Query 031642
Match_columns 156
No_of_seqs 100 out of 173
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 03:22:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031642.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031642hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03670 competence damage-ind 99.9 2E-22 4.3E-27 169.0 12.1 109 29-146 128-244 (252)
2 COG1058 CinA Predicted nucleot 99.8 1.4E-19 3.1E-24 153.3 12.6 117 29-148 121-247 (255)
3 PRK00549 competence damage-ind 99.7 9.3E-17 2E-21 142.1 11.4 123 28-153 119-253 (414)
4 PRK01215 competence damage-ind 99.5 1.9E-13 4.2E-18 115.3 13.2 112 28-144 122-246 (264)
5 PRK03673 hypothetical protein; 99.4 1.5E-12 3.2E-17 115.9 11.4 121 29-153 121-249 (396)
6 TIGR00200 cinA_nterm competenc 99.2 3.2E-10 6.8E-15 101.3 11.9 122 29-153 120-254 (413)
7 cd00885 cinA Competence-damage 98.0 9.5E-06 2.1E-10 64.4 4.9 45 28-74 118-169 (170)
8 PF00936 BMC: BMC domain; Int 84.1 2.1 4.6E-05 29.9 4.2 48 102-150 18-65 (75)
9 cd07049 BMC_EutL_repeat1 ethan 83.8 2.8 6.1E-05 32.1 5.0 65 85-152 26-102 (103)
10 cd07046 BMC_PduU-EutS 1,2-prop 83.2 12 0.00026 28.6 8.3 92 42-151 8-100 (110)
11 cd04905 ACT_CM-PDT C-terminal 80.0 15 0.00033 24.8 7.2 62 85-146 3-69 (80)
12 smart00877 BMC Bacterial micro 71.9 12 0.00026 26.2 5.0 45 104-149 19-63 (75)
13 COG4097 Predicted ferric reduc 69.5 11 0.00025 35.1 5.6 61 49-115 318-378 (438)
14 cd06169 BMC Bacterial Micro-Co 68.4 16 0.00035 24.4 4.9 43 103-146 18-61 (62)
15 PF08753 NikR_C: NikR C termin 67.6 38 0.00082 23.7 6.8 55 90-145 8-65 (78)
16 PF00994 MoCF_biosynth: Probab 65.2 5.7 0.00012 29.8 2.4 34 38-73 103-143 (144)
17 cd07053 BMC_PduT_repeat1 1,2-p 65.0 19 0.00042 25.5 4.9 47 103-150 18-64 (76)
18 COG2921 Uncharacterized conser 60.7 34 0.00075 25.8 5.8 54 92-145 24-82 (90)
19 cd04882 ACT_Bt0572_2 C-termina 60.0 39 0.00085 21.0 6.2 55 88-145 4-59 (65)
20 KOG0070 GTP-binding ADP-ribosy 60.0 12 0.00027 31.0 3.7 27 123-149 87-113 (181)
21 COG3622 Hfi Hydroxypyruvate is 57.2 9.8 0.00021 33.4 2.7 78 42-120 94-212 (260)
22 PF14492 EFG_II: Elongation Fa 55.8 65 0.0014 22.2 7.4 64 81-148 3-68 (75)
23 cd04906 ACT_ThrD-I_1 First of 55.4 67 0.0014 22.3 6.3 51 93-145 11-64 (85)
24 cd04904 ACT_AAAH ACT domain of 53.2 69 0.0015 21.7 6.8 55 92-147 9-67 (74)
25 smart00267 GGDEF diguanylate c 52.7 39 0.00084 23.3 4.7 31 121-151 83-113 (163)
26 PF03927 NapD: NapD protein; 52.1 31 0.00067 24.4 4.2 47 95-145 15-62 (79)
27 COG0035 Upp Uracil phosphoribo 51.6 58 0.0013 27.7 6.4 56 45-113 122-180 (210)
28 cd02575 PseudoU_synth_EcTruD P 50.5 65 0.0014 27.8 6.6 66 77-145 61-137 (253)
29 cd07556 Nucleotidyl_cyc_III Cl 50.0 44 0.00096 22.8 4.7 48 97-148 31-78 (133)
30 cd04886 ACT_ThrD-II-like C-ter 48.3 64 0.0014 19.9 6.8 59 88-146 3-67 (73)
31 PF03808 Glyco_tran_WecB: Glyc 47.5 34 0.00073 26.8 4.2 60 90-149 54-127 (172)
32 KOG0071 GTP-binding ADP-ribosy 47.3 21 0.00046 29.7 3.0 28 123-150 87-114 (180)
33 cd04874 ACT_Af1403 N-terminal 47.2 68 0.0015 19.9 5.8 57 86-145 3-62 (72)
34 cd04908 ACT_Bt0572_1 N-termina 46.7 79 0.0017 20.5 6.2 54 87-145 5-59 (66)
35 cd04884 ACT_CBS C-terminal ACT 45.8 84 0.0018 20.6 5.8 59 88-150 4-66 (72)
36 cd04880 ACT_AAAH-PDT-like ACT 44.9 89 0.0019 20.6 6.2 55 93-147 9-68 (75)
37 cd07045 BMC_CcmK_like Carbon d 44.7 76 0.0016 22.7 5.3 46 103-149 18-63 (84)
38 PF11209 DUF2993: Protein of u 44.2 19 0.0004 28.4 2.2 40 93-132 10-55 (225)
39 cd04909 ACT_PDH-BS C-terminal 42.6 90 0.0019 20.0 7.6 59 85-145 3-64 (69)
40 COG1925 FruB Phosphotransferas 40.8 36 0.00078 25.0 3.1 28 124-154 61-88 (88)
41 cd04931 ACT_PAH ACT domain of 40.2 1.4E+02 0.0031 21.6 6.9 64 85-148 16-83 (90)
42 PF05036 SPOR: Sporulation rel 40.0 90 0.002 19.9 4.7 58 90-148 11-70 (76)
43 cd01840 SGNH_hydrolase_yrhL_li 39.6 96 0.0021 23.0 5.4 62 47-113 51-113 (150)
44 PRK00907 hypothetical protein; 39.3 1.6E+02 0.0034 21.8 6.4 54 92-145 26-84 (92)
45 PF13684 Dak1_2: Dihydroxyacet 39.2 87 0.0019 27.3 5.8 37 81-117 264-300 (313)
46 TIGR00119 acolac_sm acetolacta 37.6 1.3E+02 0.0028 24.1 6.1 59 89-148 7-68 (157)
47 TIGR02174 CXXU_selWTH selT/sel 37.5 14 0.00029 25.6 0.5 34 95-129 13-48 (72)
48 PRK15405 ethanolamine utilizat 37.2 57 0.0012 28.0 4.2 49 101-150 50-109 (217)
49 PF03135 CagE_TrbE_VirB: CagE, 37.0 51 0.0011 26.1 3.7 30 124-153 151-180 (205)
50 smart00107 BTK Bruton's tyrosi 36.7 16 0.00035 22.9 0.7 10 21-30 16-25 (36)
51 cd02576 PseudoU_synth_ScPUS7 P 36.6 1.5E+02 0.0032 26.2 6.9 66 77-145 65-142 (371)
52 PRK05713 hypothetical protein; 36.0 1.1E+02 0.0023 25.9 5.7 93 10-114 151-254 (312)
53 PRK00341 hypothetical protein; 35.9 1.2E+02 0.0027 22.1 5.3 50 96-145 29-83 (91)
54 smart00079 PBPe Eukaryotic hom 35.7 83 0.0018 22.2 4.3 49 105-155 79-127 (134)
55 cd01949 GGDEF Diguanylate-cycl 34.9 97 0.0021 21.1 4.4 29 121-149 80-108 (158)
56 cd08431 PBP2_HupR The C-termin 34.4 54 0.0012 23.3 3.2 45 64-117 14-58 (195)
57 PF00175 NAD_binding_1: Oxidor 34.0 1.4E+02 0.003 20.3 5.1 52 52-110 2-54 (109)
58 PRK11064 wecC UDP-N-acetyl-D-m 33.8 2.6E+02 0.0056 25.1 8.0 94 46-147 75-196 (415)
59 cd06210 MMO_FAD_NAD_binding Me 33.7 1.5E+02 0.0032 23.4 5.9 95 10-113 68-169 (236)
60 PF14081 DUF4262: Domain of un 32.3 41 0.0009 25.2 2.4 31 52-84 37-70 (125)
61 TIGR03376 glycerol3P_DH glycer 32.0 2E+02 0.0044 25.4 7.0 122 20-152 57-187 (342)
62 cd07465 CRD_FZ1 Cysteine-rich 32.0 34 0.00073 26.6 1.9 28 14-41 92-123 (127)
63 PRK07114 keto-hydroxyglutarate 31.9 66 0.0014 27.1 3.8 61 81-141 41-110 (222)
64 TIGR02526 eut_PduT ethanolamin 31.8 1.3E+02 0.0028 24.9 5.4 60 90-152 104-165 (182)
65 PRK00007 elongation factor G; 31.7 1.6E+02 0.0034 28.3 6.6 63 80-147 405-470 (693)
66 TIGR03544 DivI1A_domain DivIVA 31.3 30 0.00065 20.8 1.2 24 123-146 10-33 (34)
67 PF13656 RNA_pol_L_2: RNA poly 30.7 1.8E+02 0.0038 20.5 5.2 61 87-147 4-70 (77)
68 PRK10614 multidrug efflux syst 30.6 1.2E+02 0.0026 30.5 5.8 53 97-149 626-686 (1025)
69 PRK10897 phosphohistidinoprote 30.1 68 0.0015 23.2 3.1 67 83-154 2-89 (90)
70 cd00914 PCD_DCoH_subfamily_b P 29.0 63 0.0014 22.4 2.7 60 82-147 9-73 (76)
71 PF00025 Arf: ADP-ribosylation 29.0 57 0.0012 25.0 2.7 29 123-151 84-112 (175)
72 TIGR03480 HpnN hopanoid biosyn 28.8 1.3E+02 0.0028 29.4 5.6 47 94-149 48-94 (862)
73 PF00779 BTK: BTK motif; Inte 28.8 24 0.00052 21.6 0.5 10 21-30 11-20 (32)
74 cd06215 FNR_iron_sulfur_bindin 28.7 1.9E+02 0.0042 22.5 5.7 95 10-113 63-164 (231)
75 cd07056 BMC_PduK 1,2-propanedi 28.7 2E+02 0.0044 20.2 5.3 46 103-149 18-64 (77)
76 PF11582 DUF3240: Protein of u 28.5 1.2E+02 0.0026 22.3 4.3 60 41-113 29-88 (102)
77 cd08450 PBP2_HcaR The C-termin 28.4 64 0.0014 22.8 2.7 50 59-117 8-58 (196)
78 cd04929 ACT_TPH ACT domain of 28.3 2.1E+02 0.0044 19.8 6.2 53 93-146 10-66 (74)
79 COG0206 FtsZ Cell division GTP 28.2 1.8E+02 0.0039 26.2 6.1 66 53-122 70-140 (338)
80 cd04888 ACT_PheB-BS C-terminal 28.1 1.7E+02 0.0036 18.8 6.6 58 87-146 4-66 (76)
81 cd04903 ACT_LSD C-terminal ACT 28.0 1.5E+02 0.0032 18.1 4.8 57 88-145 4-61 (71)
82 PF07364 DUF1485: Protein of u 27.6 96 0.0021 27.1 4.2 56 96-152 212-276 (292)
83 cd07460 CRD_FZ5 Cysteine-rich 27.4 42 0.00091 26.1 1.7 29 14-42 93-126 (127)
84 KOG3445 Mitochondrial/chloropl 27.4 1.5E+02 0.0032 24.2 4.9 49 98-146 45-104 (145)
85 PRK10503 multidrug efflux syst 27.2 1.6E+02 0.0034 29.9 6.0 54 96-149 639-700 (1040)
86 PRK08629 coproporphyrinogen II 26.5 1.6E+02 0.0036 26.7 5.6 94 44-146 99-193 (433)
87 cd07054 BMC_PduT_repeat2 1,2-p 26.2 1.9E+02 0.0041 20.5 4.8 45 103-148 18-64 (78)
88 PF06183 DinI: DinI-like famil 26.2 2E+02 0.0043 19.9 4.8 48 98-148 11-58 (65)
89 cd07466 CRD_FZ7 Cysteine-rich 26.2 49 0.0011 25.6 1.9 29 14-42 92-124 (125)
90 PRK08898 coproporphyrinogen II 26.1 1.7E+02 0.0037 25.9 5.5 98 44-147 71-171 (394)
91 cd00913 PCD_DCoH_subfamily_a P 26.1 73 0.0016 22.0 2.6 61 81-147 8-73 (76)
92 PRK02047 hypothetical protein; 26.1 2.6E+02 0.0056 20.3 5.6 52 94-145 26-83 (91)
93 PRK01002 nickel responsive reg 26.0 2.9E+02 0.0064 21.5 6.3 61 83-144 57-120 (141)
94 PF00338 Ribosomal_S10: Riboso 25.8 1.5E+02 0.0032 20.9 4.2 25 125-149 2-26 (97)
95 cd07462 CRD_FZ10 Cysteine-rich 25.8 48 0.001 25.8 1.8 27 14-40 93-124 (127)
96 PRK13351 elongation factor G; 25.7 2.4E+02 0.0052 26.8 6.7 65 79-148 400-467 (687)
97 PRK11895 ilvH acetolactate syn 25.6 2.7E+02 0.006 22.3 6.2 58 90-148 9-69 (161)
98 cd07448 CRD_FZ4 Cysteine-rich 25.3 45 0.00098 25.7 1.6 25 14-38 92-121 (126)
99 PF12693 GspL_C: GspL periplas 25.3 2.3E+02 0.0049 21.4 5.4 49 99-147 85-134 (157)
100 PF08945 Bclx_interact: Bcl-x 25.2 26 0.00056 22.9 0.2 27 84-110 6-33 (40)
101 PHA02755 hypothetical protein; 25.1 34 0.00073 25.8 0.8 16 107-122 5-20 (96)
102 cd06188 NADH_quinone_reductase 25.0 1.5E+02 0.0032 24.5 4.7 85 21-113 123-212 (283)
103 COG1169 MenF Isochorismate syn 24.8 3E+02 0.0064 25.8 6.9 57 62-120 160-217 (423)
104 TIGR03026 NDP-sugDHase nucleot 24.4 4.9E+02 0.011 22.9 9.6 90 47-146 77-190 (411)
105 cd08412 PBP2_PAO1_like The C-t 24.3 91 0.002 21.9 2.9 50 59-117 8-58 (198)
106 PRK12739 elongation factor G; 24.2 2.7E+02 0.0058 26.7 6.8 114 28-147 332-467 (691)
107 cd07449 CRD_FZ3 Cysteine-rich 24.0 61 0.0013 25.4 2.1 30 14-43 92-126 (127)
108 cd06191 FNR_iron_sulfur_bindin 24.0 1.9E+02 0.0041 22.7 5.0 96 10-113 62-163 (231)
109 cd04877 ACT_TyrR N-terminal AC 23.5 2.3E+02 0.0049 18.7 6.1 57 88-146 5-61 (74)
110 COG2037 Ftr Formylmethanofuran 22.9 1.4E+02 0.003 26.7 4.3 39 31-70 147-189 (297)
111 TIGR00222 panB 3-methyl-2-oxob 22.8 5.1E+02 0.011 22.6 8.9 56 96-153 117-176 (263)
112 cd04902 ACT_3PGDH-xct C-termin 22.8 2.1E+02 0.0045 18.0 4.8 43 88-130 4-47 (73)
113 TIGR00254 GGDEF diguanylate cy 22.7 2.4E+02 0.0053 19.6 4.8 29 121-149 82-110 (165)
114 cd08452 PBP2_AlsR The C-termin 22.7 82 0.0018 22.6 2.4 43 63-114 13-55 (197)
115 cd08430 PBP2_IlvY The C-termin 22.6 99 0.0021 21.7 2.8 21 95-115 36-56 (199)
116 PRK13679 hypothetical protein; 22.5 3.6E+02 0.0079 20.7 6.9 84 59-147 10-103 (168)
117 PRK00984 truD tRNA pseudouridi 22.4 3.5E+02 0.0075 24.0 6.7 65 77-144 78-153 (341)
118 cd06194 FNR_N-term_Iron_sulfur 22.4 3.3E+02 0.0072 21.1 6.0 96 10-113 56-158 (222)
119 PF05893 LuxC: Acyl-CoA reduct 22.3 71 0.0015 28.8 2.4 19 50-69 92-112 (399)
120 COG1244 Predicted Fe-S oxidore 21.9 88 0.0019 28.8 2.9 25 96-120 269-293 (358)
121 cd08444 PBP2_Cbl The C-termina 21.8 96 0.0021 22.4 2.7 26 59-89 8-34 (198)
122 PRK00311 panB 3-methyl-2-oxobu 21.8 2.1E+02 0.0046 24.7 5.1 56 96-153 118-177 (264)
123 cd08416 PBP2_MdcR The C-termin 21.8 81 0.0018 22.3 2.2 50 59-117 8-58 (199)
124 TIGR00177 molyb_syn molybdenum 21.8 1.1E+02 0.0025 23.1 3.1 36 31-68 103-141 (144)
125 cd06204 CYPOR NADPH cytochrome 21.8 5.8E+02 0.013 22.8 8.2 90 50-148 269-361 (416)
126 TIGR01709 typeII_sec_gspL gene 21.6 2.3E+02 0.0049 24.8 5.4 55 93-147 304-362 (384)
127 TIGR02793 nikR nickel-responsi 21.5 2.8E+02 0.0061 21.5 5.3 52 92-144 61-115 (129)
128 cd07464 CRD_FZ2 Cysteine-rich 21.4 64 0.0014 25.1 1.7 28 14-41 92-123 (127)
129 PRK04460 nickel responsive reg 21.3 2.8E+02 0.006 21.8 5.3 52 92-144 63-117 (137)
130 PRK13111 trpA tryptophan synth 21.2 42 0.00091 28.6 0.7 32 50-83 16-49 (258)
131 TIGR00484 EF-G translation elo 21.1 3.8E+02 0.0083 25.6 7.1 63 80-147 403-468 (689)
132 cd08415 PBP2_LysR_opines_like 21.1 1.3E+02 0.0027 21.1 3.1 24 96-119 37-60 (196)
133 TIGR00094 tRNA_TruD_broad tRNA 21.1 4.5E+02 0.0097 23.3 7.2 65 77-145 78-154 (387)
134 COG0159 TrpA Tryptophan syntha 21.1 75 0.0016 27.8 2.3 68 50-119 21-103 (265)
135 PRK07560 elongation factor EF- 21.1 3.1E+02 0.0066 26.6 6.5 62 81-147 388-452 (731)
136 cd04887 ACT_MalLac-Enz ACT_Mal 21.1 2.4E+02 0.0052 18.1 6.4 59 88-146 4-64 (74)
137 PF12687 DUF3801: Protein of u 21.0 1.5E+02 0.0032 24.5 3.9 61 81-147 32-94 (204)
138 KOG1014 17 beta-hydroxysteroid 20.9 1.3E+02 0.0027 27.2 3.6 26 123-148 73-98 (312)
139 PRK13239 alkylmercury lyase; P 20.9 48 0.001 28.0 1.0 66 58-130 16-89 (206)
140 cd00488 PCD_DCoH PCD_DCoH: The 20.8 96 0.0021 21.2 2.4 59 83-147 9-72 (75)
141 cd06209 BenDO_FAD_NAD Benzoate 20.7 3E+02 0.0065 21.6 5.5 94 10-113 63-163 (228)
142 cd08422 PBP2_CrgA_like The C-t 20.7 89 0.0019 21.8 2.2 26 59-89 9-35 (197)
143 PF12646 DUF3783: Domain of un 20.6 2.7E+02 0.0058 18.4 5.2 53 49-109 2-55 (58)
144 PF05798 Phage_FRD3: Bacteriop 20.4 91 0.002 22.7 2.2 30 102-134 16-48 (75)
145 TIGR01127 ilvA_1Cterm threonin 20.3 5.7E+02 0.012 22.2 9.2 90 50-145 278-373 (380)
146 cd08434 PBP2_GltC_like The sub 20.3 1.1E+02 0.0024 21.2 2.6 50 59-117 8-58 (195)
147 cd02393 PNPase_KH Polynucleoti 20.2 1.4E+02 0.0031 19.7 3.0 39 98-143 21-60 (61)
148 cd07454 CRD_LIN_17 Cysteine-ri 20.2 54 0.0012 25.3 1.1 23 14-36 93-117 (124)
149 cd08436 PBP2_LTTR_like_3 The C 20.1 1.1E+02 0.0023 21.4 2.5 51 59-118 8-59 (194)
150 PRK02240 GTP cyclohydrolase II 20.0 1.3E+02 0.0027 26.4 3.4 54 92-147 22-80 (254)
No 1
>PRK03670 competence damage-inducible protein A; Provisional
Probab=99.88 E-value=2e-22 Score=168.96 Aligned_cols=109 Identities=14% Similarity=0.133 Sum_probs=94.9
Q ss_pred CCCCc-eeeCCCcccceeEeC----eEEEecCCCCchH-HHHHHH-HHHhHHhCCCccCCceEEEEEEec-CCchhhhhh
Q 031642 29 VPPNC-CITTSCSYLWYIKCQ----NVIILTATNVTEL-DKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQP 100 (156)
Q Consensus 29 ~~~~~-~I~NpvS~APGF~ig----NV~VMAGV~VP~I-~aMl~~-l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~~ 100 (156)
+|.++ -|+||+..||||.++ |||+|+| ||+. +.||+. ++|.|.+ .+++++++.+. .+||+||+.
T Consensus 128 ~P~ga~~l~N~~g~ApG~~~~~~~~~v~~lPG--vP~e~~~M~~~~v~p~l~~------~~~~~~~~~~~~~~Es~la~~ 199 (252)
T PRK03670 128 LPEGAEPLENTEGAAPGAYIEHKGTKIFVLPG--MPREMKAMLEKEVLPRLGE------RKFVQKKFLAEITDESKLAPI 199 (252)
T ss_pred CCCCCEECCCCCCcCceEEEEECCeEEEEeCC--ChHHHHHHHHHHHHHhhcc------CCeEEEEEEeCCCCHHHHHHH
Confidence 55554 589999999999999 8999999 7997 779998 9999743 46889988876 899999999
Q ss_pred HHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhh
Q 031642 101 LSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 101 L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
|++++++|+ |+|||||+..+.++.|++||.|++++++|.++|++.
T Consensus 200 l~~~~~~~~-v~igSyP~~~~~~~~l~~~g~~~~~~~~a~~~l~~~ 244 (252)
T PRK03670 200 LEEALERFN-VKIHSSPKGFGKYIGIIIFAEDEEEIEKAVEFMEER 244 (252)
T ss_pred HHHHHHHCC-ceEecCCCCCCCcEEEEEEECCHHHHHHHHHHHHHh
Confidence 999999996 999999983334678999999999999999999654
No 2
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=99.82 E-value=1.4e-19 Score=153.33 Aligned_cols=117 Identities=21% Similarity=0.241 Sum_probs=101.8
Q ss_pred CCCCc-eeeCCCcccceeEeC----eEEEecCCCCchH-HHHHHHHHHhHHhCCCccCCceEEEEEEec-CCchhhhhhH
Q 031642 29 VPPNC-CITTSCSYLWYIKCQ----NVIILTATNVTEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQPL 101 (156)
Q Consensus 29 ~~~~~-~I~NpvS~APGF~ig----NV~VMAGV~VP~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~~L 101 (156)
+|.+| =|+||++.||||.++ |||+||| ||+. +.||+..++++.++ .-...++.|+++++. .+||.||+.|
T Consensus 121 ~P~Ga~~l~NpvG~APG~~v~~~~~~v~~lPG--vP~Em~~M~e~~~~~~l~~-~~~~~~~~~~~~~~~gi~ES~la~~L 197 (255)
T COG1058 121 LPEGAEVLDNPVGTAPGFVVEGNGKNVYVLPG--VPSEMKPMFENVLLPLLTG-RFPSTKYYSRVLRVFGIGESSLAPTL 197 (255)
T ss_pred CCCCCEeCCCCCCCCCeeEEecCCeEEEEeCC--CCHHHHHHHHHHHHHHhhc-cCCCCceEEEEEEEcCCChHHHHHHH
Confidence 56665 478999999999999 9999999 7996 88999999998766 222378999999998 8999999999
Q ss_pred HHHHHhCCCceeeccccccCCCe-E--EEEEecCHHHHHHHHHHHHhhhc
Q 031642 102 SKLCLEFPDLHIGCYRKSRQGPL-I--ISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 102 ~~Iq~~~Pdv~IGSYP~~~~g~~-~--lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
.+++++||+++|+|||++.+..+ . |..++.|.+.++++.+++.+++.
T Consensus 198 ~~i~~~~~~~~i~s~p~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~i~ 247 (255)
T COG1058 198 KDLQDEQPNVTIASYPKDGEVRLRELVIRAEARDEEEADALLRWLEGRLR 247 (255)
T ss_pred HHHHhcCCCCEEEecCCCCceeccceEEEEecCCHHHHHHHHHHHHHHHH
Confidence 99999999999999998876644 3 55555999999999999998875
No 3
>PRK00549 competence damage-inducible protein A; Provisional
Probab=99.70 E-value=9.3e-17 Score=142.11 Aligned_cols=123 Identities=14% Similarity=0.141 Sum_probs=98.1
Q ss_pred cCCCCce-eeCCCcccceeEeC----eEEEecCCCCchH-HHHHHH-HHHhHHhCCCccCCceEEEEEEec-CCchhhhh
Q 031642 28 KVPPNCC-ITTSCSYLWYIKCQ----NVIILTATNVTEL-DKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQ 99 (156)
Q Consensus 28 ~~~~~~~-I~NpvS~APGF~ig----NV~VMAGV~VP~I-~aMl~~-l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~ 99 (156)
.+|.++- |+||+..||||.++ +||+||| ||+. +.||+. +.|.|+.- +..+.++.++++++. ++|++||+
T Consensus 119 ~~P~ga~~l~N~~GtApG~~~~~~~~~i~~lPG--vP~Em~~m~~~~v~p~l~~~-~~~~~~~~~~~l~~~gi~Es~l~~ 195 (414)
T PRK00549 119 LIPEGATVLPNPVGTAPGMIIEVDGKTYIVLPG--PPSELKPMFEEYVVPYLSSA-KGTGEVLYSRVLRFFGIGESQLAT 195 (414)
T ss_pred cCCCCCEECcCCCCcCCeEEEEECCEEEEEeCC--CcHHHHHHHHHHhHHHHHhh-cCCCceEEEEEEEEcCCCHHHHHH
Confidence 4666665 57999999999998 5999999 7996 779998 88998742 122357899999875 79999999
Q ss_pred hHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHH----HHHhhhccCCcc
Q 031642 100 PLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIE----SLFKKFHRGAFS 153 (156)
Q Consensus 100 ~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~----~l~~~~~~~~f~ 153 (156)
.|++++.+||+++||+||++..-.+.|+++|.|.++++++.+ +|++.+.+..|+
T Consensus 196 ~L~~l~~~~~~v~ig~~~~~~~~~vrl~~~~~~~~~~~~~~~~~~~~i~~~lg~~~~~ 253 (414)
T PRK00549 196 TLRDLIDNQTNPTIAPYAKDGEVTLRLTAKARSEEEAEKLIDPLEEEIRDRVGDYFYG 253 (414)
T ss_pred HHHHHHhcCCCCEEEECccCCEEEEEEEEecCCHHHHHHHHHHHHHHHHHHhccceec
Confidence 999999999999999999763335679999999988776555 455555555553
No 4
>PRK01215 competence damage-inducible protein A; Provisional
Probab=99.52 E-value=1.9e-13 Score=115.28 Aligned_cols=112 Identities=13% Similarity=0.199 Sum_probs=86.5
Q ss_pred cCCCCc-eeeCCCcccceeEeC----eEEEecCCCCchH-HHHHHH-HHHhHHhCCCccCCceEEEEEEec-CCchhhhh
Q 031642 28 KVPPNC-CITTSCSYLWYIKCQ----NVIILTATNVTEL-DKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQ 99 (156)
Q Consensus 28 ~~~~~~-~I~NpvS~APGF~ig----NV~VMAGV~VP~I-~aMl~~-l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~ 99 (156)
-+|.++ .|+||+..||||.+. +||+|+| +|+- ..||+. +.|.|+.= .+..+.++++++. ++|++||+
T Consensus 122 ~~P~ga~~l~N~~Gtapg~~~~~~~~~i~~LPG--~P~e~~~m~~~~v~p~l~~~---~~~~~~~~~~~~~Gi~Es~l~~ 196 (264)
T PRK01215 122 MMPPGAVPLENPVGTAPGILIEHGGKDIVALPG--VPREMEAIFENFVEPLLKNR---PPLKYYEDSILVEGVMESDLAP 196 (264)
T ss_pred eCCCCCEecCCCCCcCCeEEEEECCEEEEEeCC--ChHHHHHHHHHHHHHHHhcc---CCCcEEEEEEEECCCCHHHHHH
Confidence 356554 588999999999875 5999999 7996 779998 77988631 1257889999976 79999999
Q ss_pred hHHHHHHhCCCceeecccc-cc--CCC--eEEEEEecCHHHHHHHHHHHH
Q 031642 100 PLSKLCLEFPDLHIGCYRK-SR--QGP--LIISFEGKDQARIEAAIESLF 144 (156)
Q Consensus 100 ~L~~Iq~~~Pdv~IGSYP~-~~--~g~--~~lVvRG~D~~~l~aA~~~l~ 144 (156)
.|.++..+||++.|||||. +. .+. +.|+.+|.|.+..++..+++.
T Consensus 197 ~l~~l~~~~~~~~~~s~p~~~~~~~~~v~vrl~~~~~~~~~~~~~~~~~~ 246 (264)
T PRK01215 197 YVKELVKKYDRVYVKSHPKGYEVSKPILEIQIAGSGEREEEAKVKVEKVL 246 (264)
T ss_pred HHHHHHHhCCCCEEecCccceecCCCeEEEEEEEecCCHHHHHHHHHHHH
Confidence 9999999999999999965 22 223 357777888777666444333
No 5
>PRK03673 hypothetical protein; Provisional
Probab=99.42 E-value=1.5e-12 Score=115.85 Aligned_cols=121 Identities=18% Similarity=0.124 Sum_probs=96.1
Q ss_pred CCCCc-eeeCCCcccceeEeC----eEEEecCCCCchH-HHHHHH-HHHhHHhCCCccCCceEEEEEEec-CCchhhhhh
Q 031642 29 VPPNC-CITTSCSYLWYIKCQ----NVIILTATNVTEL-DKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQP 100 (156)
Q Consensus 29 ~~~~~-~I~NpvS~APGF~ig----NV~VMAGV~VP~I-~aMl~~-l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~~ 100 (156)
+|.++ .|+||+..||||.++ +||+||| ||+- +.||+. +.|.|+.- +.....+.++++.+. .+|+++++.
T Consensus 121 ~P~ga~~l~N~~GtApG~~~~~~~~~i~~LPG--vP~Emk~M~~~~v~p~L~~~-~~~~~~~~~~~l~~~Gi~ES~l~~~ 197 (396)
T PRK03673 121 LPASAEMIDNPVGTACGFALQLNRCLMFFTPG--VPSEFKVMVEQEILPRLRER-FSLPEPPLCLRLTTFGRSESDLAQS 197 (396)
T ss_pred CCCCCeeccCCCccCCcEEEEECCEEEEEECC--ChHHHHHHHHHHHHHHHHhh-cCCCCceEEEEEEECCCCHHHHHHH
Confidence 45554 578999999999996 3999999 7996 779977 99998752 222235778888765 799999999
Q ss_pred HHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhccCCcc
Q 031642 101 LSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFS 153 (156)
Q Consensus 101 L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f~ 153 (156)
|++++ ..+++.||-|+.+..-.+.|+.++.|.+.++++.++|++.+.+..|.
T Consensus 198 l~~l~-~~~~~~i~~~~~~~~v~vrlt~~~~~~~~~~~~~~~i~~~lg~~v~~ 249 (396)
T PRK03673 198 LDPLP-LPPGVVMGYRSSMPIIELKLTGPASQRQAMEQLWQQVRRVAGQSVIF 249 (396)
T ss_pred HHHHh-cCCCCEEeecCCCCeEEEEEEEccCCHHHHHHHHHHHHHHhCCcEEE
Confidence 99997 45799999887653335678888999877888999999988776664
No 6
>TIGR00200 cinA_nterm competence/damage-inducible protein CinA N-terminal domain. cinA is a DNA damage- or competence-inducible protein that is polycistronic with recA in a number of species
Probab=99.17 E-value=3.2e-10 Score=101.29 Aligned_cols=122 Identities=11% Similarity=0.017 Sum_probs=92.4
Q ss_pred CCCCc-eeeCCCcccceeEe-C--e--EEEecCCCCchH-HHHHHH-HHHhHHhCCCccCCceEEEEEEec-CCchhhhh
Q 031642 29 VPPNC-CITTSCSYLWYIKC-Q--N--VIILTATNVTEL-DKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQ 99 (156)
Q Consensus 29 ~~~~~-~I~NpvS~APGF~i-g--N--V~VMAGV~VP~I-~aMl~~-l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~ 99 (156)
+|.++ .|+||+..||||.+ . | ||.|+| ||+- +.||+. +.|.|+.- +.....+.++++++. .+|+++++
T Consensus 120 ~p~ga~~l~N~~G~APG~~~~~~~~~~i~~LPG--~P~e~~~m~~~~v~p~l~~~-~~~~~~~~~~~~~~~Gi~ES~l~~ 196 (413)
T TIGR00200 120 LPAGAEFLANPVGTAPGMFAVQLNRCLMLFTPG--VPSEFRVMVEHEALPRLRER-FSLPQPIVSLVLRFFGIGESQLEA 196 (413)
T ss_pred CCCCCEECCCCCCCCCeeEEEecCCEEEEEeCC--CcHHHHHHHHHHhhHHHHHh-cCCCceEEEEEEEECCCCHHHHHH
Confidence 45554 67999999999544 3 4 667999 7996 779987 78998642 112246889999876 89999999
Q ss_pred hHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHH----HHHHHHhhhccCCcc
Q 031642 100 PLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEA----AIESLFKKFHRGAFS 153 (156)
Q Consensus 100 ~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~a----A~~~l~~~~~~~~f~ 153 (156)
.|.++..++++..++-|++..+..+.++.++.|.+..++ +.++|++.+.+..|+
T Consensus 197 ~l~~~~~~~~~~~~~~~~~~~~v~vrl~~~~~~~~~a~~~~~~~~~~i~~~lg~~~~~ 254 (413)
T TIGR00200 197 DLADSLDTLTNPTGAPMAYRGEVPLRELKLTGPESEQQRAMEKLWLDIKRVAGQSVIG 254 (413)
T ss_pred HHHHHHhcCCCCeEEEecCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHhCcceec
Confidence 999999999999999999764445679999988776655 555566666655553
No 7
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=97.99 E-value=9.5e-06 Score=64.44 Aligned_cols=45 Identities=16% Similarity=0.189 Sum_probs=38.6
Q ss_pred cCCCCcee-eCCCcccceeEeC----eEEEecCCCCchH-HHHHH-HHHHhHHh
Q 031642 28 KVPPNCCI-TTSCSYLWYIKCQ----NVIILTATNVTEL-DKEWN-CLIELLRS 74 (156)
Q Consensus 28 ~~~~~~~I-~NpvS~APGF~ig----NV~VMAGV~VP~I-~aMl~-~l~p~L~~ 74 (156)
.+|.++-+ .|++..||||.++ |||+|+| ||+. ++||+ .+.|.|+.
T Consensus 118 ~~p~ga~~i~N~~G~apg~~~~~~~~~i~~lPG--~P~e~~~m~~~~~~~~l~~ 169 (170)
T cd00885 118 MLPEGATLLPNPVGTAPGFSVEHNGKNVFLLPG--VPSEMKPMLEEEVLPRLRE 169 (170)
T ss_pred cCCCCCEECcCCCCEeeEEEEEeCCeEEEEECC--ChHHHHHHHHHHHHHHHhc
Confidence 36777765 9999999999999 8999999 7996 88999 68898753
No 8
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=84.10 E-value=2.1 Score=29.88 Aligned_cols=48 Identities=13% Similarity=0.189 Sum_probs=41.0
Q ss_pred HHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhccC
Q 031642 102 SKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRG 150 (156)
Q Consensus 102 ~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~ 150 (156)
.+.+.+.-||++..|-...+|.+.+.++| |...+++|+++..+.+.+.
T Consensus 18 aD~alKaa~V~l~~~~~~~~g~~~~~i~G-~vs~V~~Av~a~~~~~~~~ 65 (75)
T PF00936_consen 18 ADAALKAANVELVEIELICGGKVTVIITG-DVSAVKAAVDAAEEAAGKK 65 (75)
T ss_dssp HHHHHHHSSEEEEEEEEESTTEEEEEEEE-SHHHHHHHHHHHHHHHHHT
T ss_pred HHHHhhcCCEEEEEEEecCCCeEEEEEEE-CHHHHHHHHHHHHHHHhhc
Confidence 45667778999999998886777899999 9999999999999988654
No 9
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=83.80 E-value=2.8 Score=32.09 Aligned_cols=65 Identities=15% Similarity=0.244 Sum_probs=47.0
Q ss_pred EEEEEec-CCchhhhhhHHHHHHhCCCceeecccccc-----------CCCeEEEEEecCHHHHHHHHHHHHhhhccCCc
Q 031642 85 SKSLTTN-LSDLEAAQPLSKLCLEFPDLHIGCYRKSR-----------QGPLIISFEGKDQARIEAAIESLFKKFHRGAF 152 (156)
Q Consensus 85 S~tv~~~-~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~-----------~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f 152 (156)
|--+-+. -+|..|-+ .+++.+--||+|| ||... .|.+.+.+-|.|.+.+++|.+++.+.++..++
T Consensus 26 sIGIlt~~~~e~~iiA--~DeAtKaa~vev~-~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~~~ 102 (103)
T cd07049 26 SLGIITADSDDVTYTA--LDEATKAAEVEVV-YARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENEAY 102 (103)
T ss_pred eEEEEEeCCCcceeeh--hhhhhhhcCeEEE-EEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcccC
Confidence 4444333 46765544 4677788899999 88755 22345669999999999999999999987654
No 10
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=83.15 E-value=12 Score=28.62 Aligned_cols=92 Identities=13% Similarity=0.135 Sum_probs=55.6
Q ss_pred cceeEeCeEEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEE-ecCCchhhhhhHHHHHHhCCCceeecccccc
Q 031642 42 LWYIKCQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLT-TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR 120 (156)
Q Consensus 42 APGF~igNV~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~-~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~ 120 (156)
-||.++-=.||++.+ =|++.. .|. +..+.. -|--+- +.--|+.|.+ + +.+.+--||++|+++.+
T Consensus 8 v~gk~i~~~~vI~~v-~~~l~~-------~l~---~~~~~~-~alGile~~~~~~~i~A-a-D~A~KaA~Vel~~~~~~- 72 (110)
T cd07046 8 VPGKQITLAHLIANP-DPEIYQ-------KLG---LNPGVD-EAIGILTITPSEAAIIA-A-DIATKAADVEIGFLDRF- 72 (110)
T ss_pred cCcceEEEEEEecCC-CHHHHH-------HhC---CCCCcC-ceEEEEEecCHHHHHHH-H-HHHHhhcCeEEEEEeCC-
Confidence 488888888888884 344422 221 111121 122222 2334443433 2 33444459999998744
Q ss_pred CCCeEEEEEecCHHHHHHHHHHHHhhhccCC
Q 031642 121 QGPLIISFEGKDQARIEAAIESLFKKFHRGA 151 (156)
Q Consensus 121 ~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~ 151 (156)
.-.+++.| |.+.+++|+++..+.+++..
T Consensus 73 --~g~vii~G-dvsaV~aAl~a~~~~~~~~~ 100 (110)
T cd07046 73 --SGALVITG-DVSEVESALEAVVDYLRETL 100 (110)
T ss_pred --eEEEEEEE-CHHHHHHHHHHHHHHHhhcc
Confidence 22567999 99999999999999997654
No 11
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=79.98 E-value=15 Score=24.85 Aligned_cols=62 Identities=19% Similarity=0.116 Sum_probs=44.4
Q ss_pred EEEEEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCC-e--EEEEEec-CHHHHHHHHHHHHhh
Q 031642 85 SKSLTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGP-L--IISFEGK-DQARIEAAIESLFKK 146 (156)
Q Consensus 85 S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~-~--~lVvRG~-D~~~l~aA~~~l~~~ 146 (156)
|-.+...-.-|.+|+.|+.+++..=++ +|.|+|..++.. + .+-+.|. +...++++.+.|++.
T Consensus 3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~~~~~~~~~~~l~~l~~~ 69 (80)
T cd04905 3 SIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEGHIEDPNVAEALEELKRL 69 (80)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEECCCCCHHHHHHHHHHHHh
Confidence 334444445688999999998887666 999999754332 2 3556665 678889999888874
No 12
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=71.92 E-value=12 Score=26.18 Aligned_cols=45 Identities=22% Similarity=0.351 Sum_probs=36.7
Q ss_pred HHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 104 LCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 104 Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
...+--||.+-.|....+|.+.+.+.| |...+++|+++..+...+
T Consensus 19 ~a~KaA~V~l~~~~~~~~g~~~~~v~G-dvs~V~~Av~a~~~~~~~ 63 (75)
T smart00877 19 AALKAANVELVGYESIGGGKVTVIITG-DVAAVRAAVEAGLEAAER 63 (75)
T ss_pred HHhhhcCcEEEEEEecCCCEEEEEEEE-cHHHHHHHHHHHHHHHhh
Confidence 344455999999888777777899999 999999999998887753
No 13
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=69.53 E-value=11 Score=35.10 Aligned_cols=61 Identities=20% Similarity=0.177 Sum_probs=49.0
Q ss_pred eEEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeec
Q 031642 49 NVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 115 (156)
Q Consensus 49 NV~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGS 115 (156)
.|+|-.|+-+-.+.+||+.+.++ ++- .|+.--.-.=+-.|+..|+.|++++++.|.+.|=+
T Consensus 318 QVWIAGGIGITPFis~l~~l~~~-~s~-----~~V~L~Y~~~n~e~~~y~~eLr~~~qkl~~~~lHi 378 (438)
T COG4097 318 QVWIAGGIGITPFISMLFTLAER-KSD-----PPVHLFYCSRNWEEALYAEELRALAQKLPNVVLHI 378 (438)
T ss_pred cEEEecCcCcchHHHHHHhhccc-ccC-----CceEEEEEecCCchhHHHHHHHHHHhcCCCeEEEE
Confidence 69999998888889999999983 233 56554443333589999999999999999999988
No 14
>cd06169 BMC Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypo
Probab=68.42 E-value=16 Score=24.41 Aligned_cols=43 Identities=16% Similarity=0.295 Sum_probs=32.6
Q ss_pred HHHHhCCCceeecccccc-CCCeEEEEEecCHHHHHHHHHHHHhh
Q 031642 103 KLCLEFPDLHIGCYRKSR-QGPLIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 103 ~Iq~~~Pdv~IGSYP~~~-~g~~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
+.+.+--+|.+..|-..+ .+...+.++| |...+++|+++.++.
T Consensus 18 D~a~KaA~V~l~~~~~~~~~g~~~~~i~G-~~s~V~~A~~a~~~~ 61 (62)
T cd06169 18 DAAVKAADVELVGIERAGGGGLVTLIIRG-DVSAVKAAVEAAEQA 61 (62)
T ss_pred HHHhhhcCeEEEEEEecCCCcEEEEEEEE-CHHHHHHHHHHHHhh
Confidence 344455599999998887 4556799999 559999999887653
No 15
>PF08753 NikR_C: NikR C terminal nickel binding domain; InterPro: IPR014864 NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This protein corresponds to the C-terminal regulatory domain which contains four nickel binding sites at the tetramer interface []. ; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 2WVB_B 2WVD_C 3QSI_B 3LGH_A 2CAD_A ....
Probab=67.58 E-value=38 Score=23.74 Aligned_cols=55 Identities=20% Similarity=0.246 Sum_probs=42.2
Q ss_pred ecCCchhhhhhHHHHHHhCCCceeeccccccCCCe---EEEEEecCHHHHHHHHHHHHh
Q 031642 90 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL---IISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 90 ~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~---~lVvRG~D~~~l~aA~~~l~~ 145 (156)
-+-...++...|.+||.+|.|+-+.|.=..-++.. .+++||. .+++.+-.++|.+
T Consensus 8 ydh~~~~l~~~l~~iqH~~~~~I~s~~Hvhl~~~~ClEvivv~G~-~~~I~~l~~~l~~ 65 (78)
T PF08753_consen 8 YDHHKRELSERLTEIQHEYHDIIISSLHVHLDHDNCLEVIVVRGP-ADRIKELAEKLRS 65 (78)
T ss_dssp EETTSTTHHHHHHHHHHHTTTCEEEEEEEEESSSEEEEEEEEEEE-HHHHHHHHHHHHT
T ss_pred EcCCchhHHHHHHHHHHhCcCeEEEeeEEeecCCCeEEEEEEEcC-HHHHHHHHHHHhc
Confidence 34456789999999999999999999887776653 4899985 5566666666654
No 16
>PF00994 MoCF_biosynth: Probable molybdopterin binding domain; InterPro: IPR001453 Eukaryotic and prokaryotic molybdoenzymes require a molybdopterin cofactor (MoCF) for their activity. The biosynthesis of this cofactor involves a complex multistep enzymatic pathway. One of the eukaryotic proteins involved in this pathway is the Drosophila protein cinnamon [] which is highly similar to gephyrin, a rat microtubule-associated protein which was thought to anchor the glycine receptor to subsynaptic microtubules. Cinnamon and gephyrin are evolutionary related, in their N-terminal half, to the Escherichia coli MoCF biosynthesis proteins mog/chlG and moaB/chlA2 and, in their C-terminal half, to E. coli moeA/chlE.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 3TCR_B 1O8O_B 1O8Q_G 1EAV_D 1O8N_C 1UUX_A 1UUY_A 2G2C_A 2G4R_C 3K6A_F ....
Probab=65.23 E-value=5.7 Score=29.82 Aligned_cols=34 Identities=18% Similarity=0.008 Sum_probs=27.0
Q ss_pred CCcccceeEeC-----eEEEecCCCCchH-HHHHHHHH-HhHH
Q 031642 38 SCSYLWYIKCQ-----NVIILTATNVTEL-DKEWNCLI-ELLR 73 (156)
Q Consensus 38 pvS~APGF~ig-----NV~VMAGV~VP~I-~aMl~~l~-p~L~ 73 (156)
|...++++.++ .||.|+| .|.- ..|++.++ |.|+
T Consensus 103 p~~~~~~~~~~~~~~~~v~~LPG--~P~~~~~~~~~~v~P~L~ 143 (144)
T PF00994_consen 103 PTGLAPGAYLSRKGGKPVFGLPG--NPVAAKVMLEVLVLPLLR 143 (144)
T ss_dssp TCETEGGGGGTSSETTEEEEE-S--SHHHHHHHHHHHHHHHHH
T ss_pred ccceeeEEEeeCCCCcEEEEcCC--CHHHHHHHHHHHHHHhcC
Confidence 77888888776 5999999 6985 66888888 9875
No 17
>cd07053 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=64.97 E-value=19 Score=25.52 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=34.9
Q ss_pred HHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhccC
Q 031642 103 KLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRG 150 (156)
Q Consensus 103 ~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~ 150 (156)
+...+--+|+|..|-....|.+.++++| |-+.+++|+++-++...+.
T Consensus 18 D~~lKaa~V~l~~~~~~~~Gk~~vii~G-dvsaV~~Av~a~~~~~~~~ 64 (76)
T cd07053 18 DAMLKAANVELVLAKTICPGKYIIIVSG-DVGAVQAAVDAGKEIGGKY 64 (76)
T ss_pred HHHhhcCceEEEEEEeecCCEEEEEEEE-cHHHHHHHHHHHHHHhCCc
Confidence 3444556899999876666777888887 7778888888888776543
No 18
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=60.67 E-value=34 Score=25.78 Aligned_cols=54 Identities=17% Similarity=0.110 Sum_probs=37.6
Q ss_pred CCchhhhhhHHHHHHhCCCceeecc--ccccCCC---eEEEEEecCHHHHHHHHHHHHh
Q 031642 92 LSDLEAAQPLSKLCLEFPDLHIGCY--RKSRQGP---LIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 92 ~~Eg~IA~~L~~Iq~~~Pdv~IGSY--P~~~~g~---~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
.+++-+-+.+.-+|.--|+.+.+-- .-+..|. +.|.+|.+|.+++|+.-.+|.+
T Consensus 24 a~~~l~~~vv~vvqr~ap~~~~~~~~~k~SSkGnY~svsI~i~A~~~EQ~e~ly~eL~~ 82 (90)
T COG2921 24 AGPELEDQVVEVVQRHAPGDYTPRVSWKPSSKGNYLSVSITIRATNIEQVEALYRELRK 82 (90)
T ss_pred cchhHHHHHHHHHHHHCCcccCceeeeccCCCCceEEEEEEEEECCHHHHHHHHHHHhh
Confidence 4455444555666666699888765 2222343 4699999999999999888875
No 19
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=60.02 E-value=39 Score=20.99 Aligned_cols=55 Identities=22% Similarity=0.213 Sum_probs=35.3
Q ss_pred EEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCCeEEEEEecCHHHHHHHHHHHHh
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
+...-..|.+++.++.|++..=++ ++..++....+...++++=.+ .+.+.+.|++
T Consensus 4 v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~---~~~~~~~L~~ 59 (65)
T cd04882 4 VEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTED---IEKAIEVLQE 59 (65)
T ss_pred EEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCC---HHHHHHHHHH
Confidence 455667899999999999887666 455555322344456666665 4455555544
No 20
>KOG0070 consensus GTP-binding ADP-ribosylation factor Arf1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=59.99 E-value=12 Score=31.04 Aligned_cols=27 Identities=33% Similarity=0.484 Sum_probs=24.6
Q ss_pred CeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 123 PLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 123 ~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
++..|+.|.|.+|++.|.++|..++..
T Consensus 87 ~lIfVvDS~Dr~Ri~eak~eL~~~l~~ 113 (181)
T KOG0070|consen 87 GLIFVVDSSDRERIEEAKEELHRMLAE 113 (181)
T ss_pred EEEEEEeCCcHHHHHHHHHHHHHHHcC
Confidence 467999999999999999999999864
No 21
>COG3622 Hfi Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]
Probab=57.17 E-value=9.8 Score=33.43 Aligned_cols=78 Identities=14% Similarity=0.170 Sum_probs=52.5
Q ss_pred cceeEeCeEEEecCCCCch-H--HHHHHHHHHhHHhCC--C-ccCCceEEE-----------------------------
Q 031642 42 LWYIKCQNVIILTATNVTE-L--DKEWNCLIELLRSGG--L-SLMEPYTSK----------------------------- 86 (156)
Q Consensus 42 APGF~igNV~VMAGV~VP~-I--~aMl~~l~p~L~~G~--L-~~gap~~S~----------------------------- 86 (156)
|=+.-+.+||+|||+ +|. . .+|+......|+--. | ..|..++-+
T Consensus 94 a~aLg~~~vh~mag~-~p~~~~~~~~~~t~venLr~aAd~l~~~gi~~liEplN~~d~PG~~l~~~~~al~li~~V~~~N 172 (260)
T COG3622 94 ATALGCKQVHCLAGI-PPEGVDTEAMWATFVENLRYAADLLAAEGIRLLIEPLNLRDMPGYFLTSQEQALALIDEVGRPN 172 (260)
T ss_pred HHHhCCCceeeeecC-CCCCccHHHHHHHHHHHHHHHHHHHHhcCCEEEEecCCCCCCCCcccccHHHHHHHHHHhCCCC
Confidence 334556799999996 545 4 558877777664321 0 111222211
Q ss_pred ------EEEecCCchhhhhhHHHHHHhCCCceeecccccc
Q 031642 87 ------SLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR 120 (156)
Q Consensus 87 ------tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~ 120 (156)
.-++...||+++.-|++.....-+|.|-|=|-..
T Consensus 173 l~lq~D~YH~Q~~eGnL~~~lr~~~~~ighvQiAdvP~Rh 212 (260)
T COG3622 173 LFLQLDLYHAQIMEGNLTRLLREYLPKIGHVQIADVPGRH 212 (260)
T ss_pred eEeehhHHHHHHhccHHHHHHHHhhhhhceeeecCCCCCC
Confidence 1234568999999999999999999999999655
No 22
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=55.80 E-value=65 Score=22.15 Aligned_cols=64 Identities=20% Similarity=0.303 Sum_probs=51.0
Q ss_pred CceEEEEEEecC--CchhhhhhHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 81 EPYTSKSLTTNL--SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 81 ap~~S~tv~~~~--~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
.|+++.+|...- .+..+.+.|.+|..+-|.+.+.- .+..-.+++.|.=.-.++-+.+.|++.+.
T Consensus 3 ~Pv~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~~----d~et~e~~l~g~Gelhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 3 PPVLSVAIEPKNKEDEPKLSEALQKLSEEDPSLRVER----DEETGELILSGMGELHLEVLLERLKRRFG 68 (75)
T ss_dssp S-SEEEEEEESSHHHHHHHHHHHHHHHHH-TTSEEEE----ETTTSEEEEEESSHHHHHHHHHHHHHTTC
T ss_pred CCeEEEEEEECCHhHHHHHHHHHHHHHhcCCeEEEEE----cchhceEEEEECCHHHHHHHHHHHHHHHC
Confidence 688999998773 78889999999999999998632 12223599999999999999999998874
No 23
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=55.38 E-value=67 Score=22.26 Aligned_cols=51 Identities=8% Similarity=0.028 Sum_probs=36.0
Q ss_pred CchhhhhhHHHHHHhCCCceeeccccccCC--CeEEEEEecC-HHHHHHHHHHHHh
Q 031642 93 SDLEAAQPLSKLCLEFPDLHIGCYRKSRQG--PLIISFEGKD-QARIEAAIESLFK 145 (156)
Q Consensus 93 ~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g--~~~lVvRG~D-~~~l~aA~~~l~~ 145 (156)
.=|.++..|+.|. ..++..=.|.+...+ .+.++++-+| .+.++++.+.|++
T Consensus 11 ~PG~L~~ll~~l~--~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~ 64 (85)
T cd04906 11 RPGSFKKFCELIG--PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKS 64 (85)
T ss_pred CCcHHHHHHHHhC--CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHH
Confidence 3478888888777 345554456554322 4568899999 9999998888876
No 24
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=53.20 E-value=69 Score=21.67 Aligned_cols=55 Identities=18% Similarity=0.079 Sum_probs=41.9
Q ss_pred CCchhhhhhHHHHHHhC-CCceeeccccccC-CC--eEEEEEecCHHHHHHHHHHHHhhh
Q 031642 92 LSDLEAAQPLSKLCLEF-PDLHIGCYRKSRQ-GP--LIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 92 ~~Eg~IA~~L~~Iq~~~-Pdv~IGSYP~~~~-g~--~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
-.-|.+++.|+.+++.. .=..|=|.|.... +. |-|-+.| +.+.+++|.++|++..
T Consensus 9 ~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~-~~~~~~~~l~~L~~~~ 67 (74)
T cd04904 9 EEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEV-DRGDLDQLISSLRRVV 67 (74)
T ss_pred CCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEc-ChHHHHHHHHHHHHhc
Confidence 35688999999999886 5678999996543 33 3588889 4556999999998754
No 25
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=52.68 E-value=39 Score=23.26 Aligned_cols=31 Identities=6% Similarity=0.102 Sum_probs=26.4
Q ss_pred CCCeEEEEEecCHHHHHHHHHHHHhhhccCC
Q 031642 121 QGPLIISFEGKDQARIEAAIESLFKKFHRGA 151 (156)
Q Consensus 121 ~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~ 151 (156)
++.|.+++.+.|.+.++...++|.+.+....
T Consensus 83 ~~~f~ii~~~~~~~~~~~~~~~l~~~~~~~~ 113 (163)
T smart00267 83 GDEFALLLPETSLEEAIALAERILQQLREPI 113 (163)
T ss_pred CceEEEEecCCCHHHHHHHHHHHHHHHhCcc
Confidence 5679999999999999999999998886543
No 26
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=52.12 E-value=31 Score=24.41 Aligned_cols=47 Identities=9% Similarity=0.239 Sum_probs=35.3
Q ss_pred hhhhhhHHHHHHhCCCcee-eccccccCCCeEEEEEecCHHHHHHHHHHHHh
Q 031642 95 LEAAQPLSKLCLEFPDLHI-GCYRKSRQGPLIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 95 g~IA~~L~~Iq~~~Pdv~I-GSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
+.+++..++ -+++|+++| |+ ..+|++.+|+.+.|...+.+..++|++
T Consensus 15 ~~~~~v~~~-l~~~~gvEVh~~---~~~GKiVVtiE~~~~~~~~~~~~~i~~ 62 (79)
T PF03927_consen 15 ERLEEVAEA-LAAIPGVEVHAV---DEDGKIVVTIEAESSEEEVDLIDAINA 62 (79)
T ss_dssp CCHHHHHHH-HCCSTTEEEEEE---ETTTEEEEEEEESSHHHHHHHHHHHCC
T ss_pred hhHHHHHHH-HHcCCCcEEEee---CCCCeEEEEEEeCChHHHHHHHHHHHc
Confidence 355554444 457899998 43 335889999999999999999998865
No 27
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=51.58 E-value=58 Score=27.69 Aligned_cols=56 Identities=18% Similarity=0.170 Sum_probs=36.9
Q ss_pred eEeCeEEEecCCCCchH---HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCcee
Q 031642 45 IKCQNVIILTATNVTEL---DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHI 113 (156)
Q Consensus 45 F~igNV~VMAGV~VP~I---~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~I 113 (156)
..=++|+|+.. -+ ..|...+.-..+.| |..=++.=.-...+|| +.+++++||||.|
T Consensus 122 ~~~~~viv~DP----MLATG~s~i~ai~~L~~~G----~~~~I~~v~~vAapeG-----i~~v~~~~p~v~I 180 (210)
T COG0035 122 IDERTVIVLDP----MLATGGSAIAAIDLLKKRG----GPKNIKVVSLVAAPEG-----IKAVEKAHPDVEI 180 (210)
T ss_pred ccCCeEEEECc----hhhccHhHHHHHHHHHHhC----CCceEEEEEEEecHHH-----HHHHHHhCCCCeE
Confidence 45578888875 44 33777777555443 1433333333556787 8999999999987
No 28
>cd02575 PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Probab=50.51 E-value=65 Score=27.77 Aligned_cols=66 Identities=18% Similarity=0.287 Sum_probs=43.5
Q ss_pred CccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccC---------CCeEEEEEecC--HHHHHHHHHHHHh
Q 031642 77 LSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ---------GPLIISFEGKD--QARIEAAIESLFK 145 (156)
Q Consensus 77 L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~---------g~~~lVvRG~D--~~~l~aA~~~l~~ 145 (156)
|+.-.-+..+.+.+..+ +...+.+.++ ..+++.|+.+=+... .+|.|++|+.+ .+.++++.++|.+
T Consensus 61 lKDk~AvT~Q~~sv~~~-~~~~~~~~~~--~~~~i~i~~~~~~~~kL~~G~L~GNrF~I~lR~v~~~~~~l~~~l~~i~~ 137 (253)
T cd02575 61 LKDRHAVTTQWFSVHLP-GKEAPDLSAL--QLEGVKILEVTRHNRKLRRGHLKGNRFVIRLRGVSGNADKLEQRLETIAQ 137 (253)
T ss_pred cccCceeeEEEEEEEcC-ccCchhHHhc--cCCCeEEEEEEecCCCcCCCcccCCEEEEEEecCCCCHHHHHHHHHHHHh
Confidence 66666677776666543 2333344444 378999998865442 14789999985 6777787777764
No 29
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=49.99 E-value=44 Score=22.78 Aligned_cols=48 Identities=15% Similarity=-0.013 Sum_probs=32.6
Q ss_pred hhhhHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 97 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 97 IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
+++.|.++-..|.+. ++. +.++.|.+++.+.+.+++.+++.++.+.+.
T Consensus 31 ~~~~l~~~~~~~~~~-~~r---~~~d~f~~l~~~~~~~~~~~~~~~i~~~~~ 78 (133)
T cd07556 31 LAGRFDSLIRRSGDL-KIK---TIGDEFMVVSGLDHPAAAVAFAEDMREAVS 78 (133)
T ss_pred HHHHHHHHHHHcCcE-EEE---eecceEEEEECchHHHHHHHHHHHHHHHHH
Confidence 455555555554443 443 336678899998888888888888888764
No 30
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=48.27 E-value=64 Score=19.88 Aligned_cols=59 Identities=15% Similarity=0.168 Sum_probs=40.1
Q ss_pred EEecCCchhhhhhHHHHHHhCCCc-eeecccccc---CCC--eEEEEEecCHHHHHHHHHHHHhh
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSR---QGP--LIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~---~g~--~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
+.+.-.-|.+++.++.|.+..=++ +|-+++... ++. +.+.+...|.+.+++.+++|++.
T Consensus 3 v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~~ 67 (73)
T cd04886 3 VELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALREA 67 (73)
T ss_pred EEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHHc
Confidence 344556788999888887775554 444544332 232 35888889989999988888763
No 31
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=47.52 E-value=34 Score=26.84 Aligned_cols=60 Identities=18% Similarity=0.154 Sum_probs=38.9
Q ss_pred ecCCchhhhhhHHHHHHhCCCcee-ecccc-ccCC------------CeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 90 TNLSDLEAAQPLSKLCLEFPDLHI-GCYRK-SRQG------------PLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 90 ~~~~Eg~IA~~L~~Iq~~~Pdv~I-GSYP~-~~~g------------~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
..-.|+.++...+.++++||++.| |.|+- |++. +..||+-|--.-+=|.=+.+.++.+..
T Consensus 54 lG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~vglG~PkQE~~~~~~~~~l~~ 127 (172)
T PF03808_consen 54 LGGSEEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINASGPDIVFVGLGAPKQERWIARHRQRLPA 127 (172)
T ss_pred EeCCHHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCC
Confidence 445788899999999999999998 67753 3211 122555555555555555555555544
No 32
>KOG0071 consensus GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.30 E-value=21 Score=29.68 Aligned_cols=28 Identities=29% Similarity=0.405 Sum_probs=25.1
Q ss_pred CeEEEEEecCHHHHHHHHHHHHhhhccC
Q 031642 123 PLIISFEGKDQARIEAAIESLFKKFHRG 150 (156)
Q Consensus 123 ~~~lVvRG~D~~~l~aA~~~l~~~~~~~ 150 (156)
++.+|+.+.|.+++++|..+|+..+..-
T Consensus 87 glIFV~Dsa~~dr~eeAr~ELh~ii~~~ 114 (180)
T KOG0071|consen 87 GLIFVVDSADRDRIEEARNELHRIINDR 114 (180)
T ss_pred eEEEEEeccchhhHHHHHHHHHHHhCCH
Confidence 5789999999999999999999988643
No 33
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=47.23 E-value=68 Score=19.86 Aligned_cols=57 Identities=14% Similarity=0.126 Sum_probs=35.4
Q ss_pred EEEEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCC--eEEEEEecCHHHHHHHHHHHHh
Q 031642 86 KSLTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGP--LIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 86 ~tv~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~--~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
-++...-.+|.+++.+..+++..-++ ++-.++.. ++. +.+.+++. +.++++.++|++
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~-~~~~~~~i~~~~~--~~~~~~~~~L~~ 62 (72)
T cd04874 3 LSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIER-EGKARIYMELEGV--GDIEELVEELRS 62 (72)
T ss_pred EEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccC-CCeEEEEEEEecc--ccHHHHHHHHhC
Confidence 34555667899999999998876555 34455542 232 34666665 555566666554
No 34
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=46.67 E-value=79 Score=20.47 Aligned_cols=54 Identities=17% Similarity=-0.017 Sum_probs=35.9
Q ss_pred EEEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCCeEEEEEecCHHHHHHHHHHHHh
Q 031642 87 SLTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 87 tv~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
++...-.-|.+|+.++.+.++.=++ ++++++.. +...+.++..|. ++|.+.|++
T Consensus 5 ~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~--~~~~~rl~~~~~---~~~~~~L~~ 59 (66)
T cd04908 5 SVFLENKPGRLAAVTEILSEAGINIRALSIADTS--EFGILRLIVSDP---DKAKEALKE 59 (66)
T ss_pred EEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecC--CCCEEEEEECCH---HHHHHHHHH
Confidence 4556667899999999998888777 78776632 244566666553 344444443
No 35
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.80 E-value=84 Score=20.55 Aligned_cols=59 Identities=8% Similarity=-0.009 Sum_probs=37.6
Q ss_pred EEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCC---eEEEEEecCHHHHHHHHHHHHhhhccC
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGP---LIISFEGKDQARIEAAIESLFKKFHRG 150 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~---~~lVvRG~D~~~l~aA~~~l~~~~~~~ 150 (156)
+...-.=|.+|+.++-|.+..=++ ++..++...+.+ ..+.+.+.+... .++|.+.|+++
T Consensus 4 v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~e~~~~----~~~i~~~L~~~ 66 (72)
T cd04884 4 FLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTPMDRSK----ENELIEELKAK 66 (72)
T ss_pred EEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEEecchH----HHHHHHHHhCc
Confidence 444556789999999998888887 888888643332 335555644444 44455555444
No 36
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=44.88 E-value=89 Score=20.59 Aligned_cols=55 Identities=18% Similarity=0.181 Sum_probs=42.7
Q ss_pred CchhhhhhHHHHHHhC-CCceeecccccc-CCC--eEEEEEec-CHHHHHHHHHHHHhhh
Q 031642 93 SDLEAAQPLSKLCLEF-PDLHIGCYRKSR-QGP--LIISFEGK-DQARIEAAIESLFKKF 147 (156)
Q Consensus 93 ~Eg~IA~~L~~Iq~~~-Pdv~IGSYP~~~-~g~--~~lVvRG~-D~~~l~aA~~~l~~~~ 147 (156)
.-|.+++.|+.+++.. .=++|=|+|... .+. |.|-+.|. +...++++.++|++..
T Consensus 9 ~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~~ 68 (75)
T cd04880 9 KPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRVT 68 (75)
T ss_pred cCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhC
Confidence 4688999999999886 556899999665 333 35777786 7899999999998754
No 37
>cd07045 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carbox
Probab=44.66 E-value=76 Score=22.74 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=34.3
Q ss_pred HHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 103 KLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 103 ~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
+...+--+|+|-.|-...+|.+.++++| |.+.+++|+++.++...+
T Consensus 18 D~~lKaA~V~l~~~~~~~~gk~~vii~G-dvsaV~~Av~a~~~~~~~ 63 (84)
T cd07045 18 DAALKAANVTLVGYEKVGGGLVTVKITG-DVAAVKAAVEAGAAAAER 63 (84)
T ss_pred HHHhhhCCeEEEEEEecCCcEEEEEEEE-cHHHHHHHHHHHHHHHhc
Confidence 3445566899998887755556677777 778889999888887764
No 38
>PF11209 DUF2993: Protein of unknown function (DUF2993); InterPro: IPR021373 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=44.15 E-value=19 Score=28.36 Aligned_cols=40 Identities=20% Similarity=0.331 Sum_probs=26.4
Q ss_pred CchhhhhhHHHHH--HhCCCceeeccccc-c--CCCe-EEEEEecC
Q 031642 93 SDLEAAQPLSKLC--LEFPDLHIGCYRKS-R--QGPL-IISFEGKD 132 (156)
Q Consensus 93 ~Eg~IA~~L~~Iq--~~~Pdv~IGSYP~~-~--~g~~-~lVvRG~D 132 (156)
-|..++..|++-. .+-|+|+||..||. . .|.+ .+.+.+++
T Consensus 10 ~e~~i~~~l~~~~~~~~~~~V~i~g~P~l~qll~G~~~~v~v~~~~ 55 (225)
T PF11209_consen 10 AEKQIADALRAQLDLAEDPEVSIGGFPFLTQLLGGRLDSVTVDAPG 55 (225)
T ss_pred HHHHHHHHHHHhcCCCCCceEEEcCcCcHHHHhCCEeCeEEEEeCC
Confidence 4666777776555 56799999999975 2 5554 34444444
No 39
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=42.62 E-value=90 Score=19.97 Aligned_cols=59 Identities=22% Similarity=0.031 Sum_probs=38.1
Q ss_pred EEEEEecCCchhhhhhHHHHHHhCCCc-eeeccccccC--CCeEEEEEecCHHHHHHHHHHHHh
Q 031642 85 SKSLTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQ--GPLIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 85 S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~--g~~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
.-++...-.-|.+++.++.+++..-++ ++-.++...+ +...+++|. ++..+++.+.|++
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~--~~~~~~~~~~L~~ 64 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKT--QEDRERAKEILKE 64 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECC--HHHHHHHHHHHHH
Confidence 445556667788999999998888887 4544453211 224577773 3466777776665
No 40
>COG1925 FruB Phosphotransferase system, HPr-related proteins [Carbohydrate transport and metabolism]
Probab=40.79 E-value=36 Score=24.97 Aligned_cols=28 Identities=32% Similarity=0.421 Sum_probs=21.1
Q ss_pred eEEEEEecCHHHHHHHHHHHHhhhccCCccc
Q 031642 124 LIISFEGKDQARIEAAIESLFKKFHRGAFSE 154 (156)
Q Consensus 124 ~~lVvRG~D~~~l~aA~~~l~~~~~~~~f~~ 154 (156)
+.|..+|.|+++ |+++|.++|..+.|-|
T Consensus 61 i~i~a~G~de~~---Al~aL~~li~~~~~~e 88 (88)
T COG1925 61 IELSAEGEDEEE---ALEALSELIESGFGEE 88 (88)
T ss_pred EEEEEeCccHHH---HHHHHHHHHHhhccCC
Confidence 459999999875 7778888887666643
No 41
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=40.16 E-value=1.4e+02 Score=21.55 Aligned_cols=64 Identities=16% Similarity=0.076 Sum_probs=46.7
Q ss_pred EEEEEecCCchhhhhhHHHHHHhC-CCceeeccccccC-CC--eEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 85 SKSLTTNLSDLEAAQPLSKLCLEF-PDLHIGCYRKSRQ-GP--LIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 85 S~tv~~~~~Eg~IA~~L~~Iq~~~-Pdv~IGSYP~~~~-g~--~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
|--+.+.-.-|.++..|..+++.. .=..|-|.|.... +. |-|=+.|.+..++++|.++|++.+.
T Consensus 16 slif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg~~~~~~~~~l~~L~~~~~ 83 (90)
T cd04931 16 SLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDKKSAPALDPIIKSLRNDIG 83 (90)
T ss_pred EEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCCCHHHHHHHHHHHHHhC
Confidence 333333445688999999999875 6678999996543 33 4578888766899999999988653
No 42
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=40.03 E-value=90 Score=19.86 Aligned_cols=58 Identities=19% Similarity=0.056 Sum_probs=34.7
Q ss_pred ecCCchhhhhhHHHHHHhCCCceeeccccccCCCeEEEEEe-cCHHHHHHHHHHHH-hhhc
Q 031642 90 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEG-KDQARIEAAIESLF-KKFH 148 (156)
Q Consensus 90 ~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG-~D~~~l~aA~~~l~-~~~~ 148 (156)
+...+.+....+.+|+..+++..+ .+....++-+.|.+-. .|.++.+++.++|+ +...
T Consensus 11 s~~~~~~A~~~~~~l~~~g~~~~~-~~~~~~~~~yrV~~G~f~~~~~A~~~~~~l~~~~~~ 70 (76)
T PF05036_consen 11 SFSSEENAERLLAKLKKKGPDAYV-VQVSKGGPWYRVRVGPFSSREEAEAALRKLKKAAGP 70 (76)
T ss_dssp EES-HHHHHHHHHHHHHHT------EEEEEETTCEEEEECCECTCCHHHHHHHHHHHHHTS
T ss_pred EcCCHHHHHHHHHHHHhcCCCcce-EEEecCCceEEEEECCCCCHHHHHHHHHHHhHhhCC
Confidence 345677788889999999999887 3332222334566644 67788888999998 4443
No 43
>cd01840 SGNH_hydrolase_yrhL_like yrhL-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 the Ser-His-Asp(Glu) triad found in other serine hydrolases. Most members of this sub-family appear to co-occur with N-terminal acyltransferase domains. Might be involved in lipid metabolism.
Probab=39.59 E-value=96 Score=23.03 Aligned_cols=62 Identities=13% Similarity=0.076 Sum_probs=42.8
Q ss_pred eCeEEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEec-CCchhhhhhHHHHHHhCCCcee
Q 031642 47 CQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQPLSKLCLEFPDLHI 113 (156)
Q Consensus 47 igNV~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~~L~~Iq~~~Pdv~I 113 (156)
-+.|+|+=|+|=...++.++.++..++.| ++++--+.... ....++.+.+.+++++||++.+
T Consensus 51 ~d~vvi~lGtNd~~~~~nl~~ii~~~~~~-----~~ivlv~~~~~~~~~~~~n~~~~~~a~~~~~v~~ 113 (150)
T cd01840 51 RKTVVIGLGTNGPFTKDQLDELLDALGPD-----RQVYLVNPHVPRPWEPDVNAYLLDAAKKYKNVTI 113 (150)
T ss_pred CCeEEEEecCCCCCCHHHHHHHHHHcCCC-----CEEEEEECCCCcchHHHHHHHHHHHHHHCCCcEE
Confidence 36789999987654566777777776444 56655555432 2345677889999999998775
No 44
>PRK00907 hypothetical protein; Provisional
Probab=39.32 E-value=1.6e+02 Score=21.81 Aligned_cols=54 Identities=17% Similarity=0.108 Sum_probs=34.8
Q ss_pred CCchhhhhhHHHHHHhCCCceeecc--ccccCCCe---EEEEEecCHHHHHHHHHHHHh
Q 031642 92 LSDLEAAQPLSKLCLEFPDLHIGCY--RKSRQGPL---IISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 92 ~~Eg~IA~~L~~Iq~~~Pdv~IGSY--P~~~~g~~---~lVvRG~D~~~l~aA~~~l~~ 145 (156)
..++=.++.++-+++..|+.+-.+. .-++.|.+ .+.++.++.+++++--++|.+
T Consensus 26 a~~~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~GkY~Svtv~i~ats~eQld~iY~~L~~ 84 (92)
T PRK00907 26 AERGLETELPRLLAATGVELLQERISWKHSSSGKYVSVRIGFRAESREQYDAAHQALRD 84 (92)
T ss_pred CchhHHHHHHHHHHHhCCCCCcCcEEeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 3455445555555666687654443 22445654 599999999999987776654
No 45
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=39.19 E-value=87 Score=27.33 Aligned_cols=37 Identities=19% Similarity=0.264 Sum_probs=30.1
Q ss_pred CceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccc
Q 031642 81 EPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 117 (156)
Q Consensus 81 ap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP 117 (156)
.-++..-..-...|.+.....+.|+.+||+++|..|+
T Consensus 264 ~elvTi~~G~~~~~~~a~~l~~~l~~~~p~~eve~~~ 300 (313)
T PF13684_consen 264 GELVTIYYGEDVSEEEAEALAEFLEEKYPDVEVEVYD 300 (313)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHhCCeEEEEEE
Confidence 6666666555578888888888999999999999987
No 46
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=37.56 E-value=1.3e+02 Score=24.08 Aligned_cols=59 Identities=10% Similarity=-0.007 Sum_probs=40.2
Q ss_pred EecCCchhhhhhHHHHHHhCCCc-eeeccccccCCC--eEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 89 TTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGP--LIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 89 ~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~--~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
.+.-.=|.++...+-+..+.=++ |+..+|...++- +.+++.| |...+++-.+.|.+++.
T Consensus 7 ~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~-d~~~i~qi~kQl~Kli~ 68 (157)
T TIGR00119 7 LVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVG-DDKVLEQITKQLNKLVD 68 (157)
T ss_pred EEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEEC-CHHHHHHHHHHHhcCcc
Confidence 34444566666666666655555 788888643442 3578888 88999999999988764
No 47
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=37.48 E-value=14 Score=25.56 Aligned_cols=34 Identities=24% Similarity=0.238 Sum_probs=23.1
Q ss_pred hhhhhhHHHHHHhCCC--ceeeccccccCCCeEEEEE
Q 031642 95 LEAAQPLSKLCLEFPD--LHIGCYRKSRQGPLIISFE 129 (156)
Q Consensus 95 g~IA~~L~~Iq~~~Pd--v~IGSYP~~~~g~~~lVvR 129 (156)
...+..-.+|..+||| +++-.+|- +.|.|.|.+.
T Consensus 13 ~Ra~~l~q~L~~~Fp~~~v~~~~~~~-~~G~Fev~~~ 48 (72)
T TIGR02174 13 PRAAWLKQELLEEFPDLEIEGENTPP-TTGAFEVTVN 48 (72)
T ss_pred HHHHHHHHHHHHHCCCCeeEEeeecC-CCcEEEEEEC
Confidence 3445566789999999 77777773 3566666553
No 48
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=37.18 E-value=57 Score=28.00 Aligned_cols=49 Identities=16% Similarity=0.268 Sum_probs=38.0
Q ss_pred HHHHHHhCCCceeecccccc-----------CCCeEEEEEecCHHHHHHHHHHHHhhhccC
Q 031642 101 LSKLCLEFPDLHIGCYRKSR-----------QGPLIISFEGKDQARIEAAIESLFKKFHRG 150 (156)
Q Consensus 101 L~~Iq~~~Pdv~IGSYP~~~-----------~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~ 150 (156)
-.+.+.+--+|+|+ |+... .|.+.+++-|.|.+.+++|++...+.+++.
T Consensus 50 AaDeA~KAAnVevv-~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~ 109 (217)
T PRK15405 50 ALDEATKQAMVEVV-YARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENG 109 (217)
T ss_pred HHHHHHhhcceEEE-EEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhh
Confidence 34566667889999 55544 345678999999999999999999988753
No 49
>PF03135 CagE_TrbE_VirB: CagE, TrbE, VirB family, component of type IV transporter system; InterPro: IPR018145 This domain is found in (amongst others): the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration []. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro []. Similar type IV transport systems are also found in other bacteria. This domain is also found in proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.; GO: 0005524 ATP binding
Probab=36.99 E-value=51 Score=26.11 Aligned_cols=30 Identities=10% Similarity=0.212 Sum_probs=25.9
Q ss_pred eEEEEEecCHHHHHHHHHHHHhhhccCCcc
Q 031642 124 LIISFEGKDQARIEAAIESLFKKFHRGAFS 153 (156)
Q Consensus 124 ~~lVvRG~D~~~l~aA~~~l~~~~~~~~f~ 153 (156)
+.|+++|.|.+.++.++.++.+.|..--|.
T Consensus 151 ~~i~v~~~~~~~l~~~~~~v~~~l~~~G~~ 180 (205)
T PF03135_consen 151 FTIVVFADDPEELDDKVAEVSSALNNLGFV 180 (205)
T ss_pred EEEEEEcCCHHHHHHHHHHHHHHHHHCCCE
Confidence 469999999999999999999998755553
No 50
>smart00107 BTK Bruton's tyrosine kinase Cys-rich motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
Probab=36.70 E-value=16 Score=22.93 Aligned_cols=10 Identities=40% Similarity=1.458 Sum_probs=8.0
Q ss_pred CceeeeccCC
Q 031642 21 PRWLCCRKVP 30 (156)
Q Consensus 21 ~~~~~~~~~~ 30 (156)
-+|+||....
T Consensus 16 G~W~CC~q~~ 25 (36)
T smart00107 16 GKWLCCQQSE 25 (36)
T ss_pred CeEccCCCcC
Confidence 5799998755
No 51
>cd02576 PseudoU_synth_ScPUS7 PseudoU_synth_ScPUS7: Pseudouridine synthase, TruD family. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=36.57 E-value=1.5e+02 Score=26.21 Aligned_cols=66 Identities=17% Similarity=0.218 Sum_probs=44.4
Q ss_pred CccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccC---------CCeEEEEEecC---HHHHHHHHHHHH
Q 031642 77 LSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ---------GPLIISFEGKD---QARIEAAIESLF 144 (156)
Q Consensus 77 L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~---------g~~~lVvRG~D---~~~l~aA~~~l~ 144 (156)
++.-.-+..+.+.+.. ...+.|.++....+++.|+..-+.+. ..|.|++|+.+ .+.++++.++|+
T Consensus 65 ~KDk~AvT~Q~vsi~~---~~~~~l~~~~~~~~~i~i~~~~~~~~~l~~G~l~GN~F~I~lR~v~~~~~~~l~~~l~~l~ 141 (371)
T cd02576 65 TKDKRAVTVQRVSVKK---VTASRLKALNSKLRGIRVGNFEYKDEPLKLGDLKGNEFTIVIRNVKADSEELIKQALESLK 141 (371)
T ss_pred cccccceeEEEEEecC---CCHHHHHHHhccCCCeEEEeeEecCCCcCcccCCCCeEEEEEccCCcccHHHHHHHHHHHH
Confidence 6666667777666543 23445777776678999998775442 14789999985 566777777665
Q ss_pred h
Q 031642 145 K 145 (156)
Q Consensus 145 ~ 145 (156)
+
T Consensus 142 ~ 142 (371)
T cd02576 142 E 142 (371)
T ss_pred h
Confidence 4
No 52
>PRK05713 hypothetical protein; Provisional
Probab=35.99 E-value=1.1e+02 Score=25.89 Aligned_cols=93 Identities=14% Similarity=0.073 Sum_probs=55.0
Q ss_pred hHHhHHhcCcCCceeeeccCCCCceeeCCCcccce----eEe----Ce-EEEecCCCCchHHHHHHHHHHhHHhCCCccC
Q 031642 10 LVVRRLLGYKYPRWLCCRKVPPNCCITTSCSYLWY----IKC----QN-VIILTATNVTELDKEWNCLIELLRSGGLSLM 80 (156)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~I~NpvS~APG----F~i----gN-V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~g 80 (156)
+.+|+.-+=++-.|| .+..++.-|. ++...| |.- .+ |+|-+|+-+.-+.+|+..++.. + ..
T Consensus 151 ~~I~~~~~G~~s~~l--~~l~~Gd~v~--l~~p~gg~~~~~~~~~~~~~vlIAgGtGiaP~~s~l~~~~~~---~---~~ 220 (312)
T PRK05713 151 FHIDCSRPGAFCDAA--RQLQVGDLLR--LGELRGGALHYDPDWQERPLWLLAAGTGLAPLWGILREALRQ---G---HQ 220 (312)
T ss_pred EEEEEcCCCccchhh--hcCCCCCEEE--EccCCCCceEecCCCCCCcEEEEecCcChhHHHHHHHHHHhc---C---CC
Confidence 455544344666787 4677887776 555553 221 23 5666676567777788876532 2 11
Q ss_pred CceEEEEEEecCCchh--hhhhHHHHHHhCCCceee
Q 031642 81 EPYTSKSLTTNLSDLE--AAQPLSKLCLEFPDLHIG 114 (156)
Q Consensus 81 ap~~S~tv~~~~~Eg~--IA~~L~~Iq~~~Pdv~IG 114 (156)
.++.- ++....+.+ ..+.|.+++++||++.+.
T Consensus 221 ~~v~l--~~g~r~~~d~~~~~el~~l~~~~~~~~~~ 254 (312)
T PRK05713 221 GPIRL--LHLARDSAGHYLAEPLAALAGRHPQLSVE 254 (312)
T ss_pred CcEEE--EEEcCchHHhhhHHHHHHHHHHCCCcEEE
Confidence 23211 122333333 478899999999998875
No 53
>PRK00341 hypothetical protein; Provisional
Probab=35.93 E-value=1.2e+02 Score=22.06 Aligned_cols=50 Identities=12% Similarity=0.216 Sum_probs=32.4
Q ss_pred hhhhhHHHHHHhCCCceeecc--ccccCCCe---EEEEEecCHHHHHHHHHHHHh
Q 031642 96 EAAQPLSKLCLEFPDLHIGCY--RKSRQGPL---IISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv~IGSY--P~~~~g~~---~lVvRG~D~~~l~aA~~~l~~ 145 (156)
++.+.+.+|-.+|.+.+-.+. ..++.|.+ .+.++-++.+++++--++|.+
T Consensus 29 ~~~~~V~~iv~~~~~~~~~~~~~k~Ss~GkY~S~tv~i~~~s~~q~~~iy~~L~~ 83 (91)
T PRK00341 29 GFKDLVIEILQKHADVDLSTLAERQSSNGKYTTVQLHIVATDEDQLQDINSALRA 83 (91)
T ss_pred hHHHHHHHHHHHhCCCcccceeeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 345555555556655543322 23556654 599999999999998777765
No 54
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=35.67 E-value=83 Score=22.21 Aligned_cols=49 Identities=14% Similarity=0.055 Sum_probs=33.9
Q ss_pred HHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhccCCcccc
Q 031642 105 CLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHRGAFSEV 155 (156)
Q Consensus 105 q~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f~~~ 155 (156)
.++++++.+..-++ ....+.+.+| ++.+..+..-.+|.++.+.|.+.++
T Consensus 79 ~~~~~~~~~~~~~~-~~~~~~ia~~-k~~~l~~~vn~~l~~l~~~G~~~~l 127 (134)
T smart00079 79 LSQNCDLMTVGENF-GRKGYGIAFP-KGSPLRDDLSRAILKLSESGELQKL 127 (134)
T ss_pred HhCCCCeEEcCccc-CCCceEEEec-CCCHHHHHHHHHHHHHHhcCcHHHH
Confidence 34467766554443 3346788888 4557788888889999888887654
No 55
>cd01949 GGDEF Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.
Probab=34.89 E-value=97 Score=21.11 Aligned_cols=29 Identities=24% Similarity=0.271 Sum_probs=24.6
Q ss_pred CCCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 121 QGPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 121 ~g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
++.|.+++.+.|...+++..+.|.+.+..
T Consensus 80 ~~~f~~l~~~~~~~~~~~~~~~l~~~~~~ 108 (158)
T cd01949 80 GDEFAILLPGTDLEEAEALAERLREAIEE 108 (158)
T ss_pred CCeEEEEeCCCCHHHHHHHHHHHHHHhcC
Confidence 56789999999999998889999888764
No 56
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=34.40 E-value=54 Score=23.29 Aligned_cols=45 Identities=22% Similarity=0.070 Sum_probs=23.7
Q ss_pred HHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccc
Q 031642 64 EWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 117 (156)
Q Consensus 64 Ml~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP 117 (156)
.+..++..+..- .|=+.-.+ .|+...+.+.++.+.-=|+-|..++
T Consensus 14 ~l~~~l~~~~~~-----~P~v~i~i----~~~~~~~~~~~l~~g~~D~~i~~~~ 58 (195)
T cd08431 14 PLYPLIAEFYQL-----NKATRIRL----SEEVLGGTWDALASGRADLVIGATG 58 (195)
T ss_pred HHHHHHHHHHHH-----CCCCceEE----EEeccchHHHHHhCCCCCEEEEecC
Confidence 444555554433 55444444 3334444566676666677776543
No 57
>PF00175 NAD_binding_1: Oxidoreductase NAD-binding domain ; InterPro: IPR001433 Bacterial ferredoxin-NADP+ reductase may be bound to the thylakoid membrane or anchored to the thylakoid-bound phycobilisomes. Chloroplast ferredoxin-NADP+ reductase (1.18.1.2 from EC) may play a key role in regulating the relative amounts of cyclic and non-cyclic electron flow to meet the demands of the plant for ATP and reducing power. It is involved in the final step in the linear photosynthetic electron transport chain and has also been implicated in cyclic electron flow around photosystem I where its role would be to return electrons from ferredoxin to the cytochrome B-F complex. This domain is present in a variety of proteins that include, bacterial flavohemoprotein, mammalian NADH-cytochrome b5 reductase, eukaryotic NADPH-cytochrome P450 reductase, nitrate reductase from plants, nitric-oxide synthase, bacterial vanillate demethylase, as well as others.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1UMK_A 1CNE_A 2CND_A 1CNF_A 4FK8_A 4F7D_A 2XNJ_B 1FDR_A 1JB9_A 3LVB_A ....
Probab=34.01 E-value=1.4e+02 Score=20.34 Aligned_cols=52 Identities=21% Similarity=0.233 Sum_probs=31.4
Q ss_pred EecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEecC-CchhhhhhHHHHHHhCCC
Q 031642 52 ILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNL-SDLEAAQPLSKLCLEFPD 110 (156)
Q Consensus 52 VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~-~Eg~IA~~L~~Iq~~~Pd 110 (156)
|-+|+-+..+.+|++.+... ... .++.-- ..+.. .|--..+.|.++++++|+
T Consensus 2 IagGtGIaP~~s~l~~~~~~-~~~-----~~v~l~-~~~r~~~~~~~~~~l~~~~~~~~~ 54 (109)
T PF00175_consen 2 IAGGTGIAPFLSMLRYLLER-NDN-----RKVTLF-YGARTPEDLLFRDELEALAQEYPN 54 (109)
T ss_dssp EEEGGGGHHHHHHHHHHHHH-TCT-----SEEEEE-EEESSGGGSTTHHHHHHHHHHSTT
T ss_pred eecceeHHHHHHHHHHHHHh-CCC-----CCEEEE-EEEcccccccchhHHHHHHhhccc
Confidence 44554466677788888865 322 333221 11222 333446999999999998
No 58
>PRK11064 wecC UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional
Probab=33.81 E-value=2.6e+02 Score=25.08 Aligned_cols=94 Identities=14% Similarity=0.151 Sum_probs=54.4
Q ss_pred EeCeEEEecCCCCc---------h-HHHHHHHHHHhHHhCCCccCCceEEEEEEecC-CchhhhhhHHHHHHh--C----
Q 031642 46 KCQNVIILTATNVT---------E-LDKEWNCLIELLRSGGLSLMEPYTSKSLTTNL-SDLEAAQPLSKLCLE--F---- 108 (156)
Q Consensus 46 ~igNV~VMAGV~VP---------~-I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~-~Eg~IA~~L~~Iq~~--~---- 108 (156)
..+-|+|+-+ .| + +...++.+.+.|+.| +-++-+|- +.. .--+++..|.+-... +
T Consensus 75 ~aDvvii~vp--tp~~~~~~~dl~~v~~~~~~i~~~l~~g-----~iVI~~ST-v~pgtt~~~~~~l~~~~~~~~~~~~~ 146 (415)
T PRK11064 75 PADAFLIAVP--TPFKGDHEPDLTYVEAAAKSIAPVLKKG-----DLVILEST-SPVGATEQMAEWLAEARPDLTFPQQA 146 (415)
T ss_pred cCCEEEEEcC--CCCCCCCCcChHHHHHHHHHHHHhCCCC-----CEEEEeCC-CCCCHHHHHHHHHHHhccCCcccccc
Confidence 4678888888 46 3 455667788776555 65554442 221 222355555543222 3
Q ss_pred ---CCceeecccccc-CCCe-------EEEEEecCHHHHHHHHHHHHhhh
Q 031642 109 ---PDLHIGCYRKSR-QGPL-------IISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 109 ---Pdv~IGSYP~~~-~g~~-------~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
.|..+.+.|.+- +|.. ..++=|.|++..+++..-++.+.
T Consensus 147 g~~~~f~v~~~PE~~~~G~~~~~~~~~~~vvgG~~~~~~~~~~~ly~~~~ 196 (415)
T PRK11064 147 GEQADINIAYCPERVLPGQVMVELIKNDRVIGGMTPVCSARASELYKIFL 196 (415)
T ss_pred cCCCCeEEEECCCccCCCChhhhhcCCCEEEEeCCHHHHHHHHHHHHHhc
Confidence 367789999654 4532 25666668888777654444443
No 59
>cd06210 MMO_FAD_NAD_binding Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water.
Probab=33.67 E-value=1.5e+02 Score=23.37 Aligned_cols=95 Identities=19% Similarity=0.230 Sum_probs=49.7
Q ss_pred hHHhHHhcCcCCceeee-ccCCCCceeeCCCccccee--EeCe-EEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEE
Q 031642 10 LVVRRLLGYKYPRWLCC-RKVPPNCCITTSCSYLWYI--KCQN-VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTS 85 (156)
Q Consensus 10 ~~~~~~~~~~~~~~~~~-~~~~~~~~I~NpvS~APGF--~igN-V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S 85 (156)
+.+|+.=+=.+-.||+. -++-...-|..|......- .-++ |+|-+|+-+..+.+|+..+... + .+ ..
T Consensus 68 ~~i~~~~~G~~s~~l~~~~~~Gd~v~i~gP~G~f~l~~~~~~~~vliagGtGiaP~~~~l~~~~~~---~-----~~-~~ 138 (236)
T cd06210 68 FLIRLLPGGAFSTYLETRAKVGQRLNLRGPLGAFGLRENGLRPRWFVAGGTGLAPLLSMLRRMAEW---G-----EP-QE 138 (236)
T ss_pred EEEEEcCCCccchhhhhCcCCCCEEEEecCcceeeecCCCCccEEEEccCcchhHHHHHHHHHHhc---C-----CC-ce
Confidence 33444322235577765 3333334566665542111 1134 5555666566667777776532 2 21 12
Q ss_pred EEEE-ecCCchhh--hhhHHHHHHhCCCcee
Q 031642 86 KSLT-TNLSDLEA--AQPLSKLCLEFPDLHI 113 (156)
Q Consensus 86 ~tv~-~~~~Eg~I--A~~L~~Iq~~~Pdv~I 113 (156)
.++. ....+.++ .+.|.+++++||++.+
T Consensus 139 v~l~~~~r~~~~~~~~~~l~~l~~~~~~~~~ 169 (236)
T cd06210 139 ARLFFGVNTEAELFYLDELKRLADSLPNLTV 169 (236)
T ss_pred EEEEEecCCHHHhhhHHHHHHHHHhCCCeEE
Confidence 2332 33344444 4889999999998774
No 60
>PF14081 DUF4262: Domain of unknown function (DUF4262)
Probab=32.30 E-value=41 Score=25.16 Aligned_cols=31 Identities=19% Similarity=0.261 Sum_probs=23.3
Q ss_pred EecCCCCch-H-HHHHHHHHHhHHhCC-CccCCceE
Q 031642 52 ILTATNVTE-L-DKEWNCLIELLRSGG-LSLMEPYT 84 (156)
Q Consensus 52 VMAGV~VP~-I-~aMl~~l~p~L~~G~-L~~gap~~ 84 (156)
++-| +|. + ..+|+.+..+.+.|. +..|..+.
T Consensus 37 iv~G--L~~~~a~~lLn~l~~~v~~g~~~~~G~~~~ 70 (125)
T PF14081_consen 37 IVFG--LPPETAHSLLNELADRVRAGERFEPGQRYD 70 (125)
T ss_pred EEEC--CCHHHHHHHHHHHHHHHhcCCCCCCCcEEe
Confidence 7889 566 5 669999999999885 55555543
No 61
>TIGR03376 glycerol3P_DH glycerol-3-phosphate dehydrogenase (NAD(+)). Members of this protein family are the eukaryotic enzyme, glycerol-3-phosphate dehydrogenase (NAD(+)) (EC 1.1.1.8). Enzymatic activity for 1.1.1.8 is defined as sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH. Note the very similar reactions of enzymes defined as EC 1.1.1.94 and 1.1.99.5, assigned to families of proteins in the bacteria.
Probab=32.03 E-value=2e+02 Score=25.45 Aligned_cols=122 Identities=15% Similarity=0.093 Sum_probs=70.1
Q ss_pred CCceeeeccCCCCceeeCCCcccceeEeCeEEEecCCCCch--HHHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhh
Q 031642 20 YPRWLCCRKVPPNCCITTSCSYLWYIKCQNVIILTATNVTE--LDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEA 97 (156)
Q Consensus 20 ~~~~~~~~~~~~~~~I~NpvS~APGF~igNV~VMAGV~VP~--I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~I 97 (156)
-+++|.=.+.|+|..+.+-... -..=-.++|+| ||+ ++..++.+.+.|+.+ .+++|.+=-....+|..
T Consensus 57 n~~ylpgi~Lp~~i~at~dl~e--al~~ADiIIlA---VPs~~i~~vl~~l~~~l~~~-----~~iVs~tKGie~~~~~~ 126 (342)
T TIGR03376 57 NVKYLPGIKLPANLVAVPDLVE--AAKGADILVFV---IPHQFLEGICKQLKGHVKPN-----ARAISCIKGLEVSKDGV 126 (342)
T ss_pred CccccCCCcCCCCeEEECCHHH--HHhcCCEEEEE---CChHHHHHHHHHHHhhcCCC-----CEEEEEeCCcccCCCcC
Confidence 4555555567888777554322 12222477776 488 366888888886655 88888664444443344
Q ss_pred hhhHHHHHHhCCCceee--ccccccC----C-CeEEEEEecCHHHHHHHHHHHHhhhccCCc
Q 031642 98 AQPLSKLCLEFPDLHIG--CYRKSRQ----G-PLIISFEGKDQARIEAAIESLFKKFHRGAF 152 (156)
Q Consensus 98 A~~L~~Iq~~~Pdv~IG--SYP~~~~----g-~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f 152 (156)
--+=+-|++.+ +..++ |=|.+-. + ...+|+=+.|.+.-...++.++++|....|
T Consensus 127 ~~~se~i~e~l-~~~~~~lsGP~~A~Eva~~~pt~~~ia~~~~~~~~~~a~~~~~lf~~~~f 187 (342)
T TIGR03376 127 KLLSDIIEEEL-GIPCGVLSGANLANEVAKEKFSETTVGYRDPADFDVDARVLKALFHRPYF 187 (342)
T ss_pred ccHHHHHHHHh-CCCeEEeeCcchHHHHHcCCCceEEEEeCCCcchHHHHHHHHHHhCCCCE
Confidence 33333333344 22333 2233321 2 236888888865555677778888876666
No 62
>cd07465 CRD_FZ1 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 1 (Fz1) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 1 (Fz1) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata.
Probab=32.01 E-value=34 Score=26.60 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=23.2
Q ss_pred HHhcCcCCceeeeccCCCC----ceeeCCCcc
Q 031642 14 RLLGYKYPRWLCCRKVPPN----CCITTSCSY 41 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~----~~I~NpvS~ 41 (156)
..+|+.+|..|-|.+.|.. -||+.+.+.
T Consensus 92 ~~fg~~WP~~l~C~~fP~~~~~~~C~~~~~~~ 123 (127)
T cd07465 92 NKFGFQWPDTLRCEKFPVHGAGELCVGQNTSE 123 (127)
T ss_pred HHhCCCCCCcCCcccCCCCCCCCcccCCCCCC
Confidence 4589999999999999986 599766654
No 63
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=31.93 E-value=66 Score=27.06 Aligned_cols=61 Identities=8% Similarity=-0.067 Sum_probs=40.9
Q ss_pred CceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccC--------CCe-EEEEEecCHHHHHHHHH
Q 031642 81 EPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ--------GPL-IISFEGKDQARIEAAIE 141 (156)
Q Consensus 81 ap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~--------g~~-~lVvRG~D~~~l~aA~~ 141 (156)
-+.+-.|+++.-..-.|.....+++++||++-||.==-... -+- -||--+.|.+-++.|.+
T Consensus 41 i~~iEiT~~tp~a~~~i~~l~~~~~~~~p~~~vGaGTVl~~e~a~~a~~aGA~FiVsP~~~~~v~~~~~~ 110 (222)
T PRK07114 41 ARVFEFTNRGDFAHEVFAELVKYAAKELPGMILGVGSIVDAATAALYIQLGANFIVTPLFNPDIAKVCNR 110 (222)
T ss_pred CCEEEEeCCCCcHHHHHHHHHHHHHhhCCCeEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHH
Confidence 88888888777666667666667788999999997211110 011 26667778777777664
No 64
>TIGR02526 eut_PduT ethanolamine utilization protein, PduT homolog. This gene shows up in ethanolamine utilization operons in which a proteinaceous coat organelle is also encoded. It is closely related to the PduT protein in propane-diol operons with the same structure.
Probab=31.84 E-value=1.3e+02 Score=24.89 Aligned_cols=60 Identities=13% Similarity=0.175 Sum_probs=40.3
Q ss_pred ecCCchhhhhhHHHHHHhCCCceeecccccc--CCCeEEEEEecCHHHHHHHHHHHHhhhccCCc
Q 031642 90 TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR--QGPLIISFEGKDQARIEAAIESLFKKFHRGAF 152 (156)
Q Consensus 90 ~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~--~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f 152 (156)
+.--+..|.+ + +.+.+--+|.+.-|..+. .|.+.++++| |-+.+++|+++..+.+.++.+
T Consensus 104 ~~~~~~ai~A-A-D~a~Kaa~V~l~~~~~~~g~gG~~~v~itG-dVsaV~aAv~a~~~~~~~~~~ 165 (182)
T TIGR02526 104 ISQVGSGLNA-L-DEALKKSAIHLVKLTLGAGIGGKFVAIFTG-EVSSVEEGMRILQETAEPKKI 165 (182)
T ss_pred ecCHHHHHHH-H-HHHhhhcCeEEEEEEEecCcCceEEEEEEE-cHHHHHHHHHHHHHHHhhCCe
Confidence 3334555544 2 334444599999987665 3456688888 677799999998888865533
No 65
>PRK00007 elongation factor G; Reviewed
Probab=31.65 E-value=1.6e+02 Score=28.33 Aligned_cols=63 Identities=17% Similarity=0.284 Sum_probs=52.4
Q ss_pred CCceEEEEEEecC--CchhhhhhHHHHHHhCCCceeeccccccCCCe-EEEEEecCHHHHHHHHHHHHhhh
Q 031642 80 MEPYTSKSLTTNL--SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL-IISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 80 gap~~S~tv~~~~--~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~-~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
-.|+++.+|...- .+..+.+.|.+|+.+.|.+.+ ..+... .+++.|.-+-.||-+.++|++.|
T Consensus 405 ~~Pv~~~aIep~~~~d~~kL~~aL~~L~~eDpsl~v-----~~~~etge~~l~g~GelHLei~~~rL~~~~ 470 (693)
T PRK00007 405 PEPVISVAVEPKTKADQEKMGIALQKLAEEDPSFRV-----STDEETGQTIIAGMGELHLDIIVDRMKREF 470 (693)
T ss_pred CCceEEEEEEECCcccHHHHHHHHHHHHHhCCeEEE-----EEcCCCCCEEEEEecHHhHHHHHHHHHHHh
Confidence 3689999998764 679999999999999999986 223333 48899999999999999999987
No 66
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=31.30 E-value=30 Score=20.82 Aligned_cols=24 Identities=17% Similarity=0.319 Sum_probs=19.0
Q ss_pred CeEEEEEecCHHHHHHHHHHHHhh
Q 031642 123 PLIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 123 ~~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
.|.-++||-|+++||+..+.+.+.
T Consensus 10 ~F~~~~rGY~~~eVD~fLd~v~~~ 33 (34)
T TIGR03544 10 RFKKKLRGYDAAEVDAFLDRVADD 33 (34)
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHh
Confidence 344446999999999999988764
No 67
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=30.65 E-value=1.8e+02 Score=20.47 Aligned_cols=61 Identities=21% Similarity=0.273 Sum_probs=41.2
Q ss_pred EEEecCCchhhhhhHHHHHHhCCCceeecccccc--CCCeEEEEEecCH----HHHHHHHHHHHhhh
Q 031642 87 SLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR--QGPLIISFEGKDQ----ARIEAAIESLFKKF 147 (156)
Q Consensus 87 tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~--~g~~~lVvRG~D~----~~l~aA~~~l~~~~ 147 (156)
++....-+=.++-.|+..-.+.|+|.+=.|---. +..+.|.++-+.. +.+.+|.+.+.+.+
T Consensus 4 ~f~i~~EDHTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~ 70 (77)
T PF13656_consen 4 TFTIYGEDHTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGITPIEALKKALEDLIKIC 70 (77)
T ss_dssp EEEEES--HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHH
T ss_pred EEEEeCCCccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence 3444445567888999999999999999997644 3445666666644 55666666666655
No 68
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=30.61 E-value=1.2e+02 Score=30.52 Aligned_cols=53 Identities=13% Similarity=0.062 Sum_probs=34.9
Q ss_pred hhhhHHHHHHhCCCceeeccccc--c-CC-----CeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 97 AAQPLSKLCLEFPDLHIGCYRKS--R-QG-----PLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 97 IA~~L~~Iq~~~Pdv~IGSYP~~--~-~g-----~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
+.+.|.+--+++|++.+=..+.. . +| ++.+.+.|.|.+.++++.+++++.+++
T Consensus 626 i~~~lr~~l~~~pg~~~~~~~~~~~~~~g~~~~~~i~i~l~G~d~~~L~~~a~~i~~~L~~ 686 (1025)
T PRK10614 626 VIDRLRVKLAKEPGANLFLMAVQDIRVGGRQSNASYQYTLLSDDLAALREWEPKIRKALAA 686 (1025)
T ss_pred HHHHHHHHHhcCCCcEEEecCCcccCcCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHhc
Confidence 34444444445788763222211 1 11 367999999999999999999999853
No 69
>PRK10897 phosphohistidinoprotein-hexose phosphotransferase component of N-regulated PTS system (Npr); Provisional
Probab=30.09 E-value=68 Score=23.24 Aligned_cols=67 Identities=15% Similarity=0.234 Sum_probs=41.0
Q ss_pred eEEEEEEecCCchhhh---hhHHHHHHhC-CCceeeccc--cccC--------------C-CeEEEEEecCHHHHHHHHH
Q 031642 83 YTSKSLTTNLSDLEAA---QPLSKLCLEF-PDLHIGCYR--KSRQ--------------G-PLIISFEGKDQARIEAAIE 141 (156)
Q Consensus 83 ~~S~tv~~~~~Eg~IA---~~L~~Iq~~~-Pdv~IGSYP--~~~~--------------g-~~~lVvRG~D~~~l~aA~~ 141 (156)
|+++++....+.|-=| ..|.+++++| -++.| .|- ..-+ | .+.|.+.|.|+++ |.+
T Consensus 2 m~~~~v~V~n~~GLHARPAa~lv~~a~~f~s~v~l-~~~~g~~~~akSil~lm~Lg~~~G~~i~v~~~G~De~~---A~~ 77 (90)
T PRK10897 2 TVKQTVEIKNKLGMHARPAMKLFELVQGFDAEVLL-RNDEGTEAEANSVIALLMLDSAKGRQIEVEATGPQEEE---ALA 77 (90)
T ss_pred cEEEEEEECCCCCccHHHHHHHHHHHhhCCCEEEE-EeCCCcEEchHhHHHHHHhCCCCCCEEEEEEECcCHHH---HHH
Confidence 5677777777666544 4566777788 56666 221 1112 1 2459999999965 566
Q ss_pred HHHhhhccCCccc
Q 031642 142 SLFKKFHRGAFSE 154 (156)
Q Consensus 142 ~l~~~~~~~~f~~ 154 (156)
+|.++|.. .|.|
T Consensus 78 ~l~~~~~~-~~~e 89 (90)
T PRK10897 78 AVIALFNS-GFDE 89 (90)
T ss_pred HHHHHHHh-ccCC
Confidence 66666654 4654
No 70
>cd00914 PCD_DCoH_subfamily_b PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon
Probab=28.99 E-value=63 Score=22.36 Aligned_cols=60 Identities=12% Similarity=0.021 Sum_probs=37.2
Q ss_pred ceEEEEEEec-CCchh-hhhhHHHH---HHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 82 PYTSKSLTTN-LSDLE-AAQPLSKL---CLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 82 p~~S~tv~~~-~~Eg~-IA~~L~~I---q~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
.-+.|+.... ..++- +...++++ ...|||+++|. +.+.|.+...|...|...--++++.+
T Consensus 9 ~~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHPdi~~~~------~~V~v~l~Thd~~glT~~D~~lA~~i 73 (76)
T cd00914 9 DAIHKSFKFKDFNEAFGFMTRVALEAEKMNHHPEWFNVY------NKVDITLTTHDAGGLTERDIKLAKFI 73 (76)
T ss_pred CeEEEEEEeCCHHHHHHHHHHHHHHHHHhCCCCCEEEec------cEEEEEEEeCCCCCcCHHHHHHHHHH
Confidence 3578888765 45553 44444444 45689998862 45778887777666655555555544
No 71
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=28.98 E-value=57 Score=25.01 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=25.3
Q ss_pred CeEEEEEecCHHHHHHHHHHHHhhhccCC
Q 031642 123 PLIISFEGKDQARIEAAIESLFKKFHRGA 151 (156)
Q Consensus 123 ~~~lVvRG~D~~~l~aA~~~l~~~~~~~~ 151 (156)
++..|+.+.|.+++++|.+.|.+++....
T Consensus 84 ~iIfVvDssd~~~l~e~~~~L~~ll~~~~ 112 (175)
T PF00025_consen 84 GIIFVVDSSDPERLQEAKEELKELLNDPE 112 (175)
T ss_dssp EEEEEEETTGGGGHHHHHHHHHHHHTSGG
T ss_pred eeEEEEecccceeecccccchhhhcchhh
Confidence 56799999999999999999999887433
No 72
>TIGR03480 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921.
Probab=28.82 E-value=1.3e+02 Score=29.36 Aligned_cols=47 Identities=23% Similarity=0.304 Sum_probs=35.1
Q ss_pred chhhhhhHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 94 DLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 94 Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
+....+...+++++||+. ++.+.+|++|.|.++..+|++++.+.+++
T Consensus 48 ~~~~~~~~~~~~~~f~~~---------~~~i~vvv~~~~~e~~~~~a~~l~~~l~~ 94 (862)
T TIGR03480 48 DLPFRQDERAYEKAFPQD---------EDTIVVVIEGPTPEQASRAAERLAEKLAA 94 (862)
T ss_pred CCchhHHHHHHHHhcCCc---------cCeEEEEEeCCCHHHHHHHHHHHHHHHhc
Confidence 334444566777766653 24578899999999999999999998864
No 73
>PF00779 BTK: BTK motif; InterPro: IPR001562 The Btk-type zinc finger or Btk motif (BM) is a conserved zinc-binding motif containing conserved cysteines and a histidine that is present in certain eukaryotic signalling proteins. The motif is named after Bruton's tyrosine kinase (Btk), an enzyme which is essential for B cell maturation in humans and mice [, ]. Btk is a member of the Tec family of protein tyrosine kinases (PTK). These kinases contain a conserved Tec homology (TH) domain between the N-terminal pleckstrin homology (PH) domain (IPR001849 from INTERPRO) and the Src homology 3 (SH3) domain (IPR001452 from INTERPRO). The N-terminal of the TH domain is highly conserved and known as the Btf motif, while the C-terminal region of the TH domain contains a proline-rich region (PRR). The Btk motif contains a conserved His and three Cys residues that form a zinc finger (although these differ from known zinc finger topologies), while PRRs are commonly involved in protein-protein interactions, including interactions with G proteins [, ]. The TH domain may be of functional importance in various signalling pathways in different species []. A complete TH domain, containing both the Btk and PRR regions, has not been found outside the Tec family; however, the Btk motif on its own does occur in other proteins, usually C-terminal to a PH domain (note that although a Btk motif always occurs C-terminal to a PH domain, not all PH domains are followed by a Btk motif). The crystal structures of Btk show that the Btk-type zinc finger has a globular core, formed by a long loop which is held together by a zinc ion, and that the Btk motif is packed against the PH domain []. The zinc-binding residues are a histidine and three cysteines, which are fully conserved in the Btk motif []. Proteins known to contain a Btk-type zinc finger include: Mammalian Bruton's tyrosine kinase (Btk), a protein tyrosine kinase involved in modulation of diverse cellular processes. Mutations affecting Btk are the cause of X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency in mice. Mammalian Tec, Bmx, and Itk proteins, which are tyrosine protein kinases of the Tec subfamily. Drosophila tyrosine-protein kinase Btk29A, which is required for the development of proper ring canals and of male genitalia and required for adult survival. Mammalian Ras GTPase-activating proteins (RasGAP), which regulate the activation of inactive GDP-bound Ras by converting GDP to GTP. ; GO: 0035556 intracellular signal transduction; PDB: 2E6I_A 2YS2_A 2Z0P_A 1B55_A 1BTK_B 1BWN_A.
Probab=28.81 E-value=24 Score=21.64 Aligned_cols=10 Identities=40% Similarity=1.524 Sum_probs=7.0
Q ss_pred CceeeeccCC
Q 031642 21 PRWLCCRKVP 30 (156)
Q Consensus 21 ~~~~~~~~~~ 30 (156)
-+|+||+...
T Consensus 11 g~W~CC~q~~ 20 (32)
T PF00779_consen 11 GKWLCCKQTD 20 (32)
T ss_dssp TCESSSS-SS
T ss_pred CcCcCCCCcC
Confidence 4899998653
No 74
>cd06215 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur pr
Probab=28.70 E-value=1.9e+02 Score=22.50 Aligned_cols=95 Identities=16% Similarity=0.237 Sum_probs=52.2
Q ss_pred hHHhHHhcCcCCceeee-ccCCCCceeeCCCcccceeE---eCe-EEEecCCCCchHHHHHHHHHHhHHhCCCccCCceE
Q 031642 10 LVVRRLLGYKYPRWLCC-RKVPPNCCITTSCSYLWYIK---CQN-VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYT 84 (156)
Q Consensus 10 ~~~~~~~~~~~~~~~~~-~~~~~~~~I~NpvS~APGF~---igN-V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~ 84 (156)
+.+++.-+=..-+|++. -+.-...-|..|... .... -++ |+|-.|+-+..+.+|++.+... + ...++.
T Consensus 63 ~~vk~~~~G~~s~~l~~~~~~G~~v~i~gP~G~-f~~~~~~~~~~vlIagG~Giap~~~~l~~~~~~---~---~~~~v~ 135 (231)
T cd06215 63 ITVKRVPGGLVSNWLHDNLKVGDELWASGPAGE-FTLIDHPADKLLLLSAGSGITPMMSMARWLLDT---R---PDADIV 135 (231)
T ss_pred EEEEEcCCCcchHHHHhcCCCCCEEEEEcCcce-eEeCCCCCCcEEEEecCcCcchHHHHHHHHHhc---C---CCCcEE
Confidence 34554443356678864 333345567777654 2221 134 5666666667777788777532 2 112222
Q ss_pred EEEEEecCC--chhhhhhHHHHHHhCCCcee
Q 031642 85 SKSLTTNLS--DLEAAQPLSKLCLEFPDLHI 113 (156)
Q Consensus 85 S~tv~~~~~--Eg~IA~~L~~Iq~~~Pdv~I 113 (156)
. +..... |-...+.|.+++++++++.+
T Consensus 136 l--~~~~r~~~~~~~~~~l~~l~~~~~~~~~ 164 (231)
T cd06215 136 F--IHSARSPADIIFADELEELARRHPNFRL 164 (231)
T ss_pred E--EEecCChhhhhHHHHHHHHHHHCCCeEE
Confidence 1 223333 33456889999999887653
No 75
>cd07056 BMC_PduK 1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat 1l. PduK proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduK might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view.
Probab=28.69 E-value=2e+02 Score=20.25 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=33.2
Q ss_pred HHHHhCCCceeeccccccC-CCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 103 KLCLEFPDLHIGCYRKSRQ-GPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 103 ~Iq~~~Pdv~IGSYP~~~~-g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
+...+--||+|..|..... |.+.++++| |-+.+++|+++-.+...+
T Consensus 18 D~~lKaA~V~l~~~~~~~g~G~~~viv~G-dvsaV~~Av~a~~~~~~~ 64 (77)
T cd07056 18 DRMAKTANVRLLGLENTKGSGWMTVKISG-DVAAVNAAIEAGKQTAGA 64 (77)
T ss_pred HHHHhhCceEEEEEEeccCceEEEEEEEe-eHHHHHHHHHHHHHHHhc
Confidence 4455667999999976554 445577777 677788888888877764
No 76
>PF11582 DUF3240: Protein of unknown function (DUF3240); InterPro: IPR021634 This family of proteins with unknown function appears to be restricted to Proteobacteria. ; PDB: 3CE8_A.
Probab=28.51 E-value=1.2e+02 Score=22.29 Aligned_cols=60 Identities=13% Similarity=0.010 Sum_probs=28.4
Q ss_pred ccceeEeCeEEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCcee
Q 031642 41 YLWYIKCQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHI 113 (156)
Q Consensus 41 ~APGF~igNV~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~I 113 (156)
..|||.+-++.=... .. ..-+..++.++- ++ ...+.+-+.|-+..+-|++|+++|++..|
T Consensus 29 ~v~GFt~~~~~g~g~---~~---~~~s~~EQV~G~-----~~--~~~~~~~~~~~~~~~Ll~~L~~~~~~~~i 88 (102)
T PF11582_consen 29 GVSGFTSSPAEGHGS---RH---SLLSAAEQVSGR-----AR--RVRFQVILPEEDAEELLAALKQEFAGTGI 88 (102)
T ss_dssp T----EEEEEEEEE-------------------EE-----EE--EEEEEEEEEGGGHHHHHHHHHHHTTTS--
T ss_pred ccCCceEeeccccCC---cc---cCCCHHHhcccc-----cc--eEEEEEEECHHHHHHHHHHHHHHcCCCCc
Confidence 357788777776665 11 222333333222 22 23334456788899999999999987654
No 77
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=28.44 E-value=64 Score=22.75 Aligned_cols=50 Identities=14% Similarity=-0.004 Sum_probs=25.7
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccc
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 117 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP 117 (156)
|.+ ...+..++..+..- .|-+.-++... .-.+.+..+.+.-=|+.|...|
T Consensus 8 ~~~~~~~l~~~l~~~~~~-----~P~i~l~i~~~----~~~~~~~~l~~~~~Dl~i~~~~ 58 (196)
T cd08450 8 PGAEVQWLPEVLPILREE-----HPDLDVELSSL----FSPQLAEALMRGKLDVAFMRPE 58 (196)
T ss_pred hhhhhhhHHHHHHHHHhh-----CCCcEEEEEec----ChHHHHHHHhcCCccEEEEeCC
Confidence 455 44666666665544 66666555432 2233344555544455554443
No 78
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.28 E-value=2.1e+02 Score=19.83 Aligned_cols=53 Identities=15% Similarity=0.177 Sum_probs=40.5
Q ss_pred CchhhhhhHHHHHHhC-CCceeeccccccCC-C--eEEEEEecCHHHHHHHHHHHHhh
Q 031642 93 SDLEAAQPLSKLCLEF-PDLHIGCYRKSRQG-P--LIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 93 ~Eg~IA~~L~~Iq~~~-Pdv~IGSYP~~~~g-~--~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
.-|.+++.|..+++.. .=..|-|.|..... . |-|-+.|... .+++|.++|++-
T Consensus 10 ~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e~~~~-~i~~~l~~l~~~ 66 (74)
T cd04929 10 EVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCECDQR-RLDELVQLLKRE 66 (74)
T ss_pred CCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEcCHH-HHHHHHHHHHHh
Confidence 4688999999998875 66789999965533 3 4588888664 899999988774
No 79
>COG0206 FtsZ Cell division GTPase [Cell division and chromosome partitioning]
Probab=28.17 E-value=1.8e+02 Score=26.23 Aligned_cols=66 Identities=9% Similarity=-0.016 Sum_probs=41.7
Q ss_pred ecCCCCchH-HH-HHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhh-hHHHHHHhC--CCceeeccccccCC
Q 031642 53 LTATNVTEL-DK-EWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQ-PLSKLCLEF--PDLHIGCYRKSRQG 122 (156)
Q Consensus 53 MAGV~VP~I-~a-Ml~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~-~L~~Iq~~~--Pdv~IGSYP~~~~g 122 (156)
.||- .|++ ++ +-+++- .++.. |. |+-|+..+--..-+-|.-|+ .+.++++++ +-+.+..|||..+|
T Consensus 70 GaGa-~P~vG~~aAee~~~-~I~~~-l~-g~dmvfitaG~GGGTGtGaaPVvakiake~g~ltvavvt~Pf~~EG 140 (338)
T COG0206 70 GAGA-NPEVGRAAAEESIE-EIEEA-LK-GADMVFVTAGMGGGTGTGAAPVVAEIAKELGALTVAVVTLPFSFEG 140 (338)
T ss_pred CCCC-CcHHHHHHHHHHHH-HHHHH-hc-cCCeEEEEeeecCCccccccHHHHHHHHhcCCcEEEEEEecchhcC
Confidence 4554 6998 33 444333 33333 22 24465655555556666554 588999985 78999999998876
No 80
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.13 E-value=1.7e+02 Score=18.77 Aligned_cols=58 Identities=16% Similarity=0.126 Sum_probs=40.0
Q ss_pred EEEecCCchhhhhhHHHHHHhCCCceeecccccc--CC--CeEEEEEecCHH-HHHHHHHHHHhh
Q 031642 87 SLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR--QG--PLIISFEGKDQA-RIEAAIESLFKK 146 (156)
Q Consensus 87 tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~--~g--~~~lVvRG~D~~-~l~aA~~~l~~~ 146 (156)
.+.+.-..|.+++.++.|++. +++|=+.-... ++ .+.+.+.-.|.+ .+++-+++|+++
T Consensus 4 ~i~~~d~~g~l~~I~~~la~~--~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i 66 (76)
T cd04888 4 SLLLEHRPGVLSKVLNTIAQV--RGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELREI 66 (76)
T ss_pred EEEecCCCchHHHHHHHHHHc--CCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcC
Confidence 455555678899988888777 44444443322 22 246889889998 999998888764
No 81
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.04 E-value=1.5e+02 Score=18.12 Aligned_cols=57 Identities=18% Similarity=0.096 Sum_probs=30.7
Q ss_pred EEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCCeEEEEEecCHHHHHHHHHHHHh
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGPLIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
+.+.-..|.+++.+..+.+..-++ ++-.++...++...+.++=.+. .++++.++|++
T Consensus 4 i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v~~~-~~~~~i~~l~~ 61 (71)
T cd04903 4 VVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQP-IDEEVIEEIKK 61 (71)
T ss_pred EEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEeCCC-CCHHHHHHHHc
Confidence 345567788888888886664443 2323332112223344554444 56666666654
No 82
>PF07364 DUF1485: Protein of unknown function (DUF1485); InterPro: IPR015995 Proteins in this entry are involved in degradation of the cyanobacterial heptapeptide hepatotoxin microcystin LR, and are encoded in the mlr gene cluster []. MlrC from Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) is believed to mediate the last step of peptidolytic degradation of the tetrapeptide. It is suspected to be a metallopeptidase based on homology to known peptidases and its inhibition by metal chelators. The proteins encoded by the mlr cluster may be involved in cell wall peptidoglycan cycling and subsequently act fortuitously in hydrolysis of microcystin LR. This entry represents the N-terminal region of these proteins.; PDB: 3IUU_A.
Probab=27.55 E-value=96 Score=27.07 Aligned_cols=56 Identities=18% Similarity=0.181 Sum_probs=34.9
Q ss_pred hhhhhHHHHHHhCCCc---e-eecccccc--CCCeEEEEEec-CHHHHHHHHHHHHhhh--ccCCc
Q 031642 96 EAAQPLSKLCLEFPDL---H-IGCYRKSR--QGPLIISFEGK-DQARIEAAIESLFKKF--HRGAF 152 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv---~-IGSYP~~~--~g~~~lVvRG~-D~~~l~aA~~~l~~~~--~~~~f 152 (156)
+|-+.+.+++++ |+| | ++-|||.+ +-+..+++-+. |++..++++++|.+.+ .++.|
T Consensus 212 ~l~~~~~~~e~~-~gVl~vsv~~GFp~aD~p~~G~sV~v~~d~d~~~a~~~A~~la~~~w~~R~~f 276 (292)
T PF07364_consen 212 SLYARARELEAR-PGVLDVSVFAGFPWADVPDCGASVLVVTDGDAALAEAAADELADEIWARRDEF 276 (292)
T ss_dssp HHHHHHHHHHTS-TT--EEEEE---TT---SS-SEEEEEEES-SSSSHHHHHHHHHHHHHHTGGGS
T ss_pred HHHHHHHHHhcC-CCeEEEEEecCcccccCccCCcEEEEEcCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 455566666666 543 3 47799876 33666677777 9999999999999887 44455
No 83
>cd07460 CRD_FZ5 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 5 (Fz5) receptor.proteins. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 5 (Fz5) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz5 plays critical regulating roles in the yolk sac and placental angiogenesis, in the maturation of the Paneth cell phenotype, in governing the neural potential of progenitors in the developing retina, and in neuronal s
Probab=27.44 E-value=42 Score=26.14 Aligned_cols=29 Identities=21% Similarity=0.584 Sum_probs=23.7
Q ss_pred HHhcCcCCceeeeccCCCCc-----eeeCCCccc
Q 031642 14 RLLGYKYPRWLCCRKVPPNC-----CITTSCSYL 42 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~-----~I~NpvS~A 42 (156)
+.+|+.+|..|-|.+.|.+- |++.+.+.|
T Consensus 93 ~~fg~~WP~~l~C~~fP~~~~~~~~C~~~~~~~~ 126 (127)
T cd07460 93 RQYGFAWPERMNCDRLPVLGDPETLCMDYNRTEA 126 (127)
T ss_pred HHhCCCCCCcCChhhCCCCCCCCCccCCCCCCCC
Confidence 56899999999999999764 887766654
No 84
>KOG3445 consensus Mitochondrial/chloroplast ribosomal protein 36a [Translation, ribosomal structure and biogenesis]
Probab=27.39 E-value=1.5e+02 Score=24.17 Aligned_cols=49 Identities=22% Similarity=0.242 Sum_probs=37.4
Q ss_pred hhhHHHHHHhCCCcee------ecccccc----CCCe-EEEEEecCHHHHHHHHHHHHhh
Q 031642 98 AQPLSKLCLEFPDLHI------GCYRKSR----QGPL-IISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 98 A~~L~~Iq~~~Pdv~I------GSYP~~~----~g~~-~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
-..|.++++++|+|.| |+-|.-+ +|+. .+++|-.|++.+..=++.|++.
T Consensus 45 e~~L~~~a~enP~v~i~v~~rrg~hP~lraeY~NGre~vicvrnms~eevs~~~~lL~ds 104 (145)
T KOG3445|consen 45 ESELPDLARENPGVVIYVEPRRGQHPLLRAEYLNGRERVICVRNMSQEEVSKKATLLRDS 104 (145)
T ss_pred HHHHHHHHhhCCCeEEEEeccCCCCceEEEEecCCceEEEeeccCCHHHHHHHHHHHhcc
Confidence 3459999999999988 5555533 3444 5899999999999888877653
No 85
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=27.20 E-value=1.6e+02 Score=29.86 Aligned_cols=54 Identities=7% Similarity=0.165 Sum_probs=37.3
Q ss_pred hhhhhHHHHHHhCCCceeecccccc-------C-CCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 96 EAAQPLSKLCLEFPDLHIGCYRKSR-------Q-GPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv~IGSYP~~~-------~-g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
++.+.|++--.++|++.+-..|... . ..+.+.+.|.|.+.++++++++++.+++
T Consensus 639 ~v~~~lr~~l~~~p~~~~~~~~~~~~~~~~~~~~~~v~i~l~G~d~~~L~~~a~~l~~~l~~ 700 (1040)
T PRK10503 639 KVIARLQTAVAKVPGVDLYLQPTQDLTIDTQVSRTQYQFTLQATSLDALSTWVPKLMEKLQQ 700 (1040)
T ss_pred HHHHHHHHHHhcCCCcEEeccCCccccccCCCCCCCeEEEEECCCHHHHHHHHHHHHHHHhc
Confidence 5555565555567887653333111 1 1467999999999999999999998864
No 86
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=26.52 E-value=1.6e+02 Score=26.67 Aligned_cols=94 Identities=15% Similarity=0.080 Sum_probs=54.6
Q ss_pred eeEeCeEEEecCCCCchH-HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccCC
Q 031642 44 YIKCQNVIILTATNVTEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQG 122 (156)
Q Consensus 44 GF~igNV~VMAGV~VP~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g 122 (156)
|..++-||+.-|+ |++ ...|..++..++.- -++..-|+.++ ++.-=.+-|..+.+...-+|||=== +.+.
T Consensus 99 ~~~~~siy~GGGT--Ps~l~~~L~~ll~~i~~~-----f~i~eis~E~~-P~~lt~e~L~~l~~~vnrlsiGVQS-~~d~ 169 (433)
T PRK08629 99 GYDFESMYVGGGT--TTILEDELAKTLELAKKL-----FSIKEVSCESD-PNHLDPPKLKQLKGLIDRLSIGVQS-FNDD 169 (433)
T ss_pred CCceEEEEECCCc--cccCHHHHHHHHHHHHHh-----CCCceEEEEeC-cccCCHHHHHHHHHhCCeEEEecCc-CCHH
Confidence 5678889999995 997 66777888777654 23322333332 3332334566666667778888511 1111
Q ss_pred CeEEEEEecCHHHHHHHHHHHHhh
Q 031642 123 PLIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 123 ~~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
-....=|+.+....+++.++++++
T Consensus 170 vLk~~gR~h~~~~~~~~~~~l~~~ 193 (433)
T PRK08629 170 ILKMVDRYEKFGSGQETFEKIMKA 193 (433)
T ss_pred HHHHcCCCCChhHHHHHHHHHHHH
Confidence 123444666666666666666654
No 87
>cd07054 BMC_PduT_repeat2 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=26.23 E-value=1.9e+02 Score=20.52 Aligned_cols=45 Identities=22% Similarity=0.270 Sum_probs=31.7
Q ss_pred HHHHhCCCceeecccccc--CCCeEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 103 KLCLEFPDLHIGCYRKSR--QGPLIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 103 ~Iq~~~Pdv~IGSYP~~~--~g~~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
+...+--||+|-.|-..+ +|++.++++| |-..+++|+++-.+...
T Consensus 18 D~mlKaA~V~l~~~~~~~~~~Gk~~v~v~G-dvsaV~~Av~a~~~~~~ 64 (78)
T cd07054 18 DAALKAADVQLIEIRLAMGIGGKSFVVLTG-DVSAVEAAVEAAEAVVG 64 (78)
T ss_pred HHHhhhCCeEEEEEEEccccCCEEEEEEEe-eHHHHHHHHHHHHHHHh
Confidence 344455689998885332 4567777777 77788888888887765
No 88
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=26.23 E-value=2e+02 Score=19.90 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=26.3
Q ss_pred hhhHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 98 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 98 A~~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
++...+|...|||..+== ...+.-.|.+.|...+.=+...+-|+++++
T Consensus 11 ~EL~kRl~~~yPd~~v~V---r~~s~~~l~v~g~~~~~k~~i~~iLqe~we 58 (65)
T PF06183_consen 11 SELTKRLHRQYPDAEVRV---RPGSANGLSVSGGKKDDKERIEEILQEMWE 58 (65)
T ss_dssp HHHHHHHHHH-SS-EEEE---EEESS-EEEEES--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCceEee---eecccCccccCCcCchHHHHHHHHHHHHHh
Confidence 345678899999988621 112334677887776655555555666654
No 89
>cd07466 CRD_FZ7 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 7 (Fz7) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 7 (Fz7) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Xenopus Fz7 is important in Wnt/beta-catenin signaling pathways controlling the transcriptional activation of target genes Siamois and Xnr3 in the animal caps of late blastula.
Probab=26.18 E-value=49 Score=25.63 Aligned_cols=29 Identities=24% Similarity=0.650 Sum_probs=23.3
Q ss_pred HHhcCcCCceeeeccCCCC----ceeeCCCccc
Q 031642 14 RLLGYKYPRWLCCRKVPPN----CCITTSCSYL 42 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~----~~I~NpvS~A 42 (156)
+.+|+.+|..|-|.+.|.. -||.-+.+.|
T Consensus 92 ~~fg~~WP~~l~C~~fP~~~~~~~Ci~~~~~~~ 124 (125)
T cd07466 92 NKFGFQWPERLRCENFPVHGAGEICVGQNTSDA 124 (125)
T ss_pred HHhCCCCCCcCCcccCCCCCCCCcCcCCCCCCC
Confidence 3589999999999999976 5887665544
No 90
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=26.13 E-value=1.7e+02 Score=25.90 Aligned_cols=98 Identities=24% Similarity=0.187 Sum_probs=62.2
Q ss_pred eeEeCeEEEecCCCCchH--HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHh-CCCceeecccccc
Q 031642 44 YIKCQNVIILTATNVTEL--DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLE-FPDLHIGCYRKSR 120 (156)
Q Consensus 44 GF~igNV~VMAGV~VP~I--~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~-~Pdv~IGSYP~~~ 120 (156)
|-+++.||+.-|+ |++ .++|..|+..++.- +... +-...|+.++ ++.--.+.|..+.+. +--+|||===+.
T Consensus 71 ~~~i~siy~GGGT--Ps~L~~~~L~~ll~~i~~~-~~~~-~~~eit~E~~-p~~~~~e~L~~l~~~GvnrisiGvQS~~- 144 (394)
T PRK08898 71 GRQVHTVFIGGGT--PSLLSAAGLDRLLSDVRAL-LPLD-PDAEITLEAN-PGTFEAEKFAQFRASGVNRLSIGIQSFN- 144 (394)
T ss_pred CCceeEEEECCCC--cCCCCHHHHHHHHHHHHHh-CCCC-CCCeEEEEEC-CCCCCHHHHHHHHHcCCCeEEEecccCC-
Confidence 4578999999995 996 66999999988766 2211 1124555554 344445778888876 567888851110
Q ss_pred CCCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 121 QGPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 121 ~g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
+.-....=|+.+.+.+.+|++.+++.+
T Consensus 145 ~~~L~~l~R~~~~~~~~~~i~~~~~~~ 171 (394)
T PRK08898 145 DAHLKALGRIHDGAEARAAIEIAAKHF 171 (394)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHhC
Confidence 111223346778888888887777654
No 91
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=26.11 E-value=73 Score=22.01 Aligned_cols=61 Identities=10% Similarity=0.155 Sum_probs=38.9
Q ss_pred CceEEEEEEec-CCchh-hhhhHHHHH---HhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 81 EPYTSKSLTTN-LSDLE-AAQPLSKLC---LEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 81 ap~~S~tv~~~-~~Eg~-IA~~L~~Iq---~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
.+-+.|+.... ..++. ++..+++++ ..|||+++|. +.+.|.+...|...|.+---+|++.+
T Consensus 8 ~~~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHP~i~~~~------~~V~v~l~Th~~~glT~~D~~lA~~i 73 (76)
T cd00913 8 GLKLERTFRFKNFVEALEFVNAVGEIAEAEGHHPDLSLGW------GRVRVTWWTHSIGGLSENDFIMAAKI 73 (76)
T ss_pred CCeEEEEEEcCCHHHHHHHHHHHHHHHHHcCCCCCEEEec------cEEEEEEEeCCCCCCCHHHHHHHHHH
Confidence 34678888765 45553 444455554 5689999873 46778887777665655555555544
No 92
>PRK02047 hypothetical protein; Provisional
Probab=26.06 E-value=2.6e+02 Score=20.28 Aligned_cols=52 Identities=17% Similarity=0.265 Sum_probs=33.5
Q ss_pred chhhhhhHHHHHHhC-CCceeecc--ccccCCCe---EEEEEecCHHHHHHHHHHHHh
Q 031642 94 DLEAAQPLSKLCLEF-PDLHIGCY--RKSRQGPL---IISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 94 Eg~IA~~L~~Iq~~~-Pdv~IGSY--P~~~~g~~---~lVvRG~D~~~l~aA~~~l~~ 145 (156)
+.++.+.+.+|..+| |+++--+. ..++.|.+ .+.++-.+.+++++--++|.+
T Consensus 26 ~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~GkY~Svtv~v~v~s~eq~~~iY~~L~~ 83 (91)
T PRK02047 26 HPEFADTIFKVVSVHDPEFDLEKIEERPSSGGNYTGLTITVRATSREQLDNIYRALTG 83 (91)
T ss_pred cHhHHHHHHHHHHHhCCCCccCceEEccCCCCeEEEEEEEEEECCHHHHHHHHHHHhh
Confidence 344666666666666 66543222 12445654 599999999999987777654
No 93
>PRK01002 nickel responsive regulator; Provisional
Probab=26.00 E-value=2.9e+02 Score=21.51 Aligned_cols=61 Identities=15% Similarity=0.215 Sum_probs=43.7
Q ss_pred eEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccCCCe---EEEEEecCHHHHHHHHHHHH
Q 031642 83 YTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL---IISFEGKDQARIEAAIESLF 144 (156)
Q Consensus 83 ~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~---~lVvRG~D~~~l~aA~~~l~ 144 (156)
+=.-++--+-...++...|.+||.+|-|+-+.|+=..-++.. .+++||. .+++.+=..+|.
T Consensus 57 ~GvItivydh~~~~l~~~l~~iqH~~~~~Iiss~Hvhld~~~ClEvivv~G~-~~~I~~l~~kL~ 120 (141)
T PRK01002 57 VGTISVIYDHHSTGVMEKLTDIQHDYSDLIVASLHIHLDHDHCLEVIVVRGD-AKEIRELTEKLM 120 (141)
T ss_pred EEEEEEEEeccchhHHHHHHHHHHhccCeEEEeeeeecCCCcEEEEEEEEcC-HHHHHHHHHHHh
Confidence 333444334456788999999999999999999876665552 4889985 456666666665
No 94
>PF00338 Ribosomal_S10: Ribosomal protein S10p/S20e; InterPro: IPR001848 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor []. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_J 3U5G_U 3O30_N 3O2Z_N 3IZB_J 3U5C_U 3R2C_J 3R2D_J 2ZKQ_j 2XQD_J ....
Probab=25.85 E-value=1.5e+02 Score=20.91 Aligned_cols=25 Identities=16% Similarity=0.215 Sum_probs=22.6
Q ss_pred EEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 125 IISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 125 ~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
.|.++|.|...|+.+...+.++...
T Consensus 2 ~I~l~s~d~~~l~~~~~~i~~~~~~ 26 (97)
T PF00338_consen 2 RIKLKSYDKKLLESYVKFIHKLAKN 26 (97)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHHHC
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999998764
No 95
>cd07462 CRD_FZ10 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 10 (Fz10) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 10 (Fz10) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. The cellular functon of Fz10 is unknown.
Probab=25.82 E-value=48 Score=25.80 Aligned_cols=27 Identities=26% Similarity=0.672 Sum_probs=22.0
Q ss_pred HHhcCcCCceeeeccCCCCc-----eeeCCCc
Q 031642 14 RLLGYKYPRWLCCRKVPPNC-----CITTSCS 40 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~-----~I~NpvS 40 (156)
..+||.+|..|-|.+.|.+- |++.|.+
T Consensus 93 ~~~g~~WP~~l~C~~fP~~~~~~~lc~~~~~~ 124 (127)
T cd07462 93 EQFNFKWPDSLDCSKLPNKNDPNYLCMEAPNN 124 (127)
T ss_pred HHhCCCCCCcCCcccCCCCCCCCcccCCCCCC
Confidence 35899999999999999765 8876653
No 96
>PRK13351 elongation factor G; Reviewed
Probab=25.66 E-value=2.4e+02 Score=26.82 Aligned_cols=65 Identities=25% Similarity=0.379 Sum_probs=52.8
Q ss_pred cCCceEEEEEEecC--CchhhhhhHHHHHHhCCCceeeccccccCCCe-EEEEEecCHHHHHHHHHHHHhhhc
Q 031642 79 LMEPYTSKSLTTNL--SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL-IISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 79 ~gap~~S~tv~~~~--~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~-~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
.-.|+++.+|...- .+..+.+.|.+|+++.|.+.+ ..+... .+++.|.-+-.||-+.++|++.+.
T Consensus 400 ~~~pv~~~~Iep~~~~d~~kL~~aL~~L~~eDpsl~v-----~~~~etge~ii~g~GelHLei~~~rL~~~~~ 467 (687)
T PRK13351 400 FPEPVVSLAVEPERRGDEQKLAEALEKLVWEDPSLRV-----EEDEETGQTILSGMGELHLEVALERLRREFK 467 (687)
T ss_pred CCCccEEEEEEECCcccHHHHHHHHHHHHHhCCeEEE-----EECCCCCCEEEEEecHHHHHHHHHHHHHHhC
Confidence 34688999998774 568899999999999999885 223334 588999999999999999999763
No 97
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=25.62 E-value=2.7e+02 Score=22.33 Aligned_cols=58 Identities=14% Similarity=0.062 Sum_probs=37.9
Q ss_pred ecCCchhhhhhHHHHHHhCCCc-eeeccccccCCC--eEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 90 TNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGP--LIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 90 ~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~--~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
+.-.=|.++...+-+..+-=++ |+..+|...++- +.|++.| |...+++....|.+++.
T Consensus 9 veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~-~~~~i~qi~kQl~KLid 69 (161)
T PRK11895 9 VENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSG-DEQVIEQITKQLNKLID 69 (161)
T ss_pred EcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEEC-CHHHHHHHHHHHhcccc
Confidence 3344455666555555554444 778888643442 3466666 89999999999988764
No 98
>cd07448 CRD_FZ4 Cysteine-rich Wnt-binding domain of the frizzled 4 (Fz4) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 4 (Fz4) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and the Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Frizzled 4 (Fz4) activates the Ca(2+)/calmodulin-dependent protein kinase II and protein kinase C of the Wnt/Ca(2+) signaling pathway during retinal angiogenesis. Mutations in Fz4 lead to familial exudative vitreoretinopathy (FEVR
Probab=25.32 E-value=45 Score=25.74 Aligned_cols=25 Identities=32% Similarity=0.874 Sum_probs=20.1
Q ss_pred HHhcCcCCceeeeccCCCCc-----eeeCC
Q 031642 14 RLLGYKYPRWLCCRKVPPNC-----CITTS 38 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~-----~I~Np 38 (156)
+.+|+.+|..|-|.+.|.+- ||+.|
T Consensus 92 ~~~g~~WP~~l~C~~fP~~~~~~~~C~~~~ 121 (126)
T cd07448 92 KEFGFPWPEALNCSKFPPQNNHNHMCMEGP 121 (126)
T ss_pred HHhCCCCCCcCCcccCCCCCCCCCccCCCC
Confidence 46899999999999999764 66543
No 99
>PF12693 GspL_C: GspL periplasmic domain; PDB: 2W7V_A.
Probab=25.32 E-value=2.3e+02 Score=21.36 Aligned_cols=49 Identities=16% Similarity=0.267 Sum_probs=36.4
Q ss_pred hhHHHHHHhCCCceeeccccccC-CCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 99 QPLSKLCLEFPDLHIGCYRKSRQ-GPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 99 ~~L~~Iq~~~Pdv~IGSYP~~~~-g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
..|...-...|++.+=+-.|..+ +.+.|-+.+.|.+.+|+...++.+.|
T Consensus 85 ~~l~~~~~~~~~~~l~~l~y~~~~~~L~l~~~a~~~~~le~l~~~l~~~~ 134 (157)
T PF12693_consen 85 AALAPALQQVPGIQLQSLRYDAGRGELRLQLEAPSFQALEQLRAALAAQL 134 (157)
T ss_dssp GGHHHHHHTSTT-EEEEEEEETTTTEEEEEEEESSSHHHHHHHHHHHTTE
T ss_pred HHHHHHhccCCCCceEEEEEcCCCcEEEEEeccCCHHHHHHHHHHHHhhc
Confidence 33444445678999999887543 35789999999999999888888764
No 100
>PF08945 Bclx_interact: Bcl-x interacting, BH3 domain; InterPro: IPR015040 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Members of this entry induce apoptosis. The isoform BimL is more potent than the isoform BimEL. They form heterodimers with a number of antiapoptotic Bcl-2 proteins including Mcl-1, Bcl-2, Bcl-X(L), BFL-1, and BHRF1, but do not heterodimerise with proapoptotic proteins such as BAD, BOK, BAX or BAK. They are peripheral membrane proteins, associated with intracytoplasmic membranes. The BH3 motif is required for Bcl-2 binding and cytotoxicity. After antigen-driven expansion, the majority of T cells involved in an immune response die rapidly by apoptosis dependent on the Bcl-2 related proteins; Bim and Bax or Bak []. Bcl-xL regulates Bax and Bim is an important regulator of bcl-x deficiency induced cell death during hematopoiesis and testicular development in mice []. Bim(L) displaces Bcl-x(L) in the mitochondria and promotes Bax translocation during TNFalpha-induced apoptosis []. A potent inhibitor of antiapoptotic Bcl-2 family members, including Bcl-X(L), is AT-101 []. The immunophilin protein FKBP8 and its splice variant are Bcl-XL-interacting proteins and regulate the apoptotic signalling pathways in the RPE []. This protein is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11 []. ; PDB: 2NL9_B 2V6Q_B 3KJ0_B 3KJ1_B 3FDL_B 3D7V_B 3IO8_D 2K7W_B 2VM6_B 3IO9_B ....
Probab=25.23 E-value=26 Score=22.90 Aligned_cols=27 Identities=22% Similarity=0.313 Sum_probs=16.5
Q ss_pred EEEEEEecC-CchhhhhhHHHHHHhCCC
Q 031642 84 TSKSLTTNL-SDLEAAQPLSKLCLEFPD 110 (156)
Q Consensus 84 ~S~tv~~~~-~Eg~IA~~L~~Iq~~~Pd 110 (156)
.|++..+++ +|=-||..|++|-++|-.
T Consensus 6 qsq~~P~~~~PE~wiAqELRRIgDEFna 33 (40)
T PF08945_consen 6 QSQAEPVDMRPEIWIAQELRRIGDEFNA 33 (40)
T ss_dssp ---------HHHHHHHHHHHHHHHHHHH
T ss_pred hhhcCCccCCHHHHHHHHHHHHHHHhcc
Confidence 355666664 899999999999999864
No 101
>PHA02755 hypothetical protein; Provisional
Probab=25.13 E-value=34 Score=25.82 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=12.5
Q ss_pred hCCCceeeccccccCC
Q 031642 107 EFPDLHIGCYRKSRQG 122 (156)
Q Consensus 107 ~~Pdv~IGSYP~~~~g 122 (156)
-+|.+.|||||---+|
T Consensus 5 i~~gm~igsypdavqg 20 (96)
T PHA02755 5 ISGGMAIGSYPDAVQG 20 (96)
T ss_pred CCCCcccccCcccccC
Confidence 3688999999965555
No 102
>cd06188 NADH_quinone_reductase Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain.
Probab=24.97 E-value=1.5e+02 Score=24.51 Aligned_cols=85 Identities=15% Similarity=0.111 Sum_probs=46.5
Q ss_pred CceeeeccCCCCceeeCCCcccceeE--eCe-EEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhh
Q 031642 21 PRWLCCRKVPPNCCITTSCSYLWYIK--CQN-VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEA 97 (156)
Q Consensus 21 ~~~~~~~~~~~~~~I~NpvS~APGF~--igN-V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~I 97 (156)
-+||+.-++-...-|..|....- +. -++ |+|-+|+-+..+.+|+..++.. + ..+.++. -+.....+.++
T Consensus 123 S~~L~~l~~Gd~v~i~gP~G~f~-l~~~~~~~vlIAgGtGItP~~s~l~~~~~~---~--~~~~~v~--l~~g~r~~~d~ 194 (283)
T cd06188 123 SSYIFNLKPGDKVTASGPFGEFF-IKDTDREMVFIGGGAGMAPLRSHIFHLLKT---L--KSKRKIS--FWYGARSLKEL 194 (283)
T ss_pred hhHHhcCCCCCEEEEECcccccc-ccCCCCcEEEEEecccHhHHHHHHHHHHhc---C--CCCceEE--EEEecCCHHHh
Confidence 36786544444455666653321 11 122 5666676566677788776532 1 0012321 13344445544
Q ss_pred --hhhHHHHHHhCCCcee
Q 031642 98 --AQPLSKLCLEFPDLHI 113 (156)
Q Consensus 98 --A~~L~~Iq~~~Pdv~I 113 (156)
.+.|.+++++||++.+
T Consensus 195 ~~~~el~~l~~~~~~~~~ 212 (283)
T cd06188 195 FYQEEFEALEKEFPNFKY 212 (283)
T ss_pred hHHHHHHHHHHHCCCeEE
Confidence 5889999999998653
No 103
>COG1169 MenF Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.77 E-value=3e+02 Score=25.80 Aligned_cols=57 Identities=16% Similarity=0.132 Sum_probs=45.9
Q ss_pred HHHHHHHHHhHHhCCCccCCceEEEEEEecC-CchhhhhhHHHHHHhCCCceeecccccc
Q 031642 62 DKEWNCLIELLRSGGLSLMEPYTSKSLTTNL-SDLEAAQPLSKLCLEFPDLHIGCYRKSR 120 (156)
Q Consensus 62 ~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~-~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~ 120 (156)
..+++..+.+++.| +..+-+++|.+...+ ..-+.+..|.++-+.+|+.++=.++...
T Consensus 160 ~~~v~~A~~~i~~~--~l~KVVLAR~~~l~~~~pi~~~~~L~~l~~~n~~~Y~F~~~~~~ 217 (423)
T COG1169 160 LQLVEQALALIAQG--ELDKVVLARALDLTFDAPIDAAALLARLRAQNPNCYHFLVALGD 217 (423)
T ss_pred HHHHHHHHHHHhcC--CcceEEEeeeecccCCCCCCHHHHHHHHHHhCCCceEEEEecCC
Confidence 55888888888887 456789999999886 5889999999999999987665555433
No 104
>TIGR03026 NDP-sugDHase nucleotide sugar dehydrogenase. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
Probab=24.36 E-value=4.9e+02 Score=22.91 Aligned_cols=90 Identities=14% Similarity=0.094 Sum_probs=48.5
Q ss_pred eCeEEEecCCCCch----------HHHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHh------CCC
Q 031642 47 CQNVIILTATNVTE----------LDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLE------FPD 110 (156)
Q Consensus 47 igNV~VMAGV~VP~----------I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~------~Pd 110 (156)
.+-|+++-++ |. +....+.+.+.++.| .-++..| +.+-|...+....+.++ +.|
T Consensus 77 advvii~vpt--~~~~~~~~d~~~v~~~~~~i~~~l~~g-----~lvi~~S---Tv~pgt~~~l~~~~~~~~~g~~~~~d 146 (411)
T TIGR03026 77 ADVIIICVPT--PLKEDGSPDLSYVESAAETIAKHLRKG-----ATVVLES---TVPPGTTEEVVKPILERASGLKLGED 146 (411)
T ss_pred CCEEEEEeCC--CCCCCCCcChHHHHHHHHHHHHhcCCC-----CEEEEeC---cCCCCchHHHHHHHHHhhcCCCCCCC
Confidence 4667777663 52 455566677665544 6555433 23223222222233222 567
Q ss_pred ceeecccccc-CCCe-------EEEEEecCHHHHHHHHHHHHhh
Q 031642 111 LHIGCYRKSR-QGPL-------IISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 111 v~IGSYP~~~-~g~~-------~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
..+.+-|-+- +|.. .-++=|.|.+..+++.+-+..+
T Consensus 147 ~~v~~~Pe~~~~G~~~~~~~~~~~iv~G~~~~~~~~~~~l~~~~ 190 (411)
T TIGR03026 147 FYLAYNPEFLREGNAVHDLLNPDRIVGGETEEAGEAVAELYAPI 190 (411)
T ss_pred ceEEECCCcCCCCChhhhhcCCCEEEEeCCHHHHHHHHHHHHHh
Confidence 7888888665 4432 1455566777776655544444
No 105
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=24.30 E-value=91 Score=21.90 Aligned_cols=50 Identities=14% Similarity=0.011 Sum_probs=26.3
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccc
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 117 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP 117 (156)
+.+ ...+..++..++.- .|-+.-.+. ++.-.+....+.+.-=|+-|...|
T Consensus 8 ~~~~~~~l~~~l~~~~~~-----~P~i~l~i~----~~~~~~~~~~l~~~~~D~~i~~~~ 58 (198)
T cd08412 8 STLAPYYLPGLLRRFREA-----YPGVEVRVV----EGNQEELEEGLRSGELDLALTYDL 58 (198)
T ss_pred cccchhhhHHHHHHHHHH-----CCCcEEEEE----ECCHHHHHHHHHcCCCcEEEEcCC
Confidence 444 33555555565444 665555554 333344455555555566666544
No 106
>PRK12739 elongation factor G; Reviewed
Probab=24.24 E-value=2.7e+02 Score=26.72 Aligned_cols=114 Identities=12% Similarity=0.207 Sum_probs=73.6
Q ss_pred cCCCCceeeCCCcccceeEeCeEEEecC---CCCchHHH-HHHHHH--HhHHhCC-C------------ccCCceEEEEE
Q 031642 28 KVPPNCCITTSCSYLWYIKCQNVIILTA---TNVTELDK-EWNCLI--ELLRSGG-L------------SLMEPYTSKSL 88 (156)
Q Consensus 28 ~~~~~~~I~NpvS~APGF~igNV~VMAG---V~VP~I~a-Ml~~l~--p~L~~G~-L------------~~gap~~S~tv 88 (156)
++-++.=|.|+-+.. ..+++++++|.| +.|+++.+ .+-.|. ..++.|+ | ..-.|++..+|
T Consensus 332 tL~~g~~v~~~~~~~-~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~gdtl~~~~~~~~l~~~~~~~Pv~~~ai 410 (691)
T PRK12739 332 VLESGSYVLNTTKGK-KERIGRLLQMHANKREEIKEVYAGDIAAAVGLKDTTTGDTLCDEKAPIILESMEFPEPVISLAV 410 (691)
T ss_pred EEcCCCEEEeCCCCc-eEEecceEEEecCCcccccccCCCCEEEEeCCCcccCCCEEeCCCCccccCCCCCCCceEEEEE
Confidence 344555666655443 467888888876 11222211 111111 0112332 2 22368888998
Q ss_pred EecC--CchhhhhhHHHHHHhCCCceeeccccccCCCe-EEEEEecCHHHHHHHHHHHHhhh
Q 031642 89 TTNL--SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL-IISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 89 ~~~~--~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~-~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
...- .+..+.+.|.+|+++.|.+.+ ..+... .+++.|.-+-.||-+.++|++.|
T Consensus 411 ep~~~~d~~kL~~aL~~L~~eDpsl~v-----~~~~etge~il~g~GelHLei~~~rL~~~f 467 (691)
T PRK12739 411 EPKTKADQDKMGLALQKLAEEDPTFRV-----ETDEETGQTIISGMGELHLDIIVDRMKREF 467 (691)
T ss_pred EECCcccHHHHHHHHHHHHHhCCeEEE-----EEcCCCCCEEEEEecHHHHHHHHHHHHHHh
Confidence 8663 678899999999999999986 223333 58889999999999999999987
No 107
>cd07449 CRD_FZ3 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 3 (Fz3) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 3 (Fz3) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz3 plays a vital role in the anterior-posterior guidance of commissural axons. Knockout mice without Fz3 show defects in fiber tracts in the rostral CNS.
Probab=24.04 E-value=61 Score=25.36 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=24.3
Q ss_pred HHhcCcCCceeeeccCCCCc-----eeeCCCcccc
Q 031642 14 RLLGYKYPRWLCCRKVPPNC-----CITTSCSYLW 43 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~-----~I~NpvS~AP 43 (156)
+.+|+.+|..|-|.+.|... |++-..|+.|
T Consensus 92 ~~fg~~WP~~L~C~~fP~~~~~~~~c~~~~~~~~~ 126 (127)
T cd07449 92 EMFGVPWPEDMECSRFPDCDEPYPRLVDLSLSGEP 126 (127)
T ss_pred HHhCCCCCCcCCcccCCCCCCCcccccccccCCCC
Confidence 46899999999999999865 7776666655
No 108
>cd06191 FNR_iron_sulfur_binding Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with a C-terminal iron-sulfur binding cluster domain. FNR was intially identified as a chloroplast reductase activity catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methnae assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in
Probab=23.99 E-value=1.9e+02 Score=22.71 Aligned_cols=96 Identities=14% Similarity=0.145 Sum_probs=50.4
Q ss_pred hHHhHHhcCcCCceeee-ccCCCCceeeCCCccccee--EeCeE-EEecCCCCchHHHHHHHHHHhHHhCCCccCCceEE
Q 031642 10 LVVRRLLGYKYPRWLCC-RKVPPNCCITTSCSYLWYI--KCQNV-IILTATNVTELDKEWNCLIELLRSGGLSLMEPYTS 85 (156)
Q Consensus 10 ~~~~~~~~~~~~~~~~~-~~~~~~~~I~NpvS~APGF--~igNV-~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S 85 (156)
+.|++.-+=+.-.|++- -+.-...=|.-|....+-- .-+|+ +|-+|+-+..+.+|+..+... ..+ .++.
T Consensus 62 ~~v~~~~~G~~s~~l~~~~~~Gd~v~i~gP~G~f~l~~~~~~~~lliagG~Gitp~~s~~~~~~~~-~~~-----~~v~- 134 (231)
T cd06191 62 ITVKRVPGGRVSNYLREHIQPGMTVEVMGPQGHFVYQPQPPGRYLLVAAGSGITPLMAMIRATLQT-APE-----SDFT- 134 (231)
T ss_pred EEEEECCCCccchHHHhcCCCCCEEEEeCCccceEeCCCCCCcEEEEecCccHhHHHHHHHHHHhc-CCC-----CCEE-
Confidence 33444333346677763 2333334466665432211 12464 455566567777788877642 111 3332
Q ss_pred EEEEecCCchh--hhhhHHHHHHhCCCcee
Q 031642 86 KSLTTNLSDLE--AAQPLSKLCLEFPDLHI 113 (156)
Q Consensus 86 ~tv~~~~~Eg~--IA~~L~~Iq~~~Pdv~I 113 (156)
-+.....+.+ ..+.|.+++++++++.+
T Consensus 135 -l~~~~r~~~~~~~~~el~~l~~~~~~~~~ 163 (231)
T cd06191 135 -LIHSARTPADMIFAQELRELADKPQRLRL 163 (231)
T ss_pred -EEEecCCHHHHhHHHHHHHHHHhCCCeEE
Confidence 1223333333 46789999999988765
No 109
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=23.46 E-value=2.3e+02 Score=18.71 Aligned_cols=57 Identities=9% Similarity=0.134 Sum_probs=40.9
Q ss_pred EEecCCchhhhhhHHHHHHhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhh
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
+.+.-.-|-+++.+..|++. ++.|-+.=...++...+.+...|.+.+++..++|++.
T Consensus 5 I~~~dr~Gll~dI~~~i~~~--~~nI~~~~~~~~~~i~l~i~v~~~~~L~~li~~L~~i 61 (74)
T cd04877 5 ITCEDRLGITQEVLDLLVEH--NIDLRGIEIDPKGRIYLNFPTIEFEKLQTLMPEIRRI 61 (74)
T ss_pred EEEEccchHHHHHHHHHHHC--CCceEEEEEecCCeEEEEeEecCHHHHHHHHHHHhCC
Confidence 44555678788888888664 6666555544333367889999999999999988763
No 110
>COG2037 Ftr Formylmethanofuran:tetrahydromethanopterin formyltransferase [Energy production and conversion]
Probab=22.94 E-value=1.4e+02 Score=26.73 Aligned_cols=39 Identities=18% Similarity=0.154 Sum_probs=30.6
Q ss_pred CCceeeCCCcccceeEeCeEEEecCCCCch-H---HHHHHHHHH
Q 031642 31 PNCCITTSCSYLWYIKCQNVIILTATNVTE-L---DKEWNCLIE 70 (156)
Q Consensus 31 ~~~~I~NpvS~APGF~igNV~VMAGV~VP~-I---~aMl~~l~p 70 (156)
+.--|++-+..+-|+-=||+|+|+=. .++ + ++-+++|..
T Consensus 147 geFiiE~~~Gy~~giaGgnf~im~es-~~saL~Aa~aAV~Ai~~ 189 (297)
T COG2037 147 GEFIIERRIGYAEGIAGGNFWIMCES-QDSALEAAEAAVDAIEE 189 (297)
T ss_pred cceEEeeccchhhhccCceEEEEecC-cHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999995 666 4 336666664
No 111
>TIGR00222 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase. Members of this family are 3-methyl-2-oxobutanoate hydroxymethyltransferase, the first enzyme of the pantothenate biosynthesis pathway. An alternate name is ketopantoate hydroxymethyltransferase.
Probab=22.84 E-value=5.1e+02 Score=22.56 Aligned_cols=56 Identities=20% Similarity=0.186 Sum_probs=42.3
Q ss_pred hhhhhHHHHHHhCCCc--eeecccccc--CCCeEEEEEecCHHHHHHHHHHHHhhhccCCcc
Q 031642 96 EAAQPLSKLCLEFPDL--HIGCYRKSR--QGPLIISFEGKDQARIEAAIESLFKKFHRGAFS 153 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv--~IGSYP~~~--~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f~ 153 (156)
++++.++.+.+.-=.| .||==|..- .|++.+ .|++.++.++++++.+++-+.|+|.
T Consensus 117 ~~~~~i~~l~~~gIpV~gHiGltPq~a~~~ggy~~--qgrt~~~a~~~i~~A~a~e~AGA~~ 176 (263)
T TIGR00222 117 WLVETVQMLTERGVPVVGHLGLTPQSVNILGGYKV--QGKDEEAAKKLLEDALALEEAGAQL 176 (263)
T ss_pred hHHHHHHHHHHCCCCEEEecCCCceeEeecCCeee--cCCCHHHHHHHHHHHHHHHHcCCCE
Confidence 4677777777765444 478778643 344554 4999999999999999999999986
No 112
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=22.76 E-value=2.1e+02 Score=18.02 Aligned_cols=43 Identities=7% Similarity=-0.075 Sum_probs=28.1
Q ss_pred EEecCCchhhhhhHHHHHHhCCCc-eeeccccccCCCeEEEEEe
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSRQGPLIISFEG 130 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~~g~~~lVvRG 130 (156)
+...-..|.+|..+..++++.=++ ++.+++...++...+++|=
T Consensus 4 v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v 47 (73)
T cd04902 4 VRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSV 47 (73)
T ss_pred EEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEe
Confidence 345567899999888888776655 4666665444444455553
No 113
>TIGR00254 GGDEF diguanylate cyclase (GGDEF) domain. The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein.
Probab=22.72 E-value=2.4e+02 Score=19.62 Aligned_cols=29 Identities=10% Similarity=0.143 Sum_probs=24.3
Q ss_pred CCCeEEEEEecCHHHHHHHHHHHHhhhcc
Q 031642 121 QGPLIISFEGKDQARIEAAIESLFKKFHR 149 (156)
Q Consensus 121 ~g~~~lVvRG~D~~~l~aA~~~l~~~~~~ 149 (156)
++.|.+++.+.|.+..++..+.+.+.+.+
T Consensus 82 ~~~f~il~~~~~~~~~~~l~~~i~~~~~~ 110 (165)
T TIGR00254 82 GEEFVVILPGTPLEDALSKAERLRDAINS 110 (165)
T ss_pred CCeEEEEeCCCChHHHHHHHHHHHHHHHh
Confidence 45788999999998999889999887754
No 114
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=22.67 E-value=82 Score=22.62 Aligned_cols=43 Identities=14% Similarity=0.101 Sum_probs=19.7
Q ss_pred HHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceee
Q 031642 63 KEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIG 114 (156)
Q Consensus 63 aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IG 114 (156)
..+..++..++.- -|=+.-++. ++.-.+.+..+.+.-=|+-|.
T Consensus 13 ~~l~~~l~~~~~~-----~P~v~i~i~----~~~~~~~~~~l~~~~~Dl~i~ 55 (197)
T cd08452 13 EFLPPIVREYRKK-----FPSVKVELR----ELSSPDQVEELLKGRIDIGFL 55 (197)
T ss_pred hHHHHHHHHHHHH-----CCCcEEEEE----ecChHHHHHHHHCCCccEEEe
Confidence 3555555555433 453333332 334444455555544444443
No 115
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=22.61 E-value=99 Score=21.73 Aligned_cols=21 Identities=19% Similarity=0.213 Sum_probs=10.5
Q ss_pred hhhhhhHHHHHHhCCCceeec
Q 031642 95 LEAAQPLSKLCLEFPDLHIGC 115 (156)
Q Consensus 95 g~IA~~L~~Iq~~~Pdv~IGS 115 (156)
+.-.+.++.+.+..=|+-|..
T Consensus 36 ~~~~~~~~~l~~g~~Dl~i~~ 56 (199)
T cd08430 36 GDPADAIDKVLNGEADIAIAA 56 (199)
T ss_pred CCHHHHHHHHHCCCCCEEEEe
Confidence 333444555555555555544
No 116
>PRK13679 hypothetical protein; Provisional
Probab=22.55 E-value=3.6e+02 Score=20.71 Aligned_cols=84 Identities=15% Similarity=0.103 Sum_probs=45.7
Q ss_pred ch-HHHHHHHHHHhHHhCCCccCCceEEEEEEec----CCch---hhhhhHHHHHHhCC--CceeeccccccCCCeEEEE
Q 031642 59 TE-LDKEWNCLIELLRSGGLSLMEPYTSKSLTTN----LSDL---EAAQPLSKLCLEFP--DLHIGCYRKSRQGPLIISF 128 (156)
Q Consensus 59 P~-I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~----~~Eg---~IA~~L~~Iq~~~P--dv~IGSYP~~~~g~~~lVv 128 (156)
|+ ++..++.+...+..++ .+ +-..|+.. ..|. ++.+.|.++.+.++ +++++++=.|....-.|.+
T Consensus 10 p~~~~~~l~~~~~~~~~~~----~~-v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~F~~~~~vl~l 84 (168)
T PRK13679 10 SKKIQDFANSYRKRYDPHY----AL-IPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAPTNNVIYF 84 (168)
T ss_pred CHHHHHHHHHHHHhhCccc----cc-CCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEeccccCCCCCCEEEE
Confidence 44 5778888877764331 21 22244433 3332 34666667776554 6888777555422223444
Q ss_pred EecCHHHHHHHHHHHHhhh
Q 031642 129 EGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 129 RG~D~~~l~aA~~~l~~~~ 147 (156)
.-.+.+.|.+-.++|++.+
T Consensus 85 ~~~~~~~L~~L~~~l~~~~ 103 (168)
T PRK13679 85 KVEKTEELEELHERLHSGD 103 (168)
T ss_pred EccCCHHHHHHHHHHHhcc
Confidence 4444567777666666543
No 117
>PRK00984 truD tRNA pseudouridine synthase D; Reviewed
Probab=22.44 E-value=3.5e+02 Score=24.05 Aligned_cols=65 Identities=15% Similarity=0.217 Sum_probs=40.9
Q ss_pred CccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccC---------CCeEEEEEecC--HHHHHHHHHHHH
Q 031642 77 LSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ---------GPLIISFEGKD--QARIEAAIESLF 144 (156)
Q Consensus 77 L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~---------g~~~lVvRG~D--~~~l~aA~~~l~ 144 (156)
++.-.-+..+.+.+..+ +...+.|.++ +.+++.|+..=+... .+|.|++|+.+ .+.++++.+.|+
T Consensus 78 ~KDk~AvT~Q~~si~~~-~~~~~~~~~~--~~~~~~i~~~~~~~~~l~~G~l~GN~F~I~lR~~~~~~~~~~~~l~~l~ 153 (341)
T PRK00984 78 LKDRHAVTTQWFSIHLP-GKEEPDLSAF--QLEGLEILELGRHNRKLRLGDLKGNRFTIRLREVSKDRDKVEQRLEEIA 153 (341)
T ss_pred cCcCCeeeEEEEEEECC-CCChhhHhhc--ccCCeEEEEEEccCCCCCCCcCCCCEEEEEEecCCCCHHHHHHHHHHHH
Confidence 66666677776666431 1112334444 678999887655432 14789999995 666777766665
No 118
>cd06194 FNR_N-term_Iron_sulfur_binding Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second e
Probab=22.44 E-value=3.3e+02 Score=21.15 Aligned_cols=96 Identities=15% Similarity=0.139 Sum_probs=50.1
Q ss_pred hHHhHHhcCcCCceeeec-cCCCCceeeCCCcccce---eEeCeE-EEecCCCCchHHHHHHHHHHhHHhCCCccCCceE
Q 031642 10 LVVRRLLGYKYPRWLCCR-KVPPNCCITTSCSYLWY---IKCQNV-IILTATNVTELDKEWNCLIELLRSGGLSLMEPYT 84 (156)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~-~~~~~~~I~NpvS~APG---F~igNV-~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~ 84 (156)
+.+++.-+=.+-+||+-. +.-...=|..|.....- ..-.++ +|-.|+-+..+.+|++.++.. + ...++.
T Consensus 56 ~~i~~~~~G~~s~~l~~~~~~G~~v~i~gP~G~~~~~~~~~~~~~v~iagG~Giap~~~~l~~~~~~---~---~~~~v~ 129 (222)
T cd06194 56 FHIRRKPNGAFSGWLGEEARPGHALRLQGPFGQAFYRPEYGEGPLLLVGAGTGLAPLWGIARAALRQ---G---HQGEIR 129 (222)
T ss_pred EEEEeccCCccchHHHhccCCCCEEEEecCcCCeeccCCCCCCCEEEEecCcchhhHHHHHHHHHhc---C---CCccEE
Confidence 334443333456777753 44444456666543211 112354 455565566677788777643 1 001221
Q ss_pred EEEEEecC--CchhhhhhHHHHHHhCCCcee
Q 031642 85 SKSLTTNL--SDLEAAQPLSKLCLEFPDLHI 113 (156)
Q Consensus 85 S~tv~~~~--~Eg~IA~~L~~Iq~~~Pdv~I 113 (156)
- +.... .+-.+.+.|.++++++|++.+
T Consensus 130 l--~~~~r~~~~~~~~~el~~l~~~~~~~~~ 158 (222)
T cd06194 130 L--VHGARDPDDLYLHPALLWLAREHPNFRY 158 (222)
T ss_pred E--EEecCChhhccCHHHHHHHHHHCCCeEE
Confidence 1 22222 233467889999999998764
No 119
>PF05893 LuxC: Acyl-CoA reductase (LuxC); InterPro: IPR008670 This family consists of several bacterial Acyl-CoA reductase (LuxC) proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalysed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0008218 bioluminescence, 0055114 oxidation-reduction process
Probab=22.30 E-value=71 Score=28.78 Aligned_cols=19 Identities=21% Similarity=0.092 Sum_probs=14.3
Q ss_pred EEEecCCCCchH--HHHHHHHH
Q 031642 50 VIILTATNVTEL--DKEWNCLI 69 (156)
Q Consensus 50 V~VMAGV~VP~I--~aMl~~l~ 69 (156)
.||+|| |||-+ ..++..|+
T Consensus 92 ~Hi~ag-Nvp~~~~~S~~~~lL 112 (399)
T PF05893_consen 92 FHIAAG-NVPLVGFYSLVRGLL 112 (399)
T ss_pred EEEcCC-CccchHHHHHHHHHH
Confidence 499999 89997 44666555
No 120
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.93 E-value=88 Score=28.78 Aligned_cols=25 Identities=16% Similarity=-0.047 Sum_probs=22.6
Q ss_pred hhhhhHHHHHHhCCCceeecccccc
Q 031642 96 EAAQPLSKLCLEFPDLHIGCYRKSR 120 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv~IGSYP~~~ 120 (156)
.|++.|.+..+.+|++.|+|||..-
T Consensus 269 SivEVL~~~~~~~~~~~i~sdp~G~ 293 (358)
T COG1244 269 SIVEVLREAKKTGPMLRILSDPVGA 293 (358)
T ss_pred HHHHHHHHHHhcCCCCceeecCCCC
Confidence 4789999999999999999999765
No 121
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=21.82 E-value=96 Score=22.37 Aligned_cols=26 Identities=8% Similarity=0.066 Sum_probs=13.2
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEE
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLT 89 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~ 89 (156)
|.+ ...+..++..++.- -|=+.-++.
T Consensus 8 ~~~~~~~l~~~l~~~~~~-----~P~v~l~i~ 34 (198)
T cd08444 8 HTQARYALPWVVQAFKEQ-----FPNVHLVLH 34 (198)
T ss_pred chhhhhhhhHHHHHHHHH-----CCCeEEEEE
Confidence 455 44555555565443 454444443
No 122
>PRK00311 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed
Probab=21.81 E-value=2.1e+02 Score=24.71 Aligned_cols=56 Identities=25% Similarity=0.338 Sum_probs=42.1
Q ss_pred hhhhhHHHHHHhCCCc--eeecccccc--CCCeEEEEEecCHHHHHHHHHHHHhhhccCCcc
Q 031642 96 EAAQPLSKLCLEFPDL--HIGCYRKSR--QGPLIISFEGKDQARIEAAIESLFKKFHRGAFS 153 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv--~IGSYP~~~--~g~~~lVvRG~D~~~l~aA~~~l~~~~~~~~f~ 153 (156)
++++.+.++.++-=.| .||==|++. .|++.+ .|++.++.+++.++.++.-+.|+|.
T Consensus 118 ~~~~~I~al~~agIpV~gHiGL~pq~~~~~gg~~i--~grt~~~a~~~i~ra~a~~eAGA~~ 177 (264)
T PRK00311 118 EVAETIKRLVERGIPVMGHLGLTPQSVNVLGGYKV--QGRDEEAAEKLLEDAKALEEAGAFA 177 (264)
T ss_pred HHHHHHHHHHHCCCCEeeeecccceeecccCCeee--ecCCHHHHHHHHHHHHHHHHCCCCE
Confidence 5777788887664333 567777654 234444 8999999999999999999999985
No 123
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=21.79 E-value=81 Score=22.26 Aligned_cols=50 Identities=20% Similarity=-0.025 Sum_probs=28.3
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccc
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 117 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP 117 (156)
+.+ ...+..++..+..- .|=+.-.+.. +.-.+.++.+.+.-=|+-|...|
T Consensus 8 ~~~~~~~l~~~l~~~~~~-----~P~i~l~i~~----~~~~~~~~~l~~~~~Dl~i~~~~ 58 (199)
T cd08416 8 YSLTVNTVPRIIMGLKLR-----RPELDIELTL----GSNKDLLKKLKDGELDAILVATP 58 (199)
T ss_pred hHHHHhhhHHHHHHHHHh-----CCCeEEEEEE----cCcHHHHHHHhCCCCCEEEEecC
Confidence 555 45666666665554 6665555543 22334455566665677776555
No 124
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=21.76 E-value=1.1e+02 Score=23.12 Aligned_cols=36 Identities=6% Similarity=-0.167 Sum_probs=26.4
Q ss_pred CCceeeCCCcccceeEeCe--EEEecCCCCchH-HHHHHHH
Q 031642 31 PNCCITTSCSYLWYIKCQN--VIILTATNVTEL-DKEWNCL 68 (156)
Q Consensus 31 ~~~~I~NpvS~APGF~igN--V~VMAGV~VP~I-~aMl~~l 68 (156)
+.....+|-+.+.+++++| |+.|+| .|.= ..+|+.+
T Consensus 103 ~~~~~~~PG~~~~~~~~~~~~v~~LPG--~P~aa~~~~~~~ 141 (144)
T TIGR00177 103 FTAVLSRPGKPATAGVRGGTLIFGLPG--NPVSALVTFEVL 141 (144)
T ss_pred cchhhCCCCCceEEEEECCEEEEECCC--CHHHHHHHHHHH
Confidence 3445678888888888887 888999 5773 5577654
No 125
>cd06204 CYPOR NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredo
Probab=21.76 E-value=5.8e+02 Score=22.80 Aligned_cols=90 Identities=18% Similarity=0.078 Sum_probs=47.3
Q ss_pred EEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEecC-Cchh--hhhhHHHHHHhCCCceeeccccccCCCeEE
Q 031642 50 VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNL-SDLE--AAQPLSKLCLEFPDLHIGCYRKSRQGPLII 126 (156)
Q Consensus 50 V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~-~Eg~--IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~~l 126 (156)
|.|-+|+-+--+.+|+....-..+.| -..| ++.- +.... .+.+ ..+.|.+++++++.+.+- +-+++++.
T Consensus 269 ImIa~GtGIAP~~s~l~~~~~~~~~~-~~~~-~v~L--~~G~R~~~~d~ly~~el~~~~~~~~~~~l~-~a~Sr~~~--- 340 (416)
T cd06204 269 IMIGPGTGVAPFRGFIQERAALKESG-KKVG-PTLL--FFGCRHPDEDFIYKDELEEYAKLGGLLELV-TAFSREQP--- 340 (416)
T ss_pred EEEeCCcchHHHHHHHHHHHHHhhcc-CccC-CEEE--EEcCCCCCcccchHHHHHHHHHcCCceEEE-EEECcCCC---
Confidence 77888877777888988765433233 0111 2211 22222 3233 578899999887766542 22233322
Q ss_pred EEEecCHHHHHHHHHHHHhhhc
Q 031642 127 SFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 127 VvRG~D~~~l~aA~~~l~~~~~ 148 (156)
-+|.-++++.+..+++.+.+.
T Consensus 341 -~k~yVq~~i~~~~~~~~~~l~ 361 (416)
T cd06204 341 -KKVYVQHRLAEHAEQVWELIN 361 (416)
T ss_pred -CCcchHHHHHHhHHHHHHHHH
Confidence 022334556555555555554
No 126
>TIGR01709 typeII_sec_gspL general secretion pathway protein L. This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=21.64 E-value=2.3e+02 Score=24.77 Aligned_cols=55 Identities=22% Similarity=0.302 Sum_probs=43.2
Q ss_pred CchhhhhhHHHHHHhC---CCceeecccccc-CCCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 93 SDLEAAQPLSKLCLEF---PDLHIGCYRKSR-QGPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 93 ~Eg~IA~~L~~Iq~~~---Pdv~IGSYP~~~-~g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
+..++...|++++..+ |++.+-|-.|.. .+.+.+-+++.|.+.+++..+++.+.|
T Consensus 304 ~~~~fl~lL~~l~~al~~~~~~~l~sL~y~~~~~~L~l~l~a~~~~~le~l~~~l~~g~ 362 (384)
T TIGR01709 304 SGQGFLDLLAALATALGQLPGLQLQSLDFDGARGELRLKLEAPSDADLEQLRSRLARGF 362 (384)
T ss_pred CcchHHHHHHHHHHHhccCCCCceeEEeEcCCCCEEEEEEecCChHHHHHHHHHHhhhc
Confidence 3457888888888755 689999988775 345789999999999999888886433
No 127
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=21.45 E-value=2.8e+02 Score=21.47 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=40.0
Q ss_pred CCchhhhhhHHHHHHhCCCceeeccccccCCC--e-EEEEEecCHHHHHHHHHHHH
Q 031642 92 LSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGP--L-IISFEGKDQARIEAAIESLF 144 (156)
Q Consensus 92 ~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~--~-~lVvRG~D~~~l~aA~~~l~ 144 (156)
-...++...|.+||.+|-|+-+=|.=..-++. + .+++||. ..++++-+++|.
T Consensus 61 H~~~~l~~~l~~iqH~~~d~Iiss~HvHld~~~ClEvivv~G~-~~~I~~l~~~l~ 115 (129)
T TIGR02793 61 HSKRDLPRRLTQTQHHHHDLSVATLHVHLDHDDCLEVSVLKGD-MGDVQHFADHVI 115 (129)
T ss_pred CCchhHHHHHHHHHHhhccEEEEEEEEecCCCceEEEEEEEcC-HHHHHHHHHHHH
Confidence 35678999999999999999988877665655 2 4999995 556666666665
No 128
>cd07464 CRD_FZ2 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 2 (Fz2) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 2 (Fz2) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz2 is involved in the Wnt/beta-catenin signaling pathway and in the activation of protein kinase C and calcium/calmodulin-dependent protein kinase (CaM kinase).
Probab=21.37 E-value=64 Score=25.10 Aligned_cols=28 Identities=25% Similarity=0.679 Sum_probs=22.8
Q ss_pred HHhcCcCCceeeeccCCCCc----eeeCCCcc
Q 031642 14 RLLGYKYPRWLCCRKVPPNC----CITTSCSY 41 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~----~I~NpvS~ 41 (156)
+-+|+.+|..|-|.+.|..- ||+.+.+.
T Consensus 92 ~~fg~~WP~~l~C~~fP~~~~~~~C~~~~~~~ 123 (127)
T cd07464 92 NKFGFQWPERLRCENFPRHGAEQICVGQNHSE 123 (127)
T ss_pred HHhCCCCCCcCCcccCCCCCCCCcCCCCCCCC
Confidence 45899999999999999974 88665553
No 129
>PRK04460 nickel responsive regulator; Provisional
Probab=21.28 E-value=2.8e+02 Score=21.78 Aligned_cols=52 Identities=17% Similarity=0.195 Sum_probs=40.3
Q ss_pred CCchhhhhhHHHHHHhCCCceeeccccccCCCe---EEEEEecCHHHHHHHHHHHH
Q 031642 92 LSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL---IISFEGKDQARIEAAIESLF 144 (156)
Q Consensus 92 ~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~---~lVvRG~D~~~l~aA~~~l~ 144 (156)
-..+++...|.++|.+|-|+-+=|+=..-++.- .+++||. ..++++=+++|.
T Consensus 63 H~~~~l~~~l~~iqH~~~d~Iiss~HvHld~~~ClEvivv~G~-~~~I~~L~~~l~ 117 (137)
T PRK04460 63 HHVSDLAQKLTEIQHDHHDEIISSLHVHLDHHNCLEVLVLKGK-AKEIKKIADRLI 117 (137)
T ss_pred CCcchHHHHHHHHHHhhhceEEEEEEEecCCCcEEEEEEEEcC-HHHHHHHHHHHH
Confidence 356788999999999999999999877666652 4888985 566666666666
No 130
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=21.16 E-value=42 Score=28.59 Aligned_cols=32 Identities=19% Similarity=0.375 Sum_probs=24.6
Q ss_pred EEEecCCCCchHHHHHHHHHHhHHhCC--CccCCce
Q 031642 50 VIILTATNVTELDKEWNCLIELLRSGG--LSLMEPY 83 (156)
Q Consensus 50 V~VMAGV~VP~I~aMl~~l~p~L~~G~--L~~gap~ 83 (156)
.|++|| -|.++.-++.+....++|. |+.|-|+
T Consensus 16 ~yi~aG--~P~~~~~~~~~~~l~~~Gad~iElGiPf 49 (258)
T PRK13111 16 PYITAG--DPDLETSLEIIKALVEAGADIIELGIPF 49 (258)
T ss_pred EEEeCC--CCCHHHHHHHHHHHHHCCCCEEEECCCC
Confidence 599999 7999877777776655664 7777776
No 131
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=21.15 E-value=3.8e+02 Score=25.63 Aligned_cols=63 Identities=16% Similarity=0.230 Sum_probs=52.1
Q ss_pred CCceEEEEEEecC--CchhhhhhHHHHHHhCCCceeeccccccCCCe-EEEEEecCHHHHHHHHHHHHhhh
Q 031642 80 MEPYTSKSLTTNL--SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPL-IISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 80 gap~~S~tv~~~~--~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~~-~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
-.|+++.+|...- .+..+.+.|.+|+.+.|.+.+ ..+... ..++.|.-+-.||-+.++|++.+
T Consensus 403 ~~Pvl~~~i~p~~~~d~~kL~~aL~~L~~eDpsl~v-----~~~~etge~il~g~GelHLei~~~~L~~~~ 468 (689)
T TIGR00484 403 PEPVISLAVEPKTKADQEKMGIALGKLAEEDPTFRT-----FTDPETGQTIIAGMGELHLDIIVDRMKREF 468 (689)
T ss_pred CCceEEEEEEECCcccHHHHHHHHHHHHHhCCEEEE-----EECCCCCCEEEEEeeHHHHHHHHHHHHHHh
Confidence 4689999998774 678999999999999999986 223333 47889999999999999999976
No 132
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=21.11 E-value=1.3e+02 Score=21.13 Aligned_cols=24 Identities=8% Similarity=0.079 Sum_probs=14.3
Q ss_pred hhhhhHHHHHHhCCCceeeccccc
Q 031642 96 EAAQPLSKLCLEFPDLHIGCYRKS 119 (156)
Q Consensus 96 ~IA~~L~~Iq~~~Pdv~IGSYP~~ 119 (156)
.-.+..+.+.+.-=|+.|+..|..
T Consensus 37 ~~~~~~~~l~~~~~Dl~i~~~~~~ 60 (196)
T cd08415 37 SSSTVVEAVLSGQADLGLASLPLD 60 (196)
T ss_pred chHHHHHHHHcCCccEEEEeCCCC
Confidence 333445566666667777766643
No 133
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=21.09 E-value=4.5e+02 Score=23.32 Aligned_cols=65 Identities=11% Similarity=0.139 Sum_probs=41.0
Q ss_pred CccCCceEEEEEEecCC-chhhhhhHHHHHHhCCCceeeccccccC---------CCeEEEEEecC--HHHHHHHHHHHH
Q 031642 77 LSLMEPYTSKSLTTNLS-DLEAAQPLSKLCLEFPDLHIGCYRKSRQ---------GPLIISFEGKD--QARIEAAIESLF 144 (156)
Q Consensus 77 L~~gap~~S~tv~~~~~-Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~---------g~~~lVvRG~D--~~~l~aA~~~l~ 144 (156)
++.-.-+..+-+....+ +. .+.......+++.|+..=+.+. .+|.|++|+.+ .+.++++.+.|+
T Consensus 78 ~KDk~AvT~Q~~s~~~~~~~----~~~~~~~~~~~~~v~~~~~~~~~l~~G~l~GN~F~I~lR~~~~~~~~~~~~l~~l~ 153 (387)
T TIGR00094 78 TKDKRAVTEQWVCLRVKGEE----EPDLSNFQLKGVKILEYNRHNRKIRLGDLKGNRFTIRLREVEPNGDELEERLNELC 153 (387)
T ss_pred cccccceeEEEEEeccCchh----hhhHhhcccCCcEEEEEEecCCCcCcccCCCCEEEEEEecCCCCHHHHHHHHHHHH
Confidence 66666677776654432 21 1222344678999998755431 25789999886 566777777775
Q ss_pred h
Q 031642 145 K 145 (156)
Q Consensus 145 ~ 145 (156)
+
T Consensus 154 ~ 154 (387)
T TIGR00094 154 K 154 (387)
T ss_pred h
Confidence 4
No 134
>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=21.09 E-value=75 Score=27.81 Aligned_cols=68 Identities=12% Similarity=0.181 Sum_probs=46.8
Q ss_pred EEEecCCCCchHHHHHHHHHHhHHhCC--CccCCceE-------------EEEEEecCCchhhhhhHHHHHHhCCCceee
Q 031642 50 VIILTATNVTELDKEWNCLIELLRSGG--LSLMEPYT-------------SKSLTTNLSDLEAAQPLSKLCLEFPDLHIG 114 (156)
Q Consensus 50 V~VMAGV~VP~I~aMl~~l~p~L~~G~--L~~gap~~-------------S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IG 114 (156)
+|+|+| =|.++.-++-+.-..++|. |+.|-|+. .|.+.....--++-+.+.++-++++++.|+
T Consensus 21 ~yit~G--dP~~e~s~e~i~~L~~~GaD~iELGvPfSDPvADGP~Iq~A~~rAL~~g~t~~~~lel~~~~r~~~~~~Piv 98 (265)
T COG0159 21 PYVTAG--DPDLETSLEIIKTLVEAGADILELGVPFSDPVADGPTIQAAHLRALAAGVTLEDTLELVEEIRAKGVKVPIV 98 (265)
T ss_pred EEEeCC--CCCHHHHHHHHHHHHhCCCCEEEecCCCCCcCccCHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCCCCEE
Confidence 699999 7999877777775555555 88888872 122222333445667788888888998888
Q ss_pred ccccc
Q 031642 115 CYRKS 119 (156)
Q Consensus 115 SYP~~ 119 (156)
-+=++
T Consensus 99 lm~Y~ 103 (265)
T COG0159 99 LMTYY 103 (265)
T ss_pred EEEec
Confidence 65543
No 135
>PRK07560 elongation factor EF-2; Reviewed
Probab=21.09 E-value=3.1e+02 Score=26.57 Aligned_cols=62 Identities=15% Similarity=0.159 Sum_probs=51.6
Q ss_pred CceEEEEEEecC--CchhhhhhHHHHHHhCCCceeeccccccCCC-eEEEEEecCHHHHHHHHHHHHhhh
Q 031642 81 EPYTSKSLTTNL--SDLEAAQPLSKLCLEFPDLHIGCYRKSRQGP-LIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 81 ap~~S~tv~~~~--~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~-~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
.|+++.+|...- .+-.+.+.|.+|+++.|.+.+ ..+.. -.+++.|.-+-.|+-+.++|++.+
T Consensus 388 ~Pv~~~aI~p~~~~d~~kL~~aL~~L~~eDPsl~v-----~~~~etge~~l~g~GElHLei~~~rL~~~~ 452 (731)
T PRK07560 388 EPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLVV-----KINEETGEHLLSGMGELHLEVITYRIKRDY 452 (731)
T ss_pred CCeEEEEEEECCHHHHHHHHHHHHHHHhhCCcEEE-----EEcCCCCCeEEEcCCHHHHHHHHHHHHHHh
Confidence 689999998763 678899999999999999886 22322 358899999999999999998876
No 136
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.05 E-value=2.4e+02 Score=18.05 Aligned_cols=59 Identities=7% Similarity=-0.089 Sum_probs=40.8
Q ss_pred EEecCCchhhhhhHHHHHHhCCCceeeccccccCCC--eEEEEEecCHHHHHHHHHHHHhh
Q 031642 88 LTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGP--LIISFEGKDQARIEAAIESLFKK 146 (156)
Q Consensus 88 v~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~g~--~~lVvRG~D~~~l~aA~~~l~~~ 146 (156)
+.+.-..|.+|+....|++..-++.==+.....++. ..+.+.-+|.+.+++.+++|++.
T Consensus 4 v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~~~l~~i~~~L~~i 64 (74)
T cd04887 4 LELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSEEHAETIVAAVRAL 64 (74)
T ss_pred EEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCHHHHHHHHHHHhcC
Confidence 445567888999999998876655311112122233 35899999999999999998764
No 137
>PF12687 DUF3801: Protein of unknown function (DUF3801); InterPro: IPR024234 This functionally uncharacterised protein family is found in bacteria. Proteins found in this family are typically between 158 and 187 amino acids in length and include the PcfB protein.
Probab=20.98 E-value=1.5e+02 Score=24.53 Aligned_cols=61 Identities=15% Similarity=0.233 Sum_probs=40.1
Q ss_pred CceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccccccC--CCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 81 EPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ--GPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 81 ap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~~~~--g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
.++.+.. +.+++|-+ +.+.+..| +|..=-.+-... +.+.|.|++.|++.+.+|.+++....
T Consensus 32 ~~l~~i~----i~~~~lk~-F~k~AkKy-GV~yav~kdk~~~~~~~~V~FkA~Da~~i~~af~~~~~~~ 94 (204)
T PF12687_consen 32 KGLKNIE----ITDEDLKE-FKKEAKKY-GVDYAVKKDKSTGPGKYDVFFKAKDADVINRAFKEFSAKK 94 (204)
T ss_pred CCceEEe----cCHhhHHH-HHHHHHHc-CCceEEeeccCCCCCcEEEEEEcCcHHHHHHHHHHHHHHh
Confidence 5554443 45666655 78888877 344333331112 24679999999999999999987654
No 138
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=20.94 E-value=1.3e+02 Score=27.22 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=23.5
Q ss_pred CeEEEEEecCHHHHHHHHHHHHhhhc
Q 031642 123 PLIISFEGKDQARIEAAIESLFKKFH 148 (156)
Q Consensus 123 ~~~lVvRG~D~~~l~aA~~~l~~~~~ 148 (156)
|+++|+-|+++++|++..++|.+.-.
T Consensus 73 G~nvvLIsRt~~KL~~v~kEI~~~~~ 98 (312)
T KOG1014|consen 73 GFNVVLISRTQEKLEAVAKEIEEKYK 98 (312)
T ss_pred CCEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 68899999999999999999988654
No 139
>PRK13239 alkylmercury lyase; Provisional
Probab=20.89 E-value=48 Score=27.98 Aligned_cols=66 Identities=21% Similarity=0.206 Sum_probs=41.0
Q ss_pred CchH-HHHHHHHHHhHHhCCCccCCceEEEEEE--ecCCchhhhhhHHHHHH----hCCCceeecccccc-CCCeEEEEE
Q 031642 58 VTEL-DKEWNCLIELLRSGGLSLMEPYTSKSLT--TNLSDLEAAQPLSKLCL----EFPDLHIGCYRKSR-QGPLIISFE 129 (156)
Q Consensus 58 VP~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~--~~~~Eg~IA~~L~~Iq~----~~Pdv~IGSYP~~~-~g~~~lVvR 129 (156)
-|.- ..++-.|+-.|..| .|+.-.++. +..++.++...|.++.. ..-++ || ||++. +-...+.+-
T Consensus 16 ~~~~~~~~~~~llr~la~G-----~pvt~~~lA~~~~~~~~~v~~~L~~l~~~~~d~~g~i-v~-~plS~~pT~H~v~v~ 88 (206)
T PRK13239 16 EPGGTATLLVPLLRLLAKG-----RPVSVTTLAAALGWPVEEVEAVLEAMPDTEYDEDGRI-IG-YGLTLRPTPHRFEVD 88 (206)
T ss_pred CCCcchHHHHHHHHHHHcC-----CCCCHHHHHHHhCCCHHHHHHHHHhCCCeEECCCCCE-Ee-ccccCCCcCcEEEEC
Confidence 3443 45666677666666 887666555 33688888888888762 22245 78 99876 333445553
Q ss_pred e
Q 031642 130 G 130 (156)
Q Consensus 130 G 130 (156)
|
T Consensus 89 G 89 (206)
T PRK13239 89 G 89 (206)
T ss_pred C
Confidence 3
No 140
>cd00488 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carc
Probab=20.85 E-value=96 Score=21.24 Aligned_cols=59 Identities=10% Similarity=0.136 Sum_probs=35.5
Q ss_pred eEEEEEEec-CCchh-hhhhHHHHH---HhCCCceeeccccccCCCeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 83 YTSKSLTTN-LSDLE-AAQPLSKLC---LEFPDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 83 ~~S~tv~~~-~~Eg~-IA~~L~~Iq---~~~Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
-+.|+.... ..++- +...+++++ ..|||++++. +.+.|.+-..|..-|...--++++.+
T Consensus 9 ~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHP~i~~~~------~~V~v~l~Th~~~glt~~D~~lA~~i 72 (75)
T cd00488 9 ALERTFKFKDFKEAIAFVNRVAELAEALNHHPDISNVY------NKVTVTLTTHDAGGLTENDFILAAKI 72 (75)
T ss_pred cEEEEEEcCCHHHHHHHHHHHHHHHHHcCCCCCEEEee------eEEEEEEEeCCCCCCCHHHHHHHHHH
Confidence 467777655 33332 444444444 5689998863 45778887777665655555555544
No 141
>cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.
Probab=20.71 E-value=3e+02 Score=21.56 Aligned_cols=94 Identities=15% Similarity=0.203 Sum_probs=46.0
Q ss_pred hHHhHHhcCcCCceeee-ccCCCCceeeCCCcccceeE--eCe-EEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEE
Q 031642 10 LVVRRLLGYKYPRWLCC-RKVPPNCCITTSCSYLWYIK--CQN-VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTS 85 (156)
Q Consensus 10 ~~~~~~~~~~~~~~~~~-~~~~~~~~I~NpvS~APGF~--igN-V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S 85 (156)
+.||+.-+=..-+||+. -++-...=|..|.... -+. -++ |+|-+|+-+..+.+|++.+... + +...
T Consensus 63 ~~i~~~~~G~~s~~l~~~l~~G~~v~v~gP~G~~-~~~~~~~~~vlia~GtGIaP~~~ll~~~~~~---~------~~~~ 132 (228)
T cd06209 63 FLIRLLPGGAMSSYLRDRAQPGDRLTLTGPLGSF-YLREVKRPLLMLAGGTGLAPFLSMLDVLAED---G------SAHP 132 (228)
T ss_pred EEEEEcCCCcchhhHHhccCCCCEEEEECCcccc-eecCCCCeEEEEEcccCHhHHHHHHHHHHhc---C------CCCc
Confidence 44444322224567765 3333333344443221 000 133 5566676566667777776542 1 1111
Q ss_pred EE-EEecCCchhh--hhhHHHHHHhCCCcee
Q 031642 86 KS-LTTNLSDLEA--AQPLSKLCLEFPDLHI 113 (156)
Q Consensus 86 ~t-v~~~~~Eg~I--A~~L~~Iq~~~Pdv~I 113 (156)
.+ +.....+.++ .+.|.++++++|++.+
T Consensus 133 v~l~~~~r~~~~~~~~~~l~~l~~~~~~~~~ 163 (228)
T cd06209 133 VHLVYGVTRDADLVELDRLEALAERLPGFSF 163 (228)
T ss_pred EEEEEecCCHHHhccHHHHHHHHHhCCCeEE
Confidence 12 2222333333 4789999999997653
No 142
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=20.71 E-value=89 Score=21.75 Aligned_cols=26 Identities=12% Similarity=0.054 Sum_probs=13.1
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEE
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLT 89 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~ 89 (156)
|.+ ...+..++..++.- -|=+.-++.
T Consensus 9 ~~~~~~~l~~~l~~~~~~-----~P~v~i~i~ 35 (197)
T cd08422 9 VSFGRLHLAPLLAEFLAR-----YPDVRLELV 35 (197)
T ss_pred HHHHHHHHHHHHHHHHHh-----CCceEEEEe
Confidence 444 33445555554433 565555554
No 143
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.64 E-value=2.7e+02 Score=18.44 Aligned_cols=53 Identities=19% Similarity=0.283 Sum_probs=34.7
Q ss_pred eEEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEec-CCchhhhhhHHHHHHhCC
Q 031642 49 NVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQPLSKLCLEFP 109 (156)
Q Consensus 49 NV~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~-~~Eg~IA~~L~~Iq~~~P 109 (156)
.+.+|.|. + ...++.++..++.-| .+..-+.+-+. .-+=.+.+-+.+|.++|-
T Consensus 2 ~~ll~~g~--~--~~el~~~l~~~r~~~----~~~~~kAvlT~tN~~Wt~~~L~~El~~Eh~ 55 (58)
T PF12646_consen 2 EFLLFSGF--S--GEELDKFLDALRKAG----IPIPLKAVLTPTNINWTLKDLLEELKEEHE 55 (58)
T ss_pred CEEEECCC--C--HHHHHHHHHHHHHcC----CCcceEEEECCCcccCcHHHHHHHHHHHHH
Confidence 46788883 2 345556666665554 45555555555 467788899999998874
No 144
>PF05798 Phage_FRD3: Bacteriophage FRD3 protein; InterPro: IPR008765 This is a group of proteins of unknown function from bacteriophage T2 and related phage.
Probab=20.35 E-value=91 Score=22.73 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=22.2
Q ss_pred HHHHHhCCCceeeccccccCCC---eEEEEEecCHH
Q 031642 102 SKLCLEFPDLHIGCYRKSRQGP---LIISFEGKDQA 134 (156)
Q Consensus 102 ~~Iq~~~Pdv~IGSYP~~~~g~---~~lVvRG~D~~ 134 (156)
+-|.++||+++|-|- .+.. +.|++.|.=++
T Consensus 16 EvIRNRyPelsi~si---~d~~f~~~~i~i~GPle~ 48 (75)
T PF05798_consen 16 EVIRNRYPELSITSI---QDSKFCSIQIVIEGPLED 48 (75)
T ss_pred HHHHccCCceEEEEe---ecCCcceEEEEEeccHHH
Confidence 457899999999983 3443 46999997544
No 145
>TIGR01127 ilvA_1Cterm threonine dehydratase, medium form. A form of threonine dehydratase with two copies of the C-terminal domain Pfam:PF00585 is described by TIGR01124. This model describes a phylogenetically distinct form with a single copy of pfam00585. This form branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any pfam00585 domain. Many members of this model are found in species with other Ile biosynthetic enzymes.
Probab=20.34 E-value=5.7e+02 Score=22.18 Aligned_cols=90 Identities=17% Similarity=0.163 Sum_probs=56.2
Q ss_pred EEEecCCCCchHHHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCc-eeecccccc---CCC--
Q 031642 50 VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDL-HIGCYRKSR---QGP-- 123 (156)
Q Consensus 50 V~VMAGV~VP~I~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv-~IGSYP~~~---~g~-- 123 (156)
|+|+.|=|+. ..++..++.+ | |......+.-++...-.=|.+++.++.|.+..-++ +|--+..+. .+.
T Consensus 278 v~i~sGGn~d--~d~l~~vi~~---g-l~~~gr~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~~~~~~ 351 (380)
T TIGR01127 278 AVVLSGGNID--LNLLNKIIEK---G-LVKSGRKVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIPPGFAM 351 (380)
T ss_pred EEEeCCCCCC--HHHHHHHHHH---H-HHhCCCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCCCceEE
Confidence 6788885543 3355555433 2 33334455666666667788999888888776665 564432211 122
Q ss_pred eEEEEEecCHHHHHHHHHHHHh
Q 031642 124 LIISFEGKDQARIEAAIESLFK 145 (156)
Q Consensus 124 ~~lVvRG~D~~~l~aA~~~l~~ 145 (156)
+.+++..+|.+.+++-.++|++
T Consensus 352 v~v~vet~~~~~~~~i~~~L~~ 373 (380)
T TIGR01127 352 VEITLETRGKEHLDEILKILRD 373 (380)
T ss_pred EEEEEEeCCHHHHHHHHHHHHH
Confidence 4588888888888777777765
No 146
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=20.30 E-value=1.1e+02 Score=21.21 Aligned_cols=50 Identities=20% Similarity=0.060 Sum_probs=25.2
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeccc
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 117 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP 117 (156)
+.+ ...+..++..+..- .|=+.-++.. +.-.+..+.+.+..=|+-|...|
T Consensus 8 ~~~~~~~l~~~l~~~~~~-----~P~i~i~i~~----~~~~~~~~~l~~~~~Dl~i~~~~ 58 (195)
T cd08434 8 HSLGTSLVPDLIRAFRKE-----YPNVTFELHQ----GSTDELLDDLKNGELDLALCSPV 58 (195)
T ss_pred chhhhhhhHHHHHHHHHh-----CCCeEEEEec----CcHHHHHHHHHcCCccEEEEccC
Confidence 444 34555555555443 5554444443 33344455666655566665444
No 147
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.24 E-value=1.4e+02 Score=19.68 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=27.8
Q ss_pred hhhHHHHHHhC-CCceeeccccccCCCeEEEEEecCHHHHHHHHHHH
Q 031642 98 AQPLSKLCLEF-PDLHIGCYRKSRQGPLIISFEGKDQARIEAAIESL 143 (156)
Q Consensus 98 A~~L~~Iq~~~-Pdv~IGSYP~~~~g~~~lVvRG~D~~~l~aA~~~l 143 (156)
+..+.+||+++ =.++|.. ++ .+.+.|.|.+.+++|.+.+
T Consensus 21 G~~ik~I~~~tg~~I~i~~-----~g--~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 21 GKTIKKIIEETGVKIDIED-----DG--TVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred chHHHHHHHHHCCEEEeCC-----CC--EEEEEeCCHHHHHHHHHHh
Confidence 45577777776 4455543 22 5899999999999998765
No 148
>cd07454 CRD_LIN_17 Cysteine-rich domain (CRD) of LIN_17. A cysteine-rich domain (CRD) is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with the
Probab=20.15 E-value=54 Score=25.34 Aligned_cols=23 Identities=26% Similarity=0.649 Sum_probs=18.8
Q ss_pred HHhcCcCCceeeeccCCCC--ceee
Q 031642 14 RLLGYKYPRWLCCRKVPPN--CCIT 36 (156)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~--~~I~ 36 (156)
+.+||.+|..|-|.+.|.. -||+
T Consensus 93 ~~fg~~WP~~l~C~~fP~~~~~C~~ 117 (124)
T cd07454 93 EEFGIGWPEPLNCAQFPDPPELCMK 117 (124)
T ss_pred HHhCCCCCCCCChhhCCCCCCCCCC
Confidence 4689999999999999975 3654
No 149
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=20.13 E-value=1.1e+02 Score=21.39 Aligned_cols=51 Identities=16% Similarity=0.076 Sum_probs=27.2
Q ss_pred chH-HHHHHHHHHhHHhCCCccCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeecccc
Q 031642 59 TEL-DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRK 118 (156)
Q Consensus 59 P~I-~aMl~~l~p~L~~G~L~~gap~~S~tv~~~~~Eg~IA~~L~~Iq~~~Pdv~IGSYP~ 118 (156)
+.+ ...+..++..+..- .|=+.-++.. +.-.+.+..+.+.-=|+-|...|.
T Consensus 8 ~~~~~~~l~~~l~~~~~~-----~P~v~i~i~~----~~~~~~~~~l~~~~~Dl~i~~~~~ 59 (194)
T cd08436 8 TSLAAVDLPELLARFHRR-----HPGVDIRLRQ----AGSDDLLAAVREGRLDLAFVGLPE 59 (194)
T ss_pred hHHHHHHHHHHHHHHHHH-----CCCcEEEEec----CCHHHHHHHHHcCCccEEEEecCC
Confidence 445 44555555555444 5554555433 333345566666666777765553
No 150
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=20.02 E-value=1.3e+02 Score=26.43 Aligned_cols=54 Identities=15% Similarity=0.134 Sum_probs=39.7
Q ss_pred CCchhh----hhhHHHHHHhCCCceeeccccccCC-CeEEEEEecCHHHHHHHHHHHHhhh
Q 031642 92 LSDLEA----AQPLSKLCLEFPDLHIGCYRKSRQG-PLIISFEGKDQARIEAAIESLFKKF 147 (156)
Q Consensus 92 ~~Eg~I----A~~L~~Iq~~~Pdv~IGSYP~~~~g-~~~lVvRG~D~~~l~aA~~~l~~~~ 147 (156)
.+|.+| |....+|++.+-+ +|+|+||..+ .+..+.-|-|.+.++.+.+++.+..
T Consensus 22 rRE~dlQ~lQsrLya~L~~~~~~--~ggl~Ff~RgDN~iavtNGI~~~~~~~i~e~I~n~~ 80 (254)
T PRK02240 22 RRESDLQALQSRLYADLAQQFGA--RDGYVFFTRFDNMIAVTNGIDLEDHARIQESIRNRY 80 (254)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHh--CCCEEEeccCceEEEEcCCCCHHHHHHHHHHHHhcC
Confidence 466665 3334455555555 7999998754 5778889999999999999998763
Done!