Query 032904
Match_columns 130
No_of_seqs 107 out of 527
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:23:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01101 V_ATP_synt_F vacuola 100.0 1.7E-35 3.7E-40 214.1 13.1 112 10-121 3-114 (115)
2 KOG3432 Vacuolar H+-ATPase V1 100.0 5.4E-36 1.2E-40 214.4 10.3 115 10-124 5-119 (121)
3 PRK01395 V-type ATP synthase s 100.0 1.4E-31 3E-36 190.4 12.1 101 12-125 3-104 (104)
4 PRK03957 V-type ATP synthase s 100.0 2E-31 4.3E-36 188.1 11.9 99 13-125 1-99 (100)
5 PRK02228 V-type ATP synthase s 100.0 2.3E-29 5E-34 177.5 11.5 97 13-125 1-99 (100)
6 PRK01189 V-type ATP synthase s 100.0 7.3E-29 1.6E-33 176.6 9.9 99 12-125 2-102 (104)
7 PF01990 ATP-synt_F: ATP synth 99.9 9.8E-27 2.1E-31 161.6 9.6 92 15-118 1-95 (95)
8 COG1436 NtpG Archaeal/vacuolar 99.9 1.9E-26 4.1E-31 164.4 8.3 99 12-125 2-103 (104)
9 COG4075 Uncharacterized conser 94.4 0.058 1.3E-06 38.6 3.6 75 23-101 27-103 (110)
10 PF10126 Nit_Regul_Hom: Unchar 90.5 0.45 9.8E-06 34.4 3.9 71 24-100 28-102 (110)
11 PLN00124 succinyl-CoA ligase [ 83.9 7.1 0.00015 34.0 8.2 64 39-102 317-388 (422)
12 PF06506 PrpR_N: Propionate ca 74.5 30 0.00065 25.8 8.1 86 10-120 75-164 (176)
13 COG0045 SucC Succinyl-CoA synt 70.9 30 0.00065 30.1 8.1 84 13-102 256-352 (387)
14 PF01886 DUF61: Protein of unk 69.8 15 0.00033 27.1 5.4 70 56-125 20-101 (132)
15 PF07085 DRTGG: DRTGG domain; 68.8 8.6 0.00019 26.2 3.7 14 21-34 51-64 (105)
16 PRK14046 malate--CoA ligase su 65.1 62 0.0014 27.7 9.0 82 13-100 257-351 (392)
17 PRK06555 pyrophosphate--fructo 64.7 19 0.00041 31.3 5.8 30 49-78 241-270 (403)
18 PF00549 Ligase_CoA: CoA-ligas 63.6 37 0.00081 25.5 6.6 53 52-104 58-121 (153)
19 cd02067 B12-binding B12 bindin 63.5 38 0.00083 23.2 6.3 85 26-128 22-109 (119)
20 cd06340 PBP1_ABC_ligand_bindin 60.1 86 0.0019 25.2 8.6 71 21-97 17-100 (347)
21 PRK04115 hypothetical protein; 57.2 34 0.00074 25.6 5.3 69 56-124 23-102 (137)
22 cd06348 PBP1_ABC_ligand_bindin 57.1 97 0.0021 24.6 8.4 72 21-98 17-98 (344)
23 COG2074 2-phosphoglycerate kin 55.5 71 0.0015 26.9 7.3 36 89-127 85-120 (299)
24 PF13458 Peripla_BP_6: Peripla 55.1 62 0.0014 25.3 6.9 70 22-97 20-99 (343)
25 TIGR01016 sucCoAbeta succinyl- 54.6 1.3E+02 0.0028 25.3 9.0 83 12-100 256-351 (386)
26 PF13419 HAD_2: Haloacid dehal 53.5 34 0.00074 23.6 4.7 68 53-123 80-149 (176)
27 cd06332 PBP1_aromatic_compound 53.1 85 0.0018 24.4 7.3 70 22-97 18-95 (333)
28 PF11965 DUF3479: Domain of un 51.7 24 0.00052 27.0 3.8 44 57-100 49-94 (164)
29 PRK00696 sucC succinyl-CoA syn 49.3 1.6E+02 0.0034 24.7 9.2 96 12-119 256-364 (388)
30 PLN02235 ATP citrate (pro-S)-l 49.1 1.2E+02 0.0026 26.6 8.2 73 39-113 297-389 (423)
31 cd01833 XynB_like SGNH_hydrola 48.0 62 0.0013 22.7 5.3 37 53-89 26-74 (157)
32 COG5623 CLP1 Predicted GTPase 47.9 64 0.0014 28.0 6.1 59 53-113 235-295 (424)
33 cd06360 PBP1_alkylbenzenes_lik 47.5 1.4E+02 0.0029 23.4 7.7 53 43-97 41-95 (336)
34 PF01791 DeoC: DeoC/LacD famil 47.1 29 0.00063 27.0 3.8 57 50-107 15-72 (236)
35 PRK12862 malic enzyme; Reviewe 46.5 46 0.001 31.2 5.5 83 7-91 65-159 (763)
36 TIGR00706 SppA_dom signal pept 46.4 91 0.002 23.9 6.4 52 51-102 14-72 (207)
37 PRK12702 mannosyl-3-phosphogly 44.8 64 0.0014 27.2 5.6 43 53-96 21-63 (302)
38 cd01973 Nitrogenase_VFe_beta_l 44.8 1.2E+02 0.0027 26.3 7.6 25 11-35 304-332 (454)
39 COG3616 Predicted amino acid a 44.1 2.1E+02 0.0046 24.7 8.8 79 18-105 72-151 (368)
40 cd06366 PBP1_GABAb_receptor Li 42.7 1.7E+02 0.0037 23.2 8.7 73 21-96 15-95 (350)
41 cd07014 S49_SppA Signal peptid 42.6 1.1E+02 0.0024 22.6 6.2 51 50-100 22-80 (177)
42 cd07019 S49_SppA_1 Signal pept 42.1 1.1E+02 0.0023 23.6 6.2 52 51-102 22-81 (211)
43 PRK08366 vorA 2-ketoisovalerat 42.0 96 0.0021 26.6 6.4 52 14-74 3-54 (390)
44 TIGR02836 spore_IV_A stage IV 41.1 96 0.0021 27.9 6.3 61 62-123 140-211 (492)
45 cd01575 PBP1_GntR Ligand-bindi 40.7 1.5E+02 0.0033 22.0 8.5 79 10-88 114-199 (268)
46 PLN02225 1-deoxy-D-xylulose-5- 40.6 18 0.00039 33.7 1.8 36 9-45 209-244 (701)
47 COG2083 Uncharacterized protei 40.3 63 0.0014 24.3 4.4 71 55-125 25-106 (140)
48 cd06331 PBP1_AmiC_like Type I 39.8 1.4E+02 0.003 23.6 6.7 56 40-97 40-97 (333)
49 cd02070 corrinoid_protein_B12- 39.7 1.3E+02 0.0027 23.0 6.2 82 25-128 104-191 (201)
50 cd07022 S49_Sppa_36K_type Sign 39.1 1.4E+02 0.003 22.9 6.4 51 51-101 26-83 (214)
51 cd06358 PBP1_NHase Type I peri 38.5 1.3E+02 0.0029 23.8 6.4 53 42-97 42-96 (333)
52 PF03709 OKR_DC_1_N: Orn/Lys/A 38.2 89 0.0019 21.8 4.8 53 43-99 18-75 (115)
53 COG0157 NadC Nicotinate-nucleo 38.1 1.2E+02 0.0027 25.3 6.2 64 52-127 198-261 (280)
54 PLN03194 putative disease resi 37.2 60 0.0013 25.5 4.1 36 53-88 68-105 (187)
55 PF09612 HtrL_YibB: Bacterial 36.8 1.3E+02 0.0029 24.8 6.2 52 52-103 26-79 (271)
56 PRK15404 leucine ABC transport 36.5 2.4E+02 0.0052 23.1 8.3 83 10-96 23-121 (369)
57 TIGR01286 nifK nitrogenase mol 36.2 1.9E+02 0.0042 25.7 7.6 46 11-65 362-411 (515)
58 CHL00129 rpl1 ribosomal protei 36.1 1.1E+02 0.0024 24.4 5.6 59 11-87 70-128 (229)
59 cd06356 PBP1_Amide_Urea_BP_lik 35.9 1.7E+02 0.0038 23.3 6.7 69 22-96 18-96 (334)
60 TIGR01169 rplA_bact ribosomal 35.8 1.1E+02 0.0024 24.4 5.5 85 11-120 69-155 (227)
61 cd06334 PBP1_ABC_ligand_bindin 35.8 2.4E+02 0.0052 22.9 8.0 71 21-97 17-96 (351)
62 PRK10653 D-ribose transporter 35.3 1.5E+02 0.0032 23.0 6.1 91 6-97 20-113 (295)
63 PRK04220 2-phosphoglycerate ki 35.2 66 0.0014 26.9 4.2 31 90-123 89-119 (301)
64 PRK14166 bifunctional 5,10-met 35.0 1.6E+02 0.0034 24.5 6.4 52 15-73 35-95 (282)
65 cd02071 MM_CoA_mut_B12_BD meth 34.9 1.6E+02 0.0034 20.5 6.6 54 25-91 21-77 (122)
66 TIGR02370 pyl_corrinoid methyl 34.8 1.3E+02 0.0028 23.0 5.6 83 26-128 107-193 (197)
67 cd00403 Ribosomal_L1 Ribosomal 34.7 2E+02 0.0044 21.8 6.7 88 11-121 51-144 (208)
68 cd06335 PBP1_ABC_ligand_bindin 34.3 2E+02 0.0043 23.1 6.8 56 41-98 41-98 (347)
69 cd06359 PBP1_Nba_like Type I p 34.2 1.4E+02 0.0031 23.6 6.0 70 22-97 18-95 (333)
70 TIGR03336 IOR_alpha indolepyru 33.7 1.3E+02 0.0028 27.0 6.2 54 14-76 2-55 (595)
71 cd07018 S49_SppA_67K_type Sign 33.1 1.6E+02 0.0034 22.8 5.9 52 49-100 28-87 (222)
72 CHL00200 trpA tryptophan synth 32.3 2.7E+02 0.0059 22.5 8.7 89 19-119 107-200 (263)
73 PRK06696 uridine kinase; Valid 32.0 1E+02 0.0022 23.6 4.6 41 77-120 6-46 (223)
74 cd06330 PBP1_Arsenic_SBP_like 31.9 2.3E+02 0.005 22.4 6.8 54 43-98 43-98 (346)
75 cd06353 PBP1_BmpA_Med_like Per 31.9 1.4E+02 0.0031 23.4 5.5 63 11-75 119-187 (258)
76 TIGR02717 AcCoA-syn-alpha acet 31.7 3.4E+02 0.0074 23.5 8.9 71 50-127 353-432 (447)
77 TIGR02329 propionate_PrpR prop 31.7 1.2E+02 0.0025 27.2 5.4 52 10-72 95-150 (526)
78 PRK08367 porA pyruvate ferredo 31.6 1.5E+02 0.0032 25.5 5.9 53 13-74 3-55 (394)
79 PRK10792 bifunctional 5,10-met 31.5 97 0.0021 25.7 4.6 42 26-74 57-99 (285)
80 PF08645 PNK3P: Polynucleotide 31.2 1.8E+02 0.004 21.4 5.7 65 54-119 33-110 (159)
81 PF06309 Torsin: Torsin; Inte 31.0 1.3E+02 0.0028 22.1 4.8 62 52-120 16-77 (127)
82 cd06357 PBP1_AmiC Periplasmic 31.0 2.2E+02 0.0047 23.1 6.7 70 21-96 17-96 (360)
83 TIGR02014 BchZ chlorophyllide 31.0 1.1E+02 0.0024 27.0 5.1 54 12-76 280-341 (468)
84 PRK07896 nicotinate-nucleotide 30.9 1.7E+02 0.0037 24.3 6.0 63 52-126 209-272 (289)
85 cd06344 PBP1_ABC_ligand_bindin 30.6 2.5E+02 0.0055 22.2 6.9 54 42-97 41-96 (332)
86 cd06337 PBP1_ABC_ligand_bindin 30.0 1.7E+02 0.0036 23.7 5.8 54 42-97 44-99 (357)
87 PF11305 DUF3107: Protein of u 29.8 1.1E+02 0.0024 20.6 3.8 31 45-76 15-45 (74)
88 PRK09622 porA pyruvate flavodo 29.6 1.2E+02 0.0025 26.1 5.0 53 13-74 9-61 (407)
89 PF00578 AhpC-TSA: AhpC/TSA fa 29.6 1.7E+02 0.0037 19.3 5.7 43 54-97 47-89 (124)
90 PRK09029 O-succinylbenzoic aci 29.5 2.2E+02 0.0047 23.5 6.5 68 52-122 366-457 (458)
91 COG0447 MenB Dihydroxynaphthoi 29.3 64 0.0014 26.6 3.1 25 51-75 47-71 (282)
92 TIGR00126 deoC deoxyribose-pho 29.2 2.8E+02 0.006 21.8 6.7 59 45-104 10-68 (211)
93 TIGR02364 dha_pts dihydroxyace 29.0 2.1E+02 0.0046 20.5 5.6 35 53-88 14-55 (125)
94 cd06328 PBP1_SBP_like_2 Peripl 28.9 2.5E+02 0.0054 22.4 6.6 54 43-98 44-99 (333)
95 PRK01018 50S ribosomal protein 28.7 1.2E+02 0.0026 20.8 4.1 38 64-101 29-68 (99)
96 cd06343 PBP1_ABC_ligand_bindin 28.3 2.4E+02 0.0053 22.5 6.4 54 42-97 49-104 (362)
97 PF01408 GFO_IDH_MocA: Oxidore 28.3 1.4E+02 0.0031 19.8 4.4 42 59-103 54-98 (120)
98 PRK07232 bifunctional malic en 28.2 1.2E+02 0.0026 28.6 5.1 80 8-89 58-149 (752)
99 cd01016 TroA Metal binding pro 28.2 79 0.0017 25.3 3.6 38 47-85 191-228 (276)
100 CHL00076 chlB photochlorophyll 28.2 3.4E+02 0.0074 24.1 7.8 25 11-35 304-333 (513)
101 PF08747 DUF1788: Domain of un 28.1 2.3E+02 0.0049 20.5 5.6 50 53-102 47-103 (126)
102 PRK12360 4-hydroxy-3-methylbut 28.0 72 0.0016 26.4 3.3 20 3-22 107-126 (281)
103 PRK14177 bifunctional 5,10-met 27.9 1E+02 0.0022 25.6 4.2 41 26-73 57-98 (284)
104 PF14639 YqgF: Holliday-juncti 27.9 89 0.0019 23.3 3.5 37 52-88 48-90 (150)
105 cd06355 PBP1_FmdD_like Peripla 27.8 2.4E+02 0.0052 22.7 6.4 71 21-97 17-97 (348)
106 PF08937 DUF1863: MTH538 TIR-l 27.8 1E+02 0.0022 21.7 3.7 51 53-103 58-112 (130)
107 COG1658 Small primase-like pro 27.6 2.5E+02 0.0054 20.6 7.4 66 13-87 10-77 (127)
108 cd01971 Nitrogenase_VnfN_like 27.5 2.2E+02 0.0049 24.3 6.4 55 12-74 293-354 (427)
109 PF02873 MurB_C: UDP-N-acetyle 27.3 56 0.0012 23.0 2.2 37 24-62 49-85 (105)
110 PF03796 DnaB_C: DnaB-like hel 27.3 1.2E+02 0.0025 23.7 4.3 32 43-74 105-137 (259)
111 TIGR01279 DPOR_bchN light-inde 27.3 2.1E+02 0.0045 24.4 6.1 66 11-89 273-343 (407)
112 cd06301 PBP1_rhizopine_binding 27.2 2.7E+02 0.0058 20.8 6.5 52 44-96 34-86 (272)
113 TIGR03710 OAFO_sf 2-oxoacid:ac 26.8 2.4E+02 0.0052 25.3 6.6 57 11-76 190-246 (562)
114 PRK05424 rplA 50S ribosomal pr 26.7 1.7E+02 0.0038 23.2 5.2 59 11-87 70-128 (230)
115 TIGR03669 urea_ABC_arch urea A 26.7 2.5E+02 0.0055 23.3 6.4 69 22-96 19-97 (374)
116 cd06327 PBP1_SBP_like_1 Peripl 26.3 3.2E+02 0.007 21.5 6.8 55 41-97 40-96 (334)
117 PRK14189 bifunctional 5,10-met 26.3 1.3E+02 0.0028 24.9 4.6 40 27-73 57-97 (285)
118 PRK06106 nicotinate-nucleotide 26.1 1.9E+02 0.0041 24.0 5.4 61 52-126 204-264 (281)
119 cd00363 PFK Phosphofructokinas 25.9 1.2E+02 0.0026 25.4 4.3 51 51-102 205-265 (338)
120 cd01841 NnaC_like NnaC (CMP-Ne 25.7 2.5E+02 0.0053 19.9 8.3 73 13-89 1-85 (174)
121 COG0561 Cof Predicted hydrolas 25.7 1.9E+02 0.0041 22.3 5.2 45 52-97 22-66 (264)
122 PRK03202 6-phosphofructokinase 25.4 2.3E+02 0.005 23.7 5.9 54 47-101 193-249 (320)
123 PRK02842 light-independent pro 25.3 3E+02 0.0064 23.6 6.7 65 11-87 289-358 (427)
124 TIGR02417 fruct_sucro_rep D-fr 25.2 3.3E+02 0.0072 21.2 8.3 75 10-93 176-264 (327)
125 PTZ00029 60S ribosomal protein 25.2 2.4E+02 0.0052 22.2 5.7 59 11-86 60-124 (216)
126 PRK04017 hypothetical protein; 25.2 2.9E+02 0.0062 20.5 6.4 62 14-87 24-91 (132)
127 PRK14484 phosphotransferase ma 25.0 2.7E+02 0.0059 20.2 6.3 11 78-88 45-55 (124)
128 PRK15424 propionate catabolism 24.9 1.7E+02 0.0038 26.3 5.4 52 10-72 105-160 (538)
129 COG0616 SppA Periplasmic serin 24.7 2E+02 0.0044 23.8 5.5 52 52-103 82-140 (317)
130 cd02525 Succinoglycan_BP_ExoA 24.7 2.5E+02 0.0054 20.6 5.5 48 53-100 13-64 (249)
131 PRK14190 bifunctional 5,10-met 24.7 1.5E+02 0.0033 24.5 4.6 41 26-73 56-97 (284)
132 cd01019 ZnuA Zinc binding prot 24.7 1.7E+02 0.0036 23.6 4.8 40 47-87 209-248 (286)
133 PRK09875 putative hydrolase; P 24.6 4E+02 0.0086 21.9 7.3 86 23-117 39-145 (292)
134 PRK14192 bifunctional 5,10-met 24.6 1.1E+02 0.0025 25.0 3.9 55 15-76 38-100 (283)
135 PF05193 Peptidase_M16_C: Pept 24.6 1.6E+02 0.0035 20.2 4.2 37 51-87 3-39 (184)
136 PRK09545 znuA high-affinity zi 24.6 1.8E+02 0.0038 23.9 5.0 40 47-87 233-272 (311)
137 PRK07714 hypothetical protein; 24.4 1.4E+02 0.0029 20.4 3.7 43 53-100 24-68 (100)
138 TIGR02463 MPGP_rel mannosyl-3- 24.0 2.6E+02 0.0057 20.8 5.6 43 53-96 19-62 (221)
139 PRK14171 bifunctional 5,10-met 24.0 1.5E+02 0.0033 24.6 4.5 41 27-74 57-98 (288)
140 cd06382 PBP1_iGluR_Kainate N-t 23.9 3.6E+02 0.0078 21.2 7.9 80 14-97 1-93 (327)
141 PF00154 RecA: recA bacterial 23.9 2.4E+02 0.0053 23.7 5.8 60 11-75 80-139 (322)
142 COG3412 Uncharacterized protei 23.8 3.1E+02 0.0067 20.4 6.3 21 68-88 3-25 (129)
143 COG0218 Predicted GTPase [Gene 23.8 3.7E+02 0.0081 21.3 6.9 76 43-121 111-197 (200)
144 PRK04031 DNA primase; Provisio 23.7 5.1E+02 0.011 22.8 10.1 102 5-121 162-265 (408)
145 PF00185 OTCace: Aspartate/orn 23.6 2E+02 0.0042 21.2 4.7 22 12-33 2-29 (158)
146 cd04179 DPM_DPG-synthase_like 23.6 1.8E+02 0.0038 20.4 4.4 65 53-121 10-80 (185)
147 PF01012 ETF: Electron transfe 23.5 1.8E+02 0.004 20.9 4.5 59 12-77 34-100 (164)
148 PF00532 Peripla_BP_1: Peripla 23.1 3.8E+02 0.0082 21.1 6.6 87 9-96 115-211 (279)
149 PRK09627 oorA 2-oxoglutarate-a 23.1 2.7E+02 0.0059 23.7 6.0 54 14-76 3-56 (375)
150 COG0673 MviM Predicted dehydro 22.7 2.3E+02 0.0051 22.4 5.3 63 59-124 59-121 (342)
151 cd01017 AdcA Metal binding pro 22.7 1.3E+02 0.0027 24.1 3.8 64 16-87 174-240 (282)
152 COG1154 Dxs Deoxyxylulose-5-ph 22.3 37 0.00081 31.3 0.7 45 7-51 133-179 (627)
153 PRK08576 hypothetical protein; 22.2 3.9E+02 0.0084 23.5 6.9 64 52-118 39-103 (438)
154 TIGR01282 nifD nitrogenase mol 22.2 3.9E+02 0.0084 23.4 6.9 64 11-86 334-401 (466)
155 PF04989 CmcI: Cephalosporin h 22.2 39 0.00084 26.8 0.7 42 81-125 24-69 (206)
156 TIGR00705 SppA_67K signal pept 22.1 2.6E+02 0.0057 25.2 6.0 50 52-101 331-388 (584)
157 PRK07119 2-ketoisovalerate fer 22.1 1.6E+02 0.0036 24.7 4.5 51 13-74 3-53 (352)
158 PRK04203 rpl1P 50S ribosomal p 22.0 3.9E+02 0.0084 20.9 6.7 62 11-88 57-124 (215)
159 PRK14072 6-phosphofructokinase 22.0 1.9E+02 0.0041 25.1 4.9 29 50-78 220-248 (416)
160 PF06348 DUF1059: Protein of u 21.9 1.4E+02 0.003 18.6 3.1 41 43-86 15-55 (57)
161 TIGR01452 PGP_euk phosphoglyco 21.9 4E+02 0.0088 21.0 8.8 23 12-34 85-107 (279)
162 PF01729 QRPTase_C: Quinolinat 21.8 1.3E+02 0.0028 22.8 3.4 62 52-125 90-152 (169)
163 cd06349 PBP1_ABC_ligand_bindin 21.8 4E+02 0.0087 21.0 8.2 72 21-98 17-98 (340)
164 cd02007 TPP_DXS Thiamine pyrop 21.8 83 0.0018 24.0 2.4 85 11-103 97-192 (195)
165 TIGR01334 modD putative molybd 21.8 3.1E+02 0.0068 22.5 6.0 62 52-125 198-260 (277)
166 cd01974 Nitrogenase_MoFe_beta 21.8 5E+02 0.011 22.2 7.4 46 11-65 302-351 (435)
167 PF08282 Hydrolase_3: haloacid 21.8 1.5E+02 0.0032 21.7 3.7 43 53-96 18-60 (254)
168 TIGR01662 HAD-SF-IIIA HAD-supe 21.7 2.7E+02 0.0059 18.9 6.6 36 53-89 28-71 (132)
169 PF12163 HobA: DNA replication 21.7 2.3E+02 0.0049 22.2 4.8 44 55-100 33-82 (180)
170 PRK11579 putative oxidoreducta 21.6 3.1E+02 0.0066 22.4 5.9 60 58-119 55-114 (346)
171 TIGR02329 propionate_PrpR prop 21.6 4.4E+02 0.0095 23.6 7.2 86 16-118 148-257 (526)
172 cd02069 methionine_synthase_B1 21.6 3.3E+02 0.0072 21.2 5.8 87 26-128 111-201 (213)
173 PF07905 PucR: Purine cataboli 21.6 1.3E+02 0.0029 21.1 3.3 49 52-101 58-108 (123)
174 PF05872 DUF853: Bacterial pro 21.5 1.5E+02 0.0033 26.7 4.3 34 53-87 277-321 (502)
175 TIGR02717 AcCoA-syn-alpha acet 21.5 5.3E+02 0.012 22.2 8.8 96 13-118 8-119 (447)
176 PF00378 ECH: Enoyl-CoA hydrat 21.4 2.9E+02 0.0063 21.2 5.5 49 52-100 27-99 (245)
177 PTZ00103 60S ribosomal protein 21.2 1.4E+02 0.0031 26.0 3.9 53 67-126 156-209 (390)
178 PF00763 THF_DHG_CYH: Tetrahyd 21.0 2E+02 0.0044 20.2 4.2 40 26-72 53-93 (117)
179 PRK05583 ribosomal protein L7A 20.9 2.1E+02 0.0046 19.9 4.2 41 53-97 23-65 (104)
180 TIGR01485 SPP_plant-cyano sucr 20.9 2.6E+02 0.0056 21.5 5.1 44 53-97 24-69 (249)
181 PRK00087 4-hydroxy-3-methylbut 20.8 1.2E+02 0.0027 27.5 3.7 20 3-22 104-123 (647)
182 cd06257 DnaJ DnaJ domain or J- 20.4 1.3E+02 0.0029 17.3 2.7 15 50-64 12-26 (55)
183 cd07393 MPP_DR1119 Deinococcus 20.4 3.5E+02 0.0076 20.8 5.8 63 53-118 29-97 (232)
184 PF02401 LYTB: LytB protein; 20.4 93 0.002 25.7 2.6 24 4-27 103-128 (281)
185 TIGR01487 SPP-like sucrose-pho 20.3 2.5E+02 0.0053 21.0 4.8 42 53-95 21-62 (215)
186 TIGR01482 SPP-subfamily Sucros 20.1 3.1E+02 0.0068 20.3 5.3 43 53-96 18-60 (225)
187 cd00959 DeoC 2-deoxyribose-5-p 20.1 4E+02 0.0086 20.2 6.9 40 47-87 11-50 (203)
188 PF05116 S6PP: Sucrose-6F-phos 20.1 2E+02 0.0044 22.6 4.4 40 54-93 19-61 (247)
189 PRK09590 celB cellobiose phosp 20.1 3.1E+02 0.0068 19.1 5.7 57 59-120 42-104 (104)
190 PLN02616 tetrahydrofolate dehy 20.0 1.7E+02 0.0037 25.3 4.1 40 27-73 128-168 (364)
No 1
>TIGR01101 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit
Probab=100.00 E-value=1.7e-35 Score=214.09 Aligned_cols=112 Identities=54% Similarity=0.937 Sum_probs=107.9
Q ss_pred ccccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcC
Q 032904 10 AASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHN 89 (130)
Q Consensus 10 ~~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~ 89 (130)
.++.+||||||+||++||+||||+.+...+++||++++++|+.+|++++|+++++++|||||+|||++++++++.|++|+
T Consensus 3 ~~~~~IaVIGD~Dtv~GF~LaGi~~~~~~~~~nf~~v~~~t~~eei~~~~~~~l~~~digIIlIte~~a~~i~~~I~~~~ 82 (115)
T TIGR01101 3 EKGKLIAVIGDEDTVVGFLLGGIGEINKNRHPNFLVVDKNTTVSEIEDCFNRFLKRDDIAIILINQHIAEMIRHAVDAHT 82 (115)
T ss_pred CCCcEEEEEecHHHHHHHHHhCCCccccccccceeeecCCCCHHHHHHHHHHHhhcCCeEEEEEcHHHHHHhHHHHHhcC
Confidence 45689999999999999999999998888899999999999999999999999999999999999999999999999999
Q ss_pred CCccEEEEcCCCCCCCChhhHHHHHHHHhhcc
Q 032904 90 KPIPAILEIPSKDHPYDPAQDSVLSRVKNLVS 121 (130)
Q Consensus 90 ~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiG 121 (130)
+.+|+||+|||+.++|++++|+|+++|++++|
T Consensus 83 ~~~PaIieIP~k~~~y~~~~d~i~~~~~~~~~ 114 (115)
T TIGR01101 83 RSIPAVLEIPSKDHPYDASKDSILRRARGMFN 114 (115)
T ss_pred CcCCEEEEECCCCCCCCCcccHHHHHHHHHcC
Confidence 99999999999999999999999999999988
No 2
>KOG3432 consensus Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion]
Probab=100.00 E-value=5.4e-36 Score=214.44 Aligned_cols=115 Identities=60% Similarity=0.981 Sum_probs=111.1
Q ss_pred ccccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcC
Q 032904 10 AASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHN 89 (130)
Q Consensus 10 ~~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~ 89 (130)
..++.||||||+||++||+|+|++.++.+++|||++++..|+.++++++|+++++|+|++||+|+|.+|++||+.|+.|+
T Consensus 5 ~~~~liavIgDEDT~tGfLlaGvg~v~~~r~~Nf~vv~~~Tt~~eiedaF~~f~~RdDIaIiLInq~~Ae~iR~~vD~h~ 84 (121)
T KOG3432|consen 5 DKRTLIAVIGDEDTVTGFLLAGVGEVNENREPNFLVVDSKTTVEEIEDAFKSFTARDDIAIILINQFIAEMIRDRVDAHT 84 (121)
T ss_pred ccCcEEEEeccccceeeeeeecccccccCCCCCEEEEeccCCHHHHHHHHHhhccccCeEEEEEhHHHHHHHHHHHHhcc
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCC
Q 032904 90 KPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVES 124 (130)
Q Consensus 90 ~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi 124 (130)
+..|+|++||||++||++++|+|.+++++.+|-+-
T Consensus 85 ~~vPAvLeIpSKdhPYd~~kDSiL~R~r~~f~~e~ 119 (121)
T KOG3432|consen 85 QAVPAVLEIPSKDHPYDPSKDSILRRARGLFGPED 119 (121)
T ss_pred ccCCeeEEecCCCCCCCchHHHHHHHHHhccChhh
Confidence 99999999999999999999999999999998653
No 3
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=99.97 E-value=1.4e-31 Score=190.42 Aligned_cols=101 Identities=20% Similarity=0.395 Sum_probs=93.3
Q ss_pred ccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcC-C
Q 032904 12 SALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHN-K 90 (130)
Q Consensus 12 ~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~-~ 90 (130)
.+|||||||+||++||||+|+++ |+++++ ++++++++++. ++|||||+|||++++.+++.+++|+ +
T Consensus 3 ~~kIaVIGD~dtv~GFrLaGi~~--------~~v~~~----ee~~~~i~~l~-~~d~gII~Ite~~a~~i~~~i~~~~~~ 69 (104)
T PRK01395 3 MYKIGVVGDKDSILPFKALGIDV--------FPVIDE----QEAINTLRKLA-MEDYGIIYITEQIAADIPETIERYDNQ 69 (104)
T ss_pred ceeEEEEECHHHHHHHHHcCCee--------EEecCh----HHHHHHHHHHh-cCCcEEEEEcHHHHHHhHHHHHHhcCC
Confidence 47999999999999999999964 788776 99999999876 8999999999999999999999996 6
Q ss_pred CccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 91 PIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 91 ~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
..|+|++|||++|+.+.+.++|+++|+||||+||+
T Consensus 70 ~~P~Il~IP~~~g~~~~g~~~i~~~v~kAIG~~i~ 104 (104)
T PRK01395 70 VLPAIILIPSNQGSLGIGLSRIQDNVEKAVGQNIL 104 (104)
T ss_pred CCCEEEEeCCCCCCccccHHHHHHHHHHHhCcccC
Confidence 99999999999998876788999999999999985
No 4
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=99.97 E-value=2e-31 Score=188.13 Aligned_cols=99 Identities=34% Similarity=0.593 Sum_probs=92.0
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCc
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPI 92 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~ 92 (130)
+|||||||+||++||||+|++++ |++.++ +|++++|+++++++|||||+||+++++.+++.++ +..
T Consensus 1 mkIaVIgD~dtv~GFrLaGi~~~-------~~v~~~----ee~~~~l~~l~~~~d~gII~ite~~~~~i~~~i~---~~~ 66 (100)
T PRK03957 1 MKIAVVGDRDTVTGFRLAGLTEV-------YEVKNP----EEAKNAIKELVENDEIGIIIITERIAEEIRDLIS---VAL 66 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCCce-------EEeCCH----HHHHHHHHHHhhCCCeEEEEEcHHHHHHHHHHHh---cCC
Confidence 48999999999999999999876 676554 9999999999999999999999999999999988 778
Q ss_pred cEEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 93 PAILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 93 P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
|+|++||+++|+++.++++|+++|+||+|+||-
T Consensus 67 P~Ii~IP~~~g~~~~~~~~i~~~v~raiG~dI~ 99 (100)
T PRK03957 67 PIIVEIPDKSGSIERENDPVKELVRRAIGVEMK 99 (100)
T ss_pred CEEEEECCCCCCCccchHHHHHHHHHHhCcccc
Confidence 999999999999999889999999999999983
No 5
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=99.96 E-value=2.3e-29 Score=177.51 Aligned_cols=97 Identities=19% Similarity=0.364 Sum_probs=87.4
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh-c-CC
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS-H-NK 90 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~-~-~~ 90 (130)
+|||||||+||++||||+|++++ |++.++ +|++++|+++++++|||||+|||++++.+.+.+++ + ++
T Consensus 1 mkIaVIGD~dtv~GFrLaGi~~~-------~~~~~~----ee~~~~l~~l~~~~d~gII~Ite~~~~~i~e~i~~~~~~~ 69 (100)
T PRK02228 1 MEIAVIGSPEFTTGFRLAGIRKV-------YEVPDD----EKLDEAVEEVLEDDDVGILVMHDDDLEKLPRRLRRTLEES 69 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCceE-------EeeCCH----HHHHHHHHHHhhCCCEEEEEEehhHhHhhHHHHHHHHhcC
Confidence 58999999999999999999886 556443 89999999999999999999999999999999998 4 49
Q ss_pred CccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 91 PIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 91 ~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
..|+|++||+..|+ ++|+++|+||||+||-
T Consensus 70 ~~P~ii~IP~~~~~-----~~i~~~v~raIG~di~ 99 (100)
T PRK02228 70 VEPTVVTLGGGGGS-----GGLREKIKRAIGVDLW 99 (100)
T ss_pred CCCEEEEECCCccc-----hHHHHHHHHHhCcccc
Confidence 99999999986664 7899999999999984
No 6
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=99.96 E-value=7.3e-29 Score=176.58 Aligned_cols=99 Identities=18% Similarity=0.311 Sum_probs=83.7
Q ss_pred ccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHH-HHHhhcC-
Q 032904 12 SALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIR-FLVDSHN- 89 (130)
Q Consensus 12 ~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~-~~i~~~~- 89 (130)
.+|||||||+||++||||+|++++ |++.++ +++++.+ +.+++++||||++||++++.+. +++++|+
T Consensus 2 ~~kIaVvGd~DtilGFrlaGi~~v-------~~~~~~----e~~~~~~-~~l~~~~~gII~iTE~~a~~i~~~~i~~~~~ 69 (104)
T PRK01189 2 MSCITVIGERDVVLGFRLLGIGDT-------IEAEGK----DLVKKFL-EIFNNPKCKYIFVSESTKNMFDKNTLRSLES 69 (104)
T ss_pred CceEEEEcCHHHHHHHHHcCCceE-------EEcCCH----HHHHHHH-HHHhcCCeEEEEEEHHHHhhCCHHHHHHHhc
Confidence 368999999999999999999887 777554 6665544 4667999999999999999999 7999986
Q ss_pred CCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 90 KPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 90 ~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
+..|+||+||.++ ..+ +++|+++|++|+|+||.
T Consensus 70 ~~~P~II~Ipipg-~~~--~~~i~~~ik~aiGvd~~ 102 (104)
T PRK01189 70 SSKPLVVFIPLPG-ISE--EESIEEMAKRILGIDIG 102 (104)
T ss_pred cCCCeEEEEeCCC-Ccc--chhHHHHHHHHhccccc
Confidence 9999999877763 322 57999999999999983
No 7
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=99.94 E-value=9.8e-27 Score=161.59 Aligned_cols=92 Identities=40% Similarity=0.621 Sum_probs=85.1
Q ss_pred EEEEechhhHHHHHHhcccccccCCcceeEEe-cCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhc--CCC
Q 032904 15 IAMIADEDTVVGFLLAGVGNVDLRRKTNYLIV-DSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSH--NKP 91 (130)
Q Consensus 15 IaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~-~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~--~~~ 91 (130)
||||||+||++||||+|+++ |++. + .++++++|+++++++|+|||++|+++++.+++.++++ ++.
T Consensus 1 IavIGd~~~v~gFrLaGv~~--------~~~~~~----~ee~~~~l~~l~~~~~~gIIii~e~~~~~~~~~l~~~~~~~~ 68 (95)
T PF01990_consen 1 IAVIGDRDTVLGFRLAGVEG--------VYVNTD----PEEAEEALKELLKDEDVGIIIITEDLAEKIRDELDEYREESS 68 (95)
T ss_dssp EEEEE-HHHHHHHHHTTSEE--------EEESHS----HHHHHHHHHHHHHHTTEEEEEEEHHHHTTHHHHHHHHHHTSS
T ss_pred CEEEeCHHHHHHHHHcCCCC--------ccCCCC----HHHHHHHHHHHhcCCCccEEEeeHHHHHHHHHHHHHHHhccC
Confidence 79999999999999999988 4665 5 4999999999999999999999999999999999999 589
Q ss_pred ccEEEEcCCCCCCCChhhHHHHHHHHh
Q 032904 92 IPAILEIPSKDHPYDPAQDSVLSRVKN 118 (130)
Q Consensus 92 ~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ 118 (130)
.|+|++||++.++++.+.++|+++|||
T Consensus 69 ~P~iv~IP~~~~~~~~~~~~i~~~v~r 95 (95)
T PF01990_consen 69 LPLIVEIPSKEGSMGREKDSIRELVKR 95 (95)
T ss_dssp SSEEEEESTTCCCTSSCCHHHHHHHHH
T ss_pred CceEEEcCCCCCCCCcchHHHHHHhcC
Confidence 999999999999988889999999986
No 8
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=99.93 E-value=1.9e-26 Score=164.36 Aligned_cols=99 Identities=33% Similarity=0.526 Sum_probs=85.4
Q ss_pred ccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHH-HHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhc--
Q 032904 12 SALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIK-QIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSH-- 88 (130)
Q Consensus 12 ~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~e-ei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~-- 88 (130)
+++||||||+||++||||+|++++ |++.++ + ++.++++.+.++ |||||+||+++++++++.++++
T Consensus 2 ~~~I~VIGd~dtvtGFrLaGv~~~-------~v~~~~----~~~~~~~~~~l~~~-~~~iIiite~~a~~i~~~i~~~~~ 69 (104)
T COG1436 2 MMKIAVIGDRDTVTGFRLAGVRVV-------YVADDE----EDELRAALRVLAED-DVGIILITEDLAEKIREEIRRIIR 69 (104)
T ss_pred ceEEEEEEccchhhceeeecceeE-------EEecCh----hHHHHHHHHhhccC-CceEEEEeHHHHhhhHHHHHHHhh
Confidence 479999999999999999999986 556554 4 688999988755 9999999999999999999999
Q ss_pred CCCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 89 NKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 89 ~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
.+.+|+||+|||++ . .+.+.++++|+|+||+++.
T Consensus 70 ~~~~P~iv~IPs~~-~--~~~~~~~~~I~k~vG~~i~ 103 (104)
T COG1436 70 SSVLPAIVEIPSPG-K--EEEEPLRELIRRAVGVDIG 103 (104)
T ss_pred ccCccEEEEeCCCC-C--CccchHHHHHHHHHhhhhc
Confidence 48899999999972 2 2247899999999999985
No 9
>COG4075 Uncharacterized conserved protein, homolog of nitrogen regulatory protein PII [Function unknown]
Probab=94.40 E-value=0.058 Score=38.60 Aligned_cols=75 Identities=16% Similarity=0.281 Sum_probs=49.9
Q ss_pred hHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEE-EEehhhHHHHHHHHhhc-CCCccEEEEcCC
Q 032904 23 TVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIV-LISQYVANRIRFLVDSH-NKPIPAILEIPS 100 (130)
Q Consensus 23 tv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digII-lIte~~a~~i~~~i~~~-~~~~P~Iv~IPs 100 (130)
-+|||-|.--.|+.+.+-.+|...++ ++.+-++++++. ++-+-|. ++.|...+.|.+.+.+- .+..=+|++||=
T Consensus 27 GiTGFfl~eYrGvsPd~wkgf~~~ED---pE~aik~i~D~s-~~AVlI~tVV~Ee~vekie~~~~Ekla~eryTIi~ipI 102 (110)
T COG4075 27 GITGFFLHEYRGVSPDKWKGFSKEED---PESAIKAIRDLS-DKAVLIGTVVKEEKVEKIEELLKEKLANERYTIIEIPI 102 (110)
T ss_pred CcceEEEEEecCcChhHhcCcccccC---HHHHHHHHHHhh-hceEEEEEecCHHHHHHHHHHHHHHhcCCceEEEEeee
Confidence 36777777666666667777777543 588888888875 3332222 45678888888877653 455668899885
Q ss_pred C
Q 032904 101 K 101 (130)
Q Consensus 101 ~ 101 (130)
.
T Consensus 103 ~ 103 (110)
T COG4075 103 E 103 (110)
T ss_pred e
Confidence 3
No 10
>PF10126 Nit_Regul_Hom: Uncharacterized protein, homolog of nitrogen regulatory protein PII; InterPro: IPR019296 This family consists of various hypothetical archaeal proteins. It includes a putative nitrogen regulatory protein PII homolog.
Probab=90.50 E-value=0.45 Score=34.39 Aligned_cols=71 Identities=17% Similarity=0.339 Sum_probs=43.6
Q ss_pred HHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEE---EEehhhHHHHHHHHhh-cCCCccEEEEcC
Q 032904 24 VVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIV---LISQYVANRIRFLVDS-HNKPIPAILEIP 99 (130)
Q Consensus 24 v~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digII---lIte~~a~~i~~~i~~-~~~~~P~Iv~IP 99 (130)
++||-|-=..|..+.+-.+|...++ ++.+-++++++.. + +|+ +++++.++.|.+.+.+ ++...=+|++||
T Consensus 28 ITGFyl~eYkGmSP~~wkgf~l~ED---pe~ai~~I~d~s~--~-aV~I~TVV~~~~~~~i~~~i~ekL~~eryTii~iP 101 (110)
T PF10126_consen 28 ITGFYLHEYKGMSPQDWKGFLLDED---PEMAIKAINDLSE--N-AVLIGTVVDEEKVEKIEKLIKEKLKNERYTIIEIP 101 (110)
T ss_pred ccEEEeEeecCCChHHhcCcccccC---HHHHHHHHHHhcc--C-cEEEEEEECHHHHHHHHHHHHHHhcCCceEEEEee
Confidence 4566655444444444444654332 4777777777642 2 333 4668888888888866 356666888888
Q ss_pred C
Q 032904 100 S 100 (130)
Q Consensus 100 s 100 (130)
=
T Consensus 102 i 102 (110)
T PF10126_consen 102 I 102 (110)
T ss_pred E
Confidence 4
No 11
>PLN00124 succinyl-CoA ligase [GDP-forming] subunit beta; Provisional
Probab=83.94 E-value=7.1 Score=33.98 Aligned_cols=64 Identities=20% Similarity=0.376 Sum_probs=51.3
Q ss_pred CcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--------ehhhHHHHHHHHhhcCCCccEEEEcCCCC
Q 032904 39 RKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--------SQYVANRIRFLVDSHNKPIPAILEIPSKD 102 (130)
Q Consensus 39 ~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--------te~~a~~i~~~i~~~~~~~P~Iv~IPs~~ 102 (130)
+--||.=..-.++.+.+.++|+-+++++.+-+||| |+.+|+-|-+.+.++....|.||-+.+.+
T Consensus 317 ~pANFlD~GG~a~~~~v~~a~~ii~~d~~vk~iliNIfGGI~~cd~iA~gii~a~~~~~~~~pivvRl~Gtn 388 (422)
T PLN00124 317 SPANFLDVGGNASEQQVVEAFKILTSDDKVKAILVNIFGGIMKCDVIASGIVNAAKQVGLKVPLVVRLEGTN 388 (422)
T ss_pred CcceeeecCCCCCHHHHHHHHHHHhcCCCCcEEEEEecCCccchHHHHHHHHHHHHhcCCCCcEEEEcCCCC
Confidence 34578877777888999999999999999999998 46677766666666667799999887755
No 12
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 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 [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=74.50 E-value=30 Score=25.84 Aligned_cols=86 Identities=20% Similarity=0.257 Sum_probs=54.2
Q ss_pred ccccEEEEEechhhHHHH----HHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHH
Q 032904 10 AASALIAMIADEDTVVGF----LLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLV 85 (130)
Q Consensus 10 ~~~~kIaVIGD~dtv~GF----rLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i 85 (130)
....+||++|-+..+.++ .+.|++-. .|...+ .+|++..++++. ++.+.+|+=.....+..+.
T Consensus 75 ~~~~~Iavv~~~~~~~~~~~~~~ll~~~i~------~~~~~~----~~e~~~~i~~~~-~~G~~viVGg~~~~~~A~~-- 141 (176)
T PF06506_consen 75 KYGPKIAVVGYPNIIPGLESIEELLGVDIK------IYPYDS----EEEIEAAIKQAK-AEGVDVIVGGGVVCRLARK-- 141 (176)
T ss_dssp CCTSEEEEEEESS-SCCHHHHHHHHT-EEE------EEEESS----HHHHHHHHHHHH-HTT--EEEESHHHHHHHHH--
T ss_pred hcCCcEEEEecccccHHHHHHHHHhCCceE------EEEECC----HHHHHHHHHHHH-HcCCcEEECCHHHHHHHHH--
Confidence 345899999998777654 45677432 244544 499999999887 5678888877665444432
Q ss_pred hhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhc
Q 032904 86 DSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLV 120 (130)
Q Consensus 86 ~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ai 120 (130)
..+|.++.- .+.++|+..+.+|+
T Consensus 142 ----~gl~~v~i~--------sg~esi~~Al~eA~ 164 (176)
T PF06506_consen 142 ----LGLPGVLIE--------SGEESIRRALEEAL 164 (176)
T ss_dssp ----TTSEEEESS----------HHHHHHHHHHHH
T ss_pred ----cCCcEEEEE--------ecHHHHHHHHHHHH
Confidence 557765432 23578888888875
No 13
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=70.89 E-value=30 Score=30.12 Aligned_cols=84 Identities=20% Similarity=0.290 Sum_probs=64.3
Q ss_pred cEEEEEechh-----hHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--------hhhHH
Q 032904 13 ALIAMIADED-----TVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--------QYVAN 79 (130)
Q Consensus 13 ~kIaVIGD~d-----tv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt--------e~~a~ 79 (130)
-.|++|++-. |.-=-+|.|-+. .||+=+.-..+.+.+.++|+-+++++.+-.|||+ +.+|+
T Consensus 256 G~IG~ivNGAGLaMaTmDii~~~Gg~P------ANFLDvGGgA~~e~v~~a~~~il~d~~vk~IfVNIfGGI~rcD~vA~ 329 (387)
T COG0045 256 GNIGCIVNGAGLAMATMDIVKLYGGKP------ANFLDVGGGATAERVKEAFKLILSDPNVKAIFVNIFGGITRCDEVAE 329 (387)
T ss_pred CcEEEEecChhHHHHHHHHHHHcCCCC------cceeecCCCCCHHHHHHHHHHHhcCCCccEEEEEEccCcCccHHHHH
Confidence 4688888732 222344556644 4788666677889999999999999999999986 55788
Q ss_pred HHHHHHhhcCCCccEEEEcCCCC
Q 032904 80 RIRFLVDSHNKPIPAILEIPSKD 102 (130)
Q Consensus 80 ~i~~~i~~~~~~~P~Iv~IPs~~ 102 (130)
-+-.-+.++....|+||-+-+.+
T Consensus 330 GIi~Al~e~~~~vPlVVRL~GtN 352 (387)
T COG0045 330 GIIAALKEVGVNVPLVVRLEGTN 352 (387)
T ss_pred HHHHHHHhcCCCCCEEEEcCCCC
Confidence 88888888888899999997755
No 14
>PF01886 DUF61: Protein of unknown function DUF61; InterPro: IPR002746 The proteins in this entry are functionally uncharacterised.
Probab=69.77 E-value=15 Score=27.12 Aligned_cols=70 Identities=20% Similarity=0.320 Sum_probs=47.2
Q ss_pred HHHHHHHhcCCCeeEEEE-------ehhhHHHHHHHHhhc---CCCccEEEEc-CCCC-CCCChhhHHHHHHHHhhcccC
Q 032904 56 EDAFKEFTSREDIAIVLI-------SQYVANRIRFLVDSH---NKPIPAILEI-PSKD-HPYDPAQDSVLSRVKNLVSVE 123 (130)
Q Consensus 56 ~~~~~~l~~~~digIIlI-------te~~a~~i~~~i~~~---~~~~P~Iv~I-Ps~~-g~~~~~~d~I~~~Vk~aiGid 123 (130)
+.+|.++++.++-.|++- ...-.+.+.+.+..+ +-.+|.|+++ |+.+ |.+-.....=.+.|++++|.+
T Consensus 20 rktL~eLL~ee~P~i~lrdG~~h~f~k~ELe~L~~~lp~~~~~~lrLPIile~~~~~~~g~~~V~g~~e~k~i~~ilg~~ 99 (132)
T PF01886_consen 20 RKTLKELLEEEKPSIILRDGSRHRFDKEELERLAEILPEYEWSKLRLPIILEIDPTLGEGSYRVRGKEEVKAISKILGKE 99 (132)
T ss_pred hhhHHHHHhCCCCeEEecCCCEEEEcHHHHHHHHHhCCHHHHhceeccEEEEEeccCCCceEEEeCHHHHHHHHHHhCCC
Confidence 477889997777777763 333556677766664 3679999999 7743 444332233567788888887
Q ss_pred Cc
Q 032904 124 SV 125 (130)
Q Consensus 124 i~ 125 (130)
..
T Consensus 100 ~~ 101 (132)
T PF01886_consen 100 RE 101 (132)
T ss_pred cc
Confidence 63
No 15
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=68.83 E-value=8.6 Score=26.24 Aligned_cols=14 Identities=29% Similarity=0.406 Sum_probs=6.3
Q ss_pred hhhHHHHHHhcccc
Q 032904 21 EDTVVGFLLAGVGN 34 (130)
Q Consensus 21 ~dtv~GFrLaGi~~ 34 (130)
.|.+.....+|+.+
T Consensus 51 ~di~~~a~~~~i~~ 64 (105)
T PF07085_consen 51 EDIQLAAIEAGIAC 64 (105)
T ss_dssp HHHHHHHCCTTECE
T ss_pred HHHHHHHHHhCCCE
Confidence 44444444444444
No 16
>PRK14046 malate--CoA ligase subunit beta; Provisional
Probab=65.06 E-value=62 Score=27.67 Aligned_cols=82 Identities=18% Similarity=0.313 Sum_probs=49.8
Q ss_pred cEEEEEechh--hHHH---HHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh--------hhHH
Q 032904 13 ALIAMIADED--TVVG---FLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ--------YVAN 79 (130)
Q Consensus 13 ~kIaVIGD~d--tv~G---FrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte--------~~a~ 79 (130)
-.|++|++-- +.+. ....|.. ..||+=.....+.+.+.++|+.+++++++..|++.- .+++
T Consensus 257 G~ig~i~nGaGl~m~t~D~i~~~gg~------paNPlDlgg~a~~e~~~~aL~~ll~Dp~VdaVlv~i~ggi~~~~~vA~ 330 (392)
T PRK14046 257 GDIGCIVNGAGLAMATMDMIKLAGGE------PANFLDVGGGASPERVAKAFRLVLSDRNVKAILVNIFAGINRCDWVAE 330 (392)
T ss_pred CcEEEEeCCccHHHHHHHHHHhcCCC------CcCCEEecCCCCHHHHHHHHHHHHcCCCCCEEEEEcCCCCCCHHHHHH
Confidence 4688888721 2222 2333432 245664444467799999999999999998888632 2444
Q ss_pred HHHHHHhhcCCCccEEEEcCC
Q 032904 80 RIRFLVDSHNKPIPAILEIPS 100 (130)
Q Consensus 80 ~i~~~i~~~~~~~P~Iv~IPs 100 (130)
.+.+...+.....|+++-+.+
T Consensus 331 ~Ii~a~~~~~~~kPvvv~l~G 351 (392)
T PRK14046 331 GVVQAAREVGIDVPLVVRLAG 351 (392)
T ss_pred HHHHHHHhcCCCCcEEEEcCC
Confidence 444434332346798887744
No 17
>PRK06555 pyrophosphate--fructose-6-phosphate 1-phosphotransferase; Validated
Probab=64.68 E-value=19 Score=31.34 Aligned_cols=30 Identities=7% Similarity=0.083 Sum_probs=24.7
Q ss_pred CCcHHHHHHHHHHHhcCCCeeEEEEehhhH
Q 032904 49 KTTIKQIEDAFKEFTSREDIAIVLISQYVA 78 (130)
Q Consensus 49 ~~~~eei~~~~~~l~~~~digIIlIte~~a 78 (130)
..+.+++.+.+++.++++.++||+++|.+.
T Consensus 241 ~~~~e~~~~~ik~~~~~k~~~iIvVaEG~~ 270 (403)
T PRK06555 241 AFDLEAEAERLKAVMDEVGNVNIFLSEGAG 270 (403)
T ss_pred CCCHHHHHHHHHHHHHhCCCEEEEEeCCCC
Confidence 346688888888888889999999999973
No 18
>PF00549 Ligase_CoA: CoA-ligase; InterPro: IPR005811 This entry represents a domain found in both the alpha and beta chains of succinyl-CoA synthase (6.2.1.4 from EC (GDP-forming) and 6.2.1.5 from EC (ADP-forming)) [, ]. This domain can also be found in ATP citrate synthase (2.3.3.8 from EC) and malate-CoA ligase (6.2.1.9 from EC). Some members of the domain utilise ATP others use GTP.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3DMY_B 3MWE_B 3PFF_A 3MWD_B 2YV1_A 1EUC_A 2FP4_A 1EUD_A 2FPI_A 2FPG_A ....
Probab=63.64 E-value=37 Score=25.52 Aligned_cols=53 Identities=8% Similarity=0.156 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehh--------hHHHHHHHHhhcC---CCccEEEEcCCCCCC
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQY--------VANRIRFLVDSHN---KPIPAILEIPSKDHP 104 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~--------~a~~i~~~i~~~~---~~~P~Iv~IPs~~g~ 104 (130)
.+...+.|..+.+++++++||+.=. .+..+-+.+.+.+ ...|+|+.+=+....
T Consensus 58 ~~~~~~~l~~~~~Dp~v~vIlvd~~~G~g~~~~~A~~l~~a~~~~~~~~~~~pvVa~v~GT~~d 121 (153)
T PF00549_consen 58 PSTRNEALEIEAADPEVKVILVDIVGGIGSCEDPAAGLIPAIKEAKAEGRKKPVVARVCGTNAD 121 (153)
T ss_dssp SSHHHHHHHHHHTSTTESEEEEEEESSSSSHHHHHHHHHHHHSHCTHTTT-SEEEEEEESTTCH
T ss_pred HHHHHHHHHHHhcCCCccEEEEEeccccCchHHHHHHHHHHHHhccccCCCCcEEEEeeeecCC
Confidence 5788999999999999999999833 3444444444444 577999999776644
No 19
>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=63.45 E-value=38 Score=23.21 Aligned_cols=85 Identities=11% Similarity=-0.012 Sum_probs=45.1
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe-hhhHHHHHHHHhhcCCCcc--EEEEcCCCC
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS-QYVANRIRFLVDSHNKPIP--AILEIPSKD 102 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt-e~~a~~i~~~i~~~~~~~P--~Iv~IPs~~ 102 (130)
-|+..|++.+ | ...+++.+++.+++.+. +.|+=.|-.+ ..-...+++.++.+++..| ..+-+.+..
T Consensus 22 ~l~~~G~~V~-------~--lg~~~~~~~l~~~~~~~--~pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vGG~~ 90 (119)
T cd02067 22 ALRDAGFEVI-------D--LGVDVPPEEIVEAAKEE--DADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVGGAI 90 (119)
T ss_pred HHHHCCCEEE-------E--CCCCCCHHHHHHHHHHc--CCCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEECCC
Confidence 3556677543 1 23456678777776643 4443333333 4455666776666654444 445566654
Q ss_pred CCCChhhHHHHHHHHhhcccCCcccc
Q 032904 103 HPYDPAQDSVLSRVKNLVSVESVASD 128 (130)
Q Consensus 103 g~~~~~~d~I~~~Vk~aiGidi~~~~ 128 (130)
-+..+ ..-+.+|+|-+..+
T Consensus 91 ~~~~~-------~~~~~~G~D~~~~~ 109 (119)
T cd02067 91 VTRDF-------KFLKEIGVDAYFGP 109 (119)
T ss_pred CChhH-------HHHHHcCCeEEECC
Confidence 33111 13457788765543
No 20
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=60.08 E-value=86 Score=25.18 Aligned_cols=71 Identities=14% Similarity=0.198 Sum_probs=47.6
Q ss_pred hhhHHHHHHh-----------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhh
Q 032904 21 EDTVVGFLLA-----------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDS 87 (130)
Q Consensus 21 ~dtv~GFrLa-----------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~ 87 (130)
.+...|++|+ |+.+ ++-.+++.|...+++...+.+++|++++++-+|+ .+...+..+...+++
T Consensus 17 ~~~~~g~~lA~~~iN~~GGi~~i~G----~~v~lv~~D~~~~~~~a~~~~~~li~~~~v~aiiG~~~s~~~~a~~~~~~~ 92 (347)
T cd06340 17 QQCKAGAELAVEEINAAGGIKSLGG----AKLELVFGDSQGNPDIGATEAERLITEEGVVALVGAYQSAVTLAASQVAER 92 (347)
T ss_pred HHHHHHHHHHHHHHHhcCCccCCCC----ceEEEEEecCCCCHHHHHHHHHHHhccCCceEEecccchHhHHHHHHHHHH
Confidence 4456788887 2333 2334566676667788999999999877776666 345556677777776
Q ss_pred cCCCccEEEE
Q 032904 88 HNKPIPAILE 97 (130)
Q Consensus 88 ~~~~~P~Iv~ 97 (130)
+ ..|.|..
T Consensus 93 ~--~ip~i~~ 100 (347)
T cd06340 93 Y--GVPFVVD 100 (347)
T ss_pred h--CCCEEec
Confidence 4 4777754
No 21
>PRK04115 hypothetical protein; Provisional
Probab=57.24 E-value=34 Score=25.64 Aligned_cols=69 Identities=17% Similarity=0.237 Sum_probs=45.2
Q ss_pred HHHHHHHhcCCCeeEEE-------EehhhHHHHHHHHhhc--CCCccEEEEcCCCC--CCCChhhHHHHHHHHhhcccCC
Q 032904 56 EDAFKEFTSREDIAIVL-------ISQYVANRIRFLVDSH--NKPIPAILEIPSKD--HPYDPAQDSVLSRVKNLVSVES 124 (130)
Q Consensus 56 ~~~~~~l~~~~digIIl-------Ite~~a~~i~~~i~~~--~~~~P~Iv~IPs~~--g~~~~~~d~I~~~Vk~aiGidi 124 (130)
+.+|.++++.++-.|++ +..+=.+.+++.++.+ +-.+|.|+++-+.. |.+-.....=-+-|++++|.+.
T Consensus 23 rktL~eLL~e~~P~i~lrdGs~h~~kr~ELe~L~~~l~~~~~~lrLPIile~~~~~~~g~~~VrG~~evk~IskiLg~~~ 102 (137)
T PRK04115 23 RKTLCELLKEDKPHVILRDGSRHRIKRRELEFLKELLDEDACRLRLPIILEIDSSLGEGAIVVRGKEEVKVISKILGKED 102 (137)
T ss_pred HHHHHHHHhCCCCeEEecCCceEEecHHHHHHHHHhccchhhheeeeEEEEEecCCCceEEEEcCHHHHHHHHHHhCccc
Confidence 57888999767777766 3333455667766554 36799999987755 4332211224567889999885
No 22
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=57.13 E-value=97 Score=24.60 Aligned_cols=72 Identities=18% Similarity=0.280 Sum_probs=47.3
Q ss_pred hhhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCC
Q 032904 21 EDTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNK 90 (130)
Q Consensus 21 ~dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~ 90 (130)
++...|++|+ |+.+ ++-.+++.|...+++...++.++|+.++.+-+|+= +......+....++ .
T Consensus 17 ~~~~~g~~~a~~~iNa~ggi~G----~~v~lv~~D~~~~p~~a~~~~~~li~~~~v~~iiG~~~s~~~~a~~~~~~~--~ 90 (344)
T cd06348 17 QEQLAGLKLAEDRFNQAGGVNG----RPIKLVIEDSGGDEAEAINAFQTLINKDRVLAIIGPTLSQQAFAADPIAER--A 90 (344)
T ss_pred HhHHHHHHHHHHHHhhcCCcCC----cEEEEEEecCCCChHHHHHHHHHHhhhcCceEEECCCCcHHHHhhhHHHHh--C
Confidence 4677788775 5644 23346777777788999999999997767755552 23344455555555 4
Q ss_pred CccEEEEc
Q 032904 91 PIPAILEI 98 (130)
Q Consensus 91 ~~P~Iv~I 98 (130)
..|.|..-
T Consensus 91 ~ip~i~~~ 98 (344)
T cd06348 91 GVPVVGPS 98 (344)
T ss_pred CCCEEecc
Confidence 57877643
No 23
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=55.45 E-value=71 Score=26.85 Aligned_cols=36 Identities=17% Similarity=0.237 Sum_probs=27.3
Q ss_pred CCCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCccc
Q 032904 89 NKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESVAS 127 (130)
Q Consensus 89 ~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~~~ 127 (130)
+...|+||.|.+..|- |+.+|...+-+-+|+++..|
T Consensus 85 ~~~~p~IILIGGasGV---GkStIA~ElA~rLgI~~vis 120 (299)
T COG2074 85 KMKRPLIILIGGASGV---GKSTIAGELARRLGIRSVIS 120 (299)
T ss_pred ccCCCeEEEecCCCCC---ChhHHHHHHHHHcCCceeec
Confidence 3778999999987764 56777777777777777654
No 24
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=55.13 E-value=62 Score=25.33 Aligned_cols=70 Identities=21% Similarity=0.253 Sum_probs=46.6
Q ss_pred hhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCCC
Q 032904 22 DTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNKP 91 (130)
Q Consensus 22 dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~~ 91 (130)
+...|++|+ ||.+. +-.+++.|...+.+...+..++++.++++-+|+- +...+..+.+.+++ ..
T Consensus 20 ~~~~g~~~a~~~~N~~ggi~G~----~i~l~~~D~~~~~~~a~~~~~~l~~~~~v~~vvg~~~s~~~~~~~~~~~~--~~ 93 (343)
T PF13458_consen 20 DFLRGAELAVDEINAAGGINGR----KIELVVYDDGGDPAQAVQAARKLIDDDGVDAVVGPLSSAQAEAVAPIAEE--AG 93 (343)
T ss_dssp HHHHHHHHHHHHHHHTTEETTE----EEEEEEEE-TT-HHHHHHHHHHHHHTSTESEEEESSSHHHHHHHHHHHHH--HT
T ss_pred HHHHHHHHHHHHHHHhCCcCCc----cceeeeccCCCChHHHHHHHHHhhhhcCcEEEEecCCcHHHHHHHHHHHh--cC
Confidence 445666665 44332 2335666666678999999999998788877775 46677788887877 44
Q ss_pred ccEEEE
Q 032904 92 IPAILE 97 (130)
Q Consensus 92 ~P~Iv~ 97 (130)
.|.|.+
T Consensus 94 ip~i~~ 99 (343)
T PF13458_consen 94 IPYISP 99 (343)
T ss_dssp -EEEES
T ss_pred cEEEEe
Confidence 777773
No 25
>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=54.59 E-value=1.3e+02 Score=25.27 Aligned_cols=83 Identities=18% Similarity=0.271 Sum_probs=50.9
Q ss_pred ccEEEEEechh-----hHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh--------hhH
Q 032904 12 SALIAMIADED-----TVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ--------YVA 78 (130)
Q Consensus 12 ~~kIaVIGD~d-----tv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte--------~~a 78 (130)
.-+|++|++-- |.--+...|.. ..||+=.....+.+.+.++|+.+++++++..|++.- .++
T Consensus 256 ~G~i~~i~nG~Gl~~~t~D~~~~~g~~------~aNplDlgg~a~~~~~~~al~~l~~dp~vd~ilv~i~gg~~~~~~va 329 (386)
T TIGR01016 256 DGNIGCMVNGAGLAMATMDIIKLYGGE------PANFLDVGGGASAERVREALKLVLSDKSVKVVFINIFGGITRCDLVA 329 (386)
T ss_pred CCcEEEEECCccHHHHHHHHHHHcCCC------CCCcEEecCCCCHHHHHHHHHHHHcCCCCCEEEEECCCCCCCHHHHH
Confidence 35688888721 22233445543 235664344467799999999999999998888632 244
Q ss_pred HHHHHHHhhcCCCccEEEEcCC
Q 032904 79 NRIRFLVDSHNKPIPAILEIPS 100 (130)
Q Consensus 79 ~~i~~~i~~~~~~~P~Iv~IPs 100 (130)
+.+.+...++....|+++-+.+
T Consensus 330 ~~i~~a~~~~~~~kPvvv~~~g 351 (386)
T TIGR01016 330 KGLVEALKEVGVNVPVVVRLEG 351 (386)
T ss_pred HHHHHHHHhcCCCCcEEEEeCC
Confidence 4444444443333798887743
No 26
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=53.54 E-value=34 Score=23.63 Aligned_cols=68 Identities=13% Similarity=0.262 Sum_probs=45.7
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcC--CCccEEEEcCCCCCCCChhhHHHHHHHHhhcccC
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHN--KPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVE 123 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~--~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGid 123 (130)
..+.+.|+.+- +..+-+.++|..-.+.++..+..+. ...+.|+.- +..+...+..+.++..+++. |++
T Consensus 80 ~~~~~~L~~l~-~~~~~~~i~Sn~~~~~~~~~l~~~~~~~~f~~i~~~-~~~~~~Kp~~~~~~~~~~~~-~~~ 149 (176)
T PF13419_consen 80 PGVRELLERLK-AKGIPLVIVSNGSRERIERVLERLGLDDYFDEIISS-DDVGSRKPDPDAYRRALEKL-GIP 149 (176)
T ss_dssp TTHHHHHHHHH-HTTSEEEEEESSEHHHHHHHHHHTTHGGGCSEEEEG-GGSSSSTTSHHHHHHHHHHH-TSS
T ss_pred hhhhhhhhhcc-cccceeEEeecCCccccccccccccccccccccccc-chhhhhhhHHHHHHHHHHHc-CCC
Confidence 45778888774 5689999999998888988888875 234556533 33344555556565555554 543
No 27
>cd06332 PBP1_aromatic_compounds_like Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes. This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.
Probab=53.14 E-value=85 Score=24.45 Aligned_cols=70 Identities=19% Similarity=0.180 Sum_probs=43.3
Q ss_pred hhHHHHHHh------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCCCcc
Q 032904 22 DTVVGFLLA------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNKPIP 93 (130)
Q Consensus 22 dtv~GFrLa------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~~~P 93 (130)
+...|++++ |+.+ ++-.+++.|.+.+++...+.+++|+.++.+-.|+. +......+.+.+++ ...|
T Consensus 18 ~~~~g~~~a~~~~~~~i~G----~~i~l~~~d~~~~~~~~~~~~~~l~~~~~v~~iig~~~s~~~~~~~~~~~~--~~ip 91 (333)
T cd06332 18 DIRDGFELALKQLGGKLGG----RPVEVVVEDDELKPDVAVQAARKLIEQDKVDVVVGPVFSNVALAVVPSLTE--SGTF 91 (333)
T ss_pred HHHHHHHHHHHHhCCCcCC----eEEEEEEecCCCCHHHHHHHHHHHHHHcCCcEEEcCCccHHHHHHHHHHhh--cCCe
Confidence 456677776 3322 12224555656667888999999997767766666 34444455555665 4567
Q ss_pred EEEE
Q 032904 94 AILE 97 (130)
Q Consensus 94 ~Iv~ 97 (130)
.|..
T Consensus 92 ~v~~ 95 (333)
T cd06332 92 LISP 95 (333)
T ss_pred EEec
Confidence 7664
No 28
>PF11965 DUF3479: Domain of unknown function (DUF3479); InterPro: IPR022571 This functionally uncharacterised domain, found N-terminal to PF02514 from PFAM, occurs in magnesium chelatase subunit H, which is involved in chlorophyll biosynthesis. It is found in bacteria, green plants and archaea. It is around 160 amino acids in length.; GO: 0016851 magnesium chelatase activity
Probab=51.70 E-value=24 Score=27.01 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=31.9
Q ss_pred HHHHHHhcCCC--eeEEEEehhhHHHHHHHHhhcCCCccEEEEcCC
Q 032904 57 DAFKEFTSRED--IAIVLISQYVANRIRFLVDSHNKPIPAILEIPS 100 (130)
Q Consensus 57 ~~~~~l~~~~d--igIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs 100 (130)
+.+++-+++-| +|=.+-.++.++.+.+.++..+...|+++-.+|
T Consensus 49 ~~~~~aia~ADii~~smlF~ed~v~~l~~~L~~~r~~~~a~i~~~s 94 (164)
T PF11965_consen 49 EECEAAIARADIIFGSMLFIEDHVRPLLPALEARRDHCPAMIIFES 94 (164)
T ss_pred HHHHHHHHhCCEEEeehhhhHHHHHHHHHHHHHHHccCCEEEEEcC
Confidence 44555555667 344455577788999999987777898888888
No 29
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=49.32 E-value=1.6e+02 Score=24.74 Aligned_cols=96 Identities=17% Similarity=0.230 Sum_probs=54.4
Q ss_pred ccEEEEEechh--hH---HHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--------hhhH
Q 032904 12 SALIAMIADED--TV---VGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--------QYVA 78 (130)
Q Consensus 12 ~~kIaVIGD~d--tv---~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt--------e~~a 78 (130)
.-+|++|++-- .+ -.+...|. ...|++=.....+.+.+..+++.+++++++..|++. +.++
T Consensus 256 ~~~i~ii~ng~G~~~~~~D~l~~~g~------~~~NPvDl~g~~~~e~~~~aL~~l~~d~~vd~vlv~~~~~~~~~~~va 329 (388)
T PRK00696 256 DGNIGCMVNGAGLAMATMDIIKLYGG------EPANFLDVGGGATAERVAEAFKIILSDPNVKAILVNIFGGITRCDVIA 329 (388)
T ss_pred CCcEEEEECCchHHHHHHHHHHHcCC------CcCCeEEecCCCCHHHHHHHHHHHhcCCCCCEEEEEeCCCCCCHHHHH
Confidence 46789998842 11 12222344 223555333335679999999999998988777753 2344
Q ss_pred HHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhh
Q 032904 79 NRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNL 119 (130)
Q Consensus 79 ~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~a 119 (130)
+.+.+...+++...|+++.+.+ . . .+..++.++++
T Consensus 330 ~~i~~~~~~~~~~kPvv~~~~g-~-~----~~~~~~~L~~~ 364 (388)
T PRK00696 330 EGIIAAVKEVGVTVPLVVRLEG-T-N----VELGKKILAES 364 (388)
T ss_pred HHHHHHHHhcCCCCcEEEEeCC-C-C----HHHHHHHHHHC
Confidence 4444433332246788777644 1 1 23455555553
No 30
>PLN02235 ATP citrate (pro-S)-lyase
Probab=49.11 E-value=1.2e+02 Score=26.64 Aligned_cols=73 Identities=10% Similarity=0.007 Sum_probs=46.3
Q ss_pred CcceeEEecCCCcHHHHHHHHHHHh----cCCCeeEEEEe--------hhhH---HHHHHHHhhcC-----CCccEEEEc
Q 032904 39 RKTNYLIVDSKTTIKQIEDAFKEFT----SREDIAIVLIS--------QYVA---NRIRFLVDSHN-----KPIPAILEI 98 (130)
Q Consensus 39 ~~~nf~v~~~~~~~eei~~~~~~l~----~~~digIIlIt--------e~~a---~~i~~~i~~~~-----~~~P~Iv~I 98 (130)
+-.||.=+.-.++.+.+.++|+-++ +++++-.|+|. ..+| +-|-+-+.++. ...|+||-+
T Consensus 297 ~pANFlDvGG~a~~e~v~~a~~iil~~~~~~~~vk~ilvnIfGGI~rcd~VA~tf~GIi~A~~e~~~kl~~~~vpivVRl 376 (423)
T PLN02235 297 ELGNYAEYSGAPNEEEVLQYARVVIDCATANPDGRKRALLIGGGIANFTDVAATFNGIIRALREKESKLKAARMHIFVRR 376 (423)
T ss_pred CCceeeecCCCCCHHHHHHHHHHHHhhhhcCCCCcEEEEEEecccccchhhhhhhhHHHHHHHHhhhccccCCccEEEEC
Confidence 3457886677788899999999887 67766555443 4455 33333333332 358999988
Q ss_pred CCCCCCCChhhHHHH
Q 032904 99 PSKDHPYDPAQDSVL 113 (130)
Q Consensus 99 Ps~~g~~~~~~d~I~ 113 (130)
.+.+. +.++.-|+
T Consensus 377 ~GtN~--eeG~~il~ 389 (423)
T PLN02235 377 GGPNY--QKGLAKMR 389 (423)
T ss_pred CCCCH--HHHHHHHH
Confidence 77663 34444333
No 31
>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=48.03 E-value=62 Score=22.66 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhcCCCeeEEEE--e----------hhhHHHHHHHHhhcC
Q 032904 53 KQIEDAFKEFTSREDIAIVLI--S----------QYVANRIRFLVDSHN 89 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlI--t----------e~~a~~i~~~i~~~~ 89 (130)
.++.+.+.+.+...+..+|+| - +.+.+.++..|+.++
T Consensus 26 ~~~~~~~~~~~~~~~pd~vvi~~G~ND~~~~~~~~~~~~~~~~~i~~i~ 74 (157)
T cd01833 26 DQIAAAAADWVLAAKPDVVLLHLGTNDLVLNRDPDTAPDRLRALIDQMR 74 (157)
T ss_pred HHHHHHhhhccccCCCCEEEEeccCcccccCCCHHHHHHHHHHHHHHHH
Confidence 667777766665455444444 2 224566666776664
No 32
>COG5623 CLP1 Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]
Probab=47.88 E-value=64 Score=27.97 Aligned_cols=59 Identities=14% Similarity=0.189 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHH
Q 032904 53 KQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVL 113 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~ 113 (130)
|.+.+.++.++++-++.|++ =+|.+...++..-+... .-.|+.||+.+|-.+.+++..+
T Consensus 235 Enla~~~htiI~~f~vnivvVlgsErLy~s~k~~~~~~~--~n~iffiskldG~~~ve~e~~r 295 (424)
T COG5623 235 ENLAAFYHTIIKRFEVNIVVVLGSERLYHSLKVIAEKLM--INRIFFISKLDGFVEVEKEVGR 295 (424)
T ss_pred HHHHHHHHHHHHheeeeEEEEEcchHHHHHHHHHHhHHh--hhheeeecccCCeeehHHHHHH
Confidence 44555566666666655554 46888888887766532 2239999999997776655554
No 33
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=47.52 E-value=1.4e+02 Score=23.44 Aligned_cols=53 Identities=9% Similarity=0.153 Sum_probs=33.0
Q ss_pred eEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--hhhHHHHHHHHhhcCCCccEEEE
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--QYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~~digIIlIt--e~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
+++.|...+++...+.+++|+.++.+..|+-. ......+.+.+++ ...|.|..
T Consensus 41 l~~~D~~~~~~~~~~~~~~lv~~~~v~~iig~~~s~~~~~~~~~~~~--~~ip~v~~ 95 (336)
T cd06360 41 FVVEDDEAKPDVAVEKARKLIEQDKVDVVVGPVHSGEALAMVKVLRE--PGTPLINP 95 (336)
T ss_pred EEEcCCCCChHHHHHHHHHHHHHhCCcEEEccCccHhHHHHHHHHHh--cCceEEec
Confidence 45556555678888999999876777665544 2233344455554 45776653
No 34
>PF01791 DeoC: DeoC/LacD family aldolase; InterPro: IPR002915 This family includes the enzyme deoxyribose-phosphate aldolase, which is involved in nucleotide metabolism. 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde The family also includes a group of related bacterial proteins of unknown function, see examples Q57843 from SWISSPROT and P76143 from SWISSPROT.; GO: 0016829 lyase activity; PDB: 2A4A_A 1VCV_B 1P1X_A 1KTN_B 1JCL_A 1JCJ_A 1MZH_A 3GKF_D 3GLC_L 3GND_N ....
Probab=47.08 E-value=29 Score=27.01 Aligned_cols=57 Identities=12% Similarity=0.133 Sum_probs=44.8
Q ss_pred CcHH-HHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCCh
Q 032904 50 TTIK-QIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDP 107 (130)
Q Consensus 50 ~~~e-ei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~ 107 (130)
++.. ++++.+++.+ ...+.=|+++..+....++.+....-..++|+-+|........
T Consensus 15 ~~~~~~~~~~~~~a~-~~~~~av~v~p~~~~~~~~~~~~~~~~~~~vi~fp~g~~~~~~ 72 (236)
T PF01791_consen 15 MTGEEDIKKLCREAI-EYGFDAVCVTPGYVKPAAELLAGSGVKVGLVIGFPFGTSTTEP 72 (236)
T ss_dssp HHHHHHHHHHHHHHH-HHTSSEEEEEGGGHHHHHHHSTTSTSEEEEEESTTTSSSTHHH
T ss_pred CCchhhHHHHHHHHH-HhCCCEEEECHHHHHHHHHHhhccccccceEEEeCCCCCcccc
Confidence 3444 8999999887 4588889999999999988887654568899999987766443
No 35
>PRK12862 malic enzyme; Reviewed
Probab=46.45 E-value=46 Score=31.25 Aligned_cols=83 Identities=10% Similarity=0.090 Sum_probs=54.2
Q ss_pred hhcccccEEEEEechhhHHHHHHhcccc-ccc-----------CCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe
Q 032904 7 IRTAASALIAMIADEDTVVGFLLAGVGN-VDL-----------RRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74 (130)
Q Consensus 7 ~~~~~~~kIaVIGD~dtv~GFrLaGi~~-~~~-----------~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt 74 (130)
.|+.....++||.|-.-|+|+-=.|..+ .-. -+-.-|.+.-++.+++|+-++++.+. +.+|.|=+.
T Consensus 65 ~~t~~~n~v~vvtdg~~vLGlGd~G~~~~~pv~egK~~l~~~~~gi~~~~i~~~~~d~d~~v~~v~~~~--p~f~~i~~E 142 (763)
T PRK12862 65 RYTSRGNLVAVVSNGTAVLGLGNIGPLASKPVMEGKAVLFKKFAGIDVFDIELDESDPDKLVEIVAALE--PTFGGINLE 142 (763)
T ss_pred hcccCCcEEEEEechhhhccccccCcccccchHHHHHHHHHhhcCCCccccccCCCCHHHHHHHHHHhC--CCcceeeee
Confidence 3556667899999999999986655543 100 00001332222346799999998775 788888887
Q ss_pred hhhHHHHHHHHhhcCCC
Q 032904 75 QYVANRIRFLVDSHNKP 91 (130)
Q Consensus 75 e~~a~~i~~~i~~~~~~ 91 (130)
+--+...-..+++|+..
T Consensus 143 D~~~~~~f~i~~~~~~~ 159 (763)
T PRK12862 143 DIKAPECFYIERELRER 159 (763)
T ss_pred cccCchHHHHHHHHHhc
Confidence 77666777777777643
No 36
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=46.37 E-value=91 Score=23.88 Aligned_cols=52 Identities=10% Similarity=0.171 Sum_probs=38.8
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEehh-------hHHHHHHHHhhcCCCccEEEEcCCCC
Q 032904 51 TIKQIEDAFKEFTSREDIAIVLISQY-------VANRIRFLVDSHNKPIPAILEIPSKD 102 (130)
Q Consensus 51 ~~eei~~~~~~l~~~~digIIlIte~-------~a~~i~~~i~~~~~~~P~Iv~IPs~~ 102 (130)
+.+++.++|+++.+++++.-|++.-+ ..+.+.+.|.++++..|++..+.+..
T Consensus 14 s~~~l~~~l~~a~~d~~i~~vvl~~~s~Gg~~~~~~~l~~~i~~~~~~kpvia~v~g~a 72 (207)
T TIGR00706 14 SPEDFDKKIKRIKDDKSIKALLLRINSPGGTVVASEEIYEKLKKLKAKKPVVASMGGVA 72 (207)
T ss_pred CHHHHHHHHHHHhhCCCccEEEEEecCCCCCHHHHHHHHHHHHHhcCCCCEEEEECCcc
Confidence 35889999999988888876666432 34567777777766789999987654
No 37
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=44.83 E-value=64 Score=27.17 Aligned_cols=43 Identities=21% Similarity=0.252 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAIL 96 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv 96 (130)
+...++++++. +..+-||+.|.+....++...+++....|.|+
T Consensus 21 ~~a~~aL~~Lk-~~GI~vVlaTGRt~~ev~~l~~~Lgl~~p~I~ 63 (302)
T PRK12702 21 GAARQALAALE-RRSIPLVLYSLRTRAQLEHLCRQLRLEHPFIC 63 (302)
T ss_pred HHHHHHHHHHH-HCCCEEEEEcCCCHHHHHHHHHHhCCCCeEEE
Confidence 66888899886 67999999999999888888888765558776
No 38
>cd01973 Nitrogenase_VFe_beta_like Nitrogenase_VFe_beta -like: Nitrogenase VFe protein, beta subunit like. This group contains proteins similar to the beta subunits of the VFe protein of the vanadium-dependent (V-) nitrogenase. Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V-nitrogenase there is a molybdenum (Mo)-dependent nitrogenase and an iron only (Fe-) nitrogenase. The Mo-nitrogenase is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe p
Probab=44.78 E-value=1.2e+02 Score=26.32 Aligned_cols=25 Identities=24% Similarity=0.361 Sum_probs=19.9
Q ss_pred cccEEEEEechhhHHHHHH----hccccc
Q 032904 11 ASALIAMIADEDTVVGFLL----AGVGNV 35 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrL----aGi~~~ 35 (130)
..+|+++.||.+.+.|+.= .|++-+
T Consensus 304 ~Gkrv~i~g~~~~~~~l~~fl~elGm~~~ 332 (454)
T cd01973 304 ANKKVAIFGHPDLVIGLAEFCLEVEMKPV 332 (454)
T ss_pred CCCeEEEEcCHHHHHHHHHHHHHCCCeEE
Confidence 4689999999999988765 677654
No 39
>COG3616 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]
Probab=44.13 E-value=2.1e+02 Score=24.66 Aligned_cols=79 Identities=20% Similarity=0.211 Sum_probs=57.9
Q ss_pred EechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCC-eeEEEEehhhHHHHHHHHhhcCCCccEEE
Q 032904 18 IADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSRED-IAIVLISQYVANRIRFLVDSHNKPIPAIL 96 (130)
Q Consensus 18 IGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~d-igIIlIte~~a~~i~~~i~~~~~~~P~Iv 96 (130)
...-...--|.-+||.++ ++. .+ .........|.++.++.+ +.+++=+..-++.+.+...+...++.+.|
T Consensus 72 ~~tl~eae~~a~aGi~dI-------l~a-~p-~~~~~~~~~L~~l~~~~~~~~~~iDs~~~~~~l~~~~~~~~~pl~v~i 142 (368)
T COG3616 72 CATLGEAEVFADAGIDDI-------LLA-YP-LPGRAALAALAELLADPPRISVLIDSVEQLDALAALARDAGKPLRVLI 142 (368)
T ss_pred eechHHHHHHHccCccce-------EEe-cC-CCchhHHHHHHHhcCCCCceEEEeCCHHHHHHHHHHHHhcCCCeeEEE
Confidence 344444555677888876 444 32 244777788998988888 99999998888888888877778889999
Q ss_pred EcCCCCCCC
Q 032904 97 EIPSKDHPY 105 (130)
Q Consensus 97 ~IPs~~g~~ 105 (130)
|+-+..+-.
T Consensus 143 E~D~G~~R~ 151 (368)
T COG3616 143 EIDSGLHRS 151 (368)
T ss_pred EeCCCCCcc
Confidence 998755433
No 40
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=42.70 E-value=1.7e+02 Score=23.23 Aligned_cols=73 Identities=14% Similarity=0.171 Sum_probs=46.0
Q ss_pred hhhHHHHHHhccccccc------CCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCCCc
Q 032904 21 EDTVVGFLLAGVGNVDL------RRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNKPI 92 (130)
Q Consensus 21 ~dtv~GFrLaGi~~~~~------~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~~~ 92 (130)
.+...|++|+ ++.+|. ..+-.+++.|...++....+..++|+.++.+-.|+= +......+.+..+++ ..
T Consensus 15 ~~~~~~~~lA-v~~iN~~gg~~~g~~i~~~~~D~~~~~~~a~~~a~~l~~~~~v~~viG~~~s~~~~a~~~~~~~~--~i 91 (350)
T cd06366 15 KAALPAIEMA-LEDVNADNSILPGYRLVLHVRDSKCDPVQAASAALDLLENKPVVAIIGPQCSSVAEFVAEVANEW--NV 91 (350)
T ss_pred HHHHHHHHHH-HHHHhcCCCcCCCcEEEEEecCCCCCHHHHHHHHHHHhccCCceEEECCCcHHHHHHHHHHhhcC--Ce
Confidence 3567788776 111111 122336666766678899999999998777766664 455666667766653 46
Q ss_pred cEEE
Q 032904 93 PAIL 96 (130)
Q Consensus 93 P~Iv 96 (130)
|.|-
T Consensus 92 p~i~ 95 (350)
T cd06366 92 PVLS 95 (350)
T ss_pred eEEe
Confidence 7665
No 41
>cd07014 S49_SppA Signal peptide peptidase A. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is an intramembrane enzyme found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be ClpP-like serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain, cleaving peptide bonds in the plane of the lipid bilayer. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal p
Probab=42.62 E-value=1.1e+02 Score=22.58 Aligned_cols=51 Identities=6% Similarity=0.069 Sum_probs=38.1
Q ss_pred CcHHHHHHHHHHHhcCCCeeEEEEehh-------hHHHHHHHHhhcC-CCccEEEEcCC
Q 032904 50 TTIKQIEDAFKEFTSREDIAIVLISQY-------VANRIRFLVDSHN-KPIPAILEIPS 100 (130)
Q Consensus 50 ~~~eei~~~~~~l~~~~digIIlIte~-------~a~~i~~~i~~~~-~~~P~Iv~IPs 100 (130)
.+.+++.++|+++.+++++..|+++=+ ..+.+++.+.+++ ...|+|.-+.+
T Consensus 22 ~~~~~l~~~l~~a~~d~~v~~vvl~~~~~gg~~~~~~~~~~~i~~~~~~~kpVia~v~G 80 (177)
T cd07014 22 VSGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVASGGG 80 (177)
T ss_pred cCHHHHHHHHHHHhcCCCceEEEEEeeCCCcCHHHHHHHHHHHHHHHhCCCCEEEEECC
Confidence 346899999999998899988877743 2345666676664 78899988863
No 42
>cd07019 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-te
Probab=42.11 E-value=1.1e+02 Score=23.59 Aligned_cols=52 Identities=6% Similarity=0.089 Sum_probs=38.8
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEehh-------hHHHHHHHHhhcC-CCccEEEEcCCCC
Q 032904 51 TIKQIEDAFKEFTSREDIAIVLISQY-------VANRIRFLVDSHN-KPIPAILEIPSKD 102 (130)
Q Consensus 51 ~~eei~~~~~~l~~~~digIIlIte~-------~a~~i~~~i~~~~-~~~P~Iv~IPs~~ 102 (130)
+.+++.++|+++..++++..|+++-+ -.+.+++.+..++ ...|+|..+.+..
T Consensus 22 ~~~~l~~~l~~a~~d~~v~~ivL~~~s~Gg~~~~~~~~~~~l~~~~~~~kpVia~v~g~a 81 (211)
T cd07019 22 GGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSAGGAA 81 (211)
T ss_pred CHHHHHHHHHHHhhCCCceEEEEEEcCCCcCHHHHHHHHHHHHHHHhCCCCEEEEECCee
Confidence 45899999999999999998888622 2245566666654 6889999987653
No 43
>PRK08366 vorA 2-ketoisovalerate ferredoxin oxidoreductase subunit alpha; Reviewed
Probab=41.99 E-value=96 Score=26.65 Aligned_cols=52 Identities=15% Similarity=0.117 Sum_probs=43.4
Q ss_pred EEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe
Q 032904 14 LIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74 (130)
Q Consensus 14 kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt 74 (130)
++.+-|++....|.+.+|++ |..-.|=|+--++-+.+.++..+.++++.++.
T Consensus 3 ~~~l~GNeAiA~ga~~ag~~---------~~a~YPITPsTei~e~la~~~~~G~~~~~~~~ 54 (390)
T PRK08366 3 RKVVSGNYAAAYAALHARVQ---------VVAAYPITPQTSIIEKIAEFIANGEADIQYVP 54 (390)
T ss_pred cEEeeHHHHHHHHHHHhCCC---------EEEEECCCChhHHHHHHHHHhhCCCCCeEEEE
Confidence 57789999999999999995 45566667778999999999986678787777
No 44
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=41.05 E-value=96 Score=27.86 Aligned_cols=61 Identities=15% Similarity=0.285 Sum_probs=39.8
Q ss_pred Hhc-CCCeeEEEEehh---------hHHHHHHHHhhcC-CCccEEEEcCCCCCCCChhhHHHHHHHHhhcccC
Q 032904 62 FTS-REDIAIVLISQY---------VANRIRFLVDSHN-KPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVE 123 (130)
Q Consensus 62 l~~-~~digIIlIte~---------~a~~i~~~i~~~~-~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGid 123 (130)
.+. ..++||++.|+. +.+.=...|++++ ...|.|+.+-+.+ |+.++...+.+.+++..|+-
T Consensus 140 VI~dhstIgivVtTDgsi~dI~Re~y~~aEe~~i~eLk~~~kPfiivlN~~d-p~~~et~~l~~~l~eky~vp 211 (492)
T TIGR02836 140 VIQEHSTIGVVVTTDGTITDIPREDYVEAEERVIEELKELNKPFIILLNSTH-PYHPETEALRQELEEKYDVP 211 (492)
T ss_pred HHHhcCcEEEEEEcCCCccccccccchHHHHHHHHHHHhcCCCEEEEEECcC-CCCchhHHHHHHHHHHhCCc
Confidence 444 779999998744 4444445566664 7799999998877 33333455666666666643
No 45
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR 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,
Probab=40.71 E-value=1.5e+02 Score=22.02 Aligned_cols=79 Identities=11% Similarity=0.035 Sum_probs=41.3
Q ss_pred ccccEEEEEechhh--HHHHHHhccccccc-CC-c-ceeEEecCCCcHHHHHHHHHHHhcC-CC-eeEEEEehhhHHHHH
Q 032904 10 AASALIAMIADEDT--VVGFLLAGVGNVDL-RR-K-TNYLIVDSKTTIKQIEDAFKEFTSR-ED-IAIVLISQYVANRIR 82 (130)
Q Consensus 10 ~~~~kIaVIGD~dt--v~GFrLaGi~~~~~-~~-~-~nf~v~~~~~~~eei~~~~~~l~~~-~d-igIIlIte~~a~~i~ 82 (130)
...++|++|++... ...-|..|+...=. ++ . ..+.......+.++..+++++++++ ++ -||+..++.++..+-
T Consensus 114 ~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~ 193 (268)
T cd01575 114 RGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFCSNDDLALGAL 193 (268)
T ss_pred CCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEECCcHHHHHHH
Confidence 45678999998542 33345555432200 01 1 1122222233457778888888854 34 455555566665444
Q ss_pred HHHhhc
Q 032904 83 FLVDSH 88 (130)
Q Consensus 83 ~~i~~~ 88 (130)
..+.+.
T Consensus 194 ~~l~~~ 199 (268)
T cd01575 194 FECQRR 199 (268)
T ss_pred HHHHHh
Confidence 445443
No 46
>PLN02225 1-deoxy-D-xylulose-5-phosphate synthase
Probab=40.62 E-value=18 Score=33.71 Aligned_cols=36 Identities=14% Similarity=0.286 Sum_probs=27.0
Q ss_pred cccccEEEEEechhhHHHHHHhcccccccCCcceeEE
Q 032904 9 TAASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLI 45 (130)
Q Consensus 9 ~~~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v 45 (130)
...++-||||||-...-|+-+-|..+.-.. ..|.+|
T Consensus 209 g~~~~vvaVIGDGaltgGma~EaLN~~g~~-~~~liv 244 (701)
T PLN02225 209 GKRDRVVAVIDNATITAGQAYEAMSNAGYL-DSNMIV 244 (701)
T ss_pred CCCCcEEEEEcCcchhhhhHHHHHhhhhcc-CCCEEE
Confidence 455677999999999999999999776332 334553
No 47
>COG2083 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.26 E-value=63 Score=24.25 Aligned_cols=71 Identities=17% Similarity=0.239 Sum_probs=44.4
Q ss_pred HHHHHHHHhcCCCeeEEEE--ehhh-----HHHHHHHHhhc---CCCccEEEEcCCCCCC-CChhhHHHHHHHHhhcccC
Q 032904 55 IEDAFKEFTSREDIAIVLI--SQYV-----ANRIRFLVDSH---NKPIPAILEIPSKDHP-YDPAQDSVLSRVKNLVSVE 123 (130)
Q Consensus 55 i~~~~~~l~~~~digIIlI--te~~-----a~~i~~~i~~~---~~~~P~Iv~IPs~~g~-~~~~~d~I~~~Vk~aiGid 123 (130)
.+.+|++|++.++--|.+= |+++ .+.+.+.+++. +-.+|.+++|-|..+. .-....-=-+-|++++|.|
T Consensus 25 ~rktL~ELL~ee~P~V~~rDG~~hyfkr~ELE~La~~ldE~e~~rlrlPivlEi~s~~~~~i~Irgk~evkvI~kvlG~e 104 (140)
T COG2083 25 KRKTLEELLREERPHVTLRDGTEHYFKRRELEFLAQILDEDEIPRLRLPIVLEISSGERGAIYIRGKVEVKVIKKVLGFE 104 (140)
T ss_pred hhhHHHHHHhccCCeEEccCCceeeeeHHHHHHHHhhcchhhhhhccccEEEEeccCCCceEEEecchhhhhHHHHhcch
Confidence 6788999997777666654 2333 34566666664 3679999999983221 1111112235678999988
Q ss_pred Cc
Q 032904 124 SV 125 (130)
Q Consensus 124 i~ 125 (130)
..
T Consensus 105 ~~ 106 (140)
T COG2083 105 EV 106 (140)
T ss_pred hh
Confidence 64
No 48
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=39.76 E-value=1.4e+02 Score=23.65 Aligned_cols=56 Identities=7% Similarity=0.029 Sum_probs=40.0
Q ss_pred cceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--hhhHHHHHHHHhhcCCCccEEEE
Q 032904 40 KTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--QYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 40 ~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt--e~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
+..+++.|...+++...++.++|+.++++.+|+=. ......+.+.+++ ...|+|..
T Consensus 40 ~i~l~~~D~~~~p~~a~~~a~~Li~~~~V~aiiG~~~s~~~~a~~~~~~~--~~vp~i~~ 97 (333)
T cd06331 40 PLELVVEDPASDPAFAAKAARRLIRDDKVDAVFGCYTSASRKAVLPVVER--GRGLLFYP 97 (333)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHHhccCCcEEEecccHHHHHHHHHHHHh--cCceEEeC
Confidence 33466777777889999999999977788777754 4444567777776 45777764
No 49
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=39.66 E-value=1.3e+02 Score=22.98 Aligned_cols=82 Identities=13% Similarity=0.168 Sum_probs=45.6
Q ss_pred HHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe---hhhHHHHHHHHhhcCCCcc---EEEEc
Q 032904 25 VGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS---QYVANRIRFLVDSHNKPIP---AILEI 98 (130)
Q Consensus 25 ~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt---e~~a~~i~~~i~~~~~~~P---~Iv~I 98 (130)
.-|+..|++.+ |+ ..+++.+++.++..+. +.| +|.++ ..-...+++.++.++...| +-|-+
T Consensus 104 ~~l~~~G~~vi-------~l--G~~~p~~~l~~~~~~~--~~d--~v~lS~~~~~~~~~~~~~i~~lr~~~~~~~~~i~v 170 (201)
T cd02070 104 TMLEANGFEVI-------DL--GRDVPPEEFVEAVKEH--KPD--ILGLSALMTTTMGGMKEVIEALKEAGLRDKVKVMV 170 (201)
T ss_pred HHHHHCCCEEE-------EC--CCCCCHHHHHHHHHHc--CCC--EEEEeccccccHHHHHHHHHHHHHCCCCcCCeEEE
Confidence 45677777654 22 3456778888877644 334 44444 3445667777777653333 33444
Q ss_pred CCCCCCCChhhHHHHHHHHhhcccCCcccc
Q 032904 99 PSKDHPYDPAQDSVLSRVKNLVSVESVASD 128 (130)
Q Consensus 99 Ps~~g~~~~~~d~I~~~Vk~aiGidi~~~~ 128 (130)
.+..-+ .+ ..+.+|.|..+.+
T Consensus 171 GG~~~~----~~-----~~~~~GaD~~~~d 191 (201)
T cd02070 171 GGAPVN----QE-----FADEIGADGYAED 191 (201)
T ss_pred ECCcCC----HH-----HHHHcCCcEEECC
Confidence 443211 12 4566799987754
No 50
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=39.12 E-value=1.4e+02 Score=22.92 Aligned_cols=51 Identities=8% Similarity=0.085 Sum_probs=37.9
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEehh-------hHHHHHHHHhhcCCCccEEEEcCCC
Q 032904 51 TIKQIEDAFKEFTSREDIAIVLISQY-------VANRIRFLVDSHNKPIPAILEIPSK 101 (130)
Q Consensus 51 ~~eei~~~~~~l~~~~digIIlIte~-------~a~~i~~~i~~~~~~~P~Iv~IPs~ 101 (130)
...++.++|+++.+++++..|++.-+ -.+.+.+.|.+++...|+|.-+.+.
T Consensus 26 ~~~~l~~~l~~a~~d~~i~~Vvl~~~s~gg~~~~~~~l~~~l~~~~~~KpViA~v~g~ 83 (214)
T cd07022 26 SYEGIAAAIRAALADPDVRAIVLDIDSPGGEVAGVFELADAIRAARAGKPIVAFVNGL 83 (214)
T ss_pred cHHHHHHHHHHHhhCCCCcEEEEEEeCCCCcHHHHHHHHHHHHHHhcCCCEEEEECCc
Confidence 35899999999988889977777421 2455677777765578999988764
No 51
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=38.55 E-value=1.3e+02 Score=23.79 Aligned_cols=53 Identities=15% Similarity=0.253 Sum_probs=38.9
Q ss_pred eeEEecCCCcHHHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhhcCCCccEEEE
Q 032904 42 NYLIVDSKTTIKQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 42 nf~v~~~~~~~eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
.+.+.|..-++....+..++|+.++++-.|+ .+...+..+.+.++ ...|.|..
T Consensus 42 ~l~~~D~~~~p~~a~~~a~~Li~~~~v~aviG~~~s~~a~a~~~~~~---~~vp~i~~ 96 (333)
T cd06358 42 ELVIVDDGSPPAEAAAAAARLVDEGGVDAIIGWHTSAVRNAVAPVVA---GRVPYVYT 96 (333)
T ss_pred EEEEECCCCChHHHHHHHHHHHHhCCCcEEEecCcHHHHHHHHHHHh---cCceEEeC
Confidence 4556666667788999999999887777777 55666777777776 55777764
No 52
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=38.23 E-value=89 Score=21.76 Aligned_cols=53 Identities=26% Similarity=0.214 Sum_probs=32.5
Q ss_pred eEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehh-----hHHHHHHHHhhcCCCccEEEEcC
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQY-----VANRIRFLVDSHNKPIPAILEIP 99 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~~digIIlIte~-----~a~~i~~~i~~~~~~~P~Iv~IP 99 (130)
|.++.... .+++...++ +..+++-|+|+-+ ....+=+.+...+...|+.+...
T Consensus 18 ~~vv~~~~-~dd~~~~i~---~~~~i~avvi~~d~~~~~~~~~ll~~i~~~~~~iPVFl~~~ 75 (115)
T PF03709_consen 18 REVVDADS-TDDALAIIE---SFTDIAAVVISWDGEEEDEAQELLDKIRERNFGIPVFLLAE 75 (115)
T ss_dssp TEEEEESS-HHHHHHHHH---CTTTEEEEEEECHHHHHHHHHHHHHHHHHHSTT-EEEEEES
T ss_pred CEEEEeCC-hHHHHHHHH---hCCCeeEEEEEcccccchhHHHHHHHHHHhCCCCCEEEEec
Confidence 44444422 265666555 6679999999933 33444444666678899888765
No 53
>COG0157 NadC Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]
Probab=38.07 E-value=1.2e+02 Score=25.26 Aligned_cols=64 Identities=13% Similarity=0.220 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCccc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESVAS 127 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~~~ 127 (130)
.+|++++++ -..-||++.+.-.+.+++.+..+.....+++|..+ +...+.+..+. ..|+|...+
T Consensus 198 le~~~eAl~-----agaDiImLDNm~~e~~~~av~~l~~~~~~~lEaSG-----gIt~~ni~~yA--~tGVD~IS~ 261 (280)
T COG0157 198 LEEAEEALE-----AGADIIMLDNMSPEELKEAVKLLGLAGRALLEASG-----GITLENIREYA--ETGVDVISV 261 (280)
T ss_pred HHHHHHHHH-----cCCCEEEecCCCHHHHHHHHHHhccCCceEEEEeC-----CCCHHHHHHHh--hcCCCEEEe
Confidence 466666554 24568999999999999999886555578899843 34567898888 678886554
No 54
>PLN03194 putative disease resistance protein; Provisional
Probab=37.17 E-value=60 Score=25.50 Aligned_cols=36 Identities=6% Similarity=0.001 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHH--HHHHHHhhc
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVAN--RIRFLVDSH 88 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~--~i~~~i~~~ 88 (130)
+.+...+.+.+..-.++|+++++++++ ...+++...
T Consensus 68 ~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~~I 105 (187)
T PLN03194 68 DKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELALI 105 (187)
T ss_pred CcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHHHH
Confidence 556667777777889999999999875 666666654
No 55
>PF09612 HtrL_YibB: Bacterial protein of unknown function (HtrL_YibB); InterPro: IPR011735 The protein from this rare, uncharacterised protein family is designated HtrL or YibB in Escherichia coli, where its gene is found in a region of LPS core biosynthesis genes []. Homologs are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein.
Probab=36.85 E-value=1.3e+02 Score=24.84 Aligned_cols=52 Identities=13% Similarity=0.189 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcC-CCccE-EEEcCCCCC
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHN-KPIPA-ILEIPSKDH 103 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~-~~~P~-Iv~IPs~~g 103 (130)
.+.-.+-|+.++.=+.-=||+.++...+.+++.-.+++ ...|. |++++=+.-
T Consensus 26 ~~~Y~~yf~~la~L~N~mVIfTd~~~~e~I~~iR~~~~L~~Ktt~Ii~~dl~~~ 79 (271)
T PF09612_consen 26 NETYFEYFEFLAKLKNNMVIFTDESSKEFIKKIRKKHGLEDKTTVIITIDLKDF 79 (271)
T ss_pred HHHHHHHHHHHHhhcCCEEEEEChHHHHHHHHHHHhcCcCCCceEEEEecHHHh
Confidence 48888889989887788899999999999999888776 67787 777766553
No 56
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=36.53 E-value=2.4e+02 Score=23.13 Aligned_cols=83 Identities=16% Similarity=0.109 Sum_probs=51.9
Q ss_pred ccccEEEEEech---------hhHHHHHHhccccccc-----CCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe-
Q 032904 10 AASALIAMIADE---------DTVVGFLLAGVGNVDL-----RRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS- 74 (130)
Q Consensus 10 ~~~~kIaVIGD~---------dtv~GFrLaGi~~~~~-----~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt- 74 (130)
...-+|++++.. +...|++++ ++.+|. .++-.+++.|...+++...+..++|+. +++-.|+=.
T Consensus 23 ~~~I~IG~l~plSG~~a~~G~~~~~g~~~a-v~~iNa~GGi~G~~ielv~~D~~~~p~~a~~~~~~Li~-~~V~~iiG~~ 100 (369)
T PRK15404 23 ADDIKIAIVGPMSGPVAQYGDMEFTGARQA-IEDINAKGGIKGDKLEGVEYDDACDPKQAVAVANKVVN-DGIKYVIGHL 100 (369)
T ss_pred CCceEEEEeecCCCcchhcCHhHHHHHHHH-HHHHHhcCCCCCeEEEEEeecCCCCHHHHHHHHHHHHh-CCceEEEcCC
Confidence 345788888642 467777776 333221 123346677766778899999999995 667666653
Q ss_pred -hhhHHHHHHHHhhcCCCccEEE
Q 032904 75 -QYVANRIRFLVDSHNKPIPAIL 96 (130)
Q Consensus 75 -e~~a~~i~~~i~~~~~~~P~Iv 96 (130)
......+.+..++ ...|+|.
T Consensus 101 ~s~~~~a~~~~~~~--~~ip~i~ 121 (369)
T PRK15404 101 CSSSTQPASDIYED--EGILMIT 121 (369)
T ss_pred CchhHHHhHHHHHH--CCCeEEe
Confidence 3444455565665 4456665
No 57
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain. This model represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length.
Probab=36.17 E-value=1.9e+02 Score=25.73 Aligned_cols=46 Identities=22% Similarity=0.318 Sum_probs=30.1
Q ss_pred cccEEEEEechhhHHHH----HHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcC
Q 032904 11 ASALIAMIADEDTVVGF----LLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSR 65 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GF----rLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~ 65 (130)
..+|+||.||+|.+.|+ .=.|++-+ .++... ...+.++.++.++..
T Consensus 362 ~GKrvaI~gdpd~~~~l~~fL~ElGmepv-------~v~~~~--~~~~~~~~l~~ll~~ 411 (515)
T TIGR01286 362 HGKRFAIYGDPDFVMGLVRFVLELGCEPV-------HILCTN--GTKRWKAEMKALLAA 411 (515)
T ss_pred cCceEEEECCHHHHHHHHHHHHHCCCEEE-------EEEeCC--CCHHHHHHHHHHHhc
Confidence 35899999999999994 33566543 333322 225667777777754
No 58
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=36.12 E-value=1.1e+02 Score=24.44 Aligned_cols=59 Identities=12% Similarity=0.214 Sum_probs=45.8
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
...+|+|+++.+...==+-+|..- + .. +|+.+.+++.. .++-.++-|.++...+.. |-+
T Consensus 70 k~~kV~Vfa~~~~~~eAk~aGad~----------v-g~----edLi~~ik~~~--~~fd~~iAt~d~m~~l~k-Lgr 128 (229)
T CHL00129 70 KTIRIAVLTNEEKITEAKNAGADI----------V-GS----DDLIEEITKGN--LDFDLLIATPDMMPKLAK-LGR 128 (229)
T ss_pred CCcEEEEECChHhHHHHHHcCCCE----------e-CH----HHHHHHHHcCc--ccCCEEEECHHHHHHHHH-hcC
Confidence 458999999988887778899842 2 33 88888887764 578889999999888876 554
No 59
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=35.93 E-value=1.7e+02 Score=23.30 Aligned_cols=69 Identities=17% Similarity=0.224 Sum_probs=46.9
Q ss_pred hhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhhcCCC
Q 032904 22 DTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDSHNKP 91 (130)
Q Consensus 22 dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~~~~~ 91 (130)
+...|++|+ ||.| ++-.+++.|...+++......++|+.++++-+|+ .+......+.+.++++ .
T Consensus 18 ~~~~g~~la~~~iNa~gGi~G----r~v~lv~~D~~~~p~~a~~~~~~Li~~~~V~aiiG~~~s~~~~a~~~~~~~~--~ 91 (334)
T cd06356 18 PKVHATQLAVDEINASGGILG----REVELVDYDTQSDNERYQQYAQRLALQDKVDVVWGGISSASREAIRPIMDRT--K 91 (334)
T ss_pred HHHHHHHHHHHHHHhcCCCCC----ceEEEEEECCCCCHHHHHHHHHHHHHhCCCCEEEeCcchHHHHHHHHHHHhc--C
Confidence 455666553 5544 2334677777777899999999999877777777 3444556677777764 4
Q ss_pred ccEEE
Q 032904 92 IPAIL 96 (130)
Q Consensus 92 ~P~Iv 96 (130)
.|.|.
T Consensus 92 vp~i~ 96 (334)
T cd06356 92 QLYFY 96 (334)
T ss_pred ceEEe
Confidence 66665
No 60
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=35.78 E-value=1.1e+02 Score=24.36 Aligned_cols=85 Identities=16% Similarity=0.187 Sum_probs=55.8
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCC
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNK 90 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~ 90 (130)
...||+|++|.+...==+-+|+.- + .. +|+.+.+++.. .+|-.++-|.++...+. .+-+.-
T Consensus 69 k~~kV~Vfa~~~~~~~Ak~aGa~~----------v-g~----~eLi~~ik~~~--~~fd~~iat~~~m~~l~-~Lg~iL- 129 (227)
T TIGR01169 69 KTVRVAVFAKGEKAEEAKAAGADY----------V-GS----DDLIEKIKKGW--LDFDVVIATPDMMRVVG-KLGRIL- 129 (227)
T ss_pred CCcEEEEEcCchhHHHHHHcCCCE----------e-CH----HHHHHHHHcCC--ccCCEEEECHHHHHHHH-Hhcccc-
Confidence 457999999988887778899842 2 33 88888777664 56888899999888887 555431
Q ss_pred Ccc-EEEEcCCCC-CCCChhhHHHHHHHHhhc
Q 032904 91 PIP-AILEIPSKD-HPYDPAQDSVLSRVKNLV 120 (130)
Q Consensus 91 ~~P-~Iv~IPs~~-g~~~~~~d~I~~~Vk~ai 120 (130)
-| -. +|+.. |+.. +.|.+.|++.-
T Consensus 130 -GPrGl--MP~~k~gtv~---~di~~~I~~~k 155 (227)
T TIGR01169 130 -GPRGL--MPNPKTGTVT---ADVAKAVKNAK 155 (227)
T ss_pred -ccccC--CCCCCCCCcc---ccHHHHHHHHH
Confidence 11 01 35544 2211 23666776654
No 61
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=35.76 E-value=2.4e+02 Score=22.94 Aligned_cols=71 Identities=13% Similarity=0.170 Sum_probs=45.0
Q ss_pred hhhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE-ehhhHHHHHHHHhhcCCC
Q 032904 21 EDTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI-SQYVANRIRFLVDSHNKP 91 (130)
Q Consensus 21 ~dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI-te~~a~~i~~~i~~~~~~ 91 (130)
.....|++|+ ||.+. +-.+++.|...+++...+..++|+.++++.+|+- +......+.+.+++ ..
T Consensus 17 ~~~~~g~~la~~~iNa~GGI~Gr----~ielv~~D~~~~p~~a~~~a~~Li~~~~V~~i~~~~S~~~~a~~~~~~~--~~ 90 (351)
T cd06334 17 IPYAAGFADYFKYINEDGGINGV----KLEWEECDTGYEVPRGVECYERLKGEDGAVAFQGWSTGITEALIPKIAA--DK 90 (351)
T ss_pred hhHHHHHHHHHHHHHHcCCcCCe----EEEEEEecCCCCcHHHHHHHHHHhccCCcEEEecCcHHHHHHhhHHHhh--cC
Confidence 4466777765 66442 2235666766778999999999998777766532 12233455566665 45
Q ss_pred ccEEEE
Q 032904 92 IPAILE 97 (130)
Q Consensus 92 ~P~Iv~ 97 (130)
.|+|..
T Consensus 91 vp~i~~ 96 (351)
T cd06334 91 IPLMSG 96 (351)
T ss_pred CcEEec
Confidence 777764
No 62
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=35.28 E-value=1.5e+02 Score=23.02 Aligned_cols=91 Identities=16% Similarity=0.177 Sum_probs=42.4
Q ss_pred hhhcccccEEEEEec--hhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHH
Q 032904 6 QIRTAASALIAMIAD--EDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRF 83 (130)
Q Consensus 6 ~~~~~~~~kIaVIGD--~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~ 83 (130)
+.+++....|+++-. .+....-.+.|++..=....-+..+.+...+.++..+.++.+..+.--|||+.. .-.+...+
T Consensus 20 ~~~~~~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~~~d~~~~~~~~~~l~~~~~dgiii~~-~~~~~~~~ 98 (295)
T PRK10653 20 SANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINP-TDSDAVGN 98 (295)
T ss_pred CCccccCCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecCCCCHHHHHHHHHHHHHcCCCEEEEcC-CChHHHHH
Confidence 455556788997764 222233333344322111111122333222346667778777654323555543 32333334
Q ss_pred HHhhcC-CCccEEEE
Q 032904 84 LVDSHN-KPIPAILE 97 (130)
Q Consensus 84 ~i~~~~-~~~P~Iv~ 97 (130)
.+..++ ...|+|+.
T Consensus 99 ~l~~~~~~~ipvV~~ 113 (295)
T PRK10653 99 AVKMANQANIPVITL 113 (295)
T ss_pred HHHHHHHCCCCEEEE
Confidence 444443 45787764
No 63
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=35.17 E-value=66 Score=26.92 Aligned_cols=31 Identities=10% Similarity=0.164 Sum_probs=24.1
Q ss_pred CCccEEEEcCCCCCCCChhhHHHHHHHHhhcccC
Q 032904 90 KPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVE 123 (130)
Q Consensus 90 ~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGid 123 (130)
...|+++.|-+..|+ |+..+-..+-+.+|..
T Consensus 89 ~~~p~iIlI~G~sgs---GKStlA~~La~~l~~~ 119 (301)
T PRK04220 89 SKEPIIILIGGASGV---GTSTIAFELASRLGIR 119 (301)
T ss_pred CCCCEEEEEECCCCC---CHHHHHHHHHHHhCCC
Confidence 468999999887776 5677888887777766
No 64
>PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=34.96 E-value=1.6e+02 Score=24.47 Aligned_cols=52 Identities=10% Similarity=0.283 Sum_probs=33.7
Q ss_pred EEEEechhhHHHH--------HHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEE
Q 032904 15 IAMIADEDTVVGF--------LLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLI 73 (130)
Q Consensus 15 IaVIGD~dtv~GF--------rLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlI 73 (130)
|..+||...-..+ .-.|+... ...-.++++++++.+.++++=+++++ |||+-
T Consensus 35 ii~vg~d~as~~Yv~~k~k~a~~~Gi~~~-------~~~l~~~~t~~~l~~~I~~lN~D~~V~GIivq 95 (282)
T PRK14166 35 VILVGDNPASQTYVKSKAKACEECGIKSL-------VYHLNENTTQNELLALINTLNHDDSVHGILVQ 95 (282)
T ss_pred EEEeCCCHHHHHHHHHHHHHHHHcCCEEE-------EEECCCCCCHHHHHHHHHHHhCCCCCCEEEEe
Confidence 5556764433333 34588654 23345567889999999999777787 66654
No 65
>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=34.86 E-value=1.6e+02 Score=20.53 Aligned_cols=54 Identities=15% Similarity=0.113 Sum_probs=32.1
Q ss_pred HHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe---hhhHHHHHHHHhhcCCC
Q 032904 25 VGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS---QYVANRIRFLVDSHNKP 91 (130)
Q Consensus 25 ~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt---e~~a~~i~~~i~~~~~~ 91 (130)
.-|+..|++.+ |. ..+++.+++.++..+. +.-+|.|+ +...+.+++.++.+++.
T Consensus 21 ~~l~~~G~~vi-------~l--G~~vp~e~~~~~a~~~----~~d~V~iS~~~~~~~~~~~~~~~~L~~~ 77 (122)
T cd02071 21 RALRDAGFEVI-------YT--GLRQTPEEIVEAAIQE----DVDVIGLSSLSGGHMTLFPEVIELLREL 77 (122)
T ss_pred HHHHHCCCEEE-------EC--CCCCCHHHHHHHHHHc----CCCEEEEcccchhhHHHHHHHHHHHHhc
Confidence 44777788654 22 3345667777766643 34444444 55667778877777543
No 66
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=34.83 E-value=1.3e+02 Score=23.04 Aligned_cols=83 Identities=7% Similarity=0.038 Sum_probs=44.9
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCC-eeEEEEehhhHHHHHHHHhhcCCC-cc--EEEEcCCC
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSRED-IAIVLISQYVANRIRFLVDSHNKP-IP--AILEIPSK 101 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~d-igIIlIte~~a~~i~~~i~~~~~~-~P--~Iv~IPs~ 101 (130)
-|+..|++.+ |+ ..+++.+++.+++++. +.| +++=+....-...+++.++.+++. .| .-+-+.+.
T Consensus 107 ~l~~~G~~vi-------~L--G~~vp~e~~v~~~~~~--~pd~v~lS~~~~~~~~~~~~~i~~l~~~~~~~~v~i~vGG~ 175 (197)
T TIGR02370 107 MLRANGFDVI-------DL--GRDVPIDTVVEKVKKE--KPLMLTGSALMTTTMYGQKDINDKLKEEGYRDSVKFMVGGA 175 (197)
T ss_pred HHHhCCcEEE-------EC--CCCCCHHHHHHHHHHc--CCCEEEEccccccCHHHHHHHHHHHHHcCCCCCCEEEEECh
Confidence 3667777654 22 4567788888877754 334 333333344455667777776422 21 33334332
Q ss_pred CCCCChhhHHHHHHHHhhcccCCcccc
Q 032904 102 DHPYDPAQDSVLSRVKNLVSVESVASD 128 (130)
Q Consensus 102 ~g~~~~~~d~I~~~Vk~aiGidi~~~~ 128 (130)
. +....-+.+|.|-++.+
T Consensus 176 ~---------~~~~~~~~~gad~~~~d 193 (197)
T TIGR02370 176 P---------VTQDWADKIGADVYGEN 193 (197)
T ss_pred h---------cCHHHHHHhCCcEEeCC
Confidence 2 11223456799987765
No 67
>cd00403 Ribosomal_L1 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.
Probab=34.69 E-value=2e+02 Score=21.76 Aligned_cols=88 Identities=10% Similarity=0.162 Sum_probs=55.8
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcC---CCeeEEEEehhhHHHHHHHHhh
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSR---EDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~---~digIIlIte~~a~~i~~~i~~ 87 (130)
...+|+|+.+.+...-=+.+|..- + . .+++.+.++..-.+ .+|-+.+.+..+...+...+-+
T Consensus 51 ~~~~i~v~~~d~~~~~a~~~~a~v----------i-g----~~~L~~~~~~~~~~~l~~~~D~fla~~~~~~~~~~~lgk 115 (208)
T cd00403 51 KDVKVCVFAKDEQAKEAKAAGADV----------V-G----GEDLKKKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGK 115 (208)
T ss_pred CCeEEEEEcChHhHHHHHHcCCCE----------E-c----HHHHHHHhhcchhhhhhhcCCEEEECHHHHHHHHHHhcc
Confidence 568999999977665556666632 2 2 26777766554321 6788888888888777776765
Q ss_pred c---CCCccEEEEcCCCCCCCChhhHHHHHHHHhhcc
Q 032904 88 H---NKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVS 121 (130)
Q Consensus 88 ~---~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiG 121 (130)
. +...|..+. ++ ..+.+.+.|+++.+
T Consensus 116 ~~~~k~k~P~~~~-----~t---~~~~l~~~i~~~~~ 144 (208)
T cd00403 116 VLGPRGKMPNPKT-----GT---VTEDLAKAIEEAKS 144 (208)
T ss_pred ccccCCCCCcCCC-----CC---CcccHHHHHHHHHh
Confidence 3 344443331 11 12458888888776
No 68
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=34.34 E-value=2e+02 Score=23.07 Aligned_cols=56 Identities=18% Similarity=0.098 Sum_probs=40.0
Q ss_pred ceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--hhhHHHHHHHHhhcCCCccEEEEc
Q 032904 41 TNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--QYVANRIRFLVDSHNKPIPAILEI 98 (130)
Q Consensus 41 ~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt--e~~a~~i~~~i~~~~~~~P~Iv~I 98 (130)
-.+++.|...+++...+..++|++++++-.|+=. ......+.+.+++ ...|+|-+.
T Consensus 41 i~lv~~D~~~~p~~a~~~a~~Li~~~~V~aiiG~~~s~~~~a~~~~~~~--~~vp~i~~~ 98 (347)
T cd06335 41 LELVERDDRGNPARGLQNAQELAADEKVVAVLGGLHTPVALANLEFIQQ--NKIPLIGPW 98 (347)
T ss_pred EEEEeccCCCCcHHHHHHHHHHhccCCeEEEEcCCCCHHHHhhhHHHHh--cCCcEEecC
Confidence 3467777777789999999999987788766653 3345556677776 457877644
No 69
>cd06359 PBP1_Nba_like Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway. This group includes the type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized.
Probab=34.19 E-value=1.4e+02 Score=23.61 Aligned_cols=70 Identities=19% Similarity=0.123 Sum_probs=45.5
Q ss_pred hhHHHHHHh------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCCCcc
Q 032904 22 DTVVGFLLA------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNKPIP 93 (130)
Q Consensus 22 dtv~GFrLa------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~~~P 93 (130)
+...|++|+ |+.+. +-.++..|...+++...+..++|+.++++-+|+= +......+.+.+++ ...|
T Consensus 18 ~~~~g~~lAv~~inggi~G~----~i~l~~~D~~~~p~~a~~~~~~lv~~~~v~~viG~~~s~~~~a~~~~~~~--~~ip 91 (333)
T cd06359 18 DMRDGFQLALKQLGGKLGGL----PVEVVVEDDGLKPDVAKQAAERLIKRDKVDFVTGVVFSNVLLAVVPPVLE--SGTF 91 (333)
T ss_pred HHHHHHHHHHHHhCCccCCE----EEEEEecCCCCChHHHHHHHHHHHhhcCCcEEEccCCcHHHHHHHHHHHH--cCCe
Confidence 445566652 55442 3335666666667889999999997777777763 45556667777776 4567
Q ss_pred EEEE
Q 032904 94 AILE 97 (130)
Q Consensus 94 ~Iv~ 97 (130)
+|-.
T Consensus 92 ~i~~ 95 (333)
T cd06359 92 YIST 95 (333)
T ss_pred EEec
Confidence 7653
No 70
>TIGR03336 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit. Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase.
Probab=33.70 E-value=1.3e+02 Score=26.99 Aligned_cols=54 Identities=20% Similarity=0.223 Sum_probs=43.4
Q ss_pred EEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehh
Q 032904 14 LIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQY 76 (130)
Q Consensus 14 kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~ 76 (130)
|+.+-|++....|.+.+|++ |+.-.|=|+--++-+.|.+++++.++-++...++
T Consensus 2 ~~~~~GneA~A~g~~~ag~~---------~~~~YPiTP~t~i~e~l~~~~~~~~~~~~~~~~E 55 (595)
T TIGR03336 2 KELLLGNEAIARGALEAGVG---------VAAAYPGTPSSEITDTLAKVAKRAGVYFEWSVNE 55 (595)
T ss_pred ceeecHHHHHHHHHHHcCCE---------EEEecCCCCHHHHHHHHHHhhhhccEEEEECcCH
Confidence 56788999999999999995 5667777888999999999987666655555544
No 71
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=33.10 E-value=1.6e+02 Score=22.81 Aligned_cols=52 Identities=10% Similarity=0.197 Sum_probs=40.6
Q ss_pred CCcHHHHHHHHHHHhcCCCeeEEEEehh-------hHHHHHHHHhhcC-CCccEEEEcCC
Q 032904 49 KTTIKQIEDAFKEFTSREDIAIVLISQY-------VANRIRFLVDSHN-KPIPAILEIPS 100 (130)
Q Consensus 49 ~~~~eei~~~~~~l~~~~digIIlIte~-------~a~~i~~~i~~~~-~~~P~Iv~IPs 100 (130)
.++.+++.+.|+++.+++++..|++.=. -.+.+++.|.+++ ...|+|..+.+
T Consensus 28 ~~~~~~l~~~l~~a~~d~~ik~vvL~~~s~gg~~~~~~el~~~i~~~~~~~kpVia~~~~ 87 (222)
T cd07018 28 ELSLRDLLEALEKAAEDDRIKGIVLDLDGLSGGLAKLEELRQALERFRASGKPVIAYADG 87 (222)
T ss_pred CccHHHHHHHHHHHhcCCCeEEEEEECCCCCCCHHHHHHHHHHHHHHHHhCCeEEEEeCC
Confidence 3456999999999998889998888843 3467788887775 67898887664
No 72
>CHL00200 trpA tryptophan synthase alpha subunit; Provisional
Probab=32.25 E-value=2.7e+02 Score=22.52 Aligned_cols=89 Identities=12% Similarity=0.147 Sum_probs=49.4
Q ss_pred echhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE-Eehhh-HHHHHHHHhhcCCCccEEE
Q 032904 19 ADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL-ISQYV-ANRIRFLVDSHNKPIPAIL 96 (130)
Q Consensus 19 GD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl-Ite~~-a~~i~~~i~~~~~~~P~Iv 96 (130)
|-+.++-=++=+|+.++ .+.|- +.+|..+.++.+ +..++..|+ ++... .++++...+. ...+=-+|
T Consensus 107 G~e~F~~~~~~aGvdgv--------iipDL--P~ee~~~~~~~~-~~~gi~~I~lv~PtT~~eri~~i~~~-a~gFIY~v 174 (263)
T CHL00200 107 GINKFIKKISQAGVKGL--------IIPDL--PYEESDYLISVC-NLYNIELILLIAPTSSKSRIQKIARA-APGCIYLV 174 (263)
T ss_pred CHHHHHHHHHHcCCeEE--------EecCC--CHHHHHHHHHHH-HHcCCCEEEEECCCCCHHHHHHHHHh-CCCcEEEE
Confidence 44556666788999885 55443 467877766655 455655554 44444 4677765543 22233444
Q ss_pred EcCCCCCCCC---hhhHHHHHHHHhh
Q 032904 97 EIPSKDHPYD---PAQDSVLSRVKNL 119 (130)
Q Consensus 97 ~IPs~~g~~~---~~~d~I~~~Vk~a 119 (130)
..|+..|... .....+.+++|+.
T Consensus 175 S~~GvTG~~~~~~~~~~~~i~~ir~~ 200 (263)
T CHL00200 175 STTGVTGLKTELDKKLKKLIETIKKM 200 (263)
T ss_pred cCCCCCCCCccccHHHHHHHHHHHHh
Confidence 5677666421 2233445555543
No 73
>PRK06696 uridine kinase; Validated
Probab=32.01 E-value=1e+02 Score=23.61 Aligned_cols=41 Identities=7% Similarity=0.080 Sum_probs=28.3
Q ss_pred hHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhc
Q 032904 77 VANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLV 120 (130)
Q Consensus 77 ~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ai 120 (130)
+.+.|.+.+.......|.||-|-+..|+ ||..+.+.+.+.+
T Consensus 6 ~~~~la~~~~~~~~~~~~iI~I~G~sgs---GKSTlA~~L~~~l 46 (223)
T PRK06696 6 LIKELAEHILTLNLTRPLRVAIDGITAS---GKTTFADELAEEI 46 (223)
T ss_pred HHHHHHHHHHHhCCCCceEEEEECCCCC---CHHHHHHHHHHHH
Confidence 3444555554434567899999887776 5788888888877
No 74
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=31.88 E-value=2.3e+02 Score=22.37 Aligned_cols=54 Identities=15% Similarity=0.148 Sum_probs=38.8
Q ss_pred eEEecCCCcHHHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhhcCCCccEEEEc
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDSHNKPIPAILEI 98 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~~~~~~P~Iv~I 98 (130)
+.+.|...+++...++.++|+.++++-.|+ ++......+.+.+++ ...|+|..-
T Consensus 43 ~~~~D~~~~~~~a~~~a~~li~~~~v~aiig~~~s~~~~~~~~~~~~--~~ip~i~~~ 98 (346)
T cd06330 43 LVVRDEAGKPDEAIREARELVENEGVDMLIGLISSGVALAVAPVAEE--LKVFFIATD 98 (346)
T ss_pred EEEecCCCCHHHHHHHHHHHHhccCCcEEEcccchHHHHHHHHHHHH--cCCeEEEcC
Confidence 566666667788999999999876776666 455566667777776 457877743
No 75
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=31.86 E-value=1.4e+02 Score=23.43 Aligned_cols=63 Identities=11% Similarity=0.125 Sum_probs=38.1
Q ss_pred cccEEEEEech------hhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh
Q 032904 11 ASALIAMIADE------DTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ 75 (130)
Q Consensus 11 ~~~kIaVIGD~------dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte 75 (130)
...+|++||-. +...||.. |+..++++-+........-.+.+...++-..++ +..+-||+-.-
T Consensus 119 ~t~kVG~I~g~~~~~~~~~~~gF~~-G~~~~~p~~~v~~~~~g~~~D~~~a~~~a~~l~-~~G~DvI~~~~ 187 (258)
T cd06353 119 KTNKVGYVAAFPIPEVVRGINAFAL-GARSVNPDATVKVIWTGSWFDPAKEKEAALALI-DQGADVIYQHT 187 (258)
T ss_pred cCCcEEEEcCcccHHHHHHHHHHHH-HHHHHCCCcEEEEEEecCCCCcHHHHHHHHHHH-HCCCcEEEecC
Confidence 45789999986 56678885 887554433211112222223466777777777 45677777664
No 76
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=31.73 E-value=3.4e+02 Score=23.45 Aligned_cols=71 Identities=14% Similarity=0.112 Sum_probs=41.3
Q ss_pred CcHHHHHHHHHHHhcCCCeeEEEEeh---------hhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhc
Q 032904 50 TTIKQIEDAFKEFTSREDIAIVLISQ---------YVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLV 120 (130)
Q Consensus 50 ~~~eei~~~~~~l~~~~digIIlIte---------~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ai 120 (130)
.+.+.+..+++.++++++++.|++.- .+++.+.+...++ ..+|+++..++... .+..++..+++
T Consensus 353 ~~~~~~~~al~~l~~dp~vd~Vlv~~~~~~~~~~~~~a~~l~~~~~~~-~~KPvv~~~~gg~~-----~~~~~~~L~~~- 425 (447)
T TIGR02717 353 ATPERYAKALKTVAEDENVDGVVVVLTPTAMTDPEEVAKGIIEGAKKS-NEKPVVAGFMGGKS-----VDPAKRILEEN- 425 (447)
T ss_pred CCHHHHHHHHHHHHcCCCCCEEEEEccCCccCCHHHHHHHHHHHHHhc-CCCcEEEEecCCcc-----HHHHHHHHHhC-
Confidence 45689999999999988988776432 1333344333332 26798777654211 13345545443
Q ss_pred ccCCccc
Q 032904 121 SVESVAS 127 (130)
Q Consensus 121 Gidi~~~ 127 (130)
|+-.|.+
T Consensus 426 Gip~f~~ 432 (447)
T TIGR02717 426 GIPNYTF 432 (447)
T ss_pred CCCccCC
Confidence 5555443
No 77
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=31.67 E-value=1.2e+02 Score=27.21 Aligned_cols=52 Identities=13% Similarity=0.191 Sum_probs=37.1
Q ss_pred ccccEEEEEechhhHHHHHH----hcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE
Q 032904 10 AASALIAMIADEDTVVGFLL----AGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL 72 (130)
Q Consensus 10 ~~~~kIaVIGD~dtv~GFrL----aGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl 72 (130)
+...||||||=+.++.|++. .|++-. -|..++. +|++..++++. +..+.+|+
T Consensus 95 ~~~~~ia~vg~~~~~~~~~~~~~ll~~~i~------~~~~~~~----~e~~~~~~~l~-~~G~~~vi 150 (526)
T TIGR02329 95 RIASSIGVVTHQDTPPALRRFQAAFNLDIV------QRSYVTE----EDARSCVNDLR-ARGIGAVV 150 (526)
T ss_pred hcCCcEEEEecCcccHHHHHHHHHhCCceE------EEEecCH----HHHHHHHHHHH-HCCCCEEE
Confidence 34589999999999999983 455422 1445454 99999999886 45666654
No 78
>PRK08367 porA pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed
Probab=31.62 E-value=1.5e+02 Score=25.52 Aligned_cols=53 Identities=17% Similarity=0.147 Sum_probs=43.7
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt 74 (130)
.++.+-|++....|.+.+|++ |..-.|=|+--++-+.+.+++.+.+++..++.
T Consensus 3 ~~~~~~GNeAvA~aa~~Ag~~---------v~a~YPITPsTei~e~la~~~~~g~~~~~~v~ 55 (394)
T PRK08367 3 IRTVMKANEAAAWAAKLAKPK---------VIAAFPITPSTLVPEKISEFVANGELDAEFIK 55 (394)
T ss_pred eeEeccHHHHHHHHHHHhCCC---------EEEEECCCCccHHHHHHHHHhhcCCcCeEEEE
Confidence 467889999999999999996 35556666678899999999987778878877
No 79
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=31.52 E-value=97 Score=25.71 Aligned_cols=42 Identities=12% Similarity=0.076 Sum_probs=29.2
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEEe
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLIS 74 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlIt 74 (130)
.+.-.|+... .+.-+++++++|+.+.++++=+++++ |||+--
T Consensus 57 ~a~~~Gi~~~-------~~~l~~~~s~~el~~~I~~lN~d~~V~GIlvql 99 (285)
T PRK10792 57 ACEEVGFVSR-------SYDLPETTSEAELLALIDELNADPTIDGILVQL 99 (285)
T ss_pred HHHHcCCEEE-------EEECCCCCCHHHHHHHHHHHhCCCCCCEEEEeC
Confidence 3445688654 23345567889999999999777777 666643
No 80
>PF08645 PNK3P: Polynucleotide kinase 3 phosphatase; InterPro: IPR013954 Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin []. ; PDB: 2FPW_A 2FPR_A 2FPX_A 2FPS_A 2FPU_B 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B 3U7G_A ....
Probab=31.21 E-value=1.8e+02 Score=21.40 Aligned_cols=65 Identities=14% Similarity=0.253 Sum_probs=37.4
Q ss_pred HHHHHHHHHhcCCCeeEEEEehh----------hHHHHHHHHhhc--CCCccEEEEcCCCCCCC-ChhhHHHHHHHHhh
Q 032904 54 QIEDAFKEFTSREDIAIVLISQY----------VANRIRFLVDSH--NKPIPAILEIPSKDHPY-DPAQDSVLSRVKNL 119 (130)
Q Consensus 54 ei~~~~~~l~~~~digIIlIte~----------~a~~i~~~i~~~--~~~~P~Iv~IPs~~g~~-~~~~d~I~~~Vk~a 119 (130)
.+.++|+++. +.+|.||++|+. -.+.+...++.+ ....|+.+.++.....+ .|..-.+...+++.
T Consensus 33 ~v~~~L~~l~-~~Gy~IvIvTNQ~gi~~~~~~~~~~~~~~ki~~il~~l~ip~~~~~a~~~d~~RKP~~GM~~~~~~~~ 110 (159)
T PF08645_consen 33 GVPEALRELH-KKGYKIVIVTNQSGIGRGMGEKDLENFHEKIENILKELGIPIQVYAAPHKDPCRKPNPGMWEFALKDY 110 (159)
T ss_dssp THHHHHHHHH-HTTEEEEEEEE-CCCCCTBTCCHHHHHHHHHHHHHHHCTS-EEEEECGCSSTTSTTSSHHHHHHCCCT
T ss_pred hHHHHHHHHH-hcCCeEEEEeCccccccccccchHHHHHHHHHHHHHHcCCceEEEecCCCCCCCCCchhHHHHHHHhc
Confidence 4888999885 788999999976 122333333332 15688887777655433 33333344444443
No 81
>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor
Probab=31.02 E-value=1.3e+02 Score=22.14 Aligned_cols=62 Identities=16% Similarity=0.155 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLV 120 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ai 120 (130)
.+.++..|++-+ +|==+..+.+.+.+++-+...+...|+|+..=+ +.+-|+..+.+.|-+++
T Consensus 16 ~~~L~~~L~~~l----~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG---~tGtGKn~v~~liA~~l 77 (127)
T PF06309_consen 16 ITGLEKDLQRNL----FGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHG---WTGTGKNFVSRLIAEHL 77 (127)
T ss_pred HHHHHHHHHHHc----cCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeec---CCCCcHHHHHHHHHHHH
Confidence 466777777665 343334455666677777665688999997755 44457899998887763
No 82
>cd06357 PBP1_AmiC Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon are induced.
Probab=31.02 E-value=2.2e+02 Score=23.10 Aligned_cols=70 Identities=14% Similarity=0.136 Sum_probs=45.9
Q ss_pred hhhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCC
Q 032904 21 EDTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNK 90 (130)
Q Consensus 21 ~dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~ 90 (130)
.+...|++|+ ||.+ ++-.+++.|..-+++...++.++|+.++++-.|+= +......+...+++.
T Consensus 17 ~~~~~g~~la~~~iN~~GGi~G----~~ielv~~D~~~~p~~a~~~a~~li~~~~V~aiiG~~~s~~~~a~~~~~~~~-- 90 (360)
T cd06357 17 RSQRNGALLAIEEINAAGGVLG----RELEPVEYDPGGDPDAYRALAERLLREDGVRVIFGCYTSSSRKAVLPVVERH-- 90 (360)
T ss_pred HHHHHHHHHHHHHHhhcCCCCC----eEEEEEEECCCCCHHHHHHHHHHHHhhCCCcEEEeCccHHHHHHHHHHHHhc--
Confidence 4556777764 3433 22246666766678999999999998888888873 344445666767763
Q ss_pred CccEEE
Q 032904 91 PIPAIL 96 (130)
Q Consensus 91 ~~P~Iv 96 (130)
..|.+.
T Consensus 91 ~~~~~~ 96 (360)
T cd06357 91 DALLWY 96 (360)
T ss_pred CceEEe
Confidence 355554
No 83
>TIGR02014 BchZ chlorophyllide reductase subunit Z. This model represents the Z subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Probab=31.00 E-value=1.1e+02 Score=26.99 Aligned_cols=54 Identities=17% Similarity=0.243 Sum_probs=33.8
Q ss_pred ccEEEEEechhhHHHH---HH--hcccccccCCcceeEEecC---CCcHHHHHHHHHHHhcCCCeeEEEEehh
Q 032904 12 SALIAMIADEDTVVGF---LL--AGVGNVDLRRKTNYLIVDS---KTTIKQIEDAFKEFTSREDIAIVLISQY 76 (130)
Q Consensus 12 ~~kIaVIGD~dtv~GF---rL--aGi~~~~~~~~~nf~v~~~---~~~~eei~~~~~~l~~~~digIIlIte~ 76 (130)
.+++||.||+|.+.|+ .. .|+..+ |.+... +++..++++.+ ++.+..+||=|+.
T Consensus 280 ~k~vaI~gd~d~~~gl~~fL~~ElGm~~~-------~~~t~~v~~~~D~~~i~~~i----~~~~p~ll~Gss~ 341 (468)
T TIGR02014 280 TARFGIVASETYARGIRHVLEDELGLPCL-------FSLARKAGSKTDNNAVRKEI----VQKQPLVLYGSMN 341 (468)
T ss_pred CceEEEEcCHHHHHHHHHHHHHHCCCceE-------EEeecceeecCCHHHHHHHH----hhcCCCEEEEChH
Confidence 4689999999999998 33 577654 433221 12346666544 4456777776664
No 84
>PRK07896 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=30.94 E-value=1.7e+02 Score=24.31 Aligned_cols=63 Identities=17% Similarity=0.295 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCcc-EEEEcCCCCCCCChhhHHHHHHHHhhcccCCcc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIP-AILEIPSKDHPYDPAQDSVLSRVKNLVSVESVA 126 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P-~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~~ 126 (130)
.+|+.+++ ....-+|++...-.+.+++.+..++...| +.++. +.+...+.+.++. ..|+|...
T Consensus 209 l~ea~eal-----~~gaDiI~LDnm~~e~vk~av~~~~~~~~~v~iea-----SGGI~~~ni~~yA--~tGvD~Is 272 (289)
T PRK07896 209 LEQLDEVL-----AEGAELVLLDNFPVWQTQEAVQRRDARAPTVLLES-----SGGLTLDTAAAYA--ETGVDYLA 272 (289)
T ss_pred HHHHHHHH-----HcCCCEEEeCCCCHHHHHHHHHHHhccCCCEEEEE-----ECCCCHHHHHHHH--hcCCCEEE
Confidence 35555553 24577899998889999999987654455 45555 3334567899998 57877654
No 85
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=30.58 E-value=2.5e+02 Score=22.15 Aligned_cols=54 Identities=9% Similarity=-0.010 Sum_probs=37.6
Q ss_pred eeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh--hhHHHHHHHHhhcCCCccEEEE
Q 032904 42 NYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ--YVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 42 nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte--~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
.+++.|...+++...++.++|+.++.+-+|+=.. .....+.+.+++ ...|.|..
T Consensus 41 elv~~D~~~~p~~a~~~a~~li~~~~v~aiiG~~~s~~~~a~~~~~~~--~~ip~i~~ 96 (332)
T cd06344 41 KVVIANDGNDPEIAKKVADELVKDPEILGVVGHYSSDATLAALDIYQK--AKLVLISP 96 (332)
T ss_pred EEEEECCCCChHHHHHHHHHHhcccCceEEEcCCCcHHHHHHHHHHhh--cCceEEcc
Confidence 4667777778899999999999877776666432 344456677776 44666654
No 86
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=30.03 E-value=1.7e+02 Score=23.69 Aligned_cols=54 Identities=13% Similarity=0.237 Sum_probs=38.6
Q ss_pred eeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--hhhHHHHHHHHhhcCCCccEEEE
Q 032904 42 NYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--QYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 42 nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt--e~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
.+++.|...+++...++.++|+.++++-+|+-+ ......+.+.+++ ...|+|..
T Consensus 44 ~lv~~D~~~~p~~a~~~a~~li~~d~v~~iiG~~~s~~~~a~~~~~~~--~~ip~i~~ 99 (357)
T cd06337 44 EIIVRDSQSNPNRAGLVAQELILTDKVDLLLAGGTPDTTNPVSDQCEA--NGVPCIST 99 (357)
T ss_pred EEEEecCCCCHHHHHHHHHHHHhccCccEEEecCCcchhhHHHHHHHH--hCCCeEEe
Confidence 366667767889999999999988888777743 3344455666665 55787763
No 87
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=29.77 E-value=1.1e+02 Score=20.56 Aligned_cols=31 Identities=10% Similarity=0.321 Sum_probs=22.4
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCeeEEEEehh
Q 032904 45 IVDSKTTIKQIEDAFKEFTSREDIAIVLISQY 76 (130)
Q Consensus 45 v~~~~~~~eei~~~~~~l~~~~digIIlIte~ 76 (130)
+.+.+.+.+|+.+++.+.++..+ +++-+++.
T Consensus 15 ~ies~~s~dev~~~v~~Al~~~~-~~l~LtD~ 45 (74)
T PF11305_consen 15 VIESDQSADEVEAAVTDALADGS-GVLTLTDE 45 (74)
T ss_pred EEecCCCHHHHHHHHHHHHhCCC-ceEEEEeC
Confidence 33445678999999999996554 77766653
No 88
>PRK09622 porA pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed
Probab=29.63 E-value=1.2e+02 Score=26.12 Aligned_cols=53 Identities=8% Similarity=0.043 Sum_probs=42.5
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt 74 (130)
.++.+-|++....|...+|++ |+.-.|=|+--|+-+.+.+++.+..++..++.
T Consensus 9 ~~~~~~GNeAiA~ga~~Ag~~---------~~a~YPITPsTeI~e~la~~~~~g~~~~~~vq 61 (407)
T PRK09622 9 EIEVWDGNTAASNALRQAQID---------VVAAYPITPSTPIVQNYGSFKANGYVDGEFVM 61 (407)
T ss_pred eeeecchHHHHHHHHHHhCCC---------EEEEECCCCccHHHHHHHHHhhCCCcCcEEEe
Confidence 578899999999999999996 45556667778899999999877666655543
No 89
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=29.63 E-value=1.7e+02 Score=19.33 Aligned_cols=43 Identities=14% Similarity=0.435 Sum_probs=32.9
Q ss_pred HHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEE
Q 032904 54 QIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 54 ei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
++.+..+++ ++.++.+|.|+.+-.+.++..++++.-..|++.-
T Consensus 47 ~l~~~~~~~-~~~~~~vi~is~d~~~~~~~~~~~~~~~~~~~~D 89 (124)
T PF00578_consen 47 ELNELYKKY-KDKGVQVIGISTDDPEEIKQFLEEYGLPFPVLSD 89 (124)
T ss_dssp HHHHHHHHH-HTTTEEEEEEESSSHHHHHHHHHHHTCSSEEEEE
T ss_pred HHHHHhhhh-ccceEEeeecccccccchhhhhhhhccccccccC
Confidence 344444433 4779999999999999888888887777887765
No 90
>PRK09029 O-succinylbenzoic acid--CoA ligase; Provisional
Probab=29.47 E-value=2.2e+02 Score=23.48 Aligned_cols=68 Identities=12% Similarity=0.087 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhcCCCeeE---------------EEEe-----hhhHHHHHHHHhhcCCCcc-EEEE---cCCCCCCCCh
Q 032904 52 IKQIEDAFKEFTSREDIAI---------------VLIS-----QYVANRIRFLVDSHNKPIP-AILE---IPSKDHPYDP 107 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digI---------------IlIt-----e~~a~~i~~~i~~~~~~~P-~Iv~---IPs~~g~~~~ 107 (130)
..|+++.+.+.-.=.|..+ +... +.+.+.+++.+..|+ .| .++. +| +..+...
T Consensus 366 p~eiE~~l~~~~~v~~~~v~~~~~~~~~~~~~a~v~~~~~~~~~~l~~~~~~~l~~~~--~P~~~~~~~~~p-~t~~gKi 442 (458)
T PRK09029 366 PEEIERVINQHPLVQQVFVVPVADAEFGQRPVAVVESDSEAAVVNLAEWLQDKLARFQ--QPVAYYLLPPEL-KNGGIKI 442 (458)
T ss_pred HHHHHHHHhcCCCcceEEEEccCCcccCceEEEEEEcCcccCHHHHHHHHHhhchhcc--CCeEEEEecccc-cCcCCCc
Confidence 5899998877532222222 2211 224556666666655 45 2332 55 4444444
Q ss_pred hhHHHHHHHHhhccc
Q 032904 108 AQDSVLSRVKNLVSV 122 (130)
Q Consensus 108 ~~d~I~~~Vk~aiGi 122 (130)
.+..|++.++.+.+-
T Consensus 443 ~r~~L~~~~~~~~~~ 457 (458)
T PRK09029 443 SRQALKEWVAQQLGN 457 (458)
T ss_pred CHHHHHHHHHhccCC
Confidence 556688888776653
No 91
>COG0447 MenB Dihydroxynaphthoic acid synthase [Coenzyme metabolism]
Probab=29.27 E-value=64 Score=26.60 Aligned_cols=25 Identities=20% Similarity=0.541 Sum_probs=21.8
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEeh
Q 032904 51 TIKQIEDAFKEFTSREDIAIVLISQ 75 (130)
Q Consensus 51 ~~eei~~~~~~l~~~~digIIlIte 75 (130)
|..|+-.+|...-.+.++|+|++|-
T Consensus 47 TV~Em~~Af~~Ar~d~~vGvi~lTG 71 (282)
T COG0447 47 TVDEMIDAFADARDDPNVGVILLTG 71 (282)
T ss_pred cHHHHHHHHHhhhcCCCccEEEEec
Confidence 5688889999888888999999993
No 92
>TIGR00126 deoC deoxyribose-phosphate aldolase. Deoxyribose-phosphate aldolase is involved in the catabolism of nucleotides and deoxyriibonucleotides. The catalytic process is as follows: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde. It is found in both gram-postive and gram-negative bacteria.
Probab=29.15 E-value=2.8e+02 Score=21.80 Aligned_cols=59 Identities=14% Similarity=0.110 Sum_probs=42.4
Q ss_pred EecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCC
Q 032904 45 IVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHP 104 (130)
Q Consensus 45 v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~ 104 (130)
...++.|.+++++..++.. +..++=+.+........++.+....-..=++|-.|.-..+
T Consensus 10 ~L~p~~t~~~i~~lc~~A~-~~~~~avcv~p~~v~~a~~~l~~~~v~v~tVigFP~G~~~ 68 (211)
T TIGR00126 10 ALKADTTEEDIITLCAQAK-TYKFAAVCVNPSYVPLAKELLKGTEVRICTVVGFPLGAST 68 (211)
T ss_pred CCCCCCCHHHHHHHHHHHH-hhCCcEEEeCHHHHHHHHHHcCCCCCeEEEEeCCCCCCCc
Confidence 4466778899999999876 5688888888888888888886432223355666665544
No 93
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=28.98 E-value=2.1e+02 Score=20.53 Aligned_cols=35 Identities=14% Similarity=0.313 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhcCCCeeEEEEe----hh---hHHHHHHHHhhc
Q 032904 53 KQIEDAFKEFTSREDIAIVLIS----QY---VANRIRFLVDSH 88 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIt----e~---~a~~i~~~i~~~ 88 (130)
+.+.+..+.+. .++..|..+. .. .+++|++.|+++
T Consensus 14 ~Gi~~~~~~~~-g~~~~i~~~gg~~d~~~gt~~~~I~~ai~~~ 55 (125)
T TIGR02364 14 EGIKELIKQMA-GDDVTIISAGGTDDGRLGTSPDKIIEAIEKA 55 (125)
T ss_pred HHHHHHHHHHc-CCCccEEEEecCCCCCccchHHHHHHHHHHh
Confidence 44555555554 3455555553 11 456777777775
No 94
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=28.87 E-value=2.5e+02 Score=22.39 Aligned_cols=54 Identities=15% Similarity=0.118 Sum_probs=39.3
Q ss_pred eEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCCCccEEEEc
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNKPIPAILEI 98 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~~~P~Iv~I 98 (130)
+++.|...+++....+.++|+.++++-.|+= +......+.+.+++ ...|.|...
T Consensus 44 lv~~D~~~~p~~a~~~~~~li~~~~V~avvG~~~S~~~~a~~~~~~~--~~ip~i~~~ 99 (333)
T cd06328 44 VIVKDDAGNPEVAVSLARELIGDDGVDILVGSTSSGVALAVLPVAEE--NKKILIVEP 99 (333)
T ss_pred EEEecCCCChHHHHHHHHHHHHhcCCeEEEccCCcHHHHHHHHHHHH--hCCcEEecC
Confidence 5666777788999999999998888777763 45566666676776 457777643
No 95
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=28.73 E-value=1.2e+02 Score=20.84 Aligned_cols=38 Identities=13% Similarity=0.079 Sum_probs=28.2
Q ss_pred cCCCeeEEEEehhhHHHHHHHHhhc--CCCccEEEEcCCC
Q 032904 64 SREDIAIVLISQYVANRIRFLVDSH--NKPIPAILEIPSK 101 (130)
Q Consensus 64 ~~~digIIlIte~~a~~i~~~i~~~--~~~~P~Iv~IPs~ 101 (130)
++.....++|.+++.+..++.+..+ ....|.+...+++
T Consensus 29 ~~gkaklViiA~D~~~~~~~~i~~~c~~~~Ip~~~~~~tk 68 (99)
T PRK01018 29 KLGKAKLVIVASNCPKDIKEDIEYYAKLSGIPVYEYEGSS 68 (99)
T ss_pred HcCCceEEEEeCCCCHHHHHHHHHHHHHcCCCEEEECCCH
Confidence 4677899999999888888888765 2567877655443
No 96
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=28.28 E-value=2.4e+02 Score=22.46 Aligned_cols=54 Identities=6% Similarity=0.194 Sum_probs=37.4
Q ss_pred eeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCCCccEEEE
Q 032904 42 NYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 42 nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
.+++.|...+.+...+..++|+.++++-.|+= +......+.+.+++ ...|+|-.
T Consensus 49 ~l~~~D~~~~~~~a~~~a~~li~~~~v~avvG~~~s~~~~~~~~~~~~--~~ip~i~~ 104 (362)
T cd06343 49 ELIVEDDGYSPPKTVEQTRKLVESDEVFAMVGGLGTPTNLAVQKYLNE--KKVPQLFP 104 (362)
T ss_pred EEEEecCCCChHHHHHHHHHHHhhcCeEEEEecCCcHHHHHhHHHHHh--cCCceEec
Confidence 35666766677888999999997777766663 34555566666766 44777764
No 97
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=28.26 E-value=1.4e+02 Score=19.83 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=27.1
Q ss_pred HHHHhcCCCeeEEEEehhhH---HHHHHHHhhcCCCccEEEEcCCCCC
Q 032904 59 FKEFTSREDIAIVLISQYVA---NRIRFLVDSHNKPIPAILEIPSKDH 103 (130)
Q Consensus 59 ~~~l~~~~digIIlIte~~a---~~i~~~i~~~~~~~P~Iv~IPs~~g 103 (130)
++++++++++-+++|+..-. +.+...++ ...|+++|=|--..
T Consensus 54 ~~~ll~~~~~D~V~I~tp~~~h~~~~~~~l~---~g~~v~~EKP~~~~ 98 (120)
T PF01408_consen 54 LEELLADEDVDAVIIATPPSSHAEIAKKALE---AGKHVLVEKPLALT 98 (120)
T ss_dssp HHHHHHHTTESEEEEESSGGGHHHHHHHHHH---TTSEEEEESSSSSS
T ss_pred HHHHHHhhcCCEEEEecCCcchHHHHHHHHH---cCCEEEEEcCCcCC
Confidence 56677766777777765543 34444444 56699999987653
No 98
>PRK07232 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed
Probab=28.21 E-value=1.2e+02 Score=28.64 Aligned_cols=80 Identities=14% Similarity=0.132 Sum_probs=50.2
Q ss_pred hcccccEEEEEechhhHHHHHHhcccc-ccc-----------CCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh
Q 032904 8 RTAASALIAMIADEDTVVGFLLAGVGN-VDL-----------RRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ 75 (130)
Q Consensus 8 ~~~~~~kIaVIGD~dtv~GFrLaGi~~-~~~-----------~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte 75 (130)
|+.....++||.|-.-|+|+-=.|..+ ... -+-.-|.+.-++.+.+|+-++++.+. +.+|.|=+.+
T Consensus 58 ~t~~~n~v~vvtdg~~vLGlGd~G~~a~~pv~egK~~l~~~~~gid~~~i~~~~~d~de~v~~v~~~~--p~~g~i~~ED 135 (752)
T PRK07232 58 YTARGNLVAVISNGTAVLGLGNIGALASKPVMEGKGVLFKKFAGIDVFDIEVDEEDPDKFIEAVAALE--PTFGGINLED 135 (752)
T ss_pred cccCCcEEEEEccchhhccccccccccCccHHHHHHHHHHhhcCCCccccccCCCCHHHHHHHHHHhC--CCccEEeeee
Confidence 455567799999999999986555541 100 00001333222346788999888664 7898888776
Q ss_pred hhHHHHHHHHhhcC
Q 032904 76 YVANRIRFLVDSHN 89 (130)
Q Consensus 76 ~~a~~i~~~i~~~~ 89 (130)
--+...-+.+++|+
T Consensus 136 ~~~p~~f~i~~~~~ 149 (752)
T PRK07232 136 IKAPECFYIEEKLR 149 (752)
T ss_pred cCCchHHHHHHHHH
Confidence 65556666666664
No 99
>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=28.21 E-value=79 Score=25.34 Aligned_cols=38 Identities=13% Similarity=0.275 Sum_probs=26.1
Q ss_pred cCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHH
Q 032904 47 DSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLV 85 (130)
Q Consensus 47 ~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i 85 (130)
+.+++..++.+..+ +++..++..||.......+.-+.|
T Consensus 191 ~~eps~~~l~~l~~-~ik~~~v~~if~e~~~~~~~~~~l 228 (276)
T cd01016 191 DSEAGLRDINELVD-LIVERKIKAIFVESSVNQKSIEAL 228 (276)
T ss_pred ccCCCHHHHHHHHH-HHHHcCCCEEEEeCCCCHHHHHHH
Confidence 44556788887666 556889999999877555444444
No 100
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=28.19 E-value=3.4e+02 Score=24.05 Aligned_cols=25 Identities=16% Similarity=0.243 Sum_probs=19.5
Q ss_pred cccEEEEEechhhHHHHH--Hh---ccccc
Q 032904 11 ASALIAMIADEDTVVGFL--LA---GVGNV 35 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFr--La---Gi~~~ 35 (130)
..+|++|+||...+.|+. |. |++.+
T Consensus 304 ~Gkrv~I~gd~~~a~~l~~~L~~ELGm~vv 333 (513)
T CHL00076 304 TGKKAVVFGDATHAASMTKILAREMGIRVS 333 (513)
T ss_pred CCCEEEEEcCchHHHHHHHHHHHhCCCEEE
Confidence 348999999999999974 44 77643
No 101
>PF08747 DUF1788: Domain of unknown function (DUF1788); InterPro: IPR014858 This entry represents a putative uncharacterised protein of length around 200 amino acids.
Probab=28.08 E-value=2.3e+02 Score=20.55 Aligned_cols=50 Identities=16% Similarity=0.291 Sum_probs=33.3
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehh--hHH--HHHHHHhhcC---CCccEEEEcCCCC
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQY--VAN--RIRFLVDSHN---KPIPAILEIPSKD 102 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~--~a~--~i~~~i~~~~---~~~P~Iv~IPs~~ 102 (130)
+.+.+.+.+-...++-.|++||-= ++- +....+++++ ...|+|+.-|+.-
T Consensus 47 ~~i~~~i~~~~~~~~~~vv~ltGvG~l~P~~R~h~lL~~l~~~~~~~plv~FyPG~y 103 (126)
T PF08747_consen 47 EKIAEYIQEELEDDDRDVVFLTGVGSLFPFIRSHELLNNLQPKFGNVPLVVFYPGEY 103 (126)
T ss_pred HHHHHHHHHhccCCCCcEEEEeCcchhcchhhHHHHHHHHHHHhcCCeEEEECCcee
Confidence 666666666555677889999843 322 4444556553 5789999999854
No 102
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=28.02 E-value=72 Score=26.40 Aligned_cols=20 Identities=15% Similarity=0.130 Sum_probs=14.8
Q ss_pred CchhhhcccccEEEEEechh
Q 032904 3 NRPQIRTAASALIAMIADED 22 (130)
Q Consensus 3 ~~~~~~~~~~~kIaVIGD~d 22 (130)
+.+..+.+..+.|.++||++
T Consensus 107 ~~v~~~~~~Gy~iviiG~~~ 126 (281)
T PRK12360 107 NIVEEYYNKGYSIIIVGDKN 126 (281)
T ss_pred HHHHHHHhCCCEEEEEcCCC
Confidence 34566667789999999943
No 103
>PRK14177 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.92 E-value=1e+02 Score=25.61 Aligned_cols=41 Identities=15% Similarity=0.305 Sum_probs=28.6
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEE
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLI 73 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlI 73 (130)
-+.-.|+... .....++++++++.+.++++=+++++ |||+-
T Consensus 57 ~~~~~Gi~~~-------~~~l~~~~s~~el~~~I~~lN~D~~V~GIlvq 98 (284)
T PRK14177 57 ACHKVGMGSE-------MIRLKEQTTTEELLGVIDKLNLDPNVDGILLQ 98 (284)
T ss_pred HHHHcCCEEE-------EEECCCCCCHHHHHHHHHHHhCCCCCCeEEEc
Confidence 4455788653 23345566889999999998777787 66654
No 104
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=27.88 E-value=89 Score=23.27 Aligned_cols=37 Identities=14% Similarity=0.294 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhcCCCeeEEEE------ehhhHHHHHHHHhhc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLI------SQYVANRIRFLVDSH 88 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlI------te~~a~~i~~~i~~~ 88 (130)
.++..+.|++|+.+...-+|.| +.++.+.+++.+.++
T Consensus 48 ~~~~~~~l~~~i~~~kP~vI~v~g~~~~s~~l~~~v~~~v~~~ 90 (150)
T PF14639_consen 48 KEEDMERLKKFIEKHKPDVIAVGGNSRESRKLYDDVRDIVEEL 90 (150)
T ss_dssp SHHHHHHHHHHHHHH--SEEEE--SSTHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCeEEEEcCCChhHHHHHHHHHHHHHHh
Confidence 3677788888998888888998 566778888888775
No 105
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=27.84 E-value=2.4e+02 Score=22.68 Aligned_cols=71 Identities=14% Similarity=0.151 Sum_probs=44.9
Q ss_pred hhhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhhcCC
Q 032904 21 EDTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDSHNK 90 (130)
Q Consensus 21 ~dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~~~~ 90 (130)
+....|++|+ ||.| ++-.++..|...++++..+..++|+.++++-+|+ .+......+...+++ .
T Consensus 17 ~~~~~g~~la~~~iN~~GGi~G----~~ielv~~D~~~~p~~a~~~a~~Li~~~~V~~iiG~~~S~~~~a~~~~~~~--~ 90 (348)
T cd06355 17 TTLKDAELLAIEEINAAGGVLG----RKIEAVVEDGASDWPTFAEKARKLLTQDKVAAVFGCWTSASRKAVLPVFER--H 90 (348)
T ss_pred hhHHHHHHHHHHHHHhcCCCCC----cEEEEEEeCCCCCHHHHHHHHHHHHHhCCCcEEEeccchhhHHHHHHHHhc--c
Confidence 4556666654 5543 2333556666667899999999999877776666 334445556666665 3
Q ss_pred CccEEEE
Q 032904 91 PIPAILE 97 (130)
Q Consensus 91 ~~P~Iv~ 97 (130)
..|+|.+
T Consensus 91 ~~~~i~~ 97 (348)
T cd06355 91 NGLLFYP 97 (348)
T ss_pred CCceecC
Confidence 3566543
No 106
>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.
Probab=27.75 E-value=1e+02 Score=21.65 Aligned_cols=51 Identities=22% Similarity=0.322 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhH--HHHHHHHhhc-CCCccEEE-EcCCCCC
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVA--NRIRFLVDSH-NKPIPAIL-EIPSKDH 103 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a--~~i~~~i~~~-~~~~P~Iv-~IPs~~g 103 (130)
+.+.+.+++-++.-++-|+|++.+.. ..++-+|+.- +...|+|. .+|+...
T Consensus 58 ~~ik~~I~~~i~~s~~~IVLig~~T~~s~wV~~EI~~A~~~~~~Ii~V~~~~~~~ 112 (130)
T PF08937_consen 58 EYIKRKIRERIKNSSVTIVLIGPNTAKSKWVNWEIEYALKKGKPIIGVYLPGLKD 112 (130)
T ss_dssp TTHHHHHHHHHHTEEEEEEE--TT----HHHHHHHHHHTTT---EEEEETT--SG
T ss_pred HHHHHHHHHHHhcCCEEEEEeCCCcccCcHHHHHHHHHHHCCCCEEEEECCCCCC
Confidence 37889999999999999999999875 5788888874 58889665 5555543
No 107
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=27.56 E-value=2.5e+02 Score=20.60 Aligned_cols=66 Identities=12% Similarity=0.163 Sum_probs=39.6
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhh--HHHHHHHHhh
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYV--ANRIRFLVDS 87 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~--a~~i~~~i~~ 87 (130)
..+-|+=.++-..-.+-+|+.++ |.+....+...+..+.++... ..-|||++|+.= -++||..+.+
T Consensus 10 ~~vIVVEGK~D~~~l~~~~~~~~-------i~~~g~~i~~~~~ie~i~~~~--~~k~VIILTD~D~~Ge~Irk~l~~ 77 (127)
T COG1658 10 KEVIVVEGKDDTASLKRLGDAGV-------IITNGSAINSLETIELIKKAQ--KYKGVIILTDPDRKGERIRKKLKE 77 (127)
T ss_pred CceEEEeCCcHHHHHHHhcCCce-------EEEcCCccchHHHHHHHHHhh--ccCCEEEEeCCCcchHHHHHHHHH
Confidence 45566666777778888888887 666554333244444444433 567788888652 2455555544
No 108
>cd01971 Nitrogenase_VnfN_like Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like. This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-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 protien 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=27.49 E-value=2.2e+02 Score=24.25 Aligned_cols=55 Identities=16% Similarity=0.183 Sum_probs=33.3
Q ss_pred ccEEEEEechhhHHHH---H--HhcccccccCCcceeEEecCCCcHHHHHHHHHHHhc--CCCeeEEEEe
Q 032904 12 SALIAMIADEDTVVGF---L--LAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTS--REDIAIVLIS 74 (130)
Q Consensus 12 ~~kIaVIGD~dtv~GF---r--LaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~--~~digIIlIt 74 (130)
.++++|.||.+.+.|+ . =.|++-+ ..+.... +.++.++.+++.++ ..+..+++.+
T Consensus 293 ~k~vai~~~~~~~~~l~~~L~~elGm~~~-------~~~~~~~-~~~~~~~~~~~~~~~~~~~~~v~~~~ 354 (427)
T cd01971 293 PRRFAVIADSTYALGLARFLVNELGWVPA-------KQVITDN-PPEKYRSAIENEFEAEGVSAEVVFSE 354 (427)
T ss_pred CceEEEECChHHHHHHHHHHHHhcCCceE-------EEEecCC-CCHHHHHHHHHHHHhcCCCCcEEEec
Confidence 4899999999999988 3 3788654 3333332 24666666655432 2234455544
No 109
>PF02873 MurB_C: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; InterPro: IPR011601 This entry represents a C-terminal conserved region of UDP-N-acetylenolpyruvoylglucosamine reductase 1.1.1.158 from EC, which is also called UDP-N-acetylmuramate dehydrogenase. It is a part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide, which is a precursor of bacterial peptidoglycan. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 1MBB_A 2Q85_A 2MBR_A 1UXY_A 1MBT_A 1HSK_A 2GQU_A 2GQT_A 3I99_A 3TX1_A.
Probab=27.33 E-value=56 Score=23.04 Aligned_cols=37 Identities=16% Similarity=0.364 Sum_probs=22.0
Q ss_pred HHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHH
Q 032904 24 VVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEF 62 (130)
Q Consensus 24 v~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l 62 (130)
.-||+..|+.- ..++.||++.....|-.++.+.++.+
T Consensus 49 lKG~~iG~a~v--S~kHanfivN~g~Ata~dv~~Li~~v 85 (105)
T PF02873_consen 49 LKGFRIGGAQV--SEKHANFIVNHGGATAADVLALIEEV 85 (105)
T ss_dssp -TT-EETTEEE---SSSTTEEEE-SS--HHHHHHHHHHH
T ss_pred CCCCeeCcCEe--chhhCCeEEECCCCCHHHHHHHHHHH
Confidence 35677777753 46788899988877777777655543
No 110
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli 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. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=27.28 E-value=1.2e+02 Score=23.70 Aligned_cols=32 Identities=22% Similarity=0.456 Sum_probs=24.3
Q ss_pred eEEecCCCcHHHHHHHHHHHhcC-CCeeEEEEe
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSR-EDIAIVLIS 74 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~-~digIIlIt 74 (130)
|+...++.+.+++++.++.+..+ .++.+|+|.
T Consensus 105 ~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~ID 137 (259)
T PF03796_consen 105 YIEDTPSLTIDDIESKIRRLKREGKKVDVVFID 137 (259)
T ss_dssp EEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEE
T ss_pred EEECCCCCCHHHHHHHHHHHHhhccCCCEEEec
Confidence 55556677888898888888766 788888887
No 111
>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=27.27 E-value=2.1e+02 Score=24.39 Aligned_cols=66 Identities=9% Similarity=-0.007 Sum_probs=0.0
Q ss_pred cccEEEEEechhhHHHHH-----HhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHH
Q 032904 11 ASALIAMIADEDTVVGFL-----LAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLV 85 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFr-----LaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i 85 (130)
..+|++|.||.+.+.++. | |++.+ .+..+..+.+..++.++.+.. +..++.+.=...+.+.+
T Consensus 273 ~Gkrv~i~gd~~~~~~l~~~L~el-Gm~~v--------~~~t~~~~~~~~~~~~~~l~~----~~~v~~~~d~~~l~~~i 339 (407)
T TIGR01279 273 RGKKIFFFGDNLLELPLARFLKRC-GMEVV--------ECGTPYIHRRFHAAELALLEG----GVRIVEQPDFHRQLQRI 339 (407)
T ss_pred CCCEEEEECCchHHHHHHHHHHHC-CCEEE--------EecCCCCChHHHHHHHhhcCC----CCeEEeCCCHHHHHHHH
Q ss_pred hhcC
Q 032904 86 DSHN 89 (130)
Q Consensus 86 ~~~~ 89 (130)
.+++
T Consensus 340 ~~~~ 343 (407)
T TIGR01279 340 RATR 343 (407)
T ss_pred HhcC
No 112
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=27.22 E-value=2.7e+02 Score=20.84 Aligned_cols=52 Identities=15% Similarity=0.210 Sum_probs=26.7
Q ss_pred EEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhc-CCCccEEE
Q 032904 44 LIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSH-NKPIPAIL 96 (130)
Q Consensus 44 ~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~-~~~~P~Iv 96 (130)
++.+...+.++..+.++.+++..==|||+..-. .....+.+..+ +...|+|+
T Consensus 34 ~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~-~~~~~~~~~~l~~~~iPvv~ 86 (272)
T cd06301 34 QFEDAKNDVATQLSQVENFIAQGVDAIIVVPVD-TAATAPIVKAANAAGIPLVY 86 (272)
T ss_pred EEeCCCCCHHHHHHHHHHHHHcCCCEEEEecCc-hhhhHHHHHHHHHCCCeEEE
Confidence 333333345677788888876543444444322 22223333333 26678775
No 113
>TIGR03710 OAFO_sf 2-oxoacid:acceptor oxidoreductase, alpha subunit. The genes for this enzyme in Prevotella intermedia 17, Persephonella marina EX-H1 and Picrophilus torridus DSM 9790 are in close proximity to a variety of TCA cycle genes. Persephonella marina and P. torridus are believed to encode complete TCA cycles, and none of these contains the lipoate-based 2-oxoglutarate dehydrogenase (E1/E2/E3) system. That system is presumed to be replaced by this one. In fact, the lipoate system is absent in most organisms possessing a member of this family, providing additional circumstantial evidence that many of these enzymes are capable of acting as 2-oxoglutarate dehydrogenases and supporting flux through TCA cycles in either the forward or reverse directions.
Probab=26.75 E-value=2.4e+02 Score=25.28 Aligned_cols=57 Identities=14% Similarity=0.204 Sum_probs=43.0
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehh
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQY 76 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~ 76 (130)
...++.+-|++....|.+.+|++ |..-.|=|+--++-+.+.+++.+.++-++-..++
T Consensus 190 ~~~~~~l~GNeAvA~ga~~ag~~---------~~~~YPiTPsTei~e~la~~~~~~~~~~~q~E~E 246 (562)
T TIGR03710 190 DGDRILISGNEAIALGAIAAGLR---------FYAAYPITPASDILEFLAKHLKKFGVVVVQAEDE 246 (562)
T ss_pred CCcEEEeehHHHHHHHHHHhCCc---------eecccCCCChhHHHHHHHHhhhhhCcEEEeeccH
Confidence 44678999999999999999995 4566666777889999998876555444444444
No 114
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=26.71 E-value=1.7e+02 Score=23.24 Aligned_cols=59 Identities=12% Similarity=0.155 Sum_probs=43.2
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
...||+|++|.+...==+-+|+.- + .. +|+.+.+++=. -+|-.++-|.++...+.. |-+
T Consensus 70 k~~kI~Vfa~~~~~~~Ak~aGa~~----------v-g~----eeLi~~ik~~~--~~fd~~iat~~~m~~l~~-Lg~ 128 (230)
T PRK05424 70 KTVRVAVFAKGEKAEEAKAAGADI----------V-GG----EDLIEKIKGGW--LDFDVVIATPDMMGKVGK-LGR 128 (230)
T ss_pred CCcEEEEECChHhHHHHHHcCCCE----------e-CH----HHHHHHHhcCC--CcCCEEEECHHHHHHHHH-hcc
Confidence 457999999998887778899842 2 33 77777665332 378889999998888765 554
No 115
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=26.71 E-value=2.5e+02 Score=23.26 Aligned_cols=69 Identities=14% Similarity=0.196 Sum_probs=46.9
Q ss_pred hhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE--EehhhHHHHHHHHhhcCCC
Q 032904 22 DTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL--ISQYVANRIRFLVDSHNKP 91 (130)
Q Consensus 22 dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl--Ite~~a~~i~~~i~~~~~~ 91 (130)
+...|++|+ ||.| ++-.+++.|...+++...+..++|+.++.+-+|+ .+......+...+++ ..
T Consensus 19 ~~~~G~~lAv~~iNa~GGi~G----r~ielv~~D~~~~p~~a~~~a~~li~~d~v~~viG~~~S~~~~A~~~~~~~--~~ 92 (374)
T TIGR03669 19 PKWHASQLAIEEINKSGGILG----RQIELIDPDPQSDNERYQELTRRLLNRDKVDALWAGYSSATREAIRPIIDR--NE 92 (374)
T ss_pred HHHHHHHHHHHHHHhcCCCCC----ceeEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEcCCchHHHHHHHHHHHh--cC
Confidence 456777765 4433 2334677777778899999999999877777766 345556666666665 44
Q ss_pred ccEEE
Q 032904 92 IPAIL 96 (130)
Q Consensus 92 ~P~Iv 96 (130)
.|.|.
T Consensus 93 ~~~i~ 97 (374)
T TIGR03669 93 QLYFY 97 (374)
T ss_pred ceEEc
Confidence 67665
No 116
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=26.35 E-value=3.2e+02 Score=21.51 Aligned_cols=55 Identities=13% Similarity=0.207 Sum_probs=37.9
Q ss_pred ceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe--hhhHHHHHHHHhhcCCCccEEEE
Q 032904 41 TNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS--QYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 41 ~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt--e~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
-.+++.|...+++...+..++|+.++++-+|+=. ......+.+.+++ ...|+|..
T Consensus 40 v~l~~~D~~~~p~~a~~~~~~l~~~~~V~aviG~~~s~~~~a~~~~~~~--~~vp~i~~ 96 (334)
T cd06327 40 IELVVADHQNKADVAAAKAREWIDRDGVDMIVGGPNSAVALAVQEVARE--KKKIYIVT 96 (334)
T ss_pred EEEEEecCCCCchHHHHHHHHHHhhcCceEEECCccHHHHHHHHHHHHH--hCceEEec
Confidence 3466667766778999999999987777777653 4455566666666 44666653
No 117
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.29 E-value=1.3e+02 Score=24.92 Aligned_cols=40 Identities=10% Similarity=0.057 Sum_probs=27.6
Q ss_pred HHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEE
Q 032904 27 FLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLI 73 (130)
Q Consensus 27 FrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlI 73 (130)
+.-.|++.. ...-+.+++++++.+.++++=+++++ |||+-
T Consensus 57 ~~~~Gi~~~-------~~~l~~~~~~~~l~~~I~~lN~d~~V~GIlvq 97 (285)
T PRK14189 57 CEDNGFHSL-------KDRYPADLSEAELLARIDELNRDPKIHGILVQ 97 (285)
T ss_pred HHHcCCEEE-------EEECCCCCCHHHHHHHHHHHcCCCCCCeEEEe
Confidence 445688653 23345567889999999998777776 66654
No 118
>PRK06106 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=26.10 E-value=1.9e+02 Score=23.95 Aligned_cols=61 Identities=15% Similarity=0.173 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCCcc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVESVA 126 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~~ 126 (130)
.+|+++++ .-..-+|++...-.+.+++.++..+...| ++. +.+...+.+.++. ..|+|...
T Consensus 204 leea~ea~-----~~gaDiI~LDn~s~e~l~~av~~~~~~~~--lea-----SGGI~~~ni~~yA--~tGVD~Is 264 (281)
T PRK06106 204 LDQLEEAL-----ELGVDAVLLDNMTPDTLREAVAIVAGRAI--TEA-----SGRITPETAPAIA--ASGVDLIS 264 (281)
T ss_pred HHHHHHHH-----HcCCCEEEeCCCCHHHHHHHHHHhCCCce--EEE-----ECCCCHHHHHHHH--hcCCCEEE
Confidence 46666654 34678999999999999999987654444 554 3345568899998 56888654
No 119
>cd00363 PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases. Some members evolved by gene duplication and thus have a large C-terminal/N-terminal extension comprising a second PFK domain. Generally, ATP-PFKs are allosteric homotetramers, and PPi-PFKs are dimeric and nonallosteric except for plant PPi-PFKs which are allosteric heterotetramers.
Probab=25.91 E-value=1.2e+02 Score=25.44 Aligned_cols=51 Identities=14% Similarity=0.130 Sum_probs=33.4
Q ss_pred cHHHHHHHHHHHhcC-CCeeEEEEehhhH---------HHHHHHHhhcCCCccEEEEcCCCC
Q 032904 51 TIKQIEDAFKEFTSR-EDIAIVLISQYVA---------NRIRFLVDSHNKPIPAILEIPSKD 102 (130)
Q Consensus 51 ~~eei~~~~~~l~~~-~digIIlIte~~a---------~~i~~~i~~~~~~~P~Iv~IPs~~ 102 (130)
..+++.+.+++-.++ +.++||+++|.+. ..+.+.|++.- ...+-..+|+..
T Consensus 205 ~~~~~~~~i~~r~~~~~~~~vivvsEG~~~~~~~~~~~~~l~~~i~~~~-~~~~r~~~lGy~ 265 (338)
T cd00363 205 WEEEMVDVIKKRRERGKRHGIVIVAEGAIDFIPKPITEKLLAKLVEERL-GFDTRATVLGHV 265 (338)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEEeCCCccccccCchHHHHHHHHHHHc-CCceEEeecCcc
Confidence 356666666665554 7899999999855 56677776532 244556667643
No 120
>cd01841 NnaC_like NnaC (CMP-NeuNAc synthetase) _like subfamily of 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 two of the three components of typical Ser-His-Asp(Glu) triad from other serine hydrolases. E. coli NnaC appears to be involved in polysaccharide synthesis.
Probab=25.73 E-value=2.5e+02 Score=19.88 Aligned_cols=73 Identities=12% Similarity=0.136 Sum_probs=36.0
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHH-HHHh-cCCCeeEEEEe----------hhhHHH
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAF-KEFT-SREDIAIVLIS----------QYVANR 80 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~-~~l~-~~~digIIlIt----------e~~a~~ 80 (130)
++|.++||+-|- |+.+.+.... ....-|.-+ .-.|+ .++.+.+ ..+. ..+|+-+|++- +.+.+.
T Consensus 1 ~~iv~~GdS~t~-~~~~~~~~~~-~~~v~n~g~-~G~t~-~~~~~~~~~~~~~~~pd~v~i~~G~ND~~~~~~~~~~~~~ 76 (174)
T cd01841 1 KNIVFIGDSLFE-GWPLYEAEGK-GKTVNNLGI-AGISS-RQYLEHIEPQLIQKNPSKVFLFLGTNDIGKEVSSNQFIKW 76 (174)
T ss_pred CCEEEEcchhhh-cCchhhhccC-CCeEEeccc-ccccH-HHHHHHHHHHHHhcCCCEEEEEeccccCCCCCCHHHHHHH
Confidence 479999998764 5555443210 001111111 22333 5555556 3343 24566666543 224556
Q ss_pred HHHHHhhcC
Q 032904 81 IRFLVDSHN 89 (130)
Q Consensus 81 i~~~i~~~~ 89 (130)
++..++.++
T Consensus 77 ~~~l~~~~~ 85 (174)
T cd01841 77 YRDIIEQIR 85 (174)
T ss_pred HHHHHHHHH
Confidence 666666664
No 121
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=25.71 E-value=1.9e+02 Score=22.31 Aligned_cols=45 Identities=11% Similarity=0.146 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEE
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILE 97 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~ 97 (130)
.++..++|+++. ++++-+++.|-+-...+++.++.+....|+|..
T Consensus 22 ~~~~~~al~~~~-~~g~~v~iaTGR~~~~~~~~~~~l~~~~~~I~~ 66 (264)
T COG0561 22 SPETKEALARLR-EKGVKVVLATGRPLPDVLSILEELGLDGPLITF 66 (264)
T ss_pred CHHHHHHHHHHH-HCCCEEEEECCCChHHHHHHHHHcCCCccEEEe
Confidence 377888888665 789999999999889999989888755576653
No 122
>PRK03202 6-phosphofructokinase; Provisional
Probab=25.42 E-value=2.3e+02 Score=23.69 Aligned_cols=54 Identities=11% Similarity=0.203 Sum_probs=35.5
Q ss_pred cCCCcHHHHHHHHHHHhcC-CCeeEEEEehhhH--HHHHHHHhhcCCCccEEEEcCCC
Q 032904 47 DSKTTIKQIEDAFKEFTSR-EDIAIVLISQYVA--NRIRFLVDSHNKPIPAILEIPSK 101 (130)
Q Consensus 47 ~~~~~~eei~~~~~~l~~~-~digIIlIte~~a--~~i~~~i~~~~~~~P~Iv~IPs~ 101 (130)
+...+.+++.+.+++-.++ +.+++|+++|.+. +.+.+.+++.-. ..+-..+|+.
T Consensus 193 E~~~~~~~l~~~i~~r~~~g~~~~vivvsEg~~~~~~l~~~i~~~~~-~~~r~~~lG~ 249 (320)
T PRK03202 193 EVPFDIEELCAKIKKGRERGKKHAIIVVAEGVMPAEELAKEIEERTG-LETRVTVLGH 249 (320)
T ss_pred CCCCCHHHHHHHHHHHHHhcCCcEEEEEeCCCCCHHHHHHHHHHHhC-CceEEcccch
Confidence 3344678888888877765 8899999999954 345555554311 3455666663
No 123
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=25.27 E-value=3e+02 Score=23.56 Aligned_cols=65 Identities=9% Similarity=0.124 Sum_probs=37.8
Q ss_pred cccEEEEEechhhHH---HHHH--hcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHH
Q 032904 11 ASALIAMIADEDTVV---GFLL--AGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLV 85 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~---GFrL--aGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i 85 (130)
..+|++|.||.+.+. .|.+ .|++.+ .+.....+.+..++.++.+. + ++.++.+.-...+.+.|
T Consensus 289 ~Gkrvai~g~~~~~~~la~~L~eelGm~~v--------~v~t~~~~~~~~~~~~~~l~--~--~~~v~~~~D~~~l~~~i 356 (427)
T PRK02842 289 RGKRVFFLPDSQLEIPLARFLSRECGMELV--------EVGTPYLNRRFLAAELALLP--D--GVRIVEGQDVERQLDRI 356 (427)
T ss_pred CCcEEEEECCchhHHHHHHHHHHhCCCEEE--------EeCCCCCCHHHHHHHHHhcc--C--CCEEEECCCHHHHHHHH
Confidence 357999999987544 4554 477654 23232233455566676553 2 44566655555555656
Q ss_pred hh
Q 032904 86 DS 87 (130)
Q Consensus 86 ~~ 87 (130)
.+
T Consensus 357 ~~ 358 (427)
T PRK02842 357 RA 358 (427)
T ss_pred HH
Confidence 55
No 124
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=25.23 E-value=3.3e+02 Score=21.25 Aligned_cols=75 Identities=9% Similarity=0.047 Sum_probs=42.3
Q ss_pred ccccEEEEEechh-------hHHHHHHh----cccccccCCcceeEEecCCCcHHHHHHHHHHHhcC-C-C-eeEEEEeh
Q 032904 10 AASALIAMIADED-------TVVGFLLA----GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSR-E-D-IAIVLISQ 75 (130)
Q Consensus 10 ~~~~kIaVIGD~d-------tv~GFrLa----Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~-~-d-igIIlIte 75 (130)
...++|++++... -..||+-+ |+.. .+... .+.+.++..+.++++++. + . -||+..++
T Consensus 176 ~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~-------~~~~~-~~~~~~~~~~~~~~ll~~~~~~~~Ai~~~~D 247 (327)
T TIGR02417 176 QHADEFWYLGAQPELSVSRDRLAGFRQALKQATLEV-------EWVYG-GNYSRESGYQMFAKLCARLGRLPQALFTTSY 247 (327)
T ss_pred CCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCCh-------HhEEe-CCCChHHHHHHHHHHHhcCCCCCcEEEEcCc
Confidence 4567999998533 23444422 3211 12222 223346677788888864 2 2 57777777
Q ss_pred hhHHHHHHHHhhcCCCcc
Q 032904 76 YVANRIRFLVDSHNKPIP 93 (130)
Q Consensus 76 ~~a~~i~~~i~~~~~~~P 93 (130)
.++--+-..+.++. ..|
T Consensus 248 ~~A~g~~~al~~~g-~vP 264 (327)
T TIGR02417 248 TLLEGVLDYMLERP-LLD 264 (327)
T ss_pred HHHHHHHHHHHHcC-CCC
Confidence 77766655666655 555
No 125
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=25.22 E-value=2.4e+02 Score=22.16 Aligned_cols=59 Identities=15% Similarity=0.171 Sum_probs=41.6
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHH------HHHHhcCCCeeEEEEehhhHHHHHHH
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDA------FKEFTSREDIAIVLISQYVANRIRFL 84 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~------~~~l~~~~digIIlIte~~a~~i~~~ 84 (130)
...+|||++|.+...=-+-+|+.- + .. +++.+. .++++ .+|-+++-+.++...+...
T Consensus 60 k~~~v~V~a~~~~~~~Ak~aGa~v----------v-g~----edL~~~~k~~k~~kkl~--~~fD~flA~~~im~~l~ri 122 (216)
T PTZ00029 60 PNLKVCVLGDAVHCDEAKKLGLDF----------M-DI----EGLKKFNKNKKLVKKLA--KKYDAFLASQSLLPQIPRL 122 (216)
T ss_pred CCcEEEEECCcHHHHHHHHcCCCE----------e-cH----HHHHHhhhhHHHHhccc--ccCCEEEECHHHHHHHHHH
Confidence 457999999999888889999842 2 32 667653 33343 3677888999988877654
Q ss_pred Hh
Q 032904 85 VD 86 (130)
Q Consensus 85 i~ 86 (130)
|=
T Consensus 123 LG 124 (216)
T PTZ00029 123 LG 124 (216)
T ss_pred hc
Confidence 43
No 126
>PRK04017 hypothetical protein; Provisional
Probab=25.20 E-value=2.9e+02 Score=20.46 Aligned_cols=62 Identities=11% Similarity=0.246 Sum_probs=33.1
Q ss_pred EEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh------hhHHHHHHHHhh
Q 032904 14 LIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ------YVANRIRFLVDS 87 (130)
Q Consensus 14 kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte------~~a~~i~~~i~~ 87 (130)
++.|+=.++-..-.+-+|+++. ..+.+... ..+.. +++..+.-+||++|+ +++..+.+.+..
T Consensus 24 ~vIVVEGk~D~~~L~~lGv~~~-------iI~t~g~~-~~~~~----e~ia~~~r~VIILTD~D~~GekIr~~l~~~l~~ 91 (132)
T PRK04017 24 APIIVEGKRDVESLRKLGVEGE-------IIKVSRTP-LAEIA----ELIASRGKEVIILTDFDRKGEELAKKLSEYLQG 91 (132)
T ss_pred CEEEEeCccHHHHHHHcCCCcc-------EEEECCee-cchHH----HHHHhcCCeEEEEECCCcchHHHHHHHHHHHHh
Confidence 4444444444556778888653 44444321 12222 223456779999997 455555554443
No 127
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=25.01 E-value=2.7e+02 Score=20.16 Aligned_cols=11 Identities=9% Similarity=0.271 Sum_probs=4.8
Q ss_pred HHHHHHHHhhc
Q 032904 78 ANRIRFLVDSH 88 (130)
Q Consensus 78 a~~i~~~i~~~ 88 (130)
.+++++.|+++
T Consensus 45 ~~~i~~ai~~~ 55 (124)
T PRK14484 45 FDQIQEAIEKN 55 (124)
T ss_pred HHHHHHHHHhc
Confidence 34444444443
No 128
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=24.88 E-value=1.7e+02 Score=26.26 Aligned_cols=52 Identities=12% Similarity=0.169 Sum_probs=37.4
Q ss_pred ccccEEEEEechhhHHHHHH----hcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEE
Q 032904 10 AASALIAMIADEDTVVGFLL----AGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVL 72 (130)
Q Consensus 10 ~~~~kIaVIGD~dtv~GFrL----aGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIl 72 (130)
+...||||||=+.++.|++. .|++-. -|..++ .+|++..++++. ...|.+|+
T Consensus 105 ~~~~~iavv~~~~~~~~~~~~~~~l~~~i~------~~~~~~----~~e~~~~v~~lk-~~G~~~vv 160 (538)
T PRK15424 105 KLTSSIGVVTYQETIPALVAFQKTFNLRIE------QRSYVT----EEDARGQINELK-ANGIEAVV 160 (538)
T ss_pred hcCCcEEEEecCcccHHHHHHHHHhCCceE------EEEecC----HHHHHHHHHHHH-HCCCCEEE
Confidence 34589999999999999883 455321 144444 499999999886 46676665
No 129
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=24.71 E-value=2e+02 Score=23.77 Aligned_cols=52 Identities=13% Similarity=0.147 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhcCCC-eeEEEEehh------hHHHHHHHHhhcCCCccEEEEcCCCCC
Q 032904 52 IKQIEDAFKEFTSRED-IAIVLISQY------VANRIRFLVDSHNKPIPAILEIPSKDH 103 (130)
Q Consensus 52 ~eei~~~~~~l~~~~d-igIIlIte~------~a~~i~~~i~~~~~~~P~Iv~IPs~~g 103 (130)
.+.+.+.|+.+..+++ =||+|.=+. .++.|.+.|.+++...|++|.+|+..-
T Consensus 82 ~~~~~~~l~~~~~~~~vk~vvL~inSPGG~v~as~~i~~~l~~l~~~~PV~v~v~~~AA 140 (317)
T COG0616 82 GDDIEEILRAARADPSVKAVVLRINSPGGSVVASELIARALKRLRAKKPVVVSVGGYAA 140 (317)
T ss_pred HHHHHHHHHHHhcCCCCceEEEEEECcCCchhHHHHHHHHHHHHhhcCCEEEEECCeec
Confidence 4788888998887664 455544332 568888889988644499999998653
No 130
>cd02525 Succinoglycan_BP_ExoA ExoA is involved in the biosynthesis of succinoglycan. Succinoglycan Biosynthesis Protein ExoA catalyzes the formation of a beta-1,3 linkage of the second sugar (glucose) of the succinoglycan with the galactose on the lipid carrie. Succinoglycan is an acidic exopolysaccharide that is important for invasion of the nodules. Succinoglycan is a high-molecular-weight polymer composed of repeating octasaccharide units. These units are synthesized on membrane-bound isoprenoid lipid carriers, beginning with galactose followed by seven glucose molecules, and modified by the addition of acetate, succinate, and pyruvate. ExoA is a membrane protein with a transmembrance domain at c-terminus.
Probab=24.69 E-value=2.5e+02 Score=20.55 Aligned_cols=48 Identities=21% Similarity=0.269 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhcC----CCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCC
Q 032904 53 KQIEDAFKEFTSR----EDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPS 100 (130)
Q Consensus 53 eei~~~~~~l~~~----~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs 100 (130)
+.+.++|+.+.+. .++-||++...-.+...+.+..+....|.|..+..
T Consensus 13 ~~l~~~l~sl~~q~~~~~~~evivvd~~s~d~~~~~~~~~~~~~~~v~~i~~ 64 (249)
T cd02525 13 KYIEELLESLLNQSYPKDLIEIIVVDGGSTDGTREIVQEYAAKDPRIRLIDN 64 (249)
T ss_pred hhHHHHHHHHHhccCCCCccEEEEEeCCCCccHHHHHHHHHhcCCeEEEEeC
Confidence 5566666666532 34567777655444444444444333454444443
No 131
>PRK14190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.67 E-value=1.5e+02 Score=24.52 Aligned_cols=41 Identities=10% Similarity=0.097 Sum_probs=28.3
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEE
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLI 73 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlI 73 (130)
-+.-.|+... .....++.+++|+.++++++=+++++ |||+-
T Consensus 56 ~a~~~Gi~~~-------~~~l~~~~~~~el~~~I~~lN~D~~V~GIlvq 97 (284)
T PRK14190 56 AAEKVGIYSE-------LYEFPADITEEELLALIDRLNADPRINGILVQ 97 (284)
T ss_pred HHHHcCCEEE-------EEECCCCCCHHHHHHHHHHHhCCCCCCEEEEe
Confidence 3455688654 23345567889999999998777776 66554
No 132
>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=24.65 E-value=1.7e+02 Score=23.61 Aligned_cols=40 Identities=10% Similarity=0.058 Sum_probs=29.6
Q ss_pred cCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 47 DSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 47 ~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
+.+.+..++.+.++ .+++.++..||.......+.-+.|.+
T Consensus 209 ~~eps~~~l~~l~~-~ik~~~v~~If~e~~~~~~~~~~ia~ 248 (286)
T cd01019 209 EIDPGAKRLAKIRK-EIKEKGATCVFAEPQFHPKIAETLAE 248 (286)
T ss_pred CCCCCHHHHHHHHH-HHHHcCCcEEEecCCCChHHHHHHHH
Confidence 34567788888777 55689999999987776666666654
No 133
>PRK09875 putative hydrolase; Provisional
Probab=24.63 E-value=4e+02 Score=21.92 Aligned_cols=86 Identities=15% Similarity=0.198 Sum_probs=49.0
Q ss_pred hHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh-----------------hhHHHHHHHH
Q 032904 23 TVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ-----------------YVANRIRFLV 85 (130)
Q Consensus 23 tv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte-----------------~~a~~i~~~i 85 (130)
-+.-|+-+|...+ .-+..... --=-+.++++.++..+-||.-|- .+++.+-++|
T Consensus 39 el~~~~~~Gg~ti-------Vd~T~~g~--GRd~~~l~~is~~tgv~Iv~~TG~y~~~~~p~~~~~~~~e~la~~~i~ei 109 (292)
T PRK09875 39 EMNDLMTRGVRNV-------IEMTNRYM--GRNAQFMLDVMRETGINVVACTGYYQDAFFPEHVATRSVQELAQEMVDEI 109 (292)
T ss_pred HHHHHHHhCCCeE-------EecCCCcc--CcCHHHHHHHHHHhCCcEEEcCcCCCCccCCHHHhcCCHHHHHHHHHHHH
Confidence 4567999998653 11111111 00124566677777888888763 3455555555
Q ss_pred hhc---CCCccEEE-EcCCCCCCCChhhHHHHHHHH
Q 032904 86 DSH---NKPIPAIL-EIPSKDHPYDPAQDSVLSRVK 117 (130)
Q Consensus 86 ~~~---~~~~P~Iv-~IPs~~g~~~~~~d~I~~~Vk 117 (130)
.+. ...+|-+| +|.+..+...+....+.+.+-
T Consensus 110 ~~Gi~gt~ikaGvIGeiG~~~~~it~~E~kvl~Aaa 145 (292)
T PRK09875 110 EQGIDGTELKAGIIAEIGSSEGKITPLEEKVFIAAA 145 (292)
T ss_pred HHhhccCCCcccEEEEEecCCCCCCHHHHHHHHHHH
Confidence 553 26688888 998877544343344444443
No 134
>PRK14192 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.61 E-value=1.1e+02 Score=25.00 Aligned_cols=55 Identities=15% Similarity=0.253 Sum_probs=37.4
Q ss_pred EEEEech-hh-------HHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehh
Q 032904 15 IAMIADE-DT-------VVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQY 76 (130)
Q Consensus 15 IaVIGD~-dt-------v~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~ 76 (130)
|..+||. ++ ..-|+-.|++.. |...+++.+++++.+.++++-+++++-=|+++--
T Consensus 38 ~i~vg~~~~s~~Y~~~~~~~~~~~Gi~~~-------~~~l~~~~~~~~l~~~i~~Ln~d~~v~Gi~VqlP 100 (283)
T PRK14192 38 TILVGDDPASATYVRMKGNACRRVGMDSL-------KVELPQETTTEQLLAKIEELNANPDVHGILLQHP 100 (283)
T ss_pred EEEeCCChhHHHHHHHHHHHHHHcCCeEE-------EEECCCCCCHHHHHHHHHHHhCCCCCCEEEEeCC
Confidence 5556763 32 235677799876 6666656778999999999977667644555533
No 135
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=24.59 E-value=1.6e+02 Score=20.19 Aligned_cols=37 Identities=14% Similarity=0.447 Sum_probs=25.4
Q ss_pred cHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 51 TIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 51 ~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
+.+++++.++++.......++++.+--.+.+...+++
T Consensus 3 t~e~l~~f~~~~y~p~n~~l~i~Gd~~~~~~~~~i~~ 39 (184)
T PF05193_consen 3 TLEDLRAFYKKFYRPSNMTLVIVGDIDPDELEKLIEK 39 (184)
T ss_dssp -HHHHHHHHHHHSSGGGEEEEEEESSGHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCccceEEEEEcCccHHHHHHHHHh
Confidence 4689999999999777787777775444444444444
No 136
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=24.58 E-value=1.8e+02 Score=23.93 Aligned_cols=40 Identities=5% Similarity=0.009 Sum_probs=29.1
Q ss_pred cCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 47 DSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 47 ~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
+.+.+..++.+..+ .+++.++.+||.......+.-+.|.+
T Consensus 233 ~~eps~~~l~~l~~-~ik~~~v~~If~e~~~~~~~~~~la~ 272 (311)
T PRK09545 233 EIQPGAQRLHEIRT-QLVEQKATCVFAEPQFRPAVIESVAK 272 (311)
T ss_pred CCCCCHHHHHHHHH-HHHHcCCCEEEecCCCChHHHHHHHH
Confidence 34557788888777 44688999999998876665555554
No 137
>PRK07714 hypothetical protein; Provisional
Probab=24.37 E-value=1.4e+02 Score=20.44 Aligned_cols=43 Identities=9% Similarity=0.138 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhc--CCCccEEEEcCC
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSH--NKPIPAILEIPS 100 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~--~~~~P~Iv~IPs 100 (130)
+++.++++ +....++++.++..+..++.+..+ ....|.+. .++
T Consensus 24 ~~v~~al~----~g~~~lViiA~D~s~~~~~ki~~~~~~~~vp~~~-~~s 68 (100)
T PRK07714 24 ELVLKEVR----SGKAKLVLLSEDASVNTTKKITDKCTYYNVPMRK-VEN 68 (100)
T ss_pred HHHHHHHH----hCCceEEEEeCCCCHHHHHHHHHHHHhcCCCEEE-eCC
Confidence 44555443 567899999999998888888764 25678764 344
No 138
>TIGR02463 MPGP_rel mannosyl-3-phosphoglycerate phosphatase-related protein. This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbor-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (TIGR02460). Members of this family are like to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate.
Probab=24.04 E-value=2.6e+02 Score=20.81 Aligned_cols=43 Identities=14% Similarity=0.237 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCC-ccEEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKP-IPAIL 96 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~-~P~Iv 96 (130)
+...++|+++. +..+-+++.|-+-...++..++.+... .|.|-
T Consensus 19 ~~~~~~l~~l~-~~gi~~~i~TgR~~~~~~~~~~~l~~~~~~~I~ 62 (221)
T TIGR02463 19 QPAAPWLTRLQ-EAGIPVILCTSKTAAEVEYLQKALGLTGDPYIA 62 (221)
T ss_pred HHHHHHHHHHH-HCCCeEEEEcCCCHHHHHHHHHHcCCCCCcEEE
Confidence 44778888874 678999999999998888888877533 56663
No 139
>PRK14171 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=23.95 E-value=1.5e+02 Score=24.61 Aligned_cols=41 Identities=10% Similarity=0.220 Sum_probs=28.2
Q ss_pred HHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEEe
Q 032904 27 FLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLIS 74 (130)
Q Consensus 27 FrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlIt 74 (130)
+.-.|++.. ...-+.+.+++++.+.++++=+++++ |||+--
T Consensus 57 a~~~Gi~~~-------~~~l~~~~~~~~l~~~I~~LN~D~~V~GIlvql 98 (288)
T PRK14171 57 AHKIGIDTL-------LVNLSTTIHTNDLISKINELNLDNEISGIIVQL 98 (288)
T ss_pred HHHcCCEEE-------EEECCCCCCHHHHHHHHHHHcCCCCCCEEEEeC
Confidence 344588653 23345567889999999998777777 666643
No 140
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=23.89 E-value=3.6e+02 Score=21.16 Aligned_cols=80 Identities=18% Similarity=0.251 Sum_probs=46.4
Q ss_pred EEEEEec----hhhHHHHHHhcccccccC------CcceeEEecCC-CcHHHHHHHHHHHhcCCCeeEEE--EehhhHHH
Q 032904 14 LIAMIAD----EDTVVGFLLAGVGNVDLR------RKTNYLIVDSK-TTIKQIEDAFKEFTSREDIAIVL--ISQYVANR 80 (130)
Q Consensus 14 kIaVIGD----~dtv~GFrLaGi~~~~~~------~~~nf~v~~~~-~~~eei~~~~~~l~~~~digIIl--Ite~~a~~ 80 (130)
+|+.|-+ .....||+|| ++.+|.. .+-.+.+.+.+ .+..++..+..+++.+ ++..|+ .+...+..
T Consensus 1 ~iG~i~~~~~g~~~~~a~~lA-v~~iN~~ggil~g~~l~~~~~d~~~~~~~~a~~~~~~li~~-~V~aiiG~~~S~~~~a 78 (327)
T cd06382 1 RIGAIFDDDDDSGEELAFRYA-IDRINREKELLANTTLEYDIKRVKPDDSFETTKKVCDLLQQ-GVAAIFGPSSSEASSI 78 (327)
T ss_pred CeEEEecCCCchHHHHHHHHH-HHHhcccccccCCceEEEEEEEecCCCcHHHHHHhhhhhhc-CcEEEECCCChhHHHH
Confidence 3555544 6778888886 3444332 11123444433 3457788888888865 665555 34555666
Q ss_pred HHHHHhhcCCCccEEEE
Q 032904 81 IRFLVDSHNKPIPAILE 97 (130)
Q Consensus 81 i~~~i~~~~~~~P~Iv~ 97 (130)
+.+..+++ ..|.|..
T Consensus 79 v~~~~~~~--~vP~Is~ 93 (327)
T cd06382 79 VQSICDAK--EIPHIQT 93 (327)
T ss_pred HHHHHhcc--CCCceec
Confidence 66766653 4676663
No 141
>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []. In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....
Probab=23.88 E-value=2.4e+02 Score=23.72 Aligned_cols=60 Identities=20% Similarity=0.254 Sum_probs=37.2
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEeh
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQ 75 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte 75 (130)
.....++|.-+.+...=.+..+ |+|.++ .+++.|++ .+++..+.+.+++...+.+|++..
T Consensus 80 ~g~~~a~ID~e~~ld~~~a~~l-Gvdl~r---llv~~P~~-~E~al~~~e~lirsg~~~lVVvDS 139 (322)
T PF00154_consen 80 QGGICAFIDAEHALDPEYAESL-GVDLDR---LLVVQPDT-GEQALWIAEQLIRSGAVDLVVVDS 139 (322)
T ss_dssp TT-EEEEEESSS---HHHHHHT-T--GGG---EEEEE-SS-HHHHHHHHHHHHHTTSESEEEEE-
T ss_pred ccceeEEecCcccchhhHHHhc-Cccccc---eEEecCCc-HHHHHHHHHHHhhcccccEEEEec
Confidence 3567888888888877555533 333333 45556654 477888899999889999999885
No 142
>COG3412 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.80 E-value=3.1e+02 Score=20.39 Aligned_cols=21 Identities=24% Similarity=0.418 Sum_probs=8.9
Q ss_pred eeEEEEe--hhhHHHHHHHHhhc
Q 032904 68 IAIVLIS--QYVANRIRFLVDSH 88 (130)
Q Consensus 68 igIIlIt--e~~a~~i~~~i~~~ 88 (130)
|||++++ .++++-+.+.+.+.
T Consensus 3 vgiVIVSHS~~lAeGv~~li~em 25 (129)
T COG3412 3 VGIVIVSHSKELAEGVAELIREM 25 (129)
T ss_pred ceEEEEeCCHHHHHHHHHHHHHH
Confidence 3444443 22444444444443
No 143
>COG0218 Predicted GTPase [General function prediction only]
Probab=23.79 E-value=3.7e+02 Score=21.28 Aligned_cols=76 Identities=12% Similarity=0.208 Sum_probs=44.2
Q ss_pred eEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhh---H--------HHHHHHHhhcCCCccEEEEcCCCCCCCChhhHH
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYV---A--------NRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDS 111 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~---a--------~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~ 111 (130)
+++.|......+....+-+++...++.++++-.++ . ..+++.+...-...|.++..|+..+- +.+.
T Consensus 111 vlliD~r~~~~~~D~em~~~l~~~~i~~~vv~tK~DKi~~~~~~k~l~~v~~~l~~~~~~~~~~~~~ss~~k~---Gi~~ 187 (200)
T COG0218 111 VLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKK---GIDE 187 (200)
T ss_pred EEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEccccCChhHHHHHHHHHHHHhcCCCCccceEEEEeccccc---CHHH
Confidence 56667666667766667777777888888776553 1 12222222111233337778886653 2466
Q ss_pred HHHHHHhhcc
Q 032904 112 VLSRVKNLVS 121 (130)
Q Consensus 112 I~~~Vk~aiG 121 (130)
+++.+.+.++
T Consensus 188 l~~~i~~~~~ 197 (200)
T COG0218 188 LKAKILEWLK 197 (200)
T ss_pred HHHHHHHHhh
Confidence 7777766553
No 144
>PRK04031 DNA primase; Provisional
Probab=23.69 E-value=5.1e+02 Score=22.83 Aligned_cols=102 Identities=13% Similarity=0.175 Sum_probs=59.6
Q ss_pred hhhhcccccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehh--hHHHHH
Q 032904 5 PQIRTAASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQY--VANRIR 82 (130)
Q Consensus 5 ~~~~~~~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~--~a~~i~ 82 (130)
|+..-.....|.|+=.+.-|..+.-+|+.++ +...-.. +.+.+.++++ .. +||+.++. .-++++
T Consensus 162 Agp~i~k~~~iIVVEG~~DVi~L~~aGi~nv--------VAt~GT~----l~~~i~~l~k-~~-~Vil~~DgD~aGe~I~ 227 (408)
T PRK04031 162 AGPNVDDSDAIIVVEGRADVLNLLRYGIKNA--------IAVEGTN----VPETIIELSK-KK-TVTAFLDGDRGGELIL 227 (408)
T ss_pred cCcccccCCeEEEEeCHHHHHHHHhcccceE--------EEeCCcc----cHHHHHHHhc-CC-CEEEEECCCHHHHHHH
Confidence 3344344566777777888889999999876 4444322 3344556665 33 45554433 336666
Q ss_pred HHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhcc
Q 032904 83 FLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVS 121 (130)
Q Consensus 83 ~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiG 121 (130)
..+... .....|...|...++-....+.|.+.+++++-
T Consensus 228 k~l~~v-~~~d~VaraP~G~dVE~ls~eeI~kAL~~~~p 265 (408)
T PRK04031 228 KELLQV-ADIDYVARAPPGKEVEELTKKEIAKALRNKVP 265 (408)
T ss_pred HHHHhh-cceeEEecCCCCCChhhCCHHHHHHHHHhcCC
Confidence 666542 22345677776555544455667777666553
No 145
>PF00185 OTCace: Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; InterPro: IPR006131 This family contains two related enzymes: Aspartate carbamoyltransferase (2.1.3.2 from EC) (ATCase) catalyzes the conversion of aspartate and carbamoyl phosphate to carbamoylaspartate, the second step in the de novo biosynthesis of pyrimidine nucleotides []. In prokaryotes ATCase consists of two subunits: a catalytic chain (gene pyrB) and a regulatory chain (gene pyrI), while in eukaryotes it is a domain in a multi- functional enzyme (called URA2 in yeast, rudimentary in Drosophila, and CAD in mammals []) that also catalyzes other steps of the biosynthesis of pyrimidines. Ornithine carbamoyltransferase (2.1.3.3 from EC) (OTCase) catalyzes the conversion of ornithine and carbamoyl phosphate to citrulline. In mammals this enzyme participates in the urea cycle [] and is located in the mitochondrial matrix. In prokaryotes and eukaryotic microorganisms it is involved in the biosynthesis of arginine. In some bacterial species it is also involved in the degradation of arginine [] (the arginine deaminase pathway). It has been shown [] that these two enzymes are evolutionary related. The predicted secondary structure of both enzymes are similar and there are some regions of sequence similarities. One of these regions includes three residues which have been shown, by crystallographic studies [], to be implicated in binding the phosphoryl group of carbamoyl phosphate and is described by IPR006132 from INTERPRO. The carboxyl-terminal, aspartate/ornithine-binding domain is connected to the amino-terminal domain by two alpha-helices, which comprise a hinge between domains [].; GO: 0016597 amino acid binding, 0016743 carboxyl- or carbamoyltransferase activity, 0006520 cellular amino acid metabolic process; PDB: 1ML4_A 4EP1_B 3Q98_A 3E2P_A 2RGW_E 4EKN_B 2G7M_E 3D6N_B 3M4J_A 3L06_A ....
Probab=23.61 E-value=2e+02 Score=21.23 Aligned_cols=22 Identities=18% Similarity=0.163 Sum_probs=16.4
Q ss_pred ccEEEEEech------hhHHHHHHhccc
Q 032904 12 SALIAMIADE------DTVVGFLLAGVG 33 (130)
Q Consensus 12 ~~kIaVIGD~------dtv~GFrLaGi~ 33 (130)
..+|++|||. ..+.++...|++
T Consensus 2 gl~i~~vGD~~~rv~~Sl~~~~~~~g~~ 29 (158)
T PF00185_consen 2 GLKIAYVGDGHNRVAHSLIELLAKFGME 29 (158)
T ss_dssp TEEEEEESSTTSHHHHHHHHHHHHTTSE
T ss_pred CCEEEEECCCCChHHHHHHHHHHHcCCE
Confidence 4789999994 345677777886
No 146
>cd04179 DPM_DPG-synthase_like DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily. DPM1 is the catalytic subunit of eukaryotic dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. In higher eukaryotes,the enzyme has three subunits, DPM1, DPM2 and DPM3. DPM is synthesized from dolichol phosphate and GDP-Man on the cytosolic surface of the ER membrane by DPM synthase and then is flipped onto the luminal side and used as a donor substrate. In lower eukaryotes, such as Saccharomyces cerevisiae and Trypanosoma brucei, DPM synthase consists of a single component (Dpm1p and TbDpm1, respectively) that possesses one predicted transmembrane region near the C terminus for anchoring to the ER membrane. In contrast, the Dpm1 homologues of higher eukaryotes, namely fission yeast, fungi, and animals, have no transmembrane region, suggesting the ex
Probab=23.57 E-value=1.8e+02 Score=20.35 Aligned_cols=65 Identities=9% Similarity=0.157 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhcC----CCeeEEEEehhhHHHHHHHHhhcCCCcc--EEEEcCCCCCCCChhhHHHHHHHHhhcc
Q 032904 53 KQIEDAFKEFTSR----EDIAIVLISQYVANRIRFLVDSHNKPIP--AILEIPSKDHPYDPAQDSVLSRVKNLVS 121 (130)
Q Consensus 53 eei~~~~~~l~~~----~digIIlIte~~a~~i~~~i~~~~~~~P--~Iv~IPs~~g~~~~~~d~I~~~Vk~aiG 121 (130)
+.+.++++.+.+. ..+-||++...-.+...+.+.++....| .++.-+...|. . ..+..-++.|-|
T Consensus 10 ~~l~~~l~sl~~~~~~~~~~eiivvd~~s~d~~~~~~~~~~~~~~~~~~~~~~~n~G~-~---~a~n~g~~~a~g 80 (185)
T cd04179 10 ENIPELVERLLAVLEEGYDYEIIVVDDGSTDGTAEIARELAARVPRVRVIRLSRNFGK-G---AAVRAGFKAARG 80 (185)
T ss_pred hhHHHHHHHHHHHhccCCCEEEEEEcCCCCCChHHHHHHHHHhCCCeEEEEccCCCCc-c---HHHHHHHHHhcC
Confidence 5556666666544 3678888876654444444444432233 23333333332 1 345555565555
No 147
>PF01012 ETF: Electron transfer flavoprotein domain; InterPro: IPR014730 Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) []. ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP [, , , , ]. ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical alpha-beta-alpha sandwich fold, while domain II forms an alpha-beta-alpha sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides. This entry represents the N-terminal domain of both the alpha and beta subunits from Group I and Group II ETFs.; PDB: 1EFP_B 3FET_B 3IH5_B 2A1T_S 1EFV_B 1T9G_S 2A1U_B 1O96_E 1O94_C 3CLU_C ....
Probab=23.52 E-value=1.8e+02 Score=20.91 Aligned_cols=59 Identities=20% Similarity=0.271 Sum_probs=38.6
Q ss_pred ccEEEEEec-hhhHHH----HHHhcccccccCCcceeEEecCCC---cHHHHHHHHHHHhcCCCeeEEEEehhh
Q 032904 12 SALIAMIAD-EDTVVG----FLLAGVGNVDLRRKTNYLIVDSKT---TIKQIEDAFKEFTSREDIAIVLISQYV 77 (130)
Q Consensus 12 ~~kIaVIGD-~dtv~G----FrLaGi~~~~~~~~~nf~v~~~~~---~~eei~~~~~~l~~~~digIIlIte~~ 77 (130)
.--..++|+ .+..-- +...|++.+ |.+.++.. ..+...++|.++++..+..+|++....
T Consensus 34 ~v~av~~G~~~~~~~~l~~~l~~~G~d~v-------~~~~~~~~~~~~~~~~a~~l~~~~~~~~~~lVl~~~t~ 100 (164)
T PF01012_consen 34 EVTAVVLGPAEEAAEALRKALAKYGADKV-------YHIDDPALAEYDPEAYADALAELIKEEGPDLVLFGSTS 100 (164)
T ss_dssp EEEEEEEETCCCHHHHHHHHHHSTTESEE-------EEEE-GGGTTC-HHHHHHHHHHHHHHHT-SEEEEESSH
T ss_pred eEEEEEEecchhhHHHHhhhhhhcCCcEE-------EEecCccccccCHHHHHHHHHHHHHhcCCCEEEEcCcC
Confidence 455778886 333322 233699877 77766543 357788899999988788899988653
No 148
>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=23.09 E-value=3.8e+02 Score=21.12 Aligned_cols=87 Identities=16% Similarity=0.134 Sum_probs=50.2
Q ss_pred cccccE-EEEEechh--hHHHHHHhccccccc-C---CcceeEEecCCCcHHHHHHHHHHHhcCC-Ce-eEEEEehhhHH
Q 032904 9 TAASAL-IAMIADED--TVVGFLLAGVGNVDL-R---RKTNYLIVDSKTTIKQIEDAFKEFTSRE-DI-AIVLISQYVAN 79 (130)
Q Consensus 9 ~~~~~k-IaVIGD~d--tv~GFrLaGi~~~~~-~---~~~nf~v~~~~~~~eei~~~~~~l~~~~-di-gIIlIte~~a~ 79 (130)
....++ |+++|.+. +...-|+.|+...=. + -...++.. .+.+.+...+++++++++. ++ ||+..++.+|-
T Consensus 115 ~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~-~~~~~~~g~~~~~~ll~~~p~idai~~~nd~~A~ 193 (279)
T PF00532_consen 115 KKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIFE-GDFDYESGYEAARELLESHPDIDAIFCANDMMAI 193 (279)
T ss_dssp HTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEEE-SSSSHHHHHHHHHHHHHTSTT-SEEEESSHHHHH
T ss_pred hcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCcccccc-cCCCHHHHHHHHHHHHhhCCCCEEEEEeCHHHHH
Confidence 456788 99999843 334445544432100 0 11223433 3456788889999999765 54 55555666776
Q ss_pred HHHHHHhhcC-CCccEEE
Q 032904 80 RIRFLVDSHN-KPIPAIL 96 (130)
Q Consensus 80 ~i~~~i~~~~-~~~P~Iv 96 (130)
-+-..+.+.. ...|--|
T Consensus 194 ga~~~l~~~gr~~ip~di 211 (279)
T PF00532_consen 194 GAIRALRERGRLKIPEDI 211 (279)
T ss_dssp HHHHHHHHTT-TCTTTEE
T ss_pred HHHHHHHHcCCcccChhh
Confidence 6666666654 5567443
No 149
>PRK09627 oorA 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed
Probab=23.08 E-value=2.7e+02 Score=23.73 Aligned_cols=54 Identities=9% Similarity=0.036 Sum_probs=41.0
Q ss_pred EEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehh
Q 032904 14 LIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQY 76 (130)
Q Consensus 14 kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~ 76 (130)
++.+-|++....|...+|++ |..-.|=|+--++-+.+.+++.+.+...+-..++
T Consensus 3 ~~~~~GNeAiA~ga~~ag~~---------~~a~YPITPsTeI~e~la~~~~~~g~~~vq~E~E 56 (375)
T PRK09627 3 EIISTGNELVAKAAIECGCR---------FFGGYPITPSSEIAHEMSVLLPKCGGTFIQMEDE 56 (375)
T ss_pred ceEechHHHHHHHHHHhCCC---------EEEEeCCCChhHHHHHHHHHHHHcCCEEEEcCCH
Confidence 67889999999999999995 5666777777889998888876544444444443
No 150
>COG0673 MviM Predicted dehydrogenases and related proteins [General function prediction only]
Probab=22.71 E-value=2.3e+02 Score=22.42 Aligned_cols=63 Identities=14% Similarity=0.139 Sum_probs=43.4
Q ss_pred HHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhcccCC
Q 032904 59 FKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSVES 124 (130)
Q Consensus 59 ~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi 124 (130)
+.++++++++-+++|...-.....-.+..++...++++|=|--... .+-+.|.+..+++ |.-+
T Consensus 59 ~~~ll~~~~iD~V~Iatp~~~H~e~~~~AL~aGkhVl~EKPla~t~--~ea~~l~~~a~~~-~~~l 121 (342)
T COG0673 59 LEELLADPDIDAVYIATPNALHAELALAALEAGKHVLCEKPLALTL--EEAEELVELARKA-GVKL 121 (342)
T ss_pred HHHHhcCCCCCEEEEcCCChhhHHHHHHHHhcCCEEEEcCCCCCCH--HHHHHHHHHHHHc-CCce
Confidence 6778888888888888766555555455555777899988875543 2335677777777 6544
No 151
>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=22.67 E-value=1.3e+02 Score=24.07 Aligned_cols=64 Identities=9% Similarity=0.148 Sum_probs=39.4
Q ss_pred EEEechhhHHHHHHhcccccccCCcceeE---EecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 16 AMIADEDTVVGFLLAGVGNVDLRRKTNYL---IVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 16 aVIGD~dtv~GFrLaGi~~~~~~~~~nf~---v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
.|+.-...-+=++-.|++.+ .+ ..+.+.+..++.+..+ ++++..+..||.....-.+.-+.|.+
T Consensus 174 ~v~~H~af~Y~~~~~gl~~~-------~~~~~~~~~eps~~~l~~l~~-~ik~~~v~~if~e~~~~~~~~~~la~ 240 (282)
T cd01017 174 FVTQHAAFGYLARRYGLKQI-------AIVGVSPEVEPSPKQLAELVE-FVKKSDVKYIFFEENASSKIAETLAK 240 (282)
T ss_pred EEEecccHHHHHHHCCCeEE-------ecccCCCCCCCCHHHHHHHHH-HHHHcCCCEEEEeCCCChHHHHHHHH
Confidence 44444444444555566433 11 1244567788888776 45688999999998876655555553
No 152
>COG1154 Dxs Deoxyxylulose-5-phosphate synthase [Coenzyme metabolism / Lipid metabolism]
Probab=22.25 E-value=37 Score=31.28 Aligned_cols=45 Identities=18% Similarity=0.354 Sum_probs=31.1
Q ss_pred hhcccccEEEEEechhhHHHHHHhcccccccCCcceeE--EecCCCc
Q 032904 7 IRTAASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYL--IVDSKTT 51 (130)
Q Consensus 7 ~~~~~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~--v~~~~~~ 51 (130)
.-+.+++-||||||-...-|+-+-++.+.-.....|++ +.|++++
T Consensus 133 ~~g~~~~vvaVIGDGAlt~GmA~EALN~ag~~~~~~~iVILNDNeMS 179 (627)
T COG1154 133 LKGEDRNVVAVIGDGALTGGMAFEALNNAGADLKSNLIVILNDNEMS 179 (627)
T ss_pred hcCCCCcEEEEECCccccchHHHHHHhhhhhccCCCEEEEEeCCCcc
Confidence 34456778999999999999999988776322224455 3455554
No 153
>PRK08576 hypothetical protein; Provisional
Probab=22.20 E-value=3.9e+02 Score=23.54 Aligned_cols=64 Identities=14% Similarity=0.250 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEE-EcCCCCCCCChhhHHHHHHHHh
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAIL-EIPSKDHPYDPAQDSVLSRVKN 118 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv-~IPs~~g~~~~~~d~I~~~Vk~ 118 (130)
.++++..+++.+..+.+-|+++-++=.+...+...+ .+-|..+ .+|.+. --+.-.+.|...++.
T Consensus 39 ~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~-vrn~r~~~~~~~~~~ 103 (438)
T PRK08576 39 FEEVEDNLEEALEDDYFPILLLGREEKDLAEELIKE--LPPNSYVRVVPRKR-VRNMRVEELYWNLEE 103 (438)
T ss_pred HHHHHHHHHhhcccCCceEEEecccchHHHHHHHhh--cCCCeEEEEccchh-hhhccHHHHHHHHHH
Confidence 489999999999888899999998866666664443 4456666 556544 222223455555553
No 154
>TIGR01282 nifD nitrogenase molybdenum-iron protein alpha chain. Nitrogenase consists of alpha (NifD) and beta (NifK) subunits of the molybdenum-iron protein and an ATP-binding iron-sulfur protein (NifH). This model describes a large clade of NifD proteins, but excludes a lineage that contains putative NifD and NifD homologs from species with vanadium-dependent nitrogenases.
Probab=22.18 E-value=3.9e+02 Score=23.36 Aligned_cols=64 Identities=11% Similarity=0.104 Sum_probs=36.3
Q ss_pred cccEEEEEe---chhhHHHHHH-hcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHh
Q 032904 11 ASALIAMIA---DEDTVVGFLL-AGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVD 86 (130)
Q Consensus 11 ~~~kIaVIG---D~dtv~GFrL-aGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~ 86 (130)
..+|+++.| +.+.+.+|.. .|++-+ .+...-...++.+..++.+. + +.+++.+.=...+.+.+.
T Consensus 334 ~GKrv~i~~g~~~~~~~~~~l~ELGmevv--------~~g~~~~~~~~~~~~~~~~~---~-~~~i~~~~d~~el~~~i~ 401 (466)
T TIGR01282 334 EGKTVMLYVGGLRPRHVIGAFEDLGMEVI--------GTGYEFAHNDDYERTTKYMK---D-GTLIYDDVTHYEFEEFVE 401 (466)
T ss_pred CCCEEEEECCCCcHHHHHHHHHHCCCEEE--------EEeeecCCHHHHHHHHHhcC---C-CeEEeeCCCHHHHHHHHH
Confidence 458899998 7999999866 677643 22121112466766665443 2 455565533333334343
No 155
>PF04989 CmcI: Cephalosporin hydroxylase; InterPro: IPR007072 This entry contains Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) []. Members of this family are about 220 amino acids long. It also includes the CmcI protein O85726 from SWISSPROT, which is presumed to represent the cephalosporin-7--hydroxylase []. However this has not been experimentally verified.; GO: 0008168 methyltransferase activity, 0008610 lipid biosynthetic process; PDB: 2BR4_B 2BR3_E 2BR5_E 2BM8_J 2BM9_E.
Probab=22.17 E-value=39 Score=26.83 Aligned_cols=42 Identities=14% Similarity=0.040 Sum_probs=23.0
Q ss_pred HHHHHhhcCCCcc-EEEEcCCCCCCCChhhHHHHHHH---HhhcccCCc
Q 032904 81 IRFLVDSHNKPIP-AILEIPSKDHPYDPAQDSVLSRV---KNLVSVESV 125 (130)
Q Consensus 81 i~~~i~~~~~~~P-~Iv~IPs~~g~~~~~~d~I~~~V---k~aiGidi~ 125 (130)
+++.|-++ .| +|+|+..-+|..-.=-.++.+++ .+.+|+||-
T Consensus 24 ~qeli~~~---kPd~IIE~Gi~~GGSli~~A~ml~~~~~~~~VigiDId 69 (206)
T PF04989_consen 24 YQELIWEL---KPDLIIETGIAHGGSLIFWASMLELLGGKGKVIGIDID 69 (206)
T ss_dssp HHHHHHHH-----SEEEEE--TTSHHHHHHHHHHHHTT---EEEEEES-
T ss_pred HHHHHHHh---CCCeEEEEecCCCchHHHHHHHHHHhCCCceEEEEeCC
Confidence 45555543 46 99999998864222123456666 688999993
No 156
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both.
Probab=22.12 E-value=2.6e+02 Score=25.25 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEe-------hhhHHHHHHHHhhcC-CCccEEEEcCCC
Q 032904 52 IKQIEDAFKEFTSREDIAIVLIS-------QYVANRIRFLVDSHN-KPIPAILEIPSK 101 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIt-------e~~a~~i~~~i~~~~-~~~P~Iv~IPs~ 101 (130)
.+.+.+.|+++..++++.-|++. -..++.+++.|.+++ ...|+|+-+-+.
T Consensus 331 ~~~~~~~l~~a~~D~~VkaIVLrinSpGGs~~ase~i~~~i~~~~~~gKPVva~~~g~ 388 (584)
T TIGR00705 331 GDTVAALLRVARSDPDIKAVVLRINSPGGSVFASEIIRRELARAQARGKPVIVSMGAM 388 (584)
T ss_pred HHHHHHHHHHHhhCCCceEEEEEecCCCCCHHHHHHHHHHHHHHHhCCCcEEEEECCc
Confidence 36788888888888887666665 235678888888775 448888877553
No 157
>PRK07119 2-ketoisovalerate ferredoxin reductase; Validated
Probab=22.08 E-value=1.6e+02 Score=24.70 Aligned_cols=51 Identities=14% Similarity=0.133 Sum_probs=39.3
Q ss_pred cEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEEe
Q 032904 13 ALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74 (130)
Q Consensus 13 ~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlIt 74 (130)
.|+.+-|++....|.+.+|++ |+.-.|=|+--++-+.+.++.+ +++.+++.
T Consensus 3 ~~~~~~GNeAiA~ga~~ag~~---------~~a~YPiTPsTeI~e~la~~~~--~~~~~~vq 53 (352)
T PRK07119 3 EKVLMKGNEAIAEAAIRAGCR---------CYFGYPITPQSEIPEYMSRRLP--EVGGVFVQ 53 (352)
T ss_pred eeeeehHHHHHHHHHHHhCCC---------EEEEeCCCCchHHHHHHHHHHH--HhCCEEEe
Confidence 367899999999999999996 4566666777888888888875 55555543
No 158
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=22.04 E-value=3.9e+02 Score=20.88 Aligned_cols=62 Identities=18% Similarity=0.234 Sum_probs=44.4
Q ss_pred cccEEEEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHH------HHHhcCCCeeEEEEehhhHHHHHHH
Q 032904 11 ASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAF------KEFTSREDIAIVLISQYVANRIRFL 84 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~------~~l~~~~digIIlIte~~a~~i~~~ 84 (130)
...+|+|+++.+...--+-+|+. |++ .. +++++.. +++. .+|-+++-+.++...+...
T Consensus 57 k~~~V~vf~~~~~~~~Ak~aGa~---------~v~-~~----e~L~~i~~~~k~~rkl~--~~fD~~lA~~~im~~l~k~ 120 (215)
T PRK04203 57 KEVKIAVIAKGELALQAKEAGAD---------YVI-TR----EELEELGGDKRAAKKLA--NEYDFFIAEADLMPLIGRY 120 (215)
T ss_pred CCcEEEEEcChHhHHHHHHcCCC---------EEe-CH----HHHHHHhcChHHHhhhh--hcCCEEEECHHHHHHHHHH
Confidence 45799999998888888889985 233 32 5555432 2333 4688899999999988887
Q ss_pred Hhhc
Q 032904 85 VDSH 88 (130)
Q Consensus 85 i~~~ 88 (130)
+-+.
T Consensus 121 LGk~ 124 (215)
T PRK04203 121 LGPV 124 (215)
T ss_pred Hhhh
Confidence 7663
No 159
>PRK14072 6-phosphofructokinase; Provisional
Probab=21.98 E-value=1.9e+02 Score=25.14 Aligned_cols=29 Identities=10% Similarity=0.174 Sum_probs=24.5
Q ss_pred CcHHHHHHHHHHHhcCCCeeEEEEehhhH
Q 032904 50 TTIKQIEDAFKEFTSREDIAIVLISQYVA 78 (130)
Q Consensus 50 ~~~eei~~~~~~l~~~~digIIlIte~~a 78 (130)
.+.+++.+.+++.++++.++||+++|.+.
T Consensus 220 ~~~~~~~~~i~~~~~~~~~~ivvVaEG~~ 248 (416)
T PRK14072 220 FDEEKFLADVRAIVKRYGYCVVVVSEGIR 248 (416)
T ss_pred CCHHHHHHHHHHHHHhCCCeEEEEecCcc
Confidence 35688888888888888999999999984
No 160
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=21.92 E-value=1.4e+02 Score=18.59 Aligned_cols=41 Identities=22% Similarity=0.313 Sum_probs=30.4
Q ss_pred eEEecCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHh
Q 032904 43 YLIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVD 86 (130)
Q Consensus 43 f~v~~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~ 86 (130)
|.+..+ +++|+.+.+..=+ +..-|+--+++.+.+.||..|.
T Consensus 15 ~~~~a~--tedEll~~~~~Ha-~~~Hg~~~~~~el~~~ir~~I~ 55 (57)
T PF06348_consen 15 FVIRAE--TEDELLEAVVEHA-REVHGMTEIPEELREKIRSAIK 55 (57)
T ss_pred eEEeeC--CHHHHHHHHHHHH-HHhcCCccCCHHHHHHHHHHhh
Confidence 555432 4688888888776 5667888889999999988775
No 161
>TIGR01452 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this alignment have been annotated as pNPPases due to this association.
Probab=21.86 E-value=4e+02 Score=21.00 Aligned_cols=23 Identities=17% Similarity=0.192 Sum_probs=18.9
Q ss_pred ccEEEEEechhhHHHHHHhcccc
Q 032904 12 SALIAMIADEDTVVGFLLAGVGN 34 (130)
Q Consensus 12 ~~kIaVIGD~dtv~GFrLaGi~~ 34 (130)
..++.++|+.....-|+-.|+.-
T Consensus 85 ~~~v~~iG~~~~~~~l~~~g~~~ 107 (279)
T TIGR01452 85 PKAVYVIGEEGLRAELDAAGIRL 107 (279)
T ss_pred CCEEEEEcCHHHHHHHHHCCCEE
Confidence 36799999998888888888853
No 162
>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....
Probab=21.85 E-value=1.3e+02 Score=22.84 Aligned_cols=62 Identities=11% Similarity=0.245 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCcc-EEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIP-AILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P-~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
.+|++++++ -..-+|.+...-.+.+++.++.++...| +.++.- .+...+.+.++. ..|+|..
T Consensus 90 ~ee~~ea~~-----~g~d~I~lD~~~~~~~~~~v~~l~~~~~~v~ie~S-----GGI~~~ni~~ya--~~gvD~i 152 (169)
T PF01729_consen 90 LEEAEEALE-----AGADIIMLDNMSPEDLKEAVEELRELNPRVKIEAS-----GGITLENIAEYA--KTGVDVI 152 (169)
T ss_dssp HHHHHHHHH-----TT-SEEEEES-CHHHHHHHHHHHHHHTTTSEEEEE-----SSSSTTTHHHHH--HTT-SEE
T ss_pred HHHHHHHHH-----hCCCEEEecCcCHHHHHHHHHHHhhcCCcEEEEEE-----CCCCHHHHHHHH--hcCCCEE
Confidence 467776655 3478899999988888888886542222 555653 234457788888 5666654
No 163
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=21.84 E-value=4e+02 Score=20.97 Aligned_cols=72 Identities=25% Similarity=0.224 Sum_probs=46.9
Q ss_pred hhhHHHHHHh--------cccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCeeEEEE--ehhhHHHHHHHHhhcCC
Q 032904 21 EDTVVGFLLA--------GVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLI--SQYVANRIRFLVDSHNK 90 (130)
Q Consensus 21 ~dtv~GFrLa--------Gi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~digIIlI--te~~a~~i~~~i~~~~~ 90 (130)
.....|++|+ ||.+ ++-.+.+.|...+.....+..++|++++++-+|+= +......+.+.+++ .
T Consensus 17 ~~~~~g~~~a~~~iN~~ggi~G----~~i~l~~~D~~~~~~~a~~~a~~li~~~~V~~i~G~~~s~~~~a~~~~~~~--~ 90 (340)
T cd06349 17 TQWKRAFDLALDEINAAGGVGG----RPLNIVFEDSKSDPRQAVTIAQKFVADPRIVAVLGDFSSGVSMAASPIYQR--A 90 (340)
T ss_pred ccHHHHHHHHHHHHHhhCCcCC----eEEEEEEeCCCCChHHHHHHHHHHhccCCeEEEECCCccHhHHHhHHHHHh--C
Confidence 4455676665 5543 23346677777778899999999998777776654 34455566676765 4
Q ss_pred CccEEEEc
Q 032904 91 PIPAILEI 98 (130)
Q Consensus 91 ~~P~Iv~I 98 (130)
..|.|..-
T Consensus 91 ~vp~i~~~ 98 (340)
T cd06349 91 GLVQLSPT 98 (340)
T ss_pred CCeEEecC
Confidence 56766543
No 164
>cd02007 TPP_DXS Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products with important pharmaceutical activity. DXS catalyzes a transketolase-type condensation of pyruvate with D-glyceraldehyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide. The formation of DXP leads to the formation of the terpene precursor IPP (isopentyl diphosphate) and to the formation of thiamine (vitamin B1) and pyridoxal (vitamin B6).
Probab=21.83 E-value=83 Score=24.04 Aligned_cols=85 Identities=13% Similarity=0.139 Sum_probs=44.1
Q ss_pred cccEEEEEechhhHH-----HHHHhcccccccCCcceeEEecCCCc----HHHHHHHHHHHhcCCCeeEEE-EehhhHHH
Q 032904 11 ASALIAMIADEDTVV-----GFLLAGVGNVDLRRKTNYLIVDSKTT----IKQIEDAFKEFTSREDIAIVL-ISQYVANR 80 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~-----GFrLaGi~~~~~~~~~nf~v~~~~~~----~eei~~~~~~l~~~~digIIl-Ite~~a~~ 80 (130)
.++-++++||-++-. ++..|+... .+--+++.++... .+...+.++ .-.+.++. +.-+-.+.
T Consensus 97 ~~~vv~~~GDG~~~eG~~~Eal~~A~~~~----~~li~vvdnN~~~~~~~~~~~~~~~~----a~G~~~~~~vdG~d~~~ 168 (195)
T cd02007 97 KRKVIAVIGDGALTGGMAFEALNNAGYLK----SNMIVILNDNEMSISPNVGTPGNLFE----ELGFRYIGPVDGHNIEA 168 (195)
T ss_pred CCeEEEEEcccccccChHHHHHHHHHHhC----CCEEEEEECCCcccCCCCCCHHHHHH----hcCCCccceECCCCHHH
Confidence 456799999988764 445555431 1111334443221 112333333 23455554 55444555
Q ss_pred HHHHHhhcC-CCccEEEEcCCCCC
Q 032904 81 IRFLVDSHN-KPIPAILEIPSKDH 103 (130)
Q Consensus 81 i~~~i~~~~-~~~P~Iv~IPs~~g 103 (130)
+.+.+++.+ ...|.+|++-+..|
T Consensus 169 l~~a~~~a~~~~~P~~I~~~T~kg 192 (195)
T cd02007 169 LIKVLKEVKDLKGPVLLHVVTKKG 192 (195)
T ss_pred HHHHHHHHHhCCCCEEEEEEEecc
Confidence 555555432 56799887765543
No 165
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=21.81 E-value=3.1e+02 Score=22.54 Aligned_cols=62 Identities=8% Similarity=0.119 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCcc-EEEEcCCCCCCCChhhHHHHHHHHhhcccCCc
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIP-AILEIPSKDHPYDPAQDSVLSRVKNLVSVESV 125 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P-~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGidi~ 125 (130)
.++++++++ -..-+|+++..-.+.+++.+...+...| .+++.- .+...+.+.++. ..|+|+.
T Consensus 198 leea~ea~~-----~GaDiI~lDn~~~e~l~~~v~~l~~~~~~~~leas-----GGI~~~ni~~ya--~~GvD~i 260 (277)
T TIGR01334 198 IEQALTVLQ-----ASPDILQLDKFTPQQLHHLHERLKFFDHIPTLAAA-----GGINPENIADYI--EAGIDLF 260 (277)
T ss_pred HHHHHHHHH-----cCcCEEEECCCCHHHHHHHHHHHhccCCCEEEEEE-----CCCCHHHHHHHH--hcCCCEE
Confidence 455555432 3577899998888999998887654344 566763 334567899987 5688875
No 166
>cd01974 Nitrogenase_MoFe_beta Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems. Mo-nitrogenase consists of the MoFe protein (component 1) and the Fe protein (component 2). MoFe is an alpha2beta2 tetramer. This group contains the beta subunit of the MoFe protein. Each alphabeta pair of MoFe contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction.
Probab=21.77 E-value=5e+02 Score=22.21 Aligned_cols=46 Identities=20% Similarity=0.324 Sum_probs=27.8
Q ss_pred cccEEEEEechhhHHHH----HHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcC
Q 032904 11 ASALIAMIADEDTVVGF----LLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSR 65 (130)
Q Consensus 11 ~~~kIaVIGD~dtv~GF----rLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~ 65 (130)
..++++|.||.+.+.|+ .=.|.+-+ .++... .....++.++.+++.
T Consensus 302 ~gkrv~i~g~~~~~~~la~~L~elGm~v~-------~~~~~~--~~~~~~~~~~~~l~~ 351 (435)
T cd01974 302 HGKKFALYGDPDFLIGLTSFLLELGMEPV-------HVLTGN--GGKRFEKEMQALLDA 351 (435)
T ss_pred CCCEEEEEcChHHHHHHHHHHHHCCCEEE-------EEEeCC--CCHHHHHHHHHHHhh
Confidence 35899999999998874 33455443 233221 224556666666643
No 167
>PF08282 Hydrolase_3: haloacid dehalogenase-like hydrolase; InterPro: IPR013200 The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification []. This HAD domain is found in several distinct enzymes including: Phospholipid-transporting ATPase 1 (3.6.3.1 from EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [] 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (3.1.3.45 from EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [] Mannosyl-3-phosphoglycerate phosphatase (3.1.3.70 from EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [] Phosphoglycolate phopshatase (3.1.3.18 from EC), which catalyses the dephosphorylation of 2-phosphoglycolate [] ; PDB: 2B30_B 3R4C_A 1XVI_B 3IJ5_B 3MMZ_C 3L7Y_A 1XPJ_C 1RLT_B 1RLM_B 2HF2_A ....
Probab=21.75 E-value=1.5e+02 Score=21.75 Aligned_cols=43 Identities=19% Similarity=0.176 Sum_probs=35.1
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAIL 96 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv 96 (130)
++..++|+++. +..+=+++.|-+-...++..+..+.-..|+|.
T Consensus 18 ~~~~~al~~l~-~~g~~~~i~TGR~~~~~~~~~~~~~~~~~~I~ 60 (254)
T PF08282_consen 18 PETIEALKELQ-EKGIKLVIATGRSYSSIKRLLKELGIDDYFIC 60 (254)
T ss_dssp HHHHHHHHHHH-HTTCEEEEECSSTHHHHHHHHHHTTHCSEEEE
T ss_pred HHHHHHHHhhc-ccceEEEEEccCcccccccccccccchhhhcc
Confidence 78889999887 47899999999999889988887764456665
No 168
>TIGR01662 HAD-SF-IIIA HAD-superfamily hydrolase, subfamily IIIA. In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme.
Probab=21.72 E-value=2.7e+02 Score=18.92 Aligned_cols=36 Identities=14% Similarity=0.334 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhh--------HHHHHHHHhhcC
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYV--------ANRIRFLVDSHN 89 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~--------a~~i~~~i~~~~ 89 (130)
..+.++|+.|. +..+-+.++|..- .+.++..+..+.
T Consensus 28 ~~v~~~l~~L~-~~g~~l~i~Sn~~~~~~~~~~~~~~~~~l~~~~ 71 (132)
T TIGR01662 28 PEVPDALAELK-EAGYKVVIVTNQSGIGRGKFSSGRVARRLEELG 71 (132)
T ss_pred CCHHHHHHHHH-HCCCEEEEEECCccccccHHHHHHHHHHHHHCC
Confidence 55778888775 5689999999987 677777777765
No 169
>PF12163 HobA: DNA replication regulator; InterPro: IPR021011 This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology []. HobA is a novel protein essential for initiation of H. pylori chromosome replication. It interacts specifically via DnaA with the oriC-DnaA complex. It is possible that HobA is essential for the correct formation and stabilisation of the orisome by facilitating the spatial positioning of DnaA at oriC [].; PDB: 2UVP_D 2WP0_A.
Probab=21.70 E-value=2.3e+02 Score=22.23 Aligned_cols=44 Identities=18% Similarity=0.270 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCCeeEEEEehhhHHHHHH----HHhhcCCCcc--EEEEcCC
Q 032904 55 IEDAFKEFTSREDIAIVLISQYVANRIRF----LVDSHNKPIP--AILEIPS 100 (130)
Q Consensus 55 i~~~~~~l~~~~digIIlIte~~a~~i~~----~i~~~~~~~P--~Iv~IPs 100 (130)
+..+++.+++ ...+|++|+.--+...+ .|+..+...| =|+.|++
T Consensus 33 ~a~~l~~il~--G~s~iliTD~~R~WF~~Yil~~IN~~~~~RP~lPi~~l~~ 82 (180)
T PF12163_consen 33 IASALSHILN--GGSFILITDEEREWFEEYILSNINNSHKNRPLLPIFSLKS 82 (180)
T ss_dssp HHHHHHHHHT--T-EEEEEE-GGGHHHHHHHHHHHS-SSTTS----EEESTT
T ss_pred HHHHHHHHhC--CCeEEEEeCchhHHHHHHHHHhcCcccCCCCcceEEeccc
Confidence 6688898883 78999999986555555 4554456677 3455665
No 170
>PRK11579 putative oxidoreductase; Provisional
Probab=21.63 E-value=3.1e+02 Score=22.36 Aligned_cols=60 Identities=7% Similarity=0.057 Sum_probs=37.6
Q ss_pred HHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhh
Q 032904 58 AFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNL 119 (130)
Q Consensus 58 ~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~a 119 (130)
.+.++++++++-+++|+..-.....-.+..++...++++|=|--... .+-+.|.+..++.
T Consensus 55 ~~~ell~~~~vD~V~I~tp~~~H~~~~~~al~aGkhVl~EKPla~t~--~ea~~l~~~a~~~ 114 (346)
T PRK11579 55 EPQHLFNDPNIDLIVIPTPNDTHFPLAKAALEAGKHVVVDKPFTVTL--SQARELDALAKSA 114 (346)
T ss_pred CHHHHhcCCCCCEEEEcCCcHHHHHHHHHHHHCCCeEEEeCCCCCCH--HHHHHHHHHHHHh
Confidence 36778888888888888765544444444455678888887764432 2224455555543
No 171
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=21.62 E-value=4.4e+02 Score=23.57 Aligned_cols=86 Identities=14% Similarity=0.134 Sum_probs=53.9
Q ss_pred EEEechhhHHHHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhc-----C------------------CCeeEEE
Q 032904 16 AMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTS-----R------------------EDIAIVL 72 (130)
Q Consensus 16 aVIGD~dtv~GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~-----~------------------~digIIl 72 (130)
+||||.-++.=-+-.|+.++ ++.+. +.+..+|++.+. + ..+.=|+
T Consensus 148 ~viG~~~~~~~A~~~gl~~i--------li~s~----esi~~a~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~ii 215 (526)
T TIGR02329 148 AVVGAGLITDLAEQAGLHGV--------FLYSA----DSVRQAFDDALDVARATRLRQAATLRSATRNQLRTRYRLDDLL 215 (526)
T ss_pred EEECChHHHHHHHHcCCceE--------EEecH----HHHHHHHHHHHHHHHHHHHHHHhHHHHHhhhhhccccchhhee
Confidence 57899888888889999886 44443 677776665542 0 0111144
Q ss_pred EehhhHHHHHHHHhhc-CCCccEEEEcCCCCCCCChhhHHHHHHHHh
Q 032904 73 ISQYVANRIRFLVDSH-NKPIPAILEIPSKDHPYDPAQDSVLSRVKN 118 (130)
Q Consensus 73 Ite~~a~~i~~~i~~~-~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ 118 (130)
=.......+++.+..+ ....|+++.= ..+-|++.+-+.|..
T Consensus 216 G~S~~m~~~~~~i~~~A~~~~pVLI~G-----E~GTGKe~lA~~IH~ 257 (526)
T TIGR02329 216 GASAPMEQVRALVRLYARSDATVLILG-----ESGTGKELVAQAIHQ 257 (526)
T ss_pred eCCHHHHHHHHHHHHHhCCCCcEEEEC-----CCCcCHHHHHHHHHH
Confidence 4455667777878776 4666766642 223356777777764
No 172
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=21.60 E-value=3.3e+02 Score=21.18 Aligned_cols=87 Identities=15% Similarity=0.048 Sum_probs=46.9
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCC-eeEEEEehhhHHHHHHHHhhcCCCcc-EEEEcCCCCC
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSRED-IAIVLISQYVANRIRFLVDSHNKPIP-AILEIPSKDH 103 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~d-igIIlIte~~a~~i~~~i~~~~~~~P-~Iv~IPs~~g 103 (130)
-|+..|++.+ |+ ..+.+.+++.++..+. +.| +|+=++.......+++.++.++...| .-|-+.+.
T Consensus 111 ~l~~~G~~Vi-------~L--G~~vp~e~~v~~~~~~--~~~~V~lS~~~~~~~~~~~~~i~~L~~~~~~~~i~vGG~-- 177 (213)
T cd02069 111 ILSNNGYEVI-------DL--GVMVPIEKILEAAKEH--KADIIGLSGLLVPSLDEMVEVAEEMNRRGIKIPLLIGGA-- 177 (213)
T ss_pred HHHhCCCEEE-------EC--CCCCCHHHHHHHHHHc--CCCEEEEccchhccHHHHHHHHHHHHhcCCCCeEEEECh--
Confidence 3566677654 22 3456778888877755 333 34433445556677777777753322 33344332
Q ss_pred CCChhhHHHHH--HHHhhcccCCcccc
Q 032904 104 PYDPAQDSVLS--RVKNLVSVESVASD 128 (130)
Q Consensus 104 ~~~~~~d~I~~--~Vk~aiGidi~~~~ 128 (130)
+.. ++ ..+ ..++.+|.|-.+.|
T Consensus 178 ~~~--~~-~~~~~~~~~~~gad~y~~d 201 (213)
T cd02069 178 ATS--RK-HTAVKIAPEYDGPVVYVKD 201 (213)
T ss_pred hcC--HH-HHhhhhccccCCCceEecC
Confidence 211 12 222 23567898876654
No 173
>PF07905 PucR: Purine catabolism regulatory protein-like family; InterPro: IPR012914 This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138 from SWISSPROT). PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression []. The other members of this family are also putative regulatory proteins.
Probab=21.59 E-value=1.3e+02 Score=21.06 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhc--CCCccEEEEcCCC
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSH--NKPIPAILEIPSK 101 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~--~~~~P~Iv~IPs~ 101 (130)
+++..+.++++.+..--|+++=+......+.+.+-++ +..+|+| ++|..
T Consensus 58 ~~~~~~~i~~L~~~~~agL~i~~~~~~~~iP~~~i~~A~~~~lPli-~ip~~ 108 (123)
T PF07905_consen 58 EEELREFIRELAEKGAAGLGIKTGRYLDEIPEEIIELADELGLPLI-EIPWE 108 (123)
T ss_pred HHHHHHHHHHHHHCCCeEEEEeccCccccCCHHHHHHHHHcCCCEE-EeCCC
Confidence 3569999999987777777776665555555554443 3668864 67773
No 174
>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold. This family is restricted to bacterial proteins, none of which have currently been characterised.
Probab=21.49 E-value=1.5e+02 Score=26.69 Aligned_cols=34 Identities=18% Similarity=0.460 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehh-----------hHHHHHHHHhh
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQY-----------VANRIRFLVDS 87 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~-----------~a~~i~~~i~~ 87 (130)
+.++...+ ++..+.+||.||||. +-.+|+|.+..
T Consensus 277 ~~ieqvvr-LIRSKGVGv~fvTQ~P~DiP~~VL~QLGnrIQHaLRA 321 (502)
T PF05872_consen 277 DKIEQVVR-LIRSKGVGVYFVTQNPTDIPDDVLGQLGNRIQHALRA 321 (502)
T ss_pred HHHHHHHH-HhhccCceEEEEeCCCCCCCHHHHHhhhhHHHHHHhc
Confidence 44445444 677899999999987 34566665544
No 175
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=21.45 E-value=5.3e+02 Score=22.25 Aligned_cols=96 Identities=14% Similarity=0.218 Sum_probs=50.3
Q ss_pred cEEEEEechhhH--HHHHH------hcccccccCCcceeEEecCCCc-H--HHHHHHHHHHhcCCCeeEEEEehhhH-HH
Q 032904 13 ALIAMIADEDTV--VGFLL------AGVGNVDLRRKTNYLIVDSKTT-I--KQIEDAFKEFTSREDIAIVLISQYVA-NR 80 (130)
Q Consensus 13 ~kIaVIGD~dtv--~GFrL------aGi~~~~~~~~~nf~v~~~~~~-~--eei~~~~~~l~~~~digIIlIte~~a-~~ 80 (130)
+.|||||-.+.- +|.++ .|+.+. -|+| ++... . ...-..+.++-...|++||++..+.. +.
T Consensus 8 ~siavvGaS~~~~~~g~~~~~~l~~~gf~g~------v~~V-np~~~~i~G~~~~~sl~~lp~~~Dlavi~vp~~~~~~~ 80 (447)
T TIGR02717 8 KSVAVIGASRDPGKVGYAIMKNLIEGGYKGK------IYPV-NPKAGEILGVKAYPSVLEIPDPVDLAVIVVPAKYVPQV 80 (447)
T ss_pred CEEEEEccCCCCCchHHHHHHHHHhCCCCCc------EEEE-CCCCCccCCccccCCHHHCCCCCCEEEEecCHHHHHHH
Confidence 679999985421 23332 355321 2555 43221 0 11123355555567999999997754 44
Q ss_pred HHHHHhhcCCCccEEEEcCCCCCCCCh----hhHHHHHHHHh
Q 032904 81 IRFLVDSHNKPIPAILEIPSKDHPYDP----AQDSVLSRVKN 118 (130)
Q Consensus 81 i~~~i~~~~~~~P~Iv~IPs~~g~~~~----~~d~I~~~Vk~ 118 (130)
+++..+ ...+.++.|.+.....+. -++.+.+..++
T Consensus 81 l~e~~~---~gv~~~vi~s~gf~e~g~~g~~~~~~l~~~a~~ 119 (447)
T TIGR02717 81 VEECGE---KGVKGAVVITAGFKEVGEEGAELEQELVEIARK 119 (447)
T ss_pred HHHHHh---cCCCEEEEECCCccccCcchHHHHHHHHHHHHH
Confidence 455444 445677777664433221 13456666554
No 176
>PF00378 ECH: Enoyl-CoA hydratase/isomerase family; InterPro: IPR001753 The crotonase superfamily is comprised of mechanistically diverse proteins that share a conserved trimeric quaternary structure (sometimes a hexamer consisting of a dimer of trimers), the core of which consists of 4 turns of a (beta/beta/alpha)n superhelix. Some enzymes in the superfamily have been shown to display dehalogenase, hydratase, and isomerase activities, while others have been implicated in carbon-carbon bond formation and cleavage as well as the hydrolysis of thioesters []. However, these different enzymes share the need to stabilise an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two structurally conserved peptidic NH groups that provide hydrogen bonds to the carbonyl moieties of the acyl-CoA substrates and form an "oxyanion hole". The CoA thioester derivatives bind in a characteristic hooked shape and a conserved tunnel binds the pantetheine group of CoA, which links the 3'-phosphate ADP binding site to the site of reaction []. Enzymes in the crotonase superfamily include: Enoyl-CoA hydratase (crotonase; 4.2.1.17 from EC), which catalyses the hydratation of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA []. 3-2trans-enoyl-CoA isomerase (or dodecenoyl-CoA isomerise; 5.3.3.8 from EC), which shifts the 3-double bond of the intermediates of unsaturated fatty acid oxidation to the 2-trans position []. 3-hydroxbutyryl-CoA dehydratase (crotonase; 4.2.1.55 from EC), a bacterial enzyme involved in the butyrate/butanol-producing pathway. 4-Chlorobenzoyl-CoA dehalogenase (3.8.1.6 from EC), a Pseudomonas enzyme which catalyses the conversion of 4-chlorobenzoate-CoA to 4-hydroxybenzoate-CoA []. Dienoyl-CoA isomerise, which catalyses the isomerisation of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA []. Naphthoate synthase (MenB, or DHNA synthetase; 4.1.3.36 from EC), a bacterial enzyme involved in the biosynthesis of menaquinone (vitamin K2) []. Carnitine racemase (gene caiD), which catalyses the reversible conversion of crotonobetaine to L-carnitine in Escherichia coli []. Methylmalonyl CoA decarboxylase (MMCD; 4.1.1.41 from EC), which has a hexameric structure (dimer of trimers) []. Carboxymethylproline synthase (CarB), which is involved in carbapenem biosynthesis []. 6-oxo camphor hydrolase, which catalyses the desymmetrisation of bicyclic beta-diketones to optically active keto acids []. The alpha subunit of fatty oxidation complex, a multi-enzyme complex that catalyses the last three reactions in the fatty acid beta-oxidation cycle []. AUH protein, a bifunctional RNA-binding homologue of enoyl-CoA hydratase []. This entry represents the core domain found in crotonase superfamily members.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2VRE_B 3RSI_A 1HZD_F 2ZQR_E 2ZQQ_D 3R9S_C 1O8U_E 1SZO_C 3MOY_A 2UZF_A ....
Probab=21.42 E-value=2.9e+02 Score=21.22 Aligned_cols=49 Identities=27% Similarity=0.427 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhcCCCeeEEEEehh-----------------------hHHHHHHHHhhc-CCCccEEEEcCC
Q 032904 52 IKQIEDAFKEFTSREDIAIVLISQY-----------------------VANRIRFLVDSH-NKPIPAILEIPS 100 (130)
Q Consensus 52 ~eei~~~~~~l~~~~digIIlIte~-----------------------~a~~i~~~i~~~-~~~~P~Iv~IPs 100 (130)
.+++.++|..+-+++++.+|+++.. +.+.+.+.+..+ ..+.|+|-.|-+
T Consensus 27 ~~~l~~~l~~~~~d~~v~vvv~~~~~~~F~~G~Dl~~~~~~~~~~~~~~~~~~~~l~~~l~~~~kp~Iaav~G 99 (245)
T PF00378_consen 27 LDELEEALDEAEADPDVKVVVISGGGKAFCAGADLKEFLNSDEEEAREFFRRFQELLSRLANFPKPTIAAVNG 99 (245)
T ss_dssp HHHHHHHHHHHHHSTTESEEEEEESTSESBESB-HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSEEEEEESS
T ss_pred HHHHHHHHHHHHhcCCccEEEEeecccccccccchhhhhccccccccccchhhccccccchhhhhheeecccc
Confidence 5788899999988999988888732 123333334443 378899988755
No 177
>PTZ00103 60S ribosomal protein L3; Provisional
Probab=21.24 E-value=1.4e+02 Score=26.05 Aligned_cols=53 Identities=15% Similarity=0.084 Sum_probs=34.1
Q ss_pred CeeEEEEehhhHHHHHHHHhhcCCCccEEEEcCCCCCCCChhhHHHHHHHHhhccc-CCcc
Q 032904 67 DIAIVLISQYVANRIRFLVDSHNKPIPAILEIPSKDHPYDPAQDSVLSRVKNLVSV-ESVA 126 (130)
Q Consensus 67 digIIlIte~~a~~i~~~i~~~~~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~aiGi-di~~ 126 (130)
+|-+|.-|+- ..+. +.+..|-|+||.=..|+...-.++-.+++.+.|.+ |+|.
T Consensus 156 ~IRvi~hTqp------~~~~-l~kKkp~imEiqv~GGsv~~k~d~a~~llgk~i~v~dvF~ 209 (390)
T PTZ00103 156 VIRVIAHTQP------SKLP-LGQKKAHVMEIQVNGGSVAEKVDFAKSLLEKEVPVDSVFQ 209 (390)
T ss_pred EEEEEEEcch------hhcC-cCCcCccEEEEeecCCCHHHHHHHHHHHhcCeechhhhcc
Confidence 5667766662 1122 44778999999988877554456666666666666 5554
No 178
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=20.99 E-value=2e+02 Score=20.16 Aligned_cols=40 Identities=5% Similarity=0.148 Sum_probs=25.2
Q ss_pred HHHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEE
Q 032904 26 GFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVL 72 (130)
Q Consensus 26 GFrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIl 72 (130)
-+.-.|++.. ......+++.+++.+.++++-+++++ ||++
T Consensus 53 ~~~~~Gi~~~-------~~~l~~~~~~~el~~~i~~lN~D~~V~GIlv 93 (117)
T PF00763_consen 53 AAEKLGIEFE-------LIELPEDISEEELLELIEKLNEDPSVHGILV 93 (117)
T ss_dssp HHHHHT-EEE-------EEEE-TTSSHHHHHHHHHHHHH-TT-SEEEE
T ss_pred HHHHcCCceE-------EEECCCCcCHHHHHHHHHHHhCCCCCCEEEE
Confidence 4556788654 33445677889999999988777765 5544
No 179
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=20.90 E-value=2.1e+02 Score=19.90 Aligned_cols=41 Identities=22% Similarity=0.353 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhc-C-CCccEEEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSH-N-KPIPAILE 97 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~-~-~~~P~Iv~ 97 (130)
++++++++ +..+..+++.++.++..++.+..+ + ...|.+..
T Consensus 23 ~~v~~aik----~gk~~lVI~A~D~s~~~kkki~~~~~~~~vp~~~~ 65 (104)
T PRK05583 23 NKCEEAIK----KKKVYLIIISNDISENSKNKFKNYCNKYNIPYIEG 65 (104)
T ss_pred HHHHHHHH----cCCceEEEEeCCCCHhHHHHHHHHHHHcCCCEEEe
Confidence 44555444 567899999999998888888775 2 45676554
No 180
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=20.90 E-value=2.6e+02 Score=21.54 Aligned_cols=44 Identities=11% Similarity=0.130 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCcc--EEEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIP--AILE 97 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P--~Iv~ 97 (130)
+++.+.++++. +..+.+++.|-+-...++..+.++....| +|+.
T Consensus 24 ~~~~~~i~~~~-~~gi~fv~aTGR~~~~~~~~~~~~~~~~p~~~I~~ 69 (249)
T TIGR01485 24 LRLNALLEDHR-GEDSLLVYSTGRSPHSYKELQKQKPLLTPDIWVTS 69 (249)
T ss_pred HHHHHHHHHhh-ccCceEEEEcCCCHHHHHHHHhcCCCCCCCEEEEc
Confidence 66777777765 67789999999999999988887766667 5553
No 181
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=20.77 E-value=1.2e+02 Score=27.54 Aligned_cols=20 Identities=10% Similarity=0.160 Sum_probs=15.4
Q ss_pred CchhhhcccccEEEEEechh
Q 032904 3 NRPQIRTAASALIAMIADED 22 (130)
Q Consensus 3 ~~~~~~~~~~~kIaVIGD~d 22 (130)
+.+..+.+..+.|.++||++
T Consensus 104 ~~~~~~~~~g~~ivi~G~~~ 123 (647)
T PRK00087 104 KLAKKYYEEGYQIVIVGDKN 123 (647)
T ss_pred HHHHHHHhCCCEEEEEeCCC
Confidence 44566777889999999954
No 182
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=20.44 E-value=1.3e+02 Score=17.26 Aligned_cols=15 Identities=13% Similarity=0.419 Sum_probs=12.0
Q ss_pred CcHHHHHHHHHHHhc
Q 032904 50 TTIKQIEDAFKEFTS 64 (130)
Q Consensus 50 ~~~eei~~~~~~l~~ 64 (130)
.+.+++++++++++.
T Consensus 12 ~~~~~ik~~y~~l~~ 26 (55)
T cd06257 12 ASDEEIKKAYRKLAL 26 (55)
T ss_pred CCHHHHHHHHHHHHH
Confidence 356999999999864
No 183
>cd07393 MPP_DR1119 Deinococcus radiodurans DR1119 and related proteins, metallophosphatase domain. DR1119 is an uncharacterized Deinococcus radiodurans protein with a metallophosphatase domain. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordinat
Probab=20.42 E-value=3.5e+02 Score=20.82 Aligned_cols=63 Identities=10% Similarity=0.128 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHH-----HHHHHHhhcC-CCccEEEEcCCCCCCCChhhHHHHHHHHh
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVAN-----RIRFLVDSHN-KPIPAILEIPSKDHPYDPAQDSVLSRVKN 118 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~-----~i~~~i~~~~-~~~P~Iv~IPs~~g~~~~~~d~I~~~Vk~ 118 (130)
+++.+.++.++ ++.-+|+++-++.. .....++.++ ...| ++-+|+.+..+....+.+++.+++
T Consensus 29 ~~i~~~~~~~~--~~~D~viiaGDl~~~~~~~~~~~~l~~l~~l~~~-v~~V~GNHD~~~~~~~~~~~~l~~ 97 (232)
T cd07393 29 EKIKENWDNVV--APEDIVLIPGDISWAMKLEEAKLDLAWIDALPGT-KVLLKGNHDYWWGSASKLRKALEE 97 (232)
T ss_pred HHHHHHHHhcC--CCCCEEEEcCCCccCCChHHHHHHHHHHHhCCCC-eEEEeCCccccCCCHHHHHHHHHh
Confidence 45555555555 26788888877652 2223333332 2345 567999887554445667666655
No 184
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=20.40 E-value=93 Score=25.69 Aligned_cols=24 Identities=21% Similarity=0.326 Sum_probs=14.6
Q ss_pred chhhhcccccEEEEEechh--hHHHH
Q 032904 4 RPQIRTAASALIAMIADED--TVVGF 27 (130)
Q Consensus 4 ~~~~~~~~~~kIaVIGD~d--tv~GF 27 (130)
.+..+.+..+.|.++||+. -+.|+
T Consensus 103 ~v~~~~~~Gy~iviiG~~~HpEv~gi 128 (281)
T PF02401_consen 103 IVRKYAKEGYQIVIIGDKNHPEVIGI 128 (281)
T ss_dssp HHHHHHHCT-EEEEES-TT-HHHHHH
T ss_pred HHHHHHhcCCEEEEECCCCCceEEEe
Confidence 4556667789999999943 44444
No 185
>TIGR01487 SPP-like sucrose-phosphate phosphatase-like hydrolase, Archaeal. TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases.
Probab=20.25 E-value=2.5e+02 Score=20.97 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAI 95 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~I 95 (130)
++..++++++. +..+-+++.|-+-...++..++.+....|+|
T Consensus 21 ~~~~~~i~~l~-~~g~~~~~~TGR~~~~~~~~~~~l~~~~~~i 62 (215)
T TIGR01487 21 ERAIEAIRKAE-KKGIPVSLVTGNTVPFARALAVLIGTSGPVV 62 (215)
T ss_pred HHHHHHHHHHH-HCCCEEEEEcCCcchhHHHHHHHhCCCCcEE
Confidence 56788888885 5789999999998888888777665444654
No 186
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=20.14 E-value=3.1e+02 Score=20.25 Aligned_cols=43 Identities=21% Similarity=0.263 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhhcCCCccEEE
Q 032904 53 KQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAIL 96 (130)
Q Consensus 53 eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~~~~~~P~Iv 96 (130)
++..++++++. +..+-+++.|-+-...+++.+..+....|+|.
T Consensus 18 ~~~~~al~~l~-~~Gi~~~~aTGR~~~~~~~~~~~l~~~~~~i~ 60 (225)
T TIGR01482 18 ESALEAIRKAE-SVGIPVVLVTGNSVQFARALAKLIGTPDPVIA 60 (225)
T ss_pred HHHHHHHHHHH-HCCCEEEEEcCCchHHHHHHHHHhCCCCeEEE
Confidence 55667788775 67889999998888777777666654456653
No 187
>cd00959 DeoC 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. DERA belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2-deoxyribose 5-phosphate. DERA is unique in catalyzing the aldol reaction between two aldehydes, and its broad substrate specificity confers considerable utility as a biocatalyst, offering an environmentally benign alternative to chiral transition metal catalysis of the asymmetric aldol reaction.
Probab=20.12 E-value=4e+02 Score=20.22 Aligned_cols=40 Identities=15% Similarity=0.108 Sum_probs=31.6
Q ss_pred cCCCcHHHHHHHHHHHhcCCCeeEEEEehhhHHHHHHHHhh
Q 032904 47 DSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDS 87 (130)
Q Consensus 47 ~~~~~~eei~~~~~~l~~~~digIIlIte~~a~~i~~~i~~ 87 (130)
.+..+.+++++.+++..+ ..+.-+.++.......++.+..
T Consensus 11 ~p~~t~~~i~~~~~~a~~-~~~~av~v~p~~v~~~~~~l~~ 50 (203)
T cd00959 11 KPDATEEDIRKLCDEAKE-YGFAAVCVNPCFVPLAREALKG 50 (203)
T ss_pred CCCCCHHHHHHHHHHHHH-cCCCEEEEcHHHHHHHHHHcCC
Confidence 356678999999998884 4588888998888888887754
No 188
>PF05116 S6PP: Sucrose-6F-phosphate phosphohydrolase; InterPro: IPR006380 This family of sequences represent sucrose phosphate phosphohydrolase (SPP) from plants and cyanobacteria []. SPP is a member of the Class IIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.; PDB: 1TJ5_A 2B1Q_A 1TJ4_A 1S2O_A 1U2T_A 2D2V_A 1TJ3_A 1U2S_A 2B1R_A 3GYG_B ....
Probab=20.11 E-value=2e+02 Score=22.56 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=27.6
Q ss_pred HHHHHHHHHhc---CCCeeEEEEehhhHHHHHHHHhhcCCCcc
Q 032904 54 QIEDAFKEFTS---REDIAIVLISQYVANRIRFLVDSHNKPIP 93 (130)
Q Consensus 54 ei~~~~~~l~~---~~digIIlIte~~a~~i~~~i~~~~~~~P 93 (130)
.....|.++++ +.++..+++|-+-.+.+++.+.++..+.|
T Consensus 19 ~~~~~l~~~l~~~~~~~~~~v~~TGRs~~~~~~~~~~~~l~~P 61 (247)
T PF05116_consen 19 EALARLEELLEQQARPEILFVYVTGRSLESVLRLLREYNLPQP 61 (247)
T ss_dssp HHHHHHHHHHHHHHCCGEEEEEE-SS-HHHHHHHHHHCT-EE-
T ss_pred HHHHHHHHHHHHhhCCCceEEEECCCCHHHHHHHHHhCCCCCC
Confidence 34444555554 89999999999999999999988765555
No 189
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=20.10 E-value=3.1e+02 Score=19.05 Aligned_cols=57 Identities=11% Similarity=0.100 Sum_probs=35.4
Q ss_pred HHHHhcCCCeeEEEEehhhHHH---HHHHHhhcCCCccEEEEcCCCC-CC--CChhhHHHHHHHHhhc
Q 032904 59 FKEFTSREDIAIVLISQYVANR---IRFLVDSHNKPIPAILEIPSKD-HP--YDPAQDSVLSRVKNLV 120 (130)
Q Consensus 59 ~~~l~~~~digIIlIte~~a~~---i~~~i~~~~~~~P~Iv~IPs~~-g~--~~~~~d~I~~~Vk~ai 120 (130)
+.+.+..+++-+|+++.++.-. +++..+. ...|+.+ ||... +| |+. +.+.+.+++++
T Consensus 42 ~~~~~~~~~~DvIll~PQi~~~~~~i~~~~~~--~~ipv~~-I~~~~Y~~~~~~~--~~~~~~~~~~~ 104 (104)
T PRK09590 42 GEKAIAAAEYDLYLVSPQTKMYFKQFEEAGAK--VGKPVVQ-IPPQAYIPIPMGI--EKMAKLILENI 104 (104)
T ss_pred HHHhhccCCCCEEEEChHHHHHHHHHHHHhhh--cCCCEEE-eCHHHcCCCccCH--HHHHHHHHhcC
Confidence 3334445678899999887644 4444443 4577766 66655 54 544 66788777653
No 190
>PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=20.00 E-value=1.7e+02 Score=25.32 Aligned_cols=40 Identities=10% Similarity=0.198 Sum_probs=26.8
Q ss_pred HHHhcccccccCCcceeEEecCCCcHHHHHHHHHHHhcCCCe-eEEEE
Q 032904 27 FLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDI-AIVLI 73 (130)
Q Consensus 27 FrLaGi~~~~~~~~~nf~v~~~~~~~eei~~~~~~l~~~~di-gIIlI 73 (130)
..-.|++.. -+.-.++++++|+.+.++++=+++++ |||+-
T Consensus 128 ~e~~GI~~~-------~~~lpe~~te~ell~~I~~LN~D~~V~GIlVQ 168 (364)
T PLN02616 128 CDSVGINSF-------EVRLPEDSTEQEVLKFISGFNNDPSVHGILVQ 168 (364)
T ss_pred HHHcCCEEE-------EEECCCCCCHHHHHHHHHHHcCCCCCCEEEEe
Confidence 445688643 12224566788999999999777776 66654
Done!