Query 030251
Match_columns 180
No_of_seqs 152 out of 1047
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:53:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030251.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030251hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00109 Holliday junction res 100.0 6E-44 1.3E-48 277.7 15.9 134 25-163 3-137 (138)
2 PF03652 UPF0081: Uncharacteri 100.0 1E-45 2.3E-50 286.7 5.4 134 26-163 1-135 (135)
3 COG0816 Predicted endonuclease 100.0 2.2E-43 4.7E-48 275.3 14.2 138 25-166 1-139 (141)
4 TIGR00250 RNAse_H_YqgF RNAse H 100.0 4.8E-43 1E-47 270.2 14.1 129 29-162 1-130 (130)
5 smart00732 YqgFc Likely ribonu 99.6 5.8E-15 1.3E-19 106.4 10.8 98 26-130 1-99 (99)
6 PRK00039 ruvC Holliday junctio 98.3 2.5E-05 5.3E-10 62.5 12.5 104 25-135 1-113 (164)
7 PF02075 RuvC: Crossover junct 97.7 0.00022 4.7E-09 56.1 8.7 101 28-135 1-110 (149)
8 cd00529 RuvC_resolvase Hollida 97.6 0.00061 1.3E-08 53.6 10.0 94 27-123 1-103 (154)
9 TIGR00228 ruvC crossover junct 97.6 0.00076 1.6E-08 53.8 10.5 101 28-135 1-109 (156)
10 COG2183 Tex Transcriptional ac 97.3 0.0031 6.8E-08 61.0 12.1 93 26-125 330-424 (780)
11 PF04312 DUF460: Protein of un 97.2 0.0045 9.7E-08 48.4 9.8 109 24-154 30-138 (138)
12 PF14639 YqgF: Holliday-juncti 97.0 0.012 2.6E-07 46.5 10.7 95 26-126 5-109 (150)
13 COG0817 RuvC Holliday junction 96.9 0.0017 3.7E-08 51.9 4.8 100 29-135 1-109 (160)
14 COG2433 Uncharacterized conser 96.7 0.015 3.3E-07 55.0 10.4 109 26-156 244-352 (652)
15 PRK05082 N-acetylmannosamine k 95.1 0.15 3.3E-06 43.2 8.8 102 27-133 2-115 (291)
16 COG1940 NagC Transcriptional r 94.9 0.15 3.1E-06 43.7 8.1 109 23-135 3-127 (314)
17 PRK09557 fructokinase; Reviewe 94.8 0.16 3.5E-06 43.3 8.1 103 27-134 1-116 (301)
18 COG1548 Predicted transcriptio 94.7 0.1 2.2E-06 45.3 6.4 99 26-133 3-108 (330)
19 PRK13310 N-acetyl-D-glucosamin 93.6 0.41 8.8E-06 40.8 8.1 103 27-134 1-116 (303)
20 PF04848 Pox_A22: Poxvirus A22 93.6 2.9 6.3E-05 32.9 12.2 119 26-155 1-133 (143)
21 PRK13311 N-acetyl-D-glucosamin 92.9 0.78 1.7E-05 38.3 8.7 103 27-134 1-116 (256)
22 PRK13321 pantothenate kinase; 92.3 2 4.4E-05 36.1 10.4 57 27-85 1-63 (256)
23 PF07318 DUF1464: Protein of u 92.2 1 2.2E-05 40.2 8.8 114 30-156 1-138 (343)
24 COG1214 Inactive homolog of me 91.7 0.76 1.6E-05 38.3 7.0 94 26-132 1-102 (220)
25 PRK12408 glucokinase; Provisio 91.2 0.58 1.3E-05 41.0 6.1 98 21-123 11-118 (336)
26 TIGR03725 bact_YeaZ universal 91.0 1.8 3.8E-05 35.2 8.4 86 28-122 1-92 (202)
27 TIGR00744 ROK_glcA_fam ROK fam 90.5 1.3 2.8E-05 37.8 7.5 100 29-134 1-117 (318)
28 PF00480 ROK: ROK family; Int 90.0 0.5 1.1E-05 36.8 4.2 100 30-135 1-112 (179)
29 TIGR01766 tspaseT_teng_C trans 89.9 0.95 2.1E-05 31.2 5.2 60 67-127 13-82 (82)
30 PRK13318 pantothenate kinase; 89.7 1.7 3.6E-05 36.6 7.4 58 27-86 1-64 (258)
31 PRK00292 glk glucokinase; Prov 89.6 1.6 3.5E-05 37.5 7.5 95 26-131 2-108 (316)
32 PF01548 DEDD_Tnp_IS110: Trans 89.6 1.4 3.1E-05 33.2 6.4 85 28-130 1-85 (144)
33 PRK15080 ethanolamine utilizat 88.6 12 0.00027 31.6 12.0 107 11-130 7-131 (267)
34 PRK14101 bifunctional glucokin 87.3 1.8 4E-05 41.2 6.8 66 23-91 15-84 (638)
35 PF14239 RRXRR: RRXRR protein 85.9 0.71 1.5E-05 37.6 2.8 23 25-47 50-72 (176)
36 PRK09698 D-allose kinase; Prov 85.1 4.9 0.00011 34.1 7.8 103 26-132 4-122 (302)
37 TIGR01865 cas_Csn1 CRISPR-asso 77.8 2 4.3E-05 42.4 3.1 23 27-49 2-24 (805)
38 PRK09472 ftsA cell division pr 76.6 13 0.00029 33.5 7.9 63 25-87 7-84 (420)
39 TIGR03723 bact_gcp putative gl 76.6 14 0.0003 32.2 7.7 88 28-122 1-108 (314)
40 PRK09605 bifunctional UGMP fam 74.9 15 0.00033 34.0 7.9 93 26-125 1-110 (535)
41 PRK09604 UGMP family protein; 74.9 30 0.00065 30.4 9.4 91 26-123 1-111 (332)
42 PRK09982 universal stress prot 74.9 14 0.00029 27.8 6.4 46 67-121 92-137 (142)
43 PRK13320 pantothenate kinase; 74.8 13 0.00027 31.4 6.8 53 26-85 2-55 (244)
44 PF07282 OrfB_Zn_ribbon: Putat 72.4 2.4 5.1E-05 28.4 1.5 45 114-158 15-68 (69)
45 PF03309 Pan_kinase: Type III 71.0 24 0.00051 28.6 7.4 57 28-85 1-60 (206)
46 smart00842 FtsA Cell division 70.9 21 0.00046 28.2 7.0 60 28-87 1-75 (187)
47 TIGR00749 glk glucokinase, pro 70.4 15 0.00032 31.7 6.3 61 29-91 1-68 (316)
48 PF11104 PilM_2: Type IV pilus 69.4 11 0.00025 32.7 5.5 60 30-89 1-72 (340)
49 PRK03011 butyrate kinase; Prov 68.6 32 0.0007 30.7 8.3 129 26-161 2-166 (358)
50 PF02844 GARS_N: Phosphoribosy 67.7 10 0.00023 28.0 4.2 40 67-119 51-90 (100)
51 PRK13322 pantothenate kinase; 66.9 57 0.0012 27.5 9.1 53 27-85 1-54 (246)
52 PRK13324 pantothenate kinase; 66.7 28 0.00061 29.7 7.2 57 27-85 1-64 (258)
53 COG1646 Predicted phosphate-bi 65.5 20 0.00043 30.6 5.9 48 67-122 30-77 (240)
54 PF05378 Hydant_A_N: Hydantoin 65.3 18 0.00039 28.9 5.5 57 29-86 2-64 (176)
55 COG0418 PyrC Dihydroorotase [N 64.6 8.7 0.00019 34.2 3.7 51 84-138 130-189 (344)
56 PRK15027 xylulokinase; Provisi 64.3 17 0.00037 33.2 5.8 50 27-76 1-58 (484)
57 TIGR01312 XylB D-xylulose kina 64.1 17 0.00036 32.9 5.6 21 29-49 1-21 (481)
58 PRK13928 rod shape-determining 63.2 72 0.0016 27.6 9.3 99 29-129 6-110 (336)
59 TIGR01174 ftsA cell division p 63.1 32 0.00068 30.3 7.1 61 28-88 2-77 (371)
60 PTZ00340 O-sialoglycoprotein e 63.0 40 0.00086 30.2 7.7 90 26-122 1-108 (345)
61 PF03464 eRF1_2: eRF1 domain 2 62.9 18 0.00039 27.3 4.9 95 28-131 4-118 (133)
62 PRK00047 glpK glycerol kinase; 61.9 23 0.00051 32.4 6.2 23 27-49 6-28 (498)
63 PF03932 CutC: CutC family; I 61.6 21 0.00045 29.6 5.3 60 72-140 79-142 (201)
64 PF07066 DUF3882: Lactococcus 61.5 22 0.00048 28.3 5.1 64 25-89 1-75 (159)
65 PF00532 Peripla_BP_1: Peripla 61.3 47 0.001 27.9 7.6 89 69-166 47-147 (279)
66 PRK10116 universal stress prot 61.3 39 0.00084 24.7 6.4 47 67-121 91-137 (142)
67 PF00370 FGGY_N: FGGY family o 61.1 29 0.00062 28.4 6.1 50 27-76 1-58 (245)
68 TIGR01175 pilM type IV pilus a 61.1 51 0.0011 28.4 8.0 64 26-89 3-78 (348)
69 PF05188 MutS_II: MutS domain 60.4 62 0.0013 23.4 13.4 121 27-167 2-130 (137)
70 COG3513 Predicted CRISPR-assoc 60.3 7.7 0.00017 38.7 2.9 24 24-47 2-25 (1088)
71 PF02579 Nitro_FeMo-Co: Dinitr 59.5 42 0.00092 22.9 6.0 50 68-134 43-92 (94)
72 PRK15118 universal stress glob 59.2 45 0.00097 24.5 6.4 47 67-122 92-138 (144)
73 TIGR03192 benz_CoA_bzdQ benzoy 58.3 40 0.00086 29.6 6.7 53 24-78 30-82 (293)
74 PF13727 CoA_binding_3: CoA-bi 57.8 31 0.00067 25.9 5.4 45 67-121 130-174 (175)
75 TIGR00555 panK_eukar pantothen 57.7 82 0.0018 27.3 8.5 90 28-135 2-92 (279)
76 TIGR01769 GGGP geranylgeranylg 57.7 35 0.00076 28.2 6.0 47 67-121 13-59 (205)
77 PHA02942 putative transposase; 57.6 15 0.00032 33.1 4.1 86 76-165 264-371 (383)
78 cd03412 CbiK_N Anaerobic cobal 57.2 33 0.00071 25.8 5.4 47 81-136 3-50 (127)
79 PRK13317 pantothenate kinase; 57.1 77 0.0017 27.2 8.3 87 25-135 1-88 (277)
80 PTZ00294 glycerol kinase-like 56.8 28 0.00062 32.0 5.9 23 27-49 3-25 (504)
81 PRK10966 exonuclease subunit S 56.5 63 0.0014 29.3 8.0 71 65-139 26-102 (407)
82 cd03409 Chelatase_Class_II Cla 55.9 57 0.0012 22.6 6.2 54 81-140 2-60 (101)
83 PRK13326 pantothenate kinase; 55.5 99 0.0022 26.4 8.6 22 26-47 6-27 (262)
84 cd03416 CbiX_SirB_N Sirohydroc 54.0 64 0.0014 22.6 6.2 57 81-141 2-60 (101)
85 TIGR00329 gcp_kae1 metallohydr 53.6 1.4E+02 0.0031 25.7 9.4 89 29-123 1-108 (305)
86 TIGR00241 CoA_E_activ CoA-subs 53.4 43 0.00093 27.8 6.0 47 28-77 2-48 (248)
87 PRK00923 sirohydrochlorin coba 53.4 52 0.0011 24.2 5.9 55 80-140 3-61 (126)
88 PF03237 Terminase_6: Terminas 53.2 64 0.0014 26.9 7.1 61 24-85 224-290 (384)
89 COG1070 XylB Sugar (pentulose 52.3 44 0.00095 30.9 6.4 23 24-46 2-24 (502)
90 PLN02295 glycerol kinase 52.1 39 0.00084 31.2 6.0 49 28-76 2-58 (512)
91 PHA02533 17 large terminase pr 51.8 98 0.0021 29.2 8.7 62 21-85 310-378 (534)
92 COG4012 Uncharacterized protei 51.0 1.3E+02 0.0028 26.6 8.5 98 26-139 1-99 (342)
93 PF00012 HSP70: Hsp70 protein; 50.2 14 0.00031 34.2 2.9 18 28-45 1-18 (602)
94 PF14331 ImcF-related_N: ImcF- 49.9 49 0.0011 28.1 5.9 55 66-121 9-75 (266)
95 PRK10939 autoinducer-2 (AI-2) 48.9 52 0.0011 30.4 6.3 24 26-49 3-26 (520)
96 TIGR01314 gntK_FGGY gluconate 48.7 39 0.00084 31.1 5.4 23 28-50 2-24 (505)
97 PRK10331 L-fuculokinase; Provi 48.0 44 0.00096 30.4 5.6 23 27-49 3-25 (470)
98 TIGR00671 baf pantothenate kin 47.9 70 0.0015 26.8 6.5 55 28-85 1-56 (243)
99 PF11215 DUF3010: Protein of u 47.1 76 0.0017 24.9 6.0 62 65-136 48-111 (138)
100 PRK14878 UGMP family protein; 47.0 76 0.0016 27.7 6.7 90 29-124 1-105 (323)
101 PRK09545 znuA high-affinity zi 46.9 64 0.0014 28.0 6.3 43 94-140 235-277 (311)
102 cd02067 B12-binding B12 bindin 46.9 86 0.0019 22.6 6.1 53 67-126 39-92 (119)
103 TIGR00619 sbcd exonuclease Sbc 46.4 98 0.0021 25.9 7.1 52 66-121 27-81 (253)
104 TIGR01768 GGGP-family geranylg 46.2 62 0.0013 27.2 5.8 45 68-121 17-61 (223)
105 cd01018 ZntC Metal binding pro 45.9 62 0.0013 27.2 5.9 51 94-152 200-250 (266)
106 PRK14046 malate--CoA ligase su 45.8 1.2E+02 0.0026 27.4 8.0 87 47-140 281-367 (392)
107 cd01988 Na_H_Antiporter_C The 45.6 36 0.00077 24.2 3.9 22 67-88 83-104 (132)
108 TIGR01311 glycerol_kin glycero 45.6 52 0.0011 30.1 5.7 24 27-50 2-25 (493)
109 TIGR01315 5C_CHO_kinase FGGY-f 45.0 56 0.0012 30.5 5.9 23 28-50 2-24 (541)
110 PRK11572 copper homeostasis pr 44.6 79 0.0017 27.1 6.3 60 72-140 80-143 (248)
111 PF02310 B12-binding: B12 bind 44.4 1.1E+02 0.0025 21.7 6.5 48 68-122 41-88 (121)
112 PRK15005 universal stress prot 44.1 46 0.00099 24.3 4.3 19 67-85 96-114 (144)
113 TIGR01016 sucCoAbeta succinyl- 43.8 1.2E+02 0.0026 26.9 7.7 85 47-138 281-365 (386)
114 PF13407 Peripla_BP_4: Peripla 43.7 92 0.002 24.8 6.4 48 64-124 42-89 (257)
115 COG1521 Pantothenate kinase ty 43.7 60 0.0013 27.8 5.4 18 27-44 1-18 (251)
116 TIGR02529 EutJ ethanolamine ut 43.4 1.9E+02 0.0041 24.0 8.4 91 30-130 1-104 (239)
117 cd06294 PBP1_ycjW_transcriptio 43.4 1.3E+02 0.0027 24.0 7.1 19 67-85 49-67 (270)
118 PRK13410 molecular chaperone D 43.0 25 0.00054 34.0 3.3 22 25-46 1-22 (668)
119 PF00582 Usp: Universal stress 42.9 1.1E+02 0.0023 21.1 6.0 49 67-121 91-139 (140)
120 PF13167 GTP-bdg_N: GTP-bindin 42.8 1.3E+02 0.0028 21.9 7.2 70 65-138 8-80 (95)
121 cd03413 CbiK_C Anaerobic cobal 42.7 1.1E+02 0.0023 22.3 6.0 55 81-140 3-57 (103)
122 cd02812 PcrB_like PcrB_like pr 42.1 79 0.0017 26.5 5.8 48 67-122 14-61 (219)
123 cd05781 DNA_polB_B3_exo DEDDy 42.1 1.6E+02 0.0036 23.5 7.6 22 64-86 49-70 (188)
124 PF07355 GRDB: Glycine/sarcosi 42.0 84 0.0018 28.3 6.2 58 62-125 64-123 (349)
125 cd01989 STK_N The N-terminal d 41.7 47 0.001 24.4 4.1 19 67-85 92-110 (146)
126 PRK13927 rod shape-determining 41.7 2.2E+02 0.0048 24.3 9.2 27 26-52 5-31 (334)
127 PLN02757 sirohydrochlorine fer 41.2 1.1E+02 0.0023 24.0 6.2 56 79-138 14-71 (154)
128 PF00072 Response_reg: Respons 40.5 1.2E+02 0.0025 20.7 6.7 62 68-139 33-94 (112)
129 PF13911 AhpC-TSA_2: AhpC/TSA 40.3 71 0.0015 22.9 4.7 47 69-129 4-50 (115)
130 PRK00290 dnaK molecular chaper 40.3 27 0.00058 33.3 3.0 21 26-46 2-22 (627)
131 cd01017 AdcA Metal binding pro 39.6 1E+02 0.0023 26.0 6.3 44 93-140 202-245 (282)
132 PRK04123 ribulokinase; Provisi 39.6 71 0.0015 29.7 5.7 23 26-48 3-26 (548)
133 COG0420 SbcD DNA repair exonuc 39.6 1.1E+02 0.0024 27.0 6.7 53 66-121 28-81 (390)
134 PRK13331 pantothenate kinase; 39.5 1.1E+02 0.0023 26.2 6.3 25 24-48 5-29 (251)
135 PF06180 CbiK: Cobalt chelatas 39.3 56 0.0012 28.0 4.6 64 49-121 76-147 (262)
136 TIGR02628 fuculo_kin_coli L-fu 39.2 77 0.0017 28.8 5.8 23 27-49 2-24 (465)
137 TIGR01234 L-ribulokinase L-rib 39.1 69 0.0015 29.7 5.5 23 27-49 2-25 (536)
138 cd03414 CbiX_SirB_C Sirohydroc 39.0 1.1E+02 0.0025 21.9 5.7 56 81-140 3-60 (117)
139 cd01400 6PGL 6PGL: 6-Phosphogl 38.5 93 0.002 25.4 5.7 49 67-125 12-62 (219)
140 PRK13411 molecular chaperone D 38.1 33 0.00072 33.0 3.3 21 26-46 2-22 (653)
141 cd06297 PBP1_LacI_like_12 Liga 38.1 1.5E+02 0.0033 23.9 7.0 18 68-85 45-62 (269)
142 TIGR03275 methan_mark_8 putati 38.1 1.2E+02 0.0027 26.1 6.4 59 27-105 155-213 (259)
143 PRK13929 rod-share determining 37.8 1.4E+02 0.0031 25.8 7.1 70 26-96 4-74 (335)
144 cd02064 FAD_synthetase_N FAD s 37.6 1.2E+02 0.0026 24.0 6.0 64 68-139 89-160 (180)
145 cd00851 MTH1175 This uncharact 37.3 1.3E+02 0.0029 20.7 5.7 48 68-132 53-100 (103)
146 CHL00094 dnaK heat shock prote 37.3 31 0.00068 32.8 3.0 21 26-46 2-22 (621)
147 PLN02669 xylulokinase 36.9 88 0.0019 29.5 5.9 27 23-49 5-31 (556)
148 cd01019 ZnuA Zinc binding prot 35.4 1.3E+02 0.0029 25.5 6.4 43 93-139 210-252 (286)
149 COG0443 DnaK Molecular chapero 35.4 57 0.0012 31.1 4.4 22 25-46 4-25 (579)
150 TIGR02260 benz_CoA_red_B benzo 35.2 1.9E+02 0.0041 26.3 7.6 60 67-133 339-405 (413)
151 PF01869 BcrAD_BadFG: BadF/Bad 35.2 1.2E+02 0.0027 25.1 6.0 22 29-50 1-22 (271)
152 TIGR02026 BchE magnesium-proto 35.1 1.6E+02 0.0035 27.2 7.3 72 62-140 223-299 (497)
153 PF14450 FtsA: Cell division p 35.0 37 0.00079 25.1 2.5 19 28-46 1-19 (120)
154 PRK10606 btuE putative glutath 34.5 65 0.0014 26.0 4.1 39 67-105 43-84 (183)
155 TIGR03722 arch_KAE1 universal 34.4 2.8E+02 0.0061 24.0 8.3 89 29-123 1-105 (322)
156 cd01844 SGNH_hydrolase_like_6 34.2 1.6E+02 0.0035 22.4 6.2 51 70-122 49-100 (177)
157 cd01829 SGNH_hydrolase_peri2 S 34.2 1.1E+02 0.0025 23.5 5.4 50 68-122 98-148 (200)
158 cd00984 DnaB_C DnaB helicase C 34.1 2E+02 0.0042 23.1 6.9 60 63-123 108-171 (242)
159 PRK04169 geranylgeranylglycery 34.0 1.2E+02 0.0026 25.6 5.7 41 72-121 26-66 (232)
160 PF03358 FMN_red: NADPH-depend 33.7 1.1E+02 0.0024 22.8 5.0 49 67-121 61-112 (152)
161 PF06723 MreB_Mbl: MreB/Mbl pr 33.7 96 0.0021 27.4 5.3 107 27-134 2-113 (326)
162 COG4020 Uncharacterized protei 33.5 67 0.0014 28.2 4.1 61 26-86 3-65 (332)
163 PRK15456 universal stress prot 33.4 44 0.00095 24.6 2.7 20 67-86 94-113 (142)
164 PRK13329 pantothenate kinase; 33.2 3E+02 0.0064 23.2 8.6 18 27-44 2-19 (249)
165 cd01137 PsaA Metal binding pro 33.1 1.4E+02 0.0031 25.4 6.2 45 92-140 207-251 (287)
166 PRK11678 putative chaperone; P 33.0 41 0.00088 31.0 2.9 18 28-45 2-19 (450)
167 PRK12359 flavodoxin FldB; Prov 32.4 51 0.0011 26.4 3.1 28 82-109 138-166 (172)
168 PF03709 OKR_DC_1_N: Orn/Lys/A 32.4 2E+02 0.0043 21.0 6.3 53 68-128 27-80 (115)
169 PF00155 Aminotran_1_2: Aminot 32.0 2.1E+02 0.0045 24.2 7.1 55 67-127 132-192 (363)
170 COG4820 EutJ Ethanolamine util 31.8 88 0.0019 26.7 4.4 42 6-47 6-50 (277)
171 COG1924 Activator of 2-hydroxy 30.8 1.8E+02 0.0038 26.7 6.5 51 24-77 133-183 (396)
172 COG0363 NagB 6-phosphogluconol 30.7 1.3E+02 0.0028 25.4 5.4 52 68-127 18-75 (238)
173 cd06547 GH85_ENGase Endo-beta- 30.5 2.6E+02 0.0056 24.8 7.5 58 65-123 90-149 (339)
174 PTZ00400 DnaK-type molecular c 30.5 47 0.001 32.0 3.0 21 25-45 40-60 (663)
175 cd05785 DNA_polB_like2_exo Unc 30.5 2.8E+02 0.006 22.6 7.2 21 65-86 60-80 (207)
176 cd06271 PBP1_AglR_RafR_like Li 30.2 2.7E+02 0.0058 21.9 7.1 19 67-85 48-66 (268)
177 TIGR00290 MJ0570_dom MJ0570-re 30.0 1.7E+02 0.0036 24.5 5.9 37 67-107 74-110 (223)
178 PF12641 Flavodoxin_3: Flavodo 29.9 2.3E+02 0.005 22.3 6.4 30 77-109 38-67 (160)
179 COG4126 Hydantoin racemase [Am 29.7 82 0.0018 26.7 4.0 41 65-119 161-201 (230)
180 PTZ00009 heat shock 70 kDa pro 29.5 57 0.0012 31.3 3.4 21 25-45 3-23 (653)
181 PTZ00186 heat shock 70 kDa pre 29.5 50 0.0011 31.9 3.0 22 25-46 26-47 (657)
182 KOG0237 Glycinamide ribonucleo 29.5 1.4E+02 0.0031 29.1 5.9 71 67-140 57-145 (788)
183 KOG4013 Predicted Cu2+ homeost 29.5 1.1E+02 0.0025 25.7 4.7 42 71-121 87-129 (255)
184 cd00338 Ser_Recombinase Serine 29.4 1.9E+02 0.0041 20.8 5.7 53 67-127 54-107 (137)
185 PRK13790 phosphoribosylamine-- 29.2 1.8E+02 0.0039 25.8 6.3 20 67-86 16-35 (379)
186 TIGR00615 recR recombination p 29.1 95 0.002 25.7 4.2 28 67-94 123-151 (195)
187 cd00248 Mth938-like Mth938-lik 29.1 2.2E+02 0.0048 20.8 5.8 55 67-135 41-95 (109)
188 PRK13844 recombination protein 28.9 96 0.0021 25.8 4.2 28 67-94 127-155 (200)
189 cd00950 DHDPS Dihydrodipicolin 28.9 1.3E+02 0.0028 25.2 5.2 61 67-134 84-151 (284)
190 cd01124 KaiC KaiC is a circadi 28.7 2.5E+02 0.0055 21.2 6.5 58 66-127 83-142 (187)
191 cd01828 sialate_O-acetylestera 28.7 2.5E+02 0.0055 21.0 6.8 54 66-122 37-94 (169)
192 PLN02271 serine hydroxymethylt 28.5 1.8E+02 0.0038 28.1 6.4 38 67-109 287-324 (586)
193 TIGR00289 conserved hypothetic 28.3 2E+02 0.0042 24.1 6.0 37 67-107 74-110 (222)
194 PRK00994 F420-dependent methyl 28.2 3.3E+02 0.0071 23.6 7.3 67 63-140 45-111 (277)
195 TIGR03190 benz_CoA_bzdN benzoy 28.2 1.8E+02 0.0038 26.0 6.1 53 66-126 301-354 (377)
196 PRK01433 hscA chaperone protei 27.9 62 0.0013 30.9 3.3 19 26-44 19-37 (595)
197 cd08165 MPP_MPPE1 human MPPE1 27.8 2.7E+02 0.0058 21.4 6.4 52 67-121 27-82 (156)
198 KOG4184 Predicted sugar kinase 27.6 94 0.002 28.5 4.2 68 66-135 226-300 (478)
199 PF06490 FleQ: Flagellar regul 27.5 2.4E+02 0.0051 20.5 5.8 47 71-127 35-81 (109)
200 cd00458 SugarP_isomerase Sugar 27.0 2.1E+02 0.0046 22.3 5.8 52 67-125 9-60 (169)
201 cd00562 NifX_NifB This CD repr 27.0 2.1E+02 0.0046 19.6 5.9 51 68-134 51-101 (102)
202 PRK11175 universal stress prot 26.9 1.7E+02 0.0037 24.3 5.6 20 67-86 96-115 (305)
203 COG1433 Uncharacterized conser 26.8 2.9E+02 0.0062 21.0 6.5 53 68-137 55-107 (121)
204 cd06300 PBP1_ABC_sugar_binding 26.8 3.3E+02 0.0071 21.7 7.2 44 67-123 50-93 (272)
205 TIGR01198 pgl 6-phosphoglucono 26.7 1.8E+02 0.004 24.0 5.6 37 81-125 29-66 (233)
206 PF04412 DUF521: Protein of un 26.7 2.2E+02 0.0047 26.1 6.5 90 23-132 242-337 (400)
207 PRK10854 exopolyphosphatase; P 26.6 2.1E+02 0.0046 26.7 6.5 92 22-122 7-117 (513)
208 TIGR03471 HpnJ hopanoid biosyn 26.5 3.4E+02 0.0073 24.7 7.8 70 62-140 228-299 (472)
209 TIGR03123 one_C_unchar_1 proba 26.5 3.6E+02 0.0079 23.8 7.7 94 29-127 1-100 (318)
210 KOG1220 Phosphoglucomutase/pho 26.3 1.5E+02 0.0033 28.6 5.5 47 73-127 93-142 (607)
211 KOG1856 Transcription elongati 26.3 3E+02 0.0066 28.9 7.8 58 66-125 654-711 (1299)
212 PF01182 Glucosamine_iso: Gluc 26.0 1.6E+02 0.0034 23.7 5.0 54 66-125 9-62 (199)
213 KOG2707 Predicted metalloprote 26.0 1E+02 0.0022 28.2 4.1 39 11-52 19-58 (405)
214 COG3703 ChaC Uncharacterized p 25.9 76 0.0017 26.2 3.1 23 23-45 55-77 (190)
215 COG0145 HyuA N-methylhydantoin 25.8 2.6E+02 0.0056 27.4 7.1 59 25-85 1-64 (674)
216 cd01987 USP_OKCHK USP domain i 25.7 74 0.0016 22.6 2.7 21 67-87 74-94 (124)
217 KOG0968 DNA polymerase zeta, c 25.5 1.6E+02 0.0035 31.0 5.7 71 35-108 701-781 (1488)
218 PLN03226 serine hydroxymethylt 25.5 2.2E+02 0.0048 26.3 6.4 19 67-85 172-190 (475)
219 TIGR02350 prok_dnaK chaperone 25.3 61 0.0013 30.5 2.8 19 28-46 2-20 (595)
220 PRK13328 pantothenate kinase; 25.0 4.2E+02 0.0091 22.3 9.9 83 27-110 2-112 (255)
221 COG2410 Predicted nuclease (RN 24.9 3.9E+02 0.0083 21.9 7.1 22 26-47 1-23 (178)
222 COG2205 KdpD Osmosensitive K+ 24.9 3.2E+02 0.007 27.7 7.6 55 66-126 322-377 (890)
223 PF14606 Lipase_GDSL_3: GDSL-l 24.9 2.3E+02 0.0051 22.9 5.7 53 67-122 48-100 (178)
224 KOG3289 Uncharacterized conser 24.9 2E+02 0.0044 23.7 5.3 95 71-167 64-170 (199)
225 COG0151 PurD Phosphoribosylami 24.7 1.9E+02 0.0042 26.8 5.7 70 67-139 52-139 (428)
226 PRK05183 hscA chaperone protei 24.7 71 0.0015 30.5 3.1 20 26-45 19-38 (616)
227 cd01545 PBP1_SalR Ligand-bindi 24.6 3.4E+02 0.0073 21.4 6.7 18 67-84 45-62 (270)
228 PRK00696 sucC succinyl-CoA syn 24.6 3.8E+02 0.0082 23.8 7.6 84 48-138 282-365 (388)
229 PF03088 Str_synth: Strictosid 24.5 1.7E+02 0.0038 20.9 4.4 24 13-38 26-49 (89)
230 TIGR03566 FMN_reduc_MsuE FMN r 24.5 1.6E+02 0.0035 22.8 4.7 49 67-121 59-107 (174)
231 cd06282 PBP1_GntR_like_2 Ligan 24.4 3.5E+02 0.0076 21.2 7.0 11 75-85 52-62 (266)
232 TIGR03191 benz_CoA_bzdO benzoy 24.4 2.1E+02 0.0046 26.1 6.0 47 67-121 350-397 (430)
233 TIGR00111 pelota probable tran 24.4 2.4E+02 0.0053 25.0 6.3 145 11-166 121-273 (351)
234 PLN03184 chloroplast Hsp70; Pr 24.4 78 0.0017 30.6 3.3 40 7-46 8-59 (673)
235 PF00875 DNA_photolyase: DNA p 24.2 3.2E+02 0.007 20.7 6.4 18 68-85 78-95 (165)
236 TIGR02717 AcCoA-syn-alpha acet 24.2 5.5E+02 0.012 23.4 9.6 73 63-140 355-428 (447)
237 PRK14457 ribosomal RNA large s 24.2 4.1E+02 0.009 23.6 7.7 89 65-157 240-339 (345)
238 PF13941 MutL: MutL protein 24.1 3.2E+02 0.007 25.5 7.2 65 68-139 115-179 (457)
239 TIGR03729 acc_ester putative p 24.1 2.5E+02 0.0053 22.9 5.9 47 67-121 21-67 (239)
240 COG0655 WrbA Multimeric flavod 24.0 1.3E+02 0.0028 24.2 4.1 35 67-106 66-100 (207)
241 cd06292 PBP1_LacI_like_10 Liga 23.6 3.8E+02 0.0082 21.3 7.1 17 68-84 45-61 (273)
242 PF01884 PcrB: PcrB family; I 23.4 2.6E+02 0.0056 23.6 5.9 44 68-122 22-66 (230)
243 PRK07667 uridine kinase; Provi 23.3 2.9E+02 0.0062 21.8 6.0 53 67-125 3-57 (193)
244 cd05784 DNA_polB_II_exo DEDDy 23.3 3.9E+02 0.0084 21.5 6.8 28 65-96 53-80 (193)
245 PF09298 FAA_hydrolase_N: Fuma 23.1 39 0.00085 25.0 0.8 12 34-45 14-25 (107)
246 cd00293 USP_Like Usp: Universa 22.8 96 0.0021 21.2 2.8 21 67-87 82-102 (130)
247 PF01297 TroA: Periplasmic sol 22.8 2.9E+02 0.0064 22.6 6.2 39 96-138 184-222 (256)
248 PRK07179 hypothetical protein; 22.7 2.6E+02 0.0057 24.5 6.2 51 67-126 170-221 (407)
249 TIGR00696 wecB_tagA_cpsF bacte 22.7 4E+02 0.0087 21.2 7.3 55 66-131 36-90 (177)
250 COG2102 Predicted ATPases of P 22.6 2.4E+02 0.0052 23.9 5.5 38 67-108 75-112 (223)
251 PF02833 DHHA2: DHHA2 domain; 22.6 1.1E+02 0.0024 22.4 3.2 48 30-85 26-73 (127)
252 COG3854 SpoIIIAA ncharacterize 22.5 2.4E+02 0.0051 24.7 5.5 53 70-127 129-182 (308)
253 PRK05627 bifunctional riboflav 22.4 3E+02 0.0065 24.0 6.3 64 68-139 103-175 (305)
254 PF00701 DHDPS: Dihydrodipicol 22.4 2.6E+02 0.0056 23.6 5.8 50 67-123 85-135 (289)
255 COG3643 Glutamate formiminotra 22.3 1E+02 0.0023 26.7 3.3 47 79-128 87-133 (302)
256 TIGR03286 methan_mark_15 putat 22.3 3.1E+02 0.0067 25.2 6.6 25 24-48 142-166 (404)
257 PRK13930 rod shape-determining 22.2 86 0.0019 26.8 2.9 19 26-44 8-26 (335)
258 cd01833 XynB_like SGNH_hydrola 21.9 3.3E+02 0.0071 20.0 6.3 55 68-122 67-124 (157)
259 cd06311 PBP1_ABC_sugar_binding 21.9 4.2E+02 0.009 21.2 7.2 44 68-123 50-93 (274)
260 cd02071 MM_CoA_mut_B12_BD meth 21.7 3.3E+02 0.0071 19.9 7.8 79 67-153 39-118 (122)
261 PTZ00285 glucosamine-6-phospha 21.5 1.8E+02 0.0038 24.4 4.6 55 67-125 17-75 (253)
262 KOG0104 Molecular chaperones G 21.4 1.4E+02 0.0031 29.9 4.4 31 23-57 19-49 (902)
263 cd06309 PBP1_YtfQ_like Peripla 21.3 4.2E+02 0.0092 21.1 6.8 42 68-122 46-87 (273)
264 PRK10569 NAD(P)H-dependent FMN 21.2 2E+02 0.0044 23.0 4.8 49 67-121 57-105 (191)
265 TIGR01753 flav_short flavodoxi 21.2 2.3E+02 0.005 20.4 4.7 40 79-121 46-86 (140)
266 COG0079 HisC Histidinol-phosph 21.2 2.4E+02 0.0052 25.0 5.6 51 67-125 135-186 (356)
267 TIGR02263 benz_CoA_red_C benzo 21.1 2.1E+02 0.0046 25.5 5.2 48 67-122 310-358 (380)
268 PF09872 DUF2099: Uncharacteri 21.0 4.6E+02 0.0099 22.7 6.9 56 29-104 157-212 (258)
269 PRK13556 azoreductase; Provisi 21.0 2.3E+02 0.0051 22.6 5.1 39 68-109 78-117 (208)
270 COG0386 BtuE Glutathione perox 20.9 2E+02 0.0042 23.2 4.4 39 67-105 43-84 (162)
271 TIGR00683 nanA N-acetylneurami 20.9 2.5E+02 0.0055 23.9 5.5 52 67-124 85-137 (290)
272 PRK02724 hypothetical protein; 20.8 3.1E+02 0.0068 20.5 5.2 48 27-76 9-56 (104)
273 PRK10355 xylF D-xylose transpo 20.8 5.3E+02 0.012 22.0 8.7 44 68-124 72-115 (330)
274 TIGR03858 LLM_2I7G probable ox 20.7 1.8E+02 0.004 25.2 4.7 25 63-87 288-312 (337)
275 PLN02721 threonine aldolase 20.7 3.1E+02 0.0068 23.0 6.1 54 67-125 120-180 (353)
276 TIGR00502 nagB glucosamine-6-p 20.6 2.2E+02 0.0048 23.8 5.0 55 67-125 17-75 (259)
277 PF01026 TatD_DNase: TatD rela 20.6 3E+02 0.0065 22.7 5.8 92 66-161 73-168 (255)
278 PF10035 DUF2179: Uncharacteri 20.3 1.2E+02 0.0027 19.0 2.7 19 67-85 29-47 (55)
279 PF08608 Wyosine_form: Wyosine 20.3 1.4E+02 0.0031 20.0 3.0 28 93-125 26-53 (62)
280 PF00464 SHMT: Serine hydroxym 20.2 2.4E+02 0.0053 25.7 5.5 34 67-105 158-191 (399)
281 cd00615 Orn_deC_like Ornithine 20.1 3E+02 0.0065 23.1 5.8 50 67-126 142-193 (294)
282 PF00255 GSHPx: Glutathione pe 20.0 2.2E+02 0.0047 21.1 4.3 40 67-106 39-81 (108)
No 1
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=100.00 E-value=6e-44 Score=277.72 Aligned_cols=134 Identities=31% Similarity=0.514 Sum_probs=125.5
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHH
Q 030251 25 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLF 103 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F 103 (180)
.+++||||||++|||||+||+.+.+|+|+.++.+++... .+++|.+++++|++++||||+|++ ||+.++++..++.|
T Consensus 3 ~~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~--~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f 80 (138)
T PRK00109 3 SGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTP--DWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKF 80 (138)
T ss_pred CCcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCch--HHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHH
Confidence 578999999999999999999999999999999875443 479999999999999999999999 99999999999999
Q ss_pred HHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030251 104 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN 163 (180)
Q Consensus 104 ~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~ 163 (180)
+++|++. + ++||++|||||||++|++.|++.|.+++++|+.+|++||++|||+||++
T Consensus 81 ~~~L~~~--~-~~~v~~~DEr~TT~~A~~~l~~~~~~~~~~k~~vD~~AA~iILq~yL~~ 137 (138)
T PRK00109 81 ANRLEGR--F-GLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLDS 137 (138)
T ss_pred HHHHHHH--h-CCCEEEEcCCcCHHHHHHHHHHcCCChhhcccchhHHHHHHHHHHHHhc
Confidence 9999984 5 8999999999999999999999998888888999999999999999985
No 2
>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=1e-45 Score=286.66 Aligned_cols=134 Identities=34% Similarity=0.555 Sum_probs=123.2
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFI 104 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~ 104 (180)
|++||||||++|||||+||+.+.+|+|+++|.+.+.. .++++|.+++++|+++.||||+|++ ||+++++++.+++|+
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 6899999999999999999999999999999976543 3489999999999999999999999 999999999999999
Q ss_pred HHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030251 105 DDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN 163 (180)
Q Consensus 105 ~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~ 163 (180)
++|++. +|++||++|||||||.+|++.|++.|.+++++|+.+|++||++|||+||++
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 999985 579999999999999999999999999999999999999999999999974
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=2.2e-43 Score=275.29 Aligned_cols=138 Identities=28% Similarity=0.478 Sum_probs=129.0
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHH
Q 030251 25 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLF 103 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F 103 (180)
++++||||||+||||||+||+.+.+|+|+++|.+.+... ..|+.|.+++.+|+++.||||+|++ +|+.++.++.+++|
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 378999999999999999999999999999999887653 2389999999999999999999999 99999999999999
Q ss_pred HHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhhhhh
Q 030251 104 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANR 166 (180)
Q Consensus 104 ~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~~~~ 166 (180)
+++|+++ | ++||++||||+||++|++.|.+.|.+++++|+.+|++||++|||+||+....
T Consensus 80 ~~~L~~r--~-~lpv~l~DERltTv~A~~~L~~~~~~~~~rk~~iD~~AA~~ILq~~ld~~~~ 139 (141)
T COG0816 80 AERLKKR--F-NLPVVLWDERLSTVEAERMLIEAGVSRKKRKGVIDSLAAVLILESYLDRNHA 139 (141)
T ss_pred HHHHHHh--c-CCCEEEEcCccCHHHHHHHHHHcCCchhhhcchhHHHHHHHHHHHHHHhhhh
Confidence 9999984 6 8999999999999999999999999999999999999999999999997653
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=4.8e-43 Score=270.19 Aligned_cols=129 Identities=26% Similarity=0.345 Sum_probs=121.5
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHH
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDL 107 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L 107 (180)
||||||++|||||+||+.+.+|+|+.++..++.. ..++.|.+++++|+++.||||+|++ ||+++++++.|++|+++|
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 6999999999999999999999999999876433 3479999999999999999999999 999999999999999999
Q ss_pred HhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHh
Q 030251 108 SATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLD 162 (180)
Q Consensus 108 ~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~ 162 (180)
++. + ++||++|||||||.+|++.|++.|++++++|+.+|++||++|||+||+
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 984 5 899999999999999999999999999989999999999999999995
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=5.8e-15 Score=106.36 Aligned_cols=98 Identities=24% Similarity=0.456 Sum_probs=83.4
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFI 104 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~ 104 (180)
+++||||+|..+||+|+.|+.+.+..+..+....+ .+.+++.|.+++.++++++|+||.|-. +|....... ..|.
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 35899999999999999999999998877665322 234689999999999999999999999 998776554 7899
Q ss_pred HHHHhccCCCCCcEEEecccccHHHH
Q 030251 105 DDLSATKKLEDMKYAYWNEGFTSKGV 130 (180)
Q Consensus 105 ~~L~~~~~~~~lpV~~~DEr~TT~~A 130 (180)
+.|++. + ++||+++||+.||.+|
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=98.27 E-value=2.5e-05 Score=62.54 Aligned_cols=104 Identities=18% Similarity=0.198 Sum_probs=68.0
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceec--cceeeeCCCCC-----hhhHHHHHHHHHHhhCCCEEEEecccC--CCCCch
Q 030251 25 RGRFLGLDVGDKYVGLSISDPKNKIAS--PLSVLLRKKNT-----IDLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAA 95 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~~~~a~--Pl~~i~~~~~~-----~~~~~~~L~~li~e~~i~~iVVGlP~~--dG~~s~ 95 (180)
+++|||||+|..++|+|+.+..+.-.. -.++|..+... ...+.+.|.+++++|+|+.++|=-|+- |...+-
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 478999999999999999886654222 23466544221 124468999999999999999998877 333333
Q ss_pred HHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 96 DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 96 ~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
..-+++-.+..... +. ++||+.+ |..+.+...-
T Consensus 81 ~l~~arGvi~la~~--~~-~ipv~ey----~P~~VKk~vt 113 (164)
T PRK00039 81 KLGQARGVAILAAA--QR-GLPVAEY----TPLQVKKAVV 113 (164)
T ss_pred HHHHHHHHHHHHHH--Hc-CCCEEEE----CHHHhhhhhc
Confidence 33334444443333 23 8998865 6666665543
No 7
>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=97.74 E-value=0.00022 Score=56.06 Aligned_cols=101 Identities=17% Similarity=0.229 Sum_probs=57.1
Q ss_pred EEEEecCCCeEEEEEecCCCceec--cceeeeCCCC-C----hhhHHHHHHHHHHhhCCCEEEEecccC-CC-CCchHHH
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIAS--PLSVLLRKKN-T----IDLMAEDFRSLISEFNLEGFIVGYPFN-RQ-QNAADAV 98 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~--Pl~~i~~~~~-~----~~~~~~~L~~li~e~~i~~iVVGlP~~-dG-~~s~~~~ 98 (180)
|||||+|..++|.|+-+..+.-.. ..++|..... + ...+.+.|.+++++|+|+.++|=-|.. .. +..-..-
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 799999999999999987543222 2346665432 1 123468899999999999999998877 32 2222233
Q ss_pred HHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 99 QVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 99 ~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
+++-.+...... .++||.. +|..+.++.+-
T Consensus 81 ~arGvi~l~~~~---~~i~v~~----y~P~~vKk~vt 110 (149)
T PF02075_consen 81 QARGVILLAAAQ---RGIPVFE----YTPSEVKKAVT 110 (149)
T ss_dssp HHHHHHHHHHHT---TT--EEE----EEHHHHHHHHT
T ss_pred HHHHHHHHHHHH---cCCeEEE----ECHHHHHHHhh
Confidence 455555544432 3888775 47777777654
No 8
>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=97.64 E-value=0.00061 Score=53.59 Aligned_cols=94 Identities=14% Similarity=0.231 Sum_probs=57.9
Q ss_pred eEEEEecCCCeEEEEEecCCCceec--cceeeeCCCCC-----hhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchH-H
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIAS--PLSVLLRKKNT-----IDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAAD-A 97 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~--Pl~~i~~~~~~-----~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~-~ 97 (180)
+|||||+|..++|+|+.+..+.... -.++|...... ...+.+.|.+++.+|+|+.++|=-+.- .+..+.. .
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 6899999999999999875543322 23466654221 134578999999999999999987665 3322221 1
Q ss_pred HHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 98 VQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 98 ~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
..++..+-..... .++||..++-
T Consensus 81 ~~~~Gvi~~~~~~---~~i~v~e~~P 103 (154)
T cd00529 81 GQARGALILALAN---RNLPVFEYTP 103 (154)
T ss_pred HHHHHHHHHHHHH---cCCCEEEEcc
Confidence 1122222222221 2788877653
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=97.64 E-value=0.00076 Score=53.77 Aligned_cols=101 Identities=14% Similarity=0.221 Sum_probs=65.5
Q ss_pred EEEEecCCCeEEEEEecCCCcee--ccceeeeCCCCCh----hhHHHHHHHHHHhhCCCEEEEecccC--CCCCchHHHH
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIA--SPLSVLLRKKNTI----DLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQ 99 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a--~Pl~~i~~~~~~~----~~~~~~L~~li~e~~i~~iVVGlP~~--dG~~s~~~~~ 99 (180)
|||||+|..++|.||-+..+.-. --.++|..++... ....+.|.+++++|+|+.+.|=-++. |.+.+-..-+
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 69999999999999987544332 2235666543221 23468899999999999999988776 3344344444
Q ss_pred HHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 100 VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 100 v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
++-.+-.... + .++||+ -||..+.+..+-
T Consensus 81 arGvilla~~--~-~~ipv~----Ey~P~~vKkavt 109 (156)
T TIGR00228 81 ARGVAIVAAV--N-QELPVF----EYAARQVKQTVV 109 (156)
T ss_pred HHHHHHHHHH--H-cCCCEE----EECHHHHHHHhc
Confidence 5554433332 1 389988 356666655544
No 10
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.33 E-value=0.0031 Score=61.01 Aligned_cols=93 Identities=18% Similarity=0.271 Sum_probs=67.1
Q ss_pred CeEEEEecCCCe-EEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHH
Q 030251 26 GRFLGLDVGDKY-VGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLF 103 (180)
Q Consensus 26 ~~iLalD~G~kr-iGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F 103 (180)
..+||||+|.+. |=+|+.|..+.+..-..+++... ...+...+.|..++..|+|+.|.|| +||-|..+.+ |
T Consensus 330 ~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIG----ngTaSrete~---f 402 (780)
T COG2183 330 KATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIG----NGTASRETEK---F 402 (780)
T ss_pred cceeecCCccccccEEEEEcCCCceeceeEEEcCCCccchHHHHHHHHHHHHHhCceEEEEe----cCCcchhHHH---H
Confidence 389999999655 66899999887776544554432 1233446888999999999999999 9999976654 5
Q ss_pred HHHHHhccCCCCCcEEEecccc
Q 030251 104 IDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 104 ~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
+..|-+.....++..+.+.|..
T Consensus 403 v~~vl~~~~~~~~~~viVsEag 424 (780)
T COG2183 403 VADVLKELPKEKVLKVIVSEAG 424 (780)
T ss_pred HHHHHHhccCCCCcEEEEcccc
Confidence 5555553223477888888754
No 11
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=97.22 E-value=0.0045 Score=48.38 Aligned_cols=109 Identities=15% Similarity=0.174 Sum_probs=71.7
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHH
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLF 103 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F 103 (180)
+..-|+|+|+|+ .+|+|+-|-.|. ++.+...++.+ ..++-++|.+|+-=.||== |=+.-+ . +
T Consensus 30 ~~~lIVGiDPG~-ttgiAildL~G~---~l~l~S~R~~~----~~evi~~I~~~G~PviVAt----DV~p~P--~----~ 91 (138)
T PF04312_consen 30 RRYLIVGIDPGT-TTGIAILDLDGE---LLDLKSSRNMS----RSEVIEWISEYGKPVIVAT----DVSPPP--E----T 91 (138)
T ss_pred CCCEEEEECCCc-eeEEEEEecCCc---EEEEEeecCCC----HHHHHHHHHHcCCEEEEEe----cCCCCc--H----H
Confidence 457799999998 589999998875 44455555433 4778888888866545444 434333 3 4
Q ss_pred HHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHHHH
Q 030251 104 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAV 154 (180)
Q Consensus 104 ~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~ 154 (180)
.++|+.. | +-..+.=++.+|..|=.++..+.+. +-.....=|++||+
T Consensus 92 V~Kia~~--f-~A~ly~P~~dlsveeK~~l~~~~~~-~~~n~HeRDALAAA 138 (138)
T PF04312_consen 92 VKKIARS--F-NAVLYTPERDLSVEEKQELAREYSE-RYENDHERDALAAA 138 (138)
T ss_pred HHHHHHH--h-CCcccCCCCcCCHHHHHHHHHhhCC-CCCCchHHhHhhcC
Confidence 4455542 3 4445555899999988888776664 22233456888885
No 12
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=97.02 E-value=0.012 Score=46.47 Aligned_cols=95 Identities=14% Similarity=0.214 Sum_probs=46.3
Q ss_pred CeEEEEecCCCe----EEEEEecCCCceeccceeeeC--CCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHH
Q 030251 26 GRFLGLDVGDKY----VGLSISDPKNKIASPLSVLLR--KKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQ 99 (180)
Q Consensus 26 ~~iLalD~G~kr----iGvAvsd~~~~~a~Pl~~i~~--~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~ 99 (180)
.++|||-+|.-+ +-.|+-|..|.+.--+..... .........+.|.++|.+++|+.|+|| | .+..+.+
T Consensus 5 ~rVla~~~g~g~~~~~~~~v~ld~~G~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~kP~vI~v~-----g-~~~~s~~ 78 (150)
T PF14639_consen 5 PRVLALSWGSGDGDDAVFCVVLDENGEVLDHLKLVYNERDRERKEEDMERLKKFIEKHKPDVIAVG-----G-NSRESRK 78 (150)
T ss_dssp --EEEEE-TT--TTS-EEEEEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--------SSTHHHH
T ss_pred CEEEEEEcCCCCCCCCEEEEEECCCCcEEEEEEEcCCccchHHHHHHHHHHHHHHHHcCCeEEEEc-----C-CChhHHH
Confidence 589999999766 556788888877653333111 111223446899999999999999996 3 2334444
Q ss_pred HHHHHHHHHhc----cCCCCCcEEEeccccc
Q 030251 100 VKLFIDDLSAT----KKLEDMKYAYWNEGFT 126 (180)
Q Consensus 100 v~~F~~~L~~~----~~~~~lpV~~~DEr~T 126 (180)
..++.+.+-+. ...+.++|+++||...
T Consensus 79 l~~~v~~~v~~~~~~~~~~~i~V~~v~~~~A 109 (150)
T PF14639_consen 79 LYDDVRDIVEELDEDEQMPPIPVVIVDDEVA 109 (150)
T ss_dssp HHHHHHHHHHHTTB-TTS-B--EEE---TTH
T ss_pred HHHHHHHHHHHhhhcccCCCceEEEECcHHH
Confidence 43333333221 1235799999999764
No 13
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=96.88 E-value=0.0017 Score=51.85 Aligned_cols=100 Identities=15% Similarity=0.223 Sum_probs=64.7
Q ss_pred EEEecCCCeEEEEEecCCCceeccc--eeeeCCCCC-----hhhHHHHHHHHHHhhCCCEEEEecccC--CCCCchHHHH
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPL--SVLLRKKNT-----IDLMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQ 99 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl--~~i~~~~~~-----~~~~~~~L~~li~e~~i~~iVVGlP~~--dG~~s~~~~~ 99 (180)
||||+|..+||.+|-+..+.-.+++ ++|...+.. ...+.+.|.+++++|+|+.+.|=-.+- |-+..-..-+
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 6899999999999999887766555 466654221 124568889999999999999998876 3333333333
Q ss_pred HHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 100 VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 100 v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
+|-.+-.... + .++||.. ||..+.+...-
T Consensus 81 ARGv~~la~~--~-~~l~v~e----Y~p~~VKkavv 109 (160)
T COG0817 81 ARGVALLAAA--R-RGLPVFE----YTPNQVKKAVV 109 (160)
T ss_pred HHHHHHHHHH--H-cCCChhh----ccHHHHHHHhh
Confidence 3333332222 1 2788764 45555555443
No 14
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=96.72 E-value=0.015 Score=54.98 Aligned_cols=109 Identities=15% Similarity=0.160 Sum_probs=78.3
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 105 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~ 105 (180)
.-|.|||+|. .+|+|+-|-+|.+. .+..+++.+ ..++-++|.+|+-=.||-= |=++-+ .|++
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 58999999988643 344444432 5889999999977666655 666665 5677
Q ss_pred HHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHHHHHH
Q 030251 106 DLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGI 156 (180)
Q Consensus 106 ~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iI 156 (180)
+|+.. | +-+.+.=|+++|+.+=+..++..+++-. ....=|++||++-
T Consensus 306 KiAas--f-~A~ly~P~~dLsveEK~~~~r~~~~~~~-ddH~RDALAAA~k 352 (652)
T COG2433 306 KIAAS--F-NAVLYTPDRDLSVEEKQEALRTLKISVS-DDHERDALAAAYK 352 (652)
T ss_pred HHHHH--c-CCcccCCcccCCHHHHHHHHhhcCCCCC-CchHHHHHHHHHH
Confidence 77764 4 5566666899999999887776665532 2345699999864
No 15
>PRK05082 N-acetylmannosamine kinase; Provisional
Probab=95.14 E-value=0.15 Score=43.19 Aligned_cols=102 Identities=12% Similarity=0.140 Sum_probs=67.1
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhh--CCCEEEEecccC-C-CCC---ch---
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEF--NLEGFIVGYPFN-R-QQN---AA--- 95 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~--~i~~iVVGlP~~-d-G~~---s~--- 95 (180)
.++|+|+|..++-+++.|..+.+-.. ..++... ...+.+.+.|.+++++. ++.+|.||.|=. + +.. ++
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 58999999999999999987655431 2333321 23344567788877764 678999999844 3 211 11
Q ss_pred -HHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHH
Q 030251 96 -DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELL 133 (180)
Q Consensus 96 -~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~ 133 (180)
.... ..+.+.|++. + ++||++.++-.+...|+..
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=94.91 E-value=0.15 Score=43.73 Aligned_cols=109 Identities=14% Similarity=0.149 Sum_probs=68.9
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCC-----hhhHHHHHHHHHHhh----CCCEEEEecccC-CCC
Q 030251 23 SKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNT-----IDLMAEDFRSLISEF----NLEGFIVGYPFN-RQQ 92 (180)
Q Consensus 23 ~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~-----~~~~~~~L~~li~e~----~i~~iVVGlP~~-dG~ 92 (180)
+.++.++|||+|..+|=+|+.|..+.+-.- ..++....+ .+.+.+.+++++.++ .+.+|.++.|.. +..
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 457899999999999999999988765321 222222211 123345555555543 466677777766 432
Q ss_pred C----chHHHH--HHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 93 N----AADAVQ--VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 93 ~----s~~~~~--v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
. .+.... --.|.+.|++. + ++||...++-..-.-|+..+-
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 12478889984 5 799999999888888877754
No 17
>PRK09557 fructokinase; Reviewed
Probab=94.81 E-value=0.16 Score=43.31 Aligned_cols=103 Identities=17% Similarity=0.081 Sum_probs=64.7
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh-----CCCEEEEecccC----CCCCc---
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFN----RQQNA--- 94 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~i~~iVVGlP~~----dG~~s--- 94 (180)
++||+|+|..++-+++.|..+.+-.- ..++....+.+.+++.|.+++++. .+.+|.||.|=. +|...
T Consensus 1 ~~lgidig~t~~~~~l~d~~g~i~~~-~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgi~~pG~vd~~~g~i~~~~ 79 (301)
T PRK09557 1 MRIGIDLGGTKIEVIALDDAGEELFR-KRLPTPRDDYQQTIEAIATLVDMAEQATGQRGTVGVGIPGSISPYTGLVKNAN 79 (301)
T ss_pred CEEEEEECCCcEEEEEECCCCCEEEE-EEecCCCCCHHHHHHHHHHHHHHHHhhcCCceEEEecCcccCcCCCCeEEecC
Confidence 37999999999999999977654322 333333223344567777776664 357799999732 23211
Q ss_pred -hHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHh
Q 030251 95 -ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 134 (180)
Q Consensus 95 -~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 134 (180)
.+. .--.+.+.|++. + ++||++.+.--....|+.++
T Consensus 80 ~~~~-~~~~l~~~l~~~--~-~~pv~~~NDa~aaA~aE~~~ 116 (301)
T PRK09557 80 STWL-NGQPLDKDLSAR--L-NREVRLANDANCLAVSEAVD 116 (301)
T ss_pred Cccc-cCCCHHHHHHHH--H-CCCEEEccchhHHHHHHHHh
Confidence 110 112355667763 5 78999888877777776554
No 18
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=94.70 E-value=0.1 Score=45.34 Aligned_cols=99 Identities=21% Similarity=0.230 Sum_probs=62.5
Q ss_pred CeEEEEecCCCeEEEEEecCCCc----eeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNK----IASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQV 100 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~----~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v 100 (180)
+++||||+|...+-+|.+|.... +-.|+ +++ .+.+-+.|+++..+++++.+=|=+--. -.-....++-+
T Consensus 3 ~kilGiDIGGAntk~a~~DG~~~~~d~~YlPM----Wk~--k~rL~~~Lkei~~k~~~~~vgvvMTaELaD~f~tk~eGV 76 (330)
T COG1548 3 MKILGIDIGGANTKIASSDGDNYKIDHIYLPM----WKK--KDRLEETLKEIVHKDNVDYVGVVMTAELADAFKTKAEGV 76 (330)
T ss_pred ceEEEeeccCccchhhhccCCeeeeeEEEecc----ccc--hhHHHHHHHHHhccCCcceeEEEeeHHHHHHhhhHHhHH
Confidence 68999999999999999987642 22331 122 234567788888777777443332222 12233345566
Q ss_pred HHHHHHHHhccCCCCCcEEEecc--cccHHHHHHH
Q 030251 101 KLFIDDLSATKKLEDMKYAYWNE--GFTSKGVELL 133 (180)
Q Consensus 101 ~~F~~~L~~~~~~~~lpV~~~DE--r~TT~~A~~~ 133 (180)
+..++...+. | +.||+++|= ++-|.+|.+.
T Consensus 77 e~Ii~~v~~A--f-~~pv~~v~~~G~~~ssEa~~~ 108 (330)
T COG1548 77 EDIIDTVEKA--F-NCPVYVVDVNGNFLSSEALKN 108 (330)
T ss_pred HHHHHHHHHh--c-CCceEEEeccCcCcChhHhcC
Confidence 7777888874 6 889988883 3334466553
No 19
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional
Probab=93.58 E-value=0.41 Score=40.81 Aligned_cols=103 Identities=19% Similarity=0.173 Sum_probs=64.6
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhC-----CCEEEEecccC-C---CCCch--
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN-----LEGFIVGYPFN-R---QQNAA-- 95 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~-----i~~iVVGlP~~-d---G~~s~-- 95 (180)
+++|+|+|..+|-+++.|..+.+... ..++....+.+.+.+.|.+++++.. +.+|-||.|=. | |....
T Consensus 1 ~~lgidig~t~i~~~l~d~~g~i~~~-~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~igia~pG~vd~~~g~~~~~~ 79 (303)
T PRK13310 1 MYYGFDIGGTKIELGVFNEKLELQWE-ERVPTPRDSYDAFLDAVCELVAEADQRFGCKGSVGIGIPGMPETEDGTLYAAN 79 (303)
T ss_pred CeEEEEeCCCcEEEEEECCCCcEEEE-EEecCCCcCHHHHHHHHHHHHHHHHhhcCCcceEEEeCCCcccCCCCEEeccC
Confidence 36999999999999999977644432 2333322334455677777776532 34788998844 3 32111
Q ss_pred --HHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHh
Q 030251 96 --DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 134 (180)
Q Consensus 96 --~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 134 (180)
.... -.+.+.|++. + ++||++.+.-..-..|+.++
T Consensus 80 ~~~w~~-~~l~~~l~~~--~-~~pV~ieNDa~aaalaE~~~ 116 (303)
T PRK13310 80 VPAASG-KPLRADLSAR--L-GRDVRLDNDANCFALSEAWD 116 (303)
T ss_pred cccccC-CcHHHHHHHH--H-CCCeEEeccHhHHHHHHhhh
Confidence 0111 2466778763 5 89999988877766666443
No 20
>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=93.57 E-value=2.9 Score=32.88 Aligned_cols=119 Identities=13% Similarity=0.151 Sum_probs=65.7
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCC--CCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRK--KNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLF 103 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~--~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F 103 (180)
+.++|||+|.+..|..+-+..+.. +..+.-. +-..+..-.-+..+++ ++++.|+|=- +...++ ..++..|
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 458999999999999999975533 2222211 1112222233344444 8999999973 223333 3345567
Q ss_pred HHHHHhccCCCCCcEEEecccc-----------cHHHHHHHhccCCCCCCCCC-CCCcHHHHHH
Q 030251 104 IDDLSATKKLEDMKYAYWNEGF-----------TSKGVELLLNPLDLHPVEYK-TILDKFAAVG 155 (180)
Q Consensus 104 ~~~L~~~~~~~~lpV~~~DEr~-----------TT~~A~~~l~~~g~~~~~~k-~~iD~~AA~i 155 (180)
.+..-. .++..|..+|=.+ |-..++.++.+.+...--.+ +.+|++|=++
T Consensus 73 I~~~f~---~~~~kv~~v~p~~~~~~Y~~RKk~SVe~~~~~~~~~~~~~~i~~~kK~DDlADa~ 133 (143)
T PF04848_consen 73 IHGYFY---IKNTKVICVSPKMKGWSYRERKKRSVEVFKNWIKEFGIDDFIPKSKKKDDLADAF 133 (143)
T ss_pred HHHHhc---cCCceEEEECcccccCCHHHHHHHHHHHHHHHHHhCCchhhchhhccchHHHHHH
Confidence 665543 2366788887543 33444445554443221112 3557776554
No 21
>PRK13311 N-acetyl-D-glucosamine kinase; Provisional
Probab=92.91 E-value=0.78 Score=38.32 Aligned_cols=103 Identities=17% Similarity=0.129 Sum_probs=66.5
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhC-----CCEEEEeccc--C-C-CCCc---
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN-----LEGFIVGYPF--N-R-QQNA--- 94 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~-----i~~iVVGlP~--~-d-G~~s--- 94 (180)
+++|+|+|..++-+++.|..+.+-. ...++....+.+.+++.+.+++++.. +.+|-||.|= + + |...
T Consensus 1 ~~lgidiggt~i~~~l~d~~g~i~~-~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgv~~pG~vd~~~g~i~~~~ 79 (256)
T PRK13311 1 MYYGFDMGGTKIELGVFDENLQRIW-HKRVPTPREDYPQLLQILRDLTEEADTYCGVQGSVGIGIPGLPNADDGTVFTAN 79 (256)
T ss_pred CEEEEEECCCcEEEEEECCCCCEEE-EEEecCCCcCHHHHHHHHHHHHHHHHhhcCCCceEEEEecCcEECCCCEEEccC
Confidence 3799999999999999997764432 23333332333456777777776542 3478888884 2 2 3211
Q ss_pred -hHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHh
Q 030251 95 -ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 134 (180)
Q Consensus 95 -~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 134 (180)
+.... ..+++.|+++ + ++||.+-++-.+...|+.+.
T Consensus 80 ~~~w~~-~~l~~~l~~~--~-~~pV~leNDanaaAlaE~~~ 116 (256)
T PRK13311 80 VPSAMG-QPLQADLSRL--I-QREVRIDNDANCFALSEAWD 116 (256)
T ss_pred CCcccC-CChHHHHHHH--H-CCCEEEEchhhHHHHHHHHh
Confidence 11111 3677778773 5 78999998888877777654
No 22
>PRK13321 pantothenate kinase; Reviewed
Probab=92.26 E-value=2 Score=36.14 Aligned_cols=57 Identities=23% Similarity=0.286 Sum_probs=39.9
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhh-----CCCEEEEe
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEF-----NLEGFIVG 85 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~-----~i~~iVVG 85 (180)
++|+||+|..+|=+|+-|......+ ..++... ...+.+...+.++++++ +++.++|+
T Consensus 1 MiL~IDIGnT~ik~gl~~~~~i~~~--~~~~T~~~~~~~~~~~~l~~l~~~~~~~~~~i~~i~vs 63 (256)
T PRK13321 1 MLLLIDVGNTNIKLGVFDGDRLLRS--FRLPTDKSRTSDELGILLLSLFRHAGLDPEDIRAVVIS 63 (256)
T ss_pred CEEEEEECCCeEEEEEEECCEEEEE--EEEecCCCCCHHHHHHHHHHHHHHcCCChhhCCeEEEE
Confidence 3799999999999999985432222 2333322 22345678888888876 48999999
No 23
>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=92.19 E-value=1 Score=40.22 Aligned_cols=114 Identities=13% Similarity=0.172 Sum_probs=69.9
Q ss_pred EEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh-CCCEEEE----ecccC-CCCCchH-------
Q 030251 30 GLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIV----GYPFN-RQQNAAD------- 96 (180)
Q Consensus 30 alD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~i~~iVV----GlP~~-dG~~s~~------- 96 (180)
|+|+||+-+-+++.|..+.+.. ...+++.....+ -..|.+.++++ +++.|+. |+|+. -...++.
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 6899999999999998666654 344544332222 24567777777 9998886 67776 2221111
Q ss_pred -----HHH----HHHHHHHHHhccCCCCCcEEEec--ccccHHHHHHHhccCCCCCCCCCCCCcHHHHHHH
Q 030251 97 -----AVQ----VKLFIDDLSATKKLEDMKYAYWN--EGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGI 156 (180)
Q Consensus 97 -----~~~----v~~F~~~L~~~~~~~~lpV~~~D--Er~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iI 156 (180)
... .++|.+.+++. ++|+++.. -.+.|+-+++-+.. -.-+.-|++|-+..
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 111 46677777652 67877776 47777777665431 11234467776654
No 24
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=91.71 E-value=0.76 Score=38.27 Aligned_cols=94 Identities=15% Similarity=0.170 Sum_probs=60.0
Q ss_pred CeEEEEecCCCeEEEEEecC--CCceeccceeeeCCCCChhhHHHHHHHHHHhh-----CCCEEEEecccCCCCCchHH-
Q 030251 26 GRFLGLDVGDKYVGLSISDP--KNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFNRQQNAADA- 97 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~--~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~i~~iVVGlP~~dG~~s~~~- 97 (180)
+++|+||--++.+++|+-+. ...++.-.... +......+...+.+++.+. +++.|+|| .|=-|-..
T Consensus 1 m~iLaiDTs~~~~s~ai~~~~~~~vl~~~~~~~--~r~hse~l~~~i~~ll~~~~~~~~dld~iav~----~GPGSFTGl 74 (220)
T COG1214 1 MKILAIDTSTSALSVALYLADDGKVLAEHTEKL--KRNHAERLMPMIDELLKEAGLSLQDLDAIAVA----KGPGSFTGL 74 (220)
T ss_pred CcEEEEEcChhhhhhheeecCCCcEEEEEEEec--cccHHHHHHHHHHHHHHHcCCCHHHCCEEEEc----cCCCcccch
Confidence 47999999999999998876 44445532222 2222335567777887776 68899999 44322222
Q ss_pred HHHHHHHHHHHhccCCCCCcEEEecccccHHHHHH
Q 030251 98 VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 132 (180)
Q Consensus 98 ~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 132 (180)
+---.||+-|.-. . ++|++=+ ||.++-.
T Consensus 75 RIG~~~AkgLA~~--l-~iplvgv----ssL~~~A 102 (220)
T COG1214 75 RIGVAFAKGLALA--L-NIPLVGV----SSLEALA 102 (220)
T ss_pred hhHHHHHHHHHHH--c-CCCEEEe----CHHHHHH
Confidence 2336788888853 2 7787754 4555443
No 25
>PRK12408 glucokinase; Provisional
Probab=91.18 E-value=0.58 Score=41.03 Aligned_cols=98 Identities=13% Similarity=0.125 Sum_probs=57.5
Q ss_pred ccCCCCeEEEEecCCCeEEEEEecCCCcee-----ccceeeeCCCCChhhHHHHHHHHHHh-hCCCEEEEeccc--C-CC
Q 030251 21 KVSKRGRFLGLDVGDKYVGLSISDPKNKIA-----SPLSVLLRKKNTIDLMAEDFRSLISE-FNLEGFIVGYPF--N-RQ 91 (180)
Q Consensus 21 ~~~~~~~iLalD~G~kriGvAvsd~~~~~a-----~Pl~~i~~~~~~~~~~~~~L~~li~e-~~i~~iVVGlP~--~-dG 91 (180)
+++++-++|++|+|..+|=+|+.|..+.+. .-....+... .+.+.+.+.+++.+ .++..+.||.|= . +|
T Consensus 11 ~~~~~~~~L~~DIGGT~i~~al~d~~g~~~~~~~~~~~~~~~t~~--~~~~~~~i~~~~~~~~~~~~igIg~pG~~~~~g 88 (336)
T PRK12408 11 AVPRPESFVAADVGGTHVRVALVCASPDAAKPVELLDYRTYRCAD--YPSLAAILADFLAECAPVRRGVIASAGYALDDG 88 (336)
T ss_pred cCcccccEEEEEcChhhhheeEEeccCCccccccccceeEecCCC--ccCHHHHHHHHHhcCCCcCEEEEEecCCceECC
Confidence 346777899999999999999998655421 1112333221 12334556666653 358899999974 3 55
Q ss_pred CCchHHHHHHHHHHHHHhccCCCCCc-EEEecc
Q 030251 92 QNAADAVQVKLFIDDLSATKKLEDMK-YAYWNE 123 (180)
Q Consensus 92 ~~s~~~~~v~~F~~~L~~~~~~~~lp-V~~~DE 123 (180)
......-.-..+.+.|++. + ++| |.+.+.
T Consensus 89 ~v~~~nl~w~~~~~~l~~~--~-~~~~V~l~ND 118 (336)
T PRK12408 89 RVITANLPWTLSPEQIRAQ--L-GLQAVHLVND 118 (336)
T ss_pred EEEecCCCCccCHHHHHHH--c-CCCeEEEeec
Confidence 4221000012355777763 4 775 887654
No 26
>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=91.01 E-value=1.8 Score=35.23 Aligned_cols=86 Identities=14% Similarity=0.158 Sum_probs=56.0
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh-----CCCEEEEecccCCCCCchH-HHHHH
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGYPFNRQQNAAD-AVQVK 101 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~i~~iVVGlP~~dG~~s~~-~~~v~ 101 (180)
+|+||--+..++||+.+....++.-. ........+.+...|++++++. +++.|+|| .|=-|-. .+-.-
T Consensus 1 iLaidTs~~~~sval~~~~~~~~~~~--~~~~~~h~~~l~~~i~~~l~~~~~~~~~i~~iav~----~GPGSfTGlRig~ 74 (202)
T TIGR03725 1 ILAIDTSTEALSVALLDDGEILAERS--EEAGRNHSEILLPMIEELLAEAGLSLQDLDAIAVG----VGPGSFTGLRIGL 74 (202)
T ss_pred CEEEECCCcceEEEEEECCEEEEEEe--ehhhHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEe----cCCChHHhHHHHH
Confidence 58999999999999998654444321 1111122335567777777774 68899998 4433322 34447
Q ss_pred HHHHHHHhccCCCCCcEEEec
Q 030251 102 LFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 102 ~F~~~L~~~~~~~~lpV~~~D 122 (180)
.+++-|... . ++|++-++
T Consensus 75 ~~akgla~~--~-~~p~~~vs 92 (202)
T TIGR03725 75 ATAKGLALA--L-GIPLVGVS 92 (202)
T ss_pred HHHHHHHHH--h-CCCEEecC
Confidence 889999863 3 78877653
No 27
>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=90.46 E-value=1.3 Score=37.80 Aligned_cols=100 Identities=17% Similarity=0.199 Sum_probs=61.4
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh---------hCCCEEEEecccC-C---CCC--
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE---------FNLEGFIVGYPFN-R---QQN-- 93 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e---------~~i~~iVVGlP~~-d---G~~-- 93 (180)
+|+|+|..++-+++.|..+.+-.- ...+.. ...+.+++.|.+++++ .++.+|.||.|=. | |..
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 589999999999999977654321 233322 2223345555555444 2578899999843 3 321
Q ss_pred c--hHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHh
Q 030251 94 A--ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 134 (180)
Q Consensus 94 s--~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 134 (180)
+ ..... ..+.+.|++. + ++||++.+.-.+..-|+.++
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 0 00111 1366677763 5 79999998888877776654
No 28
>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=90.02 E-value=0.5 Score=36.78 Aligned_cols=100 Identities=12% Similarity=0.208 Sum_probs=64.9
Q ss_pred EEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh----hCCCEEEEecccC-C-CC------CchHH
Q 030251 30 GLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE----FNLEGFIVGYPFN-R-QQ------NAADA 97 (180)
Q Consensus 30 alD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e----~~i~~iVVGlP~~-d-G~------~s~~~ 97 (180)
|||+|..++=+++.|..+.+..- ..++.. .+.+.+++.|.+++++ +...+|-|+.|=. + ++ .....
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 445543 3333445555555554 4444899998854 2 22 12222
Q ss_pred HHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 98 VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 98 ~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
.. ..+.+.|++. + ++||.+.+.--....|+..+.
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 3577788874 5 799999998777777766643
No 29
>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=89.88 E-value=0.95 Score=31.22 Aligned_cols=60 Identities=12% Similarity=0.083 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCC---ch-HHHH-----HHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQN---AA-DAVQ-----VKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~---s~-~~~~-----v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
...|.+...+ .++.||||-..+ .+.. +. ..+. -..|.+.|+-.....|++|+.+||.+||
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 3455555555 679999997653 2221 11 1111 1334444543222249999999999997
No 30
>PRK13318 pantothenate kinase; Reviewed
Probab=89.66 E-value=1.7 Score=36.63 Aligned_cols=58 Identities=17% Similarity=0.269 Sum_probs=38.8
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhhC-----CCEEEEec
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEFN-----LEGFIVGY 86 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~-----i~~iVVGl 86 (180)
++|+||+|..+|=+|+.|. +.+... ..++... ...+.+.+.+.++++.++ +++|+||-
T Consensus 1 MiL~IDIGnT~iK~al~d~-g~i~~~-~~~~t~~~~~~~~~~~~l~~l~~~~~~~~~~i~~I~iss 64 (258)
T PRK13318 1 MLLAIDVGNTNTVFGLYEG-GKLVAH-WRISTDSRRTADEYGVWLKQLLGLSGLDPEDITGIIISS 64 (258)
T ss_pred CEEEEEECCCcEEEEEEEC-CEEEEE-EEEeCCCCCCHHHHHHHHHHHHHHcCCCcccCceEEEEE
Confidence 3799999999999999984 433321 2333321 122345677888887664 78999994
No 31
>PRK00292 glk glucokinase; Provisional
Probab=89.64 E-value=1.6 Score=37.51 Aligned_cols=95 Identities=9% Similarity=0.043 Sum_probs=57.7
Q ss_pred CeEEEEecCCCeEEEEEecC-CCc-eeccceeeeCCCCChhhHHHHHHHHHHh---hCCCEEEEecccC-CC-CC----c
Q 030251 26 GRFLGLDVGDKYVGLSISDP-KNK-IASPLSVLLRKKNTIDLMAEDFRSLISE---FNLEGFIVGYPFN-RQ-QN----A 94 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~-~~~-~a~Pl~~i~~~~~~~~~~~~~L~~li~e---~~i~~iVVGlP~~-dG-~~----s 94 (180)
..+||+|+|..+|=+++.|. .+. +.+ ..++... .+.+.+.|.+++.+ .++.+|.||.|=- |. +. .
T Consensus 2 ~~~lgiDIGgT~i~~~l~~~~~~~~~~~--~~~~~~~--~~~~~~~l~~~l~~~~~~~~~gigIg~pG~vd~~~i~~~n~ 77 (316)
T PRK00292 2 KPALVGDIGGTNARFALCDWANGEIEQI--KTYATAD--YPSLEDAIRAYLADEHGVQVRSACFAIAGPVDGDEVRMTNH 77 (316)
T ss_pred ceEEEEEcCccceEEEEEecCCCceeee--EEEecCC--CCCHHHHHHHHHHhccCCCCceEEEEEeCcccCCEEEecCC
Confidence 35899999999999999983 443 222 3333322 12345677777765 3588999999854 32 21 1
Q ss_pred hHHHHHHHHHHHHHhccCCCCCc-EEEecccccHHHHH
Q 030251 95 ADAVQVKLFIDDLSATKKLEDMK-YAYWNEGFTSKGVE 131 (180)
Q Consensus 95 ~~~~~v~~F~~~L~~~~~~~~lp-V~~~DEr~TT~~A~ 131 (180)
.+. ...+.|++. + ++| |++.+.--.-.-|+
T Consensus 78 ~w~----~~~~~l~~~--~-~~p~v~l~ND~~aaalgE 108 (316)
T PRK00292 78 HWA----FSIAAMKQE--L-GLDHLLLINDFTAQALAI 108 (316)
T ss_pred Ccc----cCHHHHHHH--h-CCCeEEEEecHHHHHccc
Confidence 111 124667763 4 786 88877654444443
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=89.61 E-value=1.4 Score=33.19 Aligned_cols=85 Identities=13% Similarity=0.088 Sum_probs=54.1
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHH
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDL 107 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L 107 (180)
++|||+|....=+++.++.+....+ ..+..... . +.++.+.+.++. .++||+=- -|..+. .++..|
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 5899999999999999998844333 44543322 2 577777777775 56666311 243342 345556
Q ss_pred HhccCCCCCcEEEecccccHHHH
Q 030251 108 SATKKLEDMKYAYWNEGFTSKGV 130 (180)
Q Consensus 108 ~~~~~~~~lpV~~~DEr~TT~~A 130 (180)
.+. +++|+.++=+......
T Consensus 67 ~~~----g~~v~~vnp~~~~~~~ 85 (144)
T PF01548_consen 67 QDA----GIEVVVVNPLQVKRFR 85 (144)
T ss_pred ecc----cccccccccccccccc
Confidence 652 7889998766555433
No 33
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=88.57 E-value=12 Score=31.63 Aligned_cols=107 Identities=16% Similarity=0.224 Sum_probs=60.3
Q ss_pred hHHHHHHhhh--ccCCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCC--------CChhhHHHHHHHHHH---hh
Q 030251 11 LRLFEQMLKR--KVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK--------NTIDLMAEDFRSLIS---EF 77 (180)
Q Consensus 11 ~~~~~~~~~~--~~~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~--------~~~~~~~~~L~~li~---e~ 77 (180)
++.|-+.+.+ .++....++|||+|+.+|=+.+.+.... ++....... .+.+....-|+++++ ++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~iDiGSssi~~vv~~~~~~---~~~~~~~~~~~vr~G~i~di~~a~~~i~~~~~~ae~~ 83 (267)
T PRK15080 7 LQKFAALINKTPVATESPLKVGVDLGTANIVLAVLDEDGQ---PVAGALEWADVVRDGIVVDFIGAVTIVRRLKATLEEK 83 (267)
T ss_pred HHHHHHHhcCCCCCCCCCEEEEEEccCceEEEEEEcCCCC---EEEEEeccccccCCCEEeeHHHHHHHHHHHHHHHHHH
Confidence 4556666554 2345678999999999999888765442 233332211 112222333443333 33
Q ss_pred ---CCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEE-EecccccHHHH
Q 030251 78 ---NLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYA-YWNEGFTSKGV 130 (180)
Q Consensus 78 ---~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~-~~DEr~TT~~A 130 (180)
.+..+++..|-+ +-.. -+.+.+-++.. ++++. +++|.+....+
T Consensus 84 ~g~~i~~v~~~vp~~~~~~~------~~~~~~~~~~a----Gl~~~~ii~e~~A~a~~ 131 (267)
T PRK15080 84 LGRELTHAATAIPPGTSEGD------PRAIINVVESA----GLEVTHVLDEPTAAAAV 131 (267)
T ss_pred hCCCcCeEEEEeCCCCCchh------HHHHHHHHHHc----CCceEEEechHHHHHHH
Confidence 478899999987 3211 12344555542 66766 77777654443
No 34
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=87.28 E-value=1.8 Score=41.16 Aligned_cols=66 Identities=12% Similarity=0.184 Sum_probs=47.3
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh---CCCEEEEecccC-CC
Q 030251 23 SKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF---NLEGFIVGYPFN-RQ 91 (180)
Q Consensus 23 ~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~---~i~~iVVGlP~~-dG 91 (180)
...+++||+|+|.-+|=+|+.|..+.+.. ...++.... +.+.+.+.+++.+. .+.++.||.|=- |+
T Consensus 15 ~~~~~~L~iDIGGT~ir~al~~~~g~i~~-~~~~~t~~~--~~~~~~i~~~l~~~~~~~~~~igig~pGpVd~ 84 (638)
T PRK14101 15 HADGPRLLADVGGTNARFALETGPGEITQ-IRVYPGADY--PTLTDAIRKYLKDVKIGRVNHAAIAIANPVDG 84 (638)
T ss_pred CCCCCEEEEEcCchhheeeeecCCCcccc-eeEEecCCC--CCHHHHHHHHHHhcCCCCcceEEEEEecCccC
Confidence 34578999999999999999987765533 245554432 34567777777765 488999999866 54
No 35
>PF14239 RRXRR: RRXRR protein
Probab=85.93 E-value=0.71 Score=37.59 Aligned_cols=23 Identities=30% Similarity=0.517 Sum_probs=19.8
Q ss_pred CCeEEEEecCCCeEEEEEecCCC
Q 030251 25 RGRFLGLDVGDKYVGLSISDPKN 47 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~~ 47 (180)
..-.|+||+|.+.+|+|+.+...
T Consensus 50 qpi~lgiDpGsk~tGiav~~~~~ 72 (176)
T PF14239_consen 50 QPIRLGIDPGSKTTGIAVVSEKK 72 (176)
T ss_pred cCEEEEECCCCCeEEEEEEeCCE
Confidence 35679999999999999998763
No 36
>PRK09698 D-allose kinase; Provisional
Probab=85.14 E-value=4.9 Score=34.07 Aligned_cols=103 Identities=15% Similarity=0.260 Sum_probs=61.6
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCC-C---hhhHHHHHHHHHHhh--CCCEEEEecccC-C---CC--C
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKN-T---IDLMAEDFRSLISEF--NLEGFIVGYPFN-R---QQ--N 93 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~-~---~~~~~~~L~~li~e~--~i~~iVVGlP~~-d---G~--~ 93 (180)
..++|+|+|..++-+++.|..+.+-. ...++.... . .+.+.+.+.+++.+. ++.+|-||.|=. | |. .
T Consensus 4 ~~~lgidig~t~i~~~l~d~~g~i~~-~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~i~gigia~pG~vd~~~g~i~~ 82 (302)
T PRK09698 4 NVVLGIDMGGTHIRFCLVDAEGEILH-CEKKRTAEVIAPDLVSGLGEMIDEYLRRFNARCHGIVMGFPALVSKDRRTVIS 82 (302)
T ss_pred cEEEEEEcCCcEEEEEEEcCCCCEEE-EEEeCCccccchHHHHHHHHHHHHHHHHcCCCeeEEEEeCCcceeCCCCEEEe
Confidence 67899999999999999997765432 122322211 1 233445556666654 578999999843 3 21 0
Q ss_pred chHH----HHHHHHHHHHHhccCCCCCcEEEecccccHHHHHH
Q 030251 94 AADA----VQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 132 (180)
Q Consensus 94 s~~~----~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 132 (180)
++.. -.-..+.+.|++. + ++||++.+.--....|+.
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 1112466777763 4 899998887665544443
No 37
>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=77.79 E-value=2 Score=42.43 Aligned_cols=23 Identities=39% Similarity=0.622 Sum_probs=20.2
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~ 49 (180)
.+||||.|+..||.||.|.....
T Consensus 2 y~LGLDiGt~SvGWAVv~~d~~~ 24 (805)
T TIGR01865 2 YILGLDIGIASVGWAIVEDDYKV 24 (805)
T ss_pred ceeEEeecccceeEEEEeccccc
Confidence 58999999999999999977543
No 38
>PRK09472 ftsA cell division protein FtsA; Reviewed
Probab=76.63 E-value=13 Score=33.48 Aligned_cols=63 Identities=13% Similarity=0.255 Sum_probs=40.4
Q ss_pred CCeEEEEecCCCeEEEEEec--CCC-ceeccceeeeCCC------CChhhHHHHHHHHHHh------hCCCEEEEecc
Q 030251 25 RGRFLGLDVGDKYVGLSISD--PKN-KIASPLSVLLRKK------NTIDLMAEDFRSLISE------FNLEGFIVGYP 87 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd--~~~-~~a~Pl~~i~~~~------~~~~~~~~~L~~li~e------~~i~~iVVGlP 87 (180)
...+.|||+|+.+|=+.+++ +.+ .-.......+... .+.+.+.+.|++.+++ .+++.+++|.|
T Consensus 7 ~~~i~~lDIGsskv~~vv~~~~~~~~~~i~g~~~~~s~gi~~G~I~d~~~~~~aI~~av~~ae~~~g~~i~~v~v~i~ 84 (420)
T PRK09472 7 RKLVVGLEIGTAKVAALVGEVLPDGMVNIIGVGSCPSRGMDKGGVNDLESVVKCVQRAIDQAELMADCQISSVYLALS 84 (420)
T ss_pred CCEEEEEEcccceEEEEEEEEcCCCCEEEEEEEEccCCCccCCEEEcHHHHHHHHHHHHHHHHHHhCCcccEEEEEec
Confidence 34688999999999887876 222 1122222223211 1234556778888777 57999999988
No 39
>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=76.56 E-value=14 Score=32.23 Aligned_cols=88 Identities=13% Similarity=0.186 Sum_probs=53.9
Q ss_pred EEEEecCCCeEEEEEecCCC-ceecccee-----------eeC--CCCChhhHHHHHHHHHHh-----hCCCEEEEeccc
Q 030251 28 FLGLDVGDKYVGLSISDPKN-KIASPLSV-----------LLR--KKNTIDLMAEDFRSLISE-----FNLEGFIVGYPF 88 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~-~~a~Pl~~-----------i~~--~~~~~~~~~~~L~~li~e-----~~i~~iVVGlP~ 88 (180)
|||||--...+++|+.|... .++.-..+ .+. .....+.+...|.+++++ .+++.|.|+
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 011122345666666665 468999998
Q ss_pred CCCCCchHHH-HHHHHHHHHHhccCCCCCcEEEec
Q 030251 89 NRQQNAADAV-QVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 89 ~dG~~s~~~~-~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
.|=-+-..- ....+|+-|... + ++|++.++
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 443333333 337888888863 3 78988884
No 40
>PRK09605 bifunctional UGMP family protein/serine/threonine protein kinase; Validated
Probab=74.89 E-value=15 Score=33.99 Aligned_cols=93 Identities=11% Similarity=0.059 Sum_probs=55.7
Q ss_pred CeEEEEecCCCeEEEEEecCCC-ceeccceeeeCC----------CCChhhHHHHHHHHHHh-----hCCCEEEEecccC
Q 030251 26 GRFLGLDVGDKYVGLSISDPKN-KIASPLSVLLRK----------KNTIDLMAEDFRSLISE-----FNLEGFIVGYPFN 89 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~-~~a~Pl~~i~~~----------~~~~~~~~~~L~~li~e-----~~i~~iVVGlP~~ 89 (180)
|.|||||-=..-+.+|+.+..+ .++.-..++... ......+...+.+++++ .+++.|.|+
T Consensus 1 m~il~iets~~~~s~a~~~~~~~~~~~~~~~~~~~~gg~~p~~~~~~H~~~l~~~i~~~l~~~~~~~~~id~iav~---- 76 (535)
T PRK09605 1 MIVLGIEGTAWKTSAGIVDSDGDVLFNESDPYKPPSGGIHPREAAEHHAEAIPKVIKEALEEAGLKPEDIDLVAFS---- 76 (535)
T ss_pred CEEEEEEccccceEEEEEeCCCcEEEEEEeeccCCcCCCChHHHHHHHHHHHHHHHHHHHHHcCCCHhhCCEEEEC----
Confidence 4799999999999999999543 333321221100 00111234555666665 457999999
Q ss_pred CCCCchH-HHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 90 RQQNAAD-AVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 90 dG~~s~~-~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
.|--+.. -.....||+.|+.. + ++|++.++.-.
T Consensus 77 ~gPg~~~~l~vg~~~ak~la~~--~-~~~~~~v~h~~ 110 (535)
T PRK09605 77 QGPGLGPCLRVVATAARALALS--L-DVPLIGVNHCV 110 (535)
T ss_pred CCCCcHhhHHHHHHHHHHHHHH--h-CCCeecccHHH
Confidence 3322222 23347789999874 4 78888875433
No 41
>PRK09604 UGMP family protein; Validated
Probab=74.87 E-value=30 Score=30.35 Aligned_cols=91 Identities=13% Similarity=0.145 Sum_probs=54.1
Q ss_pred CeEEEEecCCCeEEEEEecCC-Cceecc-cee----------eeCC--CCChhhHHHHHHHHHHhh-----CCCEEEEec
Q 030251 26 GRFLGLDVGDKYVGLSISDPK-NKIASP-LSV----------LLRK--KNTIDLMAEDFRSLISEF-----NLEGFIVGY 86 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~-~~~a~P-l~~----------i~~~--~~~~~~~~~~L~~li~e~-----~i~~iVVGl 86 (180)
|.+||||--...+++|+.|.. ..++.- ... ++.. ....+.+...+++++++. +++.|+|+.
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 011 1100 001122334466666653 589999993
Q ss_pred -ccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 87 -PFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 87 -P~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
| |..+. -+....+++.|... + ++|++.++.
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 22222 33446788888863 3 788888853
No 42
>PRK09982 universal stress protein UspD; Provisional
Probab=74.87 E-value=14 Score=27.75 Aligned_cols=46 Identities=4% Similarity=0.008 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.|.+..+++++|.||+| .+ .+...... ..++++-+. ..+||..+
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 5888999999999999999 55 34433333 366666653 36787654
No 43
>PRK13320 pantothenate kinase; Reviewed
Probab=74.78 E-value=13 Score=31.41 Aligned_cols=53 Identities=17% Similarity=0.312 Sum_probs=36.0
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh-CCCEEEEe
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIVG 85 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~i~~iVVG 85 (180)
+++|.||.|..+|=+|+.+....+.+ ..+. .+.+...+.+++..+ +++.++|.
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 56999999999999999985443322 1222 123356666776665 58888887
No 44
>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=72.39 E-value=2.4 Score=28.40 Aligned_cols=45 Identities=20% Similarity=0.087 Sum_probs=26.8
Q ss_pred CCCcEEEecccccHHHHHHH--hccCCCCCC-------CCCCCCcHHHHHHHHH
Q 030251 114 EDMKYAYWNEGFTSKGVELL--LNPLDLHPV-------EYKTILDKFAAVGILQ 158 (180)
Q Consensus 114 ~~lpV~~~DEr~TT~~A~~~--l~~~g~~~~-------~~k~~iD~~AA~iILq 158 (180)
.|++|+.+||.+||..--.= ......+.+ .....=|-.||.-|++
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 38999999999998854210 000000100 0123569999999886
No 45
>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=70.95 E-value=24 Score=28.63 Aligned_cols=57 Identities=19% Similarity=0.339 Sum_probs=39.4
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceee---eCCCCChhhHHHHHHHHHHhhCCCEEEEe
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVL---LRKKNTIDLMAEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i---~~~~~~~~~~~~~L~~li~e~~i~~iVVG 85 (180)
+|.||.|..||=+|+.+...... +...+ .......+.+...+..++.+.+.+.+++.
T Consensus 1 ~L~iDiGNT~ik~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~is 60 (206)
T PF03309_consen 1 ILLIDIGNTRIKWALFDGDKLID-PSGRISHSTALDSSSDELLELLESLLPQPKIDAVIIS 60 (206)
T ss_dssp EEEEEE-SSEEEEEEEETTEEEE--EEEE-EEECTTSSHHHHHHHHHHHHHCTTCGEEEEE
T ss_pred CEEEEECCCeEEEEEEECCEEEe-eeeEEEecccccccHHHHHHHHHHHhccccCCcEEEE
Confidence 68999999999999999775554 11222 11222234557888888998888888888
No 46
>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=70.86 E-value=21 Score=28.23 Aligned_cols=60 Identities=17% Similarity=0.300 Sum_probs=36.6
Q ss_pred EEEEecCCCeEEEEEecCC--C-ceeccceeeeCCC------CChhhHHHHHHHHHHhh------CCCEEEEecc
Q 030251 28 FLGLDVGDKYVGLSISDPK--N-KIASPLSVLLRKK------NTIDLMAEDFRSLISEF------NLEGFIVGYP 87 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~--~-~~a~Pl~~i~~~~------~~~~~~~~~L~~li~e~------~i~~iVVGlP 87 (180)
+.|||+|+.+|=+.++... + .-.......+... .+.+.+.+.|++.+++- +++.+++|.|
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 1111222222211 12344567777777754 5789999987
No 47
>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=70.40 E-value=15 Score=31.70 Aligned_cols=61 Identities=11% Similarity=0.048 Sum_probs=38.9
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhC------CCEEEEecccC-CC
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN------LEGFIVGYPFN-RQ 91 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~------i~~iVVGlP~~-dG 91 (180)
|++|+|..+|=+|+.|..+.......+.... ..+.+.+.|.+++.+.+ +..+.||.|-- +|
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 6899999999999998754322223443322 22345678888877643 55577777654 44
No 48
>PF11104 PilM_2: Type IV pilus assembly protein PilM;; PDB: 2YCH_A.
Probab=69.42 E-value=11 Score=32.74 Aligned_cols=60 Identities=18% Similarity=0.333 Sum_probs=36.6
Q ss_pred EEecCCCeEEEEEecCCCc---------eeccceeeeCCC-CChhhHHHHHHHHHHhhCC--CEEEEecccC
Q 030251 30 GLDVGDKYVGLSISDPKNK---------IASPLSVLLRKK-NTIDLMAEDFRSLISEFNL--EGFIVGYPFN 89 (180)
Q Consensus 30 alD~G~kriGvAvsd~~~~---------~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~i--~~iVVGlP~~ 89 (180)
|||+|+..|-++-....+. ...|-..+.... .+.+.+.+.|++++.++++ ..+++++|-+
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 7999999999997665421 123333333211 2345678999999999876 6799999854
No 49
>PRK03011 butyrate kinase; Provisional
Probab=68.57 E-value=32 Score=30.72 Aligned_cols=129 Identities=12% Similarity=0.166 Sum_probs=69.7
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCC----------CChhhHHHHHHHHHHhh-----CCCEEEEec----
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK----------NTIDLMAEDFRSLISEF-----NLEGFIVGY---- 86 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~----------~~~~~~~~~L~~li~e~-----~i~~iVVGl---- 86 (180)
.+||.|.+|+..+=+|+-+....+.. .++.... ...+.-.+.+.+.+.+. ++++| +|-
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 68999999999999999987654443 3333210 11122245666677765 45555 888
Q ss_pred -ccCCCCC----------------chHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCc
Q 030251 87 -PFNRQQN----------------AADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILD 149 (180)
Q Consensus 87 -P~~dG~~----------------s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD 149 (180)
|.+.|+. .....-.--.+.++.+. + ++|++.+|=-+....-... +-.|+..-.||---.
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 7776765 22222222233344432 4 7888777753333221111 112444333445555
Q ss_pred HHHHHHHHHHHH
Q 030251 150 KFAAVGILQEYL 161 (180)
Q Consensus 150 ~~AA~iILq~yL 161 (180)
.++-..+.++|=
T Consensus 155 gln~~~va~~~a 166 (358)
T PRK03011 155 ALNQKAVARRVA 166 (358)
T ss_pred HHhHHHHHHHHH
Confidence 666666666663
No 50
>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=67.71 E-value=10 Score=27.96 Aligned_cols=40 Identities=23% Similarity=0.291 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEE
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA 119 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~ 119 (180)
.+.|.+++.+++|+.+||| .+. -.+.-.++.|.+. ++|++
T Consensus 51 ~~~l~~~a~~~~idlvvvG------PE~---pL~~Gl~D~l~~~----gi~vf 90 (100)
T PF02844_consen 51 PEELADFAKENKIDLVVVG------PEA---PLVAGLADALRAA----GIPVF 90 (100)
T ss_dssp HHHHHHHHHHTTESEEEES------SHH---HHHTTHHHHHHHT----T-CEE
T ss_pred HHHHHHHHHHcCCCEEEEC------ChH---HHHHHHHHHHHHC----CCcEE
Confidence 6899999999999999999 333 3445677788874 67765
No 51
>PRK13322 pantothenate kinase; Reviewed
Probab=66.91 E-value=57 Score=27.46 Aligned_cols=53 Identities=13% Similarity=0.122 Sum_probs=32.1
Q ss_pred eEEEEecCCCeEEEEEecC-CCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEe
Q 030251 27 RFLGLDVGDKYVGLSISDP-KNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~-~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVG 85 (180)
++|.||.|..+|=+++.+. ...+.+ .. .....+.+...+..+ ..+.++.++|.
T Consensus 1 M~L~IDiGNT~iK~~l~~~~~~~~~~-~~----~~~t~~~~~~~l~~~-~~~~i~~v~vs 54 (246)
T PRK13322 1 MILELDCGNSRLKWRVIDNGGQIIEH-GA----HLDSPAELLLGLANL-ASLAPTRCRIV 54 (246)
T ss_pred CEEEEEeCCCcEEEEEEcCCCchhhh-cc----ccCCHHHHHHHHHhC-CccCCCEEEEE
Confidence 3899999999999999985 332221 11 111122333445333 44468999998
No 52
>PRK13324 pantothenate kinase; Reviewed
Probab=66.67 E-value=28 Score=29.70 Aligned_cols=57 Identities=18% Similarity=0.290 Sum_probs=36.3
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeC--CCCChhhHHHHHHHHHHhh-----CCCEEEEe
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLR--KKNTIDLMAEDFRSLISEF-----NLEGFIVG 85 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~--~~~~~~~~~~~L~~li~e~-----~i~~iVVG 85 (180)
++|++|.|..+|=+++.|......+ . .+.. .....+++...|..++..+ .++.+++.
T Consensus 1 MiL~iDiGNT~ik~gl~~~~~~~~~-~-r~~t~~~~~t~de~~~~l~~~~~~~~~~~~~i~~viis 64 (258)
T PRK13324 1 MLLVMDMGNSHIHIGVFDGDRIVSQ-I-RYATSSVDSTSDQMGVFLRQALRENSVDLGKIDGCGIS 64 (258)
T ss_pred CEEEEEeCCCceEEEEEECCEEEEE-E-EEecCccccchHHHHHHHHHHHHhcCCCccCCCeEEEE
Confidence 3899999999999999985433221 1 2222 1112344556677777653 57888888
No 53
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=65.49 E-value=20 Score=30.64 Aligned_cols=48 Identities=10% Similarity=0.293 Sum_probs=40.7
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
.+++.+.+.+..-|+|.|| |+.+-....+.++.++++++ +++||++.-
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 4777888888999999999 88888778899999999963 389988874
No 54
>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=65.31 E-value=18 Score=28.92 Aligned_cols=57 Identities=19% Similarity=0.362 Sum_probs=39.7
Q ss_pred EEEecCCCeEEEEEecCC-CceeccceeeeCCCCChhhHHHHHHHHHHhh-----CCCEEEEec
Q 030251 29 LGLDVGDKYVGLSISDPK-NKIASPLSVLLRKKNTIDLMAEDFRSLISEF-----NLEGFIVGY 86 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~-~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-----~i~~iVVGl 86 (180)
+|||+|.-.+=..+.|+. +.+++ .++.........-+.+.|.++..++ +++.|++|-
T Consensus 2 igIDvGGT~TD~v~~d~~~~~~~~-~K~~Tt~~d~~~gi~~al~~l~~~~~~~~~~i~~v~~gT 64 (176)
T PF05378_consen 2 IGIDVGGTFTDAVLLDEDTGVVAT-AKVPTTPDDPAEGILEALDALLEESGIDPSDIDRVRHGT 64 (176)
T ss_pred eeEecCCCcEEEEEEeCCCCEEEE-EEeCCCCcCHHHHHHHHHHhhhcccCCChhhCcEEEecc
Confidence 799999999988888887 45554 3444442222234568888888765 689999983
No 55
>COG0418 PyrC Dihydroorotase [Nucleotide transport and metabolism]
Probab=64.64 E-value=8.7 Score=34.16 Aligned_cols=51 Identities=16% Similarity=0.294 Sum_probs=35.1
Q ss_pred EecccC-CCCCchH--------HHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCC
Q 030251 84 VGYPFN-RQQNAAD--------AVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD 138 (180)
Q Consensus 84 VGlP~~-dG~~s~~--------~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g 138 (180)
+|+|+. .|..... +..+...-+.|.+ +||.+.|++ |..||++|-+..++.+
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 577777 7765433 2333334446666 488888877 9999999999887654
No 56
>PRK15027 xylulokinase; Provisional
Probab=64.32 E-value=17 Score=33.21 Aligned_cols=50 Identities=12% Similarity=0.239 Sum_probs=31.1
Q ss_pred eEEEEecCCCeEEEEEecCCCcee----ccceeeeCC----CCChhhHHHHHHHHHHh
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIA----SPLSVLLRK----KNTIDLMAEDFRSLISE 76 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a----~Pl~~i~~~----~~~~~~~~~~L~~li~e 76 (180)
.+||||+|+..+=.++-|..+.+. .++...... +.+.+.+|+.+.+.+++
T Consensus 1 ~~lgID~GTts~Ka~l~d~~G~vva~~~~~~~~~~~~~g~~eqd~~~~w~~~~~~~~~ 58 (484)
T PRK15027 1 MYIGIDLGTSGVKVILLNEQGEVVASQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKA 58 (484)
T ss_pred CEEEEEecccceEEEEEcCCCCEEEEEeecccccCCCCCccccCHHHHHHHHHHHHHH
Confidence 379999999999999999876554 333222111 22444556666555443
No 57
>TIGR01312 XylB D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization.
Probab=64.06 E-value=17 Score=32.86 Aligned_cols=21 Identities=29% Similarity=0.537 Sum_probs=18.7
Q ss_pred EEEecCCCeEEEEEecCCCce
Q 030251 29 LGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~ 49 (180)
||||+|+..+=+++.|..+.+
T Consensus 1 lgIDiGtt~ik~~l~d~~g~i 21 (481)
T TIGR01312 1 LGIDLGTSGVKALLVDEQGEV 21 (481)
T ss_pred CceeecCcceEEEEECCCCCE
Confidence 589999999999999987754
No 58
>PRK13928 rod shape-determining protein Mbl; Provisional
Probab=63.20 E-value=72 Score=27.57 Aligned_cols=99 Identities=17% Similarity=0.231 Sum_probs=51.5
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCC-hhhHHHHHHHHHHhhCCCEEEEecccCCCCCchH---HHHHHHHH
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNT-IDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAAD---AVQVKLFI 104 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~-~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~---~~~v~~F~ 104 (180)
+|||+|+.++=++..+....+..|=.+-...+.+ .-.+-++-.+... ..+..+.+..|..+|..... ....+.+.
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 8999999999999976555555653222221111 0001122222221 23677888899887755443 33445555
Q ss_pred HHHHhccCCCCCc--EEEecccccHHH
Q 030251 105 DDLSATKKLEDMK--YAYWNEGFTSKG 129 (180)
Q Consensus 105 ~~L~~~~~~~~lp--V~~~DEr~TT~~ 129 (180)
+++.....+ .-| ++-+-..+|..+
T Consensus 85 ~~~~~~~~~-~~p~~vitvP~~~~~~~ 110 (336)
T PRK13928 85 NKACGKRFF-SKPRIMICIPTGITSVE 110 (336)
T ss_pred HHHhccCCC-CCCeEEEEeCCCCCHHH
Confidence 555432112 345 444555555544
No 59
>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=63.10 E-value=32 Score=30.25 Aligned_cols=61 Identities=16% Similarity=0.230 Sum_probs=38.1
Q ss_pred EEEEecCCCeEEEEEecCC--C-ceeccceeeeCC---C---CChhhHHHHHHHHHHh------hCCCEEEEeccc
Q 030251 28 FLGLDVGDKYVGLSISDPK--N-KIASPLSVLLRK---K---NTIDLMAEDFRSLISE------FNLEGFIVGYPF 88 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~--~-~~a~Pl~~i~~~---~---~~~~~~~~~L~~li~e------~~i~~iVVGlP~ 88 (180)
++|||+|+.+|=+++.... + .-.......+.. + .+.+.+.+.|++.+++ .+++.++++.|=
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 578899999873
No 60
>PTZ00340 O-sialoglycoprotein endopeptidase-like protein; Provisional
Probab=63.05 E-value=40 Score=30.17 Aligned_cols=90 Identities=11% Similarity=0.096 Sum_probs=54.1
Q ss_pred CeEEEEecCCCeEEEEEecCCC-ceeccc---------eeeeCC--CCChhhHHHHHHHHHHh-----hCCCEEEEeccc
Q 030251 26 GRFLGLDVGDKYVGLSISDPKN-KIASPL---------SVLLRK--KNTIDLMAEDFRSLISE-----FNLEGFIVGYPF 88 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~-~~a~Pl---------~~i~~~--~~~~~~~~~~L~~li~e-----~~i~~iVVGlP~ 88 (180)
+.+||||-=...+++|+.|..+ .++.-. ++++.. ......+..-+++++++ .+++.|.|.
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 4699999999999999998543 333211 222211 00112233445555554 468999998
Q ss_pred CCCCCchHHHH-HHHHHHHHHhccCCCCCcEEEec
Q 030251 89 NRQQNAADAVQ-VKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 89 ~dG~~s~~~~~-v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
.|=-...+-+ ...||+.|+.. + ++|++-++
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 4433323333 37888888874 3 78887664
No 61
>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=62.89 E-value=18 Score=27.31 Aligned_cols=95 Identities=13% Similarity=0.158 Sum_probs=49.3
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCC-------------hhhHHHHHHHHHHhh------CCCEEEEeccc
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNT-------------IDLMAEDFRSLISEF------NLEGFIVGYPF 88 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~-------------~~~~~~~L~~li~e~------~i~~iVVGlP~ 88 (180)
++.+|.|...||+.-+.......+=-..++.+... ...++.++.+-+.++ .+++|||+-|
T Consensus 4 ~v~id~g~A~i~~l~~~~~~~~~~i~~~ip~K~~~Gg~s~~rf~r~~~~~~f~~~i~~~l~~~f~~~~~~~~~iIiaGP- 82 (133)
T PF03464_consen 4 IVVIDEGEANICLLRGYGTEILQRIESNIPGKHKKGGQSQRRFEREKALEKFFKEIAEALKKYFLVNFDDVKCIIIAGP- 82 (133)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHHHHHHHHHHHHHHHHHHHHHHHHHCCCHTTTCSEEEEEES-
T ss_pred EEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEECC-
Confidence 68899999999998665332222211122322210 123455555555555 8999999943
Q ss_pred CCCCCchHHHHHHHHHHHHHhccCCCC-CcEEEecccccHHHHH
Q 030251 89 NRQQNAADAVQVKLFIDDLSATKKLED-MKYAYWNEGFTSKGVE 131 (180)
Q Consensus 89 ~dG~~s~~~~~v~~F~~~L~~~~~~~~-lpV~~~DEr~TT~~A~ 131 (180)
+... ..|.+.+.......+ ..+..+|=..+...+-
T Consensus 83 -----Gf~k---~~f~~~l~~~~~~~~~~~i~~~~~s~~~~~gl 118 (133)
T PF03464_consen 83 -----GFTK---EEFYKYLKAEARRKDKKKIVVVDTSSGGESGL 118 (133)
T ss_dssp -----TTHH---HHHHHHHHHHHHHHTCCEEEEEE-SSSCHHHH
T ss_pred -----HHHH---HHHHHHHHHhhHhhcCCEEEEEECCCCCHHHH
Confidence 3222 246555554211112 3466666555555543
No 62
>PRK00047 glpK glycerol kinase; Provisional
Probab=61.86 E-value=23 Score=32.44 Aligned_cols=23 Identities=30% Similarity=0.309 Sum_probs=19.7
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~ 49 (180)
.+||||+|+..+=+++-|..+.+
T Consensus 6 ~~lgiD~GTts~Ka~l~d~~g~~ 28 (498)
T PRK00047 6 YILALDQGTTSSRAIIFDHDGNI 28 (498)
T ss_pred EEEEEecCCCceEEEEECCCCCE
Confidence 58999999999999999977543
No 63
>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=61.57 E-value=21 Score=29.55 Aligned_cols=60 Identities=15% Similarity=0.268 Sum_probs=38.0
Q ss_pred HHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe---cccccHHHHHHHhccCCCC
Q 030251 72 SLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW---NEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 72 ~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~---DEr~TT~~A~~~l~~~g~~ 140 (180)
+.+.+.++++||+| .|+ ||+... ..++++.+.. .++|++|. |+-....+|.+.|.+.|++
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 34556789999999 566 888764 2333443332 27888874 8888899998888876764
No 64
>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=61.53 E-value=22 Score=28.34 Aligned_cols=64 Identities=14% Similarity=0.312 Sum_probs=40.0
Q ss_pred CCeEEEEecCCCe-----EEEEEecCCCceeccceeeeCCCCC----hhhHHHHHHHHHHhhCC--CEEEEecccC
Q 030251 25 RGRFLGLDVGDKY-----VGLSISDPKNKIASPLSVLLRKKNT----IDLMAEDFRSLISEFNL--EGFIVGYPFN 89 (180)
Q Consensus 25 ~~~iLalD~G~kr-----iGvAvsd~~~~~a~Pl~~i~~~~~~----~~~~~~~L~~li~e~~i--~~iVVGlP~~ 89 (180)
|..+|+||+-+.- +|.|+-+....+..... ...+... ....+++|+.++++++. .-|||--|.-
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 4679999999998 99999975444343321 1212111 12346889999999863 3456655543
No 65
>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=61.34 E-value=47 Score=27.94 Aligned_cols=89 Identities=11% Similarity=0.056 Sum_probs=49.5
Q ss_pred HHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhcc------C---CC-CCcEEEecccccHHHHHHHhccCC
Q 030251 69 DFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATK------K---LE-DMKYAYWNEGFTSKGVELLLNPLD 138 (180)
Q Consensus 69 ~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~------~---~~-~lpV~~~DEr~TT~~A~~~l~~~g 138 (180)
+..+.+.++++++||+- +.. .. .+ .+...++... + .+ ++|.+..|.+-...+|-+.|.+.|
T Consensus 47 ~~i~~l~~~~vDGiI~~-s~~-~~-~~------~l~~~~~~~iPvV~~~~~~~~~~~~~~V~~D~~~a~~~a~~~Li~~G 117 (279)
T PF00532_consen 47 EYIELLLQRRVDGIILA-SSE-ND-DE------ELRRLIKSGIPVVLIDRYIDNPEGVPSVYIDNYEAGYEATEYLIKKG 117 (279)
T ss_dssp HHHHHHHHTTSSEEEEE-SSS-CT-CH------HHHHHHHTTSEEEEESS-SCTTCTSCEEEEEHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHhcCCCEEEEe-ccc-CC-hH------HHHHHHHcCCCEEEEEeccCCcccCCEEEEcchHHHHHHHHHHHhcc
Confidence 55566788999999998 222 11 11 1222222100 0 12 445555665566667778888777
Q ss_pred CCC--CCCCCCCcHHHHHHHHHHHHhhhhh
Q 030251 139 LHP--VEYKTILDKFAAVGILQEYLDNANR 166 (180)
Q Consensus 139 ~~~--~~~k~~iD~~AA~iILq~yL~~~~~ 166 (180)
-++ .--....+...+..=+++|.+....
T Consensus 118 h~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~ 147 (279)
T PF00532_consen 118 HRRPIAFIGGPEDSSTSRERLQGYRDALKE 147 (279)
T ss_dssp CCSTEEEEEESTTTHHHHHHHHHHHHHHHH
T ss_pred cCCeEEEEecCcchHHHHHHHHHHHHHHHH
Confidence 554 1122445555677777777766544
No 66
>PRK10116 universal stress protein UspC; Provisional
Probab=61.30 E-value=39 Score=24.70 Aligned_cols=47 Identities=9% Similarity=0.080 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.|.+.++++++|.||+|- -..+...... ..++++-.. .++||..+
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 57888999999999999993 2222222222 345566553 37888766
No 67
>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=61.14 E-value=29 Score=28.39 Aligned_cols=50 Identities=24% Similarity=0.369 Sum_probs=30.5
Q ss_pred eEEEEecCCCeEEEEEecCCCcee----ccceeeeCC----CCChhhHHHHHHHHHHh
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIA----SPLSVLLRK----KNTIDLMAEDFRSLISE 76 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a----~Pl~~i~~~----~~~~~~~~~~L~~li~e 76 (180)
.+||||+|+..+=+++-|..+.+. .|+...... ..+++.+|+.+.+.+++
T Consensus 1 y~lgiDiGTts~K~~l~d~~g~iv~~~~~~~~~~~~~~g~~e~d~~~~~~~~~~~~~~ 58 (245)
T PF00370_consen 1 YYLGIDIGTTSVKAVLFDEDGKIVASASRPYPYYTPEPGWAEQDPDEIWEAICEALKE 58 (245)
T ss_dssp EEEEEEECSSEEEEEEEETTSCEEEEEEEEETEBCSSTTEEEE-HHHHHHHHHHHHHH
T ss_pred CEEEEEEcccceEEEEEeCCCCEEEEEEEeeeeccccccccccChHHHHHHHHHHHHH
Confidence 379999999999999999776443 222222111 12445566666655554
No 68
>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=61.14 E-value=51 Score=28.36 Aligned_cols=64 Identities=17% Similarity=0.303 Sum_probs=41.1
Q ss_pred CeEEEEecCCCeEEEEEecCCCc--ee-------ccceeeeCCC-CChhhHHHHHHHHHHhhCC--CEEEEecccC
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNK--IA-------SPLSVLLRKK-NTIDLMAEDFRSLISEFNL--EGFIVGYPFN 89 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~--~a-------~Pl~~i~~~~-~~~~~~~~~L~~li~e~~i--~~iVVGlP~~ 89 (180)
..++|||+|...|=++.....+. .. .|-..+.... .+.+.+...|++++.+.+. ..+++++|-+
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 57899999999999888874221 11 2222222111 1234567888888888754 5799999854
No 69
>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=60.43 E-value=62 Score=23.41 Aligned_cols=121 Identities=13% Similarity=0.151 Sum_probs=72.5
Q ss_pred eEEEEec--CCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHH
Q 030251 27 RFLGLDV--GDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFI 104 (180)
Q Consensus 27 ~iLalD~--G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~ 104 (180)
.++||-. ....+|+|.+|..+.-.. +..+. + ..+|...+..++|..||+. ++...... ....
T Consensus 2 yl~aI~~~~~~~~~gla~~D~sTGe~~-~~~~~------d--~~~L~~~L~~~~P~EIi~~----~~~~~~~~---~~~~ 65 (137)
T PF05188_consen 2 YLAAIYEKNDEDSYGLAYIDLSTGEFY-VTEFE------D--YSELKSELARLSPREIIIP----EGFSSSDI---SALL 65 (137)
T ss_dssp EEEEEEEETCSSEEEEEEEETTTTEEE-EEEEE------C--HHHHHHHHHHH-ESEEEEE----TTCSHHHH---HHHH
T ss_pred EEEEEEEecCCCEEEEEEEECCCCEEE-EEEeC------C--HHHHHHHHHhcCCeEEEEc----CCCccccc---chhh
Confidence 3567777 777799999997654333 23332 1 5788999999999999999 77766543 1111
Q ss_pred HHHHhccCCCCCcEE-EecccccHHHHHHHhcc-CCCCCCCC----CCCCcHHHHHHHHHHHHhhhhhh
Q 030251 105 DDLSATKKLEDMKYA-YWNEGFTSKGVELLLNP-LDLHPVEY----KTILDKFAAVGILQEYLDNANRK 167 (180)
Q Consensus 105 ~~L~~~~~~~~lpV~-~~DEr~TT~~A~~~l~~-~g~~~~~~----k~~iD~~AA~iILq~yL~~~~~~ 167 (180)
..+.. ....+. ..+..+.+..+.+.+.+ .+...-+. ...-..++|.--|=.||......
T Consensus 66 ~~~~~----~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~Al~all~Yl~~t~~~ 130 (137)
T PF05188_consen 66 SSLKN----SFFKVTETPSWYFDSEFASEDIEEQFGVADLDGFGLEEDKELALSALGALLKYLEETQKS 130 (137)
T ss_dssp HCCTT----TCCEEEEETCGGGSHHHHHHHHHHHCTSSSTCCCTTGGGGHHHHHHHHHHHHHHHHTTTC
T ss_pred hhhcc----ccceeeecchhhhhhHHHHHHHHHhhccccccccCccCCCHHHHHHHHHHHHHHHHHCcc
Confidence 11221 122333 34566667667665542 22211111 34456788888999999876544
No 70
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=60.27 E-value=7.7 Score=38.69 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=20.6
Q ss_pred CCCeEEEEecCCCeEEEEEecCCC
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPKN 47 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~~ 47 (180)
.+..+||||+|+..||.|++..+.
T Consensus 2 ~~~yilglDIGi~SVGWAvve~de 25 (1088)
T COG3513 2 KKAYILGLDIGINSVGWAVVEDDE 25 (1088)
T ss_pred CcceEEEeeccccceeeEEeeccc
Confidence 457899999999999999997543
No 71
>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=59.52 E-value=42 Score=22.92 Aligned_cols=50 Identities=12% Similarity=0.060 Sum_probs=36.7
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHh
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 134 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 134 (180)
..+.+++.+++++.+|+| ..++ .....|++. ++.|+.. ...+-.+|-+.|
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 556777777999999999 4554 345567763 8899988 777777776554
No 72
>PRK15118 universal stress global response regulator UspA; Provisional
Probab=59.18 E-value=45 Score=24.54 Aligned_cols=47 Identities=9% Similarity=0.077 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
.+.|.+.++++++|.||+| .- +......-..++++-+. ..+||..+-
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 11112233566666653 368888774
No 73
>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=58.28 E-value=40 Score=29.57 Aligned_cols=53 Identities=11% Similarity=0.157 Sum_probs=31.5
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhC
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFN 78 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~ 78 (180)
..+..+|||+|+..+=+++-|.. .+.. ...++......+...+-|.++.++..
T Consensus 30 ~~m~~~GIDiGStt~K~Vlld~~-~i~~-~~~~~tg~~~~~~a~~~l~~~l~~~g 82 (293)
T TIGR03192 30 AKIITCGIDVGSVSSQAVLVCDG-ELYG-YNSMRTGNNSPDSAKNALQGIMDKIG 82 (293)
T ss_pred cccEEEEEEeCchhEEEEEEeCC-EEEE-EEeecCCCCHHHHHHHHHHHHHHHcC
Confidence 34678999999999999999954 3332 23333322112222355566666554
No 74
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=57.78 E-value=31 Score=25.92 Aligned_cols=45 Identities=20% Similarity=0.484 Sum_probs=29.9
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.+.+++++++++.|+|=+|.+ ....++++.+.+++. +++|.++
T Consensus 130 ~~~l~~~~~~~~id~v~ial~~~------~~~~i~~ii~~~~~~----~v~v~~v 174 (175)
T PF13727_consen 130 LDDLPELVREHDIDEVIIALPWS------EEEQIKRIIEELENH----GVRVRVV 174 (175)
T ss_dssp GGGHHHHHHHHT--EEEE--TTS-------HHHHHHHHHHHHTT----T-EEEE-
T ss_pred HHHHHHHHHhCCCCEEEEEcCcc------CHHHHHHHHHHHHhC----CCEEEEe
Confidence 47789999999999999998876 124667888888863 6777654
No 75
>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=57.72 E-value=82 Score=27.33 Aligned_cols=90 Identities=13% Similarity=0.137 Sum_probs=56.8
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh-CCCEEEEecccCCCCCchHHHHHHHHHHH
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF-NLEGFIVGYPFNRQQNAADAVQVKLFIDD 106 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~-~i~~iVVGlP~~dG~~s~~~~~v~~F~~~ 106 (180)
.+|||.|..-+=+++.|..+.+-. ..+++++. +.+++.|++..... .+..|.+ -|.-+ ..|++.
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 56665542 23444454443322 1222222 23333 357777
Q ss_pred HHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 107 LSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 107 L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
+... + ++++...||=-+...+-+.+.
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 7762 3 678889999888888877764
No 76
>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=57.67 E-value=35 Score=28.22 Aligned_cols=47 Identities=6% Similarity=0.140 Sum_probs=36.9
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
+.++.+.+.+...|.|.|| |+.+-....+.+..+.+++. .++||++.
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 4556667788899999999 77666667788888899873 37999875
No 77
>PHA02942 putative transposase; Provisional
Probab=57.56 E-value=15 Score=33.13 Aligned_cols=86 Identities=9% Similarity=-0.050 Sum_probs=47.4
Q ss_pred hhCCCEEEEecccC-CCCCchHHHHH---------HHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCC----
Q 030251 76 EFNLEGFIVGYPFN-RQQNAADAVQV---------KLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHP---- 141 (180)
Q Consensus 76 e~~i~~iVVGlP~~-dG~~s~~~~~v---------~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~---- 141 (180)
+++++.|||+-..+ ........+.+ ..|...|+-.....|++|+.+|+++||..-- ..|-..
T Consensus 264 ~~~~~~IviEdL~gm~k~~~~l~k~~~~~~~~~~~~~l~~~LeYKA~~~G~~Vv~V~p~yTSq~Cs----~CG~~~~~l~ 339 (383)
T PHA02942 264 DLGANVIKLEDLKNLIKDVNKLPAEFRDKLYLMQYHRIQYWIEWQAKKHGMIVEFVNPSYSSVSCP----KCGHKMVEIA 339 (383)
T ss_pred hCCCCEEEEccHHHHHhcccccchHHHHHhhhhhHHHHHHHHHHHHHHhCCEEEEECCCCCCccCC----CCCCccCcCC
Confidence 45678899997643 21111111111 2222333322222489999999999986432 222111
Q ss_pred -CC-------CCCCCcHHHHHHHHHHHHhhhh
Q 030251 142 -VE-------YKTILDKFAAVGILQEYLDNAN 165 (180)
Q Consensus 142 -~~-------~k~~iD~~AA~iILq~yL~~~~ 165 (180)
+. -...-|-.||.-|+...+....
T Consensus 340 ~r~f~C~~CG~~~drD~nAA~NI~~rg~~~~~ 371 (383)
T PHA02942 340 HRYFHCPSCGYENDRDVIAIMNLNGRGSLTLS 371 (383)
T ss_pred CCEEECCCCCCEeCcHHHHHHHHHHHHHHHhc
Confidence 10 1245699999999988765543
No 78
>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=57.19 E-value=33 Score=25.83 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=31.0
Q ss_pred EEEEecccCCCCCchHHH-HHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhcc
Q 030251 81 GFIVGYPFNRQQNAADAV-QVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNP 136 (180)
Q Consensus 81 ~iVVGlP~~dG~~s~~~~-~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~ 136 (180)
.+++| -|+..+.+. .+..+++.+++. +|+.+|.+ -|||...++.|..
T Consensus 3 illv~----fGS~~~~~~~~~~~i~~~l~~~--~p~~~V~~---afts~~i~~~l~~ 50 (127)
T cd03412 3 ILLVS----FGTSYPTAEKTIDAIEDKVRAA--FPDYEVRW---AFTSRMIRKKLKK 50 (127)
T ss_pred EEEEe----CCCCCHHHHHHHHHHHHHHHHH--CCCCeEEE---EecHHHHHHHHHh
Confidence 46888 888887554 568899999874 66667654 3555554444443
No 79
>PRK13317 pantothenate kinase; Provisional
Probab=57.05 E-value=77 Score=27.24 Aligned_cols=87 Identities=11% Similarity=0.030 Sum_probs=50.1
Q ss_pred CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh-hCCCEEEEecccCCCCCchHHHHHHHH
Q 030251 25 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE-FNLEGFIVGYPFNRQQNAADAVQVKLF 103 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e-~~i~~iVVGlP~~dG~~s~~~~~v~~F 103 (180)
|+..+|||+|...+=+++.|....+.. .+..++ ..+.+.+++.+ .++..|++= |.-+. .|
T Consensus 1 m~~~iGIDiGstt~K~v~~~~~~~~~~--~~~~~~------~~~~~~~~l~~~~~~~~i~~T-----G~g~~------~~ 61 (277)
T PRK13317 1 MEMKIGIDAGGTLTKIVYLEEKKQRTF--KTEYSA------EGKKVIDWLINLQDIEKICLT-----GGKAG------YL 61 (277)
T ss_pred CCceEEEEeCcccEEEEEEcCCCeEEE--EeeccH------HHHHHHHHhhccCCceEEEEE-----Ccchh------hh
Confidence 356899999999999999887665442 222221 13445555433 345544442 33221 23
Q ss_pred HHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 104 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 104 ~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
++.+. . ++|++.+||=-.+..+-+.+.
T Consensus 62 ~~~~~----~-~~~~~~v~E~~a~~~g~~~l~ 88 (277)
T PRK13317 62 QQLLN----Y-GYPIAEFVEFEATGLGVRYLL 88 (277)
T ss_pred hHHHh----c-CCCeeeeHHHHHHHHHHHHHH
Confidence 33222 2 678777899777776666553
No 80
>PTZ00294 glycerol kinase-like protein; Provisional
Probab=56.84 E-value=28 Score=31.97 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=20.6
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~ 49 (180)
.+||||+|+..|=+++-|..+.+
T Consensus 3 ~~lgiDiGTts~Ka~l~d~~G~~ 25 (504)
T PTZ00294 3 YIGSIDQGTTSTRFIIFDEKGNV 25 (504)
T ss_pred EEEEEecCCCceEEEEECCCCCE
Confidence 68999999999999999988755
No 81
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=56.52 E-value=63 Score=29.28 Aligned_cols=71 Identities=15% Similarity=0.091 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHhhCCCEEEEecccC-CCCCchHHH-HHHHHHHHHHhccCCCCCcEEEe----cccccHHHHHHHhccCC
Q 030251 65 LMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAV-QVKLFIDDLSATKKLEDMKYAYW----NEGFTSKGVELLLNPLD 138 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~-~v~~F~~~L~~~~~~~~lpV~~~----DEr~TT~~A~~~l~~~g 138 (180)
.++++|.+++.+++++.|||.-=+- .+..+..+. ...+|..+|++. ++||+++ |-.-.......+|...|
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 335677778752 6788877 32222334456666655
Q ss_pred C
Q 030251 139 L 139 (180)
Q Consensus 139 ~ 139 (180)
+
T Consensus 102 i 102 (407)
T PRK10966 102 T 102 (407)
T ss_pred c
Confidence 4
No 82
>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=55.91 E-value=57 Score=22.59 Aligned_cols=54 Identities=13% Similarity=0.141 Sum_probs=31.2
Q ss_pred EEEEecccCCCCCc--hHHHHHHHHHHHHHhccCCCCCc--EEEecc-cccHHHHHHHhccCCCC
Q 030251 81 GFIVGYPFNRQQNA--ADAVQVKLFIDDLSATKKLEDMK--YAYWNE-GFTSKGVELLLNPLDLH 140 (180)
Q Consensus 81 ~iVVGlP~~dG~~s--~~~~~v~~F~~~L~~~~~~~~lp--V~~~DE-r~TT~~A~~~l~~~g~~ 140 (180)
.|++| .|+.. +....+..+++.|++. ++..+ +.|... .-+..++-+.+...|.+
T Consensus 2 lllv~----HGs~~~s~~~~~~~~~~~~l~~~--~~~~~v~~a~~~~~~P~i~~~l~~l~~~g~~ 60 (101)
T cd03409 2 LLVVG----HGSPYKDPYKKDIEAQAHNLAES--LPDFPYYVGFQSGLGPDTEEAIRELAEEGYQ 60 (101)
T ss_pred EEEEE----CCCCCCccHHHHHHHHHHHHHHH--CCCCCEEEEEECCCCCCHHHHHHHHHHcCCC
Confidence 35666 66665 4455667777777764 32333 345554 56666666666555543
No 83
>PRK13326 pantothenate kinase; Reviewed
Probab=55.54 E-value=99 Score=26.38 Aligned_cols=22 Identities=14% Similarity=0.359 Sum_probs=19.3
Q ss_pred CeEEEEecCCCeEEEEEecCCC
Q 030251 26 GRFLGLDVGDKYVGLSISDPKN 47 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~ 47 (180)
.++|+||+|..+|=+++-+...
T Consensus 6 ~~~L~IDiGNT~ik~glf~~~~ 27 (262)
T PRK13326 6 SSQLIIDIGNTSISFALYKDNK 27 (262)
T ss_pred cEEEEEEeCCCeEEEEEEECCE
Confidence 5789999999999999999654
No 84
>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=53.97 E-value=64 Score=22.64 Aligned_cols=57 Identities=11% Similarity=0.059 Sum_probs=37.9
Q ss_pred EEEEecccCCCCCchHH-HHHHHHHHHHHhccCCCCCcEEEecc-cccHHHHHHHhccCCCCC
Q 030251 81 GFIVGYPFNRQQNAADA-VQVKLFIDDLSATKKLEDMKYAYWNE-GFTSKGVELLLNPLDLHP 141 (180)
Q Consensus 81 ~iVVGlP~~dG~~s~~~-~~v~~F~~~L~~~~~~~~lpV~~~DE-r~TT~~A~~~l~~~g~~~ 141 (180)
.++|| .|+.++.+ ..+..+++.+++......+.+-|.+. .-|-.++-+.+...|.++
T Consensus 2 ivlv~----hGS~~~~~~~~~~~l~~~l~~~~~~~~v~~afle~~~p~~~~~l~~l~~~g~~~ 60 (101)
T cd03416 2 LLLVG----HGSRDPRAAEALEALAERLRERLPGDEVELAFLELAEPSLAEALDELAAQGATR 60 (101)
T ss_pred EEEEE----cCCCCHHHHHHHHHHHHHHHhhCCCCcEEEEEEEcCCCCHHHHHHHHHHcCCCE
Confidence 47788 89988644 46789999998742122344556766 667777777777666543
No 85
>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=53.63 E-value=1.4e+02 Score=25.69 Aligned_cols=89 Identities=15% Similarity=0.117 Sum_probs=51.7
Q ss_pred EEEecCCCeEEEEEecCC-Cceeccceee-----------eC--CCCChhhHHHHHHHHHHh-----hCCCEEEEecccC
Q 030251 29 LGLDVGDKYVGLSISDPK-NKIASPLSVL-----------LR--KKNTIDLMAEDFRSLISE-----FNLEGFIVGYPFN 89 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~-~~~a~Pl~~i-----------~~--~~~~~~~~~~~L~~li~e-----~~i~~iVVGlP~~ 89 (180)
||||--...+++|+.|.. ..++.-..+. +. .......+...+++++++ .+++.|.|+.=
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 689999999999999852 3343211110 10 000122334556666665 35799999930
Q ss_pred CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 90 RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 90 dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
-|..+. .+....+|+.|... + ++|++.++.
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 122222 33346788888863 3 789888853
No 86
>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=53.44 E-value=43 Score=27.76 Aligned_cols=47 Identities=19% Similarity=0.202 Sum_probs=27.4
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF 77 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~ 77 (180)
++|||.|+..+=.++-|....+++- ... .....+.+.+.|.+++.+.
T Consensus 2 ~lGIDiGtts~K~vl~d~g~il~~~--~~~-~~~~~~~~~~~l~~~~~~~ 48 (248)
T TIGR00241 2 SLGIDSGSTTTKMVLMEDGKVIGYK--WLD-TTPVIEETARAILEALKEA 48 (248)
T ss_pred EEEEEcChhheEEEEEcCCEEEEEE--Eec-CCCCHHHHHHHHHHHHHHc
Confidence 7899999999999999832233321 122 1212223345566666554
No 87
>PRK00923 sirohydrochlorin cobaltochelatase; Reviewed
Probab=53.37 E-value=52 Score=24.25 Aligned_cols=55 Identities=9% Similarity=-0.048 Sum_probs=35.4
Q ss_pred CEEEEecccCCCCCchHH-HHHHHHHHHHHhccCCCCCcE--EEec-ccccHHHHHHHhccCCCC
Q 030251 80 EGFIVGYPFNRQQNAADA-VQVKLFIDDLSATKKLEDMKY--AYWN-EGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 80 ~~iVVGlP~~dG~~s~~~-~~v~~F~~~L~~~~~~~~lpV--~~~D-Er~TT~~A~~~l~~~g~~ 140 (180)
..|+|| .|+..+.+ ..+..|++.++++ .+..+| -|.+ ..-|-.++-+.+...|.+
T Consensus 3 ~lvlv~----hGS~~~~~~~~~~~~~~~l~~~--~~~~~v~~afle~~~P~l~~~l~~l~~~g~~ 61 (126)
T PRK00923 3 GLLLVG----HGSRLPYNKEVVTKIAEKIKEK--HPFYIVEVGFMEFNEPTIPEALKKLIGTGAD 61 (126)
T ss_pred EEEEEe----CCCCChHHHHHHHHHHHHHHHh--CCCCeEEEEEEEcCCCCHHHHHHHHHHcCCC
Confidence 357888 88888665 6778889988874 333344 4555 345566666666655554
No 88
>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=53.23 E-value=64 Score=26.94 Aligned_cols=61 Identities=13% Similarity=0.185 Sum_probs=31.0
Q ss_pred CCCeEEEEecC----CCeEEEEEe--cCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEe
Q 030251 24 KRGRFLGLDVG----DKYVGLSIS--DPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 24 ~~~~iLalD~G----~kriGvAvs--d~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVG 85 (180)
....++|+|+| ...+++.+. ......-. +............+.+.|.+++..+++..|++=
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 34678999999 555556665 22222211 122222222334557899999999999999885
No 89
>COG1070 XylB Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]
Probab=52.33 E-value=44 Score=30.87 Aligned_cols=23 Identities=26% Similarity=0.362 Sum_probs=20.4
Q ss_pred CCCeEEEEecCCCeEEEEEecCC
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~ 46 (180)
.+..+||||.|+..+=..+-|..
T Consensus 2 ~~~~~lgIDiGTt~~Kavl~d~~ 24 (502)
T COG1070 2 MMKYVLGIDIGTTSVKAVLFDED 24 (502)
T ss_pred CccEEEEEEcCCCcEEEEEEeCC
Confidence 46789999999999998888887
No 90
>PLN02295 glycerol kinase
Probab=52.08 E-value=39 Score=31.19 Aligned_cols=49 Identities=12% Similarity=0.138 Sum_probs=31.8
Q ss_pred EEEEecCCCeEEEEEecCCCcee----ccceeeeCC----CCChhhHHHHHHHHHHh
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIA----SPLSVLLRK----KNTIDLMAEDFRSLISE 76 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a----~Pl~~i~~~----~~~~~~~~~~L~~li~e 76 (180)
+||||.|+..+=.++-|..+.+. .++.+.... +.+++.+|+.+.+.+++
T Consensus 2 vlgID~GTts~Ka~l~d~~G~~~~~~~~~~~~~~~~~G~~Eqdp~~~w~~~~~~i~~ 58 (512)
T PLN02295 2 VGAIDQGTTSTRFIIYDRDARPVASHQVEFTQIYPQAGWVEHDPMEILESVLTCIAK 58 (512)
T ss_pred EEEEecCCCceEEEEECCCCCEEEEEeecccccCCCCCcEeeCHHHHHHHHHHHHHH
Confidence 79999999999999999887663 444332221 12445567666554433
No 91
>PHA02533 17 large terminase protein; Provisional
Probab=51.81 E-value=98 Score=29.25 Aligned_cols=62 Identities=18% Similarity=0.229 Sum_probs=42.3
Q ss_pred ccCCCCeEEEEecC----CCeEEEEEecCCCceeccceeee---CCCCChhhHHHHHHHHHHhhCCCEEEEe
Q 030251 21 KVSKRGRFLGLDVG----DKYVGLSISDPKNKIASPLSVLL---RKKNTIDLMAEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 21 ~~~~~~~iLalD~G----~kriGvAvsd~~~~~a~Pl~~i~---~~~~~~~~~~~~L~~li~e~~i~~iVVG 85 (180)
+.+....++|+|++ ....++.|.|+.. .|..++. .+..+.....+.|.++.+.|++..|.|=
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 34456789999998 4667788887642 2344444 3333444567999999999998877764
No 92
>COG4012 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.97 E-value=1.3e+02 Score=26.62 Aligned_cols=98 Identities=13% Similarity=0.118 Sum_probs=57.0
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 105 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~ 105 (180)
+.+|++|+|.-..-|-.-|. ..--++..+.+..-. .+.++|+.+.+ ..+..+++|-|.- |..+. ++|-+
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-DPENSLRMVMPSPTS---TLAQRLRFMLR-EGPYLALIGVPMG-GGPTT-----RAVRR 69 (342)
T ss_pred CceEEEEecCCceeEEEecC-CcccceeEeecCchH---HHHHHHHHHhc-cCCcEEEEeeecC-CChhh-----HHHHH
Confidence 46999999988887776664 333355555554321 23566666655 4568899998876 43332 34555
Q ss_pred HHHhccCCCCCcEEEe-cccccHHHHHHHhccCCC
Q 030251 106 DLSATKKLEDMKYAYW-NEGFTSKGVELLLNPLDL 139 (180)
Q Consensus 106 ~L~~~~~~~~lpV~~~-DEr~TT~~A~~~l~~~g~ 139 (180)
.|++ +.+|+-- |--+|-..--+++.++|+
T Consensus 70 hlk~-----G~rVyatedAAlT~hddleRv~emgi 99 (342)
T COG4012 70 HLKK-----GTRVYATEDAALTLHDDLERVEEMGI 99 (342)
T ss_pred HHhc-----CCeeEechhhhhhhhcCHHHHHhhCe
Confidence 6665 5566532 233343333445555554
No 93
>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=50.22 E-value=14 Score=34.20 Aligned_cols=18 Identities=17% Similarity=0.460 Sum_probs=15.2
Q ss_pred EEEEecCCCeEEEEEecC
Q 030251 28 FLGLDVGDKYVGLSISDP 45 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~ 45 (180)
++|||+|+..+.||+.+.
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 94
>PF14331 ImcF-related_N: ImcF-related N-terminal domain
Probab=49.94 E-value=49 Score=28.11 Aligned_cols=55 Identities=16% Similarity=0.209 Sum_probs=36.1
Q ss_pred HHHHHHHHHHhhC----CCEEEEecccC---CCCC-----chHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 66 MAEDFRSLISEFN----LEGFIVGYPFN---RQQN-----AADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 66 ~~~~L~~li~e~~----i~~iVVGlP~~---dG~~-----s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.|..+.+++.+++ +++|||=+|.. +++. ...+..+++-.+.|.+.... .+||+++
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 EWQAFLDLLRRHRPRQPLNGVILTVSVDDLLNADEAERELEALARALRQRLEELQRTLGV-RLPVYVV 75 (266)
T ss_pred HHHHHHHHHHhcCCCCCCCEEEEEEEHHHHhcCChhhhHHHHHHHHHHHHHHHHHHHhCC-CCCeEee
Confidence 4788888888764 79999999976 3333 33355555555555554333 7898865
No 95
>PRK10939 autoinducer-2 (AI-2) kinase; Provisional
Probab=48.92 E-value=52 Score=30.38 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=20.7
Q ss_pred CeEEEEecCCCeEEEEEecCCCce
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~ 49 (180)
..+||||+|+..+=+++-|..+.+
T Consensus 3 ~~~lgID~GTts~Ka~l~d~~G~~ 26 (520)
T PRK10939 3 SYLMALDAGTGSIRAVIFDLNGNQ 26 (520)
T ss_pred cEEEEEecCCCceEEEEECCCCCE
Confidence 469999999999999999988643
No 96
>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=48.67 E-value=39 Score=31.06 Aligned_cols=23 Identities=22% Similarity=0.476 Sum_probs=20.1
Q ss_pred EEEEecCCCeEEEEEecCCCcee
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIA 50 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a 50 (180)
+||||+|+..+=+++-|..+.+.
T Consensus 2 ~lgiDiGtt~~K~~l~d~~g~i~ 24 (505)
T TIGR01314 2 MIGVDIGTTSTKAVLFEENGKIV 24 (505)
T ss_pred EEEEeccccceEEEEEcCCCCEE
Confidence 79999999999999999887553
No 97
>PRK10331 L-fuculokinase; Provisional
Probab=47.97 E-value=44 Score=30.37 Aligned_cols=23 Identities=35% Similarity=0.348 Sum_probs=20.1
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~ 49 (180)
.+||||+|+..+=+++-|..+.+
T Consensus 3 ~~lgID~GTt~~Ka~l~d~~G~~ 25 (470)
T PRK10331 3 VILVLDCGATNVRAIAVDRQGKI 25 (470)
T ss_pred eEEEEecCCCceEEEEEcCCCcE
Confidence 58999999999999999987654
No 98
>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=47.87 E-value=70 Score=26.82 Aligned_cols=55 Identities=18% Similarity=0.243 Sum_probs=33.6
Q ss_pred EEEEecCCCeEEEEEecCCCceeccceeeeCC-CCChhhHHHHHHHHHHhhCCCEEEEe
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIASPLSVLLRK-KNTIDLMAEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~-~~~~~~~~~~L~~li~e~~i~~iVVG 85 (180)
+|++|+|..+|=+|+-+....... -.++.. ....+.+...|..++.+ +++.+++.
T Consensus 1 ~L~iDiGNT~i~~g~~~~~~~~~~--~r~~t~~~~t~de~~~~l~~~~~~-~i~~v~vs 56 (243)
T TIGR00671 1 LLLIDVGNTRIVFALNSGNKVYQF--WRLATNLMKTYDEHSEFLKELFGK-SLNKAFIS 56 (243)
T ss_pred CEEEEECCCcEEEEEEECCEEEEE--EEecCCCccChHHHHHHHHHHHHh-hCCEEEEE
Confidence 478999999999999885432221 122211 11223444556666655 48888888
No 99
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=47.14 E-value=76 Score=24.88 Aligned_cols=62 Identities=10% Similarity=0.195 Sum_probs=43.0
Q ss_pred hHHHHHHHHHHhhCCCEEEEecccC--CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhcc
Q 030251 65 LMAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNP 136 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGlP~~--dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~ 136 (180)
.+...+.+++++|+|+.|||=-=.. .+.-|+.+.+.+.-++.+. +++|.++ |+..-++.++.
T Consensus 48 ~Fq~~f~kl~~dy~Vd~VvIk~R~~KGKfAGga~~FKmEaaIQL~~------~~~V~lv----s~~~ik~~lKr 111 (138)
T PF11215_consen 48 KFQFTFAKLMEDYKVDKVVIKERATKGKFAGGAVGFKMEAAIQLID------DVEVELV----SPATIKAQLKR 111 (138)
T ss_pred HHHHHHHHHHHHcCCCEEEEEecccCCCccCCchhHHHHHHHHhcC------CCcEEEE----CHHHHHHHHhc
Confidence 4568899999999999999975333 5556666777666655443 6777765 56666666553
No 100
>PRK14878 UGMP family protein; Provisional
Probab=47.04 E-value=76 Score=27.71 Aligned_cols=90 Identities=12% Similarity=0.134 Sum_probs=51.9
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCC----------CChhhHHHHHHHHHHh-----hCCCEEEEecccCCCCC
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKK----------NTIDLMAEDFRSLISE-----FNLEGFIVGYPFNRQQN 93 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~----------~~~~~~~~~L~~li~e-----~~i~~iVVGlP~~dG~~ 93 (180)
||||-=..-+++|+.+....++.-..+..+.. .....+...+++++++ .+++.|.|+.- -|..
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 57887788899999885444443322221110 0011234566667666 46899999931 1222
Q ss_pred chHHHHHHHHHHHHHhccCCCCCcEEEeccc
Q 030251 94 AADAVQVKLFIDDLSATKKLEDMKYAYWNEG 124 (180)
Q Consensus 94 s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr 124 (180)
+ .-+....|++.|+.. + ++|++.++.-
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 123336778888863 3 7788888653
No 101
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=46.94 E-value=64 Score=28.00 Aligned_cols=43 Identities=9% Similarity=0.115 Sum_probs=36.1
Q ss_pred chHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCC
Q 030251 94 AADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 94 s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 140 (180)
.+..+.+.++++.+++. +++++|++..+++..++.+-.+.|.+
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 34578888999999974 89999999999999999888777753
No 102
>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=46.91 E-value=86 Score=22.62 Aligned_cols=53 Identities=13% Similarity=0.046 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCC-CCcEEEeccccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLE-DMKYAYWNEGFT 126 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~-~lpV~~~DEr~T 126 (180)
.+++.+.+.+++++.|++. .+.+.....+.++++.+++. .+ +++|.+--=-.+
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 44455667788999999884 44 666665544433
No 103
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.40 E-value=98 Score=25.88 Aligned_cols=52 Identities=13% Similarity=0.215 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhhCCCEEEEecccC-CCCCchHH-HHHHHHHHHHHhccCCCC-CcEEEe
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFN-RQQNAADA-VQVKLFIDDLSATKKLED-MKYAYW 121 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~-~~v~~F~~~L~~~~~~~~-lpV~~~ 121 (180)
.++++.+++.+++++.||++-=+. +...+..+ ....+|.++|.+. + +||+++
T Consensus 27 ~l~~l~~~~~~~~~D~lli~GDi~d~~~p~~~~~~~~~~~l~~l~~~----~~i~v~~i 81 (253)
T TIGR00619 27 FLDDLLEFAKAEQIDALLVAGDVFDTANPPAEAQELFNAFFRNLSDA----NPIPIVVI 81 (253)
T ss_pred HHHHHHHHHHHcCCCEEEECCccCCCCCCCHHHHHHHHHHHHHHHhc----CCceEEEE
Confidence 468888888899999988875555 44444433 2345676777652 4 888877
No 104
>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=46.23 E-value=62 Score=27.21 Aligned_cols=45 Identities=9% Similarity=0.259 Sum_probs=35.9
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.++.+-+.+...+.|+|| ||.+-....+.+...++++ + .+||++.
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 445556677889999999 8887777788889999996 4 5998875
No 105
>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=45.90 E-value=62 Score=27.16 Aligned_cols=51 Identities=16% Similarity=0.292 Sum_probs=39.5
Q ss_pred chHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCCCCCCCcHHH
Q 030251 94 AADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFA 152 (180)
Q Consensus 94 s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~A 152 (180)
.+..+.+.++.+.+++. +++++|++...++..++..-++.|.+ -..+|.++
T Consensus 200 eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~la~~~g~~----v~~ld~~~ 250 (266)
T cd01018 200 EPSPADLKRLIDLAKEK----GVRVVFVQPQFSTKSAEAIAREIGAK----VVTIDPLA 250 (266)
T ss_pred CCCHHHHHHHHHHHHHc----CCCEEEEcCCCCcHHHHHHHHHcCCe----EEEeCCcH
Confidence 34577888999999974 78999999999999998887777764 23456554
No 106
>PRK14046 malate--CoA ligase subunit beta; Provisional
Probab=45.82 E-value=1.2e+02 Score=27.40 Aligned_cols=87 Identities=15% Similarity=0.076 Sum_probs=51.3
Q ss_pred CceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccccc
Q 030251 47 NKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 126 (180)
Q Consensus 47 ~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~T 126 (180)
+..+.|+.+- ...+.+.+...|+.+.++-+++.|+|..+ . | .......++.+++.+++. . ++.||+.+-..-.
T Consensus 281 g~paNPlDlg--g~a~~e~~~~aL~~ll~Dp~VdaVlv~i~-g-g-i~~~~~vA~~Ii~a~~~~-~-~~kPvvv~l~G~~ 353 (392)
T PRK14046 281 GEPANFLDVG--GGASPERVAKAFRLVLSDRNVKAILVNIF-A-G-INRCDWVAEGVVQAAREV-G-IDVPLVVRLAGTN 353 (392)
T ss_pred CCCcCCEEec--CCCCHHHHHHHHHHHHcCCCCCEEEEEcC-C-C-CCCHHHHHHHHHHHHHhc-C-CCCcEEEEcCCCC
Confidence 3446677662 22344555677777777889999998766 2 2 221133445555555431 1 2567755444446
Q ss_pred HHHHHHHhccCCCC
Q 030251 127 SKGVELLLNPLDLH 140 (180)
Q Consensus 127 T~~A~~~l~~~g~~ 140 (180)
..++++.|.++|+.
T Consensus 354 ~e~~~~iL~~~Gip 367 (392)
T PRK14046 354 VEEGRKILAESGLP 367 (392)
T ss_pred HHHHHHHHHHcCCC
Confidence 67778888888764
No 107
>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=45.65 E-value=36 Score=24.19 Aligned_cols=22 Identities=18% Similarity=0.131 Sum_probs=19.0
Q ss_pred HHHHHHHHHhhCCCEEEEeccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPF 88 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~ 88 (180)
.+.|.+++++++++.||+|..-
T Consensus 83 ~~~I~~~a~~~~~dlIV~G~~~ 104 (132)
T cd01988 83 ASGILRTAKERQADLIIMGWHG 104 (132)
T ss_pred HHHHHHHHHhcCCCEEEEecCC
Confidence 5889999999999999999543
No 108
>TIGR01311 glycerol_kin glycerol kinase. This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases.
Probab=45.61 E-value=52 Score=30.13 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=20.3
Q ss_pred eEEEEecCCCeEEEEEecCCCcee
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIA 50 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a 50 (180)
.+||||+|+..|=+++-|..+.+.
T Consensus 2 ~~lgiDiGtt~iKa~l~d~~g~~l 25 (493)
T TIGR01311 2 YILAIDQGTTSSRAIVFDKDGNIV 25 (493)
T ss_pred eEEEEecCCCceEEEEECCCCCEE
Confidence 479999999999999999776443
No 109
>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=44.96 E-value=56 Score=30.46 Aligned_cols=23 Identities=30% Similarity=0.538 Sum_probs=19.9
Q ss_pred EEEEecCCCeEEEEEecCCCcee
Q 030251 28 FLGLDVGDKYVGLSISDPKNKIA 50 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~~~~a 50 (180)
+||||+|+..|=+++-|..+.+.
T Consensus 2 ~lgID~GTts~Ka~l~d~~G~i~ 24 (541)
T TIGR01315 2 YIGVDVGTGSARACIIDSTGDIL 24 (541)
T ss_pred EEEEEecCcCEEEEEEcCCCCEE
Confidence 79999999999999999876543
No 110
>PRK11572 copper homeostasis protein CutC; Provisional
Probab=44.56 E-value=79 Score=27.08 Aligned_cols=60 Identities=10% Similarity=0.199 Sum_probs=41.0
Q ss_pred HHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEE---ecccccHHHHHHHhccCCCC
Q 030251 72 SLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAY---WNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 72 ~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~---~DEr~TT~~A~~~l~~~g~~ 140 (180)
+.+.+..+++||+| -|+ +|+.... ..++|-+. ..++|++| +|+--...+|.+.|.+.|+.
T Consensus 80 ~~~~~~GadGvV~G-~L~~dg~vD~~------~~~~Li~~--a~~~~vTFHRAfD~~~d~~~al~~l~~lG~~ 143 (248)
T PRK11572 80 ATVRELGFPGLVTG-VLDVDGHVDMP------RMRKIMAA--AGPLAVTFHRAFDMCANPLNALKQLADLGVA 143 (248)
T ss_pred HHHHHcCCCEEEEe-eECCCCCcCHH------HHHHHHHH--hcCCceEEechhhccCCHHHHHHHHHHcCCC
Confidence 34556789999999 466 8886642 22233322 12688887 48877888898888887874
No 111
>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=44.45 E-value=1.1e+02 Score=21.67 Aligned_cols=48 Identities=4% Similarity=-0.005 Sum_probs=33.3
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+++.+.+.+++++.|.+.. ..+.....+.++++.+++. .|+++|+.=-
T Consensus 41 ~~l~~~~~~~~pd~V~iS~-----~~~~~~~~~~~l~~~~k~~--~p~~~iv~GG 88 (121)
T PF02310_consen 41 EELVEALRAERPDVVGISV-----SMTPNLPEAKRLARAIKER--NPNIPIVVGG 88 (121)
T ss_dssp HHHHHHHHHTTCSEEEEEE-----SSSTHHHHHHHHHHHHHTT--CTTSEEEEEE
T ss_pred HHHHHHHhcCCCcEEEEEc-----cCcCcHHHHHHHHHHHHhc--CCCCEEEEEC
Confidence 7778888888999888873 2445566677888887763 4566665543
No 112
>PRK15005 universal stress protein F; Provisional
Probab=44.14 E-value=46 Score=24.32 Aligned_cols=19 Identities=11% Similarity=0.216 Sum_probs=17.1
Q ss_pred HHHHHHHHHhhCCCEEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVG 85 (180)
.+.|.+.++++++|.||+|
T Consensus 96 ~~~I~~~a~~~~~DLIV~G 114 (144)
T PRK15005 96 KDRILELAKKIPADMIIIA 114 (144)
T ss_pred HHHHHHHHHHcCCCEEEEe
Confidence 5788889999999999999
No 113
>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=43.82 E-value=1.2e+02 Score=26.89 Aligned_cols=85 Identities=12% Similarity=0.074 Sum_probs=50.2
Q ss_pred CceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccccc
Q 030251 47 NKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 126 (180)
Q Consensus 47 ~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~T 126 (180)
+..+.|+.+- ...+.+.+.+.|+.+.++-+++.|+|-++ |........++.+++.+++. . ++.||+.+-....
T Consensus 281 ~~~aNplDlg--g~a~~~~~~~al~~l~~dp~vd~ilv~i~---gg~~~~~~va~~i~~a~~~~-~-~~kPvvv~~~g~~ 353 (386)
T TIGR01016 281 GEPANFLDVG--GGASAERVREALKLVLSDKSVKVVFINIF---GGITRCDLVAKGLVEALKEV-G-VNVPVVVRLEGTN 353 (386)
T ss_pred CCCCCcEEec--CCCCHHHHHHHHHHHHcCCCCCEEEEECC---CCCCCHHHHHHHHHHHHHhc-C-CCCcEEEEeCCcc
Confidence 3445666652 22334455677777777889999998655 22222234445666655542 1 1367755544445
Q ss_pred HHHHHHHhccCC
Q 030251 127 SKGVELLLNPLD 138 (180)
Q Consensus 127 T~~A~~~l~~~g 138 (180)
..+++++|.+.|
T Consensus 354 ~~~~~~~L~~~G 365 (386)
T TIGR01016 354 VEEGKKILAESG 365 (386)
T ss_pred HHHHHHHHHHcC
Confidence 667788888877
No 114
>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=43.74 E-value=92 Score=24.84 Aligned_cols=48 Identities=17% Similarity=0.183 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccc
Q 030251 64 DLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 124 (180)
Q Consensus 64 ~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr 124 (180)
....+.+++++. .++++||+..+-.+.. ..+.+++.+. ++||+++|-.
T Consensus 42 ~~q~~~i~~~i~-~~~d~Iiv~~~~~~~~--------~~~l~~~~~~----gIpvv~~d~~ 89 (257)
T PF13407_consen 42 EEQIEQIEQAIS-QGVDGIIVSPVDPDSL--------APFLEKAKAA----GIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHHHHHH-TTESEEEEESSSTTTT--------HHHHHHHHHT----TSEEEEESST
T ss_pred HHHHHHHHHHHH-hcCCEEEecCCCHHHH--------HHHHHHHhhc----CceEEEEecc
Confidence 333566777765 5599999983222111 1355566653 7899988755
No 115
>COG1521 Pantothenate kinase type III (Bvg accessory factor family protein) [Transcription]
Probab=43.68 E-value=60 Score=27.81 Aligned_cols=18 Identities=17% Similarity=0.447 Sum_probs=16.8
Q ss_pred eEEEEecCCCeEEEEEec
Q 030251 27 RFLGLDVGDKYVGLSISD 44 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd 44 (180)
++|.||+|..++=+|+.+
T Consensus 1 ~~L~iDiGNT~~~~a~~~ 18 (251)
T COG1521 1 MLLLIDIGNTRIVFALYE 18 (251)
T ss_pred CeEEEEeCCCeEEEEEec
Confidence 479999999999999998
No 116
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=43.36 E-value=1.9e+02 Score=23.95 Aligned_cols=91 Identities=12% Similarity=0.216 Sum_probs=47.3
Q ss_pred EEecCCCeEEEEEecCCC-cee---ccceeeeCCC-CChh---hHHHHHHHHHHh---hCCCEEEEecccC-CCCCchHH
Q 030251 30 GLDVGDKYVGLSISDPKN-KIA---SPLSVLLRKK-NTID---LMAEDFRSLISE---FNLEGFIVGYPFN-RQQNAADA 97 (180)
Q Consensus 30 alD~G~kriGvAvsd~~~-~~a---~Pl~~i~~~~-~~~~---~~~~~L~~li~e---~~i~~iVVGlP~~-dG~~s~~~ 97 (180)
|||+|+..|=+-+.+... .+| .|-..+.... .+.+ .++.++.+..++ ..+..+|++.|-+ +...-
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 689999999877755444 222 1111111100 1122 233444443323 3578999999988 54322
Q ss_pred HHHHHHHHHHHhccCCCCCc-EEEecccccHHHH
Q 030251 98 VQVKLFIDDLSATKKLEDMK-YAYWNEGFTSKGV 130 (180)
Q Consensus 98 ~~v~~F~~~L~~~~~~~~lp-V~~~DEr~TT~~A 130 (180)
+...+.++.. +++ +.+++|.+....+
T Consensus 78 ---~a~~~a~~~a----Gl~~~~li~ep~Aaa~~ 104 (239)
T TIGR02529 78 ---KVIVNVIESA----GIEVLHVLDEPTAAAAV 104 (239)
T ss_pred ---HHHHHHHHHc----CCceEEEeehHHHHHHH
Confidence 2333444442 555 4566677655443
No 117
>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=43.36 E-value=1.3e+02 Score=24.00 Aligned_cols=19 Identities=26% Similarity=0.583 Sum_probs=15.2
Q ss_pred HHHHHHHHHhhCCCEEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVG 85 (180)
.+.+..++..+++++||+-
T Consensus 49 ~~~~~~~~~~~~~dgiii~ 67 (270)
T cd06294 49 LEEVKKMIQQKRVDGFILL 67 (270)
T ss_pred HHHHHHHHHHcCcCEEEEe
Confidence 4677777888889998886
No 118
>PRK13410 molecular chaperone DnaK; Provisional
Probab=43.02 E-value=25 Score=34.00 Aligned_cols=22 Identities=23% Similarity=0.515 Sum_probs=18.8
Q ss_pred CCeEEEEecCCCeEEEEEecCC
Q 030251 25 RGRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~ 46 (180)
|+.++|||+|+..+-||+.+..
T Consensus 1 m~~viGIDlGTt~s~va~~~~g 22 (668)
T PRK13410 1 MGRIVGIDLGTTNSVVAVMEGG 22 (668)
T ss_pred CCcEEEEEeCCCcEEEEEEECC
Confidence 3679999999999999998654
No 119
>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=42.91 E-value=1.1e+02 Score=21.13 Aligned_cols=49 Identities=10% Similarity=0.021 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.|.+.+++++++.||+|-.-..+... ...-.++++|-+. . .+||..+
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 6899999999999999999765311110 0112355555553 2 6787654
No 120
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=42.78 E-value=1.3e+02 Score=21.88 Aligned_cols=70 Identities=11% Similarity=0.105 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHhhC--CCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCC
Q 030251 65 LMAEDFRSLISEFN--LEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD 138 (180)
Q Consensus 65 ~~~~~L~~li~e~~--i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g 138 (180)
..+++|..|++.-+ +.+-|+-.... |...--..-++.+.++.++. .++.++.+|..+|..+.+.+-...|
T Consensus 8 ~~l~El~~L~~t~g~~vv~~~~q~~~~~~p~~~iG~GK~eei~~~~~~----~~~d~vvfd~~Lsp~Q~rNLe~~~~ 80 (95)
T PF13167_consen 8 ESLEELEELAETAGYEVVGTVVQKRRKPDPKTYIGSGKVEEIKELIEE----LDADLVVFDNELSPSQQRNLEKALG 80 (95)
T ss_pred HHHHHHHHHHHHCCCeEEEEEEecCCCCCcceeechhHHHHHHHHHhh----cCCCEEEECCCCCHHHHHHHHHHHC
Confidence 34688888888643 22223332222 22211122344444444443 2677888888899998887654444
No 121
>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=42.70 E-value=1.1e+02 Score=22.30 Aligned_cols=55 Identities=7% Similarity=-0.071 Sum_probs=33.1
Q ss_pred EEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCC
Q 030251 81 GFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 81 ~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 140 (180)
.++|| .|+..+.....+.|++.+++.. ...+.+-+..=.-|-.++-+.+...|.+
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 8888876677788888887631 1234455665333444455555555544
No 122
>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=42.10 E-value=79 Score=26.45 Aligned_cols=48 Identities=10% Similarity=0.241 Sum_probs=34.9
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
...|.+++.+...+.|+|| ||.+-. ....+..+.+++..+ .+||++.-
T Consensus 14 ~~~~~~~~~~~gtdai~vG-----GS~~v~-~~~~~~~~~ik~~~~--~~Pvilfp 61 (219)
T cd02812 14 DEEIAKLAEESGTDAIMVG-----GSDGVS-STLDNVVRLIKRIRR--PVPVILFP 61 (219)
T ss_pred HHHHHHHHHhcCCCEEEEC-----Cccchh-hhHHHHHHHHHHhcC--CCCEEEeC
Confidence 3668888888899999999 887665 566667777776311 38887654
No 123
>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=42.07 E-value=1.6e+02 Score=23.45 Aligned_cols=22 Identities=27% Similarity=0.679 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHhhCCCEEEEec
Q 030251 64 DLMAEDFRSLISEFNLEGFIVGY 86 (180)
Q Consensus 64 ~~~~~~L~~li~e~~i~~iVVGl 86 (180)
..++..+.+++++++|+ +++|+
T Consensus 49 ~~lL~~F~~~i~~~dPd-~i~gy 70 (188)
T cd05781 49 RKIIREFVKYVKEYDPD-IIVGY 70 (188)
T ss_pred HHHHHHHHHHHHHcCCC-EEEec
Confidence 35689999999999999 55696
No 124
>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=41.96 E-value=84 Score=28.34 Aligned_cols=58 Identities=12% Similarity=0.209 Sum_probs=42.1
Q ss_pred ChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEE--Eecccc
Q 030251 62 TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA--YWNEGF 125 (180)
Q Consensus 62 ~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~--~~DEr~ 125 (180)
+.+...+++.+.++++++|.+|.|=-+|-|.++..|-.+- +.+++. + ++|++ +..|.-
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 3456689999999999999999995555899998877654 344442 3 67865 556653
No 125
>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=41.72 E-value=47 Score=24.36 Aligned_cols=19 Identities=11% Similarity=0.433 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhCCCEEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVG 85 (180)
.+.|.+..++++++.||+|
T Consensus 92 ~~~I~~~a~~~~~dlIV~G 110 (146)
T cd01989 92 AKAIVEYVADHGITKLVMG 110 (146)
T ss_pred HHHHHHHHHHcCCCEEEEe
Confidence 5778888999999999999
No 126
>PRK13927 rod shape-determining protein MreB; Provisional
Probab=41.71 E-value=2.2e+02 Score=24.28 Aligned_cols=27 Identities=19% Similarity=0.295 Sum_probs=18.2
Q ss_pred CeEEEEecCCCeEEEEEecCCCceecc
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASP 52 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~P 52 (180)
.+.+|||+|+.++=+...+....+..|
T Consensus 5 ~~~igIDlGt~~~~i~~~~~~~~~~~p 31 (334)
T PRK13927 5 SNDLGIDLGTANTLVYVKGKGIVLNEP 31 (334)
T ss_pred cceeEEEcCcceEEEEECCCcEEEecC
Confidence 457999999998777665544333444
No 127
>PLN02757 sirohydrochlorine ferrochelatase
Probab=41.18 E-value=1.1e+02 Score=24.02 Aligned_cols=56 Identities=9% Similarity=-0.086 Sum_probs=31.7
Q ss_pred CCEEEEecccCCCCCchHH-HHHHHHHHHHHhccCCCCCcEEEec-ccccHHHHHHHhccCC
Q 030251 79 LEGFIVGYPFNRQQNAADA-VQVKLFIDDLSATKKLEDMKYAYWN-EGFTSKGVELLLNPLD 138 (180)
Q Consensus 79 i~~iVVGlP~~dG~~s~~~-~~v~~F~~~L~~~~~~~~lpV~~~D-Er~TT~~A~~~l~~~g 138 (180)
...++|| .|+..+.+ ..+++|++.|++...++.+.+.|.. ..-|-.+|-+.+.+.|
T Consensus 14 ~~lllvg----HGSrd~~a~~~~~~la~~l~~~~~~~~V~~aFle~~~Psl~eal~~l~~~g 71 (154)
T PLN02757 14 DGVVIVD----HGSRRKESNLMLEEFVAMYKQKTGHPIVEPAHMELAEPSIKDAFGRCVEQG 71 (154)
T ss_pred cEEEEEe----CCCCCHHHHHHHHHHHHHHHhhCCCCcEEEEEEecCCCCHHHHHHHHHHCC
Confidence 4567888 78877765 5557888888764222233445555 3344455544443333
No 128
>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=40.54 E-value=1.2e+02 Score=20.65 Aligned_cols=62 Identities=10% Similarity=0.088 Sum_probs=43.0
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCC
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 139 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 139 (180)
.++.+.+.+..++.+++++-..+ ..+ ..+++.|++. .++.|++++=...++....+.+ +.|.
T Consensus 33 ~~~~~~~~~~~~d~iiid~~~~~-~~~------~~~~~~i~~~--~~~~~ii~~t~~~~~~~~~~~~-~~g~ 94 (112)
T PF00072_consen 33 EEALELLKKHPPDLIIIDLELPD-GDG------LELLEQIRQI--NPSIPIIVVTDEDDSDEVQEAL-RAGA 94 (112)
T ss_dssp HHHHHHHHHSTESEEEEESSSSS-SBH------HHHHHHHHHH--TTTSEEEEEESSTSHHHHHHHH-HTTE
T ss_pred HHHHHHhcccCceEEEEEeeecc-ccc------cccccccccc--cccccEEEecCCCCHHHHHHHH-HCCC
Confidence 55667778889999999965553 222 3677778764 3588988887777766666666 4444
No 129
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=40.28 E-value=71 Score=22.93 Aligned_cols=47 Identities=6% Similarity=0.068 Sum_probs=30.4
Q ss_pred HHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHH
Q 030251 69 DFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKG 129 (180)
Q Consensus 69 ~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~ 129 (180)
+...-+++-+++.|||| -|+... ++.|.+.. .+ ..| +++|+....-.
T Consensus 4 ~~~~~l~~~gv~lv~I~----~g~~~~----~~~f~~~~----~~-p~~-ly~D~~~~lY~ 50 (115)
T PF13911_consen 4 RRKPELEAAGVKLVVIG----CGSPEG----IEKFCELT----GF-PFP-LYVDPERKLYK 50 (115)
T ss_pred HhHHHHHHcCCeEEEEE----cCCHHH----HHHHHhcc----CC-CCc-EEEeCcHHHHH
Confidence 34555666899999999 566522 56777542 25 568 78898544333
No 130
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=40.28 E-value=27 Score=33.26 Aligned_cols=21 Identities=19% Similarity=0.571 Sum_probs=17.9
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030251 26 GRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~ 46 (180)
+.++|||+|+..+-+|+.++.
T Consensus 2 ~~viGIDlGTt~s~va~~~~g 22 (627)
T PRK00290 2 GKIIGIDLGTTNSCVAVMEGG 22 (627)
T ss_pred CcEEEEEeCcccEEEEEEECC
Confidence 469999999999999998643
No 131
>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=39.60 E-value=1e+02 Score=25.97 Aligned_cols=44 Identities=20% Similarity=0.295 Sum_probs=35.9
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCC
Q 030251 93 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 93 ~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 140 (180)
..+..+.+.++.+.+++. +++++|++..+++..++.+-++.|.+
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 345578889999999974 79999999999999998877776654
No 132
>PRK04123 ribulokinase; Provisional
Probab=39.58 E-value=71 Score=29.66 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=19.4
Q ss_pred CeEEEEecCCCeEEEEEecC-CCc
Q 030251 26 GRFLGLDVGDKYVGLSISDP-KNK 48 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~-~~~ 48 (180)
..+||||.|+..+=+++-|. .+.
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 133
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=39.57 E-value=1.1e+02 Score=27.03 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.++.+++.+.++|.|||+-=+- .+..+..+ +..|.+.|.+-. ..++||+.+
T Consensus 28 ~f~~~l~~a~~~~vD~vliAGDlFd~~~Ps~~a--~~~~~~~l~~l~-~~~Ipv~~I 81 (390)
T COG0420 28 AFDELLEIAKEEKVDFVLIAGDLFDTNNPSPRA--LKLFLEALRRLK-DAGIPVVVI 81 (390)
T ss_pred HHHHHHHHHHHccCCEEEEccccccCCCCCHHH--HHHHHHHHHHhc-cCCCcEEEe
Confidence 468889999999999999996666 55555544 345666666521 237999877
No 134
>PRK13331 pantothenate kinase; Reviewed
Probab=39.46 E-value=1.1e+02 Score=26.19 Aligned_cols=25 Identities=12% Similarity=0.203 Sum_probs=21.3
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCc
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPKNK 48 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~~~ 48 (180)
..+++|+||+|..+|=+++-+....
T Consensus 5 ~~~~~L~iDiGNT~~~~g~f~~~~~ 29 (251)
T PRK13331 5 TSNEWLALMIGNSRLHWGYFSGETL 29 (251)
T ss_pred CCCcEEEEEeCCCcEEEEEEECCEE
Confidence 4589999999999999999986543
No 135
>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=39.29 E-value=56 Score=28.03 Aligned_cols=64 Identities=14% Similarity=0.325 Sum_probs=39.6
Q ss_pred eeccceeeeCCCCChhhHHHHHHHHHHhhC--CCEEEEecccC-C-CCCchHHHHHHHHHHHHHhccCCC----CCcEEE
Q 030251 49 IASPLSVLLRKKNTIDLMAEDFRSLISEFN--LEGFIVGYPFN-R-QQNAADAVQVKLFIDDLSATKKLE----DMKYAY 120 (180)
Q Consensus 49 ~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~--i~~iVVGlP~~-d-G~~s~~~~~v~~F~~~L~~~~~~~----~lpV~~ 120 (180)
..+|+.+++.. + ++.|.+.++.+. .+.|+||.|+- . |.. +....++++++.|.+. ++ +-.++|
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 45777777643 2 678888888775 68999999998 3 555 6677888999999873 32 334666
Q ss_pred e
Q 030251 121 W 121 (180)
Q Consensus 121 ~ 121 (180)
+
T Consensus 147 m 147 (262)
T PF06180_consen 147 M 147 (262)
T ss_dssp E
T ss_pred E
Confidence 5
No 136
>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=39.22 E-value=77 Score=28.82 Aligned_cols=23 Identities=26% Similarity=0.277 Sum_probs=19.7
Q ss_pred eEEEEecCCCeEEEEEecCCCce
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~ 49 (180)
.+||||+|+..+=+++-|..+.+
T Consensus 2 ~ilgiD~GTss~K~~l~d~~g~~ 24 (465)
T TIGR02628 2 VILVLDCGATNLRAIAINRQGKI 24 (465)
T ss_pred eEEEEecCCCcEEEEEEcCCCCE
Confidence 38999999999999999987643
No 137
>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=39.14 E-value=69 Score=29.74 Aligned_cols=23 Identities=17% Similarity=0.134 Sum_probs=19.2
Q ss_pred eEEEEecCCCeEEEEEec-CCCce
Q 030251 27 RFLGLDVGDKYVGLSISD-PKNKI 49 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd-~~~~~ 49 (180)
.+||||.|+.-+=+++-| ..+.+
T Consensus 2 ~~lgiD~GTss~Ka~l~d~~~G~~ 25 (536)
T TIGR01234 2 YAIGVDFGTLSGRALAVDVATGEE 25 (536)
T ss_pred eEEEEecCCCceEEEEEECCCCcE
Confidence 489999999999999999 65533
No 138
>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=39.00 E-value=1.1e+02 Score=21.89 Aligned_cols=56 Identities=16% Similarity=0.112 Sum_probs=34.5
Q ss_pred EEEEecccCCCCCchH-HHHHHHHHHHHHhccCCCCCcEEEecc-cccHHHHHHHhccCCCC
Q 030251 81 GFIVGYPFNRQQNAAD-AVQVKLFIDDLSATKKLEDMKYAYWNE-GFTSKGVELLLNPLDLH 140 (180)
Q Consensus 81 ~iVVGlP~~dG~~s~~-~~~v~~F~~~L~~~~~~~~lpV~~~DE-r~TT~~A~~~l~~~g~~ 140 (180)
.|+|| .|+..+. ...+..+++.+++...+..+.+.|++. .-|-.+|-..+.+.|.+
T Consensus 3 ~llv~----HGS~~~~~~~~~~~l~~~l~~~~~~~~v~~afle~~~P~~~~~l~~l~~~g~~ 60 (117)
T cd03414 3 VVLVG----RGSSDPDANADVAKIARLLEEGTGFARVETAFAAATRPSLPEALERLRALGAR 60 (117)
T ss_pred EEEEc----CCCCCHHHHHHHHHHHHHHHHhcCCCeEEEEEecCCCCCHHHHHHHHHHcCCC
Confidence 46788 8887554 457788999998642111234457774 56666666666555543
No 139
>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=38.48 E-value=93 Score=25.44 Aligned_cols=49 Identities=14% Similarity=0.139 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhc--cCCCCCcEEEecccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSAT--KKLEDMKYAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~--~~~~~lpV~~~DEr~ 125 (180)
.+.+.+.+++.+ .+++|+ .|..++. .+-+.|.+. ..+.++-++++|||+
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 445555554443 466666 5666663 344455532 134567789999997
No 140
>PRK13411 molecular chaperone DnaK; Provisional
Probab=38.12 E-value=33 Score=32.96 Aligned_cols=21 Identities=19% Similarity=0.545 Sum_probs=18.1
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030251 26 GRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~ 46 (180)
+.++|||+|+..+=+|+.++.
T Consensus 2 ~~viGIDlGTt~s~va~~~~g 22 (653)
T PRK13411 2 GKVIGIDLGTTNSCVAVLEGG 22 (653)
T ss_pred CcEEEEEeCcccEEEEEEECC
Confidence 569999999999999997653
No 141
>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=38.09 E-value=1.5e+02 Score=23.86 Aligned_cols=18 Identities=11% Similarity=0.287 Sum_probs=12.2
Q ss_pred HHHHHHHHhhCCCEEEEe
Q 030251 68 EDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVG 85 (180)
+.+.+.+..+++++||+-
T Consensus 45 ~~~~~~l~~~~vdgvi~~ 62 (269)
T cd06297 45 RYLESTTLAYLTDGLLLA 62 (269)
T ss_pred HHHHHHHHhcCCCEEEEe
Confidence 444455667788888886
No 142
>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=38.08 E-value=1.2e+02 Score=26.09 Aligned_cols=59 Identities=22% Similarity=0.259 Sum_probs=40.2
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHH
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 105 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~ 105 (180)
...|++.|-|||+|-++++ ....+|+++-.++.++.+++|.=. .|-..+.++.+-+.++
T Consensus 155 v~~Aie~Gyk~IaVTv~~~-------------------~~a~~iRe~e~~~~~~~~if~VHt-TGis~eea~~~~~~aD 213 (259)
T TIGR03275 155 VEKAIELGYKKIAVTVADA-------------------EDAKAIRELESESGIDIIIFAVHT-TGIDREDAEEVVQYAD 213 (259)
T ss_pred HHHHHHcCCceEEEEecCH-------------------HHHHHHHHhccccCCcEEEEEEEC-CCCCHHHHHHHHHhhh
Confidence 3356888999998887742 115778888888899999999433 4665555555444444
No 143
>PRK13929 rod-share determining protein MreBH; Provisional
Probab=37.77 E-value=1.4e+02 Score=25.82 Aligned_cols=70 Identities=11% Similarity=0.134 Sum_probs=34.7
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCCh-hhHHHHHHHHHHhhCCCEEEEecccCCCCCchH
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTI-DLMAEDFRSLISEFNLEGFIVGYPFNRQQNAAD 96 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~-~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~ 96 (180)
.+.+|||+|+..+=+...+....+-.|-.+....+... -.+=++-.+.. ...++.+++-.|+.+|.....
T Consensus 4 ~~~~giDlGt~~~~i~~~~~~~~~~~ps~va~~~~~~~~~~vG~~A~~~~-~~~p~~~~~~~pi~~G~I~d~ 74 (335)
T PRK13929 4 STEIGIDLGTANILVYSKNKGIILNEPSVVAVDTETKAVLAIGTEAKNMI-GKTPGKIVAVRPMKDGVIADY 74 (335)
T ss_pred CCeEEEEcccccEEEEECCCcEEecCCcEEEEECCCCeEEEeCHHHHHhh-hcCCCcEEEEecCCCCccCCH
Confidence 34699999999996654332222224422222111110 00011222222 234677777799997775443
No 144
>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=37.60 E-value=1.2e+02 Score=23.96 Aligned_cols=64 Identities=19% Similarity=0.217 Sum_probs=37.2
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCC--CchHHHHHHHHHHHHHhccCCCCCcEEEec------ccccHHHHHHHhccCCC
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQ--NAADAVQVKLFIDDLSATKKLEDMKYAYWN------EGFTSKGVELLLNPLDL 139 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~--~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D------Er~TT~~A~~~l~~~g~ 139 (180)
+.+.+++...+++.+|||.-..-|. .+. ....+++ .++ . ++.|+.++ +..||..-++.+.+..+
T Consensus 89 ~Fi~~il~~~~~~~ivvG~Df~FG~~~~g~-~~~L~~~---~~~---~-g~~v~~v~~~~~~~~~iSST~IR~~i~~G~i 160 (180)
T cd02064 89 EFVEDLLVKLNAKHVVVGFDFRFGKGRSGD-AELLKEL---GKK---Y-GFEVTVVPPVTLDGERVSSTRIREALAEGDV 160 (180)
T ss_pred HHHHHHHhhcCCeEEEEccCCCCCCCCCCC-HHHHHHh---hhh---c-CcEEEEeCcEecCCcEEcHHHHHHHHHhCCH
Confidence 4455666556899999997654121 111 1112222 222 2 56666665 47899988888875443
No 145
>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=37.33 E-value=1.3e+02 Score=20.72 Aligned_cols=48 Identities=15% Similarity=0.075 Sum_probs=32.7
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHH
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 132 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 132 (180)
..+.+++.+++++.+|+| ..++ .....|++. ++.++..++ .+-.+|-+
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 556777777999999998 3333 234567763 789988887 45555543
No 146
>CHL00094 dnaK heat shock protein 70
Probab=37.25 E-value=31 Score=32.83 Aligned_cols=21 Identities=19% Similarity=0.520 Sum_probs=18.1
Q ss_pred CeEEEEecCCCeEEEEEecCC
Q 030251 26 GRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~ 46 (180)
+.++|||+|+..+-+|+.++.
T Consensus 2 ~~viGIDlGTt~s~va~~~~g 22 (621)
T CHL00094 2 GKVVGIDLGTTNSVVAVMEGG 22 (621)
T ss_pred CceEEEEeCcccEEEEEEECC
Confidence 579999999999999998653
No 147
>PLN02669 xylulokinase
Probab=36.87 E-value=88 Score=29.45 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=23.1
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCce
Q 030251 23 SKRGRFLGLDVGDKYVGLSISDPKNKI 49 (180)
Q Consensus 23 ~~~~~iLalD~G~kriGvAvsd~~~~~ 49 (180)
|....+||||+||..+=.++-|..+.+
T Consensus 5 ~~~~~~LGiD~GT~s~Ka~l~d~~g~v 31 (556)
T PLN02669 5 PEDSLFLGFDSSTQSLKATVLDSNLRI 31 (556)
T ss_pred CCCCeEEEEecccCCeEEEEEcCCCCE
Confidence 556779999999999999999988765
No 148
>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=35.41 E-value=1.3e+02 Score=25.50 Aligned_cols=43 Identities=12% Similarity=0.091 Sum_probs=35.7
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCC
Q 030251 93 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 139 (180)
Q Consensus 93 ~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 139 (180)
..+..+.+.++.+.+++. +++++|.+...++..++.+-++.|.
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 445578888899999873 8999999999999999988877775
No 149
>COG0443 DnaK Molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=35.41 E-value=57 Score=31.05 Aligned_cols=22 Identities=14% Similarity=0.305 Sum_probs=19.8
Q ss_pred CCeEEEEecCCCeEEEEEecCC
Q 030251 25 RGRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~ 46 (180)
++.++|||+|+-.+=||+.++.
T Consensus 4 ~~~~iGIDlGTTNS~vA~~~~~ 25 (579)
T COG0443 4 AKKAIGIDLGTTNSVVAVMRGG 25 (579)
T ss_pred CceEEEEEcCCCcEEEEEEeCC
Confidence 3579999999999999999966
No 150
>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=35.24 E-value=1.9e+02 Score=26.31 Aligned_cols=60 Identities=10% Similarity=0.254 Sum_probs=37.7
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe-----cccc-cHHHHHHH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW-----NEGF-TSKGVELL 133 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~-----DEr~-TT~~A~~~ 133 (180)
.+.|.+++++|++|+||.=.... +....+... ..+.+.+. . |+|+..+ |+|. +..+.+.+
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 655443322 22344431 2 7886655 4555 33444443
No 151
>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=35.23 E-value=1.2e+02 Score=25.08 Aligned_cols=22 Identities=27% Similarity=0.410 Sum_probs=19.3
Q ss_pred EEEecCCCeEEEEEecCCCcee
Q 030251 29 LGLDVGDKYVGLSISDPKNKIA 50 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a 50 (180)
||||-|..+|=+.+.|..+.+.
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 152
>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=35.07 E-value=1.6e+02 Score=27.19 Aligned_cols=72 Identities=13% Similarity=0.207 Sum_probs=46.7
Q ss_pred ChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe-ccccc----HHHHHHHhcc
Q 030251 62 TIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW-NEGFT----SKGVELLLNP 136 (180)
Q Consensus 62 ~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~-DEr~T----T~~A~~~l~~ 136 (180)
+.+.++++|+.+++++++..|.+. |++.....+.+.+|.+.|.++. .+.+.+. .-|.+ +.+--+.|++
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 446678999999999999998887 6665544567788999988641 1444432 22322 2344455666
Q ss_pred CCCC
Q 030251 137 LDLH 140 (180)
Q Consensus 137 ~g~~ 140 (180)
+|..
T Consensus 296 aG~~ 299 (497)
T TIGR02026 296 AGLV 299 (497)
T ss_pred hCCc
Confidence 6653
No 153
>PF14450 FtsA: Cell division protein FtsA; PDB: 1E4F_T 4A2B_A 4A2A_A 1E4G_T.
Probab=35.05 E-value=37 Score=25.05 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=16.0
Q ss_pred EEEEecCCCeEEEEEecCC
Q 030251 28 FLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~ 46 (180)
+.+||+|+.+|.+++....
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 5789999999999999863
No 154
>PRK10606 btuE putative glutathione peroxidase; Provisional
Probab=34.48 E-value=65 Score=25.96 Aligned_cols=39 Identities=15% Similarity=0.319 Sum_probs=28.6
Q ss_pred HHHHHHHHHhhCC-CEEEEecccC--CCCCchHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNL-EGFIVGYPFN--RQQNAADAVQVKLFID 105 (180)
Q Consensus 67 ~~~L~~li~e~~i-~~iVVGlP~~--dG~~s~~~~~v~~F~~ 105 (180)
...|.++.++|+- +..|+|.|.+ .+.+......+++|++
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 5788888888875 4668899987 3454445577788876
No 155
>TIGR03722 arch_KAE1 universal archaeal protein Kae1. This family represents the archaeal protein Kae1. Its partner Bud32 is fused with it in about half of the known archaeal genomes. The pair, which appears universal in the archaea, corresponds to EKC/KEOPS complex in eukaryotes. A recent characterization of the member from Pyrococcus abyssi, as an iron-binding, atypical DNA-binding protein with an apurinic lyase activity, challenges the common annotation of close homologs as O-sialoglycoprotein endopeptidase. The latter annotation is based on a characterized protein from the bacterium Pasteurella haemolytica.
Probab=34.42 E-value=2.8e+02 Score=23.99 Aligned_cols=89 Identities=12% Similarity=0.110 Sum_probs=49.6
Q ss_pred EEEecCCCeEEEEEecCCC-ceeccceeeeCCCC----------ChhhHHHHHHHHHHhh-----CCCEEEEecccCCCC
Q 030251 29 LGLDVGDKYVGLSISDPKN-KIASPLSVLLRKKN----------TIDLMAEDFRSLISEF-----NLEGFIVGYPFNRQQ 92 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~-~~a~Pl~~i~~~~~----------~~~~~~~~L~~li~e~-----~i~~iVVGlP~~dG~ 92 (180)
||||--..-+++|+.+..+ .++.-..+...... ....+...+++++++- +++.|+|+.-. |.
T Consensus 1 Lgiets~~~~s~al~~~~~~i~~~~~~~~~~~~gg~~p~~~~~~H~~~l~~~i~~~l~~~~~~~~did~Iavt~gP--g~ 78 (322)
T TIGR03722 1 LGIEGTAHTFGVGIVDEDGEILANVSDTYVPEKGGIHPREAAEHHAEVAPKLIKEALEEAGVSLEDIDAVAFSQGP--GL 78 (322)
T ss_pred CEEeccccceEEEEEECCCeEEEEEEeecccCcCCcChhHHHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecCC--ch
Confidence 5788877889999988433 33322222111000 0112335566666653 58999999411 22
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 93 NAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 93 ~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
.+ .-.....|++.|+.. + ++|++.++.
T Consensus 79 ~~-~l~vg~~~ak~la~~--~-~~p~~~v~h 105 (322)
T TIGR03722 79 GP-CLRVGATAARALALK--L-NKPLVGVNH 105 (322)
T ss_pred HH-hHHHHHHHHHHHHHH--h-CCCeechhh
Confidence 21 122335678888863 4 788888854
No 156
>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=34.24 E-value=1.6e+02 Score=22.45 Aligned_cols=51 Identities=14% Similarity=0.123 Sum_probs=34.7
Q ss_pred HHHHHHhhCCCEEEEecccCC-CCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 70 FRSLISEFNLEGFIVGYPFNR-QQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 70 L~~li~e~~i~~iVVGlP~~d-G~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+.+++..++++.|||-+=-|| +...+..+..+.+.+.+++. .|+.||+++.
T Consensus 49 ~~~~~~~~~pd~vii~~G~ND~~~~~~~~~~~~~~i~~i~~~--~p~~~iil~~ 100 (177)
T cd01844 49 VAELLRDVPADLYIIDCGPNIVGAEAMVRERLGPLVKGLRET--HPDTPILLVS 100 (177)
T ss_pred HHHHHHhcCCCEEEEEeccCCCccHHHHHHHHHHHHHHHHHH--CcCCCEEEEe
Confidence 456667789999988654452 22224567778888888874 5677888765
No 157
>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=34.24 E-value=1.1e+02 Score=23.51 Aligned_cols=50 Identities=14% Similarity=0.158 Sum_probs=26.3
Q ss_pred HHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 68 EDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+.+.+.+++.++..|++|.|.. ....++......+..+.+.+. ..+.|+|
T Consensus 98 ~~lv~~~~~~~~~vili~~pp~~~~~~~~~~~~~~~~~~~~a~~-----~~~~~id 148 (200)
T cd01829 98 DELLNVARAKGVPVIWVGLPAMRSPKLSADMVYLNSLYREEVAK-----AGGEFVD 148 (200)
T ss_pred HHHHHHHHhCCCcEEEEcCCCCCChhHhHHHHHHHHHHHHHHHH-----cCCEEEE
Confidence 3344445557888899998776 433333333333333334331 2356666
No 158
>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=34.12 E-value=2e+02 Score=23.13 Aligned_cols=60 Identities=13% Similarity=0.151 Sum_probs=36.9
Q ss_pred hhhHHHHHHHHHHhhCCCEEEEecccC---CCC-CchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 63 IDLMAEDFRSLISEFNLEGFIVGYPFN---RQQ-NAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 63 ~~~~~~~L~~li~e~~i~~iVVGlP~~---dG~-~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
.+.+.+.+..++.+++++.|||=. ++ .+. .......+..+.+.|+.-.+-.+++|+++-+
T Consensus 108 ~~~l~~~i~~~~~~~~~~~vvID~-l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q 171 (242)
T cd00984 108 VSDIRSRARRLKKEHGLGLIVIDY-LQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQ 171 (242)
T ss_pred HHHHHHHHHHHHHhcCCCEEEEcC-chhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecc
Confidence 345567777888888999999973 43 232 2334445566666666321113788888764
No 159
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=34.04 E-value=1.2e+02 Score=25.55 Aligned_cols=41 Identities=17% Similarity=0.326 Sum_probs=33.2
Q ss_pred HHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 72 SLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 72 ~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
+.+.+...+.|+|| |+.+-....+.++.+++++ + ++||++.
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 55666889999999 8887777788889999986 3 6898875
No 160
>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=33.75 E-value=1.1e+02 Score=22.80 Aligned_cols=49 Identities=20% Similarity=0.303 Sum_probs=32.7
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHH---hccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLS---ATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~---~~~~~~~lpV~~~ 121 (180)
++++.+.+. +.|+||+|-|...|+.+... +.|.+++. .. .+.+-++.++
T Consensus 61 ~~~~~~~l~--~aD~iI~~sP~y~~~~s~~l---K~~lD~~~~~~~~-~~~~K~~~~i 112 (152)
T PF03358_consen 61 VQELYDKLK--EADGIIFASPVYNGSVSGQL---KNFLDRLSCWFRR-ALRGKPVAII 112 (152)
T ss_dssp HHHHHHHHH--HSSEEEEEEEEBTTBE-HHH---HHHHHTHHHTHTT-TTTTSEEEEE
T ss_pred HHHHHhcee--cCCeEEEeecEEcCcCChhh---hHHHHHhcccccc-ccCCCEEEEE
Confidence 466666665 68999999999977766644 56777775 22 2446666655
No 161
>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=33.67 E-value=96 Score=27.43 Aligned_cols=107 Identities=14% Similarity=0.206 Sum_probs=53.1
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCC-CChhhHHHHHHHHHHhhCCCEEEEecccCCCCCc---hHHHHHHH
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK-NTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNA---ADAVQVKL 102 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~-~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s---~~~~~v~~ 102 (180)
+-+|||+|+.++=|.+.+....+..|=.+-.... ...-.+=++=.+++ ...++.|.+=.|+.+|-.+ .....++.
T Consensus 2 ~~igIDLGT~~t~i~~~~~Giv~~epSvVA~~~~~~~i~avG~~A~~m~-gktp~~i~~~~Pl~~GvI~D~~~~~~~l~~ 80 (326)
T PF06723_consen 2 KDIGIDLGTSNTRIYVKGKGIVLNEPSVVAYDKDTGKILAVGDEAKAML-GKTPDNIEVVRPLKDGVIADYEAAEEMLRY 80 (326)
T ss_dssp SEEEEEE-SSEEEEEETTTEEEEEEES-EEEETTT--EEEESHHHHTTT-TS-GTTEEEE-SEETTEESSHHHHHHHHHH
T ss_pred CceEEecCcccEEEEECCCCEEEecCcEEEEECCCCeEEEEhHHHHHHh-hcCCCccEEEccccCCcccCHHHHHHHHHH
Confidence 4589999999998877775445555532221111 11000001111222 2357778888898877554 33446677
Q ss_pred HHHHHHhccCCCCCc-EEEecccccHHHHHHHh
Q 030251 103 FIDDLSATKKLEDMK-YAYWNEGFTSKGVELLL 134 (180)
Q Consensus 103 F~~~L~~~~~~~~lp-V~~~DEr~TT~~A~~~l 134 (180)
|.++......+.... ++=+.-..|.+|-+..+
T Consensus 81 ~l~k~~~~~~~~~p~vvi~vP~~~T~verrA~~ 113 (326)
T PF06723_consen 81 FLKKALGRRSFFRPRVVICVPSGITEVERRALI 113 (326)
T ss_dssp HHHHHHTSS-SS--EEEEEE-SS--HHHHHHHH
T ss_pred HHHHhccCCCCCCCeEEEEeCCCCCHHHHHHHH
Confidence 877777631232222 44556777777765543
No 162
>COG4020 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.49 E-value=67 Score=28.17 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=39.3
Q ss_pred CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHH--HHhhCCCEEEEec
Q 030251 26 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSL--ISEFNLEGFIVGY 86 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~l--i~e~~i~~iVVGl 86 (180)
+..+|+|.|+.=|-+|+-|.+...-+-+.--+.+.......+++|.+- +.-++++.|-+-+
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 568999999999999999977766554443333222112335555554 4446788777654
No 163
>PRK15456 universal stress protein UspG; Provisional
Probab=33.39 E-value=44 Score=24.65 Aligned_cols=20 Identities=15% Similarity=0.401 Sum_probs=18.1
Q ss_pred HHHHHHHHHhhCCCEEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGY 86 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGl 86 (180)
.+.|.+..++++++.||+|-
T Consensus 94 ~~~I~~~a~~~~~DLIVmG~ 113 (142)
T PRK15456 94 RDEVNELAEELGADVVVIGS 113 (142)
T ss_pred HHHHHHHHhhcCCCEEEEcC
Confidence 57899999999999999993
No 164
>PRK13329 pantothenate kinase; Reviewed
Probab=33.18 E-value=3e+02 Score=23.21 Aligned_cols=18 Identities=33% Similarity=0.654 Sum_probs=16.7
Q ss_pred eEEEEecCCCeEEEEEec
Q 030251 27 RFLGLDVGDKYVGLSISD 44 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd 44 (180)
++|-||.|..||=.|+.|
T Consensus 2 m~LliD~GNTriKw~~~~ 19 (249)
T PRK13329 2 TFLAIDVGNTRLKWGLYD 19 (249)
T ss_pred CEEEEEcCcchheeeEec
Confidence 488999999999999998
No 165
>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=33.08 E-value=1.4e+02 Score=25.41 Aligned_cols=45 Identities=7% Similarity=0.141 Sum_probs=36.9
Q ss_pred CCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCC
Q 030251 92 QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 92 ~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 140 (180)
...+..+.+.++.+.+++. +++++|++..+++..++..-++.|.+
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 3446688889999999973 89999999999999998887777764
No 166
>PRK11678 putative chaperone; Provisional
Probab=32.96 E-value=41 Score=30.98 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=16.1
Q ss_pred EEEEecCCCeEEEEEecC
Q 030251 28 FLGLDVGDKYVGLSISDP 45 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~ 45 (180)
++|||+||..+=||+.+.
T Consensus 2 ~iGID~GTtNs~va~~~~ 19 (450)
T PRK11678 2 FIGFDYGTANCSVAVMRD 19 (450)
T ss_pred eEEEecCccceeeEEeeC
Confidence 689999999999999863
No 167
>PRK12359 flavodoxin FldB; Provisional
Probab=32.44 E-value=51 Score=26.38 Aligned_cols=28 Identities=11% Similarity=0.292 Sum_probs=24.1
Q ss_pred EEEecccC-CCCCchHHHHHHHHHHHHHh
Q 030251 82 FIVGYPFN-RQQNAADAVQVKLFIDDLSA 109 (180)
Q Consensus 82 iVVGlP~~-dG~~s~~~~~v~~F~~~L~~ 109 (180)
-.||||++ +.......+++.++.+.|+.
T Consensus 138 ~f~gl~lD~~nq~~~t~~ri~~W~~~~~~ 166 (172)
T PRK12359 138 LFVGLALDEVNQYDLSDERIQQWCEQILL 166 (172)
T ss_pred EEEEEEEcCCCchhhhHHHHHHHHHHHHH
Confidence 48999999 88877788999999998875
No 168
>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=32.40 E-value=2e+02 Score=21.00 Aligned_cols=53 Identities=9% Similarity=0.265 Sum_probs=36.9
Q ss_pred HHHHHHHHh-hCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHH
Q 030251 68 EDFRSLISE-FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 128 (180)
Q Consensus 68 ~~L~~li~e-~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~ 128 (180)
+....+++. -.+.++||-+ + .........+.+.+.++ .+ ++||++.=|+.++.
T Consensus 27 dd~~~~i~~~~~i~avvi~~---d---~~~~~~~~~ll~~i~~~-~~-~iPVFl~~~~~~~~ 80 (115)
T PF03709_consen 27 DDALAIIESFTDIAAVVISW---D---GEEEDEAQELLDKIRER-NF-GIPVFLLAERDTTE 80 (115)
T ss_dssp HHHHHHHHCTTTEEEEEEEC---H---HHHHHHHHHHHHHHHHH-ST-T-EEEEEESCCHHH
T ss_pred HHHHHHHHhCCCeeEEEEEc---c---cccchhHHHHHHHHHHh-CC-CCCEEEEecCCCcc
Confidence 555666666 4788999985 3 45556667888888875 34 99999988876444
No 169
>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=32.03 E-value=2.1e+02 Score=24.23 Aligned_cols=55 Identities=9% Similarity=0.192 Sum_probs=38.2
Q ss_pred HHHHHHHHHhh-----CCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 67 AEDFRSLISEF-----NLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 67 ~~~L~~li~e~-----~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
.+.|.+.++++ ++..+++--|-| .|..-+ ....+++++.+++. ++ ++++||.|..
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 68888988886 578999999999 887443 34456677777762 44 4557887654
No 170
>COG4820 EutJ Ethanolamine utilization protein, possible chaperonin [Amino acid transport and metabolism]
Probab=31.77 E-value=88 Score=26.68 Aligned_cols=42 Identities=12% Similarity=0.165 Sum_probs=32.1
Q ss_pred ccccchHHHHHHhhh---ccCCCCeEEEEecCCCeEEEEEecCCC
Q 030251 6 KYVKPLRLFEQMLKR---KVSKRGRFLGLDVGDKYVGLSISDPKN 47 (180)
Q Consensus 6 ~~~~~~~~~~~~~~~---~~~~~~~iLalD~G~kriGvAvsd~~~ 47 (180)
..-.-+|.|...++. .++...-++|+|.|+..|=.-+.|.++
T Consensus 6 ~~n~rlq~~aal~nk~~~~ad~sk~~vGVDLGT~~iV~~vlD~d~ 50 (277)
T COG4820 6 WLNPRLQTAAALCNKTPIAADESKLWVGVDLGTCDIVSMVLDRDG 50 (277)
T ss_pred hhhHHHHHHHHHhcCCccccccCceEEEeecccceEEEEEEcCCC
Confidence 344457788887764 235567899999999999999999865
No 171
>COG1924 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]
Probab=30.81 E-value=1.8e+02 Score=26.73 Aligned_cols=51 Identities=14% Similarity=0.178 Sum_probs=33.7
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF 77 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~ 77 (180)
+.+.+||||.|+..+=.++.+....+... .+......+. ..+.+++..++-
T Consensus 133 ~~~~~LGID~GSTtTK~VLm~d~~~I~~~--~~~~t~g~p~-~~~~l~~~le~l 183 (396)
T COG1924 133 QGMYTLGIDSGSTTTKAVLMEDGKEILYG--FYVSTKGRPI-AEKALKEALEEL 183 (396)
T ss_pred cCcEEEEEecCCcceeEEEEeCCCeEEEE--EEEcCCCChh-HHHHHHHHHHHc
Confidence 55899999999999999999887756653 3333333322 235555555553
No 172
>COG0363 NagB 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]
Probab=30.71 E-value=1.3e+02 Score=25.36 Aligned_cols=52 Identities=8% Similarity=0.030 Sum_probs=29.9
Q ss_pred HHHHHHHHhhCCC--EEEEecccCCCCCchHHHHHHHHHHHHHhc----cCCCCCcEEEecccccH
Q 030251 68 EDFRSLISEFNLE--GFIVGYPFNRQQNAADAVQVKLFIDDLSAT----KKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 68 ~~L~~li~e~~i~--~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~----~~~~~lpV~~~DEr~TT 127 (180)
+.|...+.+-... .+++|+ .|..++. .|-+.|.+. ..+.++-+++.|||+=+
T Consensus 18 ~~i~~~~~~~~~~~~~~~l~L---sgGsTP~-----~~ye~L~~~~~~~~~w~~v~~f~~DEr~vp 75 (238)
T COG0363 18 EIIADKLQAAKAERGRAVLAL---SGGSTPL-----ALYEALVKLPQGQLDWSKVTIFNLDERVVP 75 (238)
T ss_pred HHHHHHHHhhhhccCcEEEEE---CCCCCHH-----HHHHHHHhhhccCCCchheEEEeccccccC
Confidence 4444444433322 578887 5666663 344444432 23567779999999743
No 173
>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=30.55 E-value=2.6e+02 Score=24.79 Aligned_cols=58 Identities=12% Similarity=0.286 Sum_probs=41.5
Q ss_pred hHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhcc--CCCCCcEEEecc
Q 030251 65 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATK--KLEDMKYAYWNE 123 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~--~~~~lpV~~~DE 123 (180)
.++++|.++++.++.+++.|-.--. +...+.......|.+.|.+.. ..++..|++.|=
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 4689999999999999988873222 223456777788888887642 235778888874
No 174
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=30.47 E-value=47 Score=32.05 Aligned_cols=21 Identities=24% Similarity=0.536 Sum_probs=17.9
Q ss_pred CCeEEEEecCCCeEEEEEecC
Q 030251 25 RGRFLGLDVGDKYVGLSISDP 45 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~ 45 (180)
++.++|||+|+..+-+|+.+.
T Consensus 40 ~~~viGIDlGTt~s~va~~~~ 60 (663)
T PTZ00400 40 TGDIVGIDLGTTNSCVAIMEG 60 (663)
T ss_pred cCcEEEEEECcccEEEEEEeC
Confidence 457999999999999998753
No 175
>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=30.45 E-value=2.8e+02 Score=22.56 Aligned_cols=21 Identities=24% Similarity=0.357 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHhhCCCEEEEec
Q 030251 65 LMAEDFRSLISEFNLEGFIVGY 86 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGl 86 (180)
.++.++.+++.+++|+ ||+|+
T Consensus 60 ~lL~~f~~~i~~~dPd-ii~g~ 80 (207)
T cd05785 60 ELLEELVAIIRERDPD-VIEGH 80 (207)
T ss_pred HHHHHHHHHHHHhCCC-EEecc
Confidence 5689999999999998 88996
No 176
>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=30.18 E-value=2.7e+02 Score=21.94 Aligned_cols=19 Identities=26% Similarity=0.476 Sum_probs=14.9
Q ss_pred HHHHHHHHHhhCCCEEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVG 85 (180)
.+.+.+++.++++++||+.
T Consensus 48 ~~~~~~~~~~~~vdgiii~ 66 (268)
T cd06271 48 LEVYRRLVESGLVDGVIIS 66 (268)
T ss_pred HHHHHHHHHcCCCCEEEEe
Confidence 4667777777889999985
No 177
>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=30.04 E-value=1.7e+02 Score=24.53 Aligned_cols=37 Identities=11% Similarity=0.369 Sum_probs=26.7
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDL 107 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L 107 (180)
.+.|.+.+++.+++++|.| |=....+...+++.++++
T Consensus 74 ~e~l~~~l~~~gv~~vv~G----dI~s~~qr~~~e~v~~~l 110 (223)
T TIGR00290 74 VEELKGILHTLDVEAVVFG----AIYSEYQKTRIERVCREL 110 (223)
T ss_pred HHHHHHHHHHcCCCEEEEC----CcccHHHHHHHHHHHHhc
Confidence 6888888888899999999 655555555555554444
No 178
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=29.86 E-value=2.3e+02 Score=22.29 Aligned_cols=30 Identities=13% Similarity=0.320 Sum_probs=22.5
Q ss_pred hCCCEEEEecccCCCCCchHHHHHHHHHHHHHh
Q 030251 77 FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 109 (180)
Q Consensus 77 ~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~ 109 (180)
.+.|.|.+|.+.+.|+..+ .+++|.+.|+.
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 4678999999888777665 55678887764
No 179
>COG4126 Hydantoin racemase [Amino acid transport and metabolism]
Probab=29.71 E-value=82 Score=26.74 Aligned_cols=41 Identities=17% Similarity=0.240 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEE
Q 030251 65 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA 119 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~ 119 (180)
.++.+..+-++|-+.+.||+| -+..+. .+++|++. | ++||+
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 446778888888999999999 454443 46678874 5 78864
No 180
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=29.53 E-value=57 Score=31.34 Aligned_cols=21 Identities=24% Similarity=0.602 Sum_probs=18.0
Q ss_pred CCeEEEEecCCCeEEEEEecC
Q 030251 25 RGRFLGLDVGDKYVGLSISDP 45 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~ 45 (180)
.+.++|||+|+..+=||+.+.
T Consensus 3 ~~~~iGIDlGTt~s~va~~~~ 23 (653)
T PTZ00009 3 KGPAIGIDLGTTYSCVGVWKN 23 (653)
T ss_pred cccEEEEEeCcccEEEEEEeC
Confidence 467999999999999998764
No 181
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=29.48 E-value=50 Score=31.92 Aligned_cols=22 Identities=27% Similarity=0.631 Sum_probs=19.0
Q ss_pred CCeEEEEecCCCeEEEEEecCC
Q 030251 25 RGRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~ 46 (180)
++.++|||+|+..+-+|+.+..
T Consensus 26 ~~~viGIDLGTTnS~vA~~~~~ 47 (657)
T PTZ00186 26 QGDVIGVDLGTTYSCVATMDGD 47 (657)
T ss_pred cceEEEEEeCcCeEEEEEEeCC
Confidence 4679999999999999998753
No 182
>KOG0237 consensus Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism]
Probab=29.47 E-value=1.4e+02 Score=29.14 Aligned_cols=71 Identities=18% Similarity=0.206 Sum_probs=48.4
Q ss_pred HHHHHHHHHhhCCCEEEEec--ccCCC----------------CCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHH
Q 030251 67 AEDFRSLISEFNLEGFIVGY--PFNRQ----------------QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 128 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGl--P~~dG----------------~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~ 128 (180)
++.|.+++.+|+|..+|+|= ||-+| ....|.+--+.|++.+-.+ +++|-.-|+----+.
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 69999999999999999983 44333 2334455567898888764 378854443323347
Q ss_pred HHHHHhccCCCC
Q 030251 129 GVELLLNPLDLH 140 (180)
Q Consensus 129 ~A~~~l~~~g~~ 140 (180)
+|..++...+++
T Consensus 134 ~a~sfi~~~~~~ 145 (788)
T KOG0237|consen 134 EAKSFIQSATDK 145 (788)
T ss_pred HHHHHHHhCCCc
Confidence 888888766543
No 183
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=29.46 E-value=1.1e+02 Score=25.72 Aligned_cols=42 Identities=10% Similarity=0.301 Sum_probs=27.3
Q ss_pred HHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 71 RSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 71 ~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.++++++..+++|+| .++ ||+.... .++.. +... .++||.|.
T Consensus 87 v~llk~~GAdGfVFG-aLt~dgsid~~--~C~si---~~~~---rplPVTFH 129 (255)
T KOG4013|consen 87 VELLKKAGADGFVFG-ALTSDGSIDRT--SCQSI---IETA---RPLPVTFH 129 (255)
T ss_pred HHHHHHcCCCceEEe-ecCCCCCcCHH--HHHHH---HHhc---CCCceeee
Confidence 467889999999999 577 8876632 22222 2221 26898874
No 184
>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=29.44 E-value=1.9e+02 Score=20.85 Aligned_cols=53 Identities=8% Similarity=0.018 Sum_probs=37.4
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
+.++.+.+.+..++.|||--+-. .-.. ..+..|.+.|... +++++.+++.+.+
T Consensus 54 ~~~ll~~~~~~~~d~ivv~~~~Rl~R~~----~~~~~~~~~l~~~----gi~l~~~~~~~~~ 107 (137)
T cd00338 54 LQRLLADVKAGKIDVVLVEKLDRLSRNL----VDLLELLELLEAH----GVRVVTADGEIDL 107 (137)
T ss_pred HHHHHHHHHcCCCCEEEEEecchhhCCH----HHHHHHHHHHHHC----CCEEEEecCCccc
Confidence 67777888878899999986544 2222 2445677777762 8999999976654
No 185
>PRK13790 phosphoribosylamine--glycine ligase; Provisional
Probab=29.19 E-value=1.8e+02 Score=25.78 Aligned_cols=20 Identities=10% Similarity=0.242 Sum_probs=17.5
Q ss_pred HHHHHHHHHhhCCCEEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGY 86 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGl 86 (180)
.+.|.+++++++++.+|+|-
T Consensus 16 ~~~l~~~~~~~~id~vi~g~ 35 (379)
T PRK13790 16 HQAILDFAKQQNVDWVVIGP 35 (379)
T ss_pred HHHHHHHHHHhCCCEEEECC
Confidence 58889999999999999883
No 186
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.13 E-value=95 Score=25.67 Aligned_cols=28 Identities=7% Similarity=0.051 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNA 94 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s 94 (180)
++.|.+.+++.+++.||+.+..+ .|..+
T Consensus 123 i~~L~~Ri~~~~v~EVIlAt~~tvEGe~T 151 (195)
T TIGR00615 123 IAALLKRLQEESVKEVILATNPTVEGEAT 151 (195)
T ss_pred HHHHHHHHhcCCCcEEEEeCCCCchHHHH
Confidence 68888888888999999998888 77544
No 187
>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=29.12 E-value=2.2e+02 Score=20.80 Aligned_cols=55 Identities=15% Similarity=0.124 Sum_probs=34.0
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLN 135 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~ 135 (180)
.+.|..++....++.+||| -|..... --.+..+.|.+. ++.+... +|.+|=+.|.
T Consensus 41 ~~~l~~~~~~~~peiliiG----TG~~~~~--~~~~~~~~l~~~----gI~vE~m----~T~aAcrTyN 95 (109)
T cd00248 41 PEALLPLLAEDRPDILLIG----TGAEIAF--LPRALRAALRAA----GIGVEVM----STGAACRTYN 95 (109)
T ss_pred HHHHHHHHhhCCCCEEEEc----CCCCCCc--CCHHHHHHHHHc----CCeEEEe----CcHHHHHHHH
Confidence 4677777665459999999 6665521 113445566663 6676554 4667766553
No 188
>PRK13844 recombination protein RecR; Provisional
Probab=28.93 E-value=96 Score=25.76 Aligned_cols=28 Identities=7% Similarity=0.232 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNA 94 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s 94 (180)
++.|.+.+.+.+++.||+.+..+ .|..+
T Consensus 127 i~~L~~Ri~~~~v~EVIlAt~~t~EGe~T 155 (200)
T PRK13844 127 LDILQQIIADRKIDEVILAISPTVEGETT 155 (200)
T ss_pred HHHHHHHHhcCCCcEEEEeCCCCccHHHH
Confidence 68888989888999999999888 77544
No 189
>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=28.92 E-value=1.3e+02 Score=25.25 Aligned_cols=61 Identities=11% Similarity=0.162 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccc------ccHHHHHHHh
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG------FTSKGVELLL 134 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr------~TT~~A~~~l 134 (180)
.-++.+...+.+++++++.-|.. .-+. ..+.+|-+.+.+. .++||+++|-- +|...-+++.
T Consensus 84 ~~~~a~~a~~~G~d~v~~~~P~~~~~~~----~~l~~~~~~ia~~---~~~pi~lYn~P~~~g~~ls~~~~~~L~ 151 (284)
T cd00950 84 AIELTKRAEKAGADAALVVTPYYNKPSQ----EGLYAHFKAIAEA---TDLPVILYNVPGRTGVNIEPETVLRLA 151 (284)
T ss_pred HHHHHHHHHHcCCCEEEEcccccCCCCH----HHHHHHHHHHHhc---CCCCEEEEEChhHhCCCCCHHHHHHHh
Confidence 35667778889999999999977 4432 3455666677663 37999998853 4444444444
No 190
>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=28.71 E-value=2.5e+02 Score=21.25 Aligned_cols=58 Identities=9% Similarity=0.161 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhhCCCEEEEecccC--CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFN--RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~--dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
+...+...+.+++++.+||=-|-. +.........+..+...|++ . +..++++.+....
T Consensus 83 ~~~~i~~~~~~~~~~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~---~-g~tvi~v~~~~~~ 142 (187)
T cd01124 83 LIQRLKDAIEEFKAKRVVIDSVSGLLLMEQSTARLEIRRLLFALKR---F-GVTTLLTSEQSGL 142 (187)
T ss_pred HHHHHHHHHHHhCCCEEEEeCcHHHhhcChHHHHHHHHHHHHHHHH---C-CCEEEEEeccccC
Confidence 357778888889999999997765 33233344556667777775 2 7888888776554
No 191
>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=28.66 E-value=2.5e+02 Score=20.97 Aligned_cols=54 Identities=7% Similarity=0.140 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhhCCCEEEEecccC-CCCC---chHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFN-RQQN---AADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~-dG~~---s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+.+.|.+.+ ..+++.||+-+-.| -+.. ....+..+.+.+.+.+. .++.+|+++.
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 456777766 67899999988877 3322 33345556666666653 3577887764
No 192
>PLN02271 serine hydroxymethyltransferase
Probab=28.54 E-value=1.8e+02 Score=28.13 Aligned_cols=38 Identities=11% Similarity=0.079 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHh
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 109 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~ 109 (180)
+++|.+++.+.++..||+| ++.....-.+++|++...+
T Consensus 287 yd~lek~a~~~rPKLII~g-----~Saypr~~D~~~i~eIAde 324 (586)
T PLN02271 287 YDKLEEKALDFRPKILICG-----GSSYPREWDYARFRQIADK 324 (586)
T ss_pred HHHHHHHhhhcCCeEEEEC-----chhccCcCCHHHHHHHHHH
Confidence 6899998899999999998 3333332334445444443
No 193
>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=28.28 E-value=2e+02 Score=24.08 Aligned_cols=37 Identities=16% Similarity=0.376 Sum_probs=26.8
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDL 107 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L 107 (180)
.+.|.+.+.+.++++||.| +=....|...+++.++++
T Consensus 74 ~~~l~~~l~~~gv~~vv~G----dI~s~~qr~~~e~vc~~~ 110 (222)
T TIGR00289 74 VEDLAGQLGELDVEALCIG----AIESNYQKSRIDKVCREL 110 (222)
T ss_pred HHHHHHHHHHcCCCEEEEC----ccccHHHHHHHHHHHHHc
Confidence 5778888888899999999 655555655555555544
No 194
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=28.24 E-value=3.3e+02 Score=23.64 Aligned_cols=67 Identities=13% Similarity=0.094 Sum_probs=44.6
Q ss_pred hhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCC
Q 030251 63 IDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 63 ~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~ 140 (180)
++..-+...+.+++|+++-+|+.-|-- +..++.. +| +.|+.. ++|.+.+-..-|++.. ..|.+.|+.
T Consensus 45 pe~~~~~~~~~~~~~~pDf~i~isPN~-a~PGP~~--AR---E~l~~~----~iP~IvI~D~p~~K~~-d~l~~~g~G 111 (277)
T PRK00994 45 PEEVEEVVKKMLEEWKPDFVIVISPNP-AAPGPKK--AR---EILKAA----GIPCIVIGDAPGKKVK-DAMEEQGLG 111 (277)
T ss_pred HHHHHHHHHHHHHhhCCCEEEEECCCC-CCCCchH--HH---HHHHhc----CCCEEEEcCCCccchH-HHHHhcCCc
Confidence 344344567777999999999997754 3344422 12 235542 7898888888888755 777877763
No 195
>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=28.21 E-value=1.8e+02 Score=25.96 Aligned_cols=53 Identities=15% Similarity=0.151 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccccc
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 126 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~T 126 (180)
-.+.|.++++++++|+||.=.... +-...+.. . ..+.|++. |+|+..+|=.++
T Consensus 301 R~~~i~~lv~~~~~DGVI~~~~kfC~~~~~e~~-~---lk~~l~e~----GIP~L~iE~D~~ 354 (377)
T TIGR03190 301 RYDHVLGLAKEYNVQGAIFLQQKFCDPHEGDYP-D---LKRHLEAN----GIPTLFLEFDIT 354 (377)
T ss_pred HHHHHHHHHHHhCCCEEEEecccCCCcchhhhH-H---HHHHHHHC----CCCEEEEecCCC
Confidence 368899999999999999987777 65544432 2 22345542 899888864455
No 196
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=27.89 E-value=62 Score=30.87 Aligned_cols=19 Identities=21% Similarity=0.338 Sum_probs=16.9
Q ss_pred CeEEEEecCCCeEEEEEec
Q 030251 26 GRFLGLDVGDKYVGLSISD 44 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd 44 (180)
..++|||+|+....||+..
T Consensus 19 ~~viGIDlGTT~S~va~~~ 37 (595)
T PRK01433 19 QIAVGIDFGTTNSLIAIAT 37 (595)
T ss_pred ceEEEEEcCcccEEEEEEe
Confidence 4689999999999999974
No 197
>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=27.83 E-value=2.7e+02 Score=21.39 Aligned_cols=52 Identities=10% Similarity=-0.031 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCch---HHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAA---DAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~---~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
...+.+++.+.+++.||+.-=+. ++.... ....+.+|.+.+.. .++.|++++
T Consensus 27 ~~~~~~~i~~~~pd~vv~~GDl~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~i~~v 82 (156)
T cd08165 27 ERSFQTSLWLLQPDVVFVLGDLFDEGKWSTDEEWEDYVERFKKMFGH---PPDLPLHVV 82 (156)
T ss_pred HHHHHHHHHhcCCCEEEECCCCCCCCccCCHHHHHHHHHHHHHHhcc---CCCCeEEEE
Confidence 45788899999999999875444 333221 12234455554442 236788775
No 198
>KOG4184 consensus Predicted sugar kinase [Carbohydrate transport and metabolism; General function prediction only]
Probab=27.64 E-value=94 Score=28.52 Aligned_cols=68 Identities=15% Similarity=0.177 Sum_probs=47.6
Q ss_pred HHHHHHHHHHhhCCCEEEEe-cccCCC-CCchHHHHHHHHHHHHHhccCCCCCcEE-----EecccccHHHHHHHhc
Q 030251 66 MAEDFRSLISEFNLEGFIVG-YPFNRQ-QNAADAVQVKLFIDDLSATKKLEDMKYA-----YWNEGFTSKGVELLLN 135 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVG-lP~~dG-~~s~~~~~v~~F~~~L~~~~~~~~lpV~-----~~DEr~TT~~A~~~l~ 135 (180)
..+.+-+-+++++|+.+||- +-+-++ +...+.++.+...+.|.+- .+++|++ +.||-|+|.--+..|-
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 35777788899999999884 333322 3335556667777777762 4689987 5788888888876654
No 199
>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=27.51 E-value=2.4e+02 Score=20.51 Aligned_cols=47 Identities=9% Similarity=-0.076 Sum_probs=30.8
Q ss_pred HHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 71 RSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 71 ~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
.....+..-..++|| .|+.+ ....+.+.|.+. ++.+||.+..|.-+.
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 233445555553 678999999988877
No 200
>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=27.03 E-value=2.1e+02 Score=22.27 Aligned_cols=52 Identities=15% Similarity=0.230 Sum_probs=26.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
.+.+.+.+++.+. ++||+ .|..++. ...+.+++..... .+..+-+++.|||+
T Consensus 9 ~~~i~~~~~~~~~--~~i~l---sgGsTp~-~~y~~L~~~~~~~-~w~~v~~f~~DEr~ 60 (169)
T cd00458 9 EDKXEKLLEEKDD--MVIGL---GTGSTPA-YFYKLLGEKLKRG-EISDIVGFPTDERY 60 (169)
T ss_pred HHHHHHHHHhCCC--EEEEE---CCCccHH-HHHHHHHhhhhhC-CccceEEEECcccc
Confidence 4555665655554 44554 2444432 2223333332221 14467788999985
No 201
>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=27.02 E-value=2.1e+02 Score=19.56 Aligned_cols=51 Identities=20% Similarity=0.060 Sum_probs=35.3
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHh
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLL 134 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l 134 (180)
..+.+++...+++.+|+| ..++ ....+|++. ++.|+..++..|-.+|-+.|
T Consensus 51 ~~~~~~l~~~~v~~vi~~------~iG~------~a~~~l~~~----gI~v~~~~~~~~v~eal~~~ 101 (102)
T cd00562 51 KLAARLLALEGCDAVLVG------GIGG------PAAAKLEAA----GIKPIKAAEGGTIEEALEAL 101 (102)
T ss_pred hHHHHHHHHCCCcEEEEc------ccCc------cHHHHHHHc----CCEEEEcCCCCcHHHHHHhh
Confidence 345667777899999999 3444 234467763 88998888766777665543
No 202
>PRK11175 universal stress protein UspE; Provisional
Probab=26.89 E-value=1.7e+02 Score=24.28 Aligned_cols=20 Identities=5% Similarity=-0.230 Sum_probs=18.1
Q ss_pred HHHHHHHHHhhCCCEEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGY 86 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGl 86 (180)
.+.|.+.+.++++|.||+|.
T Consensus 96 ~~~i~~~a~~~~~DLiV~G~ 115 (305)
T PRK11175 96 FEAIIQEVIAGGHDLVVKMT 115 (305)
T ss_pred HHHHHHHHHhcCCCEEEEeC
Confidence 58899999999999999993
No 203
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=26.84 E-value=2.9e+02 Score=21.01 Aligned_cols=53 Identities=13% Similarity=-0.003 Sum_probs=39.3
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccC
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPL 137 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~ 137 (180)
-.+.+++.+++++.+|++ ..++.+.. .|++. ++.|+..++ -|..+|-..+...
T Consensus 55 ~~~a~~l~~~gvdvvi~~------~iG~~a~~------~l~~~----GIkv~~~~~-~~V~e~i~~~~~g 107 (121)
T COG1433 55 IRIAELLVDEGVDVVIAS------NIGPNAYN------ALKAA----GIKVYVAPG-GTVEEAIKAFLEG 107 (121)
T ss_pred HHHHHHHHHcCCCEEEEC------ccCHHHHH------HHHHc----CcEEEecCC-CCHHHHHHHHhcC
Confidence 457889999999999999 55554333 46653 789998888 7788887776543
No 204
>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=26.78 E-value=3.3e+02 Score=21.70 Aligned_cols=44 Identities=16% Similarity=0.302 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
.+.+..++. +++++||+. ....... ....+.+.+. ++||+++|-
T Consensus 50 ~~~~~~~~~-~~vdgiIi~----~~~~~~~----~~~l~~~~~~----~iPvv~~~~ 93 (272)
T cd06300 50 IADIRNLIA-QGVDAIIIN----PASPTAL----NPVIEEACEA----GIPVVSFDG 93 (272)
T ss_pred HHHHHHHHH-cCCCEEEEe----CCChhhh----HHHHHHHHHC----CCeEEEEec
Confidence 455666555 599999997 2221111 1123445542 788888873
No 205
>TIGR01198 pgl 6-phosphogluconolactonase. This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with
Probab=26.69 E-value=1.8e+02 Score=23.99 Aligned_cols=37 Identities=11% Similarity=0.183 Sum_probs=22.6
Q ss_pred EEEEecccCCCCCchHHHHHHHHHHHHHh-ccCCCCCcEEEecccc
Q 030251 81 GFIVGYPFNRQQNAADAVQVKLFIDDLSA-TKKLEDMKYAYWNEGF 125 (180)
Q Consensus 81 ~iVVGlP~~dG~~s~~~~~v~~F~~~L~~-~~~~~~lpV~~~DEr~ 125 (180)
.+++++ .|..++. .+-+.|.+ ...+..+-+++.|||+
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 5666652 44445553 1234577799999997
No 206
>PF04412 DUF521: Protein of unknown function (DUF521); InterPro: IPR007506 This is a group of hypothetical proteins.
Probab=26.67 E-value=2.2e+02 Score=26.06 Aligned_cols=90 Identities=9% Similarity=0.058 Sum_probs=56.7
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhh------CCCEEEEecccCCCCCchH
Q 030251 23 SKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF------NLEGFIVGYPFNRQQNAAD 96 (180)
Q Consensus 23 ~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~------~i~~iVVGlP~~dG~~s~~ 96 (180)
-.+-.+.|+-+--....-|.... .+++.-. .+.|.+..++. ++|.|++|-|-- .
T Consensus 242 ~~m~Hi~GvTPEa~~~~~a~~~~-------~e~i~i~-------~~dl~~~~~~l~~~~~~~~D~V~lGcPH~------S 301 (400)
T PF04412_consen 242 VAMFHIVGVTPEAPTLEAAFGGK-------AERITIT-------DADLEEVYEELNTAGDEKVDLVALGCPHL------S 301 (400)
T ss_pred eeeEEEeCCCCCCCcchhhhcCC-------ceEEEeC-------HHHHHHHHHHhccCCCCCCCEEEECCCCC------C
Confidence 33456667777766666665543 2333322 24445555554 899999995544 4
Q ss_pred HHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHH
Q 030251 97 AVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVEL 132 (180)
Q Consensus 97 ~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~ 132 (180)
..+++++++.|+.+..-+++++..+=-|.+-..|++
T Consensus 302 ~~El~~ia~ll~gr~~~~~~~~~i~t~~~v~~~a~~ 337 (400)
T PF04412_consen 302 LEELREIAELLEGRKVHPNVPLWITTSRAVYELAER 337 (400)
T ss_pred HHHHHHHHHHHhCCCCCCCceEEEECCHHHHHHHHh
Confidence 556778888898753225788888777777777665
No 207
>PRK10854 exopolyphosphatase; Provisional
Probab=26.57 E-value=2.1e+02 Score=26.65 Aligned_cols=92 Identities=14% Similarity=0.143 Sum_probs=56.9
Q ss_pred cCCCCeEEEEecCCCeEEEEEecCCCceeccceee----eC-----CCCC--------hhhHHHHHHHHHHhhCCCE-EE
Q 030251 22 VSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVL----LR-----KKNT--------IDLMAEDFRSLISEFNLEG-FI 83 (180)
Q Consensus 22 ~~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i----~~-----~~~~--------~~~~~~~L~~li~e~~i~~-iV 83 (180)
-|++..+-+||+|+-.|=+.|.+....-...+... .- ..+. .-..+....+++++++++. .+
T Consensus 7 ~~~~~~~A~IDIGSNSirL~I~e~~~~~~~~i~~~k~~vrLg~g~~~~g~Ls~e~~~r~~~~L~~F~~~~~~~~v~~v~~ 86 (513)
T PRK10854 7 SPRPQEFAAVDLGSNSFHMVIARVVDGAMQIIGRLKQRVHLADGLDSDNMLSEEAMERGLNCLSLFAERLQGFSPANVCI 86 (513)
T ss_pred CCCCCEEEEEEeccchheEEEEEecCCcEEEeeeeeEEEECCCCcCCCCCcCHHHHHHHHHHHHHHHHHHHhCCCCeEEE
Confidence 36778899999999999999987542211211111 10 0010 1134677788888999864 45
Q ss_pred EecccCCCCCc-hHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 84 VGYPFNRQQNA-ADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 84 VGlP~~dG~~s-~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
|| |.. ..+.....|.+++++. .|++|..++
T Consensus 87 vA------TsAlReA~N~~~fl~~i~~~---tGl~i~vIs 117 (513)
T PRK10854 87 VG------THTLRQALNATDFLKRAEKV---IPYPIEIIS 117 (513)
T ss_pred Ee------hHHHHcCcCHHHHHHHHHHH---HCCCeEEeC
Confidence 55 322 2234457899999874 388888876
No 208
>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=26.53 E-value=3.4e+02 Score=24.73 Aligned_cols=70 Identities=9% Similarity=0.176 Sum_probs=44.9
Q ss_pred ChhhHHHHHHHHHHhh-CCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEE-ecccccHHHHHHHhccCCC
Q 030251 62 TIDLMAEDFRSLISEF-NLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAY-WNEGFTSKGVELLLNPLDL 139 (180)
Q Consensus 62 ~~~~~~~~L~~li~e~-~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~-~DEr~TT~~A~~~l~~~g~ 139 (180)
..+.++++|+.+.+.+ .+..|.++ |++.+...+.+.++.+.|.+. ++.... ..-.+ +.+--+.|.++|.
T Consensus 228 s~e~V~~Ei~~~~~~~~~~~~i~f~----Dd~f~~~~~~~~~l~~~l~~~----~i~~~~~~~~~~-~~e~l~~l~~aG~ 298 (472)
T TIGR03471 228 SAESVIEEVKYALENFPEVREFFFD----DDTFTDDKPRAEEIARKLGPL----GVTWSCNARANV-DYETLKVMKENGL 298 (472)
T ss_pred CHHHHHHHHHHHHHhcCCCcEEEEe----CCCCCCCHHHHHHHHHHHhhc----CceEEEEecCCC-CHHHHHHHHHcCC
Confidence 3456789999988877 78889888 777766667788888888763 333211 11123 3344455666665
Q ss_pred C
Q 030251 140 H 140 (180)
Q Consensus 140 ~ 140 (180)
+
T Consensus 299 ~ 299 (472)
T TIGR03471 299 R 299 (472)
T ss_pred C
Confidence 4
No 209
>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=26.47 E-value=3.6e+02 Score=23.82 Aligned_cols=94 Identities=18% Similarity=0.273 Sum_probs=50.5
Q ss_pred EEEecCCCeEEEEEecCCCceec-cceeee-CCCCChhhHHHHHHHHHHhhCC-CEEEEecccC-CCCCchHHHHHHHHH
Q 030251 29 LGLDVGDKYVGLSISDPKNKIAS-PLSVLL-RKKNTIDLMAEDFRSLISEFNL-EGFIVGYPFN-RQQNAADAVQVKLFI 104 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~-Pl~~i~-~~~~~~~~~~~~L~~li~e~~i-~~iVVGlP~~-dG~~s~~~~~v~~F~ 104 (180)
+|+|+|...+=+|..|+.+.+.. -...++ .++. +.+-+.|.+++++.+. +.+.|=+-=. -.-......=|+..+
T Consensus 1 ~G~DiGGA~~K~a~~~~~g~~~~v~~~~~plW~~~--~~L~~~l~~~~~~~~~~~~~avtMTgELaD~f~~r~~GV~~i~ 78 (318)
T TIGR03123 1 LGIDIGGANTKAAELDEDGRIKEVHQLYCPLWKGN--DKLAETLKEISQDLSSADNVAVTMTGELADCFEDKAEGVEFIL 78 (318)
T ss_pred CccccccceeeeEEecCCCceeEEEEecCcccCCc--hHHHHHHHHHHHhcCccceEEEEeehhhhhhhcCHHHHHHHHH
Confidence 58999999999998886663332 000111 2222 2334667777766665 4444443211 111224455667777
Q ss_pred HHHHhccCCCCCcEEEe--cccccH
Q 030251 105 DDLSATKKLEDMKYAYW--NEGFTS 127 (180)
Q Consensus 105 ~~L~~~~~~~~lpV~~~--DEr~TT 127 (180)
+.+++. |++ |+.++ |=.+.|
T Consensus 79 ~~~~~~--~~~-~~~i~~s~GG~~s 100 (318)
T TIGR03123 79 AAVESA--FGS-PVSVFASDGGFVS 100 (318)
T ss_pred HHHHHh--cCC-CeEEEecCCCCcc
Confidence 778774 633 55544 444434
No 210
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=26.34 E-value=1.5e+02 Score=28.56 Aligned_cols=47 Identities=17% Similarity=0.204 Sum_probs=30.8
Q ss_pred HHHhhCC---CEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 73 LISEFNL---EGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 73 li~e~~i---~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
.+.+.-+ -+||||. ||..+. ++||+..+......+++|++.+|--+|
T Consensus 93 yl~~~~~~~~~giviG~---D~R~~S-----~~fA~l~a~vf~~~g~~v~lf~~~v~T 142 (607)
T KOG1220|consen 93 YLKNQFPSKNLGIVIGH---DGRYNS-----KRFAELVAAVFLLNGFKVYLFSELVPT 142 (607)
T ss_pred HHHHhCCcccceEEEec---CCccch-----HHHHHHHHHHHHhCCceEEEeccccCC
Confidence 4444445 4999996 888775 567776665322248999999954433
No 211
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=26.27 E-value=3e+02 Score=28.91 Aligned_cols=58 Identities=9% Similarity=0.088 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
+.+.+++.|+..+|+.|.|+-+-. ........|+.....|.-...++.+||+++|+-+
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 346788999999999999984411 1233344555555544432224689999999754
No 212
>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=26.01 E-value=1.6e+02 Score=23.66 Aligned_cols=54 Identities=9% Similarity=0.065 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
+.+.|.+.+.+.+. ++||+ .|..++. ...+.+++.-+....+.++-+++.|||+
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 45677777776644 66665 3555543 2234455544221123466789999998
No 213
>KOG2707 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=26.01 E-value=1e+02 Score=28.17 Aligned_cols=39 Identities=21% Similarity=0.405 Sum_probs=29.6
Q ss_pred hHHHHHHhhhccCCC-CeEEEEecCCCeEEEEEecCCCceecc
Q 030251 11 LRLFEQMLKRKVSKR-GRFLGLDVGDKYVGLSISDPKNKIASP 52 (180)
Q Consensus 11 ~~~~~~~~~~~~~~~-~~iLalD~G~kriGvAvsd~~~~~a~P 52 (180)
++.|.+-++. .- -++|||.--=.=+++||.|+.+.+..+
T Consensus 19 lr~f~~~~~t---r~sy~VLgIETSCDDTavaVVd~~~~~~~~ 58 (405)
T KOG2707|consen 19 LRLFRCFIRT---RLSYKVLGIETSCDDTAVAVVDEFSHVLSS 58 (405)
T ss_pred HHHhccchhh---hhheeeeeEecccCcceeeeecccccccch
Confidence 5566655442 22 339999999999999999999888877
No 214
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=25.88 E-value=76 Score=26.19 Aligned_cols=23 Identities=35% Similarity=0.572 Sum_probs=20.1
Q ss_pred CCCCeEEEEecCCCeEEEEEecC
Q 030251 23 SKRGRFLGLDVGDKYVGLSISDP 45 (180)
Q Consensus 23 ~~~~~iLalD~G~kriGvAvsd~ 45 (180)
..+|.+|++|.|..-+|||.-=|
T Consensus 55 ~~PGlvl~L~~GGsc~GvafRip 77 (190)
T COG3703 55 EQPGLVLGLDRGGSCEGVAYRIP 77 (190)
T ss_pred CCCceEEEeeCCCcEEEEEEEcC
Confidence 46799999999999999998754
No 215
>COG0145 HyuA N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=25.78 E-value=2.6e+02 Score=27.43 Aligned_cols=59 Identities=19% Similarity=0.240 Sum_probs=37.9
Q ss_pred CCeEEEEecCCCeEEEEEecCCC-ceeccceeeeCCCCChhhHHHHHHHHHHhh----CCCEEEEe
Q 030251 25 RGRFLGLDVGDKYVGLSISDPKN-KIASPLSVLLRKKNTIDLMAEDFRSLISEF----NLEGFIVG 85 (180)
Q Consensus 25 ~~~iLalD~G~kriGvAvsd~~~-~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~----~i~~iVVG 85 (180)
++..+|||.|.-.+=+.+-|..+ .+.. .+++...+ ........+.+++..+ +++.+++|
T Consensus 1 ~~~~iGID~GGTfTDaV~~~~~~g~~~~-~K~lTtP~-~~~~~~~~~~~~~~~~~~~~~i~~v~~g 64 (674)
T COG0145 1 MMLRIGIDVGGTFTDAVLLDEDGGVLAT-IKVLTTPD-LPSGIVNAGIRLALELLEGSEVDLVVHG 64 (674)
T ss_pred CceEEEEEcCCCcEeEEEEeCCCCEEEE-EEccCCCC-chhhHHHHHHHHHhhccccccccEEEEe
Confidence 35689999999999888888765 3332 33333322 2222345566666664 69999999
No 216
>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=25.69 E-value=74 Score=22.56 Aligned_cols=21 Identities=29% Similarity=0.419 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhCCCEEEEecc
Q 030251 67 AEDFRSLISEFNLEGFIVGYP 87 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP 87 (180)
.+.|.+.+++++++.||+|..
T Consensus 74 ~~~I~~~~~~~~~dllviG~~ 94 (124)
T cd01987 74 AEAIVEFAREHNVTQIVVGKS 94 (124)
T ss_pred HHHHHHHHHHcCCCEEEeCCC
Confidence 588999999999999999953
No 217
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=25.50 E-value=1.6e+02 Score=30.96 Aligned_cols=71 Identities=18% Similarity=0.295 Sum_probs=46.2
Q ss_pred CCeEEEEEecCC---Cceeccc-------eeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHH
Q 030251 35 DKYVGLSISDPK---NKIASPL-------SVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFI 104 (180)
Q Consensus 35 ~kriGvAvsd~~---~~~a~Pl-------~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~ 104 (180)
..++||+|.|.. -...+++ .++... ... ++++++.+++..|.|| |++|+-.++++-|-..+++..|.
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 IVSVGVIVVDKVCPDSHVQTTTLGGIYGCRVVVME-SEL-ELFEEVAKLIVQYDPD-ILLGYEIHNLSWGYLIERAKLLG 777 (1488)
T ss_pred eeeeeEEEEeccCccccccccccCCcCCceEEEeh-hHH-HHHHHHHHHHHhcCcc-eeeeeeecccchHHHHHHHHHhc
Confidence 778999999933 2222221 222211 122 5689999999999999 89999888777776666555544
Q ss_pred HHHH
Q 030251 105 DDLS 108 (180)
Q Consensus 105 ~~L~ 108 (180)
-.|-
T Consensus 778 ~di~ 781 (1488)
T KOG0968|consen 778 IDIS 781 (1488)
T ss_pred chHH
Confidence 4433
No 218
>PLN03226 serine hydroxymethyltransferase; Provisional
Probab=25.50 E-value=2.2e+02 Score=26.30 Aligned_cols=19 Identities=16% Similarity=0.176 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhCCCEEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVG 85 (180)
.+.|.+++.++++..||+|
T Consensus 172 ~d~Le~~l~~~~pklIv~~ 190 (475)
T PLN03226 172 YDKLEKKAMLFRPKLIIAG 190 (475)
T ss_pred HHHHHHHHhhcCCeEEEEe
Confidence 6899999988899999997
No 219
>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=25.31 E-value=61 Score=30.51 Aligned_cols=19 Identities=16% Similarity=0.468 Sum_probs=16.5
Q ss_pred EEEEecCCCeEEEEEecCC
Q 030251 28 FLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 28 iLalD~G~kriGvAvsd~~ 46 (180)
++|||+|+..+-+|+.++.
T Consensus 2 viGIDlGtt~s~va~~~~g 20 (595)
T TIGR02350 2 IIGIDLGTTNSCVAVMEGG 20 (595)
T ss_pred EEEEEeCcccEEEEEEECC
Confidence 7999999999999987653
No 220
>PRK13328 pantothenate kinase; Reviewed
Probab=25.01 E-value=4.2e+02 Score=22.33 Aligned_cols=83 Identities=11% Similarity=0.100 Sum_probs=45.4
Q ss_pred eEEEEecCCCeEEEEEecCCCceec----cc-----------------eeeeCCCCChhhHHHHHHHHHHh-hC-CCEEE
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIAS----PL-----------------SVLLRKKNTIDLMAEDFRSLISE-FN-LEGFI 83 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~----Pl-----------------~~i~~~~~~~~~~~~~L~~li~e-~~-i~~iV 83 (180)
++|-||.|..|+=.|+.+....... +. .++- .+.....+-..+.+.+++ +. +.-++
T Consensus 2 M~LliDiGNTriKwa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v-sSV~~p~~~~~l~~~l~~~~~~~~~~~ 80 (255)
T PRK13328 2 MILLIDAGNSRIKWAWADAGRPWVHSGAFAHGLDAALAPDWSALPAPRGAWI-SNVAGPAVAARLDALLAARWPGLPVTW 80 (255)
T ss_pred cEEEEEeCccceeEEEEcCCCceeecchhcccchHHHHHHHHhCCCCCeEEE-EecCChhHHHHHHHHHHHHhCCCCeEE
Confidence 4899999999999999985421111 00 0010 011101234667777776 33 66666
Q ss_pred Eecc-----cCCCCCchHHHHHHHHHHHHHhc
Q 030251 84 VGYP-----FNRQQNAADAVQVKLFIDDLSAT 110 (180)
Q Consensus 84 VGlP-----~~dG~~s~~~~~v~~F~~~L~~~ 110 (180)
+.-+ +.++...+..-=+.+++.-+...
T Consensus 81 v~~~~~~~gl~~~Y~~p~~LG~DR~~a~vaA~ 112 (255)
T PRK13328 81 VRSRAAQCGVRNGYREPAQLGSDRWAGLIGAR 112 (255)
T ss_pred EecCccCCCceeCCCChhhccHHHHHHHHHHH
Confidence 7632 22344445555556666666653
No 221
>COG2410 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=24.93 E-value=3.9e+02 Score=21.86 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=16.7
Q ss_pred CeEEEEecCCCe-EEEEEecCCC
Q 030251 26 GRFLGLDVGDKY-VGLSISDPKN 47 (180)
Q Consensus 26 ~~iLalD~G~kr-iGvAvsd~~~ 47 (180)
+++-|+|+|.|+ +|+|+--+..
T Consensus 1 mmy~GIDla~k~~tavavl~~~~ 23 (178)
T COG2410 1 MMYAGIDLAVKRSTAVAVLIEGR 23 (178)
T ss_pred CcccccccccCCCceEEEEECCE
Confidence 356799999888 7888876654
No 222
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=24.90 E-value=3.2e+02 Score=27.67 Aligned_cols=55 Identities=11% Similarity=0.037 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhhCCCEEEEecccCCCCCchHHHH-HHHHHHHHHhccCCCCCcEEEeccccc
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQ-VKLFIDDLSATKKLEDMKYAYWNEGFT 126 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~-v~~F~~~L~~~~~~~~lpV~~~DEr~T 126 (180)
+.+.|.++.+++++..||||-|.. +.+... -..|+++|... .+++.|+.+.....
T Consensus 322 v~~~i~~ya~~~~~TkiViG~~~~----~rw~~~~~~~l~~~L~~~--~~~idv~ii~~~~~ 377 (890)
T COG2205 322 VAKAIARYAREHNATKIVIGRSRR----SRWRRLFKGSLADRLARE--APGIDVHIVALDAP 377 (890)
T ss_pred HHHHHHHHHHHcCCeeEEeCCCcc----hHHHHHhcccHHHHHHhc--CCCceEEEeeCCCC
Confidence 478999999999999999995443 333222 16788888874 46788887764433
No 223
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=24.87 E-value=2.3e+02 Score=22.92 Aligned_cols=53 Identities=11% Similarity=0.135 Sum_probs=39.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
-.++.+++.+-..+.+|+-.=.| .+.....+.+..|.+.|.+. .|+.||+++.
T Consensus 48 e~~~a~~ia~~~a~~~~ld~~~N-~~~~~~~~~~~~fv~~iR~~--hP~tPIllv~ 100 (178)
T PF14606_consen 48 EPEVADLIAEIDADLIVLDCGPN-MSPEEFRERLDGFVKTIREA--HPDTPILLVS 100 (178)
T ss_dssp -HHHHHHHHHS--SEEEEEESHH-CCTTTHHHHHHHHHHHHHTT---SSS-EEEEE
T ss_pred CHHHHHHHhcCCCCEEEEEeecC-CCHHHHHHHHHHHHHHHHHh--CCCCCEEEEe
Confidence 36778888888889999875444 66677888999999999985 5799999886
No 224
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=24.85 E-value=2e+02 Score=23.75 Aligned_cols=95 Identities=14% Similarity=0.090 Sum_probs=58.7
Q ss_pred HHHHHhh--CCCEEEEecccCCCCC--chHHHHHHHHHHHHHhccCCCCCcEEEec-ccccHHHHHHH---hccCCCCCC
Q 030251 71 RSLISEF--NLEGFIVGYPFNRQQN--AADAVQVKLFIDDLSATKKLEDMKYAYWN-EGFTSKGVELL---LNPLDLHPV 142 (180)
Q Consensus 71 ~~li~e~--~i~~iVVGlP~~dG~~--s~~~~~v~~F~~~L~~~~~~~~lpV~~~D-Er~TT~~A~~~---l~~~g~~~~ 142 (180)
..+|+.| +-..+|+|+=..+-+. .+...-+.+.|.++++. |++-+++.+| -++|+.--+.. |...|.+.+
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 3455665 5678899973223222 22344556788889874 7888888887 45554332222 234555544
Q ss_pred CCC----CCCcHHHHHHHHHHHHhhhhhh
Q 030251 143 EYK----TILDKFAAVGILQEYLDNANRK 167 (180)
Q Consensus 143 ~~k----~~iD~~AA~iILq~yL~~~~~~ 167 (180)
.++ ..-|-..|-.+|+.+|+++.-.
T Consensus 142 ~~d~~~~~~~d~~e~~~~ls~ll~~~~~r 170 (199)
T KOG3289|consen 142 PKDKTLVQWSDWLEGRQMLSALLESRAYR 170 (199)
T ss_pred ecCCchhhhhcchhHHHHHHHHHhhhhhh
Confidence 443 2358889999999999887543
No 225
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=24.66 E-value=1.9e+02 Score=26.79 Aligned_cols=70 Identities=17% Similarity=0.184 Sum_probs=47.1
Q ss_pred HHHHHHHHHhhCCCEEEEec--ccCCC----------------CCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHH
Q 030251 67 AEDFRSLISEFNLEGFIVGY--PFNRQ----------------QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 128 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGl--P~~dG----------------~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~ 128 (180)
.+.|.++..+++++.+|||= ||-.| ....+-+--+.|++.+-++ + ++|-.-...=.+..
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 58999999999999999993 22222 2233344457899998875 3 78843333333667
Q ss_pred HHHHHhccCCC
Q 030251 129 GVELLLNPLDL 139 (180)
Q Consensus 129 ~A~~~l~~~g~ 139 (180)
+|+..+.+.|.
T Consensus 129 ~a~ayi~~~g~ 139 (428)
T COG0151 129 EAKAYIDEKGA 139 (428)
T ss_pred HHHHHHHHcCC
Confidence 77887776554
No 226
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=24.66 E-value=71 Score=30.50 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=17.5
Q ss_pred CeEEEEecCCCeEEEEEecC
Q 030251 26 GRFLGLDVGDKYVGLSISDP 45 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd~ 45 (180)
..++|||+|+..+-||+.+.
T Consensus 19 ~~~iGIDlGTt~s~va~~~~ 38 (616)
T PRK05183 19 RLAVGIDLGTTNSLVATVRS 38 (616)
T ss_pred CeEEEEEeccccEEEEEEEC
Confidence 47899999999999999754
No 227
>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=24.60 E-value=3.4e+02 Score=21.45 Aligned_cols=18 Identities=33% Similarity=0.621 Sum_probs=11.9
Q ss_pred HHHHHHHHHhhCCCEEEE
Q 030251 67 AEDFRSLISEFNLEGFIV 84 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVV 84 (180)
...+.+.+..+++++||+
T Consensus 45 ~~~~~~~l~~~~vdgiii 62 (270)
T cd01545 45 AERVRALLQRSRVDGVIL 62 (270)
T ss_pred HHHHHHHHHHCCCCEEEE
Confidence 355666666677777766
No 228
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=24.57 E-value=3.8e+02 Score=23.77 Aligned_cols=84 Identities=18% Similarity=0.094 Sum_probs=47.0
Q ss_pred ceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccH
Q 030251 48 KIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 48 ~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT 127 (180)
..+.|+.+.- ..+.+.+...|+.+.+.-+++.|++-++ |........++.+++..++. . .+.||+.+-=....
T Consensus 282 ~~~NPvDl~g--~~~~e~~~~aL~~l~~d~~vd~vlv~~~---~~~~~~~~va~~i~~~~~~~-~-~~kPvv~~~~g~~~ 354 (388)
T PRK00696 282 EPANFLDVGG--GATAERVAEAFKIILSDPNVKAILVNIF---GGITRCDVIAEGIIAAVKEV-G-VTVPLVVRLEGTNV 354 (388)
T ss_pred CcCCeEEecC--CCCHHHHHHHHHHHhcCCCCCEEEEEeC---CCCCCHHHHHHHHHHHHHhc-C-CCCcEEEEeCCCCH
Confidence 4556766622 2344455567777777788999998654 22222233445555544431 1 25677554322355
Q ss_pred HHHHHHhccCC
Q 030251 128 KGVELLLNPLD 138 (180)
Q Consensus 128 ~~A~~~l~~~g 138 (180)
.++++.|.+.|
T Consensus 355 ~~~~~~L~~~G 365 (388)
T PRK00696 355 ELGKKILAESG 365 (388)
T ss_pred HHHHHHHHHCC
Confidence 67777788777
No 229
>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=24.48 E-value=1.7e+02 Score=20.87 Aligned_cols=24 Identities=25% Similarity=0.331 Sum_probs=16.5
Q ss_pred HHHHHhhhccCCCCeEEEEecCCCeE
Q 030251 13 LFEQMLKRKVSKRGRFLGLDVGDKYV 38 (180)
Q Consensus 13 ~~~~~~~~~~~~~~~iLalD~G~kri 38 (180)
-++.+++. ...||++-.|+-++.+
T Consensus 26 ~~~~~le~--~~~GRll~ydp~t~~~ 49 (89)
T PF03088_consen 26 WVYDLLEG--RPTGRLLRYDPSTKET 49 (89)
T ss_dssp HHHHHHHT-----EEEEEEETTTTEE
T ss_pred eeeeeecC--CCCcCEEEEECCCCeE
Confidence 34455554 4579999999999998
No 230
>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=24.48 E-value=1.6e+02 Score=22.80 Aligned_cols=49 Identities=18% Similarity=0.151 Sum_probs=31.9
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
+.++.+.+. +.|+||+|-|..+|+.+.+.+. |.+++... .+.+-|+.++
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 466666666 5899999999998888776554 55554321 1335566554
No 231
>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=24.40 E-value=3.5e+02 Score=21.22 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=7.4
Q ss_pred HhhCCCEEEEe
Q 030251 75 SEFNLEGFIVG 85 (180)
Q Consensus 75 ~e~~i~~iVVG 85 (180)
..+++++||+.
T Consensus 52 ~~~~vdgiii~ 62 (266)
T cd06282 52 LRQRVDGLILT 62 (266)
T ss_pred HhcCCCEEEEe
Confidence 33678887775
No 232
>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=24.37 E-value=2.1e+02 Score=26.14 Aligned_cols=47 Identities=11% Similarity=0.206 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.|.++++++++|+||.=.=.. +....+.. .++++. ++. |+|+..+
T Consensus 350 ~~~l~~li~e~~vDGVI~~~~~~C~~~s~e~~-~ik~~l---~~~----GIP~L~i 397 (430)
T TIGR03191 350 SEMMLNIARDWNVDGCMLHLNRGCEGLSIGIM-ENRLAI---AKA----GIPIMTF 397 (430)
T ss_pred HHHHHHHHHHHCCCEEEEcCCCCCccchHhHH-HHHHHH---HHc----CCCEEEE
Confidence 69999999999999999864333 33333333 345544 332 7886655
No 233
>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=24.36 E-value=2.4e+02 Score=24.98 Aligned_cols=145 Identities=13% Similarity=0.050 Sum_probs=68.7
Q ss_pred hHHHHHHhhhccCCCCeEEEEecCCCeEEEEEecCCCceeccceeeeCCC------CChhhHHHHHHHHHHhh-CCCEEE
Q 030251 11 LRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKK------NTIDLMAEDFRSLISEF-NLEGFI 83 (180)
Q Consensus 11 ~~~~~~~~~~~~~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~------~~~~~~~~~L~~li~e~-~i~~iV 83 (180)
+.....|+++.....--++.+|-|...||+--+......++=-..+|.+. .....++.++.+.+.++ ++++||
T Consensus 121 le~L~ea~~~~~~~~~~~vv~d~g~A~i~ll~~~~~~~~~~i~~~iP~K~~~~~~e~~~~~Ff~~v~~~l~~~~~v~~iI 200 (351)
T TIGR00111 121 LKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEEIQKIEYHMPGKKRTLKFGELRKEFYKEIAKKLLNFDDLKTII 200 (351)
T ss_pred HHHHHHHhccccCCcEEEEEEeCCcEEEEEEcCCEEEEEEEEEEeCCCCcccchhHHHHHHHHHHHHHHHhhhcccCEEE
Confidence 34444555431112245678999999999877764433333111232221 11124566666666665 799999
Q ss_pred EecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCC-CCCCCCCCCCcHHHHHHHHHHHHh
Q 030251 84 VGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD-LHPVEYKTILDKFAAVGILQEYLD 162 (180)
Q Consensus 84 VGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g-~~~~~~k~~iD~~AA~iILq~yL~ 162 (180)
|+ +++.... .|.+.|.+...-.....+..|=+++...+-.-+...+ +.+ .-...-..-..-+++.|++
T Consensus 201 ia------GPGf~k~---~f~~~l~~~~~~~~~k~ii~~~s~g~~~gl~EvL~~~~v~~--~l~d~k~~~E~~~l~~f~~ 269 (351)
T TIGR00111 201 VA------GPGFYKN---DFYDFIFERYPEEANKAVLENCSTGGRAGINEVLKRGLVAR--ILQETRYAKEIMVIDEFLE 269 (351)
T ss_pred EE------CCHHHHH---HHHHHHHHHhhhhhCCcEEEecCCCchhHHHHHHhChHHHH--HHhhhhHHHHHHHHHHHHH
Confidence 99 3444333 4555554321000123344452222233322221111 110 0112223334678999998
Q ss_pred hhhh
Q 030251 163 NANR 166 (180)
Q Consensus 163 ~~~~ 166 (180)
....
T Consensus 270 ~l~k 273 (351)
T TIGR00111 270 HLAK 273 (351)
T ss_pred HHhc
Confidence 7644
No 234
>PLN03184 chloroplast Hsp70; Provisional
Probab=24.36 E-value=78 Score=30.62 Aligned_cols=40 Identities=20% Similarity=0.372 Sum_probs=28.0
Q ss_pred cccchHHHHHHhhh---cc------C---CCCeEEEEecCCCeEEEEEecCC
Q 030251 7 YVKPLRLFEQMLKR---KV------S---KRGRFLGLDVGDKYVGLSISDPK 46 (180)
Q Consensus 7 ~~~~~~~~~~~~~~---~~------~---~~~~iLalD~G~kriGvAvsd~~ 46 (180)
++-|--.|..|-|+ ++ | .++.++|||+|+..+-+|+.++.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viGIDlGTt~s~va~~~~g 59 (673)
T PLN03184 8 FSTPTAAFLKMGKRRGNGARRRAGGPLRVVAEKVVGIDLGTTNSAVAAMEGG 59 (673)
T ss_pred CCCCCcchhhhhhhhccccccccCCCccccCCCEEEEEeCcCcEEEEEEECC
Confidence 55666677777665 11 1 12469999999999999987643
No 235
>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=24.22 E-value=3.2e+02 Score=20.74 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=8.0
Q ss_pred HHHHHHHHhhCCCEEEEe
Q 030251 68 EDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVG 85 (180)
+.|.+++++++++.|+.-
T Consensus 78 ~~l~~l~~~~~~~~V~~~ 95 (165)
T PF00875_consen 78 EVLPELAKEYGATAVYFN 95 (165)
T ss_dssp HHHHHHHHHHTESEEEEE
T ss_pred HHHHHHHHhcCcCeeEec
Confidence 334444444444444443
No 236
>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=24.20 E-value=5.5e+02 Score=23.41 Aligned_cols=73 Identities=11% Similarity=0.132 Sum_probs=41.0
Q ss_pred hhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEE-EecccccHHHHHHHhccCCCC
Q 030251 63 IDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYA-YWNEGFTSKGVELLLNPLDLH 140 (180)
Q Consensus 63 ~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~-~~DEr~TT~~A~~~l~~~g~~ 140 (180)
.+.+.+-|+.+.++-+++.++|.+.... . +.....++.+++..++. .+.||. .+.+.....++++.|.+.|+.
T Consensus 355 ~~~~~~al~~l~~dp~vd~Vlv~~~~~~-~-~~~~~~a~~l~~~~~~~---~~KPvv~~~~gg~~~~~~~~~L~~~Gip 428 (447)
T TIGR02717 355 PERYAKALKTVAEDENVDGVVVVLTPTA-M-TDPEEVAKGIIEGAKKS---NEKPVVAGFMGGKSVDPAKRILEENGIP 428 (447)
T ss_pred HHHHHHHHHHHHcCCCCCEEEEEccCCc-c-CCHHHHHHHHHHHHHhc---CCCcEEEEecCCccHHHHHHHHHhCCCC
Confidence 3455566667777778999998875321 1 11133445555544431 134553 444444566677778777764
No 237
>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=24.19 E-value=4.1e+02 Score=23.57 Aligned_cols=89 Identities=16% Similarity=0.071 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCC---cEEEec----ccccHHH---HHHHh
Q 030251 65 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDM---KYAYWN----EGFTSKG---VELLL 134 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~l---pV~~~D----Er~TT~~---A~~~l 134 (180)
.+++.+.+...+.+. .|.+=+|+=.| .+...+.++++++.|+.. .. .+ |+.-+. ++.|..+ ..+.|
T Consensus 240 ~l~~~~~~y~~~~gr-~I~iey~LIpG-vNDs~e~a~~La~~l~~l-~~-~VnLIPynp~~~~~~~~ps~e~i~~f~~~L 315 (345)
T PRK14457 240 NLLEDCRHYVAITGR-RVSFEYILLGG-VNDLPEHAEELANLLRGF-QS-HVNLIPYNPIDEVEFQRPSPKRIQAFQRVL 315 (345)
T ss_pred HHHHHHHHHHHHhCC-EEEEEEEEECC-cCCCHHHHHHHHHHHhcC-CC-eEEEecCCCCCCCCCCCCCHHHHHHHHHHH
Confidence 445666666665532 46666766522 222334445555555531 00 11 221111 2333333 23445
Q ss_pred ccCCCCCCCCC-CCCcHHHHHHHH
Q 030251 135 NPLDLHPVEYK-TILDKFAAVGIL 157 (180)
Q Consensus 135 ~~~g~~~~~~k-~~iD~~AA~iIL 157 (180)
...|+.-..++ .=.|-.|||--|
T Consensus 316 ~~~Gi~vtvR~~~G~di~aaCGqL 339 (345)
T PRK14457 316 EQRGVAVSVRASRGLDANAACGQL 339 (345)
T ss_pred HHCCCeEEEeCCCCCchhhccccc
Confidence 56677543333 335777787655
No 238
>PF13941 MutL: MutL protein
Probab=24.13 E-value=3.2e+02 Score=25.47 Aligned_cols=65 Identities=15% Similarity=0.192 Sum_probs=52.3
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCC
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDL 139 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~ 139 (180)
.+|++ |.+-+||.|++= -|+.+....-+.+-|+.|.+. .+ .+||++.-=+--..++++.|.+.+.
T Consensus 115 ~~l~~-i~~~~PDiILLa----GGtDgG~~~~il~nA~~La~~-~~-~~pVIyAGN~~a~~~v~~il~~~~~ 179 (457)
T PF13941_consen 115 EDLEE-IREIRPDIILLA----GGTDGGNKEVILHNAEMLAEA-NL-RIPVIYAGNKAAQDEVEEILEKAGK 179 (457)
T ss_pred HHHHH-HhccCCCEEEEe----CCccCCchHHHHHHHHHHHhC-CC-CCcEEEECCHHHHHHHHHHHHhCCC
Confidence 45555 567899998886 689888888899999999975 44 7899999888888888888885543
No 239
>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=24.10 E-value=2.5e+02 Score=22.86 Aligned_cols=47 Identities=13% Similarity=0.241 Sum_probs=30.5
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
++.+.+.+.+.+++.||+. |...........|.+.|.+. .+.||+++
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 4666676777889999887 54443233445666667652 25788877
No 240
>COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only]
Probab=24.03 E-value=1.3e+02 Score=24.22 Aligned_cols=35 Identities=26% Similarity=0.395 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDD 106 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~ 106 (180)
++.|.+.+. +.|+||+|-|...|+.|.+. +.|.++
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 466666555 58999999999977766644 467777
No 241
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. 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 repressor.
Probab=23.55 E-value=3.8e+02 Score=21.29 Aligned_cols=17 Identities=12% Similarity=0.276 Sum_probs=11.5
Q ss_pred HHHHHHHHhhCCCEEEE
Q 030251 68 EDFRSLISEFNLEGFIV 84 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVV 84 (180)
.++.+.+...+++++++
T Consensus 45 ~~~i~~l~~~~vdgiIi 61 (273)
T cd06292 45 ADYVEDLLARGVRGVVF 61 (273)
T ss_pred HHHHHHHHHcCCCEEEE
Confidence 34444455578999998
No 242
>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=23.42 E-value=2.6e+02 Score=23.63 Aligned_cols=44 Identities=14% Similarity=0.168 Sum_probs=27.0
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCC-chHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQN-AADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~-s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+++.+.+.+...|.|+|| |+. +.... +....+++. +++||++.-
T Consensus 22 ~~~~~~~~~~gtDai~VG-----GS~~~~~~d---~vv~~ik~~---~~lPvilfP 66 (230)
T PF01884_consen 22 EEALEAACESGTDAIIVG-----GSDTGVTLD---NVVALIKRV---TDLPVILFP 66 (230)
T ss_dssp HHHHHHHHCTT-SEEEEE------STHCHHHH---HHHHHHHHH---SSS-EEEET
T ss_pred HHHHHHHHhcCCCEEEEC-----CCCCccchH---HHHHHHHhc---CCCCEEEeC
Confidence 444555578899999999 877 44333 445556652 389998874
No 243
>PRK07667 uridine kinase; Provisional
Probab=23.32 E-value=2.9e+02 Score=21.82 Aligned_cols=53 Identities=8% Similarity=0.160 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCc--EEEecccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMK--YAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lp--V~~~DEr~ 125 (180)
.++|.+.+.+++...+|||+== +.-+..+-.++.+++.|.+. +++ ++-.|..+
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 22334455567777777652 455 55555544
No 244
>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=23.31 E-value=3.9e+02 Score=21.51 Aligned_cols=28 Identities=11% Similarity=0.249 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHhhCCCEEEEecccCCCCCchH
Q 030251 65 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAAD 96 (180)
Q Consensus 65 ~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~ 96 (180)
.++..+.+++.+++|+ ||+|+ |+..-..
T Consensus 53 ~lL~~f~~~i~~~dPD-vi~g~---N~~~FD~ 80 (193)
T cd05784 53 SLLLALIAWFAQYDPD-IIIGW---NVINFDL 80 (193)
T ss_pred HHHHHHHHHHHhhCCC-EEEEC---CCcCcCH
Confidence 5689999999999999 88896 4444443
No 245
>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=23.11 E-value=39 Score=25.01 Aligned_cols=12 Identities=33% Similarity=0.509 Sum_probs=10.3
Q ss_pred CCCeEEEEEecC
Q 030251 34 GDKYVGLSISDP 45 (180)
Q Consensus 34 G~kriGvAvsd~ 45 (180)
+..|+||||+|.
T Consensus 14 ~~pR~gvaIGd~ 25 (107)
T PF09298_consen 14 PSPRVGVAIGDQ 25 (107)
T ss_dssp ESEEEEEEETTE
T ss_pred CCCeeEEEECCE
Confidence 678999999984
No 246
>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=22.83 E-value=96 Score=21.22 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=19.0
Q ss_pred HHHHHHHHHhhCCCEEEEecc
Q 030251 67 AEDFRSLISEFNLEGFIVGYP 87 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP 87 (180)
.+.|.+.+++.+++.+|+|..
T Consensus 82 ~~~i~~~~~~~~~dlvvig~~ 102 (130)
T cd00293 82 AEAILEAAEELGADLIVMGSR 102 (130)
T ss_pred HHHHHHHHHHcCCCEEEEcCC
Confidence 589999999999999999954
No 247
>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=22.80 E-value=2.9e+02 Score=22.62 Aligned_cols=39 Identities=18% Similarity=0.202 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCC
Q 030251 96 DAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLD 138 (180)
Q Consensus 96 ~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g 138 (180)
..+.+.++.+.+++. ++++++.+...++..++.+-++.|
T Consensus 184 s~~~l~~l~~~ik~~----~v~~i~~e~~~~~~~~~~la~~~g 222 (256)
T PF01297_consen 184 SPKDLAELIKLIKEN----KVKCIFTEPQFSSKLAEALAKETG 222 (256)
T ss_dssp -HHHHHHHHHHHHHT----T-SEEEEETTS-THHHHHHHHCCT
T ss_pred CHHHHHHHHHHhhhc----CCcEEEecCCCChHHHHHHHHHcC
Confidence 344444555555542 455555555555554444433333
No 248
>PRK07179 hypothetical protein; Provisional
Probab=22.67 E-value=2.6e+02 Score=24.50 Aligned_cols=51 Identities=12% Similarity=0.083 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 126 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~T 126 (180)
.+.|.+.+++.....|++--|.+ .|...+. .+.++..++ . ++ ++++||-++
T Consensus 170 ~~~l~~~l~~~~~~lV~v~~v~n~tG~i~pl----~~I~~l~~~---~-~~-~livDea~~ 221 (407)
T PRK07179 170 VDHLRRQIERHGPGIIVVDSVYSTTGTIAPL----ADIVDIAEE---F-GC-VLVVDESHS 221 (407)
T ss_pred HHHHHHHHHhcCCeEEEECCCCCCCCccccH----HHHHHHHHH---c-CC-EEEEECccc
Confidence 57788888776677777877777 8887773 334444444 2 43 677888876
No 249
>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=22.65 E-value=4e+02 Score=21.24 Aligned_cols=55 Identities=11% Similarity=0.077 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHH
Q 030251 66 MAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVE 131 (180)
Q Consensus 66 ~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~ 131 (180)
++..|.+...+.+..-+++| |++. .+.+.+++|++ ++|++.|...+=.++..+..
T Consensus 36 l~~~l~~~~~~~~~~vfllG-----~~~~----v~~~~~~~l~~--~yP~l~i~g~~g~f~~~~~~ 90 (177)
T TIGR00696 36 LMEELCQRAGKEKLPIFLYG-----GKPD----VLQQLKVKLIK--EYPKLKIVGAFGPLEPEERK 90 (177)
T ss_pred HHHHHHHHHHHcCCeEEEEC-----CCHH----HHHHHHHHHHH--HCCCCEEEEECCCCChHHHH
Confidence 46777777777778888999 4443 34567778887 37889988777777655443
No 250
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=22.62 E-value=2.4e+02 Score=23.88 Aligned_cols=38 Identities=13% Similarity=0.413 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLS 108 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~ 108 (180)
.+.|.+.+..-++++||.| +=-..-|..++++.++++.
T Consensus 75 ve~L~~~l~~l~~d~iv~G----aI~s~yqk~rve~lc~~lG 112 (223)
T COG2102 75 VEELKEALRRLKVDGIVAG----AIASEYQKERVERLCEELG 112 (223)
T ss_pred HHHHHHHHHhCcccEEEEc----hhhhHHHHHHHHHHHHHhC
Confidence 6889999999999999999 6666667777777777765
No 251
>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=22.61 E-value=1.1e+02 Score=22.36 Aligned_cols=48 Identities=27% Similarity=0.410 Sum_probs=32.1
Q ss_pred EEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEe
Q 030251 30 GLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 30 alD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVG 85 (180)
-++.|..++|++.... .++..+.... +.+.+.+.++..+++.+.+++=
T Consensus 26 ~f~~~~~~vgis~v~~-----~~~~~~~~~~---~~~~~~l~~~~~~~~ld~l~lm 73 (127)
T PF02833_consen 26 EFEFGGKKVGISQVET-----MDLEELLSRK---DELLEELEEFCEERKLDLLFLM 73 (127)
T ss_dssp EEEETTEEEEEEEEEE-----S-HHHHHTTH---HHHHHHHHHHHHHTT-SEEEEE
T ss_pred eeecCCeEEEEEeeee-----cCHHHHHHHH---HHHHHHHHHHHHhCCCCEEEEE
Confidence 3566999999987632 3333333221 3568999999999999987765
No 252
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=22.54 E-value=2.4e+02 Score=24.74 Aligned_cols=53 Identities=17% Similarity=0.093 Sum_probs=31.4
Q ss_pred HHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhc-cCCCCCcEEEecccccH
Q 030251 70 FRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSAT-KKLEDMKYAYWNEGFTS 127 (180)
Q Consensus 70 L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~-~~~~~lpV~~~DEr~TT 127 (180)
+..+...-....+++|-|-. |..+-. +..|+.++.. ..|.+..|..+|||---
T Consensus 129 i~~ly~~g~lntLiigpP~~-GKTTlL----RdiaR~~s~g~~~~l~kkv~IiDersEI 182 (308)
T COG3854 129 IKDLYQNGWLNTLIIGPPQV-GKTTLL----RDIARLLSDGINQFLPKKVGIIDERSEI 182 (308)
T ss_pred HHHHHhcCceeeEEecCCCC-ChHHHH----HHHHHHhhccccccCCceEEEEeccchh
Confidence 44444544566999996554 655543 4444444431 02456789999998543
No 253
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=22.39 E-value=3e+02 Score=24.01 Aligned_cols=64 Identities=19% Similarity=0.212 Sum_probs=36.7
Q ss_pred HHHHHH-HHhhCCCEEEEecccCCCC--CchHHHHHHHHHHHHHhccCCCCCcEEEe------cccccHHHHHHHhccCC
Q 030251 68 EDFRSL-ISEFNLEGFIVGYPFNRQQ--NAADAVQVKLFIDDLSATKKLEDMKYAYW------NEGFTSKGVELLLNPLD 138 (180)
Q Consensus 68 ~~L~~l-i~e~~i~~iVVGlP~~dG~--~s~~~~~v~~F~~~L~~~~~~~~lpV~~~------DEr~TT~~A~~~l~~~g 138 (180)
+.++++ +...+++.||||.=..-|. .+. ....+++ .++ + +..|+.+ +++.||..-++.+.+..
T Consensus 103 ~Fi~~~l~~~l~~~~iVvG~Df~FG~~~~G~-~~~L~~~---~~~---~-g~~v~~v~~~~~~~~~ISST~IR~~I~~G~ 174 (305)
T PRK05627 103 EFIEDLLVKGLNAKHVVVGFDFRFGKKRAGD-FELLKEA---GKE---F-GFEVTIVPEVKEDGERVSSTAIRQALAEGD 174 (305)
T ss_pred HHHHHHHHhccCCCEEEECCCCCCCCCCCCC-HHHHHHH---HHH---c-CcEEEEeccEecCCCcCchHHHHHHHHcCC
Confidence 445554 4558999999996443121 111 1222222 222 2 4555555 46899999999887644
Q ss_pred C
Q 030251 139 L 139 (180)
Q Consensus 139 ~ 139 (180)
+
T Consensus 175 i 175 (305)
T PRK05627 175 L 175 (305)
T ss_pred H
Confidence 3
No 254
>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=22.37 E-value=2.6e+02 Score=23.57 Aligned_cols=50 Identities=10% Similarity=0.254 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
.-++.+..++..+++++|.-|.. ..+.. .+.+|-+.+.+. +++||+++|.
T Consensus 85 ~i~~a~~a~~~Gad~v~v~~P~~~~~s~~----~l~~y~~~ia~~---~~~pi~iYn~ 135 (289)
T PF00701_consen 85 AIELARHAQDAGADAVLVIPPYYFKPSQE----ELIDYFRAIADA---TDLPIIIYNN 135 (289)
T ss_dssp HHHHHHHHHHTT-SEEEEEESTSSSCCHH----HHHHHHHHHHHH---SSSEEEEEEB
T ss_pred HHHHHHHHhhcCceEEEEeccccccchhh----HHHHHHHHHHhh---cCCCEEEEEC
Confidence 35556667889999999999988 54433 344555666653 4899998885
No 255
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=22.27 E-value=1e+02 Score=26.72 Aligned_cols=47 Identities=11% Similarity=0.060 Sum_probs=32.5
Q ss_pred CCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHH
Q 030251 79 LEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 128 (180)
Q Consensus 79 i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~ 128 (180)
..-+|==.|+.|-+..+-.+..+.|++++.+. + ++||+++.+.-|--
T Consensus 87 A~DViPfvPl~d~tteecveiske~gkrvgee--l-giPVylYe~aatrp 133 (302)
T COG3643 87 AADVIPFVPLKDTTTEECVEISKELGKRVGEE--L-GIPVYLYEDAATRP 133 (302)
T ss_pred ccceeceeecccccHHHHHHHHHHHHHHhhHh--h-CCcEEEehhhccCc
Confidence 44455556777555555556668999999874 5 89999997655543
No 256
>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=22.25 E-value=3.1e+02 Score=25.23 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=20.2
Q ss_pred CCCeEEEEecCCCeEEEEEecCCCc
Q 030251 24 KRGRFLGLDVGDKYVGLSISDPKNK 48 (180)
Q Consensus 24 ~~~~iLalD~G~kriGvAvsd~~~~ 48 (180)
..+..+|||.|+..+=+++-|....
T Consensus 142 ~~g~~lGIDiGSTttK~Vl~dd~~I 166 (404)
T TIGR03286 142 QEGLTLGIDSGSTTTKAVVMEDNEV 166 (404)
T ss_pred cCCEEEEEEcChhheeeEEEcCCeE
Confidence 3467999999999999999885433
No 257
>PRK13930 rod shape-determining protein MreB; Provisional
Probab=22.18 E-value=86 Score=26.78 Aligned_cols=19 Identities=16% Similarity=0.368 Sum_probs=14.8
Q ss_pred CeEEEEecCCCeEEEEEec
Q 030251 26 GRFLGLDVGDKYVGLSISD 44 (180)
Q Consensus 26 ~~iLalD~G~kriGvAvsd 44 (180)
.+.+|||+|+..+-+++.+
T Consensus 8 ~~~vgiDlGt~~t~i~~~~ 26 (335)
T PRK13930 8 SKDIGIDLGTANTLVYVKG 26 (335)
T ss_pred ccceEEEcCCCcEEEEECC
Confidence 3569999999988777653
No 258
>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=21.92 E-value=3.3e+02 Score=19.97 Aligned_cols=55 Identities=5% Similarity=-0.008 Sum_probs=23.1
Q ss_pred HHHHHHHHhh--CCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 68 EDFRSLISEF--NLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 68 ~~L~~li~e~--~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+++.+.+++. ++.-+++++|.. +...........+..+++.+.....+..+.++|
T Consensus 67 ~~~i~~i~~~~p~~~ii~~~~~p~~~~~~~~~~~~~n~~l~~~~~~~~~~~~~v~~vd 124 (157)
T cd01833 67 RALIDQMRAANPDVKIIVATLIPTTDASGNARIAEYNAAIPGVVADLRTAGSPVVLVD 124 (157)
T ss_pred HHHHHHHHHhCCCeEEEEEeCCCCCCcchhHHHHHHHHHHHHHHHHHhcCCCCEEEEe
Confidence 4444445555 345556666544 333223333333333333321001124567776
No 259
>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=21.90 E-value=4.2e+02 Score=21.17 Aligned_cols=44 Identities=9% Similarity=0.218 Sum_probs=25.5
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecc
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNE 123 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DE 123 (180)
..+.+.+..+++++||+. |.+ ... +....+++.+. ++||+++|-
T Consensus 50 ~~~~~~l~~~~vDgiii~-~~~---~~~----~~~~i~~~~~~----gIpvV~~d~ 93 (274)
T cd06311 50 NAQQDLLINRKIDALVIL-PFE---SAP----LTQPVAKAKKA----GIFVVVVDR 93 (274)
T ss_pred HHHHHHHHHcCCCEEEEe-CCC---chh----hHHHHHHHHHC----CCeEEEEcC
Confidence 455565566789999996 333 111 11223344442 789888874
No 260
>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=21.66 E-value=3.3e+02 Score=19.89 Aligned_cols=79 Identities=9% Similarity=0.027 Sum_probs=48.7
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCCC-CC
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVE-YK 145 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~-~k 145 (180)
.+++.+.+.+++++.|++. ++.......++++++.|++.+ ++++++. +-=+..+.+ ...|.+.|+..-- .+
T Consensus 39 ~e~~~~~a~~~~~d~V~iS-----~~~~~~~~~~~~~~~~L~~~~-~~~i~i~-~GG~~~~~~-~~~~~~~G~d~~~~~~ 110 (122)
T cd02071 39 PEEIVEAAIQEDVDVIGLS-----SLSGGHMTLFPEVIELLRELG-AGDILVV-GGGIIPPED-YELLKEMGVAEIFGPG 110 (122)
T ss_pred HHHHHHHHHHcCCCEEEEc-----ccchhhHHHHHHHHHHHHhcC-CCCCEEE-EECCCCHHH-HHHHHHCCCCEEECCC
Confidence 4778888899999988886 455566777899999999852 3244444 433333333 3456667764322 23
Q ss_pred CCCcHHHH
Q 030251 146 TILDKFAA 153 (180)
Q Consensus 146 ~~iD~~AA 153 (180)
...+++++
T Consensus 111 ~~~~~~~~ 118 (122)
T cd02071 111 TSIEEIID 118 (122)
T ss_pred CCHHHHHH
Confidence 34444443
No 261
>PTZ00285 glucosamine-6-phosphate isomerase; Provisional
Probab=21.52 E-value=1.8e+02 Score=24.35 Aligned_cols=55 Identities=9% Similarity=0.063 Sum_probs=26.9
Q ss_pred HHHHHHHHHh---hCCCEEEEecccCCCCCchHHHHHHHHHHHHHh-ccCCCCCcEEEecccc
Q 030251 67 AEDFRSLISE---FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA-TKKLEDMKYAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e---~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~-~~~~~~lpV~~~DEr~ 125 (180)
.+.+.+.+.+ .+=..+++++ .|..++. ..-+.+++...+ ...+..+-|+++|||+
T Consensus 17 a~~i~~~i~~~~~~~~~~~~i~l---sgG~tP~-~~y~~L~~~~~~~~i~w~~v~if~~DEr~ 75 (253)
T PTZ00285 17 SNYIIKRINDFKPTSDRPFVLGL---PTGSTPL-PTYQELIRAYREGRVSFSNVVTFNMDEYV 75 (253)
T ss_pred HHHHHHHHHHHhhhcCCCeEEEE---cCCCCHH-HHHHHHHHHHhhcCCchhHeEEECCcEEe
Confidence 3444444443 1223456665 4555542 222334433221 1134566789999997
No 262
>KOG0104 consensus Molecular chaperones GRP170/SIL1, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=21.38 E-value=1.4e+02 Score=29.89 Aligned_cols=31 Identities=19% Similarity=0.589 Sum_probs=25.7
Q ss_pred CCCCeEEEEecCCCeEEEEEecCCCceeccceeee
Q 030251 23 SKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLL 57 (180)
Q Consensus 23 ~~~~~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~ 57 (180)
+...-+|+||||+..|-+||..| | .|+.++-
T Consensus 19 ~~~~AvmsVDlGse~~Kv~vVkP-G---vPmeIvL 49 (902)
T KOG0104|consen 19 SSALAVMSVDLGSEWIKVAVVKP-G---VPMEIVL 49 (902)
T ss_pred cchhhheeeecccceeEEEEecC-C---CCeEEee
Confidence 56678999999999999999998 3 6766653
No 263
>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=21.32 E-value=4.2e+02 Score=21.12 Aligned_cols=42 Identities=14% Similarity=0.247 Sum_probs=23.6
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
+.+..++ .+++++||+. |.+ ... +....+.+.+. ++||+++|
T Consensus 46 ~~i~~l~-~~~vdgiIi~-~~~---~~~----~~~~i~~~~~~----~iPvV~~~ 87 (273)
T cd06309 46 SAIRSFI-AQGVDVIILA-PVV---ETG----WDPVLKEAKAA----GIPVILVD 87 (273)
T ss_pred HHHHHHH-HcCCCEEEEc-CCc---ccc----chHHHHHHHHC----CCCEEEEe
Confidence 4555554 4689999996 333 110 01233445542 67888776
No 264
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=21.24 E-value=2e+02 Score=23.05 Aligned_cols=49 Identities=18% Similarity=0.264 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
+.++.+.+. +.|+||||-|..+|+.+...+. |.+++... .+.+-|+..+
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 466666665 5899999999998888876554 55444321 1334555544
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=21.17 E-value=2.3e+02 Score=20.43 Aligned_cols=40 Identities=15% Similarity=0.268 Sum_probs=24.9
Q ss_pred CCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEe
Q 030251 79 LEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYW 121 (180)
Q Consensus 79 i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~ 121 (180)
.+.||+|-|-. .|... ...++.|.++|... .+.+.++..+
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 68899999988 66443 13456677777642 2345555544
No 266
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=21.17 E-value=2.4e+02 Score=25.04 Aligned_cols=51 Identities=10% Similarity=0.156 Sum_probs=37.0
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
.+.+...+.+ +++.|+|.-|-| .|+.-. ...+++|++.+.. --++.+||-|
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 4677777776 899999999999 998775 3445566555542 2378889876
No 267
>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=21.06 E-value=2.1e+02 Score=25.52 Aligned_cols=48 Identities=8% Similarity=0.029 Sum_probs=33.0
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEec
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWN 122 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~D 122 (180)
.+.|.++++++++|+||.=.-.. +-...+ ... ..+.|++. |+|+..+|
T Consensus 310 ~~~i~~lvke~~aDGVI~~~~~~C~~~~~e-~~~---lk~~l~e~----GIP~L~id 358 (380)
T TIGR02263 310 GKYLLDQVRKNAAEGVIFAAPSFCDPALLE-RPM---LAARCKEH----GIPQIAFK 358 (380)
T ss_pred HHHHHHHHHHhCCCEEEEhHhhcCChhhhh-HHH---HHHHHHHC----CCCEEEEE
Confidence 68999999999999999986655 433332 222 23345442 89988775
No 268
>PF09872 DUF2099: Uncharacterized protein conserved in archaea (DUF2099); InterPro: IPR009181 The exact function of this protein is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=20.99 E-value=4.6e+02 Score=22.70 Aligned_cols=56 Identities=18% Similarity=0.291 Sum_probs=37.7
Q ss_pred EEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHH
Q 030251 29 LGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFI 104 (180)
Q Consensus 29 LalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~ 104 (180)
.|++.|-|||+|-+.++. ...+|+++=.+..++.+++|.=. .|-..+.++.+-+.+
T Consensus 157 kAie~Gyk~IaVTV~~~~-------------------~A~~iRele~~~~~~~~if~VHt-TGis~eeA~~l~~~~ 212 (258)
T PF09872_consen 157 KAIEMGYKRIAVTVADAE-------------------DAKKIRELEKEEGVNIYIFGVHT-TGISEEEAERLFEYA 212 (258)
T ss_pred HHHHcCCceEEEEecCHH-------------------HHHHHHHhhccCCCceEEEEEEc-cCCCHHHHHHHHHHh
Confidence 468889999998887521 14677777777899999999533 455555444443333
No 269
>PRK13556 azoreductase; Provisional
Probab=20.97 E-value=2.3e+02 Score=22.63 Aligned_cols=39 Identities=13% Similarity=0.252 Sum_probs=27.2
Q ss_pred HHHHHHHHh-hCCCEEEEecccCCCCCchHHHHHHHHHHHHHh
Q 030251 68 EDFRSLISE-FNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSA 109 (180)
Q Consensus 68 ~~L~~li~e-~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~ 109 (180)
+...+++++ ...|.||++.|..+++.... .+.|.+++..
T Consensus 78 ~~~~~~~~~l~~AD~iVi~~P~yn~~~Pa~---LK~~iD~v~~ 117 (208)
T PRK13556 78 AVADKYLNQFLEADKVVFAFPLWNFTIPAV---LHTYIDYLNR 117 (208)
T ss_pred HHHHHHHHHHHHCCEEEEeccccccCCcHH---HHHHHHHHhc
Confidence 444455444 36999999999997776654 4567777775
No 270
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=20.93 E-value=2e+02 Score=23.22 Aligned_cols=39 Identities=21% Similarity=0.449 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhCCCE-EEEecccC--CCCCchHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNLEG-FIVGYPFN--RQQNAADAVQVKLFID 105 (180)
Q Consensus 67 ~~~L~~li~e~~i~~-iVVGlP~~--dG~~s~~~~~v~~F~~ 105 (180)
.+.|..|.+.|+-.+ .|+|.|-| .|.+-...++|.+|.+
T Consensus 43 YegLe~Ly~ky~~~Gf~VLgFPcNQF~~QEPg~~eEI~~fC~ 84 (162)
T COG0386 43 YEGLEALYKKYKDKGFEVLGFPCNQFGGQEPGSDEEIAKFCQ 84 (162)
T ss_pred HHHHHHHHHHHhhCCcEEEeccccccccCCCCCHHHHHHHHH
Confidence 688999999986554 67899999 7788888888999976
No 271
>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=20.91 E-value=2.5e+02 Score=23.94 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=35.9
Q ss_pred HHHHHHHHHhhCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccc
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 124 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr 124 (180)
.-++.+...+.+++++++.-|.. ..+. +.+.+|-+.+.+. .+++|++++|--
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 5442 3455555566442 336899988864
No 272
>PRK02724 hypothetical protein; Provisional
Probab=20.84 E-value=3.1e+02 Score=20.46 Aligned_cols=48 Identities=19% Similarity=0.126 Sum_probs=34.6
Q ss_pred eEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHh
Q 030251 27 RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISE 76 (180)
Q Consensus 27 ~iLalD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e 76 (180)
-+|=+=...+.||||+-.-.+.-.+|++....=..+ ..|++|+..++.
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 456666778999999999888888999877531111 237888877764
No 273
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=20.76 E-value=5.3e+02 Score=21.96 Aligned_cols=44 Identities=9% Similarity=0.209 Sum_probs=24.2
Q ss_pred HHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccc
Q 030251 68 EDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 124 (180)
Q Consensus 68 ~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr 124 (180)
+.+.. +..+++++||+- |.+ .+.. ....+.+.+. ++||+++|..
T Consensus 72 ~~i~~-l~~~~vDGiIi~-~~~---~~~~----~~~l~~~~~~----~iPvV~id~~ 115 (330)
T PRK10355 72 SQIEN-MINRGVDVLVII-PYN---GQVL----SNVIKEAKQE----GIKVLAYDRM 115 (330)
T ss_pred HHHHH-HHHcCCCEEEEe-CCC---hhhH----HHHHHHHHHC----CCeEEEECCC
Confidence 33444 445799999996 222 1111 1233455542 6788888754
No 274
>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=20.74 E-value=1.8e+02 Score=25.20 Aligned_cols=25 Identities=24% Similarity=0.492 Sum_probs=16.3
Q ss_pred hhhHHHHHHHHHHhhCCCEEEEecc
Q 030251 63 IDLMAEDFRSLISEFNLEGFIVGYP 87 (180)
Q Consensus 63 ~~~~~~~L~~li~e~~i~~iVVGlP 87 (180)
++.+.++|.++.++..++.+++..|
T Consensus 288 Pe~V~e~i~~~~~~~G~d~~~l~~~ 312 (337)
T TIGR03858 288 PETVAEKIADTIETLGLDRFMLHYS 312 (337)
T ss_pred HHHHHHHHHHHHHHcCCCeEEEEec
Confidence 4556667776666667777777643
No 275
>PLN02721 threonine aldolase
Probab=20.66 E-value=3.1e+02 Score=22.97 Aligned_cols=54 Identities=4% Similarity=-0.100 Sum_probs=32.6
Q ss_pred HHHHHHHHHhh------CCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 67 AEDFRSLISEF------NLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e~------~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
++.|.+.+.++ ++..|++--|.+ .|........++++++..++. +++++. ||-+
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 343333344456777767652 666544 8754
No 276
>TIGR00502 nagB glucosamine-6-phosphate isomerase. The set of proteins recognized by this model includes a closely related pair from Bacillus subtilis, one of which is uncharacterized but included as a member of the orthologous set.
Probab=20.62 E-value=2.2e+02 Score=23.78 Aligned_cols=55 Identities=18% Similarity=0.216 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhC---CCEEEEecccCCCCCchHHHHHHHHHHHHHh-ccCCCCCcEEEecccc
Q 030251 67 AEDFRSLISEFN---LEGFIVGYPFNRQQNAADAVQVKLFIDDLSA-TKKLEDMKYAYWNEGF 125 (180)
Q Consensus 67 ~~~L~~li~e~~---i~~iVVGlP~~dG~~s~~~~~v~~F~~~L~~-~~~~~~lpV~~~DEr~ 125 (180)
.+.+.+.+.+.. -..+++++ .|..++.. .-+.+++.... ...+.++-+++.|||+
T Consensus 17 a~~i~~~i~~~~~~~~~~~~i~l---sgGstP~~-~y~~L~~~~~~~~i~w~~v~~f~~DEr~ 75 (259)
T TIGR00502 17 ARHIANRINEFKPTAARPFVLGL---PTGGTPIG-TYKQLIELHQAGKISFQNVTTFNMDEYA 75 (259)
T ss_pred HHHHHHHHHHhCccccCceEEEE---cCCCChHH-HHHHHHHHhhccCCchhHeEEEeCeecC
Confidence 455555566522 33466776 35555421 12333332211 1124466789999996
No 277
>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=20.59 E-value=3e+02 Score=22.73 Aligned_cols=92 Identities=14% Similarity=0.246 Sum_probs=49.1
Q ss_pred HHHHHHHH--HHhhCCCEE-EEecccCCCCCchHHHHHHHHHHHHHhccCCCCCcEEEecccccHHHHHHHhccCCCCCC
Q 030251 66 MAEDFRSL--ISEFNLEGF-IVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPV 142 (180)
Q Consensus 66 ~~~~L~~l--i~e~~i~~i-VVGlP~~dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~ 142 (180)
.++.|.++ +.+.++.+| =|||++..........+.+-|.+.|+-...+ ++||.+...+ +..+.-+.+++.+...
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 35777777 555566556 6899985112222333444555555432123 7888877766 5666666776655221
Q ss_pred CCCCCCcHHHHHH-HHHHHH
Q 030251 143 EYKTILDKFAAVG-ILQEYL 161 (180)
Q Consensus 143 ~~k~~iD~~AA~i-ILq~yL 161 (180)
.+..+..+.+.. .++.|+
T Consensus 150 -~~~i~H~f~g~~~~~~~~~ 168 (255)
T PF01026_consen 150 -LRVIFHCFSGSPEEAKKFL 168 (255)
T ss_dssp -SEEEETT--S-HHHHHHHH
T ss_pred -eeEEEecCCCCHHHHHHHH
Confidence 144455544433 455555
No 278
>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=20.31 E-value=1.2e+02 Score=18.99 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=15.2
Q ss_pred HHHHHHHHHhhCCCEEEEe
Q 030251 67 AEDFRSLISEFNLEGFIVG 85 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVG 85 (180)
+.+|.+++++..++++|+=
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 279
>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=20.30 E-value=1.4e+02 Score=19.97 Aligned_cols=28 Identities=21% Similarity=0.189 Sum_probs=18.6
Q ss_pred CchHHHHHHHHHHHHHhccCCCCCcEEEecccc
Q 030251 93 NAADAVQVKLFIDDLSATKKLEDMKYAYWNEGF 125 (180)
Q Consensus 93 ~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~ 125 (180)
.-+....|.+|+++|.+. ++....+|+-
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 345678899999999973 3466666653
No 280
>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=20.17 E-value=2.4e+02 Score=25.70 Aligned_cols=34 Identities=18% Similarity=0.303 Sum_probs=21.5
Q ss_pred HHHHHHHHHhhCCCEEEEecccCCCCCchHHHHHHHHHH
Q 030251 67 AEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 105 (180)
Q Consensus 67 ~~~L~~li~e~~i~~iVVGlP~~dG~~s~~~~~v~~F~~ 105 (180)
++++.+++++++|+.||+| ++.-...-..++|.+
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 343344444455544
No 281
>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=20.06 E-value=3e+02 Score=23.06 Aligned_cols=50 Identities=10% Similarity=0.191 Sum_probs=35.1
Q ss_pred HHHHHHHHHh-hCCCEEEEecccC-CCCCchHHHHHHHHHHHHHhccCCCCCcEEEeccccc
Q 030251 67 AEDFRSLISE-FNLEGFIVGYPFN-RQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFT 126 (180)
Q Consensus 67 ~~~L~~li~e-~~i~~iVVGlP~~-dG~~s~~~~~v~~F~~~L~~~~~~~~lpV~~~DEr~T 126 (180)
.+.|++.+.+ .++..+++-.| + .|...+ ++++++.+++. ++ .+++||-+.
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 887665 34555556552 54 577888765
No 282
>PF00255 GSHPx: Glutathione peroxidase; InterPro: IPR000889 Glutathione peroxidase (GSHPx) (1.11.1.9 from EC) is an enzyme that catalyses the reduction of hydroxyperoxides by glutathione [, ]. Its main function is to protect against the damaging effect of endogenously formed hydroxyperoxides. In higher vertebrates, several forms of GSHPx are known, including a ubiquitous cytosolic form (GSHPx-1), a gastrointestinal cytosolic form (GSHPx-GI), a plasma secreted form (GSHPx-P), and an epididymal secretory form (GSHPx-EP). In addition to these characterised forms, the sequence of a protein of unknown function [] has been shown to be evolutionary related to those of GSHPx's. In filarial nematode parasites, the major soluble cuticular protein (gp29) is a secreted GSHPx, which may provide a mechanism of resistance to the immune reaction of the mammalian host by neutralising the products of the oxidative burst of leukocytes []. The Escherichia coli protein btuE, a periplasmic protein involved in vitamin B12 transport, is evolutionarily related to GSHPxs, although the significance of this relationship is unclear. The structure of bovine seleno-glutathione peroxidase has been determined []. The protein belongs to the alpha-beta class, with a 3 layer(aba) sandwich architecture. The catalyic site of GSHPx contains a conserved residue which is either a cysteine or, in many eukaryotic GSHPx, a selenocysteine []. ; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 3E0U_A 2VUP_A 2RM5_A 2RM6_A 3DWV_B 2P31_B 2R37_B 1GP1_B 2F8A_B 3KIJ_C ....
Probab=20.04 E-value=2.2e+02 Score=21.09 Aligned_cols=40 Identities=18% Similarity=0.339 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhC-CCEEEEecccC--CCCCchHHHHHHHHHHH
Q 030251 67 AEDFRSLISEFN-LEGFIVGYPFN--RQQNAADAVQVKLFIDD 106 (180)
Q Consensus 67 ~~~L~~li~e~~-i~~iVVGlP~~--dG~~s~~~~~v~~F~~~ 106 (180)
...|.++-+++. =...|+|.|-+ .+.+......++.|+..
T Consensus 39 y~~L~~L~~ky~~~gl~ILaFPcnqFg~QEp~~~~ei~~~~~~ 81 (108)
T PF00255_consen 39 YKQLNELYEKYKDKGLEILAFPCNQFGNQEPGSNEEIKEFCKE 81 (108)
T ss_dssp HHHHHHHHHHHGGGTEEEEEEEBSTTTTTTSSCHHHHHHHHCH
T ss_pred cHHHHHHHHHHhcCCeEEEeeehHHhccccCCCHHHHHHHHHh
Confidence 678888888887 46779999998 45666667778888664
Done!