Query 033395
Match_columns 120
No_of_seqs 103 out of 175
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 13:22:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033395.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033395hhsearch_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 3.3E-26 7.2E-31 183.8 9.9 106 1-115 125-236 (252)
2 COG1058 CinA Predicted nucleot 99.9 2.7E-24 5.9E-29 174.5 10.2 110 1-113 118-235 (255)
3 PRK00549 competence damage-ind 99.8 1.4E-20 3E-25 159.4 9.6 110 1-113 117-232 (414)
4 PRK01215 competence damage-ind 99.7 1.7E-16 3.7E-21 128.2 9.4 109 1-114 120-239 (264)
5 PRK03673 hypothetical protein; 99.6 1.6E-15 3.4E-20 129.1 10.0 106 1-110 118-229 (396)
6 TIGR00200 cinA_nterm competenc 99.5 4.8E-14 1.1E-18 120.3 10.2 110 1-113 117-233 (413)
7 cd00885 cinA Competence-damage 99.1 7E-11 1.5E-15 89.8 4.3 49 1-51 116-169 (170)
8 PF00994 MoCF_biosynth: Probab 86.8 0.39 8.4E-06 34.6 1.6 35 15-50 103-143 (144)
9 TIGR00177 molyb_syn molybdenum 72.7 4.8 0.0001 29.3 3.3 35 10-45 105-141 (144)
10 COG4097 Predicted ferric reduc 61.5 22 0.00048 31.8 5.6 61 26-92 318-378 (438)
11 COG3622 Hfi Hydroxypyruvate is 57.9 8.5 0.00019 32.3 2.4 77 21-97 96-212 (260)
12 COG0035 Upp Uracil phosphoribo 52.5 66 0.0014 26.1 6.6 56 22-90 122-180 (210)
13 PF14081 DUF4262: Domain of un 51.1 17 0.00037 26.0 2.8 33 29-61 37-70 (125)
14 PF08753 NikR_C: NikR C termin 50.4 67 0.0014 21.4 5.4 46 65-110 6-54 (78)
15 cd01840 SGNH_hydrolase_yrhL_li 48.6 50 0.0011 23.5 4.9 62 24-90 51-113 (150)
16 PF13684 Dak1_2: Dihydroxyacet 47.9 67 0.0015 26.8 6.2 41 57-97 263-303 (313)
17 PRK07114 keto-hydroxyglutarate 47.7 60 0.0013 26.1 5.7 36 57-92 40-75 (222)
18 cd04910 ACT_AK-Ectoine_1 ACT d 46.4 83 0.0018 21.1 5.4 51 30-90 11-69 (71)
19 cd08431 PBP2_HupR The C-termin 42.8 35 0.00075 23.2 3.2 18 76-93 40-57 (195)
20 cd00452 KDPG_aldolase KDPG and 41.8 1.1E+02 0.0023 23.0 6.0 53 28-92 8-60 (190)
21 PF04459 DUF512: Protein of un 40.9 44 0.00096 26.5 3.9 64 29-97 54-134 (204)
22 smart00852 MoCF_biosynth Proba 39.9 41 0.00088 23.8 3.3 30 13-43 104-133 (135)
23 cd08450 PBP2_HcaR The C-termin 37.0 40 0.00087 22.8 2.8 16 78-93 42-57 (196)
24 PHA02755 hypothetical protein; 33.9 19 0.00041 25.9 0.7 16 84-99 5-20 (96)
25 TIGR00550 nadA quinolinate syn 33.6 72 0.0016 26.8 4.3 63 25-98 53-117 (310)
26 COG5489 Uncharacterized conser 33.2 62 0.0013 23.9 3.3 44 10-68 31-77 (107)
27 COG0379 NadA Quinolinate synth 32.2 43 0.00093 28.9 2.7 75 25-110 70-149 (324)
28 PF03345 DDOST_48kD: Oligosacc 32.2 41 0.00089 29.7 2.7 61 58-118 148-216 (423)
29 PF09846 DUF2073: Uncharacteri 32.2 20 0.00043 26.4 0.6 48 70-117 33-84 (104)
30 TIGR02036 dsdC D-serine deamin 32.2 94 0.002 24.3 4.5 24 69-92 106-129 (302)
31 PF12646 DUF3783: Domain of un 30.6 1.4E+02 0.0031 18.8 5.5 53 26-86 2-55 (58)
32 cd08412 PBP2_PAO1_like The C-t 30.0 66 0.0014 21.6 2.9 19 76-94 40-58 (198)
33 COG0206 FtsZ Cell division GTP 29.3 1.7E+02 0.0037 25.2 5.9 44 57-100 95-141 (338)
34 cd08430 PBP2_IlvY The C-termin 29.1 65 0.0014 21.7 2.8 12 77-88 18-29 (199)
35 COG0245 IspF 2C-methyl-D-eryth 28.9 1.2E+02 0.0026 23.8 4.5 48 18-72 85-136 (159)
36 cd08452 PBP2_AlsR The C-termin 28.6 58 0.0013 22.4 2.5 16 75-90 39-54 (197)
37 cd08444 PBP2_Cbl The C-termina 28.6 64 0.0014 22.3 2.7 6 43-48 16-21 (198)
38 TIGR01182 eda Entner-Doudoroff 28.5 2.3E+02 0.005 22.4 6.1 53 28-92 12-64 (204)
39 PRK15092 DNA-binding transcrip 28.2 2E+02 0.0043 23.0 5.8 22 69-90 109-130 (310)
40 cd08416 PBP2_MdcR The C-termin 28.0 56 0.0012 22.1 2.3 47 39-94 12-58 (199)
41 PF08945 Bclx_interact: Bcl-x 27.8 22 0.00049 22.0 0.2 26 62-87 7-33 (40)
42 PRK05718 keto-hydroxyglutarate 26.9 2.8E+02 0.006 21.9 6.3 54 27-92 18-71 (212)
43 cd08422 PBP2_CrgA_like The C-t 26.6 63 0.0014 21.6 2.3 10 86-95 48-57 (197)
44 cd08434 PBP2_GltC_like The sub 26.6 76 0.0016 21.1 2.7 20 75-94 39-58 (195)
45 cd08415 PBP2_LysR_opines_like 26.5 89 0.0019 21.0 3.1 19 77-95 41-59 (196)
46 cd08436 PBP2_LTTR_like_3 The C 26.2 73 0.0016 21.3 2.6 20 76-95 40-59 (194)
47 PRK11899 prephenate dehydratas 25.9 67 0.0014 26.6 2.7 29 69-97 247-276 (279)
48 cd08461 PBP2_DntR_like_3 The C 25.9 67 0.0014 21.8 2.4 42 41-91 14-55 (198)
49 PF11582 DUF3240: Protein of u 25.7 1.5E+02 0.0032 20.8 4.2 66 11-90 23-88 (102)
50 PF14492 EFG_II: Elongation Fa 25.6 1.1E+02 0.0024 20.0 3.3 34 58-91 3-38 (75)
51 PF01081 Aldolase: KDPG and KH 25.3 1.8E+02 0.004 22.9 5.0 53 28-92 12-64 (196)
52 cd08448 PBP2_LTTR_aromatics_li 25.0 79 0.0017 21.2 2.6 15 77-91 41-55 (197)
53 TIGR03339 phn_lysR aminoethylp 25.0 1.7E+02 0.0037 21.9 4.6 23 70-92 95-117 (279)
54 PF02445 NadA: Quinolinate syn 25.0 1.5E+02 0.0033 25.2 4.7 62 25-97 47-110 (296)
55 PRK11242 DNA-binding transcrip 24.9 1.8E+02 0.0039 22.1 4.8 25 69-93 101-125 (296)
56 cd08421 PBP2_LTTR_like_1 The C 24.7 99 0.0022 20.8 3.0 16 76-91 40-55 (198)
57 COG0011 Uncharacterized conser 24.6 1.1E+02 0.0024 22.1 3.3 51 32-87 13-63 (100)
58 PRK09986 DNA-binding transcrip 24.4 2.2E+02 0.0048 21.6 5.2 30 61-90 99-128 (294)
59 cd08479 PBP2_CrgA_like_9 The C 24.2 61 0.0013 22.0 1.9 9 58-66 27-35 (198)
60 PRK15016 isochorismate synthas 24.2 3E+02 0.0064 24.1 6.5 68 26-95 116-185 (391)
61 cd08447 PBP2_LTTR_aromatics_li 24.2 85 0.0018 21.2 2.6 33 58-94 26-58 (198)
62 cd08485 PBP2_ClcR The C-termin 24.0 1.1E+02 0.0024 21.1 3.3 17 76-92 41-57 (198)
63 COG1031 Uncharacterized Fe-S o 23.5 98 0.0021 28.6 3.5 14 22-35 398-411 (560)
64 COG4187 RocB Arginine degradat 23.5 68 0.0015 29.5 2.5 28 63-98 21-48 (553)
65 cd08481 PBP2_GcdR_like The C-t 23.4 55 0.0012 22.0 1.5 9 58-66 26-34 (194)
66 PRK14997 LysR family transcrip 23.2 1.9E+02 0.0042 22.2 4.7 25 69-93 102-126 (301)
67 cd08464 PBP2_DntR_like_2 The C 23.1 80 0.0017 21.3 2.3 13 79-91 43-55 (200)
68 KOG2754 Oligosaccharyltransfer 23.1 76 0.0017 28.5 2.7 34 85-118 204-239 (443)
69 cd08453 PBP2_IlvR The C-termin 22.9 1E+02 0.0023 20.9 2.9 47 39-94 12-58 (200)
70 cd00914 PCD_DCoH_subfamily_b P 22.5 1.1E+02 0.0024 20.2 2.8 49 59-113 9-62 (76)
71 PF05798 Phage_FRD3: Bacteriop 22.5 85 0.0018 21.8 2.3 30 79-108 16-45 (75)
72 cd08471 PBP2_CrgA_like_2 The C 22.3 61 0.0013 21.9 1.6 11 41-51 15-25 (201)
73 PF14681 UPRTase: Uracil phosp 22.1 66 0.0014 24.9 1.9 16 77-92 165-180 (207)
74 PF02514 CobN-Mg_chel: CobN/Ma 22.0 47 0.001 32.6 1.3 27 5-32 359-389 (1098)
75 cd08441 PBP2_MetR The C-termin 22.0 1.3E+02 0.0028 20.5 3.2 8 58-65 26-33 (198)
76 cd08458 PBP2_NocR The C-termin 22.0 1.1E+02 0.0023 21.0 2.8 21 73-93 37-57 (196)
77 cd08440 PBP2_LTTR_like_4 TThe 21.9 1.3E+02 0.0027 20.0 3.1 15 78-92 42-56 (197)
78 cd06210 MMO_FAD_NAD_binding Me 21.8 3.5E+02 0.0076 20.3 6.5 57 25-90 109-169 (236)
79 cd08473 PBP2_CrgA_like_4 The C 21.7 75 0.0016 21.4 2.0 11 41-51 17-27 (202)
80 PF11209 DUF2993: Protein of u 21.6 43 0.00093 25.1 0.8 27 70-96 10-38 (225)
81 cd08449 PBP2_XapR The C-termin 21.6 1.1E+02 0.0025 20.4 2.8 46 41-95 14-59 (197)
82 cd08478 PBP2_CrgA The C-termin 21.5 73 0.0016 21.7 1.9 23 71-93 15-37 (199)
83 TIGR00543 isochor_syn isochori 21.5 3.3E+02 0.0071 23.1 6.1 56 37-94 91-147 (351)
84 TIGR01531 glyc_debranch glycog 21.2 1.8E+02 0.0038 30.0 5.0 64 19-94 506-591 (1464)
85 cd08488 PBP2_AmpR The C-termin 21.0 74 0.0016 21.8 1.8 9 58-66 26-34 (191)
86 PF02153 PDH: Prephenate dehyd 20.9 1.4E+02 0.0031 23.5 3.7 80 26-118 47-144 (258)
87 TIGR01091 upp uracil phosphori 20.9 2.5E+02 0.0055 21.7 5.0 15 76-90 163-177 (207)
88 cd08427 PBP2_LTTR_like_2 The C 20.8 99 0.0021 20.7 2.4 13 79-91 43-55 (195)
89 cd08460 PBP2_DntR_like_1 The C 20.7 1E+02 0.0022 21.1 2.5 18 77-94 40-57 (200)
90 PRK06015 keto-hydroxyglutarate 20.6 4.1E+02 0.0089 21.0 6.2 32 57-92 29-60 (201)
91 cd08470 PBP2_CrgA_like_1 The C 20.5 66 0.0014 21.8 1.5 21 41-66 15-35 (197)
92 cd08435 PBP2_GbpR The C-termin 20.4 97 0.0021 20.8 2.3 22 74-95 38-59 (201)
93 cd08442 PBP2_YofA_SoxR_like Th 20.3 1.2E+02 0.0026 20.3 2.7 14 78-91 42-55 (193)
94 cd08467 PBP2_SyrM The C-termin 20.3 1.1E+02 0.0024 21.1 2.6 42 41-91 14-55 (200)
95 KOG3457 Sec61 protein transloc 20.0 59 0.0013 23.3 1.2 14 18-31 52-65 (88)
No 1
>PRK03670 competence damage-inducible protein A; Provisional
Probab=99.93 E-value=3.3e-26 Score=183.83 Aligned_cols=106 Identities=18% Similarity=0.182 Sum_probs=92.3
Q ss_pred CCCCCCcccccccCCCCCCCeeEEC----cEEEecCCChhHHHHHHHH-HHHHHHhCCCcCCCceEEEEEEec-CCchhh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTELDKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEA 74 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i~----NV~VmAGvpvP~i~aMl~~-l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~I 74 (120)
||++|+|| ++|+||+..||||.++ |||+|||||. .|+.||+. ++|.|.+ .++.++++.+. .+||+|
T Consensus 125 mA~~P~ga-~~l~N~~g~ApG~~~~~~~~~v~~lPGvP~-e~~~M~~~~v~p~l~~------~~~~~~~~~~~~~~Es~l 196 (252)
T PRK03670 125 MAYLPEGA-EPLENTEGAAPGAYIEHKGTKIFVLPGMPR-EMKAMLEKEVLPRLGE------RKFVQKKFLAEITDESKL 196 (252)
T ss_pred eeCCCCCC-EECCCCCCcCceEEEEECCeEEEEeCCChH-HHHHHHHHHHHHhhcc------CCeEEEEEEeCCCCHHHH
Confidence 89999995 8999999999999999 8999999554 57889998 9999854 56889988876 799999
Q ss_pred hhhHHHHHHhCCCceeeecccccCCCeEEEEeeecccceee
Q 033395 75 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKVKDSATW 115 (120)
Q Consensus 75 A~~L~~i~~~~pdv~IGSYP~~~~g~~~~V~rg~D~~~~~~ 115 (120)
|+.|++++++|+ |+|||||+..+.++.+++||+|++++..
T Consensus 197 a~~l~~~~~~~~-v~igSyP~~~~~~~~l~~~g~~~~~~~~ 236 (252)
T PRK03670 197 APILEEALERFN-VKIHSSPKGFGKYIGIIIFAEDEEEIEK 236 (252)
T ss_pred HHHHHHHHHHCC-ceEecCCCCCCCcEEEEEEECCHHHHHH
Confidence 999999999996 9999999833346788999999977653
No 2
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=99.91 E-value=2.7e-24 Score=174.46 Aligned_cols=110 Identities=25% Similarity=0.321 Sum_probs=94.4
Q ss_pred CCCCCCcccccccCCCCCCCeeEEC----cEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEec-CCchhhh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAA 75 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i~----NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~IA 75 (120)
||.+|+|| ++|+||+..||||.|+ |||+|||||. +|+.||+..++.+..+ .-...++.|+++++. .+||.||
T Consensus 118 ~A~~P~Ga-~~l~NpvG~APG~~v~~~~~~v~~lPGvP~-Em~~M~e~~~~~~l~~-~~~~~~~~~~~~~~~gi~ES~la 194 (255)
T COG1058 118 QAMLPEGA-EVLDNPVGTAPGFVVEGNGKNVYVLPGVPS-EMKPMFENVLLPLLTG-RFPSTKYYSRVLRVFGIGESSLA 194 (255)
T ss_pred hccCCCCC-EeCCCCCCCCCeeEEecCCeEEEEeCCCCH-HHHHHHHHHHHHHhhc-cCCCCceEEEEEEEcCCChHHHH
Confidence 89999995 8999999999999999 9999999776 6899999999998764 111278999999988 8999999
Q ss_pred hhHHHHHHhCCCceeeecccccCCCe-EE--EEeeecccce
Q 033395 76 QPLSKLCLEFPDLHIGCYRKSRQGPL-II--SFEGKVKDSA 113 (120)
Q Consensus 76 ~~L~~i~~~~pdv~IGSYP~~~~g~~-~~--V~rg~D~~~~ 113 (120)
+.|.+++++||+++|+|||++.+..+ .+ ..+++|.+.+
T Consensus 195 ~~L~~i~~~~~~~~i~s~p~~~~~~~~~~~i~~~~~~~~~~ 235 (255)
T COG1058 195 PTLKDLQDEQPNVTIASYPKDGEVRLRELVIRAEARDEEEA 235 (255)
T ss_pred HHHHHHHhcCCCCEEEecCCCCceeccceEEEEecCCHHHH
Confidence 99999999999999999999998755 34 4444666543
No 3
>PRK00549 competence damage-inducible protein A; Provisional
Probab=99.83 E-value=1.4e-20 Score=159.37 Aligned_cols=110 Identities=22% Similarity=0.249 Sum_probs=93.0
Q ss_pred CCCCCCcccccccCCCCCCCeeEEC----cEEEecCCChhHHHHHHHH-HHHHHHhCCCcCCCceEEEEEEec-CCchhh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTELDKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEA 74 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i~----NV~VmAGvpvP~i~aMl~~-l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~I 74 (120)
||.+|+|| ++|+||+..||||.++ +||+|||||. +|+.||++ +.|.|+.- +..+.++.++++++. .+|++|
T Consensus 117 qA~~P~ga-~~l~N~~GtApG~~~~~~~~~i~~lPGvP~-Em~~m~~~~v~p~l~~~-~~~~~~~~~~~l~~~gi~Es~l 193 (414)
T PRK00549 117 QALIPEGA-TVLPNPVGTAPGMIIEVDGKTYIVLPGPPS-ELKPMFEEYVVPYLSSA-KGTGEVLYSRVLRFFGIGESQL 193 (414)
T ss_pred hhcCCCCC-EECcCCCCcCCeEEEEECCEEEEEeCCCcH-HHHHHHHHHhHHHHHhh-cCCCceEEEEEEEEcCCCHHHH
Confidence 79999995 8999999999999998 5999999666 68999998 88998731 112357899999765 799999
Q ss_pred hhhHHHHHHhCCCceeeecccccCCCeEEEEeeecccce
Q 033395 75 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKVKDSA 113 (120)
Q Consensus 75 A~~L~~i~~~~pdv~IGSYP~~~~g~~~~V~rg~D~~~~ 113 (120)
++.|.+++.+|++++||+||++..-.+.++++|.|.+.+
T Consensus 194 ~~~L~~l~~~~~~v~ig~~~~~~~~~vrl~~~~~~~~~~ 232 (414)
T PRK00549 194 ATTLRDLIDNQTNPTIAPYAKDGEVTLRLTAKARSEEEA 232 (414)
T ss_pred HHHHHHHHhcCCCCEEEECccCCEEEEEEEEecCCHHHH
Confidence 999999999999999999998744456778999987654
No 4
>PRK01215 competence damage-inducible protein A; Provisional
Probab=99.68 E-value=1.7e-16 Score=128.21 Aligned_cols=109 Identities=17% Similarity=0.234 Sum_probs=87.6
Q ss_pred CCCCCCcccccccCCCCCCCeeEEC----cEEEecCCChhHHHHHHHH-HHHHHHhCCCcCCCceEEEEEEec-CCchhh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTELDKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEA 74 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i~----NV~VmAGvpvP~i~aMl~~-l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~I 74 (120)
||.+|+|| ++|+|++..||||.+. +||+|||+|. .++.||+. +.|.|+. + .+..+.++++++. .+|++|
T Consensus 120 ~A~~P~ga-~~l~N~~Gtapg~~~~~~~~~i~~LPG~P~-e~~~m~~~~v~p~l~~--~-~~~~~~~~~~~~~Gi~Es~l 194 (264)
T PRK01215 120 MAMMPPGA-VPLENPVGTAPGILIEHGGKDIVALPGVPR-EMEAIFENFVEPLLKN--R-PPLKYYEDSILVEGVMESDL 194 (264)
T ss_pred eeeCCCCC-EecCCCCCcCCeEEEEECCEEEEEeCCChH-HHHHHHHHHHHHHHhc--c-CCCcEEEEEEEECCCCHHHH
Confidence 68999995 7999999999999885 5999999666 68889998 7799875 2 2357889999976 799999
Q ss_pred hhhHHHHHHhCCCceeeeccc-c--cCCC--eEEEEeeeccccee
Q 033395 75 AQPLSKLCLEFPDLHIGCYRK-S--RQGP--LIISFEGKVKDSAT 114 (120)
Q Consensus 75 A~~L~~i~~~~pdv~IGSYP~-~--~~g~--~~~V~rg~D~~~~~ 114 (120)
|+.|.++..+||++.|||||. + ..+. +.++.+|.|.+.+.
T Consensus 195 ~~~l~~l~~~~~~~~~~s~p~~~~~~~~~v~vrl~~~~~~~~~~~ 239 (264)
T PRK01215 195 APYVKELVKKYDRVYVKSHPKGYEVSKPILEIQIAGSGEREEEAK 239 (264)
T ss_pred HHHHHHHHHhCCCCEEecCccceecCCCeEEEEEEEecCCHHHHH
Confidence 999999999999999999965 2 2333 44466677665543
No 5
>PRK03673 hypothetical protein; Provisional
Probab=99.63 E-value=1.6e-15 Score=129.07 Aligned_cols=106 Identities=22% Similarity=0.139 Sum_probs=84.9
Q ss_pred CCCCCCcccccccCCCCCCCeeEEC----cEEEecCCChhHHHHHHHH-HHHHHHhCCCcCCCceEEEEEEec-CCchhh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTELDKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLEA 74 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i~----NV~VmAGvpvP~i~aMl~~-l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~I 74 (120)
||.+|+|| ++|+||+..||||.++ +||+|||||. +|+.||+. +.|.|+.- +.....+.++++.+. .+|+++
T Consensus 118 QA~~P~ga-~~l~N~~GtApG~~~~~~~~~i~~LPGvP~-Emk~M~~~~v~p~L~~~-~~~~~~~~~~~l~~~Gi~ES~l 194 (396)
T PRK03673 118 QAELPASA-EMIDNPVGTACGFALQLNRCLMFFTPGVPS-EFKVMVEQEILPRLRER-FSLPEPPLCLRLTTFGRSESDL 194 (396)
T ss_pred hccCCCCC-eeccCCCccCCcEEEEECCEEEEEECCChH-HHHHHHHHHHHHHHHhh-cCCCCceEEEEEEECCCCHHHH
Confidence 69999995 8999999999999996 3999999666 68999987 99998851 121245778888764 799999
Q ss_pred hhhHHHHHHhCCCceeeecccccCCCeEEEEeeecc
Q 033395 75 AQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKVK 110 (120)
Q Consensus 75 A~~L~~i~~~~pdv~IGSYP~~~~g~~~~V~rg~D~ 110 (120)
++.|.+++ ..+++.||-|+.+..-.+.++.++.|.
T Consensus 195 ~~~l~~l~-~~~~~~i~~~~~~~~v~vrlt~~~~~~ 229 (396)
T PRK03673 195 AQSLDPLP-LPPGVVMGYRSSMPIIELKLTGPASQR 229 (396)
T ss_pred HHHHHHHh-cCCCCEEeecCCCCeEEEEEEEccCCH
Confidence 99999997 457999998877754456667777765
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=99.53 E-value=4.8e-14 Score=120.26 Aligned_cols=110 Identities=18% Similarity=0.115 Sum_probs=89.5
Q ss_pred CCCCCCcccccccCCCCCCCeeEE-C--c--EEEecCCChhHHHHHHHH-HHHHHHhCCCcCCCceEEEEEEec-CCchh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKC-Q--N--VIILTATNVTELDKEWNC-LIELLRSGGLSLMEPYTSKSLTTN-LSDLE 73 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i-~--N--V~VmAGvpvP~i~aMl~~-l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~ 73 (120)
||.+|+|| ++|+||+..||||.+ . | ||.|||+|. +++.||+. +.|.|+.- +.....+.++++++. .+|++
T Consensus 117 qA~~p~ga-~~l~N~~G~APG~~~~~~~~~~i~~LPG~P~-e~~~m~~~~v~p~l~~~-~~~~~~~~~~~~~~~Gi~ES~ 193 (413)
T TIGR00200 117 QALLPAGA-EFLANPVGTAPGMFAVQLNRCLMLFTPGVPS-EFRVMVEHEALPRLRER-FSLPQPIVSLVLRFFGIGESQ 193 (413)
T ss_pred hcCCCCCC-EECCCCCCCCCeeEEEecCCEEEEEeCCCcH-HHHHHHHHHhhHHHHHh-cCCCceEEEEEEEECCCCHHH
Confidence 79999995 899999999999544 3 4 677999777 78999988 78998751 112246889999876 79999
Q ss_pred hhhhHHHHHHhCCCceeeecccccCCCeEEEEeeecccce
Q 033395 74 AAQPLSKLCLEFPDLHIGCYRKSRQGPLIISFEGKVKDSA 113 (120)
Q Consensus 74 IA~~L~~i~~~~pdv~IGSYP~~~~g~~~~V~rg~D~~~~ 113 (120)
+++.|.++..++++..++-|+++.+-.+.++.++.|.+.+
T Consensus 194 l~~~l~~~~~~~~~~~~~~~~~~~~v~vrl~~~~~~~~~a 233 (413)
T TIGR00200 194 LEADLADSLDTLTNPTGAPMAYRGEVPLRELKLTGPESEQ 233 (413)
T ss_pred HHHHHHHHHhcCCCCeEEEecCCCeEEEEEEEecCCHHHH
Confidence 9999999999999999999998866677778888876654
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=99.11 E-value=7e-11 Score=89.80 Aligned_cols=49 Identities=29% Similarity=0.391 Sum_probs=43.4
Q ss_pred CCCCCCcccccccCCCCCCCeeEEC----cEEEecCCChhHHHHHHH-HHHHHHHh
Q 033395 1 MALLPEGTTELLHHDKLLLPLIKCQ----NVIILTATNVTELDKEWN-CLIELLRS 51 (120)
Q Consensus 1 MAriPeGaa~LI~npvs~APGf~i~----NV~VmAGvpvP~i~aMl~-~l~p~L~~ 51 (120)
||.+|+|+ ++|.|++..||||.++ |||+|||+|. +|++||+ .+.|.|+.
T Consensus 116 ~a~~p~ga-~~i~N~~G~apg~~~~~~~~~i~~lPG~P~-e~~~m~~~~~~~~l~~ 169 (170)
T cd00885 116 QAMLPEGA-TLLPNPVGTAPGFSVEHNGKNVFLLPGVPS-EMKPMLEEEVLPRLRE 169 (170)
T ss_pred eecCCCCC-EECcCCCCEeeEEEEEeCCeEEEEECCChH-HHHHHHHHHHHHHHhc
Confidence 79999995 8999999999999999 8999999555 5899999 68888753
No 8
>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=86.84 E-value=0.39 Score=34.62 Aligned_cols=35 Identities=26% Similarity=0.178 Sum_probs=24.4
Q ss_pred CCCCCCeeEEC-----cEEEecCCChhHHHHHHHHHH-HHHH
Q 033395 15 DKLLLPLIKCQ-----NVIILTATNVTELDKEWNCLI-ELLR 50 (120)
Q Consensus 15 pvs~APGf~i~-----NV~VmAGvpvP~i~aMl~~l~-p~L~ 50 (120)
|...++++.++ .||.|||.|+ ....|++.++ |.|+
T Consensus 103 p~~~~~~~~~~~~~~~~v~~LPG~P~-~~~~~~~~~v~P~L~ 143 (144)
T PF00994_consen 103 PTGLAPGAYLSRKGGKPVFGLPGNPV-AAKVMLEVLVLPLLR 143 (144)
T ss_dssp TCETEGGGGGTSSETTEEEEE-SSHH-HHHHHHHHHHHHHHH
T ss_pred ccceeeEEEeeCCCCcEEEEcCCCHH-HHHHHHHHHHHHhcC
Confidence 44456776665 5999999555 4677888887 8875
No 9
>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=72.71 E-value=4.8 Score=29.32 Aligned_cols=35 Identities=11% Similarity=-0.020 Sum_probs=26.4
Q ss_pred ccccCCCCCCCeeEECc--EEEecCCChhHHHHHHHHH
Q 033395 10 ELLHHDKLLLPLIKCQN--VIILTATNVTELDKEWNCL 45 (120)
Q Consensus 10 ~LI~npvs~APGf~i~N--V~VmAGvpvP~i~aMl~~l 45 (120)
++..+|...+.+++++| ||.|||.|. ....+|+.+
T Consensus 105 ~~~~~PG~~~~~~~~~~~~v~~LPG~P~-aa~~~~~~~ 141 (144)
T TIGR00177 105 AVLSRPGKPATAGVRGGTLIFGLPGNPV-SALVTFEVL 141 (144)
T ss_pred hhhCCCCCceEEEEECCEEEEECCCCHH-HHHHHHHHH
Confidence 46788888888889988 899999555 455566654
No 10
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=61.54 E-value=22 Score=31.81 Aligned_cols=61 Identities=20% Similarity=0.160 Sum_probs=48.1
Q ss_pred cEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 26 NVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 26 NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
.|+|=.|+=+--+.+||+.+.++ ++ -.|+.--...=+-.|...|+.|++++++.|.++|=+
T Consensus 318 QVWIAGGIGITPFis~l~~l~~~-~s-----~~~V~L~Y~~~n~e~~~y~~eLr~~~qkl~~~~lHi 378 (438)
T COG4097 318 QVWIAGGIGITPFISMLFTLAER-KS-----DPPVHLFYCSRNWEEALYAEELRALAQKLPNVVLHI 378 (438)
T ss_pred cEEEecCcCcchHHHHHHhhccc-cc-----CCceEEEEEecCCchhHHHHHHHHHHhcCCCeEEEE
Confidence 69999997776689999999983 33 256655443334589999999999999999999988
No 11
>COG3622 Hfi Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]
Probab=57.95 E-value=8.5 Score=32.26 Aligned_cols=77 Identities=13% Similarity=0.173 Sum_probs=51.0
Q ss_pred eeEECcEEEecCCChhHH--HHHHHHHHHHHHhCC--C-cCCCceEEE--------------------------------
Q 033395 21 LIKCQNVIILTATNVTEL--DKEWNCLIELLRSGG--L-SLMEPYTSK-------------------------------- 63 (120)
Q Consensus 21 Gf~i~NV~VmAGvpvP~i--~aMl~~l~p~L~~G~--L-~~G~p~~S~-------------------------------- 63 (120)
+.-|.+||+|||++-+.. .+|+.....+|+--. | ..|..++-+
T Consensus 96 aLg~~~vh~mag~~p~~~~~~~~~~t~venLr~aAd~l~~~gi~~liEplN~~d~PG~~l~~~~~al~li~~V~~~Nl~l 175 (260)
T COG3622 96 ALGCKQVHCLAGIPPEGVDTEAMWATFVENLRYAADLLAAEGIRLLIEPLNLRDMPGYFLTSQEQALALIDEVGRPNLFL 175 (260)
T ss_pred HhCCCceeeeecCCCCCccHHHHHHHHHHHHHHHHHHHHhcCCEEEEecCCCCCCCCcccccHHHHHHHHHHhCCCCeEe
Confidence 345789999999763343 447776666654210 0 012222211
Q ss_pred ---EEEecCCchhhhhhHHHHHHhCCCceeeeccccc
Q 033395 64 ---SLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR 97 (120)
Q Consensus 64 ---tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~ 97 (120)
.-++...||+++.-|++.....-+|+|-|-|--.
T Consensus 176 q~D~YH~Q~~eGnL~~~lr~~~~~ighvQiAdvP~Rh 212 (260)
T COG3622 176 QLDLYHAQIMEGNLTRLLREYLPKIGHVQIADVPGRH 212 (260)
T ss_pred ehhHHHHHHhccHHHHHHHHhhhhhceeeecCCCCCC
Confidence 1234568999999999999999999999988755
No 12
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=52.46 E-value=66 Score=26.11 Aligned_cols=56 Identities=18% Similarity=0.170 Sum_probs=35.3
Q ss_pred eEECcEEEecCCChhHH---HHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCcee
Q 033395 22 IKCQNVIILTATNVTEL---DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHI 90 (120)
Q Consensus 22 f~i~NV~VmAGvpvP~i---~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~I 90 (120)
..=++|+|+-. -+ -.|...+.-..+-| |..=++.=.....+|| +.+++++||||.|
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 44568888765 33 23666666444332 3433333333556888 8999999999987
No 13
>PF14081 DUF4262: Domain of unknown function (DUF4262)
Probab=51.08 E-value=17 Score=26.03 Aligned_cols=33 Identities=18% Similarity=0.190 Sum_probs=24.5
Q ss_pred EecCCChhHHHHHHHHHHHHHHhCC-CcCCCceE
Q 033395 29 ILTATNVTELDKEWNCLIELLRSGG-LSLMEPYT 61 (120)
Q Consensus 29 VmAGvpvP~i~aMl~~l~p~L~~G~-L~~G~p~~ 61 (120)
++-|+|.-....+|+.+..+.+.|. +..|....
T Consensus 37 iv~GL~~~~a~~lLn~l~~~v~~g~~~~~G~~~~ 70 (125)
T PF14081_consen 37 IVFGLPPETAHSLLNELADRVRAGERFEPGQRYD 70 (125)
T ss_pred EEECCCHHHHHHHHHHHHHHHhcCCCCCCCcEEe
Confidence 8889766445779999999999875 55555443
No 14
>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=50.43 E-value=67 Score=21.41 Aligned_cols=46 Identities=13% Similarity=0.193 Sum_probs=36.2
Q ss_pred EEecCCchhhhhhHHHHHHhCCCceeeecccccCCCeEE---EEeeecc
Q 033395 65 LTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQGPLII---SFEGKVK 110 (120)
Q Consensus 65 v~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~~g~~~~---V~rg~D~ 110 (120)
+--+-...++...|.+||.+|.|+-+.|.=..-+....+ ++||.-.
T Consensus 6 ~vydh~~~~l~~~l~~iqH~~~~~I~s~~Hvhl~~~~ClEvivv~G~~~ 54 (78)
T PF08753_consen 6 IVYDHHKRELSERLTEIQHEYHDIIISSLHVHLDHDNCLEVIVVRGPAD 54 (78)
T ss_dssp EEEETTSTTHHHHHHHHHHHTTTCEEEEEEEEESSSEEEEEEEEEEEHH
T ss_pred EEEcCCchhHHHHHHHHHHhCcCeEEEeeEEeecCCCeEEEEEEEcCHH
Confidence 334455678999999999999999999988777766555 8898644
No 15
>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=48.61 E-value=50 Score=23.47 Aligned_cols=62 Identities=13% Similarity=0.060 Sum_probs=43.2
Q ss_pred ECcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEec-CCchhhhhhHHHHHHhCCCcee
Q 033395 24 CQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQPLSKLCLEFPDLHI 90 (120)
Q Consensus 24 i~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~IA~~L~~i~~~~pdv~I 90 (120)
-+.|+|+=|++=...++.++.++..++. +.+++-.+.... .-+.++.+.+.+++++||++.+
T Consensus 51 ~d~vvi~lGtNd~~~~~nl~~ii~~~~~-----~~~ivlv~~~~~~~~~~~~n~~~~~~a~~~~~v~~ 113 (150)
T cd01840 51 RKTVVIGLGTNGPFTKDQLDELLDALGP-----DRQVYLVNPHVPRPWEPDVNAYLLDAAKKYKNVTI 113 (150)
T ss_pred CCeEEEEecCCCCCCHHHHHHHHHHcCC-----CCEEEEEECCCCcchHHHHHHHHHHHHHHCCCcEE
Confidence 3788999998875456677777776543 366655555432 2345777889999999998775
No 16
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=47.89 E-value=67 Score=26.75 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=31.1
Q ss_pred CCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeeccccc
Q 033395 57 MEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR 97 (120)
Q Consensus 57 G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~ 97 (120)
+.-++..-..-...|.+.......|+++||+++|..|+--.
T Consensus 263 ~~elvTi~~G~~~~~~~a~~l~~~l~~~~p~~eve~~~GgQ 303 (313)
T PF13684_consen 263 DGELVTIYYGEDVSEEEAEALAEFLEEKYPDVEVEVYDGGQ 303 (313)
T ss_pred CCeEEEEEecCCCCHHHHHHHHHHHHHHhCCeEEEEEECCC
Confidence 45566655555578888888888999999999999986543
No 17
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=47.71 E-value=60 Score=26.07 Aligned_cols=36 Identities=11% Similarity=0.069 Sum_probs=29.2
Q ss_pred CCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 57 MEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 57 G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
|-+.+-.|+++....-.|.....+++++||++-||.
T Consensus 40 Gi~~iEiT~~tp~a~~~i~~l~~~~~~~~p~~~vGa 75 (222)
T PRK07114 40 GARVFEFTNRGDFAHEVFAELVKYAAKELPGMILGV 75 (222)
T ss_pred CCCEEEEeCCCCcHHHHHHHHHHHHHhhCCCeEEee
Confidence 688999998887766667666667788999999986
No 18
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=46.35 E-value=83 Score=21.12 Aligned_cols=51 Identities=14% Similarity=0.015 Sum_probs=36.2
Q ss_pred ecCCChhHH-HHHHHHHHHHHHhCCCcCCCceEEE-------EEEecCCchhhhhhHHHHHHhCCCcee
Q 033395 30 LTATNVTEL-DKEWNCLIELLRSGGLSLMEPYTSK-------SLTTNLSDLEAAQPLSKLCLEFPDLHI 90 (120)
Q Consensus 30 mAGvpvP~i-~aMl~~l~p~L~~G~L~~G~p~~S~-------tv~~~~~Eg~IA~~L~~i~~~~pdv~I 90 (120)
|-| .+.+ +..++.|... +..++++ |.+...+...+...+.+|+++||+-+|
T Consensus 11 MvG--~~g~d~~i~~~l~~~--------~v~ii~K~~nANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 11 MVG--EVGYDLEILELLQRF--------KVSIIAKDTNANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred ccC--ChhHHHHHHHHHHHc--------CCeEEEEecCCCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 667 4455 4477766643 4677776 334455777889999999999998776
No 19
>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=42.83 E-value=35 Score=23.24 Aligned_cols=18 Identities=28% Similarity=0.244 Sum_probs=8.9
Q ss_pred hhHHHHHHhCCCceeeec
Q 033395 76 QPLSKLCLEFPDLHIGCY 93 (120)
Q Consensus 76 ~~L~~i~~~~pdv~IGSY 93 (120)
+.+.++.+.-=|+-|..+
T Consensus 40 ~~~~~l~~g~~D~~i~~~ 57 (195)
T cd08431 40 GTWDALASGRADLVIGAT 57 (195)
T ss_pred hHHHHHhCCCCCEEEEec
Confidence 334455555555555443
No 20
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=41.85 E-value=1.1e+02 Score=23.04 Aligned_cols=53 Identities=26% Similarity=0.300 Sum_probs=34.1
Q ss_pred EEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 28 IILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 28 ~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
-|+-|.+...+..+.+.+.. | |.+++.-++... .-.+.+.+++++||++.||.
T Consensus 8 ~i~r~~~~~~~~~~~~~l~~----~----G~~~vev~~~~~----~~~~~i~~l~~~~~~~~iGa 60 (190)
T cd00452 8 AVLRGDDAEDALALAEALIE----G----GIRAIEITLRTP----GALEAIRALRKEFPEALIGA 60 (190)
T ss_pred EEEEcCCHHHHHHHHHHHHH----C----CCCEEEEeCCCh----hHHHHHHHHHHHCCCCEEEE
Confidence 35566554445556555553 2 587776665422 23447999999999999885
No 21
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=40.90 E-value=44 Score=26.54 Aligned_cols=64 Identities=17% Similarity=0.163 Sum_probs=38.0
Q ss_pred EecCCChhH----------------HHHHHHHHHHHHHhCCCcCCCceEEEEEEec-CCchhhhhhHHHHHHhCCCceee
Q 033395 29 ILTATNVTE----------------LDKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQPLSKLCLEFPDLHIG 91 (120)
Q Consensus 29 VmAGvpvP~----------------i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~IA~~L~~i~~~~pdv~IG 91 (120)
++||.|+|. ++..++.....|+. |. .+=.+.++-|. +..-.+...+.++ ++++++.+=
T Consensus 54 l~Ag~p~P~~~~Y~~fpQlenGVGm~r~f~~e~~~~l~~--l~--~~~~~v~ivTG~la~~~l~~~~~~l-~~~~~~~v~ 128 (204)
T PF04459_consen 54 LLAGRPLPDAEFYEDFPQLENGVGMVRLFLDEWEEALRK--LP--KKPRRVTIVTGVLAYPFLKPLVEKL-NRIPGLEVE 128 (204)
T ss_pred HHcCCCCCChhhcCCCcccCCCeeEhHHHHHHHHHHHhh--cC--CCCeeEEEEeeHHHHHHHHHHHHHH-hccCCCeEE
Confidence 388888877 23344555555444 33 22223444444 3555566666677 777999999
Q ss_pred eccccc
Q 033395 92 CYRKSR 97 (120)
Q Consensus 92 SYP~~~ 97 (120)
-||--.
T Consensus 129 V~~V~N 134 (204)
T PF04459_consen 129 VVPVKN 134 (204)
T ss_pred EEEeec
Confidence 888644
No 22
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=39.89 E-value=41 Score=23.77 Aligned_cols=30 Identities=13% Similarity=-0.022 Sum_probs=19.6
Q ss_pred cCCCCCCCeeEECcEEEecCCChhHHHHHHH
Q 033395 13 HHDKLLLPLIKCQNVIILTATNVTELDKEWN 43 (120)
Q Consensus 13 ~npvs~APGf~i~NV~VmAGvpvP~i~aMl~ 43 (120)
.|+....+|+.=.-||.|||.|. ....+++
T Consensus 104 ~~~~~~~~g~~~~~i~~LPG~P~-~~~~~~~ 133 (135)
T smart00852 104 ANLSGTAPGFRGKLVFGLPGSPV-AARAMLE 133 (135)
T ss_pred ccccCcCCeEeCcEEEECCCCHH-HHHHHHH
Confidence 36667778875346999999554 3444544
No 23
>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=37.03 E-value=40 Score=22.77 Aligned_cols=16 Identities=13% Similarity=-0.185 Sum_probs=6.9
Q ss_pred HHHHHHhCCCceeeec
Q 033395 78 LSKLCLEFPDLHIGCY 93 (120)
Q Consensus 78 L~~i~~~~pdv~IGSY 93 (120)
+..+.+.-=|+.|...
T Consensus 42 ~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 42 AEALMRGKLDVAFMRP 57 (196)
T ss_pred HHHHhcCCccEEEEeC
Confidence 3444444444444433
No 24
>PHA02755 hypothetical protein; Provisional
Probab=33.92 E-value=19 Score=25.85 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=13.0
Q ss_pred hCCCceeeecccccCC
Q 033395 84 EFPDLHIGCYRKSRQG 99 (120)
Q Consensus 84 ~~pdv~IGSYP~~~~g 99 (120)
-++.+.|||||---+|
T Consensus 5 i~~gm~igsypdavqg 20 (96)
T PHA02755 5 ISGGMAIGSYPDAVQG 20 (96)
T ss_pred CCCCcccccCcccccC
Confidence 3688999999987665
No 25
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=33.61 E-value=72 Score=26.83 Aligned_cols=63 Identities=14% Similarity=0.220 Sum_probs=45.0
Q ss_pred CcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEE--EEEEecCCchhhhhhHHHHHHhCCCceeeecccccC
Q 033395 25 QNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTS--KSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ 98 (120)
Q Consensus 25 ~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S--~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~~ 98 (120)
.+++|+.| | .+++....++ ..++.++. -.=.|..-+.--++.+.++.++|||.-|=+||....
T Consensus 53 ~~~IvF~g--v-~fMae~a~~l--------~p~k~vilp~~~a~C~~a~~~~~~~i~~lk~~~Pda~vvah~n~~a 117 (310)
T TIGR00550 53 ADIIVFCG--V-HFMGETAKIL--------NPEKTVLMPDLGAGCSMADMCPPEEFKKLKERHPDAFVVTYVNTTA 117 (310)
T ss_pred CCEEEEeC--C-chHHHHHHHh--------CCCCEEEccCCCCCCccccccCHHHHHHHHHHCCCCEEEEECCCCH
Confidence 46799999 7 6555444432 12466666 233366777777888999999999999999999773
No 26
>COG5489 Uncharacterized conserved protein [Function unknown]
Probab=33.23 E-value=62 Score=23.93 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=31.7
Q ss_pred ccccCCCCC---CCeeEECcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEec
Q 033395 10 ELLHHDKLL---LPLIKCQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTN 68 (120)
Q Consensus 10 ~LI~npvs~---APGf~i~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~ 68 (120)
.||+|.... ||-|+ |++| -++|-+-|..... + |..|+|.++...
T Consensus 31 ~lvPn~~~s~~~aPdfR-----V~~g--g~eiGAaW~k~s~---~-----G~dYlsvkLddP 77 (107)
T COG5489 31 RLVPNESKSGDNAPDFR-----VTAG--GVEIGAAWNKTSN---S-----GRDYLSVKLDDP 77 (107)
T ss_pred EEcccCCCCCCCCCcEE-----EEec--Ccchhhhhhhhcc---c-----CcceEEEEecCC
Confidence 477777654 89999 4555 5589888988732 2 689999887543
No 27
>COG0379 NadA Quinolinate synthase [Coenzyme metabolism]
Probab=32.23 E-value=43 Score=28.95 Aligned_cols=75 Identities=13% Similarity=0.172 Sum_probs=50.3
Q ss_pred CcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEE--ecCCchhhhhhHHHHHHhCCCceeeecccccCC---
Q 033395 25 QNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLT--TNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQG--- 99 (120)
Q Consensus 25 ~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~--~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~~g--- 99 (120)
.+++|++| | .|++.-..++.- -+.++.=... |++.++-=++.+++.+++|||...=+|=-....
T Consensus 70 Ad~IVf~G--V-~FMaETAkiLnP--------eK~VL~Pd~~AgCsmA~~~~~~~~~~~~~~~P~~~vV~YvNtsA~vKA 138 (324)
T COG0379 70 ADTIVFAG--V-HFMAETAKILNP--------EKTVLLPDLEAGCSMADMITAEEVRAFKEKHPDAPVVTYVNTSAEVKA 138 (324)
T ss_pred CCEEEEec--e-eehHhhHhhcCC--------CCeEecCCCCCCCCcccCCCHHHHHHHHHHCCCCceEEEeeChHHHHh
Confidence 47899999 8 766644444321 2446655555 667888889999999999999998888665421
Q ss_pred CeEEEEeeecc
Q 033395 100 PLIISFEGKVK 110 (120)
Q Consensus 100 ~~~~V~rg~D~ 110 (120)
...+++.+.++
T Consensus 139 ~~Di~cTSsNA 149 (324)
T COG0379 139 EADICCTSSNA 149 (324)
T ss_pred hcCeEEecchH
Confidence 23345544443
No 28
>PF03345 DDOST_48kD: Oligosaccharyltransferase 48 kDa subunit beta; InterPro: IPR005013 During N-linked glycosylation of proteins, oligosaccharide chains are assembled on the carrier molecule dolichyl pyrophosphate in the following order: 2 molecules of N-acetylglucosamine (GlcNAc), 9 molecules of mannose, and 3 molecules of glucose. These 14-residue oligosaccharide cores are then transferred to asparagine residues on nascent polypeptide chains in the endoplasmic reticulum (ER). As proteins progress through the Golgi apparatus, the oligosaccharide cores are modified by trimming and extension to generate a diverse array of glycosylated proteins [, ]. The oligosaccharyl transferase complex (OST complex) 2.4.1.119 from EC transfers 14-sugar branched oligosaccharides from dolichyl pyrophosphate to asparagine residues []. The complex contains nine protein subunits: Ost1p, Ost2p, Ost3p, Ost4p, Ost5p, Ost6p, Stt3p, Swp1p, and Wbp1p, all of which are integral membrane proteins of the ER. The OST complex interacts with the Sec61p pore complex [] involved in protein import into the ER. This entry represents subunits OST3 and OST6. OST3 is homologous to OST6 [], and several lines of evidence indicate that they are alternative members of the OST complex. Disruption of both OST3 and OST6 causes severe underglycosylation of soluble and membrane-bound glycoproteins and a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation []. This entry also includes the magnesium transporter protein 1, also known as OST3 homologue B, which might be involved in N-glycosylation through its association with the oligosaccharyl transferase (OST) complex. Wbp1p is the beta subunit of the OST complex, one of the original six subunits purified []. Wbp1 is essential [, ], but conditional mutants have decreased transferase activity [, ]. Wbp1p is homologous to mammalian OST48 [].; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0018279 protein N-linked glycosylation via asparagine, 0005789 endoplasmic reticulum membrane
Probab=32.21 E-value=41 Score=29.66 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=38.7
Q ss_pred CceEEEEEEecCCchhhh-hhHHHHHHhC---CCceeeec--ccccCCC--eEEEEeeecccceeeecc
Q 033395 58 EPYTSKSLTTNLSDLEAA-QPLSKLCLEF---PDLHIGCY--RKSRQGP--LIISFEGKVKDSATWISS 118 (120)
Q Consensus 58 ~p~~S~tv~~~~~Eg~IA-~~L~~i~~~~---pdv~IGSY--P~~~~g~--~~~V~rg~D~~~~~~~~~ 118 (120)
.|++=+-+...++..... ..|++=...| |+-.+..| |+..+.. +...+-+++.+|++|++|
T Consensus 148 ~pilf~G~g~~l~~n~l~~pIL~a~~Tays~~~~~~~~~~~~~~~~G~q~~LVsa~QarNNARv~~~GS 216 (423)
T PF03345_consen 148 KPILFRGVGHLLDNNPLVFPILRAPSTAYSYDPKEPIEEYDDPWAAGSQISLVSAFQARNNARVVFSGS 216 (423)
T ss_pred CcEEEEeEEEEecCCCceeeeeccCCceeccccccccccccchhhccccceEEEEEecccCcEEEEEec
Confidence 355545544444333332 3455555555 67777777 8776443 444899999999999988
No 29
>PF09846 DUF2073: Uncharacterized protein conserved in archaea (DUF2073); InterPro: IPR012017 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.20 E-value=20 Score=26.40 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=31.7
Q ss_pred Cchh-hhhhHHHHH-HhCCCceeeeccccc-CCCeEE-EEeeecccceeeec
Q 033395 70 SDLE-AAQPLSKLC-LEFPDLHIGCYRKSR-QGPLII-SFEGKVKDSATWIS 117 (120)
Q Consensus 70 ~Eg~-IA~~L~~i~-~~~pdv~IGSYP~~~-~g~~~~-V~rg~D~~~~~~~~ 117 (120)
-|+. |-.-..+|. +.|+.++|=|||... +.+|-- ++..+...+.|-|.
T Consensus 33 Ee~~LIE~TM~eI~~d~F~GIEiesyp~~~~~~~f~~rl~gk~~~~rlTVIG 84 (104)
T PF09846_consen 33 EESKLIEMTMTEIDPDEFSGIEIESYPSKEADKSFLGRLLGKKSRERLTVIG 84 (104)
T ss_pred HHHHHHHHHHHhcCccccCceEEEecCcccccccHHHHHhCCCCCCCeEEEc
Confidence 3444 344578888 999999999999988 333321 45555555666654
No 30
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=32.15 E-value=94 Score=24.33 Aligned_cols=24 Identities=4% Similarity=0.237 Sum_probs=20.2
Q ss_pred CCchhhhhhHHHHHHhCCCceeee
Q 033395 69 LSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 69 ~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
+...-+++.|..+.++||++.|=.
T Consensus 106 ~~~~~l~~~l~~f~~~~P~i~l~l 129 (302)
T TIGR02036 106 FAQCWLVPRIGDFTRRYPSISLTV 129 (302)
T ss_pred HHHHHHHHHHHHHHHHCCCceEEE
Confidence 567889999999999999887654
No 31
>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=30.63 E-value=1.4e+02 Score=18.79 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=35.0
Q ss_pred cEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEec-CCchhhhhhHHHHHHhCC
Q 033395 26 NVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTN-LSDLEAAQPLSKLCLEFP 86 (120)
Q Consensus 26 NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~-~~Eg~IA~~L~~i~~~~p 86 (120)
.+.+|.|.+-. .++.++..++.- |.+..-+++-+. .-+=.+.+-+.+|.++|-
T Consensus 2 ~~ll~~g~~~~----el~~~l~~~r~~----~~~~~~kAvlT~tN~~Wt~~~L~~El~~Eh~ 55 (58)
T PF12646_consen 2 EFLLFSGFSGE----ELDKFLDALRKA----GIPIPLKAVLTPTNINWTLKDLLEELKEEHE 55 (58)
T ss_pred CEEEECCCCHH----HHHHHHHHHHHc----CCCcceEEEECCCcccCcHHHHHHHHHHHHH
Confidence 46788895553 444455555543 345556666655 467788999999998874
No 32
>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=30.01 E-value=66 Score=21.65 Aligned_cols=19 Identities=16% Similarity=-0.129 Sum_probs=9.3
Q ss_pred hhHHHHHHhCCCceeeecc
Q 033395 76 QPLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 76 ~~L~~i~~~~pdv~IGSYP 94 (120)
+....+.+.-=|+.|...|
T Consensus 40 ~~~~~l~~~~~D~~i~~~~ 58 (198)
T cd08412 40 ELEEGLRSGELDLALTYDL 58 (198)
T ss_pred HHHHHHHcCCCcEEEEcCC
Confidence 3344455555555555443
No 33
>COG0206 FtsZ Cell division GTPase [Cell division and chromosome partitioning]
Probab=29.28 E-value=1.7e+02 Score=25.17 Aligned_cols=44 Identities=9% Similarity=-0.036 Sum_probs=32.8
Q ss_pred CCceEEEEEEecCCchhhhh-hHHHHHHhC--CCceeeecccccCCC
Q 033395 57 MEPYTSKSLTTNLSDLEAAQ-PLSKLCLEF--PDLHIGCYRKSRQGP 100 (120)
Q Consensus 57 G~p~~S~tv~~~~~Eg~IA~-~L~~i~~~~--pdv~IGSYP~~~~g~ 100 (120)
|.-+...|--...+-|.-|+ .+.++++++ +-+++..|||..+|+
T Consensus 95 g~dmvfitaG~GGGTGtGaaPVvakiake~g~ltvavvt~Pf~~EG~ 141 (338)
T COG0206 95 GADMVFVTAGMGGGTGTGAAPVVAEIAKELGALTVAVVTLPFSFEGS 141 (338)
T ss_pred cCCeEEEEeeecCCccccccHHHHHHHHhcCCcEEEEEEecchhcCc
Confidence 46666666555566776555 488999986 779999999998873
No 34
>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=29.07 E-value=65 Score=21.69 Aligned_cols=12 Identities=17% Similarity=0.412 Sum_probs=4.6
Q ss_pred hHHHHHHhCCCc
Q 033395 77 PLSKLCLEFPDL 88 (120)
Q Consensus 77 ~L~~i~~~~pdv 88 (120)
.|.+++++||++
T Consensus 18 ~l~~~~~~~P~v 29 (199)
T cd08430 18 ILERFRAQHPQV 29 (199)
T ss_pred HHHHHHHHCCCc
Confidence 333333333333
No 35
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=28.89 E-value=1.2e+02 Score=23.77 Aligned_cols=48 Identities=15% Similarity=0.043 Sum_probs=33.1
Q ss_pred CCCeeEECcEE--EecCCCh--hHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCch
Q 033395 18 LLPLIKCQNVI--ILTATNV--TELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDL 72 (120)
Q Consensus 18 ~APGf~i~NV~--VmAGvpv--P~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg 72 (120)
.+=|+++.||= |.+=-|- |.+++|.+.|...| +.+.....|.++..|+
T Consensus 85 ~~~g~~i~Nvd~tii~~~PK~~P~~~amr~~ia~~L-------~i~~~~invKatT~E~ 136 (159)
T COG0245 85 REKGYRIGNVDITIIAQRPKLGPYREAMRANIAELL-------GIPVDRINVKATTTEK 136 (159)
T ss_pred HHhCcEEEeEEEEEEEecCcccchHHHHHHHHHHHh-------CCCchheEEEEeccCc
Confidence 34689999974 4555333 55688999999988 4667666666665554
No 36
>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=28.60 E-value=58 Score=22.39 Aligned_cols=16 Identities=13% Similarity=0.108 Sum_probs=6.8
Q ss_pred hhhHHHHHHhCCCcee
Q 033395 75 AQPLSKLCLEFPDLHI 90 (120)
Q Consensus 75 A~~L~~i~~~~pdv~I 90 (120)
.+.+..+.+.-=|+-|
T Consensus 39 ~~~~~~l~~~~~Dl~i 54 (197)
T cd08452 39 PDQVEELLKGRIDIGF 54 (197)
T ss_pred HHHHHHHHCCCccEEE
Confidence 3344444444334433
No 37
>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=28.57 E-value=64 Score=22.29 Aligned_cols=6 Identities=0% Similarity=0.196 Sum_probs=2.2
Q ss_pred HHHHHH
Q 033395 43 NCLIEL 48 (120)
Q Consensus 43 ~~l~p~ 48 (120)
..++..
T Consensus 16 ~~~l~~ 21 (198)
T cd08444 16 PWVVQA 21 (198)
T ss_pred hHHHHH
Confidence 333333
No 38
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=28.47 E-value=2.3e+02 Score=22.42 Aligned_cols=53 Identities=25% Similarity=0.245 Sum_probs=32.3
Q ss_pred EEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 28 IILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 28 ~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
-|+-+.+.-......+.+. .| |-+++-.|+++. . -.+.+.++.++||++.||-
T Consensus 12 aVlr~~~~e~a~~~~~al~----~~----Gi~~iEit~~t~---~-a~~~i~~l~~~~~~~~vGA 64 (204)
T TIGR01182 12 PVIRIDDVDDALPLAKALI----EG----GLRVLEVTLRTP---V-ALDAIRLLRKEVPDALIGA 64 (204)
T ss_pred EEEecCCHHHHHHHHHHHH----Hc----CCCEEEEeCCCc---c-HHHHHHHHHHHCCCCEEEE
Confidence 3555543322333444444 33 588877776543 2 3345888899999999985
No 39
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=28.17 E-value=2e+02 Score=22.97 Aligned_cols=22 Identities=18% Similarity=0.295 Sum_probs=17.1
Q ss_pred CCchhhhhhHHHHHHhCCCcee
Q 033395 69 LSDLEAAQPLSKLCLEFPDLHI 90 (120)
Q Consensus 69 ~~Eg~IA~~L~~i~~~~pdv~I 90 (120)
+...-++..|.+++++||++.|
T Consensus 109 ~~~~~l~~~l~~f~~~~P~i~i 130 (310)
T PRK15092 109 TADTILPFLLNRVSSVYPKLAL 130 (310)
T ss_pred HHHHHHHHHHHHHHHHCCCcEE
Confidence 3445577889999999998765
No 40
>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=28.02 E-value=56 Score=22.11 Aligned_cols=47 Identities=19% Similarity=-0.048 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeecc
Q 033395 39 DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 39 ~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP 94 (120)
...+..++..+.. -.|=+...+.. +.-.+.++.+.+.-=|+-|...|
T Consensus 12 ~~~l~~~l~~~~~-----~~P~i~l~i~~----~~~~~~~~~l~~~~~Dl~i~~~~ 58 (199)
T cd08416 12 VNTVPRIIMGLKL-----RRPELDIELTL----GSNKDLLKKLKDGELDAILVATP 58 (199)
T ss_pred HhhhHHHHHHHHH-----hCCCeEEEEEE----cCcHHHHHHHhCCCCCEEEEecC
Confidence 3345555555444 25554444432 22223344555555566665544
No 41
>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=27.80 E-value=22 Score=22.03 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=16.4
Q ss_pred EEEEEecC-CchhhhhhHHHHHHhCCC
Q 033395 62 SKSLTTNL-SDLEAAQPLSKLCLEFPD 87 (120)
Q Consensus 62 S~tv~~~~-~Eg~IA~~L~~i~~~~pd 87 (120)
|++..+++ +|=-||..|++|-++|-.
T Consensus 7 sq~~P~~~~PE~wiAqELRRIgDEFna 33 (40)
T PF08945_consen 7 SQAEPVDMRPEIWIAQELRRIGDEFNA 33 (40)
T ss_dssp --------HHHHHHHHHHHHHHHHHHH
T ss_pred hhcCCccCCHHHHHHHHHHHHHHHhcc
Confidence 55555564 899999999999999854
No 42
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=26.85 E-value=2.8e+02 Score=21.94 Aligned_cols=54 Identities=19% Similarity=0.273 Sum_probs=33.1
Q ss_pred EEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 27 VIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 27 V~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
|-|+-+.+........+.+. .| |-..+-.|++.. ++ -+.++++.++||++.||.
T Consensus 18 iaV~r~~~~~~a~~i~~al~----~~----Gi~~iEitl~~~--~~--~~~I~~l~~~~p~~~IGA 71 (212)
T PRK05718 18 VPVIVINKLEDAVPLAKALV----AG----GLPVLEVTLRTP--AA--LEAIRLIAKEVPEALIGA 71 (212)
T ss_pred EEEEEcCCHHHHHHHHHHHH----Hc----CCCEEEEecCCc--cH--HHHHHHHHHHCCCCEEEE
Confidence 34566644433333444444 33 577777775443 32 355888999999999996
No 43
>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=26.61 E-value=63 Score=21.57 Aligned_cols=10 Identities=30% Similarity=0.013 Sum_probs=4.7
Q ss_pred CCceeeeccc
Q 033395 86 PDLHIGCYRK 95 (120)
Q Consensus 86 pdv~IGSYP~ 95 (120)
=|+-|+..|.
T Consensus 48 ~D~~i~~~~~ 57 (197)
T cd08422 48 FDLAIRIGEL 57 (197)
T ss_pred ccEEEEeCCC
Confidence 4455554443
No 44
>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=26.55 E-value=76 Score=21.12 Aligned_cols=20 Identities=20% Similarity=-0.014 Sum_probs=10.2
Q ss_pred hhhHHHHHHhCCCceeeecc
Q 033395 75 AQPLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 75 A~~L~~i~~~~pdv~IGSYP 94 (120)
.+..+.+.+..=|+-|...|
T Consensus 39 ~~~~~~l~~~~~Dl~i~~~~ 58 (195)
T cd08434 39 DELLDDLKNGELDLALCSPV 58 (195)
T ss_pred HHHHHHHHcCCccEEEEccC
Confidence 34445555555555555444
No 45
>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=26.49 E-value=89 Score=20.96 Aligned_cols=19 Identities=11% Similarity=0.048 Sum_probs=10.4
Q ss_pred hHHHHHHhCCCceeeeccc
Q 033395 77 PLSKLCLEFPDLHIGCYRK 95 (120)
Q Consensus 77 ~L~~i~~~~pdv~IGSYP~ 95 (120)
..+.+.+.-=|+.|+..|.
T Consensus 41 ~~~~l~~~~~Dl~i~~~~~ 59 (196)
T cd08415 41 VVEAVLSGQADLGLASLPL 59 (196)
T ss_pred HHHHHHcCCccEEEEeCCC
Confidence 3445555555666665554
No 46
>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=26.24 E-value=73 Score=21.26 Aligned_cols=20 Identities=15% Similarity=-0.036 Sum_probs=11.0
Q ss_pred hhHHHHHHhCCCceeeeccc
Q 033395 76 QPLSKLCLEFPDLHIGCYRK 95 (120)
Q Consensus 76 ~~L~~i~~~~pdv~IGSYP~ 95 (120)
+.+..+.+.-=|+-|...|.
T Consensus 40 ~~~~~l~~~~~Dl~i~~~~~ 59 (194)
T cd08436 40 DLLAAVREGRLDLAFVGLPE 59 (194)
T ss_pred HHHHHHHcCCccEEEEecCC
Confidence 34555555555666655443
No 47
>PRK11899 prephenate dehydratase; Provisional
Probab=25.93 E-value=67 Score=26.56 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=22.2
Q ss_pred CCchhhhhhHHHHHHhCCCce-eeeccccc
Q 033395 69 LSDLEAAQPLSKLCLEFPDLH-IGCYRKSR 97 (120)
Q Consensus 69 ~~Eg~IA~~L~~i~~~~pdv~-IGSYP~~~ 97 (120)
..+..+.+.|.+|++.-..+. +||||..+
T Consensus 247 ~~d~~v~~aL~~l~~~~~~~kvLGsYp~~~ 276 (279)
T PRK11899 247 PEDRNVALALEELRFFSEEVRILGVYPAHP 276 (279)
T ss_pred CCCHHHHHHHHHHHHhcCcEEEeeeecCcc
Confidence 345668889999998777764 69999754
No 48
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=25.86 E-value=67 Score=21.79 Aligned_cols=42 Identities=19% Similarity=0.097 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceee
Q 033395 41 EWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIG 91 (120)
Q Consensus 41 Ml~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IG 91 (120)
.+..++..+.. .-|=+..++... .-.+.+..+.+.-=|+-|.
T Consensus 14 ~l~~~l~~f~~-----~~P~v~i~i~~~----~~~~~~~~l~~~~~Di~i~ 55 (198)
T cd08461 14 ILPPLLAALRQ-----EAPGVRVAIRDL----ESDNLEAQLERGEVDLALT 55 (198)
T ss_pred HhHHHHHHHHH-----HCCCcEEEEeeC----CcccHHHHHhcCCCcEEEe
Confidence 44555555443 245445554432 2223345555554555554
No 49
>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=25.70 E-value=1.5e+02 Score=20.79 Aligned_cols=66 Identities=15% Similarity=0.016 Sum_probs=32.4
Q ss_pred cccCCCCCCCeeEECcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCcee
Q 033395 11 LLHHDKLLLPLIKCQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHI 90 (120)
Q Consensus 11 LI~npvs~APGf~i~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~I 90 (120)
|+..| ...|||.+-++.--.. - . ..-+..++.+|- . -...+.+-+.|-+..+.|.+|+++|++..|
T Consensus 23 Ll~~~-~~v~GFt~~~~~g~g~--~--~--~~~s~~EQV~G~-----~--~~~~~~~~~~~~~~~~Ll~~L~~~~~~~~i 88 (102)
T PF11582_consen 23 LLELP-DGVSGFTSSPAEGHGS--R--H--SLLSAAEQVSGR-----A--RRVRFQVILPEEDAEELLAALKQEFAGTGI 88 (102)
T ss_dssp HTT---TT----EEEEEEEEE-------------------EE-----E--EEEEEEEEEEGGGHHHHHHHHHHHTTTS--
T ss_pred HHHhc-CccCCceEeeccccCC--c--c--cCCCHHHhcccc-----c--ceEEEEEEECHHHHHHHHHHHHHHcCCCCc
Confidence 44442 2578999999988776 2 1 223344444331 2 233444556889999999999999987654
No 50
>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=25.60 E-value=1.1e+02 Score=20.01 Aligned_cols=34 Identities=24% Similarity=0.332 Sum_probs=23.4
Q ss_pred CceEEEEEEecC--CchhhhhhHHHHHHhCCCceee
Q 033395 58 EPYTSKSLTTNL--SDLEAAQPLSKLCLEFPDLHIG 91 (120)
Q Consensus 58 ~p~~S~tv~~~~--~Eg~IA~~L~~i~~~~pdv~IG 91 (120)
.|+++.+|...- .+-.+.+.|.+|.++-|.+.+-
T Consensus 3 ~Pv~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~ 38 (75)
T PF14492_consen 3 PPVLSVAIEPKNKEDEPKLSEALQKLSEEDPSLRVE 38 (75)
T ss_dssp S-SEEEEEEESSHHHHHHHHHHHHHHHHH-TTSEEE
T ss_pred CCeEEEEEEECCHhHHHHHHHHHHHHHhcCCeEEEE
Confidence 577777777663 6677778888888888877753
No 51
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=25.34 E-value=1.8e+02 Score=22.85 Aligned_cols=53 Identities=25% Similarity=0.293 Sum_probs=31.0
Q ss_pred EEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 28 IILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 28 ~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
=|+-+.+........+.+. .| |-+.+..|+++.. -.+.+.++.++|||+-||-
T Consensus 12 aVir~~~~~~a~~~~~al~----~g----Gi~~iEiT~~t~~----a~~~I~~l~~~~p~~~vGA 64 (196)
T PF01081_consen 12 AVIRGDDPEDAVPIAEALI----EG----GIRAIEITLRTPN----ALEAIEALRKEFPDLLVGA 64 (196)
T ss_dssp EEETTSSGGGHHHHHHHHH----HT----T--EEEEETTSTT----HHHHHHHHHHHHTTSEEEE
T ss_pred EEEEcCCHHHHHHHHHHHH----HC----CCCEEEEecCCcc----HHHHHHHHHHHCCCCeeEE
Confidence 3455544433344444444 34 5777777665432 3466888999999999985
No 52
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=24.99 E-value=79 Score=21.15 Aligned_cols=15 Identities=20% Similarity=0.018 Sum_probs=6.7
Q ss_pred hHHHHHHhCCCceee
Q 033395 77 PLSKLCLEFPDLHIG 91 (120)
Q Consensus 77 ~L~~i~~~~pdv~IG 91 (120)
....+.+..=|+.|.
T Consensus 41 ~~~~l~~~~~Di~i~ 55 (197)
T cd08448 41 QIEALLRGELDLGFV 55 (197)
T ss_pred HHHHHHcCCcceEEE
Confidence 344444444444444
No 53
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=24.99 E-value=1.7e+02 Score=21.87 Aligned_cols=23 Identities=4% Similarity=0.275 Sum_probs=18.0
Q ss_pred CchhhhhhHHHHHHhCCCceeee
Q 033395 70 SDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 70 ~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
...-+...|.+++++||++.|=-
T Consensus 95 ~~~~~~~~l~~~~~~~p~v~l~i 117 (279)
T TIGR03339 95 APYYVLDLVARFRQRYPGIEVSV 117 (279)
T ss_pred hHHHHHHHHHHHHHHCCCcEEEE
Confidence 34567889999999999876643
No 54
>PF02445 NadA: Quinolinate synthetase A protein; InterPro: IPR003473 Quinolinate synthetase catalyzes the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid []. This synthesis requires two enzymes, an FAD-containing "B protein" and an "A protein".; GO: 0008987 quinolinate synthetase A activity, 0009435 NAD biosynthetic process; PDB: 2QS0_A 1WZU_A.
Probab=24.95 E-value=1.5e+02 Score=25.21 Aligned_cols=62 Identities=18% Similarity=0.268 Sum_probs=36.2
Q ss_pred CcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEE--EecCCchhhhhhHHHHHHhCCCceeeeccccc
Q 033395 25 QNVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSL--TTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSR 97 (120)
Q Consensus 25 ~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv--~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~ 97 (120)
..++|+.| | .|++.-..++-- .+.++-=.. .|.+.+..=++.+.++.++|||.-.=||=-..
T Consensus 47 a~~IVfcG--V-~FMAEtAkIL~P--------~K~VllPd~~AgC~MAdm~~~~~v~~~k~~~p~~~vV~YVNss 110 (296)
T PF02445_consen 47 ADIIVFCG--V-HFMAETAKILNP--------DKKVLLPDPEAGCPMADMATAEDVRELKEEYPDAAVVTYVNSS 110 (296)
T ss_dssp SSEEEEES----HHHHHHHHHH-T--------TSEEE-SS--------TT--HHHHHHHHHHSTTS-EEEESSS-
T ss_pred CCEEEEec--c-eehHhhHHhhCC--------CCEEEecCCCCCCchhhhCCHHHHHHHHHHCCCCeEEEEecCh
Confidence 36899999 8 777655554421 244443333 36788999999999999999999988886544
No 55
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=24.86 E-value=1.8e+02 Score=22.13 Aligned_cols=25 Identities=4% Similarity=0.195 Sum_probs=20.0
Q ss_pred CCchhhhhhHHHHHHhCCCceeeec
Q 033395 69 LSDLEAAQPLSKLCLEFPDLHIGCY 93 (120)
Q Consensus 69 ~~Eg~IA~~L~~i~~~~pdv~IGSY 93 (120)
....-+...|.+++++||++.|=.+
T Consensus 101 ~~~~~l~~~l~~~~~~~p~~~i~~~ 125 (296)
T PRK11242 101 FTAYLIGPLIDAFHARYPGITLTIR 125 (296)
T ss_pred hhhhhhHHHHHHHHHHCCCCEEEEE
Confidence 4666789999999999999876544
No 56
>cd08421 PBP2_LTTR_like_1 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=24.71 E-value=99 Score=20.83 Aligned_cols=16 Identities=19% Similarity=0.071 Sum_probs=7.0
Q ss_pred hhHHHHHHhCCCceee
Q 033395 76 QPLSKLCLEFPDLHIG 91 (120)
Q Consensus 76 ~~L~~i~~~~pdv~IG 91 (120)
+.+..+.+.-=|+-|.
T Consensus 40 ~~~~~l~~~~~D~~i~ 55 (198)
T cd08421 40 DIVRAVAEGRADLGIV 55 (198)
T ss_pred HHHHHHhcCCceEEEE
Confidence 3344444443344444
No 57
>COG0011 Uncharacterized conserved protein [Function unknown]
Probab=24.61 E-value=1.1e+02 Score=22.11 Aligned_cols=51 Identities=14% Similarity=0.079 Sum_probs=36.1
Q ss_pred CCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCC
Q 033395 32 ATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPD 87 (120)
Q Consensus 32 GvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pd 87 (120)
|+.-|++-+-++.+..-|+.- |-++.--.. .+.=||++.+.|+.|++.|.-
T Consensus 13 gt~~~svs~yVa~~i~~lk~~----glky~~~pm-~T~iEg~~del~~~ik~~~Ea 63 (100)
T COG0011 13 GTGGPSVSKYVAEAIEILKES----GLKYQLGPM-GTVIEGELDELMEAVKEAHEA 63 (100)
T ss_pred CCCCCCHHHHHHHHHHHHHHc----CCceeecCc-ceEEEecHHHHHHHHHHHHHH
Confidence 445666777777888888775 466644333 334599999999999999854
No 58
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=24.40 E-value=2.2e+02 Score=21.61 Aligned_cols=30 Identities=7% Similarity=-0.017 Sum_probs=21.2
Q ss_pred EEEEEEecCCchhhhhhHHHHHHhCCCcee
Q 033395 61 TSKSLTTNLSDLEAAQPLSKLCLEFPDLHI 90 (120)
Q Consensus 61 ~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~I 90 (120)
++..+........+.+.|.+++++||++.|
T Consensus 99 l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l 128 (294)
T PRK09986 99 IEIGIVGTALWGRLRPAMRHFLKENPNVEW 128 (294)
T ss_pred EEEEEehHHhHHHHHHHHHHHHHhCCCeEE
Confidence 344433345566778889999999999766
No 59
>cd08479 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. 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 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 gene a
Probab=24.22 E-value=61 Score=21.97 Aligned_cols=9 Identities=22% Similarity=0.132 Sum_probs=3.7
Q ss_pred CceEEEEEE
Q 033395 58 EPYTSKSLT 66 (120)
Q Consensus 58 ~p~~S~tv~ 66 (120)
-|-+..++.
T Consensus 27 ~P~i~i~~~ 35 (198)
T cd08479 27 YPELEVQLE 35 (198)
T ss_pred CCCeEEEEE
Confidence 444444443
No 60
>PRK15016 isochorismate synthase EntC; Provisional
Probab=24.22 E-value=3e+02 Score=24.12 Aligned_cols=68 Identities=12% Similarity=0.003 Sum_probs=49.4
Q ss_pred cEEEecCCChhH-HHHHHHHHHHHHHhCCCcCCCceEEEEEEecC-CchhhhhhHHHHHHhCCCceeeeccc
Q 033395 26 NVIILTATNVTE-LDKEWNCLIELLRSGGLSLMEPYTSKSLTTNL-SDLEAAQPLSKLCLEFPDLHIGCYRK 95 (120)
Q Consensus 26 NV~VmAGvpvP~-i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~-~Eg~IA~~L~~i~~~~pdv~IGSYP~ 95 (120)
++....-+|-+. .+.+++..+..++.|. .-+-++||.+.... ...+....|.+|.+.+|.-..-.+++
T Consensus 116 ~~~~~~~~p~~~~y~~~V~~a~~~i~~G~--l~KVVLsR~~~l~~~~~~d~~~l~~~L~~~nP~~y~f~~~~ 185 (391)
T PRK15016 116 NVVERQAIPEQTTFEAMVARAAALTATPQ--VDKVVLSRLIDITTDAAIDSGALLERLIAQNPVSYNFHVPL 185 (391)
T ss_pred ceeecccCCCHHHHHHHHHHHHHHHHcCC--ccEEEcCcEEeecCCCCCCHHHHHHHHHHhCCCCeEEEEEc
Confidence 455555545544 6889999999998873 33568899987665 45677888999999999976555543
No 61
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=24.18 E-value=85 Score=21.17 Aligned_cols=33 Identities=15% Similarity=0.034 Sum_probs=14.7
Q ss_pred CceEEEEEEecCCchhhhhhHHHHHHhCCCceeeecc
Q 033395 58 EPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 58 ~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP 94 (120)
.|-+.-.+. ++.-.+.+..+.+..=|+-|...|
T Consensus 26 ~P~i~v~~~----~~~~~~~~~~l~~g~~D~~i~~~~ 58 (198)
T cd08447 26 LPDVDLVLR----EMVTTDQIEALESGRIDLGLLRPP 58 (198)
T ss_pred CCCeEEEEE----eCCHHHHHHHHHcCCceEEEecCC
Confidence 454444443 233344445555544455554333
No 62
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of 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 th
Probab=24.00 E-value=1.1e+02 Score=21.10 Aligned_cols=17 Identities=18% Similarity=0.186 Sum_probs=8.2
Q ss_pred hhHHHHHHhCCCceeee
Q 033395 76 QPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 76 ~~L~~i~~~~pdv~IGS 92 (120)
+.+..+.+..=|+.|+.
T Consensus 41 ~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 41 RQIEALDAGTIDIGFGR 57 (198)
T ss_pred HHHHHHHcCCccEEEec
Confidence 34445555444555543
No 63
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=23.53 E-value=98 Score=28.61 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=11.8
Q ss_pred eEECcEEEecCCCh
Q 033395 22 IKCQNVIILTATNV 35 (120)
Q Consensus 22 f~i~NV~VmAGvpv 35 (120)
+-|.+|.+.||+|.
T Consensus 398 INIRqV~~fpgT~~ 411 (560)
T COG1031 398 INIRQVVVFPGTPM 411 (560)
T ss_pred eeeeeEeecCCCch
Confidence 45789999999887
No 64
>COG4187 RocB Arginine degradation protein (predicted deacylase) [Amino acid transport and metabolism]
Probab=23.47 E-value=68 Score=29.53 Aligned_cols=28 Identities=18% Similarity=0.100 Sum_probs=22.1
Q ss_pred EEEEecCCchhhhhhHHHHHHhCCCceeeecccccC
Q 033395 63 KSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRKSRQ 98 (120)
Q Consensus 63 ~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~~~~ 98 (120)
-+|.-+.+|+.+|+-|-.+ +|+||+|++
T Consensus 21 ~SvtgT~GE~a~ad~l~~v--------L~~~pYFqe 48 (553)
T COG4187 21 PSVTGTPGEGAFADRLLGV--------LGELPYFQE 48 (553)
T ss_pred cccCCCcccccHHHHHHHH--------HhcCchhhh
Confidence 3455667999999999876 688888874
No 65
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=23.45 E-value=55 Score=21.97 Aligned_cols=9 Identities=22% Similarity=0.346 Sum_probs=4.1
Q ss_pred CceEEEEEE
Q 033395 58 EPYTSKSLT 66 (120)
Q Consensus 58 ~p~~S~tv~ 66 (120)
-|=+.-++.
T Consensus 26 ~P~i~i~i~ 34 (194)
T cd08481 26 HPDITVNLV 34 (194)
T ss_pred CCCceEEEE
Confidence 454444444
No 66
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=23.15 E-value=1.9e+02 Score=22.22 Aligned_cols=25 Identities=20% Similarity=0.358 Sum_probs=19.2
Q ss_pred CCchhhhhhHHHHHHhCCCceeeec
Q 033395 69 LSDLEAAQPLSKLCLEFPDLHIGCY 93 (120)
Q Consensus 69 ~~Eg~IA~~L~~i~~~~pdv~IGSY 93 (120)
....-+.+.|.+++++||++.|=..
T Consensus 102 ~~~~~l~~~l~~~~~~~P~i~i~~~ 126 (301)
T PRK14997 102 LLHVHIGPMLAKFMARYPDVSLQLE 126 (301)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEE
Confidence 4556677889999999999887543
No 67
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=23.14 E-value=80 Score=21.33 Aligned_cols=13 Identities=38% Similarity=0.230 Sum_probs=4.8
Q ss_pred HHHHHhCCCceee
Q 033395 79 SKLCLEFPDLHIG 91 (120)
Q Consensus 79 ~~i~~~~pdv~IG 91 (120)
..+...-=|+-|.
T Consensus 43 ~~l~~g~~D~~i~ 55 (200)
T cd08464 43 DMLDRGEIDLAIG 55 (200)
T ss_pred HHHhcCcccEEEe
Confidence 3333333344443
No 68
>KOG2754 consensus Oligosaccharyltransferase, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.06 E-value=76 Score=28.47 Aligned_cols=34 Identities=12% Similarity=0.348 Sum_probs=27.9
Q ss_pred CCCceeeecccccCCC-eEE-EEeeecccceeeecc
Q 033395 85 FPDLHIGCYRKSRQGP-LII-SFEGKVKDSATWISS 118 (120)
Q Consensus 85 ~pdv~IGSYP~~~~g~-~~~-V~rg~D~~~~~~~~~ 118 (120)
+|+-.+-|||+-.+.+ +-+ ++.+++.+|+-|+.|
T Consensus 204 np~a~~s~np~a~Gs~~~LV~~lQarNNARvv~sGS 239 (443)
T KOG2754|consen 204 NPEAKVSCNPWAAGSQTLLVSGLQARNNARVVFSGS 239 (443)
T ss_pred CcccccccCccccccceEEEEeeeccCCceEEEecc
Confidence 4888999999988544 333 999999999999987
No 69
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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, 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, they can interact with a cognate membrane transport
Probab=22.88 E-value=1e+02 Score=20.92 Aligned_cols=47 Identities=17% Similarity=0.020 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeecc
Q 033395 39 DKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 39 ~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP 94 (120)
...+..++..+.. --|-+.-++. ++.-.+.+..+.+.-=|+-|...|
T Consensus 12 ~~~l~~~l~~~~~-----~~P~i~l~i~----~~~~~~~~~~l~~g~~D~~i~~~~ 58 (200)
T cd08453 12 YSVLPELVRRFRE-----AYPDVELQLR----EATSDVQLEALLAGEIDAGIVIPP 58 (200)
T ss_pred hHHHHHHHHHHHH-----hCCCceEEEE----eCCHHHHHHHHHcCCCCEEEEecC
Confidence 3355566666544 2454444443 233344455666555555555443
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=22.52 E-value=1.1e+02 Score=20.17 Aligned_cols=49 Identities=8% Similarity=-0.008 Sum_probs=30.1
Q ss_pred ceEEEEEEec-CCchh-hhhhHHHHH---HhCCCceeeecccccCCCeEEEEeeecccce
Q 033395 59 PYTSKSLTTN-LSDLE-AAQPLSKLC---LEFPDLHIGCYRKSRQGPLIISFEGKVKDSA 113 (120)
Q Consensus 59 p~~S~tv~~~-~~Eg~-IA~~L~~i~---~~~pdv~IGSYP~~~~g~~~~V~rg~D~~~~ 113 (120)
.-+.|+.... ..++- +...+++++ ..|||+++|. +.+.+.+.-.|...+
T Consensus 9 ~~l~r~f~f~~f~~a~~f~~~va~~ae~~~HHPdi~~~~------~~V~v~l~Thd~~gl 62 (76)
T cd00914 9 DAIHKSFKFKDFNEAFGFMTRVALEAEKMNHHPEWFNVY------NKVDITLTTHDAGGL 62 (76)
T ss_pred CeEEEEEEeCCHHHHHHHHHHHHHHHHHhCCCCCEEEec------cEEEEEEEeCCCCCc
Confidence 3578888765 45553 444444444 5689998763 556666666665543
No 71
>PF05798 Phage_FRD3: Bacteriophage FRD3 protein; InterPro: IPR008765 This is a group of proteins of unknown function from bacteriophage T2 and related phage.
Probab=22.45 E-value=85 Score=21.79 Aligned_cols=30 Identities=23% Similarity=0.392 Sum_probs=18.8
Q ss_pred HHHHHhCCCceeeecccccCCCeEEEEeee
Q 033395 79 SKLCLEFPDLHIGCYRKSRQGPLIISFEGK 108 (120)
Q Consensus 79 ~~i~~~~pdv~IGSYP~~~~g~~~~V~rg~ 108 (120)
+-|.++||+++|-|---...-.+.+++.|-
T Consensus 16 EvIRNRyPelsi~si~d~~f~~~~i~i~GP 45 (75)
T PF05798_consen 16 EVIRNRYPELSITSIQDSKFCSIQIVIEGP 45 (75)
T ss_pred HHHHccCCceEEEEeecCCcceEEEEEecc
Confidence 457899999999983222212344476664
No 72
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. 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 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 gene a
Probab=22.32 E-value=61 Score=21.95 Aligned_cols=11 Identities=9% Similarity=-0.158 Sum_probs=5.6
Q ss_pred HHHHHHHHHHh
Q 033395 41 EWNCLIELLRS 51 (120)
Q Consensus 41 Ml~~l~p~L~~ 51 (120)
.+..++..+..
T Consensus 15 ~l~~~l~~~~~ 25 (201)
T cd08471 15 HVLPIITDFLD 25 (201)
T ss_pred HHHHHHHHHHH
Confidence 55555555544
No 73
>PF14681 UPRTase: Uracil phosphoribosyltransferase; PDB: 1V9S_B 1UPF_A 1UPU_D 1JLR_B 1BD4_A 1BD3_C 1JLS_D 1XTV_C 1XTU_H 3G6W_C ....
Probab=22.10 E-value=66 Score=24.95 Aligned_cols=16 Identities=38% Similarity=0.561 Sum_probs=13.7
Q ss_pred hHHHHHHhCCCceeee
Q 033395 77 PLSKLCLEFPDLHIGC 92 (120)
Q Consensus 77 ~L~~i~~~~pdv~IGS 92 (120)
.|.+++++||++.|=.
T Consensus 165 Gl~~l~~~~P~v~I~t 180 (207)
T PF14681_consen 165 GLERLLKAFPDVRIYT 180 (207)
T ss_dssp HHHHHHHHSTTSEEEE
T ss_pred HHHHHHHhCCCeEEEE
Confidence 4999999999999743
No 74
>PF02514 CobN-Mg_chel: CobN/Magnesium Chelatase; InterPro: IPR003672 This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN may play a role in cobalt insertion reactions and is implicated in the conversion of precorrin-2 to cobyrinic acid in cobalamin biosynthesis []. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis as the third subunit of light-independent protochlorophyllide reductase in bacteria and plants [].; GO: 0009058 biosynthetic process
Probab=22.02 E-value=47 Score=32.65 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=19.2
Q ss_pred CCccccccc----CCCCCCCeeEECcEEEecC
Q 033395 5 PEGTTELLH----HDKLLLPLIKCQNVIILTA 32 (120)
Q Consensus 5 PeGaa~LI~----npvs~APGf~i~NV~VmAG 32 (120)
|+| .-.+. +..-.-||++.|||+|++=
T Consensus 359 ppg-~~mv~~~~~~~~~vIpgi~~GNV~i~~Q 389 (1098)
T PF02514_consen 359 PPG-DIMVYEDNGGGYFVIPGIRFGNVFIGPQ 389 (1098)
T ss_pred Ccc-CCcceecccCCEEEEEeeeeCCEEEEeC
Confidence 555 23455 4445679999999999974
No 75
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=22.00 E-value=1.3e+02 Score=20.45 Aligned_cols=8 Identities=25% Similarity=0.132 Sum_probs=3.4
Q ss_pred CceEEEEE
Q 033395 58 EPYTSKSL 65 (120)
Q Consensus 58 ~p~~S~tv 65 (120)
.|-+.-.+
T Consensus 26 ~P~i~i~i 33 (198)
T cd08441 26 WPDVELDL 33 (198)
T ss_pred CCCeEEEE
Confidence 44444444
No 76
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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=21.95 E-value=1.1e+02 Score=21.01 Aligned_cols=21 Identities=24% Similarity=0.251 Sum_probs=9.7
Q ss_pred hhhhhHHHHHHhCCCceeeec
Q 033395 73 EAAQPLSKLCLEFPDLHIGCY 93 (120)
Q Consensus 73 ~IA~~L~~i~~~~pdv~IGSY 93 (120)
.-.+.+..+.+.-=|+-|...
T Consensus 37 ~~~~~~~~l~~g~~Dl~i~~~ 57 (196)
T cd08458 37 PSQTVLELVSLQHYDLGISIL 57 (196)
T ss_pred ChHHHHHHHHcCCCCEEEEec
Confidence 344444555444444444433
No 77
>cd08440 PBP2_LTTR_like_4 TThe 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 funct
Probab=21.85 E-value=1.3e+02 Score=19.97 Aligned_cols=15 Identities=20% Similarity=0.215 Sum_probs=6.7
Q ss_pred HHHHHHhCCCceeee
Q 033395 78 LSKLCLEFPDLHIGC 92 (120)
Q Consensus 78 L~~i~~~~pdv~IGS 92 (120)
++.+.+.-=|+-|..
T Consensus 42 ~~~l~~g~~D~~i~~ 56 (197)
T cd08440 42 IEAVRSGEVDFGIGS 56 (197)
T ss_pred HHHHHcCCccEEEEe
Confidence 344444334555543
No 78
>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=21.82 E-value=3.5e+02 Score=20.26 Aligned_cols=57 Identities=19% Similarity=0.232 Sum_probs=31.4
Q ss_pred CcEEEec-CCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEE-ecCCchhh--hhhHHHHHHhCCCcee
Q 033395 25 QNVIILT-ATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLT-TNLSDLEA--AQPLSKLCLEFPDLHI 90 (120)
Q Consensus 25 ~NV~VmA-GvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~-~~~~Eg~I--A~~L~~i~~~~pdv~I 90 (120)
++++..| |+=+.-+.+|+..+... +.+ ...++. +...+.++ .+.|.+++++||++.+
T Consensus 109 ~~~vliagGtGiaP~~~~l~~~~~~--------~~~-~~v~l~~~~r~~~~~~~~~~l~~l~~~~~~~~~ 169 (236)
T cd06210 109 RPRWFVAGGTGLAPLLSMLRRMAEW--------GEP-QEARLFFGVNTEAELFYLDELKRLADSLPNLTV 169 (236)
T ss_pred ccEEEEccCcchhHHHHHHHHHHhc--------CCC-ceEEEEEecCCHHHhhhHHHHHHHHHhCCCeEE
Confidence 3555555 53344456666665432 122 122332 33444444 4889999999998774
No 79
>cd08473 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. 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 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 gene a
Probab=21.71 E-value=75 Score=21.44 Aligned_cols=11 Identities=9% Similarity=-0.040 Sum_probs=4.9
Q ss_pred HHHHHHHHHHh
Q 033395 41 EWNCLIELLRS 51 (120)
Q Consensus 41 Ml~~l~p~L~~ 51 (120)
.+..++..+..
T Consensus 17 ~l~~~l~~~~~ 27 (202)
T cd08473 17 LLAPLLPRFMA 27 (202)
T ss_pred HHHHHHHHHHH
Confidence 44444444433
No 80
>PF11209 DUF2993: Protein of unknown function (DUF2993); InterPro: IPR021373 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=21.64 E-value=43 Score=25.13 Aligned_cols=27 Identities=22% Similarity=0.294 Sum_probs=20.4
Q ss_pred CchhhhhhHHHHH--HhCCCceeeecccc
Q 033395 70 SDLEAAQPLSKLC--LEFPDLHIGCYRKS 96 (120)
Q Consensus 70 ~Eg~IA~~L~~i~--~~~pdv~IGSYP~~ 96 (120)
-|..++..|++-. .+-|+|+||..||.
T Consensus 10 ~e~~i~~~l~~~~~~~~~~~V~i~g~P~l 38 (225)
T PF11209_consen 10 AEKQIADALRAQLDLAEDPEVSIGGFPFL 38 (225)
T ss_pred HHHHHHHHHHHhcCCCCCceEEEcCcCcH
Confidence 4666777776555 56799999999985
No 81
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=21.59 E-value=1.1e+02 Score=20.43 Aligned_cols=46 Identities=11% Similarity=0.096 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceeeeccc
Q 033395 41 EWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGCYRK 95 (120)
Q Consensus 41 Ml~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGSYP~ 95 (120)
.+..++..+.. --|=+.-.+. ++.-.+.+..+.+..=|+-|+.++.
T Consensus 14 ~l~~~l~~~~~-----~~P~i~i~~~----~~~~~~~~~~l~~~~~Dl~i~~~~~ 59 (197)
T cd08449 14 GLGPALRRFKR-----QYPNVTVRFH----ELSPEAQKAALLSKRIDLGFVRFAD 59 (197)
T ss_pred hHHHHHHHHHH-----HCCCeEEEEE----ECCHHHHHHHHhCCCccEEEecccc
Confidence 45555555443 2444444443 2333344455555555666665553
No 82
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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 gene and activates the expression of the mdaB gene wh
Probab=21.49 E-value=73 Score=21.69 Aligned_cols=23 Identities=17% Similarity=0.212 Sum_probs=18.3
Q ss_pred chhhhhhHHHHHHhCCCceeeec
Q 033395 71 DLEAAQPLSKLCLEFPDLHIGCY 93 (120)
Q Consensus 71 Eg~IA~~L~~i~~~~pdv~IGSY 93 (120)
..-+...|.+++++||++.|-..
T Consensus 15 ~~~l~~~l~~f~~~~P~v~i~~~ 37 (199)
T cd08478 15 LHLLAPLIAKFRERYPDIELELV 37 (199)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEE
Confidence 34567889999999999888654
No 83
>TIGR00543 isochor_syn isochorismate synthases. This enzyme interconverts chorismate and isochorismate. In E. coli, different loci encode isochorismate synthases for the pathways of menaquinone biosynthesis and enterobactin biosynthesis (via salicilate) and fail to complement each other. Among isochorismate synthases, the N-terminal domain is poorly conserved.
Probab=21.47 E-value=3.3e+02 Score=23.11 Aligned_cols=56 Identities=20% Similarity=0.272 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHhCCCcCCCceEEEEEEecC-CchhhhhhHHHHHHhCCCceeeecc
Q 033395 37 ELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNL-SDLEAAQPLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 37 ~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~-~Eg~IA~~L~~i~~~~pdv~IGSYP 94 (120)
..+.+++..+..++.|. .-+-++|+.+.... ..-+..+.|.++.+++|+..+-.|.
T Consensus 91 ~~~~~v~~a~~~I~~G~--l~KvVLar~~~~~~~~~~~~~~~l~~L~~~~p~~y~f~~~ 147 (351)
T TIGR00543 91 AWRTAVEEALENIRQGP--LDKVVLARALTLKFADDIDPIAVLANLRQQYPNAYIFLLE 147 (351)
T ss_pred HHHHHHHHHHHHHHcCC--ccEEEcccEEEEecCCCCCHHHHHHHHHHhCCcCEEEEEE
Confidence 46778999999988862 23457899887765 4557889999999999986655444
No 84
>TIGR01531 glyc_debranch glycogen debranching enzymye. glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4--1,4-glucantransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site directed mutagenesis studies in S. cerevisiae indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this model belong to the larger alpha-amylase family. The model covers eukaryotic proteins with a seed composed of human, nematode and yeast sequences. Yeast seed sequence is well characterized. The model is quite rigorous; either query sequence yields large bit score or it fails to hit the model altogether. There doesn't appear to be any middle ground.
Probab=21.17 E-value=1.8e+02 Score=30.05 Aligned_cols=64 Identities=14% Similarity=0.276 Sum_probs=42.6
Q ss_pred CCeeEECcEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCc--eEEEEEEecCCchhh--------------------hh
Q 033395 19 LPLIKCQNVIILTATNVTELDKEWNCLIELLRSGGLSLMEP--YTSKSLTTNLSDLEA--------------------AQ 76 (120)
Q Consensus 19 APGf~i~NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p--~~S~tv~~~~~Eg~I--------------------A~ 76 (120)
.=||||+|.| .||...-+-|||.-..- .| ++-..+-+.-.|-|. +.
T Consensus 506 F~G~RiDNCH---STPlhVaeylLd~AR~v---------nPnLyV~AELFTGSee~D~~Fv~rLGInsLIREAm~a~~~~ 573 (1464)
T TIGR01531 506 FDGVRIDNCH---STPIHVAEYLLDAARKY---------NPNLYVVAELFTGSETLDNVFVNRLGISSLIREAMSAWDSH 573 (1464)
T ss_pred hcceeeeccc---CCcHHHHHHHHHHHhhc---------CCCeEEEeeecCCcHHHHHHHHHHhhHHHHHHHHHhcCCHH
Confidence 3599999999 57774447799876643 33 333333333333222 45
Q ss_pred hHHHHHHhCCCceeeecc
Q 033395 77 PLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 77 ~L~~i~~~~pdv~IGSYP 94 (120)
.|+++.-+|-.-.||||.
T Consensus 574 El~rlv~r~GG~PIGs~~ 591 (1464)
T TIGR01531 574 EEGRLVYRYGGRPVGSFK 591 (1464)
T ss_pred HhhhHHHHhCCccccccc
Confidence 689999999999999993
No 85
>cd08488 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsibl
Probab=21.02 E-value=74 Score=21.75 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=3.9
Q ss_pred CceEEEEEE
Q 033395 58 EPYTSKSLT 66 (120)
Q Consensus 58 ~p~~S~tv~ 66 (120)
-|-+.-++.
T Consensus 26 ~P~v~i~~~ 34 (191)
T cd08488 26 HPFIDLRLS 34 (191)
T ss_pred CCCcEEEEE
Confidence 444444444
No 86
>PF02153 PDH: Prephenate dehydrogenase; InterPro: IPR003099 Members of this family are prephenate dehydrogenases 1.3.1.12 from EC involved in tyrosine biosynthesis. ; GO: 0004665 prephenate dehydrogenase (NADP+) activity, 0008977 prephenate dehydrogenase activity, 0006571 tyrosine biosynthetic process, 0055114 oxidation-reduction process; PDB: 2F1K_B 2PV7_A 3DZB_B 3KTD_B 3B1F_A 2G5C_D 3GGP_C 3GGG_C 3GGO_D.
Probab=20.93 E-value=1.4e+02 Score=23.53 Aligned_cols=80 Identities=11% Similarity=0.226 Sum_probs=44.1
Q ss_pred cEEEecCCChhHHHHHHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCC-Cce-eeecccccC-----
Q 033395 26 NVIILTATNVTELDKEWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFP-DLH-IGCYRKSRQ----- 98 (120)
Q Consensus 26 NV~VmAGvpvP~i~aMl~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~p-dv~-IGSYP~~~~----- 98 (120)
.|.|++ ||+..+...++.+.|.++.| .-+ .-. ++... .++.++++..| ++. ||+-|-+-.
T Consensus 47 Dlvvla-vP~~~~~~~l~~~~~~~~~~-----~iv-~Dv--~SvK~----~~~~~~~~~~~~~~~~v~~HPM~G~e~~G~ 113 (258)
T PF02153_consen 47 DLVVLA-VPVSAIEDVLEEIAPYLKPG-----AIV-TDV--GSVKA----PIVEAMERLLPEGVRFVGGHPMAGPEKSGP 113 (258)
T ss_dssp SEEEE--S-HHHHHHHHHHHHCGS-TT-----SEE-EE----S-CH----HHHHHHHHHHTSSGEEEEEEESCSTSSSSG
T ss_pred CEEEEc-CCHHHHHHHHHHhhhhcCCC-----cEE-EEe--CCCCH----HHHHHHHHhcCcccceeecCCCCCCccccc
Confidence 577776 47766888999999976653 433 221 23332 33444444445 555 888887665
Q ss_pred ---------CCeEEEEeee--cccceeeecc
Q 033395 99 ---------GPLIISFEGK--VKDSATWISS 118 (120)
Q Consensus 99 ---------g~~~~V~rg~--D~~~~~~~~~ 118 (120)
|+..+++.+. |.+.+.|+..
T Consensus 114 ~~a~~~lf~g~~~il~p~~~~~~~~~~~~~~ 144 (258)
T PF02153_consen 114 EAADADLFEGRNWILCPGEDTDPEALELVEE 144 (258)
T ss_dssp GG-TTTTTTTSEEEEEECTTS-HHHHHHHHH
T ss_pred hhhcccccCCCeEEEeCCCCChHHHHHHHHH
Confidence 4556666554 5455666544
No 87
>TIGR01091 upp uracil phosphoribosyltransferase. that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins.
Probab=20.91 E-value=2.5e+02 Score=21.67 Aligned_cols=15 Identities=20% Similarity=0.397 Sum_probs=12.9
Q ss_pred hhHHHHHHhCCCcee
Q 033395 76 QPLSKLCLEFPDLHI 90 (120)
Q Consensus 76 ~~L~~i~~~~pdv~I 90 (120)
+.+.+|+++||++.|
T Consensus 163 ~gl~~l~~~~p~v~i 177 (207)
T TIGR01091 163 EGIEAVEKAHPDVDI 177 (207)
T ss_pred HHHHHHHHHCCCCEE
Confidence 449999999999986
No 88
>cd08427 PBP2_LTTR_like_2 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=20.78 E-value=99 Score=20.70 Aligned_cols=13 Identities=15% Similarity=-0.059 Sum_probs=5.0
Q ss_pred HHHHHhCCCceee
Q 033395 79 SKLCLEFPDLHIG 91 (120)
Q Consensus 79 ~~i~~~~pdv~IG 91 (120)
+.+.+.-=|+-|.
T Consensus 43 ~~l~~g~~Dl~i~ 55 (195)
T cd08427 43 ARVDAGELDAAIV 55 (195)
T ss_pred HHHHCCCCCEEEE
Confidence 3333333344443
No 89
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=20.73 E-value=1e+02 Score=21.14 Aligned_cols=18 Identities=28% Similarity=0.230 Sum_probs=9.5
Q ss_pred hHHHHHHhCCCceeeecc
Q 033395 77 PLSKLCLEFPDLHIGCYR 94 (120)
Q Consensus 77 ~L~~i~~~~pdv~IGSYP 94 (120)
.+..+.+.-=|+-|+..+
T Consensus 40 ~~~~l~~g~~D~~i~~~~ 57 (200)
T cd08460 40 DVDALREGRIDLEIGVLG 57 (200)
T ss_pred HHHHHHCCCccEEEecCC
Confidence 345555555555555444
No 90
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=20.59 E-value=4.1e+02 Score=21.02 Aligned_cols=32 Identities=19% Similarity=0.217 Sum_probs=22.7
Q ss_pred CCceEEEEEEecCCchhhhhhHHHHHHhCCCceeee
Q 033395 57 MEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIGC 92 (120)
Q Consensus 57 G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IGS 92 (120)
|-+.+-.|+++.- -.+.+.++.++||++-||.
T Consensus 29 Gi~~iEit~~tp~----a~~~I~~l~~~~~~~~vGA 60 (201)
T PRK06015 29 GLPAIEITLRTPA----ALDAIRAVAAEVEEAIVGA 60 (201)
T ss_pred CCCEEEEeCCCcc----HHHHHHHHHHHCCCCEEee
Confidence 5777777765432 2245778899999999986
No 91
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. 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 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 gene
Probab=20.53 E-value=66 Score=21.79 Aligned_cols=21 Identities=10% Similarity=-0.047 Sum_probs=9.7
Q ss_pred HHHHHHHHHHhCCCcCCCceEEEEEE
Q 033395 41 EWNCLIELLRSGGLSLMEPYTSKSLT 66 (120)
Q Consensus 41 Ml~~l~p~L~~G~L~~G~p~~S~tv~ 66 (120)
.+..++..++. --|-+.-++.
T Consensus 15 ~l~~~l~~f~~-----~~P~v~l~i~ 35 (197)
T cd08470 15 FIAPLVNDFMQ-----RYPKLEVDIE 35 (197)
T ss_pred HHHHHHHHHHH-----HCCCeEEEEE
Confidence 44444445444 2454444444
No 92
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of 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 ma
Probab=20.36 E-value=97 Score=20.78 Aligned_cols=22 Identities=27% Similarity=0.200 Sum_probs=11.9
Q ss_pred hhhhHHHHHHhCCCceeeeccc
Q 033395 74 AAQPLSKLCLEFPDLHIGCYRK 95 (120)
Q Consensus 74 IA~~L~~i~~~~pdv~IGSYP~ 95 (120)
-.+....+.+..=|+-|..+|.
T Consensus 38 ~~~~~~~l~~~~~Dl~i~~~~~ 59 (201)
T cd08435 38 SDELLEGLRAGELDLAIGRLAD 59 (201)
T ss_pred HHHHHHHHHcCCccEEEEecCc
Confidence 3344455555555666665543
No 93
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=20.32 E-value=1.2e+02 Score=20.26 Aligned_cols=14 Identities=7% Similarity=-0.211 Sum_probs=5.7
Q ss_pred HHHHHHhCCCceee
Q 033395 78 LSKLCLEFPDLHIG 91 (120)
Q Consensus 78 L~~i~~~~pdv~IG 91 (120)
+..+.+.-=|+-|.
T Consensus 42 ~~~l~~g~~Dl~i~ 55 (193)
T cd08442 42 IQAVLEGRLDGAFV 55 (193)
T ss_pred HHHHHCCCccEEEE
Confidence 33344433444443
No 94
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=20.32 E-value=1.1e+02 Score=21.09 Aligned_cols=42 Identities=21% Similarity=0.096 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhCCCcCCCceEEEEEEecCCchhhhhhHHHHHHhCCCceee
Q 033395 41 EWNCLIELLRSGGLSLMEPYTSKSLTTNLSDLEAAQPLSKLCLEFPDLHIG 91 (120)
Q Consensus 41 Ml~~l~p~L~~G~L~~G~p~~S~tv~~~~~Eg~IA~~L~~i~~~~pdv~IG 91 (120)
.+..++..++. --|=++-++. |+.-.+.++++.+.-=|+-|.
T Consensus 14 ~l~~~l~~~~~-----~~P~i~l~~~----~~~~~~~~~~l~~g~~D~~i~ 55 (200)
T cd08467 14 LLPRLAPRLRE-----RAPGLDLRLC----PIGDDLAERGLEQGTIDLAVG 55 (200)
T ss_pred HHHHHHHHHHh-----hCCCCEEEEe----cCCcccHHHHhhCCCcCEEEe
Confidence 44555555443 1444444443 333334556665544455554
No 95
>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=20.04 E-value=59 Score=23.31 Aligned_cols=14 Identities=29% Similarity=0.420 Sum_probs=11.9
Q ss_pred CCCeeEECcEEEec
Q 033395 18 LLPLIKCQNVIILT 31 (120)
Q Consensus 18 ~APGf~i~NV~VmA 31 (120)
.||||+++-|.||=
T Consensus 52 da~GlKV~PvvVLv 65 (88)
T KOG3457|consen 52 DAPGLKVDPVVVLV 65 (88)
T ss_pred CCCCceeCCeeehh
Confidence 58999999988873
Done!