Query 030738
Match_columns 172
No_of_seqs 180 out of 460
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:50:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030738.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030738hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02289 ribulose-bisphosphate 100.0 1.2E-90 2.6E-95 566.1 17.0 157 9-167 18-176 (176)
2 CHL00130 rbcS ribulose-1,5-bis 100.0 1.3E-59 2.9E-64 372.0 13.3 103 57-170 3-107 (138)
3 cd03527 RuBisCO_small Ribulose 100.0 2.2E-59 4.8E-64 353.7 13.1 99 57-166 1-99 (99)
4 PF00101 RuBisCO_small: Ribulo 100.0 1.2E-56 2.6E-61 338.4 12.2 99 58-167 1-99 (99)
5 COG4451 RbcS Ribulose bisphosp 100.0 1.9E-48 4.1E-53 303.9 12.4 104 55-169 6-109 (127)
6 cd00307 RuBisCO_small_like Rib 100.0 5.2E-46 1.1E-50 273.7 10.9 82 70-166 1-84 (84)
7 PF12338 RbcS: Ribulose-1,5-bi 98.6 2.5E-08 5.5E-13 66.6 1.6 28 6-35 18-45 (45)
8 PF05036 SPOR: Sporulation rel 70.5 15 0.00032 24.1 5.0 62 69-146 14-75 (76)
9 KOG4068 Uncharacterized conser 61.1 8.2 0.00018 32.4 2.8 37 67-119 65-101 (174)
10 PF01329 Pterin_4a: Pterin 4 a 58.8 5.9 0.00013 29.1 1.4 59 66-145 3-62 (95)
11 PF10557 Cullin_Nedd8: Cullin 56.4 12 0.00026 25.8 2.6 20 67-86 41-60 (68)
12 PF04208 MtrA: Tetrahydrometha 56.3 11 0.00023 31.9 2.7 26 119-144 130-155 (176)
13 PRK08176 pdxK pyridoxal-pyrido 55.9 39 0.00084 28.8 6.1 70 56-153 57-127 (281)
14 TIGR02802 Pal_lipo peptidoglyc 54.6 22 0.00048 25.5 3.9 29 125-153 14-42 (104)
15 PF08410 DUF1737: Domain of un 54.6 14 0.00031 25.5 2.7 24 64-87 8-31 (54)
16 PF05871 ESCRT-II: ESCRT-II co 52.8 14 0.00031 29.5 2.8 37 67-119 60-96 (139)
17 PF09967 DUF2201: VWA-like dom 52.2 18 0.0004 27.7 3.2 31 124-155 14-44 (126)
18 PRK00964 tetrahydromethanopter 48.4 16 0.00034 32.0 2.6 27 119-145 134-160 (225)
19 PF13174 TPR_6: Tetratricopept 46.3 24 0.00053 19.4 2.4 20 124-143 14-33 (33)
20 PF08784 RPA_C: Replication pr 44.8 26 0.00056 25.4 3.0 22 64-86 74-95 (102)
21 KOG2499 Beta-N-acetylhexosamin 44.8 65 0.0014 31.5 6.3 79 68-149 247-334 (542)
22 PF13986 DUF4224: Domain of un 44.7 25 0.00054 23.2 2.6 19 68-86 3-30 (47)
23 PTZ00344 pyridoxal kinase; Pro 44.2 89 0.0019 26.7 6.6 30 55-85 45-74 (296)
24 PF13663 DUF4148: Domain of un 44.1 19 0.00042 24.7 2.0 26 67-92 18-43 (58)
25 PF08756 YfkB: YfkB-like domai 44.1 64 0.0014 26.7 5.4 59 63-146 8-67 (153)
26 TIGR01111 mtrA N5-methyltetrah 43.8 21 0.00045 31.4 2.7 26 119-144 134-159 (238)
27 PF12122 DUF3582: Protein of u 42.9 62 0.0013 24.5 4.8 52 69-139 8-60 (101)
28 COG1867 TRM1 N2,N2-dimethylgua 42.7 16 0.00034 34.1 1.9 64 63-134 273-344 (380)
29 cd01169 HMPP_kinase 4-amino-5- 41.3 49 0.0011 26.6 4.4 54 67-153 50-103 (242)
30 PF01522 Polysacc_deac_1: Poly 41.0 90 0.002 22.1 5.3 47 70-140 43-89 (123)
31 PF03701 UPF0181: Uncharacteri 38.2 40 0.00086 23.3 2.8 24 62-85 2-28 (51)
32 PF13079 DUF3916: Protein of u 38.0 20 0.00044 29.5 1.6 46 104-150 13-73 (153)
33 cd01300 YtcJ_like YtcJ_like me 38.0 50 0.0011 29.8 4.3 51 103-153 36-93 (479)
34 PF09639 YjcQ: YjcQ protein; 37.9 33 0.00072 24.9 2.6 29 66-94 20-48 (88)
35 COG4063 MtrA Tetrahydromethano 37.2 32 0.0007 30.0 2.8 27 118-144 132-158 (238)
36 KOG0792 Protein tyrosine phosp 36.1 91 0.002 33.1 6.1 76 39-139 972-1058(1144)
37 PRK10802 peptidoglycan-associa 35.9 55 0.0012 26.6 3.9 30 125-154 83-112 (173)
38 PRK10985 putative hydrolase; P 35.7 2.8E+02 0.006 23.6 9.2 100 37-151 36-139 (324)
39 cd08587 PI-PLCXDc_like Catalyt 35.3 55 0.0012 28.0 3.9 30 119-148 87-116 (288)
40 PRK00823 phhB pterin-4-alpha-c 35.2 42 0.00091 24.7 2.8 61 65-145 3-64 (97)
41 TIGR03687 pupylate_cterm ubiqu 35.1 10 0.00022 24.1 -0.5 23 124-146 3-25 (33)
42 cd00741 Lipase Lipase. Lipase 35.0 63 0.0014 24.4 3.8 26 126-151 11-36 (153)
43 cd01173 pyridoxal_pyridoxamine 34.7 1.2E+02 0.0025 24.9 5.6 63 64-153 48-111 (254)
44 PF05902 4_1_CTD: 4.1 protein 34.4 45 0.00098 26.4 3.0 21 125-145 82-103 (114)
45 PRK05114 hypothetical protein; 34.4 48 0.001 23.5 2.8 23 62-84 2-27 (59)
46 PRK15358 pathogenicity island 34.4 37 0.00081 29.6 2.7 15 68-82 25-39 (239)
47 PF09778 Guanylate_cyc_2: Guan 34.2 43 0.00092 28.9 3.0 29 138-170 157-185 (212)
48 cd05782 DNA_polB_like1_exo Unc 33.7 1.4E+02 0.003 24.7 6.0 79 61-152 17-101 (208)
49 PRK13697 cytochrome c6; Provis 33.5 48 0.001 23.9 2.9 19 67-85 89-110 (111)
50 COG1724 Predicted RNA binding 32.7 48 0.001 24.0 2.6 23 62-87 1-23 (66)
51 PF11918 DUF3436: Domain of un 32.6 34 0.00075 23.9 1.8 17 65-81 35-51 (55)
52 PF10096 DUF2334: Uncharacteri 31.6 1.5E+02 0.0033 25.1 6.0 75 70-152 54-128 (243)
53 cd06297 PBP1_LacI_like_12 Liga 31.5 39 0.00085 27.2 2.3 28 129-157 195-222 (269)
54 PF10104 Brr6_like_C_C: Di-sul 31.3 32 0.0007 27.1 1.7 16 126-141 40-55 (135)
55 CHL00123 rps6 ribosomal protei 31.0 46 0.00099 24.7 2.4 75 56-141 5-87 (97)
56 TIGR03045 PS_II_C550 cytochrom 30.7 55 0.0012 26.8 3.1 28 56-83 120-147 (159)
57 cd03323 D-glucarate_dehydratas 30.5 1.9E+02 0.0041 26.3 6.7 65 57-153 156-221 (395)
58 PF05524 PEP-utilisers_N: PEP- 30.3 12 0.00026 28.0 -0.9 23 68-92 77-99 (123)
59 PLN02749 Uncharacterized prote 29.9 51 0.0011 27.7 2.7 29 57-85 4-32 (173)
60 PRK07708 hypothetical protein; 29.7 3.3E+02 0.0072 23.0 7.7 87 51-168 7-100 (219)
61 PRK12799 motB flagellar motor 29.6 2.5E+02 0.0055 26.5 7.5 33 119-152 158-196 (421)
62 PHA00422 hypothetical protein 29.5 13 0.00029 27.0 -0.7 21 127-147 5-25 (69)
63 cd08557 PI-PLCc_bacteria_like 28.8 82 0.0018 25.8 3.8 29 123-152 78-106 (271)
64 cd06354 PBP1_BmpA_PnrA_like Pe 28.5 61 0.0013 26.4 3.0 33 131-167 197-233 (265)
65 PHA01346 hypothetical protein 28.4 48 0.001 22.6 1.9 19 65-83 29-47 (53)
66 cd03799 GT1_amsK_like This is 28.1 83 0.0018 25.5 3.7 28 64-92 8-35 (355)
67 PHA02103 hypothetical protein 28.0 60 0.0013 26.0 2.7 28 116-143 37-68 (135)
68 cd01543 PBP1_XylR Ligand-bindi 27.8 55 0.0012 26.1 2.6 26 128-154 185-210 (265)
69 COG2885 OmpA Outer membrane pr 27.7 87 0.0019 25.0 3.7 27 125-151 97-123 (190)
70 PRK08944 motB flagellar motor 26.9 3.7E+02 0.008 23.9 7.8 29 124-153 192-220 (302)
71 PF12720 DUF3807: Protein of u 26.7 52 0.0011 27.3 2.3 23 62-84 39-70 (172)
72 PF00388 PI-PLC-X: Phosphatidy 26.6 51 0.0011 25.2 2.1 23 123-145 66-88 (146)
73 cd08588 PI-PLCc_At5g67130_like 26.2 1E+02 0.0022 26.8 4.1 47 122-169 74-131 (270)
74 PF09424 YqeY: Yqey-like prote 25.9 55 0.0012 26.0 2.2 22 63-84 85-107 (143)
75 cd01213 tensin Tensin Phosphot 25.9 1.3E+02 0.0028 24.2 4.3 72 69-168 23-108 (138)
76 PF02757 YLP: YLP motif; Inte 25.8 32 0.00069 16.1 0.5 6 63-68 3-8 (9)
77 cd08811 CARD_IPS1 Caspase acti 25.8 33 0.00071 25.8 0.8 14 60-73 22-35 (84)
78 CHL00133 psbV photosystem II c 25.7 85 0.0018 26.0 3.3 19 65-83 130-148 (163)
79 cd06293 PBP1_LacI_like_11 Liga 25.7 53 0.0011 26.1 2.1 26 129-155 189-217 (269)
80 PF13529 Peptidase_C39_2: Pept 25.3 59 0.0013 23.0 2.1 23 139-166 121-143 (144)
81 PF13590 DUF4136: Domain of un 25.2 63 0.0014 24.1 2.3 38 56-93 14-61 (151)
82 cd07185 OmpA_C-like Peptidogly 25.0 1.3E+02 0.0029 20.8 3.9 29 125-153 16-44 (106)
83 PF00034 Cytochrom_C: Cytochro 25.0 80 0.0017 20.4 2.6 17 67-83 74-90 (91)
84 PF08708 PriCT_1: Primase C te 24.8 75 0.0016 21.5 2.5 21 65-85 50-70 (71)
85 TIGR00703 conserved hypothetic 24.7 63 0.0014 28.1 2.4 29 110-139 193-221 (223)
86 PF07864 DUF1651: Protein of u 24.4 65 0.0014 22.7 2.1 21 69-89 51-71 (75)
87 cd06286 PBP1_CcpB_like Ligand- 24.1 64 0.0014 25.4 2.3 27 128-155 189-215 (260)
88 PF05639 Pup: Pup-like protein 24.0 22 0.00047 25.9 -0.4 24 123-146 38-61 (69)
89 cd02969 PRX_like1 Peroxiredoxi 23.9 1.3E+02 0.0027 23.2 3.9 32 121-152 35-66 (171)
90 PF14326 DUF4384: Domain of un 23.9 88 0.0019 22.0 2.7 20 140-159 16-35 (83)
91 cd08037 LARP_1 La RNA-binding 23.8 61 0.0013 23.5 1.9 10 71-80 2-11 (73)
92 PF14740 DUF4471: Domain of un 23.4 65 0.0014 28.8 2.4 41 51-91 244-288 (289)
93 cd08616 PI-PLCXD1c Catalytic d 23.3 86 0.0019 27.4 3.1 28 119-147 93-120 (290)
94 PF06486 DUF1093: Protein of u 23.2 1.2E+02 0.0026 21.1 3.3 23 144-166 29-51 (78)
95 CHL00183 petJ cytochrome c553; 23.1 82 0.0018 22.9 2.5 18 66-83 86-103 (108)
96 PF11181 YflT: Heat induced st 23.0 79 0.0017 23.2 2.4 19 69-87 8-26 (103)
97 PRK10401 DNA-binding transcrip 23.0 64 0.0014 27.2 2.2 27 129-156 252-278 (346)
98 smart00540 LEM in nuclear memb 22.9 53 0.0012 21.7 1.3 22 64-88 2-23 (44)
99 PF00993 MHC_II_alpha: Class I 22.9 60 0.0013 23.7 1.7 25 114-138 38-66 (82)
100 PF03354 Terminase_1: Phage Te 22.6 2.5E+02 0.0055 25.9 6.1 79 49-157 299-383 (477)
101 TIGR00687 pyridox_kin pyridoxa 22.6 1.8E+02 0.004 24.4 4.9 61 66-153 52-113 (286)
102 cd06296 PBP1_CatR_like Ligand- 22.4 84 0.0018 24.8 2.6 38 128-166 192-233 (270)
103 PRK11041 DNA-binding transcrip 22.3 65 0.0014 26.3 2.0 28 128-156 227-254 (309)
104 PF06100 Strep_67kDa_ant: Stre 22.3 23 0.00051 34.1 -0.6 39 103-143 150-188 (500)
105 PRK09967 putative outer membra 22.3 1.3E+02 0.0029 24.1 3.8 29 125-153 66-94 (160)
106 PF01168 Ala_racemase_N: Alani 22.2 3.2E+02 0.0069 21.6 6.0 55 37-94 60-120 (218)
107 PRK06925 flagellar motor prote 22.0 1.3E+02 0.0028 25.3 3.8 29 125-154 132-160 (230)
108 PRK10510 putative outer membra 21.9 1.3E+02 0.0029 25.3 3.9 29 125-153 126-154 (219)
109 cd06270 PBP1_GalS_like Ligand 21.8 68 0.0015 25.5 2.0 35 120-155 181-217 (268)
110 PF03230 Antirestrict: Antires 21.4 34 0.00074 25.9 0.2 12 108-119 5-16 (94)
111 PRK13618 psbV cytochrome c-550 21.3 1E+02 0.0023 25.4 3.0 27 57-83 122-148 (163)
112 PF13442 Cytochrome_CBB3: Cyto 21.2 86 0.0019 20.6 2.1 14 67-80 54-67 (67)
113 PF08069 Ribosomal_S13_N: Ribo 20.8 37 0.00081 23.9 0.3 21 68-88 28-48 (60)
114 PF07802 GCK: GCK domain; Int 20.8 66 0.0014 23.6 1.6 21 127-147 41-61 (76)
115 TIGR00166 S6 ribosomal protein 20.8 2.5E+02 0.0054 20.2 4.7 76 57-142 1-82 (93)
116 PRK13617 psbV cytochrome c-550 20.7 1.2E+02 0.0026 25.4 3.3 26 58-83 130-155 (170)
117 PRK09041 motB flagellar motor 20.4 5.6E+02 0.012 23.0 7.7 74 72-154 121-203 (317)
118 PF13463 HTH_27: Winged helix 20.3 2.5E+02 0.0054 18.0 4.3 29 67-95 29-57 (68)
119 TIGR01431 adm_rel adenosine de 20.3 1.3E+02 0.0028 28.5 3.8 28 125-155 268-298 (479)
120 PF13412 HTH_24: Winged helix- 20.3 1.4E+02 0.003 18.5 2.9 19 68-86 29-47 (48)
121 PRK10014 DNA-binding transcrip 20.2 83 0.0018 26.2 2.3 35 121-155 248-292 (342)
122 PRK00453 rpsF 30S ribosomal pr 20.2 2.8E+02 0.006 20.5 4.9 76 57-142 2-84 (108)
123 PF13193 AMP-binding_C: AMP-bi 20.2 2.7E+02 0.0059 18.4 4.7 33 132-164 1-35 (73)
124 KOG0729 26S proteasome regulat 20.1 41 0.00088 31.3 0.4 45 120-170 179-223 (435)
125 PF02671 PAH: Paired amphipath 20.0 45 0.00097 21.1 0.5 20 123-142 18-37 (47)
No 1
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=100.00 E-value=1.2e-90 Score=566.12 Aligned_cols=157 Identities=53% Similarity=1.089 Sum_probs=151.7
Q ss_pred cccccccccccCCcccccccccccCCC-CccccCCcccceeeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCee
Q 030738 9 PVAGSGYLGLKPTSKALLPVKDSIAWS-SKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIP 87 (172)
Q Consensus 9 ~~~va~f~glks~~~~~fp~~~~~~~~-~~~~sng~r~~cm~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p 87 (172)
++||+||+||||+++ ||+++|.+++ ++.+|||+||+|||||||+|+|||||||||||||||||+|||+|||+|||+|
T Consensus 18 as~vapf~gLKs~~~--fp~~~k~~~~~~~~~sng~rv~cmqvw~~~~~kkfETfSYLPpLtdeqI~kQVeYli~~GW~p 95 (176)
T PLN02289 18 ATMVAPFTGLKSSAA--FPVTRKANNDITSIASNGGRVSCMQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVP 95 (176)
T ss_pred ccccccccccccccc--CcceeeccccccccccCCceeEEEEeecccCccceeeeecCCCCCHHHHHHHHHHHHhCCCee
Confidence 478999999999999 9999997655 7788999999999999999999999999999999999999999999999999
Q ss_pred EEEeccC-CceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecC
Q 030738 88 CLEFDEV-GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166 (172)
Q Consensus 88 ~lEfad~-~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP 166 (172)
||||+++ +++||||+++|||||||||+|||||||||+|++|||+||+||+|+|||+|||||||||++|+||++||||||
T Consensus 96 clEf~~~~~~~~r~~~~s~~yyD~rYWtMWKLPMFg~tD~~~Vl~Ei~eC~kayP~~yIRiigFDn~rqvq~~sFiv~rP 175 (176)
T PLN02289 96 CLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKP 175 (176)
T ss_pred eeeeccCCceeEecCCCCCCcccCceeEEeccccCCCCCHHHHHHHHHHHHHHCCcceEEEEEEECCCCEEEEEEEEecC
Confidence 9999966 899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C
Q 030738 167 T 167 (172)
Q Consensus 167 ~ 167 (172)
.
T Consensus 176 ~ 176 (176)
T PLN02289 176 P 176 (176)
T ss_pred C
Confidence 5
No 2
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=100.00 E-value=1.3e-59 Score=371.95 Aligned_cols=103 Identities=34% Similarity=0.776 Sum_probs=99.2
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHH
Q 030738 57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC 136 (172)
Q Consensus 57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C 136 (172)
.||||||||||||||||++||+|||+|||+|||||++++++ | |+||+|||||||||+|++|||+||+||
T Consensus 3 ~~~eTfSyLPpLTdeqI~kQI~Y~i~~GW~p~iEft~~~~~-~----------~~YW~MWkLPMFg~tD~~~Vl~Ei~~C 71 (138)
T CHL00130 3 LTQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDPHP-R----------NSYWELWGLPLFDVKDPAAVMFEINEC 71 (138)
T ss_pred eeeceeccCCCCCHHHHHHHHHHHHhcCCeEEEEecCCCCc-C----------ccEEeeeCCccCCCCCHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999987 3 999999999999999999999999999
Q ss_pred HHHCCCCeEEEEeeecCCCeEE--EEEEEecCCCCC
Q 030738 137 KKAYPNAYIRCLAFNNQKQGQC--MSFLIQKPTTTT 170 (172)
Q Consensus 137 ~k~~P~~YIRliGfDn~rqvq~--~sfIV~RP~~~~ 170 (172)
+|+|||+|||||||||.+|+|| ++||||||.+..
T Consensus 72 rkayP~~yIRl~gFDn~rq~Q~~~~sFiV~rP~~ep 107 (138)
T CHL00130 72 RKQKPNGYIKVNAFDASRGVESCVLSFIVNRPANEP 107 (138)
T ss_pred HHHCCCcEEEEEEeeCCCcEEEeEEEEEEeCCCCCC
Confidence 9999999999999999999999 999999997653
No 3
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=100.00 E-value=2.2e-59 Score=353.70 Aligned_cols=99 Identities=60% Similarity=1.297 Sum_probs=96.6
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHH
Q 030738 57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC 136 (172)
Q Consensus 57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C 136 (172)
+|||||||||||||+||++||+|||+|||+|||||+|+++ |+++||+|||||||||+|++|||+||++|
T Consensus 1 ~~~~t~sylp~lt~~~i~~QI~yll~qG~~~~lE~ad~~~-----------~~~~yW~mwklP~f~~~d~~~Vl~ei~~C 69 (99)
T cd03527 1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTEPEH-----------YDNRYWTMWKLPMFGCTDPAQVLREIEAC 69 (99)
T ss_pred CcccccccCCCCCHHHHHHHHHHHHhCCCEEEEEcccCCC-----------CCCCEEeeccCCCCCCCCHHHHHHHHHHH
Confidence 6899999999999999999999999999999999999984 56999999999999999999999999999
Q ss_pred HHHCCCCeEEEEeeecCCCeEEEEEEEecC
Q 030738 137 KKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166 (172)
Q Consensus 137 ~k~~P~~YIRliGfDn~rqvq~~sfIV~RP 166 (172)
+++|||+|||||||||++|+||++||||||
T Consensus 70 ~~~~p~~YVRliG~D~~~q~~~~~fIv~RP 99 (99)
T cd03527 70 RKAYPDHYVRVVGFDNYKQSQCMSFIVHRP 99 (99)
T ss_pred HHHCCCCeEEEEEEeCCccEEEEEEEeeCc
Confidence 999999999999999999999999999999
No 4
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=100.00 E-value=1.2e-56 Score=338.43 Aligned_cols=99 Identities=44% Similarity=1.011 Sum_probs=89.8
Q ss_pred ccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHH
Q 030738 58 KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECK 137 (172)
Q Consensus 58 kfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~ 137 (172)
|||||||||||||+||++||+|||+|||+|||||+|++++ | ++||+|||||||||+|++|||+||++|+
T Consensus 1 k~et~S~lP~l~~~~i~~Qv~~ll~qG~~i~iE~ad~r~~-r----------~~~W~mW~~p~~~~~~~~~Vl~el~~c~ 69 (99)
T PF00101_consen 1 KFETFSYLPPLTDEEIAKQVRYLLSQGWIIGIEHADPRRF-R----------TSYWQMWKLPMFGCTDPAQVLAELEACL 69 (99)
T ss_dssp --STTTTSS---HHHHHHHHHHHHHTT-EEEEEEESCGGS-T----------SSS-EEESSEBTTBSSHHHHHHHHHHHH
T ss_pred CCcccccCCCCCHHHHHHHHHhhhhcCceeeEEecCCCCC-C----------CCEeecCCCCCcCCCCHHHHHHHHHHHH
Confidence 7999999999999999999999999999999999999965 3 9999999999999999999999999999
Q ss_pred HHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 030738 138 KAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167 (172)
Q Consensus 138 k~~P~~YIRliGfDn~rqvq~~sfIV~RP~ 167 (172)
++|||+|||||||||++|+||++||||||.
T Consensus 70 ~~~p~~yVRlig~D~~~q~r~~~~iVqRP~ 99 (99)
T PF00101_consen 70 AEHPGEYVRLIGFDNKRQRRVLEFIVQRPN 99 (99)
T ss_dssp HHSTTSEEEEEEEETTTTEEEEEEEEEGGT
T ss_pred HhCCCceEEEEEEcCcccEEEEEEEEECCC
Confidence 999999999999999999999999999995
No 5
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=100.00 E-value=1.9e-48 Score=303.87 Aligned_cols=104 Identities=32% Similarity=0.749 Sum_probs=100.9
Q ss_pred CccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHH
Q 030738 55 NNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQ 134 (172)
Q Consensus 55 ~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie 134 (172)
.+..++||||||+|||+||++||+|||.|||+|++||+|+++| | +.||+|||+||||..++.+||+|||
T Consensus 6 ~~~~~~~~s~lp~Ltd~qi~~QVrylL~QGykigvE~~d~rrp-r----------tgsWt~wg~p~f~~~~~~evlaele 74 (127)
T COG4451 6 KNSRYKTLSSLPPLTDEQIAEQVRYLLSQGYKIGVEYVDDRRP-R----------TGSWTMWGTPMFGAKTAGEVLAELE 74 (127)
T ss_pred CCCcccceecCCcCcHHHHHHHHHHHHhCCcccceeecccCCc-c----------cceeeecCCccccccchHHHHHHHH
Confidence 6889999999999999999999999999999999999999977 4 9999999999999999999999999
Q ss_pred HHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCC
Q 030738 135 ECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTT 169 (172)
Q Consensus 135 ~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~ 169 (172)
+|+++||++|||||||||++|+|++|||||||.+.
T Consensus 75 ~Cr~dhp~eYIRliGfDp~gkrrv~sfIVhRPng~ 109 (127)
T COG4451 75 ACRADHPGEYIRLIGFDPKGKRRVVSFIVHRPNGN 109 (127)
T ss_pred HHHHhCCCCeEEEEEecCCCceEEEEEEEECCCCC
Confidence 99999999999999999999999999999999864
No 6
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=100.00 E-value=5.2e-46 Score=273.71 Aligned_cols=82 Identities=18% Similarity=0.415 Sum_probs=80.1
Q ss_pred hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCC--CCHHHHHHHHHHHHHHCCCCeEEE
Q 030738 70 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGC--NDSSQILNEIQECKKAYPNAYIRC 147 (172)
Q Consensus 70 d~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~--td~sqVl~Eie~C~k~~P~~YIRl 147 (172)
|+||.+||+|||+|||+|||||+|+ +|||||||||||+| +|++|||+||++|+++|||+||||
T Consensus 1 d~~i~~QI~yll~qG~~~~iE~~d~---------------~rywt~w~lp~f~~~~~~~~~Vl~el~~c~~~~p~~YVRl 65 (84)
T cd00307 1 SEDVVEQVRQLLAQGYKIGLEHADA---------------RRFRTSSWQSCGPIEGRSEAQVLAALEACLAEHPGEYVRL 65 (84)
T ss_pred CHHHHHHHHHHHHCCCEeEEEECCC---------------CccHhhhcCCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEE
Confidence 6899999999999999999999986 48999999999999 999999999999999999999999
Q ss_pred EeeecCCCeEEEEEEEecC
Q 030738 148 LAFNNQKQGQCMSFLIQKP 166 (172)
Q Consensus 148 iGfDn~rqvq~~sfIV~RP 166 (172)
|||||++|+|++|||||||
T Consensus 66 ig~D~~~q~~~~~fIv~RP 84 (84)
T cd00307 66 IGIDPKAKRRVLEIIIQRP 84 (84)
T ss_pred EEEeCCccEEEEEEEeeCc
Confidence 9999999999999999999
No 7
>PF12338 RbcS: Ribulose-1,5-bisphosphate carboxylase small subunit; InterPro: IPR024680 This domain is found in the N-terminal region of the small subunit of ribulose-1,5-bisphosphate in plants. It contains a conserved APF sequence motif. There are also two completely conserved residues (L and P) that may be functionally important.
Probab=98.56 E-value=2.5e-08 Score=66.55 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=24.4
Q ss_pred ccCcccccccccccCCcccccccccccCCC
Q 030738 6 FTAPVAGSGYLGLKPTSKALLPVKDSIAWS 35 (172)
Q Consensus 6 ~a~~~~va~f~glks~~~~~fp~~~~~~~~ 35 (172)
.++++|||||+||||+++ ||++||.++|
T Consensus 18 ~aqa~mVAPFtGLKS~a~--fPvtrK~~nd 45 (45)
T PF12338_consen 18 PAQASMVAPFTGLKSTAA--FPVTRKSNND 45 (45)
T ss_pred ccccceeecccccccccc--CccccccCCC
Confidence 356689999999999999 9999998654
No 8
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=70.47 E-value=15 Score=24.07 Aligned_cols=62 Identities=19% Similarity=0.312 Sum_probs=32.1
Q ss_pred ChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEE
Q 030738 69 SDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIR 146 (172)
Q Consensus 69 td~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~~YIR 146 (172)
+.++..+.++.|..+|...-+.....+ +.+|...=.|.=.-.++.+++.+|. .+.+++++|+
T Consensus 14 ~~~~A~~~~~~l~~~g~~~~~~~~~~~--------------~~~yrV~~G~f~~~~~A~~~~~~l~--~~~~~~~~vv 75 (76)
T PF05036_consen 14 SEENAERLLAKLKKKGPDAYVVQVSKG--------------GPWYRVRVGPFSSREEAEAALRKLK--KAAGPDAFVV 75 (76)
T ss_dssp -HHHHHHHHHHHHHHT-----EEEEEE--------------TTCEEEEECCECTCCHHHHHHHHHH--HHHTS--EEE
T ss_pred CHHHHHHHHHHHHhcCCCcceEEEecC--------------CceEEEEECCCCCHHHHHHHHHHHh--HhhCCCCEEE
Confidence 567778888999999877554222221 2222222224344445566666666 6899999986
No 9
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.07 E-value=8.2 Score=32.44 Aligned_cols=37 Identities=27% Similarity=0.464 Sum_probs=31.4
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCC
Q 030738 67 SLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLP 119 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLP 119 (172)
-|+.+-|..-+++|-++|- +|+.|++ | ++||-||+.|
T Consensus 65 ~Ls~~~i~~Il~~l~k~g~---~e~~Dk~---r----------t~f~I~Wrs~ 101 (174)
T KOG4068|consen 65 RLSQEFIDEILEELEKKGL---AEPTDKR---R----------TRFFIYWRSL 101 (174)
T ss_pred cCCHHHHHHHHHHHHHccC---CcccccC---c----------eEEEEEEcCH
Confidence 4677788888999999996 7999988 5 8999999865
No 10
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=58.76 E-value=5.9 Score=29.10 Aligned_cols=59 Identities=22% Similarity=0.397 Sum_probs=32.2
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCC-CHHHHHHHHHHHHHHCCCCe
Q 030738 66 PSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCN-DSSQILNEIQECKKAYPNAY 144 (172)
Q Consensus 66 P~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~t-d~sqVl~Eie~C~k~~P~~Y 144 (172)
|+||++||.+.+..| .||...- . ....|. |+.+=|... +--.-++++.+-..-||+-.
T Consensus 3 ~~Ls~~ei~~~L~~l--~~W~~~~--~--~~l~r~---------------f~f~~f~~a~~f~~~Va~~ae~~~HHP~i~ 61 (95)
T PF01329_consen 3 PPLSEEEIAEALAEL--PGWKLDG--G--GRLERT---------------FKFKDFAEAVEFVNRVAALAEEENHHPDIS 61 (95)
T ss_dssp SB-THHHHHHHHHTS--TTSEEET--S--SEEEEE---------------EE-SSHHHHHHHHHHHHHHHHHHT---EEE
T ss_pred CCCCHHHHHHhhhcC--cCCEECC--C--CcEEEE---------------EEeCCHHHHHHHHHHHHHHHHHhCCCCCeE
Confidence 789999999999977 8998763 1 333331 233322211 22334556666777788755
Q ss_pred E
Q 030738 145 I 145 (172)
Q Consensus 145 I 145 (172)
+
T Consensus 62 ~ 62 (95)
T PF01329_consen 62 L 62 (95)
T ss_dssp E
T ss_pred e
Confidence 4
No 11
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=56.41 E-value=12 Score=25.79 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=16.1
Q ss_pred CCChHHHHHHHHHHHhCCCe
Q 030738 67 SLSDDSIAKEIDYMLKKGWI 86 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~qGw~ 86 (172)
+.+..+|.++|++||.+||.
T Consensus 41 ~~~~~~ik~~Ie~LIekeyi 60 (68)
T PF10557_consen 41 PPSVSDIKKRIESLIEKEYI 60 (68)
T ss_dssp ---HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHHHhhhh
Confidence 35899999999999999984
No 12
>PF04208 MtrA: Tetrahydromethanopterin S-methyltransferase, subunit A ; InterPro: IPR013340 This domain is mostly found in N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A (MtrA) in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. 5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the N-terminal region of what appears to be a fusion of the MtrA and MtrF proteins [, ]. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism. ; GO: 0008168 methyltransferase activity, 0030269 tetrahydromethanopterin S-methyltransferase activity
Probab=56.28 E-value=11 Score=31.91 Aligned_cols=26 Identities=35% Similarity=0.621 Sum_probs=24.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCe
Q 030738 119 PMFGCNDSSQILNEIQECKKAYPNAY 144 (172)
Q Consensus 119 Pmfg~td~sqVl~Eie~C~k~~P~~Y 144 (172)
-|+|.+|...+.+.|++|...-|++|
T Consensus 130 d~ig~eD~~~I~~~I~e~~~kdpga~ 155 (176)
T PF04208_consen 130 DMIGEEDPEAIQAKIKECISKDPGAF 155 (176)
T ss_pred eeecCCCHHHHHHHHHHHHhcCCccC
Confidence 79999999999999999999999887
No 13
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=55.88 E-value=39 Score=28.79 Aligned_cols=70 Identities=9% Similarity=0.195 Sum_probs=44.6
Q ss_pred ccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHH-HH
Q 030738 56 NKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNE-IQ 134 (172)
Q Consensus 56 ~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~E-ie 134 (172)
.--|+.+.. ++++++.+.+|++-+...+... +|+ .+|..|++..+..+++.+ ++
T Consensus 57 ~~~y~~~~~-~~~~~~~i~~~l~~~~~~~~l~--~~d----------------------~i~~G~l~s~~~~~~i~~~l~ 111 (281)
T PRK08176 57 TPHYPTFYG-GAIPDEWFSGYLRALQERDALR--QLR----------------------AVTTGYMGSASQIKILAEWLT 111 (281)
T ss_pred CCCCCCcCC-eeCCHHHHHHHHHHHHhcCccc--cCC----------------------EEEECCCCCHHHHHHHHHHHH
Confidence 334666654 3688999999999988876420 111 157888887665555555 55
Q ss_pred HHHHHCCCCeEEEEeeecC
Q 030738 135 ECKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 135 ~C~k~~P~~YIRliGfDn~ 153 (172)
+.+..+|+ ++++ +||+
T Consensus 112 ~~~~~~~~--~~vv-~DPv 127 (281)
T PRK08176 112 ALRADHPD--LLIM-VDPV 127 (281)
T ss_pred HHHHHCCC--CcEE-eCCc
Confidence 55545576 3455 9997
No 14
>TIGR02802 Pal_lipo peptidoglycan-associated lipoprotein. Members of this protein are Pal (also called OprL), the Peptidoglycan-Associated Lipoprotein of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients. Members of this family contain a hydrodrophobic lipoprotein signal sequence, a conserved N-terminal cleavage and modification site, a poorly conserved low-complexity region, together comprising about 65 amino acids, and a well-conserved C-terminal domain. The seed alignment for this model includes only the conserved C-terminal domain.
Probab=54.58 E-value=22 Score=25.51 Aligned_cols=29 Identities=14% Similarity=0.243 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfDn~ 153 (172)
+..++|.+|.+.++.+|+..|+|.|+-..
T Consensus 14 ~~~~~L~~~a~~l~~~~~~~i~I~Ghtd~ 42 (104)
T TIGR02802 14 EAQAILDAHAAYLKKNPSVRVTIEGHTDE 42 (104)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEEecCC
Confidence 45679999999999999999999999654
No 15
>PF08410 DUF1737: Domain of unknown function (DUF1737); InterPro: IPR013619 This domain of unknown function is found at the N terminus of bacterial and viral hypothetical proteins.
Probab=54.56 E-value=14 Score=25.49 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=20.2
Q ss_pred CCCCCChHHHHHHHHHHHhCCCee
Q 030738 64 YLPSLSDDSIAKEIDYMLKKGWIP 87 (172)
Q Consensus 64 yLP~ltd~qi~kQV~ylL~qGw~p 87 (172)
+|=--+|+++.+.|...|++||.+
T Consensus 8 ~lt~~d~~~fc~rVt~aL~~GW~l 31 (54)
T PF08410_consen 8 VLTGPDDSAFCHRVTEALNEGWQL 31 (54)
T ss_pred EEECCChHHHHHHHHHHHHcCCEe
Confidence 344558999999999999999975
No 16
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=52.80 E-value=14 Score=29.52 Aligned_cols=37 Identities=27% Similarity=0.515 Sum_probs=26.5
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCC
Q 030738 67 SLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLP 119 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLP 119 (172)
-|+.+.+..=+++|+++| -.|+.|++ + +++|-+|+-|
T Consensus 60 ~L~~e~~~~Il~~Lv~~g---~aew~~~~---~----------~~~~I~Wrt~ 96 (139)
T PF05871_consen 60 RLSPEFIREILDELVQKG---NAEWIDKS---K----------TRCLIYWRTP 96 (139)
T ss_dssp E--HHHHHHHHHHHHCTT---SEEECSTT---S----------CEEEE-SS-H
T ss_pred CCCHHHHHHHHHHHHhcC---CeEEeeCC---C----------CEEEEEeCCH
Confidence 478899999999999999 46666655 2 6889999864
No 17
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=52.17 E-value=18 Score=27.71 Aligned_cols=31 Identities=16% Similarity=0.379 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEEEEeeecCCC
Q 030738 124 NDSSQILNEIQECKKAYPNAYIRCLAFNNQKQ 155 (172)
Q Consensus 124 td~sqVl~Eie~C~k~~P~~YIRliGfDn~rq 155 (172)
.+..+.|+||....+.+ +.-|+||-||..-|
T Consensus 14 ~~l~~fl~ev~~i~~~~-~~~v~vi~~D~~v~ 44 (126)
T PF09967_consen 14 EELRRFLSEVAGILRRF-PAEVHVIQFDAEVQ 44 (126)
T ss_pred HHHHHHHHHHHHHHHhC-CCCEEEEEECCEee
Confidence 35678899999999999 66699999999743
No 18
>PRK00964 tetrahydromethanopterin S-methyltransferase subunit A; Provisional
Probab=48.43 E-value=16 Score=31.97 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=25.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCeE
Q 030738 119 PMFGCNDSSQILNEIQECKKAYPNAYI 145 (172)
Q Consensus 119 Pmfg~td~sqVl~Eie~C~k~~P~~YI 145 (172)
-|+|.+|+..+-+.|++|...-|++|-
T Consensus 134 d~i~~eD~~~I~a~I~ec~~kdpga~~ 160 (225)
T PRK00964 134 DLIDTEDPGAITAKIKECIAKDPGAFD 160 (225)
T ss_pred eeecCCCHHHHHHHHHHHHccCCCCCC
Confidence 799999999999999999999999775
No 19
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=46.26 E-value=24 Score=19.35 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHHHHHHCCCC
Q 030738 124 NDSSQILNEIQECKKAYPNA 143 (172)
Q Consensus 124 td~sqVl~Eie~C~k~~P~~ 143 (172)
.|.++.+..++++.+.||+.
T Consensus 14 g~~~~A~~~~~~~~~~~P~s 33 (33)
T PF13174_consen 14 GDYDEAIEYFQRLIKRYPDS 33 (33)
T ss_dssp CHHHHHHHHHHHHHHHSTTS
T ss_pred cCHHHHHHHHHHHHHHCcCC
Confidence 46788899999999999984
No 20
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=44.85 E-value=26 Score=25.39 Aligned_cols=22 Identities=27% Similarity=0.661 Sum_probs=18.8
Q ss_pred CCCCCChHHHHHHHHHHHhCCCe
Q 030738 64 YLPSLSDDSIAKEIDYMLKKGWI 86 (172)
Q Consensus 64 yLP~ltd~qi~kQV~ylL~qGw~ 86 (172)
-| -|++++|.+-|++|++.|.+
T Consensus 74 ~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 74 QL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HS-TS-HHHHHHHHHHHHHTTSE
T ss_pred Hh-CcCHHHHHHHHHHHHhCCeE
Confidence 45 78999999999999999975
No 21
>KOG2499 consensus Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism]
Probab=44.80 E-value=65 Score=31.47 Aligned_cols=79 Identities=23% Similarity=0.487 Sum_probs=58.6
Q ss_pred CChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccC--Ccceeecc-CCCCCCCCH-----HHHHHH-HHHHHH
Q 030738 68 LSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYD--GRYWTMWK-LPMFGCNDS-----SQILNE-IQECKK 138 (172)
Q Consensus 68 ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd--~ryWtmWk-LPmfg~td~-----sqVl~E-ie~C~k 138 (172)
.|.+|+++-|+|.--.|-++-.||+-.+|.- +=.|||=+ ...|.-|. .|.||-=|| =+||.| +++-..
T Consensus 247 YT~eDv~evV~yarlRGIRVlpEfD~PgHt~---sWg~g~~~fl~p~~~~~~~~~~~gplnP~~n~tydvls~i~~dv~e 323 (542)
T KOG2499|consen 247 YTREDVSEVVEYARLRGIRVLPEFDTPGHTG---SWGPGYPDFLTPCWSSFEVQPPFGPLNPTNNHTYDVLSEIFEDVSE 323 (542)
T ss_pred ecHHHHHHHHHHHHhccceeeecccCCcccc---cccCCCCcccCCcccccccCCCCcCCCCCchhHHHHHHHHHHHHHH
Confidence 3899999999999999999999999988752 23344433 34444444 477776444 378888 688889
Q ss_pred HCCCCeEEEEe
Q 030738 139 AYPNAYIRCLA 149 (172)
Q Consensus 139 ~~P~~YIRliG 149 (172)
.||+.|+.+=|
T Consensus 324 vFp~~~~HlGG 334 (542)
T KOG2499|consen 324 VFPDEFFHLGG 334 (542)
T ss_pred hCcHHHeecCC
Confidence 99999998744
No 22
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=44.72 E-value=25 Score=23.20 Aligned_cols=19 Identities=26% Similarity=0.632 Sum_probs=15.4
Q ss_pred CChHHH---------HHHHHHHHhCCCe
Q 030738 68 LSDDSI---------AKEIDYMLKKGWI 86 (172)
Q Consensus 68 ltd~qi---------~kQV~ylL~qGw~ 86 (172)
||+||| .+|++.|-++||.
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~ 30 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIP 30 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCe
Confidence 677776 4799999999964
No 23
>PTZ00344 pyridoxal kinase; Provisional
Probab=44.25 E-value=89 Score=26.74 Aligned_cols=30 Identities=10% Similarity=0.111 Sum_probs=23.2
Q ss_pred CccccccccCCCCCChHHHHHHHHHHHhCCC
Q 030738 55 NNKKFEALSYLPSLSDDSIAKEIDYMLKKGW 85 (172)
Q Consensus 55 ~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw 85 (172)
|...|+.+ .-|+++++++.+|++.+.+.+.
T Consensus 45 ~~~~~~~~-~g~~i~~~~~~~~l~~l~~~~~ 74 (296)
T PTZ00344 45 NHTGYPVI-KGHRLDLNELITLMDGLRANNL 74 (296)
T ss_pred CCCCCCCc-cCeeCCHHHHHHHHHHHHhcCC
Confidence 34446663 4589999999999999988765
No 24
>PF13663 DUF4148: Domain of unknown function (DUF4148)
Probab=44.14 E-value=19 Score=24.65 Aligned_cols=26 Identities=23% Similarity=0.386 Sum_probs=22.8
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEec
Q 030738 67 SLSDDSIAKEIDYMLKKGWIPCLEFD 92 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~qGw~p~lEfa 92 (172)
+||.+|+..++.-+-++|+.|..|..
T Consensus 18 ~~TRAqV~aEL~~a~~~G~~~~~~~~ 43 (58)
T PF13663_consen 18 PLTRAQVRAELAQAEAAGYLPSGESD 43 (58)
T ss_pred cccHHHHHHHHHHHHHcCCCCCCCCC
Confidence 79999999999999999998775543
No 25
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 YfkB is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=44.08 E-value=64 Score=26.72 Aligned_cols=59 Identities=31% Similarity=0.578 Sum_probs=42.3
Q ss_pred cCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecc-CCCCCCCCHHHHHHHHHHHHHHCC
Q 030738 63 SYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWK-LPMFGCNDSSQILNEIQECKKAYP 141 (172)
Q Consensus 63 SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWk-LPmfg~td~sqVl~Eie~C~k~~P 141 (172)
|=||-||-+|+.+-|..||.- | |..-|-+.+ ||.+-|.+-.+=++=|..- ++-|
T Consensus 8 s~L~vLsL~e~r~aIh~LLd~---------------R---------d~~~WMLFGTLPfy~Cs~~eeD~~Ll~RL-~~~~ 62 (153)
T PF08756_consen 8 SNLEVLSLDEMREAIHRLLDI---------------R---------DPNVWMLFGTLPFYPCSDDEEDLALLKRL-RSEP 62 (153)
T ss_pred hhCccCCHHHHHHHHHHHHhc---------------c---------CCCeeEEecccccccCCCCHHHHHHHHHH-HhCC
Confidence 459999999999999999852 3 356787777 7999999776655444443 3445
Q ss_pred CCeEE
Q 030738 142 NAYIR 146 (172)
Q Consensus 142 ~~YIR 146 (172)
|-=||
T Consensus 63 NVTvR 67 (153)
T PF08756_consen 63 NVTVR 67 (153)
T ss_pred CCeee
Confidence 55554
No 26
>TIGR01111 mtrA N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit A. coenzyme M methyltransferase subunit A in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.
Probab=43.83 E-value=21 Score=31.44 Aligned_cols=26 Identities=23% Similarity=0.563 Sum_probs=24.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCe
Q 030738 119 PMFGCNDSSQILNEIQECKKAYPNAY 144 (172)
Q Consensus 119 Pmfg~td~sqVl~Eie~C~k~~P~~Y 144 (172)
-|+|.+|...+-+.|++|...-|++|
T Consensus 134 dlI~~eD~~~I~~~I~ec~~kdpGa~ 159 (238)
T TIGR01111 134 NLIDVEDMGAITSKVKECASKDPGAF 159 (238)
T ss_pred eeecCCCHHHHHHHHHHHHhcCCCCC
Confidence 79999999999999999999999987
No 27
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=42.93 E-value=62 Score=24.51 Aligned_cols=52 Identities=19% Similarity=0.273 Sum_probs=32.7
Q ss_pred ChHHHHH-HHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHH
Q 030738 69 SDDSIAK-EIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKA 139 (172)
Q Consensus 69 td~qi~k-QV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~ 139 (172)
+++..+. =++||..+|-..-|+-++. .-|.+|-. +..+.++|..|+++.++.
T Consensus 8 ~n~r~AqaF~DYl~sqgI~~~i~~~~~----------------~~~~lwl~---de~~~~~a~~el~~Fl~n 60 (101)
T PF12122_consen 8 NNPRAAQAFIDYLASQGIELQIEPEGQ----------------GQFALWLH---DEEHLEQAEQELEEFLQN 60 (101)
T ss_dssp SSHHHHHHHHHHHHHTT--EEEE-SSS----------------E--EEEES----GGGHHHHHHHHHHHHHS
T ss_pred CCHHHHHHHHHHHHHCCCeEEEEECCC----------------CceEEEEe---CHHHHHHHHHHHHHHHHC
Confidence 4444444 4899999993333554332 22566754 888999999999999864
No 28
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=42.74 E-value=16 Score=34.12 Aligned_cols=64 Identities=16% Similarity=0.196 Sum_probs=45.9
Q ss_pred cCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCcee-------ecCCCCCCccCCcce-eeccCCCCCCCCHHHHHHHHH
Q 030738 63 SYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVH-------RENSKMPGYYDGRYW-TMWKLPMFGCNDSSQILNEIQ 134 (172)
Q Consensus 63 SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~-------R~~~~sp~yyd~ryW-tmWkLPmfg~td~sqVl~Eie 134 (172)
-||.||-|+++.+.+.-+..+. |+....+.. -|-..+|.|||..-| .+||++. ...+.|+.+|.
T Consensus 273 lW~GpL~d~~f~e~~l~~~~~~-----~l~~~~~~~klL~~i~~E~~~~p~fydl~~ias~l~~s~---p~~~~vv~~L~ 344 (380)
T COG1867 273 LWLGPLHDEEFIEEMLEIAEGL-----ELGTKKRALKLLKLIKKELDISPLFYDLHRIASKLGLSA---PPLEEVVEALR 344 (380)
T ss_pred cccCcccCHHHHHHHHHHhhcc-----ccccHHHHHHHHHHHHhhcCCCceEEEHHHHHHHhCCCC---CCHHHHHHHHH
Confidence 4799999999999998888776 555322111 144567999999887 6788865 45667777775
No 29
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=41.33 E-value=49 Score=26.63 Aligned_cols=54 Identities=24% Similarity=0.527 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEE
Q 030738 67 SLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIR 146 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~~YIR 146 (172)
+++.+.+.+|++.++++ ++++ . .|..|++.. +.+..|.+..+++|+ ++
T Consensus 50 ~~~~~~~~~~l~~~~~~-----~~~~----~------------------i~~G~l~~~---~~~~~i~~~~~~~~~--~~ 97 (242)
T cd01169 50 PVPPEFVAAQLDAVLED-----IPVD----A------------------IKIGMLGSA---EIIEAVAEALKDYPD--IP 97 (242)
T ss_pred ECCHHHHHHHHHHHHhC-----CCCC----E------------------EEECCCCCH---HHHHHHHHHHHhCCC--Cc
Confidence 36789999999999883 1111 1 466777743 455556666677776 45
Q ss_pred EEeeecC
Q 030738 147 CLAFNNQ 153 (172)
Q Consensus 147 liGfDn~ 153 (172)
++ ||++
T Consensus 98 vv-~Dpv 103 (242)
T cd01169 98 VV-LDPV 103 (242)
T ss_pred EE-ECCc
Confidence 55 9986
No 30
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=41.00 E-value=90 Score=22.10 Aligned_cols=47 Identities=13% Similarity=0.253 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHC
Q 030738 70 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAY 140 (172)
Q Consensus 70 d~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~ 140 (172)
-++-.++++.|++.||.++. .+ |.-+-+...+.+++..||+.|++..
T Consensus 43 ~~~~~~~l~~l~~~G~ei~~----H~--------------------~~H~~~~~~~~~~~~~ei~~~~~~l 89 (123)
T PF01522_consen 43 VERYPDQLRELAAAGHEIGN----HG--------------------WSHPNLSTLSPEELRREIERSREIL 89 (123)
T ss_dssp HHHHHHHHHHHHHTT-EEEE----E---------------------SSSSCGGGS-HHHHHHHHHHHHHHH
T ss_pred cccccccchhHHHHHHHHHh----cC--------------------CcccccccCCHHHHHHHHHHHHHHH
Confidence 34447899999999976653 11 2222225667889999999998764
No 31
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=38.22 E-value=40 Score=23.30 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=18.6
Q ss_pred ccCCCCCChHHH---HHHHHHHHhCCC
Q 030738 62 LSYLPSLSDDSI---AKEIDYMLKKGW 85 (172)
Q Consensus 62 ~SyLP~ltd~qi---~kQV~ylL~qGw 85 (172)
|.-||.||-+|- .++|+-|.++|-
T Consensus 2 ~~~lp~LtHeeQQ~AvE~Iq~LMaqGm 28 (51)
T PF03701_consen 2 FNDLPSLTHEEQQQAVERIQELMAQGM 28 (51)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHhcc
Confidence 456999998764 567889999983
No 32
>PF13079 DUF3916: Protein of unknown function (DUF3916)
Probab=37.97 E-value=20 Score=29.45 Aligned_cols=46 Identities=22% Similarity=0.598 Sum_probs=27.5
Q ss_pred CCCccCCcceeeccCCCCC-----CCCHHH--------HHHHHHHHHHHCC--CCeEEEEee
Q 030738 104 MPGYYDGRYWTMWKLPMFG-----CNDSSQ--------ILNEIQECKKAYP--NAYIRCLAF 150 (172)
Q Consensus 104 sp~yyd~ryWtmWkLPmfg-----~td~sq--------Vl~Eie~C~k~~P--~~YIRliGf 150 (172)
.+.+|+.+||. ||||.-. ..-+-+ .|...+.-.+.-| .+..||++.
T Consensus 13 p~~~~~~~YW~-~kiPv~~~fi~s~~t~~~vkr~c~Q~LIn~a~~Li~~kp~~~~~yRV~~~ 73 (153)
T PF13079_consen 13 PSTFYNDGYWN-WKIPVSQSFIESKKTPRKVKRLCIQTLINAAEHLIQAKPDDENTYRVVCL 73 (153)
T ss_pred CCcccCCccee-EecccCHHHHhccCCcHHHHHHHHHHHHHHHHHHHhCCcCcCCceEEEEE
Confidence 35578889999 9998642 222222 2333444445556 778887653
No 33
>cd01300 YtcJ_like YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling.
Probab=37.96 E-value=50 Score=29.84 Aligned_cols=51 Identities=22% Similarity=0.412 Sum_probs=39.4
Q ss_pred CCCCccCCccee------eccCCCCCCCCHHHHHHHHHHHHHHCC-CCeEEEEeeecC
Q 030738 103 KMPGYYDGRYWT------MWKLPMFGCNDSSQILNEIQECKKAYP-NAYIRCLAFNNQ 153 (172)
Q Consensus 103 ~sp~yyd~ryWt------mWkLPmfg~td~sqVl~Eie~C~k~~P-~~YIRliGfDn~ 153 (172)
..||+-|.+-.- ...+.+.++.+.++++..|.++.++.| +.+|...|+|+.
T Consensus 36 ~~PGfiD~H~H~~~~~~~~~~~~l~~~~s~~e~~~~l~~~~~~~~~~~wi~~~g~~~~ 93 (479)
T cd01300 36 VLPGFIDSHSHLLLGGLSLLWLDLSGVTSKEEALARIREDAAAAPPGEWILGFGWDES 93 (479)
T ss_pred EccCcccccccchhhcccceeecCCCCCCHHHHHHHHHHHHHhCCCCCeEEECCcCHH
Confidence 467777765432 234567899999999999999988875 679999999976
No 34
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=37.89 E-value=33 Score=24.94 Aligned_cols=29 Identities=14% Similarity=0.330 Sum_probs=23.5
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccC
Q 030738 66 PSLSDDSIAKEIDYMLKKGWIPCLEFDEV 94 (172)
Q Consensus 66 P~ltd~qi~kQV~ylL~qGw~p~lEfad~ 94 (172)
|..+++++.+.++.|.+.|++-|+.+.+.
T Consensus 20 ~~~~~~~~~~il~~L~d~GyI~G~~~~~~ 48 (88)
T PF09639_consen 20 PDITDSYWSDILRMLQDEGYIKGVSVVRY 48 (88)
T ss_dssp HTS-HHHHHHHHHHHHHHTSEE--EESSS
T ss_pred cchhHHHHHHHHHHHHHCCCccceEEEec
Confidence 56778999999999999999999999865
No 35
>COG4063 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A [Coenzyme metabolism]
Probab=37.25 E-value=32 Score=30.02 Aligned_cols=27 Identities=26% Similarity=0.633 Sum_probs=25.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCe
Q 030738 118 LPMFGCNDSSQILNEIQECKKAYPNAY 144 (172)
Q Consensus 118 LPmfg~td~sqVl~Eie~C~k~~P~~Y 144 (172)
+-++++.|++++-+-|++|+..-|++|
T Consensus 132 vdlid~eD~~~I~~~v~ecv~kdpga~ 158 (238)
T COG4063 132 VDLIDVEDPDEITAKVEECVEKDPGAY 158 (238)
T ss_pred ehhcccCCHHHHHHHHHHHHhcCCCcc
Confidence 378999999999999999999999887
No 36
>KOG0792 consensus Protein tyrosine phosphatase PTPMEG, contains FERM domain [Signal transduction mechanisms]
Probab=36.07 E-value=91 Score=33.05 Aligned_cols=76 Identities=24% Similarity=0.516 Sum_probs=52.0
Q ss_pred ccCCcccceeeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccC--CceeecCC---CCCCccCCcce
Q 030738 39 VSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEV--GYVHRENS---KMPGYYDGRYW 113 (172)
Q Consensus 39 ~sng~r~~cm~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~--~~~~R~~~---~sp~yyd~ryW 113 (172)
-.-|||+.|-|-||-++ ++|..| .++.+..+|.+. ++++|+.. .-. +.+-
T Consensus 972 e~EggR~KchqYWPr~~---~~t~~y------------------grf~v~~~~~~~t~~y~tr~m~l~~~~t----~eeR 1026 (1144)
T KOG0792|consen 972 EVEGGRVKCHQYWPRLG---HETMEY------------------GRFQVTCVFEQQTTCYVTREMTLKDLQT----REER 1026 (1144)
T ss_pred hhhcCeeccccccCCCC---ccceec------------------cceEEEEEEecccccEEEEeEEEeeccC----Ccee
Confidence 45789999999999987 777666 788999999853 77777542 222 5677
Q ss_pred eeccC-----CCCCCC-CHHHHHHHHHHHHHH
Q 030738 114 TMWKL-----PMFGCN-DSSQILNEIQECKKA 139 (172)
Q Consensus 114 tmWkL-----Pmfg~t-d~sqVl~Eie~C~k~ 139 (172)
+.|-| |==||- |+...|.=|++-+..
T Consensus 1027 ~V~hLQYtaWPDHg~P~D~~~FL~Fleevrsv 1058 (1144)
T KOG0792|consen 1027 TVWHLQYTAWPDHGVPDDPNDFLDFLEEVRSV 1058 (1144)
T ss_pred eeeeeeecccccCCCCCChHHHHHHHHHHHHH
Confidence 77776 555664 566555545554443
No 37
>PRK10802 peptidoglycan-associated outer membrane lipoprotein; Provisional
Probab=35.93 E-value=55 Score=26.60 Aligned_cols=30 Identities=13% Similarity=0.262 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecCC
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFNNQK 154 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfDn~r 154 (172)
+..++|.+|.+.++.+|+..|+|.|.-..+
T Consensus 83 ~~~~~L~~~a~~L~~~p~~~v~I~GhtD~~ 112 (173)
T PRK10802 83 DFAQMLDAHANFLRSNPSYKVTVEGHADER 112 (173)
T ss_pred HHHHHHHHHHHHHHhCCCceEEEEEecCCC
Confidence 567899999999999999999999985543
No 38
>PRK10985 putative hydrolase; Provisional
Probab=35.75 E-value=2.8e+02 Score=23.64 Aligned_cols=100 Identities=11% Similarity=0.184 Sum_probs=55.5
Q ss_pred ccccCCcccceeeeeccCCccccccccCCCCCChH----HHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcc
Q 030738 37 KTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDD----SIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRY 112 (172)
Q Consensus 37 ~~~sng~r~~cm~vw~p~~~kkfeT~SyLP~ltd~----qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ry 112 (172)
-...+|+.+.+.-.+.|-....-.++-+|+-++.. -+...+++|.++||...+ +.- |.+..+|+-....|
T Consensus 36 ~~~~dg~~~~l~w~~~~~~~~~~p~vll~HG~~g~~~~~~~~~~~~~l~~~G~~v~~-~d~-----rG~g~~~~~~~~~~ 109 (324)
T PRK10985 36 LELPDGDFVDLAWSEDPAQARHKPRLVLFHGLEGSFNSPYAHGLLEAAQKRGWLGVV-MHF-----RGCSGEPNRLHRIY 109 (324)
T ss_pred EECCCCCEEEEecCCCCccCCCCCEEEEeCCCCCCCcCHHHHHHHHHHHHCCCEEEE-EeC-----CCCCCCccCCcceE
Confidence 34567777666422223222334678888888643 355688999999996654 321 43333342111112
Q ss_pred eeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEeee
Q 030738 113 WTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFN 151 (172)
Q Consensus 113 WtmWkLPmfg~td~sqVl~Eie~C~k~~P~~YIRliGfD 151 (172)
.......+..-|+..+++++..=+=++|++
T Consensus 110 ---------~~~~~~D~~~~i~~l~~~~~~~~~~~vG~S 139 (324)
T PRK10985 110 ---------HSGETEDARFFLRWLQREFGHVPTAAVGYS 139 (324)
T ss_pred ---------CCCchHHHHHHHHHHHHhCCCCCEEEEEec
Confidence 112233444445555667887778888886
No 39
>cd08587 PI-PLCXDc_like Catalytic domain of phosphatidylinositol-specific phospholipase C X domain containing and similar proteins. This family corresponds to the catalytic domain present in phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD) which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs mainly found in eukaryota. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs and their bacterial homologs contain a single TIM-barrel type catalytic domain, X domain, which is more closely related to that of bacterial PI-PLCs. Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may be
Probab=35.34 E-value=55 Score=28.01 Aligned_cols=30 Identities=7% Similarity=0.237 Sum_probs=25.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCeEEEE
Q 030738 119 PMFGCNDSSQILNEIQECKKAYPNAYIRCL 148 (172)
Q Consensus 119 Pmfg~td~sqVl~Eie~C~k~~P~~YIRli 148 (172)
.+++.....+||.||.+-+++||++.|=|-
T Consensus 87 ~~~~~~~~~~~l~~i~~fl~~~p~Evvil~ 116 (288)
T cd08587 87 GLYSGEPVDEVLEDVNDFLDEHPKEVVILD 116 (288)
T ss_pred ecccccCHHHHHHHHHHHHHhCCCcEEEEE
Confidence 455558899999999999999999998664
No 40
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=35.22 E-value=42 Score=24.72 Aligned_cols=61 Identities=23% Similarity=0.335 Sum_probs=37.1
Q ss_pred CCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCC-CCCHHHHHHHHHHHHHHCCCC
Q 030738 65 LPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFG-CNDSSQILNEIQECKKAYPNA 143 (172)
Q Consensus 65 LP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg-~td~sqVl~Eie~C~k~~P~~ 143 (172)
.|+|+++||.+.+..| .||...-+ .....|+ ++.+-|. .-+--..++++.+-..-||+-
T Consensus 3 ~~~Ls~~ei~~~l~~l--~gW~~~~~---~~~l~r~---------------f~f~~f~~a~~f~~~Va~~ae~~~HHP~i 62 (97)
T PRK00823 3 AEKLSDEEIAELLPQL--PGWTLVGD---RDAIERT---------------FKFKNFNEAFAFMNRVAEIAEEEDHHPDW 62 (97)
T ss_pred CCCCCHHHHHHHhhcC--CCCeEeCC---cCeEEEE---------------EEeCCHHHHHHHHHHHHHHHHHcCCCCCE
Confidence 4789999998877665 69988311 1123331 2444332 223445677778888888975
Q ss_pred eE
Q 030738 144 YI 145 (172)
Q Consensus 144 YI 145 (172)
-+
T Consensus 63 ~~ 64 (97)
T PRK00823 63 FN 64 (97)
T ss_pred EE
Confidence 43
No 41
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=35.14 E-value=10 Score=24.10 Aligned_cols=23 Identities=17% Similarity=0.450 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEE
Q 030738 124 NDSSQILNEIQECKKAYPNAYIR 146 (172)
Q Consensus 124 td~sqVl~Eie~C~k~~P~~YIR 146 (172)
.+.+.+|.||+..+.++..+|||
T Consensus 3 ~~~D~lLDeId~vLe~NAe~FV~ 25 (33)
T TIGR03687 3 EGVDDLLDEIDGVLESNAEEFVR 25 (33)
T ss_pred chHHHHHHHHHHHHHHhHHHHHH
Confidence 36789999999999999998887
No 42
>cd00741 Lipase Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site.
Probab=34.96 E-value=63 Score=24.35 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHCCCCeEEEEeee
Q 030738 126 SSQILNEIQECKKAYPNAYIRCLAFN 151 (172)
Q Consensus 126 ~sqVl~Eie~C~k~~P~~YIRliGfD 151 (172)
..++..++++++++||+.-|-|+|.-
T Consensus 11 ~~~i~~~~~~~~~~~p~~~i~v~GHS 36 (153)
T cd00741 11 ANLVLPLLKSALAQYPDYKIHVTGHS 36 (153)
T ss_pred HHHHHHHHHHHHHHCCCCeEEEEEcC
Confidence 35788899999999999999999863
No 43
>cd01173 pyridoxal_pyridoxamine_kinase Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and require its precursors in the form of vitamin B6 (pyridoxal, pyridoxine, and pyridoxamine) from their diet. Pyridoxal kinase encoding genes are also found in many other species including yeast and bacteria.
Probab=34.74 E-value=1.2e+02 Score=24.88 Aligned_cols=63 Identities=16% Similarity=0.268 Sum_probs=39.5
Q ss_pred CCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHH-HHHHHHHCCC
Q 030738 64 YLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNE-IQECKKAYPN 142 (172)
Q Consensus 64 yLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~E-ie~C~k~~P~ 142 (172)
.-|+++++++.++++.+...+-. .++ . .+ |..|++..+..+++.+ |+++++..|+
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~--~~~---~------------------~v-~~G~l~~~~~~~~~~~~l~~~~~~~~~ 103 (254)
T cd01173 48 TGFVLSAEELEDLLEGLEALGLL--LEY---D------------------AV-LTGYLGSAEQVEAVAEIVKRLKEKNPN 103 (254)
T ss_pred CCeecCHHHHHHHHHHHHHcCCc--ccC---C------------------EE-EEecCCCHHHHHHHHHHHHHHHHhCCC
Confidence 35889999999999998875410 011 0 11 4556666556566655 6777665566
Q ss_pred CeEEEEeeecC
Q 030738 143 AYIRCLAFNNQ 153 (172)
Q Consensus 143 ~YIRliGfDn~ 153 (172)
++++ +|++
T Consensus 104 --~~vv-~Dpv 111 (254)
T cd01173 104 --LLYV-CDPV 111 (254)
T ss_pred --ceEE-ECCC
Confidence 4555 9986
No 44
>PF05902 4_1_CTD: 4.1 protein C-terminal domain (CTD); InterPro: IPR008379 There is a unique sequence domain at the C terminus of all known 4.1 proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24 kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates [].; GO: 0003779 actin binding, 0005198 structural molecule activity, 0005856 cytoskeleton
Probab=34.44 E-value=45 Score=26.38 Aligned_cols=21 Identities=33% Similarity=0.544 Sum_probs=18.1
Q ss_pred CHHHHHHH-HHHHHHHCCCCeE
Q 030738 125 DSSQILNE-IQECKKAYPNAYI 145 (172)
Q Consensus 125 d~sqVl~E-ie~C~k~~P~~YI 145 (172)
|-+|+|++ |.||+..|||--|
T Consensus 82 DhDqaLa~aI~eAk~q~Pdm~V 103 (114)
T PF05902_consen 82 DHDQALAQAIKEAKEQHPDMSV 103 (114)
T ss_pred chHHHHHHHHHHHHHhCCCceE
Confidence 56899987 9999999999765
No 45
>PRK05114 hypothetical protein; Provisional
Probab=34.42 E-value=48 Score=23.52 Aligned_cols=23 Identities=26% Similarity=0.533 Sum_probs=18.1
Q ss_pred ccCCCCCChHHHH---HHHHHHHhCC
Q 030738 62 LSYLPSLSDDSIA---KEIDYMLKKG 84 (172)
Q Consensus 62 ~SyLP~ltd~qi~---kQV~ylL~qG 84 (172)
|.-||.||-+|-. ++|+.|.++|
T Consensus 2 ~~~lp~LtHeeQQ~AVErIq~LMaqG 27 (59)
T PRK05114 2 FAGLPSLTHEQQQKAVERIQELMAQG 27 (59)
T ss_pred CCCcccCCHHHHHHHHHHHHHHHHcc
Confidence 4569999988654 5788889888
No 46
>PRK15358 pathogenicity island 2 effector protein SseF; Provisional
Probab=34.42 E-value=37 Score=29.60 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=12.5
Q ss_pred CChHHHHHHHHHHHh
Q 030738 68 LSDDSIAKEIDYMLK 82 (172)
Q Consensus 68 ltd~qi~kQV~ylL~ 82 (172)
||.|||.+|-+|.+.
T Consensus 25 ltpeqi~qqrdya~h 39 (239)
T PRK15358 25 LTPEQIRQQRDYAIH 39 (239)
T ss_pred cCHHHHHHHHHHHHH
Confidence 899999999887654
No 47
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=34.22 E-value=43 Score=28.85 Aligned_cols=29 Identities=14% Similarity=0.426 Sum_probs=24.5
Q ss_pred HHCCCCeEEEEeeecCCCeEEEEEEEecCCCCC
Q 030738 138 KAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 170 (172)
Q Consensus 138 k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~~ 170 (172)
..|-+|||=|.|||...+. |+++.|+...
T Consensus 157 ~~Y~GHYVVlcGyd~~~~~----~~yrdPa~~~ 185 (212)
T PF09778_consen 157 PDYQGHYVVLCGYDAATKE----FEYRDPASSD 185 (212)
T ss_pred CCccEEEEEEEeecCCCCe----EEEeCCcccc
Confidence 5799999999999998874 8888887654
No 48
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=33.72 E-value=1.4e+02 Score=24.66 Aligned_cols=79 Identities=16% Similarity=0.162 Sum_probs=45.4
Q ss_pred cccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCC----CCCCcc--CCcceeeccCCCCCCCCHHHHHHHHH
Q 030738 61 ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENS----KMPGYY--DGRYWTMWKLPMFGCNDSSQILNEIQ 134 (172)
Q Consensus 61 T~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~----~sp~yy--d~ryWtmWkLPmfg~td~sqVl~Eie 134 (172)
.+.++++++|+++.++-...-+ |.+...+...+.+ .|-.++ ++.....| -..+.|+.++|.+.-
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~l~~~~~~Iv~Is~~~~~~~~~~~~~~---~~~~~~E~elL~~F~ 86 (208)
T cd05782 17 RLYLLLELDDLEVLEKRFAQRL-------EKSGSDFLPLPFHKVVSISALYRDDDGGFLKVR---TLDGADEKELLEDFF 86 (208)
T ss_pred hhccCCCcchHHHHHHHHHHHH-------HhcCCCCCccccCceEEEEEEEEecCCCeEEEe---ecCCCCHHHHHHHHH
Confidence 3335667999999887766543 2221111111111 122232 23334444 445778999999999
Q ss_pred HHHHHCCCCeEEEEeeec
Q 030738 135 ECKKAYPNAYIRCLAFNN 152 (172)
Q Consensus 135 ~C~k~~P~~YIRliGfDn 152 (172)
+..++|.. .|+||+-
T Consensus 87 ~~i~~~~p---~lv~yNg 101 (208)
T cd05782 87 QLIEKKNP---RLVSFNG 101 (208)
T ss_pred HHHHHhCC---EEEecCC
Confidence 99999732 5888864
No 49
>PRK13697 cytochrome c6; Provisional
Probab=33.55 E-value=48 Score=23.95 Aligned_cols=19 Identities=47% Similarity=0.882 Sum_probs=16.2
Q ss_pred CCChHHHHHHHHHHHh---CCC
Q 030738 67 SLSDDSIAKEIDYMLK---KGW 85 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~---qGw 85 (172)
.|||+||.+=|.||.. +||
T Consensus 89 ~ls~~di~~l~~Yi~~~~~~~~ 110 (111)
T PRK13697 89 RLSPDQIEDVAAYVLEQAEKGW 110 (111)
T ss_pred CCCHHHHHHHHHHHHHHHHccC
Confidence 5799999999999987 466
No 50
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=32.70 E-value=48 Score=23.96 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=18.3
Q ss_pred ccCCCCCChHHHHHHHHHHHhCCCee
Q 030738 62 LSYLPSLSDDSIAKEIDYMLKKGWIP 87 (172)
Q Consensus 62 ~SyLP~ltd~qi~kQV~ylL~qGw~p 87 (172)
.|+||+|+-.++.|. |.+.||.-
T Consensus 1 ms~lp~~~~ke~ik~---Le~~Gf~~ 23 (66)
T COG1724 1 MSKLPRMKAKEVIKA---LEKDGFQL 23 (66)
T ss_pred CCcCCcCCHHHHHHH---HHhCCcEE
Confidence 489999999998765 56789863
No 51
>PF11918 DUF3436: Domain of unknown function (DUF3436); InterPro: IPR024591 This uncharacterised N-terminal domain is associated with the interphotoreceptor retinol-binding protein family. It is about 50 amino acids in length and has two conserved sequence motifs: DPRL and SYEP.
Probab=32.60 E-value=34 Score=23.89 Aligned_cols=17 Identities=18% Similarity=0.440 Sum_probs=14.5
Q ss_pred CCCCChHHHHHHHHHHH
Q 030738 65 LPSLSDDSIAKEIDYML 81 (172)
Q Consensus 65 LP~ltd~qi~kQV~ylL 81 (172)
||+|+.||+..+|+--|
T Consensus 35 ~~~Lt~EqLla~lq~~i 51 (55)
T PF11918_consen 35 LPNLTPEQLLAMLQKSI 51 (55)
T ss_pred CCCcCHHHHHHHHHhhe
Confidence 69999999999987544
No 52
>PF10096 DUF2334: Uncharacterized protein conserved in bacteria (DUF2334); InterPro: IPR018763 This group of proteins has no known function.
Probab=31.55 E-value=1.5e+02 Score=25.08 Aligned_cols=75 Identities=11% Similarity=0.133 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEe
Q 030738 70 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLA 149 (172)
Q Consensus 70 d~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~~YIRliG 149 (172)
+.+..+-++|+.++||.+.|-=-... +. +. ..+.-++.|+.-.-.+.+.+.+-+-|++-++..-..=|+..|
T Consensus 54 ~~~f~~~L~~~~~~Gg~I~lHGYtHq--~~--~~----~sg~~~ef~~~~~~~~~~~~~a~~ri~~gl~~l~~~gi~p~~ 125 (243)
T PF10096_consen 54 NPEFVEYLRYLQARGGEIVLHGYTHQ--YG--NS----VSGDGFEFWDSEFDAGDSEEEAKERIEKGLEILAELGIYPVG 125 (243)
T ss_pred hHHHHHHHHHHHhcCCEEEEEeccee--cC--CC----cccccceeccccccccCCHHHHHHHHHHHHHHHHHCCCcccE
Confidence 77999999999999999997422211 10 00 113334555532222345666666677777776666667777
Q ss_pred eec
Q 030738 150 FNN 152 (172)
Q Consensus 150 fDn 152 (172)
|-+
T Consensus 126 f~a 128 (243)
T PF10096_consen 126 FEA 128 (243)
T ss_pred EEC
Confidence 643
No 53
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=31.51 E-value=39 Score=27.20 Aligned_cols=28 Identities=18% Similarity=0.288 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHCCCCeEEEEeeecCCCeE
Q 030738 129 ILNEIQECKKAYPNAYIRCLAFNNQKQGQ 157 (172)
Q Consensus 129 Vl~Eie~C~k~~P~~YIRliGfDn~rqvq 157 (172)
|++.+.++-..-|+. |.|+|||+....+
T Consensus 195 ~~~~l~~~g~~vP~d-i~vvg~d~~~~~~ 222 (269)
T cd06297 195 ALQEAVELGLTVGED-VRVVGFDDHPFAR 222 (269)
T ss_pred HHHHHHHcCCCCCCc-eEEEEECCchhhc
Confidence 444444433344765 8999999985433
No 54
>PF10104 Brr6_like_C_C: Di-sulfide bridge nucleocytoplasmic transport domain; InterPro: IPR018767 This entry represents the highly conserved C-terminal region of Brr6-like proteins, including Brl1, which are found in fungi. Brr6 from Saccharomyces cerevisiae (Baker's yeast) is an essential nuclear envelope integral membrane protein that is required for mRNA nuclear export []. Brr6 is involved in the nuclear pore complex (NPC) distribution and nuclear envelope morphology. Brr6 interacts with Brl1, which is also involved in mRNA and protein export from the nucleus []. The conserved C-terminal region carries four highly conserved cysteine residues. It is suggested that members of the family interact with each other via di-sulphide bridges to form a complex that is involved in nucleocytoplasmic transport.; GO: 0015031 protein transport, 0051028 mRNA transport, 0016021 integral to membrane
Probab=31.34 E-value=32 Score=27.08 Aligned_cols=16 Identities=44% Similarity=0.864 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHCC
Q 030738 126 SSQILNEIQECKKAYP 141 (172)
Q Consensus 126 ~sqVl~Eie~C~k~~P 141 (172)
..+++.|+++|+++|-
T Consensus 40 ~~~~~~ei~~C~~~Y~ 55 (135)
T PF10104_consen 40 KLELLQEIAQCKKEYE 55 (135)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4588999999999983
No 55
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=31.01 E-value=46 Score=24.66 Aligned_cols=75 Identities=21% Similarity=0.371 Sum_probs=43.7
Q ss_pred cccccc-ccCCCCCChHHHHHHHH---HHHh-CCCeeEEEeccC---CceeecCCCCCCccCCcceeeccCCCCCCCCHH
Q 030738 56 NKKFEA-LSYLPSLSDDSIAKEID---YMLK-KGWIPCLEFDEV---GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS 127 (172)
Q Consensus 56 ~kkfeT-~SyLP~ltd~qi~kQV~---ylL~-qGw~p~lEfad~---~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~s 127 (172)
.++||| |-.=|+|+|+++.+-++ .+|. +|=.+ ++.++- +..|.=. .+-+|.|.-+ -|.+ +.
T Consensus 5 mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i-~~~~~wG~r~LAY~I~----k~~~G~Yv~~----~f~~--~~ 73 (97)
T CHL00123 5 LNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKN-ISVQNRGKRKLSYKIN----KYEDGIYIQM----NYSG--NG 73 (97)
T ss_pred ccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEE-EEEEeecCeeeeEEcC----CCCEEEEEEE----EEEE--CH
Confidence 478999 78889999998876544 4454 56443 333322 2222211 2334555432 2444 45
Q ss_pred HHHHHHHHHHHHCC
Q 030738 128 QILNEIQECKKAYP 141 (172)
Q Consensus 128 qVl~Eie~C~k~~P 141 (172)
++++||+.-.+-..
T Consensus 74 ~~i~eler~lri~e 87 (97)
T CHL00123 74 KLVNSLEKALKLDE 87 (97)
T ss_pred HHHHHHHHHhCCCC
Confidence 89999998775443
No 56
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=30.73 E-value=55 Score=26.84 Aligned_cols=28 Identities=11% Similarity=0.203 Sum_probs=22.2
Q ss_pred ccccccccCCCCCChHHHHHHHHHHHhC
Q 030738 56 NKKFEALSYLPSLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 56 ~kkfeT~SyLP~ltd~qi~kQV~ylL~q 83 (172)
.|.|.=+.-...|||+||..=..||+.|
T Consensus 120 ~k~~~~mP~~~~LsdeEL~avAaYIl~q 147 (159)
T TIGR03045 120 IRSADIFPKMRNLTDEDLRLIAGHILVQ 147 (159)
T ss_pred cCcccccCCcCCCCHHHHHHHHHHHHHh
Confidence 3555555556679999999999999986
No 57
>cd03323 D-glucarate_dehydratase D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilized by coordination to the essential Mg2+ ion.
Probab=30.50 E-value=1.9e+02 Score=26.25 Aligned_cols=65 Identities=12% Similarity=0.205 Sum_probs=43.4
Q ss_pred cccccccCCCCCChHHHHHHHHHHHh-CCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHH
Q 030738 57 KKFEALSYLPSLSDDSIAKEIDYMLK-KGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQE 135 (172)
Q Consensus 57 kkfeT~SyLP~ltd~qi~kQV~ylL~-qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~ 135 (172)
+-++|++|....+.|++.+|++.++. +|++-. |+- +|-.|+.+-++-|++
T Consensus 156 ~~~~~~~~~~~~~~e~~~~~a~~~~~~~Gf~~~----------------------------KiK-vG~~~~~~di~~v~a 206 (395)
T cd03323 156 YPWFRDRWGEALTPEGVVRLARAAIDRYGFKSF----------------------------KLK-GGVLPGEEEIEAVKA 206 (395)
T ss_pred ccccccccccCCCHHHHHHHHHHHHHhcCCcEE----------------------------EEe-cCCCCHHHHHHHHHH
Confidence 34566677666788999999998885 686311 221 133456677778888
Q ss_pred HHHHCCCCeEEEEeeecC
Q 030738 136 CKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 136 C~k~~P~~YIRliGfDn~ 153 (172)
.+++.|+ ++|. +|.+
T Consensus 207 vRea~~~--~~l~-vDaN 221 (395)
T cd03323 207 LAEAFPG--ARLR-LDPN 221 (395)
T ss_pred HHHhCCC--CcEE-EeCC
Confidence 9999975 4444 5765
No 58
>PF05524 PEP-utilisers_N: PEP-utilising enzyme, N-terminal; InterPro: IPR008731 This sequence identifies proteins which are a component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), a major carbohydrate active transport system. The PTS system is found throughout the bacterial kingdom, and is responsible for the coupled phosphorylation and translocation of numerous sugars across the cytoplasmic membrane []. This entry represents the N-terminal domain of enzyme I (EIN) which transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) which in turn phosphorylates a group of membrane-associated proteins, known as enzyme II. The N-terminal domain of EI (EIN) extends from residues 1 to 259 and can be phosphorylated in a fully reversible manner by phosphorylated HPr. EIN, however, cannot be autophosphorylated by PEP [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0008965 phosphoenolpyruvate-protein phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2WQD_A 2XDF_B 2HWG_A 3EZB_A 2L5H_A 3EZA_A 1EZB_A 2EZA_A 1EZA_A 1EZC_A ....
Probab=30.27 E-value=12 Score=28.00 Aligned_cols=23 Identities=22% Similarity=0.517 Sum_probs=17.3
Q ss_pred CChHHHHHHHHHHHhCCCeeEEEec
Q 030738 68 LSDDSIAKEIDYMLKKGWIPCLEFD 92 (172)
Q Consensus 68 ltd~qi~kQV~ylL~qGw~p~lEfa 92 (172)
|.|+++.++|.-+|.+|. +.|++
T Consensus 77 L~D~~l~~~v~~~I~~~~--~Ae~A 99 (123)
T PF05524_consen 77 LEDPELIDEVEELIREGK--NAEYA 99 (123)
T ss_dssp HT-HHHHHHHHHHHHHH----HHHH
T ss_pred hcCHhHHHHHHHHHhccC--CHHHH
Confidence 689999999999999997 66655
No 59
>PLN02749 Uncharacterized protein At1g47420
Probab=29.90 E-value=51 Score=27.70 Aligned_cols=29 Identities=31% Similarity=0.539 Sum_probs=26.0
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhCCC
Q 030738 57 KKFEALSYLPSLSDDSIAKEIDYMLKKGW 85 (172)
Q Consensus 57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw 85 (172)
..+|+.|.||..+|.+|.+-..-|++-.|
T Consensus 4 ~fs~d~~~lP~i~Dp~i~~afkdLma~sW 32 (173)
T PLN02749 4 RFSEDVSHLPEISDPEILKAFKDLMAASW 32 (173)
T ss_pred ccccccccCCCCCCHHHHHHHHHHHhcch
Confidence 35688999999999999999999998877
No 60
>PRK07708 hypothetical protein; Validated
Probab=29.68 E-value=3.3e+02 Score=23.02 Aligned_cols=87 Identities=17% Similarity=0.246 Sum_probs=53.2
Q ss_pred eccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHH
Q 030738 51 WNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQIL 130 (172)
Q Consensus 51 w~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl 130 (172)
|.=...|+.+|.-+--.++-+|...-.+-+-+-|..--|||-|.. +.+|| +
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~--------------~~~~~---------------~ 57 (219)
T PRK07708 7 WTYKTKKGLQTELTSDWMNIEEALQLAEDFEKTGRVKELEFYDEM--------------DTEWS---------------L 57 (219)
T ss_pred EEEEcCCCceeEEEeccccHHHHHHHHHHHhhcCCceeEEEecCC--------------CCEee---------------H
Confidence 444455666664444455566666666777788999999999865 78887 2
Q ss_pred HHHHHHHHH---CCCCeEEEEeeec----CCCeEEEEEEEecCCC
Q 030738 131 NEIQECKKA---YPNAYIRCLAFNN----QKQGQCMSFLIQKPTT 168 (172)
Q Consensus 131 ~Eie~C~k~---~P~~YIRliGfDn----~rqvq~~sfIV~RP~~ 168 (172)
+|+.+-.++ -|+. +.+ =||- ..+.-.++++|..|.+
T Consensus 58 k~~~~~~~~~~~ep~~-~~v-Y~DGs~~~n~g~aG~GvVI~~~~g 100 (219)
T PRK07708 58 KELKKLSKEVEEEPHE-ILV-YFDGGFDKETKLAGLGIVIYYKQG 100 (219)
T ss_pred HHHhhhhhhhccCCCc-EEE-EEeeccCCCCCCcEEEEEEEECCC
Confidence 444444433 3443 222 2554 3455677888876543
No 61
>PRK12799 motB flagellar motor protein MotB; Reviewed
Probab=29.63 E-value=2.5e+02 Score=26.51 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=26.7
Q ss_pred CCCCCC------CHHHHHHHHHHHHHHCCCCeEEEEeeec
Q 030738 119 PMFGCN------DSSQILNEIQECKKAYPNAYIRCLAFNN 152 (172)
Q Consensus 119 Pmfg~t------d~sqVl~Eie~C~k~~P~~YIRliGfDn 152 (172)
+||+.. +..++|.+|..-++.+|+ .|+|.|.=.
T Consensus 158 ~lF~~GSA~L~p~~~~iL~~ia~~L~~~pn-~I~I~GHTD 196 (421)
T PRK12799 158 PMFKMGSAQVEPYMRDILRAIAPILNDIPN-KLSLSGHTD 196 (421)
T ss_pred cccCCCCcccCHHHHHHHHHHHHHHHcCCC-cEEEEEEcC
Confidence 556554 457899999999999999 699999843
No 62
>PHA00422 hypothetical protein
Probab=29.46 E-value=13 Score=27.00 Aligned_cols=21 Identities=29% Similarity=0.729 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHCCCCeEEE
Q 030738 127 SQILNEIQECKKAYPNAYIRC 147 (172)
Q Consensus 127 sqVl~Eie~C~k~~P~~YIRl 147 (172)
=.||++|..|-+.|...|||-
T Consensus 5 L~vL~~ik~~pk~fQSn~vR~ 25 (69)
T PHA00422 5 LKVLAAIKSCPKTFQSNYVRN 25 (69)
T ss_pred HHHHHHHHhCcHHHHHHHHhh
Confidence 479999999999999999984
No 63
>cd08557 PI-PLCc_bacteria_like Catalytic domain of bacterial phosphatidylinositol-specific phospholipase C and similar proteins. This subfamily corresponds to the catalytic domain present in bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and their sequence homologs found in eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Its catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. Eukaryotic homologs in this family are named as phosphatidylinositol-specific phospholipase C X
Probab=28.77 E-value=82 Score=25.79 Aligned_cols=29 Identities=17% Similarity=0.277 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeEEEEeeec
Q 030738 123 CNDSSQILNEIQECKKAYPNAYIRCLAFNN 152 (172)
Q Consensus 123 ~td~sqVl~Eie~C~k~~P~~YIRliGfDn 152 (172)
+....+||.||..-+++||++.|=|. |..
T Consensus 78 ~~~~~~vL~~i~~fl~~~p~E~vil~-~~~ 106 (271)
T cd08557 78 GQTLEDVLNEVKDFLDAHPSEVVILD-LEH 106 (271)
T ss_pred cccHHHHHHHHHHHHHHCCCcEEEEE-EEc
Confidence 58899999999999999999988665 543
No 64
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=28.47 E-value=61 Score=26.42 Aligned_cols=33 Identities=9% Similarity=0.191 Sum_probs=21.6
Q ss_pred HHHHHHHHHCCCCeEEEEeeecCCCeE----EEEEEEecCC
Q 030738 131 NEIQECKKAYPNAYIRCLAFNNQKQGQ----CMSFLIQKPT 167 (172)
Q Consensus 131 ~Eie~C~k~~P~~YIRliGfDn~rqvq----~~sfIV~RP~ 167 (172)
.-+.+|++.- |.|+|||+.-..+ .+..|.+++.
T Consensus 197 gv~~al~~~g----isIvGfD~~~~~~~~~p~lttv~~~~~ 233 (265)
T cd06354 197 GVFQAAKEAG----VYAIGVDSDQYYLAPGVVLTSMVKRVD 233 (265)
T ss_pred HHHHHHHhcC----CeEEEecCcccccCCCcEEEEEeehhH
Confidence 3344454443 9999999976655 5566666664
No 65
>PHA01346 hypothetical protein
Probab=28.44 E-value=48 Score=22.60 Aligned_cols=19 Identities=37% Similarity=0.644 Sum_probs=17.1
Q ss_pred CCCCChHHHHHHHHHHHhC
Q 030738 65 LPSLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 65 LP~ltd~qi~kQV~ylL~q 83 (172)
=|+++.|.|-.+++.||++
T Consensus 29 dpdfsqekihaeldsllrk 47 (53)
T PHA01346 29 DPDFSQEKIHAELDSLLRK 47 (53)
T ss_pred CCCccHHHHHHHHHHHHHH
Confidence 3899999999999999975
No 66
>cd03799 GT1_amsK_like This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor.
Probab=28.11 E-value=83 Score=25.50 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=24.2
Q ss_pred CCCCCChHHHHHHHHHHHhCCCeeEEEec
Q 030738 64 YLPSLSDDSIAKEIDYMLKKGWIPCLEFD 92 (172)
Q Consensus 64 yLP~ltd~qi~kQV~ylL~qGw~p~lEfa 92 (172)
.+|+.++.-+.++++.|.++||.+.+ ++
T Consensus 8 ~~~~~~~~~~~~~~~~L~~~g~~v~v-~~ 35 (355)
T cd03799 8 EFPRLSETFILREILALEAAGHEVEI-FS 35 (355)
T ss_pred CCCCcchHHHHHHHHHHHhCCCeEEE-EE
Confidence 35788999999999999999999987 54
No 67
>PHA02103 hypothetical protein
Probab=27.99 E-value=60 Score=26.02 Aligned_cols=28 Identities=18% Similarity=0.616 Sum_probs=21.3
Q ss_pred ccCCCCCCCCHHHHH----HHHHHHHHHCCCC
Q 030738 116 WKLPMFGCNDSSQIL----NEIQECKKAYPNA 143 (172)
Q Consensus 116 WkLPmfg~td~sqVl----~Eie~C~k~~P~~ 143 (172)
|.+|.++....+.-| -=++.|+.+||+.
T Consensus 37 ~e~pai~~~~~~~ei~rl~~f~~kck~~yp~g 68 (135)
T PHA02103 37 YEIPAIDADRTKAEIVRLITFMDKCKAEYPRG 68 (135)
T ss_pred EeccccccchhhHHHHHHHHHHHHHHhhCCCC
Confidence 889999887655332 3368999999985
No 68
>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=27.79 E-value=55 Score=26.11 Aligned_cols=26 Identities=23% Similarity=0.431 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHCCCCeEEEEeeecCC
Q 030738 128 QILNEIQECKKAYPNAYIRCLAFNNQK 154 (172)
Q Consensus 128 qVl~Eie~C~k~~P~~YIRliGfDn~r 154 (172)
.+++.+.+.-..-|+. |.|+|||+..
T Consensus 185 g~~~~l~~~g~~vp~d-i~vigfd~~~ 210 (265)
T cd01543 185 QLLEACRRAGIAVPEE-VAVLGVDNDE 210 (265)
T ss_pred HHHHHHHHhCCCCCCc-eEEEeeCCch
Confidence 3455555544455665 9999999874
No 69
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=27.74 E-value=87 Score=24.98 Aligned_cols=27 Identities=19% Similarity=0.210 Sum_probs=25.2
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeee
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFN 151 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfD 151 (172)
+..++|.+|.+-++.+|..-|+|.|.=
T Consensus 97 ~~~~~L~~~a~~L~~~p~~~i~V~GHT 123 (190)
T COG2885 97 KAQATLDELAKYLKKNPITRILVEGHT 123 (190)
T ss_pred hHHHHHHHHHHHHHhCCCcEEEEEecC
Confidence 688999999999999999999999973
No 70
>PRK08944 motB flagellar motor protein MotB; Reviewed
Probab=26.92 E-value=3.7e+02 Score=23.89 Aligned_cols=29 Identities=17% Similarity=0.240 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 030738 124 NDSSQILNEIQECKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 124 td~sqVl~Eie~C~k~~P~~YIRliGfDn~ 153 (172)
.+..++|.+|.+.++.+|+ .|+|.|.=..
T Consensus 192 ~~~~~~L~~ia~~L~~~~~-~I~I~GHTD~ 220 (302)
T PRK08944 192 PKFKPVVRKIGELLKDVPG-IITVSGHTDN 220 (302)
T ss_pred HHHHHHHHHHHHHHHhCCC-eEEEEEecCC
Confidence 3567899999999999998 6999998443
No 71
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=26.72 E-value=52 Score=27.35 Aligned_cols=23 Identities=35% Similarity=0.686 Sum_probs=19.2
Q ss_pred ccCCCC-----CChHHHH----HHHHHHHhCC
Q 030738 62 LSYLPS-----LSDDSIA----KEIDYMLKKG 84 (172)
Q Consensus 62 ~SyLP~-----ltd~qi~----kQV~ylL~qG 84 (172)
|-|.|+ ||||||+ .+|+-|+++.
T Consensus 39 LGYYpDGVKRTLTDEQI~IFRHSEI~aL~Rer 70 (172)
T PF12720_consen 39 LGYYPDGVKRTLTDEQIEIFRHSEIQALRRER 70 (172)
T ss_pred cccCCCCCcccccHHHHHHHHHHHHHHHHHHH
Confidence 889997 9999997 5788888763
No 72
>PF00388 PI-PLC-X: Phosphatidylinositol-specific phospholipase C, X domain This entry is for the whole phospholipase C protein; InterPro: IPR000909 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), a eukaryotic intracellular enzyme, plays an important role in signal transduction processes []. It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as the 'X-box' and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains, and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. By profile analysis, we could show that sequences with significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic counterparts.; GO: 0004629 phospholipase C activity, 0006629 lipid metabolic process, 0035556 intracellular signal transduction; PDB: 2FJU_B 2ZKM_X 3V18_A 3V1H_A 3V16_A 3QR1_D 3EA3_A 3EA1_A 2OR2_A 1T6M_B ....
Probab=26.62 E-value=51 Score=25.23 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeE
Q 030738 123 CNDSSQILNEIQECKKAYPNAYI 145 (172)
Q Consensus 123 ~td~sqVl~Eie~C~k~~P~~YI 145 (172)
.....+||.+|.+.+.+||++.|
T Consensus 66 ~~~~~dvL~~i~~fl~~~p~E~V 88 (146)
T PF00388_consen 66 GITFEDVLNDIRDFLFEHPSEPV 88 (146)
T ss_dssp EEEHHHHHHHHHHHTTHSTTS-E
T ss_pred eEeHHHHHHHHHHHHhcCCCeEE
Confidence 35688999999999999999988
No 73
>cd08588 PI-PLCc_At5g67130_like Catalytic domain of Arabidopsis thaliana PI-PLC X domain-containing protein At5g67130 and its uncharacterized homologs. This subfamily corresponds to the catalytic domain present in Arabidopsis thaliana PI-PLC X domain-containing protein At5g67130 and its uncharacterized homologs. Members in this family show high sequence similarity to bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), which participates in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG).
Probab=26.24 E-value=1e+02 Score=26.83 Aligned_cols=47 Identities=17% Similarity=0.242 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCC-----------eEEEEEEEecCCCC
Q 030738 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQ-----------GQCMSFLIQKPTTT 169 (172)
Q Consensus 122 g~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rq-----------vq~~sfIV~RP~~~ 169 (172)
+......+|.||..-+++||++-|=|+ |.+.-. ...+.-++++|...
T Consensus 74 ~~~~~~d~L~~i~~fL~~nP~EvV~l~-l~~~~~~~~~~~~~~~~~~gl~~~~y~p~~~ 131 (270)
T cd08588 74 DGGPLSDVLREVVDFLDANPNEVVTLF-LEDYVSPGPLLRSKLFRVAGLTDLVYVPDAM 131 (270)
T ss_pred CCccHHHHHHHHHHHHHhCCCcEEEEE-EEeCCCcchHHHHHHhhhcCccceEEcCCCC
Confidence 457899999999999999999998877 443321 12456677777543
No 74
>PF09424 YqeY: Yqey-like protein; InterPro: IPR019004 Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; YOR215C is not an essential gene. ; PDB: 1NG6_A.
Probab=25.89 E-value=55 Score=26.03 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=15.2
Q ss_pred cCCC-CCChHHHHHHHHHHHhCC
Q 030738 63 SYLP-SLSDDSIAKEIDYMLKKG 84 (172)
Q Consensus 63 SyLP-~ltd~qi~kQV~ylL~qG 84 (172)
+||| .||+++|.+-|+-.|..-
T Consensus 85 ~yLP~~lseeEi~~~v~~~i~e~ 107 (143)
T PF09424_consen 85 EYLPKQLSEEEIEAIVEEAIAEL 107 (143)
T ss_dssp GGS-----HHHHHHHHHHHHHHT
T ss_pred HhCcCCCCHHHHHHHHHHHHHHh
Confidence 6888 589999999999888753
No 75
>cd01213 tensin Tensin Phosphotyrosine-binding (PTB) domain. Tensin Phosphotyrosine-binding (PTB) domain. Tensin is a a focal adhesion protein, which contains a C-terminal SH2 domain followed by a PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=25.86 E-value=1.3e+02 Score=24.23 Aligned_cols=72 Identities=13% Similarity=0.253 Sum_probs=47.5
Q ss_pred ChHHHHHHHHHHHhCCCee-E--EEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHH-HHHHCCCCe
Q 030738 69 SDDSIAKEIDYMLKKGWIP-C--LEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQE-CKKAYPNAY 144 (172)
Q Consensus 69 td~qi~kQV~ylL~qGw~p-~--lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~-C~k~~P~~Y 144 (172)
+.+.|.|-|+.++++.-.| . .+|. .|. =++++.+.++ +. -++.||-.=
T Consensus 23 g~~av~kAv~~~l~~~~~~~~t~vh~k----------VS~----------qGItLtDn~r--------k~ffrrhypl~~ 74 (138)
T cd01213 23 GNEAIKKAIAQCSGQAPDPQATEVHFK----------VSS----------QGITLTDNTR--------KKFFRRHYKVDS 74 (138)
T ss_pred CcHHHHHHHHHHHhcCCCCCceEEEEE----------EEc----------CCeeeecccc--------ceeehhhCCcCe
Confidence 5778889999999653222 1 1221 000 1455665443 11 345699999
Q ss_pred EEEEeeecCC----------CeEEEEEEEecCCC
Q 030738 145 IRCLAFNNQK----------QGQCMSFLIQKPTT 168 (172)
Q Consensus 145 IRliGfDn~r----------qvq~~sfIV~RP~~ 168 (172)
|-..|+|+.- +.++.+||+.+|.+
T Consensus 75 Vs~ca~dp~n~~~~~~~~~~~kriFgFVar~~~~ 108 (138)
T cd01213 75 VIFCAIDPEERMWENEGAIAKARIFAFVARIPHS 108 (138)
T ss_pred EEEEeeCCccccccccccccccEEEEEEEecCCC
Confidence 9999999973 47899999999977
No 76
>PF02757 YLP: YLP motif; InterPro: IPR004019 The YLP motif is found in one or several copies in various Drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in the human Erbb-2 and ErbB-4 receptor protein-tyrosine kinases (2.7.10.1 from EC) may suggest it could be a substrate for tyrosine kinases. ErbBs (1-4) are single-pass transmembrane proteins that activate a wide variety of signalling pathways, including those involved in proliferation, migration, differentiation, survival, and apoptosis; they are frequently misregulated in cancer []. ErbB-2 is an essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. ErbB-4 specifically binds and is activated by neuregulins, NRG-2, NRG-3, heparin-binding EGF-like growth factor, betacellulin and NTAK [].
Probab=25.76 E-value=32 Score=16.15 Aligned_cols=6 Identities=50% Similarity=1.209 Sum_probs=4.4
Q ss_pred cCCCCC
Q 030738 63 SYLPSL 68 (172)
Q Consensus 63 SyLP~l 68 (172)
-||||.
T Consensus 3 eYLpP~ 8 (9)
T PF02757_consen 3 EYLPPV 8 (9)
T ss_pred cccCCC
Confidence 388886
No 77
>cd08811 CARD_IPS1 Caspase activation and recruitment domain (CARD) found in IPS-1. Caspase activation and recruitment domain (CARD) found in IPS-1 (Interferon beta promoter stimulator protein 1), also known as CARDIF, VISA or MAVS. IPS-1 is an adaptor protein that plays an important role in interferon induction in response to viral infection. It is crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. The CARD of IPS-1 associates with the CARDs of two RNA helicases, RIG-I and MDA5, which bind viral DNA in the cytoplasm during the initial stage of intracellular antiviral response, leading to the induction of type I interferons. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homo
Probab=25.75 E-value=33 Score=25.82 Aligned_cols=14 Identities=43% Similarity=0.738 Sum_probs=11.4
Q ss_pred ccccCCCCCChHHH
Q 030738 60 EALSYLPSLSDDSI 73 (172)
Q Consensus 60 eT~SyLP~ltd~qi 73 (172)
|=+.|||.||+.+=
T Consensus 22 eiLP~LpCLT~~Dq 35 (84)
T cd08811 22 EILPYLPCLTASDQ 35 (84)
T ss_pred HhcCccccCchhhH
Confidence 45889999999863
No 78
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=25.74 E-value=85 Score=25.97 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=17.0
Q ss_pred CCCCChHHHHHHHHHHHhC
Q 030738 65 LPSLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 65 LP~ltd~qi~kQV~ylL~q 83 (172)
...||||||..=..|||.|
T Consensus 130 ~~~LsdeEL~aVAaYIl~q 148 (163)
T CHL00133 130 MRSLTDEDLYAIAGHILLQ 148 (163)
T ss_pred CCCCCHHHHHHHHHHHHhc
Confidence 3679999999999999987
No 79
>cd06293 PBP1_LacI_like_11 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=25.70 E-value=53 Score=26.15 Aligned_cols=26 Identities=8% Similarity=0.314 Sum_probs=16.3
Q ss_pred HHHHHHHHHH---HCCCCeEEEEeeecCCC
Q 030738 129 ILNEIQECKK---AYPNAYIRCLAFNNQKQ 155 (172)
Q Consensus 129 Vl~Eie~C~k---~~P~~YIRliGfDn~rq 155 (172)
.+.-+.+|++ .-|+. |+|+|||+...
T Consensus 189 a~g~~~al~~~g~~vp~d-i~i~g~d~~~~ 217 (269)
T cd06293 189 AIGLLEVLRERGLSIPGD-MSLVGFDDVGP 217 (269)
T ss_pred HHHHHHHHHHcCCCCccc-eEEEeecCchH
Confidence 3344444444 44554 99999999753
No 80
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=25.33 E-value=59 Score=23.04 Aligned_cols=23 Identities=13% Similarity=0.517 Sum_probs=15.9
Q ss_pred HCCCCeEEEEeeecCCCeEEEEEEEecC
Q 030738 139 AYPNAYIRCLAFNNQKQGQCMSFLIQKP 166 (172)
Q Consensus 139 ~~P~~YIRliGfDn~rqvq~~sfIV~RP 166 (172)
...+|||=|+|+|... .|+|+-|
T Consensus 121 ~~~~H~vvi~Gy~~~~-----~~~v~DP 143 (144)
T PF13529_consen 121 TYGGHYVVIIGYDEDG-----YVYVNDP 143 (144)
T ss_dssp -TTEEEEEEEEE-SSE------EEEE-T
T ss_pred CcCCEEEEEEEEeCCC-----EEEEeCC
Confidence 3578999999999965 7777766
No 81
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=25.18 E-value=63 Score=24.08 Aligned_cols=38 Identities=21% Similarity=0.474 Sum_probs=23.7
Q ss_pred ccccccccCCCC---------CChHHHHHHHHH-HHhCCCeeEEEecc
Q 030738 56 NKKFEALSYLPS---------LSDDSIAKEIDY-MLKKGWIPCLEFDE 93 (172)
Q Consensus 56 ~kkfeT~SyLP~---------ltd~qi~kQV~y-lL~qGw~p~lEfad 93 (172)
-..|.||+++|+ |.++.|.+.|+- |-++|++...|-+|
T Consensus 14 f~~ykTy~~~~~~~~~~~~~~~~~~~i~~~v~~~L~~~G~~~~~~~aD 61 (151)
T PF13590_consen 14 FSQYKTYAFVPSSSDPAQSNPLDDQRIQDAVEQELAAKGYRRVPENAD 61 (151)
T ss_pred CCCCCeEEEecCCcCccccCcHHHHHHHHHHHHHHHHCCCeecccCCC
Confidence 346788888887 334455555543 44589999844443
No 82
>cd07185 OmpA_C-like Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA. OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.
Probab=25.04 E-value=1.3e+02 Score=20.80 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfDn~ 153 (172)
+..+.|.+|....+.+|+..|.|+|+-..
T Consensus 16 ~~~~~l~~~~~~l~~~~~~~v~v~g~a~~ 44 (106)
T cd07185 16 EAKPLLDKLAEVLKKNPDAKIRIEGHTDS 44 (106)
T ss_pred HHHHHHHHHHHHHHHCCCceEEEEEEeCC
Confidence 45788899999999999999999998654
No 83
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=25.04 E-value=80 Score=20.40 Aligned_cols=17 Identities=35% Similarity=0.421 Sum_probs=15.5
Q ss_pred CCChHHHHHHHHHHHhC
Q 030738 67 SLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~q 83 (172)
.|||+||..=|.||...
T Consensus 74 ~ls~~e~~~l~ayl~sl 90 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRSL 90 (91)
T ss_dssp TSSHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 79999999999999864
No 84
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=24.78 E-value=75 Score=21.52 Aligned_cols=21 Identities=19% Similarity=0.401 Sum_probs=18.4
Q ss_pred CCCCChHHHHHHHHHHHhCCC
Q 030738 65 LPSLSDDSIAKEIDYMLKKGW 85 (172)
Q Consensus 65 LP~ltd~qi~kQV~ylL~qGw 85 (172)
-|||.++||..=++.+.+--|
T Consensus 50 ~~PL~~~Ev~~i~kSi~k~~~ 70 (71)
T PF08708_consen 50 SPPLPESEVKAIAKSIAKWTW 70 (71)
T ss_pred CCCCCHHHHHHHHHHHHHhcc
Confidence 899999999999998887655
No 85
>TIGR00703 conserved hypothetical protein. The function of this family is unknown. These proteins are from 222 to 233 residues in length, lack hydrophobic stretches, and are found so far only in thermophiles.
Probab=24.73 E-value=63 Score=28.11 Aligned_cols=29 Identities=28% Similarity=0.478 Sum_probs=22.0
Q ss_pred CcceeeccCCCCCCCCHHHHHHHHHHHHHH
Q 030738 110 GRYWTMWKLPMFGCNDSSQILNEIQECKKA 139 (172)
Q Consensus 110 ~ryWtmWkLPmfg~td~sqVl~Eie~C~k~ 139 (172)
+|||--|-||.+..-|. .+-.+++..+..
T Consensus 193 ~rYrl~WllPTiaLFD~-dIa~kvdk~Lg~ 221 (223)
T TIGR00703 193 NRYRLSWLLPTIALFDI-DIANKVDKVLGM 221 (223)
T ss_pred CceEEEEecchhhhhhH-HHHHHHHHHHhh
Confidence 69999999999888876 566666665543
No 86
>PF07864 DUF1651: Protein of unknown function (DUF1651); InterPro: IPR012447 The proteins in this entry have not been characterised.
Probab=24.36 E-value=65 Score=22.65 Aligned_cols=21 Identities=19% Similarity=0.442 Sum_probs=17.6
Q ss_pred ChHHHHHHHHHHHhCCCeeEE
Q 030738 69 SDDSIAKEIDYMLKKGWIPCL 89 (172)
Q Consensus 69 td~qi~kQV~ylL~qGw~p~l 89 (172)
+.++-.+.=..|+++||..|-
T Consensus 51 ~~~~A~e~W~~L~~~GW~~~~ 71 (75)
T PF07864_consen 51 TREEARELWKELQKTGWRRCE 71 (75)
T ss_pred EHHHHHHHHHHHHHcCCEECC
Confidence 667777788999999999883
No 87
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to 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. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=24.10 E-value=64 Score=25.44 Aligned_cols=27 Identities=22% Similarity=0.375 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHCCCCeEEEEeeecCCC
Q 030738 128 QILNEIQECKKAYPNAYIRCLAFNNQKQ 155 (172)
Q Consensus 128 qVl~Eie~C~k~~P~~YIRliGfDn~rq 155 (172)
.|++.+.++...-|+. |.|+|||+...
T Consensus 189 ~~~~~l~~~g~~ip~d-i~v~g~d~~~~ 215 (260)
T cd06286 189 GIITEAKKQGIRVPED-LAIIGFDNQPI 215 (260)
T ss_pred HHHHHHHHcCCCCCcc-eEEEeecCccc
Confidence 5666666655555665 99999998753
No 88
>PF05639 Pup: Pup-like protein; InterPro: IPR008515 This family consists of several short bacterial proteins formely known as (DUF797). It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD) []. Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages []. The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup []). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. ; PDB: 3M91_D 3M9D_I.
Probab=24.03 E-value=22 Score=25.88 Aligned_cols=24 Identities=21% Similarity=0.513 Sum_probs=16.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeEE
Q 030738 123 CNDSSQILNEIQECKKAYPNAYIR 146 (172)
Q Consensus 123 ~td~sqVl~Eie~C~k~~P~~YIR 146 (172)
..+.+.+|.||+..+..+..+|||
T Consensus 38 ~~~vD~lLDeID~vLE~NAeeFVr 61 (69)
T PF05639_consen 38 TDDVDDLLDEIDSVLETNAEEFVR 61 (69)
T ss_dssp HCCHHHHHHHHTTTSSSC------
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHH
Confidence 358899999999999999999998
No 89
>cd02969 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.
Probab=23.89 E-value=1.3e+02 Score=23.19 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCeEEEEeeec
Q 030738 121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNN 152 (172)
Q Consensus 121 fg~td~sqVl~Eie~C~k~~P~~YIRliGfDn 152 (172)
..|..-.+.+.+|++-.++|++.-+++|||..
T Consensus 35 t~Cp~c~~~~~~l~~l~~~~~~~~v~~v~is~ 66 (171)
T cd02969 35 NHCPYVKAIEDRLNRLAKEYGAKGVAVVAINS 66 (171)
T ss_pred CCCccHHHHHHHHHHHHHHHhhCCeEEEEEec
Confidence 35777777788999999999988899999954
No 90
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=23.86 E-value=88 Score=22.01 Aligned_cols=20 Identities=5% Similarity=0.164 Sum_probs=16.9
Q ss_pred CCCCeEEEEeeecCCCeEEE
Q 030738 140 YPNAYIRCLAFNNQKQGQCM 159 (172)
Q Consensus 140 ~P~~YIRliGfDn~rqvq~~ 159 (172)
.-++||+|+.+|+..++..+
T Consensus 16 ~~~~Yl~l~~~~~~G~v~~L 35 (83)
T PF14326_consen 16 NRDGYLYLFYIDADGKVTLL 35 (83)
T ss_pred CCCeEEEEEEECCCCCEEEE
Confidence 45789999999999888765
No 91
>cd08037 LARP_1 La RNA-binding domain of La-related protein 1. This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=23.81 E-value=61 Score=23.50 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=5.7
Q ss_pred HHHHHHHHHH
Q 030738 71 DSIAKEIDYM 80 (172)
Q Consensus 71 ~qi~kQV~yl 80 (172)
+.|.+||+|-
T Consensus 2 ~~I~~QvEyY 11 (73)
T cd08037 2 DYIKRQIEYY 11 (73)
T ss_pred hHHHHHHHHh
Confidence 4566666653
No 92
>PF14740 DUF4471: Domain of unknown function (DUF4471)
Probab=23.43 E-value=65 Score=28.82 Aligned_cols=41 Identities=15% Similarity=0.333 Sum_probs=30.6
Q ss_pred eccCCccccccccCCCCCChHHHHH---HHH-HHHhCCCeeEEEe
Q 030738 51 WNPINNKKFEALSYLPSLSDDSIAK---EID-YMLKKGWIPCLEF 91 (172)
Q Consensus 51 w~p~~~kkfeT~SyLP~ltd~qi~k---QV~-ylL~qGw~p~lEf 91 (172)
+-|=+.=-.||--||-+|..||+.. +|. .+...||+|+.+|
T Consensus 244 ~a~~A~LvvEtaKfmvdLrKEq~~~F~~kv~eLA~~aG~~p~~~~ 288 (289)
T PF14740_consen 244 LAPDAVLVVETAKFMVDLRKEQLQEFVKKVKELAKAAGFKPVTNF 288 (289)
T ss_pred hCCCCEEEEEcchhheeCCHHHHHHHHHHHHHHHHHCCCcccccC
Confidence 3444455679999999999999875 444 4456899999876
No 93
>cd08616 PI-PLCXD1c Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1. This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, members in this group contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to
Probab=23.31 E-value=86 Score=27.39 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=24.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCeEEE
Q 030738 119 PMFGCNDSSQILNEIQECKKAYPNAYIRC 147 (172)
Q Consensus 119 Pmfg~td~sqVl~Eie~C~k~~P~~YIRl 147 (172)
.+|+. ..++||.||.+-+.+||++.|=|
T Consensus 93 g~~~~-~~~~~L~~i~~fl~~~p~Evvil 120 (290)
T cd08616 93 GLYGI-LVKEILEEINDFLTEHPKEVVIL 120 (290)
T ss_pred eccch-hHHHHHHHHHHHHHHCCCcEEEE
Confidence 45666 89999999999999999998854
No 94
>PF06486 DUF1093: Protein of unknown function (DUF1093); InterPro: IPR006542 These are a family of small (about 115 amino acids) uncharacterised proteins with N-terminal signal sequences, found exclusively in Gram-positive organisms. Most genomes that have any members of this family have at least two members.; PDB: 3NPP_B 2K5Q_A 2K5W_A.
Probab=23.21 E-value=1.2e+02 Score=21.15 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=17.8
Q ss_pred eEEEEeeecCCCeEEEEEEEecC
Q 030738 144 YIRCLAFNNQKQGQCMSFLIQKP 166 (172)
Q Consensus 144 YIRliGfDn~rqvq~~sfIV~RP 166 (172)
.=+|.|||..-+.+-|.|-+.+|
T Consensus 29 ~Y~l~~yd~~G~~k~l~f~~~~~ 51 (78)
T PF06486_consen 29 EYTLKGYDEDGKEKTLTFTASKP 51 (78)
T ss_dssp EEEEEEEETT--EEEEEEEESS-
T ss_pred EEEEEEECCCCCEEEEEEEecCC
Confidence 34799999999999999999877
No 95
>CHL00183 petJ cytochrome c553; Provisional
Probab=23.13 E-value=82 Score=22.92 Aligned_cols=18 Identities=33% Similarity=0.580 Sum_probs=15.5
Q ss_pred CCCChHHHHHHHHHHHhC
Q 030738 66 PSLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 66 P~ltd~qi~kQV~ylL~q 83 (172)
+.|||+|+.+=+.||..+
T Consensus 86 ~~Ls~~ei~~i~aYi~~~ 103 (108)
T CHL00183 86 GRLSDEDIEDVANYVLSQ 103 (108)
T ss_pred CCCCHHHHHHHHHHHHHh
Confidence 458999999999999864
No 96
>PF11181 YflT: Heat induced stress protein YflT
Probab=22.97 E-value=79 Score=23.21 Aligned_cols=19 Identities=11% Similarity=0.331 Sum_probs=17.2
Q ss_pred ChHHHHHHHHHHHhCCCee
Q 030738 69 SDDSIAKEIDYMLKKGWIP 87 (172)
Q Consensus 69 td~qi~kQV~ylL~qGw~p 87 (172)
+++|+...|+-|.++||..
T Consensus 8 ~~~E~~~~I~~L~~~Gy~~ 26 (103)
T PF11181_consen 8 NEEEALSAIEELKAQGYSE 26 (103)
T ss_pred CHHHHHHHHHHHHHcCCCc
Confidence 7899999999999999864
No 97
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=22.96 E-value=64 Score=27.18 Aligned_cols=27 Identities=15% Similarity=0.292 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHCCCCeEEEEeeecCCCe
Q 030738 129 ILNEIQECKKAYPNAYIRCLAFNNQKQG 156 (172)
Q Consensus 129 Vl~Eie~C~k~~P~~YIRliGfDn~rqv 156 (172)
|++.+.+.-..-|++ |.|||||+....
T Consensus 252 ~~~al~~~G~~vP~d-isvigfD~~~~~ 278 (346)
T PRK10401 252 ALTALKDNGIAIPLH-LSIIGFDDIPIA 278 (346)
T ss_pred HHHHHHHcCCCCCCc-eEEEEeCCchHH
Confidence 334444333334666 999999997533
No 98
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=22.93 E-value=53 Score=21.69 Aligned_cols=22 Identities=27% Similarity=0.354 Sum_probs=15.3
Q ss_pred CCCCCChHHHHHHHHHHHhCCCeeE
Q 030738 64 YLPSLSDDSIAKEIDYMLKKGWIPC 88 (172)
Q Consensus 64 yLP~ltd~qi~kQV~ylL~qGw~p~ 88 (172)
.+..|||+||.+++ ++.|..|+
T Consensus 2 d~~~LSd~eL~~~L---~~~G~~~g 23 (44)
T smart00540 2 DVDRLSDAELRAEL---KQYGLPPG 23 (44)
T ss_pred chhHcCHHHHHHHH---HHcCCCCC
Confidence 35679999999874 55565443
No 99
>PF00993 MHC_II_alpha: Class II histocompatibility antigen, alpha domain; InterPro: IPR001003 Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response. Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection) []. MHC class II molecules are comprised of two membrane-spanning chains, alpha and beta, of similar size. Both chains consist of two globular domains (N- and C-terminal), and a transmembrane segment to anchor them to the membrane []. A groove in the structure acts as the peptide-binding site. This entry represents the N-terminal domain (also called alpha-1 domain) of the alpha chain. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane, 0042613 MHC class II protein complex; PDB: 3LQZ_A 2ICW_D 1SJH_A 1KG0_A 1D6E_A 1D5M_A 1ZGL_G 1SJE_A 1J8H_A 2IAM_A ....
Probab=22.90 E-value=60 Score=23.65 Aligned_cols=25 Identities=40% Similarity=0.749 Sum_probs=19.5
Q ss_pred eeccCCCCCCC---C-HHHHHHHHHHHHH
Q 030738 114 TMWKLPMFGCN---D-SSQILNEIQECKK 138 (172)
Q Consensus 114 tmWkLPmfg~t---d-~sqVl~Eie~C~k 138 (172)
+.|.||.|.-- + ..+.+++|.-||.
T Consensus 38 ~V~~lP~F~~~~~f~~~~~a~~~~~~ck~ 66 (82)
T PF00993_consen 38 TVWRLPEFADPASFDGYQGALANIAICKH 66 (82)
T ss_dssp EEESSGGHHGTEBE-THHHHHHHHHHHHH
T ss_pred EEeeCCccccccCCccHHHHHHHHHHHHH
Confidence 56999988432 4 8999999999985
No 100
>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.56 E-value=2.5e+02 Score=25.86 Aligned_cols=79 Identities=16% Similarity=0.229 Sum_probs=49.7
Q ss_pred eeeccCCccccccccCCCCCChHHHHHH----HHH--HHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCC
Q 030738 49 KTWNPINNKKFEALSYLPSLSDDSIAKE----IDY--MLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFG 122 (172)
Q Consensus 49 ~vw~p~~~kkfeT~SyLP~ltd~qi~kQ----V~y--lL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg 122 (172)
-+|+.-+.--+.+..|+|.-.-+++.+. |.| ..++||- |.-.+..
T Consensus 299 ~~~~~~~~~~~~~~~f~p~~~~~~~~~~~~~~~~y~~w~~~G~~--l~~~~g~--------------------------- 349 (477)
T PF03354_consen 299 FLFPDDDKYYVKSHFFIPESALDKREKRDKDKIPYREWADEGWC--LTITPGN--------------------------- 349 (477)
T ss_pred EEEEECCeEEEEeeeECCccccchhhhhcccchhHHHHHHcCCe--EeccCCC---------------------------
Confidence 3565545334477899996655543331 333 4566763 4433322
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeE
Q 030738 123 CNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQ 157 (172)
Q Consensus 123 ~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq 157 (172)
..|.++|..-|.+..++| +-.|+.||||+..-.+
T Consensus 350 ~iD~~~v~~~i~~~~~~~-~~~v~~i~yD~~~a~~ 383 (477)
T PF03354_consen 350 VIDYDEVEEWIIELIDKY-GFDVQEIGYDPWNATQ 383 (477)
T ss_pred cccHHHHHHHHHHHHHhc-CcCccEEEEehhhhHH
Confidence 348889999988877774 2379999999985544
No 101
>TIGR00687 pyridox_kin pyridoxal kinase. ThiD and related proteins form an outgroup.
Probab=22.56 E-value=1.8e+02 Score=24.38 Aligned_cols=61 Identities=15% Similarity=0.209 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHH-HHHHHHHCCCCe
Q 030738 66 PSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNE-IQECKKAYPNAY 144 (172)
Q Consensus 66 P~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~E-ie~C~k~~P~~Y 144 (172)
++++++++.++++.+.+.+..- +++ . .+..+++..+..+++.+ |+++++..|+.
T Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~--~~d-------------------~---v~~G~l~~~~~~~~~~~~l~~~~~~~~~~- 106 (286)
T TIGR00687 52 QVLPPDELTELVDGLAAINKLN--QCD-------------------A---VLSGYLGSAEQVAMVVGIVRQVKQANPQA- 106 (286)
T ss_pred eECCHHHHHHHHHHHHhcCccc--cCC-------------------E---EEECCCCCHHHHHHHHHHHHHHHHhCCCC-
Confidence 6788999999999886655421 111 1 25677776666666666 67777777763
Q ss_pred EEEEeeecC
Q 030738 145 IRCLAFNNQ 153 (172)
Q Consensus 145 IRliGfDn~ 153 (172)
.++ +|++
T Consensus 107 -~vv-~Dpv 113 (286)
T TIGR00687 107 -LYV-CDPV 113 (286)
T ss_pred -cEE-ECCe
Confidence 233 7884
No 102
>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=22.39 E-value=84 Score=24.84 Aligned_cols=38 Identities=11% Similarity=0.238 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHCCCCeEEEEeeecCCCeEE----EEEEEecC
Q 030738 128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQC----MSFLIQKP 166 (172)
Q Consensus 128 qVl~Eie~C~k~~P~~YIRliGfDn~rqvq~----~sfIV~RP 166 (172)
.+++.|++....-|+. |.|+|||+..-.+. +..|.|.|
T Consensus 192 ~~~~~l~~~g~~~p~~-i~v~~~d~~~~~~~~~~~~~~i~~~~ 233 (270)
T cd06296 192 GVYEAARERGLRIPED-LSVVGFDDLPEARWVSPPLTTVRQPL 233 (270)
T ss_pred HHHHHHHHhCCCCCCc-eEEEEECChhhhcccCCCceEecCCH
Confidence 3455555554444665 88999998754332 34455444
No 103
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=22.34 E-value=65 Score=26.29 Aligned_cols=28 Identities=11% Similarity=0.261 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHCCCCeEEEEeeecCCCe
Q 030738 128 QILNEIQECKKAYPNAYIRCLAFNNQKQG 156 (172)
Q Consensus 128 qVl~Eie~C~k~~P~~YIRliGfDn~rqv 156 (172)
.|++.+++....-|+. |.|+|||+..-.
T Consensus 227 gv~~al~~~g~~ip~d-i~vvg~D~~~~~ 254 (309)
T PRK11041 227 GALSQAKRMGLRVPQD-LSIIGFDDIDLA 254 (309)
T ss_pred HHHHHHHHcCCCCCcc-eEEEEeCCchhh
Confidence 4555555555555654 799999997433
No 104
>PF06100 Strep_67kDa_ant: Streptococcal 67 kDa myosin-cross-reactive antigen like family ; InterPro: IPR010354 Members of this family are thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis [].
Probab=22.32 E-value=23 Score=34.07 Aligned_cols=39 Identities=15% Similarity=0.474 Sum_probs=27.3
Q ss_pred CCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCCC
Q 030738 103 KMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNA 143 (172)
Q Consensus 103 ~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~~ 143 (172)
=++.+|++.||.||.- ||+-+.-.- ..|...++..|-.+
T Consensus 150 F~~~FF~SnFW~~W~T-~FAFqpWhS-a~E~rRyl~Rf~h~ 188 (500)
T PF06100_consen 150 FSESFFESNFWYMWST-MFAFQPWHS-AVEFRRYLHRFIHE 188 (500)
T ss_pred cchhhhcCchhHhHHH-hhccCcchh-HHHHHHHHHHHHHh
Confidence 4688999999999997 887765432 34666666555443
No 105
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=22.26 E-value=1.3e+02 Score=24.07 Aligned_cols=29 Identities=10% Similarity=0.027 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfDn~ 153 (172)
+..++|.+|-+-++.+|...|+|+|+-..
T Consensus 66 ~~~~~L~~ia~~l~~~~~~~v~I~GhTD~ 94 (160)
T PRK09967 66 ESQQQIQTMAAKLASTGLTHARMDGHTDN 94 (160)
T ss_pred HHHHHHHHHHHHHHhCCCceEEEEEEcCC
Confidence 67789999999999999999999998543
No 106
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel. This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alanine racemase activity.; PDB: 3KW3_A 1B54_A 1CT5_A 2ODO_B 2RJG_A 3B8V_D 2RJH_D 3B8T_D 3B8W_B 3B8U_A ....
Probab=22.23 E-value=3.2e+02 Score=21.64 Aligned_cols=55 Identities=18% Similarity=0.224 Sum_probs=36.2
Q ss_pred ccccCCcccceeeeeccCCccccccc---cCCCCCChHHHHHHHHHHHh---CCCeeEEEeccC
Q 030738 37 KTVSNGSKTRCMKTWNPINNKKFEAL---SYLPSLSDDSIAKEIDYMLK---KGWIPCLEFDEV 94 (172)
Q Consensus 37 ~~~sng~r~~cm~vw~p~~~kkfeT~---SyLP~ltd~qi~kQV~ylL~---qGw~p~lEfad~ 94 (172)
....+| .-..++.|+..++++.+ ..-+-+++.+..+.++-... ..+.+.||.+-.
T Consensus 60 ~lr~~g---~~il~l~~~~~~~~~~~~~~~~~~~v~s~~~~~~l~~~~~~~~~~~~v~l~vdtG 120 (218)
T PF01168_consen 60 ELREAG---APILVLGPIPPEELEELVEYNIIPTVDSLEQLEALSKAAKKQGKPLKVHLKVDTG 120 (218)
T ss_dssp HHHHTT---SEEEEESESTGGGHHHHHHTTEEEEE-SHHHHHHHHHHHHHHTSTEEEEEEBESS
T ss_pred hHHhcC---CceEEEcCCChhhHHHHhhCcEEEEEchhhHHHHHHHHHHHcCCceEEEEeeccc
Confidence 445566 34556666666666443 45667778777788877774 778888888854
No 107
>PRK06925 flagellar motor protein MotS; Reviewed
Probab=22.02 E-value=1.3e+02 Score=25.29 Aligned_cols=29 Identities=17% Similarity=0.293 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecCC
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFNNQK 154 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfDn~r 154 (172)
+..++|.+|.+.++.+|+ .|+|.|+-...
T Consensus 132 ~~~~~L~~ia~~l~~~~~-~I~I~GhTD~~ 160 (230)
T PRK06925 132 QAEPFLHKIGVLLSTIPN-DIKVEGHTDSR 160 (230)
T ss_pred hHHHHHHHHHHHHHhCCC-eEEEEEeCCCC
Confidence 567899999999999999 69999986544
No 108
>PRK10510 putative outer membrane lipoprotein; Provisional
Probab=21.91 E-value=1.3e+02 Score=25.32 Aligned_cols=29 Identities=14% Similarity=0.407 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 030738 125 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 153 (172)
Q Consensus 125 d~sqVl~Eie~C~k~~P~~YIRliGfDn~ 153 (172)
+..+.|.+|.+-++.||+.-|+|.|+=..
T Consensus 126 ~~~~~L~~ia~~L~~~p~~~I~I~GhTD~ 154 (219)
T PRK10510 126 AGANTLTGVAMVLKEYPKTAVNVVGYTDS 154 (219)
T ss_pred HHHHHHHHHHHHHHhCCCceEEEEEecCC
Confidence 45688999999999999999999998543
No 109
>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=21.79 E-value=68 Score=25.48 Aligned_cols=35 Identities=17% Similarity=0.396 Sum_probs=20.1
Q ss_pred CCCCCCH--HHHHHHHHHHHHHCCCCeEEEEeeecCCC
Q 030738 120 MFGCNDS--SQILNEIQECKKAYPNAYIRCLAFNNQKQ 155 (172)
Q Consensus 120 mfg~td~--sqVl~Eie~C~k~~P~~YIRliGfDn~rq 155 (172)
.|.++|. ..|++.++++...=|+. |.|+|||+.-.
T Consensus 181 i~~~~d~~a~g~~~~l~~~g~~ip~d-i~v~g~d~~~~ 217 (268)
T cd06270 181 VFCANDEMAAGAISALREHGISVPQD-VSIIGFDDVLL 217 (268)
T ss_pred EEEcCcHHHHHHHHHHHHcCCCCCCc-eeEEEecCchH
Confidence 3444443 23455555544444554 88999999644
No 110
>PF03230 Antirestrict: Antirestriction protein; InterPro: IPR004914 This family includes various protein that are involved in antirestriction. The ArdB protein efficiently inhibits restriction by members of the three known families of type I systems of Escherichia coli [].; PDB: 2WJ9_B 2KMG_A.
Probab=21.43 E-value=34 Score=25.87 Aligned_cols=12 Identities=50% Similarity=1.392 Sum_probs=6.2
Q ss_pred cCCcceeeccCC
Q 030738 108 YDGRYWTMWKLP 119 (172)
Q Consensus 108 yd~ryWtmWkLP 119 (172)
|+|.||..|+|+
T Consensus 5 Y~Gg~W~f~~ls 16 (94)
T PF03230_consen 5 YDGGYWEFYTLS 16 (94)
T ss_dssp -----EEEEEET
T ss_pred CCCCeeEEEEeC
Confidence 789999999985
No 111
>PRK13618 psbV cytochrome c-550; Provisional
Probab=21.26 E-value=1e+02 Score=25.41 Aligned_cols=27 Identities=15% Similarity=0.265 Sum_probs=21.9
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhC
Q 030738 57 KKFEALSYLPSLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 57 kkfeT~SyLP~ltd~qi~kQV~ylL~q 83 (172)
|++.=|.=+..|||||+..=..|||.|
T Consensus 122 k~~~~mP~~~~Lsd~eL~ava~yll~~ 148 (163)
T PRK13618 122 KSADIFTAMRNLTDKDLEAIAGHILVQ 148 (163)
T ss_pred CccccCCCCCCCCHHHHHHHHHHHHhc
Confidence 555555556689999999999999986
No 112
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=21.19 E-value=86 Score=20.55 Aligned_cols=14 Identities=36% Similarity=0.572 Sum_probs=12.7
Q ss_pred CCChHHHHHHHHHH
Q 030738 67 SLSDDSIAKEIDYM 80 (172)
Q Consensus 67 ~ltd~qi~kQV~yl 80 (172)
.|||+|+.+=++||
T Consensus 54 ~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 54 QLSDEEIEALAAYI 67 (67)
T ss_dssp TSTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHC
Confidence 68999999999987
No 113
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 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 [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=20.84 E-value=37 Score=23.93 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=17.9
Q ss_pred CChHHHHHHHHHHHhCCCeeE
Q 030738 68 LSDDSIAKEIDYMLKKGWIPC 88 (172)
Q Consensus 68 ltd~qi~kQV~ylL~qGw~p~ 88 (172)
++.|||.++|--|-++|+.|+
T Consensus 28 ~~~~eVe~~I~klakkG~tpS 48 (60)
T PF08069_consen 28 YSPEEVEELIVKLAKKGLTPS 48 (60)
T ss_dssp S-HHHHHHHHHHHCCTTHCHH
T ss_pred CCHHHHHHHHHHHHHcCCCHH
Confidence 688999999999999998774
No 114
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=20.77 E-value=66 Score=23.57 Aligned_cols=21 Identities=14% Similarity=0.271 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHCCCCeEEE
Q 030738 127 SQILNEIQECKKAYPNAYIRC 147 (172)
Q Consensus 127 sqVl~Eie~C~k~~P~~YIRl 147 (172)
.++..-|..|..+|||.|=-|
T Consensus 41 ~e~~~~L~kCM~ahsdYY~P~ 61 (76)
T PF07802_consen 41 FEATAALRKCMEAHSDYYEPI 61 (76)
T ss_pred HHHHHHHHHHHHhchhHHHHH
Confidence 467778999999999988433
No 115
>TIGR00166 S6 ribosomal protein S6. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.
Probab=20.76 E-value=2.5e+02 Score=20.16 Aligned_cols=76 Identities=17% Similarity=0.194 Sum_probs=43.1
Q ss_pred ccccc-ccCCCCCChH--HHHHHHHHHH-hCC-CeeEEEeccC-CceeecCCCCCCccCCcceeeccCCCCCCCCHHHHH
Q 030738 57 KKFEA-LSYLPSLSDD--SIAKEIDYML-KKG-WIPCLEFDEV-GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQIL 130 (172)
Q Consensus 57 kkfeT-~SyLP~ltd~--qi~kQV~ylL-~qG-w~p~lEfad~-~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl 130 (172)
++||+ |-.=|.++++ ++.+++..+| ++| =+..+|.=.. ..+|.=. .+.+|.||.| -|.+ +.+.+
T Consensus 1 ~~YE~~~Il~p~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~----k~~~G~Y~~~----~f~~--~~~~i 70 (93)
T TIGR00166 1 RHYEIIFLVRPTLSEEVKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIK----KQLRAHYVLM----NFSG--EAQVI 70 (93)
T ss_pred CceeEEEEECCCCcHHHHHHHHHHHHHHHhCCCEEEEEEeecceecceEcC----CCceEEEEEE----EEEe--CHHHH
Confidence 46888 4455667765 4455565554 454 4455664432 2333211 3456788753 2444 45899
Q ss_pred HHHHHHHHHCCC
Q 030738 131 NEIQECKKAYPN 142 (172)
Q Consensus 131 ~Eie~C~k~~P~ 142 (172)
+||+.-.+-.++
T Consensus 71 ~el~~~lr~~~~ 82 (93)
T TIGR00166 71 KEFERTARINDN 82 (93)
T ss_pred HHHHHHhcCCcC
Confidence 999987776554
No 116
>PRK13617 psbV cytochrome c-550; Provisional
Probab=20.66 E-value=1.2e+02 Score=25.37 Aligned_cols=26 Identities=15% Similarity=0.287 Sum_probs=19.7
Q ss_pred ccccccCCCCCChHHHHHHHHHHHhC
Q 030738 58 KFEALSYLPSLSDDSIAKEIDYMLKK 83 (172)
Q Consensus 58 kfeT~SyLP~ltd~qi~kQV~ylL~q 83 (172)
++..|-=++.|||||+..=..||+.+
T Consensus 130 ~~~imP~~~~LsdeeL~alAayLl~~ 155 (170)
T PRK13617 130 SADLYPAMRDLNDEDLRLMAGYILVA 155 (170)
T ss_pred ccccCcccCCCCHHHHHHHHHHHHhc
Confidence 33334334579999999999999987
No 117
>PRK09041 motB flagellar motor protein MotB; Validated
Probab=20.39 E-value=5.6e+02 Score=23.03 Aligned_cols=74 Identities=14% Similarity=0.162 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhCC-----Ce--eEEEeccCCceeecCCCC--CCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCC
Q 030738 72 SIAKEIDYMLKKG-----WI--PCLEFDEVGYVHRENSKM--PGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPN 142 (172)
Q Consensus 72 qi~kQV~ylL~qG-----w~--p~lEfad~~~~~R~~~~s--p~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~ 142 (172)
++.++|+..|... .. +-++-++++..-+ -... -.+|+....+ | ..+..++|.+|..-++.+|+
T Consensus 121 ~l~~~l~~~l~~~~~~~~l~~~v~v~~~~~Gl~I~-i~d~~~~~lF~~gsa~---L----~~~~~~~L~~ia~~L~~~~~ 192 (317)
T PRK09041 121 KLKQELDQAIESNPKLRQFKPQLLIDLTQEGLRIQ-IVDSQNRPMFATGSAE---V----EPYMRDILREIAPVLNDVPN 192 (317)
T ss_pred HHHHHHHHHHHhhhhHHHhhcceeEEEcCCceEEE-EEcCCCccccCCCCcc---c----CHHHHHHHHHHHHHHHhCCC
Confidence 5677777776653 22 3344444443222 1111 1244444322 2 23567899999999999998
Q ss_pred CeEEEEeeecCC
Q 030738 143 AYIRCLAFNNQK 154 (172)
Q Consensus 143 ~YIRliGfDn~r 154 (172)
.|+|.|.-..+
T Consensus 193 -~I~I~GHTD~~ 203 (317)
T PRK09041 193 -RISLSGHTDAT 203 (317)
T ss_pred -eEEEEEecCCC
Confidence 69999985543
No 118
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=20.33 E-value=2.5e+02 Score=18.01 Aligned_cols=29 Identities=14% Similarity=0.156 Sum_probs=20.0
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEeccCC
Q 030738 67 SLSDDSIAKEIDYMLKKGWIPCLEFDEVG 95 (172)
Q Consensus 67 ~ltd~qi~kQV~ylL~qGw~p~lEfad~~ 95 (172)
.++...+.++|+-|++.||+=-.+-++++
T Consensus 29 ~~~~~~vs~~i~~L~~~glv~~~~~~~d~ 57 (68)
T PF13463_consen 29 GISKSTVSRIIKKLEEKGLVEKERDPHDK 57 (68)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEEEESSCT
T ss_pred CcCHHHHHHHHHHHHHCCCEEecCCCCcC
Confidence 46778999999999999998333333333
No 119
>TIGR01431 adm_rel adenosine deaminase-related growth factor. Members of this family have been described as secreted proteins with growth factor activity and regions of adenosine deaminase homology in insects, mollusks, and vertebrates.
Probab=20.29 E-value=1.3e+02 Score=28.49 Aligned_cols=28 Identities=25% Similarity=0.360 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHHH---HCCCCeEEEEeeecCCC
Q 030738 125 DSSQILNEIQECKK---AYPNAYIRCLAFNNQKQ 155 (172)
Q Consensus 125 d~sqVl~Eie~C~k---~~P~~YIRliGfDn~rq 155 (172)
+++++...++.|.+ .||+ .|+|||=.-|
T Consensus 268 ~~~~~~~~~~~a~~~k~~~p~---~vvGfDL~G~ 298 (479)
T TIGR01431 268 DKEELDNYIKVAMELKEKYPD---FVAGFDLVGQ 298 (479)
T ss_pred CHHHHHHHHHHHHHHHhhCCC---eEEEEeccCC
Confidence 56777777777754 5787 3899997654
No 120
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=20.28 E-value=1.4e+02 Score=18.48 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=13.9
Q ss_pred CChHHHHHHHHHHHhCCCe
Q 030738 68 LSDDSIAKEIDYMLKKGWI 86 (172)
Q Consensus 68 ltd~qi~kQV~ylL~qGw~ 86 (172)
+|...+.+.++.|.++|++
T Consensus 29 is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 29 ISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp S-HHHHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHHHHCcCc
Confidence 5666677778889998875
No 121
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=20.22 E-value=83 Score=26.22 Aligned_cols=35 Identities=9% Similarity=0.078 Sum_probs=21.0
Q ss_pred CCCCCHH--HHHHHHHHHHHHCCC--------CeEEEEeeecCCC
Q 030738 121 FGCNDSS--QILNEIQECKKAYPN--------AYIRCLAFNNQKQ 155 (172)
Q Consensus 121 fg~td~s--qVl~Eie~C~k~~P~--------~YIRliGfDn~rq 155 (172)
|..+|.. .++..+.+.....|. .=|.|||||+..-
T Consensus 248 ~~~nd~~A~g~~~~l~~~g~~vp~~~~~~~~p~di~vigfd~~~~ 292 (342)
T PRK10014 248 VCYNETIAMGAWFGLLRAGRQSGESGVDRYFEQQVALAAFTDVPE 292 (342)
T ss_pred EECCcHHHHHHHHHHHHcCCCCCCccccccccCceEEEEecCchH
Confidence 4444543 345555555555665 1399999999743
No 122
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=20.21 E-value=2.8e+02 Score=20.48 Aligned_cols=76 Identities=16% Similarity=0.229 Sum_probs=42.9
Q ss_pred ccccc-ccCCCCCChHHHHHH---HHHHHh-C-CCeeEEEeccC-CceeecCCCCCCccCCcceeeccCCCCCCCCHHHH
Q 030738 57 KKFEA-LSYLPSLSDDSIAKE---IDYMLK-K-GWIPCLEFDEV-GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQI 129 (172)
Q Consensus 57 kkfeT-~SyLP~ltd~qi~kQ---V~ylL~-q-Gw~p~lEfad~-~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqV 129 (172)
++||+ |-.=|.|+++++.+- +..+|. + |=+..+|.-.. +.+|. --.+.+|.|+.| -|.+ +.+.
T Consensus 2 ~~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~----I~k~~~G~Y~~~----~f~~--~~~~ 71 (108)
T PRK00453 2 RKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYP----INKLRKGHYVLL----NFEA--PPAA 71 (108)
T ss_pred CceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEecccccccceE----cCCCcEEEEEEE----EEEe--CHHH
Confidence 57887 566688898877654 554554 3 44444554322 22332 112345666542 2444 5588
Q ss_pred HHHHHHHHHHCCC
Q 030738 130 LNEIQECKKAYPN 142 (172)
Q Consensus 130 l~Eie~C~k~~P~ 142 (172)
++||+.-.+-.++
T Consensus 72 i~el~~~l~~~~~ 84 (108)
T PRK00453 72 IAELERLFRINED 84 (108)
T ss_pred HHHHHHHhCCCCC
Confidence 8999987665444
No 123
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=20.17 E-value=2.7e+02 Score=18.39 Aligned_cols=33 Identities=12% Similarity=0.231 Sum_probs=22.3
Q ss_pred HHHHHHHHCCCC-eEEEEeee-cCCCeEEEEEEEe
Q 030738 132 EIQECKKAYPNA-YIRCLAFN-NQKQGQCMSFLIQ 164 (172)
Q Consensus 132 Eie~C~k~~P~~-YIRliGfD-n~rqvq~~sfIV~ 164 (172)
|||++...||+- =+=++|.. ...+.+++.|++-
T Consensus 1 EIE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~ 35 (73)
T PF13193_consen 1 EIESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVL 35 (73)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEE
T ss_pred CHHHHHhcCCCccEEEEEEEEcccccccceeEEEe
Confidence 899999999971 11244554 4466778888863
No 124
>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]
Probab=20.05 E-value=41 Score=31.27 Aligned_cols=45 Identities=22% Similarity=0.371 Sum_probs=36.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCCC
Q 030738 120 MFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 170 (172)
Q Consensus 120 mfg~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~~ 170 (172)
.-||.+.-+-|.|+-|.--.||.-||+| |||+-+.+ +.|-|+|..
T Consensus 179 vggckeqieklrevve~pll~perfv~l-gidppkgv-----llygppgtg 223 (435)
T KOG0729|consen 179 VGGCKEQIEKLREVVELPLLHPERFVNL-GIDPPKGV-----LLYGPPGTG 223 (435)
T ss_pred ccchHHHHHHHHHHHhccccCHHHHhhc-CCCCCCce-----EEeCCCCCc
Confidence 4578888888999999999999999996 89999876 456676653
No 125
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=20.02 E-value=45 Score=21.12 Aligned_cols=20 Identities=20% Similarity=0.396 Sum_probs=16.5
Q ss_pred CCCHHHHHHHHHHHHHHCCC
Q 030738 123 CNDSSQILNEIQECKKAYPN 142 (172)
Q Consensus 123 ~td~sqVl~Eie~C~k~~P~ 142 (172)
.-|.++|+.+|.+..+.|||
T Consensus 18 ~~~~~~v~~~v~~Ll~~hpd 37 (47)
T PF02671_consen 18 RISRSEVIEEVSELLRGHPD 37 (47)
T ss_dssp CSCHHHHHHHHHHHTTT-HH
T ss_pred CCCHHHHHHHHHHHHccCHH
Confidence 45788999999999999986
Done!