Query psy9845
Match_columns 261
No_of_seqs 195 out of 1230
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 21:08:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9845.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9845hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0830|consensus 100.0 1E-53 2.3E-58 384.8 8.6 146 4-149 67-222 (254)
2 PTZ00254 40S ribosomal protein 100.0 5.3E-50 1.2E-54 361.7 11.9 125 4-128 96-222 (249)
3 TIGR01012 Sa_S2_E_A ribosomal 100.0 3.2E-40 6.9E-45 289.0 10.3 109 4-112 86-196 (196)
4 PRK04020 rps2P 30S ribosomal p 100.0 1.3E-36 2.7E-41 267.8 9.1 109 4-112 92-202 (204)
5 COG0052 RpsB Ribosomal protein 100.0 5E-29 1.1E-33 226.0 8.8 77 19-95 151-227 (252)
6 PRK12311 rpsB 30S ribosomal pr 99.9 5.3E-26 1.2E-30 212.1 8.4 73 21-93 149-221 (326)
7 PRK05299 rpsB 30S ribosomal pr 99.9 9.5E-26 2.1E-30 203.8 8.6 74 21-94 154-227 (258)
8 TIGR01011 rpsB_bact ribosomal 99.9 1.3E-25 2.8E-30 199.0 9.0 73 21-93 152-224 (225)
9 cd01425 RPS2 Ribosomal protein 99.9 1.8E-25 3.9E-30 192.4 8.1 87 4-90 81-193 (193)
10 CHL00067 rps2 ribosomal protei 99.9 1.3E-24 2.9E-29 193.0 8.6 72 21-92 158-229 (230)
11 PF00318 Ribosomal_S2: Ribosom 99.9 1.4E-22 3.1E-27 176.8 7.3 73 20-92 139-211 (211)
12 KOG0832|consensus 99.7 6.4E-18 1.4E-22 153.1 7.9 70 24-93 173-242 (251)
13 cd05710 SIS_1 A subgroup of th 77.8 14 0.0003 29.3 7.3 61 22-82 45-113 (120)
14 TIGR00393 kpsF KpsF/GutQ famil 75.2 15 0.00033 32.1 7.6 75 21-95 44-136 (268)
15 PRK12570 N-acetylmuramic acid- 74.8 11 0.00025 35.2 7.0 83 22-108 125-224 (296)
16 PRK08674 bifunctional phosphog 71.9 16 0.00035 34.0 7.3 74 21-96 75-159 (337)
17 cd06295 PBP1_CelR Ligand bindi 70.7 9.8 0.00021 32.3 5.2 45 23-68 63-107 (275)
18 cd05008 SIS_GlmS_GlmD_1 SIS (S 69.9 24 0.00052 27.2 6.8 46 22-67 44-95 (126)
19 TIGR00441 gmhA phosphoheptose 67.4 17 0.00037 30.1 5.8 51 21-71 76-132 (154)
20 PRK00331 glucosamine--fructose 64.6 23 0.0005 35.6 7.1 74 23-96 335-423 (604)
21 PRK00414 gmhA phosphoheptose i 63.7 42 0.00092 29.1 7.8 54 18-71 105-164 (192)
22 TIGR00274 N-acetylmuramic acid 63.2 32 0.0007 32.2 7.4 83 22-108 124-223 (291)
23 PRK10892 D-arabinose 5-phospha 62.9 40 0.00087 30.8 7.9 47 21-67 91-143 (326)
24 PRK05441 murQ N-acetylmuramic 62.1 44 0.00095 31.3 8.1 74 22-95 129-219 (299)
25 PRK13936 phosphoheptose isomer 61.0 55 0.0012 28.4 8.0 65 20-84 107-183 (197)
26 TIGR03127 RuMP_HxlB 6-phospho 59.9 86 0.0019 26.1 8.7 48 20-67 68-121 (179)
27 cd05005 SIS_PHI Hexulose-6-pho 58.6 98 0.0021 25.9 8.9 51 21-71 72-130 (179)
28 cd06278 PBP1_LacI_like_2 Ligan 58.0 23 0.00051 29.5 5.1 45 23-68 53-97 (266)
29 cd06271 PBP1_AglR_RafR_like Li 56.7 27 0.00059 29.1 5.3 44 23-67 58-101 (268)
30 cd06294 PBP1_ycjW_transcriptio 56.5 27 0.00059 29.2 5.2 36 23-59 59-94 (270)
31 cd05006 SIS_GmhA Phosphoheptos 55.5 80 0.0017 26.3 7.9 49 21-69 98-152 (177)
32 PRK11302 DNA-binding transcrip 55.1 55 0.0012 29.0 7.2 48 22-69 173-225 (284)
33 PRK10886 DnaA initiator-associ 54.7 67 0.0014 28.5 7.6 47 15-61 100-151 (196)
34 cd05007 SIS_Etherase N-acetylm 54.3 56 0.0012 29.8 7.2 82 22-107 116-214 (257)
35 PF04493 Endonuclease_5: Endon 53.3 25 0.00055 31.7 4.8 70 3-72 63-142 (206)
36 cd05017 SIS_PGI_PMI_1 The memb 52.1 29 0.00062 27.3 4.4 57 21-78 40-107 (119)
37 TIGR01135 glmS glucosamine--fr 50.3 64 0.0014 32.5 7.5 75 22-96 336-425 (607)
38 PRK13938 phosphoheptose isomer 49.7 83 0.0018 27.8 7.4 56 16-71 105-168 (196)
39 cd05009 SIS_GlmS_GlmD_2 SIS (S 47.9 1.3E+02 0.0029 23.5 8.1 76 20-95 57-141 (153)
40 cd06307 PBP1_uncharacterized_s 47.3 57 0.0012 27.8 5.8 31 24-54 58-90 (275)
41 PRK11337 DNA-binding transcrip 47.0 93 0.002 27.9 7.4 49 21-69 184-238 (292)
42 cd06274 PBP1_FruR Ligand bindi 47.0 77 0.0017 26.7 6.5 44 23-67 54-97 (264)
43 cd06283 PBP1_RegR_EndR_KdgR_li 46.5 94 0.002 25.9 6.9 44 23-67 54-97 (267)
44 PRK14101 bifunctional glucokin 45.3 69 0.0015 32.6 7.0 50 21-70 512-566 (638)
45 cd06285 PBP1_LacI_like_7 Ligan 45.2 96 0.0021 26.1 6.8 35 23-58 54-88 (265)
46 cd06267 PBP1_LacI_sugar_bindin 44.8 90 0.0019 25.5 6.4 36 23-59 54-89 (264)
47 cd05014 SIS_Kpsf KpsF-like pro 43.8 57 0.0012 25.2 4.9 48 22-69 45-98 (128)
48 cd06300 PBP1_ABC_sugar_binding 43.5 42 0.0009 28.5 4.4 44 23-67 59-104 (272)
49 PRK13937 phosphoheptose isomer 43.1 1.2E+02 0.0025 26.1 7.1 48 21-68 103-156 (188)
50 cd06318 PBP1_ABC_sugar_binding 42.3 58 0.0012 27.7 5.1 35 23-58 54-90 (282)
51 cd06279 PBP1_LacI_like_3 Ligan 42.2 59 0.0013 28.1 5.2 43 23-67 55-97 (283)
52 PF06925 MGDG_synth: Monogalac 41.8 58 0.0013 27.0 4.9 36 23-59 88-127 (169)
53 COG1165 MenD 2-succinyl-6-hydr 41.4 42 0.00091 35.0 4.8 80 7-93 53-158 (566)
54 PRK11382 frlB fructoselysine-6 40.5 1.1E+02 0.0024 28.6 7.2 49 23-71 91-145 (340)
55 PF01380 SIS: SIS domain SIS d 39.9 89 0.0019 23.8 5.4 50 24-73 53-110 (131)
56 cd01574 PBP1_LacI Ligand-bindi 39.5 1.5E+02 0.0032 24.8 7.1 35 23-58 55-89 (264)
57 COG0449 GlmS Glucosamine 6-pho 39.2 86 0.0019 32.9 6.6 74 26-99 332-420 (597)
58 cd06273 PBP1_GntR_like_1 This 37.8 77 0.0017 26.6 5.1 31 24-54 55-85 (268)
59 COG1515 Nfi Deoxyinosine 3'end 36.9 26 0.00056 32.3 2.3 56 2-57 68-133 (212)
60 cd01575 PBP1_GntR Ligand-bindi 36.8 1.9E+02 0.0041 24.1 7.2 35 23-57 54-88 (268)
61 PRK02947 hypothetical protein; 36.8 1.8E+02 0.0039 26.2 7.6 38 20-57 102-143 (246)
62 PTZ00295 glucosamine-fructose- 36.6 1.2E+02 0.0027 31.0 7.3 47 24-70 369-421 (640)
63 COG1737 RpiR Transcriptional r 36.2 1.5E+02 0.0033 27.1 7.1 49 21-69 174-228 (281)
64 COG3535 Uncharacterized conser 36.1 41 0.00088 33.3 3.6 38 23-72 294-331 (357)
65 cd06311 PBP1_ABC_sugar_binding 35.8 1.8E+02 0.0039 24.7 7.1 34 23-57 59-94 (274)
66 cd06299 PBP1_LacI_like_13 Liga 35.3 1.7E+02 0.0038 24.4 6.9 44 23-67 54-97 (265)
67 PRK15408 autoinducer 2-binding 34.8 1E+02 0.0022 28.7 5.8 44 23-67 79-124 (336)
68 cd06296 PBP1_CatR_like Ligand- 34.6 92 0.002 26.2 5.1 34 23-57 54-87 (270)
69 COG2103 Predicted sugar phosph 34.4 88 0.0019 30.3 5.4 68 37-108 146-226 (298)
70 cd06292 PBP1_LacI_like_10 Liga 34.2 84 0.0018 26.5 4.8 35 23-58 54-93 (273)
71 cd06298 PBP1_CcpA_like Ligand- 33.8 96 0.0021 25.9 5.1 32 23-54 54-85 (268)
72 PF10087 DUF2325: Uncharacteri 33.6 78 0.0017 24.3 4.2 37 16-52 40-80 (97)
73 PF11238 DUF3039: Protein of u 33.2 30 0.00066 26.2 1.7 19 38-56 15-33 (58)
74 PF13580 SIS_2: SIS domain; PD 33.2 44 0.00095 27.2 2.9 41 14-54 91-137 (138)
75 PRK15482 transcriptional regul 32.7 3.2E+02 0.0069 24.6 8.5 49 22-70 180-234 (285)
76 cd06305 PBP1_methylthioribose_ 32.5 81 0.0017 26.6 4.4 36 23-59 54-91 (273)
77 cd06306 PBP1_TorT-like TorT-li 31.9 1.8E+02 0.0038 25.0 6.5 31 23-53 56-87 (268)
78 cd05013 SIS_RpiR RpiR-like pro 31.2 2.3E+02 0.005 21.3 7.7 49 23-71 59-113 (139)
79 cd01141 TroA_d Periplasmic bin 31.1 74 0.0016 26.2 3.9 31 23-53 68-98 (186)
80 TIGR02128 G6PI_arch bifunction 31.0 1.5E+02 0.0032 28.0 6.3 60 21-81 63-133 (308)
81 PRK11557 putative DNA-binding 31.0 75 0.0016 28.2 4.2 48 22-69 173-226 (278)
82 cd06270 PBP1_GalS_like Ligand 30.0 2.2E+02 0.0048 24.0 6.7 36 22-58 53-88 (268)
83 PTZ00394 glucosamine-fructose- 30.0 1.3E+02 0.0029 31.3 6.3 48 23-70 400-453 (670)
84 cd06308 PBP1_sensor_kinase_lik 29.8 1.3E+02 0.0028 25.5 5.3 34 23-57 55-90 (270)
85 cd06272 PBP1_hexuronate_repres 29.5 1.1E+02 0.0023 25.8 4.7 36 23-59 50-85 (261)
86 COG1879 RbsB ABC-type sugar tr 29.5 1E+02 0.0023 27.5 4.9 38 22-60 89-128 (322)
87 PRK14987 gluconate operon tran 29.1 1.2E+02 0.0027 26.8 5.2 35 23-57 118-152 (331)
88 cd06297 PBP1_LacI_like_12 Liga 28.1 2.5E+02 0.0053 24.0 6.7 35 23-58 54-88 (269)
89 cd06319 PBP1_ABC_sugar_binding 27.9 3E+02 0.0065 23.2 7.1 35 23-58 54-90 (277)
90 cd06289 PBP1_MalI_like Ligand- 27.8 1.6E+02 0.0035 24.5 5.4 45 23-68 54-99 (268)
91 cd06317 PBP1_ABC_sugar_binding 27.7 2E+02 0.0043 24.1 6.0 35 23-58 55-91 (275)
92 cd06559 Endonuclease_V Endonuc 27.1 63 0.0014 29.1 3.0 53 4-56 68-130 (208)
93 PRK14089 ipid-A-disaccharide s 26.5 75 0.0016 30.5 3.6 40 14-53 66-108 (347)
94 cd06282 PBP1_GntR_like_2 Ligan 26.5 3E+02 0.0065 22.9 6.8 35 23-58 54-89 (266)
95 PRK07765 para-aminobenzoate sy 26.4 79 0.0017 27.9 3.5 32 23-54 45-83 (214)
96 cd06277 PBP1_LacI_like_1 Ligan 26.2 1.4E+02 0.0031 25.2 4.9 41 23-65 57-97 (268)
97 TIGR02417 fruct_sucro_rep D-fr 25.3 1.5E+02 0.0032 26.2 5.0 47 23-70 115-162 (327)
98 cd01542 PBP1_TreR_like Ligand- 24.8 1.6E+02 0.0034 24.6 4.8 31 23-53 54-84 (259)
99 COG1929 Glycerate kinase [Carb 24.4 78 0.0017 31.6 3.3 40 17-56 277-325 (378)
100 PF06136 DUF966: Domain of unk 24.4 70 0.0015 30.9 3.0 31 59-93 15-45 (337)
101 cd06325 PBP1_ABC_uncharacteriz 24.1 41 0.00089 28.4 1.3 42 16-57 176-221 (281)
102 cd01147 HemV-2 Metal binding p 23.8 1.4E+02 0.0031 25.5 4.5 32 23-54 73-105 (262)
103 cd01545 PBP1_SalR Ligand-bindi 23.7 1.9E+02 0.004 24.2 5.1 35 23-58 55-90 (270)
104 PRK11543 gutQ D-arabinose 5-ph 23.3 1.7E+02 0.0037 26.5 5.1 48 20-67 85-138 (321)
105 PRK11617 endonuclease V; Provi 22.9 80 0.0017 29.1 2.9 70 3-75 71-150 (224)
106 PRK10014 DNA-binding transcrip 22.3 1.9E+02 0.0042 25.6 5.2 44 23-67 119-163 (342)
107 cd01149 HutB Hemin binding pro 22.1 1.2E+02 0.0027 25.8 3.8 31 23-53 57-87 (235)
108 cd06301 PBP1_rhizopine_binding 21.9 1.7E+02 0.0038 24.6 4.6 34 23-57 55-90 (272)
109 PRK00994 F420-dependent methyl 21.9 1.2E+02 0.0025 29.2 3.8 36 22-57 58-97 (277)
110 PF01497 Peripla_BP_2: Peripla 21.8 1.3E+02 0.0028 25.1 3.8 34 23-56 59-92 (238)
111 cd06302 PBP1_LsrB_Quorum_Sensi 21.5 2.4E+02 0.0053 24.8 5.6 34 23-57 55-90 (298)
112 cd06288 PBP1_sucrose_transcrip 20.9 2.4E+02 0.0052 23.5 5.2 46 23-70 55-100 (269)
113 cd06320 PBP1_allose_binding Pe 20.7 1.7E+02 0.0038 24.7 4.4 35 23-58 56-92 (275)
114 cd06314 PBP1_tmGBP Periplasmic 20.6 3.6E+02 0.0077 22.9 6.3 33 23-57 54-88 (271)
115 PLN02981 glucosamine:fructose- 20.5 3.8E+02 0.0082 28.1 7.5 45 24-68 410-460 (680)
116 cd01543 PBP1_XylR Ligand-bindi 20.2 2E+02 0.0042 24.4 4.6 45 23-70 49-93 (265)
No 1
>KOG0830|consensus
Probab=100.00 E-value=1e-53 Score=384.84 Aligned_cols=146 Identities=62% Similarity=1.088 Sum_probs=135.2
Q ss_pred cccccccccc--CchhhhcccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHH
Q psy9845 4 LSSRTGLFIF--PNLQFQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMW 81 (261)
Q Consensus 4 ~~~i~Grfip--lTNQIQaaFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~ 81 (261)
-.||.|||.| ||||||++|+|||||||||||.|||+|+|+||+|+|||+||||||+|+||||+|||||||.|||++||
T Consensus 67 atpiag~ftpg~ftn~iq~~f~epr~lvvtdpr~d~q~~~E~s~~n~p~ialcnTDSpL~~VDIAIPcNNKG~hSVgl~w 146 (254)
T KOG0830|consen 67 ATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLCYVDIAIPCNNKGAHSVGVMW 146 (254)
T ss_pred CCcccccccccccchHHHHhhcCCceeeecCcccccchhhhhhhcCCceEEEecCCCccceeeeeeecCCCCcccchhhh
Confidence 3589999999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCC-CCCcccccccccccCchhhhhhhHhhhhhhhhhhc------CCccccccCCCC-CCCCC
Q psy9845 82 WLLAREVLRFRGTIPR-EPKWDVVVDLFFYRDPEEAEKEEQAGKESAAAIAD------KPADEFAAHAPT-ESWND 149 (261)
Q Consensus 82 wlLAreVLr~rGtIs~-e~pWEVmPDLyFYRDPEEiEKEeqaaae~a~~~~~------~~~~e~~~~~~~-~~w~~ 149 (261)
|||+|+||+|||+|++ .|+|++||||||||||||+|||||+++++++++++ +++++|+++++. .+|..
T Consensus 147 w~LareVLrmrgtis~~~~~~~~m~dl~FyrDpeE~e~eeqAa~~ka~t~eefqge~ta~a~eftatq~~vadw~e 222 (254)
T KOG0830|consen 147 WMLAREVLRMRGTISRLQHPWEVMPDLYFYRDPEETEKEEQAAAEKAVTKEEFQGEWTAPAPEFTATQPEVADWSE 222 (254)
T ss_pred hhhhHHHHHHHhhhhhhccchhhcCCcccccCccccchhhhcccchhhcccccccccccCCccccccCcccccccc
Confidence 9999999999999997 99999999999999999999999999999887653 667788766554 45543
No 2
>PTZ00254 40S ribosomal protein SA; Provisional
Probab=100.00 E-value=5.3e-50 Score=361.69 Aligned_cols=125 Identities=65% Similarity=1.093 Sum_probs=120.9
Q ss_pred cccccccccc--CchhhhcccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHH
Q psy9845 4 LSSRTGLFIF--PNLQFQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMW 81 (261)
Q Consensus 4 ~~~i~Grfip--lTNQIQaaFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~ 81 (261)
-.||.|||+| |||+++..|++||||||+||+.|||||+||+|+||||||||||||+|++|||+|||||||.+||+|||
T Consensus 96 ~~~i~~Rw~pGtlTN~~~~~f~~P~llIV~Dp~~d~qAI~EA~~lnIPvIal~DTds~p~~VDy~IP~Ndds~~SI~li~ 175 (249)
T PTZ00254 96 ASAIAGRFTPGTFTNQIQKKFMEPRLLIVTDPRTDHQAIREASYVNIPVIALCDTDSPLEYVDIAIPCNNRGKESIALMY 175 (249)
T ss_pred CeEECCcccCCCCCCccccccCCCCEEEEeCCCcchHHHHHHHHhCCCEEEEecCCCCcccCceeeCCCCchHHHHHHHH
Confidence 4689999999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCCCCcccccccccccCchhhhhhhHhhhhhhh
Q psy9845 82 WLLAREVLRFRGTIPREPKWDVVVDLFFYRDPEEAEKEEQAGKESAA 128 (261)
Q Consensus 82 wlLAreVLr~rGtIs~e~pWEVmPDLyFYRDPEEiEKEeqaaae~a~ 128 (261)
|+|+|+||++||+|+++++|+|||||||||||||+||||+++++++.
T Consensus 176 ~lLar~Vl~~rG~~~r~~~~~v~~d~f~~r~~~~~~~~~~~~~~~~~ 222 (249)
T PTZ00254 176 WLLAREVLRLRGTLPRDEEWDVMVDLFFWRDPEEAEEKEEAAAETAG 222 (249)
T ss_pred HHHHHHHHHhhCccccCCCCCcCceeccccChhhhhhHHHHHHhhcc
Confidence 99999999999999999999999999999999999999998877543
No 3
>TIGR01012 Sa_S2_E_A ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria.
Probab=100.00 E-value=3.2e-40 Score=289.01 Aligned_cols=109 Identities=53% Similarity=0.988 Sum_probs=107.0
Q ss_pred cccccccccc--CchhhhcccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHH
Q psy9845 4 LSSRTGLFIF--PNLQFQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMW 81 (261)
Q Consensus 4 ~~~i~Grfip--lTNQIQaaFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~ 81 (261)
-.|++|||+| |||+.+..|++|++|||+||+.|+|||+||+++||||||||||||+|++|||+|||||||.+||+|++
T Consensus 86 ~~~v~~RWlgGtLTN~~~~~~~~Pdlliv~dp~~~~~Av~EA~~l~IP~Iai~DTn~dp~~vdypIP~Ndds~~Si~li~ 165 (196)
T TIGR01012 86 ARAIAGRFTPGTFTNPMQKAFREPEVVVVTDPRADHQALKEASEVGIPIVALCDTDNPLRYVDLVIPTNNKGRHSLALIY 165 (196)
T ss_pred CceECCeeCCCCCCCccccccCCCCEEEEECCccccHHHHHHHHcCCCEEEEeeCCCCCccCCEEECCCCchHHHHHHHH
Confidence 4689999999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCCCCcccccccccccC
Q psy9845 82 WLLAREVLRFRGTIPREPKWDVVVDLFFYRD 112 (261)
Q Consensus 82 wlLAreVLr~rGtIs~e~pWEVmPDLyFYRD 112 (261)
|+|+++||++||+++++++|+||||+|||||
T Consensus 166 ~lla~ail~~~g~~~~~~~~~~~~d~f~~~~ 196 (196)
T TIGR01012 166 WLLAREILRMRGTISRDQDWDVMYEEFFYRD 196 (196)
T ss_pred HHHHHHHHHhhCccCCCCCCccChhhhcccC
Confidence 9999999999999999999999999999997
No 4
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=100.00 E-value=1.3e-36 Score=267.76 Aligned_cols=109 Identities=40% Similarity=0.609 Sum_probs=106.4
Q ss_pred cccccccccc--CchhhhcccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHH
Q psy9845 4 LSSRTGLFIF--PNLQFQAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMW 81 (261)
Q Consensus 4 ~~~i~Grfip--lTNQIQaaFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~ 81 (261)
-.|++|||+| |||+....|.+|++|||+||+.||+||+||+++||||||||||||+|++|||+|||||||.+||+|++
T Consensus 92 ~~~v~~RWlgG~LTN~~~~~~~~Pdliiv~dp~~~~~AI~EA~kl~IP~IaivDTn~dp~~VdypIP~Ndds~~SI~li~ 171 (204)
T PRK04020 92 AKAITGRFIPGTLTNPSLKGYIEPDVVVVTDPRGDAQAVKEAIEVGIPVVALCDTDNLTSNVDLVIPTNNKGRKALALVY 171 (204)
T ss_pred CeeecCccCCCcCcCcchhccCCCCEEEEECCcccHHHHHHHHHhCCCEEEEEeCCCCcccCceeECCCCchHHHHHHHH
Confidence 4689999999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCCCCcccccccccccC
Q psy9845 82 WLLAREVLRFRGTIPREPKWDVVVDLFFYRD 112 (261)
Q Consensus 82 wlLAreVLr~rGtIs~e~pWEVmPDLyFYRD 112 (261)
|+|+++|+++||+++++++|+||+|+|++|.
T Consensus 172 ~ll~~aIl~~kg~~~~~~~~~v~~~~f~~~~ 202 (204)
T PRK04020 172 WLLAREILRERGEIKPDEDLPVPVEDFETKL 202 (204)
T ss_pred HHHHHHHHHhhCccCCCCCCCcCHHHHhhhh
Confidence 9999999999999999999999999999875
No 5
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=5e-29 Score=225.99 Aligned_cols=77 Identities=36% Similarity=0.580 Sum_probs=72.7
Q ss_pred hcccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhhCCC
Q psy9845 19 QAAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRGTI 95 (261)
Q Consensus 19 QaaFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~rGtI 95 (261)
+.|.+.|++|||+||+.|+|||.||.++||||||||||||+|++|||+||||||+.+||.|++|+|+++|++++|..
T Consensus 151 k~m~~~Pd~l~ViDp~~e~iAv~EA~klgIPVvAlvDTn~dpd~VD~~IP~Ndda~rsi~Li~~~lA~ai~e~r~~~ 227 (252)
T COG0052 151 KDMKGLPDVLFVIDPRKEKIAVKEANKLGIPVVALVDTNCDPDGVDYVIPGNDDAIRSIALIYWLLARAILEGRGGA 227 (252)
T ss_pred hhccCCCCEEEEeCCcHhHHHHHHHHHcCCCEEEEecCCCCCccCceeecCCChHHHHHHHHHHHHHHHHHHHhccc
Confidence 33455699999999999999999999999999999999999999999999999999999999999999999999854
No 6
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=99.93 E-value=5.3e-26 Score=212.11 Aligned_cols=73 Identities=27% Similarity=0.328 Sum_probs=70.6
Q ss_pred ccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhhC
Q psy9845 21 AFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 93 (261)
Q Consensus 21 aFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~rG 93 (261)
|.++|++|||+||+.|++||+||.++||||||||||||+|++|||||||||||.+||.|++|+|+++|+.++.
T Consensus 149 m~~~Pd~viv~d~~~e~~AI~EA~kl~IPvIaivDTn~dp~~IdypIP~NDds~~si~li~~~la~ai~~g~~ 221 (326)
T PRK12311 149 MGGLPDLLFVIDTNKEDIAIQEAQRLGIPVAAIVDTNCDPDGITYPVPGNDDAGRAIALYCDLIARAAIDGIS 221 (326)
T ss_pred cccCCCEEEEeCCccchHHHHHHHHcCCCEEEEeeCCCCccccceeecCCCchHHHHHHHHHHHHHHHHHHHh
Confidence 4469999999999999999999999999999999999999999999999999999999999999999999985
No 7
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=99.92 E-value=9.5e-26 Score=203.82 Aligned_cols=74 Identities=32% Similarity=0.383 Sum_probs=71.7
Q ss_pred ccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhhCC
Q psy9845 21 AFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRGT 94 (261)
Q Consensus 21 aFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~rGt 94 (261)
|.++|++|||+||..|++||+||.++||||||||||||+|++|||||||||||.+||.|++|+|+++|++++|.
T Consensus 154 m~~~Pd~iii~d~~~~~~ai~Ea~kl~IPiIaivDTn~dp~~IdypIP~Ndds~~si~li~~~l~~ai~~g~~~ 227 (258)
T PRK05299 154 MGGLPDALFVVDPNKEHIAVKEARKLGIPVVAIVDTNCDPDGVDYPIPGNDDAIRSIKLYTSKIADAILEGRQG 227 (258)
T ss_pred cccCCCEEEEeCCCccHHHHHHHHHhCCCEEEEeeCCCCCcccceeeecCCchHHHHHHHHHHHHHHHHHHhhc
Confidence 44799999999999999999999999999999999999999999999999999999999999999999999984
No 8
>TIGR01011 rpsB_bact ribosomal protein S2, bacterial type. TIGR01012 describes the archaeal and cytosolic forms.
Probab=99.92 E-value=1.3e-25 Score=198.98 Aligned_cols=73 Identities=34% Similarity=0.468 Sum_probs=70.7
Q ss_pred ccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhhC
Q psy9845 21 AFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 93 (261)
Q Consensus 21 aFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~rG 93 (261)
|.++|++|||+||..|++||+||.++||||||||||||+|++|||||||||||.+||.|++|+|+++|+++++
T Consensus 152 m~~~Pd~vii~d~~~~~~ai~Ea~~l~IP~I~ivDTn~~p~~idypIP~Ndds~~si~li~~~l~~ai~~g~~ 224 (225)
T TIGR01011 152 MKKLPDLLFVIDPVKEKIAVAEARKLGIPVVAIVDTNCDPDLVDYPIPGNDDAIRSIRLLTNLIADAVLEGKQ 224 (225)
T ss_pred cccCCCEEEEeCCCccHHHHHHHHHcCCCEEEEeeCCCCCcccceeeecCCchHHHHHHHHHHHHHHHHHHhc
Confidence 4479999999999999999999999999999999999999999999999999999999999999999999975
No 9
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=99.92 E-value=1.8e-25 Score=192.35 Aligned_cols=87 Identities=38% Similarity=0.576 Sum_probs=82.1
Q ss_pred cccccccccc--Cchhhhc------------------------ccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCC
Q psy9845 4 LSSRTGLFIF--PNLQFQA------------------------AFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 4 ~~~i~Grfip--lTNQIQa------------------------aFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTD 57 (261)
-.++.+||++ |||..+. ++++|++|||+||..|+++|+||+++|||||||||||
T Consensus 81 ~~~i~~rw~~G~LTN~~~~~~~~~~~~~~~~~~~~k~~~g~~~~~~~Pdlviv~~~~~~~~ai~Ea~~l~IP~I~i~Dtn 160 (193)
T cd01425 81 SFYVNGRWLGGTLTNWKTIRKSIKRLKKLEKEKLEKNLGGIKDMFRLPDLVIVLDPRKEHQAIREASKLGIPVIAIVDTN 160 (193)
T ss_pred CeeecCeecCCcCCCHHHHHHHHHHHHHHHHHHHHHhcccccccccCCCEEEEeCCccchHHHHHHHHcCCCEEEEecCC
Confidence 3578999998 9997643 8999999999999999999999999999999999999
Q ss_pred CCCCcceeeccCCCCCcchHHHHHHHHHHHHHH
Q psy9845 58 SPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLR 90 (261)
Q Consensus 58 SpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr 90 (261)
+++++|||||||||||.+|+.|++|+|+++|++
T Consensus 161 ~~~~~i~ypIP~Nd~s~~si~li~~~l~~ai~~ 193 (193)
T cd01425 161 CDPDLIDYPIPANDDSIRSIALILWLLARAILE 193 (193)
T ss_pred CCCccceEEeecCCchHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999974
No 10
>CHL00067 rps2 ribosomal protein S2
Probab=99.91 E-value=1.3e-24 Score=193.01 Aligned_cols=72 Identities=24% Similarity=0.391 Sum_probs=69.6
Q ss_pred ccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhh
Q psy9845 21 AFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFR 92 (261)
Q Consensus 21 aFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~r 92 (261)
|.++|++|||+||..|++||+||.++|||||||||||++|++|||+|||||||.+||.|++++|+++|++++
T Consensus 158 m~~~P~~iiv~d~~~~~~ai~Ea~~l~IPvIaivDTn~~p~~idypIP~Ndds~~si~li~~~l~~ai~~G~ 229 (230)
T CHL00067 158 MTKLPDIVIIIDQQEEYTALRECRKLGIPTISILDTNCDPDLADIPIPANDDAIASIKLILNKLTTAICEGR 229 (230)
T ss_pred cccCCCEEEEeCCcccHHHHHHHHHcCCCEEEEEeCCCCccccceeeecCCchHHHHHHHHHHHHHHHHHhc
Confidence 447999999999999999999999999999999999999999999999999999999999999999999875
No 11
>PF00318 Ribosomal_S2: Ribosomal protein S2; InterPro: IPR001865 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal S2 proteins have been shown to belong to a family that includes 40S ribosomal subunit 40kDa proteins, putative laminin-binding proteins, NAB-1 protein and 29.3kDa protein from Haloarcula marismortui [, ]. The laminin-receptor proteins are thus predicted to be the eukaryotic homologue of the eubacterial S2 risosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2QNH_c 3MR8_B 3PYS_B 3MS0_B 3PYN_B 1VOZ_B 2OW8_c 3PYQ_B 3D5C_B 3PYU_B ....
Probab=99.87 E-value=1.4e-22 Score=176.77 Aligned_cols=73 Identities=34% Similarity=0.528 Sum_probs=66.7
Q ss_pred cccCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhh
Q psy9845 20 AAFREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFR 92 (261)
Q Consensus 20 aaFrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~r 92 (261)
.+.+.|++|||+||..|+++|+||.++|||||||||||+++++|||||||||||..||.|++++|+++|+++|
T Consensus 139 ~l~~~P~~vii~~~~~~~~~i~Ea~~l~IP~i~i~Dtn~~~~~i~ypIp~N~~s~~si~~i~~~l~~ai~~g~ 211 (211)
T PF00318_consen 139 NLKKLPDLVIILDPNKNKNAIREANKLNIPTIAIVDTNCNPSLIDYPIPANDDSIKSIYLILNLLAKAILEGK 211 (211)
T ss_dssp TCSSSBSEEEESSTTTTHHHHHHHHHTTS-EEEEESTTS-GTTSSEEEES-SSSHHHHHHHHHHHHHHHHHTC
T ss_pred cccccCcEEEEecccccchhHHHHHhcCceEEEeecCCCCccccceEeecCCccHHHHHHHHHHHHHHHHhcC
Confidence 3456799999999999999999999999999999999999999999999999999999999999999999875
No 12
>KOG0832|consensus
Probab=99.73 E-value=6.4e-18 Score=153.15 Aligned_cols=70 Identities=33% Similarity=0.568 Sum_probs=67.4
Q ss_pred CCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCCCcchHHHHHHHHHHHHHHhhC
Q psy9845 24 EPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 93 (261)
Q Consensus 24 EPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~rG 93 (261)
.||+|||.|+..+|.||+||++++||||||+||||+|++|+||||+|||+..|+.|++.+|.++|.+++.
T Consensus 173 ~~D~vvvln~~e~~sAilEA~K~~IPTIgIVDtN~~P~liTYpVPaNDDs~~sv~f~~~l~k~ai~~g~~ 242 (251)
T KOG0832|consen 173 TPDLVVVLNPEENHSAILEAAKMAIPTIGIVDTNCNPELITYPVPANDDSPASVEFILNLLKRAIARGKQ 242 (251)
T ss_pred CcceeEecCcccccHHHHHHHHhCCCeEEEecCCCCccceeeccCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999999999999999999999999999999999999999999998764
No 13
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=77.77 E-value=14 Score=29.29 Aligned_cols=61 Identities=16% Similarity=0.262 Sum_probs=38.4
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCCC--CcchHHHHHH
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNNK--SPHSIGLMWW 82 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNNd--s~~SVgLi~w 82 (261)
..+-+++|++....+. .+++.|...|.|+|+|++. ++++ .+.|+.|..... -.+-+.+.+.
T Consensus 45 ~~~~dl~I~iS~SG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l~~~~~~~~~~~~~~~~~ 113 (120)
T cd05710 45 LTEKSVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDSPLAKLADYVIVYGFEIDAVEEKYLLLY 113 (120)
T ss_pred CCCCcEEEEEeCCCCChHHHHHHHHHHHcCCeEEEEECCCCCcHHHhCCEEEEccCCcCccchHHHHHH
Confidence 3455787777655443 3667888999999999986 4454 346666655444 3344444433
No 14
>TIGR00393 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli.
Probab=75.24 E-value=15 Score=32.12 Aligned_cols=75 Identities=17% Similarity=0.157 Sum_probs=46.0
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCC---------CCcch---HHHHHH
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNN---------KSPHS---IGLMWW 82 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNN---------ds~~S---VgLi~w 82 (261)
.+.+-+++|++...... .+++.|...|+|||+|++. ++++ .+.|+.|.... ....| .-++.-
T Consensus 44 ~~~~~d~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~~s~l~~~~d~~l~~~~~~~~~~~~~~~~~s~~~~~~l~d 123 (268)
T TIGR00393 44 MVEPNDVVLMISYSGESLELLNLIPHLKRLSHKIIAFTGSPNSSLARAADYVLDIKVEKEACPINLAPTTSTTLTLALGD 123 (268)
T ss_pred CCCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEEECCCCCcccccCCEEEEcCCCcccCCCCCccHHHHHHHHHHHH
Confidence 45667888887755443 3668899999999999985 4554 34666665421 11122 223334
Q ss_pred HHHHHHHHhhCCC
Q psy9845 83 LLAREVLRFRGTI 95 (261)
Q Consensus 83 lLAreVLr~rGtI 95 (261)
+|...+...+|..
T Consensus 124 ~l~~~~~~~~~~~ 136 (268)
T TIGR00393 124 ALAVALMRARNFS 136 (268)
T ss_pred HHHHHHHHHHCcC
Confidence 4666666666653
No 15
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=74.76 E-value=11 Score=35.16 Aligned_cols=83 Identities=19% Similarity=0.203 Sum_probs=59.8
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCCC-cceeeccCC--C---------CCcchHHHHHHHH
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPLR-FVDIAIPCN--N---------KSPHSIGLMWWLL 84 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL~-~VDiaIPcN--N---------ds~~SVgLi~wlL 84 (261)
+.+-|++|++....+. .+++.|...|.+||+|++. ++++. +.|+.|-.. . ++..+..+++.+|
T Consensus 125 l~~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~~IaIT~~~~s~La~~aD~~I~~~~g~E~~~~st~~~s~taqk~vLd~L 204 (296)
T PRK12570 125 LTADDVVVGIAASGRTPYVIGALEYAKQIGATTIALSCNPDSPIAKIADIAISPVVGPEVLTGSTRLKSGTAQKMVLNML 204 (296)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEeeCcCCccccccchHHHHHHHHHHHHHH
Confidence 4567888888766654 4778999999999999865 44443 477777421 1 2345778889999
Q ss_pred HHHHHHhhCCCCCCCCcccccccc
Q psy9845 85 AREVLRFRGTIPREPKWDVVVDLF 108 (261)
Q Consensus 85 AreVLr~rGtIs~e~pWEVmPDLy 108 (261)
.-.+....|..-..+ |.|+-
T Consensus 205 ~t~~~~r~Gk~~~n~----mvd~~ 224 (296)
T PRK12570 205 STASMIRLGKSYQNL----MVDVK 224 (296)
T ss_pred HHHHHHhcchhhcCe----EEEee
Confidence 999988888876554 77753
No 16
>PRK08674 bifunctional phosphoglucose/phosphomannose isomerase; Validated
Probab=71.93 E-value=16 Score=34.02 Aligned_cols=74 Identities=19% Similarity=0.295 Sum_probs=52.3
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecCCCCCCcc-------eeeccCCCCCcchHHHHHHHHHHHHH
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNTESPLRFV-------DIAIPCNNKSPHSIGLMWWLLAREVL 89 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDTDSpL~~V-------DiaIPcNNds~~SVgLi~wlLAreVL 89 (261)
...+-+++|++.-..+. .+++.|...|+++|+|++ +++|.-. -+.||.+.-+..|.++++..|. .+|
T Consensus 75 ~~~~~dlvI~iS~SG~T~e~~~a~~~a~~~ga~vIaIT~-~~~L~~~a~~~~~~~i~ip~~~~~r~s~~~ll~~l~-~~l 152 (337)
T PRK08674 75 FVDEKTLVIAVSYSGNTEETLSAVEQALKRGAKIIAITS-GGKLKEMAKEHGLPVIIVPGGYQPRAALGYLFTPLL-KIL 152 (337)
T ss_pred cCCCCcEEEEEcCCCCCHHHHHHHHHHHHCCCeEEEECC-CchHHHHHHhcCCeEEEeCCCCcchhhHHHHHHHHH-HHH
Confidence 34566788887655443 466788899999999996 5555433 6788988877788777776554 567
Q ss_pred HhhCCCC
Q psy9845 90 RFRGTIP 96 (261)
Q Consensus 90 r~rGtIs 96 (261)
...|.++
T Consensus 153 ~~~Gl~~ 159 (337)
T PRK08674 153 EKLGLIP 159 (337)
T ss_pred HHcCCCc
Confidence 7777654
No 17
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=70.68 E-value=9.8 Score=32.30 Aligned_cols=45 Identities=9% Similarity=0.070 Sum_probs=32.2
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeecc
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIP 68 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIP 68 (261)
+.++.||+.....+...+.++...|||+|.+ |++.+-....+..+
T Consensus 63 ~~~dgiii~~~~~~~~~~~~~~~~~ipvV~~-~~~~~~~~~~~V~~ 107 (275)
T cd06295 63 GRADGVILIGQHDQDPLPERLAETGLPFVVW-GRPLPGQPYCYVGS 107 (275)
T ss_pred CCCCEEEEeCCCCChHHHHHHHhCCCCEEEE-CCccCCCCCCEEEE
Confidence 5789999887666667789999999999966 77654333344443
No 18
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=69.94 E-value=24 Score=27.18 Aligned_cols=46 Identities=17% Similarity=0.226 Sum_probs=30.9
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecCCC-CC-Ccceeec
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNTES-PL-RFVDIAI 67 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDTDS-pL-~~VDiaI 67 (261)
..+-+++|++....+. .+++.|...|.++|+|++... ++ .+.|+.|
T Consensus 44 ~~~~d~~I~iS~sG~t~e~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l 95 (126)
T cd05008 44 LDEDTLVIAISQSGETADTLAALRLAKEKGAKTVAITNVVGSTLAREADYVL 95 (126)
T ss_pred CCCCcEEEEEeCCcCCHHHHHHHHHHHHcCCeEEEEECCCCChHHHhCCEEE
Confidence 4566777776544332 366889999999999999744 33 3355544
No 19
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=67.41 E-value=17 Score=30.13 Aligned_cols=51 Identities=12% Similarity=0.176 Sum_probs=35.3
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEec-CCCCCC-cceeeccCCC
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCN-TESPLR-FVDIAIPCNN 71 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcD-TDSpL~-~VDiaIPcNN 71 (261)
..++-+++|++...... .+++.|...|+|+|+|++ .++++. +.|+.|...+
T Consensus 76 ~~~~~D~~i~iS~sG~t~~~~~~~~~a~~~g~~ii~iT~~~~s~l~~~ad~~l~~~~ 132 (154)
T TIGR00441 76 LGQKGDVLLGISTSGNSKNVLKAIEAAKDKGMKTITLAGKDGGKMAGLADIELRVPH 132 (154)
T ss_pred hCCCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEEeCC
Confidence 34677888887755443 356788999999999997 466663 4666665444
No 20
>PRK00331 glucosamine--fructose-6-phosphate aminotransferase; Reviewed
Probab=64.62 E-value=23 Score=35.55 Aligned_cols=74 Identities=19% Similarity=0.259 Sum_probs=46.5
Q ss_pred CCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCCC---------CcchHHHHHHHHHHH
Q psy9845 23 REPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNNK---------SPHSIGLMWWLLARE 87 (261)
Q Consensus 23 rEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNNd---------s~~SVgLi~wlLAre 87 (261)
...+++|++...-+ ..+++.|...|+|||+|++. +|++ .+.|+.|+.+.. +..+.-+++.+|+-.
T Consensus 335 ~~~dlvI~iS~SG~T~e~i~a~~~ak~~ga~~IaIT~~~~S~La~~aD~~l~~~~~~e~~~~~tks~~s~l~~l~lL~~~ 414 (604)
T PRK00331 335 SPKTLVIAISQSGETADTLAALRLAKELGAKTLAICNVPGSTIARESDAVLYTHAGPEIGVASTKAFTAQLAVLYLLALA 414 (604)
T ss_pred CCCeEEEEEcCCCCCHHHHHHHHHHHHCCCCEEEEECCCCChhHHhcCcEEEecCcCccchhhhHHHHHHHHHHHHHHHH
Confidence 55678887765554 34677888899999999985 5655 457777776531 222333445555555
Q ss_pred HHHhhCCCC
Q psy9845 88 VLRFRGTIP 96 (261)
Q Consensus 88 VLr~rGtIs 96 (261)
+...+|.++
T Consensus 415 ~~~~~g~~~ 423 (604)
T PRK00331 415 LAKARGTLS 423 (604)
T ss_pred HHHHcCCCC
Confidence 555555543
No 21
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=63.70 E-value=42 Score=29.12 Aligned_cols=54 Identities=20% Similarity=0.257 Sum_probs=37.8
Q ss_pred hhcccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCC
Q psy9845 18 FQAAFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNN 71 (261)
Q Consensus 18 IQaaFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNN 71 (261)
+....++-|++|++...... .+++.|...|+|||+|+.. ++++ .+.|+.|..+.
T Consensus 105 ~~~~~~~~Dv~I~iS~SG~t~~~i~~~~~ak~~g~~iI~iT~~~~s~l~~~ad~~l~~~~ 164 (192)
T PRK00414 105 VEAVGREGDVLLGISTSGNSGNIIKAIEAARAKGMKVITLTGKDGGKMAGLADIEIRVPH 164 (192)
T ss_pred HHHhCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEEEeCC
Confidence 34456777898887755443 4667889999999999974 5555 34677666555
No 22
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=63.23 E-value=32 Score=32.16 Aligned_cols=83 Identities=16% Similarity=0.141 Sum_probs=56.6
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCC-----------CCCcchHHHHHHHH
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCN-----------NKSPHSIGLMWWLL 84 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcN-----------Nds~~SVgLi~wlL 84 (261)
+.+-|++|++-..... .++..|...|.+||+|+.. ++++ .+.|+.|... -++.-+..+++.+|
T Consensus 124 l~~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~tIaIT~~~~s~La~~aD~~I~~~~g~E~~~~st~~~s~~aqk~iLd~L 203 (291)
T TIGR00274 124 LTKNDVVVGIAASGRTPYVIAGLQYARSLGALTISIACNPKSAASEIADIAIETIVGPEILTGSSRLKAGTAQKMVLNML 203 (291)
T ss_pred CCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEecCCCCccccccchhhHHHHHHHHHHHH
Confidence 5566888887665553 3668899999999999753 4443 4567777542 12345566788899
Q ss_pred HHHHHHhhCCCCCCCCcccccccc
Q psy9845 85 AREVLRFRGTIPREPKWDVVVDLF 108 (261)
Q Consensus 85 AreVLr~rGtIs~e~pWEVmPDLy 108 (261)
+-.+....|..-..+ |.|+-
T Consensus 204 ~t~~~~~~gk~~~n~----mvd~~ 223 (291)
T TIGR00274 204 STASMIKLGKVYENL----MVDVQ 223 (291)
T ss_pred HHHHHHhcchhhcCe----EEeee
Confidence 888888888765443 77753
No 23
>PRK10892 D-arabinose 5-phosphate isomerase; Provisional
Probab=62.91 E-value=40 Score=30.76 Aligned_cols=47 Identities=13% Similarity=0.238 Sum_probs=32.5
Q ss_pred ccCCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecCC-CCCC-cceeec
Q psy9845 21 AFREPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNTE-SPLR-FVDIAI 67 (261)
Q Consensus 21 aFrEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDTD-SpL~-~VDiaI 67 (261)
...+-+++|+..-..+ ..+++.|...|+|||+|++.. |++. +.|+.|
T Consensus 91 ~~~~~d~~I~iS~sG~t~~~~~~~~~ak~~g~~vi~iT~~~~s~la~~ad~~l 143 (326)
T PRK10892 91 MVTPQDVVIAISNSGESSEILALIPVLKRLHVPLICITGRPESSMARAADIHL 143 (326)
T ss_pred cCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCcEEEEECCCCCcccccCCEEE
Confidence 4556678887765433 346788999999999999864 5443 455555
No 24
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=62.06 E-value=44 Score=31.26 Aligned_cols=74 Identities=19% Similarity=0.162 Sum_probs=52.5
Q ss_pred cCCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEec-CCCCC-CcceeeccCCC-----------CCcchHHHHHHHH
Q psy9845 22 FREPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCN-TESPL-RFVDIAIPCNN-----------KSPHSIGLMWWLL 84 (261)
Q Consensus 22 FrEPrLLVVTDPraD----hQALtEAS~VNIPtIALcD-TDSpL-~~VDiaIPcNN-----------ds~~SVgLi~wlL 84 (261)
+..-|++|++-.... ..+++.|...|.+||+|++ .++++ .+.|+.|.... ++..+..+++.+|
T Consensus 129 l~~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~tI~IT~~~~s~La~~aD~~I~~~~g~E~~~~st~~~s~taqk~iLn~l 208 (299)
T PRK05441 129 LTAKDVVVGIAASGRTPYVIGALEYARERGALTIGISCNPGSPLSKEADIAIEVVVGPEVLTGSTRMKAGTAQKLVLNMI 208 (299)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhhHhCCEEEEcCCCCccccccccccchhHHHHHHHHH
Confidence 566788888765443 3477899999999999996 44554 34677775432 2344678889999
Q ss_pred HHHHHHhhCCC
Q psy9845 85 AREVLRFRGTI 95 (261)
Q Consensus 85 AreVLr~rGtI 95 (261)
...+....|..
T Consensus 209 st~~~~~~gkv 219 (299)
T PRK05441 209 STGVMIRLGKV 219 (299)
T ss_pred HHHHHHHccHH
Confidence 98888877764
No 25
>PRK13936 phosphoheptose isomerase; Provisional
Probab=60.99 E-value=55 Score=28.39 Aligned_cols=65 Identities=15% Similarity=0.195 Sum_probs=39.9
Q ss_pred cccCCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEecCC-CCCCc----ce--eeccCCCCC-cchHHHHHHHH
Q psy9845 20 AAFREPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFCNTE-SPLRF----VD--IAIPCNNKS-PHSIGLMWWLL 84 (261)
Q Consensus 20 aaFrEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALcDTD-SpL~~----VD--iaIPcNNds-~~SVgLi~wlL 84 (261)
...+.-|++|++....... +++.|...|+|||+|++.+ +++.- .| +.||..+.+ ...+.++.+-+
T Consensus 107 ~~~~~~Dv~i~iS~sG~t~~~~~~~~~ak~~g~~iI~IT~~~~s~l~~l~~~ad~~l~v~~~~~~~~~e~~~~~~h~ 183 (197)
T PRK13936 107 ALGQPGDVLLAISTSGNSANVIQAIQAAHEREMHVVALTGRDGGKMASLLLPEDVEIRVPAERTARIQEVHLLAIHC 183 (197)
T ss_pred HhCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCChhhhhhccCCEEEEeCCCcHHHHHHHHHHHHHH
Confidence 3446778888877554433 5678999999999999844 44432 34 445554432 34445544433
No 26
>TIGR03127 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin.
Probab=59.94 E-value=86 Score=26.06 Aligned_cols=48 Identities=19% Similarity=0.309 Sum_probs=32.1
Q ss_pred cccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCCC-cceeec
Q psy9845 20 AAFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPLR-FVDIAI 67 (261)
Q Consensus 20 aaFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL~-~VDiaI 67 (261)
....+-+++|+..-.... .+++.|...|+|||+|++. +|++. +.|+.|
T Consensus 68 ~~~~~~Dv~I~iS~sG~t~~~i~~~~~ak~~g~~ii~IT~~~~s~la~~ad~~l 121 (179)
T TIGR03127 68 PSIKKGDLLIAISGSGETESLVTVAKKAKEIGATVAAITTNPESTLGKLADVVV 121 (179)
T ss_pred CCCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEECCCCCchHHhCCEEE
Confidence 445667888887754433 3556789999999999985 44443 355544
No 27
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=58.65 E-value=98 Score=25.87 Aligned_cols=51 Identities=22% Similarity=0.348 Sum_probs=33.5
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecCC-CCCC-ccee--eccCCC
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNTE-SPLR-FVDI--AIPCNN 71 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDTD-SpL~-~VDi--aIPcNN 71 (261)
...+-+++|+....... .+++.|...|+|+|+|+|+. +++. +.|+ .+|++.
T Consensus 72 ~~~~~D~vI~iS~sG~t~~~i~~~~~ak~~g~~iI~IT~~~~s~la~~ad~~l~~~~~~ 130 (179)
T cd05005 72 AIGPGDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPDSPLAKLADVVVVIPAAT 130 (179)
T ss_pred CCCCCCEEEEEcCCCCcHHHHHHHHHHHHCCCeEEEEECCCCCchHHhCCEEEEeCCcc
Confidence 34566788877654443 35678899999999999964 4442 3455 445543
No 28
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=58.01 E-value=23 Score=29.48 Aligned_cols=45 Identities=20% Similarity=0.093 Sum_probs=31.6
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeecc
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIP 68 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIP 68 (261)
+..+.+|+.....+...++++...|||+|.+ |++.+...+++...
T Consensus 53 ~~vdgiii~~~~~~~~~~~~~~~~~ipvV~~-~~~~~~~~~~~v~~ 97 (266)
T cd06278 53 YRVDGVIVTSGTLSSELAEECRRNGIPVVLI-NRYVDGPGVDAVCS 97 (266)
T ss_pred cCCCEEEEecCCCCHHHHHHHhhcCCCEEEE-CCccCCCCCCEEEE
Confidence 5688888876555566788898999999987 65544444555443
No 29
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=56.73 E-value=27 Score=29.11 Aligned_cols=44 Identities=5% Similarity=-0.062 Sum_probs=30.0
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+..+.+|+.....+...+.++...|||+|.+ |++.+...+++..
T Consensus 58 ~~vdgiii~~~~~~~~~~~~~~~~~ipvV~~-~~~~~~~~~~~V~ 101 (268)
T cd06271 58 GLVDGVIISRTRPDDPRVALLLERGFPFVTH-GRTELGDPHPWVD 101 (268)
T ss_pred CCCCEEEEecCCCCChHHHHHHhcCCCEEEE-CCcCCCCCCCeEe
Confidence 4589899876655555678888899999966 6654433344444
No 30
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=56.46 E-value=27 Score=29.24 Aligned_cols=36 Identities=8% Similarity=0.103 Sum_probs=27.6
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESP 59 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSp 59 (261)
+.++.||+..+..+...+.++...|||+|.+ |++.+
T Consensus 59 ~~~dgiii~~~~~~~~~~~~~~~~~ipvV~~-~~~~~ 94 (270)
T cd06294 59 KRVDGFILLYSREDDPIIDYLKEEKFPFVVI-GKPED 94 (270)
T ss_pred cCcCEEEEecCcCCcHHHHHHHhcCCCEEEE-CCCCC
Confidence 3489999987666667788888899999987 55443
No 31
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=55.52 E-value=80 Score=26.34 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=34.7
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCCC-cceeeccC
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPLR-FVDIAIPC 69 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL~-~VDiaIPc 69 (261)
..++-|++|++.-+.+. .+++.|...|+|||+|++. ++++. +.|+.|-.
T Consensus 98 ~~~~~Dv~I~iS~SG~t~~~i~~~~~ak~~Ga~vI~IT~~~~s~La~~aD~~l~~ 152 (177)
T cd05006 98 LGQPGDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGGKLLELADIEIHV 152 (177)
T ss_pred hCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchhhhCCEEEEe
Confidence 46778998888755553 4668889999999999986 45443 35555543
No 32
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=55.14 E-value=55 Score=28.97 Aligned_cols=48 Identities=19% Similarity=0.171 Sum_probs=34.0
Q ss_pred cCCCCEEEEeCCCCC-c---hhHHHHhhcCCCEEEEecCCCCCCc-ceeeccC
Q psy9845 22 FREPRLLVVTDPHTD-H---QPITEAAYVNIPVIAFCNTESPLRF-VDIAIPC 69 (261)
Q Consensus 22 FrEPrLLVVTDPraD-h---QALtEAS~VNIPtIALcDTDSpL~~-VDiaIPc 69 (261)
..+-+++|++.-... . .+++.|...|.+||+|++.++++.- .|+.|..
T Consensus 173 ~~~~D~vI~iS~sG~t~~~~~~~~~ak~~g~~vI~IT~~~s~l~~~ad~~l~~ 225 (284)
T PRK11302 173 SSDGDVVVLISHTGRTKSLVELAQLARENGATVIAITSAGSPLAREATLALTL 225 (284)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEECCCCChhHHhCCEEEec
Confidence 356678777764443 3 3568899999999999998777643 5666654
No 33
>PRK10886 DnaA initiator-associating protein DiaA; Provisional
Probab=54.69 E-value=67 Score=28.47 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=35.4
Q ss_pred chhhhcccCCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEec-CCCCCC
Q psy9845 15 NLQFQAAFREPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFCN-TESPLR 61 (261)
Q Consensus 15 TNQIQaaFrEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALcD-TDSpL~ 61 (261)
..|++...++-|++|++....+.. +++.|...|+|||+|+. .++++.
T Consensus 100 ~~ql~~~~~~gDvli~iS~SG~s~~v~~a~~~Ak~~G~~vI~IT~~~~s~l~ 151 (196)
T PRK10886 100 AKQVRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELA 151 (196)
T ss_pred HHHHHHcCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCChhh
Confidence 346677788899999887766544 55778899999999997 344444
No 34
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=54.31 E-value=56 Score=29.77 Aligned_cols=82 Identities=21% Similarity=0.229 Sum_probs=55.4
Q ss_pred cCCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCC-----------CCcchHHHHHHHH
Q psy9845 22 FREPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNN-----------KSPHSIGLMWWLL 84 (261)
Q Consensus 22 FrEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNN-----------ds~~SVgLi~wlL 84 (261)
+.+-|++|++.-... ..+++.|...|.|||+|++. ++++ .+.|+.|-... ++.-+..+++.+|
T Consensus 116 l~~~DvvI~IS~SG~T~~vi~al~~Ak~~Ga~~I~It~~~~s~L~~~aD~~I~~~~g~E~~~~st~~~s~~aqk~vLn~L 195 (257)
T cd05007 116 LTERDVVIGIAASGRTPYVLGALRYARARGALTIGIACNPGSPLLQLADIAIALITGPEVVAGSTRLKAGTAQKLALNML 195 (257)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEECCCCChhHHhCCEEEEcCCCCccccCccccccHHHHHHHHHHH
Confidence 456678877765444 34678999999999999754 4544 23566664432 2345678888999
Q ss_pred HHHHHHhhCCCCCCCCccccccc
Q psy9845 85 AREVLRFRGTIPREPKWDVVVDL 107 (261)
Q Consensus 85 AreVLr~rGtIs~e~pWEVmPDL 107 (261)
.-.+....|.+-.. .|.||
T Consensus 196 ~t~~~~~~g~v~~n----~mvd~ 214 (257)
T cd05007 196 STAVMIRLGKVYGN----LMVDV 214 (257)
T ss_pred HHHHHHHcchHHHH----HHHHh
Confidence 88888888876433 36664
No 35
>PF04493 Endonuclease_5: Endonuclease V; InterPro: IPR007581 Endonuclease V is specific for single-stranded DNA, for duplex DNA that contains uracil, or that is damaged []. Matrix metalloproteinase-1 (MMP-1) is the major enzyme responsible for collagen 1 digestion. It is induced by exposure to sunlight, but is reduced with treatment of DNA repair enzyme endonuclease V []. This family consequently has potential medical importance []. This endonuclease also appears in bifunctional enzymes, such as the bifunctional methyltransferase/endonuclease in Thermoplasma acidophilum.; GO: 0004519 endonuclease activity, 0006281 DNA repair; PDB: 3GA2_A 2W36_A 3HD0_A 2W35_B 3GOC_B.
Probab=53.31 E-value=25 Score=31.68 Aligned_cols=70 Identities=14% Similarity=0.176 Sum_probs=35.8
Q ss_pred Ccccccccccc-----CchhhhcccCCCCEEEEe-----CCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCC
Q psy9845 3 SLSSRTGLFIF-----PNLQFQAAFREPRLLVVT-----DPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNK 72 (261)
Q Consensus 3 ~~~~i~Grfip-----lTNQIQaaFrEPrLLVVT-----DPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNd 72 (261)
...||-|-|-| +..-++....+|++|+|= +||.=-.|-.=+-.+|+|||++--+----+..+...+.+..
T Consensus 63 ~~PYiPG~LafRE~P~~l~~l~~l~~~~dvilvDG~G~~HpR~~GlA~HlGv~l~iPtIGVAK~~l~g~~~~~~~~~~~~ 142 (206)
T PF04493_consen 63 SFPYIPGFLAFRELPCILEALEKLKNKPDVILVDGHGILHPRRFGLASHLGVLLDIPTIGVAKSLLYGDGEEFEEPGRKR 142 (206)
T ss_dssp -S-SSTT-GGGGTHHHHHHHHHTSSS--SCEEEES-SSSSTTS--HHHHHHHHHTS-EEEEESS-TTSTT-EE----SST
T ss_pred CcCccCCceehhhHHHHHHHHHHhcccCCEEEEeCceeecCCCcChhheeeeccCCCEEEEeCcccccCCcccchhcccc
Confidence 45677777775 555566667789988874 34443345555677899999997664333223555555543
No 36
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=52.05 E-value=29 Score=27.28 Aligned_cols=57 Identities=12% Similarity=0.130 Sum_probs=37.8
Q ss_pred ccCCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecCCCCCC-c------ceeeccCCCCCcchHH
Q psy9845 21 AFREPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNTESPLR-F------VDIAIPCNNKSPHSIG 78 (261)
Q Consensus 21 aFrEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDTDSpL~-~------VDiaIPcNNds~~SVg 78 (261)
...+-+++|++....+ ..+++.|...|+++|+|++ ++++. + .-+.+|.++-++.|.-
T Consensus 40 ~~~~~dl~I~iS~SG~t~e~i~~~~~a~~~g~~iI~IT~-~~~l~~~~~~~~~~~~~~p~~~~~r~s~~ 107 (119)
T cd05017 40 FVDRKTLVIAVSYSGNTEETLSAVEQAKERGAKIVAITS-GGKLLEMAREHGVPVIIIPKGLQPRAAFP 107 (119)
T ss_pred CCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEeC-CchHHHHHHHcCCcEEECCCCCCCceeHH
Confidence 4456678888765544 3356788889999999995 44443 1 2377788776665543
No 37
>TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing). The member from Methanococcus jannaschii contains an intein.
Probab=50.27 E-value=64 Score=32.48 Aligned_cols=75 Identities=19% Similarity=0.265 Sum_probs=46.4
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCCC---------CcchHHHHHHHHHH
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNNK---------SPHSIGLMWWLLAR 86 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNNd---------s~~SVgLi~wlLAr 86 (261)
..+.+++|++...-+. .+++-|...|++||+|++. +|++ .+.|+.|+.+.. +..+.-+++.+|+-
T Consensus 336 ~~~~dlvI~iS~SG~T~e~v~a~~~ak~~ga~~IaIT~~~~S~La~~ad~~l~~~~~~e~~~~~tks~~s~l~~l~lL~~ 415 (607)
T TIGR01135 336 VDKDTLVIAISQSGETADTLAALRLAKELGAKTLGICNVPGSTLVRESDHTLYTRAGPEIGVASTKAFTTQLTVLYLLAL 415 (607)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHcCCcEEEEECCCCChHHhhcCceEEecCCCccchhhhHHHHHHHHHHHHHHH
Confidence 3566788887655443 4667788889999999985 6666 356666665431 12223344556666
Q ss_pred HHHHhhCCCC
Q psy9845 87 EVLRFRGTIP 96 (261)
Q Consensus 87 eVLr~rGtIs 96 (261)
.+...+|.++
T Consensus 416 ~l~~~~g~~~ 425 (607)
T TIGR01135 416 KLAKARGTLS 425 (607)
T ss_pred HHHHHcCCCC
Confidence 6655556543
No 38
>PRK13938 phosphoheptose isomerase; Provisional
Probab=49.69 E-value=83 Score=27.82 Aligned_cols=56 Identities=18% Similarity=0.310 Sum_probs=39.8
Q ss_pred hhhhcccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCC-Ccceeec--cCCC
Q psy9845 16 LQFQAAFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPL-RFVDIAI--PCNN 71 (261)
Q Consensus 16 NQIQaaFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL-~~VDiaI--PcNN 71 (261)
.++.....+-|++|+.....+. .+++.|...|+|||+|++. ++++ ++.|+.| |.++
T Consensus 105 ~~~~~~~~~~DllI~iS~SG~t~~vi~a~~~Ak~~G~~vI~iT~~~~s~La~~aD~~l~v~~~e 168 (196)
T PRK13938 105 RALEGSARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFLINVPSRD 168 (196)
T ss_pred HHHHhcCCCCCEEEEEcCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCChhhhhCCEEEEeCCCc
Confidence 4566778888999998766543 4668889999999999974 4444 3355544 5543
No 39
>cd05009 SIS_GlmS_GlmD_2 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=47.87 E-value=1.3e+02 Score=23.51 Aligned_cols=76 Identities=21% Similarity=0.215 Sum_probs=45.4
Q ss_pred cccCCCCEEEEeCCCCC-----chhHHHHhhcCCCEEEEecCCCCCCccee--eccCCCC--CcchHHHHHHHHHHHHHH
Q psy9845 20 AAFREPRLLVVTDPHTD-----HQPITEAAYVNIPVIAFCNTESPLRFVDI--AIPCNNK--SPHSIGLMWWLLAREVLR 90 (261)
Q Consensus 20 aaFrEPrLLVVTDPraD-----hQALtEAS~VNIPtIALcDTDSpL~~VDi--aIPcNNd--s~~SVgLi~wlLAreVLr 90 (261)
.+..+-+++|++.+... ...++.+...|.++|+|.+.+.+....|+ .+|.-.+ +.-..-+.+++|+..+-.
T Consensus 57 ~~~~~~~~vi~is~~g~t~~~~~~~~~~~~~~~~~vi~it~~~~s~~~~d~~i~~~~~~~~~~~~~~~~~~q~la~~~a~ 136 (153)
T cd05009 57 ALVDEGTPVIFLAPEDRLEEKLESLIKEVKARGAKVIVITDDGDAKDLADVVIRVPATVEELSPLLYIVPLQLLAYHLAV 136 (153)
T ss_pred hhccCCCcEEEEecCChhHHHHHHHHHHHHHcCCEEEEEecCCcccccCCeEEECCCCchhHHHHHHHHHHHHHHHHHHH
Confidence 33445566666664322 24667888899999999877643334444 4443222 122334446888888887
Q ss_pred hhCCC
Q psy9845 91 FRGTI 95 (261)
Q Consensus 91 ~rGtI 95 (261)
.+|..
T Consensus 137 ~~g~~ 141 (153)
T cd05009 137 ARGID 141 (153)
T ss_pred HcCCC
Confidence 77754
No 40
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=47.28 E-value=57 Score=27.75 Aligned_cols=31 Identities=13% Similarity=0.330 Sum_probs=23.1
Q ss_pred CCCEEEEeCCCCC--chhHHHHhhcCCCEEEEe
Q psy9845 24 EPRLLVVTDPHTD--HQPITEAAYVNIPVIAFC 54 (261)
Q Consensus 24 EPrLLVVTDPraD--hQALtEAS~VNIPtIALc 54 (261)
..+.||+.....+ ...|.++...|||+|.+-
T Consensus 58 ~vdgiii~~~~~~~~~~~i~~~~~~~ipvV~~~ 90 (275)
T cd06307 58 RSDGVALVAPDHPQVRAAVARLAAAGVPVVTLV 90 (275)
T ss_pred cCCEEEEeCCCcHHHHHHHHHHHHCCCcEEEEe
Confidence 6898888765433 245788888999999774
No 41
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=47.01 E-value=93 Score=27.94 Aligned_cols=49 Identities=14% Similarity=0.180 Sum_probs=33.1
Q ss_pred ccCCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEecCCCCC--CcceeeccC
Q psy9845 21 AFREPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFCNTESPL--RFVDIAIPC 69 (261)
Q Consensus 21 aFrEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALcDTDSpL--~~VDiaIPc 69 (261)
...+-|++|+..-..... +++.|...|++||+|+|...++ .+.|+.|.+
T Consensus 184 ~~~~~Dl~I~iS~sG~t~~~~~~~~~ak~~g~~ii~IT~~~~s~la~~ad~~l~~ 238 (292)
T PRK11337 184 LLQEGDVVLVVSHSGRTSDVIEAVELAKKNGAKIICITNSYHSPIAKLADYVICS 238 (292)
T ss_pred cCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEEEc
Confidence 356678777766443333 4577889999999999976555 345665543
No 42
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=46.96 E-value=77 Score=26.69 Aligned_cols=44 Identities=16% Similarity=0.244 Sum_probs=28.9
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+..+.||+.....+...++++...|+|+|.+ |++.+-..+.+..
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~ipvV~~-~~~~~~~~~~~V~ 97 (264)
T cd06274 54 RQVDALIVAGSLPPDDPYYLCQKAGLPVVAL-DRPGDPSRFPSVV 97 (264)
T ss_pred cCCCEEEEcCCCCchHHHHHHHhcCCCEEEe-cCccCCCCCCEEE
Confidence 4678888876654444478888899999877 6654322344433
No 43
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=46.45 E-value=94 Score=25.89 Aligned_cols=44 Identities=18% Similarity=0.144 Sum_probs=30.0
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+..+.||+..+..+...+.++...|||+|.+ |++.+...+.+..
T Consensus 54 ~~~dgiii~~~~~~~~~l~~~~~~~ipvV~~-~~~~~~~~~~~v~ 97 (267)
T cd06283 54 YQVDGLIVNPTGNNKELYQRLAKNGKPVVLV-DRKIPELGVDTVT 97 (267)
T ss_pred cCcCEEEEeCCCCChHHHHHHhcCCCCEEEE-cCCCCCCCCCEEE
Confidence 4678888877655556688888899999987 5554333344433
No 44
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=45.30 E-value=69 Score=32.63 Aligned_cols=50 Identities=16% Similarity=0.270 Sum_probs=35.6
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecCCCCC-CcceeeccCC
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNTESPL-RFVDIAIPCN 70 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDTDSpL-~~VDiaIPcN 70 (261)
...+-+++|++.-.... .+++.|...|++||+|+|.+|++ .+.|+.|+..
T Consensus 512 ~l~~~DvvI~iS~sG~t~e~i~~~~~Ak~~Ga~vIaIT~~~spLa~~aD~~L~~~ 566 (638)
T PRK14101 512 LLGKGDVIVAVSKSGRAPELLRVLDVAMQAGAKVIAITSSNTPLAKRATVALETD 566 (638)
T ss_pred cCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEcCCCChhHhhCCEEEEcC
Confidence 34555777776543333 35678888999999999988877 4578877764
No 45
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=45.20 E-value=96 Score=26.15 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=26.9
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDS 58 (261)
+..+.+|+.....+...++++...|||+|.+ |.+.
T Consensus 54 ~~~dgiii~~~~~~~~~~~~~~~~~iPvv~~-~~~~ 88 (265)
T cd06285 54 RRVDGLILGDARSDDHFLDELTRRGVPFVLV-LRHA 88 (265)
T ss_pred cCCCEEEEecCCCChHHHHHHHHcCCCEEEE-ccCC
Confidence 4578888887666667789998899999766 5443
No 46
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=44.79 E-value=90 Score=25.52 Aligned_cols=36 Identities=19% Similarity=0.313 Sum_probs=27.0
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESP 59 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSp 59 (261)
+.++.+|+.....+...+.++...|||+|.+ +++.+
T Consensus 54 ~~~d~iii~~~~~~~~~~~~~~~~~ipvv~~-~~~~~ 89 (264)
T cd06267 54 RRVDGIILAPSRLDDELLEELAALGIPVVLV-DRPLD 89 (264)
T ss_pred cCcCEEEEecCCcchHHHHHHHHcCCCEEEe-ccccc
Confidence 5789888877665555588999999999987 44443
No 47
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=43.80 E-value=57 Score=25.16 Aligned_cols=48 Identities=13% Similarity=0.221 Sum_probs=32.8
Q ss_pred cCCCCEEEEeCCC-CC---chhHHHHhhcCCCEEEEecC-CCCCC-cceeeccC
Q psy9845 22 FREPRLLVVTDPH-TD---HQPITEAAYVNIPVIAFCNT-ESPLR-FVDIAIPC 69 (261)
Q Consensus 22 FrEPrLLVVTDPr-aD---hQALtEAS~VNIPtIALcDT-DSpL~-~VDiaIPc 69 (261)
..+-+++|+..-. .. ..+++.|...|+|||+|++. ++++. +.|+.|.+
T Consensus 45 ~~~~d~vi~iS~sG~t~~~~~~~~~a~~~g~~vi~iT~~~~s~la~~ad~~l~~ 98 (128)
T cd05014 45 VTPGDVVIAISNSGETDELLNLLPHLKRRGAPIIAITGNPNSTLAKLSDVVLDL 98 (128)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCeEEEEeCCCCCchhhhCCEEEEC
Confidence 3556777777633 33 34668899999999999995 45553 46666644
No 48
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=43.49 E-value=42 Score=28.45 Aligned_cols=44 Identities=16% Similarity=0.221 Sum_probs=28.4
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+.++.||+.....+ ...+..+...|||+|.+ |++.+...+.+..
T Consensus 59 ~~vdgiIi~~~~~~~~~~~l~~~~~~~iPvv~~-~~~~~~~~~~~v~ 104 (272)
T cd06300 59 QGVDAIIINPASPTALNPVIEEACEAGIPVVSF-DGTVTTPCAYNVN 104 (272)
T ss_pred cCCCEEEEeCCChhhhHHHHHHHHHCCCeEEEE-ecCCCCCceeEec
Confidence 47899988765433 34678888899999988 4443323344433
No 49
>PRK13937 phosphoheptose isomerase; Provisional
Probab=43.07 E-value=1.2e+02 Score=26.08 Aligned_cols=48 Identities=10% Similarity=0.154 Sum_probs=32.6
Q ss_pred ccCCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecC-CCCCC-cceeecc
Q psy9845 21 AFREPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNT-ESPLR-FVDIAIP 68 (261)
Q Consensus 21 aFrEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDT-DSpL~-~VDiaIP 68 (261)
..++-|++|+..-..+ ..+++.|...|+|||+|++. ++++. +.|+.|-
T Consensus 103 ~~~~~Dl~i~iS~sG~t~~~~~~~~~ak~~g~~~I~iT~~~~s~L~~~ad~~l~ 156 (188)
T PRK13937 103 LGRPGDVLIGISTSGNSPNVLAALEKARELGMKTIGLTGRDGGKMKELCDHLLI 156 (188)
T ss_pred hCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCeEEEEeCCCCChhHHhCCEEEE
Confidence 4467788888764433 23668889999999999884 55553 3555443
No 50
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=42.30 E-value=58 Score=27.67 Aligned_cols=35 Identities=14% Similarity=0.356 Sum_probs=24.8
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTDS 58 (261)
+.++.||+.....+ ...|+++...|||+|.+ |++.
T Consensus 54 ~~~Dgiii~~~~~~~~~~~i~~~~~~~iPvV~~-~~~~ 90 (282)
T cd06318 54 RGVNVLIINPVDPEGLVPAVAAAKAAGVPVVVV-DSSI 90 (282)
T ss_pred cCCCEEEEecCCccchHHHHHHHHHCCCCEEEe-cCCC
Confidence 46888888654333 34578888899999987 5543
No 51
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=42.21 E-value=59 Score=28.07 Aligned_cols=43 Identities=14% Similarity=0.071 Sum_probs=29.1
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+.++.+|++........++++...|+|+|.+ |++.+ ..+++.-
T Consensus 55 ~~~dgiii~~~~~~~~~~~~~~~~~ipvV~~-~~~~~-~~~~~v~ 97 (283)
T cd06279 55 ALVDGFIVYGVPRDDPLVAALLRRGLPVVVV-DQPLP-PGVPSVG 97 (283)
T ss_pred cCCCEEEEeCCCCChHHHHHHHHcCCCEEEE-ecCCC-CCCCEEe
Confidence 5678888876444456788999999999866 66654 3344444
No 52
>PF06925 MGDG_synth: Monogalactosyldiacylglycerol (MGDG) synthase; InterPro: IPR009695 This entry represents a conserved region of approximately 180 residues found towirds the N terminus of a number of plant and bacterial diacylglycerol glucosyltransferases, such as monogalactosyldiacylglycerol synthase [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009247 glycolipid biosynthetic process
Probab=41.76 E-value=58 Score=27.04 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=26.6
Q ss_pred CCCCEEEEeCCCCCch---hHHHHhhc-CCCEEEEecCCCC
Q psy9845 23 REPRLLVVTDPHTDHQ---PITEAAYV-NIPVIAFCNTESP 59 (261)
Q Consensus 23 rEPrLLVVTDPraDhQ---ALtEAS~V-NIPtIALcDTDSp 59 (261)
..||++|.|-|....- .+++-..+ ++|+++++ ||-.
T Consensus 88 ~~PD~IIsThp~~~~~~l~~lk~~~~~~~~p~~tvv-TD~~ 127 (169)
T PF06925_consen 88 FQPDLIISTHPFPAQVPLSRLKRRGRLPNIPVVTVV-TDFD 127 (169)
T ss_pred cCCCEEEECCcchhhhHHHHHHHhhcccCCcEEEEE-cCCC
Confidence 5899999999986554 24666667 79988776 6653
No 53
>COG1165 MenD 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [Coenzyme metabolism]
Probab=41.35 E-value=42 Score=35.01 Aligned_cols=80 Identities=18% Similarity=0.293 Sum_probs=57.4
Q ss_pred cccccc-cCchhhhcccCCCCEEEEeCCCC---CchhHHHHhhcCCCEEEEecCCCCCCc--------------------
Q psy9845 7 RTGLFI-FPNLQFQAAFREPRLLVVTDPHT---DHQPITEAAYVNIPVIAFCNTESPLRF-------------------- 62 (261)
Q Consensus 7 i~Grfi-plTNQIQaaFrEPrLLVVTDPra---DhQALtEAS~VNIPtIALcDTDSpL~~-------------------- 62 (261)
+++|=. ||.=|+-++...|-.||+|.--+ =+-||.||.+-++|.|-|. .|-|+++
T Consensus 53 ~DERsagFfALGlAKas~rPVavi~TSGTA~ANl~PAViEA~~srvpLIVLT-ADRP~EL~~~GAnQaI~Q~~lfgs~v~ 131 (566)
T COG1165 53 IDERSAGFFALGLAKASKRPVAVICTSGTAVANLYPAVIEANLSRVPLIVLT-ADRPPELRGCGANQAIDQTGLFGSYVR 131 (566)
T ss_pred cccchHHHHHHhhhhhcCCCEEEEEcCcchhhhccHHHHhhhhcCCceEEEe-CCCCHHHhcCCCchhhhhhhhhcccch
Confidence 445544 36678889999999999987443 2568999999999999885 5666554
Q ss_pred --ceeeccCCCCCcchHHHHHHHHHHHHHHhhC
Q psy9845 63 --VDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 93 (261)
Q Consensus 63 --VDiaIPcNNds~~SVgLi~wlLAreVLr~rG 93 (261)
+|.+.|-++.. ++|.+.+-..++-+
T Consensus 132 ~~~~L~~P~~~~~------~~~~~~~~~~~~~~ 158 (566)
T COG1165 132 ASIDLPLPEDDIE------ALWYLRTIASAAAQ 158 (566)
T ss_pred hhccCCCCCCCHH------HHHHHHHHHHHHHH
Confidence 47788887664 56666665555433
No 54
>PRK11382 frlB fructoselysine-6-P-deglycase; Provisional
Probab=40.54 E-value=1.1e+02 Score=28.63 Aligned_cols=49 Identities=10% Similarity=0.144 Sum_probs=35.6
Q ss_pred CCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecC-CCCC-CcceeeccCCC
Q psy9845 23 REPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNT-ESPL-RFVDIAIPCNN 71 (261)
Q Consensus 23 rEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDT-DSpL-~~VDiaIPcNN 71 (261)
.+-+++|++....+ ..+++.|...|.+||+|++. +|++ .+.|+.|+.+-
T Consensus 91 ~~~~lvI~iS~SGeT~e~i~al~~ak~~Ga~~I~IT~~~~S~L~~~ad~~l~~~a 145 (340)
T PRK11382 91 DDRCAVIGVSDYGKTEEVIKALELGRACGALTAAFTKRADSPITSAAEFSIDYQA 145 (340)
T ss_pred CCCCEEEEEcCCCCCHHHHHHHHHHHHcCCeEEEEECCCCChHHHhCCEEEEeCC
Confidence 34466776655444 34667888999999999986 6666 57899998873
No 55
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=39.86 E-value=89 Score=23.77 Aligned_cols=50 Identities=22% Similarity=0.346 Sum_probs=30.0
Q ss_pred CCCEEEEeCC-CCCc---hhHHHHhhcCCCEEEEecCCC-CCC-cce--eeccCCCCC
Q psy9845 24 EPRLLVVTDP-HTDH---QPITEAAYVNIPVIAFCNTES-PLR-FVD--IAIPCNNKS 73 (261)
Q Consensus 24 EPrLLVVTDP-raDh---QALtEAS~VNIPtIALcDTDS-pL~-~VD--iaIPcNNds 73 (261)
+=+++|+... +... +.++.+...|.|+|+|++... ++. +.| +.+|.++..
T Consensus 53 ~~d~vi~is~sg~~~~~~~~~~~ak~~g~~vi~iT~~~~~~l~~~ad~~l~~~~~~~~ 110 (131)
T PF01380_consen 53 PDDLVIIISYSGETRELIELLRFAKERGAPVILITSNSESPLARLADIVLYIPTGEES 110 (131)
T ss_dssp TTEEEEEEESSSTTHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEESSCGS
T ss_pred ccceeEeeeccccchhhhhhhHHHHhcCCeEEEEeCCCCCchhhhCCEEEEecCCCcc
Confidence 3366666553 3332 356889999999999997544 332 244 444554443
No 56
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=39.54 E-value=1.5e+02 Score=24.84 Aligned_cols=35 Identities=20% Similarity=0.319 Sum_probs=25.5
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDS 58 (261)
+..+.+|+.....+...+.++..-|||+|.+ |++.
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~~~~ipvv~~-~~~~ 89 (264)
T cd01574 55 QRVDGVIVNAPLDDADAALAAAPADVPVVFV-DGSP 89 (264)
T ss_pred cCCCEEEEeCCCCChHHHHHHHhcCCCEEEE-eccC
Confidence 4689998877665544567777789999997 5543
No 57
>COG0449 GlmS Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains [Cell envelope biogenesis, outer membrane]
Probab=39.21 E-value=86 Score=32.93 Aligned_cols=74 Identities=22% Similarity=0.216 Sum_probs=55.2
Q ss_pred CEEEEeCCCCC----chhHHHHhhcCCCEEEEecCCCCC--CcceeeccC---------CCCCcchHHHHHHHHHHHHHH
Q psy9845 26 RLLVVTDPHTD----HQPITEAAYVNIPVIAFCNTESPL--RFVDIAIPC---------NNKSPHSIGLMWWLLAREVLR 90 (261)
Q Consensus 26 rLLVVTDPraD----hQALtEAS~VNIPtIALcDTDSpL--~~VDiaIPc---------NNds~~SVgLi~wlLAreVLr 90 (261)
+|+|.+.+.-+ ..+|++|...|.++++|||..-+. +-.|+.+.- -.|+..+--+++++|+-.+-+
T Consensus 332 ~L~I~ISQSGETaDTl~ALr~ak~~G~~tlaItNv~gSti~Resd~~l~~~AGpEigVAsTKaftaQl~~L~lLal~~a~ 411 (597)
T COG0449 332 TLVIAISQSGETADTLAALRLAKEQGAKTLAITNVPGSTIARESDHTLLIRAGPEIGVASTKAFTAQVLALYLLALYLAK 411 (597)
T ss_pred cEEEEEccCcccHHHHHHHHHHHHcCCCEEEEEecCCChhhcccceEEEeccCCceeeecchhHHHHHHHHHHHHHHHhH
Confidence 56666555444 468999999999999999875443 235665543 357778888889999999999
Q ss_pred hhCCCCCCC
Q psy9845 91 FRGTIPREP 99 (261)
Q Consensus 91 ~rGtIs~e~ 99 (261)
.+|+++.+.
T Consensus 412 ~~g~i~~~~ 420 (597)
T COG0449 412 QRGTISEEE 420 (597)
T ss_pred hhCccchhH
Confidence 999887543
No 58
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=37.80 E-value=77 Score=26.59 Aligned_cols=31 Identities=13% Similarity=0.029 Sum_probs=24.8
Q ss_pred CCCEEEEeCCCCCchhHHHHhhcCCCEEEEe
Q psy9845 24 EPRLLVVTDPHTDHQPITEAAYVNIPVIAFC 54 (261)
Q Consensus 24 EPrLLVVTDPraDhQALtEAS~VNIPtIALc 54 (261)
..+.+|++....+.+.+.++...|||+|.+-
T Consensus 55 ~vdgiii~~~~~~~~~~~~l~~~~iPvv~~~ 85 (268)
T cd06273 55 GVDGLALIGLDHSPALLDLLARRGVPYVATW 85 (268)
T ss_pred CCCEEEEeCCCCCHHHHHHHHhCCCCEEEEc
Confidence 4788888877666677888888999999873
No 59
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=36.94 E-value=26 Score=32.28 Aligned_cols=56 Identities=18% Similarity=0.307 Sum_probs=40.6
Q ss_pred CCcccccccccc-----CchhhhcccCCCCEEEEeC-----CCCCchhHHHHhhcCCCEEEEecCC
Q psy9845 2 ISLSSRTGLFIF-----PNLQFQAAFREPRLLVVTD-----PHTDHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 2 ~~~~~i~Grfip-----lTNQIQaaFrEPrLLVVTD-----PraDhQALtEAS~VNIPtIALcDTD 57 (261)
+++.||-|-|.| +.+-+.....+|++|+|=. ||.=-.|-..+-.+|+|||++--+-
T Consensus 68 ~~~PYIPGfLaFRE~p~~l~a~~~l~~~~d~ilVDG~GiaHPR~~GlAsH~Gv~l~~PtIGVAK~~ 133 (212)
T COG1515 68 VSFPYIPGFLAFRELPLLLKALEKLSVKPDLLLVDGHGIAHPRRLGLASHIGVLLDVPTIGVAKSR 133 (212)
T ss_pred cccCcccchhhhhhhHHHHHHHHhcCCCCCEEEEcCcceecCcccChhheeeeeeCCCceeEehhh
Confidence 456677776665 4456677788999999854 5544457778888999999986553
No 60
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=36.83 E-value=1.9e+02 Score=24.12 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=26.5
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTD 57 (261)
+..+.||++....+...+..+...|||+|.+-+..
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~ipvv~~~~~~ 88 (268)
T cd01575 54 RRPAGLILTGLEHTERTRQLLRAAGIPVVEIMDLP 88 (268)
T ss_pred cCCCEEEEeCCCCCHHHHHHHHhcCCCEEEEecCC
Confidence 46899988876555566778888899999986543
No 61
>PRK02947 hypothetical protein; Provisional
Probab=36.79 E-value=1.8e+02 Score=26.25 Aligned_cols=38 Identities=21% Similarity=0.147 Sum_probs=29.1
Q ss_pred cccCCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEecCC
Q psy9845 20 AAFREPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 20 aaFrEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALcDTD 57 (261)
.....-|++|++....... +++.|...|+|||+|++..
T Consensus 102 ~~~~~~Dv~i~iS~sG~t~~~i~~~~~a~~~g~~vI~iT~~~ 143 (246)
T PRK02947 102 YDIRPGDVLIVVSNSGRNPVPIEMALEAKERGAKVIAVTSLA 143 (246)
T ss_pred cCCCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEcCCc
Confidence 3456678888887665543 5678999999999999875
No 62
>PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional
Probab=36.61 E-value=1.2e+02 Score=30.96 Aligned_cols=47 Identities=23% Similarity=0.275 Sum_probs=33.2
Q ss_pred CCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecCC-CCC-CcceeeccCC
Q psy9845 24 EPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNTE-SPL-RFVDIAIPCN 70 (261)
Q Consensus 24 EPrLLVVTDPraD----hQALtEAS~VNIPtIALcDTD-SpL-~~VDiaIPcN 70 (261)
.-+++|++-..-+ ..+++.|...|+|||+|++.. |++ +..|+.|+.+
T Consensus 369 ~~~lvI~ISqSGeT~d~i~al~~ak~~Ga~~IaITn~~~S~La~~ad~~l~~~ 421 (640)
T PTZ00295 369 EDAGVIFISQSGETLDVVRALNLADELNLPKISVVNTVGSLIARSTDCGVYLN 421 (640)
T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHHCCCCEEEEECCCCChhHHhcCEEEEeC
Confidence 4467777654444 346788889999999999865 444 5677877754
No 63
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=36.19 E-value=1.5e+02 Score=27.08 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=33.7
Q ss_pred ccCCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEecC-CCCCCc-ceeeccC
Q psy9845 21 AFREPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFCNT-ESPLRF-VDIAIPC 69 (261)
Q Consensus 21 aFrEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALcDT-DSpL~~-VDiaIPc 69 (261)
....=|++|++.-+.... .+..|...|.|||+|+|+ +||+.- .|+.+..
T Consensus 174 ~~~~~Dv~i~iS~sG~t~e~i~~a~~ak~~ga~vIaiT~~~~spla~~Ad~~L~~ 228 (281)
T COG1737 174 LLTPGDVVIAISFSGYTREIVEAAELAKERGAKVIAITDSADSPLAKLADIVLLV 228 (281)
T ss_pred hCCCCCEEEEEeCCCCcHHHHHHHHHHHHCCCcEEEEcCCCCCchhhhhceEEec
Confidence 334557888877555443 457789999999999999 787743 4544443
No 64
>COG3535 Uncharacterized conserved protein [Function unknown]
Probab=36.07 E-value=41 Score=33.29 Aligned_cols=38 Identities=32% Similarity=0.355 Sum_probs=28.7
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNK 72 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNd 72 (261)
.-|+||+++|...-..--+|.-+-|.-++ -++|||+|+
T Consensus 294 ~~PDLI~lld~~Tg~piTTe~lkyG~rV~------------V~aIP~~~~ 331 (357)
T COG3535 294 TTPDLIVLLDLNTGLPITTESLKYGQRVV------------VIAIPAPDL 331 (357)
T ss_pred ecCceEEEEecCCCCccchHHhhcCcEEE------------EEEecCcch
Confidence 46999999999876655567777676554 459999975
No 65
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=35.82 E-value=1.8e+02 Score=24.68 Aligned_cols=34 Identities=24% Similarity=0.310 Sum_probs=24.7
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTD 57 (261)
+.++.||+.....+ ...+.++...|||+|.+ |++
T Consensus 59 ~~vDgiii~~~~~~~~~~~i~~~~~~gIpvV~~-d~~ 94 (274)
T cd06311 59 RKIDALVILPFESAPLTQPVAKAKKAGIFVVVV-DRG 94 (274)
T ss_pred cCCCEEEEeCCCchhhHHHHHHHHHCCCeEEEE-cCC
Confidence 46899988743322 36688898999999986 544
No 66
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=35.31 E-value=1.7e+02 Score=24.43 Aligned_cols=44 Identities=11% Similarity=0.139 Sum_probs=29.3
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+..+.||+.....+...+.++...|||+|.+ |++.+-..+++..
T Consensus 54 ~~vdgiIi~~~~~~~~~~~~l~~~~ipvV~~-~~~~~~~~~~~v~ 97 (265)
T cd06299 54 QRVDGIIVVPHEQSAEQLEDLLKRGIPVVFV-DREITGSPIPFVT 97 (265)
T ss_pred cCCCEEEEcCCCCChHHHHHHHhCCCCEEEE-ecccCCCCCCEEE
Confidence 3578888876555556789999999999976 5543323344443
No 67
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=34.79 E-value=1e+02 Score=28.72 Aligned_cols=44 Identities=11% Similarity=0.211 Sum_probs=30.3
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+.++.|||+-...+ ...|++|...|||+|.+ |++.+.....+-|
T Consensus 79 ~~vdgIiv~~~d~~al~~~l~~a~~~gIpVV~~-d~~~~~~~~~~~V 124 (336)
T PRK15408 79 QGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTW-DSDTKPECRSYYI 124 (336)
T ss_pred cCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEe-CCCCCCccceEEE
Confidence 56899998744333 56889999999999975 5665444444434
No 68
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=34.62 E-value=92 Score=26.18 Aligned_cols=34 Identities=12% Similarity=0.253 Sum_probs=26.3
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTD 57 (261)
+..+.||++.+..+...+.++...|||+|.+ |+.
T Consensus 54 ~~~dgiii~~~~~~~~~~~~~~~~~ipvV~i-~~~ 87 (270)
T cd06296 54 RRTDGVILVTPELTSAQRAALRRTGIPFVVV-DPA 87 (270)
T ss_pred cCCCEEEEecCCCChHHHHHHhcCCCCEEEE-ecc
Confidence 4579888876665556789999999999987 443
No 69
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=34.42 E-value=88 Score=30.35 Aligned_cols=68 Identities=24% Similarity=0.244 Sum_probs=50.9
Q ss_pred chhHHHHhhcCCCEEEE-ecCCCCCCc-ceeeccC-----------CCCCcchHHHHHHHHHHHHHHhhCCCCCCCCccc
Q psy9845 37 HQPITEAAYVNIPVIAF-CNTESPLRF-VDIAIPC-----------NNKSPHSIGLMWWLLAREVLRFRGTIPREPKWDV 103 (261)
Q Consensus 37 hQALtEAS~VNIPtIAL-cDTDSpL~~-VDiaIPc-----------NNds~~SVgLi~wlLAreVLr~rGtIs~e~pWEV 103 (261)
.-+|++|..+|..||+| ||-+|++.. .||+|-- --|+...-.|+++||+..+.-.-|+.-.. .
T Consensus 146 igal~yAr~~Ga~Ti~iacNp~s~i~~~Ad~~I~~~vGPEvltGSTRlKaGTAQKlvLNMlST~~Mi~lGKvy~N----l 221 (298)
T COG2103 146 IGALEYARQRGATTIGIACNPGSAISRIADIAIEPVVGPEVLTGSTRLKAGTAQKLVLNMLSTGVMIKLGKVYGN----L 221 (298)
T ss_pred hHHHHHHHhcCCeEEEeecCCCchhhhhcCcceeeccCccccccccccccchHHHHHHHHHHHHHHHHhcccccc----e
Confidence 45899999999999999 677777654 7777732 23566677899999999887777776443 4
Q ss_pred ccccc
Q psy9845 104 VVDLF 108 (261)
Q Consensus 104 mPDLy 108 (261)
|.|+-
T Consensus 222 MVDv~ 226 (298)
T COG2103 222 MVDVK 226 (298)
T ss_pred EEEee
Confidence 77764
No 70
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=34.23 E-value=84 Score=26.52 Aligned_cols=35 Identities=26% Similarity=0.307 Sum_probs=24.7
Q ss_pred CCCCEEEEeCCCC-----CchhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHT-----DHQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPra-----DhQALtEAS~VNIPtIALcDTDS 58 (261)
+.++.||++.... ....+.++...|+|+|.+ |++.
T Consensus 54 ~~vdgiIi~~~~~~~~~~~~~~i~~~~~~~ipvV~i-~~~~ 93 (273)
T cd06292 54 RGVRGVVFISSLHADTHADHSHYERLAERGLPVVLV-NGRA 93 (273)
T ss_pred cCCCEEEEeCCCCCcccchhHHHHHHHhCCCCEEEE-cCCC
Confidence 4689888875432 234588888999999976 5544
No 71
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=33.78 E-value=96 Score=25.93 Aligned_cols=32 Identities=9% Similarity=0.065 Sum_probs=24.3
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEe
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFC 54 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALc 54 (261)
+..+.+|+.....+...+.++...|||+|.+-
T Consensus 54 ~~vdgiii~~~~~~~~~~~~l~~~~ipvV~~~ 85 (268)
T cd06298 54 KQVDGIIFMGGKISEEHREEFKRSPTPVVLAG 85 (268)
T ss_pred hcCCEEEEeCCCCcHHHHHHHhcCCCCEEEEc
Confidence 46788888765555567777777899998883
No 72
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.59 E-value=78 Score=24.31 Aligned_cols=37 Identities=19% Similarity=0.360 Sum_probs=29.0
Q ss_pred hhhhcccCCCCEEEEeCCCCCchhH----HHHhhcCCCEEE
Q psy9845 16 LQFQAAFREPRLLVVTDPHTDHQPI----TEAAYVNIPVIA 52 (261)
Q Consensus 16 NQIQaaFrEPrLLVVTDPraDhQAL----tEAS~VNIPtIA 52 (261)
.+|......+|+|||.--...|.+. .+|.+.|+|++-
T Consensus 40 ~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~~akk~~ip~~~ 80 (97)
T PF10087_consen 40 SRLPSKIKKADLVIVFTDYVSHNAMWKVKKAAKKYGIPIIY 80 (97)
T ss_pred hHHHHhcCCCCEEEEEeCCcChHHHHHHHHHHHHcCCcEEE
Confidence 3478888899999987766777755 678889999863
No 73
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=33.21 E-value=30 Score=26.15 Aligned_cols=19 Identities=37% Similarity=0.751 Sum_probs=16.0
Q ss_pred hhHHHHhhcCCCEEEEecC
Q psy9845 38 QPITEAAYVNIPVIAFCNT 56 (261)
Q Consensus 38 QALtEAS~VNIPtIALcDT 56 (261)
.-|.|+.-.|.||+|||--
T Consensus 15 ~kI~esav~G~pVvALCGk 33 (58)
T PF11238_consen 15 DKIAESAVMGTPVVALCGK 33 (58)
T ss_pred hHHHHHHhcCceeEeeeCc
Confidence 3578999999999999843
No 74
>PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D ....
Probab=33.19 E-value=44 Score=27.20 Aligned_cols=41 Identities=24% Similarity=0.221 Sum_probs=27.3
Q ss_pred Cchhhhcc--cCCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEe
Q psy9845 14 PNLQFQAA--FREPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFC 54 (261)
Q Consensus 14 lTNQIQaa--FrEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALc 54 (261)
+..++... ++.-|+||+....-... ++.+|...|++||+|.
T Consensus 91 ~~~~~~~~~~~~~gDvli~iS~SG~s~~vi~a~~~Ak~~G~~vIalT 137 (138)
T PF13580_consen 91 FARQLLALYDIRPGDVLIVISNSGNSPNVIEAAEEAKERGMKVIALT 137 (138)
T ss_dssp HHHHHHHHTT--TT-EEEEEESSS-SHHHHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEe
Confidence 44566666 78889999887655533 6689999999999985
No 75
>PRK15482 transcriptional regulator MurR; Provisional
Probab=32.69 E-value=3.2e+02 Score=24.59 Aligned_cols=49 Identities=16% Similarity=0.194 Sum_probs=33.6
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecCC-CCC-CcceeeccCC
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNTE-SPL-RFVDIAIPCN 70 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDTD-SpL-~~VDiaIPcN 70 (261)
..+-|++|+..-.... .+++.|...|.+||+|+|.. |++ .+.|+.|.+.
T Consensus 180 ~~~~Dv~i~iS~sg~t~~~~~~~~~a~~~g~~iI~IT~~~~s~la~~ad~~l~~~ 234 (285)
T PRK15482 180 LKKGDVQIAISYSGSKKEIVLCAEAARKQGATVIAITSLADSPLRRLAHFTLDTV 234 (285)
T ss_pred CCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCEEEEEeCCCCCchHHhCCEEEEcC
Confidence 4555787777644443 35678899999999999864 444 3567776554
No 76
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=32.45 E-value=81 Score=26.56 Aligned_cols=36 Identities=19% Similarity=0.331 Sum_probs=25.4
Q ss_pred CCCCEEEEeCCC--CCchhHHHHhhcCCCEEEEecCCCC
Q psy9845 23 REPRLLVVTDPH--TDHQPITEAAYVNIPVIAFCNTESP 59 (261)
Q Consensus 23 rEPrLLVVTDPr--aDhQALtEAS~VNIPtIALcDTDSp 59 (261)
+.++.||+..+. .....+.++...|||+|.+ |++.+
T Consensus 54 ~~vdgii~~~~~~~~~~~~i~~~~~~~ipvV~~-~~~~~ 91 (273)
T cd06305 54 QKVDAIIIQHGRAEVLKPWVKRALDAGIPVVAF-DVDSD 91 (273)
T ss_pred cCCCEEEEecCChhhhHHHHHHHHHcCCCEEEe-cCCCC
Confidence 468988886543 3356688899999999866 55443
No 77
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=31.91 E-value=1.8e+02 Score=24.96 Aligned_cols=31 Identities=23% Similarity=0.294 Sum_probs=23.6
Q ss_pred CCCCEEEEeCCCCCch-hHHHHhhcCCCEEEE
Q psy9845 23 REPRLLVVTDPHTDHQ-PITEAAYVNIPVIAF 53 (261)
Q Consensus 23 rEPrLLVVTDPraDhQ-ALtEAS~VNIPtIAL 53 (261)
+.++.||+.....+.. .+.++...|||+|.+
T Consensus 56 ~~vdgiI~~~~~~~~~~~~~~~~~~giPvV~~ 87 (268)
T cd06306 56 WGADAILLGAVSPDGLNEILQQVAASIPVIAL 87 (268)
T ss_pred cCCCEEEEcCCChhhHHHHHHHHHCCCCEEEe
Confidence 5789998875444332 478999999999988
No 78
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=31.19 E-value=2.3e+02 Score=21.34 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=33.6
Q ss_pred CCCCEEEEeCCCCCch----hHHHHhhcCCCEEEEecCCCC-C-CcceeeccCCC
Q psy9845 23 REPRLLVVTDPHTDHQ----PITEAAYVNIPVIAFCNTESP-L-RFVDIAIPCNN 71 (261)
Q Consensus 23 rEPrLLVVTDPraDhQ----ALtEAS~VNIPtIALcDTDSp-L-~~VDiaIPcNN 71 (261)
.+-+++|++..+.+.. +++.|+..|+++|++++...+ + .+.|+.|++..
T Consensus 59 ~~~~~~i~iS~~g~~~~~~~~~~~a~~~g~~iv~iT~~~~~~l~~~~d~~i~~~~ 113 (139)
T cd05013 59 TPGDVVIAISFSGETKETVEAAEIAKERGAKVIAITDSANSPLAKLADIVLLVSS 113 (139)
T ss_pred CCCCEEEEEeCCCCCHHHHHHHHHHHHcCCeEEEEcCCCCChhHHhcCEEEEcCC
Confidence 4567888877665533 567899999999999985443 3 24666665543
No 79
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=31.10 E-value=74 Score=26.18 Aligned_cols=31 Identities=16% Similarity=0.333 Sum_probs=21.2
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEE
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAF 53 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIAL 53 (261)
..|||+|...-..+...+..-...||||+.+
T Consensus 68 l~PDlii~~~~~~~~~~~~~l~~~gIpvv~i 98 (186)
T cd01141 68 LKPDLVILYGGFQAQTILDKLEQLGIPVLYV 98 (186)
T ss_pred cCCCEEEEecCCCchhHHHHHHHcCCCEEEe
Confidence 4699988754322222556667899999877
No 80
>TIGR02128 G6PI_arch bifunctional phosphoglucose/phosphomannose isomerase. This bifunctional isomerase is a member of the larger PGI superfamily and only distantly related to other glucose-6-phosphate isomerases. The family is limited to the archaea.
Probab=31.03 E-value=1.5e+02 Score=27.96 Aligned_cols=60 Identities=18% Similarity=0.182 Sum_probs=40.4
Q ss_pred ccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecCCCCCC-------cceeeccCCCCCcchHHHHH
Q psy9845 21 AFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNTESPLR-------FVDIAIPCNNKSPHSIGLMW 81 (261)
Q Consensus 21 aFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDTDSpL~-------~VDiaIPcNNds~~SVgLi~ 81 (261)
.....+++|++....+. .++..|...|.++|++++ ++++. ...+.||.+.-+..|+..|+
T Consensus 63 ~~~~~dlvI~iS~SG~t~e~~~a~~~A~~~g~~ii~iT~-~g~L~~~a~~~~~~~i~vP~~~~~R~s~~~~~ 133 (308)
T TIGR02128 63 FVDGKTLLIAVSYSGNTEETLSAVEEAKKKGAKVIAITS-GGRLEEMAKERGLDVIKIPKGLQPRAAFPYLL 133 (308)
T ss_pred cCCCCeEEEEEcCCCCCHHHHHHHHHHHHcCCEEEEECC-CcHHHHHHHhcCCeEEEcCCCCCCeeeHHHHH
Confidence 33555677777655443 356788889999999996 33222 34567899988888875443
No 81
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=31.00 E-value=75 Score=28.25 Aligned_cols=48 Identities=17% Similarity=0.146 Sum_probs=35.9
Q ss_pred cCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCCC-cceeeccC
Q psy9845 22 FREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPLR-FVDIAIPC 69 (261)
Q Consensus 22 FrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL~-~VDiaIPc 69 (261)
..+-|++|++.-.... .+++.|...|++||+|+|. ++++. +.|+.|.+
T Consensus 173 ~~~~Dv~I~iS~sg~~~~~~~~~~~ak~~ga~iI~IT~~~~s~la~~ad~~l~~ 226 (278)
T PRK11557 173 LSPDDLLLAISYSGERRELNLAADEALRVGAKVLAITGFTPNALQQRASHCLYT 226 (278)
T ss_pred CCCCCEEEEEcCCCCCHHHHHHHHHHHHcCCCEEEEcCCCCCchHHhCCEEEEe
Confidence 4677888888755443 4678899999999999996 45543 56777764
No 82
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=30.03 E-value=2.2e+02 Score=23.98 Aligned_cols=36 Identities=17% Similarity=0.162 Sum_probs=26.2
Q ss_pred cCCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCC
Q psy9845 22 FREPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 22 FrEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDS 58 (261)
-+.++.+|++....+...+.++...|+|+|.+ |++.
T Consensus 53 ~~~vdgii~~~~~~~~~~~~~~~~~~ipvV~~-~~~~ 88 (268)
T cd06270 53 ERRCDALILHSKALSDDELIELAAQVPPLVLI-NRHI 88 (268)
T ss_pred HcCCCEEEEecCCCCHHHHHHHhhCCCCEEEE-eccC
Confidence 36789999987544433488888899999887 5543
No 83
>PTZ00394 glucosamine-fructose-6-phosphate aminotransferase; Provisional
Probab=29.97 E-value=1.3e+02 Score=31.31 Aligned_cols=48 Identities=13% Similarity=0.145 Sum_probs=32.8
Q ss_pred CCCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecCC-CCC-CcceeeccCC
Q psy9845 23 REPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNTE-SPL-RFVDIAIPCN 70 (261)
Q Consensus 23 rEPrLLVVTDPraD----hQALtEAS~VNIPtIALcDTD-SpL-~~VDiaIPcN 70 (261)
.+-+++|++-..-+ ..+++.|...|++||+|++.. |++ +..|+.|..+
T Consensus 400 ~~~dlvI~ISqSGeT~dtl~Al~~Ak~~Ga~tIaITn~~~S~La~~AD~~l~~~ 453 (670)
T PTZ00394 400 QRDDVCFFVSQSGETADTLMALQLCKEAGAMCVGITNVVGSSISRLTHYAIHLN 453 (670)
T ss_pred CCCCEEEEEECCcCcHHHHHHHHHHHHCCCcEEEEECCCCCHHHHhcCeEEEec
Confidence 34467777654443 346788888999999998864 554 5677777653
No 84
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=29.75 E-value=1.3e+02 Score=25.52 Aligned_cols=34 Identities=24% Similarity=0.389 Sum_probs=24.0
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTD 57 (261)
+.++.+|+.....+ ...+.++...|||+|.+ |++
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~-~~~ 90 (270)
T cd06308 55 QGVDLLIISPNEAAPLTPVVEEAYRAGIPVILL-DRK 90 (270)
T ss_pred hCCCEEEEecCchhhchHHHHHHHHCCCCEEEe-CCC
Confidence 46898888754433 34578888899999966 443
No 85
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=29.52 E-value=1.1e+02 Score=25.77 Aligned_cols=36 Identities=8% Similarity=0.143 Sum_probs=26.4
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESP 59 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSp 59 (261)
+.++.+|+.....+...+++....+||+|.+ |++.+
T Consensus 50 ~~vdgii~~~~~~~~~~~~~~~~~~ipvV~~-~~~~~ 85 (261)
T cd06272 50 NRFDGVIIFGESASDVEYLYKIKLAIPVVSY-GVDYD 85 (261)
T ss_pred cCcCEEEEeCCCCChHHHHHHHHcCCCEEEE-cccCC
Confidence 3578888887666666678888889999966 65543
No 86
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=29.46 E-value=1e+02 Score=27.46 Aligned_cols=38 Identities=18% Similarity=0.392 Sum_probs=30.7
Q ss_pred cCCCCEEEE--eCCCCCchhHHHHhhcCCCEEEEecCCCCC
Q psy9845 22 FREPRLLVV--TDPHTDHQPITEAAYVNIPVIAFCNTESPL 60 (261)
Q Consensus 22 FrEPrLLVV--TDPraDhQALtEAS~VNIPtIALcDTDSpL 60 (261)
-+.++.|+| .|+..=..+|++|...|||+|.+ |++.+.
T Consensus 89 a~~~daIiv~~~d~~~~~~~v~~a~~aGIpVv~~-d~~~~~ 128 (322)
T COG1879 89 AQGVDAIIINPVDPDALTPAVKKAKAAGIPVVTV-DSDIPG 128 (322)
T ss_pred HcCCCEEEEcCCChhhhHHHHHHHHHCCCcEEEE-ecCCCC
Confidence 488999999 67777778999999999999988 454443
No 87
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=29.12 E-value=1.2e+02 Score=26.82 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=25.9
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTD 57 (261)
+..+.+|+.....+...+.++...|||+|.+.|.+
T Consensus 118 ~~vdgiI~~~~~~~~~~~~~l~~~~iPvV~~~~~~ 152 (331)
T PRK14987 118 WNIDGLILTERTHTPRTLKMIEVAGIPVVELMDSQ 152 (331)
T ss_pred cCCCEEEEcCCCCCHHHHHHHHhCCCCEEEEecCC
Confidence 46788888754445566788888899999886654
No 88
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=28.10 E-value=2.5e+02 Score=24.04 Aligned_cols=35 Identities=11% Similarity=0.083 Sum_probs=26.6
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDS 58 (261)
+.++.||++....+...+.+....|+|+|.+ |++.
T Consensus 54 ~~vdgvi~~~~~~~~~~~~~l~~~~iPvv~~-~~~~ 88 (269)
T cd06297 54 YLTDGLLLASYDLTERLAERRLPTERPVVLV-DAEN 88 (269)
T ss_pred cCCCEEEEecCccChHHHHHHhhcCCCEEEE-ccCC
Confidence 4589898887655666778888889999988 5543
No 89
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=27.95 E-value=3e+02 Score=23.17 Aligned_cols=35 Identities=14% Similarity=0.243 Sum_probs=24.1
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTDS 58 (261)
+.++.+|+.....+ ...+..+...|+|+|.+ |...
T Consensus 54 ~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~-~~~~ 90 (277)
T cd06319 54 KGVSGIIISPTNSSAAVTLLKLAAQAKIPVVIA-DIGA 90 (277)
T ss_pred cCCCEEEEcCCchhhhHHHHHHHHHCCCCEEEE-ecCC
Confidence 67898887643322 34678888899999975 5443
No 90
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=27.83 E-value=1.6e+02 Score=24.50 Aligned_cols=45 Identities=16% Similarity=0.110 Sum_probs=28.4
Q ss_pred CCCCEEEEeCCCCC-chhHHHHhhcCCCEEEEecCCCCCCcceeecc
Q psy9845 23 REPRLLVVTDPHTD-HQPITEAAYVNIPVIAFCNTESPLRFVDIAIP 68 (261)
Q Consensus 23 rEPrLLVVTDPraD-hQALtEAS~VNIPtIALcDTDSpL~~VDiaIP 68 (261)
+..+.+|+.....+ ...++++...|||+|.+ |++.+...+++..+
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~-~~~~~~~~~~~v~~ 99 (268)
T cd06289 54 HGVAGIILCPAAGTSPDLLKRLAESGIPVVLV-AREVAGAPFDYVGP 99 (268)
T ss_pred cCCCEEEEeCCCCccHHHHHHHHhcCCCEEEE-eccCCCCCCCEEee
Confidence 45788888754332 34678888999999987 44433233444443
No 91
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=27.73 E-value=2e+02 Score=24.13 Aligned_cols=35 Identities=14% Similarity=0.193 Sum_probs=24.6
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTDS 58 (261)
+.++.||+.....+ ...+.++...|||+|.+ |++.
T Consensus 55 ~~vdgiii~~~~~~~~~~~l~~~~~~~iPvV~~-~~~~ 91 (275)
T cd06317 55 QKVDGIILWPTDGQAYIPGLRKAKQAGIPVVIT-NSNI 91 (275)
T ss_pred cCCCEEEEecCCccccHHHHHHHHHCCCcEEEe-CCCC
Confidence 46898888654333 35678888999999955 5543
No 92
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown.
Probab=27.15 E-value=63 Score=29.14 Aligned_cols=53 Identities=19% Similarity=0.303 Sum_probs=31.0
Q ss_pred cccccccccc-----CchhhhcccCCCCEEEEeCCCCCc-----hhHHHHhhcCCCEEEEecC
Q psy9845 4 LSSRTGLFIF-----PNLQFQAAFREPRLLVVTDPHTDH-----QPITEAAYVNIPVIAFCNT 56 (261)
Q Consensus 4 ~~~i~Grfip-----lTNQIQaaFrEPrLLVVTDPraDh-----QALtEAS~VNIPtIALcDT 56 (261)
..||-|-+.| +..-++.....|+||+|=.-..-| .|-.=--.+|+|||++--+
T Consensus 68 ~PYIPG~LafRE~p~l~~~~~~l~~~PDlilVDG~G~~HpR~~GlA~HlGv~l~~PtIGVAK~ 130 (208)
T cd06559 68 FPYIPGLLAFREGPPLLEALEKLKTKPDLLLVDGHGIAHPRRFGLASHLGVLLDLPTIGVAKS 130 (208)
T ss_pred CCCcchhHHHhhHHHHHHHHHhCCCCCCEEEEeCCccccCCCcchhheeeeecCCCEEEEEcc
Confidence 3455563333 444455555789999985444443 2222223467899999765
No 93
>PRK14089 ipid-A-disaccharide synthase; Provisional
Probab=26.50 E-value=75 Score=30.52 Aligned_cols=40 Identities=5% Similarity=0.057 Sum_probs=31.0
Q ss_pred CchhhhcccCCCCEEEEeC-CCCCchhHHHHhhc--CCCEEEE
Q psy9845 14 PNLQFQAAFREPRLLVVTD-PHTDHQPITEAAYV--NIPVIAF 53 (261)
Q Consensus 14 lTNQIQaaFrEPrLLVVTD-PraDhQALtEAS~V--NIPtIAL 53 (261)
+-+++......||++|++| |.=+....+.+.+. |||+|=.
T Consensus 66 ~~~~~~~~~~~pd~~i~iD~p~Fnl~lak~~k~~~~~i~viyy 108 (347)
T PRK14089 66 AIKEMVELAKQADKVLLMDSSSFNIPLAKKIKKAYPKKEIIYY 108 (347)
T ss_pred HHHHHHHHhcCCCEEEEeCCCCCCHHHHHHHHhcCCCCCEEEE
Confidence 3444545557999999999 87888888899888 6999744
No 94
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=26.48 E-value=3e+02 Score=22.86 Aligned_cols=35 Identities=9% Similarity=0.106 Sum_probs=24.1
Q ss_pred CCCCEEEEeCCCCC-chhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTD-HQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraD-hQALtEAS~VNIPtIALcDTDS 58 (261)
+.++.+|+.....+ ...+.++...|||+|.+ |++.
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~-~~~~ 89 (266)
T cd06282 54 QRVDGLILTVADAATSPALDLLDAERVPYVLA-YNDP 89 (266)
T ss_pred cCCCEEEEecCCCCchHHHHHHhhCCCCEEEE-eccC
Confidence 46898888643322 23578888999999988 4443
No 95
>PRK07765 para-aminobenzoate synthase component II; Provisional
Probab=26.45 E-value=79 Score=27.91 Aligned_cols=32 Identities=13% Similarity=0.325 Sum_probs=24.1
Q ss_pred CCCCEEEEe----CCCCC---chhHHHHhhcCCCEEEEe
Q psy9845 23 REPRLLVVT----DPHTD---HQPITEAAYVNIPVIAFC 54 (261)
Q Consensus 23 rEPrLLVVT----DPraD---hQALtEAS~VNIPtIALc 54 (261)
..++.||++ +|..+ .+.++++...++|++++|
T Consensus 45 ~~~dgliisGGp~~~~~~~~~~~~i~~~~~~~~PiLGIC 83 (214)
T PRK07765 45 AQFDGVLLSPGPGTPERAGASIDMVRACAAAGTPLLGVC 83 (214)
T ss_pred cCCCEEEECCCCCChhhcchHHHHHHHHHhCCCCEEEEc
Confidence 468999997 44322 356788888899999998
No 96
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.25 E-value=1.4e+02 Score=25.17 Aligned_cols=41 Identities=15% Similarity=0.153 Sum_probs=27.4
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCccee
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDI 65 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDi 65 (261)
+..+.||+..... ...+.++...|||+|. +|.+.+...+.+
T Consensus 57 ~~vdgiii~~~~~-~~~~~~l~~~~ipvV~-~~~~~~~~~~~~ 97 (268)
T cd06277 57 GKVDGIILLGGIS-TEYIKEIKELGIPFVL-VDHYIPNEKADC 97 (268)
T ss_pred CCCCEEEEeCCCC-hHHHHHHhhcCCCEEE-EccCCCCCCCCE
Confidence 4688888876443 3447888888999995 576654433444
No 97
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=25.25 E-value=1.5e+02 Score=26.22 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=28.8
Q ss_pred CCCCEEEEeCCCC-CchhHHHHhhcCCCEEEEecCCCCCCcceeeccCC
Q psy9845 23 REPRLLVVTDPHT-DHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCN 70 (261)
Q Consensus 23 rEPrLLVVTDPra-DhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcN 70 (261)
+..+.||+..... +...+.+....+||+|. +|.+.+-..+++...-|
T Consensus 115 ~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~-~~~~~~~~~~~~V~~dn 162 (327)
T TIGR02417 115 RQVDALIVASCMPPEDAYYQKLQNEGLPVVA-LDRSLDDEHFCSVISDD 162 (327)
T ss_pred cCCCEEEEeCCCCCChHHHHHHHhcCCCEEE-EccccCCCCCCEEEeCc
Confidence 4568877765433 44567777788999985 46654333345555433
No 98
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=24.82 E-value=1.6e+02 Score=24.61 Aligned_cols=31 Identities=10% Similarity=0.214 Sum_probs=22.9
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEE
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAF 53 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIAL 53 (261)
+.++.||++....+...+..+...|||+|.+
T Consensus 54 ~~~dgii~~~~~~~~~~~~~~~~~~ipvv~~ 84 (259)
T cd01542 54 QKVDGIILLATTITDEHREAIKKLNVPVVVV 84 (259)
T ss_pred cCCCEEEEeCCCCCHHHHHHHhcCCCCEEEE
Confidence 5789999886554445556667779999987
No 99
>COG1929 Glycerate kinase [Carbohydrate transport and metabolism]
Probab=24.36 E-value=78 Score=31.63 Aligned_cols=40 Identities=23% Similarity=0.432 Sum_probs=32.3
Q ss_pred hhhcccCCCCEEEEeCCCCCchhH---------HHHhhcCCCEEEEecC
Q psy9845 17 QFQAAFREPRLLVVTDPHTDHQPI---------TEAAYVNIPVIAFCNT 56 (261)
Q Consensus 17 QIQaaFrEPrLLVVTDPraDhQAL---------tEAS~VNIPtIALcDT 56 (261)
++-.....-||+|.=.-|-|+|-+ +-|.+.++|+|+||-+
T Consensus 277 ~le~~v~daDLVITGEGr~D~Qs~~GK~pigVA~~Akk~~vPvIaiaGs 325 (378)
T COG1929 277 NLEDAVKDADLVITGEGRIDSQSLHGKTPIGVAKLAKKYGVPVIAIAGS 325 (378)
T ss_pred CHHHhhccCCEEEeCCCcccccccCCccchHHHHhhhhhCCCEEEEecc
Confidence 455666777998888899998855 5677899999999976
No 100
>PF06136 DUF966: Domain of unknown function (DUF966); InterPro: IPR010369 This is a family of plant proteins confined to monocotyledons and mosses, with unknown function
Probab=24.35 E-value=70 Score=30.89 Aligned_cols=31 Identities=16% Similarity=0.200 Sum_probs=21.4
Q ss_pred CCCcceeeccCCCCCcchHHHHHHHHHHHHHHhhC
Q psy9845 59 PLRFVDIAIPCNNKSPHSIGLMWWLLAREVLRFRG 93 (261)
Q Consensus 59 pL~~VDiaIPcNNds~~SVgLi~wlLAreVLr~rG 93 (261)
.||+|..+.+.++ +.+-=..|-|| .+||++|
T Consensus 15 HPHfieV~~~s~~-gL~LRDV~~RL---~~LRGkG 45 (337)
T PF06136_consen 15 HPHFIEVPLSSPQ-GLYLRDVKDRL---TALRGKG 45 (337)
T ss_pred CCeeEEeccCCCC-CcCHHHHHHHH---HHhhCCC
Confidence 4788999998864 55555555554 4678877
No 101
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=24.13 E-value=41 Score=28.45 Aligned_cols=42 Identities=21% Similarity=0.173 Sum_probs=24.4
Q ss_pred hhhhcccCCCCEEEEeCCCCCc---hhHHHHhh-cCCCEEEEecCC
Q psy9845 16 LQFQAAFREPRLLVVTDPHTDH---QPITEAAY-VNIPVIAFCNTE 57 (261)
Q Consensus 16 NQIQaaFrEPrLLVVTDPraDh---QALtEAS~-VNIPtIALcDTD 57 (261)
+.++.....|+.|++.+-..-. +++++... .+||+|++-|+.
T Consensus 176 ~~~~~~~~~~dai~~~~d~~a~~~~~~~~~~~~~~~ipvig~d~~~ 221 (281)
T cd06325 176 QAAQSLAGKVDAIYVPTDNTVASAMEAVVKVANEAKIPVIASDDDM 221 (281)
T ss_pred HHHHHhcccCCEEEEcCchhHHhHHHHHHHHHHHcCCCEEEcCHHH
Confidence 3444444457888876533222 33344332 479999998764
No 102
>cd01147 HemV-2 Metal binding protein HemV-2. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=23.76 E-value=1.4e+02 Score=25.53 Aligned_cols=32 Identities=13% Similarity=0.245 Sum_probs=20.2
Q ss_pred CCCCEEEEeCCCCCchhHHHHhh-cCCCEEEEe
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAY-VNIPVIAFC 54 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~-VNIPtIALc 54 (261)
-.|||||..+.......+.+... .||||+.+.
T Consensus 73 l~PDLIi~~~~~~~~~~~~~l~~~~gipvv~~~ 105 (262)
T cd01147 73 LKPDVVIDVGSDDPTSIADDLQKKTGIPVVVLD 105 (262)
T ss_pred cCCCEEEEecCCccchhHHHHHHhhCCCEEEEe
Confidence 37999998765433222333333 889999874
No 103
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=23.67 E-value=1.9e+02 Score=24.24 Aligned_cols=35 Identities=9% Similarity=0.190 Sum_probs=24.1
Q ss_pred CCCCEEEEeCCCC-CchhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHT-DHQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPra-DhQALtEAS~VNIPtIALcDTDS 58 (261)
+..+.||++.... +...+..+...|||+|.+ |++.
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvv~i-~~~~ 90 (270)
T cd01545 55 SRVDGVILTPPLSDNPELLDLLDEAGVPYVRI-APGT 90 (270)
T ss_pred CCCCEEEEeCCCCCccHHHHHHHhcCCCEEEE-ecCC
Confidence 4568888765432 345678888899999987 4443
No 104
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=23.28 E-value=1.7e+02 Score=26.53 Aligned_cols=48 Identities=13% Similarity=0.162 Sum_probs=33.8
Q ss_pred cccCCCCEEEEeCCCCCc----hhHHHHhhcCCCEEEEecC-CCCCC-cceeec
Q psy9845 20 AAFREPRLLVVTDPHTDH----QPITEAAYVNIPVIAFCNT-ESPLR-FVDIAI 67 (261)
Q Consensus 20 aaFrEPrLLVVTDPraDh----QALtEAS~VNIPtIALcDT-DSpL~-~VDiaI 67 (261)
....+-+++|+..-..+. ++++.|...|+|||+|++. +|++. +.|+.+
T Consensus 85 ~~~~~~d~~i~iS~sG~t~~~~~~~~~ak~~g~~vI~iT~~~~s~la~~ad~~l 138 (321)
T PRK11543 85 GMIESRDVMLFISYSGGAKELDLIIPRLEDKSIALLAMTGKPTSPLGLAAKAVL 138 (321)
T ss_pred CccCCCCEEEEEeCCCCcHHHHHHHHHHHHcCCeEEEEECCCCChhHHhCCEEE
Confidence 345677888887755443 3668899999999999995 55553 355555
No 105
>PRK11617 endonuclease V; Provisional
Probab=22.86 E-value=80 Score=29.12 Aligned_cols=70 Identities=13% Similarity=0.177 Sum_probs=37.5
Q ss_pred Ccccccccccc-----CchhhhcccCCCCEEEEeCCCCCch-----hHHHHhhcCCCEEEEecCCCCCCcceeeccCCCC
Q psy9845 3 SLSSRTGLFIF-----PNLQFQAAFREPRLLVVTDPHTDHQ-----PITEAAYVNIPVIAFCNTESPLRFVDIAIPCNNK 72 (261)
Q Consensus 3 ~~~~i~Grfip-----lTNQIQaaFrEPrLLVVTDPraDhQ-----ALtEAS~VNIPtIALcDTDSpL~~VDiaIPcNNd 72 (261)
...||-|-|-| +..-+.+.-..|++|+|=....-|. |-.=--.+|+|||++--+ +-+.++.-|.+.+
T Consensus 71 ~~PYIPG~LaFRE~P~~l~al~~l~~~PdlllvDG~G~~HPR~~GlA~HlGv~~~~PtIGVAK~---~L~g~~~~~~~~~ 147 (224)
T PRK11617 71 TMPYIPGFLSFREYPALLAAWEQLSQKPDLVFVDGHGIAHPRRLGVASHFGLLVDVPTIGVAKK---RLCGKFEPLSEEP 147 (224)
T ss_pred CCCcCcchHHHhhHHHHHHHHHhcCcCCCEEEEcCceeECCCCcceeeEEEeecCCCEEEEEcc---cccCCCcCccccC
Confidence 34567776654 3333344456899998844333222 111113468899999765 2233444455554
Q ss_pred Ccc
Q psy9845 73 SPH 75 (261)
Q Consensus 73 s~~ 75 (261)
|..
T Consensus 148 G~~ 150 (224)
T PRK11617 148 GSL 150 (224)
T ss_pred Cce
Confidence 443
No 106
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=22.28 E-value=1.9e+02 Score=25.56 Aligned_cols=44 Identities=20% Similarity=0.098 Sum_probs=28.7
Q ss_pred CCCCEEEEeCCCC-CchhHHHHhhcCCCEEEEecCCCCCCcceeec
Q psy9845 23 REPRLLVVTDPHT-DHQPITEAAYVNIPVIAFCNTESPLRFVDIAI 67 (261)
Q Consensus 23 rEPrLLVVTDPra-DhQALtEAS~VNIPtIALcDTDSpL~~VDiaI 67 (261)
+..+.||+..... ....+.++...|||+|.+ |...+...+++..
T Consensus 119 ~~vdgiIi~~~~~~~~~~~~~l~~~~iPvV~~-~~~~~~~~~~~V~ 163 (342)
T PRK10014 119 QGVDGVVIAGAAGSSDDLREMAEEKGIPVVFA-SRASYLDDVDTVR 163 (342)
T ss_pred CCCCEEEEeCCCCCcHHHHHHHhhcCCCEEEE-ecCCCCCCCCEEE
Confidence 4578888875432 345677888889999966 5544444455544
No 107
>cd01149 HutB Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=22.07 E-value=1.2e+02 Score=25.83 Aligned_cols=31 Identities=16% Similarity=0.413 Sum_probs=20.9
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEE
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAF 53 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIAL 53 (261)
-.|||||.+.-..+...+..-..++||++.+
T Consensus 57 l~PDlIi~~~~~~~~~~~~~l~~~gipvv~~ 87 (235)
T cd01149 57 LKPTLVIASDEAGPPEALDQLRAAGVPVVTV 87 (235)
T ss_pred cCCCEEEEcCCCCCHHHHHHHHHcCCeEEEe
Confidence 3699998765433333455556889999865
No 108
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=21.93 E-value=1.7e+02 Score=24.61 Aligned_cols=34 Identities=18% Similarity=0.252 Sum_probs=24.0
Q ss_pred CCCCEEEEeCCCC--CchhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHT--DHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPra--DhQALtEAS~VNIPtIALcDTD 57 (261)
+..+.+|+.-... ....+.++...|||+|.+ |++
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~-~~~ 90 (272)
T cd06301 55 QGVDAIIVVPVDTAATAPIVKAANAAGIPLVYV-NRR 90 (272)
T ss_pred cCCCEEEEecCchhhhHHHHHHHHHCCCeEEEe-cCC
Confidence 4678888765432 245678888999999966 554
No 109
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=21.88 E-value=1.2e+02 Score=29.24 Aligned_cols=36 Identities=19% Similarity=0.343 Sum_probs=25.8
Q ss_pred cCCCCEEEEeCCCCCch---hHHHH-hhcCCCEEEEecCC
Q psy9845 22 FREPRLLVVTDPHTDHQ---PITEA-AYVNIPVIAFCNTE 57 (261)
Q Consensus 22 FrEPrLLVVTDPraDhQ---ALtEA-S~VNIPtIALcDTD 57 (261)
-+.|+++|++.|+.-.. .-+|. +..|||+|.+.|.-
T Consensus 58 ~~~pDf~i~isPN~a~PGP~~ARE~l~~~~iP~IvI~D~p 97 (277)
T PRK00994 58 EWKPDFVIVISPNPAAPGPKKAREILKAAGIPCIVIGDAP 97 (277)
T ss_pred hhCCCEEEEECCCCCCCCchHHHHHHHhcCCCEEEEcCCC
Confidence 46899999999985432 22443 45799999997653
No 110
>PF01497 Peripla_BP_2: Periplasmic binding protein; InterPro: IPR002491 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Most bacterial importers employ a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered to the cell membrane via the acylation of a cysteine residue that is an integral component of a lipoprotein signal sequence. In planta expression of a high-affinity iron-uptake system involving the siderophore chrysobactin in Erwinia chrysanthemi 3937 contributes greatly to invasive growth of this pathogen on its natural host, African violets []. The cobalamin (vitamin B12) and the iron transport systems share many common attributes and probably evolved from the same origin [, ]. The periplasmic-binding domain is composed of two subdomains, each consisting of a central beta-sheet and surrounding alpha-helices, linked by a rigid alpha-helix. The substrate binding site is located in a cleft between the two alpha/beta subdomains [].; GO: 0005488 binding; PDB: 2X4L_A 1N4A_B 1N2Z_B 1N4D_B 4DBL_J 2QI9_F 3EIW_A 3EIX_A 3MWG_A 3MWF_A ....
Probab=21.77 E-value=1.3e+02 Score=25.13 Aligned_cols=34 Identities=21% Similarity=0.341 Sum_probs=25.1
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNT 56 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDT 56 (261)
..|||||.++-......+.+-...+|||+.+-..
T Consensus 59 l~PDlIi~~~~~~~~~~~~~~~~~~ip~~~~~~~ 92 (238)
T PF01497_consen 59 LKPDLIIGSSFYGQSEEIEKLLEAGIPVVVFDSS 92 (238)
T ss_dssp T--SEEEEETTSSCHHHHHHHHHTTSEEEEESST
T ss_pred CCCCEEEEeccccchHHHHHHhcccceEEEeecc
Confidence 3699999998875666777778889999987443
No 111
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=21.52 E-value=2.4e+02 Score=24.75 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=25.1
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTD 57 (261)
+.++.||+.....+ ...++++...|||+|.+ |++
T Consensus 55 ~~~DgiIi~~~~~~~~~~~~~~~~~~~iPvV~v-~~~ 90 (298)
T cd06302 55 QGVDAIAVVPNDPDALEPVLKKAREAGIKVVTH-DSD 90 (298)
T ss_pred cCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEE-cCC
Confidence 46899999765444 45678888999998876 544
No 112
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=20.88 E-value=2.4e+02 Score=23.55 Aligned_cols=46 Identities=7% Similarity=0.080 Sum_probs=26.0
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCN 70 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcN 70 (261)
+.++.||++....+.. .......|+|+|.+ |.+.+...+++..+-|
T Consensus 55 ~~~dgiii~~~~~~~~-~~~~~~~~ipvv~~-~~~~~~~~~~~v~~d~ 100 (269)
T cd06288 55 HRVDGIIYATMYHREV-TLPPELLSVPTVLL-NCYDADGALPSVVPDE 100 (269)
T ss_pred cCCCEEEEecCCCChh-HHHHHhcCCCEEEE-ecccCCCCCCeEEEcc
Confidence 4578888875432221 12234579999988 5544433455555544
No 113
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=20.68 E-value=1.7e+02 Score=24.74 Aligned_cols=35 Identities=17% Similarity=0.183 Sum_probs=22.6
Q ss_pred CCCCEEEEeCCCCC--chhHHHHhhcCCCEEEEecCCC
Q psy9845 23 REPRLLVVTDPHTD--HQPITEAAYVNIPVIAFCNTES 58 (261)
Q Consensus 23 rEPrLLVVTDPraD--hQALtEAS~VNIPtIALcDTDS 58 (261)
+..+.||+.....+ .+.+.++...|||+|.+ |+..
T Consensus 56 ~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~-~~~~ 92 (275)
T cd06320 56 KGYKGLLFSPISDVNLVPAVERAKKKGIPVVNV-NDKL 92 (275)
T ss_pred hCCCEEEECCCChHHhHHHHHHHHHCCCeEEEE-CCCC
Confidence 35788776532222 34578888899999965 5543
No 114
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=20.59 E-value=3.6e+02 Score=22.93 Aligned_cols=33 Identities=12% Similarity=0.147 Sum_probs=22.8
Q ss_pred CCCCEEEEeCCCC--CchhHHHHhhcCCCEEEEecCC
Q psy9845 23 REPRLLVVTDPHT--DHQPITEAAYVNIPVIAFCNTE 57 (261)
Q Consensus 23 rEPrLLVVTDPra--DhQALtEAS~VNIPtIALcDTD 57 (261)
+.++.+|+..... ....+.++.. |||+|.+ |.+
T Consensus 54 ~~vDgiIi~~~~~~~~~~~l~~~~~-~ipvV~~-~~~ 88 (271)
T cd06314 54 EGVDGIAISPIDPKAVIPALNKAAA-GIKLITT-DSD 88 (271)
T ss_pred cCCCEEEEecCChhHhHHHHHHHhc-CCCEEEe-cCC
Confidence 4678888864322 2466788878 9999987 444
No 115
>PLN02981 glucosamine:fructose-6-phosphate aminotransferase
Probab=20.50 E-value=3.8e+02 Score=28.07 Aligned_cols=45 Identities=11% Similarity=0.061 Sum_probs=30.6
Q ss_pred CCCEEEEeCCCCC----chhHHHHhhcCCCEEEEecC-CCCCC-cceeecc
Q psy9845 24 EPRLLVVTDPHTD----HQPITEAAYVNIPVIAFCNT-ESPLR-FVDIAIP 68 (261)
Q Consensus 24 EPrLLVVTDPraD----hQALtEAS~VNIPtIALcDT-DSpL~-~VDiaIP 68 (261)
.-+++|++...-+ ..+++.|...|.+||+|++. +|++. ..|+.|.
T Consensus 410 ~~~lvI~ISqSGeT~eti~Al~~Ak~~Ga~~IaITn~~~S~La~~ad~~i~ 460 (680)
T PLN02981 410 REDTAVFVSQSGETADTLRALEYAKENGALCVGITNTVGSAISRGTHCGVH 460 (680)
T ss_pred CCCeEEEEeCCcCCHHHHHHHHHHHHCCCcEEEEECCCCChhHhccCeeEE
Confidence 3467777654444 34778888999999999866 67763 3466544
No 116
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=20.19 E-value=2e+02 Score=24.43 Aligned_cols=45 Identities=11% Similarity=0.045 Sum_probs=27.9
Q ss_pred CCCCEEEEeCCCCCchhHHHHhhcCCCEEEEecCCCCCCcceeeccCC
Q psy9845 23 REPRLLVVTDPHTDHQPITEAAYVNIPVIAFCNTESPLRFVDIAIPCN 70 (261)
Q Consensus 23 rEPrLLVVTDPraDhQALtEAS~VNIPtIALcDTDSpL~~VDiaIPcN 70 (261)
+..+-+|+.. .+...+.+....++|+|.+ |...+...+++...-|
T Consensus 49 ~~vdGiI~~~--~~~~~~~~l~~~~~PvV~~-~~~~~~~~~~~v~~d~ 93 (265)
T cd01543 49 WQGDGIIARI--DDPEMAEALQKLGIPVVDV-SGSREKPGIPRVTTDN 93 (265)
T ss_pred cccceEEEEC--CCHHHHHHHhhCCCCEEEE-eCccCCCCCCEEeeCH
Confidence 3578888763 2445567777889999877 6554334455544433
Done!