Query 028759
Match_columns 204
No_of_seqs 152 out of 1139
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 16:32:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028759.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028759hhsearch_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 5.4E-40 1.2E-44 263.8 16.2 130 62-194 3-136 (138)
2 PF03652 UPF0081: Uncharacteri 100.0 2E-41 4.4E-46 271.2 7.6 130 63-194 1-134 (135)
3 COG0816 Predicted endonuclease 100.0 2.6E-40 5.6E-45 267.3 13.4 130 63-195 2-136 (141)
4 TIGR00250 RNAse_H_YqgF RNAse H 100.0 8.1E-40 1.7E-44 260.4 15.0 124 66-192 1-127 (130)
5 smart00732 YqgFc Likely ribonu 99.5 8.6E-14 1.9E-18 102.8 11.4 95 64-163 2-99 (99)
6 PRK00039 ruvC Holliday junctio 97.7 0.00049 1.1E-08 57.0 10.8 98 63-167 2-112 (164)
7 PF02075 RuvC: Crossover junct 97.5 0.0012 2.5E-08 53.7 10.4 96 65-167 1-109 (149)
8 cd00529 RuvC_resolvase Hollida 97.4 0.0025 5.4E-08 51.8 11.1 92 64-157 1-104 (154)
9 TIGR00228 ruvC crossover junct 97.2 0.0024 5.3E-08 52.8 8.7 95 65-166 1-107 (156)
10 PF04312 DUF460: Protein of un 97.1 0.0097 2.1E-07 48.4 10.9 108 62-187 31-138 (138)
11 COG2183 Tex Transcriptional ac 96.8 0.011 2.4E-07 59.4 10.8 89 62-158 329-424 (780)
12 COG2433 Uncharacterized conser 96.3 0.053 1.1E-06 53.4 11.6 121 44-189 232-352 (652)
13 COG1548 Predicted transcriptio 96.3 0.018 3.9E-07 52.0 7.7 104 63-169 3-111 (330)
14 PF14639 YqgF: Holliday-juncti 96.2 0.091 2E-06 43.0 10.8 92 62-160 4-110 (150)
15 COG0817 RuvC Holliday junction 96.0 0.013 2.9E-07 48.7 5.1 95 66-167 1-108 (160)
16 TIGR01766 tspaseT_teng_C trans 93.8 0.29 6.3E-06 35.0 6.4 61 99-160 13-82 (82)
17 PRK09557 fructokinase; Reviewe 92.1 1.2 2.5E-05 39.2 9.1 98 64-166 1-115 (301)
18 COG1940 NagC Transcriptional r 91.5 1.3 2.8E-05 39.0 8.7 103 62-167 5-126 (314)
19 PRK05082 N-acetylmannosamine k 91.1 3.8 8.1E-05 35.7 11.2 97 64-165 2-114 (291)
20 TIGR00744 ROK_glcA_fam ROK fam 89.7 1.4 3.1E-05 38.6 7.3 98 66-167 1-117 (318)
21 PF01548 DEDD_Tnp_IS110: Trans 89.1 1.8 3.8E-05 33.7 6.7 107 65-192 1-108 (144)
22 PRK13310 N-acetyl-D-glucosamin 88.6 2.7 5.8E-05 36.8 8.2 100 64-166 1-115 (303)
23 PRK13321 pantothenate kinase; 86.1 13 0.00029 32.2 11.1 55 64-118 1-64 (256)
24 PRK09698 D-allose kinase; Prov 85.5 7.9 0.00017 33.8 9.5 97 63-163 4-120 (302)
25 PF04848 Pox_A22: Poxvirus A22 85.4 19 0.00041 29.5 12.8 115 64-188 2-133 (143)
26 PRK13311 N-acetyl-D-glucosamin 84.8 8.9 0.00019 32.9 9.3 99 64-166 1-115 (256)
27 PF14239 RRXRR: RRXRR protein 84.2 2.6 5.6E-05 35.7 5.5 22 62-83 50-71 (176)
28 PF07318 DUF1464: Protein of u 83.8 5.4 0.00012 37.1 7.9 96 67-166 1-121 (343)
29 PF07282 OrfB_Zn_ribbon: Putat 82.9 1.2 2.6E-05 31.0 2.5 54 135-192 3-69 (69)
30 PRK00292 glk glucokinase; Prov 82.3 8.9 0.00019 33.9 8.5 98 64-164 3-108 (316)
31 COG4012 Uncharacterized protei 81.6 11 0.00025 34.4 8.8 96 64-172 2-99 (342)
32 PHA02942 putative transposase; 80.2 3.4 7.3E-05 38.6 5.2 81 108-192 264-365 (383)
33 TIGR03725 bact_YeaZ universal 79.9 12 0.00026 31.3 8.1 90 65-165 1-98 (202)
34 COG1214 Inactive homolog of me 79.9 8.8 0.00019 33.0 7.4 92 63-165 1-102 (220)
35 PF00480 ROK: ROK family; Int 79.7 2.7 5.8E-05 33.6 3.9 95 67-167 1-111 (179)
36 PF03932 CutC: CutC family; I 77.9 8.9 0.00019 32.9 6.7 62 104-174 79-143 (201)
37 cd03409 Chelatase_Class_II Cla 77.4 16 0.00035 26.3 7.2 56 113-173 2-60 (101)
38 PRK13318 pantothenate kinase; 77.4 15 0.00032 31.9 8.1 55 64-118 1-64 (258)
39 PRK09982 universal stress prot 75.1 12 0.00025 29.0 6.3 49 96-154 89-137 (142)
40 cd03416 CbiX_SirB_N Sirohydroc 74.4 21 0.00046 26.0 7.2 57 113-174 2-60 (101)
41 PRK12408 glucokinase; Provisio 73.8 7.1 0.00015 35.3 5.3 92 62-157 15-119 (336)
42 PRK13320 pantothenate kinase; 72.6 48 0.001 28.9 10.1 55 63-119 2-57 (244)
43 PRK14101 bifunctional glucokin 71.3 12 0.00027 36.7 6.8 65 60-124 15-84 (638)
44 COG1646 Predicted phosphate-bi 70.1 14 0.0003 32.8 6.1 49 98-155 29-77 (240)
45 PRK11572 copper homeostasis pr 67.8 31 0.00068 30.7 7.9 62 104-174 80-144 (248)
46 PF00582 Usp: Universal stress 66.0 22 0.00047 25.5 5.6 52 96-154 88-139 (140)
47 cd01988 Na_H_Antiporter_C The 65.2 16 0.00036 26.8 5.0 23 97-119 81-103 (132)
48 TIGR01865 cas_Csn1 CRISPR-asso 65.1 4.8 0.0001 41.1 2.6 19 64-82 2-20 (805)
49 PRK10116 universal stress prot 65.0 38 0.00082 25.6 7.1 50 96-154 88-137 (142)
50 PRK15080 ethanolamine utilizat 64.7 97 0.0021 27.1 11.2 89 62-160 23-128 (267)
51 PRK00923 sirohydrochlorin coba 64.1 39 0.00085 25.8 7.0 57 112-173 3-61 (126)
52 KOG0237 Glycinamide ribonucleo 62.9 19 0.00042 36.2 6.1 75 96-173 54-145 (788)
53 TIGR03723 bact_gcp putative gl 62.8 71 0.0015 28.8 9.4 85 65-156 1-109 (314)
54 PF03309 Pan_kinase: Type III 62.1 62 0.0013 27.1 8.4 78 65-155 1-85 (206)
55 PF02844 GARS_N: Phosphoribosy 61.7 15 0.00033 28.3 4.2 43 96-152 48-90 (100)
56 TIGR01769 GGGP geranylgeranylg 60.6 35 0.00076 29.3 6.7 46 100-154 14-59 (205)
57 cd01989 STK_N The N-terminal d 60.3 26 0.00055 26.6 5.4 50 97-154 90-143 (146)
58 PF03464 eRF1_2: eRF1 domain 2 59.7 56 0.0012 25.5 7.3 92 64-167 3-121 (133)
59 PF05188 MutS_II: MutS domain 59.2 73 0.0016 23.8 10.0 89 64-169 2-94 (137)
60 PRK10854 exopolyphosphatase; P 58.0 68 0.0015 30.9 8.9 101 56-168 4-127 (513)
61 PF02579 Nitro_FeMo-Co: Dinitr 56.9 64 0.0014 22.8 6.7 52 99-168 42-93 (94)
62 PRK15118 universal stress glob 56.1 53 0.0012 24.9 6.5 50 96-155 89-138 (144)
63 PRK09604 UGMP family protein; 55.8 64 0.0014 29.3 7.9 87 63-156 1-111 (332)
64 PRK13324 pantothenate kinase; 55.5 1.5E+02 0.0032 26.2 10.8 80 64-155 1-90 (258)
65 PRK09472 ftsA cell division pr 54.3 73 0.0016 29.7 8.2 58 62-119 7-84 (420)
66 cd02064 FAD_synthetase_N FAD s 54.2 26 0.00057 28.7 4.7 64 99-171 88-159 (180)
67 cd03413 CbiK_C Anaerobic cobal 53.9 72 0.0016 24.1 6.8 56 113-174 3-58 (103)
68 PRK15005 universal stress prot 53.6 28 0.00062 26.2 4.6 23 96-118 93-115 (144)
69 PRK13326 pantothenate kinase; 53.1 1.6E+02 0.0035 26.0 10.0 21 63-83 6-26 (262)
70 COG0418 PyrC Dihydroorotase [N 52.8 20 0.00044 33.2 4.1 52 116-171 130-189 (344)
71 PF14331 ImcF-related_N: ImcF- 52.2 51 0.0011 29.0 6.5 57 97-154 8-75 (266)
72 PRK09545 znuA high-affinity zi 50.8 67 0.0015 28.8 7.2 44 126-173 234-277 (311)
73 PRK10966 exonuclease subunit S 50.8 1.1E+02 0.0024 28.6 8.9 71 98-172 27-102 (407)
74 PRK09605 bifunctional UGMP fam 50.8 92 0.002 29.7 8.5 88 63-157 1-109 (535)
75 cd03414 CbiX_SirB_C Sirohydroc 50.3 78 0.0017 23.6 6.5 55 113-172 3-59 (117)
76 PRK13322 pantothenate kinase; 50.2 1E+02 0.0022 26.9 8.0 78 64-155 1-81 (246)
77 cd01018 ZntC Metal binding pro 49.4 70 0.0015 27.7 6.9 44 126-173 199-242 (266)
78 cd01017 AdcA Metal binding pro 49.4 89 0.0019 27.3 7.6 44 126-173 202-245 (282)
79 PF00012 HSP70: Hsp70 protein; 47.9 16 0.00034 34.9 2.8 18 65-82 1-18 (602)
80 PRK15456 universal stress prot 47.4 31 0.00067 26.3 3.9 50 97-154 92-141 (142)
81 KOG1220 Phosphoglucomutase/pho 46.9 42 0.00092 33.5 5.6 50 102-160 90-142 (607)
82 cd02067 B12-binding B12 bindin 46.9 1.1E+02 0.0023 22.9 6.8 80 85-173 25-104 (119)
83 cd01025 TOPRIM_recR TOPRIM_rec 46.6 65 0.0014 25.3 5.6 30 98-127 44-73 (112)
84 PF13727 CoA_binding_3: CoA-bi 46.6 40 0.00086 26.1 4.5 45 99-154 130-174 (175)
85 COG3513 Predicted CRISPR-assoc 46.5 17 0.00036 37.9 2.8 20 62-81 3-22 (1088)
86 PRK03011 butyrate kinase; Prov 46.4 1.6E+02 0.0034 27.3 9.1 89 63-156 2-129 (358)
87 cd03412 CbiK_N Anaerobic cobal 46.2 43 0.00092 26.2 4.6 49 113-171 3-52 (127)
88 PF00072 Response_reg: Respons 46.0 1E+02 0.0022 21.6 7.7 65 100-175 33-97 (112)
89 TIGR01768 GGGP-family geranylg 45.2 63 0.0014 28.2 5.9 45 100-154 17-61 (223)
90 cd00293 USP_Like Usp: Universa 44.5 45 0.00098 23.6 4.2 21 99-119 82-102 (130)
91 cd01137 PsaA Metal binding pro 44.3 1.2E+02 0.0026 26.8 7.7 46 124-173 206-251 (287)
92 cd01122 GP4d_helicase GP4d_hel 42.3 59 0.0013 27.7 5.3 59 98-156 128-189 (271)
93 PF14450 FtsA: Cell division p 41.8 76 0.0016 24.2 5.3 18 65-82 1-18 (120)
94 cd06292 PBP1_LacI_like_10 Liga 41.8 2E+02 0.0043 23.7 8.5 17 100-116 45-61 (273)
95 cd00984 DnaB_C DnaB helicase C 41.3 1.3E+02 0.0028 25.0 7.1 60 97-156 110-171 (242)
96 smart00842 FtsA Cell division 41.2 1.5E+02 0.0033 24.0 7.4 55 65-119 1-75 (187)
97 cd02812 PcrB_like PcrB_like pr 40.8 90 0.002 27.1 6.2 47 99-154 14-60 (219)
98 PRK04169 geranylgeranylglycery 40.5 78 0.0017 27.7 5.8 41 104-154 26-66 (232)
99 PLN02757 sirohydrochlorine fer 40.4 1.7E+02 0.0037 23.8 7.5 58 110-172 13-72 (154)
100 cd01987 USP_OKCHK USP domain i 40.4 1.4E+02 0.0029 21.9 6.4 24 96-119 71-94 (124)
101 PF08967 DUF1884: Domain of un 40.3 81 0.0018 23.8 5.0 34 109-158 26-60 (85)
102 TIGR02529 EutJ ethanolamine ut 39.6 2.3E+02 0.0051 24.2 8.6 59 67-125 1-75 (239)
103 TIGR00329 gcp_kae1 metallohydr 38.9 1.3E+02 0.0029 26.7 7.2 84 66-156 1-108 (305)
104 PF03808 Glyco_tran_WecB: Glyc 38.9 1.1E+02 0.0024 24.9 6.2 38 97-144 88-125 (172)
105 COG1609 PurR Transcriptional r 38.8 2.3E+02 0.005 25.3 8.7 87 71-172 57-175 (333)
106 COG3142 CutC Uncharacterized p 38.8 1.5E+02 0.0032 26.5 7.2 62 104-174 80-144 (241)
107 PLN02405 hexokinase 38.5 2.5E+02 0.0054 27.4 9.4 20 62-81 94-113 (497)
108 PF03237 Terminase_6: Terminas 38.4 1.6E+02 0.0036 25.1 7.5 103 40-155 205-317 (384)
109 PRK13317 pantothenate kinase; 37.9 2.2E+02 0.0048 25.3 8.4 86 63-168 2-88 (277)
110 PRK11175 universal stress prot 37.8 1E+02 0.0022 26.5 6.1 53 97-156 94-146 (305)
111 COG0420 SbcD DNA repair exonuc 37.7 1.2E+02 0.0026 27.6 6.9 55 97-154 27-81 (390)
112 cd01844 SGNH_hydrolase_like_6 37.3 1.4E+02 0.0029 23.6 6.4 52 102-155 49-100 (177)
113 TIGR00619 sbcd exonuclease Sbc 36.8 1.7E+02 0.0037 25.3 7.4 53 98-154 27-81 (253)
114 PLN03184 chloroplast Hsp70; Pr 36.8 40 0.00086 33.7 3.8 20 62-81 38-57 (673)
115 PTZ00400 DnaK-type molecular c 36.8 13 0.00029 36.9 0.5 56 11-82 5-60 (663)
116 COG0151 PurD Phosphoribosylami 36.4 1.1E+02 0.0023 29.5 6.4 71 98-172 51-139 (428)
117 PRK14046 malate--CoA ligase su 36.4 3E+02 0.0065 25.7 9.3 84 85-174 284-368 (392)
118 PF01261 AP_endonuc_2: Xylose 36.3 2.1E+02 0.0045 22.5 7.3 75 98-172 72-156 (213)
119 TIGR01016 sucCoAbeta succinyl- 36.2 3E+02 0.0066 25.2 9.2 81 85-171 284-365 (386)
120 COG4126 Hydantoin racemase [Am 36.0 81 0.0018 27.9 5.1 61 98-175 162-222 (230)
121 PRK11678 putative chaperone; P 35.7 39 0.00085 32.1 3.4 18 64-81 1-18 (450)
122 TIGR01174 ftsA cell division p 35.5 2.2E+02 0.0048 25.7 8.2 55 65-119 2-76 (371)
123 cd06294 PBP1_ycjW_transcriptio 34.7 1.3E+02 0.0029 24.5 6.1 20 98-117 48-67 (270)
124 cd01019 ZnuA Zinc binding prot 34.5 1.9E+02 0.0042 25.4 7.4 44 125-172 209-252 (286)
125 PF02737 3HCDH_N: 3-hydroxyacy 34.0 25 0.00054 29.0 1.6 64 114-192 3-66 (180)
126 cd00732 CheW CheW, a small reg 33.9 68 0.0015 24.5 4.0 45 33-81 45-89 (140)
127 TIGR00749 glk glucokinase, pro 33.5 1.5E+02 0.0032 26.3 6.6 88 66-158 1-101 (316)
128 PF00155 Aminotran_1_2: Aminot 33.3 97 0.0021 27.1 5.3 57 98-160 131-192 (363)
129 KOG4013 Predicted Cu2+ homeost 33.2 99 0.0021 27.3 5.1 62 103-173 87-152 (255)
130 PRK03317 histidinol-phosphate 33.2 1.3E+02 0.0029 26.7 6.3 54 98-160 148-201 (368)
131 TIGR02260 benz_CoA_red_B benzo 33.1 2.4E+02 0.0052 26.6 8.1 63 98-167 338-406 (413)
132 PF02310 B12-binding: B12 bind 33.1 1.7E+02 0.0036 21.5 5.9 61 99-168 40-100 (121)
133 TIGR00665 DnaB replicative DNA 33.0 1.5E+02 0.0032 27.5 6.7 58 99-156 294-353 (434)
134 PRK12564 carbamoyl phosphate s 33.0 64 0.0014 30.0 4.3 47 62-117 177-225 (360)
135 COG0675 Transposase and inacti 32.5 54 0.0012 28.1 3.5 77 109-192 261-345 (364)
136 TIGR00241 CoA_E_activ CoA-subs 32.4 97 0.0021 26.5 5.1 18 64-81 1-18 (248)
137 PTZ00009 heat shock 70 kDa pro 32.4 45 0.00097 33.1 3.3 21 61-81 2-22 (653)
138 cd00950 DHDPS Dihydrodipicolin 32.0 1.6E+02 0.0036 25.5 6.5 53 98-157 83-135 (284)
139 PRK13331 pantothenate kinase; 32.0 1.7E+02 0.0038 25.8 6.7 22 62-83 6-27 (251)
140 PRK07179 hypothetical protein; 31.6 1.4E+02 0.0031 27.0 6.3 53 98-159 169-221 (407)
141 TIGR00555 panK_eukar pantothen 31.6 3.8E+02 0.0081 24.1 8.8 89 65-168 2-92 (279)
142 PRK00994 F420-dependent methyl 31.5 2.8E+02 0.0061 25.1 7.8 63 99-173 49-111 (277)
143 PF11215 DUF3010: Protein of u 31.4 1.6E+02 0.0035 24.1 5.8 63 98-170 49-112 (138)
144 PF11104 PilM_2: Type IV pilus 31.4 2.2E+02 0.0047 25.5 7.3 53 67-119 1-70 (340)
145 cd06297 PBP1_LacI_like_12 Liga 31.3 1.7E+02 0.0036 24.4 6.2 17 101-117 46-62 (269)
146 PF13481 AAA_25: AAA domain; P 31.3 1.2E+02 0.0025 24.2 5.1 58 98-156 128-187 (193)
147 PRK11475 DNA-binding transcrip 31.1 3.2E+02 0.0069 22.9 8.6 67 100-174 27-94 (207)
148 PF13407 Peripla_BP_4: Peripla 30.9 1.7E+02 0.0036 24.0 6.1 45 99-157 45-89 (257)
149 PRK14457 ribosomal RNA large s 30.8 2.2E+02 0.0049 26.2 7.4 24 165-188 313-337 (345)
150 cd06533 Glyco_transf_WecG_TagA 30.8 1.7E+02 0.0038 23.8 6.1 61 99-172 88-154 (171)
151 PRK13410 molecular chaperone D 30.7 46 0.001 33.3 3.1 19 63-81 2-20 (668)
152 TIGR01175 pilM type IV pilus a 30.3 3E+02 0.0065 24.3 8.0 59 61-119 1-76 (348)
153 COG1831 Predicted metal-depend 30.3 1.8E+02 0.0038 26.6 6.4 73 99-174 110-187 (285)
154 PF09989 DUF2229: CoA enzyme a 30.2 72 0.0016 27.4 3.9 37 109-155 182-219 (221)
155 TIGR01295 PedC_BrcD bacterioci 30.2 2.2E+02 0.0047 21.8 6.3 48 99-155 13-60 (122)
156 PF06925 MGDG_synth: Monogalac 29.8 2.9E+02 0.0062 22.0 7.4 66 99-176 78-161 (169)
157 TIGR00539 hemN_rel putative ox 29.7 3.6E+02 0.0078 24.4 8.5 60 110-174 51-113 (360)
158 TIGR03568 NeuC_NnaA UDP-N-acet 29.5 3.5E+02 0.0076 24.6 8.5 75 98-186 81-182 (365)
159 PF13911 AhpC-TSA_2: AhpC/TSA 29.5 1.5E+02 0.0032 21.9 5.1 52 103-175 6-57 (115)
160 PRK01433 hscA chaperone protei 29.4 62 0.0013 31.9 3.7 19 63-81 19-37 (595)
161 PRK13325 bifunctional biotin-- 29.3 5.5E+02 0.012 25.5 10.3 21 62-82 337-357 (592)
162 PTZ00186 heat shock 70 kDa pre 29.3 62 0.0013 32.4 3.7 21 62-82 26-46 (657)
163 PRK09165 replicative DNA helic 29.2 1.7E+02 0.0036 28.2 6.5 58 99-156 330-391 (497)
164 COG1433 Uncharacterized conser 29.1 2.9E+02 0.0063 21.9 6.9 54 100-171 55-108 (121)
165 PTZ00340 O-sialoglycoprotein e 28.9 2.3E+02 0.005 26.3 7.2 91 64-165 2-114 (345)
166 PRK05627 bifunctional riboflav 28.9 1.4E+02 0.0031 26.9 5.7 65 99-170 102-173 (305)
167 cd01833 XynB_like SGNH_hydrola 28.8 2.6E+02 0.0057 21.2 7.1 57 99-155 66-124 (157)
168 PF07355 GRDB: Glycine/sarcosi 28.7 1.4E+02 0.003 28.0 5.7 51 96-153 66-116 (349)
169 TIGR03123 one_C_unchar_1 proba 28.7 3.7E+02 0.0081 24.6 8.4 93 66-166 1-107 (318)
170 PF01884 PcrB: PcrB family; I 28.7 2.5E+02 0.0054 24.7 7.0 44 100-154 22-65 (230)
171 cd00851 MTH1175 This uncharact 28.6 2.2E+02 0.0048 20.3 5.8 49 100-166 53-101 (103)
172 PF00532 Peripla_BP_1: Peripla 28.5 2.4E+02 0.0051 24.4 6.9 92 72-174 1-120 (279)
173 TIGR02263 benz_CoA_red_C benzo 28.5 1.5E+02 0.0033 27.3 5.9 50 98-155 309-358 (380)
174 COG0079 HisC Histidinol-phosph 28.3 1.7E+02 0.0036 27.0 6.1 53 99-159 135-187 (356)
175 PRK14878 UGMP family protein; 28.3 3.6E+02 0.0077 24.3 8.2 85 66-157 1-105 (323)
176 cd06281 PBP1_LacI_like_5 Ligan 27.9 2.3E+02 0.0051 23.3 6.5 14 104-117 49-62 (269)
177 cd06311 PBP1_ABC_sugar_binding 27.4 2.1E+02 0.0046 23.6 6.2 45 99-156 49-93 (274)
178 cd01016 TroA Metal binding pro 27.3 2.5E+02 0.0055 24.5 6.9 43 125-171 191-233 (276)
179 PRK00290 dnaK molecular chaper 27.0 55 0.0012 32.1 2.9 19 63-81 2-20 (627)
180 cd00338 Ser_Recombinase Serine 26.9 2.5E+02 0.0054 20.9 6.0 58 97-162 52-109 (137)
181 cd01829 SGNH_hydrolase_peri2 S 26.9 2.2E+02 0.0048 22.6 6.0 51 100-155 98-148 (200)
182 cd01545 PBP1_SalR Ligand-bindi 26.7 2.1E+02 0.0045 23.4 6.0 17 100-116 46-62 (270)
183 PRK10550 tRNA-dihydrouridine s 26.6 3.1E+02 0.0066 24.8 7.4 68 99-171 150-217 (312)
184 PRK10812 putative DNAse; Provi 26.6 4.1E+02 0.009 23.2 8.1 72 97-172 75-147 (265)
185 cd02071 MM_CoA_mut_B12_BD meth 26.4 2.9E+02 0.0063 21.0 9.9 94 85-187 25-119 (122)
186 PRK07667 uridine kinase; Provi 26.3 2.4E+02 0.0052 23.1 6.2 48 100-155 4-52 (193)
187 PF13167 GTP-bdg_N: GTP-bindin 26.2 2.9E+02 0.0063 20.9 7.7 71 98-172 9-81 (95)
188 COG1924 Activator of 2-hydroxy 26.0 1.3E+02 0.0029 28.6 5.0 26 56-81 128-153 (396)
189 PF01297 TroA: Periplasmic sol 25.9 2.7E+02 0.0058 23.7 6.6 46 124-173 179-224 (256)
190 cd00248 Mth938-like Mth938-lik 25.8 3E+02 0.0065 20.9 7.0 55 99-168 41-95 (109)
191 cd01828 sialate_O-acetylestera 25.8 3.1E+02 0.0068 21.1 6.9 22 100-122 39-60 (169)
192 PTZ00107 hexokinase; Provision 25.8 1.5E+02 0.0033 28.5 5.6 20 62-81 73-92 (464)
193 KOG0968 DNA polymerase zeta, c 25.7 2.3E+02 0.0049 31.1 7.1 106 33-141 653-781 (1488)
194 PRK05183 hscA chaperone protei 25.6 70 0.0015 31.6 3.3 19 63-81 19-37 (616)
195 PTZ00288 glucokinase 1; Provis 25.3 3.8E+02 0.0083 25.3 8.1 29 54-82 16-45 (405)
196 TIGR01917 gly_red_sel_B glycin 25.3 1.7E+02 0.0036 28.3 5.6 50 97-153 63-112 (431)
197 KOG1856 Transcription elongati 25.1 4.1E+02 0.0088 29.1 8.7 98 64-169 604-717 (1299)
198 PRK13411 molecular chaperone D 25.1 67 0.0014 31.9 3.1 19 63-81 2-20 (653)
199 TIGR01918 various_sel_PB selen 25.0 1.7E+02 0.0037 28.3 5.6 62 97-169 63-126 (431)
200 PF09547 Spore_IV_A: Stage IV 24.8 1.9E+02 0.0041 28.3 5.9 43 124-169 188-231 (492)
201 TIGR00674 dapA dihydrodipicoli 24.6 2.1E+02 0.0046 25.0 5.9 53 98-157 81-133 (285)
202 cd06271 PBP1_AglR_RafR_like Li 24.5 2.4E+02 0.0051 22.9 5.9 19 99-117 48-66 (268)
203 PRK08760 replicative DNA helic 24.5 2.4E+02 0.0052 27.0 6.7 57 99-155 328-386 (476)
204 TIGR02026 BchE magnesium-proto 24.4 3.9E+02 0.0084 25.5 8.0 68 96-172 225-298 (497)
205 TIGR03192 benz_CoA_bzdQ benzoy 24.1 3.6E+02 0.0078 24.6 7.4 20 63-82 32-51 (293)
206 COG0443 DnaK Molecular chapero 24.1 73 0.0016 31.4 3.1 19 63-81 5-23 (579)
207 PF00701 DHDPS: Dihydrodipicol 24.0 4.2E+02 0.0091 23.0 7.7 64 99-169 24-91 (289)
208 TIGR03729 acc_ester putative p 23.8 2.7E+02 0.0059 23.4 6.2 47 99-154 21-67 (239)
209 PRK05595 replicative DNA helic 23.7 2.4E+02 0.0052 26.5 6.4 57 99-155 300-358 (444)
210 PRK03170 dihydrodipicolinate s 23.7 2.8E+02 0.0062 24.2 6.5 52 98-156 84-135 (292)
211 PF00701 DHDPS: Dihydrodipicol 23.6 4.9E+02 0.011 22.6 9.0 53 97-156 83-135 (289)
212 TIGR02350 prok_dnaK chaperone 23.3 69 0.0015 31.2 2.8 17 65-81 2-18 (595)
213 CHL00094 dnaK heat shock prote 23.3 71 0.0015 31.5 2.9 19 63-81 2-20 (621)
214 PRK15005 universal stress prot 23.0 1.8E+02 0.0039 21.7 4.6 29 112-144 3-31 (144)
215 PRK08769 DNA polymerase III su 22.9 2.6E+02 0.0057 25.4 6.3 63 106-169 68-136 (319)
216 cd01972 Nitrogenase_VnfE_like 22.6 1.9E+02 0.0042 26.9 5.5 58 96-160 75-133 (426)
217 cd01715 ETF_alpha The electron 22.6 2.1E+02 0.0045 22.9 5.1 36 98-144 71-106 (168)
218 PF02833 DHHA2: DHHA2 domain; 22.5 93 0.002 23.6 2.9 50 65-117 24-73 (127)
219 cd01541 PBP1_AraR Ligand-bindi 22.3 4.4E+02 0.0096 21.6 7.8 17 100-117 46-62 (273)
220 cd06282 PBP1_GntR_like_2 Ligan 22.3 3.3E+02 0.0071 22.1 6.3 9 109-117 54-62 (266)
221 PF06180 CbiK: Cobalt chelatas 22.3 2.7E+02 0.0059 24.7 6.1 68 84-155 76-148 (262)
222 PRK08175 aminotransferase; Val 22.0 3E+02 0.0065 24.8 6.5 56 98-159 150-207 (395)
223 PF00370 FGGY_N: FGGY family o 22.0 97 0.0021 26.0 3.1 18 64-81 1-18 (245)
224 TIGR01312 XylB D-xylulose kina 22.0 1.7E+02 0.0036 27.2 5.0 16 66-81 1-16 (481)
225 PRK09112 DNA polymerase III su 21.9 3.4E+02 0.0075 24.9 6.9 67 103-169 93-164 (351)
226 PRK11175 universal stress prot 21.7 1.3E+02 0.0028 25.8 4.0 21 98-118 249-269 (305)
227 PHA02546 47 endonuclease subun 21.7 3E+02 0.0066 24.8 6.5 56 97-154 26-82 (340)
228 cd05785 DNA_polB_like2_exo Unc 21.5 3.7E+02 0.0081 22.6 6.6 22 96-118 59-80 (207)
229 smart00260 CheW Two component 21.4 1.4E+02 0.003 22.3 3.6 45 33-81 47-91 (138)
230 PF14606 Lipase_GDSL_3: GDSL-l 21.3 2.8E+02 0.0061 23.4 5.7 56 96-155 45-100 (178)
231 TIGR03772 anch_rpt_subst ancho 21.3 4.2E+02 0.0091 25.7 7.6 47 123-173 399-447 (479)
232 PRK12359 flavodoxin FldB; Prov 21.3 1.2E+02 0.0027 25.1 3.5 31 114-144 138-168 (172)
233 PF08821 CGGC: CGGC domain; I 21.2 3E+02 0.0064 21.2 5.4 52 97-153 53-104 (107)
234 cd06309 PBP1_YtfQ_like Peripla 21.2 3.5E+02 0.0075 22.3 6.3 42 100-155 46-87 (273)
235 PRK11303 DNA-binding transcrip 21.2 5.2E+02 0.011 22.0 8.5 17 101-117 108-124 (328)
236 PF14106 DUF4279: Domain of un 21.1 2.1E+02 0.0046 21.2 4.6 43 99-141 68-113 (118)
237 COG3703 ChaC Uncharacterized p 21.1 1E+02 0.0023 26.5 3.1 20 62-81 57-76 (190)
238 cd04724 Tryptophan_synthase_al 21.1 3.5E+02 0.0075 23.3 6.5 53 98-153 15-81 (242)
239 PRK14469 ribosomal RNA large s 21.1 4.2E+02 0.0092 24.0 7.3 26 165-190 308-334 (343)
240 COG1521 Pantothenate kinase ty 21.1 2.4E+02 0.0052 25.1 5.5 19 64-82 1-19 (251)
241 PLN02257 phosphoribosylamine-- 21.0 3.6E+02 0.0079 25.4 7.0 21 97-117 49-69 (434)
242 cd05560 Xcc1710_like Xcc1710_l 20.9 2.7E+02 0.0058 21.2 5.1 54 99-168 42-95 (109)
243 TIGR03722 arch_KAE1 universal 20.8 2.1E+02 0.0046 25.7 5.2 84 66-156 1-105 (322)
244 TIGR03190 benz_CoA_bzdN benzoy 20.8 2.9E+02 0.0062 25.5 6.2 54 98-159 301-354 (377)
245 PRK14463 ribosomal RNA large s 20.8 4.6E+02 0.0099 24.2 7.5 27 164-190 307-334 (349)
246 PRK03692 putative UDP-N-acetyl 20.8 3E+02 0.0066 24.1 6.1 61 99-172 146-212 (243)
247 TIGR03275 methan_mark_8 putati 20.8 1.7E+02 0.0037 26.3 4.5 61 62-138 153-213 (259)
248 PF07066 DUF3882: Lactococcus 20.7 3E+02 0.0064 23.1 5.5 57 63-120 2-74 (159)
249 TIGR03600 phage_DnaB phage rep 20.6 4.3E+02 0.0094 24.4 7.4 56 101-156 295-352 (421)
250 PF06050 HGD-D: 2-hydroxygluta 20.5 1.6E+02 0.0034 25.9 4.3 53 96-155 272-324 (349)
251 cd01141 TroA_d Periplasmic bin 20.3 3.5E+02 0.0076 21.4 6.0 34 108-156 67-100 (186)
252 cd06316 PBP1_ABC_sugar_binding 20.2 3.3E+02 0.0071 22.9 6.1 43 100-156 47-89 (294)
253 TIGR01279 DPOR_bchN light-inde 20.2 2.9E+02 0.0063 25.7 6.2 57 97-160 71-128 (407)
254 cd01143 YvrC Periplasmic bindi 20.2 4E+02 0.0087 20.9 6.3 46 108-169 58-103 (195)
255 PRK13392 5-aminolevulinate syn 20.1 4.4E+02 0.0095 23.8 7.2 50 101-159 166-218 (410)
No 1
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=100.00 E-value=5.4e-40 Score=263.80 Aligned_cols=130 Identities=32% Similarity=0.469 Sum_probs=121.1
Q ss_pred CceEEEEecCCCeEEEEEecC--CeeeeeeeEEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759 62 GGFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG 138 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~ 138 (204)
.+++||||||+||||||+||. .+|+|+.++.+++ ...+..|.+++++|++++||||+|++|||+++++++.+++|++
T Consensus 3 ~~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~ 82 (138)
T PRK00109 3 SGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFAN 82 (138)
T ss_pred CCcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHHHH
Confidence 478999999999999999995 5899999998754 3467899999999999999999999999999999999999999
Q ss_pred HHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc-cc
Q 028759 139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-IT 194 (204)
Q Consensus 139 ~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~-l~ 194 (204)
+|++++ ++||++|||||||.+|+++|++.|.+++++|+.+|++||++|||+ |+
T Consensus 83 ~L~~~~---~~~v~~~DEr~TT~~A~~~l~~~~~~~~~~k~~vD~~AA~iILq~yL~ 136 (138)
T PRK00109 83 RLEGRF---GLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLD 136 (138)
T ss_pred HHHHHh---CCCEEEEcCCcCHHHHHHHHHHcCCChhhcccchhHHHHHHHHHHHHh
Confidence 999885 899999999999999999999999888888899999999999999 65
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=2e-41 Score=271.19 Aligned_cols=130 Identities=35% Similarity=0.492 Sum_probs=119.3
Q ss_pred ceEEEEecCCCeEEEEEecC--CeeeeeeeEEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHH
Q 028759 63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR 139 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~ 139 (204)
+++||||||+||||||+||. .+|+|++++.+.+ ..+++.|.+++++|+|+.||||+|++|||+++++++.+++|+++
T Consensus 1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~ 80 (135)
T PF03652_consen 1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEE 80 (135)
T ss_dssp -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHH
T ss_pred CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHH
Confidence 57999999999999999996 4899999999653 46889999999999999999999999999999999999999999
Q ss_pred HHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc-cc
Q 028759 140 LAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-IT 194 (204)
Q Consensus 140 L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~-l~ 194 (204)
|+++++ ++||++|||||||.+|++.|++.|++++++|+.+|++||++|||+ |+
T Consensus 81 L~~~~~--~ipV~~~DEr~TT~~A~~~l~~~g~~~~k~k~~iD~~AA~iILq~yLd 134 (135)
T PF03652_consen 81 LKKRFP--GIPVILVDERLTTKEAERRLRESGLSRKKRKKKIDSIAAAIILQSYLD 134 (135)
T ss_dssp HHHHH---TSEEEEEECSCSHHCCHCCHHHTT-SHHHHCHHHCCCHHHHHHHHHHC
T ss_pred HHHhcC--CCcEEEECCChhHHHHHHHHHHcCCChhhcCccccHHHHHHHHHHHHh
Confidence 999863 999999999999999999999999999999999999999999998 54
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=2.6e-40 Score=267.30 Aligned_cols=130 Identities=32% Similarity=0.422 Sum_probs=122.7
Q ss_pred ceEEEEecCCCeEEEEEecC--CeeeeeeeEEccch--hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759 63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRGE--KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG 138 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~~--~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~ 138 (204)
+++||||||+||||||+||. .+|+|++++.+.+. ..+..|.+++++|+++.||||+|++|+|+++++++.+++|++
T Consensus 2 ~~ilalD~G~KrIGvA~sd~~~~~A~pl~~i~~~~~~~~~~~~l~~li~~~~~~~vVVGlP~~m~g~~~~~~~~~~~f~~ 81 (141)
T COG0816 2 MRILALDVGTKRIGVAVSDILGSLASPLETIKRKNGKPQDFNALLKLVKEYQVDTVVVGLPLNMDGTEGPRAELARKFAE 81 (141)
T ss_pred ceEEEEecCCceEEEEEecCCCccccchhhheeccccHhhHHHHHHHHHHhCCCEEEEecCcCCCCCcchhHHHHHHHHH
Confidence 68999999999999999995 49999999997665 378999999999999999999999999999999999999999
Q ss_pred HHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc-ccc
Q 028759 139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-ITF 195 (204)
Q Consensus 139 ~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~-l~~ 195 (204)
+|++++ ++||++||||+||++|++.|++.|++++++|+.+|++||++|||+ |+.
T Consensus 82 ~L~~r~---~lpv~l~DERltTv~A~~~L~~~~~~~~~rk~~iD~~AA~~ILq~~ld~ 136 (141)
T COG0816 82 RLKKRF---NLPVVLWDERLSTVEAERMLIEAGVSRKKRKGVIDSLAAVLILESYLDR 136 (141)
T ss_pred HHHHhc---CCCEEEEcCccCHHHHHHHHHHcCCchhhhcchhHHHHHHHHHHHHHHh
Confidence 999985 899999999999999999999999999999999999999999999 653
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=8.1e-40 Score=260.44 Aligned_cols=124 Identities=29% Similarity=0.406 Sum_probs=117.2
Q ss_pred EEEecCCCeEEEEEecC--CeeeeeeeEEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHH
Q 028759 66 LGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAV 142 (204)
Q Consensus 66 LalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~ 142 (204)
||||||+||||||+||. .+|+|++++..++ ...+..|.+++++|+++.||||+|++|||+++++++.+++|+++|++
T Consensus 1 laiD~G~kriGvA~~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L~~ 80 (130)
T TIGR00250 1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG 80 (130)
T ss_pred CeEccCCCeEEEEEECCCCCEEeceEEEEecCCcHHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHHHH
Confidence 69999999999999995 5899999998743 46789999999999999999999999999999999999999999998
Q ss_pred hhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc
Q 028759 143 RAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES 192 (204)
Q Consensus 143 ~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~ 192 (204)
++ ++||++||||+||.+|+++|++.|++++++|..+|++||++|||+
T Consensus 81 ~~---~~~v~~~DEr~TT~~A~~~l~~~g~~~~~~k~~vD~~AA~iILq~ 127 (130)
T TIGR00250 81 RF---GVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQS 127 (130)
T ss_pred Hh---CCCEEEEcCCcCHHHHHHHHHHcCCChhhccccHhHHHHHHHHHH
Confidence 85 899999999999999999999999999999999999999999998
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=99.54 E-value=8.6e-14 Score=102.80 Aligned_cols=95 Identities=26% Similarity=0.364 Sum_probs=78.5
Q ss_pred eEEEEecCCCeEEEEEecC--CeeeeeeeEEc-cchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHH
Q 028759 64 FSLGVDLGLSRTGLALSKG--FCVRPLTVLKL-RGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRL 140 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~-~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L 140 (204)
++||||+|..+||+|+.|. ....+..+... +.....+.|.+++++++++.|+||.|-.++|....... ..|.+.|
T Consensus 2 ~ilgiD~Ggt~i~~a~~d~~g~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~i~Ig~pg~v~g~~~~~~~--~~l~~~l 79 (99)
T smart00732 2 RVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETE--EAFAELL 79 (99)
T ss_pred cEEEEccCCCeEEEEEECCCCCEecCEEEEEecCcchHHHHHHHHHHHhCCCEEEEeCCcCCCCCcCHHHH--HHHHHHH
Confidence 5899999999999999983 45555554432 22456789999999999999999999999998776554 8899999
Q ss_pred HHhhccCCCcEEEEcCCCcHHHH
Q 028759 141 AVRAAERGWRVYLLDEHRTSAEA 163 (204)
Q Consensus 141 ~~~~~~~~lpV~lvDER~TT~eA 163 (204)
++++ ++||+++||.+||.+|
T Consensus 80 ~~~~---~~pv~~~nDa~st~~a 99 (99)
T smart00732 80 KERF---NLPVVLVDERLATVYA 99 (99)
T ss_pred HHhh---CCcEEEEeCCcccccC
Confidence 8875 8999999999999875
No 6
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=97.71 E-value=0.00049 Score=57.01 Aligned_cols=98 Identities=22% Similarity=0.167 Sum_probs=60.9
Q ss_pred ceEEEEecCCCeEEEEEecC--Cee--eeeeeEEccc--------hhHHHHHHHHHHHcCCCEEEEeecCCCC-CCCChh
Q 028759 63 GFSLGVDLGLSRTGLALSKG--FCV--RPLTVLKLRG--------EKLELQLLEIAQREETDEFIIGLPKSWD-GSETPQ 129 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~--~~A--~Pl~~i~~~~--------~~~~~~L~~li~e~~i~~IVVGlPl~~d-Gt~~~~ 129 (204)
+++||||+|..++|+|+.+. ... --.+++..+. ....+.|.+++++|+|+.++|=-|+-.. ....-.
T Consensus 2 m~iLGIDPgl~~tG~avi~~~~~~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~~Pd~vaiE~~f~~~n~~sa~~ 81 (164)
T PRK00039 2 MRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEYQPDEVAIEEVFFNKNPQSALK 81 (164)
T ss_pred CEEEEEccccCceeEEEEEecCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEehhhhccChHHHHH
Confidence 58999999999999999873 222 2233554321 1345789999999999999999887432 222211
Q ss_pred HHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759 130 SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 130 ~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L 167 (204)
.-+++--+.....+ .++||+.+ |..+.+...
T Consensus 82 l~~arGvi~la~~~---~~ipv~ey----~P~~VKk~v 112 (164)
T PRK00039 82 LGQARGVAILAAAQ---RGLPVAEY----TPLQVKKAV 112 (164)
T ss_pred HHHHHHHHHHHHHH---cCCCEEEE----CHHHhhhhh
Confidence 12233333333322 59999865 555555443
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=97.53 E-value=0.0012 Score=53.69 Aligned_cols=96 Identities=24% Similarity=0.229 Sum_probs=50.6
Q ss_pred EEEEecCCCeEEEEEecC--C--eeeeeeeEEccch--------hHHHHHHHHHHHcCCCEEEEeecCCCCCCCC-hhHH
Q 028759 65 SLGVDLGLSRTGLALSKG--F--CVRPLTVLKLRGE--------KLELQLLEIAQREETDEFIIGLPKSWDGSET-PQSN 131 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~--~--~A~Pl~~i~~~~~--------~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~-~~~~ 131 (204)
|||||+|..++|.|+-+. . ..--..++..+.. ...+.|.+++++|+|+.++|=-|.......+ -..-
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 799999999999999983 2 2233345553221 2357899999999999999998874322111 1111
Q ss_pred HHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759 132 KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 132 ~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L 167 (204)
+++-.+..... ..++||.. +|..+.++.+
T Consensus 81 ~arGvi~l~~~---~~~i~v~~----y~P~~vKk~v 109 (149)
T PF02075_consen 81 QARGVILLAAA---QRGIPVFE----YTPSEVKKAV 109 (149)
T ss_dssp HHHHHHHHHHH---TTT--EEE----EEHHHHHHHH
T ss_pred HHHHHHHHHHH---HcCCeEEE----ECHHHHHHHh
Confidence 22233222222 25889875 4666666654
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=97.43 E-value=0.0025 Score=51.78 Aligned_cols=92 Identities=18% Similarity=0.162 Sum_probs=55.7
Q ss_pred eEEEEecCCCeEEEEEecC--Cee--eeeeeEEccc--------hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHH
Q 028759 64 FSLGVDLGLSRTGLALSKG--FCV--RPLTVLKLRG--------EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSN 131 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~--~~A--~Pl~~i~~~~--------~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~ 131 (204)
++||||+|..++|+|+.+. ... .-..++..+. ....+.|.+++.+|+|+.++|=-+.--.+. +.+.
T Consensus 1 rILGIDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~~Pd~vaiE~~~~~~n~--~s~~ 78 (154)
T cd00529 1 RILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQFQPDVVAIERVFFAKNP--DSAL 78 (154)
T ss_pred CEEEEccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEEEhhcccCh--HHHH
Confidence 5899999999999999873 222 2234555331 134578999999999999999876632222 2222
Q ss_pred HHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759 132 KVRSVAGRLAVRAAERGWRVYLLDEH 157 (204)
Q Consensus 132 ~v~~Fa~~L~~~~~~~~lpV~lvDER 157 (204)
.+-.+-..+-..+...++||+.++-.
T Consensus 79 ~l~~~~Gvi~~~~~~~~i~v~e~~P~ 104 (154)
T cd00529 79 KLGQARGALILALANRNLPVFEYTPN 104 (154)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEccC
Confidence 22111111111122258898887644
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=97.20 E-value=0.0024 Score=52.81 Aligned_cols=95 Identities=18% Similarity=0.158 Sum_probs=58.5
Q ss_pred EEEEecCCCeEEEEEecC--Ce--eeeeeeEEccch-------hHHHHHHHHHHHcCCCEEEEeecCCC-CCCCChhHHH
Q 028759 65 SLGVDLGLSRTGLALSKG--FC--VRPLTVLKLRGE-------KLELQLLEIAQREETDEFIIGLPKSW-DGSETPQSNK 132 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~--~~--A~Pl~~i~~~~~-------~~~~~L~~li~e~~i~~IVVGlPl~~-dGt~~~~~~~ 132 (204)
+||||+|..++|.||-+. .. .--..++..+.. ...+.|.+++++|+|+.+.|=-++-. |....-..-+
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 599999999999999883 22 233345543221 23578999999999999999887743 2222222223
Q ss_pred HHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759 133 VRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166 (204)
Q Consensus 133 v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~ 166 (204)
++-.+-.... ..++||+ | ||..+.++.
T Consensus 81 arGvilla~~---~~~ipv~---E-y~P~~vKka 107 (156)
T TIGR00228 81 ARGVAIVAAV---NQELPVF---E-YAARQVKQT 107 (156)
T ss_pred HHHHHHHHHH---HcCCCEE---E-ECHHHHHHH
Confidence 3333322222 2599998 3 666655443
No 10
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=97.09 E-value=0.0097 Score=48.45 Aligned_cols=108 Identities=17% Similarity=0.124 Sum_probs=68.1
Q ss_pred CceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHH
Q 028759 62 GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLA 141 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~ 141 (204)
...|.|||+|+ .+|+|+-|-. ..++.+...++ -....+.++|.+++-=.||-= |=+.- -. ++++|+
T Consensus 31 ~~lIVGiDPG~-ttgiAildL~-G~~l~l~S~R~-~~~~evi~~I~~~G~PviVAt-----DV~p~--P~----~V~Kia 96 (138)
T PF04312_consen 31 RYLIVGIDPGT-TTGIAILDLD-GELLDLKSSRN-MSRSEVIEWISEYGKPVIVAT-----DVSPP--PE----TVKKIA 96 (138)
T ss_pred CCEEEEECCCc-eeEEEEEecC-CcEEEEEeecC-CCHHHHHHHHHHcCCEEEEEe-----cCCCC--cH----HHHHHH
Confidence 47899999998 6899999832 24455444333 234577777877766555543 43333 33 444555
Q ss_pred HhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHH
Q 028759 142 VRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAV 187 (204)
Q Consensus 142 ~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~ 187 (204)
..| +-.++.=++.+|..|=.+...+.+.+-.. ---=|++||+
T Consensus 97 ~~f---~A~ly~P~~dlsveeK~~l~~~~~~~~~n-~HeRDALAAA 138 (138)
T PF04312_consen 97 RSF---NAVLYTPERDLSVEEKQELAREYSERYEN-DHERDALAAA 138 (138)
T ss_pred HHh---CCcccCCCCcCCHHHHHHHHHhhCCCCCC-chHHhHhhcC
Confidence 543 55677778999999888888876641111 1223888885
No 11
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.80 E-value=0.011 Score=59.43 Aligned_cols=89 Identities=15% Similarity=0.233 Sum_probs=59.6
Q ss_pred CceEEEEecCCCe-EEEEEecCC--eeeeeeeEEcc----chhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHH
Q 028759 62 GGFSLGVDLGLSR-TGLALSKGF--CVRPLTVLKLR----GEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVR 134 (204)
Q Consensus 62 ~g~iLalD~G~kR-IGVAvsD~~--~A~Pl~~i~~~----~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~ 134 (204)
+..+||||+|... |=+||.|+. ...--.+++.. .....+.|..++..|+|+.|.|| +||.+.. +.
T Consensus 329 ~~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIG-----ngTaSre---te 400 (780)
T COG2183 329 PKATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIG-----NGTASRE---TE 400 (780)
T ss_pred CcceeecCCccccccEEEEEcCCCceeceeEEEcCCCccchHHHHHHHHHHHHHhCceEEEEe-----cCCcchh---HH
Confidence 3479999999655 567888843 11111122221 13455788999999999999999 8998754 45
Q ss_pred HHHHHHHHhhccCCCcEEEEcCCC
Q 028759 135 SVAGRLAVRAAERGWRVYLLDEHR 158 (204)
Q Consensus 135 ~Fa~~L~~~~~~~~lpV~lvDER~ 158 (204)
+|+..+-+..+..++..+.|.|..
T Consensus 401 ~fv~~vl~~~~~~~~~~viVsEag 424 (780)
T COG2183 401 KFVADVLKELPKEKVLKVIVSEAG 424 (780)
T ss_pred HHHHHHHHhccCCCCcEEEEcccc
Confidence 566666655433477888888764
No 12
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=96.29 E-value=0.053 Score=53.41 Aligned_cols=121 Identities=21% Similarity=0.274 Sum_probs=81.9
Q ss_pred hhhhcccccccccCCCCCCceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCC
Q 028759 44 VEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWD 123 (204)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~d 123 (204)
.=+|.|.+.++. ..|.|||||+ .+|+|+-|-. -.++.+...++ -....+.++|.+++-=.||-- |
T Consensus 232 rief~pl~~~r~-------~lIVGIDPGi-TtgiAvldld-Gevl~~~S~r~-~~~~eVve~I~~lG~PvvVAt-----D 296 (652)
T COG2433 232 RIEFVPLRPERR-------SLIVGIDPGI-TTGIAVLDLD-GEVLDLESRRG-IDRSEVVEFISELGKPVVVAT-----D 296 (652)
T ss_pred ccccccCccccc-------ceEEEeCCCc-eeeEEEEecC-CcEEeeecccc-CCHHHHHHHHHHcCCceEEEc-----c
Confidence 335667766643 5799999998 6899999832 12333333322 234688889998876666654 5
Q ss_pred CCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHH
Q 028759 124 GSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVR 189 (204)
Q Consensus 124 Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iI 189 (204)
=+.-| .|+++|+..| +-+.+.=|+++|+.|=.+.++..+++-... -.=|++||++-
T Consensus 297 Vtp~P------~~V~KiAasf---~A~ly~P~~dLsveEK~~~~r~~~~~~~dd-H~RDALAAA~k 352 (652)
T COG2433 297 VTPAP------ETVKKIAASF---NAVLYTPDRDLSVEEKQEALRTLKISVSDD-HERDALAAAYK 352 (652)
T ss_pred CCCCh------HHHHHHHHHc---CCcccCCcccCCHHHHHHHHhhcCCCCCCc-hHHHHHHHHHH
Confidence 55554 5667777764 777888899999999988777766654432 22489999863
No 13
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=96.28 E-value=0.018 Score=51.95 Aligned_cols=104 Identities=21% Similarity=0.239 Sum_probs=68.0
Q ss_pred ceEEEEecCCCeEEEEEecCCe-eeeeeeEEc--cchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHH
Q 028759 63 GFSLGVDLGLSRTGLALSKGFC-VRPLTVLKL--RGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR 139 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~~~-A~Pl~~i~~--~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~ 139 (204)
..+||||+|...+-+|.+||.. ..-+-.+++ +...+...|++++.+++++.+=|=+--..-.-....++-|+..++.
T Consensus 3 ~kilGiDIGGAntk~a~~DG~~~~~d~~YlPMWk~k~rL~~~Lkei~~k~~~~~vgvvMTaELaD~f~tk~eGVe~Ii~~ 82 (330)
T COG1548 3 MKILGIDIGGANTKIASSDGDNYKIDHIYLPMWKKKDRLEETLKEIVHKDNVDYVGVVMTAELADAFKTKAEGVEDIIDT 82 (330)
T ss_pred ceEEEeeccCccchhhhccCCeeeeeEEEeccccchhHHHHHHHHHhccCCcceeEEEeeHHHHHHhhhHHhHHHHHHHH
Confidence 6799999999999999999853 223333443 2235667888988778888554433222222223355667777888
Q ss_pred HHHhhccCCCcEEEEcCC--CcHHHHHHHHHH
Q 028759 140 LAVRAAERGWRVYLLDEH--RTSAEAVDRMIN 169 (204)
Q Consensus 140 L~~~~~~~~lpV~lvDER--~TT~eA~~~L~e 169 (204)
.++.| +.||+++|=. +-|.||.+.+.+
T Consensus 83 v~~Af---~~pv~~v~~~G~~~ssEa~~~~~~ 111 (330)
T COG1548 83 VEKAF---NCPVYVVDVNGNFLSSEALKNPRE 111 (330)
T ss_pred HHHhc---CCceEEEeccCcCcChhHhcCHHH
Confidence 88775 8999999843 334477765544
No 14
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=96.15 E-value=0.091 Score=42.98 Aligned_cols=92 Identities=16% Similarity=0.124 Sum_probs=41.5
Q ss_pred CceEEEEecCCCe----EEEEEecCC-eeeeeeeE-Ec-----cchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhH
Q 028759 62 GGFSLGVDLGLSR----TGLALSKGF-CVRPLTVL-KL-----RGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQS 130 (204)
Q Consensus 62 ~g~iLalD~G~kR----IGVAvsD~~-~A~Pl~~i-~~-----~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~ 130 (204)
+-++|||-+|.-+ +-.|+-|.. -..-...+ .. ...++.+.|.+++.+++|+.|+|| |. +..+
T Consensus 4 ~~rVla~~~g~g~~~~~~~~v~ld~~G~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~kP~vI~v~------g~-~~~s 76 (150)
T PF14639_consen 4 GPRVLALSWGSGDGDDAVFCVVLDENGEVLDHLKLVYNERDRERKEEDMERLKKFIEKHKPDVIAVG------GN-SRES 76 (150)
T ss_dssp ---EEEEE-TT--TTS-EEEEEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--------S-STHH
T ss_pred CCEEEEEEcCCCCCCCCEEEEEECCCCcEEEEEEEcCCccchHHHHHHHHHHHHHHHHcCCeEEEEc------CC-ChhH
Confidence 4679999999666 334454521 11111111 11 113456789999999999999997 42 3445
Q ss_pred HHHHHHHHHHHHhhc----cCCCcEEEEcCCCcH
Q 028759 131 NKVRSVAGRLAVRAA----ERGWRVYLLDEHRTS 160 (204)
Q Consensus 131 ~~v~~Fa~~L~~~~~----~~~lpV~lvDER~TT 160 (204)
++..++.+.+-+... ...++|+++||...+
T Consensus 77 ~~l~~~v~~~v~~~~~~~~~~~i~V~~v~~~~A~ 110 (150)
T PF14639_consen 77 RKLYDDVRDIVEELDEDEQMPPIPVVIVDDEVAR 110 (150)
T ss_dssp HHHHHHHHHHHHHTTB-TTS-B--EEE---TTHH
T ss_pred HHHHHHHHHHHHHhhhcccCCCceEEEECcHHHH
Confidence 554444444433221 136899999997643
No 15
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=95.97 E-value=0.013 Score=48.69 Aligned_cols=95 Identities=25% Similarity=0.272 Sum_probs=57.8
Q ss_pred EEEecCCCeEEEEEecC--Ceeeee--eeEEccch--------hHHHHHHHHHHHcCCCEEEEeecCC-CCCCCChhHHH
Q 028759 66 LGVDLGLSRTGLALSKG--FCVRPL--TVLKLRGE--------KLELQLLEIAQREETDEFIIGLPKS-WDGSETPQSNK 132 (204)
Q Consensus 66 LalD~G~kRIGVAvsD~--~~A~Pl--~~i~~~~~--------~~~~~L~~li~e~~i~~IVVGlPl~-~dGt~~~~~~~ 132 (204)
||||||..+||.+|-+. ....++ .+|..... .+.+.|.+++.+|+|+.+.|=-.+- -|-+..-..-+
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 68999999999999993 344444 45543311 2457888999999999999987763 22222222222
Q ss_pred HHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759 133 VRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 133 v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L 167 (204)
++-.+-.... +.++||.. ||..+.+.-.
T Consensus 81 ARGv~~la~~---~~~l~v~e----Y~p~~VKkav 108 (160)
T COG0817 81 ARGVALLAAA---RRGLPVFE----YTPNQVKKAV 108 (160)
T ss_pred HHHHHHHHHH---HcCCChhh----ccHHHHHHHh
Confidence 2222222222 24888874 5666665554
No 16
>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=93.77 E-value=0.29 Score=35.02 Aligned_cols=61 Identities=20% Similarity=0.225 Sum_probs=37.5
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCC---Ch-hHHH-----HHHHHHHHHHhhccCCCcEEEEcCCCcH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSE---TP-QSNK-----VRSVAGRLAVRAAERGWRVYLLDEHRTS 160 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~---~~-~~~~-----v~~Fa~~L~~~~~~~~lpV~lvDER~TT 160 (204)
...|.+...+ .++.||||...+..+.. +. ..+. -..|.+.|+-...++|++|..|||.+||
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 3456666666 77999999865333321 11 1111 2334555554444579999999999997
No 17
>PRK09557 fructokinase; Reviewed
Probab=92.14 E-value=1.2 Score=39.18 Aligned_cols=98 Identities=15% Similarity=0.165 Sum_probs=57.8
Q ss_pred eEEEEecCCCeEEEEEecC--C-eeeeeeeEEcc---chhHHHHHHHHHHHc-----CCCEEEEeecCCC---CCCCC--
Q 028759 64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLKLR---GEKLELQLLEIAQRE-----ETDEFIIGLPKSW---DGSET-- 127 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~--~-~A~Pl~~i~~~---~~~~~~~L~~li~e~-----~i~~IVVGlPl~~---dGt~~-- 127 (204)
++||+|+|..++-+++.|. . ..+ ..++.. .....+.+.+++++. .+.+|.||.|=.. +|...
T Consensus 1 ~~lgidig~t~~~~~l~d~~g~i~~~--~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgi~~pG~vd~~~g~i~~~ 78 (301)
T PRK09557 1 MRIGIDLGGTKIEVIALDDAGEELFR--KRLPTPRDDYQQTIEAIATLVDMAEQATGQRGTVGVGIPGSISPYTGLVKNA 78 (301)
T ss_pred CEEEEEECCCcEEEEEECCCCCEEEE--EEecCCCCCHHHHHHHHHHHHHHHHhhcCCceEEEecCcccCcCCCCeEEec
Confidence 4799999999999999993 2 211 222221 123445555555443 3567999998433 23111
Q ss_pred hhHH-HHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759 128 PQSN-KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166 (204)
Q Consensus 128 ~~~~-~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~ 166 (204)
+..- .--.+.+.|++++ ++||++.+.-.....|+.+
T Consensus 79 ~~~~~~~~~l~~~l~~~~---~~pv~~~NDa~aaA~aE~~ 115 (301)
T PRK09557 79 NSTWLNGQPLDKDLSARL---NREVRLANDANCLAVSEAV 115 (301)
T ss_pred CCccccCCCHHHHHHHHH---CCCEEEccchhHHHHHHHH
Confidence 0000 1124566777775 8999998887776666644
No 18
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=91.49 E-value=1.3 Score=38.97 Aligned_cols=103 Identities=18% Similarity=0.157 Sum_probs=61.3
Q ss_pred CceEEEEecCCCeEEEEEecCC---eeeeeeeEEccch--h----HHHHHHHHHHHc----CCCEEEEeecCCCCCCC--
Q 028759 62 GGFSLGVDLGLSRTGLALSKGF---CVRPLTVLKLRGE--K----LELQLLEIAQRE----ETDEFIIGLPKSWDGSE-- 126 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~---~A~Pl~~i~~~~~--~----~~~~L~~li~e~----~i~~IVVGlPl~~dGt~-- 126 (204)
...++|||+|..+|=+|+.|.. ........+.... . ..+.+++++.++ .+.+|.++.|-..+...
T Consensus 5 ~~~~lgidIggt~i~~~l~d~~g~~l~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~iGIgi~~pg~~~~~~~~ 84 (314)
T COG1940 5 AMTVLGIDIGGTKIKVALVDLDGEILLRERIPTPTPDPEEAILEAILALVAELLKQAQGRVAIIGIGIPGPGDVDNGTVI 84 (314)
T ss_pred CcEEEEEEecCCEEEEEEECCCCcEEEEEEEecCCCCchhHHHHHHHHHHHHHHHhcCCcCceEEEEeccceeccCCcEE
Confidence 5789999999999999999942 2222222221111 2 234455555543 35566666665444321
Q ss_pred --ChhHHHH--HHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759 127 --TPQSNKV--RSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 127 --~~~~~~v--~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L 167 (204)
.+...-. -.|++.|++.+ ++||...++-..-.-|+..+
T Consensus 85 ~~~~~~~~~~~~~l~~~L~~~~---~~Pv~veNDan~aalaE~~~ 126 (314)
T COG1940 85 VPAPNLGWWNGVDLAEELEARL---GLPVFVENDANAAALAEAWF 126 (314)
T ss_pred eecCCCCccccccHHHHHHHHH---CCCEEEecHHHHHHHHHHHh
Confidence 1111111 34788899886 89999999877777666554
No 19
>PRK05082 N-acetylmannosamine kinase; Provisional
Probab=91.13 E-value=3.8 Score=35.69 Aligned_cols=97 Identities=15% Similarity=0.101 Sum_probs=59.4
Q ss_pred eEEEEecCCCeEEEEEecC--C-eeeeeeeEEcc---c-hhHHHHHHHHHHHc--CCCEEEEeecCCCC-CCC---Ch-h
Q 028759 64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLKLR---G-EKLELQLLEIAQRE--ETDEFIIGLPKSWD-GSE---TP-Q 129 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~--~-~A~Pl~~i~~~---~-~~~~~~L~~li~e~--~i~~IVVGlPl~~d-Gt~---~~-~ 129 (204)
.++|+|+|..++-+++.|- . .+ ...++.. . ....+.+.+++.+. ++.+|.||.|=..| |.. .+ .
T Consensus 2 ~~lgvdig~~~i~~~l~dl~g~i~~--~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~igi~~pG~vd~~~~~~~~~~~ 79 (291)
T PRK05082 2 TTLAIDIGGTKIAAALVGEDGQIRQ--RRQIPTPASQTPEALRQALSALVSPLQAQADRVAVASTGIINDGILTALNPHN 79 (291)
T ss_pred cEEEEEECCCEEEEEEEcCCCcEEE--EEEecCCCCCCHHHHHHHHHHHHHHhhhcCcEEEEeCcccccCCeeEEecCCC
Confidence 4899999999999999993 2 22 1122211 1 23456666666653 67899999984332 211 10 0
Q ss_pred H--HHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHH
Q 028759 130 S--NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVD 165 (204)
Q Consensus 130 ~--~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~ 165 (204)
. -.-..+.+.|++++ ++||++.++-.+..-|+.
T Consensus 80 ~~~w~~~~l~~~l~~~~---~~pv~v~NDa~a~a~aE~ 114 (291)
T PRK05082 80 LGGLLHFPLVQTLEQLT---DLPTIALNDAQAAAWAEY 114 (291)
T ss_pred CccccCCChHHHHHHHh---CCCEEEECcHHHHHHHHH
Confidence 0 01124666777775 899999888777666654
No 20
>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=89.68 E-value=1.4 Score=38.61 Aligned_cols=98 Identities=15% Similarity=0.166 Sum_probs=56.6
Q ss_pred EEEecCCCeEEEEEecCC-eeeeeeeEEc--cchhHHHHHH----HHHHH-----cCCCEEEEeecCCCCCCCChh----
Q 028759 66 LGVDLGLSRTGLALSKGF-CVRPLTVLKL--RGEKLELQLL----EIAQR-----EETDEFIIGLPKSWDGSETPQ---- 129 (204)
Q Consensus 66 LalD~G~kRIGVAvsD~~-~A~Pl~~i~~--~~~~~~~~L~----~li~e-----~~i~~IVVGlPl~~dGt~~~~---- 129 (204)
+|+|+|..++-+++.|.. ........+. ......+.|. +++++ .++.+|-||.|=..|...+..
T Consensus 1 lgidig~t~~~~~l~d~~g~i~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~i~gIgva~pG~vd~~~g~~~~~~ 80 (318)
T TIGR00744 1 IGVDIGGTTIKLGVVDEEGNILSKWKVPTDTTPETIVDAIASAVDSFIQHIAKVGHEIVAIGIGAPGPVNRQRGTVYFAV 80 (318)
T ss_pred CEEEeCCCEEEEEEECCCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhcCCCccceEEEEEeccccccCCCCEEEecC
Confidence 589999999999999931 1111111211 1223334444 44433 257789999984443222110
Q ss_pred ---HHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759 130 ---SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 130 ---~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L 167 (204)
-.. ..+.+.|++++ ++||++.+.-....-|+..+
T Consensus 81 ~~~w~~-~~l~~~l~~~~---~~pv~v~NDa~~~alaE~~~ 117 (318)
T TIGR00744 81 NLDWKQ-EPLKEKVEARV---GLPVVVENDANAAALGEYKK 117 (318)
T ss_pred CCCCCC-CCHHHHHHHHH---CCCEEEechHHHHHHHHHHh
Confidence 011 13667787775 89999998877766666543
No 21
>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=89.11 E-value=1.8 Score=33.68 Aligned_cols=107 Identities=15% Similarity=0.079 Sum_probs=62.9
Q ss_pred EEEEecCCCeEEEEEecCCe-eeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHh
Q 028759 65 SLGVDLGLSRTGLALSKGFC-VRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVR 143 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~~~-A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~ 143 (204)
++|||+|....=+++.|... ......+.+ +...+..+.+.+.++. .++||+ ..-|..+ ..++..|..
T Consensus 1 ~vGiDv~k~~~~v~v~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~--~~~v~~--E~tg~y~------~~l~~~L~~- 68 (144)
T PF01548_consen 1 FVGIDVSKDTHDVCVIDPNGEKLRRFKFEN-DPAGLEKLLDWLASLG--PVLVVM--EATGGYW------RPLADFLQD- 68 (144)
T ss_pred eEEEEcccCeEEEEEEcCCCcEEEEEEEec-cccchhHHhhhhcccc--cccccc--ccccccc------hhhhhheec-
Confidence 58999999999999999643 344444543 3344577777777775 555653 2223333 234444554
Q ss_pred hccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc
Q 028759 144 AAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES 192 (204)
Q Consensus 144 ~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~ 192 (204)
.+.+|++++=+.....++.. + ++.+-.+.|+..-+.++..
T Consensus 69 ---~g~~v~~vnp~~~~~~~~~~----~--~~~KtD~~DA~~ia~~~~~ 108 (144)
T PF01548_consen 69 ---AGIEVVVVNPLQVKRFRKSL----G--RRAKTDKIDARAIARLLRR 108 (144)
T ss_pred ---cccccccccccccccccccc----c--ccccccccchHHHHHHHhc
Confidence 38999999765554433211 1 2223456676665555544
No 22
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional
Probab=88.61 E-value=2.7 Score=36.84 Aligned_cols=100 Identities=15% Similarity=0.118 Sum_probs=57.6
Q ss_pred eEEEEecCCCeEEEEEecC--C-eeeeeeeEE-ccchhHHHHHHHHHHHc----C-CCEEEEeecCCCCCCCCh--hHH-
Q 028759 64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLK-LRGEKLELQLLEIAQRE----E-TDEFIIGLPKSWDGSETP--QSN- 131 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~--~-~A~Pl~~i~-~~~~~~~~~L~~li~e~----~-i~~IVVGlPl~~dGt~~~--~~~- 131 (204)
+++|||+|..+|-+++.|. . ..+-....+ .......+.+.+++++. . +..|-||.|=..|-..+. ...
T Consensus 1 ~~lgidig~t~i~~~l~d~~g~i~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~igia~pG~vd~~~g~~~~~~~ 80 (303)
T PRK13310 1 MYYGFDIGGTKIELGVFNEKLELQWEERVPTPRDSYDAFLDAVCELVAEADQRFGCKGSVGIGIPGMPETEDGTLYAANV 80 (303)
T ss_pred CeEEEEeCCCcEEEEEECCCCcEEEEEEecCCCcCHHHHHHHHHHHHHHHHhhcCCcceEEEeCCCcccCCCCEEeccCc
Confidence 4799999999999999993 2 221111111 11223445566555442 2 347889988544321110 000
Q ss_pred ---HHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759 132 ---KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166 (204)
Q Consensus 132 ---~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~ 166 (204)
.--.+.+.|++++ ++||++.+.-..-..|+..
T Consensus 81 ~~w~~~~l~~~l~~~~---~~pV~ieNDa~aaalaE~~ 115 (303)
T PRK13310 81 PAASGKPLRADLSARL---GRDVRLDNDANCFALSEAW 115 (303)
T ss_pred ccccCCcHHHHHHHHH---CCCeEEeccHhHHHHHHhh
Confidence 0124667788775 8999998887666656543
No 23
>PRK13321 pantothenate kinase; Reviewed
Probab=86.07 E-value=13 Score=32.22 Aligned_cols=55 Identities=18% Similarity=0.219 Sum_probs=36.5
Q ss_pred eEEEEecCCCeEEEEEecCCeeeeeeeEEcc---c-hhHHHHHHHHHHHc-----CCCEEEEee
Q 028759 64 FSLGVDLGLSRTGLALSKGFCVRPLTVLKLR---G-EKLELQLLEIAQRE-----ETDEFIIGL 118 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~---~-~~~~~~L~~li~e~-----~i~~IVVGl 118 (204)
++|+||.|..+|=+|+.|+........++.. . ......+.++++++ +++.++|+-
T Consensus 1 MiL~IDIGnT~ik~gl~~~~~i~~~~~~~T~~~~~~~~~~~~l~~l~~~~~~~~~~i~~i~vss 64 (256)
T PRK13321 1 MLLLIDVGNTNIKLGVFDGDRLLRSFRLPTDKSRTSDELGILLLSLFRHAGLDPEDIRAVVISS 64 (256)
T ss_pred CEEEEEECCCeEEEEEEECCEEEEEEEEecCCCCCHHHHHHHHHHHHHHcCCChhhCCeEEEEe
Confidence 4799999999999999985311111122211 1 23456788888776 489999994
No 24
>PRK09698 D-allose kinase; Provisional
Probab=85.54 E-value=7.9 Score=33.79 Aligned_cols=97 Identities=14% Similarity=0.151 Sum_probs=56.8
Q ss_pred ceEEEEecCCCeEEEEEecC--C-eee---eeeeEEccc---hhHHHHHHHHHHHc--CCCEEEEeecCCCCCCCC----
Q 028759 63 GFSLGVDLGLSRTGLALSKG--F-CVR---PLTVLKLRG---EKLELQLLEIAQRE--ETDEFIIGLPKSWDGSET---- 127 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~--~-~A~---Pl~~i~~~~---~~~~~~L~~li~e~--~i~~IVVGlPl~~dGt~~---- 127 (204)
..++|+|+|..++-+++.|. . .++ |..... .. ..+.+.+.+++++. ++.+|-||.|=..|...+
T Consensus 4 ~~~lgidig~t~i~~~l~d~~g~i~~~~~~~~~~~~-~~~~~~~l~~~i~~~~~~~~~~i~gigia~pG~vd~~~g~i~~ 82 (302)
T PRK09698 4 NVVLGIDMGGTHIRFCLVDAEGEILHCEKKRTAEVI-APDLVSGLGEMIDEYLRRFNARCHGIVMGFPALVSKDRRTVIS 82 (302)
T ss_pred cEEEEEEcCCcEEEEEEEcCCCCEEEEEEeCCcccc-chHHHHHHHHHHHHHHHHcCCCeeEEEEeCCcceeCCCCEEEe
Confidence 57999999999999999992 2 222 221110 11 12234455666653 678999999844332111
Q ss_pred -hhH----HHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHH
Q 028759 128 -PQS----NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEA 163 (204)
Q Consensus 128 -~~~----~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA 163 (204)
+.. -.-..+.+.|++++ ++||++.+.-.....|
T Consensus 83 ~~~~~~~~~~~~~l~~~l~~~~---~~pv~v~NDa~aaa~~ 120 (302)
T PRK09698 83 TPNLPLTALDLYDLADKLENTL---NCPVFFSRDVNLQLLW 120 (302)
T ss_pred cCCCCccccccCCHHHHHHHHh---CCCEEEcchHhHHHHH
Confidence 100 11124667787775 8999988875554434
No 25
>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=85.39 E-value=19 Score=29.47 Aligned_cols=115 Identities=13% Similarity=0.175 Sum_probs=65.2
Q ss_pred eEEEEecCCCeEEEEEecCCeeeeeeeEEccc---hh--HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759 64 FSLGVDLGLSRTGLALSKGFCVRPLTVLKLRG---EK--LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG 138 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~---~~--~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~ 138 (204)
.++|||+|.+..|..+-+..... +..+..+. +. ....+.++++ ++++.|+|=- +...++.. ++..|.+
T Consensus 2 ii~sIDiGikNlA~~iie~~~~~-i~~~~i~~~~~~~~~~~~~~~dl~~-~~~d~VlIEr----Q~~r~~~~-~i~~fI~ 74 (143)
T PF04848_consen 2 IILSIDIGIKNLAYCIIEFEGNK-IRVIDISKVDWSRDWEYRILKDLLK-YEADTVLIER----QPPRNPNV-KIVHFIH 74 (143)
T ss_pred eEEEEecCCCceeEEEEEcCCCe-EEEEEeccCCcccchHHHHHHHHhh-ccCCEEEEec----CCCCCcch-hHHHHHH
Confidence 58999999999999999942111 33332211 11 1233444544 9999999984 34444433 4455654
Q ss_pred HHHHhhccCCCcEEEEcCCC-----------cHHHHHHHHHHcCCCccccC-CCCcHHHHHH
Q 028759 139 RLAVRAAERGWRVYLLDEHR-----------TSAEAVDRMINMGLSKSARQ-TKTDAYAAVV 188 (204)
Q Consensus 139 ~L~~~~~~~~lpV~lvDER~-----------TT~eA~~~L~e~G~~rkkrK-~~vD~~AA~i 188 (204)
..-. ..+..|..+|=.+ |-.-++..+.+.|...--.+ +++|++|=++
T Consensus 75 ~~f~---~~~~kv~~v~p~~~~~~Y~~RKk~SVe~~~~~~~~~~~~~~i~~~kK~DDlADa~ 133 (143)
T PF04848_consen 75 GYFY---IKNTKVICVSPKMKGWSYRERKKRSVEVFKNWIKEFGIDDFIPKSKKKDDLADAF 133 (143)
T ss_pred HHhc---cCCceEEEECcccccCCHHHHHHHHHHHHHHHHHhCCchhhchhhccchHHHHHH
Confidence 4432 2367888888553 33444555555443321122 4668887665
No 26
>PRK13311 N-acetyl-D-glucosamine kinase; Provisional
Probab=84.84 E-value=8.9 Score=32.93 Aligned_cols=99 Identities=14% Similarity=0.098 Sum_probs=59.3
Q ss_pred eEEEEecCCCeEEEEEecCC-eeeeeeeEEc---cchhHHHHHHHHHHHc-----CCCEEEEeecCCCC---CCC----C
Q 028759 64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKL---RGEKLELQLLEIAQRE-----ETDEFIIGLPKSWD---GSE----T 127 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~-~A~Pl~~i~~---~~~~~~~~L~~li~e~-----~i~~IVVGlPl~~d---Gt~----~ 127 (204)
+++|+|+|..++-+++.|.. .......++. +..+..+.+.+++++. .+.+|-||.|=-.| |.. .
T Consensus 1 ~~lgidiggt~i~~~l~d~~g~i~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgv~~pG~vd~~~g~i~~~~~ 80 (256)
T PRK13311 1 MYYGFDMGGTKIELGVFDENLQRIWHKRVPTPREDYPQLLQILRDLTEEADTYCGVQGSVGIGIPGLPNADDGTVFTANV 80 (256)
T ss_pred CEEEEEECCCcEEEEEECCCCCEEEEEEecCCCcCHHHHHHHHHHHHHHHHhhcCCCceEEEEecCcEECCCCEEEccCC
Confidence 47999999999999999931 1111111211 1123455666666543 23578888884222 211 0
Q ss_pred hhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759 128 PQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166 (204)
Q Consensus 128 ~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~ 166 (204)
+.-.. ..+++.|++++ ++||.+-++-.....|+.+
T Consensus 81 ~~w~~-~~l~~~l~~~~---~~pV~leNDanaaAlaE~~ 115 (256)
T PRK13311 81 PSAMG-QPLQADLSRLI---QREVRIDNDANCFALSEAW 115 (256)
T ss_pred CcccC-CChHHHHHHHH---CCCEEEEchhhHHHHHHHH
Confidence 11111 36777888775 8999999987777767654
No 27
>PF14239 RRXRR: RRXRR protein
Probab=84.25 E-value=2.6 Score=35.71 Aligned_cols=22 Identities=32% Similarity=0.453 Sum_probs=19.4
Q ss_pred CceEEEEecCCCeEEEEEecCC
Q 028759 62 GGFSLGVDLGLSRTGLALSKGF 83 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~ 83 (204)
....|+||+|.|.+|+|+.+..
T Consensus 50 qpi~lgiDpGsk~tGiav~~~~ 71 (176)
T PF14239_consen 50 QPIRLGIDPGSKTTGIAVVSEK 71 (176)
T ss_pred cCEEEEECCCCCeEEEEEEeCC
Confidence 3578999999999999999864
No 28
>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=83.82 E-value=5.4 Score=37.10 Aligned_cols=96 Identities=18% Similarity=0.115 Sum_probs=54.7
Q ss_pred EEecCCCeEEEEEecC-CeeeeeeeEEccc-hhHHHHHHHHHHHc-CCCEEEE----eecCCCCCCCCh-----------
Q 028759 67 GVDLGLSRTGLALSKG-FCVRPLTVLKLRG-EKLELQLLEIAQRE-ETDEFII----GLPKSWDGSETP----------- 128 (204)
Q Consensus 67 alD~G~kRIGVAvsD~-~~A~Pl~~i~~~~-~~~~~~L~~li~e~-~i~~IVV----GlPl~~dGt~~~----------- 128 (204)
|+|+||+-+-++..|. --..-...+++.. .+....+.+.++++ ++|.|+. |+|+..-...++
T Consensus 1 GIDpGT~s~dv~~~dd~g~v~~~~~ipt~~v~~~p~~iv~~l~~~~~~dlIa~psGyG~pl~~~~ei~d~e~~l~tl~~~ 80 (343)
T PF07318_consen 1 GIDPGTKSFDVCGLDDDGKVIFYFSIPTEEVAKNPSIIVEELEEFGDIDLIAGPSGYGLPLKRIREITDREIFLLTLIEE 80 (343)
T ss_pred CCCCCCCcEEEEEEccCCcEEEEeeccHHHhhhCHHHHHHHHHhccCCCEEEeCCcCCcccccccccchhhhhceEeecc
Confidence 6899999999999986 2222222233211 12334577777777 9998886 667543222211
Q ss_pred -hHH----HHHHHHHHHHHhhccCCCcEEEEc--CCCcHHHHHHH
Q 028759 129 -QSN----KVRSVAGRLAVRAAERGWRVYLLD--EHRTSAEAVDR 166 (204)
Q Consensus 129 -~~~----~v~~Fa~~L~~~~~~~~lpV~lvD--ER~TT~eA~~~ 166 (204)
... -.+++...+++. ++|+++.- =.+.|+-+.+.
T Consensus 81 ~~~g~~~~Glr~~~~~l~~~----~l~~~~iPgVi~LptVP~~RK 121 (343)
T PF07318_consen 81 SEVGRRIGGLRKLVRELAES----NLPAYFIPGVIHLPTVPAWRK 121 (343)
T ss_pred cccccccccHHHHHHHHHhC----CCCEEEeCceeccCCCchHhh
Confidence 001 145566666443 67777664 35666665444
No 29
>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=82.85 E-value=1.2 Score=31.02 Aligned_cols=54 Identities=28% Similarity=0.247 Sum_probs=32.7
Q ss_pred HHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccc----c---------CCCCcHHHHHHHhcc
Q 028759 135 SVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSA----R---------QTKTDAYAAVVRQES 192 (204)
Q Consensus 135 ~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkk----r---------K~~vD~~AA~iILq~ 192 (204)
+|.+.|+....+.|++|+.+||.+||..--. -|...+. + ...-|-.||.-|+++
T Consensus 3 ~~~~~L~yka~~~G~~v~~v~~~~TSq~C~~----CG~~~~~~~~~r~~~C~~Cg~~~~rD~naA~NI~~r 69 (69)
T PF07282_consen 3 QFRQRLEYKAEEYGIQVVEVDEAYTSQTCPR----CGHRNKKRRSGRVFTCPNCGFEMDRDVNAARNILRR 69 (69)
T ss_pred HHHHHHHHHHHHhCCEEEEECCCCCccCccC----cccccccccccceEEcCCCCCEECcHHHHHHHHhcC
Confidence 3444555444346999999999999885421 1111111 0 134589999988863
No 30
>PRK00292 glk glucokinase; Provisional
Probab=82.34 E-value=8.9 Score=33.94 Aligned_cols=98 Identities=15% Similarity=0.166 Sum_probs=56.4
Q ss_pred eEEEEecCCCeEEEEEec-CC-eeeeeeeEEccc-hhHHHHHHHHHHH---cCCCEEEEeecCCCCCCCChhHHH-HHHH
Q 028759 64 FSLGVDLGLSRTGLALSK-GF-CVRPLTVLKLRG-EKLELQLLEIAQR---EETDEFIIGLPKSWDGSETPQSNK-VRSV 136 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD-~~-~A~Pl~~i~~~~-~~~~~~L~~li~e---~~i~~IVVGlPl~~dGt~~~~~~~-v~~F 136 (204)
.+||+|+|..+|=+++.| .. .......++.+. ....+.+.+++++ .++..|.||.|=..|...-..+.. -...
T Consensus 3 ~~lgiDIGgT~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~gigIg~pG~vd~~~i~~~n~~w~~~ 82 (316)
T PRK00292 3 PALVGDIGGTNARFALCDWANGEIEQIKTYATADYPSLEDAIRAYLADEHGVQVRSACFAIAGPVDGDEVRMTNHHWAFS 82 (316)
T ss_pred eEEEEEcCccceEEEEEecCCCceeeeEEEecCCCCCHHHHHHHHHHhccCCCCceEEEEEeCcccCCEEEecCCCcccC
Confidence 589999999999999997 22 111122333221 2355667777764 357899999985433211000000 0112
Q ss_pred HHHHHHhhccCCCc-EEEEcCCCcHHHHH
Q 028759 137 AGRLAVRAAERGWR-VYLLDEHRTSAEAV 164 (204)
Q Consensus 137 a~~L~~~~~~~~lp-V~lvDER~TT~eA~ 164 (204)
.+.|++++ ++| |++.+.-..-.-|+
T Consensus 83 ~~~l~~~~---~~p~v~l~ND~~aaalgE 108 (316)
T PRK00292 83 IAAMKQEL---GLDHLLLINDFTAQALAI 108 (316)
T ss_pred HHHHHHHh---CCCeEEEEecHHHHHccc
Confidence 46677765 886 99888754444443
No 31
>COG4012 Uncharacterized protein conserved in archaea [Function unknown]
Probab=81.64 E-value=11 Score=34.40 Aligned_cols=96 Identities=26% Similarity=0.331 Sum_probs=64.5
Q ss_pred eEEEEecCCCeEEEEEecCC-eeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHH
Q 028759 64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAV 142 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~-~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~ 142 (204)
.+|++|+|.-..-|-.-|+. --++.-+.+........+|..+.+ +.+..+++|-| |.|..+. ++|-+.|++
T Consensus 2 kila~DvG~GTqDi~~~d~~~EnSl~mVmPspt~~~A~R~R~~~~-~g~~l~l~G~~--MGGGp~t-----ravrrhlk~ 73 (342)
T COG4012 2 KILAIDVGVGTQDIVAYDGDPENSLRMVMPSPTSTLAQRLRFMLR-EGPYLALIGVP--MGGGPTT-----RAVRRHLKK 73 (342)
T ss_pred ceEEEEecCCceeEEEecCCcccceeEeecCchHHHHHHHHHHhc-cCCcEEEEeee--cCCChhh-----HHHHHHHhc
Confidence 58999999999988888864 456666666544455667777665 56699999977 4565443 445555653
Q ss_pred hhccCCCcEEEE-cCCCcHHHHHHHHHHcCC
Q 028759 143 RAAERGWRVYLL-DEHRTSAEAVDRMINMGL 172 (204)
Q Consensus 143 ~~~~~~lpV~lv-DER~TT~eA~~~L~e~G~ 172 (204)
+.+|+-- |--+|-..--+++.++|+
T Consensus 74 -----G~rVyatedAAlT~hddleRv~emgi 99 (342)
T COG4012 74 -----GTRVYATEDAALTLHDDLERVEEMGI 99 (342)
T ss_pred -----CCeeEechhhhhhhhcCHHHHHhhCe
Confidence 6777654 334555555677778775
No 32
>PHA02942 putative transposase; Provisional
Probab=80.23 E-value=3.4 Score=38.57 Aligned_cols=81 Identities=12% Similarity=0.076 Sum_probs=47.1
Q ss_pred HcCCCEEEEeecCCCCCCCChhHHHHH---------HHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccc--
Q 028759 108 REETDEFIIGLPKSWDGSETPQSNKVR---------SVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSA-- 176 (204)
Q Consensus 108 e~~i~~IVVGlPl~~dGt~~~~~~~v~---------~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkk-- 176 (204)
+++.+.|||+...+|........+.+. .|...|+-.....|++|+.+|+++||..-- ..|...+.
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 556789999988766543222222222 222344433233699999999999986432 12321111
Q ss_pred -c---------CCCCcHHHHHHHhcc
Q 028759 177 -R---------QTKTDAYAAVVRQES 192 (204)
Q Consensus 177 -r---------K~~vD~~AA~iILq~ 192 (204)
+ ...-|-.||.-|+..
T Consensus 340 ~r~f~C~~CG~~~drD~nAA~NI~~r 365 (383)
T PHA02942 340 HRYFHCPSCGYENDRDVIAIMNLNGR 365 (383)
T ss_pred CCEEECCCCCCEeCcHHHHHHHHHHH
Confidence 1 134688999999876
No 33
>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=79.95 E-value=12 Score=31.33 Aligned_cols=90 Identities=21% Similarity=0.134 Sum_probs=58.9
Q ss_pred EEEEecCCCeEEEEEecCC--eeeeeeeEEc-cchhHHHHHHHHHHHc-----CCCEEEEeecCCCCCCCChhHHHHHHH
Q 028759 65 SLGVDLGLSRTGLALSKGF--CVRPLTVLKL-RGEKLELQLLEIAQRE-----ETDEFIIGLPKSWDGSETPQSNKVRSV 136 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~~--~A~Pl~~i~~-~~~~~~~~L~~li~e~-----~i~~IVVGlPl~~dGt~~~~~~~v~~F 136 (204)
+||||--++.++||+.+.. .+.-.....+ +.+.+...+++++++. +++.|+||.= -|+.+. .+....+
T Consensus 1 iLaidTs~~~~sval~~~~~~~~~~~~~~~~~h~~~l~~~i~~~l~~~~~~~~~i~~iav~~G---PGSfTG-lRig~~~ 76 (202)
T TIGR03725 1 ILAIDTSTEALSVALLDDGEILAERSEEAGRNHSEILLPMIEELLAEAGLSLQDLDAIAVGVG---PGSFTG-LRIGLAT 76 (202)
T ss_pred CEEEECCCcceEEEEEECCEEEEEEeehhhHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecC---CChHHh-HHHHHHH
Confidence 5899999999999998843 2221111111 2234556777777764 6888988831 356654 6677889
Q ss_pred HHHHHHhhccCCCcEEEEcCCCcHHHHHH
Q 028759 137 AGRLAVRAAERGWRVYLLDEHRTSAEAVD 165 (204)
Q Consensus 137 a~~L~~~~~~~~lpV~lvDER~TT~eA~~ 165 (204)
|+.|...+ ++|++-+ ||.+|-.
T Consensus 77 akgla~~~---~~p~~~v----ssL~~lA 98 (202)
T TIGR03725 77 AKGLALAL---GIPLVGV----SSLEALA 98 (202)
T ss_pred HHHHHHHh---CCCEEec----CHHHHHH
Confidence 99998764 8898875 4555543
No 34
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=79.91 E-value=8.8 Score=33.01 Aligned_cols=92 Identities=22% Similarity=0.108 Sum_probs=60.6
Q ss_pred ceEEEEecCCCeEEEEEecC--C--eeeeeeeEEc-cchhHHHHHHHHHHHc-----CCCEEEEeecCCCCCCCChhHHH
Q 028759 63 GFSLGVDLGLSRTGLALSKG--F--CVRPLTVLKL-RGEKLELQLLEIAQRE-----ETDEFIIGLPKSWDGSETPQSNK 132 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~--~--~A~Pl~~i~~-~~~~~~~~L~~li~e~-----~i~~IVVGlPl~~dGt~~~~~~~ 132 (204)
+.+||||--++.+++|+.+. . .+.=.....+ +.+.+...+.+++.+- +++.|+||.= -|+.+. .+.
T Consensus 1 m~iLaiDTs~~~~s~ai~~~~~~~vl~~~~~~~~r~hse~l~~~i~~ll~~~~~~~~dld~iav~~G---PGSFTG-lRI 76 (220)
T COG1214 1 MKILAIDTSTSALSVALYLADDGKVLAEHTEKLKRNHAERLMPMIDELLKEAGLSLQDLDAIAVAKG---PGSFTG-LRI 76 (220)
T ss_pred CcEEEEEcChhhhhhheeecCCCcEEEEEEEeccccHHHHHHHHHHHHHHHcCCCHHHCCEEEEccC---CCcccc-hhh
Confidence 36899999999999998776 2 2333333332 2234556777777765 6888999931 355553 455
Q ss_pred HHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHH
Q 028759 133 VRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVD 165 (204)
Q Consensus 133 v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~ 165 (204)
--.||+-|+-.+ ++|++=+ ||.++-.
T Consensus 77 G~~~AkgLA~~l---~iplvgv----ssL~~~A 102 (220)
T COG1214 77 GVAFAKGLALAL---NIPLVGV----SSLEALA 102 (220)
T ss_pred HHHHHHHHHHHc---CCCEEEe----CHHHHHH
Confidence 578888888664 8888764 5555533
No 35
>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=79.74 E-value=2.7 Score=33.56 Aligned_cols=95 Identities=18% Similarity=0.151 Sum_probs=58.0
Q ss_pred EEecCCCeEEEEEecC--C-eeeeeeeEEc--cchhHHH----HHHHHHHHcCCCEEEEeecCCCCCCC-------ChhH
Q 028759 67 GVDLGLSRTGLALSKG--F-CVRPLTVLKL--RGEKLEL----QLLEIAQREETDEFIIGLPKSWDGSE-------TPQS 130 (204)
Q Consensus 67 alD~G~kRIGVAvsD~--~-~A~Pl~~i~~--~~~~~~~----~L~~li~e~~i~~IVVGlPl~~dGt~-------~~~~ 130 (204)
|||.|..++=+++.|- . ..+ ..++. ......+ .+.++..++...+|-|+.|=..+... .+.-
T Consensus 1 gidig~~~i~~~l~d~~g~ii~~--~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~gIgi~~pG~v~~~~g~i~~~~~~~~ 78 (179)
T PF00480_consen 1 GIDIGGTSIRIALVDLDGEIIYS--ESIPTPTSPEELLDALAELIERLLADYGRSGIGISVPGIVDSEKGRIISSPNPGW 78 (179)
T ss_dssp EEEEESSEEEEEEEETTSCEEEE--EEEEHHSSHHHHHHHHHHHHHHHHHHHTCEEEEEEESSEEETTTTEEEECSSGTG
T ss_pred CEEECCCEEEEEEECCCCCEEEE--EEEECCCCHHHHHHHHHHHHHHHHhhcccccEEEeccccCcCCCCeEEecCCCCc
Confidence 7999999999999993 2 221 12221 2223333 44455555554489999884333221 1112
Q ss_pred HHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759 131 NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 131 ~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L 167 (204)
+. ..+++.|++++ ++||.+.+.-.....|+..+
T Consensus 79 ~~-~~l~~~l~~~~---~~pv~i~Nd~~~~a~ae~~~ 111 (179)
T PF00480_consen 79 EN-IPLKEELEERF---GVPVIIENDANAAALAEYWF 111 (179)
T ss_dssp TT-CEHHHHHHHHH---TSEEEEEEHHHHHHHHHHHH
T ss_pred cc-CCHHHHhhccc---ceEEEEecCCCcceeehhhc
Confidence 22 45778888886 89999999866666665543
No 36
>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=77.91 E-value=8.9 Score=32.92 Aligned_cols=62 Identities=24% Similarity=0.399 Sum_probs=42.0
Q ss_pred HHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE---cCCCcHHHHHHHHHHcCCCc
Q 028759 104 EIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL---DEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 104 ~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv---DER~TT~eA~~~L~e~G~~r 174 (204)
+.+++.+++++|+| .++.||+.. ....+.|.+.. .++|++|. |+-....+|-+.|.+.|+++
T Consensus 79 ~~~~~~GadG~VfG-~L~~dg~iD------~~~~~~Li~~a--~~~~~tFHRAfD~~~d~~~al~~L~~lG~~r 143 (201)
T PF03932_consen 79 RMLRELGADGFVFG-ALTEDGEID------EEALEELIEAA--GGMPVTFHRAFDEVPDPEEALEQLIELGFDR 143 (201)
T ss_dssp HHHHHTT-SEEEE---BETTSSB-------HHHHHHHHHHH--TTSEEEE-GGGGGSSTHHHHHHHHHHHT-SE
T ss_pred HHHHHcCCCeeEEE-eECCCCCcC------HHHHHHHHHhc--CCCeEEEeCcHHHhCCHHHHHHHHHhcCCCE
Confidence 34457899999999 577788876 34444454443 28899985 99888999999999888754
No 37
>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=77.36 E-value=16 Score=26.30 Aligned_cols=56 Identities=20% Similarity=0.297 Sum_probs=34.5
Q ss_pred EEEEeecCCCCCCCC--hhHHHHHHHHHHHHHhhccCCCcEEEEcC-CCcHHHHHHHHHHcCCC
Q 028759 113 EFIIGLPKSWDGSET--PQSNKVRSVAGRLAVRAAERGWRVYLLDE-HRTSAEAVDRMINMGLS 173 (204)
Q Consensus 113 ~IVVGlPl~~dGt~~--~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE-R~TT~eA~~~L~e~G~~ 173 (204)
.|++| .|+.. +....++++++.|+++++...+.+.+... .-+..+|-+.|.+.|++
T Consensus 2 lllv~-----HGs~~~s~~~~~~~~~~~~l~~~~~~~~v~~a~~~~~~P~i~~~l~~l~~~g~~ 60 (101)
T cd03409 2 LLVVG-----HGSPYKDPYKKDIEAQAHNLAESLPDFPYYVGFQSGLGPDTEEAIRELAEEGYQ 60 (101)
T ss_pred EEEEE-----CCCCCCccHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHcCCC
Confidence 35666 46554 55667777888887765322333445555 56777777777666653
No 38
>PRK13318 pantothenate kinase; Reviewed
Probab=77.35 E-value=15 Score=31.92 Aligned_cols=55 Identities=16% Similarity=0.154 Sum_probs=35.4
Q ss_pred eEEEEecCCCeEEEEEecCCeeeeeeeEEcc---c-hhHHHHHHHHHHHcC-----CCEEEEee
Q 028759 64 FSLGVDLGLSRTGLALSKGFCVRPLTVLKLR---G-EKLELQLLEIAQREE-----TDEFIIGL 118 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~---~-~~~~~~L~~li~e~~-----i~~IVVGl 118 (204)
++|+||.|..+|=+|+.|.........++.. . ......+.++++.++ ++.|+||.
T Consensus 1 MiL~IDIGnT~iK~al~d~g~i~~~~~~~t~~~~~~~~~~~~l~~l~~~~~~~~~~i~~I~iss 64 (258)
T PRK13318 1 MLLAIDVGNTNTVFGLYEGGKLVAHWRISTDSRRTADEYGVWLKQLLGLSGLDPEDITGIIISS 64 (258)
T ss_pred CEEEEEECCCcEEEEEEECCEEEEEEEEeCCCCCCHHHHHHHHHHHHHHcCCCcccCceEEEEE
Confidence 4799999999999999984211111222211 1 233456777777654 78999996
No 39
>PRK09982 universal stress protein UspD; Provisional
Probab=75.06 E-value=12 Score=29.03 Aligned_cols=49 Identities=16% Similarity=0.229 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
+...+.|.+.++++++|.||+| .+ .+...+.. ..++++-.. ..+||..+
T Consensus 89 G~p~~~I~~~A~~~~aDLIVmG-----~~-~~~~~~~~-~va~~V~~~---s~~pVLvv 137 (142)
T PRK09982 89 GEMPETLLEIMQKEQCDLLVCG-----HH-HSFINRLM-PAYRGMINK---MSADLLIV 137 (142)
T ss_pred cCHHHHHHHHHHHcCCCEEEEe-----CC-hhHHHHHH-HHHHHHHhc---CCCCEEEe
Confidence 3466788899999999999999 33 33333333 356666554 37888765
No 40
>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=74.39 E-value=21 Score=26.05 Aligned_cols=57 Identities=25% Similarity=0.437 Sum_probs=40.8
Q ss_pred EEEEeecCCCCCCCChhH-HHHHHHHHHHHHhhccCCCcEEEEcC-CCcHHHHHHHHHHcCCCc
Q 028759 113 EFIIGLPKSWDGSETPQS-NKVRSVAGRLAVRAAERGWRVYLLDE-HRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 113 ~IVVGlPl~~dGt~~~~~-~~v~~Fa~~L~~~~~~~~lpV~lvDE-R~TT~eA~~~L~e~G~~r 174 (204)
.++|| .|+..+.+ ..+..++++++++.+...+.+-+.+. .-+-.+|-+.+.+.|.++
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 46788 78888644 47889999998875323455666776 677888888888877543
No 41
>PRK12408 glucokinase; Provisional
Probab=73.76 E-value=7.1 Score=35.32 Aligned_cols=92 Identities=14% Similarity=0.130 Sum_probs=53.8
Q ss_pred CceEEEEecCCCeEEEEEecC--Ce-----eeeeeeEEccc-hhHHHHHHHHHHH-cCCCEEEEeecCC-C-CCCCChhH
Q 028759 62 GGFSLGVDLGLSRTGLALSKG--FC-----VRPLTVLKLRG-EKLELQLLEIAQR-EETDEFIIGLPKS-W-DGSETPQS 130 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~--~~-----A~Pl~~i~~~~-~~~~~~L~~li~e-~~i~~IVVGlPl~-~-dGt~~~~~ 130 (204)
+-++|++|+|--+|=+|+.|. .. ..-....+... ..+.+.+.+++++ .++..|.||.|=. . +|... .+
T Consensus 15 ~~~~L~~DIGGT~i~~al~d~~g~~~~~~~~~~~~~~~t~~~~~~~~~i~~~~~~~~~~~~igIg~pG~~~~~g~v~-~~ 93 (336)
T PRK12408 15 PESFVAADVGGTHVRVALVCASPDAAKPVELLDYRTYRCADYPSLAAILADFLAECAPVRRGVIASAGYALDDGRVI-TA 93 (336)
T ss_pred cccEEEEEcChhhhheeEEeccCCccccccccceeEecCCCccCHHHHHHHHHhcCCCcCEEEEEecCCceECCEEE-ec
Confidence 345899999999999999983 21 11112222111 2344556666653 4588999999864 2 44321 11
Q ss_pred HH-HHHHHHHHHHhhccCCCc-EEEEcCC
Q 028759 131 NK-VRSVAGRLAVRAAERGWR-VYLLDEH 157 (204)
Q Consensus 131 ~~-v~~Fa~~L~~~~~~~~lp-V~lvDER 157 (204)
.. -..+.+.|++++ ++| |++.+.-
T Consensus 94 nl~w~~~~~~l~~~~---~~~~V~l~ND~ 119 (336)
T PRK12408 94 NLPWTLSPEQIRAQL---GLQAVHLVNDF 119 (336)
T ss_pred CCCCccCHHHHHHHc---CCCeEEEeecH
Confidence 00 122457777764 885 9988763
No 42
>PRK13320 pantothenate kinase; Reviewed
Probab=72.57 E-value=48 Score=28.89 Aligned_cols=55 Identities=22% Similarity=0.252 Sum_probs=36.3
Q ss_pred ceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHc-CCCEEEEeec
Q 028759 63 GFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~-~i~~IVVGlP 119 (204)
.++|.||.|..+|=+|+.+.........+. ..+....+.++++.+ +++.++|.-.
T Consensus 2 ~M~L~iDiGNT~ik~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~i~~i~vsSV 57 (244)
T PRK13320 2 SMNLVIDIGNTTTKLAVFEGDELLEVFVVS--TEGVEESLEKLLAKYPAIRDAIVSSV 57 (244)
T ss_pred ceEEEEEeCCCcEEEEEEECCEEEEEEEEc--cHHHHHHHHHHHHHCCCCCEEEEEec
Confidence 469999999999999999853211222222 223445666677665 5889888843
No 43
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=71.32 E-value=12 Score=36.70 Aligned_cols=65 Identities=18% Similarity=0.200 Sum_probs=42.9
Q ss_pred CCCceEEEEecCCCeEEEEEecCC-eeeeeeeEEccc-hhHHHHHHHHHHHc---CCCEEEEeecCCCCC
Q 028759 60 WRGGFSLGVDLGLSRTGLALSKGF-CVRPLTVLKLRG-EKLELQLLEIAQRE---ETDEFIIGLPKSWDG 124 (204)
Q Consensus 60 ~~~g~iLalD~G~kRIGVAvsD~~-~A~Pl~~i~~~~-~~~~~~L~~li~e~---~i~~IVVGlPl~~dG 124 (204)
-..+++||+|+|.-+|=+|+.|.. .......++... ......+.+++++. .+..+.||.|=..|+
T Consensus 15 ~~~~~~L~iDIGGT~ir~al~~~~g~i~~~~~~~t~~~~~~~~~i~~~l~~~~~~~~~~igig~pGpVd~ 84 (638)
T PRK14101 15 HADGPRLLADVGGTNARFALETGPGEITQIRVYPGADYPTLTDAIRKYLKDVKIGRVNHAAIAIANPVDG 84 (638)
T ss_pred CCCCCEEEEEcCchhheeeeecCCCcccceeEEecCCCCCHHHHHHHHHHhcCCCCcceEEEEEecCccC
Confidence 345889999999999999988732 112223333222 34556677777654 488999999965554
No 44
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=70.09 E-value=14 Score=32.80 Aligned_cols=49 Identities=27% Similarity=0.345 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
...++.+-+.+.+.|.|.|| ||.+-....++++.++++++ +++||++.-
T Consensus 29 ~~~ei~~~~~~~GTDaImIG------GS~gvt~~~~~~~v~~ik~~---~~lPvilfP 77 (240)
T COG1646 29 EADEIAEAAAEAGTDAIMIG------GSDGVTEENVDNVVEAIKER---TDLPVILFP 77 (240)
T ss_pred ccHHHHHHHHHcCCCEEEEC------CcccccHHHHHHHHHHHHhh---cCCCEEEec
Confidence 44677788888999999999 98888888999999999976 489998863
No 45
>PRK11572 copper homeostasis protein CutC; Provisional
Probab=67.80 E-value=31 Score=30.68 Aligned_cols=62 Identities=13% Similarity=0.204 Sum_probs=45.3
Q ss_pred HHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE---cCCCcHHHHHHHHHHcCCCc
Q 028759 104 EIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL---DEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 104 ~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv---DER~TT~eA~~~L~e~G~~r 174 (204)
+.+++...++||+|. ++.||+... ...++|-+.. .++|++|. |+--...+|-+.|.+.|+.+
T Consensus 80 ~~~~~~GadGvV~G~-L~~dg~vD~------~~~~~Li~~a--~~~~vTFHRAfD~~~d~~~al~~l~~lG~~r 144 (248)
T PRK11572 80 ATVRELGFPGLVTGV-LDVDGHVDM------PRMRKIMAAA--GPLAVTFHRAFDMCANPLNALKQLADLGVAR 144 (248)
T ss_pred HHHHHcCCCEEEEee-ECCCCCcCH------HHHHHHHHHh--cCCceEEechhhccCCHHHHHHHHHHcCCCE
Confidence 445678999999994 677888773 3334444443 37899884 88888889999999988754
No 46
>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=65.99 E-value=22 Score=25.51 Aligned_cols=52 Identities=21% Similarity=0.229 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
....+.+.+.+++.++|.||+|-.-.. + ... ...-.+++.+-... .+||..+
T Consensus 88 ~~~~~~i~~~~~~~~~dliv~G~~~~~-~-~~~--~~~gs~~~~l~~~~---~~pVlvv 139 (140)
T PF00582_consen 88 GDVADAIIEFAEEHNADLIVMGSRGRS-G-LER--LLFGSVAEKLLRHA---PCPVLVV 139 (140)
T ss_dssp SSHHHHHHHHHHHTTCSEEEEESSSTT-S-TTT--SSSHHHHHHHHHHT---SSEEEEE
T ss_pred eccchhhhhccccccceeEEEeccCCC-C-ccC--CCcCCHHHHHHHcC---CCCEEEe
Confidence 456688999999999999999965421 1 111 11235566666553 6788764
No 47
>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=65.23 E-value=16 Score=26.76 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=19.9
Q ss_pred hHHHHHHHHHHHcCCCEEEEeec
Q 028759 97 KLELQLLEIAQREETDEFIIGLP 119 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlP 119 (204)
...+.|.++++++++|.||+|..
T Consensus 81 ~~~~~I~~~a~~~~~dlIV~G~~ 103 (132)
T cd01988 81 DIASGILRTAKERQADLIIMGWH 103 (132)
T ss_pred CHHHHHHHHHHhcCCCEEEEecC
Confidence 46678999999999999999964
No 48
>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=65.15 E-value=4.8 Score=41.14 Aligned_cols=19 Identities=32% Similarity=0.788 Sum_probs=17.6
Q ss_pred eEEEEecCCCeEEEEEecC
Q 028759 64 FSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~ 82 (204)
++||||.|+.-||+||.|.
T Consensus 2 y~LGLDiGt~SvGWAVv~~ 20 (805)
T TIGR01865 2 YILGLDIGIASVGWAIVED 20 (805)
T ss_pred ceeEEeecccceeEEEEec
Confidence 5899999999999999983
No 49
>PRK10116 universal stress protein UspC; Provisional
Probab=65.04 E-value=38 Score=25.55 Aligned_cols=50 Identities=22% Similarity=0.234 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
+...+.|.+.++++++|.||+|-. |. +...... ..++++-.. .++||..+
T Consensus 88 G~~~~~I~~~a~~~~~DLiV~g~~----~~-~~~~~~~-s~a~~v~~~---~~~pVLvv 137 (142)
T PRK10116 88 GELSEHILEVCRKHHFDLVICGNH----NH-SFFSRAS-CSAKRVIAS---SEVDVLLV 137 (142)
T ss_pred CCHHHHHHHHHHHhCCCEEEEcCC----cc-hHHHHHH-HHHHHHHhc---CCCCEEEE
Confidence 345678889999999999999943 22 2222222 345555544 37888876
No 50
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=64.68 E-value=97 Score=27.05 Aligned_cols=89 Identities=19% Similarity=0.209 Sum_probs=49.5
Q ss_pred CceEEEEecCCCeEEEEEecCC------eeeeeeeEEc----cch---hHHHHHHHHHHHc---CCCEEEEeecCCCCCC
Q 028759 62 GGFSLGVDLGLSRTGLALSKGF------CVRPLTVLKL----RGE---KLELQLLEIAQRE---ETDEFIIGLPKSWDGS 125 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~------~A~Pl~~i~~----~~~---~~~~~L~~li~e~---~i~~IVVGlPl~~dGt 125 (204)
.+.++|||+|+.+|=+.+.+.. ...|-..+.. +-. ..+.++.+.++++ .+..+++..|-..+-
T Consensus 23 ~~~~~~iDiGSssi~~vv~~~~~~~~~~~~~~~~~vr~G~i~di~~a~~~i~~~~~~ae~~~g~~i~~v~~~vp~~~~~- 101 (267)
T PRK15080 23 SPLKVGVDLGTANIVLAVLDEDGQPVAGALEWADVVRDGIVVDFIGAVTIVRRLKATLEEKLGRELTHAATAIPPGTSE- 101 (267)
T ss_pred CCEEEEEEccCceEEEEEEcCCCCEEEEEeccccccCCCEEeeHHHHHHHHHHHHHHHHHHhCCCcCeEEEEeCCCCCc-
Confidence 4789999999999998887621 1122222211 011 2233444444333 478999999976431
Q ss_pred CChhHHHHHHHHHHHHHhhccCCCcEE-EEcCCCcH
Q 028759 126 ETPQSNKVRSVAGRLAVRAAERGWRVY-LLDEHRTS 160 (204)
Q Consensus 126 ~~~~~~~v~~Fa~~L~~~~~~~~lpV~-lvDER~TT 160 (204)
..-+.+.+-+++. ++++. +++|.+..
T Consensus 102 -----~~~~~~~~~~~~a----Gl~~~~ii~e~~A~ 128 (267)
T PRK15080 102 -----GDPRAIINVVESA----GLEVTHVLDEPTAA 128 (267)
T ss_pred -----hhHHHHHHHHHHc----CCceEEEechHHHH
Confidence 1113344444432 77777 67776533
No 51
>PRK00923 sirohydrochlorin cobaltochelatase; Reviewed
Probab=64.15 E-value=39 Score=25.83 Aligned_cols=57 Identities=21% Similarity=0.346 Sum_probs=38.5
Q ss_pred CEEEEeecCCCCCCCChhH-HHHHHHHHHHHHhhccCCCcEEEEc-CCCcHHHHHHHHHHcCCC
Q 028759 112 DEFIIGLPKSWDGSETPQS-NKVRSVAGRLAVRAAERGWRVYLLD-EHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 112 ~~IVVGlPl~~dGt~~~~~-~~v~~Fa~~L~~~~~~~~lpV~lvD-ER~TT~eA~~~L~e~G~~ 173 (204)
..|+|| .||..+.+ ..+..|++.++++.+...+.+.|.+ ..-|-.++-+.+...|.+
T Consensus 3 ~lvlv~-----hGS~~~~~~~~~~~~~~~l~~~~~~~~v~~afle~~~P~l~~~l~~l~~~g~~ 61 (126)
T PRK00923 3 GLLLVG-----HGSRLPYNKEVVTKIAEKIKEKHPFYIVEVGFMEFNEPTIPEALKKLIGTGAD 61 (126)
T ss_pred EEEEEe-----CCCCChHHHHHHHHHHHHHHHhCCCCeEEEEEEEcCCCCHHHHHHHHHHcCCC
Confidence 357888 78887666 6888899999876431123344555 456777777787776754
No 52
>KOG0237 consensus Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism]
Probab=62.93 E-value=19 Score=36.24 Aligned_cols=75 Identities=11% Similarity=0.058 Sum_probs=52.9
Q ss_pred hhHHHHHHHHHHHcCCCEEEEe--ecCC---------------CCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCC
Q 028759 96 EKLELQLLEIAQREETDEFIIG--LPKS---------------WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHR 158 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVG--lPl~---------------~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~ 158 (204)
..++++|.++.+|++|..+|+| +|+- --+....|.+..++|++.+-.+ +++|-.-++---
T Consensus 54 ~~d~~ala~f~~e~~I~lVvvGPE~PL~~Gl~~~l~~~gi~~FGPs~~aAqlE~sK~fsK~fm~r---~~IPTA~y~~ft 130 (788)
T KOG0237|consen 54 VADFEALASFCKEHNINLVVVGPELPLVAGLADVLRSAGIPCFGPSKQAAQLEASKNFSKDFMHR---HNIPTAKYKTFT 130 (788)
T ss_pred hhhHHHHHHHHHHcceeEEEECCchhhhhhhhhhhhccCcceeCchHHHHHhhhhHHHHHHHHHh---cCCCcceeeeeC
Confidence 3578899999999999999998 2221 1122334556667888888876 599977666544
Q ss_pred cHHHHHHHHHHcCCC
Q 028759 159 TSAEAVDRMINMGLS 173 (204)
Q Consensus 159 TT~eA~~~L~e~G~~ 173 (204)
-+.+|+..++..+++
T Consensus 131 ~~e~a~sfi~~~~~~ 145 (788)
T KOG0237|consen 131 DPEEAKSFIQSATDK 145 (788)
T ss_pred CHHHHHHHHHhCCCc
Confidence 457888888876643
No 53
>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=62.84 E-value=71 Score=28.77 Aligned_cols=85 Identities=15% Similarity=0.098 Sum_probs=53.0
Q ss_pred EEEEecCCCeEEEEEecC---Ceeeeee-----------eEEc-----cchhHHHHHHHHHHH-----cCCCEEEEeecC
Q 028759 65 SLGVDLGLSRTGLALSKG---FCVRPLT-----------VLKL-----RGEKLELQLLEIAQR-----EETDEFIIGLPK 120 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~---~~A~Pl~-----------~i~~-----~~~~~~~~L~~li~e-----~~i~~IVVGlPl 120 (204)
+||||-=+..++||+.|. +.+.-.. +.+. +.+.+...+.+++++ .+++.|.|+.=
T Consensus 1 iLaIdTs~~~~sval~~~~~~il~~~~~~~~~~~~~~gGi~p~~~~~~H~~~l~~~i~~~l~~~~~~~~~id~iav~~G- 79 (314)
T TIGR03723 1 ILGIETSCDETAVAIVDDGKGLLSNIVASQIELHARYGGVVPELASRAHLEAIPPLIEEALAEAGLTLSDIDAIAVTAG- 79 (314)
T ss_pred CEEEECcccceEEEEEECCceEEEEEEeehhhhccCcCCcCcchhHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecC-
Confidence 589999999999999983 2221110 0010 112334556666665 46899999831
Q ss_pred CCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 121 ~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
-|+.+ -.+....+|+.|...+ ++|++.++.
T Consensus 80 --PGsft-glrig~~~Ak~la~~~---~~p~~~v~h 109 (314)
T TIGR03723 80 --PGLIG-ALLVGVSFAKALALAL---NKPLIGVNH 109 (314)
T ss_pred --CChHH-hHHHHHHHHHHHHHHh---CCCEEeccc
Confidence 23333 3455678888888764 899998843
No 54
>PF03309 Pan_kinase: Type III pantothenate kinase; InterPro: IPR004619 Pantothenate kinase (PanK or CoaA) catalyses the first step of the universal five step coenzyme A (CoA) biosynthesis pathway. CoA is a ubiquitous and essential cofactor in all living organsims. Pantothenate kinase catalyses the first and rate limiting step in the CoA biosynthetic pathway, which involves transferring a phosphoryl group from ATP to pantothenate, also known as vitamin B5. Three distinct types of pantothenate kinase enzymes have been identified: type I PanK enzymes are typified by the E. coli CoaA protein, type II enzymes are primarily found in eukaryotic organisms whilst type III enzymes have a wider phylogenic distribution and are not feedback inhibited by CoA []. This entry represents the type III pantothenate kinase family, such as that found in Helicobacter pylori. PanK III enzymes have a much wider phylogenic distribution than PanK I, and differs significantly in biochemical activity. PanK III enzymes are are not feedback inhibited by CoA concentration (which is also the case for PanK II enzymes), and PanK III enzymes have an unusually high Km for ATP []. ; GO: 0045893 positive regulation of transcription, DNA-dependent; PDB: 2GTD_E 3BF1_F 3BEX_D 3BF3_F 2NRH_B 2H3G_X 3DJC_J 2F9T_A 2F9W_A.
Probab=62.05 E-value=62 Score=27.06 Aligned_cols=78 Identities=22% Similarity=0.230 Sum_probs=44.8
Q ss_pred EEEEecCCCeEEEEEecCCe-eeeeeeE--E---ccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHH
Q 028759 65 SLGVDLGLSRTGLALSKGFC-VRPLTVL--K---LRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVA 137 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~~~-A~Pl~~i--~---~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa 137 (204)
+|.||.|..+|=+|+.++.. ..+...+ . ... ......+..++.+.+.+.+++. .-..+ ....+.
T Consensus 1 ~L~iDiGNT~ik~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~is------SV~~~---~~~~~~ 71 (206)
T PF03309_consen 1 ILLIDIGNTRIKWALFDGDKLIDPSGRISHSTALDSSSDELLELLESLLPQPKIDAVIIS------SVVPE---ATEQLL 71 (206)
T ss_dssp EEEEEE-SSEEEEEEEETTEEEE-EEEE-EEECTTSSHHHHHHHHHHHHHCTTCGEEEEE------ESSGH---HHHHHH
T ss_pred CEEEEECCCeEEEEEEECCEEEeeeeEEEecccccccHHHHHHHHHHHhccccCCcEEEE------EcCCH---HHHHHH
Confidence 68999999999999999642 2212222 1 111 2345678888888888888887 22222 224455
Q ss_pred HHHHHhhccCCCcEEEEc
Q 028759 138 GRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 138 ~~L~~~~~~~~lpV~lvD 155 (204)
+.+.+.+ + ++++++
T Consensus 72 ~~~~~~~---~-~~~~~~ 85 (206)
T PF03309_consen 72 EALLKRF---G-RPHFVK 85 (206)
T ss_dssp HHHHHHC---S---EEES
T ss_pred HHHHHHh---C-CCEEEE
Confidence 5555543 4 555554
No 55
>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=61.72 E-value=15 Score=28.25 Aligned_cols=43 Identities=23% Similarity=0.377 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEE
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVY 152 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~ 152 (204)
....+.|.+++++++||.+||| |.+-.+.-.+..|++. ++|+.
T Consensus 48 ~~d~~~l~~~a~~~~idlvvvG----------PE~pL~~Gl~D~l~~~----gi~vf 90 (100)
T PF02844_consen 48 ITDPEELADFAKENKIDLVVVG----------PEAPLVAGLADALRAA----GIPVF 90 (100)
T ss_dssp TT-HHHHHHHHHHTTESEEEES----------SHHHHHTTHHHHHHHT----T-CEE
T ss_pred CCCHHHHHHHHHHcCCCEEEEC----------ChHHHHHHHHHHHHHC----CCcEE
Confidence 3567899999999999999999 2333444556666654 78875
No 56
>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=60.61 E-value=35 Score=29.31 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=36.0
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
..+.+.+.+...|.|.|| |+.+-....+.+..+.+++. +++||++.
T Consensus 14 ~~ia~~v~~~gtDaI~VG------GS~gvt~~~~~~~v~~ik~~---~~lPvilf 59 (205)
T TIGR01769 14 EKIAKNAKDAGTDAIMVG------GSLGIVESNLDQTVKKIKKI---TNLPVILF 59 (205)
T ss_pred HHHHHHHHhcCCCEEEEc------CcCCCCHHHHHHHHHHHHhh---cCCCEEEE
Confidence 345556778899999999 77766667888888888875 38999874
No 57
>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=60.28 E-value=26 Score=26.64 Aligned_cols=50 Identities=18% Similarity=0.300 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHH--HHHHHHHHhhccCC--CcEEEE
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVR--SVAGRLAVRAAERG--WRVYLL 154 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~--~Fa~~L~~~~~~~~--lpV~lv 154 (204)
...+.|.+..++++++.||+|- .|. +...+... ..+.++-+.. . +||..+
T Consensus 90 ~~~~~I~~~a~~~~~dlIV~Gs----~g~-~~l~~~~~gssva~~Vi~~a---~~~c~Vlvv 143 (146)
T cd01989 90 DVAKAIVEYVADHGITKLVMGA----SSD-NHFSMKFKKSDVASSVLKEA---PDFCTVYVV 143 (146)
T ss_pred cHHHHHHHHHHHcCCCEEEEec----cCC-CceeecccCCchhHHHHhcC---CCCceEEEE
Confidence 4567889999999999999993 232 22222222 2555555542 4 677665
No 58
>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=59.73 E-value=56 Score=25.52 Aligned_cols=92 Identities=16% Similarity=0.165 Sum_probs=52.9
Q ss_pred eEEEEecCCCeEEEEEecCCeeeeeeeE----Eccc----------------hhHHHHHHHHHHHc------CCCEEEEe
Q 028759 64 FSLGVDLGLSRTGLALSKGFCVRPLTVL----KLRG----------------EKLELQLLEIAQRE------ETDEFIIG 117 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~~A~Pl~~i----~~~~----------------~~~~~~L~~li~e~------~i~~IVVG 117 (204)
-++.+|-|...||+.-+.+. ..+..+ +.+. .+++.++.+-+.++ .++.|||+
T Consensus 3 ~~v~id~g~A~i~~l~~~~~--~~~~~i~~~ip~K~~~Gg~s~~rf~r~~~~~~f~~~i~~~l~~~f~~~~~~~~~iIia 80 (133)
T PF03464_consen 3 GIVVIDEGEANICLLRGYGT--EILQRIESNIPGKHKKGGQSQRRFEREKALEKFFKEIAEALKKYFLVNFDDVKCIIIA 80 (133)
T ss_dssp EEEEEETTEEEEEEEETTEE--EEEEEEE-GHCCCSSTTCSHHHHHHHHHHHHHHHHHHHHHHHHHCCCHTTTCSEEEEE
T ss_pred EEEEEeCCCEEEEEEcCCEE--EEEEEEEecCCCccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEE
Confidence 37899999999998865543 222222 2211 02334444444444 89999999
Q ss_pred ecCCCCCCCChhHHHHHHHHHHHHHhhccCC-CcEEEEcCCCcHHHHHHHH
Q 028759 118 LPKSWDGSETPQSNKVRSVAGRLAVRAAERG-WRVYLLDEHRTSAEAVDRM 167 (204)
Q Consensus 118 lPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~-lpV~lvDER~TT~eA~~~L 167 (204)
=| |.. -..|.+.+.......+ ..+..+|=..+...+-..+
T Consensus 81 GP----Gf~------k~~f~~~l~~~~~~~~~~~i~~~~~s~~~~~gl~Ev 121 (133)
T PF03464_consen 81 GP----GFT------KEEFYKYLKAEARRKDKKKIVVVDTSSGGESGLNEV 121 (133)
T ss_dssp ES----TTH------HHHHHHHHHHHHHHHTCCEEEEEE-SSSCHHHHHHH
T ss_pred CC----HHH------HHHHHHHHHHhhHhhcCCEEEEEECCCCCHHHHHHH
Confidence 65 321 2567777765543224 5577777666666664443
No 59
>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=59.22 E-value=73 Score=23.79 Aligned_cols=89 Identities=16% Similarity=0.023 Sum_probs=52.7
Q ss_pred eEEEEec--CCCeEEEEEecCC-eeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHH
Q 028759 64 FSLGVDL--GLSRTGLALSKGF-CVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRL 140 (204)
Q Consensus 64 ~iLalD~--G~kRIGVAvsD~~-~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L 140 (204)
.++||-. ....+|+|.+|-. .-.-+..+. + ...|...+..++|.+||+. ++...... ...+
T Consensus 2 yl~aI~~~~~~~~~gla~~D~sTGe~~~~~~~--d---~~~L~~~L~~~~P~EIi~~-----~~~~~~~~------~~~~ 65 (137)
T PF05188_consen 2 YLAAIYEKNDEDSYGLAYIDLSTGEFYVTEFE--D---YSELKSELARLSPREIIIP-----EGFSSSDI------SALL 65 (137)
T ss_dssp EEEEEEEETCSSEEEEEEEETTTTEEEEEEEE--C---HHHHHHHHHHH-ESEEEEE-----TTCSHHHH------HHHH
T ss_pred EEEEEEEecCCCEEEEEEEECCCCEEEEEEeC--C---HHHHHHHHHhcCCeEEEEc-----CCCccccc------chhh
Confidence 4677777 7778999999943 222233332 1 6788888999999999999 56655432 1111
Q ss_pred HHhhccCCCcEEE-EcCCCcHHHHHHHHHH
Q 028759 141 AVRAAERGWRVYL-LDEHRTSAEAVDRMIN 169 (204)
Q Consensus 141 ~~~~~~~~lpV~l-vDER~TT~eA~~~L~e 169 (204)
. ........+.. .+..+....|.+.+.+
T Consensus 66 ~-~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 94 (137)
T PF05188_consen 66 S-SLKNSFFKVTETPSWYFDSEFASEDIEE 94 (137)
T ss_dssp H-CCTTTCCEEEEETCGGGSHHHHHHHHHH
T ss_pred h-hhccccceeeecchhhhhhHHHHHHHHH
Confidence 1 11111223333 4566677777777654
No 60
>PRK10854 exopolyphosphatase; Provisional
Probab=57.96 E-value=68 Score=30.91 Aligned_cols=101 Identities=16% Similarity=0.100 Sum_probs=62.8
Q ss_pred cCCCCCCceEEEEecCCCeEEEEEecC--Ceeeeee----eEEc------cc---h-------hHHHHHHHHHHHcCCCE
Q 028759 56 KDSLWRGGFSLGVDLGLSRTGLALSKG--FCVRPLT----VLKL------RG---E-------KLELQLLEIAQREETDE 113 (204)
Q Consensus 56 ~~~~~~~g~iLalD~G~kRIGVAvsD~--~~A~Pl~----~i~~------~~---~-------~~~~~L~~li~e~~i~~ 113 (204)
+|..+|+..+-+||.|+--|=+.|.+. .....+. ++.. ++ . ....++.+++++++++.
T Consensus 4 ~~~~~~~~~~A~IDIGSNSirL~I~e~~~~~~~~i~~~k~~vrLg~g~~~~g~Ls~e~~~r~~~~L~~F~~~~~~~~v~~ 83 (513)
T PRK10854 4 HDKSPRPQEFAAVDLGSNSFHMVIARVVDGAMQIIGRLKQRVHLADGLDSDNMLSEEAMERGLNCLSLFAERLQGFSPAN 83 (513)
T ss_pred CCCCCCCCEEEEEEeccchheEEEEEecCCcEEEeeeeeEEEECCCCcCCCCCcCHHHHHHHHHHHHHHHHHHHhCCCCe
Confidence 455567788999999999999988872 1112221 1110 11 0 12457788888999975
Q ss_pred E-EEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 114 F-IIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 114 I-VVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
+ +||- +.--.++....|.+++++.+ |++|..++. ..||.-.+.
T Consensus 84 v~~vAT------sAlReA~N~~~fl~~i~~~t---Gl~i~vIsG---~EEA~l~~~ 127 (513)
T PRK10854 84 VCIVGT------HTLRQALNATDFLKRAEKVI---PYPIEIISG---NEEARLIFM 127 (513)
T ss_pred EEEEeh------HHHHcCcCHHHHHHHHHHHH---CCCeEEeCH---HHHHHHHHh
Confidence 4 4551 11122334478999999875 999999874 356654443
No 61
>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=56.93 E-value=64 Score=22.76 Aligned_cols=52 Identities=19% Similarity=0.178 Sum_probs=38.8
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
...+.+++.+++++.+|+|- .+ ....+.|++. ++.|+.. ...+-.+|-+.|.
T Consensus 42 ~~~~~~~l~~~~v~~li~~~-------iG------~~~~~~L~~~----gI~v~~~-~~~~i~~~l~~~~ 93 (94)
T PF02579_consen 42 GDKIAKFLAEEGVDVLICGG-------IG------EGAFRALKEA----GIKVYQG-AGGDIEEALEAYL 93 (94)
T ss_dssp STHHHHHHHHTTESEEEESC-------SC------HHHHHHHHHT----TSEEEES-TSSBHHHHHHHHH
T ss_pred chhHHHHHHHcCCCEEEEeC-------CC------HHHHHHHHHC----CCEEEEc-CCCCHHHHHHHHh
Confidence 35677777779999999992 23 3555667765 8999998 7788888877664
No 62
>PRK15118 universal stress global response regulator UspA; Provisional
Probab=56.12 E-value=53 Score=24.89 Aligned_cols=50 Identities=16% Similarity=0.133 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
+.....|.+.++++++|.||+|- .|+ .... .-..++++-.. ..+||..+-
T Consensus 89 G~p~~~I~~~a~~~~~DLIV~Gs----~~~--~~~~-lgSva~~v~~~---a~~pVLvv~ 138 (144)
T PRK15118 89 GDLGQVLVDAIKKYDMDLVVCGH----HQD--FWSK-LMSSARQLINT---VHVDMLIVP 138 (144)
T ss_pred cCHHHHHHHHHHHhCCCEEEEeC----ccc--HHHH-HHHHHHHHHhh---CCCCEEEec
Confidence 35667899999999999999993 232 2222 33666666655 378988874
No 63
>PRK09604 UGMP family protein; Validated
Probab=55.78 E-value=64 Score=29.27 Aligned_cols=87 Identities=16% Similarity=0.114 Sum_probs=54.1
Q ss_pred ceEEEEecCCCeEEEEEec-C--Ceee-eeee----------EEc-----cchhHHHHHHHHHHH-----cCCCEEEEee
Q 028759 63 GFSLGVDLGLSRTGLALSK-G--FCVR-PLTV----------LKL-----RGEKLELQLLEIAQR-----EETDEFIIGL 118 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD-~--~~A~-Pl~~----------i~~-----~~~~~~~~L~~li~e-----~~i~~IVVGl 118 (204)
+.+||||--...+++|+.| + +.+. -... ++. +.+.+...+++++++ .+++.|+|+.
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 3689999999999999998 3 2211 1111 111 011233446666665 3589999995
Q ss_pred cCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 119 PKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 119 Pl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
= -|..+. -+....+|+.|...+ ++|++.++.
T Consensus 81 G---PG~~tg-lrvg~~~Ak~La~~~---~ipl~~v~h 111 (332)
T PRK09604 81 G---PGLVGA-LLVGVSFAKALALAL---NKPLIGVNH 111 (332)
T ss_pred C---CCcHHh-HHHHHHHHHHHHHHh---CCCEEeecC
Confidence 1 133332 455568899998764 899999854
No 64
>PRK13324 pantothenate kinase; Reviewed
Probab=55.48 E-value=1.5e+02 Score=26.22 Aligned_cols=80 Identities=14% Similarity=0.186 Sum_probs=45.6
Q ss_pred eEEEEecCCCeEEEEEecCC-eeeeeeeE--Ec-c-chhHHHHHHHHHHHc-----CCCEEEEeecCCCCCCCChhHHHH
Q 028759 64 FSLGVDLGLSRTGLALSKGF-CVRPLTVL--KL-R-GEKLELQLLEIAQRE-----ETDEFIIGLPKSWDGSETPQSNKV 133 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~~-~A~Pl~~i--~~-~-~~~~~~~L~~li~e~-----~i~~IVVGlPl~~dGt~~~~~~~v 133 (204)
++|+||.|..+|=+|+.|+. ........ .. . ..+....+..++.++ .++.+++.- .-| +..
T Consensus 1 MiL~iDiGNT~ik~gl~~~~~~~~~~r~~t~~~~~t~de~~~~l~~~~~~~~~~~~~i~~viisS-------VvP--~l~ 71 (258)
T PRK13324 1 MLLVMDMGNSHIHIGVFDGDRIVSQIRYATSSVDSTSDQMGVFLRQALRENSVDLGKIDGCGISS-------VVP--HLN 71 (258)
T ss_pred CEEEEEeCCCceEEEEEECCEEEEEEEEecCccccchHHHHHHHHHHHHhcCCCccCCCeEEEEe-------Ccc--hhH
Confidence 48999999999999999853 21111111 11 1 123445677777653 578888882 112 222
Q ss_pred HHHHHHHHHhhccCCCcEEEEc
Q 028759 134 RSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 134 ~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
..|.+.+.+.+ +.+++++.
T Consensus 72 ~~l~~~~~~~~---~~~~~~v~ 90 (258)
T PRK13324 72 YSLGSAVIKYF---NIKPFFIS 90 (258)
T ss_pred HHHHHHHHHHh---CCCeEEEe
Confidence 33434444444 66777775
No 65
>PRK09472 ftsA cell division protein FtsA; Reviewed
Probab=54.31 E-value=73 Score=29.72 Aligned_cols=58 Identities=10% Similarity=0.182 Sum_probs=37.2
Q ss_pred CceEEEEecCCCeEEEEEec----C-CeeeeeeeEEcc---------chhHHHHHHHHHHH------cCCCEEEEeec
Q 028759 62 GGFSLGVDLGLSRTGLALSK----G-FCVRPLTVLKLR---------GEKLELQLLEIAQR------EETDEFIIGLP 119 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD----~-~~A~Pl~~i~~~---------~~~~~~~L~~li~e------~~i~~IVVGlP 119 (204)
...+.|||.|+.+|=+.+++ + .........+.. -....+.|++.+++ .++..+++|.|
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 35689999999999887775 2 112222222211 12344567777765 57999999988
No 66
>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=54.17 E-value=26 Score=28.74 Aligned_cols=64 Identities=13% Similarity=0.217 Sum_probs=38.0
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCC--CChhHHHHHHHHHHHHHhhccCCCcEEEEc------CCCcHHHHHHHHHHc
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGS--ETPQSNKVRSVAGRLAVRAAERGWRVYLLD------EHRTSAEAVDRMINM 170 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt--~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD------ER~TT~eA~~~L~e~ 170 (204)
.+-+.+++...+++.+|||.-..- |. .+. ... |++.+...+..|+.++ +..||..-++.+.+.
T Consensus 88 ~~Fi~~il~~~~~~~ivvG~Df~F-G~~~~g~-~~~-------L~~~~~~~g~~v~~v~~~~~~~~~iSST~IR~~i~~G 158 (180)
T cd02064 88 EEFVEDLLVKLNAKHVVVGFDFRF-GKGRSGD-AEL-------LKELGKKYGFEVTVVPPVTLDGERVSSTRIREALAEG 158 (180)
T ss_pred HHHHHHHHhhcCCeEEEEccCCCC-CCCCCCC-HHH-------HHHhhhhcCcEEEEeCcEecCCcEEcHHHHHHHHHhC
Confidence 345666666669999999976542 21 111 111 2222112367777776 468999888888764
Q ss_pred C
Q 028759 171 G 171 (204)
Q Consensus 171 G 171 (204)
.
T Consensus 159 ~ 159 (180)
T cd02064 159 D 159 (180)
T ss_pred C
Confidence 3
No 67
>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=53.91 E-value=72 Score=24.14 Aligned_cols=56 Identities=13% Similarity=0.197 Sum_probs=35.6
Q ss_pred EEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCc
Q 028759 113 EFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 113 ~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~r 174 (204)
.++|| .|+..+.....+.+++.++++.+ ..+-+-+.+=.-|-.++-+.+.+.|.++
T Consensus 3 illvg-----HGSr~~~~~~~~~l~~~l~~~~~-~~v~~~~lE~~P~i~~~l~~l~~~G~~~ 58 (103)
T cd03413 3 VVFMG-----HGTDHPSNAVYAALEYVLREEDP-ANVFVGTVEGYPGLDDVLAKLKKAGIKK 58 (103)
T ss_pred EEEEE-----CCCCchhhhHHHHHHHHHHhcCC-CcEEEEEEcCCCCHHHHHHHHHHcCCCE
Confidence 46788 78887767777888888876531 2344556654445556666666666543
No 68
>PRK15005 universal stress protein F; Provisional
Probab=53.63 E-value=28 Score=26.24 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHHHcCCCEEEEee
Q 028759 96 EKLELQLLEIAQREETDEFIIGL 118 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGl 118 (204)
+...+.|.+.++++++|.||+|-
T Consensus 93 G~p~~~I~~~a~~~~~DLIV~Gs 115 (144)
T PRK15005 93 GSPKDRILELAKKIPADMIIIAS 115 (144)
T ss_pred CCHHHHHHHHHHHcCCCEEEEeC
Confidence 34667899999999999999993
No 69
>PRK13326 pantothenate kinase; Reviewed
Probab=53.08 E-value=1.6e+02 Score=25.99 Aligned_cols=21 Identities=29% Similarity=0.308 Sum_probs=18.8
Q ss_pred ceEEEEecCCCeEEEEEecCC
Q 028759 63 GFSLGVDLGLSRTGLALSKGF 83 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~~ 83 (204)
.++|+||.|..+|=+++-|+.
T Consensus 6 ~~~L~IDiGNT~ik~glf~~~ 26 (262)
T PRK13326 6 SSQLIIDIGNTSISFALYKDN 26 (262)
T ss_pred cEEEEEEeCCCeEEEEEEECC
Confidence 578999999999999999863
No 70
>COG0418 PyrC Dihydroorotase [Nucleotide transport and metabolism]
Probab=52.84 E-value=20 Score=33.23 Aligned_cols=52 Identities=29% Similarity=0.372 Sum_probs=34.7
Q ss_pred EeecCCCCCCCChh--------HHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcC
Q 028759 116 IGLPKSWDGSETPQ--------SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMG 171 (204)
Q Consensus 116 VGlPl~~dGt~~~~--------~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G 171 (204)
+|+|+...|..... +..+...-+.|.++|+ .+.|++ |..||.+|-+..++.+
T Consensus 130 ~gmpLlvHGEvt~~~vDifdrE~~Fi~~vl~pl~~~fP--~LKIV~--EHiTT~dav~~v~~~~ 189 (344)
T COG0418 130 IGMPLLVHGEVTDAEVDIFDREAAFIESVLEPLRQRFP--KLKIVL--EHITTKDAVEYVKDAN 189 (344)
T ss_pred cCCeEEEecccCCccccchhhHHHHHHHHHHHHHhhCC--cceEEE--EEeccHHHHHHHHhcC
Confidence 56666666655432 2334445556677774 666665 9999999999988755
No 71
>PF14331 ImcF-related_N: ImcF-related N-terminal domain
Probab=52.17 E-value=51 Score=28.99 Aligned_cols=57 Identities=14% Similarity=0.200 Sum_probs=39.3
Q ss_pred hHHHHHHHHHHHc----CCCEEEEeecCC--CCCCC-----ChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 97 KLELQLLEIAQRE----ETDEFIIGLPKS--WDGSE-----TPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 97 ~~~~~L~~li~e~----~i~~IVVGlPl~--~dGt~-----~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
..|..+.++++++ .+++|||=.|.. +++++ ...++.++.-.+.|.+.+. ..+|||++
T Consensus 8 ~~W~~~L~lL~~~R~r~PlnGvil~vs~~~Ll~~~~~~r~l~~~a~~lR~rL~el~~~lg-~~~PVYvv 75 (266)
T PF14331_consen 8 AEWQAFLDLLRRHRPRQPLNGVILTVSVDDLLNADEAERELEALARALRQRLEELQRTLG-VRLPVYVV 75 (266)
T ss_pred HHHHHHHHHHHhcCCCCCCCEEEEEEEHHHHhcCChhhhHHHHHHHHHHHHHHHHHHHhC-CCCCeEee
Confidence 4677888888765 468999999964 34443 3346666666666666664 57899987
No 72
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=50.85 E-value=67 Score=28.84 Aligned_cols=44 Identities=7% Similarity=0.064 Sum_probs=37.2
Q ss_pred CChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCC
Q 028759 126 ETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 126 ~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~ 173 (204)
..+..+.+.++++.+++. ++++++++..+++..++..-++.|++
T Consensus 234 ~eps~~~l~~l~~~ik~~----~v~~If~e~~~~~~~~~~la~e~g~~ 277 (311)
T PRK09545 234 IQPGAQRLHEIRTQLVEQ----KATCVFAEPQFRPAVIESVAKGTSVR 277 (311)
T ss_pred CCCCHHHHHHHHHHHHHc----CCCEEEecCCCChHHHHHHHHhcCCe
Confidence 345688889999999875 89999999999999998888887753
No 73
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=50.83 E-value=1.1e+02 Score=28.65 Aligned_cols=71 Identities=21% Similarity=0.157 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhH-HHHHHHHHHHHHhhccCCCcEEEE----cCCCcHHHHHHHHHHcCC
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQS-NKVRSVAGRLAVRAAERGWRVYLL----DEHRTSAEAVDRMINMGL 172 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~-~~v~~Fa~~L~~~~~~~~lpV~lv----DER~TT~eA~~~L~e~G~ 172 (204)
..+.|.+++.++++|.|||.==+-..+.....+ ....+|...|++. ++||+++ |-.-......+.|...|+
T Consensus 27 ~l~~l~~~i~~~~~D~viIaGDifD~~~p~~~a~~~~~~~l~~L~~~----~~~v~~I~GNHD~~~~l~~~~~~l~~~gi 102 (407)
T PRK10966 27 FLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQT----GCQLVVLAGNHDSVATLNESRDLLAFLNT 102 (407)
T ss_pred HHHHHHHHHHhcCCCEEEECCccccCCCCcHHHHHHHHHHHHHHHhc----CCcEEEEcCCCCChhhhhhHHHHHHHCCc
Confidence 356788888899999998873333233333333 2235566666643 6898887 433333345666777665
No 74
>PRK09605 bifunctional UGMP family protein/serine/threonine protein kinase; Validated
Probab=50.80 E-value=92 Score=29.75 Aligned_cols=88 Identities=15% Similarity=0.094 Sum_probs=55.9
Q ss_pred ceEEEEecCCCeEEEEEecC---CeeeeeeeEEc-------------cchhHHHHHHHHHHH-----cCCCEEEEeecCC
Q 028759 63 GFSLGVDLGLSRTGLALSKG---FCVRPLTVLKL-------------RGEKLELQLLEIAQR-----EETDEFIIGLPKS 121 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~---~~A~Pl~~i~~-------------~~~~~~~~L~~li~e-----~~i~~IVVGlPl~ 121 (204)
+.+||||-=..-+.+|+.+. ..+.-..++.. +.+.+...+.+++++ .++|.|.|+.-.
T Consensus 1 m~il~iets~~~~s~a~~~~~~~~~~~~~~~~~~~~gg~~p~~~~~~H~~~l~~~i~~~l~~~~~~~~~id~iav~~gP- 79 (535)
T PRK09605 1 MIVLGIEGTAWKTSAGIVDSDGDVLFNESDPYKPPSGGIHPREAAEHHAEAIPKVIKEALEEAGLKPEDIDLVAFSQGP- 79 (535)
T ss_pred CEEEEEEccccceEEEEEeCCCcEEEEEEeeccCCcCCCChHHHHHHHHHHHHHHHHHHHHHcCCCHhhCCEEEECCCC-
Confidence 36999999999999999983 23322222110 111233455566555 467999999432
Q ss_pred CCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759 122 WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEH 157 (204)
Q Consensus 122 ~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER 157 (204)
|..+ --+....||+.|+..+ ++|++.++..
T Consensus 80 --g~~~-~l~vg~~~ak~la~~~---~~~~~~v~h~ 109 (535)
T PRK09605 80 --GLGP-CLRVVATAARALALSL---DVPLIGVNHC 109 (535)
T ss_pred --CcHh-hHHHHHHHHHHHHHHh---CCCeecccHH
Confidence 3333 2445678899998775 8999988543
No 75
>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=50.25 E-value=78 Score=23.59 Aligned_cols=55 Identities=20% Similarity=0.297 Sum_probs=34.3
Q ss_pred EEEEeecCCCCCCCCh-hHHHHHHHHHHHHHhhccCCCcEEEEcC-CCcHHHHHHHHHHcCC
Q 028759 113 EFIIGLPKSWDGSETP-QSNKVRSVAGRLAVRAAERGWRVYLLDE-HRTSAEAVDRMINMGL 172 (204)
Q Consensus 113 ~IVVGlPl~~dGt~~~-~~~~v~~Fa~~L~~~~~~~~lpV~lvDE-R~TT~eA~~~L~e~G~ 172 (204)
.|+|| .||..+ ....++.+++.++++++...+.+.+++. .-|-.+|-+.+.+.|.
T Consensus 3 ~llv~-----HGS~~~~~~~~~~~l~~~l~~~~~~~~v~~afle~~~P~~~~~l~~l~~~g~ 59 (117)
T cd03414 3 VVLVG-----RGSSDPDANADVAKIARLLEEGTGFARVETAFAAATRPSLPEALERLRALGA 59 (117)
T ss_pred EEEEc-----CCCCCHHHHHHHHHHHHHHHHhcCCCeEEEEEecCCCCCHHHHHHHHHHcCC
Confidence 46777 677655 3457788888887765311244556664 5666777777766554
No 76
>PRK13322 pantothenate kinase; Reviewed
Probab=50.25 E-value=1e+02 Score=26.91 Aligned_cols=78 Identities=18% Similarity=0.118 Sum_probs=42.6
Q ss_pred eEEEEecCCCeEEEEEecC-CeeeeeeeEEccch-hHHHHHHHHHHHcCCCEEEEeecCCCCCCCC-hhHHHHHHHHHHH
Q 028759 64 FSLGVDLGLSRTGLALSKG-FCVRPLTVLKLRGE-KLELQLLEIAQREETDEFIIGLPKSWDGSET-PQSNKVRSVAGRL 140 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~-~~A~Pl~~i~~~~~-~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~-~~~~~v~~Fa~~L 140 (204)
++|.||.|..+|=+++.|+ .....-.. ...+. .....+..+ ..++|+.++|.- -.. +.. ..+.+.+
T Consensus 1 M~L~IDiGNT~iK~~l~~~~~~~~~~~~-~~~t~~~~~~~l~~~-~~~~i~~v~vsS------V~p~~~~---~~l~~~l 69 (246)
T PRK13322 1 MILELDCGNSRLKWRVIDNGGQIIEHGA-HLDSPAELLLGLANL-ASLAPTRCRIVS------VLSEEET---ARLVAIL 69 (246)
T ss_pred CEEEEEeCCCcEEEEEEcCCCchhhhcc-ccCCHHHHHHHHHhC-CccCCCEEEEEe------CCCHHHH---HHHHHHH
Confidence 4899999999999999884 21100000 11121 222344332 344689998871 111 222 3444555
Q ss_pred HHhhccCCCcEEEEc
Q 028759 141 AVRAAERGWRVYLLD 155 (204)
Q Consensus 141 ~~~~~~~~lpV~lvD 155 (204)
++.+ ++|++++.
T Consensus 70 ~~~~---~~~~~~v~ 81 (246)
T PRK13322 70 EKRL---GIPVVFAK 81 (246)
T ss_pred HHHh---CCCeEEEe
Confidence 5543 67777774
No 77
>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=49.43 E-value=70 Score=27.74 Aligned_cols=44 Identities=14% Similarity=0.240 Sum_probs=37.1
Q ss_pred CChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCC
Q 028759 126 ETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 126 ~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~ 173 (204)
..+..+.+.++.+.+++. ++++++++...++..++..-++.|++
T Consensus 199 ~eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~la~~~g~~ 242 (266)
T cd01018 199 KEPSPADLKRLIDLAKEK----GVRVVFVQPQFSTKSAEAIAREIGAK 242 (266)
T ss_pred CCCCHHHHHHHHHHHHHc----CCCEEEEcCCCCcHHHHHHHHHcCCe
Confidence 446688999999999875 89999999999999998777888863
No 78
>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=49.42 E-value=89 Score=27.29 Aligned_cols=44 Identities=11% Similarity=0.142 Sum_probs=36.6
Q ss_pred CChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCC
Q 028759 126 ETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 126 ~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~ 173 (204)
..+..+.+.++.+.+++. ++++++++...++..++..-++.|++
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 446688899999998875 89999999999999998877777753
No 79
>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=47.90 E-value=16 Score=34.90 Aligned_cols=18 Identities=33% Similarity=0.639 Sum_probs=15.2
Q ss_pred EEEEecCCCeEEEEEecC
Q 028759 65 SLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~ 82 (204)
++|||+|+..+.||+.+.
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 689999999999999773
No 80
>PRK15456 universal stress protein UspG; Provisional
Probab=47.37 E-value=31 Score=26.32 Aligned_cols=50 Identities=18% Similarity=0.219 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
...+.|.+.++++++|.||+|- .|. +-....+=..++++-+.. +.||..+
T Consensus 92 ~~~~~I~~~a~~~~~DLIVmG~----~g~-~~~~~llGS~a~~v~~~a---~~pVLvV 141 (142)
T PRK15456 92 SVRDEVNELAEELGADVVVIGS----RNP-SISTHLLGSNASSVIRHA---NLPVLVV 141 (142)
T ss_pred ChHHHHHHHHhhcCCCEEEEcC----CCC-CccceecCccHHHHHHcC---CCCEEEe
Confidence 4667889999999999999994 332 211122234455555542 6777654
No 81
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=46.95 E-value=42 Score=33.49 Aligned_cols=50 Identities=24% Similarity=0.352 Sum_probs=37.3
Q ss_pred HHHHHHHcCCC---EEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcH
Q 028759 102 LLEIAQREETD---EFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160 (204)
Q Consensus 102 L~~li~e~~i~---~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT 160 (204)
+.+.+.+..++ +||||. ||..+. +.||+.++.-|..-|.+|++.+|--+|
T Consensus 90 ~a~yl~~~~~~~~~giviG~----D~R~~S-----~~fA~l~a~vf~~~g~~v~lf~~~v~T 142 (607)
T KOG1220|consen 90 LAAYLKNQFPSKNLGIVIGH----DGRYNS-----KRFAELVAAVFLLNGFKVYLFSELVPT 142 (607)
T ss_pred HHHHHHHhCCcccceEEEec----CCccch-----HHHHHHHHHHHHhCCceEEEeccccCC
Confidence 44444445554 999997 898884 889999888876679999999954443
No 82
>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=46.94 E-value=1.1e+02 Score=22.90 Aligned_cols=80 Identities=16% Similarity=0.167 Sum_probs=49.0
Q ss_pred eeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHH
Q 028759 85 VRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV 164 (204)
Q Consensus 85 A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~ 164 (204)
..+.+++.....-..+.+.+.+.+++++.|++. .+.+.....+.++++.+++..+ .+++|.+-==..+. ..
T Consensus 25 ~~G~~V~~lg~~~~~~~l~~~~~~~~pdvV~iS------~~~~~~~~~~~~~i~~l~~~~~-~~~~i~vGG~~~~~-~~- 95 (119)
T cd02067 25 DAGFEVIDLGVDVPPEEIVEAAKEEDADAIGLS------GLLTTHMTLMKEVIEELKEAGL-DDIPVLVGGAIVTR-DF- 95 (119)
T ss_pred HCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEe------ccccccHHHHHHHHHHHHHcCC-CCCeEEEECCCCCh-hH-
Confidence 355566543222335678888889999977775 4445566788889999988632 14555555443332 22
Q ss_pred HHHHHcCCC
Q 028759 165 DRMINMGLS 173 (204)
Q Consensus 165 ~~L~e~G~~ 173 (204)
+.+.+.|..
T Consensus 96 ~~~~~~G~D 104 (119)
T cd02067 96 KFLKEIGVD 104 (119)
T ss_pred HHHHHcCCe
Confidence 355666653
No 83
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=46.64 E-value=65 Score=25.26 Aligned_cols=30 Identities=23% Similarity=0.259 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCC
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSET 127 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~ 127 (204)
....|.+.+++.++.+||+....++.|..+
T Consensus 44 ~i~~L~~ri~~~~i~EVIlA~~pt~EGe~T 73 (112)
T cd01025 44 NIDKLLERIAKGQVKEVILATNPTVEGEAT 73 (112)
T ss_pred CHHHHHHHHhcCCCcEEEEecCCCchHHHH
Confidence 457888888889999999999888877543
No 84
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=46.59 E-value=40 Score=26.06 Aligned_cols=45 Identities=29% Similarity=0.416 Sum_probs=29.1
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
.+.+.++++++++|.|+|=+|... ...++++.+.+++. +++|.++
T Consensus 130 ~~~l~~~~~~~~id~v~ial~~~~-------~~~i~~ii~~~~~~----~v~v~~v 174 (175)
T PF13727_consen 130 LDDLPELVREHDIDEVIIALPWSE-------EEQIKRIIEELENH----GVRVRVV 174 (175)
T ss_dssp GGGHHHHHHHHT--EEEE--TTS--------HHHHHHHHHHHHTT----T-EEEE-
T ss_pred HHHHHHHHHhCCCCEEEEEcCccC-------HHHHHHHHHHHHhC----CCEEEEe
Confidence 468889999999999999988643 34667777777764 6777654
No 85
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=46.48 E-value=17 Score=37.86 Aligned_cols=20 Identities=30% Similarity=0.717 Sum_probs=18.5
Q ss_pred CceEEEEecCCCeEEEEEec
Q 028759 62 GGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD 81 (204)
..++||+|.|+.-||.|++.
T Consensus 3 ~~yilglDIGi~SVGWAvve 22 (1088)
T COG3513 3 KAYILGLDIGINSVGWAVVE 22 (1088)
T ss_pred cceEEEeeccccceeeEEee
Confidence 46899999999999999997
No 86
>PRK03011 butyrate kinase; Provisional
Probab=46.38 E-value=1.6e+02 Score=27.29 Aligned_cols=89 Identities=19% Similarity=0.178 Sum_probs=50.9
Q ss_pred ceEEEEecCCCeEEEEEecCCeeeeeeeEEcc-----------chhH--HHHHHHHHHHc-----CCCEEEEee-----c
Q 028759 63 GFSLGVDLGLSRTGLALSKGFCVRPLTVLKLR-----------GEKL--ELQLLEIAQRE-----ETDEFIIGL-----P 119 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~-----------~~~~--~~~L~~li~e~-----~i~~IVVGl-----P 119 (204)
.+||+|.+|..-+=+|+-++....--+++... .+.. .+.+.+.+++. +++.| +|- |
T Consensus 2 ~~il~inpgststk~a~~~~~~~~~~~~~~h~~~~~~~~~~~~~q~~~r~~~i~~~l~~~g~~~~~l~av-~~RgG~~~~ 80 (358)
T PRK03011 2 MRILVINPGSTSTKIAVFEDEKPIFEETLRHSAEELEKFKTIIDQYEFRKQAILDFLKEHGIDLSELDAV-VGRGGLLKP 80 (358)
T ss_pred CEEEEEcCCCchheEEEEcCCceeeeeccccCHHHHhcCCCccchHHHHHHHHHHHHHHcCCChhcceEE-EEcCCCCcc
Confidence 47999999999999999985321111222111 1112 24677777766 44545 887 6
Q ss_pred CCCCCCC----------------ChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 120 KSWDGSE----------------TPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 120 l~~dGt~----------------~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
.+ .|+. .+.+.-.--.+.++.+. .++|++.+|=
T Consensus 81 v~-gG~~~v~~~~~~~l~~~~~~~~~~nl~~~~a~~~~~~---~~~p~~v~D~ 129 (358)
T PRK03011 81 IP-GGTYRVNEAMLEDLKNGKYGEHASNLGAIIAYEIAKE---LGIPAFIVDP 129 (358)
T ss_pred cC-CCCEEcCHHHHHHHHhcCCCCCCCCHHHHHHHHHHHh---cCCCEEEECC
Confidence 54 4665 23333333334444443 4889888876
No 87
>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=46.19 E-value=43 Score=26.16 Aligned_cols=49 Identities=12% Similarity=0.247 Sum_probs=32.4
Q ss_pred EEEEeecCCCCCCCChhH-HHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcC
Q 028759 113 EFIIGLPKSWDGSETPQS-NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMG 171 (204)
Q Consensus 113 ~IVVGlPl~~dGt~~~~~-~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G 171 (204)
.++|| -||..+.+ +.+..+++.++++++ +.+|.+ -|||....++|.+.|
T Consensus 3 illv~-----fGS~~~~~~~~~~~i~~~l~~~~p--~~~V~~---afts~~i~~~l~~~~ 52 (127)
T cd03412 3 ILLVS-----FGTSYPTAEKTIDAIEDKVRAAFP--DYEVRW---AFTSRMIRKKLKKRG 52 (127)
T ss_pred EEEEe-----CCCCCHHHHHHHHHHHHHHHHHCC--CCeEEE---EecHHHHHHHHHhcC
Confidence 47888 68887755 468899999988874 455543 366655555555443
No 88
>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=46.00 E-value=1e+02 Score=21.60 Aligned_cols=65 Identities=14% Similarity=0.212 Sum_probs=44.8
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCcc
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKS 175 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rk 175 (204)
.+..+.+.+..++.+++++-. .+..+ ..+++.|+... .+.|+.++=...++....+.+ +.|...-
T Consensus 33 ~~~~~~~~~~~~d~iiid~~~--~~~~~------~~~~~~i~~~~--~~~~ii~~t~~~~~~~~~~~~-~~g~~~~ 97 (112)
T PF00072_consen 33 EEALELLKKHPPDLIIIDLEL--PDGDG------LELLEQIRQIN--PSIPIIVVTDEDDSDEVQEAL-RAGADDY 97 (112)
T ss_dssp HHHHHHHHHSTESEEEEESSS--SSSBH------HHHHHHHHHHT--TTSEEEEEESSTSHHHHHHHH-HTTESEE
T ss_pred HHHHHHhcccCceEEEEEeee--ccccc------ccccccccccc--ccccEEEecCCCCHHHHHHHH-HCCCCEE
Confidence 455566688899999999543 33222 57788887764 488999888777777666666 5665443
No 89
>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=45.21 E-value=63 Score=28.21 Aligned_cols=45 Identities=24% Similarity=0.349 Sum_probs=35.8
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
.++.+-+.+...|.|+|| ||.+-....+.+...++++. .+||++.
T Consensus 17 ~~~~~~~~~~gtdai~vG------GS~~vt~~~~~~~v~~ik~~----~lPvilf 61 (223)
T TIGR01768 17 DEIAKAAAESGTDAILIG------GSQGVTYEKTDTLIEALRRY----GLPIILF 61 (223)
T ss_pred HHHHHHHHhcCCCEEEEc------CCCcccHHHHHHHHHHHhcc----CCCEEEe
Confidence 345556677899999999 88877778888888888853 6998874
No 90
>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=44.46 E-value=45 Score=23.60 Aligned_cols=21 Identities=24% Similarity=0.322 Sum_probs=18.7
Q ss_pred HHHHHHHHHHcCCCEEEEeec
Q 028759 99 ELQLLEIAQREETDEFIIGLP 119 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlP 119 (204)
.+.|.+.+++.+++.+|+|..
T Consensus 82 ~~~i~~~~~~~~~dlvvig~~ 102 (130)
T cd00293 82 AEAILEAAEELGADLIVMGSR 102 (130)
T ss_pred HHHHHHHHHHcCCCEEEEcCC
Confidence 678999999999999999954
No 91
>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=44.32 E-value=1.2e+02 Score=26.77 Aligned_cols=46 Identities=7% Similarity=0.044 Sum_probs=38.5
Q ss_pred CCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCC
Q 028759 124 GSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 124 Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~ 173 (204)
....+..+.+.++.+.+++. ++++++++.-.++..++..-++.|++
T Consensus 206 ~~~eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~ia~~~gv~ 251 (287)
T cd01137 206 TEEEGTPKQVATLIEQVKKE----KVPAVFVESTVNDRLMKQVAKETGAK 251 (287)
T ss_pred CCCCCCHHHHHHHHHHHHHh----CCCEEEEeCCCChHHHHHHHHHhCCc
Confidence 34557789999999999875 89999999999999998888887764
No 92
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=42.25 E-value=59 Score=27.68 Aligned_cols=59 Identities=15% Similarity=0.138 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCC---ChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSE---TPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~---~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
..+.+..++.+++++.|||=..-.+.... ......+..+...|+....+.+++|.++-+
T Consensus 128 i~~~i~~~~~~~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~~L~~la~~~~vtvll~sq 189 (271)
T cd01122 128 VLEKVRYMAVSHGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSH 189 (271)
T ss_pred HHHHHHHHHhcCCceEEEECCHHHHhccCCCchhHHHHHHHHHHHHHHHHHHhCCEEEEEec
Confidence 44667777778899999998764443221 223344556666666544445899988865
No 93
>PF14450 FtsA: Cell division protein FtsA; PDB: 1E4F_T 4A2B_A 4A2A_A 1E4G_T.
Probab=41.77 E-value=76 Score=24.20 Aligned_cols=18 Identities=28% Similarity=0.510 Sum_probs=15.5
Q ss_pred EEEEecCCCeEEEEEecC
Q 028759 65 SLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~ 82 (204)
+.+||+|+.+|.+++...
T Consensus 1 i~~iDiGs~~~~~~i~~~ 18 (120)
T PF14450_consen 1 IVVIDIGSSKTKVAIAED 18 (120)
T ss_dssp EEEEEE-SSSEEEEEEET
T ss_pred CEEEEcCCCcEEEEEEEe
Confidence 578999999999999995
No 94
>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=41.76 E-value=2e+02 Score=23.67 Aligned_cols=17 Identities=6% Similarity=0.014 Sum_probs=11.7
Q ss_pred HHHHHHHHHcCCCEEEE
Q 028759 100 LQLLEIAQREETDEFII 116 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVV 116 (204)
.++.+.+...++|++|+
T Consensus 45 ~~~i~~l~~~~vdgiIi 61 (273)
T cd06292 45 ADYVEDLLARGVRGVVF 61 (273)
T ss_pred HHHHHHHHHcCCCEEEE
Confidence 34445555579999998
No 95
>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=41.31 E-value=1.3e+02 Score=24.97 Aligned_cols=60 Identities=12% Similarity=0.140 Sum_probs=40.8
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCC-CCC-CChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSW-DGS-ETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~-dGt-~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
.+...+..++.+++++.|||=.=-.+ .+. .......+..+.+.|+....+++++|.++-+
T Consensus 110 ~l~~~i~~~~~~~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q 171 (242)
T cd00984 110 DIRSRARRLKKEHGLGLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQ 171 (242)
T ss_pred HHHHHHHHHHHhcCCCEEEEcCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecc
Confidence 34567777888889999999853222 222 2334556778888888655456999998875
No 96
>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=41.16 E-value=1.5e+02 Score=24.04 Aligned_cols=55 Identities=22% Similarity=0.375 Sum_probs=32.9
Q ss_pred EEEEecCCCeEEEEEec----C-CeeeeeeeEEcc----c-----hhHHHHHHHHHHH------cCCCEEEEeec
Q 028759 65 SLGVDLGLSRTGLALSK----G-FCVRPLTVLKLR----G-----EKLELQLLEIAQR------EETDEFIIGLP 119 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD----~-~~A~Pl~~i~~~----~-----~~~~~~L~~li~e------~~i~~IVVGlP 119 (204)
+.|||.|+.+|=+.+.. + .........+.+ + ......+++.+++ .++..+++|.|
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 47999999999988885 2 111112222211 1 2334556666654 36789999987
No 97
>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=40.84 E-value=90 Score=27.13 Aligned_cols=47 Identities=19% Similarity=0.323 Sum_probs=35.0
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
...+.+++.+...|.|+|| ||.+-. ....+..+.+++.- . .+||++.
T Consensus 14 ~~~~~~~~~~~gtdai~vG------GS~~v~-~~~~~~~~~ik~~~-~-~~Pvilf 60 (219)
T cd02812 14 DEEIAKLAEESGTDAIMVG------GSDGVS-STLDNVVRLIKRIR-R-PVPVILF 60 (219)
T ss_pred HHHHHHHHHhcCCCEEEEC------Cccchh-hhHHHHHHHHHHhc-C-CCCEEEe
Confidence 3568888888999999999 888765 66677777777642 1 3888764
No 98
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=40.49 E-value=78 Score=27.72 Aligned_cols=41 Identities=24% Similarity=0.333 Sum_probs=33.7
Q ss_pred HHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 104 EIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 104 ~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
+.+.+...|.|+|| ||.+-....+.+....+++ + ++||++.
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 55667899999999 8887777788889899886 3 7898874
No 99
>PLN02757 sirohydrochlorine ferrochelatase
Probab=40.40 E-value=1.7e+02 Score=23.77 Aligned_cols=58 Identities=12% Similarity=0.157 Sum_probs=36.0
Q ss_pred CCCEEEEeecCCCCCCCChhH-HHHHHHHHHHHHhhccCCCcEEEEc-CCCcHHHHHHHHHHcCC
Q 028759 110 ETDEFIIGLPKSWDGSETPQS-NKVRSVAGRLAVRAAERGWRVYLLD-EHRTSAEAVDRMINMGL 172 (204)
Q Consensus 110 ~i~~IVVGlPl~~dGt~~~~~-~~v~~Fa~~L~~~~~~~~lpV~lvD-ER~TT~eA~~~L~e~G~ 172 (204)
....|+|| .|+..+.+ ..++++++.|+++.....+.+.|.. ..-|-.+|-+.+.+.|.
T Consensus 13 ~~~lllvg-----HGSrd~~a~~~~~~la~~l~~~~~~~~V~~aFle~~~Psl~eal~~l~~~g~ 72 (154)
T PLN02757 13 KDGVVIVD-----HGSRRKESNLMLEEFVAMYKQKTGHPIVEPAHMELAEPSIKDAFGRCVEQGA 72 (154)
T ss_pred CcEEEEEe-----CCCCCHHHHHHHHHHHHHHHhhCCCCcEEEEEEecCCCCHHHHHHHHHHCCC
Confidence 34578888 78877765 6678888888765421123455555 44566666666655554
No 100
>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=40.37 E-value=1.4e+02 Score=21.85 Aligned_cols=24 Identities=13% Similarity=0.426 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeec
Q 028759 96 EKLELQLLEIAQREETDEFIIGLP 119 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlP 119 (204)
....+.|.+.+++++++.||+|..
T Consensus 71 ~~~~~~I~~~~~~~~~dllviG~~ 94 (124)
T cd01987 71 DDVAEAIVEFAREHNVTQIVVGKS 94 (124)
T ss_pred CcHHHHHHHHHHHcCCCEEEeCCC
Confidence 345678999999999999999964
No 101
>PF08967 DUF1884: Domain of unknown function (DUF1884); InterPro: IPR014418 This group represents an uncharacterised conserved protein.; PDB: 2PK8_A.
Probab=40.31 E-value=81 Score=23.80 Aligned_cols=34 Identities=24% Similarity=0.351 Sum_probs=19.6
Q ss_pred cCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHh-hccCCCcEEEEcCCC
Q 028759 109 EETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVR-AAERGWRVYLLDEHR 158 (204)
Q Consensus 109 ~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~-~~~~~lpV~lvDER~ 158 (204)
++||.+.+| ..|.+.++.. +...+++|+.+||=.
T Consensus 26 ~ePDivL~G----------------~ef~e~~~~~~l~~~~lkvy~i~ELg 60 (85)
T PF08967_consen 26 FEPDIVLVG----------------PEFYEFLSEEVLEVSGLKVYVIEELG 60 (85)
T ss_dssp ----EEEE-----------------HHHHHHHHH---EETTEEEEE-GGGT
T ss_pred CCCCEEEEc----------------HHHHHHHHHHHHHhhCceEEEHHhcC
Confidence 689999999 5677776543 333689999999944
No 102
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=39.57 E-value=2.3e+02 Score=24.25 Aligned_cols=59 Identities=15% Similarity=0.144 Sum_probs=33.8
Q ss_pred EEecCCCeEEEEEecCC------eeeeeeeEEcc---c----hhHHHHHHHHHHH---cCCCEEEEeecCCCCCC
Q 028759 67 GVDLGLSRTGLALSKGF------CVRPLTVLKLR---G----EKLELQLLEIAQR---EETDEFIIGLPKSWDGS 125 (204)
Q Consensus 67 alD~G~kRIGVAvsD~~------~A~Pl~~i~~~---~----~~~~~~L~~li~e---~~i~~IVVGlPl~~dGt 125 (204)
|||+|+..|=+.+.+.. .+.|-..+... + ...+.++.+..++ ..+..+||+-|-+.+..
T Consensus 1 g~dig~~~ik~v~~~~~~~~~~~~~~~~~~~~~g~I~d~~~~~~~l~~l~~~a~~~~g~~~~~vvisVP~~~~~~ 75 (239)
T TIGR02529 1 GVDLGTANIVIVVLDEDGQPVAGVMQFADVVRDGIVVDFLGAVEIVRRLKDTLEQKLGIELTHAATAIPPGTIEG 75 (239)
T ss_pred CCCcccceEEEEEEecCCCEEEEEecccccccCCeEEEhHHHHHHHHHHHHHHHHHhCCCcCcEEEEECCCCCcc
Confidence 68999999988776621 12222222211 1 1233445544332 46789999999877543
No 103
>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=38.92 E-value=1.3e+02 Score=26.73 Aligned_cols=84 Identities=15% Similarity=0.096 Sum_probs=52.2
Q ss_pred EEEecCCCeEEEEEecC---Ceeeeeee-----------EEc-----cchhHHHHHHHHHHH-----cCCCEEEEeecCC
Q 028759 66 LGVDLGLSRTGLALSKG---FCVRPLTV-----------LKL-----RGEKLELQLLEIAQR-----EETDEFIIGLPKS 121 (204)
Q Consensus 66 LalD~G~kRIGVAvsD~---~~A~Pl~~-----------i~~-----~~~~~~~~L~~li~e-----~~i~~IVVGlPl~ 121 (204)
||||--...++||+.|. +.+.-... .+. +.+.+...+.+++++ .+++.|.|+.=
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 68999999999999984 22221111 111 112233456666655 35799999851
Q ss_pred CCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 122 WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 122 ~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
-|+.+. .+....+|+.|...+ ++|++.++.
T Consensus 79 -PG~~tg-lrvg~~~Ak~la~~~---~~p~~~v~h 108 (305)
T TIGR00329 79 -PGLGGS-LRVGATFARSLALSL---DKPLIGVNH 108 (305)
T ss_pred -CCchhh-HHHHHHHHHHHHHHh---CCCEeeccc
Confidence 144443 455567899998775 899998854
No 104
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=38.90 E-value=1.1e+02 Score=24.90 Aligned_cols=38 Identities=18% Similarity=0.241 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhh
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRA 144 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~ 144 (204)
...+.+.+.|++.++|.|+||+ |.... +.|+...+..+
T Consensus 88 ~~~~~i~~~I~~~~pdiv~vgl-----G~PkQ-----E~~~~~~~~~l 125 (172)
T PF03808_consen 88 EEEEAIINRINASGPDIVFVGL-----GAPKQ-----ERWIARHRQRL 125 (172)
T ss_pred hhHHHHHHHHHHcCCCEEEEEC-----CCCHH-----HHHHHHHHHHC
Confidence 4567888899999999999996 55543 68888888876
No 105
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=38.79 E-value=2.3e+02 Score=25.35 Aligned_cols=87 Identities=21% Similarity=0.228 Sum_probs=51.7
Q ss_pred CCCeEEEEEecC---C------------eeeeeeeEEccc---hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHH
Q 028759 71 GLSRTGLALSKG---F------------CVRPLTVLKLRG---EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNK 132 (204)
Q Consensus 71 G~kRIGVAvsD~---~------------~A~Pl~~i~~~~---~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~ 132 (204)
-+..||+.+.+. . ...++.++.... ........+.+.++++|+||+=- -..+
T Consensus 57 ~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~-----~~~~----- 126 (333)
T COG1609 57 RTKTIGLVVPDITNPFFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLG-----ERPN----- 126 (333)
T ss_pred CCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEec-----CCCC-----
Confidence 466788877651 1 135555554322 23456777888889999999862 1111
Q ss_pred HHHHHHHHHHhhccCCCcEEEEcCCCc--------------HHHHHHHHHHcCC
Q 028759 133 VRSVAGRLAVRAAERGWRVYLLDEHRT--------------SAEAVDRMINMGL 172 (204)
Q Consensus 133 v~~Fa~~L~~~~~~~~lpV~lvDER~T--------------T~eA~~~L~e~G~ 172 (204)
..+.+.+.+. ++|++++|.... ..+|-+.|.+.|.
T Consensus 127 -~~~~~~l~~~----~~P~V~i~~~~~~~~~~~V~~Dn~~~~~~a~~~L~~~G~ 175 (333)
T COG1609 127 -DSLLELLAAA----GIPVVVIDRSPPGLGVPSVGIDNFAGAYLATEHLIELGH 175 (333)
T ss_pred -HHHHHHHHhc----CCCEEEEeCCCccCCCCEEEEChHHHHHHHHHHHHHCCC
Confidence 3445555553 677777775333 4566677777663
No 106
>COG3142 CutC Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]
Probab=38.77 E-value=1.5e+02 Score=26.50 Aligned_cols=62 Identities=23% Similarity=0.355 Sum_probs=46.7
Q ss_pred HHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE---cCCCcHHHHHHHHHHcCCCc
Q 028759 104 EIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL---DEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 104 ~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv---DER~TT~eA~~~L~e~G~~r 174 (204)
..+++...++||+|- ++.||+.. ..-.++|-+.. .+++|+|. ||--.-.+|-+.+.+.|+.|
T Consensus 80 ~~~~~lG~~GVV~G~-lt~dg~iD------~~~le~Li~aA--~gL~vTFHrAFD~~~d~~~ale~li~~Gv~R 144 (241)
T COG3142 80 RLARELGVQGVVLGA-LTADGNID------MPRLEKLIEAA--GGLGVTFHRAFDECPDPLEALEQLIELGVER 144 (241)
T ss_pred HHHHHcCCCcEEEee-ecCCCccC------HHHHHHHHHHc--cCCceeeehhhhhcCCHHHHHHHHHHCCCcE
Confidence 345678999999995 66788876 23344444443 38899985 89888999999999988755
No 107
>PLN02405 hexokinase
Probab=38.54 E-value=2.5e+02 Score=27.44 Aligned_cols=20 Identities=20% Similarity=0.199 Sum_probs=17.5
Q ss_pred CceEEEEecCCCeEEEEEec
Q 028759 62 GGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD 81 (204)
.|.+||||+|....=|....
T Consensus 94 ~G~flAlDlGGTNfRV~~V~ 113 (497)
T PLN02405 94 KGLFYALDLGGTNFRVLRVL 113 (497)
T ss_pred ceeEEEEecCCceEEEEEEE
Confidence 48999999999998888776
No 108
>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=38.37 E-value=1.6e+02 Score=25.08 Aligned_cols=103 Identities=14% Similarity=0.008 Sum_probs=44.9
Q ss_pred cccchhhhcccccccccCCCCCCceEEEEecC----CCeEEEEEe--c-CCeeeeeeeEEcc---chhHHHHHHHHHHHc
Q 028759 40 ALSSVEEFLPNATRRKKDSLWRGGFSLGVDLG----LSRTGLALS--K-GFCVRPLTVLKLR---GEKLELQLLEIAQRE 109 (204)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~g~iLalD~G----~kRIGVAvs--D-~~~A~Pl~~i~~~---~~~~~~~L~~li~e~ 109 (204)
++|+.+.+-....... |......++|+|+| ...+++.+. . .....-+.....+ .....+.+.+++..+
T Consensus 205 ~if~~~~~~~~~~~~~--~~~~~~~~~g~D~a~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~ 282 (384)
T PF03237_consen 205 SIFDRFWIERHVRDPI--PPPDWPIIIGVDPAGGKGGDYTAIVVWEIVDDDGFYVVDDEYERGMSPEEWAERIRELYKKY 282 (384)
T ss_dssp BSS-HHHHCC-----B----TT--EEEEEE--SSCTTB-EEEEEE-E-SSSSEEEEEEEEESSS-TTTHHHHHHHHHHHT
T ss_pred CccchHHhhccccccc--cCCCceEEEEEECCCCCccCCEEEEEEccccccceEEeeehhhcCCCHHHHHHHHHHHHhhc
Confidence 4666665544333221 33445678999999 556666665 1 1112222222211 134567888888899
Q ss_pred CCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 110 ETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 110 ~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
++..|++=- +| .+ ...++.|+......+++|....
T Consensus 283 ~~~~i~~d~----~~-~g------~~~~~~l~~~~~~~~~~~~~~~ 317 (384)
T PF03237_consen 283 NPIKIYIDA----NG-AG------ESVIEILRREGPNEGFNVKPTP 317 (384)
T ss_dssp TS--EEEEE----SC-CH------HHHHHHHHTTT--S-SSEE--H
T ss_pred CceEEEEcC----Cc-cc------cchhhhhhhhcCCceEEEEecc
Confidence 999998852 22 22 4455556654321125555553
No 109
>PRK13317 pantothenate kinase; Provisional
Probab=37.93 E-value=2.2e+02 Score=25.32 Aligned_cols=86 Identities=12% Similarity=0.176 Sum_probs=48.3
Q ss_pred ceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHH-cCCCEEEEeecCCCCCCCChhHHHHHHHHHHHH
Q 028759 63 GFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQR-EETDEFIIGLPKSWDGSETPQSNKVRSVAGRLA 141 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e-~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~ 141 (204)
+..+|||.|...+=+++-|...-.-+.....+ ..+.+.+++.+ .++..|++= |.-+ ..|++.+.
T Consensus 2 ~~~iGIDiGstt~K~v~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~i~~T------G~g~------~~~~~~~~ 66 (277)
T PRK13317 2 EMKIGIDAGGTLTKIVYLEEKKQRTFKTEYSA---EGKKVIDWLINLQDIEKICLT------GGKA------GYLQQLLN 66 (277)
T ss_pred CceEEEEeCcccEEEEEEcCCCeEEEEeeccH---HHHHHHHHhhccCCceEEEEE------Ccch------hhhhHHHh
Confidence 45789999999999999874211112222221 22344444433 345544442 3222 22333221
Q ss_pred HhhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 142 VRAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 142 ~~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
.++|++.+||=-.+..+-+.+.
T Consensus 67 -----~~~~~~~v~E~~a~~~g~~~l~ 88 (277)
T PRK13317 67 -----YGYPIAEFVEFEATGLGVRYLL 88 (277)
T ss_pred -----cCCCeeeeHHHHHHHHHHHHHH
Confidence 2788888999877777777764
No 110
>PRK11175 universal stress protein UspE; Provisional
Probab=37.79 E-value=1e+02 Score=26.45 Aligned_cols=53 Identities=8% Similarity=-0.017 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
...+.|.+.++++++|.||+|. .|...-.....-..+.+|-.. .++||.++-+
T Consensus 94 ~~~~~i~~~a~~~~~DLiV~G~----~~~~~~~~~~~gs~~~~l~~~---~~~pvlvv~~ 146 (305)
T PRK11175 94 RPFEAIIQEVIAGGHDLVVKMT----HQHDKLESVIFTPTDWHLLRK---CPCPVLMVKD 146 (305)
T ss_pred CcHHHHHHHHHhcCCCEEEEeC----CCCcHHHhhccChhHHHHHhc---CCCCEEEecc
Confidence 4567899999999999999994 333221111112333444433 3678888865
No 111
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=37.69 E-value=1.2e+02 Score=27.60 Aligned_cols=55 Identities=24% Similarity=0.212 Sum_probs=38.7
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
+.+..+.+++.+.++|.|||+==+-.. ..|-.+.+..|.+.|++. ...++||+.+
T Consensus 27 ~~f~~~l~~a~~~~vD~vliAGDlFd~--~~Ps~~a~~~~~~~l~~l-~~~~Ipv~~I 81 (390)
T COG0420 27 KAFDELLEIAKEEKVDFVLIAGDLFDT--NNPSPRALKLFLEALRRL-KDAGIPVVVI 81 (390)
T ss_pred HHHHHHHHHHHHccCCEEEEccccccC--CCCCHHHHHHHHHHHHHh-ccCCCcEEEe
Confidence 456788888999999999998443333 344456666777777654 2247999998
No 112
>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=37.25 E-value=1.4e+02 Score=23.65 Aligned_cols=52 Identities=15% Similarity=0.201 Sum_probs=34.7
Q ss_pred HHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 102 LLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 102 L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
+.+++..++++.|||-+=-|.-+......+.++++++.+++..+ +.||+++.
T Consensus 49 ~~~~~~~~~pd~vii~~G~ND~~~~~~~~~~~~~~i~~i~~~~p--~~~iil~~ 100 (177)
T cd01844 49 VAELLRDVPADLYIIDCGPNIVGAEAMVRERLGPLVKGLRETHP--DTPILLVS 100 (177)
T ss_pred HHHHHHhcCCCEEEEEeccCCCccHHHHHHHHHHHHHHHHHHCc--CCCEEEEe
Confidence 55666778999998865555322222456777888888887653 56777764
No 113
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.82 E-value=1.7e+02 Score=25.26 Aligned_cols=53 Identities=13% Similarity=0.143 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhH-HHHHHHHHHHHHhhccCC-CcEEEE
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQS-NKVRSVAGRLAVRAAERG-WRVYLL 154 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~-~~v~~Fa~~L~~~~~~~~-lpV~lv 154 (204)
.++++.+++.++++|.||++==+-.+...+..+ .....|..+|++. + +||+++
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 456788888889999888874333233333222 2234555555543 4 888887
No 114
>PLN03184 chloroplast Hsp70; Provisional
Probab=36.79 E-value=40 Score=33.71 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.7
Q ss_pred CceEEEEecCCCeEEEEEec
Q 028759 62 GGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD 81 (204)
++.++|||+|+..+-+|+.+
T Consensus 38 ~~~viGIDlGTt~s~va~~~ 57 (673)
T PLN03184 38 AEKVVGIDLGTTNSAVAAME 57 (673)
T ss_pred CCCEEEEEeCcCcEEEEEEE
Confidence 45699999999999999986
No 115
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=36.79 E-value=13 Score=36.89 Aligned_cols=56 Identities=21% Similarity=0.248 Sum_probs=33.9
Q ss_pred CCccccccCCCCccceeeccCCCcccccccccchhhhcccccccccCCCCCCceEEEEecCCCeEEEEEecC
Q 028759 11 NSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~iLalD~G~kRIGVAvsD~ 82 (204)
|..+.+-.-.+|++.+-|+|.-..-|. .+.|.- ...+.++|||+|+..+-||+.++
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~----~~~~~viGIDlGTt~s~va~~~~ 60 (663)
T PTZ00400 5 NKKLIVKSLLTPSIALVLSSAMRSLCT------------SAIRFA----KATGDIVGIDLGTTNSCVAIMEG 60 (663)
T ss_pred chhhhhhhhhccchhhhhHHHHHHHHH------------Hhhhhh----hhcCcEEEEEECcccEEEEEEeC
Confidence 333333344578887777776433331 111110 11357999999999999999863
No 116
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=36.41 E-value=1.1e+02 Score=29.51 Aligned_cols=71 Identities=17% Similarity=0.196 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHcCCCEEEEee--cCCCCC----------------CCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCc
Q 028759 98 LELQLLEIAQREETDEFIIGL--PKSWDG----------------SETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGl--Pl~~dG----------------t~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~T 159 (204)
..+.|.++.++++++.+|||= |+- .| ....+-+-.+.|++.+-++ +++|-.-...=.+
T Consensus 51 ~~~~lv~fA~~~~idl~vVGPE~pL~-~GvvD~l~~~Gi~vFGPsk~AA~lE~SK~faK~fm~k---~~IPta~y~~f~~ 126 (428)
T COG0151 51 DHEALVAFAKEKNVDLVVVGPEAPLV-AGVVDALRAAGIPVFGPTKAAAQLEGSKAFAKDFMKK---YGIPTAEYEVFTD 126 (428)
T ss_pred CHHHHHHHHHHcCCCEEEECCcHHHh-hhhHHHHHHCCCceeCcCHHHHHHHhhHHHHHHHHHH---cCCCcccccccCC
Confidence 568999999999999999981 111 11 1122444567899988887 5999555554446
Q ss_pred HHHHHHHHHHcCC
Q 028759 160 SAEAVDRMINMGL 172 (204)
Q Consensus 160 T~eA~~~L~e~G~ 172 (204)
..+|+..+.+.|.
T Consensus 127 ~e~a~ayi~~~g~ 139 (428)
T COG0151 127 PEEAKAYIDEKGA 139 (428)
T ss_pred HHHHHHHHHHcCC
Confidence 6777777777654
No 117
>PRK14046 malate--CoA ligase subunit beta; Provisional
Probab=36.40 E-value=3e+02 Score=25.71 Aligned_cols=84 Identities=8% Similarity=-0.028 Sum_probs=48.1
Q ss_pred eeeeeeEEccchh-HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHH
Q 028759 85 VRPLTVLKLRGEK-LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEA 163 (204)
Q Consensus 85 A~Pl~~i~~~~~~-~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA 163 (204)
+.|+.+-...+.+ ....|+.+..+-+++.|+|-.+ .| .......++..++.+++. ..+.||..+-.-....++
T Consensus 284 aNPlDlgg~a~~e~~~~aL~~ll~Dp~VdaVlv~i~---gg-i~~~~~vA~~Ii~a~~~~--~~~kPvvv~l~G~~~e~~ 357 (392)
T PRK14046 284 ANFLDVGGGASPERVAKAFRLVLSDRNVKAILVNIF---AG-INRCDWVAEGVVQAAREV--GIDVPLVVRLAGTNVEEG 357 (392)
T ss_pred cCCEEecCCCCHHHHHHHHHHHHcCCCCCEEEEEcC---CC-CCCHHHHHHHHHHHHHhc--CCCCcEEEEcCCCCHHHH
Confidence 5677763222223 3456777777889999998766 23 222233334444444331 036787555443466677
Q ss_pred HHHHHHcCCCc
Q 028759 164 VDRMINMGLSK 174 (204)
Q Consensus 164 ~~~L~e~G~~r 174 (204)
++.|.+.|+.-
T Consensus 358 ~~iL~~~Gipv 368 (392)
T PRK14046 358 RKILAESGLPI 368 (392)
T ss_pred HHHHHHcCCCe
Confidence 77798888643
No 118
>PF01261 AP_endonuc_2: Xylose isomerase-like TIM barrel; InterPro: IPR012307 This TIM alpha/beta barrel structure is found in xylose isomerase (P19148 from SWISSPROT) and in endonuclease IV (P12638 from SWISSPROT, 3.1.21.2 from EC). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae []. ; PDB: 3KWS_B 3DX5_A 3CQH_B 3CQI_A 3CQK_A 3CQJ_B 2G0W_B 1DXI_A 2ZDS_D 3TVA_B ....
Probab=36.32 E-value=2.1e+02 Score=22.47 Aligned_cols=75 Identities=13% Similarity=0.093 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHcCCCEEEEeec---CCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcH-------HHHHHHH
Q 028759 98 LELQLLEIAQREETDEFIIGLP---KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS-------AEAVDRM 167 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlP---l~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT-------~eA~~~L 167 (204)
...+..++.++.++..++++.+ ........+.-..+.+..+.|.+....+++.+.+-....+. .++.+.+
T Consensus 72 ~~~~~i~~a~~lg~~~i~~~~g~~~~~~~~~~~~~~~~~~~~l~~l~~~a~~~gv~i~lE~~~~~~~~~~~~~~~~~~~l 151 (213)
T PF01261_consen 72 YLKKAIDLAKRLGAKYIVVHSGRYPSGPEDDTEENWERLAENLRELAEIAEEYGVRIALENHPGPFSETPFSVEEIYRLL 151 (213)
T ss_dssp HHHHHHHHHHHHTBSEEEEECTTESSSTTSSHHHHHHHHHHHHHHHHHHHHHHTSEEEEE-SSSSSSSEESSHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCceeecCcccccccCCCHHHHHHHHHHHHHHHHhhhhhhcceEEEecccCccccchhhHHHHHHHH
Confidence 3456667777889999999976 22222222333333333334443333458887777655544 6777787
Q ss_pred HHcCC
Q 028759 168 INMGL 172 (204)
Q Consensus 168 ~e~G~ 172 (204)
.+.+-
T Consensus 152 ~~~~~ 156 (213)
T PF01261_consen 152 EEVDS 156 (213)
T ss_dssp HHHTT
T ss_pred hhcCC
Confidence 76553
No 119
>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=36.16 E-value=3e+02 Score=25.20 Aligned_cols=81 Identities=14% Similarity=0.026 Sum_probs=46.5
Q ss_pred eeeeeeEEccchh-HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHH
Q 028759 85 VRPLTVLKLRGEK-LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEA 163 (204)
Q Consensus 85 A~Pl~~i~~~~~~-~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA 163 (204)
+.|+.+-...+.. ....|+.+.++-+++.|+|-.+ |........++..++.+++. . .+.||..+-.-....++
T Consensus 284 aNplDlgg~a~~~~~~~al~~l~~dp~vd~ilv~i~----gg~~~~~~va~~i~~a~~~~-~-~~kPvvv~~~g~~~~~~ 357 (386)
T TIGR01016 284 ANFLDVGGGASAERVREALKLVLSDKSVKVVFINIF----GGITRCDLVAKGLVEALKEV-G-VNVPVVVRLEGTNVEEG 357 (386)
T ss_pred CCcEEecCCCCHHHHHHHHHHHHcCCCCCEEEEECC----CCCCCHHHHHHHHHHHHHhc-C-CCCcEEEEeCCccHHHH
Confidence 4666663222222 3456777777889999998655 32222233444444444432 0 12787665544455677
Q ss_pred HHHHHHcC
Q 028759 164 VDRMINMG 171 (204)
Q Consensus 164 ~~~L~e~G 171 (204)
+++|.+.|
T Consensus 358 ~~~L~~~G 365 (386)
T TIGR01016 358 KKILAESG 365 (386)
T ss_pred HHHHHHcC
Confidence 88898888
No 120
>COG4126 Hydantoin racemase [Amino acid transport and metabolism]
Probab=36.02 E-value=81 Score=27.91 Aligned_cols=61 Identities=25% Similarity=0.372 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCcc
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKS 175 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rk 175 (204)
++....+-++|-..+.||+| -+. ++ ..+++|++.+ ++||+ |=-....+-..-|..+|...+
T Consensus 162 l~~~~~~a~~edgAeaIiLG-----CAG---ms----~la~~Lq~~~---gvPVI--Dgv~Aav~~a~~L~~~~~~ts 222 (230)
T COG4126 162 LVIEAAEALKEDGAEAIILG-----CAG---MS----DLADQLQKAF---GVPVI--DGVAAAVKLAEGLLGMGLSTS 222 (230)
T ss_pred HHHHHHHHhhhcCCCEEEEc-----Ccc---HH----HHHHHHHHHh---CCCcc--cchHHHHHHHHHHHhhchhhh
Confidence 45567777888999999999 222 22 3377888875 88874 433333322333444555443
No 121
>PRK11678 putative chaperone; Provisional
Probab=35.75 E-value=39 Score=32.14 Aligned_cols=18 Identities=22% Similarity=0.499 Sum_probs=16.3
Q ss_pred eEEEEecCCCeEEEEEec
Q 028759 64 FSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD 81 (204)
+++|||+||..+=||+.+
T Consensus 1 ~~iGID~GTtNs~va~~~ 18 (450)
T PRK11678 1 MFIGFDYGTANCSVAVMR 18 (450)
T ss_pred CeEEEecCccceeeEEee
Confidence 468999999999999996
No 122
>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=35.51 E-value=2.2e+02 Score=25.69 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=34.7
Q ss_pred EEEEecCCCeEEEEEec----C-Cee-----eeeeeEEc----cchhHHHHHHHHHHH------cCCCEEEEeec
Q 028759 65 SLGVDLGLSRTGLALSK----G-FCV-----RPLTVLKL----RGEKLELQLLEIAQR------EETDEFIIGLP 119 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD----~-~~A-----~Pl~~i~~----~~~~~~~~L~~li~e------~~i~~IVVGlP 119 (204)
++|||.|+.+|=+++.. + ... .|...+.. +.....+.|++.+++ .++..++++.|
T Consensus 2 ~~~lDIGs~~ik~vv~~~~~~~~~~i~~~~~~~~~gi~~G~I~d~~~~~~~i~~al~~~e~~~~~~i~~v~~~v~ 76 (371)
T TIGR01174 2 IVGLDIGTSKICAIVAEVLEDGELNIIGVGTHPSRGIKKGVINDIEAAVGSIQRAIEAAELMAGCEIRSVIVSIS 76 (371)
T ss_pred EEEEEeccceEEEEEEEEcCCCCEEEEEEEEecCCCccCcEEEcHHHHHHHHHHHHHHHHHHhCCcccEEEEEEc
Confidence 68999999999998875 2 111 22211111 112345667777765 57889999987
No 123
>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=34.71 E-value=1.3e+02 Score=24.54 Aligned_cols=20 Identities=25% Similarity=0.365 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHcCCCEEEEe
Q 028759 98 LELQLLEIAQREETDEFIIG 117 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVG 117 (204)
....+.+++...++++||+-
T Consensus 48 ~~~~~~~~~~~~~~dgiii~ 67 (270)
T cd06294 48 LLEEVKKMIQQKRVDGFILL 67 (270)
T ss_pred HHHHHHHHHHHcCcCEEEEe
Confidence 34567777777788888885
No 124
>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=34.46 E-value=1.9e+02 Score=25.39 Aligned_cols=44 Identities=9% Similarity=0.114 Sum_probs=36.7
Q ss_pred CCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCC
Q 028759 125 SETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGL 172 (204)
Q Consensus 125 t~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~ 172 (204)
...+..+.+.++++.+++. ++++++.+...+...|+..-++.|.
T Consensus 209 ~~eps~~~l~~l~~~ik~~----~v~~If~e~~~~~~~~~~ia~~~g~ 252 (286)
T cd01019 209 EIDPGAKRLAKIRKEIKEK----GATCVFAEPQFHPKIAETLAEGTGA 252 (286)
T ss_pred CCCCCHHHHHHHHHHHHHc----CCcEEEecCCCChHHHHHHHHhcCc
Confidence 3556688888999988875 9999999999999999888888775
No 125
>PF02737 3HCDH_N: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; InterPro: IPR006176 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major regions of similarity in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3K6J_A 1ZCJ_A 2X58_A 1ZEJ_A 3HDH_B 2WTB_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B ....
Probab=34.01 E-value=25 Score=28.98 Aligned_cols=64 Identities=23% Similarity=0.295 Sum_probs=33.6
Q ss_pred EEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc
Q 028759 114 FIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES 192 (204)
Q Consensus 114 IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~ 192 (204)
-||| .|+-| +.+|..+... |.+|.++|..-...+.-....+..+.+..++....+-.+.-.+.+
T Consensus 3 ~ViG-----aG~mG------~~iA~~~a~~----G~~V~l~d~~~~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~ 66 (180)
T PF02737_consen 3 AVIG-----AGTMG------RGIAALFARA----GYEVTLYDRSPEALERARKRIERLLDRLVRKGRLSQEEADAALAR 66 (180)
T ss_dssp EEES------SHHH------HHHHHHHHHT----TSEEEEE-SSHHHHHHHHHHHHHHHHHHHHTTTTTHHHHHHHHHT
T ss_pred EEEc-----CCHHH------HHHHHHHHhC----CCcEEEEECChHHHHhhhhHHHHHHhhhhhhccchhhhhhhhhhh
Confidence 4778 56544 5666666653 899999998776644433332222222233344444444444444
No 126
>cd00732 CheW CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together with CheA and the methyl-accepting chemotaxis proteins (MCPs), which are involved in response modulation.
Probab=33.85 E-value=68 Score=24.49 Aligned_cols=45 Identities=18% Similarity=0.178 Sum_probs=33.8
Q ss_pred CcccccccccchhhhcccccccccCCCCCCceEEEEecCCCeEEEEEec
Q 028759 33 NFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~iLalD~G~kRIGVAvsD 81 (204)
|.+.+..+++++.+++.-..+.. -...+++-+..+..++|++|.+
T Consensus 45 ~~rg~~ipvvdl~~~lg~~~~~~----~~~~~vli~~~~~~~~gl~Vd~ 89 (140)
T cd00732 45 NLRGRIVPVIDLRKRLGLPPAED----TKNTRIIVVEVGDQVVGLLVDS 89 (140)
T ss_pred ecCCcEEEEEehHHHcCCCCCCC----CCCCEEEEEEECCEEEEEEEee
Confidence 45666788999999886543321 2346899999999999999976
No 127
>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=33.50 E-value=1.5e+02 Score=26.27 Aligned_cols=88 Identities=15% Similarity=0.117 Sum_probs=48.3
Q ss_pred EEEecCCCeEEEEEecC--CeeeeeeeEEcc-chhHHHHHHHHHHHcC------CCEEEEeecCCCCCCCChhHH---HH
Q 028759 66 LGVDLGLSRTGLALSKG--FCVRPLTVLKLR-GEKLELQLLEIAQREE------TDEFIIGLPKSWDGSETPQSN---KV 133 (204)
Q Consensus 66 LalD~G~kRIGVAvsD~--~~A~Pl~~i~~~-~~~~~~~L~~li~e~~------i~~IVVGlPl~~dGt~~~~~~---~v 133 (204)
|++|+|--+|=+|+.|. .......+.... ...+.+.+.+++.+.+ +..+.||.|-..+|..-..+. .+
T Consensus 1 l~~DIGGT~i~~glvd~~g~~l~~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~Igi~Gpv~~~~v~~~nl~w~~ 80 (316)
T TIGR00749 1 LVGDIGGTNARLALCEIAPGEISQAKTYSGLDFPSLEAVVRVYLEEHKVELKDPIAKGCFAIACPITGDWVAMTNHTWAF 80 (316)
T ss_pred CeEecCcceeeEEEEecCCCceeeeEEEecCCCCCHHHHHHHHHHhcccccCCCcCeEEEEEeCcccCCEEEecCCCCee
Confidence 68999999999999872 211112333211 2345677777776542 556778877444443211111 01
Q ss_pred HHHHHHHHHhhccCCC-cEEEEcCCC
Q 028759 134 RSVAGRLAVRAAERGW-RVYLLDEHR 158 (204)
Q Consensus 134 ~~Fa~~L~~~~~~~~l-pV~lvDER~ 158 (204)
.. ..|++.+ ++ ||++.+.-.
T Consensus 81 -~~-~~l~~~~---g~~~V~l~ND~n 101 (316)
T TIGR00749 81 -SI-AELKQNL---GFSHLEIINDFT 101 (316)
T ss_pred -CH-HHHHHhc---CCCeEEEEecHH
Confidence 23 2555543 77 588877633
No 128
>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=33.34 E-value=97 Score=27.10 Aligned_cols=57 Identities=18% Similarity=0.135 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHc-----CCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcH
Q 028759 98 LELQLLEIAQRE-----ETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160 (204)
Q Consensus 98 ~~~~L~~li~e~-----~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT 160 (204)
....|.+.+++. .+..+++-.|-|+.|..=+ ....+++++..++. ++ +.++||.+..
T Consensus 131 d~~~l~~~l~~~~~~~~~~~~v~~~~p~nPtG~~~~-~~~l~~l~~~~~~~----~~-~ii~De~y~~ 192 (363)
T PF00155_consen 131 DPEALEEALDELPSKGPRPKAVLICNPNNPTGSVLS-LEELRELAELAREY----NI-IIIVDEAYSD 192 (363)
T ss_dssp THHHHHHHHHTSHTTTETEEEEEEESSBTTTTBB---HHHHHHHHHHHHHT----TS-EEEEEETTTT
T ss_pred cccccccccccccccccccceeeecccccccccccc-cccccchhhhhccc----cc-ceeeeeceec
Confidence 467888888775 5688999999999997543 34445666665543 54 4558887764
No 129
>KOG4013 consensus Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism]
Probab=33.24 E-value=99 Score=27.26 Aligned_cols=62 Identities=19% Similarity=0.346 Sum_probs=39.1
Q ss_pred HHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE---cCCCcHHHHHH-HHHHcCCC
Q 028759 103 LEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL---DEHRTSAEAVD-RMINMGLS 173 (204)
Q Consensus 103 ~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv---DER~TT~eA~~-~L~e~G~~ 173 (204)
.++++++..+++|+| .++.||+... .-...+-... .++||.|. |=-+--+.+.+ .|.+.|.+
T Consensus 87 v~llk~~GAdGfVFG-aLt~dgsid~------~~C~si~~~~--rplPVTFHRAfD~~~D~k~~lE~~l~~lGF~ 152 (255)
T KOG4013|consen 87 VELLKKAGADGFVFG-ALTSDGSIDR------TSCQSIIETA--RPLPVTFHRAFDVAYDWKTCLEDALLDLGFK 152 (255)
T ss_pred HHHHHHcCCCceEEe-ecCCCCCcCH------HHHHHHHHhc--CCCceeeeeehhhhcCHHHHHHHHHHHhhHH
Confidence 467889999999999 5788898773 2222222222 38899885 54444455544 45565543
No 130
>PRK03317 histidinol-phosphate aminotransferase; Provisional
Probab=33.24 E-value=1.3e+02 Score=26.67 Aligned_cols=54 Identities=15% Similarity=0.147 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcH
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT 160 (204)
..+.+.+.+.+.+++.|++-.|-|+.|..-+.. ..++ |.+.. +. +.++||-++-
T Consensus 148 d~~~l~~~~~~~~~~~i~l~~p~NPtG~~~~~~-~l~~----l~~~~---~~-~lI~DE~y~~ 201 (368)
T PRK03317 148 DVDAAVAAIAEHRPDVVFLTSPNNPTGTALPLD-DVEA----ILDAA---PG-IVVVDEAYAE 201 (368)
T ss_pred CHHHHHHHHhccCCCEEEEeCCCCCCCCCCCHH-HHHH----HHHHC---Cc-eEEEeCCchh
Confidence 346777777777888899999999999876522 2223 33332 43 7788998763
No 131
>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=33.06 E-value=2.4e+02 Score=26.59 Aligned_cols=63 Identities=19% Similarity=0.170 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE-----cCCC-cHHHHHHHH
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL-----DEHR-TSAEAVDRM 167 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv-----DER~-TT~eA~~~L 167 (204)
-.+.|.++++++++|+||.=.-..-+....+. ....+.+.+. .|+|+..+ |+|+ +..+.+-++
T Consensus 338 R~~~l~~l~ke~~aDGVI~~~~~~C~~~~~e~----~~~~~~l~e~---~GIP~L~iE~D~~d~r~~d~gQ~~TRi 406 (413)
T TIGR02260 338 RVDLLEKYINEYEADGLLINSIKSCNSFSAGQ----LLMMREIEKR---TGKPAAFIETDLVDPRYFSAANVKNRL 406 (413)
T ss_pred HHHHHHHHHHHhCCCEEEEeccCCCCcchhhh----HHHHHHHHHH---cCCCEEEEEcCCCCcccCCHHHHHHHH
Confidence 35689999999999999987655444433321 2233344443 28997766 4444 334444443
No 132
>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=33.06 E-value=1.7e+02 Score=21.47 Aligned_cols=61 Identities=16% Similarity=0.196 Sum_probs=38.1
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
.+.+.+.+.+++++.|.+..+ .+.....+.++++.+++.. ++++|..=-= ..|...++.+.
T Consensus 40 ~~~l~~~~~~~~pd~V~iS~~------~~~~~~~~~~l~~~~k~~~--p~~~iv~GG~-~~t~~~~~~l~ 100 (121)
T PF02310_consen 40 PEELVEALRAERPDVVGISVS------MTPNLPEAKRLARAIKERN--PNIPIVVGGP-HATADPEEILR 100 (121)
T ss_dssp HHHHHHHHHHTTCSEEEEEES------SSTHHHHHHHHHHHHHTTC--TTSEEEEEES-SSGHHHHHHHH
T ss_pred HHHHHHHHhcCCCcEEEEEcc------CcCcHHHHHHHHHHHHhcC--CCCEEEEECC-chhcChHHHhc
Confidence 367777788889998877643 4455666677777777654 2555555433 33444555554
No 133
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=33.03 E-value=1.5e+02 Score=27.48 Aligned_cols=58 Identities=16% Similarity=0.168 Sum_probs=38.6
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCC--ChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSE--TPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~--~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
...+.++.++++++.|||-+=-.+.+.. ......+..+.+.|+....++++||.++-.
T Consensus 294 ~~~i~~~~~~~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i~vi~lsq 353 (434)
T TIGR00665 294 RAKARRLKREHGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNVPVIALSQ 353 (434)
T ss_pred HHHHHHHHHhcCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEec
Confidence 3566677778899999998654443322 234455677777777654456999998764
No 134
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=33.00 E-value=64 Score=29.99 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=24.9
Q ss_pred CceEEEEecCCCeEEEEEecCCeeeeee--eEEccchhHHHHHHHHHHHcCCCEEEEe
Q 028759 62 GGFSLGVDLGLSRTGLALSKGFCVRPLT--VLKLRGEKLELQLLEIAQREETDEFIIG 117 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~~A~Pl~--~i~~~~~~~~~~L~~li~e~~i~~IVVG 117 (204)
+.+|+.||+|.|.- +.+.+...... +++.+ ...+.+. ..++++||+.
T Consensus 177 ~~~I~viD~G~k~n---ivr~L~~~G~~v~vvp~~--~~~~~i~----~~~~DGIvLS 225 (360)
T PRK12564 177 KYKVVAIDFGVKRN---ILRELAERGCRVTVVPAT--TTAEEIL----ALNPDGVFLS 225 (360)
T ss_pred CCEEEEEeCCcHHH---HHHHHHHCCCEEEEEeCC--CCHHHHH----hcCCCEEEEe
Confidence 35899999997752 22222222222 23322 1223332 3589999996
No 135
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.54 E-value=54 Score=28.10 Aligned_cols=77 Identities=16% Similarity=0.032 Sum_probs=41.2
Q ss_pred cCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCC-Cccc-------cCCC
Q 028759 109 EETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGL-SKSA-------RQTK 180 (204)
Q Consensus 109 ~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~-~rkk-------rK~~ 180 (204)
..+..+++|.... +-..+..+ -..|.+.|+-.....+++|..++|.+||..--. .|. +.+. ..-.
T Consensus 261 ~~~~~~~~~~~~~-~~~i~~~~--~~~~~~~l~yka~~~~~~v~~~~~~~tS~~C~~----cg~~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 261 VGVETLVVEDLVK-RRSISDWA--FGELRRQLEYKAEWGGIVVKVVPPYYTSKTCPC----CGHLSGRLFKCPRCGFVHD 333 (364)
T ss_pred Eeeeeeehhhhhh-cccHhhhh--HHHHHHHHHHHHHhCCeEEEECCCCCCcccccc----cCCccceeEECCCCCCeeh
Confidence 4566666664433 22222211 123444444332223789999999999875421 122 1111 0123
Q ss_pred CcHHHHHHHhcc
Q 028759 181 TDAYAAVVRQES 192 (204)
Q Consensus 181 vD~~AA~iILq~ 192 (204)
=|-.||.-|+..
T Consensus 334 rD~naa~Ni~~~ 345 (364)
T COG0675 334 RDVNAALNIARR 345 (364)
T ss_pred hhHHHHHHHHHH
Confidence 599999999877
No 136
>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=32.44 E-value=97 Score=26.50 Aligned_cols=18 Identities=39% Similarity=0.619 Sum_probs=16.3
Q ss_pred eEEEEecCCCeEEEEEec
Q 028759 64 FSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD 81 (204)
.++|||.|+..+=.++-|
T Consensus 1 ~~lGIDiGtts~K~vl~d 18 (248)
T TIGR00241 1 ISLGIDSGSTTTKMVLME 18 (248)
T ss_pred CEEEEEcChhheEEEEEc
Confidence 378999999999999988
No 137
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=32.39 E-value=45 Score=33.11 Aligned_cols=21 Identities=29% Similarity=0.513 Sum_probs=18.3
Q ss_pred CCceEEEEecCCCeEEEEEec
Q 028759 61 RGGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 61 ~~g~iLalD~G~kRIGVAvsD 81 (204)
..+.++|||+|+..+=||+.+
T Consensus 2 ~~~~~iGIDlGTt~s~va~~~ 22 (653)
T PTZ00009 2 TKGPAIGIDLGTTYSCVGVWK 22 (653)
T ss_pred CcccEEEEEeCcccEEEEEEe
Confidence 457799999999999999986
No 138
>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=32.03 E-value=1.6e+02 Score=25.48 Aligned_cols=53 Identities=15% Similarity=0.107 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEH 157 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER 157 (204)
...++.+.+++.++++|++.-|....-+ ...+.+|.+.+.+. .++||+++|--
T Consensus 83 ~~~~~a~~a~~~G~d~v~~~~P~~~~~~----~~~l~~~~~~ia~~---~~~pi~lYn~P 135 (284)
T cd00950 83 EAIELTKRAEKAGADAALVVTPYYNKPS----QEGLYAHFKAIAEA---TDLPVILYNVP 135 (284)
T ss_pred HHHHHHHHHHHcCCCEEEEcccccCCCC----HHHHHHHHHHHHhc---CCCCEEEEECh
Confidence 3456777788899999999999754322 24566777777765 38999999863
No 139
>PRK13331 pantothenate kinase; Reviewed
Probab=31.96 E-value=1.7e+02 Score=25.83 Aligned_cols=22 Identities=23% Similarity=0.113 Sum_probs=19.6
Q ss_pred CceEEEEecCCCeEEEEEecCC
Q 028759 62 GGFSLGVDLGLSRTGLALSKGF 83 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~ 83 (204)
..++|+||+|..+|=+++-|+.
T Consensus 6 ~~~~L~iDiGNT~~~~g~f~~~ 27 (251)
T PRK13331 6 SNEWLALMIGNSRLHWGYFSGE 27 (251)
T ss_pred CCcEEEEEeCCCcEEEEEEECC
Confidence 4789999999999999999963
No 140
>PRK07179 hypothetical protein; Provisional
Probab=31.59 E-value=1.4e+02 Score=26.98 Aligned_cols=53 Identities=17% Similarity=0.150 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCc
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~T 159 (204)
..+.|.+.+++..+..|++--|.++.|...+. ++.++..++ +++ +.++||-++
T Consensus 169 d~~~l~~~l~~~~~~lV~v~~v~n~tG~i~pl----~~I~~l~~~----~~~-~livDea~~ 221 (407)
T PRK07179 169 DVDHLRRQIERHGPGIIVVDSVYSTTGTIAPL----ADIVDIAEE----FGC-VLVVDESHS 221 (407)
T ss_pred CHHHHHHHHHhcCCeEEEECCCCCCCCccccH----HHHHHHHHH----cCC-EEEEECccc
Confidence 34677777776667778888788899988873 233333332 253 678899876
No 141
>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=31.58 E-value=3.8e+02 Score=24.14 Aligned_cols=89 Identities=15% Similarity=0.183 Sum_probs=51.1
Q ss_pred EEEEecCCCeEEEEEecCCeeeeeeeEEccch-hHHHHHHHHHHHc-CCCEEEEeecCCCCCCCChhHHHHHHHHHHHHH
Q 028759 65 SLGVDLGLSRTGLALSKGFCVRPLTVLKLRGE-KLELQLLEIAQRE-ETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAV 142 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~-~~~~~L~~li~e~-~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~ 142 (204)
.+|||.|...+=++..|..--.-...++++.- +..+.|++..... .+..|.+ -|.-+ .+|++.+..
T Consensus 2 ~iGiDiGgT~~Kiv~~~~~~~~~f~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~------TGgGa------~k~~~~~~~ 69 (279)
T TIGR00555 2 RIGIDIGGTLIKVVYEEPKGRRKFKTFETTNIDKFIEWLKNQIHRHSRITTLCA------TGGGA------FKFAELIYE 69 (279)
T ss_pred eEEEEeCcceEEEEEEcCCCcEEEEEeecccHHHHHHHHHHHHHhhcCceEEEE------ECCcH------HHHHHHhcc
Confidence 58999999999999986321111334443332 2222333222211 1222222 13222 577777876
Q ss_pred hhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 143 RAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 143 ~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
.+ ++++.-.||=-+...+-+.+.
T Consensus 70 ~~---~v~~~k~dE~~a~~~g~~~ll 92 (279)
T TIGR00555 70 SA---GIQLHKFDEFDALIQGLNYLL 92 (279)
T ss_pred cc---CCcccchhHHHHHHHHHHHHh
Confidence 53 788889999888888877764
No 142
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=31.47 E-value=2.8e+02 Score=25.10 Aligned_cols=63 Identities=19% Similarity=0.257 Sum_probs=43.7
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~ 173 (204)
.+...+.+++|++|.+|+.-|-. +..||.. +|+ .|++. ++|.+.+-..-|.+ +++.|.+.|+.
T Consensus 49 ~~~~~~~~~~~~pDf~i~isPN~--a~PGP~~--ARE---~l~~~----~iP~IvI~D~p~~K-~~d~l~~~g~G 111 (277)
T PRK00994 49 EEVVKKMLEEWKPDFVIVISPNP--AAPGPKK--ARE---ILKAA----GIPCIVIGDAPGKK-VKDAMEEQGLG 111 (277)
T ss_pred HHHHHHHHHhhCCCEEEEECCCC--CCCCchH--HHH---HHHhc----CCCEEEEcCCCccc-hHHHHHhcCCc
Confidence 34677788999999999997742 3455522 222 24443 89999998877777 44888887753
No 143
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=31.42 E-value=1.6e+02 Score=24.07 Aligned_cols=63 Identities=10% Similarity=0.083 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHcCCCEEEEeecC-CCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHc
Q 028759 98 LELQLLEIAQREETDEFIIGLPK-SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINM 170 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl-~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~ 170 (204)
+...+.+++++|+|+.|||=-=. .-.+.-|..+.+++.-++.+. +++|.++ |+..-++.++..
T Consensus 49 Fq~~f~kl~~dy~Vd~VvIk~R~~KGKfAGga~~FKmEaaIQL~~------~~~V~lv----s~~~ik~~lKrn 112 (138)
T PF11215_consen 49 FQFTFAKLMEDYKVDKVVIKERATKGKFAGGAVGFKMEAAIQLID------DVEVELV----SPATIKAQLKRN 112 (138)
T ss_pred HHHHHHHHHHHcCCCEEEEEecccCCCccCCchhHHHHHHHHhcC------CCcEEEE----CHHHHHHHHhcC
Confidence 45689999999999999996321 112233444455444443332 6788774 666666666543
No 144
>PF11104 PilM_2: Type IV pilus assembly protein PilM;; PDB: 2YCH_A.
Probab=31.35 E-value=2.2e+02 Score=25.51 Aligned_cols=53 Identities=21% Similarity=0.309 Sum_probs=32.4
Q ss_pred EEecCCCeEEEEEecC----C--e-----eeeeeeEEcc----chhHHHHHHHHHHHcCC--CEEEEeec
Q 028759 67 GVDLGLSRTGLALSKG----F--C-----VRPLTVLKLR----GEKLELQLLEIAQREET--DEFIIGLP 119 (204)
Q Consensus 67 alD~G~kRIGVAvsD~----~--~-----A~Pl~~i~~~----~~~~~~~L~~li~e~~i--~~IVVGlP 119 (204)
|||+|+..|-++-... . . ..|-.++... ...+.+.|++++++.++ ..+++++|
T Consensus 1 GiDiG~~siK~v~l~~~~~~~~l~~~~~~~~p~~~i~~g~i~d~~~l~~~L~~~~~~~~~~~k~v~~aip 70 (340)
T PF11104_consen 1 GIDIGSSSIKAVELSKKGNRFQLEAFASIPLPPGAISDGEIVDPEALAEALKELLKENKIKGKKVVLAIP 70 (340)
T ss_dssp EEEE-SSEEEEEEEETTTT--EEEEEEEEE--TTSEETTEES-HHHHHHHHHHHHHHHT----EEEEEE-
T ss_pred CeecCCCeEEEEEEEEcCCccEEEEEEEEECCCCCccCCCcCCHHHHHHHHHHHHHHcCCCCCeEEEEeC
Confidence 7999999999997662 1 1 2333444321 12456789999998866 67999988
No 145
>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=31.32 E-value=1.7e+02 Score=24.39 Aligned_cols=17 Identities=18% Similarity=0.130 Sum_probs=10.7
Q ss_pred HHHHHHHHcCCCEEEEe
Q 028759 101 QLLEIAQREETDEFIIG 117 (204)
Q Consensus 101 ~L~~li~e~~i~~IVVG 117 (204)
.+.+.+..+++|+||+-
T Consensus 46 ~~~~~l~~~~vdgvi~~ 62 (269)
T cd06297 46 YLESTTLAYLTDGLLLA 62 (269)
T ss_pred HHHHHHHhcCCCEEEEe
Confidence 34444556777777775
No 146
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=31.30 E-value=1.2e+02 Score=24.16 Aligned_cols=58 Identities=24% Similarity=0.182 Sum_probs=30.0
Q ss_pred HHHHHHHHHHH-cCCCEEEEeecCCCC-CCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 98 LELQLLEIAQR-EETDEFIIGLPKSWD-GSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 98 ~~~~L~~li~e-~~i~~IVVGlPl~~d-Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
..+.+.+.+.+ ++++.|||=.=...- +.+.... .+.+|...|++...++++.|.++..
T Consensus 128 ~~~~l~~~~~~~~~~~lvviD~l~~~~~~~~~~~~-~~~~~~~~l~~la~~~~~~vi~v~H 187 (193)
T PF13481_consen 128 DLEELEAALKELYGPDLVVIDPLQSLHDGDENSNS-AVAQLMQELKRLAKEYGVAVILVHH 187 (193)
T ss_dssp HHHHHHHHHTT----SEEEEE-GGGG--S-TT-HH-HHHHHHHHHHHHHHHH--EEEEEEE
T ss_pred HHHHHHHHHhhcCCCcEEEEcCHHHHhcCCCCCHH-HHHHHHHHHHHHHHHcCCEEEEEEC
Confidence 45678888888 789999887443332 2232222 2366666666543335888887763
No 147
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=31.12 E-value=3.2e+02 Score=22.95 Aligned_cols=67 Identities=15% Similarity=0.157 Sum_probs=38.8
Q ss_pred HHHHHHHHHcCCCEEEEeecC-CCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCc
Q 028759 100 LQLLEIAQREETDEFIIGLPK-SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl-~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~r 174 (204)
..+.+.+.+..++.+|+.+.- .|.|..| -+++++|++..+ ++||.++--.-....+.+.+.+.|...
T Consensus 27 ~~~l~~~~~~~pd~vl~dl~d~~mp~~~G------l~~~~~l~~~~p--~~~iIvlt~~~~~~~~~~~~~~~Ga~g 94 (207)
T PRK11475 27 SSFQDAMSRISFSAVIFSLSAMRSERREG------LSCLTELAIKFP--RMRRLVIADDDIEARLIGSLSPSPLDG 94 (207)
T ss_pred HHHHHHhccCCCCEEEeeccccCCCCCCH------HHHHHHHHHHCC--CCCEEEEeCCCCHHHHHHHHHHcCCeE
Confidence 344445666788999866542 3334333 467788877653 788888754333333444554556543
No 148
>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=30.86 E-value=1.7e+02 Score=24.01 Aligned_cols=45 Identities=13% Similarity=0.117 Sum_probs=28.3
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEH 157 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER 157 (204)
...+.+++. .++|+||+.-+. .+.. ..+.+++++. ++||+++|-.
T Consensus 45 ~~~i~~~i~-~~~d~Iiv~~~~---~~~~------~~~l~~~~~~----gIpvv~~d~~ 89 (257)
T PF13407_consen 45 IEQIEQAIS-QGVDGIIVSPVD---PDSL------APFLEKAKAA----GIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHHH-TTESEEEEESSS---TTTT------HHHHHHHHHT----TSEEEEESST
T ss_pred HHHHHHHHH-hcCCEEEecCCC---HHHH------HHHHHHHhhc----CceEEEEecc
Confidence 345666554 679999998432 2222 3455556654 8999998755
No 149
>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=30.83 E-value=2.2e+02 Score=26.20 Aligned_cols=24 Identities=29% Similarity=0.248 Sum_probs=12.3
Q ss_pred HHHHHcCCCccccCC-CCcHHHHHH
Q 028759 165 DRMINMGLSKSARQT-KTDAYAAVV 188 (204)
Q Consensus 165 ~~L~e~G~~rkkrK~-~vD~~AA~i 188 (204)
+.|++.|+.-..|+. =.|-.||+-
T Consensus 313 ~~L~~~Gi~vtvR~~~G~di~aaCG 337 (345)
T PRK14457 313 RVLEQRGVAVSVRASRGLDANAACG 337 (345)
T ss_pred HHHHHCCCeEEEeCCCCCchhhccc
Confidence 345556765554443 245555553
No 150
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=30.75 E-value=1.7e+02 Score=23.76 Aligned_cols=61 Identities=25% Similarity=0.283 Sum_probs=40.5
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEE-----Ec-CCCcHHHHHHHHHHcCC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYL-----LD-EHRTSAEAVDRMINMGL 172 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~l-----vD-ER~TT~eA~~~L~e~G~ 172 (204)
...+.+.|.+.++|.|+||+ |...+ +.|+.+.+..+ +.+|.+ .| ...+...|=..++..|+
T Consensus 88 ~~~i~~~I~~~~pdiv~vgl-----G~PkQ-----E~~~~~~~~~l---~~~v~~~vG~~~d~~aG~~~raP~w~~~~gl 154 (171)
T cd06533 88 EEEIIERINASGADILFVGL-----GAPKQ-----ELWIARHKDRL---PVPVAIGVGGSFDFLAGTVKRAPKWMQKLGL 154 (171)
T ss_pred HHHHHHHHHHcCCCEEEEEC-----CCCHH-----HHHHHHHHHHC---CCCEEEEeceeeEeccCCcccCcHHHHHhCc
Confidence 34588888999999999996 55543 67888888775 334443 23 44455556566666554
No 151
>PRK13410 molecular chaperone DnaK; Provisional
Probab=30.67 E-value=46 Score=33.30 Aligned_cols=19 Identities=32% Similarity=0.578 Sum_probs=17.4
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
+.++|||+|+..+-||+.+
T Consensus 2 ~~viGIDlGTt~s~va~~~ 20 (668)
T PRK13410 2 GRIVGIDLGTTNSVVAVME 20 (668)
T ss_pred CcEEEEEeCCCcEEEEEEE
Confidence 5799999999999999987
No 152
>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=30.31 E-value=3e+02 Score=24.31 Aligned_cols=59 Identities=17% Similarity=0.248 Sum_probs=0.0
Q ss_pred CCceEEEEecCCCeEEEEEec----CCeeeeeeeEEccchh-----------HHHHHHHHHHHcCCCE--EEEeec
Q 028759 61 RGGFSLGVDLGLSRTGLALSK----GFCVRPLTVLKLRGEK-----------LELQLLEIAQREETDE--FIIGLP 119 (204)
Q Consensus 61 ~~g~iLalD~G~kRIGVAvsD----~~~A~Pl~~i~~~~~~-----------~~~~L~~li~e~~i~~--IVVGlP 119 (204)
....++|||+|...|=++... +....-....+..... +...|++++++.+... +++++|
T Consensus 1 ~~~~~vgiDIg~~~Ik~v~~~~~~~~~~v~~~~~~~~p~~~i~~g~i~d~~~~~~~l~~~~~~~~~~~k~v~~alp 76 (348)
T TIGR01175 1 KKSLLVGIDIGSTSVKVAQLKRSGDRYKLEHYAVEPLPAGIFTEGHIVEYQAVAEALKELLSELGINTKKAATAVP 76 (348)
T ss_pred CCCcEEEEEeccCeEEEEEEEecCCceEEEEEEEEECCCCcccCCCccCHHHHHHHHHHHHHHcCCCcceEEEEec
No 153
>COG1831 Predicted metal-dependent hydrolase (urease superfamily) [General function prediction only]
Probab=30.31 E-value=1.8e+02 Score=26.62 Aligned_cols=73 Identities=16% Similarity=0.055 Sum_probs=51.3
Q ss_pred HHHHHHHHHHcCCCEE-EEeecCCC-CCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHH---HHHHcCCC
Q 028759 99 ELQLLEIAQREETDEF-IIGLPKSW-DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVD---RMINMGLS 173 (204)
Q Consensus 99 ~~~L~~li~e~~i~~I-VVGlPl~~-dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~---~L~e~G~~ 173 (204)
.+...+++.|..+++| =||.|=-. +-..=+.+..+...|-.+++- -+.||.+.-|+++...-++ +.++.|++
T Consensus 110 lelA~k~v~eg~avaiGEvGrPHypVs~~v~~~~n~vl~~a~elA~d---vdc~vqLHtes~~~~~~~~i~~~ak~~G~~ 186 (285)
T COG1831 110 LELAAKLVEEGKAVAIGEVGRPHYPVSEEVWEASNEVLEYAMELAKD---VDCAVQLHTESLDEETYEEIAEMAKEAGIK 186 (285)
T ss_pred HHHHHHHHhccceeeeeccCCCCCCCCHHHHHHHHHHHHHHHHHhhc---CCCcEEEecCCCChHHHHHHHHHHHHhCCC
Confidence 3566778888888888 88888432 333445666677777777665 3899999999999865544 45677874
Q ss_pred c
Q 028759 174 K 174 (204)
Q Consensus 174 r 174 (204)
.
T Consensus 187 ~ 187 (285)
T COG1831 187 P 187 (285)
T ss_pred c
Confidence 3
No 154
>PF09989 DUF2229: CoA enzyme activase uncharacterised domain (DUF2229); InterPro: IPR018709 Proteins containing this domain include various bacterial hypothetical proteins, as well as CoA enzyme activases. The exact function of this domain has not, as yet, been defined.
Probab=30.24 E-value=72 Score=27.44 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=28.2
Q ss_pred cCCCEEEEeecCCC-CCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 109 EETDEFIIGLPKSW-DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 109 ~~i~~IVVGlPl~~-dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
.+..-+|+|.|++. |...+ ....++|++. |++|+..|
T Consensus 182 ~~~~Ivl~GrpY~~~D~~in------~~I~~~l~~~----G~~vit~d 219 (221)
T PF09989_consen 182 GKPAIVLLGRPYNIYDPFIN------MGIPDKLRSL----GVPVITED 219 (221)
T ss_pred CCceEEEEcCCCcCCCcccC------CchHHHHHHC----CCeeeCcc
Confidence 56889999999998 77666 4566667764 88887765
No 155
>TIGR01295 PedC_BrcD bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris.
Probab=30.19 E-value=2.2e+02 Score=21.85 Aligned_cols=48 Identities=23% Similarity=0.401 Sum_probs=36.3
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
..++.+.+...+...+.+| .+..+-|+.+....+.+.+. .+.+++++|
T Consensus 13 ~~~~~~~i~~~~~~iv~f~------~~~Cp~C~~~~P~l~~~~~~---~~~~~y~vd 60 (122)
T TIGR01295 13 VVRALEALDKKETATFFIG------RKTCPYCRKFSGTLSGVVAQ---TKAPIYYID 60 (122)
T ss_pred HHHHHHHHHcCCcEEEEEE------CCCChhHHHHhHHHHHHHHh---cCCcEEEEE
Confidence 3578888887777788899 45667777777777777765 378999998
No 156
>PF06925 MGDG_synth: Monogalactosyldiacylglycerol (MGDG) synthase; InterPro: IPR009695 This entry represents a conserved region of approximately 180 residues found towirds the N terminus of a number of plant and bacterial diacylglycerol glucosyltransferases, such as monogalactosyldiacylglycerol synthase [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009247 glycolipid biosynthetic process
Probab=29.85 E-value=2.9e+02 Score=21.99 Aligned_cols=66 Identities=20% Similarity=0.220 Sum_probs=41.4
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEE-EEcCCC-c----------------H
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVY-LLDEHR-T----------------S 160 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~-lvDER~-T----------------T 160 (204)
...|.+++++++||.||.=.|+-..-. ...|+++-...++|+. .+.. + + |
T Consensus 78 ~~~l~~~l~~~~PD~IIsThp~~~~~~-----------l~~lk~~~~~~~~p~~tvvTD-~~~~H~~W~~~~~D~y~Vas 145 (169)
T PF06925_consen 78 ARRLIRLLREFQPDLIISTHPFPAQVP-----------LSRLKRRGRLPNIPVVTVVTD-FDTVHPFWIHPGVDRYFVAS 145 (169)
T ss_pred HHHHHHHHhhcCCCEEEECCcchhhhH-----------HHHHHHhhcccCCcEEEEEcC-CCCCCcCeecCCCCEEEECC
Confidence 358999999999999999888742110 2223333111156754 3332 4 3 6
Q ss_pred HHHHHHHHHcCCCccc
Q 028759 161 AEAVDRMINMGLSKSA 176 (204)
Q Consensus 161 ~eA~~~L~e~G~~rkk 176 (204)
.++++.|.+.|+...+
T Consensus 146 e~~~~~l~~~Gi~~~~ 161 (169)
T PF06925_consen 146 EEVKEELIERGIPPER 161 (169)
T ss_pred HHHHHHHHHcCCChhH
Confidence 7888888888876543
No 157
>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase. Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo.
Probab=29.69 E-value=3.6e+02 Score=24.40 Aligned_cols=60 Identities=12% Similarity=0.202 Sum_probs=37.9
Q ss_pred CCCEEEEeecCCCCCCCChh-HHHHHHHHHHHHHhhc-cCCCcEEE-EcCCCcHHHHHHHHHHcCCCc
Q 028759 110 ETDEFIIGLPKSWDGSETPQ-SNKVRSVAGRLAVRAA-ERGWRVYL-LDEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 110 ~i~~IVVGlPl~~dGt~~~~-~~~v~~Fa~~L~~~~~-~~~lpV~l-vDER~TT~eA~~~L~e~G~~r 174 (204)
.+..|.+| .||.+-. ...+.++.+.+++.+. ..+.++.+ .+-..-|.+--+.|++.|+++
T Consensus 51 ~v~~i~~G-----GGtPs~l~~~~l~~ll~~i~~~~~~~~~~eitie~np~~lt~e~l~~l~~~Gv~r 113 (360)
T TIGR00539 51 PLESIFIG-----GGTPNTLSVEAFERLFESIYQHASLSDDCEITTEANPELITAEWCKGLKGAGINR 113 (360)
T ss_pred cccEEEeC-----CCchhcCCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCCCCHHHHHHHHHcCCCE
Confidence 38899999 8888743 5777788888876652 12344443 343333455557778877643
No 158
>TIGR03568 NeuC_NnaA UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing. This family of enzymes catalyzes the combined epimerization and UDP-hydrolysis of UDP-N-acetylglucosamine to N-acetylmannosamine. This is in contrast to the related enzyme WecB (TIGR00236) which retains the UDP moiety. NeuC acts in concert with NeuA and NeuB to synthesize CMP-N5-acetyl-neuraminate.
Probab=29.55 E-value=3.5e+02 Score=24.56 Aligned_cols=75 Identities=16% Similarity=0.162 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc--CC------------------
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD--EH------------------ 157 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD--ER------------------ 157 (204)
....+.+++.+++||.++|- |... ..++..+.... .++||..+. ||
T Consensus 81 ~~~~~~~~~~~~~Pd~vlv~------GD~~------~~la~alaA~~--~~IPv~HveaG~rs~~~~eE~~r~~i~~la~ 146 (365)
T TIGR03568 81 TIIGFSDAFERLKPDLVVVL------GDRF------EMLAAAIAAAL--LNIPIAHIHGGEVTEGAIDESIRHAITKLSH 146 (365)
T ss_pred HHHHHHHHHHHhCCCEEEEe------CCch------HHHHHHHHHHH--hCCcEEEEECCccCCCCchHHHHHHHHHHHh
Confidence 35789999999999977665 4332 23444455443 378887554 33
Q ss_pred ---CcHHHHHHHHHHcCCCcccc----CCCCcHHHH
Q 028759 158 ---RTSAEAVDRMINMGLSKSAR----QTKTDAYAA 186 (204)
Q Consensus 158 ---~TT~eA~~~L~e~G~~rkkr----K~~vD~~AA 186 (204)
-+|..|++.|...|....+- --.+|.+..
T Consensus 147 l~f~~t~~~~~~L~~eg~~~~~i~~tG~~~iD~l~~ 182 (365)
T TIGR03568 147 LHFVATEEYRQRVIQMGEDPDRVFNVGSPGLDNILS 182 (365)
T ss_pred hccCCCHHHHHHHHHcCCCCCcEEEECCcHHHHHHh
Confidence 15566777777777754321 234566543
No 159
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=29.51 E-value=1.5e+02 Score=21.94 Aligned_cols=52 Identities=13% Similarity=0.157 Sum_probs=33.1
Q ss_pred HHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCcc
Q 028759 103 LEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKS 175 (204)
Q Consensus 103 ~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rk 175 (204)
..-+++-+++.|||| -|+.. .+++|++... +..| .++|+. ++.|+..|+.+.
T Consensus 6 ~~~l~~~gv~lv~I~-----~g~~~----~~~~f~~~~~-----~p~~-ly~D~~------~~lY~~lg~~~~ 57 (115)
T PF13911_consen 6 KPELEAAGVKLVVIG-----CGSPE----GIEKFCELTG-----FPFP-LYVDPE------RKLYKALGLKRG 57 (115)
T ss_pred HHHHHHcCCeEEEEE-----cCCHH----HHHHHHhccC-----CCCc-EEEeCc------HHHHHHhCCccc
Confidence 445566899999999 46542 2677875522 4678 778883 334555566653
No 160
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=29.42 E-value=62 Score=31.92 Aligned_cols=19 Identities=21% Similarity=0.574 Sum_probs=17.2
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
..++|||+|+....||+..
T Consensus 19 ~~viGIDlGTT~S~va~~~ 37 (595)
T PRK01433 19 QIAVGIDFGTTNSLIAIAT 37 (595)
T ss_pred ceEEEEEcCcccEEEEEEe
Confidence 4689999999999999986
No 161
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=29.27 E-value=5.5e+02 Score=25.49 Aligned_cols=21 Identities=29% Similarity=0.082 Sum_probs=18.8
Q ss_pred CceEEEEecCCCeEEEEEecC
Q 028759 62 GGFSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~ 82 (204)
..++|-||.|..||=+|+.++
T Consensus 337 ~~~~LliD~GNTriKwa~~~~ 357 (592)
T PRK13325 337 SERFLLLDGGNSRLKWAWVEN 357 (592)
T ss_pred CceEEEEEcCcCceeEEEEcC
Confidence 578999999999999999873
No 162
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=29.25 E-value=62 Score=32.41 Aligned_cols=21 Identities=38% Similarity=0.552 Sum_probs=18.4
Q ss_pred CceEEEEecCCCeEEEEEecC
Q 028759 62 GGFSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~ 82 (204)
.+.++|||+|+..+-||+.++
T Consensus 26 ~~~viGIDLGTTnS~vA~~~~ 46 (657)
T PTZ00186 26 QGDVIGVDLGTTYSCVATMDG 46 (657)
T ss_pred cceEEEEEeCcCeEEEEEEeC
Confidence 357999999999999999873
No 163
>PRK09165 replicative DNA helicase; Provisional
Probab=29.19 E-value=1.7e+02 Score=28.22 Aligned_cols=58 Identities=14% Similarity=0.187 Sum_probs=39.4
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCC----CChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGS----ETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt----~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
...+.++..+++++.|||-+--.+... .......+..+.+.|+....+.++||.+.-.
T Consensus 330 ~~~ir~l~~~~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~is~~LK~lAkel~ipVi~lsQ 391 (497)
T PRK09165 330 RARARRLKRQHGLDLLVVDYLQLIRGSSKRSSDNRVQEISEITQGLKALAKELNIPVIALSQ 391 (497)
T ss_pred HHHHHHHHHhcCCCEEEEcchHhccCCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEeec
Confidence 346666777889999999886544321 1223456777777777665557999998864
No 164
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=29.07 E-value=2.9e+02 Score=21.86 Aligned_cols=54 Identities=24% Similarity=0.357 Sum_probs=39.6
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcC
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMG 171 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G 171 (204)
-.+.+++.+++++.+|++. -| +-+. ..|+.. ++.|+..++ .|..+|-+.+.+..
T Consensus 55 ~~~a~~l~~~gvdvvi~~~----iG---~~a~------~~l~~~----GIkv~~~~~-~~V~e~i~~~~~g~ 108 (121)
T COG1433 55 IRIAELLVDEGVDVVIASN----IG---PNAY------NALKAA----GIKVYVAPG-GTVEEAIKAFLEGE 108 (121)
T ss_pred HHHHHHHHHcCCCEEEECc----cC---HHHH------HHHHHc----CcEEEecCC-CCHHHHHHHHhcCC
Confidence 3688899999999999983 23 3222 235554 899999988 88888888877643
No 165
>PTZ00340 O-sialoglycoprotein endopeptidase-like protein; Provisional
Probab=28.90 E-value=2.3e+02 Score=26.32 Aligned_cols=91 Identities=14% Similarity=0.097 Sum_probs=55.8
Q ss_pred eEEEEecCCCeEEEEEec--C-Ceeeee---------eeEEcc-----chhHHHHHHHHHHH-----cCCCEEEEeecCC
Q 028759 64 FSLGVDLGLSRTGLALSK--G-FCVRPL---------TVLKLR-----GEKLELQLLEIAQR-----EETDEFIIGLPKS 121 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD--~-~~A~Pl---------~~i~~~-----~~~~~~~L~~li~e-----~~i~~IVVGlPl~ 121 (204)
++||||==...+++|+.| + +.+.-. .+++.. .+.+..-+++++++ .+++.|.|..=
T Consensus 2 ~iLgIETScd~tsvAl~~~~~~il~~~~~sq~~~~G~GvvP~~a~r~H~~~l~~~i~~~l~~a~~~~~did~Iavt~G-- 79 (345)
T PTZ00340 2 LALGIEGSANKLGVGIVTSDGEILSNVRETYITPPGTGFLPRETAQHHREHILSLVKEALEEAKITPSDISLICYTKG-- 79 (345)
T ss_pred eEEEEEccchhhEEEEEECCCcEEEEEEeeccccCCCCcCchHHHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecC--
Confidence 689999999999999997 3 233221 222211 11223344555554 46899999831
Q ss_pred CCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHH
Q 028759 122 WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVD 165 (204)
Q Consensus 122 ~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~ 165 (204)
-|.. .--+.-..||+.|...+ ++|++-++ +.+|+-
T Consensus 80 -PGl~-~~LrVG~~~Ak~LA~a~---~~PligV~----HlegHi 114 (345)
T PTZ00340 80 -PGMG-APLSVGAVVARTLSLLW---GKPLVGVN----HCVAHI 114 (345)
T ss_pred -CCcH-hhHHHHHHHHHHHHHHc---CCCEeecc----hHHHHH
Confidence 1222 23455578889998764 89998765 455553
No 166
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=28.86 E-value=1.4e+02 Score=26.93 Aligned_cols=65 Identities=11% Similarity=0.184 Sum_probs=37.1
Q ss_pred HHHHHHHH-HHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc------CCCcHHHHHHHHHHc
Q 028759 99 ELQLLEIA-QREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD------EHRTSAEAVDRMINM 170 (204)
Q Consensus 99 ~~~L~~li-~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD------ER~TT~eA~~~L~e~ 170 (204)
.+-+.+++ +..+++.||||.=..- |....- . -++.+.+.+. ++..|+.+| ++.||..-++.+.++
T Consensus 102 e~Fi~~~l~~~l~~~~iVvG~Df~F-G~~~~G--~-~~~L~~~~~~---~g~~v~~v~~~~~~~~~ISST~IR~~I~~G 173 (305)
T PRK05627 102 EEFIEDLLVKGLNAKHVVVGFDFRF-GKKRAG--D-FELLKEAGKE---FGFEVTIVPEVKEDGERVSSTAIRQALAEG 173 (305)
T ss_pred HHHHHHHHHhccCCCEEEECCCCCC-CCCCCC--C-HHHHHHHHHH---cCcEEEEeccEecCCCcCchHHHHHHHHcC
Confidence 34566644 4589999999964432 211110 0 1122222222 366666664 689999998888764
No 167
>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=28.77 E-value=2.6e+02 Score=21.21 Aligned_cols=57 Identities=14% Similarity=0.130 Sum_probs=24.6
Q ss_pred HHHHHHHHHHcCC--CEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 99 ELQLLEIAQREET--DEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 99 ~~~L~~li~e~~i--~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
.+++.+.+++..+ ..+++++|...+....+......+....+.+.....+..+.++|
T Consensus 66 ~~~~i~~i~~~~p~~~ii~~~~~p~~~~~~~~~~~~~n~~l~~~~~~~~~~~~~v~~vd 124 (157)
T cd01833 66 LRALIDQMRAANPDVKIIVATLIPTTDASGNARIAEYNAAIPGVVADLRTAGSPVVLVD 124 (157)
T ss_pred HHHHHHHHHHhCCCeEEEEEeCCCCCCcchhHHHHHHHHHHHHHHHHHhcCCCCEEEEe
Confidence 3444454555544 44556655433332223333333333333332211124577777
No 168
>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=28.75 E-value=1.4e+02 Score=28.00 Aligned_cols=51 Identities=22% Similarity=0.254 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEE
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYL 153 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~l 153 (204)
+....++.++++++++|.+|.| |--.-|..+.+|-.+- +.+++.+ ++|++.
T Consensus 66 eea~~~i~~mv~~~~pD~viaG-PaFnagrYG~acg~v~---~aV~e~~---~IP~vt 116 (349)
T PF07355_consen 66 EEALKKILEMVKKLKPDVVIAG-PAFNAGRYGVACGEVA---KAVQEKL---GIPVVT 116 (349)
T ss_pred HHHHHHHHHHHHhcCCCEEEEc-CCcCCchHHHHHHHHH---HHHHHhh---CCCEEE
Confidence 3456789999999999999999 5444688887776654 4455554 888653
No 169
>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=28.75 E-value=3.7e+02 Score=24.65 Aligned_cols=93 Identities=24% Similarity=0.246 Sum_probs=57.6
Q ss_pred EEEecCCCeEEEEEec--CC-e--e-eeeeeEEccchhHHHHHHHHHHHcCC-CEEEEeecCCCCCCCC----hhHHHHH
Q 028759 66 LGVDLGLSRTGLALSK--GF-C--V-RPLTVLKLRGEKLELQLLEIAQREET-DEFIIGLPKSWDGSET----PQSNKVR 134 (204)
Q Consensus 66 LalD~G~kRIGVAvsD--~~-~--A-~Pl~~i~~~~~~~~~~L~~li~e~~i-~~IVVGlPl~~dGt~~----~~~~~v~ 134 (204)
+|+|+|...+=+|..| +. . . .|+..++ ...++.+.|.+++++.++ +.+.|= |-|.-. ....=|+
T Consensus 1 ~G~DiGGA~~K~a~~~~~g~~~~v~~~~~plW~-~~~~L~~~l~~~~~~~~~~~~~avt----MTgELaD~f~~r~~GV~ 75 (318)
T TIGR03123 1 LGIDIGGANTKAAELDEDGRIKEVHQLYCPLWK-GNDKLAETLKEISQDLSSADNVAVT----MTGELADCFEDKAEGVE 75 (318)
T ss_pred CccccccceeeeEEecCCCceeEEEEecCcccC-CchHHHHHHHHHHHhcCccceEEEE----eehhhhhhhcCHHHHHH
Confidence 5899999999999776 22 1 1 2222232 234667788888887776 555554 455443 5667778
Q ss_pred HHHHHHHHhhccCCCcEEEE--cCCC-cHHHHHHH
Q 028759 135 SVAGRLAVRAAERGWRVYLL--DEHR-TSAEAVDR 166 (204)
Q Consensus 135 ~Fa~~L~~~~~~~~lpV~lv--DER~-TT~eA~~~ 166 (204)
..++.+++.| +-+++++ |=.+ |..+|.+.
T Consensus 76 ~i~~~~~~~~---~~~~~i~~s~GG~~s~~~a~~~ 107 (318)
T TIGR03123 76 FILAAVESAF---GSPVSVFASDGGFVSAEEALTN 107 (318)
T ss_pred HHHHHHHHhc---CCCeEEEecCCCCccHHHHHHh
Confidence 8888888886 3466555 4433 44455444
No 170
>PF01884 PcrB: PcrB family; InterPro: IPR008205 This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase, which is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) []. Some of the prokaryotic proteins in this family are related to pcrB. The Staphylococcus aureus chromosomal gene pcrA encodes a protein with significant similarity (40% identity) to two Escherichia coli helicases: the helicase II encoded by the uvrD gene and the Rep helicase. PcrB gene seems to belong to an operon containing at least one other gene, pcrBA, downstream from pcrB []. The PcrB proteins often contain an FMN binding site although the function of these proteins is still unknown.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 1VIZ_A 2F6X_B 2F6U_B 3VKD_A 3VKA_A 3VK5_B 3VKC_B 3VKB_B.
Probab=28.70 E-value=2.5e+02 Score=24.67 Aligned_cols=44 Identities=27% Similarity=0.347 Sum_probs=27.7
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
+.+.+.+.+...|.|+|| ||. ......+....+++. +++||++.
T Consensus 22 ~~~~~~~~~~gtDai~VG------GS~--~~~~~d~vv~~ik~~---~~lPvilf 65 (230)
T PF01884_consen 22 EEALEAACESGTDAIIVG------GSD--TGVTLDNVVALIKRV---TDLPVILF 65 (230)
T ss_dssp HHHHHHHHCTT-SEEEEE-------ST--HCHHHHHHHHHHHHH---SSS-EEEE
T ss_pred HHHHHHHHhcCCCEEEEC------CCC--CccchHHHHHHHHhc---CCCCEEEe
Confidence 444455588999999999 887 223345556666665 48999886
No 171
>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=28.61 E-value=2.2e+02 Score=20.28 Aligned_cols=49 Identities=27% Similarity=0.257 Sum_probs=33.3
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~ 166 (204)
..+.+++.+++++.||+|- .+ ......|+.+ ++.++..++ .+-.+|-+.
T Consensus 53 ~~~~~~l~~~~v~~vi~~~-------iG------~~~~~~l~~~----gI~v~~~~~-~~i~~vl~~ 101 (103)
T cd00851 53 GKAAEFLADEGVDVVIVGG-------IG------PRALNKLRNA----GIKVYKGAE-GTVEEAIEA 101 (103)
T ss_pred hHHHHHHHHcCCCEEEeCC-------CC------cCHHHHHHHC----CCEEEEcCC-CCHHHHHHh
Confidence 5677777779999999982 22 2334456654 899998887 566665443
No 172
>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=28.53 E-value=2.4e+02 Score=24.41 Aligned_cols=92 Identities=15% Similarity=0.204 Sum_probs=49.6
Q ss_pred CCeEEEEEecCC---e------------eeeeeeEEcc--c-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHH
Q 028759 72 LSRTGLALSKGF---C------------VRPLTVLKLR--G-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKV 133 (204)
Q Consensus 72 ~kRIGVAvsD~~---~------------A~Pl~~i~~~--~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v 133 (204)
|+.|||-+.+-. + ...+.++-.. + .+.. +..+.+.++++|+||+- +...+ .
T Consensus 1 t~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~~~~~e-~~i~~l~~~~vDGiI~~-s~~~~---~------ 69 (279)
T PF00532_consen 1 TKTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGDDEEKE-EYIELLLQRRVDGIILA-SSEND---D------ 69 (279)
T ss_dssp -CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETTTHHHH-HHHHHHHHTTSSEEEEE-SSSCT---C------
T ss_pred CCEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCCchHHH-HHHHHHHhcCCCEEEEe-cccCC---h------
Confidence 578999998831 1 2344443321 2 2233 55566788999999998 22211 1
Q ss_pred HHHHHHHHHhhc---------cC-CCcEEEEcCCCcHHHHHHHHHHcCCCc
Q 028759 134 RSVAGRLAVRAA---------ER-GWRVYLLDEHRTSAEAVDRMINMGLSK 174 (204)
Q Consensus 134 ~~Fa~~L~~~~~---------~~-~lpV~lvDER~TT~eA~~~L~e~G~~r 174 (204)
..+....+..+| .. ++|.+..|.+-...+|.+.|.+.|.++
T Consensus 70 ~~l~~~~~~~iPvV~~~~~~~~~~~~~~V~~D~~~a~~~a~~~Li~~Gh~~ 120 (279)
T PF00532_consen 70 EELRRLIKSGIPVVLIDRYIDNPEGVPSVYIDNYEAGYEATEYLIKKGHRR 120 (279)
T ss_dssp HHHHHHHHTTSEEEEESS-SCTTCTSCEEEEEHHHHHHHHHHHHHHTTCCS
T ss_pred HHHHHHHHcCCCEEEEEeccCCcccCCEEEEcchHHHHHHHHHHHhcccCC
Confidence 122222221111 01 345555555556678888888888765
No 173
>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=28.47 E-value=1.5e+02 Score=27.35 Aligned_cols=50 Identities=18% Similarity=0.210 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
-.+.|.++++++++|+||.=.-..-+ +..-......+.|++ .|+|+..+|
T Consensus 309 R~~~i~~lvke~~aDGVI~~~~~~C~----~~~~e~~~lk~~l~e----~GIP~L~id 358 (380)
T TIGR02263 309 KGKYLLDQVRKNAAEGVIFAAPSFCD----PALLERPMLAARCKE----HGIPQIAFK 358 (380)
T ss_pred HHHHHHHHHHHhCCCEEEEhHhhcCC----hhhhhHHHHHHHHHH----CCCCEEEEE
Confidence 45789999999999999998544322 222222333344544 399988885
No 174
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=28.32 E-value=1.7e+02 Score=26.98 Aligned_cols=53 Identities=17% Similarity=0.204 Sum_probs=37.1
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCc
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~T 159 (204)
.+.+...+.+ +++.|+|..|-|+.|+.-+ ...+++|++.+.. --+..+||-|-
T Consensus 135 ~~~~~~~~~~-~~~lv~i~nPNNPTG~~~~-~~~l~~l~~~~~~------~~~vVvDEAY~ 187 (356)
T COG0079 135 LDAILAAIRD-KTKLVFLCNPNNPTGTLLP-REELRALLEALPE------GGLVVIDEAYI 187 (356)
T ss_pred HHHHHHhhhc-CCCEEEEeCCCCCCCCCCC-HHHHHHHHHhCCC------CcEEEEeCchh
Confidence 3556666665 8999999999999998775 3444555555432 24888999763
No 175
>PRK14878 UGMP family protein; Provisional
Probab=28.32 E-value=3.6e+02 Score=24.33 Aligned_cols=85 Identities=14% Similarity=0.123 Sum_probs=52.5
Q ss_pred EEEecCCCeEEEEEecC--CeeeeeeeEEc-------------cchhHHHHHHHHHHH-----cCCCEEEEeecCCCCCC
Q 028759 66 LGVDLGLSRTGLALSKG--FCVRPLTVLKL-------------RGEKLELQLLEIAQR-----EETDEFIIGLPKSWDGS 125 (204)
Q Consensus 66 LalD~G~kRIGVAvsD~--~~A~Pl~~i~~-------------~~~~~~~~L~~li~e-----~~i~~IVVGlPl~~dGt 125 (204)
||||-=..-+++|+.++ +.+.-..+..+ +.+.+...+++++++ .++|.|.|+.-. |.
T Consensus 1 l~iets~~~~s~al~~~~~i~~~~~~~~~~~~gg~~p~~~~~~h~~~l~~~i~~~l~~a~~~~~did~Iavt~gP---G~ 77 (323)
T PRK14878 1 LGIESTAHTLGVGIVKEDKVLANVRDTYVPEKGGIHPREAAQHHAEVAPELLRKALEKAGISIEDIDAVAVSQGP---GL 77 (323)
T ss_pred CEEecCCcccEEEEEECCEEEEEEEEecccCcCCcCccHHHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecCC---Cc
Confidence 57787778889999874 23322222211 011233556666666 467999999522 33
Q ss_pred CChhHHHHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759 126 ETPQSNKVRSVAGRLAVRAAERGWRVYLLDEH 157 (204)
Q Consensus 126 ~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER 157 (204)
.+ .-+....||+.|+..+ ++|++.++..
T Consensus 78 ~~-~lrvg~~~Ak~la~~~---~~p~~~v~h~ 105 (323)
T PRK14878 78 GP-ALRVGATAARALALKY---NKPLVPVNHC 105 (323)
T ss_pred cc-chHHHHHHHHHHHHHh---CCCccccchH
Confidence 33 2445577899998775 8899988653
No 176
>cd06281 PBP1_LacI_like_5 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=27.87 E-value=2.3e+02 Score=23.29 Aligned_cols=14 Identities=21% Similarity=0.313 Sum_probs=9.1
Q ss_pred HHHHHcCCCEEEEe
Q 028759 104 EIAQREETDEFIIG 117 (204)
Q Consensus 104 ~li~e~~i~~IVVG 117 (204)
+.+.++++++||+-
T Consensus 49 ~~l~~~~vdgii~~ 62 (269)
T cd06281 49 RSFEQRRMDGIIIA 62 (269)
T ss_pred HHHHHcCCCEEEEe
Confidence 33555778888773
No 177
>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=27.41 E-value=2.1e+02 Score=23.61 Aligned_cols=45 Identities=13% Similarity=0.148 Sum_probs=26.1
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
...+.+.+..+++|+|||. |.+.+. +....+.+.+. ++||+++|-
T Consensus 49 ~~~~~~~l~~~~vDgiii~-~~~~~~--------~~~~i~~~~~~----gIpvV~~d~ 93 (274)
T cd06311 49 QNAQQDLLINRKIDALVIL-PFESAP--------LTQPVAKAKKA----GIFVVVVDR 93 (274)
T ss_pred HHHHHHHHHHcCCCEEEEe-CCCchh--------hHHHHHHHHHC----CCeEEEEcC
Confidence 3455555566899999996 432211 12223344432 899998873
No 178
>cd01016 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=27.29 E-value=2.5e+02 Score=24.53 Aligned_cols=43 Identities=2% Similarity=0.019 Sum_probs=35.3
Q ss_pred CCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcC
Q 028759 125 SETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMG 171 (204)
Q Consensus 125 t~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G 171 (204)
...+..+.+.++.+.+++. +++++++++-+++..|+....+.|
T Consensus 191 ~~eps~~~l~~l~~~ik~~----~v~~if~e~~~~~~~~~~l~~~~~ 233 (276)
T cd01016 191 DSEAGLRDINELVDLIVER----KIKAIFVESSVNQKSIEALQDAVK 233 (276)
T ss_pred ccCCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHHh
Confidence 3445688889999999875 899999999999999988866543
No 179
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=27.04 E-value=55 Score=32.15 Aligned_cols=19 Identities=32% Similarity=0.616 Sum_probs=16.9
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
+.++|||+|+..+-+|+.+
T Consensus 2 ~~viGIDlGTt~s~va~~~ 20 (627)
T PRK00290 2 GKIIGIDLGTTNSCVAVME 20 (627)
T ss_pred CcEEEEEeCcccEEEEEEE
Confidence 3589999999999999986
No 180
>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=26.93 E-value=2.5e+02 Score=20.90 Aligned_cols=58 Identities=14% Similarity=0.044 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHH
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAE 162 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~e 162 (204)
..+.++.+.+++..++.|||--+-...-. ...+..|.+.|... +++|+.+++.+.+..
T Consensus 52 ~~~~~ll~~~~~~~~d~ivv~~~~Rl~R~----~~~~~~~~~~l~~~----gi~l~~~~~~~~~~~ 109 (137)
T cd00338 52 PGLQRLLADVKAGKIDVVLVEKLDRLSRN----LVDLLELLELLEAH----GVRVVTADGEIDLDS 109 (137)
T ss_pred HHHHHHHHHHHcCCCCEEEEEecchhhCC----HHHHHHHHHHHHHC----CCEEEEecCCcccCC
Confidence 34567777777789999999976554222 22445566666653 899999998776543
No 181
>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=26.90 E-value=2.2e+02 Score=22.55 Aligned_cols=51 Identities=18% Similarity=0.178 Sum_probs=29.2
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
..+.+.+++.++..|++|.|..... .....+..+.+.+++..... .+.++|
T Consensus 98 ~~lv~~~~~~~~~vili~~pp~~~~---~~~~~~~~~~~~~~~~a~~~--~~~~id 148 (200)
T cd01829 98 DELLNVARAKGVPVIWVGLPAMRSP---KLSADMVYLNSLYREEVAKA--GGEFVD 148 (200)
T ss_pred HHHHHHHHhCCCcEEEEcCCCCCCh---hHhHHHHHHHHHHHHHHHHc--CCEEEE
Confidence 3444445567888999998764322 23345555655555544322 467776
No 182
>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=26.72 E-value=2.1e+02 Score=23.36 Aligned_cols=17 Identities=24% Similarity=0.368 Sum_probs=8.9
Q ss_pred HHHHHHHHHcCCCEEEE
Q 028759 100 LQLLEIAQREETDEFII 116 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVV 116 (204)
..+.+.+..+++++||+
T Consensus 46 ~~~~~~l~~~~vdgiii 62 (270)
T cd01545 46 ERVRALLQRSRVDGVIL 62 (270)
T ss_pred HHHHHHHHHCCCCEEEE
Confidence 34444444556666555
No 183
>PRK10550 tRNA-dihydrouridine synthase C; Provisional
Probab=26.62 E-value=3.1e+02 Score=24.81 Aligned_cols=68 Identities=18% Similarity=0.165 Sum_probs=46.7
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMG 171 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G 171 (204)
..++.+++++.+++.|.|--=...+|..++.+. -+.+.++++.. ++||+..--=.|..+|++.+.+.|
T Consensus 150 ~~~~a~~l~~~Gvd~i~Vh~Rt~~~~y~g~~~~--~~~i~~ik~~~---~iPVi~nGdI~t~~da~~~l~~~g 217 (312)
T PRK10550 150 KFEIADAVQQAGATELVVHGRTKEDGYRAEHIN--WQAIGEIRQRL---TIPVIANGEIWDWQSAQQCMAITG 217 (312)
T ss_pred HHHHHHHHHhcCCCEEEECCCCCccCCCCCccc--HHHHHHHHhhc---CCcEEEeCCcCCHHHHHHHHhccC
Confidence 457888888999999999522222333332211 14566777664 899999998889999999886644
No 184
>PRK10812 putative DNAse; Provisional
Probab=26.62 E-value=4.1e+02 Score=23.21 Aligned_cols=72 Identities=13% Similarity=0.080 Sum_probs=45.5
Q ss_pred hHHHHHHHHHHHcCCCEE-EEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCC
Q 028759 97 KLELQLLEIAQREETDEF-IIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGL 172 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~I-VVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~ 172 (204)
...+.|.+++.+.++..| =||+.+..+. .....+.+-|...|+-. .+.++||.+.- |-...+.-+.|++.+.
T Consensus 75 ~~~~~l~~~~~~~~vvaIGEiGLD~~~~~--~~~~~Q~~vf~~ql~lA-~e~~~Pv~iH~-r~a~~~~l~iL~~~~~ 147 (265)
T PRK10812 75 YDVEELRRLAAEEGVVAMGETGLDYYYTP--ETKVRQQESFRHHIQIG-RELNKPVIVHT-RDARADTLAILREEKV 147 (265)
T ss_pred hHHHHHHHHhcCCCEEEEEeeecCcCCCC--CCHHHHHHHHHHHHHHH-HHhCCCeEEEe-eCchHHHHHHHHhhcC
Confidence 345677777765566666 6899876432 23445556676666643 23599998884 4466677777876544
No 185
>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=26.43 E-value=2.9e+02 Score=20.96 Aligned_cols=94 Identities=12% Similarity=0.017 Sum_probs=58.1
Q ss_pred eeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHH
Q 028759 85 VRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV 164 (204)
Q Consensus 85 A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~ 164 (204)
+.+++++........+.+.+.+.+++++.|++. ++.......++++++.|++... .+++ .++==+..+. -.
T Consensus 25 ~~G~~vi~lG~~vp~e~~~~~a~~~~~d~V~iS------~~~~~~~~~~~~~~~~L~~~~~-~~i~-i~~GG~~~~~-~~ 95 (122)
T cd02071 25 DAGFEVIYTGLRQTPEEIVEAAIQEDVDVIGLS------SLSGGHMTLFPEVIELLRELGA-GDIL-VVGGGIIPPE-DY 95 (122)
T ss_pred HCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEc------ccchhhHHHHHHHHHHHHhcCC-CCCE-EEEECCCCHH-HH
Confidence 456666654333345678888889999999886 4445567778899999998632 1334 3444333333 24
Q ss_pred HHHHHcCCCccc-cCCCCcHHHHH
Q 028759 165 DRMINMGLSKSA-RQTKTDAYAAV 187 (204)
Q Consensus 165 ~~L~e~G~~rkk-rK~~vD~~AA~ 187 (204)
+.|.+.|+..-- .+...+.+++.
T Consensus 96 ~~~~~~G~d~~~~~~~~~~~~~~~ 119 (122)
T cd02071 96 ELLKEMGVAEIFGPGTSIEEIIDK 119 (122)
T ss_pred HHHHHCCCCEEECCCCCHHHHHHH
Confidence 677788875442 23445555543
No 186
>PRK07667 uridine kinase; Provisional
Probab=26.32 E-value=2.4e+02 Score=23.06 Aligned_cols=48 Identities=21% Similarity=0.474 Sum_probs=31.0
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCC-CCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDG-SETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dG-t~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
+.|.+.+.+++...+|||+ +| .-+..+-.++.+++.|.+. ++++..++
T Consensus 4 ~~~~~~~~~~~~~~~iIgI----~G~~gsGKStla~~L~~~l~~~----~~~~~~i~ 52 (193)
T PRK07667 4 NELINIMKKHKENRFILGI----DGLSRSGKTTFVANLKENMKQE----GIPFHIFH 52 (193)
T ss_pred HHHHHHHHhcCCCCEEEEE----ECCCCCCHHHHHHHHHHHHHhC----CCcEEEEE
Confidence 4566778888899999997 44 3344555566666666542 56644443
No 187
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=26.16 E-value=2.9e+02 Score=20.90 Aligned_cols=71 Identities=14% Similarity=0.109 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHc--CCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCC
Q 028759 98 LELQLLEIAQRE--ETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGL 172 (204)
Q Consensus 98 ~~~~L~~li~e~--~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~ 172 (204)
..+++..+++.- .|.+-|+-.....|...--..-++.+.++.++. .+..++.+|..+|..+.+..=+..|+
T Consensus 9 ~l~El~~L~~t~g~~vv~~~~q~~~~~~p~~~iG~GK~eei~~~~~~----~~~d~vvfd~~Lsp~Q~rNLe~~~~~ 81 (95)
T PF13167_consen 9 SLEELEELAETAGYEVVGTVVQKRRKPDPKTYIGSGKVEEIKELIEE----LDADLVVFDNELSPSQQRNLEKALGV 81 (95)
T ss_pred HHHHHHHHHHHCCCeEEEEEEecCCCCCcceeechhHHHHHHHHHhh----cCCCEEEECCCCCHHHHHHHHHHHCC
Confidence 345666666643 333334443222222221112233334333332 37788888888888888776555543
No 188
>COG1924 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]
Probab=25.96 E-value=1.3e+02 Score=28.63 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=21.6
Q ss_pred cCCCCCCceEEEEecCCCeEEEEEec
Q 028759 56 KDSLWRGGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 56 ~~~~~~~g~iLalD~G~kRIGVAvsD 81 (204)
.-+.+.++..||||.|...+=.++-+
T Consensus 128 ~~~~~~~~~~LGID~GSTtTK~VLm~ 153 (396)
T COG1924 128 KLREYQGMYTLGIDSGSTTTKAVLME 153 (396)
T ss_pred hhhhhcCcEEEEEecCCcceeEEEEe
Confidence 33567789999999999999888777
No 189
>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=25.86 E-value=2.7e+02 Score=23.65 Aligned_cols=46 Identities=11% Similarity=0.114 Sum_probs=32.2
Q ss_pred CCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCC
Q 028759 124 GSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173 (204)
Q Consensus 124 Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~ 173 (204)
....+..+.+.++.+.+++. ++++++.+...++..++..-++.|++
T Consensus 179 ~~~~ps~~~l~~l~~~ik~~----~v~~i~~e~~~~~~~~~~la~~~g~~ 224 (256)
T PF01297_consen 179 PGEEPSPKDLAELIKLIKEN----KVKCIFTEPQFSSKLAEALAKETGVK 224 (256)
T ss_dssp SSSSS-HHHHHHHHHHHHHT----T-SEEEEETTS-THHHHHHHHCCT-E
T ss_pred cccCCCHHHHHHHHHHhhhc----CCcEEEecCCCChHHHHHHHHHcCCc
Confidence 34556778888888888875 88899998888888777776666643
No 190
>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=25.82 E-value=3e+02 Score=20.89 Aligned_cols=55 Identities=22% Similarity=0.315 Sum_probs=33.1
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
.+.|..++....|+.+||| -|.... .--.+..+.|++. ++.++.. .|.+|-+.|-
T Consensus 41 ~~~l~~~~~~~~peiliiG-----TG~~~~--~~~~~~~~~l~~~----gI~vE~m----~T~aAcrTyN 95 (109)
T cd00248 41 PEALLPLLAEDRPDILLIG-----TGAEIA--FLPRALRAALRAA----GIGVEVM----STGAACRTYN 95 (109)
T ss_pred HHHHHHHHhhCCCCEEEEc-----CCCCCC--cCCHHHHHHHHHc----CCeEEEe----CcHHHHHHHH
Confidence 3566666654359999999 465442 1113344455543 7888764 5777766653
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=25.81 E-value=3.1e+02 Score=21.12 Aligned_cols=22 Identities=14% Similarity=-0.052 Sum_probs=12.5
Q ss_pred HHHHHHHHHcCCCEEEEeecCCC
Q 028759 100 LQLLEIAQREETDEFIIGLPKSW 122 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~ 122 (204)
++|.+++ ..+++.||+-+-.|.
T Consensus 39 ~~l~~~~-~~~pd~vvl~~G~ND 60 (169)
T cd01828 39 ARLDEDV-ALQPKAIFIMIGIND 60 (169)
T ss_pred HHHHHHh-ccCCCEEEEEeeccC
Confidence 4555555 456666666655543
No 192
>PTZ00107 hexokinase; Provisional
Probab=25.80 E-value=1.5e+02 Score=28.52 Aligned_cols=20 Identities=15% Similarity=0.179 Sum_probs=18.3
Q ss_pred CceEEEEecCCCeEEEEEec
Q 028759 62 GGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD 81 (204)
.|.+||||+|....=|+..+
T Consensus 73 ~G~fLAlDlGGTN~RV~~V~ 92 (464)
T PTZ00107 73 KGVYYAIDFGGTNFRAVRVS 92 (464)
T ss_pred cceEEEEecCCceEEEEEEE
Confidence 48899999999999999887
No 193
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=25.73 E-value=2.3e+02 Score=31.07 Aligned_cols=106 Identities=11% Similarity=0.083 Sum_probs=61.6
Q ss_pred CcccccccccchhhhcccccccccCCCCCC--ceEEEEecC--------CCeEEEEEecC---Cee---------eeeee
Q 028759 33 NFGQRIGALSSVEEFLPNATRRKKDSLWRG--GFSLGVDLG--------LSRTGLALSKG---FCV---------RPLTV 90 (204)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--g~iLalD~G--------~kRIGVAvsD~---~~A---------~Pl~~ 90 (204)
..++. -.++|+|..-.....-..||..-. .-+++++=- ..++||+|.|. ... ....+
T Consensus 653 ~~~~~-Lt~lsiElha~sr~dl~PDP~~D~V~~l~~~vq~dtp~pd~~si~~~gv~Vv~~~~~ds~~~t~~~~~~~~~~V 731 (1488)
T KOG0968|consen 653 EQTQL-LTILSIELHATSRGDLEPDPVFDSVASLFLCVQEDTPMPDADSIVSVGVIVVDKVCPDSHVQTTTLGGIYGCRV 731 (1488)
T ss_pred cccce-eeeeeeeccccccCCCCCCcccccchhhhhhhccCCCCCcccceeeeeEEEEeccCccccccccccCCcCCceE
Confidence 33443 345688855333333333433322 223444433 77999999992 111 23334
Q ss_pred EEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHH
Q 028759 91 LKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLA 141 (204)
Q Consensus 91 i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~ 141 (204)
..... .++++++.+++..|.|| |++|+=.+ +++-|-..+++..+.-.|-
T Consensus 732 ~~~~sE~elf~ev~~~i~q~DPD-Il~GyEi~-~~SWGyl~eR~~~l~~di~ 781 (1488)
T KOG0968|consen 732 VVMESELELFEEVAKLIVQYDPD-ILLGYEIH-NLSWGYLIERAKLLGIDIS 781 (1488)
T ss_pred EEehhHHHHHHHHHHHHHhcCcc-eeeeeeec-ccchHHHHHHHHHhcchHH
Confidence 43333 35789999999999998 67899877 4777766666555444443
No 194
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=25.61 E-value=70 Score=31.56 Aligned_cols=19 Identities=26% Similarity=0.546 Sum_probs=17.2
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
..++|||+|+..+-||+.+
T Consensus 19 ~~~iGIDlGTt~s~va~~~ 37 (616)
T PRK05183 19 RLAVGIDLGTTNSLVATVR 37 (616)
T ss_pred CeEEEEEeccccEEEEEEE
Confidence 4799999999999999975
No 195
>PTZ00288 glucokinase 1; Provisional
Probab=25.31 E-value=3.8e+02 Score=25.34 Aligned_cols=29 Identities=24% Similarity=0.550 Sum_probs=23.6
Q ss_pred cccCCCC-CCceEEEEecCCCeEEEEEecC
Q 028759 54 RKKDSLW-RGGFSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 54 ~~~~~~~-~~g~iLalD~G~kRIGVAvsD~ 82 (204)
-|+|-+| ..+.++|.|+|...+=+|+++.
T Consensus 16 ~~~~~~~~~~~~~~~~DiGgt~~R~~~~~~ 45 (405)
T PTZ00288 16 LKTDASWSSGPIFVGCDVGGTNARVGFARE 45 (405)
T ss_pred hccCcccccCCeEEEEEecCCceEEEEEec
Confidence 3577778 4567999999999999999973
No 196
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=25.27 E-value=1.7e+02 Score=28.31 Aligned_cols=50 Identities=18% Similarity=0.310 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEE
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYL 153 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~l 153 (204)
+..+.+.++++++++|.+|.| |--.-|..+.+|-.+-+ .+++.+ ++|++.
T Consensus 63 ea~~~i~~mv~k~~pDv~iaG-PaFNagrYG~acg~va~---aV~e~~---~IP~vt 112 (431)
T TIGR01917 63 EAKAKVLEMIKGANPDIFIAG-PAFNAGRYGMAAGAITK---AVQDEL---GIKAFT 112 (431)
T ss_pred HHHHHHHHHHHhcCCCEEEEc-CccCCccHHHHHHHHHH---HHHHhh---CCCeEE
Confidence 345789999999999999999 54446888887776644 345443 788654
No 197
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=25.10 E-value=4.1e+02 Score=29.12 Aligned_cols=98 Identities=14% Similarity=0.104 Sum_probs=53.3
Q ss_pred eEEEEecCCCe----EEEEEec-CCeeeeeeeEE----c---c----chhHHHHHHHHHHHcCCCEEEEeecCCCCCCCC
Q 028759 64 FSLGVDLGLSR----TGLALSK-GFCVRPLTVLK----L---R----GEKLELQLLEIAQREETDEFIIGLPKSWDGSET 127 (204)
Q Consensus 64 ~iLalD~G~kR----IGVAvsD-~~~A~Pl~~i~----~---~----~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~ 127 (204)
++||+=+|+.+ ++|-+.. |.+.--|.... . + ..++.+.++++|+..+|..|.|+-+ +-...
T Consensus 604 rvl~~~~~~~~~~a~f~v~vn~~Gd~vD~lrl~~~~kr~~~~n~~~r~~k~~d~f~kFI~~~kP~vi~v~g~---~r~~q 680 (1299)
T KOG1856|consen 604 RVLAVCGGTERSDAIFCVLVNFEGDLVDYLRLVDITKRKTLVNDEERKKKFQDLFKKFIEKKKPHVIGVSGE---NRLKQ 680 (1299)
T ss_pred eEEEeccCCCCCceEEEEEEcCCCceeeeeeccchhhhhhccchhhhhhhHHHHHHHHHHhcCCCEEEeeCC---CchhH
Confidence 88888888754 4444443 32222222111 0 1 1234567899999999999999844 11122
Q ss_pred hhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHH
Q 028759 128 PQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMIN 169 (204)
Q Consensus 128 ~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e 169 (204)
.....|+.....|...=..+.+||+++|+ |+...|.+
T Consensus 681 ~~~~~I~~~v~el~~~~~~~~ipv~~vd~-----ela~lY~n 717 (1299)
T KOG1856|consen 681 KIYEAIRQLVHELLISDQGHPIPVIYVDN-----ELARLYQN 717 (1299)
T ss_pred HHHHHHHHHHHhccccccCCCcceeeccc-----HHHHHHHh
Confidence 33344444433333220015789999997 34455554
No 198
>PRK13411 molecular chaperone DnaK; Provisional
Probab=25.06 E-value=67 Score=31.94 Aligned_cols=19 Identities=32% Similarity=0.618 Sum_probs=17.0
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
+.++|||+|+..+=||+.+
T Consensus 2 ~~viGIDlGTt~s~va~~~ 20 (653)
T PRK13411 2 GKVIGIDLGTTNSCVAVLE 20 (653)
T ss_pred CcEEEEEeCcccEEEEEEE
Confidence 3699999999999999976
No 199
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=25.03 E-value=1.7e+02 Score=28.26 Aligned_cols=62 Identities=19% Similarity=0.208 Sum_probs=42.4
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEE--EcCCCcHHHHHHHHHH
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYL--LDEHRTSAEAVDRMIN 169 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~l--vDER~TT~eA~~~L~e 169 (204)
+..+.+.++++++++|.+|.| |--.-|..+.+|-.+-+ .+++.+ ++|++. +-| . .+-+.|+.
T Consensus 63 ea~~~i~~mv~k~~pDv~iaG-PaFNagrYG~acg~va~---aV~e~~---~IP~vt~My~E-N---pgvd~yk~ 126 (431)
T TIGR01918 63 EAVARVLEMLKDKEPDIFIAG-PAFNAGRYGVACGEICK---VVQDKL---NVPAVTSMYVE-N---PGVDMFKK 126 (431)
T ss_pred HHHHHHHHHHHhcCCCEEEEc-CccCCccHHHHHHHHHH---HHHHhh---CCCeEEEeccc-C---hHHHHHhh
Confidence 445789999999999999999 54446888887776644 345443 888654 345 3 34445544
No 200
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=24.83 E-value=1.9e+02 Score=28.33 Aligned_cols=43 Identities=16% Similarity=0.202 Sum_probs=36.4
Q ss_pred CCCChhHHHHHHHHHHHHHhhccCCCcEEEEc-CCCcHHHHHHHHHH
Q 028759 124 GSETPQSNKVRSVAGRLAVRAAERGWRVYLLD-EHRTSAEAVDRMIN 169 (204)
Q Consensus 124 Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD-ER~TT~eA~~~L~e 169 (204)
.+..|.+...++.++.|++. +++||.-+| +.++...-...|.+
T Consensus 188 Ns~~P~s~et~~L~~eL~ek---Y~vpVlpvnc~~l~~~DI~~Il~~ 231 (492)
T PF09547_consen 188 NSTKPYSEETQELAEELEEK---YDVPVLPVNCEQLREEDITRILEE 231 (492)
T ss_pred eCCCCCCHHHHHHHHHHHHH---hCCcEEEeehHHcCHHHHHHHHHH
Confidence 35667778889999999998 499999999 99999998888765
No 201
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=24.57 E-value=2.1e+02 Score=25.00 Aligned_cols=53 Identities=13% Similarity=0.137 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEH 157 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER 157 (204)
..-++.+..++.+++.+++.-|.....+ .+.+.+|-+.+.+.. ++||+++|--
T Consensus 81 ~~i~~a~~a~~~Gad~v~v~pP~y~~~~----~~~i~~~~~~i~~~~---~~pi~lYn~P 133 (285)
T TIGR00674 81 EAISLTKFAEDVGADGFLVVTPYYNKPT----QEGLYQHFKAIAEEV---DLPIILYNVP 133 (285)
T ss_pred HHHHHHHHHHHcCCCEEEEcCCcCCCCC----HHHHHHHHHHHHhcC---CCCEEEEECc
Confidence 3346777788899999999999865432 245566666776653 8999999853
No 202
>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=24.49 E-value=2.4e+02 Score=22.93 Aligned_cols=19 Identities=16% Similarity=0.078 Sum_probs=14.2
Q ss_pred HHHHHHHHHHcCCCEEEEe
Q 028759 99 ELQLLEIAQREETDEFIIG 117 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVG 117 (204)
.+.+.+++.++++++||+.
T Consensus 48 ~~~~~~~~~~~~vdgiii~ 66 (268)
T cd06271 48 LEVYRRLVESGLVDGVIIS 66 (268)
T ss_pred HHHHHHHHHcCCCCEEEEe
Confidence 4566777777889998885
No 203
>PRK08760 replicative DNA helicase; Provisional
Probab=24.48 E-value=2.4e+02 Score=27.03 Aligned_cols=57 Identities=12% Similarity=0.155 Sum_probs=36.9
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCC--CCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWD--GSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~d--Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
...++.+..+++++.|||=+--.|. |........+....+.|+....+.++||+..=
T Consensus 328 ~~~~r~l~~~~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~ls 386 (476)
T PRK08760 328 RSKCRRLKREHDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELNVPVIALS 386 (476)
T ss_pred HHHHHHHHHhcCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhCCEEEEee
Confidence 3456666677889999998754453 22223445566667777665555689988764
No 204
>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=24.41 E-value=3.9e+02 Score=25.54 Aligned_cols=68 Identities=18% Similarity=0.195 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCC-CcEEEE-cCCCc----HHHHHHHHHH
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERG-WRVYLL-DEHRT----SAEAVDRMIN 169 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~-lpV~lv-DER~T----T~eA~~~L~e 169 (204)
+...++|+.+++++++..+.+. |++.+.--+.+.+|.+.|.++ + +.+.+. .-|.+ +.+--+.|++
T Consensus 225 e~Vv~Ei~~l~~~~gv~~~~~~-----Dd~f~~~~~~~~~l~~~l~~~----~~l~i~w~~~~r~~~i~~d~ell~~l~~ 295 (497)
T TIGR02026 225 KKFVDEIEWLVRTHGVGFFILA-----DEEPTINRKKFQEFCEEIIAR----NPISVTWGINTRVTDIVRDADILHLYRR 295 (497)
T ss_pred HHHHHHHHHHHHHcCCCEEEEE-----ecccccCHHHHHHHHHHHHhc----CCCCeEEEEecccccccCCHHHHHHHHH
Confidence 4567889999999999988876 554443345677888888765 3 555442 22322 3344556777
Q ss_pred cCC
Q 028759 170 MGL 172 (204)
Q Consensus 170 ~G~ 172 (204)
+|.
T Consensus 296 aG~ 298 (497)
T TIGR02026 296 AGL 298 (497)
T ss_pred hCC
Confidence 765
No 205
>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=24.12 E-value=3.6e+02 Score=24.57 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=17.9
Q ss_pred ceEEEEecCCCeEEEEEecC
Q 028759 63 GFSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD~ 82 (204)
+..+|||.|+..+=+++-|.
T Consensus 32 m~~~GIDiGStt~K~Vlld~ 51 (293)
T TIGR03192 32 IITCGIDVGSVSSQAVLVCD 51 (293)
T ss_pred cEEEEEEeCchhEEEEEEeC
Confidence 47899999999999999984
No 206
>COG0443 DnaK Molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=24.09 E-value=73 Score=31.38 Aligned_cols=19 Identities=26% Similarity=0.536 Sum_probs=18.0
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
..++|||+|+-.+=||+.+
T Consensus 5 ~~~iGIDlGTTNS~vA~~~ 23 (579)
T COG0443 5 KKAIGIDLGTTNSVVAVMR 23 (579)
T ss_pred ceEEEEEcCCCcEEEEEEe
Confidence 5799999999999999999
No 207
>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=24.05 E-value=4.2e+02 Score=23.01 Aligned_cols=64 Identities=14% Similarity=0.072 Sum_probs=39.0
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHH----HHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNK----VRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMIN 169 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~----v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e 169 (204)
..++.+.+.+.++++++++ |+.|+.... =+++++...+..+ .++||+.-=-..||.+|-+..+.
T Consensus 24 ~~~~i~~l~~~Gv~gl~~~------GstGE~~~Lt~~Er~~l~~~~~~~~~-~~~~vi~gv~~~st~~~i~~a~~ 91 (289)
T PF00701_consen 24 LKRLIDFLIEAGVDGLVVL------GSTGEFYSLTDEERKELLEIVVEAAA-GRVPVIAGVGANSTEEAIELARH 91 (289)
T ss_dssp HHHHHHHHHHTTSSEEEES------STTTTGGGS-HHHHHHHHHHHHHHHT-TSSEEEEEEESSSHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCEEEEC------CCCcccccCCHHHHHHHHHHHHHHcc-CceEEEecCcchhHHHHHHHHHH
Confidence 3445555557899999998 655543221 1223333333222 36888888788899999888654
No 208
>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=23.83 E-value=2.7e+02 Score=23.40 Aligned_cols=47 Identities=15% Similarity=0.202 Sum_probs=30.2
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEE
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLL 154 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lv 154 (204)
...+.+.+.+.++|.||+. |.-.........+.+.+.+. .+.||+++
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 4556666667889988887 54443233445666666653 26788887
No 209
>PRK05595 replicative DNA helicase; Provisional
Probab=23.70 E-value=2.4e+02 Score=26.45 Aligned_cols=57 Identities=14% Similarity=0.175 Sum_probs=38.4
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCC--ChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSE--TPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~--~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
...++++..+++++.|||=+=-.|.++. ......+....+.|+....+.++||...-
T Consensus 300 ~~~~r~~~~~~~~~~vvIDylql~~~~~~~~~r~~~v~~is~~LK~lAke~~i~vi~ls 358 (444)
T PRK05595 300 RSKCRRLKIEHGIDMILIDYLQLMSGGKGSESRQQEVSEISRSIKALAKEMECPVIALS 358 (444)
T ss_pred HHHHHHHHHhcCCCEEEEeHHHhccCCCCCccHHHHHHHHHHHHHHHHHHhCCeEEEee
Confidence 3456666677889999997765555332 23445667777777766555699998874
No 210
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=23.68 E-value=2.8e+02 Score=24.18 Aligned_cols=52 Identities=13% Similarity=0.132 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
...++.+..++.+++.+++.-|....- + .+.+.+|-+.+.+.. ++||+++|-
T Consensus 84 ~~i~~a~~a~~~G~d~v~~~pP~~~~~--~--~~~i~~~~~~ia~~~---~~pv~lYn~ 135 (292)
T PRK03170 84 EAIELTKFAEKAGADGALVVTPYYNKP--T--QEGLYQHFKAIAEAT---DLPIILYNV 135 (292)
T ss_pred HHHHHHHHHHHcCCCEEEECCCcCCCC--C--HHHHHHHHHHHHhcC---CCCEEEEEC
Confidence 445677778889999999999875332 2 245566667776653 799999984
No 211
>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=23.65 E-value=4.9e+02 Score=22.60 Aligned_cols=53 Identities=13% Similarity=0.167 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
...-++.+..++..+++++|.-|.....+ .+.+.+|.+.+.+. .++||+++|.
T Consensus 83 ~~~i~~a~~a~~~Gad~v~v~~P~~~~~s----~~~l~~y~~~ia~~---~~~pi~iYn~ 135 (289)
T PF00701_consen 83 EEAIELARHAQDAGADAVLVIPPYYFKPS----QEELIDYFRAIADA---TDLPIIIYNN 135 (289)
T ss_dssp HHHHHHHHHHHHTT-SEEEEEESTSSSCC----HHHHHHHHHHHHHH---SSSEEEEEEB
T ss_pred HHHHHHHHHHhhcCceEEEEeccccccch----hhHHHHHHHHHHhh---cCCCEEEEEC
Confidence 34456667778899999999999765433 33456666777765 4899999996
No 212
>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=23.31 E-value=69 Score=31.15 Aligned_cols=17 Identities=29% Similarity=0.624 Sum_probs=15.8
Q ss_pred EEEEecCCCeEEEEEec
Q 028759 65 SLGVDLGLSRTGLALSK 81 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD 81 (204)
++|||+|+..+-+|+.+
T Consensus 2 viGIDlGtt~s~va~~~ 18 (595)
T TIGR02350 2 IIGIDLGTTNSCVAVME 18 (595)
T ss_pred EEEEEeCcccEEEEEEE
Confidence 79999999999999986
No 213
>CHL00094 dnaK heat shock protein 70
Probab=23.30 E-value=71 Score=31.46 Aligned_cols=19 Identities=32% Similarity=0.590 Sum_probs=17.1
Q ss_pred ceEEEEecCCCeEEEEEec
Q 028759 63 GFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 63 g~iLalD~G~kRIGVAvsD 81 (204)
+.++|||+|+..+-+|+.+
T Consensus 2 ~~viGIDlGTt~s~va~~~ 20 (621)
T CHL00094 2 GKVVGIDLGTTNSVVAVME 20 (621)
T ss_pred CceEEEEeCcccEEEEEEE
Confidence 3699999999999999986
No 214
>PRK15005 universal stress protein F; Provisional
Probab=23.01 E-value=1.8e+02 Score=21.73 Aligned_cols=29 Identities=17% Similarity=0.142 Sum_probs=21.5
Q ss_pred CEEEEeecCCCCCCCChhHHHHHHHHHHHHHhh
Q 028759 112 DEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRA 144 (204)
Q Consensus 112 ~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~ 144 (204)
..|+|+. ||++...+..+-.+|..+++..
T Consensus 3 ~~ILv~~----D~s~~~~~~~a~~~a~~la~~~ 31 (144)
T PRK15005 3 RTILVPI----DISDSELTQRVISHVEAEAKID 31 (144)
T ss_pred ccEEEec----CCCchhHHHHHHHHHHHHHhcc
Confidence 4578885 8888766677788888887653
No 215
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=22.86 E-value=2.6e+02 Score=25.43 Aligned_cols=63 Identities=17% Similarity=0.237 Sum_probs=42.2
Q ss_pred HHHcCCCEEEEe-ecCCCCCC---CChhHHHHHHHHHHHHHhhccCCCcEEEEc--CCCcHHHHHHHHHH
Q 028759 106 AQREETDEFIIG-LPKSWDGS---ETPQSNKVRSVAGRLAVRAAERGWRVYLLD--EHRTSAEAVDRMIN 169 (204)
Q Consensus 106 i~e~~i~~IVVG-lPl~~dGt---~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD--ER~TT~eA~~~L~e 169 (204)
.....||..+|. .|-. .|. .+-.-.+||++.+.+...-.+-+..|+++| |++|..+|...|+-
T Consensus 68 ~~g~HPD~~~i~~~p~~-~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKt 136 (319)
T PRK08769 68 AAGTHPDLQLVSFIPNR-TGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKT 136 (319)
T ss_pred hcCCCCCEEEEecCCCc-ccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHH
Confidence 345679999986 4532 221 123466778888777654222246789988 89999999998874
No 216
>cd01972 Nitrogenase_VnfE_like Nitrogenase_VnfE_like: VnfE subunit of the VnfEN complex_like. This group in addition to VnfE contains a subset of the alpha subunit of the nitrogenase MoFe protein and NifE-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protein for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.
Probab=22.58 E-value=1.9e+02 Score=26.90 Aligned_cols=58 Identities=22% Similarity=0.193 Sum_probs=41.2
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc-CCCcH
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD-EHRTS 160 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD-ER~TT 160 (204)
+++.+.|.++.++++|+.|+|-- ....+-+...++.+++.+++.+ ++||+.++ +-|..
T Consensus 75 ~kL~~aI~~~~~~~~P~~I~V~t----tC~~~iIGdDi~~v~~~~~~~~---~~pvi~v~t~gf~g 133 (426)
T cd01972 75 KKLEDTIKEAYSRYKPKAIFVAT----SCATGIIGDDVESVVEELEDEI---GIPVVALHCEGFKG 133 (426)
T ss_pred HHHHHHHHHHHHhCCCCEEEEEC----CChHHHhccCHHHHHHHHHHhh---CCCEEEEeCCccCC
Confidence 46778899999999999777751 2223334455688888888764 89999998 55544
No 217
>cd01715 ETF_alpha The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The alpha subunit of ETF is structurally related to the bacterial nitrogen fixation protein fixB which could play a role in a redox process and feed electrons to ferredoxin.
Probab=22.57 E-value=2.1e+02 Score=22.90 Aligned_cols=36 Identities=22% Similarity=0.373 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhh
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRA 144 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~ 144 (204)
....|.+++++++++.|++| +...+ +.++-+|+.++
T Consensus 71 ~a~al~~~i~~~~p~~Vl~~-----~t~~g------~~la~rlAa~L 106 (168)
T cd01715 71 YAPALVALAKKEKPSHILAG-----ATSFG------KDLAPRVAAKL 106 (168)
T ss_pred HHHHHHHHHHhcCCCEEEEC-----CCccc------cchHHHHHHHh
Confidence 34678899999999999999 33333 57888888886
No 218
>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=22.49 E-value=93 Score=23.59 Aligned_cols=50 Identities=18% Similarity=0.221 Sum_probs=31.5
Q ss_pred EEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEe
Q 028759 65 SLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIG 117 (204)
Q Consensus 65 iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVG 117 (204)
+=-++.|..++|++-... .+++.+..+...+...+.++..+++.+.+++=
T Consensus 24 ~K~f~~~~~~vgis~v~~---~~~~~~~~~~~~~~~~l~~~~~~~~ld~l~lm 73 (127)
T PF02833_consen 24 YKEFEFGGKKVGISQVET---MDLEELLSRKDELLEELEEFCEERKLDLLFLM 73 (127)
T ss_dssp EEEEEETTEEEEEEEEEE---S-HHHHHTTHHHHHHHHHHHHHHTT-SEEEEE
T ss_pred ceeeecCCeEEEEEeeee---cCHHHHHHHHHHHHHHHHHHHHhCCCCEEEEE
Confidence 334666999999887521 22222222224567899999999999977654
No 219
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=22.33 E-value=4.4e+02 Score=21.60 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=11.7
Q ss_pred HHHHHHHHHcCCCEEEEe
Q 028759 100 LQLLEIAQREETDEFIIG 117 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVG 117 (204)
+.++.+ ..+++++||+-
T Consensus 46 ~~i~~l-~~~~vdgii~~ 62 (273)
T cd01541 46 KCLENM-LSQGIDGLIIE 62 (273)
T ss_pred HHHHHH-HHcCCCEEEEe
Confidence 445554 45799999984
No 220
>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=22.30 E-value=3.3e+02 Score=22.05 Aligned_cols=9 Identities=22% Similarity=0.508 Sum_probs=4.7
Q ss_pred cCCCEEEEe
Q 028759 109 EETDEFIIG 117 (204)
Q Consensus 109 ~~i~~IVVG 117 (204)
+++++||+.
T Consensus 54 ~~vdgiii~ 62 (266)
T cd06282 54 QRVDGLILT 62 (266)
T ss_pred cCCCEEEEe
Confidence 455555553
No 221
>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=22.28 E-value=2.7e+02 Score=24.73 Aligned_cols=68 Identities=21% Similarity=0.301 Sum_probs=39.9
Q ss_pred eeeeeeeEEccchhHHHHHHHHHHHcC--CCEEEEeecCCCC-CCCChhHHHHHHHHHHHHHhhc--cCCCcEEEEc
Q 028759 84 CVRPLTVLKLRGEKLELQLLEIAQREE--TDEFIIGLPKSWD-GSETPQSNKVRSVAGRLAVRAA--ERGWRVYLLD 155 (204)
Q Consensus 84 ~A~Pl~~i~~~~~~~~~~L~~li~e~~--i~~IVVGlPl~~d-Gt~~~~~~~v~~Fa~~L~~~~~--~~~lpV~lvD 155 (204)
..+|+-+++ +.-...|.+.++++. .+.|+||.|+-.. |.. .....++.+++.|.+.++ ..+-.++++=
T Consensus 76 ~VQplhiip---G~Ey~~l~~~v~~~~~~F~~i~~g~PLL~~~g~~-~~~~D~~~va~aL~~~~~~~~~~~a~vlmG 148 (262)
T PF06180_consen 76 VVQPLHIIP---GEEYEKLRATVEAYKHDFKKIVLGRPLLYTMGQE-NSPEDYEAVAEALAEEFPKKRKDEAVVLMG 148 (262)
T ss_dssp EEEE--SCS---SHHHHHHHHHHHHHCCCSSEEEEE--SCSS------SHHHHHHHHHHHHCCS-TT-TTEEEEEEE
T ss_pred EEeecceeC---cHhHHHHHHHHHHhhccCCeEEeccccccccccc-CChHHHHHHHHHHHHhccccCCCCEEEEEe
Confidence 357777775 334567777777654 6799999998653 544 566777888888887653 1244566663
No 222
>PRK08175 aminotransferase; Validated
Probab=22.03 E-value=3e+02 Score=24.81 Aligned_cols=56 Identities=11% Similarity=0.024 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHc--CCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCc
Q 028759 98 LELQLLEIAQRE--ETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159 (204)
Q Consensus 98 ~~~~L~~li~e~--~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~T 159 (204)
..+.|.+.+++. ++..|++..|-|+.|..-+..+. +++++..++ +++ +..+||-|.
T Consensus 150 ~~~~l~~~l~~~~~~~~~v~i~~p~NPtG~~~~~~~~-~~i~~~a~~----~~i-~ii~De~y~ 207 (395)
T PRK08175 150 FFNELERAIRESYPKPKMMILGFPSNPTAQCVELEFF-EKVVALAKR----YDV-LVVHDLAYA 207 (395)
T ss_pred cHHHHHHHHhhccCCceEEEEeCCCCCCCCCCCHHHH-HHHHHHHHH----cCc-EEEEecchH
Confidence 356777777654 67888888899999976553332 444444443 255 556788774
No 223
>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=21.99 E-value=97 Score=26.03 Aligned_cols=18 Identities=28% Similarity=0.565 Sum_probs=16.6
Q ss_pred eEEEEecCCCeEEEEEec
Q 028759 64 FSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD 81 (204)
.+||||+|+..+=+++-|
T Consensus 1 y~lgiDiGTts~K~~l~d 18 (245)
T PF00370_consen 1 YYLGIDIGTTSVKAVLFD 18 (245)
T ss_dssp EEEEEEECSSEEEEEEEE
T ss_pred CEEEEEEcccceEEEEEe
Confidence 489999999999999988
No 224
>TIGR01312 XylB D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization.
Probab=21.99 E-value=1.7e+02 Score=27.18 Aligned_cols=16 Identities=44% Similarity=0.603 Sum_probs=15.2
Q ss_pred EEEecCCCeEEEEEec
Q 028759 66 LGVDLGLSRTGLALSK 81 (204)
Q Consensus 66 LalD~G~kRIGVAvsD 81 (204)
||||+|+..+=+++.|
T Consensus 1 lgIDiGtt~ik~~l~d 16 (481)
T TIGR01312 1 LGIDLGTSGVKALLVD 16 (481)
T ss_pred CceeecCcceEEEEEC
Confidence 5899999999999999
No 225
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=21.92 E-value=3.4e+02 Score=24.91 Aligned_cols=67 Identities=18% Similarity=0.270 Sum_probs=41.6
Q ss_pred HHHHHHcCCCEEEEeecCCCCCC---CChhHHHHHHHHHHHHHhhccCCCcEEEEc--CCCcHHHHHHHHHH
Q 028759 103 LEIAQREETDEFIIGLPKSWDGS---ETPQSNKVRSVAGRLAVRAAERGWRVYLLD--EHRTSAEAVDRMIN 169 (204)
Q Consensus 103 ~~li~e~~i~~IVVGlPl~~dGt---~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD--ER~TT~eA~~~L~e 169 (204)
..+.....||.+++.-|....+. .+-....|+...+.+......-+..|+++| |+++...|...|+.
T Consensus 93 ~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~ 164 (351)
T PRK09112 93 RQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKT 164 (351)
T ss_pred HHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHH
Confidence 34445668999988877643321 111235556555555543212357899999 78998888887764
No 226
>PRK11175 universal stress protein UspE; Provisional
Probab=21.72 E-value=1.3e+02 Score=25.77 Aligned_cols=21 Identities=19% Similarity=0.324 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHcCCCEEEEee
Q 028759 98 LELQLLEIAQREETDEFIIGL 118 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGl 118 (204)
....|.+.++++++|.||+|-
T Consensus 249 ~~~~I~~~a~~~~~DLIVmG~ 269 (305)
T PRK11175 249 PEEVIPDLAEHLDAELVILGT 269 (305)
T ss_pred HHHHHHHHHHHhCCCEEEECC
Confidence 445677778888888888884
No 227
>PHA02546 47 endonuclease subunit; Provisional
Probab=21.72 E-value=3e+02 Score=24.83 Aligned_cols=56 Identities=13% Similarity=0.005 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHH-HHHhhccCCCcEEEE
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR-LAVRAAERGWRVYLL 154 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~-L~~~~~~~~lpV~lv 154 (204)
..++++.+++.+++|+.||++==+-. .. .+.......|+.. +..++...++||+++
T Consensus 26 ~~l~~ii~~a~~~~vD~VliaGDlfD-~~-~~~~~~~~~~~~~~l~~~L~~~gi~v~~I 82 (340)
T PHA02546 26 KFIKQAIEYSKAHGITTWIQLGDTFD-VR-KAITQNTMNFVREKIFDLLKEAGITLHVL 82 (340)
T ss_pred HHHHHHHHHHHHcCCCEEEECCcccC-CC-CCCCHHHHHHHHHHHHHHHHHCCCeEEEE
Confidence 34567788888999999998732221 11 1112222334433 222222237899998
No 228
>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=21.53 E-value=3.7e+02 Score=22.61 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=18.8
Q ss_pred hhHHHHHHHHHHHcCCCEEEEee
Q 028759 96 EKLELQLLEIAQREETDEFIIGL 118 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGl 118 (204)
.++..++.+++.++.|+ ||+|+
T Consensus 59 ~~lL~~f~~~i~~~dPd-ii~g~ 80 (207)
T cd05785 59 KELLEELVAIIRERDPD-VIEGH 80 (207)
T ss_pred HHHHHHHHHHHHHhCCC-EEecc
Confidence 35678999999999998 88896
No 229
>smart00260 CheW Two component signalling adaptor domain.
Probab=21.39 E-value=1.4e+02 Score=22.30 Aligned_cols=45 Identities=13% Similarity=0.180 Sum_probs=33.4
Q ss_pred CcccccccccchhhhcccccccccCCCCCCceEEEEecCCCeEEEEEec
Q 028759 33 NFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~iLalD~G~kRIGVAvsD 81 (204)
|.+.++.+++++.+++.-...... ...+++-+..+..++|+.|.+
T Consensus 47 ~~rg~~ipvvdl~~~l~~~~~~~~----~~~~viv~~~~~~~~gL~Vd~ 91 (138)
T smart00260 47 NLRGEVLPVVDLRRLLGLPPEPPT----DETRVIVVETGDRKVGLVVDS 91 (138)
T ss_pred eeCCeEEEEEEHHHHhCCCCCCCC----CccEEEEEEeCCEEEEEEEee
Confidence 556677888999998875433221 146888899999999999976
No 230
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=21.34 E-value=2.8e+02 Score=23.37 Aligned_cols=56 Identities=11% Similarity=0.144 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
......+.+++.+-..+.+|+-.=.| .+.....+.+..|.+.|.+.- ++.||.++.
T Consensus 45 ~~le~~~a~~ia~~~a~~~~ld~~~N--~~~~~~~~~~~~fv~~iR~~h--P~tPIllv~ 100 (178)
T PF14606_consen 45 GKLEPEVADLIAEIDADLIVLDCGPN--MSPEEFRERLDGFVKTIREAH--PDTPILLVS 100 (178)
T ss_dssp CS--HHHHHHHHHS--SEEEEEESHH--CCTTTHHHHHHHHHHHHHTT---SSS-EEEEE
T ss_pred cccCHHHHHHHhcCCCCEEEEEeecC--CCHHHHHHHHHHHHHHHHHhC--CCCCEEEEe
Confidence 35567888899998999999887666 566778999999999999864 489999986
No 231
>TIGR03772 anch_rpt_subst anchored repeat ABC transporter, substrate-binding protein. Members of this protein family are ABC transporter permease subunits as identified by pfam00950, but additionally contain the Actinobacterial insert domain described by TIGR03769. Some homologs (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the TIGR03769 insert that occurs just once in this protein family.
Probab=21.33 E-value=4.2e+02 Score=25.73 Aligned_cols=47 Identities=9% Similarity=0.106 Sum_probs=35.1
Q ss_pred CCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHH--HHHHHHHHcCCC
Q 028759 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSA--EAVDRMINMGLS 173 (204)
Q Consensus 123 dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~--eA~~~L~e~G~~ 173 (204)
+....+..+.+.++.+.+++. +++++|.++-+++. .++..-++.|++
T Consensus 399 ~~~~ePS~~~L~~Li~~IK~~----~V~~IF~Epq~~~~~~~l~~IA~e~Gv~ 447 (479)
T TIGR03772 399 NPAVEPSLADRRRLTRTIENL----KVPAVFLEPNLAARSTTLNEIADELGVR 447 (479)
T ss_pred CCCCCCCHHHHHHHHHHHHHc----CCCEEEEeCCCCCchHHHHHHHHHcCCc
Confidence 334456789999999999975 89999999988744 356666666653
No 232
>PRK12359 flavodoxin FldB; Provisional
Probab=21.26 E-value=1.2e+02 Score=25.09 Aligned_cols=31 Identities=6% Similarity=0.159 Sum_probs=25.6
Q ss_pred EEEeecCCCCCCCChhHHHHHHHHHHHHHhh
Q 028759 114 FIIGLPKSWDGSETPQSNKVRSVAGRLAVRA 144 (204)
Q Consensus 114 IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~ 144 (204)
-.||||+..+......-.++.+++++|+..+
T Consensus 138 ~f~gl~lD~~nq~~~t~~ri~~W~~~~~~~~ 168 (172)
T PRK12359 138 LFVGLALDEVNQYDLSDERIQQWCEQILLEM 168 (172)
T ss_pred EEEEEEEcCCCchhhhHHHHHHHHHHHHHHH
Confidence 4789999988877777799999999988654
No 233
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=21.24 E-value=3e+02 Score=21.20 Aligned_cols=52 Identities=10% Similarity=0.082 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEE
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYL 153 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~l 153 (204)
.+...++++. +++++.|-++-=...+ ...+.+-.+..+++.|++.+ +++|+.
T Consensus 53 ~~~~~~~~l~-~~~~d~IHlssC~~~~-~~~~~CP~~~~~~~~I~~~~---gi~VV~ 104 (107)
T PF08821_consen 53 KLVRRIKKLK-KNGADVIHLSSCMVKG-NPHGPCPHIDEIKKIIEEKF---GIEVVE 104 (107)
T ss_pred HHHHHHHHHH-HCCCCEEEEcCCEecC-CCCCCCCCHHHHHHHHHHHh---CCCEee
Confidence 4555666666 8999998888544432 22225566788888898875 888864
No 234
>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=21.19 E-value=3.5e+02 Score=22.29 Aligned_cols=42 Identities=21% Similarity=0.242 Sum_probs=23.6
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
+.+..+ ..+++++||+. |.+.+. +....+.+.+. ++||+++|
T Consensus 46 ~~i~~l-~~~~vdgiIi~-~~~~~~--------~~~~i~~~~~~----~iPvV~~~ 87 (273)
T cd06309 46 SAIRSF-IAQGVDVIILA-PVVETG--------WDPVLKEAKAA----GIPVILVD 87 (273)
T ss_pred HHHHHH-HHcCCCEEEEc-CCcccc--------chHHHHHHHHC----CCCEEEEe
Confidence 345554 45789999996 432211 01223344432 78888887
No 235
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=21.19 E-value=5.2e+02 Score=22.01 Aligned_cols=17 Identities=18% Similarity=0.300 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCEEEEe
Q 028759 101 QLLEIAQREETDEFIIG 117 (204)
Q Consensus 101 ~L~~li~e~~i~~IVVG 117 (204)
.+.+.+...++++||+-
T Consensus 108 ~~~~~l~~~~vdgiIi~ 124 (328)
T PRK11303 108 RCAEHLLQRQVDALIVS 124 (328)
T ss_pred HHHHHHHHcCCCEEEEc
Confidence 44444556899999984
No 236
>PF14106 DUF4279: Domain of unknown function (DUF4279)
Probab=21.12 E-value=2.1e+02 Score=21.19 Aligned_cols=43 Identities=14% Similarity=0.118 Sum_probs=33.2
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCCh---hHHHHHHHHHHHH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETP---QSNKVRSVAGRLA 141 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~---~~~~v~~Fa~~L~ 141 (204)
...|.++.++++.+..++++-..++|...+ ....+..|...|.
T Consensus 68 ~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~l~~lg 113 (118)
T PF14106_consen 68 REIIKELKEKYNLEIQFFCYFSSISGGGFPAIYLSPEIIKFLAALG 113 (118)
T ss_pred HHHHHHHHHhcCcceEEEEEEEecCCCCCcccccCHHHHHHHHhhC
Confidence 468889999999997778777777777777 7777777766654
No 237
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=21.11 E-value=1e+02 Score=26.47 Aligned_cols=20 Identities=40% Similarity=0.526 Sum_probs=17.9
Q ss_pred CceEEEEecCCCeEEEEEec
Q 028759 62 GGFSLGVDLGLSRTGLALSK 81 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD 81 (204)
+|.+|++|.|..-+|||.--
T Consensus 57 PGlvl~L~~GGsc~GvafRi 76 (190)
T COG3703 57 PGLVLGLDRGGSCEGVAYRI 76 (190)
T ss_pred CceEEEeeCCCcEEEEEEEc
Confidence 59999999999999999753
No 238
>cd04724 Tryptophan_synthase_alpha Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Indole is then channeled to the active site of the beta subunit, a PLP-dependent enzyme that catalyzes a replacement reaction to convert L-serine into L-tryptophan.
Probab=21.10 E-value=3.5e+02 Score=23.28 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHcCCCEEEEeecC---CCCCCCChhHH-----------HHHHHHHHHHHhhccCCCcEEE
Q 028759 98 LELQLLEIAQREETDEFIIGLPK---SWDGSETPQSN-----------KVRSVAGRLAVRAAERGWRVYL 153 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl---~~dGt~~~~~~-----------~v~~Fa~~L~~~~~~~~lpV~l 153 (204)
.+.+..+-+.+.++|.|=+|.|. -+||..=+.+. ..-.+.+.+++. .++|+++
T Consensus 15 ~~~~~~~~l~~~Gad~iel~iPfsdPv~DG~~I~~a~~~al~~g~~~~~~~~~~~~vr~~---~~~pv~l 81 (242)
T cd04724 15 TTLEILKALVEAGADIIELGIPFSDPVADGPVIQAASERALANGVTLKDVLELVKEIRKK---NTIPIVL 81 (242)
T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHhhc---CCCCEEE
Confidence 34444445556799999999998 67886554333 555666666654 2678766
No 239
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=21.10 E-value=4.2e+02 Score=24.04 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=14.1
Q ss_pred HHHHHcCCCccccC-CCCcHHHHHHHh
Q 028759 165 DRMINMGLSKSARQ-TKTDAYAAVVRQ 190 (204)
Q Consensus 165 ~~L~e~G~~rkkrK-~~vD~~AA~iIL 190 (204)
+.|.+.|+.-..|+ .-.|-.||+-=|
T Consensus 308 ~~l~~~gi~vtvr~~~g~di~aaCGqL 334 (343)
T PRK14469 308 EILLKNGIEAEIRREKGSDIEAACGQL 334 (343)
T ss_pred HHHHHCCCeEEEeCCCCcchhhcCccc
Confidence 34555677554443 345666666443
No 240
>COG1521 Pantothenate kinase type III (Bvg accessory factor family protein) [Transcription]
Probab=21.08 E-value=2.4e+02 Score=25.11 Aligned_cols=19 Identities=37% Similarity=0.525 Sum_probs=17.3
Q ss_pred eEEEEecCCCeEEEEEecC
Q 028759 64 FSLGVDLGLSRTGLALSKG 82 (204)
Q Consensus 64 ~iLalD~G~kRIGVAvsD~ 82 (204)
++|.||.|..++=+|+.++
T Consensus 1 ~~L~iDiGNT~~~~a~~~~ 19 (251)
T COG1521 1 MLLLIDIGNTRIVFALYEG 19 (251)
T ss_pred CeEEEEeCCCeEEEEEecC
Confidence 4799999999999999984
No 241
>PLN02257 phosphoribosylamine--glycine ligase
Probab=21.03 E-value=3.6e+02 Score=25.42 Aligned_cols=21 Identities=5% Similarity=0.169 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHcCCCEEEEe
Q 028759 97 KLELQLLEIAQREETDEFIIG 117 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVG 117 (204)
...+.|.+++++++++.+|+|
T Consensus 49 ~d~~~l~~~a~~~~id~vvvg 69 (434)
T PLN02257 49 SDSAAVISFCRKWGVGLVVVG 69 (434)
T ss_pred CCHHHHHHHHHHcCCCEEEEC
Confidence 456789999999999999998
No 242
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=20.86 E-value=2.7e+02 Score=21.25 Aligned_cols=54 Identities=13% Similarity=0.179 Sum_probs=33.7
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHH
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMI 168 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~ 168 (204)
.+.|..++. .+|+.+||| -|.....- -.+..+.|+++ ++.++. ++|.+|-+.|-
T Consensus 42 ~e~l~~l~~-~~peiliiG-----TG~~~~~~--~~~~~~~l~~~----gi~vE~----m~T~~AcrTyN 95 (109)
T cd05560 42 AAHFEALLA-LQPEVILLG-----TGERQRFP--PPALLAPLLAR----GIGVEV----MDTQAACRTYN 95 (109)
T ss_pred HHHHHHHHh-cCCCEEEEe-----cCCCCCcC--CHHHHHHHHHc----CCeEEE----ECHHHHHHHHH
Confidence 356666665 469999999 56554322 13444556654 778866 45777766653
No 243
>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=20.84 E-value=2.1e+02 Score=25.66 Aligned_cols=84 Identities=12% Similarity=0.077 Sum_probs=50.4
Q ss_pred EEEecCCCeEEEEEec-C--CeeeeeeeEEc-------------cchhHHHHHHHHHHHc-----CCCEEEEeecCCCCC
Q 028759 66 LGVDLGLSRTGLALSK-G--FCVRPLTVLKL-------------RGEKLELQLLEIAQRE-----ETDEFIIGLPKSWDG 124 (204)
Q Consensus 66 LalD~G~kRIGVAvsD-~--~~A~Pl~~i~~-------------~~~~~~~~L~~li~e~-----~i~~IVVGlPl~~dG 124 (204)
||||=-..-+++|+.+ + +.+.-...... +.+.+...+++++++- ++|.|.|+.-. |
T Consensus 1 Lgiets~~~~s~al~~~~~~i~~~~~~~~~~~~gg~~p~~~~~~H~~~l~~~i~~~l~~~~~~~~did~Iavt~gP---g 77 (322)
T TIGR03722 1 LGIEGTAHTFGVGIVDEDGEILANVSDTYVPEKGGIHPREAAEHHAEVAPKLIKEALEEAGVSLEDIDAVAFSQGP---G 77 (322)
T ss_pred CEEeccccceEEEEEECCCeEEEEEEeecccCcCCcChhHHHHHHHHHHHHHHHHHHHHcCCCHHHCCEEEEecCC---c
Confidence 5788777889999987 3 23322222211 1112334566666553 67999999532 3
Q ss_pred CCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 125 SETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 125 t~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
..+ .-+....+++.|+..+ ++|++.++.
T Consensus 78 ~~~-~l~vg~~~ak~la~~~---~~p~~~v~h 105 (322)
T TIGR03722 78 LGP-CLRVGATAARALALKL---NKPLVGVNH 105 (322)
T ss_pred hHH-hHHHHHHHHHHHHHHh---CCCeechhh
Confidence 222 2345567788888765 899999865
No 244
>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=20.84 E-value=2.9e+02 Score=25.46 Aligned_cols=54 Identities=19% Similarity=0.100 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCc
Q 028759 98 LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159 (204)
Q Consensus 98 ~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~T 159 (204)
-.+.|.++++++++|+||.=....-+-...+. . ...+.|++. |+|+..+|=.++
T Consensus 301 R~~~i~~lv~~~~~DGVI~~~~kfC~~~~~e~-~---~lk~~l~e~----GIP~L~iE~D~~ 354 (377)
T TIGR03190 301 RYDHVLGLAKEYNVQGAIFLQQKFCDPHEGDY-P---DLKRHLEAN----GIPTLFLEFDIT 354 (377)
T ss_pred HHHHHHHHHHHhCCCEEEEecccCCCcchhhh-H---HHHHHHHHC----CCCEEEEecCCC
Confidence 45689999999999999998766544443321 1 222334443 999988874455
No 245
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.78 E-value=4.6e+02 Score=24.16 Aligned_cols=27 Identities=15% Similarity=0.133 Sum_probs=15.3
Q ss_pred HHHHHHcCCCccccC-CCCcHHHHHHHh
Q 028759 164 VDRMINMGLSKSARQ-TKTDAYAAVVRQ 190 (204)
Q Consensus 164 ~~~L~e~G~~rkkrK-~~vD~~AA~iIL 190 (204)
++.|.+.|+.-..|+ .=.|-.||+-=|
T Consensus 307 ~~~L~~~gi~v~vR~~~G~di~aaCGqL 334 (349)
T PRK14463 307 HKYLLDKHVTVITRSSRGSDISAACGQL 334 (349)
T ss_pred HHHHHHCCceEEEeCCCCcchhhccCcc
Confidence 444566777665554 335666666444
No 246
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=20.77 E-value=3e+02 Score=24.06 Aligned_cols=61 Identities=16% Similarity=0.144 Sum_probs=40.1
Q ss_pred HHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEE-----Ec-CCCcHHHHHHHHHHcCC
Q 028759 99 ELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYL-----LD-EHRTSAEAVDRMINMGL 172 (204)
Q Consensus 99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~l-----vD-ER~TT~eA~~~L~e~G~ 172 (204)
.+.+.+-|.+.++|.|+||+ |..-+ +.|+.+.+..+ +.+|.+ .| -..+...|=.+++..|+
T Consensus 146 ~~~i~~~I~~s~~dil~Vgl-----G~PkQ-----E~~~~~~~~~~---~~~v~~gvGg~fD~~aG~~~RAP~w~~~~gL 212 (243)
T PRK03692 146 RQALFERIHASGAKIVTVAM-----GSPKQ-----EIFMRDCRLVY---PDALYMGVGGTYDVFTGHVKRAPKIWQNLGL 212 (243)
T ss_pred HHHHHHHHHhcCCCEEEEEC-----CCcHH-----HHHHHHHHHhC---CCCEEEEeCeEEEEecCCcCcCcHHHHHhCh
Confidence 45688888899999999996 55432 66888887764 445433 23 34445556666666654
No 247
>TIGR03275 methan_mark_8 putative methanogenesis marker protein 8. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=20.77 E-value=1.7e+02 Score=26.34 Aligned_cols=61 Identities=15% Similarity=0.283 Sum_probs=40.6
Q ss_pred CceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759 62 GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG 138 (204)
Q Consensus 62 ~g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~ 138 (204)
.|...|++.|-|||+|-++|. +...+|+++-.++.++.+++|- |..|-..+-++.+-+.+.
T Consensus 153 ~Gv~~Aie~Gyk~IaVTv~~~--------------~~a~~iRe~e~~~~~~~~if~V--HtTGis~eea~~~~~~aD 213 (259)
T TIGR03275 153 KGVEKAIELGYKKIAVTVADA--------------EDAKAIRELESESGIDIIIFAV--HTTGIDREDAEEVVQYAD 213 (259)
T ss_pred HHHHHHHHcCCceEEEEecCH--------------HHHHHHHHhccccCCcEEEEEE--ECCCCCHHHHHHHHHhhh
Confidence 355668888999998887642 3446677777777889999994 555665554554444433
No 248
>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=20.70 E-value=3e+02 Score=23.05 Aligned_cols=57 Identities=26% Similarity=0.321 Sum_probs=35.3
Q ss_pred ceEEEEecCCCe-----EEEEEecCC-e-eeeeeeEEccch-------hHHHHHHHHHHHcCCC--EEEEeecC
Q 028759 63 GFSLGVDLGLSR-----TGLALSKGF-C-VRPLTVLKLRGE-------KLELQLLEIAQREETD--EFIIGLPK 120 (204)
Q Consensus 63 g~iLalD~G~kR-----IGVAvsD~~-~-A~Pl~~i~~~~~-------~~~~~L~~li~e~~i~--~IVVGlPl 120 (204)
..+|+||+-|.- +|.|+-++. . ..... ...... .-..+|+.++++++.- .|||--|.
T Consensus 2 ~~~LslD~STs~~~~~gTG~A~~~~~~~~~~si~-~~~k~Ks~~ER~k~ias~Lk~ii~~~d~~~y~i~IE~~v 74 (159)
T PF07066_consen 2 KKVLSLDFSTSSKKGEGTGWAFFKGSDLVVGSIK-AKHKSKSFFERAKSIASELKTIIQKYDLKFYIIVIEKPV 74 (159)
T ss_pred CeeEEEEEecccCCCCCceeEEecCCeEEEeeee-ecCcccCHHHHHHHHHHHHHHHHHHhCCCcceEEEeccc
Confidence 468999999998 999999753 2 22221 111111 2346889899987543 46665543
No 249
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=20.59 E-value=4.3e+02 Score=24.36 Aligned_cols=56 Identities=14% Similarity=0.147 Sum_probs=35.5
Q ss_pred HHHHHHHHc-CCCEEEEeecCCCCC-CCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 101 QLLEIAQRE-ETDEFIIGLPKSWDG-SETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 101 ~L~~li~e~-~i~~IVVGlPl~~dG-t~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
.++++..++ +++.|||=+=-.+.+ ........+..+.+.|+....++++||+..-.
T Consensus 295 ~~r~~~~~~~~~~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~~i~Vi~lsQ 352 (421)
T TIGR03600 295 IARRIKRKKGGLDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELDVPVVLLAQ 352 (421)
T ss_pred HHHHHHHhcCCCCEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEEEecc
Confidence 444455555 688888876434443 22334556677777777655556999998764
No 250
>PF06050 HGD-D: 2-hydroxyglutaryl-CoA dehydratase, D-component ; InterPro: IPR010327 Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalysed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate [].; PDB: 3O3O_B 3O3N_D 3O3M_D.
Probab=20.51 E-value=1.6e+02 Score=25.92 Aligned_cols=53 Identities=19% Similarity=0.108 Sum_probs=30.3
Q ss_pred hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc
Q 028759 96 EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD 155 (204)
Q Consensus 96 ~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD 155 (204)
....+.+.+++++++++++|......-+. ..-....+.+.+++. .++|+..+|
T Consensus 272 ~~r~~~~~~~~~~~~~dgvi~~~~~~C~~----~~~~~~~l~~~~~~~---~gIP~l~le 324 (349)
T PF06050_consen 272 ERRIEYIDDLIEKYGADGVIFHGHKGCDP----YSYDQPLLKEALREF---LGIPVLFLE 324 (349)
T ss_dssp HCHHHHHHHHHHHTT-SEEEEEEETT-HH----HHCCHHHHHHHHHCC---HT--EEEEE
T ss_pred HhHHHHHHHHHHHhCCCEEEEhHhcCCCc----HHHHHHHHHHHHHHh---cCCCeEeec
Confidence 34567899999999999999996543211 111123344444432 199997666
No 251
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor 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 their ligands in the cleft between these domains.
Probab=20.29 E-value=3.5e+02 Score=21.38 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=21.6
Q ss_pred HcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 108 REETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 108 e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
.-+||.||.+ + +.... ...+.|++. ++|+++++.
T Consensus 67 ~l~PDlii~~-~----~~~~~------~~~~~l~~~----gIpvv~i~~ 100 (186)
T cd01141 67 ALKPDLVILY-G----GFQAQ------TILDKLEQL----GIPVLYVNE 100 (186)
T ss_pred ccCCCEEEEe-c----CCCch------hHHHHHHHc----CCCEEEeCC
Confidence 4799998775 2 22111 345556653 899999985
No 252
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.24 E-value=3.3e+02 Score=22.93 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=24.7
Q ss_pred HHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcC
Q 028759 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156 (204)
Q Consensus 100 ~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDE 156 (204)
+.+..++ ..++++||+. |...++. ....+.+.+. ++||+++|.
T Consensus 47 ~~l~~~~-~~~~dgiii~-~~~~~~~--------~~~i~~~~~~----~iPvV~~~~ 89 (294)
T cd06316 47 ADIETTI-SQKPDIIISI-PVDPVST--------AAAYKKVAEA----GIKLVFMDN 89 (294)
T ss_pred HHHHHHH-HhCCCEEEEc-CCCchhh--------hHHHHHHHHc----CCcEEEecC
Confidence 3455544 4789999995 4321111 2344455543 788888874
No 253
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme involved in bacteriochlorophyll biosynthesis. This subunit shows homology to the nitrogenase molybdenum-iron protein NifN.
Probab=20.17 E-value=2.9e+02 Score=25.67 Aligned_cols=57 Identities=12% Similarity=0.103 Sum_probs=40.8
Q ss_pred hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEc-CCCcH
Q 028759 97 KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLD-EHRTS 160 (204)
Q Consensus 97 ~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvD-ER~TT 160 (204)
++.+.|+++.+.++|+.|+|-- .....-+-..+..+++++++.. ++||+.++ +.|..
T Consensus 71 ~L~~aI~~i~~~~~P~~I~V~t----TC~se~IGDDi~~v~~~~~~~~---~~pVi~v~tpgf~g 128 (407)
T TIGR01279 71 ELDRVVEQIKRDRNPSVIFLLS----SCTPEVIKMDLEGLAERLSTNF---GVPVLFAPASGLDY 128 (407)
T ss_pred HHHHHHHHHHhhcCCCEEEEEC----CchHHHHHhhHHHHHHHHHHhh---CCCEEEeeCCCccc
Confidence 5678889999999999877761 2333445567788888887653 78888887 55653
No 254
>cd01143 YvrC Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. 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.
Probab=20.15 E-value=4e+02 Score=20.87 Aligned_cols=46 Identities=20% Similarity=0.174 Sum_probs=27.6
Q ss_pred HcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHH
Q 028759 108 REETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMIN 169 (204)
Q Consensus 108 e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e 169 (204)
+-+||.|+... +. .. ...++|++. ++|++.+|...+.....+.++.
T Consensus 58 ~l~PDlii~~~-----~~-~~------~~~~~l~~~----gi~v~~~~~~~~~~~~~~~~~~ 103 (195)
T cd01143 58 ALKPDLVIVSS-----SS-LA------ELLEKLKDA----GIPVVVLPAASSLDEIYDQIEL 103 (195)
T ss_pred ccCCCEEEEcC-----Cc-CH------HHHHHHHHc----CCcEEEeCCCCCHHHHHHHHHH
Confidence 46899877652 11 11 134566653 8899999876544555555554
No 255
>PRK13392 5-aminolevulinate synthase; Provisional
Probab=20.06 E-value=4.4e+02 Score=23.84 Aligned_cols=50 Identities=16% Similarity=0.154 Sum_probs=31.3
Q ss_pred HHHHHHHH---cCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCc
Q 028759 101 QLLEIAQR---EETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159 (204)
Q Consensus 101 ~L~~li~e---~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~T 159 (204)
.+.+.++. .+...|++-.|.++.|..-+ .+++.+..++ +++ +.++||-++
T Consensus 166 ~l~~~l~~~~~~~t~~v~i~~~~n~tG~~~~----l~~i~~l~~~----~~~-~livDea~~ 218 (410)
T PRK13392 166 DLEEQLASVDPDRPKLIAFESVYSMDGDIAP----IEAICDLADR----YNA-LTYVDEVHA 218 (410)
T ss_pred HHHHHHHhccCCCCEEEEEeCCCCCCccccc----HHHHHHHHHH----cCC-EEEEECCcc
Confidence 34444442 35678889999999998766 2223332332 253 677999887
Done!