeccCC-CCC---CchHHHHHHHHHHHHHhccCCCCCcEEEec--CcccHHHHHHHhc
Q 030509 67 RSLISEFNLEGFIVGYPFN-RQQ---NAADAVQVKLFIDDLSATKKLEDMKYAYWN--EGFTSKGVELLLN 131 (176)
Q Consensus 67 ~~li~e~~~~~iVVGlPl~-dG~---~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D--Er~TT~~A~~~l~ 131 (176)
..+.....|+.+++.-|.+ .+. .+-....+++..+.+.......+..|+++| |+++..+|..+|+
T Consensus 93 ~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk 163 (351)
T PRK09112 93 RQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILK 163 (351)
T ss_pred HHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHH
Confidence 4444566799888887866 321 111234455555555432111256799999 7899888888776
No 274
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=23.24 E-value=2.9e+02 Score=21.89 Aligned_cols=18 Identities=11% Similarity=0.368 Sum_probs=12.3
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.+..+ ..+++++||+-
T Consensus 45 ~~~i~~l-~~~~vdgii~~ 62 (273)
T cd01541 45 RKCLENM-LSQGIDGLIIE 62 (273)
T ss_pred HHHHHHH-HHcCCCEEEEe
Confidence 3555554 44789999984
No 275
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=22.76 E-value=2.2e+02 Score=24.27 Aligned_cols=51 Identities=10% Similarity=0.189 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc
Q 030509 64 EDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr 120 (176)
-++.+...+..++++++.-|.. .-+. +.+.+|-+.+.+. .+++||+++|--
T Consensus 85 i~~a~~A~~~Gad~v~v~pP~y~~~~~----~~l~~~f~~ia~a--~~~lpv~iYn~P 136 (294)
T TIGR02313 85 LELTKFAEEAGADAAMVIVPYYNKPNQ----EALYDHFAEVADA--VPDFPIIIYNIP 136 (294)
T ss_pred HHHHHHHHHcCCCEEEEcCccCCCCCH----HHHHHHHHHHHHh--ccCCCEEEEeCc
Confidence 4455667888999999999988 5443 2333444445442 237999999853
No 276
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=22.75 E-value=3.9e+02 Score=21.08 Aligned_cols=18 Identities=17% Similarity=0.392 Sum_probs=11.9
Q ss_pred HHHHHHHHHhcCCCEEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVG 81 (176)
.+.+..++. +++++||+-
T Consensus 45 ~~~l~~~~~-~~vdgii~~ 62 (273)
T cd06305 45 ADQIDQAIA-QKVDAIIIQ 62 (273)
T ss_pred HHHHHHHHH-cCCCEEEEe
Confidence 345555554 589999886
No 277
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=22.73 E-value=1.9e+02 Score=23.24 Aligned_cols=21 Identities=10% Similarity=0.425 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHhcCCCEEEEec
Q 030509 61 LMAEDFRSLISEFNLEGFIVGY 82 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGl 82 (176)
.++..+.+++.++.|+ ||+|+
T Consensus 53 ~lL~~f~~~i~~~dPD-vi~g~ 73 (193)
T cd05784 53 SLLLALIAWFAQYDPD-IIIGW 73 (193)
T ss_pred HHHHHHHHHHHhhCCC-EEEEC
Confidence 5689999999999999 78896
No 278
>PF02833 DHHA2: DHHA2 domain; InterPro: IPR004097 This domain is called DHHA2 since it is often associated with the DHH domain (IPR001667 from INTERPRO) and is diagnostic of DHH subfamily 2 members []. The domain is about 120 residues long and contains a conserved DXK motif at its amino terminus. It is present in inorganic pyrophosphatases and in exopolyphosphatase of Saccharomyces cerevisiae.; GO: 0016462 pyrophosphatase activity, 0005737 cytoplasm; PDB: 1WPP_A 1K20_A 1I74_A 2HAW_A 1WPN_A 1WPM_B 2IW4_B 1K23_D 2ENX_A 2EB0_A ....
Probab=22.67 E-value=1.1e+02 Score=22.28 Aligned_cols=49 Identities=27% Similarity=0.388 Sum_probs=32.6
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEe
Q 030509 25 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 25 LglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVG 81 (176)
=-+++|..++||+.... .++..+.... +.+.+.+.++..+++.+.+++=
T Consensus 25 K~f~~~~~~vgis~v~~-----~~~~~~~~~~---~~~~~~l~~~~~~~~ld~l~lm 73 (127)
T PF02833_consen 25 KEFEFGGKKVGISQVET-----MDLEELLSRK---DELLEELEEFCEERKLDLLFLM 73 (127)
T ss_dssp EEEEETTEEEEEEEEEE-----S-HHHHHTTH---HHHHHHHHHHHHHTT-SEEEEE
T ss_pred eeeecCCeEEEEEeeee-----cCHHHHHHHH---HHHHHHHHHHHHhCCCCEEEEE
Confidence 34667999999997632 3333333321 3567999999999999987765
No 279
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=22.63 E-value=3.2e+02 Score=23.48 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=36.3
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.-++.+..++..++++++=-|.. ..+. ......|..-.+. . ++|++++|
T Consensus 88 ai~lak~a~~~Gad~il~v~PyY~k~~~---~gl~~hf~~ia~a---~-~lPvilYN 137 (299)
T COG0329 88 AIELAKHAEKLGADGILVVPPYYNKPSQ---EGLYAHFKAIAEA---V-DLPVILYN 137 (299)
T ss_pred HHHHHHHHHhcCCCEEEEeCCCCcCCCh---HHHHHHHHHHHHh---c-CCCEEEEe
Confidence 46788899999999999999988 6653 3344455554443 2 78988887
No 280
>KOG4245 consensus Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]
Probab=22.62 E-value=1.4e+02 Score=25.26 Aligned_cols=73 Identities=16% Similarity=0.315 Sum_probs=44.6
Q ss_pred ccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 47 SPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 47 ~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
.|++|++.+. ++..+++..+.+++-.+.++=||--.+ ..-...----+-+-+++|+-..-...+...+||-|+
T Consensus 68 v~lgtlpmn~--~e~avee~~rcvk~lg~~g~eigshv~e~~ld~~d~~ply~~~e~l~~~lfvhpwdmhmwdgrl 141 (297)
T KOG4245|consen 68 VGLGTLPMNA--PELAVEEMERCVKELGFKGFEIGSHVAEKDLDAQDFFPLYAAAEELKCSLFVHPWDMHMWDGRL 141 (297)
T ss_pred cccCccCCcC--HHHHHHHHHHHHHHcCCCceeeccccccccCchHHHhHHHHHHHhheeeEEecchhhcccccch
Confidence 4678887754 334579999999999999999996555 222222222223345666532111345566777775
No 281
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=22.44 E-value=1e+02 Score=26.59 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=32.5
Q ss_pred CEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHH
Q 030509 76 EGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 124 (176)
Q Consensus 76 ~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~ 124 (176)
.-+|==.|+.|-+..+-.+-.+.|++++.+. + ++||+++.+.-|--
T Consensus 88 ~DViPfvPl~d~tteecveiske~gkrvgee--l-giPVylYe~aatrp 133 (302)
T COG3643 88 ADVIPFVPLKDTTTEECVEISKELGKRVGEE--L-GIPVYLYEDAATRP 133 (302)
T ss_pred cceeceeecccccHHHHHHHHHHHHHHhhHh--h-CCcEEEehhhccCc
Confidence 3455456777666666666678899999874 5 99999997765543
No 282
>PF01993 MTD: methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase; InterPro: IPR002844 This archaeal enzyme family is involved in formation of methane from carbon dioxide 1.5.99.9 from EC. The enzyme requires coenzyme F420 [].; GO: 0008901 ferredoxin hydrogenase activity, 0015948 methanogenesis, 0055114 oxidation-reduction process; PDB: 1U6I_D 3IQF_G 1QV9_C 3IQE_F 1U6J_G 3IQZ_D 1U6K_B.
Probab=22.43 E-value=2.8e+02 Score=23.92 Aligned_cols=86 Identities=21% Similarity=0.198 Sum_probs=47.7
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCC------
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHP------ 137 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~------ 137 (176)
+...+.+++|+++-+|+--|-- +..++...+ +.|+.. ++|.+.+-..-|.+ +++.|.+.|+.-
T Consensus 49 ~~~~~~~~~~~pdf~I~isPN~-~~PGP~~AR-----E~l~~~----~iP~IvI~D~p~~k-~kd~l~~~g~GYIivk~D 117 (276)
T PF01993_consen 49 EVVTKMLKEWDPDFVIVISPNA-AAPGPTKAR-----EMLSAK----GIPCIVISDAPTKK-AKDALEEEGFGYIIVKAD 117 (276)
T ss_dssp HHHHHHHHHH--SEEEEE-S-T-TSHHHHHHH-----HHHHHS----SS-EEEEEEGGGGG-GHHHHHHTT-EEEEETTS
T ss_pred HHHHHHHHhhCCCEEEEECCCC-CCCCcHHHH-----HHHHhC----CCCEEEEcCCCchh-hHHHHHhcCCcEEEEecC
Confidence 4456667899999999986643 445553222 345542 89988777677666 678888777621
Q ss_pred ---CCCCCCCcHHH----------------HHHHHHHHHhhh
Q 030509 138 ---VEYKTILDKFA----------------AVGILQEYLDNA 160 (176)
Q Consensus 138 ---~~~k~~iD~~A----------------A~iILq~yL~~~ 160 (176)
.-|++-+|..= |.-++|.-||..
T Consensus 118 pMIGArREFLDP~EMa~fNaD~~kVLa~tGa~RlvQ~elD~v 159 (276)
T PF01993_consen 118 PMIGARREFLDPVEMALFNADVLKVLAITGAFRLVQEELDKV 159 (276)
T ss_dssp ------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred ccccccccccCHHHHHHhhhhHHHHHHhhhHHHHHHHHHHHH
Confidence 23567777542 445677777664
No 283
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=22.35 E-value=4.8e+02 Score=22.07 Aligned_cols=58 Identities=10% Similarity=0.065 Sum_probs=34.4
Q ss_pred HHHHHHHHhcC-CCEEEEeccCCCCCCch--------HHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 64 EDFRSLISEFN-LEGFIVGYPFNRQQNAA--------DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 64 ~~L~~li~e~~-~~~iVVGlPl~dG~~s~--------~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
.++.+.+-+.. +++|+++ |+.++ ..+.++..++... .++||+.-=-..||.++-++.+
T Consensus 24 ~~~i~~~i~~G~v~gi~~~-----GstGE~~~Lt~eEr~~~~~~~~~~~~-----~~~pvi~gv~~~~t~~~i~la~ 90 (290)
T TIGR00683 24 RQIIRHNIDKMKVDGLYVG-----GSTGENFMLSTEEKKEIFRIAKDEAK-----DQIALIAQVGSVNLKEAVELGK 90 (290)
T ss_pred HHHHHHHHhCCCcCEEEEC-----CcccccccCCHHHHHHHHHHHHHHhC-----CCCcEEEecCCCCHHHHHHHHH
Confidence 44444445567 9999887 66554 2222333333322 2578877766778888877655
No 284
>PRK10812 putative DNAse; Provisional
Probab=22.26 E-value=4e+02 Score=22.32 Aligned_cols=69 Identities=13% Similarity=0.166 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCCEE-EEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 63 AEDFRSLISEFNLEGF-IVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 63 ~~~L~~li~e~~~~~i-VVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
++.|.+++.+.++.+| =|||... +.... ..+.+-|...|+-...+ ++||.+.- |-...+.-+.|.+.+.
T Consensus 77 ~~~l~~~~~~~~vvaIGEiGLD~~~~~~~~--~~Q~~vf~~ql~lA~e~-~~Pv~iH~-r~a~~~~l~iL~~~~~ 147 (265)
T PRK10812 77 VEELRRLAAEEGVVAMGETGLDYYYTPETK--VRQQESFRHHIQIGREL-NKPVIVHT-RDARADTLAILREEKV 147 (265)
T ss_pred HHHHHHHhcCCCEEEEEeeecCcCCCCCCH--HHHHHHHHHHHHHHHHh-CCCeEEEe-eCchHHHHHHHHhhcC
Confidence 6788888876666677 7899887 43322 23333444444321123 88988774 4455666677765443
No 285
>PLN02721 threonine aldolase
Probab=22.20 E-value=2.6e+02 Score=23.35 Aligned_cols=54 Identities=4% Similarity=-0.100 Sum_probs=32.0
Q ss_pred HHHHHHHHHhc------CCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 63 AEDFRSLISEF------NLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 63 ~~~L~~li~e~------~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
.+.|.+.++++ ++..+++--|.+ .|........++++++..++. +++++. ||-+
T Consensus 120 ~~~l~~~i~~~~~~~~~~~~~v~l~~~~~np~G~~~~~~~l~~l~~l~~~~----g~~liv-D~a~ 180 (353)
T PLN02721 120 LDAIEAAIRPKGDDHFPTTRLICLENTHANCGGRCLSVEYTDKVGELAKRH----GLKLHI-DGAR 180 (353)
T ss_pred HHHHHHHHHhccCCCCCcceEEEEeccccccCCccccHHHHHHHHHHHHHc----CCEEEE-Echh
Confidence 58888888764 566666655555 443333344456676666652 666544 8754
No 286
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=22.16 E-value=1e+02 Score=20.98 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=18.9
Q ss_pred HHHHHHHHHhcCCCEEEEecc
Q 030509 63 AEDFRSLISEFNLEGFIVGYP 83 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlP 83 (176)
.+.|.+.+++.+++.+|+|..
T Consensus 82 ~~~i~~~~~~~~~dlvvig~~ 102 (130)
T cd00293 82 AEAILEAAEELGADLIVMGSR 102 (130)
T ss_pred HHHHHHHHHHcCCCEEEEcCC
Confidence 588999999999999999953
No 287
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.14 E-value=99 Score=25.61 Aligned_cols=46 Identities=20% Similarity=0.021 Sum_probs=31.4
Q ss_pred CCcEEEecCcccHHHHHHHhccCC-CCCCC-------CCCCCcHHHHHHHHHHHHhhh
Q 030509 111 DMKYAYWNEGFTSKGVELLLNPLD-LHPVE-------YKTILDKFAAVGILQEYLDNA 160 (176)
Q Consensus 111 ~lpV~~~DEr~TT~~A~~~l~~~g-~~~~~-------~k~~iD~~AA~iILq~yL~~~ 160 (176)
+++|..++|.+||+.-..- | ++.+. ..-.=|-.||.-|+..++...
T Consensus 297 ~~~v~~~~~~~tS~~C~~c----g~~~~r~~~C~~cg~~~~rD~naa~Ni~~~~~~~~ 350 (364)
T COG0675 297 GIVVKVVPPYYTSKTCPCC----GHLSGRLFKCPRCGFVHDRDVNAALNIARRALGLL 350 (364)
T ss_pred CeEEEECCCCCCccccccc----CCccceeEECCCCCCeehhhHHHHHHHHHHhcccC
Confidence 6899999999998864321 2 11111 112369999999999998754
No 288
>PRK00304 hypothetical protein; Provisional
Probab=21.82 E-value=2.9e+02 Score=19.29 Aligned_cols=34 Identities=6% Similarity=-0.018 Sum_probs=24.9
Q ss_pred CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHH
Q 030509 86 RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 124 (176)
Q Consensus 86 dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~ 124 (176)
.|.+.....++.+.-+.|++ +--++.|||---|.
T Consensus 28 yg~E~sL~~kv~qv~~qL~~-----G~~vIvfse~~es~ 61 (75)
T PRK00304 28 NGDETPLETRVLRVRQALTK-----GQAVILFDPESQQC 61 (75)
T ss_pred CcccccHHHHHHHHHHHHHc-----CCEEEEECCCccee
Confidence 35577788888888888886 45688888765443
No 289
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=21.76 E-value=1.9e+02 Score=22.25 Aligned_cols=49 Identities=12% Similarity=0.144 Sum_probs=30.9
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
++.+.+.+. +.|+||++-|..+|+.+...+ .|.+++... .+.+-|+..+
T Consensus 56 ~~~l~~~i~--~AD~iI~~sP~Y~~sip~~LK---~~iD~~~~~-~l~~K~v~~~ 104 (171)
T TIGR03567 56 IKAATAQVA--QADGVVVATPVYKASYSGVLK---ALLDLLPQR-ALRGKVVLPI 104 (171)
T ss_pred HHHHHHHHH--HCCEEEEECCcccCCCCHHHH---HHHHhCChh-hhCCCEEEEE
Confidence 456666555 589999999999888877655 444444321 1224465543
No 290
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.67 E-value=4.6e+02 Score=21.55 Aligned_cols=46 Identities=15% Similarity=0.200 Sum_probs=25.9
Q ss_pred HHHHHHHHhc-CCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCccc
Q 030509 64 EDFRSLISEF-NLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 122 (176)
Q Consensus 64 ~~L~~li~e~-~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~T 122 (176)
+.+..++..+ ++++||+- |.. . . . ..+.+.+.+. ++||+++|...+
T Consensus 47 ~~i~~~~~~~~~vdgiIi~-~~~---~-~-~---~~~~~~~~~~----giPvV~~~~~~~ 93 (305)
T cd06324 47 QQARTILQRPDKPDALIFT-NEK---S-V-A---PELLRLAEGA----GVKLFLVNSGLT 93 (305)
T ss_pred HHHHHHHHhccCCCEEEEc-CCc---c-c-h---HHHHHHHHhC----CCeEEEEecCCC
Confidence 4455554432 89999995 322 1 1 1 1234455542 789998885543
No 291
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.46 E-value=3.4e+02 Score=22.02 Aligned_cols=43 Identities=12% Similarity=0.198 Sum_probs=24.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
.+.+..++ ..++++||+. |.+ ++. ....+.+... ++||+++|.
T Consensus 46 ~~~l~~~~-~~~~dgiii~-~~~~~~~--------~~~i~~~~~~----~iPvV~~~~ 89 (294)
T cd06316 46 VADIETTI-SQKPDIIISI-PVDPVST--------AAAYKKVAEA----GIKLVFMDN 89 (294)
T ss_pred HHHHHHHH-HhCCCEEEEc-CCCchhh--------hHHHHHHHHc----CCcEEEecC
Confidence 34555554 4679999995 333 211 1233445442 678877764
No 292
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=21.45 E-value=2e+02 Score=25.52 Aligned_cols=48 Identities=8% Similarity=0.031 Sum_probs=33.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
.+.|.++++++++|+||.=.-.. +-...+. .. ..+.|++. |+|+..+|
T Consensus 310 ~~~i~~lvke~~aDGVI~~~~~~C~~~~~e~-~~---lk~~l~e~----GIP~L~id 358 (380)
T TIGR02263 310 GKYLLDQVRKNAAEGVIFAAPSFCDPALLER-PM---LAARCKEH----GIPQIAFK 358 (380)
T ss_pred HHHHHHHHHHhCCCEEEEhHhhcCChhhhhH-HH---HHHHHHHC----CCCEEEEE
Confidence 68899999999999999987666 4433332 22 23345442 89988775
No 293
>PF08288 PIGA: PIGA (GPI anchor biosynthesis); InterPro: IPR013234 This domain is found on phosphatidylinositol N-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with the disease paroxysmal nocturnal haemoglobinuria [].; GO: 0006506 GPI anchor biosynthetic process
Probab=21.36 E-value=3.3e+02 Score=19.73 Aligned_cols=80 Identities=15% Similarity=0.173 Sum_probs=50.8
Q ss_pred cCCCeEEEEEecCCCc-eeccceeeeCCCCChh--hHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHh
Q 030509 29 VGDKYVGLSISDPKNK-IASPLSVLLRKKNTID--LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 105 (176)
Q Consensus 29 ~G~kriGvAvsd~~~~-~a~Pl~~i~~~~~~~~--~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~ 105 (176)
|| .|.||---....+ .--|+.++.+...-+. ..+.-++.++-.++|+ ||=| .++.|..+.++.--|+.|
T Consensus 3 yg-~R~GvRyltngLKVYYlP~~~~~~~~t~Pt~~~~~pl~R~IlirE~I~-IVHg----H~a~S~l~hE~i~hA~~m-- 74 (90)
T PF08288_consen 3 YG-DRVGVRYLTNGLKVYYLPLKVFYNQCTLPTLFGSFPLLRNILIRERID-IVHG----HQAFSTLCHEAILHARTM-- 74 (90)
T ss_pred CC-CcceeEEcCCCeEEEeecchhhhcCcchHHHHHhhHHHHHHHHHcCee-EEEe----ehhhhHHHHHHHHHHHhC--
Confidence 44 5677766554322 3356666644332221 1246678888888888 8888 788888887765444433
Q ss_pred ccCCCCCcEEEecCcc
Q 030509 106 TKKLEDMKYAYWNEGF 121 (176)
Q Consensus 106 ~~~~~~lpV~~~DEr~ 121 (176)
+++.++-|.+|
T Consensus 75 -----GlktVfTDHSL 85 (90)
T PF08288_consen 75 -----GLKTVFTDHSL 85 (90)
T ss_pred -----CCcEEeecccc
Confidence 78899999876
No 294
>cd00615 Orn_deC_like Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life.
Probab=21.31 E-value=2.8e+02 Score=23.09 Aligned_cols=50 Identities=10% Similarity=0.191 Sum_probs=34.7
Q ss_pred HHHHHHHHHh-cCCCEEEEeccCC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCccc
Q 030509 63 AEDFRSLISE-FNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 122 (176)
Q Consensus 63 ~~~L~~li~e-~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~T 122 (176)
.+.|.+.+++ .++..+++-.| + .|...+ +++.++.+++. ++ .+++||-+.
T Consensus 142 ~~~l~~~l~~~~~~k~v~l~~p-~~~G~~~d----l~~I~~~~~~~----g~-~livDeA~~ 193 (294)
T cd00615 142 PETFKKALIEHPDAKAAVITNP-TYYGICYN----LRKIVEEAHHR----GL-PVLVDEAHG 193 (294)
T ss_pred HHHHHHHHHhCCCceEEEEECC-CCCCEecC----HHHHHHHHHhc----CC-eEEEECcch
Confidence 5778888876 46888999988 7 888765 34455555542 54 577898765
No 295
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=21.24 E-value=4e+02 Score=20.73 Aligned_cols=61 Identities=10% Similarity=0.215 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHhcCCCEEEEeccCC--CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhc
Q 030509 61 LMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 131 (176)
Q Consensus 61 ~~~~~L~~li~e~~~~~iVVGlPl~--dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 131 (176)
.+...+.+++++|+|+.|||=-=.. .+.-|+.+.+.+.-.+.+ ++++|.++ |+.+-++.++
T Consensus 48 ~Fq~~f~kl~~dy~Vd~VvIk~R~~KGKfAGga~~FKmEaaIQL~------~~~~V~lv----s~~~ik~~lK 110 (138)
T PF11215_consen 48 KFQFTFAKLMEDYKVDKVVIKERATKGKFAGGAVGFKMEAAIQLI------DDVEVELV----SPATIKAQLK 110 (138)
T ss_pred HHHHHHHHHHHHcCCCEEEEEecccCCCccCCchhHHHHHHHHhc------CCCcEEEE----CHHHHHHHHh
Confidence 4567799999999999999965333 444556666655554444 26788775 5666666654
No 296
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=21.15 E-value=83 Score=27.70 Aligned_cols=26 Identities=42% Similarity=0.578 Sum_probs=21.4
Q ss_pred CCeEEEEecCCCeEEEEEecCCCcee
Q 030509 21 RGRFLGLDVGDKYVGLSISDPKNKIA 46 (176)
Q Consensus 21 ~~~iLglD~G~kriGvAvsd~~~~~a 46 (176)
..++||+++++...|||+.-....+|
T Consensus 271 ~e~vLGlPv~~~~~GvvviGGlnpia 296 (325)
T COG1693 271 SERVLGLPVADRKVGVVVIGGLNPIA 296 (325)
T ss_pred CcceeCcccCCCceEEEEEcCccccc
Confidence 47899999999999999997654333
No 297
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=21.13 E-value=2.8e+02 Score=21.95 Aligned_cols=37 Identities=16% Similarity=0.209 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCC-chHHHHHHHHHHHHH
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQN-AADAVQVKLFIDDLS 104 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~-s~~~~~v~~Fa~~L~ 104 (176)
+.+.+++++-+=-.|||| .|.. ....+.+++|++++.
T Consensus 18 ~~aa~lLk~AKRPvIivG----~ga~~~~a~e~l~~laEklg 55 (162)
T TIGR00315 18 KLVAMMIKRAKRPLLIVG----PENLEDEEKELIVKFIEKFD 55 (162)
T ss_pred HHHHHHHHcCCCcEEEEC----CCcCcccHHHHHHHHHHHHC
Confidence 455666666555669999 5554 456777788877764
No 298
>PRK06242 flavodoxin; Provisional
Probab=21.11 E-value=1.8e+02 Score=21.44 Aligned_cols=38 Identities=11% Similarity=0.051 Sum_probs=23.9
Q ss_pred CCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030509 74 NLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 117 (176)
Q Consensus 74 ~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~ 117 (176)
+.+.||+|-|...|...+ .++.|.+++.. +.+-++.++
T Consensus 43 ~~d~ii~g~pvy~~~~~~---~~~~fl~~~~~---~~~k~~~~f 80 (150)
T PRK06242 43 EYDLIGFGSGIYFGKFHK---SLLKLIEKLPP---VSGKKAFIF 80 (150)
T ss_pred HCCEEEEeCchhcCCcCH---HHHHHHHhhhh---hcCCeEEEE
Confidence 568899999977555544 45567777643 124555554
No 299
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=21.02 E-value=4.2e+02 Score=20.89 Aligned_cols=17 Identities=12% Similarity=0.210 Sum_probs=11.9
Q ss_pred HHHHHHHHhcCCCEEEEe
Q 030509 64 EDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVG 81 (176)
+.|..+ ..+++++|||.
T Consensus 47 ~~i~~l-~~~~vdgiii~ 63 (272)
T cd06301 47 SQVENF-IAQGVDAIIVV 63 (272)
T ss_pred HHHHHH-HHcCCCEEEEe
Confidence 445554 45689999997
No 300
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=20.97 E-value=4.3e+02 Score=20.96 Aligned_cols=42 Identities=12% Similarity=0.181 Sum_probs=23.0
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 118 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D 118 (176)
+.|..+ ..+++++||+. |.+ .... ....+.+.+. ++|++++|
T Consensus 46 ~~i~~l-~~~~vdgiIi~-~~~---~~~~----~~~i~~~~~~----~iPvV~~~ 87 (273)
T cd06309 46 SAIRSF-IAQGVDVIILA-PVV---ETGW----DPVLKEAKAA----GIPVILVD 87 (273)
T ss_pred HHHHHH-HHcCCCEEEEc-CCc---cccc----hHHHHHHHHC----CCCEEEEe
Confidence 445555 44689999996 333 1100 1123345442 67887776
No 301
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=20.87 E-value=1.2e+02 Score=26.26 Aligned_cols=69 Identities=16% Similarity=0.180 Sum_probs=39.7
Q ss_pred HHHHHHHH-hcCCCEEEEeccCC--CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCC
Q 030509 64 EDFRSLIS-EFNLEGFIVGYPFN--RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 135 (176)
Q Consensus 64 ~~L~~li~-e~~~~~iVVGlPl~--dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 135 (176)
+.+.+++. ..++..||||.=.. .+..+. ....+++++...-. ..-+|....||+.||..-++.+.++.+
T Consensus 87 ~Fi~~~l~~~l~~~~ivvG~Df~FG~~~~G~-~~~L~~~~~~~g~~--v~~~~~~~~~~~ISST~IR~~l~~G~i 158 (288)
T TIGR00083 87 QFIDQLIVKHLHVKFLVVGDDFRFGHDRQGD-FLLLQLFGNTTIFC--VIVKQLFCQDIRISSSAIRQALKNGDL 158 (288)
T ss_pred HHHHHHHHhccCCcEEEECCCccCCCCCCCC-HHHHHHhccccCcE--EEEeccccCCCeECHHHHHHHHHcCCH
Confidence 34556664 47999999997655 222332 23334444322200 012344556789999999998875443
No 302
>cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat
Probab=20.86 E-value=1.9e+02 Score=24.90 Aligned_cols=53 Identities=11% Similarity=0.066 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhcCCCEEE-EeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCcc
Q 030509 62 MAEDFRSLISEFNLEGFI-VGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 121 (176)
Q Consensus 62 ~~~~L~~li~e~~~~~iV-VGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~ 121 (176)
.++++.+.+++.++|.|| || -|+.-+.++-+.-+...... .+++|++.+-=..
T Consensus 66 ~v~~~~~~~~~~~~d~IiaiG----GGs~~D~aKa~a~~~~~~~~---~~~~p~i~VPTta 119 (332)
T cd08180 66 VVAKGIKKFLDFKPDIVIALG----GGSAIDAAKAIIYFAKKLGK---KKKPLFIAIPTTS 119 (332)
T ss_pred HHHHHHHHHHhcCCCEEEEEC----CchHHHHHHHHHHHHhCCCC---CCCCCEEEeCCCC
Confidence 357888888899999999 89 78888877766444332211 1367888887554
No 303
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.82 E-value=4.2e+02 Score=20.82 Aligned_cols=43 Identities=12% Similarity=0.089 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecC
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 119 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DE 119 (176)
+.+..+ ..+++++||+. ....+. +..+.+.+.+. ++|++++|-
T Consensus 47 ~~~~~l-~~~~vdgiii~----~~~~~~----~~~~l~~~~~~----~iPvV~~~~ 89 (275)
T cd06317 47 AQVEDL-IAQKVDGIILW----PTDGQA----YIPGLRKAKQA----GIPVVITNS 89 (275)
T ss_pred HHHHHH-HHcCCCEEEEe----cCCccc----cHHHHHHHHHC----CCcEEEeCC
Confidence 444444 45689999997 222111 11233455542 789888874
No 304
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=20.80 E-value=1.6e+02 Score=22.34 Aligned_cols=54 Identities=15% Similarity=0.150 Sum_probs=36.1
Q ss_pred HHHHHHHHHhcCCCEEEEeccCCCCCCc--hHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhcc
Q 030509 63 AEDFRSLISEFNLEGFIVGYPFNRQQNA--ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNP 132 (176)
Q Consensus 63 ~~~L~~li~e~~~~~iVVGlPl~dG~~s--~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~ 132 (176)
.++|.+++. ++++.|||| .|..+ .....+++|.+... ..|+. +.|.+|-.++.+
T Consensus 51 ~eEle~~le-e~~E~ivvG----TG~~G~l~l~~ea~e~~r~k~-------~~vi~----~pT~EAikr~ne 106 (121)
T COG1504 51 LEELEELLE-EGPEVIVVG----TGQSGMLELSEEAREFFRKKG-------CEVIE----LPTPEAIKRYNE 106 (121)
T ss_pred HHHHHHHHh-cCCcEEEEe----cCceeEEEeCHHHHHHHHhcC-------CeEEE----eCCHHHHHHHHH
Confidence 578888877 679999999 67655 34456666655443 33433 347888877764
No 305
>TIGR03275 methan_mark_8 putative methanogenesis marker protein 8. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=20.78 E-value=1.8e+02 Score=25.03 Aligned_cols=57 Identities=21% Similarity=0.253 Sum_probs=38.4
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHH
Q 030509 24 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFI 100 (176)
Q Consensus 24 iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa 100 (176)
..|++.|-|||+|-++++ ....+|+++-.++.++.+++|-=. .|-..+-++.+-+.+
T Consensus 156 ~~Aie~Gyk~IaVTv~~~-------------------~~a~~iRe~e~~~~~~~~if~VHt-TGis~eea~~~~~~a 212 (259)
T TIGR03275 156 EKAIELGYKKIAVTVADA-------------------EDAKAIRELESESGIDIIIFAVHT-TGIDREDAEEVVQYA 212 (259)
T ss_pred HHHHHcCCceEEEEecCH-------------------HHHHHHHHhccccCCcEEEEEEEC-CCCCHHHHHHHHHhh
Confidence 456888999998877642 115777888778899999999433 465555555444443
No 306
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=20.58 E-value=5.5e+02 Score=22.01 Aligned_cols=79 Identities=6% Similarity=-0.014 Sum_probs=45.2
Q ss_pred CceeccceeeeC-CCCChhhHHHHHHHHHHhcCCCEEEEeccCCCCCCchH-------HHHHHHHHHHHHhccCCCCCcE
Q 030509 43 NKIASPLSVLLR-KKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAAD-------AVQVKLFIDDLSATKKLEDMKY 114 (176)
Q Consensus 43 ~~~a~Pl~~i~~-~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~dG~~s~~-------~~~v~~Fa~~L~~~~~~~~lpV 114 (176)
+.++-+++.+.. .+-+.+. +.++.+.+-+..+++||+. ||.++. -.++-+++..... ..+||
T Consensus 7 Gvi~a~vTPF~~dg~vD~~a-~~~lv~~li~~Gv~gi~~~-----GttGE~~~Ls~eEr~~v~~~~v~~~~----grvpv 76 (299)
T COG0329 7 GVIPALVTPFDEDGSVDEEA-LRRLVEFLIAAGVDGLVVL-----GTTGESPTLTLEERKEVLEAVVEAVG----GRVPV 76 (299)
T ss_pred cceeccccCCCCCCCcCHHH-HHHHHHHHHHcCCCEEEEC-----CCCccchhcCHHHHHHHHHHHHHHHC----CCCcE
Confidence 334444444433 2233333 5666777777889999997 665532 2233333333332 15788
Q ss_pred EEecCcccHHHHHHHhc
Q 030509 115 AYWNEGFTSKGVELLLN 131 (176)
Q Consensus 115 ~~~DEr~TT~~A~~~l~ 131 (176)
+.-==..+|.+|-++-+
T Consensus 77 iaG~g~~~t~eai~lak 93 (299)
T COG0329 77 IAGVGSNSTAEAIELAK 93 (299)
T ss_pred EEecCCCcHHHHHHHHH
Confidence 87666777888877654
No 307
>PF14871 GHL6: Hypothetical glycosyl hydrolase 6
Probab=20.55 E-value=1.5e+02 Score=22.46 Aligned_cols=21 Identities=14% Similarity=0.694 Sum_probs=17.4
Q ss_pred hhHHHHHHHHHHhcCCCEEEE
Q 030509 60 DLMAEDFRSLISEFNLEGFIV 80 (176)
Q Consensus 60 ~~~~~~L~~li~e~~~~~iVV 80 (176)
+.+.+.|+++++.|.+|+|.+
T Consensus 110 e~~~~~i~Ei~~~y~~DGiF~ 130 (132)
T PF14871_consen 110 EFLLEQIREILDRYDVDGIFF 130 (132)
T ss_pred HHHHHHHHHHHHcCCCCEEEe
Confidence 455788999999999999875
No 308
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=20.44 E-value=4.4e+02 Score=20.91 Aligned_cols=43 Identities=12% Similarity=0.140 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecCc
Q 030509 64 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr 120 (176)
+.|..+ .+ ++++||+. |.+ .+. ...+.+.+.+. ++||+++|..
T Consensus 50 ~~i~~~-~~-~vdgiii~-~~~---~~~----~~~~i~~~~~~----~ipvV~~~~~ 92 (275)
T cd06307 50 AALLRL-GA-RSDGVALV-APD---HPQ----VRAAVARLAAA----GVPVVTLVSD 92 (275)
T ss_pred HHHHHH-Hh-cCCEEEEe-CCC---cHH----HHHHHHHHHHC----CCcEEEEeCC
Confidence 444444 45 89999996 222 111 12344556542 6788877653
No 309
>cd01016 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=20.33 E-value=2.5e+02 Score=23.54 Aligned_cols=41 Identities=15% Similarity=0.273 Sum_probs=33.3
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecCcccHHHHHHHhccC
Q 030509 89 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPL 133 (176)
Q Consensus 89 ~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~ 133 (176)
..+..+.+.++.+.+++. +++++|+.+.+++..++.+..+.
T Consensus 192 ~eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~l~~~~ 232 (276)
T cd01016 192 SEAGLRDINELVDLIVER----KIKAIFVESSVNQKSIEALQDAV 232 (276)
T ss_pred cCCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHH
Confidence 345578888899989874 89999999999999998886544
No 310
>PRK02724 hypothetical protein; Provisional
Probab=20.32 E-value=3.3e+02 Score=20.25 Aligned_cols=48 Identities=19% Similarity=0.126 Sum_probs=34.2
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh
Q 030509 23 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE 72 (176)
Q Consensus 23 ~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e 72 (176)
-+|=+=...+.||||+-+..+.-.+|++....=... ..|+.|+..++.
T Consensus 9 fvlKvlWle~~iaiAvDQ~vg~~t~PLT~yfFWPr~--DAWe~LK~~Les 56 (104)
T PRK02724 9 FILKVLWLDDNVALAVDQIVGKGTSPLTAYFFWPRN--DAWEQLKTELES 56 (104)
T ss_pred EEEEEEEeccceeEEeeeecCCCCCcCcceeecCCc--cHHHHHHHHHhc
Confidence 456666778999999998888888999876431111 237888877764
No 311
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=20.28 E-value=4.1e+02 Score=20.42 Aligned_cols=17 Identities=24% Similarity=0.513 Sum_probs=9.9
Q ss_pred HHHHHHHHhcCCCEEEEe
Q 030509 64 EDFRSLISEFNLEGFIVG 81 (176)
Q Consensus 64 ~~L~~li~e~~~~~iVVG 81 (176)
+.+..++ ..++++||+.
T Consensus 46 ~~~~~~~-~~~~d~iii~ 62 (264)
T cd06267 46 EALELLL-SRRVDGIILA 62 (264)
T ss_pred HHHHHHH-HcCcCEEEEe
Confidence 4444444 3467777776
No 312
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=20.13 E-value=3.7e+02 Score=25.18 Aligned_cols=50 Identities=10% Similarity=0.111 Sum_probs=39.3
Q ss_pred cCCCEEEEeccCCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec-CcccHHHHHHHhc
Q 030509 73 FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN-EGFTSKGVELLLN 131 (176)
Q Consensus 73 ~~~~~iVVGlPl~dG~~s~~~~~v~~Fa~~L~~~~~~~~lpV~~~D-Er~TT~~A~~~l~ 131 (176)
.+|=.||+- +..+.+..+++.++.|+++ + ++||.-+| +.++...-.+.|.
T Consensus 180 gKPFvillN------s~~P~s~et~~L~~eL~ek--Y-~vpVlpvnc~~l~~~DI~~Il~ 230 (492)
T PF09547_consen 180 GKPFVILLN------STKPYSEETQELAEELEEK--Y-DVPVLPVNCEQLREEDITRILE 230 (492)
T ss_pred CCCEEEEEe------CCCCCCHHHHHHHHHHHHH--h-CCcEEEeehHHcCHHHHHHHHH
Confidence 356555555 6667777888999999984 4 99999999 9999988877765
No 313
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=20.10 E-value=5.3e+02 Score=21.65 Aligned_cols=77 Identities=10% Similarity=0.094 Sum_probs=0.0
Q ss_pred CceeccceeeeCCCCChhhHHHHHHHHHHhc-CCCEEEEeccCCCCCCc--------hHHHHHHHHHHHHHhccCCCCCc
Q 030509 43 NKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIVGYPFNRQQNA--------ADAVQVKLFIDDLSATKKLEDMK 113 (176)
Q Consensus 43 ~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~~~~iVVGlPl~dG~~s--------~~~~~v~~Fa~~L~~~~~~~~lp 113 (176)
|.++-+++.+..+..--...++++.+.+.+. .+++|+++ |+.+ +..+.++..++.... .+|
T Consensus 3 Gv~~a~~TPf~~dg~iD~~~~~~~i~~l~~~~Gv~gi~~~-----GstGE~~~Lt~~Er~~~~~~~~~~~~~-----~~~ 72 (288)
T cd00954 3 GLIAALLTPFDENGEINEDVLRAIVDYLIEKQGVDGLYVN-----GSTGEGFLLSVEERKQIAEIVAEAAKG-----KVT 72 (288)
T ss_pred CeeeceECCCCCCCCCCHHHHHHHHHHHHhcCCCCEEEEC-----cCCcCcccCCHHHHHHHHHHHHHHhCC-----CCe
Q ss_pred EEEecCcccHHHHHHH
Q 030509 114 YAYWNEGFTSKGVELL 129 (176)
Q Consensus 114 V~~~DEr~TT~~A~~~ 129 (176)
|+.-=-..||.+|.++
T Consensus 73 viagv~~~~~~~ai~~ 88 (288)
T cd00954 73 LIAHVGSLNLKESQEL 88 (288)
T ss_pred EEeccCCCCHHHHHHH
Done!