Query 029245
Match_columns 196
No_of_seqs 195 out of 464
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:50:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029245hhsearch_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 2.1E-89 4.5E-94 569.3 17.2 161 29-191 14-176 (176)
2 CHL00130 rbcS ribulose-1,5-bis 100.0 2.1E-58 4.5E-63 372.0 13.4 102 81-193 3-106 (138)
3 cd03527 RuBisCO_small Ribulose 100.0 2.6E-58 5.5E-63 354.4 13.2 99 81-190 1-99 (99)
4 PF00101 RuBisCO_small: Ribulo 100.0 1.1E-55 2.3E-60 339.5 12.2 99 82-191 1-99 (99)
5 COG4451 RbcS Ribulose bisphosp 100.0 1.1E-47 2.4E-52 305.2 12.4 104 79-193 6-109 (127)
6 cd00307 RuBisCO_small_like Rib 100.0 4.5E-45 9.8E-50 273.8 10.9 82 94-190 1-84 (84)
7 PF12338 RbcS: Ribulose-1,5-bi 99.0 1.9E-10 4.2E-15 78.2 1.5 44 5-59 2-45 (45)
8 PF05036 SPOR: Sporulation rel 72.1 12 0.00026 25.0 5.0 62 93-170 14-75 (76)
9 KOG4068 Uncharacterized conser 63.3 6.9 0.00015 33.6 2.8 38 90-143 64-101 (174)
10 PRK08176 pdxK pyridoxal-pyrido 60.9 24 0.00053 30.7 5.8 67 83-177 60-127 (281)
11 PF01329 Pterin_4a: Pterin 4 a 54.7 7.5 0.00016 29.2 1.4 59 90-169 3-62 (95)
12 PF10557 Cullin_Nedd8: Cullin 54.0 14 0.0003 26.1 2.6 20 91-110 41-60 (68)
13 PF04208 MtrA: Tetrahydrometha 53.4 12 0.00027 32.2 2.7 26 143-168 130-155 (176)
14 TIGR02802 Pal_lipo peptidoglyc 53.0 24 0.00052 25.9 3.9 30 149-178 14-43 (104)
15 PF05871 ESCRT-II: ESCRT-II co 51.4 16 0.00034 29.9 2.9 37 91-143 60-96 (139)
16 PF08410 DUF1737: Domain of un 50.2 18 0.00039 25.6 2.7 24 88-111 8-31 (54)
17 PF08756 YfkB: YfkB-like domai 48.8 65 0.0014 27.3 6.2 59 87-170 8-67 (153)
18 PF09967 DUF2201: VWA-like dom 47.9 23 0.0005 27.7 3.3 32 148-180 14-45 (126)
19 PRK00964 tetrahydromethanopter 44.4 19 0.00041 32.1 2.5 27 143-169 134-160 (225)
20 PF13663 DUF4148: Domain of un 44.0 19 0.00042 25.2 2.1 26 91-116 18-43 (58)
21 KOG2499 Beta-N-acetylhexosamin 43.1 70 0.0015 31.9 6.3 78 93-173 248-334 (542)
22 COG1867 TRM1 N2,N2-dimethylgua 42.1 17 0.00036 34.7 2.0 64 87-158 273-344 (380)
23 PRK10985 putative hydrolase; P 41.5 2.4E+02 0.0052 24.6 9.5 99 62-175 37-139 (324)
24 TIGR01111 mtrA N5-methyltetrah 40.8 24 0.00053 31.7 2.7 26 143-168 134-159 (238)
25 PF13174 TPR_6: Tetratricopept 40.6 33 0.00072 19.2 2.4 20 148-167 14-33 (33)
26 PF13986 DUF4224: Domain of un 39.8 33 0.00071 23.2 2.6 19 92-110 3-30 (47)
27 PF08784 RPA_C: Replication pr 39.1 35 0.00077 25.2 3.0 22 88-110 74-95 (102)
28 cd01300 YtcJ_like YtcJ_like me 37.8 48 0.001 30.6 4.2 51 127-177 36-93 (479)
29 COG1724 Predicted RNA binding 37.4 36 0.00078 25.2 2.7 22 86-110 1-22 (66)
30 PF01522 Polysacc_deac_1: Poly 37.0 1.1E+02 0.0024 22.1 5.3 47 94-164 43-89 (123)
31 PF13079 DUF3916: Protein of u 36.9 21 0.00046 30.0 1.6 46 128-174 13-73 (153)
32 PF12122 DUF3582: Protein of u 36.7 82 0.0018 24.4 4.7 52 93-163 8-60 (101)
33 cd01169 HMPP_kinase 4-amino-5- 36.2 64 0.0014 26.5 4.3 54 91-177 50-103 (242)
34 PRK10802 peptidoglycan-associa 35.4 56 0.0012 27.1 3.9 30 149-178 83-112 (173)
35 PRK07708 hypothetical protein; 35.3 2.2E+02 0.0048 24.6 7.7 87 75-192 7-100 (219)
36 cd08587 PI-PLCXDc_like Catalyt 35.2 54 0.0012 28.7 4.0 30 143-172 87-116 (288)
37 PF03701 UPF0181: Uncharacteri 34.3 49 0.0011 23.4 2.8 24 86-109 2-28 (51)
38 COG4063 MtrA Tetrahydromethano 33.9 39 0.00084 30.2 2.8 27 142-168 132-158 (238)
39 cd00741 Lipase Lipase. Lipase 33.4 68 0.0015 24.7 3.9 26 150-175 11-36 (153)
40 PRK00823 phhB pterin-4-alpha-c 33.2 42 0.00092 25.2 2.6 61 89-169 3-64 (97)
41 KOG0792 Protein tyrosine phosp 33.1 1.1E+02 0.0023 33.2 6.2 79 63-163 972-1058(1144)
42 cd05782 DNA_polB_like1_exo Unc 33.1 1.4E+02 0.0031 25.1 6.0 79 85-176 17-101 (208)
43 TIGR03687 pupylate_cterm ubiqu 32.6 12 0.00026 24.3 -0.4 23 148-170 3-25 (33)
44 PRK05114 hypothetical protein; 31.6 56 0.0012 23.7 2.8 24 86-109 2-28 (59)
45 PF09639 YjcQ: YjcQ protein; 31.3 48 0.001 24.6 2.6 29 90-118 20-48 (88)
46 cd01173 pyridoxal_pyridoxamine 30.4 1.4E+02 0.0031 24.8 5.6 62 89-177 49-111 (254)
47 PF10096 DUF2334: Uncharacteri 30.3 1.6E+02 0.0035 25.5 6.0 75 94-176 54-128 (243)
48 PRK15358 pathogenicity island 30.1 48 0.001 29.6 2.7 15 92-106 25-39 (239)
49 PRK13697 cytochrome c6; Provis 29.9 60 0.0013 23.9 2.9 21 90-110 88-111 (111)
50 PF05902 4_1_CTD: 4.1 protein 29.4 61 0.0013 26.2 3.0 21 149-169 82-103 (114)
51 cd08557 PI-PLCc_bacteria_like 29.1 1.1E+02 0.0023 25.7 4.6 29 147-176 78-106 (271)
52 PHA00422 hypothetical protein 28.5 14 0.00031 27.4 -0.7 21 151-171 5-25 (69)
53 COG2885 OmpA Outer membrane pr 28.4 82 0.0018 25.7 3.7 27 149-175 97-123 (190)
54 PRK12799 motB flagellar motor 28.3 2.6E+02 0.0056 27.0 7.5 27 149-176 170-196 (421)
55 PRK08944 motB flagellar motor 28.2 3.2E+02 0.0069 24.8 7.8 29 148-177 192-220 (302)
56 PF09778 Guanylate_cyc_2: Guan 28.0 62 0.0013 28.5 3.0 29 162-194 157-185 (212)
57 cd03323 D-glucarate_dehydratas 27.9 2.1E+02 0.0046 26.5 6.7 64 82-177 157-221 (395)
58 cd06297 PBP1_LacI_like_12 Liga 27.7 46 0.001 27.4 2.2 36 145-181 184-222 (269)
59 cd03799 GT1_amsK_like This is 27.7 84 0.0018 26.0 3.7 28 88-116 8-35 (355)
60 PF10104 Brr6_like_C_C: Di-sul 27.5 41 0.00088 27.1 1.7 16 150-165 40-55 (135)
61 PTZ00344 pyridoxal kinase; Pro 27.5 1.6E+02 0.0035 25.7 5.6 29 80-109 46-74 (296)
62 cd06354 PBP1_BmpA_PnrA_like Pe 27.4 64 0.0014 26.8 3.0 33 155-191 197-233 (265)
63 PHA01346 hypothetical protein 27.4 51 0.0011 23.0 2.0 18 90-107 30-47 (53)
64 cd08588 PI-PLCc_At5g67130_like 26.7 96 0.0021 27.6 4.1 46 146-192 74-130 (270)
65 cd01213 tensin Tensin Phosphot 26.5 1.2E+02 0.0026 25.0 4.3 32 161-192 67-108 (138)
66 PF11918 DUF3436: Domain of un 25.8 53 0.0011 23.5 1.8 17 89-105 35-51 (55)
67 PF02757 YLP: YLP motif; Inte 25.5 33 0.0007 16.5 0.5 6 87-92 3-8 (9)
68 TIGR03045 PS_II_C550 cytochrom 25.4 77 0.0017 26.6 3.1 28 80-107 120-147 (159)
69 PLN02749 Uncharacterized prote 25.2 69 0.0015 27.5 2.7 29 81-109 4-32 (173)
70 cd01543 PBP1_XylR Ligand-bindi 25.1 59 0.0013 26.5 2.3 26 152-178 185-210 (265)
71 PRK09038 flagellar motor prote 24.7 4.8E+02 0.01 23.2 8.1 28 149-177 147-174 (281)
72 PF01168 Ala_racemase_N: Alani 24.4 2.6E+02 0.0057 22.6 6.0 56 61-119 60-121 (218)
73 KOG1386 Nucleoside phosphatase 24.1 23 0.00049 34.9 -0.4 59 110-172 68-131 (501)
74 cd08037 LARP_1 La RNA-binding 24.0 59 0.0013 24.1 1.9 10 95-104 2-11 (73)
75 PF00388 PI-PLC-X: Phosphatidy 24.0 55 0.0012 25.5 1.9 23 147-169 66-88 (146)
76 cd07185 OmpA_C-like Peptidogly 23.9 1.4E+02 0.0031 21.1 3.9 29 149-177 16-44 (106)
77 cd08616 PI-PLCXD1c Catalytic d 23.2 86 0.0019 28.0 3.1 28 143-171 93-120 (290)
78 cd02969 PRX_like1 Peroxiredoxi 22.9 1.3E+02 0.0029 23.6 3.9 32 145-176 35-66 (171)
79 cd08621 PI-PLCXDc_like_2 Catal 22.8 1.3E+02 0.0028 27.1 4.2 26 147-172 86-111 (300)
80 PF07864 DUF1651: Protein of u 22.6 72 0.0016 22.9 2.1 21 93-113 51-71 (75)
81 PF08708 PriCT_1: Primase C te 22.2 90 0.002 21.6 2.5 21 89-109 50-70 (71)
82 PF06486 DUF1093: Protein of u 22.0 1.3E+02 0.0027 21.5 3.3 23 168-190 29-51 (78)
83 TIGR00703 conserved hypothetic 21.8 75 0.0016 28.2 2.4 28 134-162 193-220 (223)
84 PF14740 DUF4471: Domain of un 21.8 73 0.0016 29.1 2.4 40 76-115 245-288 (289)
85 PHA02103 hypothetical protein 21.7 90 0.0019 25.6 2.7 28 140-167 37-68 (135)
86 PF13590 DUF4136: Domain of un 21.6 79 0.0017 24.1 2.3 38 80-117 14-61 (151)
87 PRK06925 flagellar motor prote 21.5 1.3E+02 0.0028 25.8 3.8 29 149-178 132-160 (230)
88 cd08811 CARD_IPS1 Caspase acti 21.5 41 0.0009 25.8 0.7 14 84-97 22-35 (84)
89 PF13193 AMP-binding_C: AMP-bi 21.4 2.7E+02 0.0058 18.9 4.7 33 156-188 1-35 (73)
90 PRK09967 putative outer membra 21.4 1.4E+02 0.003 24.5 3.8 29 149-177 66-94 (160)
91 PRK10510 putative outer membra 21.3 1.3E+02 0.0029 25.8 3.9 29 149-177 126-154 (219)
92 PF13463 HTH_27: Winged helix 21.0 2.4E+02 0.0052 18.5 4.3 30 90-119 28-57 (68)
93 PF06100 Strep_67kDa_ant: Stre 21.0 26 0.00056 34.5 -0.6 39 127-167 150-188 (500)
94 cd06286 PBP1_CcpB_like Ligand- 20.9 75 0.0016 25.6 2.1 27 152-179 189-215 (260)
95 cd08586 PI-PLCc_BcPLC_like Cat 20.8 2E+02 0.0043 25.6 4.9 34 139-172 64-97 (279)
96 PF03230 Antirestrict: Antires 20.8 35 0.00075 26.4 0.1 12 132-143 5-16 (94)
97 CHL00133 psbV photosystem II c 20.6 1.2E+02 0.0026 25.6 3.3 18 90-107 131-148 (163)
98 PF14326 DUF4384: Domain of un 20.6 1.1E+02 0.0024 22.0 2.7 20 164-183 16-35 (83)
99 CHL00123 rps6 ribosomal protei 20.6 91 0.002 23.6 2.4 75 80-165 5-87 (97)
100 PF09424 YqeY: Yqey-like prote 20.5 79 0.0017 25.7 2.2 22 87-108 85-107 (143)
101 KOG0729 26S proteasome regulat 20.4 39 0.00084 32.1 0.4 45 144-194 179-223 (435)
102 PRK10401 DNA-binding transcrip 20.3 73 0.0016 27.4 2.0 27 153-180 252-278 (346)
103 PF11181 YflT: Heat induced st 20.2 97 0.0021 23.3 2.5 19 93-111 8-26 (103)
104 PF05639 Pup: Pup-like protein 20.1 27 0.00057 26.0 -0.6 23 148-170 39-61 (69)
105 smart00540 LEM in nuclear memb 20.1 66 0.0014 21.7 1.4 22 88-112 2-23 (44)
No 1
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=100.00 E-value=2.1e-89 Score=569.28 Aligned_cols=161 Identities=52% Similarity=1.052 Sum_probs=154.6
Q ss_pred cccCceeeccccCccCccccccceecccCCC-CccccCCcccceeeeeccCCccccccccCCCCCChHHHHHHHHHHHhC
Q 029245 29 IFTAPVAGSGYLGLKPTSKALLPVKDSIAWS-SKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKK 107 (196)
Q Consensus 29 ~~a~~~~vapf~glks~~~~~fp~~~~~~~~-~~~~sng~rv~cm~vw~p~~~kkfET~SyLPpLs~~qI~kQV~ylL~q 107 (196)
..++++||+||+||||+++ ||+++|.+++ ++++||||||+|||||||+|+|||||||||||||||||+|||+|||+|
T Consensus 14 ~~~qas~vapf~gLKs~~~--fp~~~k~~~~~~~~~sng~rv~cmqvw~~~~~kkfETfSYLPpLtdeqI~kQVeYli~~ 91 (176)
T PLN02289 14 SPAQATMVAPFTGLKSSAA--FPVTRKANNDITSIASNGGRVSCMQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRN 91 (176)
T ss_pred ccccccccccccccccccc--CcceeeccccccccccCCceeEEEEeecccCccceeeeecCCCCCHHHHHHHHHHHHhC
Confidence 3457899999999999999 9999997655 778899999999999999999999999999999999999999999999
Q ss_pred CCeeEEEeccC-CceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEE
Q 029245 108 GWIPCLEFDEV-GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFL 186 (196)
Q Consensus 108 Gw~pclEfad~-~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~~P~~YVRLiGfDn~rQvq~~sfI 186 (196)
||+|||||+++ +++||||+++|||||||||+|||||||||||++|||+||+||+|+|||+|||||||||++|+||++||
T Consensus 92 GW~pclEf~~~~~~~~r~~~~s~~yyD~rYWtMWKLPMFg~tD~~~Vl~Ei~eC~kayP~~yIRiigFDn~rqvq~~sFi 171 (176)
T PLN02289 92 KWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFI 171 (176)
T ss_pred CCeeeeeeccCCceeEecCCCCCCcccCceeEEeccccCCCCCHHHHHHHHHHHHHHCCcceEEEEEEECCCCEEEEEEE
Confidence 99999999976 89999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCC
Q 029245 187 IQKPT 191 (196)
Q Consensus 187 V~RP~ 191 (196)
||||.
T Consensus 172 v~rP~ 176 (176)
T PLN02289 172 AYKPP 176 (176)
T ss_pred EecCC
Confidence 99995
No 2
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=100.00 E-value=2.1e-58 Score=372.02 Aligned_cols=102 Identities=34% Similarity=0.784 Sum_probs=98.7
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHH
Q 029245 81 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC 160 (196)
Q Consensus 81 kkfET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC 160 (196)
.||||||||||||||||+|||+|||+|||+|||||++++++ | |+||+|||||||||+|++|||+||+||
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--EEEEEecCCCC
Q 029245 161 KKAYPNAYIRCLAFNNQKQGQC--MSFLIQKPTTT 193 (196)
Q Consensus 161 ~k~~P~~YVRLiGfDn~rQvq~--~sfIV~RP~~~ 193 (196)
+|+|||+|||||||||.+|+|| ++||||||.+.
T Consensus 72 rkayP~~yIRl~gFDn~rq~Q~~~~sFiV~rP~~e 106 (138)
T CHL00130 72 RKQKPNGYIKVNAFDASRGVESCVLSFIVNRPANE 106 (138)
T ss_pred HHHCCCcEEEEEEeeCCCcEEEeEEEEEEeCCCCC
Confidence 9999999999999999999999 99999999764
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=2.6e-58 Score=354.39 Aligned_cols=99 Identities=60% Similarity=1.297 Sum_probs=96.5
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHH
Q 029245 81 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC 160 (196)
Q Consensus 81 kkfET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC 160 (196)
+|||||||||||||+||++||+|||+|||+|||||+|+++ |+++||+|||||||||+|++|||+||++|
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 5899999999999999999999999999999999999884 56999999999999999999999999999
Q ss_pred HHHCCCCeEEEEeeecCCCeEEEEEEEecC
Q 029245 161 KKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 190 (196)
Q Consensus 161 ~k~~P~~YVRLiGfDn~rQvq~~sfIV~RP 190 (196)
+++|||+|||||||||++|+||++||||||
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=1.1e-55 Score=339.46 Aligned_cols=99 Identities=44% Similarity=1.011 Sum_probs=89.7
Q ss_pred ccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHH
Q 029245 82 KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECK 161 (196)
Q Consensus 82 kfET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~ 161 (196)
||||||||||||++||++||+|||+|||+|||||+|++++ | ++||+|||||||||+|++|||+||++|+
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 7999999999999999999999999999999999999865 3 9999999999999999999999999999
Q ss_pred HHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 029245 162 KAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 191 (196)
Q Consensus 162 k~~P~~YVRLiGfDn~rQvq~~sfIV~RP~ 191 (196)
++|||+|||||||||++|+||++||||||.
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=1.1e-47 Score=305.19 Aligned_cols=104 Identities=32% Similarity=0.749 Sum_probs=100.7
Q ss_pred CccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHH
Q 029245 79 NNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQ 158 (196)
Q Consensus 79 ~~kkfET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~Eie 158 (196)
.+..|+||||||+|||+||++||+|||.|||+|++||+|++++ | +.||+|||+||||..++.+||+|||
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 029245 159 ECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTT 193 (196)
Q Consensus 159 eC~k~~P~~YVRLiGfDn~rQvq~~sfIV~RP~~~ 193 (196)
+|+++||++|||||||||++|+|++|||||||++.
T Consensus 75 ~Cr~dhp~eYIRliGfDp~gkrrv~sfIVhRPng~ 109 (127)
T COG4451 75 ACRADHPGEYIRLIGFDPKGKRRVVSFIVHRPNGN 109 (127)
T ss_pred HHHHhCCCCeEEEEEecCCCceEEEEEEEECCCCC
Confidence 99999999999999999999999999999999854
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=4.5e-45 Score=273.77 Aligned_cols=82 Identities=18% Similarity=0.415 Sum_probs=79.9
Q ss_pred hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCC--CCHHHHHHHHHHHHHHCCCCeEEE
Q 029245 94 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGC--NDSSQILNEIQECKKAYPNAYIRC 171 (196)
Q Consensus 94 ~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~--tD~sqVL~EieeC~k~~P~~YVRL 171 (196)
|+||.+||+|||+|||+|||||+|++ |||||||||||+| +|++|||+||++|+++|||+||||
T Consensus 1 d~~i~~QI~yll~qG~~~~iE~~d~~---------------rywt~w~lp~f~~~~~~~~~Vl~el~~c~~~~p~~YVRl 65 (84)
T cd00307 1 SEDVVEQVRQLLAQGYKIGLEHADAR---------------RFRTSSWQSCGPIEGRSEAQVLAALEACLAEHPGEYVRL 65 (84)
T ss_pred CHHHHHHHHHHHHCCCEeEEEECCCC---------------ccHhhhcCCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEE
Confidence 68999999999999999999999974 6999999999999 999999999999999999999999
Q ss_pred EeeecCCCeEEEEEEEecC
Q 029245 172 LAFNNQKQGQCMSFLIQKP 190 (196)
Q Consensus 172 iGfDn~rQvq~~sfIV~RP 190 (196)
|||||++|+||+|||||||
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=98.97 E-value=1.9e-10 Score=78.18 Aligned_cols=44 Identities=23% Similarity=0.213 Sum_probs=33.9
Q ss_pred CceEEecCCCccccccCccccccccccCceeeccccCccCccccccceecccCCC
Q 029245 5 SSLVFNSSGSSDVFNQCPKKMSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWS 59 (196)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~ma~~~~a~~~~vapf~glks~~~~~fp~~~~~~~~ 59 (196)
||+| || ++|+.+. -+..+|++|||||+||||+++ ||++||.+++
T Consensus 2 SSm~--Ss-aavatv~------ra~~aqa~mVAPFtGLKS~a~--fPvtrK~~nd 45 (45)
T PF12338_consen 2 SSMM--SS-AAVATVN------RASPAQASMVAPFTGLKSTAA--FPVTRKSNND 45 (45)
T ss_pred ccch--hh-hHHhhhc------cCCccccceeecccccccccc--CccccccCCC
Confidence 4555 44 6666554 345688999999999999999 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=72.14 E-value=12 Score=25.04 Aligned_cols=62 Identities=19% Similarity=0.312 Sum_probs=33.0
Q ss_pred ChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHHCCCCeEE
Q 029245 93 SDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIR 170 (196)
Q Consensus 93 s~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~~P~~YVR 170 (196)
+.++..+.++.|..+|...-+.....+ +.+|...=.|.=.-.++.+++.+|. ...+++++|+
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 567778889999999877554222221 2232222224444455667777776 6899999986
No 9
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.31 E-value=6.9 Score=33.57 Aligned_cols=38 Identities=26% Similarity=0.444 Sum_probs=31.6
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCC
Q 029245 90 PSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLP 143 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLP 143 (196)
--|+.+-|..-+++|-++|- +|+.|++ | ++||-+|+.|
T Consensus 64 R~Ls~~~i~~Il~~l~k~g~---~e~~Dk~---r----------t~f~I~Wrs~ 101 (174)
T KOG4068|consen 64 RRLSQEFIDEILEELEKKGL---AEPTDKR---R----------TRFFIYWRSL 101 (174)
T ss_pred ccCCHHHHHHHHHHHHHccC---CcccccC---c----------eEEEEEEcCH
Confidence 34677778888899999996 7999988 5 7899999865
No 10
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=60.92 E-value=24 Score=30.65 Aligned_cols=67 Identities=9% Similarity=0.174 Sum_probs=42.2
Q ss_pred cccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHH-HHHHH
Q 029245 83 FEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNE-IQECK 161 (196)
Q Consensus 83 fET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~E-ieeC~ 161 (196)
|+.+-. ++++++.+.+|++-+...+... +|+ . +|..|++..+..+++.+ +++.+
T Consensus 60 y~~~~~-~~~~~~~i~~~l~~~~~~~~l~--~~d-------------------~---i~~G~l~s~~~~~~i~~~l~~~~ 114 (281)
T PRK08176 60 YPTFYG-GAIPDEWFSGYLRALQERDALR--QLR-------------------A---VTTGYMGSASQIKILAEWLTALR 114 (281)
T ss_pred CCCcCC-eeCCHHHHHHHHHHHHhcCccc--cCC-------------------E---EEECCCCCHHHHHHHHHHHHHHH
Confidence 555543 3678999999999988876420 111 1 57788886655555555 54555
Q ss_pred HHCCCCeEEEEeeecC
Q 029245 162 KAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 162 k~~P~~YVRLiGfDn~ 177 (196)
..+|+. ++| +||+
T Consensus 115 ~~~~~~--~vv-~DPv 127 (281)
T PRK08176 115 ADHPDL--LIM-VDPV 127 (281)
T ss_pred HHCCCC--cEE-eCCc
Confidence 455773 445 8997
No 11
>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=54.74 E-value=7.5 Score=29.17 Aligned_cols=59 Identities=22% Similarity=0.405 Sum_probs=32.1
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCC-CHHHHHHHHHHHHHHCCCCe
Q 029245 90 PSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCN-DSSQILNEIQECKKAYPNAY 168 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~t-D~sqVL~EieeC~k~~P~~Y 168 (196)
|+||++||.+.+..| .||...- . +...| +| +.+=|... +--.-++++.+-..-||+-.
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--GRLER-----------TF----KFKDFAEAVEFVNRVAALAEEENHHPDIS 61 (95)
T ss_dssp SB-THHHHHHHHHTS--TTSEEET--S--SEEEE-----------EE----E-SSHHHHHHHHHHHHHHHHHHT---EEE
T ss_pred CCCCHHHHHHhhhcC--cCCEECC--C--CcEEE-----------EE----EeCCHHHHHHHHHHHHHHHHHhCCCCCeE
Confidence 789999999999976 8998763 1 33334 11 33322211 22334556666677788765
Q ss_pred E
Q 029245 169 I 169 (196)
Q Consensus 169 V 169 (196)
+
T Consensus 62 ~ 62 (95)
T PF01329_consen 62 L 62 (95)
T ss_dssp E
T ss_pred e
Confidence 4
No 12
>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=54.04 E-value=14 Score=26.08 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=16.1
Q ss_pred CCChHHHHHHHHHHHhCCCe
Q 029245 91 SLSDDSIAKEIDYMLKKGWI 110 (196)
Q Consensus 91 pLs~~qI~kQV~ylL~qGw~ 110 (196)
+.+..+|.++|++|+.+||.
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 13
>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=53.41 E-value=12 Score=32.19 Aligned_cols=26 Identities=35% Similarity=0.621 Sum_probs=24.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCe
Q 029245 143 PMFGCNDSSQILNEIQECKKAYPNAY 168 (196)
Q Consensus 143 PmFg~tD~sqVL~EieeC~k~~P~~Y 168 (196)
-|+|.+|...+.+.|++|...-|++|
T Consensus 130 d~ig~eD~~~I~~~I~e~~~kdpga~ 155 (176)
T PF04208_consen 130 DMIGEEDPEAIQAKIKECISKDPGAF 155 (176)
T ss_pred eeecCCCHHHHHHHHHHHHhcCCccC
Confidence 79999999999999999999999987
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=52.98 E-value=24 Score=25.89 Aligned_cols=30 Identities=13% Similarity=0.265 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecCC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQK 178 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~r 178 (196)
+..++|.+|.+.++.+|+..|+|.|+-...
T Consensus 14 ~~~~~L~~~a~~l~~~~~~~i~I~Ghtd~~ 43 (104)
T TIGR02802 14 EAQAILDAHAAYLKKNPSVRVTIEGHTDER 43 (104)
T ss_pred HHHHHHHHHHHHHHHCCCcEEEEEEecCCC
Confidence 456799999999999999999999996543
No 15
>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=51.36 E-value=16 Score=29.93 Aligned_cols=37 Identities=27% Similarity=0.515 Sum_probs=26.3
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCC
Q 029245 91 SLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLP 143 (196)
Q Consensus 91 pLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLP 143 (196)
-|+.+.+..=+++|+++| -.|+.+++ + +++|-+|+-|
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 46676655 2 5799999864
No 16
>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=50.17 E-value=18 Score=25.55 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=20.1
Q ss_pred CCCCCChHHHHHHHHHHHhCCCee
Q 029245 88 YLPSLSDDSIAKEIDYMLKKGWIP 111 (196)
Q Consensus 88 yLPpLs~~qI~kQV~ylL~qGw~p 111 (196)
+|=--+++++.+.|...|++||.+
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 17
>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=48.79 E-value=65 Score=27.29 Aligned_cols=59 Identities=31% Similarity=0.575 Sum_probs=43.1
Q ss_pred cCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecC-CCCCCCCCHHHHHHHHHHHHHHCC
Q 029245 87 SYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWK-LPMFGCNDSSQILNEIQECKKAYP 165 (196)
Q Consensus 87 SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWK-LPmFg~tD~sqVL~EieeC~k~~P 165 (196)
|=||-||-+|+.+-|..||.- | |..-|-+.+ ||.|-|.+-.+=++=|.. +++-|
T Consensus 8 s~L~vLsL~e~r~aIh~LLd~---------------R---------d~~~WMLFGTLPfy~Cs~~eeD~~Ll~R-L~~~~ 62 (153)
T PF08756_consen 8 SNLEVLSLDEMREAIHRLLDI---------------R---------DPNVWMLFGTLPFYPCSDDEEDLALLKR-LRSEP 62 (153)
T ss_pred hhCccCCHHHHHHHHHHHHhc---------------c---------CCCeeEEecccccccCCCCHHHHHHHHH-HHhCC
Confidence 458999999999999999852 3 346788888 799999977665544443 44456
Q ss_pred CCeEE
Q 029245 166 NAYIR 170 (196)
Q Consensus 166 ~~YVR 170 (196)
|.=||
T Consensus 63 NVTvR 67 (153)
T PF08756_consen 63 NVTVR 67 (153)
T ss_pred CCeee
Confidence 66555
No 18
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=47.92 E-value=23 Score=27.75 Aligned_cols=32 Identities=16% Similarity=0.368 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCe
Q 029245 148 NDSSQILNEIQECKKAYPNAYIRCLAFNNQKQG 180 (196)
Q Consensus 148 tD~sqVL~EieeC~k~~P~~YVRLiGfDn~rQv 180 (196)
.+..+.|+||....+.+ +.-|+||-||..-|.
T Consensus 14 ~~l~~fl~ev~~i~~~~-~~~v~vi~~D~~v~~ 45 (126)
T PF09967_consen 14 EELRRFLSEVAGILRRF-PAEVHVIQFDAEVQD 45 (126)
T ss_pred HHHHHHHHHHHHHHHhC-CCCEEEEEECCEeee
Confidence 35678899999999999 666999999987443
No 19
>PRK00964 tetrahydromethanopterin S-methyltransferase subunit A; Provisional
Probab=44.41 E-value=19 Score=32.10 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=25.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCeE
Q 029245 143 PMFGCNDSSQILNEIQECKKAYPNAYI 169 (196)
Q Consensus 143 PmFg~tD~sqVL~EieeC~k~~P~~YV 169 (196)
-|+|.+|...+-+.|++|...-|++|-
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 20
>PF13663 DUF4148: Domain of unknown function (DUF4148)
Probab=44.02 E-value=19 Score=25.20 Aligned_cols=26 Identities=23% Similarity=0.386 Sum_probs=23.0
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEec
Q 029245 91 SLSDDSIAKEIDYMLKKGWIPCLEFD 116 (196)
Q Consensus 91 pLs~~qI~kQV~ylL~qGw~pclEfa 116 (196)
+||++|+..|+.-+-+.|+.|..|..
T Consensus 18 ~~TRAqV~aEL~~a~~~G~~~~~~~~ 43 (58)
T PF13663_consen 18 PLTRAQVRAELAQAEAAGYLPSGESD 43 (58)
T ss_pred cccHHHHHHHHHHHHHcCCCCCCCCC
Confidence 79999999999999999998875544
No 21
>KOG2499 consensus Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism]
Probab=43.06 E-value=70 Score=31.91 Aligned_cols=78 Identities=23% Similarity=0.493 Sum_probs=58.3
Q ss_pred ChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccC--CcceeecC-CCCCCCCCH-----HHHHHH-HHHHHHH
Q 029245 93 SDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYD--GRYWTMWK-LPMFGCNDS-----SQILNE-IQECKKA 163 (196)
Q Consensus 93 s~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd--~rYWtMWK-LPmFg~tD~-----sqVL~E-ieeC~k~ 163 (196)
|.+++++-|+|.--.|-++-.||+..+|.- +=.|||=+ ...|.-|. .|.||--|+ =+||.| +++-...
T Consensus 248 T~eDv~evV~yarlRGIRVlpEfD~PgHt~---sWg~g~~~fl~p~~~~~~~~~~~gplnP~~n~tydvls~i~~dv~ev 324 (542)
T KOG2499|consen 248 TREDVSEVVEYARLRGIRVLPEFDTPGHTG---SWGPGYPDFLTPCWSSFEVQPPFGPLNPTNNHTYDVLSEIFEDVSEV 324 (542)
T ss_pred cHHHHHHHHHHHHhccceeeecccCCcccc---cccCCCCcccCCcccccccCCCCcCCCCCchhHHHHHHHHHHHHHHh
Confidence 899999999999999999999999988752 23344433 34444444 477776444 378888 6888899
Q ss_pred CCCCeEEEEe
Q 029245 164 YPNAYIRCLA 173 (196)
Q Consensus 164 ~P~~YVRLiG 173 (196)
||++|+.|=|
T Consensus 325 Fp~~~~HlGG 334 (542)
T KOG2499|consen 325 FPDEFFHLGG 334 (542)
T ss_pred CcHHHeecCC
Confidence 9999988744
No 22
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=42.13 E-value=17 Score=34.67 Aligned_cols=64 Identities=16% Similarity=0.196 Sum_probs=46.0
Q ss_pred cCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCcee-------ecCCCCCCccCCcce-eecCCCCCCCCCHHHHHHHHH
Q 029245 87 SYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVH-------RENSKMPGYYDGRYW-TMWKLPMFGCNDSSQILNEIQ 158 (196)
Q Consensus 87 SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~-------R~~~~sp~yyd~rYW-tMWKLPmFg~tD~sqVL~Eie 158 (196)
-||.||-|+++.+++.-+..+. |+....+.. -|-..+|.|||..=| .+||++. ...+.|+.+|.
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 144566999999887 6788866 45667777775
No 23
>PRK10985 putative hydrolase; Provisional
Probab=41.46 E-value=2.4e+02 Score=24.56 Aligned_cols=99 Identities=11% Similarity=0.208 Sum_probs=55.1
Q ss_pred cccCCcccceeeeeccCCccccccccCCCCCChH----HHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcce
Q 029245 62 TVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDD----SIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYW 137 (196)
Q Consensus 62 ~~sng~rv~cm~vw~p~~~kkfET~SyLPpLs~~----qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYW 137 (196)
...+|+.+.+.-.+.|-....-.++=+|+-++.. -+...+++|.++||.+.+ ++ +|.+..+|+-....|.
T Consensus 37 ~~~dg~~~~l~w~~~~~~~~~~p~vll~HG~~g~~~~~~~~~~~~~l~~~G~~v~~-~d-----~rG~g~~~~~~~~~~~ 110 (324)
T PRK10985 37 ELPDGDFVDLAWSEDPAQARHKPRLVLFHGLEGSFNSPYAHGLLEAAQKRGWLGVV-MH-----FRGCSGEPNRLHRIYH 110 (324)
T ss_pred ECCCCCEEEEecCCCCccCCCCCEEEEeCCCCCCCcCHHHHHHHHHHHHCCCEEEE-Ee-----CCCCCCCccCCcceEC
Confidence 4567777665422223222334578888888642 355688999999996654 32 2444444422111221
Q ss_pred eecCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEeee
Q 029245 138 TMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFN 175 (196)
Q Consensus 138 tMWKLPmFg~tD~sqVL~EieeC~k~~P~~YVRLiGfD 175 (196)
.....++..-|+..++++|..=+=++|+.
T Consensus 111 ---------~~~~~D~~~~i~~l~~~~~~~~~~~vG~S 139 (324)
T PRK10985 111 ---------SGETEDARFFLRWLQREFGHVPTAAVGYS 139 (324)
T ss_pred ---------CCchHHHHHHHHHHHHhCCCCCEEEEEec
Confidence 11233444444555667887778888886
No 24
>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=40.79 E-value=24 Score=31.69 Aligned_cols=26 Identities=23% Similarity=0.563 Sum_probs=24.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCe
Q 029245 143 PMFGCNDSSQILNEIQECKKAYPNAY 168 (196)
Q Consensus 143 PmFg~tD~sqVL~EieeC~k~~P~~Y 168 (196)
-|+|.+|...+-+.|++|...-|++|
T Consensus 134 dlI~~eD~~~I~~~I~ec~~kdpGa~ 159 (238)
T TIGR01111 134 NLIDVEDMGAITSKVKECASKDPGAF 159 (238)
T ss_pred eeecCCCHHHHHHHHHHHHhcCCCCC
Confidence 79999999999999999999999987
No 25
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=40.61 E-value=33 Score=19.20 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHHHHHHCCCC
Q 029245 148 NDSSQILNEIQECKKAYPNA 167 (196)
Q Consensus 148 tD~sqVL~EieeC~k~~P~~ 167 (196)
.|..+.+..++++++.||+.
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 26
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=39.75 E-value=33 Score=23.16 Aligned_cols=19 Identities=26% Similarity=0.632 Sum_probs=15.3
Q ss_pred CChHHH---------HHHHHHHHhCCCe
Q 029245 92 LSDDSI---------AKEIDYMLKKGWI 110 (196)
Q Consensus 92 Ls~~qI---------~kQV~ylL~qGw~ 110 (196)
||+||| .+|++.|-++||.
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 27
>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=39.09 E-value=35 Score=25.23 Aligned_cols=22 Identities=27% Similarity=0.661 Sum_probs=18.7
Q ss_pred CCCCCChHHHHHHHHHHHhCCCe
Q 029245 88 YLPSLSDDSIAKEIDYMLKKGWI 110 (196)
Q Consensus 88 yLPpLs~~qI~kQV~ylL~qGw~ 110 (196)
-| -|++++|.+-|++|++.|++
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 35 78999999999999999975
No 28
>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=37.77 E-value=48 Score=30.58 Aligned_cols=51 Identities=22% Similarity=0.412 Sum_probs=39.9
Q ss_pred CCCCccCCccee------ecCCCCCCCCCHHHHHHHHHHHHHHCC-CCeEEEEeeecC
Q 029245 127 KMPGYYDGRYWT------MWKLPMFGCNDSSQILNEIQECKKAYP-NAYIRCLAFNNQ 177 (196)
Q Consensus 127 ~sp~yyd~rYWt------MWKLPmFg~tD~sqVL~EieeC~k~~P-~~YVRLiGfDn~ 177 (196)
..||+-|.+-.- ...+.+.++.+.++++..|.++.++.| +.+|...|+|+.
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 468887775432 234567899999999999999988875 689999999976
No 29
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=37.40 E-value=36 Score=25.17 Aligned_cols=22 Identities=27% Similarity=0.533 Sum_probs=18.3
Q ss_pred ccCCCCCChHHHHHHHHHHHhCCCe
Q 029245 86 LSYLPSLSDDSIAKEIDYMLKKGWI 110 (196)
Q Consensus 86 ~SyLPpLs~~qI~kQV~ylL~qGw~ 110 (196)
+|+||+|+..++.|. |.+.||.
T Consensus 1 ms~lp~~~~ke~ik~---Le~~Gf~ 22 (66)
T COG1724 1 MSKLPRMKAKEVIKA---LEKDGFQ 22 (66)
T ss_pred CCcCCcCCHHHHHHH---HHhCCcE
Confidence 589999999998766 4678986
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=37.01 E-value=1.1e+02 Score=22.07 Aligned_cols=47 Identities=13% Similarity=0.270 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHHC
Q 029245 94 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAY 164 (196)
Q Consensus 94 ~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~~ 164 (196)
-++-.++++.|.+.||.++.= + |.-+-+...+.+++..||+.|++..
T Consensus 43 ~~~~~~~l~~l~~~G~ei~~H----~--------------------~~H~~~~~~~~~~~~~ei~~~~~~l 89 (123)
T PF01522_consen 43 VERYPDQLRELAAAGHEIGNH----G--------------------WSHPNLSTLSPEELRREIERSREIL 89 (123)
T ss_dssp HHHHHHHHHHHHHTT-EEEEE-------------------------SSSSCGGGS-HHHHHHHHHHHHHHH
T ss_pred cccccccchhHHHHHHHHHhc----C--------------------CcccccccCCHHHHHHHHHHHHHHH
Confidence 444478999999999766531 1 1222225567889999999998764
No 31
>PF13079 DUF3916: Protein of unknown function (DUF3916)
Probab=36.94 E-value=21 Score=30.00 Aligned_cols=46 Identities=22% Similarity=0.598 Sum_probs=27.4
Q ss_pred CCCccCCcceeecCCCCCC-----CCCHHH--------HHHHHHHHHHHCC--CCeEEEEee
Q 029245 128 MPGYYDGRYWTMWKLPMFG-----CNDSSQ--------ILNEIQECKKAYP--NAYIRCLAF 174 (196)
Q Consensus 128 sp~yyd~rYWtMWKLPmFg-----~tD~sq--------VL~EieeC~k~~P--~~YVRLiGf 174 (196)
.+.+|+.+||. ||||.-. .+-+-+ .|...+.-.+.-| .+..||+..
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 34578888999 9998642 222222 3334444455556 677787653
No 32
>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=36.71 E-value=82 Score=24.39 Aligned_cols=52 Identities=19% Similarity=0.273 Sum_probs=32.9
Q ss_pred ChHHHHH-HHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHH
Q 029245 93 SDDSIAK-EIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKA 163 (196)
Q Consensus 93 s~~qI~k-QV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~ 163 (196)
+++..+. =++||..+|-..-|+-.+. .-|.+|-. +..+.++|..|+++.++.
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 23566754 888999999999999864
No 33
>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=36.21 E-value=64 Score=26.53 Aligned_cols=54 Identities=24% Similarity=0.513 Sum_probs=35.5
Q ss_pred CCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHHCCCCeEE
Q 029245 91 SLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIR 170 (196)
Q Consensus 91 pLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~~P~~YVR 170 (196)
+++.+.+.+|++.++.+ ++++ . .|..|++.. +.+..|.+..+++|+ ++
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 466777643 455566666677776 45
Q ss_pred EEeeecC
Q 029245 171 CLAFNNQ 177 (196)
Q Consensus 171 LiGfDn~ 177 (196)
++ ||++
T Consensus 98 vv-~Dpv 103 (242)
T cd01169 98 VV-LDPV 103 (242)
T ss_pred EE-ECCc
Confidence 55 9986
No 34
>PRK10802 peptidoglycan-associated outer membrane lipoprotein; Provisional
Probab=35.42 E-value=56 Score=27.15 Aligned_cols=30 Identities=13% Similarity=0.262 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecCC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQK 178 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~r 178 (196)
+..++|.+|.+.++.||+..|+|.|+-..+
T Consensus 83 ~~~~~L~~~a~~L~~~p~~~v~I~GhtD~~ 112 (173)
T PRK10802 83 DFAQMLDAHANFLRSNPSYKVTVEGHADER 112 (173)
T ss_pred HHHHHHHHHHHHHHhCCCceEEEEEecCCC
Confidence 567899999999999999999999986543
No 35
>PRK07708 hypothetical protein; Validated
Probab=35.31 E-value=2.2e+02 Score=24.63 Aligned_cols=87 Identities=17% Similarity=0.246 Sum_probs=54.5
Q ss_pred eccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHH
Q 029245 75 WNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQIL 154 (196)
Q Consensus 75 w~p~~~kkfET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL 154 (196)
|.=...|+.+|.-+--.++-+|...-.+-+-+-|..--|||-|+. +.+|| +
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~--------------~~~~~---------------~ 57 (219)
T PRK07708 7 WTYKTKKGLQTELTSDWMNIEEALQLAEDFEKTGRVKELEFYDEM--------------DTEWS---------------L 57 (219)
T ss_pred EEEEcCCCceeEEEeccccHHHHHHHHHHHhhcCCceeEEEecCC--------------CCEee---------------H
Confidence 544555666665555566666666667777888999999999965 67988 2
Q ss_pred HHHHHHHHH---CCCCeEEEEeeec----CCCeEEEEEEEecCCC
Q 029245 155 NEIQECKKA---YPNAYIRCLAFNN----QKQGQCMSFLIQKPTT 192 (196)
Q Consensus 155 ~EieeC~k~---~P~~YVRLiGfDn----~rQvq~~sfIV~RP~~ 192 (196)
+||.+-.++ -|+. +.+ =||- ..+.-.++++|..|.+
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 444444443 3443 222 2443 4455678888876543
No 36
>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=35.24 E-value=54 Score=28.65 Aligned_cols=30 Identities=7% Similarity=0.237 Sum_probs=25.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCeEEEE
Q 029245 143 PMFGCNDSSQILNEIQECKKAYPNAYIRCL 172 (196)
Q Consensus 143 PmFg~tD~sqVL~EieeC~k~~P~~YVRLi 172 (196)
.+++.....+||.||.+-+++||++.|=|-
T Consensus 87 ~~~~~~~~~~~l~~i~~fl~~~p~Evvil~ 116 (288)
T cd08587 87 GLYSGEPVDEVLEDVNDFLDEHPKEVVILD 116 (288)
T ss_pred ecccccCHHHHHHHHHHHHHhCCCcEEEEE
Confidence 345558899999999999999999998663
No 37
>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=34.32 E-value=49 Score=23.37 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=18.4
Q ss_pred ccCCCCCChHHH---HHHHHHHHhCCC
Q 029245 86 LSYLPSLSDDSI---AKEIDYMLKKGW 109 (196)
Q Consensus 86 ~SyLPpLs~~qI---~kQV~ylL~qGw 109 (196)
|.-||.||-+|- .++|+-|.++|-
T Consensus 2 ~~~lp~LtHeeQQ~AvE~Iq~LMaqGm 28 (51)
T PF03701_consen 2 FNDLPSLTHEEQQQAVERIQELMAQGM 28 (51)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHhcc
Confidence 456899998865 457888999983
No 38
>COG4063 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A [Coenzyme metabolism]
Probab=33.86 E-value=39 Score=30.17 Aligned_cols=27 Identities=26% Similarity=0.633 Sum_probs=25.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCe
Q 029245 142 LPMFGCNDSSQILNEIQECKKAYPNAY 168 (196)
Q Consensus 142 LPmFg~tD~sqVL~EieeC~k~~P~~Y 168 (196)
+-++++.|++++-+-|+||+..-|++|
T Consensus 132 vdlid~eD~~~I~~~v~ecv~kdpga~ 158 (238)
T COG4063 132 VDLIDVEDPDEITAKVEECVEKDPGAY 158 (238)
T ss_pred ehhcccCCHHHHHHHHHHHHhcCCCcc
Confidence 378999999999999999999999987
No 39
>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=33.44 E-value=68 Score=24.70 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHCCCCeEEEEeee
Q 029245 150 SSQILNEIQECKKAYPNAYIRCLAFN 175 (196)
Q Consensus 150 ~sqVL~EieeC~k~~P~~YVRLiGfD 175 (196)
..++..++++++++||+.-|-|+|.-
T Consensus 11 ~~~i~~~~~~~~~~~p~~~i~v~GHS 36 (153)
T cd00741 11 ANLVLPLLKSALAQYPDYKIHVTGHS 36 (153)
T ss_pred HHHHHHHHHHHHHHCCCCeEEEEEcC
Confidence 45788899999999999999999863
No 40
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=33.17 E-value=42 Score=25.23 Aligned_cols=61 Identities=23% Similarity=0.335 Sum_probs=36.8
Q ss_pred CCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCC-CCCHHHHHHHHHHHHHHCCCC
Q 029245 89 LPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFG-CNDSSQILNEIQECKKAYPNA 167 (196)
Q Consensus 89 LPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg-~tD~sqVL~EieeC~k~~P~~ 167 (196)
.|+|+++||.+.+..| .||...-+ .....|+ ++.+-|. .-+--..++++.+-..-||+-
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 3789999998877665 69988311 1123331 2333332 223445677777778888986
Q ss_pred eE
Q 029245 168 YI 169 (196)
Q Consensus 168 YV 169 (196)
.+
T Consensus 63 ~~ 64 (97)
T PRK00823 63 FN 64 (97)
T ss_pred EE
Confidence 43
No 41
>KOG0792 consensus Protein tyrosine phosphatase PTPMEG, contains FERM domain [Signal transduction mechanisms]
Probab=33.08 E-value=1.1e+02 Score=33.21 Aligned_cols=79 Identities=23% Similarity=0.487 Sum_probs=51.7
Q ss_pred ccCCcccceeeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccC--CceeecCCCCCCccCCcceeec
Q 029245 63 VSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEV--GYVHRENSKMPGYYDGRYWTMW 140 (196)
Q Consensus 63 ~sng~rv~cm~vw~p~~~kkfET~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~--~~~~R~~~~sp~yyd~rYWtMW 140 (196)
-.-|||+.|-|-||-++ ++|+.| .++.+..+|.++ ++++|+...- .--.+.+-+.|
T Consensus 972 e~EggR~KchqYWPr~~---~~t~~y------------------grf~v~~~~~~~t~~y~tr~m~l~-~~~t~eeR~V~ 1029 (1144)
T KOG0792|consen 972 EVEGGRVKCHQYWPRLG---HETMEY------------------GRFQVTCVFEQQTTCYVTREMTLK-DLQTREERTVW 1029 (1144)
T ss_pred hhhcCeeccccccCCCC---ccceec------------------cceEEEEEEecccccEEEEeEEEe-eccCCceeeee
Confidence 34789999999999987 677665 778899999864 7777754200 00115677778
Q ss_pred CC-----CCCCCC-CHHHHHHHHHHHHHH
Q 029245 141 KL-----PMFGCN-DSSQILNEIQECKKA 163 (196)
Q Consensus 141 KL-----PmFg~t-D~sqVL~EieeC~k~ 163 (196)
-| |==||- |+...|.=||+-+..
T Consensus 1030 hLQYtaWPDHg~P~D~~~FL~Fleevrsv 1058 (1144)
T KOG0792|consen 1030 HLQYTAWPDHGVPDDPNDFLDFLEEVRSV 1058 (1144)
T ss_pred eeeecccccCCCCCChHHHHHHHHHHHHH
Confidence 76 555664 555555545544443
No 42
>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=33.05 E-value=1.4e+02 Score=25.15 Aligned_cols=79 Identities=16% Similarity=0.162 Sum_probs=45.5
Q ss_pred cccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCC----CCCCcc--CCcceeecCCCCCCCCCHHHHHHHHH
Q 029245 85 ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENS----KMPGYY--DGRYWTMWKLPMFGCNDSSQILNEIQ 158 (196)
Q Consensus 85 T~SyLPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~----~sp~yy--d~rYWtMWKLPmFg~tD~sqVL~Eie 158 (196)
.+.++++++++++..+-...-+ |.+...+...+.+ .+-.++ ++..+..| -..+.|+.++|.+.-
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 3335667999999887765543 2221111111111 122232 23334445 445778999999999
Q ss_pred HHHHHCCCCeEEEEeeec
Q 029245 159 ECKKAYPNAYIRCLAFNN 176 (196)
Q Consensus 159 eC~k~~P~~YVRLiGfDn 176 (196)
+..++|.. .|+||+-
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 43
>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=32.59 E-value=12 Score=24.33 Aligned_cols=23 Identities=17% Similarity=0.450 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEE
Q 029245 148 NDSSQILNEIQECKKAYPNAYIR 170 (196)
Q Consensus 148 tD~sqVL~EieeC~k~~P~~YVR 170 (196)
.+.+.+|.||+.-+.++..+|||
T Consensus 3 ~~~D~lLDeId~vLe~NAe~FV~ 25 (33)
T TIGR03687 3 EGVDDLLDEIDGVLESNAEEFVR 25 (33)
T ss_pred chHHHHHHHHHHHHHHhHHHHHH
Confidence 36789999999999999999887
No 44
>PRK05114 hypothetical protein; Provisional
Probab=31.64 E-value=56 Score=23.72 Aligned_cols=24 Identities=25% Similarity=0.497 Sum_probs=18.4
Q ss_pred ccCCCCCChHHHH---HHHHHHHhCCC
Q 029245 86 LSYLPSLSDDSIA---KEIDYMLKKGW 109 (196)
Q Consensus 86 ~SyLPpLs~~qI~---kQV~ylL~qGw 109 (196)
|.-||.||-+|-. ++|+.|.++|-
T Consensus 2 ~~~lp~LtHeeQQ~AVErIq~LMaqGm 28 (59)
T PRK05114 2 FAGLPSLTHEQQQKAVERIQELMAQGM 28 (59)
T ss_pred CCCcccCCHHHHHHHHHHHHHHHHccc
Confidence 4569999988654 46888888883
No 45
>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=31.33 E-value=48 Score=24.60 Aligned_cols=29 Identities=14% Similarity=0.330 Sum_probs=23.5
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccC
Q 029245 90 PSLSDDSIAKEIDYMLKKGWIPCLEFDEV 118 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~qGw~pclEfad~ 118 (196)
|..+++++.+.++.|.+.|++-|+.+.+.
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 56777999999999999999999999875
No 46
>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=30.38 E-value=1.4e+02 Score=24.84 Aligned_cols=62 Identities=18% Similarity=0.269 Sum_probs=38.9
Q ss_pred CCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHH-HHHHHHHCCCC
Q 029245 89 LPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNE-IQECKKAYPNA 167 (196)
Q Consensus 89 LPpLs~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~E-ieeC~k~~P~~ 167 (196)
-|+++++++.++++.+...+-. .+ ...+ |..|++..+..+++.+ |+++++..|+
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~--~~---------------------~~~v-~~G~l~~~~~~~~~~~~l~~~~~~~~~- 103 (254)
T cd01173 49 GFVLSAEELEDLLEGLEALGLL--LE---------------------YDAV-LTGYLGSAEQVEAVAEIVKRLKEKNPN- 103 (254)
T ss_pred CeecCHHHHHHHHHHHHHcCCc--cc---------------------CCEE-EEecCCCHHHHHHHHHHHHHHHHhCCC-
Confidence 4889999999999998875410 00 1111 4555655555565555 6777665666
Q ss_pred eEEEEeeecC
Q 029245 168 YIRCLAFNNQ 177 (196)
Q Consensus 168 YVRLiGfDn~ 177 (196)
++++ +|++
T Consensus 104 -~~vv-~Dpv 111 (254)
T cd01173 104 -LLYV-CDPV 111 (254)
T ss_pred -ceEE-ECCC
Confidence 3455 9986
No 47
>PF10096 DUF2334: Uncharacterized protein conserved in bacteria (DUF2334); InterPro: IPR018763 This group of proteins has no known function.
Probab=30.28 E-value=1.6e+02 Score=25.51 Aligned_cols=75 Identities=13% Similarity=0.149 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEe
Q 029245 94 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLA 173 (196)
Q Consensus 94 ~~qI~kQV~ylL~qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~~P~~YVRLiG 173 (196)
+.++.+-++|+.++||.+.|-=-. |.+. +.. .+.-++.|+.-.-.+.+.+++-+-|++-++..-..=|+..|
T Consensus 54 ~~~f~~~L~~~~~~Gg~I~lHGYt--Hq~~-~~~-----sg~~~ef~~~~~~~~~~~~~a~~ri~~gl~~l~~~gi~p~~ 125 (243)
T PF10096_consen 54 NPEFVEYLRYLQARGGEIVLHGYT--HQYG-NSV-----SGDGFEFWDSEFDAGDSEEEAKERIEKGLEILAELGIYPVG 125 (243)
T ss_pred hHHHHHHHHHHHhcCCEEEEEecc--eecC-CCc-----ccccceeccccccccCCHHHHHHHHHHHHHHHHHCCCcccE
Confidence 779999999999999999874222 1110 111 13445555532222445666666677777766666667776
Q ss_pred eec
Q 029245 174 FNN 176 (196)
Q Consensus 174 fDn 176 (196)
|-+
T Consensus 126 f~a 128 (243)
T PF10096_consen 126 FEA 128 (243)
T ss_pred EEC
Confidence 643
No 48
>PRK15358 pathogenicity island 2 effector protein SseF; Provisional
Probab=30.13 E-value=48 Score=29.56 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=12.6
Q ss_pred CChHHHHHHHHHHHh
Q 029245 92 LSDDSIAKEIDYMLK 106 (196)
Q Consensus 92 Ls~~qI~kQV~ylL~ 106 (196)
||.|||.+|-+|.+.
T Consensus 25 ltpeqi~qqrdya~h 39 (239)
T PRK15358 25 LTPEQIRQQRDYAIH 39 (239)
T ss_pred cCHHHHHHHHHHHHH
Confidence 799999999887654
No 49
>PRK13697 cytochrome c6; Provisional
Probab=29.89 E-value=60 Score=23.95 Aligned_cols=21 Identities=43% Similarity=0.754 Sum_probs=17.1
Q ss_pred CCCChHHHHHHHHHHHh---CCCe
Q 029245 90 PSLSDDSIAKEIDYMLK---KGWI 110 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~---qGw~ 110 (196)
-.||++||.+=|.||.+ +||+
T Consensus 88 ~~ls~~di~~l~~Yi~~~~~~~~~ 111 (111)
T PRK13697 88 DRLSPDQIEDVAAYVLEQAEKGWK 111 (111)
T ss_pred CCCCHHHHHHHHHHHHHHHHccCC
Confidence 35799999999999987 4663
No 50
>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=29.39 E-value=61 Score=26.25 Aligned_cols=21 Identities=33% Similarity=0.544 Sum_probs=18.1
Q ss_pred CHHHHHHH-HHHHHHHCCCCeE
Q 029245 149 DSSQILNE-IQECKKAYPNAYI 169 (196)
Q Consensus 149 D~sqVL~E-ieeC~k~~P~~YV 169 (196)
|-+|+|++ |.||+..|||--|
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 51
>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=29.12 E-value=1.1e+02 Score=25.70 Aligned_cols=29 Identities=17% Similarity=0.277 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeEEEEeeec
Q 029245 147 CNDSSQILNEIQECKKAYPNAYIRCLAFNN 176 (196)
Q Consensus 147 ~tD~sqVL~EieeC~k~~P~~YVRLiGfDn 176 (196)
+....+||.||..-+++||++.|-|. |..
T Consensus 78 ~~~~~~vL~~i~~fl~~~p~E~vil~-~~~ 106 (271)
T cd08557 78 GQTLEDVLNEVKDFLDAHPSEVVILD-LEH 106 (271)
T ss_pred cccHHHHHHHHHHHHHHCCCcEEEEE-EEc
Confidence 68899999999999999999988665 443
No 52
>PHA00422 hypothetical protein
Probab=28.46 E-value=14 Score=27.43 Aligned_cols=21 Identities=29% Similarity=0.729 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHCCCCeEEE
Q 029245 151 SQILNEIQECKKAYPNAYIRC 171 (196)
Q Consensus 151 sqVL~EieeC~k~~P~~YVRL 171 (196)
=.||.+|..|-+.|...|||-
T Consensus 5 L~vL~~ik~~pk~fQSn~vR~ 25 (69)
T PHA00422 5 LKVLAAIKSCPKTFQSNYVRN 25 (69)
T ss_pred HHHHHHHHhCcHHHHHHHHhh
Confidence 379999999999999999983
No 53
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=28.42 E-value=82 Score=25.69 Aligned_cols=27 Identities=19% Similarity=0.210 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeee
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFN 175 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfD 175 (196)
+..++|.+|.+-++.+|..-|+|.|.=
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 54
>PRK12799 motB flagellar motor protein MotB; Reviewed
Probab=28.30 E-value=2.6e+02 Score=27.02 Aligned_cols=27 Identities=19% Similarity=0.201 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeec
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNN 176 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn 176 (196)
+..++|.+|..-++.+|| .|+|.|.=.
T Consensus 170 ~~~~iL~~ia~~L~~~pn-~I~I~GHTD 196 (421)
T PRK12799 170 YMRDILRAIAPILNDIPN-KLSLSGHTD 196 (421)
T ss_pred HHHHHHHHHHHHHHcCCC-cEEEEEEcC
Confidence 457899999999999999 799999843
No 55
>PRK08944 motB flagellar motor protein MotB; Reviewed
Probab=28.24 E-value=3.2e+02 Score=24.81 Aligned_cols=29 Identities=17% Similarity=0.240 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 029245 148 NDSSQILNEIQECKKAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 148 tD~sqVL~EieeC~k~~P~~YVRLiGfDn~ 177 (196)
.+..++|.+|.+.++.+|+ .|+|.|.=..
T Consensus 192 ~~~~~~L~~ia~~L~~~~~-~I~I~GHTD~ 220 (302)
T PRK08944 192 PKFKPVVRKIGELLKDVPG-IITVSGHTDN 220 (302)
T ss_pred HHHHHHHHHHHHHHHhCCC-eEEEEEecCC
Confidence 3577899999999999998 6999998443
No 56
>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=27.97 E-value=62 Score=28.49 Aligned_cols=29 Identities=14% Similarity=0.426 Sum_probs=24.1
Q ss_pred HHCCCCeEEEEeeecCCCeEEEEEEEecCCCCC
Q 029245 162 KAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 194 (196)
Q Consensus 162 k~~P~~YVRLiGfDn~rQvq~~sfIV~RP~~~~ 194 (196)
..|-||||=|.|||...|. |+++-|+...
T Consensus 157 ~~Y~GHYVVlcGyd~~~~~----~~yrdPa~~~ 185 (212)
T PF09778_consen 157 PDYQGHYVVLCGYDAATKE----FEYRDPASSD 185 (212)
T ss_pred CCccEEEEEEEeecCCCCe----EEEeCCcccc
Confidence 5699999999999998874 7888887543
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=27.90 E-value=2.1e+02 Score=26.49 Aligned_cols=64 Identities=13% Similarity=0.250 Sum_probs=42.1
Q ss_pred ccccccCCCCCChHHHHHHHHHHHh-CCCeeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHH
Q 029245 82 KFEALSYLPSLSDDSIAKEIDYMLK-KGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC 160 (196)
Q Consensus 82 kfET~SyLPpLs~~qI~kQV~ylL~-qGw~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC 160 (196)
-++|++|....+.|++.+|++.++. +|++- + |+- +|-.++.+-++-|++.
T Consensus 157 ~~~~~~~~~~~~~e~~~~~a~~~~~~~Gf~~------------------------~----KiK-vG~~~~~~di~~v~av 207 (395)
T cd03323 157 PWFRDRWGEALTPEGVVRLARAAIDRYGFKS------------------------F----KLK-GGVLPGEEEIEAVKAL 207 (395)
T ss_pred cccccccccCCCHHHHHHHHHHHHHhcCCcE------------------------E----EEe-cCCCCHHHHHHHHHHH
Confidence 4556666666788999999998885 68631 1 221 1334566667778888
Q ss_pred HHHCCCCeEEEEeeecC
Q 029245 161 KKAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 161 ~k~~P~~YVRLiGfDn~ 177 (196)
+++.|+ ++|. +|.+
T Consensus 208 Rea~~~--~~l~-vDaN 221 (395)
T cd03323 208 AEAFPG--ARLR-LDPN 221 (395)
T ss_pred HHhCCC--CcEE-EeCC
Confidence 899975 4443 5765
No 58
>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=27.74 E-value=46 Score=27.35 Aligned_cols=36 Identities=17% Similarity=0.299 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHHHHHHH---HCCCCeEEEEeeecCCCeE
Q 029245 145 FGCNDSSQILNEIQECKK---AYPNAYIRCLAFNNQKQGQ 181 (196)
Q Consensus 145 Fg~tD~sqVL~EieeC~k---~~P~~YVRLiGfDn~rQvq 181 (196)
+=|.+....+.-+.+|++ .-|+. |.|||||+....+
T Consensus 184 i~~~~d~~a~g~~~~l~~~g~~vP~d-i~vvg~d~~~~~~ 222 (269)
T cd06297 184 VFASADQQALGALQEAVELGLTVGED-VRVVGFDDHPFAR 222 (269)
T ss_pred EEEcCcHHHHHHHHHHHHcCCCCCCc-eEEEEECCchhhc
Confidence 334444344444444444 44665 8999999985433
No 59
>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=27.69 E-value=84 Score=26.02 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=24.2
Q ss_pred CCCCCChHHHHHHHHHHHhCCCeeEEEec
Q 029245 88 YLPSLSDDSIAKEIDYMLKKGWIPCLEFD 116 (196)
Q Consensus 88 yLPpLs~~qI~kQV~ylL~qGw~pclEfa 116 (196)
.+|+.++.-+.++++.|.++||.+.+ ++
T Consensus 8 ~~~~~~~~~~~~~~~~L~~~g~~v~v-~~ 35 (355)
T cd03799 8 EFPRLSETFILREILALEAAGHEVEI-FS 35 (355)
T ss_pred CCCCcchHHHHHHHHHHHhCCCeEEE-EE
Confidence 35888999999999999999999987 44
No 60
>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=27.53 E-value=41 Score=27.08 Aligned_cols=16 Identities=44% Similarity=0.864 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHCC
Q 029245 150 SSQILNEIQECKKAYP 165 (196)
Q Consensus 150 ~sqVL~EieeC~k~~P 165 (196)
..+++.|+++|+++|-
T Consensus 40 ~~~~~~ei~~C~~~Y~ 55 (135)
T PF10104_consen 40 KLELLQEIAQCKKEYE 55 (135)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4588999999999983
No 61
>PTZ00344 pyridoxal kinase; Provisional
Probab=27.52 E-value=1.6e+02 Score=25.68 Aligned_cols=29 Identities=7% Similarity=0.071 Sum_probs=22.2
Q ss_pred ccccccccCCCCCChHHHHHHHHHHHhCCC
Q 029245 80 NKKFEALSYLPSLSDDSIAKEIDYMLKKGW 109 (196)
Q Consensus 80 ~kkfET~SyLPpLs~~qI~kQV~ylL~qGw 109 (196)
...|+.+ .-|+++++++.+|++.+.+.+.
T Consensus 46 ~~~~~~~-~g~~i~~~~~~~~l~~l~~~~~ 74 (296)
T PTZ00344 46 HTGYPVI-KGHRLDLNELITLMDGLRANNL 74 (296)
T ss_pred CCCCCCc-cCeeCCHHHHHHHHHHHHhcCC
Confidence 3345553 3589999999999999988765
No 62
>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=27.44 E-value=64 Score=26.84 Aligned_cols=33 Identities=9% Similarity=0.191 Sum_probs=22.1
Q ss_pred HHHHHHHHHCCCCeEEEEeeecCCCeE----EEEEEEecCC
Q 029245 155 NEIQECKKAYPNAYIRCLAFNNQKQGQ----CMSFLIQKPT 191 (196)
Q Consensus 155 ~EieeC~k~~P~~YVRLiGfDn~rQvq----~~sfIV~RP~ 191 (196)
.-+.+|++.. |.|||||+.-..+ .+..|.+++.
T Consensus 197 gv~~al~~~g----isIvGfD~~~~~~~~~p~lttv~~~~~ 233 (265)
T cd06354 197 GVFQAAKEAG----VYAIGVDSDQYYLAPGVVLTSMVKRVD 233 (265)
T ss_pred HHHHHHHhcC----CeEEEecCcccccCCCcEEEEEeehhH
Confidence 3445555443 9999999976655 5666677664
No 63
>PHA01346 hypothetical protein
Probab=27.35 E-value=51 Score=23.00 Aligned_cols=18 Identities=39% Similarity=0.754 Sum_probs=16.8
Q ss_pred CCCChHHHHHHHHHHHhC
Q 029245 90 PSLSDDSIAKEIDYMLKK 107 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~q 107 (196)
|++++|.|-.+++.||++
T Consensus 30 pdfsqekihaeldsllrk 47 (53)
T PHA01346 30 PDFSQEKIHAELDSLLRK 47 (53)
T ss_pred CCccHHHHHHHHHHHHHH
Confidence 999999999999999975
No 64
>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=26.71 E-value=96 Score=27.56 Aligned_cols=46 Identities=17% Similarity=0.252 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCC-----------eEEEEEEEecCCC
Q 029245 146 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQ-----------GQCMSFLIQKPTT 192 (196)
Q Consensus 146 g~tD~sqVL~EieeC~k~~P~~YVRLiGfDn~rQ-----------vq~~sfIV~RP~~ 192 (196)
+.....++|.||..-+++||++-|=|+ |.+... ...+.-++++|..
T Consensus 74 ~~~~~~d~L~~i~~fL~~nP~EvV~l~-l~~~~~~~~~~~~~~~~~~gl~~~~y~p~~ 130 (270)
T cd08588 74 DGGPLSDVLREVVDFLDANPNEVVTLF-LEDYVSPGPLLRSKLFRVAGLTDLVYVPDA 130 (270)
T ss_pred CCccHHHHHHHHHHHHHhCCCcEEEEE-EEeCCCcchHHHHHHhhhcCccceEEcCCC
Confidence 467899999999999999999998877 433221 1246667777754
No 65
>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=26.54 E-value=1.2e+02 Score=24.96 Aligned_cols=32 Identities=13% Similarity=0.363 Sum_probs=27.6
Q ss_pred HHHCCCCeEEEEeeecCC----------CeEEEEEEEecCCC
Q 029245 161 KKAYPNAYIRCLAFNNQK----------QGQCMSFLIQKPTT 192 (196)
Q Consensus 161 ~k~~P~~YVRLiGfDn~r----------Qvq~~sfIV~RP~~ 192 (196)
++.||-.=|-..|+|+.. +.++.+||+.+|.+
T Consensus 67 rrhypl~~Vs~ca~dp~n~~~~~~~~~~~kriFgFVar~~~~ 108 (138)
T cd01213 67 RRHYKVDSVIFCAIDPEERMWENEGAIAKARIFAFVARIPHS 108 (138)
T ss_pred hhhCCcCeEEEEeeCCccccccccccccccEEEEEEEecCCC
Confidence 456999999999999974 47899999999976
No 66
>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=25.84 E-value=53 Score=23.50 Aligned_cols=17 Identities=18% Similarity=0.440 Sum_probs=14.2
Q ss_pred CCCCChHHHHHHHHHHH
Q 029245 89 LPSLSDDSIAKEIDYML 105 (196)
Q Consensus 89 LPpLs~~qI~kQV~ylL 105 (196)
||+|+.||+..+++--+
T Consensus 35 ~~~Lt~EqLla~lq~~i 51 (55)
T PF11918_consen 35 LPNLTPEQLLAMLQKSI 51 (55)
T ss_pred CCCcCHHHHHHHHHhhe
Confidence 69999999999987544
No 67
>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=25.47 E-value=33 Score=16.54 Aligned_cols=6 Identities=50% Similarity=1.209 Sum_probs=4.4
Q ss_pred cCCCCC
Q 029245 87 SYLPSL 92 (196)
Q Consensus 87 SyLPpL 92 (196)
-||||.
T Consensus 3 eYLpP~ 8 (9)
T PF02757_consen 3 EYLPPV 8 (9)
T ss_pred cccCCC
Confidence 388885
No 68
>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=25.45 E-value=77 Score=26.58 Aligned_cols=28 Identities=11% Similarity=0.203 Sum_probs=21.8
Q ss_pred ccccccccCCCCCChHHHHHHHHHHHhC
Q 029245 80 NKKFEALSYLPSLSDDSIAKEIDYMLKK 107 (196)
Q Consensus 80 ~kkfET~SyLPpLs~~qI~kQV~ylL~q 107 (196)
.|.|.=|.-...|||+||..=..||+.|
T Consensus 120 ~k~~~~mP~~~~LsdeEL~avAaYIl~q 147 (159)
T TIGR03045 120 IRSADIFPKMRNLTDEDLRLIAGHILVQ 147 (159)
T ss_pred cCcccccCCcCCCCHHHHHHHHHHHHHh
Confidence 3445555555679999999999999986
No 69
>PLN02749 Uncharacterized protein At1g47420
Probab=25.16 E-value=69 Score=27.53 Aligned_cols=29 Identities=31% Similarity=0.539 Sum_probs=26.0
Q ss_pred cccccccCCCCCChHHHHHHHHHHHhCCC
Q 029245 81 KKFEALSYLPSLSDDSIAKEIDYMLKKGW 109 (196)
Q Consensus 81 kkfET~SyLPpLs~~qI~kQV~ylL~qGw 109 (196)
..+|+.+.||..+|.+|.+-..-|+.-.|
T Consensus 4 ~fs~d~~~lP~i~Dp~i~~afkdLma~sW 32 (173)
T PLN02749 4 RFSEDVSHLPEISDPEILKAFKDLMAASW 32 (173)
T ss_pred ccccccccCCCCCCHHHHHHHHHHHhcch
Confidence 34589999999999999999999998877
No 70
>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=25.13 E-value=59 Score=26.50 Aligned_cols=26 Identities=23% Similarity=0.431 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHCCCCeEEEEeeecCC
Q 029245 152 QILNEIQECKKAYPNAYIRCLAFNNQK 178 (196)
Q Consensus 152 qVL~EieeC~k~~P~~YVRLiGfDn~r 178 (196)
.+++.+.+.-..-|+. |.|||||+..
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 3455555544445665 9999999874
No 71
>PRK09038 flagellar motor protein MotD; Reviewed
Probab=24.74 E-value=4.8e+02 Score=23.22 Aligned_cols=28 Identities=29% Similarity=0.427 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~ 177 (196)
+..++|.+|-+.++.+|+ .|+|.|.=..
T Consensus 147 ~~~~~L~~ia~~L~~~~~-~I~I~GHTD~ 174 (281)
T PRK09038 147 QAFAILEKVAEVLKPAPN-PIHVEGFTDN 174 (281)
T ss_pred HHHHHHHHHHHHHHhCCC-eEEEEEECCC
Confidence 577899999999999998 7999998544
No 72
>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=24.37 E-value=2.6e+02 Score=22.62 Aligned_cols=56 Identities=18% Similarity=0.199 Sum_probs=37.0
Q ss_pred ccccCCcccceeeeeccCCccccccc---cCCCCCChHHHHHHHHHHHh---CCCeeEEEeccCC
Q 029245 61 KTVSNGSKTRCMKTWNPINNKKFEAL---SYLPSLSDDSIAKEIDYMLK---KGWIPCLEFDEVG 119 (196)
Q Consensus 61 ~~~sng~rv~cm~vw~p~~~kkfET~---SyLPpLs~~qI~kQV~ylL~---qGw~pclEfad~~ 119 (196)
....+| .-..++.|+..++++.+ ..-+-+++.+..++++-..+ ..+.+.||.+-..
T Consensus 60 ~lr~~g---~~il~l~~~~~~~~~~~~~~~~~~~v~s~~~~~~l~~~~~~~~~~~~v~l~vdtG~ 121 (218)
T PF01168_consen 60 ELREAG---APILVLGPIPPEELEELVEYNIIPTVDSLEQLEALSKAAKKQGKPLKVHLKVDTGM 121 (218)
T ss_dssp HHHHTT---SEEEEESESTGGGHHHHHHTTEEEEE-SHHHHHHHHHHHHHHTSTEEEEEEBESSS
T ss_pred hHHhcC---CceEEEcCCChhhHHHHhhCcEEEEEchhhHHHHHHHHHHHcCCceEEEEeecccc
Confidence 445566 34556666666666443 45677778787788887774 7788888888543
No 73
>KOG1386 consensus Nucleoside phosphatase [Nucleotide transport and metabolism]
Probab=24.09 E-value=23 Score=34.95 Aligned_cols=59 Identities=15% Similarity=0.323 Sum_probs=39.1
Q ss_pred eeEEEeccCCceeecCCCCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHH-----HCCCCeEEEE
Q 029245 110 IPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKK-----AYPNAYIRCL 172 (196)
Q Consensus 110 ~pclEfad~~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k-----~~P~~YVRLi 172 (196)
+|||||++..-|..-+..+|-|=--.= +.=+....+.+++|.-+..-++ .+.++.+|||
T Consensus 68 ~pLlefA~~~IPk~~h~~Tpl~l~ATA----GMRLL~~~~qeaIl~~l~~~l~~~s~f~f~~~~a~II 131 (501)
T KOG1386|consen 68 TPLLEFAKEHIPKEKHKETPLFLGATA----GMRLLPLAQQEAILEVLRRVLKSLSDFLFDDEWARII 131 (501)
T ss_pred HHHHHHHHhhCCHhhcCCCCeEEEecc----cceecCcccHHHHHHHHHHhcccccCCcccccccEEe
Confidence 899999988767443344443221111 2233455688899998888888 5678889998
No 74
>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=24.04 E-value=59 Score=24.12 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=6.2
Q ss_pred HHHHHHHHHH
Q 029245 95 DSIAKEIDYM 104 (196)
Q Consensus 95 ~qI~kQV~yl 104 (196)
+.|.+||+|-
T Consensus 2 ~~I~~QvEyY 11 (73)
T cd08037 2 DYIKRQIEYY 11 (73)
T ss_pred hHHHHHHHHh
Confidence 4566676663
No 75
>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=24.04 E-value=55 Score=25.55 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeE
Q 029245 147 CNDSSQILNEIQECKKAYPNAYI 169 (196)
Q Consensus 147 ~tD~sqVL~EieeC~k~~P~~YV 169 (196)
.....+||.+|.+.+.+||++.|
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 45688999999999999999987
No 76
>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=23.86 E-value=1.4e+02 Score=21.12 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~ 177 (196)
+..+.|.+|-...+.+|+..|.|+|+-..
T Consensus 16 ~~~~~l~~~~~~l~~~~~~~v~v~g~a~~ 44 (106)
T cd07185 16 EAKPLLDKLAEVLKKNPDAKIRIEGHTDS 44 (106)
T ss_pred HHHHHHHHHHHHHHHCCCceEEEEEEeCC
Confidence 45788899999999999999999998654
No 77
>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=23.16 E-value=86 Score=28.00 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=24.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCeEEE
Q 029245 143 PMFGCNDSSQILNEIQECKKAYPNAYIRC 171 (196)
Q Consensus 143 PmFg~tD~sqVL~EieeC~k~~P~~YVRL 171 (196)
.+|+. ..++||.||.+-+.+||++.|=|
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 78
>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=22.92 E-value=1.3e+02 Score=23.57 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCeEEEEeeec
Q 029245 145 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNN 176 (196)
Q Consensus 145 Fg~tD~sqVL~EieeC~k~~P~~YVRLiGfDn 176 (196)
..|..-.+.+.+|++-.++|++.-+++|||..
T Consensus 35 t~Cp~c~~~~~~l~~l~~~~~~~~v~~v~is~ 66 (171)
T cd02969 35 NHCPYVKAIEDRLNRLAKEYGAKGVAVVAINS 66 (171)
T ss_pred CCCccHHHHHHHHHHHHHHHhhCCeEEEEEec
Confidence 35777777888999999999988899999954
No 79
>cd08621 PI-PLCXDc_like_2 Catalytic domain of uncharacterized hypothetical proteins similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins. This subfamily corresponds to the catalytic domain present in a group of uncharacterized hypothetical proteins found in bacteria and fungi, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). 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, eukaryotic PI-PLCXDs 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 phosphatidyl
Probab=22.81 E-value=1.3e+02 Score=27.12 Aligned_cols=26 Identities=15% Similarity=0.249 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCeEEEE
Q 029245 147 CNDSSQILNEIQECKKAYPNAYIRCL 172 (196)
Q Consensus 147 ~tD~sqVL~EieeC~k~~P~~YVRLi 172 (196)
....++||.||..-+.+||++.|=|-
T Consensus 86 ~~~l~~vL~~v~~Fl~~~p~EvViL~ 111 (300)
T cd08621 86 GESLDDILDEVNRFTDENPGELVILN 111 (300)
T ss_pred CCcHHHHHHHHHHHHHhCCCcEEEEE
Confidence 45799999999999999999988554
No 80
>PF07864 DUF1651: Protein of unknown function (DUF1651); InterPro: IPR012447 The proteins in this entry have not been characterised.
Probab=22.58 E-value=72 Score=22.91 Aligned_cols=21 Identities=19% Similarity=0.442 Sum_probs=17.6
Q ss_pred ChHHHHHHHHHHHhCCCeeEE
Q 029245 93 SDDSIAKEIDYMLKKGWIPCL 113 (196)
Q Consensus 93 s~~qI~kQV~ylL~qGw~pcl 113 (196)
+.++-.+.=..|+++||.+|-
T Consensus 51 ~~~~A~e~W~~L~~~GW~~~~ 71 (75)
T PF07864_consen 51 TREEARELWKELQKTGWRRCE 71 (75)
T ss_pred EHHHHHHHHHHHHHcCCEECC
Confidence 667777788999999999883
No 81
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=22.21 E-value=90 Score=21.60 Aligned_cols=21 Identities=19% Similarity=0.401 Sum_probs=18.4
Q ss_pred CCCCChHHHHHHHHHHHhCCC
Q 029245 89 LPSLSDDSIAKEIDYMLKKGW 109 (196)
Q Consensus 89 LPpLs~~qI~kQV~ylL~qGw 109 (196)
-|||+++|+.+=++.+.+--|
T Consensus 50 ~~PL~~~Ev~~i~kSi~k~~~ 70 (71)
T PF08708_consen 50 SPPLPESEVKAIAKSIAKWTW 70 (71)
T ss_pred CCCCCHHHHHHHHHHHHHhcc
Confidence 799999999999998887655
No 82
>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=22.05 E-value=1.3e+02 Score=21.49 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=17.8
Q ss_pred eEEEEeeecCCCeEEEEEEEecC
Q 029245 168 YIRCLAFNNQKQGQCMSFLIQKP 190 (196)
Q Consensus 168 YVRLiGfDn~rQvq~~sfIV~RP 190 (196)
.=+|.|||..-+.+-|.|-+.+|
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 34799999999999999999876
No 83
>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=21.85 E-value=75 Score=28.25 Aligned_cols=28 Identities=29% Similarity=0.503 Sum_probs=21.1
Q ss_pred CcceeecCCCCCCCCCHHHHHHHHHHHHH
Q 029245 134 GRYWTMWKLPMFGCNDSSQILNEIQECKK 162 (196)
Q Consensus 134 ~rYWtMWKLPmFg~tD~sqVL~EieeC~k 162 (196)
+|||--|-||.+..-|. .|-.|++..+.
T Consensus 193 ~rYrl~WllPTiaLFD~-dIa~kvdk~Lg 220 (223)
T TIGR00703 193 NRYRLSWLLPTIALFDI-DIANKVDKVLG 220 (223)
T ss_pred CceEEEEecchhhhhhH-HHHHHHHHHHh
Confidence 68999999999888776 45566665544
No 84
>PF14740 DUF4471: Domain of unknown function (DUF4471)
Probab=21.77 E-value=73 Score=29.13 Aligned_cols=40 Identities=15% Similarity=0.347 Sum_probs=29.8
Q ss_pred ccCCccccccccCCCCCChHHHHH---HHH-HHHhCCCeeEEEe
Q 029245 76 NPINNKKFEALSYLPSLSDDSIAK---EID-YMLKKGWIPCLEF 115 (196)
Q Consensus 76 ~p~~~kkfET~SyLPpLs~~qI~k---QV~-ylL~qGw~pclEf 115 (196)
-|=+.=-.||--||-+|..||++. +|. .+...||+|+.+|
T Consensus 245 a~~A~LvvEtaKfmvdLrKEq~~~F~~kv~eLA~~aG~~p~~~~ 288 (289)
T PF14740_consen 245 APDAVLVVETAKFMVDLRKEQLQEFVKKVKELAKAAGFKPVTNF 288 (289)
T ss_pred CCCCEEEEEcchhheeCCHHHHHHHHHHHHHHHHHCCCcccccC
Confidence 344444569999999999999875 444 4455899999876
No 85
>PHA02103 hypothetical protein
Probab=21.67 E-value=90 Score=25.58 Aligned_cols=28 Identities=18% Similarity=0.616 Sum_probs=21.3
Q ss_pred cCCCCCCCCCHHHH----HHHHHHHHHHCCCC
Q 029245 140 WKLPMFGCNDSSQI----LNEIQECKKAYPNA 167 (196)
Q Consensus 140 WKLPmFg~tD~sqV----L~EieeC~k~~P~~ 167 (196)
|.+|.++....+.- +-=++.|+.+||+.
T Consensus 37 ~e~pai~~~~~~~ei~rl~~f~~kck~~yp~g 68 (135)
T PHA02103 37 YEIPAIDADRTKAEIVRLITFMDKCKAEYPRG 68 (135)
T ss_pred EeccccccchhhHHHHHHHHHHHHHHhhCCCC
Confidence 88999988765532 33368999999985
No 86
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=21.56 E-value=79 Score=24.06 Aligned_cols=38 Identities=21% Similarity=0.474 Sum_probs=23.7
Q ss_pred ccccccccCCCC---------CChHHHHHHHHH-HHhCCCeeEEEecc
Q 029245 80 NKKFEALSYLPS---------LSDDSIAKEIDY-MLKKGWIPCLEFDE 117 (196)
Q Consensus 80 ~kkfET~SyLPp---------Ls~~qI~kQV~y-lL~qGw~pclEfad 117 (196)
-..|.||+++|+ |.++.|.+.|+- |-++||+...|-+|
T Consensus 14 f~~ykTy~~~~~~~~~~~~~~~~~~~i~~~v~~~L~~~G~~~~~~~aD 61 (151)
T PF13590_consen 14 FSQYKTYAFVPSSSDPAQSNPLDDQRIQDAVEQELAAKGYRRVPENAD 61 (151)
T ss_pred CCCCCeEEEecCCcCccccCcHHHHHHHHHHHHHHHHCCCeecccCCC
Confidence 346778888877 344455555544 44589999845443
No 87
>PRK06925 flagellar motor protein MotS; Reviewed
Probab=21.52 E-value=1.3e+02 Score=25.79 Aligned_cols=29 Identities=17% Similarity=0.293 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecCC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQK 178 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~r 178 (196)
+..++|.+|.+.++.+|+ .|+|.|+-...
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 88
>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=21.47 E-value=41 Score=25.84 Aligned_cols=14 Identities=43% Similarity=0.738 Sum_probs=11.5
Q ss_pred ccccCCCCCChHHH
Q 029245 84 EALSYLPSLSDDSI 97 (196)
Q Consensus 84 ET~SyLPpLs~~qI 97 (196)
|=|.|||.||+.+=
T Consensus 22 eiLP~LpCLT~~Dq 35 (84)
T cd08811 22 EILPYLPCLTASDQ 35 (84)
T ss_pred HhcCccccCchhhH
Confidence 56889999998763
No 89
>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=21.38 E-value=2.7e+02 Score=18.89 Aligned_cols=33 Identities=12% Similarity=0.231 Sum_probs=22.5
Q ss_pred HHHHHHHHCCCC-eEEEEeee-cCCCeEEEEEEEe
Q 029245 156 EIQECKKAYPNA-YIRCLAFN-NQKQGQCMSFLIQ 188 (196)
Q Consensus 156 EieeC~k~~P~~-YVRLiGfD-n~rQvq~~sfIV~ 188 (196)
|||+....||+- =+=++|+. ...+.+++.|++-
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 4566778888863
No 90
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=21.36 E-value=1.4e+02 Score=24.49 Aligned_cols=29 Identities=10% Similarity=0.027 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~ 177 (196)
+..++|.+|-+-++.+|...|+|+|+-..
T Consensus 66 ~~~~~L~~ia~~l~~~~~~~v~I~GhTD~ 94 (160)
T PRK09967 66 ESQQQIQTMAAKLASTGLTHARMDGHTDN 94 (160)
T ss_pred HHHHHHHHHHHHHHhCCCceEEEEEEcCC
Confidence 67789999999999999999999998543
No 91
>PRK10510 putative outer membrane lipoprotein; Provisional
Probab=21.32 E-value=1.3e+02 Score=25.81 Aligned_cols=29 Identities=14% Similarity=0.407 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHHCCCCeEEEEeeecC
Q 029245 149 DSSQILNEIQECKKAYPNAYIRCLAFNNQ 177 (196)
Q Consensus 149 D~sqVL~EieeC~k~~P~~YVRLiGfDn~ 177 (196)
+..+.|.+|.+-++.||+..|+|.|+=..
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 92
>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=21.01 E-value=2.4e+02 Score=18.53 Aligned_cols=30 Identities=13% Similarity=0.125 Sum_probs=20.5
Q ss_pred CCCChHHHHHHHHHHHhCCCeeEEEeccCC
Q 029245 90 PSLSDDSIAKEIDYMLKKGWIPCLEFDEVG 119 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~qGw~pclEfad~~ 119 (196)
=.++...+.++|+-|+.+||+=-.+-.+++
T Consensus 28 ~~~~~~~vs~~i~~L~~~glv~~~~~~~d~ 57 (68)
T PF13463_consen 28 LGISKSTVSRIIKKLEEKGLVEKERDPHDK 57 (68)
T ss_dssp TT--HHHHHHHHHHHHHTTSEEEEEESSCT
T ss_pred HCcCHHHHHHHHHHHHHCCCEEecCCCCcC
Confidence 346778899999999999998433333333
No 93
>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=20.99 E-value=26 Score=34.50 Aligned_cols=39 Identities=15% Similarity=0.474 Sum_probs=26.9
Q ss_pred CCCCccCCcceeecCCCCCCCCCHHHHHHHHHHHHHHCCCC
Q 029245 127 KMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNA 167 (196)
Q Consensus 127 ~sp~yyd~rYWtMWKLPmFg~tD~sqVL~EieeC~k~~P~~ 167 (196)
=++.+|++.||+||.- ||+=+.-.- ..|...++..|-.+
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 34566665555443
No 94
>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=20.93 E-value=75 Score=25.57 Aligned_cols=27 Identities=22% Similarity=0.375 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHCCCCeEEEEeeecCCC
Q 029245 152 QILNEIQECKKAYPNAYIRCLAFNNQKQ 179 (196)
Q Consensus 152 qVL~EieeC~k~~P~~YVRLiGfDn~rQ 179 (196)
.|++.+.++...-|+. |.|+|||+...
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 5666666665555665 99999998753
No 95
>cd08586 PI-PLCc_BcPLC_like Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins. This subfamily corresponds to the catalytic domain present in Bacillus cereus phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and its sequence homologs found in bacteria and 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. Their 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. This family also includes some uncharacterized eukaryotic homologs, which
Probab=20.85 E-value=2e+02 Score=25.63 Aligned_cols=34 Identities=21% Similarity=0.202 Sum_probs=27.2
Q ss_pred ecCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEE
Q 029245 139 MWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCL 172 (196)
Q Consensus 139 MWKLPmFg~tD~sqVL~EieeC~k~~P~~YVRLi 172 (196)
++-.+.+......+||.+|..-+++||++.|=|.
T Consensus 64 ~~Hg~~~~~~~~~dvL~~i~~FL~~nP~E~Vil~ 97 (279)
T cd08586 64 IHHGPFYQGLTFGDVLNECYSFLDANPSETIIMS 97 (279)
T ss_pred EEccCccccCcHHHHHHHHHHHHHhCCCcEEEEE
Confidence 3444555457889999999999999999998664
No 96
>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=20.76 E-value=35 Score=26.41 Aligned_cols=12 Identities=50% Similarity=1.392 Sum_probs=6.2
Q ss_pred cCCcceeecCCC
Q 029245 132 YDGRYWTMWKLP 143 (196)
Q Consensus 132 yd~rYWtMWKLP 143 (196)
|+|.||..|+|+
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 97
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=20.61 E-value=1.2e+02 Score=25.62 Aligned_cols=18 Identities=22% Similarity=0.283 Sum_probs=16.7
Q ss_pred CCCChHHHHHHHHHHHhC
Q 029245 90 PSLSDDSIAKEIDYMLKK 107 (196)
Q Consensus 90 PpLs~~qI~kQV~ylL~q 107 (196)
..||||||..=..|||.|
T Consensus 131 ~~LsdeEL~aVAaYIl~q 148 (163)
T CHL00133 131 RSLTDEDLYAIAGHILLQ 148 (163)
T ss_pred CCCCHHHHHHHHHHHHhc
Confidence 679999999999999987
No 98
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=20.58 E-value=1.1e+02 Score=21.99 Aligned_cols=20 Identities=5% Similarity=0.164 Sum_probs=16.8
Q ss_pred CCCCeEEEEeeecCCCeEEE
Q 029245 164 YPNAYIRCLAFNNQKQGQCM 183 (196)
Q Consensus 164 ~P~~YVRLiGfDn~rQvq~~ 183 (196)
.-++||+|+.+|+..++..+
T Consensus 16 ~~~~Yl~l~~~~~~G~v~~L 35 (83)
T PF14326_consen 16 NRDGYLYLFYIDADGKVTLL 35 (83)
T ss_pred CCCeEEEEEEECCCCCEEEE
Confidence 45789999999999888765
No 99
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=20.57 E-value=91 Score=23.59 Aligned_cols=75 Identities=21% Similarity=0.371 Sum_probs=43.3
Q ss_pred cccccc-ccCCCCCChHHHHHHHH---HHHh-CCCeeEEEeccC---CceeecCCCCCCccCCcceeecCCCCCCCCCHH
Q 029245 80 NKKFEA-LSYLPSLSDDSIAKEID---YMLK-KGWIPCLEFDEV---GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS 151 (196)
Q Consensus 80 ~kkfET-~SyLPpLs~~qI~kQV~---ylL~-qGw~pclEfad~---~~~~R~~~~sp~yyd~rYWtMWKLPmFg~tD~s 151 (196)
.++||| |-.=|.|+++++.+-++ .+|. +|=.+ ++.++- +..|.=. .+-+|.|..+ -|.+ +.
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 478998 67779999998876544 4454 56443 333332 2222211 2234555432 2444 35
Q ss_pred HHHHHHHHHHHHCC
Q 029245 152 QILNEIQECKKAYP 165 (196)
Q Consensus 152 qVL~EieeC~k~~P 165 (196)
++++||+.-.+-..
T Consensus 74 ~~i~eler~lri~e 87 (97)
T CHL00123 74 KLVNSLEKALKLDE 87 (97)
T ss_pred HHHHHHHHHhCCCC
Confidence 89999998775444
No 100
>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=20.53 E-value=79 Score=25.69 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=15.0
Q ss_pred cCCC-CCChHHHHHHHHHHHhCC
Q 029245 87 SYLP-SLSDDSIAKEIDYMLKKG 108 (196)
Q Consensus 87 SyLP-pLs~~qI~kQV~ylL~qG 108 (196)
+||| .||+++|.+-|+-.+..-
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 5887 589999999998888753
No 101
>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]
Probab=20.43 E-value=39 Score=32.06 Aligned_cols=45 Identities=22% Similarity=0.371 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCCC
Q 029245 144 MFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 194 (196)
Q Consensus 144 mFg~tD~sqVL~EieeC~k~~P~~YVRLiGfDn~rQvq~~sfIV~RP~~~~ 194 (196)
.-||.+.-+-|.|+-|.---||.-||+| |||+-+.+ +.|-|+|..
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 4578888889999999999999999996 89999876 456676643
No 102
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=20.28 E-value=73 Score=27.41 Aligned_cols=27 Identities=15% Similarity=0.292 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHCCCCeEEEEeeecCCCe
Q 029245 153 ILNEIQECKKAYPNAYIRCLAFNNQKQG 180 (196)
Q Consensus 153 VL~EieeC~k~~P~~YVRLiGfDn~rQv 180 (196)
|++.+++.-..-|++ |.|||||+....
T Consensus 252 ~~~al~~~G~~vP~d-isvigfD~~~~~ 278 (346)
T PRK10401 252 ALTALKDNGIAIPLH-LSIIGFDDIPIA 278 (346)
T ss_pred HHHHHHHcCCCCCCc-eEEEEeCCchHH
Confidence 333333333334666 999999997543
No 103
>PF11181 YflT: Heat induced stress protein YflT
Probab=20.18 E-value=97 Score=23.26 Aligned_cols=19 Identities=11% Similarity=0.331 Sum_probs=17.2
Q ss_pred ChHHHHHHHHHHHhCCCee
Q 029245 93 SDDSIAKEIDYMLKKGWIP 111 (196)
Q Consensus 93 s~~qI~kQV~ylL~qGw~p 111 (196)
+++|+...|+-|.++||..
T Consensus 8 ~~~E~~~~I~~L~~~Gy~~ 26 (103)
T PF11181_consen 8 NEEEALSAIEELKAQGYSE 26 (103)
T ss_pred CHHHHHHHHHHHHHcCCCc
Confidence 6899999999999999864
No 104
>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=20.10 E-value=27 Score=26.00 Aligned_cols=23 Identities=22% Similarity=0.543 Sum_probs=15.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCeEE
Q 029245 148 NDSSQILNEIQECKKAYPNAYIR 170 (196)
Q Consensus 148 tD~sqVL~EieeC~k~~P~~YVR 170 (196)
.+.+.+|.||+.-+..+..+|||
T Consensus 39 ~~vD~lLDeID~vLE~NAeeFVr 61 (69)
T PF05639_consen 39 DDVDDLLDEIDSVLETNAEEFVR 61 (69)
T ss_dssp CCHHHHHHHHTTTSSSC------
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 58899999999999999999998
No 105
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=20.07 E-value=66 Score=21.72 Aligned_cols=22 Identities=27% Similarity=0.354 Sum_probs=16.2
Q ss_pred CCCCCChHHHHHHHHHHHhCCCeeE
Q 029245 88 YLPSLSDDSIAKEIDYMLKKGWIPC 112 (196)
Q Consensus 88 yLPpLs~~qI~kQV~ylL~qGw~pc 112 (196)
.+..|||+||.+++ ++.|..|+
T Consensus 2 d~~~LSd~eL~~~L---~~~G~~~g 23 (44)
T smart00540 2 DVDRLSDAELRAEL---KQYGLPPG 23 (44)
T ss_pred chhHcCHHHHHHHH---HHcCCCCC
Confidence 35679999999875 66676554
Done!