Query 045537
Match_columns 291
No_of_seqs 176 out of 1170
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 03:05:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045537.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045537hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00046 RNA methyltransferas 100.0 2.5E-60 5.3E-65 432.7 25.2 228 43-282 1-236 (240)
2 COG1385 Uncharacterized protei 100.0 3.7E-60 7.9E-65 432.8 21.6 230 42-281 1-242 (246)
3 PF04452 Methyltrans_RNA: RNA 100.0 1.6E-59 3.4E-64 423.3 17.1 217 54-281 1-225 (225)
4 PRK11713 16S ribosomal RNA met 100.0 6.7E-57 1.5E-61 408.6 23.3 222 44-283 1-230 (234)
5 PRK02135 hypothetical protein; 96.0 0.019 4.2E-07 51.3 6.7 78 194-275 113-190 (201)
6 PF04013 Methyltrn_RNA_2: Puta 95.7 0.022 4.7E-07 51.0 5.5 79 194-276 112-191 (199)
7 PF00588 SpoU_methylase: SpoU 92.8 0.37 8.1E-06 39.9 6.6 108 123-252 8-117 (142)
8 COG1901 Uncharacterized conser 91.9 0.54 1.2E-05 41.7 6.6 78 194-275 111-188 (197)
9 PRK11081 tRNA guanosine-2'-O-m 87.6 5.2 0.00011 36.5 9.8 111 116-252 20-134 (229)
10 TIGR01080 rplX_A_E ribosomal p 87.4 1.4 3E-05 36.2 5.2 49 54-102 25-74 (114)
11 TIGR00185 rRNA_methyl_2 rRNA m 86.8 4.8 0.0001 34.2 8.6 105 123-251 8-114 (153)
12 PRK10864 putative methyltransf 86.7 3.5 7.5E-05 40.0 8.4 107 121-251 203-312 (346)
13 TIGR00186 rRNA_methyl_3 rRNA m 84.0 8.6 0.00019 35.0 9.4 108 121-250 95-204 (237)
14 PRK01130 N-acetylmannosamine-6 83.2 4 8.7E-05 36.3 6.7 40 237-276 176-216 (221)
15 PRK15114 tRNA (cytidine/uridin 82.5 14 0.0003 34.0 10.1 114 117-253 6-130 (245)
16 PRK11181 23S rRNA (guanosine-2 78.5 15 0.00032 33.7 8.9 108 121-251 100-210 (244)
17 PRK08883 ribulose-phosphate 3- 76.4 8.9 0.00019 34.7 6.7 134 114-270 59-203 (220)
18 smart00739 KOW KOW (Kyprides, 75.1 7.1 0.00015 22.8 3.9 26 70-95 2-27 (28)
19 PF00467 KOW: KOW motif; Inte 74.8 5.3 0.00012 24.9 3.4 29 72-100 1-29 (32)
20 PF09895 DUF2122: RecB-family 72.6 14 0.00031 29.9 6.2 77 196-281 27-104 (106)
21 PRK08091 ribulose-phosphate 3- 71.9 7.6 0.00016 35.5 5.1 134 114-270 69-215 (228)
22 smart00333 TUDOR Tudor domain. 71.4 18 0.00039 24.7 5.9 34 70-103 3-37 (57)
23 cd00377 ICL_PEPM Members of th 71.1 28 0.00061 31.8 8.7 137 128-273 84-237 (243)
24 PF11717 Tudor-knot: RNA bindi 70.6 6.7 0.00015 27.5 3.6 26 70-95 1-26 (55)
25 TIGR03784 marine_sortase sorta 68.3 7.5 0.00016 34.0 4.1 42 52-93 91-132 (174)
26 smart00743 Agenet Tudor-like d 68.0 20 0.00042 25.2 5.6 35 68-102 1-37 (61)
27 PRK12281 rplX 50S ribosomal pr 66.4 15 0.00031 27.9 4.8 35 68-102 5-39 (76)
28 PRK08745 ribulose-phosphate 3- 65.4 26 0.00057 31.8 7.2 134 114-270 63-207 (223)
29 cd04726 KGPDC_HPS 3-Keto-L-gul 64.8 24 0.00051 30.5 6.6 119 132-270 68-194 (202)
30 cd05829 Sortase_E Sortase E (S 63.6 13 0.00029 31.2 4.6 42 52-93 50-96 (144)
31 cd04729 NanE N-acetylmannosami 62.2 26 0.00057 31.0 6.6 121 133-270 84-214 (219)
32 CHL00141 rpl24 ribosomal prote 61.4 20 0.00043 27.6 4.9 35 68-102 7-41 (83)
33 cd00452 KDPG_aldolase KDPG and 61.2 29 0.00062 30.2 6.5 108 132-266 67-175 (190)
34 PRK13125 trpA tryptophan synth 60.7 58 0.0013 29.5 8.7 121 128-267 88-219 (244)
35 PRK10358 putative rRNA methyla 60.5 1.1E+02 0.0023 26.1 10.4 110 117-250 3-113 (157)
36 PRK08005 epimerase; Validated 60.4 28 0.0006 31.4 6.3 130 114-270 59-199 (210)
37 PTZ00170 D-ribulose-5-phosphat 60.1 32 0.00069 31.1 6.8 133 114-270 66-209 (228)
38 TIGR00050 rRNA_methyl_1 RNA me 59.3 72 0.0016 29.0 9.0 112 117-253 5-127 (233)
39 TIGR00262 trpA tryptophan synt 58.7 38 0.00081 31.3 7.1 118 130-267 104-232 (256)
40 PRK14057 epimerase; Provisiona 57.6 49 0.0011 30.8 7.6 135 114-270 76-229 (254)
41 TIGR01079 rplX_bact ribosomal 57.2 24 0.00053 28.3 4.9 35 68-102 2-36 (104)
42 COG1756 Mra1 Uncharacterized c 56.0 48 0.001 30.3 7.0 76 195-279 137-216 (223)
43 PRK01191 rpl24p 50S ribosomal 54.9 23 0.00049 29.4 4.4 48 54-101 29-77 (120)
44 PRK00004 rplX 50S ribosomal pr 53.8 30 0.00065 27.8 4.9 35 68-102 3-37 (105)
45 COG4080 SpoU rRNA Methylase fa 52.9 38 0.00082 28.9 5.4 127 126-281 12-141 (147)
46 TIGR00405 L26e_arch ribosomal 51.1 38 0.00083 28.1 5.4 42 56-97 69-114 (145)
47 TIGR02320 PEP_mutase phosphoen 50.7 72 0.0016 30.1 7.7 144 126-278 90-256 (285)
48 PF14801 GCD14_N: tRNA methylt 50.7 21 0.00046 25.4 3.1 22 70-91 6-27 (54)
49 PTZ00194 60S ribosomal protein 49.4 24 0.00052 30.1 3.8 49 54-102 30-79 (143)
50 PRK08559 nusG transcription an 48.3 45 0.00097 28.3 5.4 49 56-104 77-131 (153)
51 PF06003 SMN: Survival motor n 47.8 37 0.00081 31.6 5.2 30 67-96 66-96 (264)
52 PF00834 Ribul_P_3_epim: Ribul 47.2 8 0.00017 34.5 0.7 134 112-268 56-200 (201)
53 PF09953 DUF2187: Uncharacteri 47.1 44 0.00096 24.1 4.3 32 69-104 3-34 (57)
54 COG0250 NusG Transcription ant 46.9 45 0.00097 29.3 5.3 49 52-100 95-154 (178)
55 PF02598 Methyltrn_RNA_3: Puta 46.3 9.2 0.0002 36.2 1.0 95 184-280 177-291 (291)
56 PRK00103 rRNA large subunit me 46.2 1.2E+02 0.0027 26.0 7.8 73 204-280 64-143 (157)
57 TIGR00693 thiE thiamine-phosph 44.3 22 0.00047 30.7 3.0 35 240-274 158-192 (196)
58 PRK06739 pyruvate kinase; Vali 43.6 1.2E+02 0.0026 29.6 8.2 71 70-146 110-183 (352)
59 PRK00278 trpC indole-3-glycero 43.2 16 0.00035 33.8 2.0 31 240-270 217-248 (260)
60 PLN02762 pyruvate kinase compl 42.6 80 0.0017 32.4 7.0 71 70-146 141-221 (509)
61 PRK04180 pyridoxal biosynthesi 42.6 34 0.00073 32.6 4.0 46 239-284 210-259 (293)
62 cd06166 Sortase_D_5 Sortase D 42.3 41 0.00089 27.3 4.1 31 63-94 58-88 (126)
63 COG0036 Rpe Pentose-5-phosphat 42.3 1.3E+02 0.0028 27.5 7.7 134 113-270 61-205 (220)
64 cd05828 Sortase_D_4 Sortase D 41.1 54 0.0012 26.6 4.7 40 53-93 45-84 (127)
65 TIGR00922 nusG transcription t 40.9 86 0.0019 26.6 6.1 51 51-101 89-153 (172)
66 PRK05826 pyruvate kinase; Prov 40.9 1.7E+02 0.0038 29.6 9.1 72 70-146 118-191 (465)
67 cd00958 DhnA Class I fructose- 40.5 2.3E+02 0.005 25.1 9.1 40 231-271 180-223 (235)
68 TIGR01182 eda Entner-Doudoroff 39.4 93 0.002 27.9 6.3 110 132-269 71-183 (204)
69 cd04508 TUDOR Tudor domains ar 39.4 1.1E+02 0.0023 19.9 5.5 31 73-103 1-33 (48)
70 PF02590 SPOUT_MTase: Predicte 38.9 91 0.002 26.7 5.9 77 200-280 60-143 (155)
71 PF06995 Phage_P2_GpU: Phage P 38.0 68 0.0015 25.9 4.8 75 23-97 9-97 (121)
72 TIGR02317 prpB methylisocitrat 37.5 2.7E+02 0.0059 26.3 9.3 146 126-278 86-245 (285)
73 PRK05609 nusG transcription an 37.0 91 0.002 26.6 5.7 49 53-101 99-160 (181)
74 PF04203 Sortase: Sortase fami 36.8 38 0.00082 27.1 3.1 34 58-94 52-85 (128)
75 COG0566 SpoU rRNA methylases [ 36.8 1.3E+02 0.0029 27.8 7.0 104 122-247 115-221 (260)
76 PF05641 Agenet: Agenet domain 36.4 96 0.0021 22.4 4.9 32 71-102 2-38 (68)
77 TIGR00343 pyridoxal 5'-phospha 36.4 49 0.0011 31.4 4.1 31 239-269 204-235 (287)
78 PLN02765 pyruvate kinase 35.6 2.7E+02 0.0059 28.7 9.6 75 70-146 142-225 (526)
79 PRK09722 allulose-6-phosphate 35.5 1.6E+02 0.0034 26.9 7.2 132 114-267 60-203 (229)
80 cd00564 TMP_TenI Thiamine mono 35.3 29 0.00062 29.3 2.3 31 240-270 156-186 (196)
81 TIGR00739 yajC preprotein tran 35.2 80 0.0017 24.2 4.5 31 68-102 36-66 (84)
82 CHL00200 trpA tryptophan synth 35.2 1.2E+02 0.0027 28.1 6.6 120 129-268 107-237 (263)
83 PF12945 YcgR_2: Flagellar pro 34.7 1.1E+02 0.0024 22.4 5.2 31 70-100 1-36 (87)
84 PF13550 Phage-tail_3: Putativ 33.2 69 0.0015 26.3 4.2 26 68-94 138-163 (164)
85 PRK00043 thiE thiamine-phospha 33.0 53 0.0011 28.4 3.6 35 237-271 163-197 (212)
86 cd04727 pdxS PdxS is a subunit 32.9 61 0.0013 30.7 4.2 31 239-269 201-232 (283)
87 COG0198 RplX Ribosomal protein 32.4 85 0.0018 25.3 4.3 34 67-100 2-35 (104)
88 PTZ00066 pyruvate kinase; Prov 32.3 1.5E+02 0.0033 30.4 7.2 72 70-146 154-228 (513)
89 PRK05585 yajC preprotein trans 32.1 88 0.0019 25.1 4.4 40 59-102 42-81 (106)
90 cd00004 Sortase Sortases are c 31.8 72 0.0016 25.7 4.0 29 64-93 59-87 (128)
91 cd02787 MopB_CT_ydeP The MopB_ 31.7 1.6E+02 0.0035 22.9 5.9 30 51-84 30-59 (112)
92 cd05830 Sortase_D_5 Sortase D 31.3 66 0.0014 26.5 3.7 29 64-93 60-88 (137)
93 TIGR03128 RuMP_HxlA 3-hexulose 31.0 41 0.00089 29.2 2.6 117 132-270 67-194 (206)
94 PLN02623 pyruvate kinase 30.0 3.2E+02 0.007 28.6 9.1 71 70-146 223-296 (581)
95 COG1188 Ribosome-associated he 29.4 66 0.0014 25.8 3.2 53 39-95 6-73 (100)
96 PF01272 GreA_GreB: Transcript 29.3 1E+02 0.0023 22.7 4.2 39 52-94 38-76 (77)
97 TIGR01076 sortase_fam LPXTG-si 29.1 93 0.002 25.6 4.3 31 62-93 56-86 (136)
98 PRK04171 ribosome biogenesis p 28.9 1.9E+02 0.0042 26.4 6.5 77 195-279 135-215 (222)
99 PRK05753 nucleoside diphosphat 28.4 1E+02 0.0022 25.7 4.4 29 66-94 98-126 (137)
100 PF11325 DUF3127: Domain of un 28.0 57 0.0012 25.3 2.6 33 54-89 40-73 (84)
101 TIGR00376 DNA helicase, putati 27.4 1.9E+02 0.0041 30.4 7.1 71 69-141 57-129 (637)
102 PF07680 DoxA: TQO small subun 27.1 1.5E+02 0.0032 25.0 5.1 53 31-91 76-132 (133)
103 PRK06247 pyruvate kinase; Prov 26.8 3.6E+02 0.0078 27.5 8.7 71 70-146 118-191 (476)
104 KOG4201 Anthranilate synthase 25.9 78 0.0017 29.2 3.4 39 233-271 237-275 (289)
105 PRK10039 hypothetical protein; 25.9 50 0.0011 27.6 2.0 17 238-254 78-94 (127)
106 PF09671 Spore_GerQ: Spore coa 25.6 1.3E+02 0.0028 23.1 4.0 41 59-99 5-52 (81)
107 PRK11320 prpB 2-methylisocitra 25.5 5.4E+02 0.012 24.3 9.2 145 126-277 91-249 (292)
108 cd06541 ASCH ASC-1 homology or 25.4 1.3E+02 0.0028 23.6 4.3 27 68-94 29-55 (105)
109 cd00288 Pyruvate_Kinase Pyruva 25.3 4.8E+02 0.01 26.6 9.3 72 70-146 118-192 (480)
110 PRK06354 pyruvate kinase; Prov 25.2 4.4E+02 0.0096 27.6 9.2 71 70-146 121-196 (590)
111 PF01052 SpoA: Surface present 24.8 1.6E+02 0.0034 21.5 4.4 39 65-104 24-72 (77)
112 PTZ00300 pyruvate kinase; Prov 24.7 3.1E+02 0.0066 27.8 7.7 68 70-146 91-165 (454)
113 TIGR01956 NusG_myco NusG famil 24.6 1.6E+02 0.0034 27.6 5.2 35 68-102 204-240 (258)
114 PF09846 DUF2073: Uncharacteri 24.4 55 0.0012 26.4 1.9 21 230-253 19-39 (104)
115 PRK05886 yajC preprotein trans 24.2 1.5E+02 0.0032 24.1 4.4 37 62-102 31-67 (109)
116 cd02792 MopB_CT_Formate-Dh-Na- 24.1 1E+02 0.0022 24.2 3.5 30 51-84 34-63 (122)
117 PF09465 LBR_tudor: Lamin-B re 24.1 2E+02 0.0043 20.6 4.5 30 68-97 4-34 (55)
118 PLN02334 ribulose-phosphate 3- 23.6 64 0.0014 28.9 2.5 34 237-270 177-210 (229)
119 TIGR00246 tRNA_RlmH_YbeA rRNA 23.6 4.2E+02 0.0091 22.6 7.4 69 208-280 66-140 (153)
120 TIGR01955 RfaH transcriptional 23.2 1.7E+02 0.0037 24.3 4.9 29 68-96 107-135 (159)
121 PF14258 DUF4350: Domain of un 23.1 1.1E+02 0.0025 21.8 3.3 24 230-253 34-58 (70)
122 PRK13307 bifunctional formalde 22.9 1.9E+02 0.004 28.7 5.7 121 131-270 240-366 (391)
123 cd06462 Peptidase_S24_S26 The 22.1 3E+02 0.0064 19.5 6.0 51 43-100 9-60 (84)
124 PRK09014 rfaH transcriptional 21.8 1.8E+02 0.0039 24.4 4.8 45 52-96 84-136 (162)
125 smart00561 MBT Present in Dros 21.7 2.7E+02 0.0059 21.7 5.5 37 67-103 25-63 (96)
126 cd06555 ASCH_PF0470_like ASC-1 20.9 1.9E+02 0.0042 23.4 4.5 36 53-94 21-57 (109)
127 COG3127 Predicted ABC-type tra 20.5 1.1E+02 0.0025 32.8 3.8 33 62-95 603-635 (829)
128 PRK04302 triosephosphate isome 20.3 1.1E+02 0.0023 27.4 3.2 37 232-270 173-210 (223)
129 PF07653 SH3_2: Variant SH3 do 20.2 1.4E+02 0.0031 20.2 3.2 23 68-90 16-40 (55)
130 PRK04950 ProP expression regul 20.2 1.5E+02 0.0033 26.9 4.1 35 69-104 166-200 (213)
131 cd02791 MopB_CT_Nitrate-R-NapA 20.2 1.1E+02 0.0025 23.9 3.1 30 51-84 34-63 (122)
No 1
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=100.00 E-value=2.5e-60 Score=432.72 Aligned_cols=228 Identities=25% Similarity=0.350 Sum_probs=194.1
Q ss_pred cccEEEe----CCcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCCccceE
Q 045537 43 GIPRFFS----QGGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQHTQWNV 118 (291)
Q Consensus 43 ~~~rff~----~~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~~~i~l 118 (291)
+|++||. .++.+.|+++++||+++|||+++||.|.++||+|+.|.|+|++++++.+.+++.+...... +.+..+
T Consensus 1 ~m~~~~~~~~~~~~~i~l~~~~~~Hl~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~~~~~~~~--~~~~~i 78 (240)
T TIGR00046 1 RMRIVYHPEQLEEATISLTEEEAHHLVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELLEGESEKR--ELPLKI 78 (240)
T ss_pred CCcEEEeCccccCCeEEEChHHHhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEEecccCCC--CCCcEE
Confidence 4667886 3456899999999999999999999999999999999999999999999888776543222 334567
Q ss_pred EEEeeccCCCcHHHHHHHHHhcCccEEEEeeccccccccccc----ccccccccchhhchhchhhhhcCCCCcceeEcCC
Q 045537 119 FAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIG----DNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPP 194 (291)
Q Consensus 119 ~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~----~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p 194 (291)
++++|+||+++|||+|||||||||++|+|+.|+ ||+++. .+|.+||+ +|+ +||||||+|+++|+|.+|
T Consensus 79 ~l~~al~K~~~~d~il~katELGv~~i~p~~s~---rs~~~~~~~~~~k~~rw~---~i~--~eA~~Q~~r~~lP~i~~~ 150 (240)
T TIGR00046 79 HLAIVLIKGKKMEFIIRKLTELGVSKIIPFNAE---RSVVKLDIEAIKKLERWQ---KIA--IEAAEQSGRNIVPEIKPP 150 (240)
T ss_pred EEEEeecCCccHHHHHHHHHHcCCCEEEEEEec---cceeccCchHHHHHHHHH---HHH--HHHHHhcCCCCCCEECCc
Confidence 788999999999999999999999999999999 997632 35788999 999 999999999999999999
Q ss_pred CCHhhhccccCCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHH
Q 045537 195 MKIDGLLPLVSQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIA 274 (291)
Q Consensus 195 ~~l~~~l~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~ 274 (291)
.+|+++++...+.+..+++++++.+....+.. ..++++++||||||||++|++.+.++||.+||||+||||||||+++
T Consensus 151 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~l~~--~~~~v~~~IGPEGGfs~~Ei~~~~~~gf~~vsLG~rILR~ETA~i~ 228 (240)
T TIGR00046 151 KNLKEKCAEAYEEALKLNFHPEASPLSANLPI--PAGNIVIIIGPEGGFSEKEIQLLKEKGFTPVLLGPRILRTETAPLY 228 (240)
T ss_pred CCHHHHHhhCcCCCeEEEECCcccchhhhhcc--CCCcEEEEECCCCCCCHHHHHHHHHCCCEEEccCCcchhhccHHHH
Confidence 99999987655445667777665443333422 2346999999999999999999999999999999999999999999
Q ss_pred HHHHHHHc
Q 045537 275 LLATLMLC 282 (291)
Q Consensus 275 ala~l~~~ 282 (291)
|+|++.++
T Consensus 229 als~~~~~ 236 (240)
T TIGR00046 229 ALSILQAL 236 (240)
T ss_pred HHHHHHHH
Confidence 99998763
No 2
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=3.7e-60 Score=432.79 Aligned_cols=230 Identities=32% Similarity=0.461 Sum_probs=197.6
Q ss_pred ccccEEEe-----CCcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCCccc
Q 045537 42 GGIPRFFS-----QGGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQHTQW 116 (291)
Q Consensus 42 ~~~~rff~-----~~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~~~i 116 (291)
|+|+|+|+ .+..+.++++++||+.+|||+++||.|.++||+|+.|.|+|++++++.+.+++.+..... ++.+.
T Consensus 1 ~~~~~~~v~~~~~~~~~~~l~~~~~~Hl~~VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i~~~~~~~--~e~~~ 78 (246)
T COG1385 1 MRMPRLFVDEELAEGATVILTGDEAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKIVEQLEPN--PELPL 78 (246)
T ss_pred CCceeEeecccccCCCEEEECchhhhhHHheeecCCCCEEEEEeCCCcEEEEEEeecCCCceEEEEEeecccC--CCCCc
Confidence 78999998 467899999999999999999999999999999999999999999999999888765433 34566
Q ss_pred eEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccc-c---ccccccchhhchhchhhhhcCCCCcceeEc
Q 045537 117 NVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGD-N---GFLSCNFYYGFIANSAFVYGGQRLHEMVLN 192 (291)
Q Consensus 117 ~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~-~---k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~ 192 (291)
.+++++++||+++|||+|||||||||+.|+|+.++ ||+.+++ + |++||+ +|+ +||||||+|+.+|+|.
T Consensus 79 ~i~l~~~i~kg~k~d~iiqkatELGv~~i~p~~te---r~~~k~~~~~~~kler~~---ki~--ieAaEQs~R~~vP~I~ 150 (246)
T COG1385 79 KITLAQAIPKGDKLELIIQKATELGVSKIIPLITE---RSVVKLDGKKAAKLERWQ---KIA--IEAAEQSGRNVVPEIK 150 (246)
T ss_pred eEEEEEEcCccHHHHHHHHHHHHhCcceEEEEeee---eeEEeccccchhHHHHHH---HHH--HHHHHhcCCCcCCeee
Confidence 78889999999999999999999999999999999 9987532 2 478888 999 9999999999999999
Q ss_pred CCCCHhhhccccCCCc-eEEEEeCCCCChhhhhc--cCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccc
Q 045537 193 PPMKIDGLLPLVSQSK-LAFVAIAEATPLVTALS--SSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVE 269 (291)
Q Consensus 193 ~p~~l~~~l~~~~~~~-~~lv~~~~~~~~~~~l~--~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtE 269 (291)
.+.+|+++++...+++ ..+.+++........+. .....++++++||||||||++|++++.++||.+|+|||||||||
T Consensus 151 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iiIGPEGGfs~~Ei~~l~~~g~~~v~LGprILRtE 230 (246)
T COG1385 151 PPESLKELLKEIDDEDALKLIYEEKAKEGLLALPLLEALPEGKVLLIIGPEGGFSEDEIELLREAGFTPVSLGPRILRTE 230 (246)
T ss_pred chhhHHHHHHhcccchhhhheeccccccccccchhhhcccCCcEEEEECCCCCCCHHHHHHHHHCCCeEeccCCceehhh
Confidence 9999999999886555 34455544332211111 11235789999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHH
Q 045537 270 TATIALLATLML 281 (291)
Q Consensus 270 TAai~ala~l~~ 281 (291)
||+++|+|++++
T Consensus 231 TAal~ala~i~~ 242 (246)
T COG1385 231 TAALAALAALQA 242 (246)
T ss_pred HHHHHHHHHHHH
Confidence 999999999964
No 3
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=100.00 E-value=1.6e-59 Score=423.33 Aligned_cols=217 Identities=33% Similarity=0.522 Sum_probs=166.8
Q ss_pred EEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCCccceEEEEeeccCCCcHHHH
Q 045537 54 VRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQHTQWNVFAAFGTLKGGRADWL 133 (291)
Q Consensus 54 v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~~~i~l~la~~l~K~~r~d~i 133 (291)
|.|+++++||+.+|||+++||.|.++||+|+.|.|+|++++++.+.+++.+...... +.+..+++++|+||+++|||+
T Consensus 1 V~L~~~~~~Hl~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~~~~~~~~--~~~~~i~L~~al~K~~~~d~i 78 (225)
T PF04452_consen 1 VELDGEEAHHLVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRILEELEIPP--EPPPEITLAQALPKGDRMDWI 78 (225)
T ss_dssp EEEEHHHHHHHHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE-----SSSSEEEEEEE--STTHHHHH
T ss_pred CEecHHHHHHHHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEeeeccCCC--CCcceEEEEEEEEcCccHHHH
Confidence 579999999999999999999999999999999999999999999998886644322 334457778899999999999
Q ss_pred HHHHHhcCccEEEEeecccccccccc-----cccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccCCCc
Q 045537 134 VEKCTELGAQSVTPLLTELHLQSRKI-----GDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVSQSK 208 (291)
Q Consensus 134 iekatELGV~~I~P~~se~~~RS~~~-----~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~~~~ 208 (291)
|||||||||++|+|+.|+ ||+.+ ..+|.+||+ +|+ +||||||+|+++|+|.+|.+|++++....+.+
T Consensus 79 l~katELGv~~i~p~~s~---rsv~k~~~~~~~~k~~R~~---~i~--~eA~kQs~r~~~P~i~~~~~l~~~l~~~~~~~ 150 (225)
T PF04452_consen 79 LQKATELGVSRIIPVISE---RSVVKSDGKKSDKKLERWQ---RIA--IEAAKQSGRTRLPEIEPPISLKELLEDIPDED 150 (225)
T ss_dssp HHHHHHTT-SEEEEEE-T---TSSS---HHHHHHHHHHHH---HHH--HHHHHHHT-SS--EEEEEEEHHHHHHHSSECS
T ss_pred HHHHHhcCCCEEEEEEee---eeeeeccchhhHHHHHHHH---HHH--HHHHHhcCCCccceeeccccHHHHhhccccCC
Confidence 999999999999999999 99642 356888999 999 99999999999999999999999998776554
Q ss_pred eEEEEeCCCCChhhhhccCCCC--C-ceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHHHHHHHHH
Q 045537 209 LAFVAIAEATPLVTALSSSRNE--S-SGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIALLATLML 281 (291)
Q Consensus 209 ~~lv~~~~~~~~~~~l~~~~~~--~-~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~ala~l~~ 281 (291)
. +++|+++......+...... + +++++||||||||++|++.+.++||.+||||+||||||||+++|+|+++|
T Consensus 151 ~-~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~~~~~g~~~vsLG~~ILR~ETAai~als~l~y 225 (225)
T PF04452_consen 151 L-LILDEDEEPSLSSLSEILNSEKSFSIAIIIGPEGGFSEEEIEFLKEAGFQPVSLGPRILRTETAAIAALSILQY 225 (225)
T ss_dssp E-EEE-TTTTCBGGGCSHTTSCHHC-EEEEEE--TT---HHHHHHHHHCTEEEEB-SSS---HHHHHHHHHHHHHH
T ss_pred E-EEEcccccccccchhhhhhcccCCcEEEEECCCCCCCHHHHHHHHHCCCEEEEcCCCEEehHHHHHHHHHHhhC
Confidence 4 88888765443333221111 1 89999999999999999999999999999999999999999999999875
No 4
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=100.00 E-value=6.7e-57 Score=408.63 Aligned_cols=222 Identities=31% Similarity=0.485 Sum_probs=186.1
Q ss_pred ccEEEe---CCcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCCccceEEE
Q 045537 44 IPRFFS---QGGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQHTQWNVFA 120 (291)
Q Consensus 44 ~~rff~---~~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~~~i~l~l 120 (291)
|+|||+ .++.+.|+++++||+.+|||+++||.|.|+||+|+.|.|+|+.++++.+.+++.+...... +.+..+++
T Consensus 1 m~~~f~~~~~~~~~~l~~~~~~Hl~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~~~~~~i~~~~~~~~--~~~~~l~l 78 (234)
T PRK11713 1 MPRLFVLLAAGETLILDGEEAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEVELEILEKLELEP--EPPLRLTL 78 (234)
T ss_pred CcEEEEecCCCCEEEEChHHHhHHHhhccCCCCCEEEEEeCCCCEEEEEEEEecCcEEEEEEEecccCCC--CCCCeEEE
Confidence 678887 5678999999999999999999999999999999999999999999999888776533222 33456778
Q ss_pred EeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccc-c----ccccccccchhhchhchhhhhcCCCCcceeEcCCC
Q 045537 121 AFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKI-G----DNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPM 195 (291)
Q Consensus 121 a~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~-~----~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~ 195 (291)
++|+||+++|||+|||||||||++|+|+.|+ ||+.. + .+|.+||+ +|+ ++|||||+|+++|+|..+.
T Consensus 79 ~~al~k~~~~e~il~k~tELGV~~i~p~~se---rs~~~~~~~~~~~k~~r~~---~i~--~~A~~Qs~r~~~P~i~~~~ 150 (234)
T PRK11713 79 AQALPKGDRLELILQKATELGVSAIIPLISE---RSVVKLDGERADKKLERWQ---KIA--IEAAEQSGRTRIPEVRPPI 150 (234)
T ss_pred EEeecCCccHHHHHHHHHHhCcCeEEEEEec---cceecccchhhHHHHHHHH---HHH--HHHHHhcCCCCCCEEcCcC
Confidence 8899999999999999999999999999999 88753 1 24778999 999 9999999999999999999
Q ss_pred CHhhhccccCCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHHH
Q 045537 196 KIDGLLPLVSQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIAL 275 (291)
Q Consensus 196 ~l~~~l~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~a 275 (291)
+|+++++...+.+. ++. ....+.. ...++++++||||||||++|++.|.++||.+|+||+||||+|||+++|
T Consensus 151 ~~~~~l~~~~~~~~----~~~---~~~~l~~-~~~~~i~viIGPEGGfs~~Ei~~l~~~g~~~vsLG~~ILR~ETA~i~a 222 (234)
T PRK11713 151 SLKEFLEELLPADL----KAG---LKLVLHP-EAGGKVLLLIGPEGGFSPEEIELLREAGFTPVSLGPRILRTETAALAA 222 (234)
T ss_pred CHHHHHhhcccccc----chh---hhhhcCc-CCCCeEEEEECCCCCCCHHHHHHHHHCCCEEeccCCCchhhhhHHHHH
Confidence 99999876533221 111 1111111 122469999999999999999999999999999999999999999999
Q ss_pred HHHHHHcc
Q 045537 276 LATLMLCS 283 (291)
Q Consensus 276 la~l~~~~ 283 (291)
+|++.++.
T Consensus 223 ls~~~~~~ 230 (234)
T PRK11713 223 LAALQALL 230 (234)
T ss_pred HHHHHHHh
Confidence 99997654
No 5
>PRK02135 hypothetical protein; Provisional
Probab=96.02 E-value=0.019 Score=51.32 Aligned_cols=78 Identities=19% Similarity=0.310 Sum_probs=61.8
Q ss_pred CCCHhhhccccCCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHH
Q 045537 194 PMKIDGLLPLVSQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATI 273 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai 273 (291)
-.+|++++..+......+++|+++.++...- ...+.+++.|=-=||+++|.+.+.+.|+..|||||..|=|.-+.+
T Consensus 113 ~~~fe~ll~~~~e~~~l~~L~e~G~~i~~~~----~~~~~~FvLgDH~~~~~ee~~~L~~~ga~~iSlGP~~l~AshcI~ 188 (201)
T PRK02135 113 RRGFEDLLEELAEGKTLYYLHEDGEDIRDVE----FPENPVFVLGDHIGFTEEEENLLKRLGAEKISLGPKMLHADHCIT 188 (201)
T ss_pred cCCHHHHHHHHhcCCcEEEEeCCCCchhhcc----CCCCCEEEEeCCCCCCHHHHHHHHHhCCeEEEeCcHHHHHHHHHH
Confidence 3689999887744456788898888776321 123455889999999999999999999999999999999887654
Q ss_pred HH
Q 045537 274 AL 275 (291)
Q Consensus 274 ~a 275 (291)
.+
T Consensus 189 ~v 190 (201)
T PRK02135 189 LI 190 (201)
T ss_pred HH
Confidence 43
No 6
>PF04013 Methyltrn_RNA_2: Putative SAM-dependent RNA methyltransferase; InterPro: IPR007158 The proteins in this family are around 200 amino acids long with the exception of O29206 from SWISSPROT that has an additional 100 amino acids at its N terminus. The function of these bacterial protein is unknown, however, they do contain several conserved histidines and aspartates that might form a metal-binding site.; PDB: 2QMM_A 3AIA_A 3AI9_X 2QWV_B.
Probab=95.67 E-value=0.022 Score=50.98 Aligned_cols=79 Identities=16% Similarity=0.256 Sum_probs=55.4
Q ss_pred CCCHhhhccccCCCceEEEEeCCCCChhhhhccCCCCC-ceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHH
Q 045537 194 PMKIDGLLPLVSQSKLAFVAIAEATPLVTALSSSRNES-SGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETAT 272 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~-~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAa 272 (291)
-.+|++++..+......+++|+++.+..+.-. .. +.+++.|=--||+++|.+.+.+.|+..|||||.-|=|.-+.
T Consensus 112 ~~~fe~ll~~~~~~~~l~~L~e~G~di~~~~~----~~~d~~FVLgDH~g~~~eee~~L~~~~a~kiSlGP~~lhAdhcI 187 (199)
T PF04013_consen 112 KGGFEDLLEELAEEYPLYYLHEDGEDIRDVEF----PGNDPVFVLGDHIGFTEEEEELLERLGAEKISLGPKSLHADHCI 187 (199)
T ss_dssp ---HHHHHHHHHCTSEEEEESTTSEEGGGS-------S-SEEEEEE-TT-SHHHHHHHHHCTTSEEEES-SS---HHHHH
T ss_pred cCCHHHHHHHHhcCCcEEEEcCCCCcHhhccc----CCCCCeEEEeCCCCCCHHHHHHHHHccCceEEeCCHHHHHHHHH
Confidence 35899999877655567888988877654321 22 67799999999999999999999999999999999998876
Q ss_pred HHHH
Q 045537 273 IALL 276 (291)
Q Consensus 273 i~al 276 (291)
+++-
T Consensus 188 ~ivh 191 (199)
T PF04013_consen 188 TIVH 191 (199)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6553
No 7
>PF00588 SpoU_methylase: SpoU rRNA Methylase family; InterPro: IPR001537 The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases [, ]. The Pet56 protein of Saccharomyces cerevisiae has been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase centre of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The Pet56 protein catalyzes the site-specific formation of 2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and E. coli 23S rRNA providing evidence for an essential modified nucleotide in rRNA [].; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 3N4J_A 3N4K_A 1IPA_A 3ONP_A 3NK6_A 3NK7_A 3IC6_A 1GZ0_D 1MXI_A 1J85_A ....
Probab=92.84 E-value=0.37 Score=39.90 Aligned_cols=108 Identities=15% Similarity=0.140 Sum_probs=67.7
Q ss_pred eccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhcc
Q 045537 123 GTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLP 202 (291)
Q Consensus 123 ~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~ 202 (291)
.+-.+..+--+++-|.-+|++.++.+... . .+-|. .-+ ..++..+ ..++| +....+++++++
T Consensus 8 ~~~~p~NlG~i~Rta~afG~~~v~l~~~~---~--------~~~~~---~~~--~r~s~g~-~~~~~-~~~~~~~~~~l~ 69 (142)
T PF00588_consen 8 NVQDPGNLGAIIRTAAAFGVDGVILVGPR---C--------ADPYN---PKV--LRASAGA-HEHLP-IRRVDDLEEALK 69 (142)
T ss_dssp S-SSHHHHHHHHHHHHHTTESEEEEESSS---S--------STTTS---HHH--HHHTTTG-HHCSH-EEEESSHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHhCCchhheeccc---c--------ccccc---ccc--ccccCCh-hhhhh-eeeeehhhhhcc
Confidence 34446778899999999999999865433 1 12233 333 3333333 22455 555578999888
Q ss_pred ccCCCceEEEEeCCC-CChhhhhccCCCCCceEEEEcCC-CCCCHHHHHHHH
Q 045537 203 LVSQSKLAFVAIAEA-TPLVTALSSSRNESSGLIIVGPE-GDFTEKEVNKIV 252 (291)
Q Consensus 203 ~~~~~~~~lv~~~~~-~~~~~~l~~~~~~~~i~lvIGPE-GGfs~~Ei~~l~ 252 (291)
.++..+..+++.+.. .++. .+ .-.+++++++|.| .|.|+++.+...
T Consensus 70 ~~~~~g~~i~~~~~~~~~~~-~~---~~~~~~~lv~G~E~~Gls~~~~~~~d 117 (142)
T PF00588_consen 70 DLKENGYTIVATSPGATPLY-EL---DFPKKVALVFGNESRGLSEEVLELCD 117 (142)
T ss_dssp HHHHTTEEEEEESTTSCEGG-GS---HTTSSEEEEEEBTTTBS-HHHHHTSS
T ss_pred cccccccccceeeecccccc-cc---ccccceEEEEcCcCCCCCcccccccc
Confidence 776555666665433 3333 12 2346899999999 799999877754
No 8
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=91.91 E-value=0.54 Score=41.73 Aligned_cols=78 Identities=15% Similarity=0.239 Sum_probs=61.4
Q ss_pred CCCHhhhccccCCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHH
Q 045537 194 PMKIDGLLPLVSQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATI 273 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai 273 (291)
-.+|++++..+......+++++++..+.+.-. ..+.++++|=-=|+++++...+.+.+...|||||--|=|+-+..
T Consensus 111 ~~~~e~ll~~l~~~~~ly~L~E~G~DI~~v~~----~~np~FIlGDH~g~t~e~~k~L~r~~~~~ISlGP~~lha~hcit 186 (197)
T COG1901 111 NGGFEALLAELAEGRSLYYLHEDGRDISEVDL----IPNPVFILGDHIGLTEEDEKLLERHAAKKISLGPLSLHADHCIT 186 (197)
T ss_pred cCCHHHHHHHHhccCcEEEEccCCccHhhccc----CCCceEEeeCCCCCCHHHHHHHHHhhCceeEeCchHHHHHHHHH
Confidence 45899988877555566778887766544322 23566889999999999999999999999999999999998765
Q ss_pred HH
Q 045537 274 AL 275 (291)
Q Consensus 274 ~a 275 (291)
.+
T Consensus 187 ~~ 188 (197)
T COG1901 187 LL 188 (197)
T ss_pred HH
Confidence 54
No 9
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=87.65 E-value=5.2 Score=36.53 Aligned_cols=111 Identities=11% Similarity=0.092 Sum_probs=66.4
Q ss_pred ceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCC
Q 045537 116 WNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPM 195 (291)
Q Consensus 116 i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~ 195 (291)
+.|++ -.+-++..+--|++-|.-.||+.++.+..+ .. +. ... . + -+....+++ +....
T Consensus 20 l~vvL-d~V~~p~NlGAIiRta~AfGv~~V~~v~~~---~~----------~~---~~~--~-~-s~Ga~~wv~-i~~~~ 77 (229)
T PRK11081 20 LTVCM-EQVHKPHNVSAIIRTADAVGVHEVHAVWPG---SR----------MR---TMG--S-T-AAGSNSWVQ-VKTHR 77 (229)
T ss_pred eEEEE-eCCCCcchHHHHHHHHHHhCCCeEEEecCC---Cc----------cc---hhh--h-h-cCCchheEE-EEEeC
Confidence 34433 367788999999999999999999765444 11 11 111 1 1 122223443 33334
Q ss_pred CHhhhccccCCCceEEEE-eCC--CCChhhhhccCCCCCceEEEEcCCC-CCCHHHHHHHH
Q 045537 196 KIDGLLPLVSQSKLAFVA-IAE--ATPLVTALSSSRNESSGLIIVGPEG-DFTEKEVNKIV 252 (291)
Q Consensus 196 ~l~~~l~~~~~~~~~lv~-~~~--~~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~l~ 252 (291)
++.+++..+...+..+++ +.. +.++.+ ..-.+++++++|.|| |.|++.++.+.
T Consensus 78 ~~~~~i~~lk~~g~~i~at~~~~~a~~l~~----~d~~~p~alV~GnE~~GlS~e~l~~~D 134 (229)
T PRK11081 78 TIGDAVAHLKGQGMQILATHLSDTAVDFRE----IDYTRPTCILMGQEKTGISQEALALAD 134 (229)
T ss_pred CHHHHHHHHHhCCCEEEEEeCCCCCccHhH----hcccCCeEEEECCCCCCCCHHHHhcCC
Confidence 788887766544444444 322 223322 123468999999998 89998877653
No 10
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=87.36 E-value=1.4 Score=36.18 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=36.4
Q ss_pred EEEcchhhhHH-HHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 54 VRVEGDEFWHM-TKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 54 v~L~~~~~~Hl-~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
..|+++...+. .+.++++.||.|.|+.|...-..++|.++..+...+.+
T Consensus 25 a~ls~elr~~y~~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~V 74 (114)
T TIGR01080 25 APLSKELREKYGKRALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYV 74 (114)
T ss_pred cccCHHHHHHcCcccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEE
Confidence 44566544444 78999999999999999655568999999866655443
No 11
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2. this is part of the trmH (spoU) family of rRNA methylases
Probab=86.85 E-value=4.8 Score=34.16 Aligned_cols=105 Identities=11% Similarity=0.118 Sum_probs=58.9
Q ss_pred eccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCC-CcceeEcCCCCHhhhc
Q 045537 123 GTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQR-LHEMVLNPPMKIDGLL 201 (291)
Q Consensus 123 ~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r-~~lP~I~~p~~l~~~l 201 (291)
.+-.+..+=-+++-|.-+|++.++ + .. ++..... .++ . ..+ .+. .++|.+ ...++.+++
T Consensus 8 ~v~dP~NlG~iiRta~afGv~~vi-~-~~---~~~~~~~---~~~------~--ra~---~~~~~~~~~~-~~~~~~~~l 67 (153)
T TIGR00185 8 EPEIPPNTGNIARTCAATGTRLHL-I-EP---LGFFLDD---KRL------K--RAG---LDYWEFVQLF-YHKSWEEFL 67 (153)
T ss_pred CCCCCChHHHHHHHHHHhCCEEEE-E-CC---CCCCCcc---HHH------H--hhc---cchHhcCCeE-EeCCHHHHH
Confidence 344577889999999999996554 3 33 3221100 111 1 221 111 233333 345888888
Q ss_pred cccCCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCC-CCCHHHHHHH
Q 045537 202 PLVSQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEG-DFTEKEVNKI 251 (291)
Q Consensus 202 ~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~l 251 (291)
+.+.+.+ .+.+..++......+ ....+.++++|.|| |.|++..+..
T Consensus 68 ~~l~~~g-v~~~~~~~~~~~~~~---~~~~~~alv~GnE~~Gls~~~l~~~ 114 (153)
T TIGR00185 68 EAEKPQK-LFALTKKGTPAHSQV---TYKLGDYLMFGPETRGLPQSILDNM 114 (153)
T ss_pred HhCcCCC-EEEEeCCCCCcceee---ccCCCCEEEECCCCCCCCHHHHhhC
Confidence 7765555 333333322211111 12345689999999 9999988876
No 12
>PRK10864 putative methyltransferase; Provisional
Probab=86.71 E-value=3.5 Score=40.05 Aligned_cols=107 Identities=13% Similarity=0.125 Sum_probs=65.8
Q ss_pred EeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhh
Q 045537 121 AFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGL 200 (291)
Q Consensus 121 a~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~ 200 (291)
.-.+-++..+=-|++-|.-+||+.|+.. + .+.. +. .+.+ + ++. ..-.++|.+ ...++.++
T Consensus 203 Ld~I~DP~NlGaIiRTA~afGv~~Vil~--~---~~~~--------~~--~kvv--R-aS~-Ga~~~v~i~-~~~nl~~~ 262 (346)
T PRK10864 203 LEDVGNPHNLGGIMRSCAHFGVKGVVVQ--D---AALL--------ES--GAAI--R-TAE-GGAEHVQPI-TGDSFVDV 262 (346)
T ss_pred EeCCCCCCcHHHHHHHHHHhCCCEEEEC--C---CCCC--------Cc--hhHH--H-Hhc-ChhhcceEE-EeCCHHHH
Confidence 3467788999999999999999999743 3 2211 11 0233 3 222 122345544 33578888
Q ss_pred ccccCCCceEEEEeC-C-CCChhhhhccCCCCCceEEEEcCCC-CCCHHHHHHH
Q 045537 201 LPLVSQSKLAFVAIA-E-ATPLVTALSSSRNESSGLIIVGPEG-DFTEKEVNKI 251 (291)
Q Consensus 201 l~~~~~~~~~lv~~~-~-~~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~l 251 (291)
+..+...+..+++.. . +.++.+ ....+++++++|.|| |++++.++..
T Consensus 263 L~~lk~~G~~Iv~t~~~~~~~l~~----~~~~~k~aLV~GnE~~GLs~~vl~~~ 312 (346)
T PRK10864 263 LDDFRQAGYTIVTTSSHKGTPLFK----ASLPAKMVLVLGQEYDGLSDAARQQG 312 (346)
T ss_pred HHHHHHCCCEEEEEeCCCCcchhh----cccCCCeEEEECCCCCCCCHHHHHhC
Confidence 877654455555543 2 223222 123468999999999 8999876664
No 13
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=84.04 E-value=8.6 Score=34.98 Aligned_cols=108 Identities=12% Similarity=0.086 Sum_probs=61.4
Q ss_pred EeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhh
Q 045537 121 AFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGL 200 (291)
Q Consensus 121 a~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~ 200 (291)
.-.+-.+..+--+++-|.-+|++.++ .++ ++. ..+. ..+ ..++. ..-.++|-.. ..++.++
T Consensus 95 Ld~v~dp~NlGaI~Rta~afG~~~vi--l~~---~~~-------~~~~---~~~--~r~s~-Ga~~~l~~~~-~~~~~~~ 155 (237)
T TIGR00186 95 LDEITDPHNLGAILRTAEAFGVDGVI--LPK---RRS-------APLN---STV--VKTSS-GAVEYVPLAR-VTNLSRT 155 (237)
T ss_pred EcCCCCCccHHHHHHHHHHcCCCEEE--ECC---CCc-------CCCC---Cce--eeeec-cccceeEEEE-eCCHHHH
Confidence 34667788899999999999999986 333 221 1121 111 11111 1112455432 3478888
Q ss_pred ccccCCCceEEEEeC-CCCChhhhhccCCCCCceEEEEcCCC-CCCHHHHHH
Q 045537 201 LPLVSQSKLAFVAIA-EATPLVTALSSSRNESSGLIIVGPEG-DFTEKEVNK 250 (291)
Q Consensus 201 l~~~~~~~~~lv~~~-~~~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~ 250 (291)
++.+.+.+..+++-. .+... +......+++++++|.|| |++++..+.
T Consensus 156 l~~l~~~g~~i~~~~~~~~~~---~~~~~~~~~~~lv~GnE~~Gls~~~l~~ 204 (237)
T TIGR00186 156 ITKLKESGFWTVGTDLDAQDT---LYQVKLTKPLALVVGNEGEGVSRLIKEN 204 (237)
T ss_pred HHHHHHCCCEEEEEecCCCcc---ccccccCCCEEEEECCCCCCcCHHHHHh
Confidence 776654444454433 22221 111223568999999998 698875544
No 14
>PRK01130 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional
Probab=83.18 E-value=4 Score=36.31 Aligned_cols=40 Identities=35% Similarity=0.353 Sum_probs=33.3
Q ss_pred EcCCCCC-CHHHHHHHHHcCCeEEecCCCccccchHHHHHH
Q 045537 237 VGPEGDF-TEKEVNKIVEAGATAVGLGPHRLRVETATIALL 276 (291)
Q Consensus 237 IGPEGGf-s~~Ei~~l~~~Gf~~vsLG~rILRtETAai~al 276 (291)
|-++||. ++++++.+.+.|+..|-+|..+.+.+...-...
T Consensus 176 via~GGI~t~~~~~~~l~~GadgV~iGsai~~~~~~~~~~~ 216 (221)
T PRK01130 176 VIAEGRINTPEQAKKALELGAHAVVVGGAITRPEEITKWFV 216 (221)
T ss_pred EEEECCCCCHHHHHHHHHCCCCEEEEchHhcCCHHHHHHHH
Confidence 3468999 699999999999999999999999877654433
No 15
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=82.46 E-value=14 Score=34.00 Aligned_cols=114 Identities=14% Similarity=0.069 Sum_probs=62.3
Q ss_pred eEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCC
Q 045537 117 NVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMK 196 (291)
Q Consensus 117 ~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~ 196 (291)
.|+|. .+-.+..+-.+++-|.-.|++.++.+.-. + +-++ ..+ .++.-+. ..++......+
T Consensus 6 ~vVLv-~~~~pgNiGaiaRa~~~fG~~~l~lv~p~----~--------~~~~---~a~---~~a~GA~-~~l~~a~i~~~ 65 (245)
T PRK15114 6 RIVLV-ETSHTGNMGSVARAMKTMGLTNLWLVNPL----V--------KPDS---QAI---ALAAGAS-DVIGNATIVDT 65 (245)
T ss_pred EEEEe-CCCCCCcHHHHHHHHHhcCCCEEEEeCCC----C--------CCcC---HHH---HHcCCch-hhcccCeEecC
Confidence 44443 34457889999999999999999976543 1 1122 212 1222221 11222222347
Q ss_pred HhhhccccCCCceEEEEeCCCCCh----h---h---hhccCCCCCceEEEEcCCC-CCCHHHHHHHHH
Q 045537 197 IDGLLPLVSQSKLAFVAIAEATPL----V---T---ALSSSRNESSGLIIVGPEG-DFTEKEVNKIVE 253 (291)
Q Consensus 197 l~~~l~~~~~~~~~lv~~~~~~~~----~---~---~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~l~~ 253 (291)
++++++.. +..+-........ . . ........+++++++|.|| |++++|++....
T Consensus 66 l~eal~~~---~~vvatt~r~~~~~~~~~~~~~~~~~~~~~~~~~~~alVFG~E~~GLs~e~l~~cd~ 130 (245)
T PRK15114 66 LDEALAGC---SLVVGTSARSRTLPWPMLDPRECGLKSVAEAANAPVALVFGRERVGLTNDELQKCHY 130 (245)
T ss_pred HHHHHhcC---CEEEEEcCCccCCcccccCHHHHHHHHHhhccCCCEEEEECCCCCCCCHHHHHhCCe
Confidence 88887643 2333222221110 0 0 0000112457999999997 999999987643
No 16
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=78.47 E-value=15 Score=33.66 Aligned_cols=108 Identities=12% Similarity=0.143 Sum_probs=63.3
Q ss_pred EeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhh
Q 045537 121 AFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGL 200 (291)
Q Consensus 121 a~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~ 200 (291)
.-.+-.+..+--+++-|.-+|++.|+. ++ ++.. .|. ..+ ..++ ...-.++|-.. ..++.++
T Consensus 100 Ld~v~dp~NlGai~Rta~a~G~~~vi~--~~---~~~~-------~~~---~~~--~r~s-~Ga~~~l~~~~-~~~~~~~ 160 (244)
T PRK11181 100 LDGVTDPHNLGACLRSADAAGVHAVIV--PK---DRSA-------QLN---ATA--KKVA-CGAAETVPLIR-VTNLART 160 (244)
T ss_pred EcCCCCcchHHHHHHHHHHcCCCEEEE--CC---CCCC-------CCC---Cce--EEec-CCHHHcCeEEE-cCCHHHH
Confidence 346778889999999999999999973 33 3221 111 111 1111 11123455433 3478888
Q ss_pred ccccCCCceEEEEe-CCC-CChhhhhccCCCCCceEEEEcCCC-CCCHHHHHHH
Q 045537 201 LPLVSQSKLAFVAI-AEA-TPLVTALSSSRNESSGLIIVGPEG-DFTEKEVNKI 251 (291)
Q Consensus 201 l~~~~~~~~~lv~~-~~~-~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~l 251 (291)
++.+.+.+..+++- .++ .++.. ....+++++++|.|| |.|++..+..
T Consensus 161 l~~l~~~g~~i~~t~~~~~~~~~~----~~~~~~~alv~G~E~~Gls~~~~~~~ 210 (244)
T PRK11181 161 MRMLQEKNIWIVGTAGEADHTLYQ----SKLTGPLALVMGAEGEGMRRLTREHC 210 (244)
T ss_pred HHHHHHCCCEEEEEeCCCCcchhh----cCCCCCEEEEECCCCCCcCHHHHHhC
Confidence 77665444445543 222 22221 123468999999998 8999776654
No 17
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=76.44 E-value=8.9 Score=34.67 Aligned_cols=134 Identities=18% Similarity=0.204 Sum_probs=77.2
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcC
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNP 193 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~ 193 (291)
.+++++|.+ + +-+..+++..+.|++.|. +-.| - .....|.- + ..++.|--.-..+++
T Consensus 59 ~~~dvHLMv---~--~p~~~i~~~~~~gad~i~-~H~E---a-----~~~~~~~l---~------~ik~~g~k~GlalnP 115 (220)
T PRK08883 59 APIDVHLMV---K--PVDRIIPDFAKAGASMIT-FHVE---A-----SEHVDRTL---Q------LIKEHGCQAGVVLNP 115 (220)
T ss_pred CCEEEEecc---C--CHHHHHHHHHHhCCCEEE-Eccc---C-----cccHHHHH---H------HHHHcCCcEEEEeCC
Confidence 456677653 2 356788999999999876 3444 1 11223332 3 333444333334666
Q ss_pred CCCHhhhccccCCCceEEEEe--CCC--CCh-------hhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecC
Q 045537 194 PMKIDGLLPLVSQSKLAFVAI--AEA--TPL-------VTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLG 262 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~--~~~--~~~-------~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG 262 (291)
..+++.+...++.-+..++.- +.. ... ...+.+.......-+.|--.||.+++.+..+.++|+..+-.|
T Consensus 116 ~Tp~~~i~~~l~~~D~vlvMtV~PGfgGq~fi~~~lekI~~l~~~~~~~~~~~~I~vdGGI~~eni~~l~~aGAd~vVvG 195 (220)
T PRK08883 116 ATPLHHLEYIMDKVDLILLMSVNPGFGGQSFIPHTLDKLRAVRKMIDESGRDIRLEIDGGVKVDNIREIAEAGADMFVAG 195 (220)
T ss_pred CCCHHHHHHHHHhCCeEEEEEecCCCCCceecHhHHHHHHHHHHHHHhcCCCeeEEEECCCCHHHHHHHHHcCCCEEEEe
Confidence 666666655444455555542 321 111 111111101111123344489999999999999999999999
Q ss_pred CCccccch
Q 045537 263 PHRLRVET 270 (291)
Q Consensus 263 ~rILRtET 270 (291)
+-|.+.+.
T Consensus 196 SaIf~~~d 203 (220)
T PRK08883 196 SAIFGQPD 203 (220)
T ss_pred HHHhCCCC
Confidence 99998876
No 18
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=75.09 E-value=7.1 Score=22.82 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=21.2
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeC
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDR 95 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k 95 (291)
.++||.|.|..|.-.-..|+|.+++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57899999999976666888888764
No 19
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=74.85 E-value=5.3 Score=24.89 Aligned_cols=29 Identities=31% Similarity=0.336 Sum_probs=23.6
Q ss_pred CCCEEEEEeCCCCEEEEEEEEeeCCceEE
Q 045537 72 TNDRVELFNGKGGLIEGCIQRIDRTGLDV 100 (291)
Q Consensus 72 ~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v 100 (291)
+||.|.+..|.-.-..|+|.+++++...+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V 29 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRV 29 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEE
Confidence 59999999996555689999998877544
No 20
>PF09895 DUF2122: RecB-family nuclease (DUF2122); InterPro: IPR018665 This family of archaeal proteins include RecB nuclease-like proteins as well as proteins of no known function.
Probab=72.64 E-value=14 Score=29.89 Aligned_cols=77 Identities=10% Similarity=0.161 Sum_probs=41.0
Q ss_pred CHhhhccccCCCceEEEEeCCCCCh-hhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHH
Q 045537 196 KIDGLLPLVSQSKLAFVAIAEATPL-VTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIA 274 (291)
Q Consensus 196 ~l~~~l~~~~~~~~~lv~~~~~~~~-~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~ 274 (291)
+++|+++.+..+...++...+.... .+.+. ...+-..++-|-|-|||+.|++.-.. ..... +..+.-+++
T Consensus 27 dl~DAiEvl~p~~V~~i~~~~~~~~~~~~~~--~~~rvllVf~G~d~gfsk~El~~g~~--v~~~~-----v~~~iG~~g 97 (106)
T PF09895_consen 27 DLKDAIEVLKPDVVYLISRSGEEEEKLEFLK--IEGRVLLVFSGSDPGFSKIELELGEA--VYIRG-----VERDIGPIG 97 (106)
T ss_pred CHHHHHHhcCCcEEEEEcCcccccccccccC--cCCcEEEEEeCCCCCCChhHhcCCce--EEeec-----cCcCcChHH
Confidence 6888888776554333332222211 12222 12345677789999999999765211 11111 334445556
Q ss_pred HHHHHHH
Q 045537 275 LLATLML 281 (291)
Q Consensus 275 ala~l~~ 281 (291)
.+|+++|
T Consensus 98 ~~ai~Ly 104 (106)
T PF09895_consen 98 EAAIILY 104 (106)
T ss_pred HHHHHHh
Confidence 6666554
No 21
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=71.88 E-value=7.6 Score=35.52 Aligned_cols=134 Identities=15% Similarity=0.088 Sum_probs=77.9
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhh--cCCCCcceeE
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVY--GGQRLHEMVL 191 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~k--Qs~r~~lP~I 191 (291)
.+++++|.+ . .-+..+++..+.|++.|. +-.| = .....+.- +.+ ++.-. ++|- .+
T Consensus 69 ~~~DvHLMv---~--~P~~~i~~~~~aGad~It-~H~E---a-----~~~~~~~l---~~I--k~~g~~~kaGl----al 125 (228)
T PRK08091 69 CFKDVHLMV---R--DQFEVAKACVAAGADIVT-LQVE---Q-----THDLALTI---EWL--AKQKTTVLIGL----CL 125 (228)
T ss_pred CCEEEEecc---C--CHHHHHHHHHHhCCCEEE-Eccc---C-----cccHHHHH---HHH--HHCCCCceEEE----EE
Confidence 456666653 2 245688999999999876 3333 1 11122222 222 22222 3333 35
Q ss_pred cCCCCHhhhccccCCCceEEEEe--CC--CCChh-------hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEe
Q 045537 192 NPPMKIDGLLPLVSQSKLAFVAI--AE--ATPLV-------TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVG 260 (291)
Q Consensus 192 ~~p~~l~~~l~~~~~~~~~lv~~--~~--~~~~~-------~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vs 260 (291)
+|..+++.+...++.-|..++.. |+ +..+. ..+.+.......-+.|.-.||.+++-+..+.++|+..+-
T Consensus 126 nP~Tp~~~i~~~l~~vD~VLiMtV~PGfgGQ~f~~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~aGaD~~V 205 (228)
T PRK08091 126 CPETPISLLEPYLDQIDLIQILTLDPRTGTKAPSDLILDRVIQVENRLGNRRVEKLISIDGSMTLELASYLKQHQIDWVV 205 (228)
T ss_pred CCCCCHHHHHHHHhhcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHCCCCEEE
Confidence 56666766655554455555543 32 11111 111111011233467899999999999999999999999
Q ss_pred cCCCccccch
Q 045537 261 LGPHRLRVET 270 (291)
Q Consensus 261 LG~rILRtET 270 (291)
.|+-+.+.+.
T Consensus 206 ~GSalF~~~d 215 (228)
T PRK08091 206 SGSALFSQGE 215 (228)
T ss_pred EChhhhCCCC
Confidence 9999988765
No 22
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=71.35 E-value=18 Score=24.72 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=26.4
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeC-CceEEEee
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDR-TGLDVVAL 103 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k-~~~~v~i~ 103 (291)
.++|+.+.+...+|.-|+|+|+++++ ..+.+...
T Consensus 3 ~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~ 37 (57)
T smart00333 3 FKVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFI 37 (57)
T ss_pred CCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEE
Confidence 47899887765679999999999988 55555443
No 23
>cd00377 ICL_PEPM Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first committed step in the glyoxylate pathway. This carbon-conserving pathway is present in most prokaryotes, lower eukaryotes and plants, but has not been observed in vertebrates. PEP mutase (PEPM) turns phosphoenolpyruvate (PEP) into phosphonopyruvate (P-pyr), an important intermediate in the formation of organophosphonates, which function as antibiotics or play a role in pathogenesis or signaling. P-pyr can be hydrolyzed by phosphonopyruvate hydrolase (PPH) to from pyruvate and phosphate. Oxaloacetate acetylhydrolase (OAH) catalyzes the hydrolytic cleavage of oxaloacetate to
Probab=71.14 E-value=28 Score=31.79 Aligned_cols=137 Identities=15% Similarity=0.108 Sum_probs=72.6
Q ss_pred CcHHHHHHHHHhcCccEEEEeecccccccccccccc---cccccchhhchhchhhhhcCCC-CcceeEcC-----C--CC
Q 045537 128 GRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNG---FLSCNFYYGFIANSAFVYGGQR-LHEMVLNP-----P--MK 196 (291)
Q Consensus 128 ~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k---~eRw~~~~kIi~~~eA~kQs~r-~~lP~I~~-----p--~~ 196 (291)
+.....+++..+.||+-|.+=-.....|+-....+. .+.+. ..+ ..+.++... ..++-+.- . .+
T Consensus 84 ~~~~~~v~~~~~~G~~gv~iED~~~~k~~g~~~~~~~~~~ee~~---~ki--~aa~~a~~~~~~~~IiARTDa~~~~~~~ 158 (243)
T cd00377 84 LNVARTVRELEEAGAAGIHIEDQVGPKKCGHHGGKVLVPIEEFV---AKI--KAARDARDDLPDFVIIARTDALLAGEEG 158 (243)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCCCccccCCCCCeecCHHHHH---HHH--HHHHHHHhccCCeEEEEEcCchhccCCC
Confidence 456677899999999999861111000111000111 12222 222 223333332 35555543 2 46
Q ss_pred Hhhhcccc-----CCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCCC-CCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 197 IDGLLPLV-----SQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEGD-FTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 197 l~~~l~~~-----~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEGG-fs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
+++.++.. .+.|..++..+....-...+.+. ...|+.+...|-+. ++.+| |.+.||..|++|+..+|+-.
T Consensus 159 ~~eai~Ra~ay~~AGAD~v~v~~~~~~~~~~~~~~~-~~~Pl~~~~~~~~~~~~~~~---l~~lG~~~v~~~~~~~~~a~ 234 (243)
T cd00377 159 LDEAIERAKAYAEAGADGIFVEGLKDPEEIRAFAEA-PDVPLNVNMTPGGNLLTVAE---LAELGVRRVSYGLALLRAAA 234 (243)
T ss_pred HHHHHHHHHHHHHcCCCEEEeCCCCCHHHHHHHHhc-CCCCEEEEecCCCCCCCHHH---HHHCCCeEEEEChHHHHHHH
Confidence 88877643 23455444333221112222222 24678787777655 78887 55579999999999888765
Q ss_pred HHH
Q 045537 271 ATI 273 (291)
Q Consensus 271 Aai 273 (291)
.++
T Consensus 235 ~a~ 237 (243)
T cd00377 235 KAM 237 (243)
T ss_pred HHH
Confidence 554
No 24
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=70.60 E-value=6.7 Score=27.52 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=21.7
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeC
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDR 95 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k 95 (291)
+++|+.+.+..++|..|.|+|.++..
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~ 26 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIRE 26 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEE
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEe
Confidence 46899999999889999999998754
No 25
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=68.29 E-value=7.5 Score=33.99 Aligned_cols=42 Identities=17% Similarity=0.151 Sum_probs=33.6
Q ss_pred cEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEe
Q 045537 52 GIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRI 93 (291)
Q Consensus 52 ~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i 93 (291)
+.+.|.+-.-.|..+.-++++||.|.|.+.+|..+..+|+++
T Consensus 91 Gn~VIAGHrdt~F~~L~~L~~GD~I~v~~~~g~~~~Y~V~~~ 132 (174)
T TIGR03784 91 GNSVIAGHRDTHFAFLQELRPGDVIRLQTPDGQWQSYQVTAT 132 (174)
T ss_pred CcEEEEeeCCccCCChhhCCCCCEEEEEECCCeEEEEEEeEE
Confidence 456676644457778889999999999999988888888765
No 26
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=68.05 E-value=20 Score=25.18 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=26.5
Q ss_pred ccCCCCCEEEEEe-CCCCEEEEEEEEeeC-CceEEEe
Q 045537 68 LRLSTNDRVELFN-GKGGLIEGCIQRIDR-TGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~d-G~g~~~~a~I~~i~k-~~~~v~i 102 (291)
++.++||.|.++. .+|.-|.|+|+++.+ +...|..
T Consensus 1 ~~~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~ 37 (61)
T smart00743 1 SDFKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRY 37 (61)
T ss_pred CCcCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEE
Confidence 4679999999876 357889999999987 4444443
No 27
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=66.43 E-value=15 Score=27.92 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=26.4
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
|+++.||.|.|.-|...=-.++|..++++.-.+.+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 39 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIV 39 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 58999999999999543347999999866554443
No 28
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=65.41 E-value=26 Score=31.80 Aligned_cols=134 Identities=17% Similarity=0.222 Sum_probs=78.0
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcC
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNP 193 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~ 193 (291)
.+++++|.+ . .-+..++...+.|++.|. +-.| = .....|.- +.+ ++.-.++|- .+++
T Consensus 63 ~~~dvHLMv---~--~P~~~i~~~~~~gad~I~-~H~E---a-----~~~~~~~l---~~I--r~~g~k~Gl----alnP 119 (223)
T PRK08745 63 APIDVHLMV---E--PVDRIVPDFADAGATTIS-FHPE---A-----SRHVHRTI---QLI--KSHGCQAGL----VLNP 119 (223)
T ss_pred CCEEEEecc---C--CHHHHHHHHHHhCCCEEE-Eccc---C-----cccHHHHH---HHH--HHCCCceeE----EeCC
Confidence 456677653 2 355678999999999876 4444 1 11223333 334 344334443 3555
Q ss_pred CCCHhhhccccCCCceEEEEe--CC--CCChh-------hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecC
Q 045537 194 PMKIDGLLPLVSQSKLAFVAI--AE--ATPLV-------TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLG 262 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~--~~--~~~~~-------~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG 262 (291)
..+++.+...++.-+.+++.. |+ +.... ..+.+.......-+.|.-.||.+.+-+..+.++|+..+-.|
T Consensus 120 ~T~~~~i~~~l~~vD~VlvMtV~PGf~GQ~fi~~~l~KI~~l~~~~~~~~~~~~IeVDGGI~~eti~~l~~aGaDi~V~G 199 (223)
T PRK08745 120 ATPVDILDWVLPELDLVLVMSVNPGFGGQAFIPSALDKLRAIRKKIDALGKPIRLEIDGGVKADNIGAIAAAGADTFVAG 199 (223)
T ss_pred CCCHHHHHHHHhhcCEEEEEEECCCCCCccccHHHHHHHHHHHHHHHhcCCCeeEEEECCCCHHHHHHHHHcCCCEEEEC
Confidence 566666554444445555543 22 11111 11111100112236678899999999999999999999999
Q ss_pred CCccccch
Q 045537 263 PHRLRVET 270 (291)
Q Consensus 263 ~rILRtET 270 (291)
+-|..++.
T Consensus 200 SaiF~~~d 207 (223)
T PRK08745 200 SAIFNAPD 207 (223)
T ss_pred hhhhCCCC
Confidence 99988765
No 29
>cd04726 KGPDC_HPS 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for L-ascorbate utilization in some eubacteria. HPS catalyzes the formation of D-arabino-3-hexulose-6-phosphate from D-ribulose 5-phosphate and formaldehyde in microorganisms that can use formaldehyde as a carbon source. Both catalyze reactions that involve the Mg2+-assisted formation and stabilization of 1,2-enediolate reaction intermediates.
Probab=64.78 E-value=24 Score=30.51 Aligned_cols=119 Identities=15% Similarity=-0.002 Sum_probs=66.7
Q ss_pred HHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccC-CCceE
Q 045537 132 WLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVS-QSKLA 210 (291)
Q Consensus 132 ~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~-~~~~~ 210 (291)
+.++++.+.|++-|+.-... - . +-.. .+ .++++..+-.....+..|.+-.+.+.... +.+..
T Consensus 68 ~~~~~~~~aGad~i~~h~~~---~------~--~~~~---~~---i~~~~~~g~~~~v~~~~~~t~~e~~~~~~~~~d~v 130 (202)
T cd04726 68 LEAEMAFKAGADIVTVLGAA---P------L--STIK---KA---VKAAKKYGKEVQVDLIGVEDPEKRAKLLKLGVDIV 130 (202)
T ss_pred HHHHHHHhcCCCEEEEEeeC---C------H--HHHH---HH---HHHHHHcCCeEEEEEeCCCCHHHHHHHHHCCCCEE
Confidence 66799999999988743332 0 0 1112 22 34445444333322345556666544222 33432
Q ss_pred EEEeCC----C---CChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 211 FVAIAE----A---TPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 211 lv~~~~----~---~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
.+ ++. . ......+...... .-+-|.+.||.+++-+..+.+.|+..+..|+-|.+++-
T Consensus 131 ~~-~~~~~~~~~~~~~~~~~i~~~~~~--~~~~i~~~GGI~~~~i~~~~~~Gad~vvvGsai~~~~d 194 (202)
T cd04726 131 IL-HRGIDAQAAGGWWPEDDLKKVKKL--LGVKVAVAGGITPDTLPEFKKAGADIVIVGRAITGAAD 194 (202)
T ss_pred EE-cCcccccccCCCCCHHHHHHHHhh--cCCCEEEECCcCHHHHHHHHhcCCCEEEEeehhcCCCC
Confidence 22 221 1 1111222211100 12457888999999999999999999999999988754
No 30
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=63.57 E-value=13 Score=31.16 Aligned_cols=42 Identities=19% Similarity=0.243 Sum_probs=30.5
Q ss_pred cEEEEcchhhhH-----HHHcccCCCCCEEEEEeCCCCEEEEEEEEe
Q 045537 52 GIVRVEGDEFWH-----MTKVLRLSTNDRVELFNGKGGLIEGCIQRI 93 (291)
Q Consensus 52 ~~v~L~~~~~~H-----l~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i 93 (291)
+.+.|.+-.-.| ..+.-++++||.|.|.+..|+.|..+|.++
T Consensus 50 Gn~viaGH~~~~g~~~~F~~L~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 50 GTAVLAGHVDSRGGPAVFFRLGDLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred CCEEEEEecCCCCCChhhcchhcCCCCCEEEEEECCCCEEEEEEeEE
Confidence 445555533222 555567999999999998898999999764
No 31
>cd04729 NanE N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.
Probab=62.19 E-value=26 Score=31.04 Aligned_cols=121 Identities=20% Similarity=0.169 Sum_probs=64.2
Q ss_pred HHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccC-CCceEE
Q 045537 133 LVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVS-QSKLAF 211 (291)
Q Consensus 133 iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~-~~~~~l 211 (291)
-++++.+.|++-|++.... +... . .+... .++ .++.++. .+|-+..+.+.++...... +.+...
T Consensus 84 ~~~~a~~aGad~I~~~~~~---~~~p--~--~~~~~---~~i--~~~~~~g---~~~iiv~v~t~~ea~~a~~~G~d~i~ 148 (219)
T cd04729 84 EVDALAAAGADIIALDATD---RPRP--D--GETLA---ELI--KRIHEEY---NCLLMADISTLEEALNAAKLGFDIIG 148 (219)
T ss_pred HHHHHHHcCCCEEEEeCCC---CCCC--C--CcCHH---HHH--HHHHHHh---CCeEEEECCCHHHHHHHHHcCCCEEE
Confidence 5699999999977665544 2110 0 01233 444 4444544 3444555566666543221 223221
Q ss_pred EEeC---C-----CCChhhhhccCCCCCceEEEEcCCCCC-CHHHHHHHHHcCCeEEecCCCccccch
Q 045537 212 VAIA---E-----ATPLVTALSSSRNESSGLIIVGPEGDF-TEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 212 v~~~---~-----~~~~~~~l~~~~~~~~i~lvIGPEGGf-s~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
+... . ..+..+.+......-.+ -|=+.||. ++++++.+.+.|+..|-.|..+.|++-
T Consensus 149 ~~~~g~t~~~~~~~~~~~~~l~~i~~~~~i--pvia~GGI~~~~~~~~~l~~GadgV~vGsal~~~~~ 214 (219)
T cd04729 149 TTLSGYTEETAKTEDPDFELLKELRKALGI--PVIAEGRINSPEQAAKALELGADAVVVGSAITRPEH 214 (219)
T ss_pred ccCccccccccCCCCCCHHHHHHHHHhcCC--CEEEeCCCCCHHHHHHHHHCCCCEEEEchHHhChHh
Confidence 1110 0 01111221111000012 22358999 689999999999999999999888764
No 32
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=61.37 E-value=20 Score=27.60 Aligned_cols=35 Identities=17% Similarity=0.294 Sum_probs=26.5
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
|+++.||.|.|.-|...==.++|.+++.+.-.+.+
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 41 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIV 41 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 58999999999999543347999999876555443
No 33
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=61.23 E-value=29 Score=30.21 Aligned_cols=108 Identities=10% Similarity=0.025 Sum_probs=63.8
Q ss_pred HHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccC-CCceE
Q 045537 132 WLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVS-QSKLA 210 (291)
Q Consensus 132 ~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~-~~~~~ 210 (291)
.-++.+.++|++.++--.+ . .-+ .+++++.+...+|.+. +++++..... +.+..
T Consensus 67 ~~~~~a~~~Ga~~i~~p~~-----------------~---~~~--~~~~~~~~~~~i~gv~---t~~e~~~A~~~Gad~i 121 (190)
T cd00452 67 EQADAAIAAGAQFIVSPGL-----------------D---PEV--VKAANRAGIPLLPGVA---TPTEIMQALELGADIV 121 (190)
T ss_pred HHHHHHHHcCCCEEEcCCC-----------------C---HHH--HHHHHHcCCcEECCcC---CHHHHHHHHHCCCCEE
Confidence 3467888899998861111 1 224 5677777666666555 6777654332 23432
Q ss_pred EEEeCCCCChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCcc
Q 045537 211 FVAIAEATPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRL 266 (291)
Q Consensus 211 lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rIL 266 (291)
-+ ++......+.+......-+ .+-+=|.||.+.+.+..+.+.|+..|..|.-+.
T Consensus 122 ~~-~p~~~~g~~~~~~l~~~~~-~~p~~a~GGI~~~n~~~~~~~G~~~v~v~s~i~ 175 (190)
T cd00452 122 KL-FPAEAVGPAYIKALKGPFP-QVRFMPTGGVSLDNAAEWLAAGVVAVGGGSLLP 175 (190)
T ss_pred EE-cCCcccCHHHHHHHHhhCC-CCeEEEeCCCCHHHHHHHHHCCCEEEEEchhcc
Confidence 22 3322111222221111101 134668899999999999999999999998887
No 34
>PRK13125 trpA tryptophan synthase subunit alpha; Provisional
Probab=60.70 E-value=58 Score=29.55 Aligned_cols=121 Identities=14% Similarity=0.038 Sum_probs=71.8
Q ss_pred CcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccCCC
Q 045537 128 GRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVSQS 207 (291)
Q Consensus 128 ~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~~~ 207 (291)
...+..++++.+.|++.++.-..- - +. .++.. + + ++.++.-|-...+.+.+..+.+.+.......
T Consensus 88 ~~~~~~i~~~~~~Gadgvii~dlp---~-----e~-~~~~~---~-~--~~~~~~~Gl~~~~~v~p~T~~e~l~~~~~~~ 152 (244)
T PRK13125 88 DSLDNFLNMARDVGADGVLFPDLL---I-----DY-PDDLE---K-Y--VEIIKNKGLKPVFFTSPKFPDLLIHRLSKLS 152 (244)
T ss_pred hCHHHHHHHHHHcCCCEEEECCCC---C-----Cc-HHHHH---H-H--HHHHHHcCCCEEEEECCCCCHHHHHHHHHhC
Confidence 457788999999999999854211 0 00 12222 3 2 4566666666677888877666654333323
Q ss_pred ceEEEEe-CCC--CChhh-------hhccCCCCCceEEEEcCCCCC-CHHHHHHHHHcCCeEEecCCCccc
Q 045537 208 KLAFVAI-AEA--TPLVT-------ALSSSRNESSGLIIVGPEGDF-TEKEVNKIVEAGATAVGLGPHRLR 267 (291)
Q Consensus 208 ~~~lv~~-~~~--~~~~~-------~l~~~~~~~~i~lvIGPEGGf-s~~Ei~~l~~~Gf~~vsLG~rILR 267 (291)
+..++.- ... ..+.. .+.+.....+ |.-+||. +++.+..+.++|+..+-.|+-++|
T Consensus 153 ~~~l~msv~~~~g~~~~~~~~~~i~~lr~~~~~~~----i~v~gGI~~~e~i~~~~~~gaD~vvvGSai~~ 219 (244)
T PRK13125 153 PLFIYYGLRPATGVPLPVSVERNIKRVRNLVGNKY----LVVGFGLDSPEDARDALSAGADGVVVGTAFIE 219 (244)
T ss_pred CCEEEEEeCCCCCCCchHHHHHHHHHHHHhcCCCC----EEEeCCcCCHHHHHHHHHcCCCEEEECHHHHH
Confidence 3333322 111 11111 1111111112 4468999 899999999999999999999987
No 35
>PRK10358 putative rRNA methylase; Provisional
Probab=60.45 E-value=1.1e+02 Score=26.13 Aligned_cols=110 Identities=11% Similarity=0.149 Sum_probs=59.8
Q ss_pred eEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCC
Q 045537 117 NVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMK 196 (291)
Q Consensus 117 ~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~ 196 (291)
+|+|. .+-.+..+-.+++-|.-.|++ .+.+ .. ++ +.|. .|.+ +. +-+.-..+++ +....+
T Consensus 3 ~ivL~-~~~dPgNlGti~Rta~a~G~~-~viv-~~---~~--------d~~~--~k~~--ra-ag~~~~~~~~-~~~~~~ 62 (157)
T PRK10358 3 NIVLF-EPEIPPNTGNIIRLCANTGFR-LHII-EP---MG--------FAWD--DKRL--RR-AGLDYHEFTA-VTRHHD 62 (157)
T ss_pred EEEEe-CCCCcChHHHHHHHHHHhCCE-EEEE-CC---CC--------CCCC--hHHH--Hh-ccccccccee-eEEcCC
Confidence 34443 345678899999999999995 5444 44 32 2232 0333 33 2122222222 333468
Q ss_pred HhhhccccCCCceEEEEeCCCCChhhhhccCCCCCceEEEEcCCC-CCCHHHHHH
Q 045537 197 IDGLLPLVSQSKLAFVAIAEATPLVTALSSSRNESSGLIIVGPEG-DFTEKEVNK 250 (291)
Q Consensus 197 l~~~l~~~~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~ 250 (291)
+.++++...+. ..+.+...+.+...... -.++.++++|.|| |.|++..+.
T Consensus 63 l~~~l~~~~~~-~v~~~~~~~~~~~~~~~---~~~~~~lvfGnE~~GLs~~~~~~ 113 (157)
T PRK10358 63 YAAFLEAENPQ-RLFALTTKGTPAHSAVS---YQDGDYLMFGPETRGLPASILDA 113 (157)
T ss_pred HHHHHHhCCCc-eEEEEeCCCCCCccccc---cCCCcEEEECCCCCCCCHHHHhc
Confidence 88888743322 23333333332221111 1345789999998 899987765
No 36
>PRK08005 epimerase; Validated
Probab=60.43 E-value=28 Score=31.42 Aligned_cols=130 Identities=11% Similarity=0.054 Sum_probs=74.8
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcC
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNP 193 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~ 193 (291)
.+++++|.+ + .=+..+++..+.|++.|. +-.| = .....|.- +.+ ++.-.++|- .+++
T Consensus 59 ~~~DvHLMv---~--~P~~~i~~~~~~gad~It-~H~E---a-----~~~~~~~l---~~I--k~~G~k~Gl----AlnP 115 (210)
T PRK08005 59 HPLSFHLMV---S--SPQRWLPWLAAIRPGWIF-IHAE---S-----VQNPSEIL---ADI--RAIGAKAGL----ALNP 115 (210)
T ss_pred CCeEEEecc---C--CHHHHHHHHHHhCCCEEE-Eccc---C-----ccCHHHHH---HHH--HHcCCcEEE----EECC
Confidence 346666643 2 244688999999999776 3333 1 11223333 333 344344443 3555
Q ss_pred CCCHhhhccccCCCceEEEEe--CC--CCChh-------hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecC
Q 045537 194 PMKIDGLLPLVSQSKLAFVAI--AE--ATPLV-------TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLG 262 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~--~~--~~~~~-------~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG 262 (291)
..+++.+...++.-|..++.. |+ +.... ..+.+.. . .. -|.-.||.+++-+..+.++|+..+-+|
T Consensus 116 ~Tp~~~i~~~l~~vD~VlvMsV~PGf~GQ~f~~~~~~KI~~l~~~~-~-~~--~I~VDGGI~~~~i~~l~~aGad~~V~G 191 (210)
T PRK08005 116 ATPLLPYRYLALQLDALMIMTSEPDGRGQQFIAAMCEKVSQSREHF-P-AA--ECWADGGITLRAARLLAAAGAQHLVIG 191 (210)
T ss_pred CCCHHHHHHHHHhcCEEEEEEecCCCccceecHHHHHHHHHHHHhc-c-cC--CEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence 555655443333345555443 22 11111 1111111 1 11 388899999999999999999999999
Q ss_pred CCccccch
Q 045537 263 PHRLRVET 270 (291)
Q Consensus 263 ~rILRtET 270 (291)
+-+.+.+.
T Consensus 192 saiF~~~d 199 (210)
T PRK08005 192 RALFTTAN 199 (210)
T ss_pred hHhhCCCC
Confidence 99997654
No 37
>PTZ00170 D-ribulose-5-phosphate 3-epimerase; Provisional
Probab=60.06 E-value=32 Score=31.09 Aligned_cols=133 Identities=13% Similarity=0.197 Sum_probs=76.8
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcC
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNP 193 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~ 193 (291)
.++.+.+. .+..+..++++.+.|++.|.. -.+ = .. +.+. ++ ++++++.|...-..+.+
T Consensus 66 ~~lDvHLm-----~~~p~~~i~~~~~~Gad~itv-H~e---a-----~~--~~~~---~~---l~~ik~~G~~~gval~p 123 (228)
T PTZ00170 66 TFLDCHLM-----VSNPEKWVDDFAKAGASQFTF-HIE---A-----TE--DDPK---AV---ARKIREAGMKVGVAIKP 123 (228)
T ss_pred CCEEEEEC-----CCCHHHHHHHHHHcCCCEEEE-ecc---C-----Cc--hHHH---HH---HHHHHHCCCeEEEEECC
Confidence 44566653 445677889999999998864 333 0 11 1133 33 35556555433345556
Q ss_pred CCCHhhhcccc--CCCceEEE-E-eCC--CCCh----hhhhccCC-CCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecC
Q 045537 194 PMKIDGLLPLV--SQSKLAFV-A-IAE--ATPL----VTALSSSR-NESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLG 262 (291)
Q Consensus 194 p~~l~~~l~~~--~~~~~~lv-~-~~~--~~~~----~~~l~~~~-~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG 262 (291)
-.+++++...+ ..-+.+++ . +++ +... ...+.... .... +.|.-.||.+++.+..+.++|+..+-+|
T Consensus 124 ~t~~e~l~~~l~~~~vD~Vl~m~v~pG~~gq~~~~~~~~ki~~~~~~~~~--~~I~VdGGI~~~ti~~~~~aGad~iVvG 201 (228)
T PTZ00170 124 KTPVEVLFPLIDTDLVDMVLVMTVEPGFGGQSFMHDMMPKVRELRKRYPH--LNIQVDGGINLETIDIAADAGANVIVAG 201 (228)
T ss_pred CCCHHHHHHHHccchhhhHHhhhcccCCCCcEecHHHHHHHHHHHHhccc--CeEEECCCCCHHHHHHHHHcCCCEEEEc
Confidence 56677764333 22232222 2 221 1111 11111100 0112 4577799999999999999999999999
Q ss_pred CCccccch
Q 045537 263 PHRLRVET 270 (291)
Q Consensus 263 ~rILRtET 270 (291)
+-|..++.
T Consensus 202 saI~~a~d 209 (228)
T PTZ00170 202 SSIFKAKD 209 (228)
T ss_pred hHHhCCCC
Confidence 99998876
No 38
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen
Probab=59.28 E-value=72 Score=28.97 Aligned_cols=112 Identities=16% Similarity=0.111 Sum_probs=62.1
Q ss_pred eEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCC
Q 045537 117 NVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMK 196 (291)
Q Consensus 117 ~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~ 196 (291)
.++|. .+-.+..+-.+++-|.-.|++.++.+... +. +. .-+ ..++ .....+++.+.-..+
T Consensus 5 ~vvL~-~~~~p~NiGaiaR~~~~fG~~~l~lv~p~----~~---------~~---~~a--~~~a-~ga~~~l~~~~v~~~ 64 (233)
T TIGR00050 5 RIVLV-EPSHSGNIGSIARAMKNMGLTELCLVNPK----SH---------LE---EEA--YALA-AGARDILDNAKVVDD 64 (233)
T ss_pred EEEEE-CCCCCCCHHHHHHHHHhCCCCEEEEeCCC----cC---------CC---HHH--HHHh-CChHHhhccCEEECC
Confidence 34443 34467889999999999999999977544 10 11 111 1111 111234443333447
Q ss_pred HhhhccccCCCceEEEEeCCCCChhh----------hhccCCCCCceEEEEcCCC-CCCHHHHHHHHH
Q 045537 197 IDGLLPLVSQSKLAFVAIAEATPLVT----------ALSSSRNESSGLIIVGPEG-DFTEKEVNKIVE 253 (291)
Q Consensus 197 l~~~l~~~~~~~~~lv~~~~~~~~~~----------~l~~~~~~~~i~lvIGPEG-Gfs~~Ei~~l~~ 253 (291)
++++++.. +..+........... .+.. ..++++++.|+|+ |++++|++....
T Consensus 65 l~eal~~~---~~vv~tt~~~~~~~~~~~~~~~~~~~~~~--~~~~~aLvFG~E~~GL~~~~l~~cd~ 127 (233)
T TIGR00050 65 LDEALDDC---DLVVGTSARSRNLQRPLLTPRELAPKLVA--YKGKIAIVFGREDSGLTNEELLKCHV 127 (233)
T ss_pred HHHHHhcC---CEEEEECCCcCCCCCCcCCHHHHHHHHHh--hcCCEEEEECCCCCCCCHHHHHhCCE
Confidence 88887643 332222221111100 0111 1357999999986 999999987543
No 39
>TIGR00262 trpA tryptophan synthase, alpha subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences.
Probab=58.73 E-value=38 Score=31.28 Aligned_cols=118 Identities=16% Similarity=0.221 Sum_probs=69.2
Q ss_pred HHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccCCCc-
Q 045537 130 ADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVSQSK- 208 (291)
Q Consensus 130 ~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~~~~- 208 (291)
++..++++.+.||+.++.-.-. .+... . . ++.+++.+-...+-+.+-.+.+.+.......+
T Consensus 104 ~e~f~~~~~~aGvdgviipDlp------------~ee~~---~-~--~~~~~~~gl~~i~lv~P~T~~eri~~i~~~~~g 165 (256)
T TIGR00262 104 VEEFYAKCKEVGVDGVLVADLP------------LEESG---D-L--VEAAKKHGVKPIFLVAPNADDERLKQIAEKSQG 165 (256)
T ss_pred HHHHHHHHHHcCCCEEEECCCC------------hHHHH---H-H--HHHHHHCCCcEEEEECCCCCHHHHHHHHHhCCC
Confidence 6788999999999997643222 12222 2 3 46777777666777777666665432222222
Q ss_pred eEEE-EeCC---CC-----ChhhhhccCCCCCceEEEEcCCCCCC-HHHHHHHHHcCCeEEecCCCccc
Q 045537 209 LAFV-AIAE---AT-----PLVTALSSSRNESSGLIIVGPEGDFT-EKEVNKIVEAGATAVGLGPHRLR 267 (291)
Q Consensus 209 ~~lv-~~~~---~~-----~~~~~l~~~~~~~~i~lvIGPEGGfs-~~Ei~~l~~~Gf~~vsLG~rILR 267 (291)
..++ ...+ .. ...+.+.......+.-+++ +||.+ ++.+..+.+.|+..|-.|+-+.|
T Consensus 166 fiy~vs~~G~TG~~~~~~~~~~~~i~~lr~~~~~pi~v--gfGI~~~e~~~~~~~~GADgvVvGSaiv~ 232 (256)
T TIGR00262 166 FVYLVSRAGVTGARNRAASALNELVKRLKAYSAKPVLV--GFGISKPEQVKQAIDAGADGVIVGSAIVK 232 (256)
T ss_pred CEEEEECCCCCCCcccCChhHHHHHHHHHhhcCCCEEE--eCCCCCHHHHHHHHHcCCCEEEECHHHHH
Confidence 3333 2211 11 1111111111111122444 89997 99999999999999999998887
No 40
>PRK14057 epimerase; Provisional
Probab=57.64 E-value=49 Score=30.81 Aligned_cols=135 Identities=16% Similarity=0.179 Sum_probs=76.7
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhh--------cCCC
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVY--------GGQR 185 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~k--------Qs~r 185 (291)
.+++++|.+ . +-+..++...+.|++.|+ +-.| = .....|.- +.+ +..+++ ++|-
T Consensus 76 ~p~DvHLMV---~--~P~~~i~~~~~aGad~It-~H~E---a-----~~~~~~~l---~~I-r~~G~k~~~~~~~~kaGl 137 (254)
T PRK14057 76 FIKDVHLMV---A--DQWTAAQACVKAGAHCIT-LQAE---G-----DIHLHHTL---SWL-GQQTVPVIGGEMPVIRGI 137 (254)
T ss_pred CCeeEEeee---C--CHHHHHHHHHHhCCCEEE-Eeec---c-----ccCHHHHH---HHH-HHcCCCcccccccceeEE
Confidence 445666653 2 356788999999999886 3333 1 11122222 222 022232 3443
Q ss_pred CcceeEcCCCCHhhhccccCCCceEEEEe--CC--CCChh-------hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHc
Q 045537 186 LHEMVLNPPMKIDGLLPLVSQSKLAFVAI--AE--ATPLV-------TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEA 254 (291)
Q Consensus 186 ~~lP~I~~p~~l~~~l~~~~~~~~~lv~~--~~--~~~~~-------~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~ 254 (291)
. ++|..+++.+...++.-|..++.. |+ +.... ..+.+.......-+.|.-.||.+++-+..+.++
T Consensus 138 A----lnP~Tp~e~i~~~l~~vD~VLvMtV~PGfgGQ~Fi~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~ti~~l~~a 213 (254)
T PRK14057 138 S----LCPATPLDVIIPILSDVEVIQLLAVNPGYGSKMRSSDLHERVAQLLCLLGDKREGKIIVIDGSLTQDQLPSLIAQ 213 (254)
T ss_pred E----ECCCCCHHHHHHHHHhCCEEEEEEECCCCCchhccHHHHHHHHHHHHHHHhcCCCceEEEECCCCHHHHHHHHHC
Confidence 3 455555665544444445555543 22 11111 111111011233477889999999999999999
Q ss_pred CCeEEecCCCccccch
Q 045537 255 GATAVGLGPHRLRVET 270 (291)
Q Consensus 255 Gf~~vsLG~rILRtET 270 (291)
|+..+-.|+-+.+.++
T Consensus 214 Gad~~V~GSalF~~~d 229 (254)
T PRK14057 214 GIDRVVSGSALFRDDR 229 (254)
T ss_pred CCCEEEEChHhhCCCC
Confidence 9999999999998765
No 41
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=57.22 E-value=24 Score=28.30 Aligned_cols=35 Identities=17% Similarity=0.322 Sum_probs=26.8
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
++++.||.|.|.-|...=-.++|.++.++.-.+.+
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 36 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIV 36 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 47899999999999655457999999866544433
No 42
>COG1756 Mra1 Uncharacterized conserved protein [Function unknown]
Probab=56.02 E-value=48 Score=30.29 Aligned_cols=76 Identities=18% Similarity=0.227 Sum_probs=50.2
Q ss_pred CCHhhhccccCCCceEEEEeCCCC--ChhhhhccCCCCCceEEEEc--CCCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 195 MKIDGLLPLVSQSKLAFVAIAEAT--PLVTALSSSRNESSGLIIVG--PEGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 195 ~~l~~~l~~~~~~~~~lv~~~~~~--~~~~~l~~~~~~~~i~lvIG--PEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
.++.++++... +..++.++.+. +.....+.. .+.++++|| |+|.|.++-.... .-+|+|.-=|-+.|
T Consensus 137 ~~l~d~l~~~~--~~~ill~e~G~~~~p~~~~~~l--~~~i~v~iG~fp~Gdf~~~~~~~~-----~~~si~~~pL~a~~ 207 (223)
T COG1756 137 NPLTDLLPENN--KVTILLHEKGELIPPKELISLL--LKGIAVIIGGFPHGDFREETEFVA-----EKYSIYDEPLSAWS 207 (223)
T ss_pred CcHHHhccccC--ceEEEEcCCCCccCHHHHHhhh--ccCceEEEeccCCCcchhhhhhhc-----ceeeecCCCccHHH
Confidence 36888887653 56778887653 333333322 123778888 8999987654433 56899999999999
Q ss_pred HHHHHHHHH
Q 045537 271 ATIALLATL 279 (291)
Q Consensus 271 Aai~ala~l 279 (291)
++-=.+...
T Consensus 208 v~~ki~~~~ 216 (223)
T COG1756 208 VCSKIVYAY 216 (223)
T ss_pred HHHHHHHHH
Confidence 876655543
No 43
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=54.95 E-value=23 Score=29.36 Aligned_cols=48 Identities=15% Similarity=0.055 Sum_probs=34.6
Q ss_pred EEEcc-hhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEE
Q 045537 54 VRVEG-DEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVV 101 (291)
Q Consensus 54 v~L~~-~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~ 101 (291)
..|+. -...|=.+-++++.||.|.|+-|...-=.++|++++++.-.+.
T Consensus 29 a~LSkeLr~~y~ir~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~ 77 (120)
T PRK01191 29 APLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIY 77 (120)
T ss_pred CccCHHHHHHhCCccceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEE
Confidence 44554 3566777889999999999999953333699999976554443
No 44
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=53.80 E-value=30 Score=27.75 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=26.4
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
++++.||.|.|+-|...=-.++|.++.++.-.+.+
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 37 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIV 37 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 57899999999999544347999999866555443
No 45
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=52.85 E-value=38 Score=28.86 Aligned_cols=127 Identities=15% Similarity=0.139 Sum_probs=66.3
Q ss_pred CCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccC
Q 045537 126 KGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVS 205 (291)
Q Consensus 126 K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~ 205 (291)
-..|+..+-+-+.-+|+++++..... =| .-.+-. -++.|-|-..-.|.+.. ..++|+++-+.
T Consensus 12 S~~rv~e~ariaygfg~k~lV~tka~---g~-----AAQsGI---------p~~~kla~k~G~~vlvf-~dL~DAlevL~ 73 (147)
T COG4080 12 SVQRVLEFARIAYGFGAKRLVLTKAK---GS-----AAQSGI---------PEVLKLAFKLGKPVLVF-PDLDDALEVLR 73 (147)
T ss_pred chHHHHHHHHHHcccCccEEEEEecc---cH-----hhhhcc---------HHHHHHHHHhCCcEEEe-hhHHHHHHhcC
Confidence 35678888899999999999854443 11 101111 12222221112333333 36999988776
Q ss_pred CCceEEEEe-C--CCCChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHHHHHHHHH
Q 045537 206 QSKLAFVAI-A--EATPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIALLATLML 281 (291)
Q Consensus 206 ~~~~~lv~~-~--~~~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~ala~l~~ 281 (291)
+. ..+..- + ..+++. . ++....+-..++-|.|+||++.|+++ |...+ .+--.+--.+.++|+++|
T Consensus 74 P~-v~ll~~~~~~~ek~~d-p-~e~ie~~vliVf~ga~~gl~k~El~l----g~~~~----y~ve~~VG~~g~lAi~Ly 141 (147)
T COG4080 74 PD-VTLLVGSASEGEKKLD-P-NEKIEGRVLIVFSGAEPGLTKRELEL----GADLR----YIVEADVGELGALAIFLY 141 (147)
T ss_pred Cc-eEEEecCcccccccCC-c-cccccceEEEEEecCCCCcChhhccc----CCcEE----EEEeccchHHHHHHHHHH
Confidence 53 333331 1 112211 0 11112245678889999999999764 32211 123445556666676654
No 46
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=51.06 E-value=38 Score=28.13 Aligned_cols=42 Identities=17% Similarity=0.180 Sum_probs=31.0
Q ss_pred EcchhhhHHHHc----ccCCCCCEEEEEeCCCCEEEEEEEEeeCCc
Q 045537 56 VEGDEFWHMTKV----LRLSTNDRVELFNGKGGLIEGCIQRIDRTG 97 (291)
Q Consensus 56 L~~~~~~Hl~kV----LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~ 97 (291)
+++++..++.+. .-+++||.|.+.+|-=.-+.|+|.+++...
T Consensus 69 i~~~ei~~l~~~~~~~~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k 114 (145)
T TIGR00405 69 IDFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESK 114 (145)
T ss_pred CCHHHHHHHhcccccccccCCCCEEEEeecCCCCCeEEEEEEcCCC
Confidence 778888887542 127799999999995444589999887433
No 47
>TIGR02320 PEP_mutase phosphoenolpyruvate phosphomutase. A closely related enzyme, phosphonopyruvate hydrolase from Variovorax sp. Pal2, is excluded from this model.
Probab=50.74 E-value=72 Score=30.07 Aligned_cols=144 Identities=15% Similarity=0.082 Sum_probs=74.1
Q ss_pred CCCcHHHHHHHHHhcCccEEEEe---eccccccccccc---ccccccccchhhchhchhhhhcC-CCCcceeEcC-----
Q 045537 126 KGGRADWLVEKCTELGAQSVTPL---LTELHLQSRKIG---DNGFLSCNFYYGFIANSAFVYGG-QRLHEMVLNP----- 193 (291)
Q Consensus 126 K~~r~d~iiekatELGV~~I~P~---~se~~~RS~~~~---~~k~eRw~~~~kIi~~~eA~kQs-~r~~lP~I~~----- 193 (291)
....+...+++..+.||.-|..= .-+ |+-... ...+--.+ .-++++.|+..+ ....++-+.-
T Consensus 90 ~~~~v~r~V~~l~~aGvaGi~iEDq~~pk---~cg~~~~~~~~~l~s~e---e~~~kI~Aa~~a~~~~~~~IiARTDa~~ 163 (285)
T TIGR02320 90 NFEHFRRLVRKLERRGVSAVCIEDKLGLK---KNSLFGNDVAQPQASVE---EFCGKIRAGKDAQTTEDFMIIARVESLI 163 (285)
T ss_pred CHHHHHHHHHHHHHcCCeEEEEeccCCCc---cccccCCCCcccccCHH---HHHHHHHHHHHhccCCCeEEEEeccccc
Confidence 44567788999999999999761 111 221100 00111112 111223455544 2334555433
Q ss_pred -CCCHhhhcccc-----CCCceEEEEe-CCC-CChhhhhccCC---CCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecC
Q 045537 194 -PMKIDGLLPLV-----SQSKLAFVAI-AEA-TPLVTALSSSR---NESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLG 262 (291)
Q Consensus 194 -p~~l~~~l~~~-----~~~~~~lv~~-~~~-~~~~~~l~~~~---~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG 262 (291)
...+++.++.. .+.|..++.. ... ..+........ .+.|++++-|+-|.+|.+| |.+.||..|+.|
T Consensus 164 ~~~~~~eAi~Ra~ay~eAGAD~ifv~~~~~~~~ei~~~~~~~~~~~p~~pl~~~~~~~~~~~~~e---L~~lG~~~v~~~ 240 (285)
T TIGR02320 164 LGKGMEDALKRAEAYAEAGADGIMIHSRKKDPDEILEFARRFRNHYPRTPLVIVPTSYYTTPTDE---FRDAGISVVIYA 240 (285)
T ss_pred ccCCHHHHHHHHHHHHHcCCCEEEecCCCCCHHHHHHHHHHhhhhCCCCCEEEecCCCCCCCHHH---HHHcCCCEEEEh
Confidence 23577777543 2345545432 111 11111111111 1236655445445666555 777899999999
Q ss_pred CCccccchHHHHHHHH
Q 045537 263 PHRLRVETATIALLAT 278 (291)
Q Consensus 263 ~rILRtETAai~ala~ 278 (291)
+.-+|+=..++-..+.
T Consensus 241 ~~~~~aa~~a~~~~~~ 256 (285)
T TIGR02320 241 NHLLRAAYAAMQQVAE 256 (285)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999987776655443
No 48
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=50.66 E-value=21 Score=25.42 Aligned_cols=22 Identities=27% Similarity=0.359 Sum_probs=13.5
Q ss_pred CCCCCEEEEEeCCCCEEEEEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQ 91 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~ 91 (291)
+++||.|.+.|.+|+.|..++.
T Consensus 6 f~~GdrVQlTD~Kgr~~Ti~L~ 27 (54)
T PF14801_consen 6 FRAGDRVQLTDPKGRKHTITLE 27 (54)
T ss_dssp --TT-EEEEEETT--EEEEE--
T ss_pred CCCCCEEEEccCCCCeeeEEEC
Confidence 5789999999999998876664
No 49
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=49.40 E-value=24 Score=30.09 Aligned_cols=49 Identities=12% Similarity=0.077 Sum_probs=35.1
Q ss_pred EEEcc-hhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 54 VRVEG-DEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 54 v~L~~-~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
..|+. -...|=.+-++++.||.|.|+-|+-.=-.++|.+++.+.-.+.+
T Consensus 30 a~LSkeLr~k~~~Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViV 79 (143)
T PTZ00194 30 APLSKELRAKYNVRSMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHI 79 (143)
T ss_pred CccCHHHHHHhCCccceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEE
Confidence 34554 46667778889999999999998533336999999766544433
No 50
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=48.35 E-value=45 Score=28.30 Aligned_cols=49 Identities=27% Similarity=0.267 Sum_probs=35.6
Q ss_pred EcchhhhHHHHcc----cCCCCCEEEEEeCCCCEEEEEEEEeeCC--ceEEEeee
Q 045537 56 VEGDEFWHMTKVL----RLSTNDRVELFNGKGGLIEGCIQRIDRT--GLDVVALE 104 (291)
Q Consensus 56 L~~~~~~Hl~kVL----Rlk~Gd~i~v~dG~g~~~~a~I~~i~k~--~~~v~i~~ 104 (291)
|+.+|...+.+.. -+++||.|.+.+|--.-+.|+|.+++.. .+.+.+..
T Consensus 77 l~~~Ei~~il~~~~~~~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~ 131 (153)
T PRK08559 77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLE 131 (153)
T ss_pred CCHHHHHHHHhccCcccCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEEC
Confidence 7777777776533 4789999999999766679999999744 34444443
No 51
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=47.79 E-value=37 Score=31.62 Aligned_cols=30 Identities=17% Similarity=0.246 Sum_probs=21.4
Q ss_pred cccCCCCCEEEEE-eCCCCEEEEEEEEeeCC
Q 045537 67 VLRLSTNDRVELF-NGKGGLIEGCIQRIDRT 96 (291)
Q Consensus 67 VLRlk~Gd~i~v~-dG~g~~~~a~I~~i~k~ 96 (291)
...-++||..... -++|..|.|+|++|+.+
T Consensus 66 ~~~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~ 96 (264)
T PF06003_consen 66 NKKWKVGDKCMAVYSEDGQYYPATIESIDEE 96 (264)
T ss_dssp TT---TT-EEEEE-TTTSSEEEEEEEEEETT
T ss_pred ccCCCCCCEEEEEECCCCCEEEEEEEEEcCC
Confidence 4468899998754 46999999999999965
No 52
>PF00834 Ribul_P_3_epim: Ribulose-phosphate 3 epimerase family; InterPro: IPR000056 Ribulose-phosphate 3-epimerase (5.1.3.1 from EC) (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Ralstonia eutropha (Alcaligenes eutrophus) two copies of the gene coding for PPE are known [], one is chromosomally encoded P40117 from SWISSPROT, the other one is on a plasmid Q04539 from SWISSPROT. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.; GO: 0004750 ribulose-phosphate 3-epimerase activity, 0005975 carbohydrate metabolic process; PDB: 3CTL_A 3CT7_D 3CU2_A 1RPX_A 3OVR_A 3OVP_A 3OVQ_B 3QC3_B 3INP_A 1TQJ_D ....
Probab=47.19 E-value=8 Score=34.52 Aligned_cols=134 Identities=19% Similarity=0.248 Sum_probs=72.6
Q ss_pred CCccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeE
Q 045537 112 QHTQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVL 191 (291)
Q Consensus 112 ~~~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I 191 (291)
...+++++|... .+ +..+++..+.|++.|. +-.| - .....++- +.+ +++-.++|- .+
T Consensus 56 ~~~~~DvHLMv~--~P---~~~i~~~~~~g~~~i~-~H~E---~-----~~~~~~~i---~~i--k~~g~k~Gi----al 112 (201)
T PF00834_consen 56 TDLPLDVHLMVE--NP---ERYIEEFAEAGADYIT-FHAE---A-----TEDPKETI---KYI--KEAGIKAGI----AL 112 (201)
T ss_dssp SSSEEEEEEESS--SG---GGHHHHHHHHT-SEEE-EEGG---G-----TTTHHHHH---HHH--HHTTSEEEE----EE
T ss_pred CCCcEEEEeeec--cH---HHHHHHHHhcCCCEEE-Eccc---c-----hhCHHHHH---HHH--HHhCCCEEE----EE
Confidence 345677777532 33 3578899999999765 4444 1 11223333 344 444344433 36
Q ss_pred cCCCCHhhhccccCCCceEEEEe--CCC--CChhh-------hhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEe
Q 045537 192 NPPMKIDGLLPLVSQSKLAFVAI--AEA--TPLVT-------ALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVG 260 (291)
Q Consensus 192 ~~p~~l~~~l~~~~~~~~~lv~~--~~~--~~~~~-------~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vs 260 (291)
.+..+++.+...++.-+..++.. ++. ..... .+.+.......-+.|.-.||.+.+-+..+.++|+..+-
T Consensus 113 nP~T~~~~~~~~l~~vD~VlvMsV~PG~~Gq~f~~~~~~KI~~l~~~~~~~~~~~~I~vDGGI~~~~~~~~~~aGad~~V 192 (201)
T PF00834_consen 113 NPETPVEELEPYLDQVDMVLVMSVEPGFGGQKFIPEVLEKIRELRKLIPENGLDFEIEVDGGINEENIKQLVEAGADIFV 192 (201)
T ss_dssp -TTS-GGGGTTTGCCSSEEEEESS-TTTSSB--HGGHHHHHHHHHHHHHHHTCGSEEEEESSESTTTHHHHHHHT--EEE
T ss_pred ECCCCchHHHHHhhhcCEEEEEEecCCCCcccccHHHHHHHHHHHHHHHhcCCceEEEEECCCCHHHHHHHHHcCCCEEE
Confidence 66667776655555556666654 221 11111 01110000112355777999999999999999999999
Q ss_pred cCCCcccc
Q 045537 261 LGPHRLRV 268 (291)
Q Consensus 261 LG~rILRt 268 (291)
.|+-+.++
T Consensus 193 ~Gs~iF~~ 200 (201)
T PF00834_consen 193 AGSAIFKA 200 (201)
T ss_dssp ESHHHHTS
T ss_pred ECHHHhCC
Confidence 99776654
No 53
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=47.07 E-value=44 Score=24.09 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=25.5
Q ss_pred cCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeee
Q 045537 69 RLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALE 104 (291)
Q Consensus 69 Rlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~ 104 (291)
.+++||.|.+-+ | +.++|..+..+++.+.+..
T Consensus 3 ~a~vGdiIefk~--g--~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 3 KAKVGDIIEFKD--G--FTGIVEKVYENSVIVDITI 34 (57)
T ss_pred ccccCcEEEEcC--C--cEEEEEEEecCcEEEEEEe
Confidence 368999999744 3 6999999999998887643
No 54
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=46.88 E-value=45 Score=29.30 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=36.8
Q ss_pred cEEEEcchhhhHHHHccc-----------CCCCCEEEEEeCCCCEEEEEEEEeeCCceEE
Q 045537 52 GIVRVEGDEFWHMTKVLR-----------LSTNDRVELFNGKGGLIEGCIQRIDRTGLDV 100 (291)
Q Consensus 52 ~~v~L~~~~~~Hl~kVLR-----------lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v 100 (291)
....+++++.+|+.+.+- .++||.|++.+|-=.-+.|.|.+++...-.+
T Consensus 95 ~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~ 154 (178)
T COG0250 95 KPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKL 154 (178)
T ss_pred CCcccCHHHHHHHHhhccccccCCcccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEE
Confidence 457889999999555554 5789999999995444789999998664333
No 55
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=46.25 E-value=9.2 Score=36.16 Aligned_cols=95 Identities=19% Similarity=0.212 Sum_probs=40.4
Q ss_pred CCCcceeEcCCCCHhhhccccC---CCceEEEEeCCCCChhhh---hccCCCCCceEEEEc---CCCCCCHHHHHH----
Q 045537 184 QRLHEMVLNPPMKIDGLLPLVS---QSKLAFVAIAEATPLVTA---LSSSRNESSGLIIVG---PEGDFTEKEVNK---- 250 (291)
Q Consensus 184 ~r~~lP~I~~p~~l~~~l~~~~---~~~~~lv~~~~~~~~~~~---l~~~~~~~~i~lvIG---PEGGfs~~Ei~~---- 250 (291)
|-.|=..+....+|.+++...+ ++++.+...+.+.+.... .... ..+.++++.| |..|.-+..-+.
T Consensus 177 g~YwGY~VR~a~sl~~v~~~~~~~~GYd~~IgtS~~G~~~~~~~~~~~~~-~~~~~LiVFGg~~~~~~~~~~~~~~~~~~ 255 (291)
T PF02598_consen 177 GYYWGYSVRIASSLSEVFTECPYPEGYDLIIGTSERGEPISSSELEIKSS-SFKHLLIVFGGWSPLEGADEIDEKLFEGG 255 (291)
T ss_dssp -S----EEEEECEHHHHHHHC------SEEEEE-TTS-BTTTSHHHHHHH-T-SEEEEE-----SSS---S---------
T ss_pred CccCCeEEEEeCCHHHHHhcCCcccccceEEEECCCCeeCchhhcccccC-CCCcEEEEEecCHHHhhcccccccccccc
Confidence 3344445555567888776543 356666666555432211 1111 3567889998 444443333221
Q ss_pred --HHHc-----CCeEEecCCCccccchHHHHHHHHHH
Q 045537 251 --IVEA-----GATAVGLGPHRLRVETATIALLATLM 280 (291)
Q Consensus 251 --l~~~-----Gf~~vsLG~rILRtETAai~ala~l~ 280 (291)
..+. ++. -+-|.|..|+|=|.+++||.+.
T Consensus 256 ~~~~~~fD~~lN~~-p~QgsrtIRtEEAv~itLa~Ln 291 (291)
T PF02598_consen 256 EDAEELFDHWLNTC-PGQGSRTIRTEEAVLITLAILN 291 (291)
T ss_dssp -------SEEEBSS-TT-SSS---HHHHHHHHHHHHH
T ss_pred ccccccCCceEecC-CCCCCCccCHHHHHHHHHHhcC
Confidence 1111 222 2348999999999999999863
No 56
>PRK00103 rRNA large subunit methyltransferase; Provisional
Probab=46.20 E-value=1.2e+02 Score=25.97 Aligned_cols=73 Identities=12% Similarity=0.171 Sum_probs=49.5
Q ss_pred cCCCceEEEEeCCCCChh-----hhhcc--CCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHHHH
Q 045537 204 VSQSKLAFVAIAEATPLV-----TALSS--SRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIALL 276 (291)
Q Consensus 204 ~~~~~~~lv~~~~~~~~~-----~~l~~--~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~al 276 (291)
+.+.+..+++++.++.+. ..+.. ......++++||.=-||+++-.+. +. ..+|||+-.+-=+-|-++.+
T Consensus 64 l~~~~~~i~LDe~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGGa~G~~~~v~~~---a~-~~lSLS~mTfpH~larlvL~ 139 (157)
T PRK00103 64 LPKGARVIALDERGKQLSSEEFAQELERWRDDGRSDVAFVIGGADGLSPAVKKR---AD-QSLSLSKLTLPHQLVRVLLA 139 (157)
T ss_pred CCCCCEEEEEcCCCCcCCHHHHHHHHHHHHhcCCccEEEEEcCccccCHHHHHh---cC-ceEEeccCCCcHHHHHHHHH
Confidence 334556777887765432 22221 112247999999999999985443 23 45999999999999988887
Q ss_pred HHHH
Q 045537 277 ATLM 280 (291)
Q Consensus 277 a~l~ 280 (291)
=++.
T Consensus 140 EQlY 143 (157)
T PRK00103 140 EQLY 143 (157)
T ss_pred HHHH
Confidence 6663
No 57
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.
Probab=44.28 E-value=22 Score=30.69 Aligned_cols=35 Identities=20% Similarity=0.293 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHcCCeEEecCCCccccchHHHH
Q 045537 240 EGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIA 274 (291)
Q Consensus 240 EGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~ 274 (291)
.||.+++.+..+.+.|+..|..|..|.++|...-+
T Consensus 158 ~GGI~~~~~~~~~~~G~~gva~~~~i~~~~dp~~~ 192 (196)
T TIGR00693 158 IGGITLENAAEVLAAGADGVAVVSAIMQAADPKAA 192 (196)
T ss_pred ECCcCHHHHHHHHHcCCCEEEEhHHhhCCCCHHHH
Confidence 38999999999999999999999999999885433
No 58
>PRK06739 pyruvate kinase; Validated
Probab=43.58 E-value=1.2e+02 Score=29.57 Aligned_cols=71 Identities=7% Similarity=0.019 Sum_probs=42.8
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCC--c-cceEEEEeeccCCCcHHHHHHHHHhcCccEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQH--T-QWNVFAAFGTLKGGRADWLVEKCTELGAQSVT 146 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~--~-~i~l~la~~l~K~~r~d~iiekatELGV~~I~ 146 (291)
+++||.|.+-|| .-..+|.+++.+.+.+++...-....... + ...+.+ -++...|+ ..|+.+.+.||+-|-
T Consensus 110 v~~Gd~IlidDG---~i~l~V~~v~~~~v~~~v~~gG~L~s~Kgvn~pg~~~~l-p~ltekD~--~di~f~~~~~vD~ia 183 (352)
T PRK06739 110 VKVGSRILMNDG---EVELIVEKVSTDKIETKVKTGGNISSHKGVNLPGAIVRL-PAITEKDK--KDIQFLLEEDVDFIA 183 (352)
T ss_pred cCCCCEEEEeCC---EEEEEEEEEeCCEEEEEEeeCcEEcCCCCeecccccCCC-CCCCHHHH--HHHHHHHHcCCCEEE
Confidence 799999998665 45678888888888777654311111100 0 011111 12333444 558899999999886
No 59
>PRK00278 trpC indole-3-glycerol-phosphate synthase; Reviewed
Probab=43.24 E-value=16 Score=33.77 Aligned_cols=31 Identities=29% Similarity=0.528 Sum_probs=27.8
Q ss_pred CCCC-CHHHHHHHHHcCCeEEecCCCccccch
Q 045537 240 EGDF-TEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 240 EGGf-s~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
|||. +++++..+.+.|+..|-.|..|+|++-
T Consensus 217 egGI~t~ed~~~~~~~Gad~vlVGsaI~~~~d 248 (260)
T PRK00278 217 ESGIFTPEDLKRLAKAGADAVLVGESLMRADD 248 (260)
T ss_pred EeCCCCHHHHHHHHHcCCCEEEECHHHcCCCC
Confidence 5555 899999999999999999999999874
No 60
>PLN02762 pyruvate kinase complex alpha subunit
Probab=42.56 E-value=80 Score=32.36 Aligned_cols=71 Identities=7% Similarity=-0.003 Sum_probs=40.8
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCC----------ccceEEEEeeccCCCcHHHHHHHHHh
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQH----------TQWNVFAAFGTLKGGRADWLVEKCTE 139 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~----------~~i~l~la~~l~K~~r~d~iiekatE 139 (291)
+++||.|.+=|| .-..+|.+++.+.+.+++...-....... +...+-+ -++...|+ .-|+-+.+
T Consensus 141 v~~Gd~IlidDG---~i~l~V~~~~~~~v~~~v~~~G~l~~~KgvNl~~~g~~~p~~~~~l-p~ltekD~--~di~f~~~ 214 (509)
T PLN02762 141 VKVGDELVVDGG---MVRFEVIEKIGPDVKCKCTDPGLLLPRANLTFWRDGSLVRERNAML-PTISSKDW--LDIDFGIS 214 (509)
T ss_pred cCCCCEEEEeCC---EEEEEEEEEECCEEEEEEEeCcEEcCCCceeeccccCCCCCCccCC-CCCCHHHH--HHHHHHHH
Confidence 789999888654 34567777777777776654311111000 0111111 12444454 44788999
Q ss_pred cCccEEE
Q 045537 140 LGAQSVT 146 (291)
Q Consensus 140 LGV~~I~ 146 (291)
.||+-|-
T Consensus 215 ~~vD~ia 221 (509)
T PLN02762 215 EGVDFIA 221 (509)
T ss_pred cCCCEEE
Confidence 9999886
No 61
>PRK04180 pyridoxal biosynthesis lyase PdxS; Provisional
Probab=42.55 E-value=34 Score=32.57 Aligned_cols=46 Identities=20% Similarity=0.297 Sum_probs=33.9
Q ss_pred CCCCC-CHHHHHHHHHcCCeEEecCCCcccc---chHHHHHHHHHHHccC
Q 045537 239 PEGDF-TEKEVNKIVEAGATAVGLGPHRLRV---ETATIALLATLMLCSD 284 (291)
Q Consensus 239 PEGGf-s~~Ei~~l~~~Gf~~vsLG~rILRt---ETAai~ala~l~~~~~ 284 (291)
.|||. |++.+..+.+.|+..|-.|.-|+++ +.++-.....+..|.|
T Consensus 210 AeGGI~TPedaa~vme~GAdgVaVGSaI~ks~dP~~~akafv~ai~~~~~ 259 (293)
T PRK04180 210 AAGGIATPADAALMMQLGADGVFVGSGIFKSGDPEKRARAIVEATTHYDD 259 (293)
T ss_pred EeCCCCCHHHHHHHHHhCCCEEEEcHHhhcCCCHHHHHHHHHHHHHHcCC
Confidence 68999 9999999999999999999999844 4444333333334433
No 62
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=42.33 E-value=41 Score=27.33 Aligned_cols=31 Identities=13% Similarity=0.157 Sum_probs=24.3
Q ss_pred HHHHcccCCCCCEEEEEeCCCCEEEEEEEEee
Q 045537 63 HMTKVLRLSTNDRVELFNGKGGLIEGCIQRID 94 (291)
Q Consensus 63 Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~ 94 (291)
+..+.-.+++||.|.+.+. ++.|..+|.++.
T Consensus 58 ~F~~L~~l~~Gd~v~v~~~-~~~~~Y~V~~~~ 88 (126)
T cd06166 58 IFNRLDEVEKGDEIKVTTK-NGTYKYKITSIF 88 (126)
T ss_pred ccCChHHCCCCCEEEEEEC-CEEEEEEEEEEE
Confidence 4444556789999999997 779999998653
No 63
>COG0036 Rpe Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
Probab=42.29 E-value=1.3e+02 Score=27.48 Aligned_cols=134 Identities=17% Similarity=0.275 Sum_probs=80.6
Q ss_pred CccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEc
Q 045537 113 HTQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLN 192 (291)
Q Consensus 113 ~~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~ 192 (291)
+.+++++|.+. .-+..+++..+.|++.|. +-.| - .....|.- +.+ ++.-.++|- .++
T Consensus 61 ~~p~DvHLMV~-----~p~~~i~~fa~agad~It-~H~E---~-----~~~~~r~i---~~I--k~~G~kaGv----~ln 117 (220)
T COG0036 61 DLPLDVHLMVE-----NPDRYIEAFAKAGADIIT-FHAE---A-----TEHIHRTI---QLI--KELGVKAGL----VLN 117 (220)
T ss_pred CCceEEEEecC-----CHHHHHHHHHHhCCCEEE-EEec---c-----CcCHHHHH---HHH--HHcCCeEEE----EEC
Confidence 45667777542 236899999999999886 4444 1 12233433 344 443333333 355
Q ss_pred CCCCHhhhccccCCCceEEEEe--CC--CCChh-------hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEec
Q 045537 193 PPMKIDGLLPLVSQSKLAFVAI--AE--ATPLV-------TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGL 261 (291)
Q Consensus 193 ~p~~l~~~l~~~~~~~~~lv~~--~~--~~~~~-------~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsL 261 (291)
|-.+++.+-..+..-|..++.. |+ +.... ..+.+....+. -+.|--.||.+.+=+..+.++|+..+-.
T Consensus 118 P~Tp~~~i~~~l~~vD~VllMsVnPGfgGQ~Fi~~~l~Ki~~lr~~~~~~~-~~~IeVDGGI~~~t~~~~~~AGad~~Va 196 (220)
T COG0036 118 PATPLEALEPVLDDVDLVLLMSVNPGFGGQKFIPEVLEKIRELRAMIDERL-DILIEVDGGINLETIKQLAAAGADVFVA 196 (220)
T ss_pred CCCCHHHHHHHHhhCCEEEEEeECCCCcccccCHHHHHHHHHHHHHhcccC-CeEEEEeCCcCHHHHHHHHHcCCCEEEE
Confidence 5556665544444446666553 32 11111 11111111122 5778889999999999999999999999
Q ss_pred CCCccccch
Q 045537 262 GPHRLRVET 270 (291)
Q Consensus 262 G~rILRtET 270 (291)
|+-+.+..-
T Consensus 197 GSalF~~~d 205 (220)
T COG0036 197 GSALFGADD 205 (220)
T ss_pred EEEEeCCcc
Confidence 999988864
No 64
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=41.07 E-value=54 Score=26.63 Aligned_cols=40 Identities=18% Similarity=0.147 Sum_probs=28.6
Q ss_pred EEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEe
Q 045537 53 IVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRI 93 (291)
Q Consensus 53 ~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i 93 (291)
.+.|.+-.-.|..+.-.++.||.|.+.+. |+.|..+|.++
T Consensus 45 n~vIaGH~~~~F~~L~~l~~Gd~i~v~~~-~~~~~Y~V~~~ 84 (127)
T cd05828 45 NIVIAGHRDTHFRFLGELEPGDIITLQTL-GGTYTYRVTST 84 (127)
T ss_pred cEEEEEeCchhhhChhcCCCCCEEEEEEC-CEEEEEEEeeE
Confidence 34444322245555556889999999998 89999999875
No 65
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=40.92 E-value=86 Score=26.62 Aligned_cols=51 Identities=16% Similarity=0.291 Sum_probs=36.4
Q ss_pred CcEEEEcc-hhhhHHHHc-----------ccCCCCCEEEEEeCCCCEEEEEEEEeeCC--ceEEE
Q 045537 51 GGIVRVEG-DEFWHMTKV-----------LRLSTNDRVELFNGKGGLIEGCIQRIDRT--GLDVV 101 (291)
Q Consensus 51 ~~~v~L~~-~~~~Hl~kV-----------LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~--~~~v~ 101 (291)
+....+++ ++...+.+. ..+++||.|.|.+|-=.-+.|.|.+++++ .+.+.
T Consensus 89 ~~p~~I~~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 89 GKPKALSEDEEVKNILNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred CeeeccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 34567888 888887642 23678999999999655568999999733 44443
No 66
>PRK05826 pyruvate kinase; Provisional
Probab=40.88 E-value=1.7e+02 Score=29.55 Aligned_cols=72 Identities=13% Similarity=0.135 Sum_probs=42.7
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCCccceEE-EEeeccC-CCcHHHHHHHHHhcCccEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQHTQWNVF-AAFGTLK-GGRADWLVEKCTELGAQSVT 146 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~~~i~l~-la~~l~K-~~r~d~iiekatELGV~~I~ 146 (291)
+++||.|.+-||. -..+|++++.+.+.+++...-... ....+++- ..+.+|- .++-.+.|+.+.+.|++.|.
T Consensus 118 v~~Gd~ilidDG~---i~l~V~~~~~~~v~~~v~~~g~l~--s~kgvnlp~~~~~lp~lte~D~~~i~~ald~g~d~I~ 191 (465)
T PRK05826 118 VKPGDILLLDDGK---LQLKVVEVDGDEVETEVKNGGPLS--NNKGINIPGGGLSLPALTEKDKADIKFAAEQGVDYIA 191 (465)
T ss_pred cCCCCEEEEeCCe---EEEEEEEEeCCEEEEEEEeCcEec--CCceeeccCcccCCCCCChhhHHHHHHHHHCCCCEEE
Confidence 7899999987763 366788888888877765432111 01111100 0001121 23344778999999999995
No 67
>cd00958 DhnA Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly divergent based on sequence similarity to other class I and class II (metal dependent) aldolase subfamilies.
Probab=40.50 E-value=2.3e+02 Score=25.09 Aligned_cols=40 Identities=28% Similarity=0.364 Sum_probs=29.8
Q ss_pred CceEEEEcCCCCCCHHH----HHHHHHcCCeEEecCCCccccchH
Q 045537 231 SSGLIIVGPEGDFTEKE----VNKIVEAGATAVGLGPHRLRVETA 271 (291)
Q Consensus 231 ~~i~lvIGPEGGfs~~E----i~~l~~~Gf~~vsLG~rILRtETA 271 (291)
-++ +++|=.|--++++ +..+.+.|+..++.|+.|+..+-.
T Consensus 180 ~pv-v~~GG~~~~~~~~~l~~~~~~~~~Ga~gv~vg~~i~~~~dp 223 (235)
T cd00958 180 VPV-VIAGGPKKDSEEEFLKMVYDAMEAGAAGVAVGRNIFQRPDP 223 (235)
T ss_pred CCE-EEeCCCCCCCHHHHHHHHHHHHHcCCcEEEechhhhcCCCH
Confidence 455 5666333346655 888899999999999999998863
No 68
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=39.36 E-value=93 Score=27.90 Aligned_cols=110 Identities=15% Similarity=0.119 Sum_probs=72.0
Q ss_pred HHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccCCCc-eE
Q 045537 132 WLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVSQSK-LA 210 (291)
Q Consensus 132 ~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~~~~-~~ 210 (291)
.-++++.+.|++-|+ +. . +. .-+ .++|++.+-.++|=+..|-....+++. +.+ ++
T Consensus 71 ~~a~~a~~aGA~Fiv---sP---~-----------~~---~~v--~~~~~~~~i~~iPG~~TptEi~~A~~~--Ga~~vK 126 (204)
T TIGR01182 71 EQLRQAVDAGAQFIV---SP---G-----------LT---PEL--AKHAQDHGIPIIPGVATPSEIMLALEL--GITALK 126 (204)
T ss_pred HHHHHHHHcCCCEEE---CC---C-----------CC---HHH--HHHHHHcCCcEECCCCCHHHHHHHHHC--CCCEEE
Confidence 457899999999885 22 1 23 455 678888888888866555544444432 222 34
Q ss_pred EEEeC-CC-CChhhhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccc
Q 045537 211 FVAIA-EA-TPLVTALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVE 269 (291)
Q Consensus 211 lv~~~-~~-~~~~~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtE 269 (291)
++.-. -+ ....+.+...- ..+-++ |=||.+.+-+..+.++|+..+.+|+.+.+.+
T Consensus 127 lFPA~~~GG~~yikal~~pl--p~i~~~--ptGGV~~~N~~~~l~aGa~~vg~Gs~L~~~~ 183 (204)
T TIGR01182 127 LFPAEVSGGVKMLKALAGPF--PQVRFC--PTGGINLANVRDYLAAPNVACGGGSWLVPKD 183 (204)
T ss_pred ECCchhcCCHHHHHHHhccC--CCCcEE--ecCCCCHHHHHHHHhCCCEEEEEChhhcCch
Confidence 44322 11 23344454322 234454 9999999999999999999999999998743
No 69
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=39.35 E-value=1.1e+02 Score=19.94 Aligned_cols=31 Identities=16% Similarity=0.068 Sum_probs=20.9
Q ss_pred CCEEEEEeC-CCCEEEEEEEEee-CCceEEEee
Q 045537 73 NDRVELFNG-KGGLIEGCIQRID-RTGLDVVAL 103 (291)
Q Consensus 73 Gd~i~v~dG-~g~~~~a~I~~i~-k~~~~v~i~ 103 (291)
|+.+.+... +|.-|+|+|.++. ...+.+...
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~~~~~~V~f~ 33 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILSDGKVEVFFV 33 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECCCCcEEEEEE
Confidence 555555444 5999999999998 445555433
No 70
>PF02590 SPOUT_MTase: Predicted SPOUT methyltransferase; InterPro: IPR003742 This family of proteins are predicted to be SPOUT methyltransferases []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1VH0_E 4FAK_A 1TO0_G 1O6D_A 1NS5_B.
Probab=38.86 E-value=91 Score=26.67 Aligned_cols=77 Identities=16% Similarity=0.264 Sum_probs=41.2
Q ss_pred hccccCCCceEEEEeCCCCChh-----hhhcc--CCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHH
Q 045537 200 LLPLVSQSKLAFVAIAEATPLV-----TALSS--SRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETAT 272 (291)
Q Consensus 200 ~l~~~~~~~~~lv~~~~~~~~~-----~~l~~--~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAa 272 (291)
+++.+...+..+++++.++.+. +.+.. ....+.++++||.=-||+++=.+. + -..+|||+-.+-=|-|-
T Consensus 60 il~~i~~~~~~i~Ld~~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGG~~G~~~~~~~~---a-~~~lSLS~mTfpH~lar 135 (155)
T PF02590_consen 60 ILKKIPPNDYVILLDERGKQLSSEEFAKKLERWMNQGKSDIVFIIGGADGLSEEVRKR---A-DEKLSLSKMTFPHQLAR 135 (155)
T ss_dssp HHCTSHTTSEEEEE-TTSEE--HHHHHHHHHHHHHTTS-EEEEEE-BTTB--HHHHHH-----SEEEES-SS---HHHHH
T ss_pred HHhhccCCCEEEEEcCCCccCChHHHHHHHHHHHhcCCceEEEEEecCCCCCHHHHhh---c-CceEEEecCCCcHHHHH
Confidence 3344444566777777765322 12221 112357999999777899863332 2 36799999999999998
Q ss_pred HHHHHHHH
Q 045537 273 IALLATLM 280 (291)
Q Consensus 273 i~ala~l~ 280 (291)
++.+=++.
T Consensus 136 lvL~EQiY 143 (155)
T PF02590_consen 136 LVLLEQIY 143 (155)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88876663
No 71
>PF06995 Phage_P2_GpU: Phage P2 GpU; InterPro: IPR009734 This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein (O64315 from SWISSPROT) which is thought to be involved in tail assembly [].
Probab=38.04 E-value=68 Score=25.91 Aligned_cols=75 Identities=23% Similarity=0.303 Sum_probs=47.8
Q ss_pred ccccceec-ccCccccCCccccccEEEe----CCcEEEEcchhhhHH------HHccc--CCCCCEEEEEeCCCCEE-EE
Q 045537 23 PLSLRAFS-SSSSDYANQSRGGIPRFFS----QGGIVRVEGDEFWHM------TKVLR--LSTNDRVELFNGKGGLI-EG 88 (291)
Q Consensus 23 ~~~~~~~~-~~~~~~~~~~~~~~~rff~----~~~~v~L~~~~~~Hl------~kVLR--lk~Gd~i~v~dG~g~~~-~a 88 (291)
.++...|+ +++..|+...|.+...... ..+.+.|++.-+.|. ...|| +..|+...+++|+|..+ ..
T Consensus 9 ~~~f~~l~r~~~~rwa~h~~ig~~p~~Q~~G~~~~~itl~g~l~~~~~~~~~~l~~Lr~~~~~g~p~~Lv~G~G~~~G~~ 88 (121)
T PF06995_consen 9 TLTFQELQRSSSARWAEHERIGGKPALQFTGPGLDTITLSGVLFPEFGGGRKELDKLRAMAESGEPLPLVIGSGKVLGKW 88 (121)
T ss_pred ccChHHheeeeccccccceeccCCCcceecCCCCceEEEEEEEehHHCCCHHHHHHHHHHHHcCCceEEEECCCceeEEE
Confidence 33334443 4567888888877654433 446777776544443 23333 46789999999988654 56
Q ss_pred EEEEeeCCc
Q 045537 89 CIQRIDRTG 97 (291)
Q Consensus 89 ~I~~i~k~~ 97 (291)
.|++++...
T Consensus 89 vI~si~e~~ 97 (121)
T PF06995_consen 89 VITSISETQ 97 (121)
T ss_pred EEEEEechh
Confidence 888887654
No 72
>TIGR02317 prpB methylisocitrate lyase. Members of this family are methylisocitrate lyase, also called (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase. This enzyme acts in propionate metabolism. It cleaves a carbon-carbon bond to convert 2-methylisocitrate to pyruvate plus succinate. Some members of this family have been annotated, incorrectly it seems, as the related protein carboxyphosphoenolpyruvate phosphomutase, which is involved in synthesizing the antibiotic bialaphos in Streptomyces hygroscopicus.
Probab=37.52 E-value=2.7e+02 Score=26.25 Aligned_cols=146 Identities=13% Similarity=0.075 Sum_probs=72.6
Q ss_pred CCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCC-cceeEc--C---CCCHhh
Q 045537 126 KGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRL-HEMVLN--P---PMKIDG 199 (291)
Q Consensus 126 K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~-~lP~I~--~---p~~l~~ 199 (291)
........++...+.||.-|..=-...-.|+-....+.+--.+ ..++|+.|+..+... .+--+. + ...+++
T Consensus 86 ~~~~v~~tv~~~~~aG~agi~IEDq~~pK~cgh~~g~~lv~~e---e~~~kI~Aa~~a~~~~d~~IiARTDa~~~~g~de 162 (285)
T TIGR02317 86 EAFNVARTVREMEDAGAAAVHIEDQVLPKRCGHLPGKELVSRE---EMVDKIAAAVDAKRDEDFVIIARTDARAVEGLDA 162 (285)
T ss_pred CHHHHHHHHHHHHHcCCeEEEEecCCCccccCCCCCccccCHH---HHHHHHHHHHHhccCCCEEEEEEcCcccccCHHH
Confidence 3455667899999999988864221100022111112222222 233344455555432 121121 1 224777
Q ss_pred hccccC-----CCceEEEEeCCCCChhhhhccCCCCCceEEEE--cCC-CCCCHHHHHHHHHcCCeEEecCCCccccchH
Q 045537 200 LLPLVS-----QSKLAFVAIAEATPLVTALSSSRNESSGLIIV--GPE-GDFTEKEVNKIVEAGATAVGLGPHRLRVETA 271 (291)
Q Consensus 200 ~l~~~~-----~~~~~lv~~~~~~~~~~~l~~~~~~~~i~lvI--GPE-GGfs~~Ei~~l~~~Gf~~vsLG~rILRtETA 271 (291)
.++... +.|..++.-.....-...+... ...|+.+.+ |+. +-+|.+| |.+.||..|+.|+.-+|+-+.
T Consensus 163 AI~Ra~ay~~AGAD~vfi~g~~~~e~i~~~~~~-i~~Pl~~n~~~~~~~p~~s~~e---L~~lGv~~v~~~~~~~~aa~~ 238 (285)
T TIGR02317 163 AIERAKAYVEAGADMIFPEALTSLEEFRQFAKA-VKVPLLANMTEFGKTPLFTADE---LREAGYKMVIYPVTAFRAMNK 238 (285)
T ss_pred HHHHHHHHHHcCCCEEEeCCCCCHHHHHHHHHh-cCCCEEEEeccCCCCCCCCHHH---HHHcCCcEEEEchHHHHHHHH
Confidence 775432 3354444221111111112221 124664333 222 2366666 677899999999999999888
Q ss_pred HHHHHHH
Q 045537 272 TIALLAT 278 (291)
Q Consensus 272 ai~ala~ 278 (291)
++.....
T Consensus 239 a~~~~~~ 245 (285)
T TIGR02317 239 AAEAVYN 245 (285)
T ss_pred HHHHHHH
Confidence 7765544
No 73
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=37.01 E-value=91 Score=26.61 Aligned_cols=49 Identities=16% Similarity=0.274 Sum_probs=34.1
Q ss_pred EEEEcchhhhHHHHc-----------ccCCCCCEEEEEeCCCCEEEEEEEEeeCC--ceEEE
Q 045537 53 IVRVEGDEFWHMTKV-----------LRLSTNDRVELFNGKGGLIEGCIQRIDRT--GLDVV 101 (291)
Q Consensus 53 ~v~L~~~~~~Hl~kV-----------LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~--~~~v~ 101 (291)
...+++++..-+.+. ..+++||.|.|.+|-=.-+.|+|.++++. .+.+.
T Consensus 99 p~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~ 160 (181)
T PRK05609 99 PTPLSEKEVEKILKQLQEGVEKPKPKVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL 160 (181)
T ss_pred cccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE
Confidence 455677777666552 34678999999999655568999999743 44443
No 74
>PF04203 Sortase: Sortase family; InterPro: IPR005754 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N ....
Probab=36.77 E-value=38 Score=27.11 Aligned_cols=34 Identities=21% Similarity=0.300 Sum_probs=25.3
Q ss_pred chhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEee
Q 045537 58 GDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRID 94 (291)
Q Consensus 58 ~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~ 94 (291)
+.-+.+| .++++||.|.+.+..|..|..+|.++.
T Consensus 52 ~~~F~~L---~~~~~gd~i~~~~~~g~~~~Y~V~~~~ 85 (128)
T PF04203_consen 52 GAMFSNL---NKLKKGDEIYLTTPDGKTYEYRVTSVK 85 (128)
T ss_dssp SSTTCGG---GGGHTT-EEEEEETSSEEEEEEEEEEE
T ss_pred Ccccccc---cccCCCCEEEEEEecCEEEEEEEEEEE
Confidence 3445554 455999999999988999999998653
No 75
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=36.76 E-value=1.3e+02 Score=27.77 Aligned_cols=104 Identities=14% Similarity=0.173 Sum_probs=58.6
Q ss_pred eeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhc
Q 045537 122 FGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLL 201 (291)
Q Consensus 122 ~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l 201 (291)
-.+-++..+--||+-|.-+||+.++.-.. |+.... .+. |+ .. +..--++|.+........++
T Consensus 115 d~V~DP~NlGaIiRtA~a~Gv~~Vi~~~~----~~~~~~-~~v--~r----~s-------~Ga~~~vp~~~~~n~~~~~~ 176 (260)
T COG0566 115 DGVTDPHNLGAIIRTADAFGVDGVILPKR----RADPLN-PKV--IR----AS-------AGAAFHVPVIRVTNLARTLL 176 (260)
T ss_pred ecCcCCcchhhHHhhHHHhCCCEEEECCC----ccCCcc-cee--EE----ec-------CChheeceeEEEeccHHHHH
Confidence 36788999999999999999999984332 222111 111 21 11 12223456554433344444
Q ss_pred cccCCCceEEEEe-CCC-CChhhhhccCCCCCceEEEEcCCC-CCCHHH
Q 045537 202 PLVSQSKLAFVAI-AEA-TPLVTALSSSRNESSGLIIVGPEG-DFTEKE 247 (291)
Q Consensus 202 ~~~~~~~~~lv~~-~~~-~~~~~~l~~~~~~~~i~lvIGPEG-Gfs~~E 247 (291)
+.....+..++.- .++ ..+... ...+++++++|-|| |.|+.=
T Consensus 177 ~~~~~~G~~v~~t~~~~~~~~~~~----~~~~~~aLvlG~Eg~Gls~~~ 221 (260)
T COG0566 177 ELLKEAGFWVVATSLDGEVDLYET----DLPKKTALVLGNEGEGLSRLL 221 (260)
T ss_pred HHHHHcCeEEEEECCCCCcchhhc----cccCCEEEEECCCCCCcCHHH
Confidence 4443344444443 333 222221 22478999999999 788763
No 76
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=36.45 E-value=96 Score=22.44 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=22.0
Q ss_pred CCCCEEEEEeC----CCCEEEEEEEEeeCC-ceEEEe
Q 045537 71 STNDRVELFNG----KGGLIEGCIQRIDRT-GLDVVA 102 (291)
Q Consensus 71 k~Gd~i~v~dG----~g~~~~a~I~~i~k~-~~~v~i 102 (291)
+.|+.|+|.-. .|.-|.|+|++..++ ...++-
T Consensus 2 ~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~~~~V~Y 38 (68)
T PF05641_consen 2 KKGDEVEVSSDEDGFRGAWFPATVLKENGDDKYLVEY 38 (68)
T ss_dssp -TT-EEEEEE-SBTT--EEEEEEEEEEETT-EEEEEE
T ss_pred CCCCEEEEEEcCCCCCcEEEEEEEEEeCCCcEEEEEE
Confidence 68999998653 477899999999888 666554
No 77
>TIGR00343 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1. This protein had been believed to be a singlet oxygen resistance protein. Subsequent work showed that it is a protein of pyridoxine (vitamin B6) biosynthesis, and that pyridoxine quenches the highly toxic singlet form of oxygen produced by light in the presence of certain chemicals.
Probab=36.44 E-value=49 Score=31.41 Aligned_cols=31 Identities=19% Similarity=0.327 Sum_probs=28.6
Q ss_pred CCCCC-CHHHHHHHHHcCCeEEecCCCccccc
Q 045537 239 PEGDF-TEKEVNKIVEAGATAVGLGPHRLRVE 269 (291)
Q Consensus 239 PEGGf-s~~Ei~~l~~~Gf~~vsLG~rILRtE 269 (291)
.|||. |++.+..+.+.|+..|-.|+-|.+++
T Consensus 204 AiGGI~TPedAa~~melGAdGVaVGSaI~ks~ 235 (287)
T TIGR00343 204 AAGGVATPADAALMMQLGADGVFVGSGIFKSS 235 (287)
T ss_pred ccCCCCCHHHHHHHHHcCCCEEEEhHHhhcCC
Confidence 78999 99999999999999999999999743
No 78
>PLN02765 pyruvate kinase
Probab=35.59 E-value=2.7e+02 Score=28.71 Aligned_cols=75 Identities=5% Similarity=-0.074 Sum_probs=44.2
Q ss_pred CCCCCEEEEEeC-----CCCEEEEEEEEeeCCceEEEeeecccccCCC---C-ccceEEEEeeccCCCcHHHHHHHHHhc
Q 045537 70 LSTNDRVELFNG-----KGGLIEGCIQRIDRTGLDVVALEDLKLVLPQ---H-TQWNVFAAFGTLKGGRADWLVEKCTEL 140 (291)
Q Consensus 70 lk~Gd~i~v~dG-----~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~---~-~~i~l~la~~l~K~~r~d~iiekatEL 140 (291)
+++||.|.+-|| +++.-..+|.+++.+.+.+++...-...... . +...+-+ -++...|+ +.+.+-+.+.
T Consensus 142 v~~Gd~IlidDG~~~g~~dg~i~l~V~~~~~~~v~~~v~~gG~L~s~~kgvnlpg~~~~l-p~ltekD~-~di~~f~~~~ 219 (526)
T PLN02765 142 VKPGDTIFVGQYLFTGSETTSVWLEVDEVKGDDVVCTVKNSATLAGSLFTLHVSQVRIDL-PTLSEKDK-EVISTWGVPN 219 (526)
T ss_pred cCCCCEEEECCcccccccCceEEEEEEEEECCEEEEEEEeCcEECCCccceeCCCCcCCC-CCCcHhHH-HHHHHHHHHc
Confidence 899999999887 4456677888888888877765431111100 0 0111111 12334443 3334789999
Q ss_pred CccEEE
Q 045537 141 GAQSVT 146 (291)
Q Consensus 141 GV~~I~ 146 (291)
||+-|-
T Consensus 220 ~vD~ia 225 (526)
T PLN02765 220 KIDFLS 225 (526)
T ss_pred CCCEEE
Confidence 999765
No 79
>PRK09722 allulose-6-phosphate 3-epimerase; Provisional
Probab=35.50 E-value=1.6e+02 Score=26.90 Aligned_cols=132 Identities=17% Similarity=0.231 Sum_probs=74.5
Q ss_pred ccceEEEEeeccCCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcC
Q 045537 114 TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNP 193 (291)
Q Consensus 114 ~~i~l~la~~l~K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~ 193 (291)
.++.++|.+. . =+..+++..+.|++.|. +-.| -+. .... +++ +.+++.|--.=-.+++
T Consensus 60 ~~~DvHLMv~--~---P~~~i~~~~~aGad~it-~H~E---a~~-------~~~~---~~i---~~Ik~~G~kaGlalnP 117 (229)
T PRK09722 60 KPLDVHLMVT--D---PQDYIDQLADAGADFIT-LHPE---TIN-------GQAF---RLI---DEIRRAGMKVGLVLNP 117 (229)
T ss_pred CCeEEEEEec--C---HHHHHHHHHHcCCCEEE-ECcc---CCc-------chHH---HHH---HHHHHcCCCEEEEeCC
Confidence 4566666542 3 34678999999999775 4444 110 1122 222 3333333222224566
Q ss_pred CCCHhhhccccCCCceEEEEe--CC--CCChh-------hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecC
Q 045537 194 PMKIDGLLPLVSQSKLAFVAI--AE--ATPLV-------TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLG 262 (291)
Q Consensus 194 p~~l~~~l~~~~~~~~~lv~~--~~--~~~~~-------~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG 262 (291)
..+++.+...++.-+.+++.. |+ +.... ..+.+.......-+.|.-.||.+++-+..+.++|+..+-.|
T Consensus 118 ~T~~~~l~~~l~~vD~VLvMsV~PGf~GQ~fi~~~l~KI~~lr~~~~~~~~~~~IeVDGGI~~~~i~~~~~aGad~~V~G 197 (229)
T PRK09722 118 ETPVESIKYYIHLLDKITVMTVDPGFAGQPFIPEMLDKIAELKALRERNGLEYLIEVDGSCNQKTYEKLMEAGADVFIVG 197 (229)
T ss_pred CCCHHHHHHHHHhcCEEEEEEEcCCCcchhccHHHHHHHHHHHHHHHhcCCCeEEEEECCCCHHHHHHHHHcCCCEEEEC
Confidence 566666554444445555543 22 11111 11111101123447789999999999999999999999999
Q ss_pred CC-ccc
Q 045537 263 PH-RLR 267 (291)
Q Consensus 263 ~r-ILR 267 (291)
+. +..
T Consensus 198 ss~iF~ 203 (229)
T PRK09722 198 TSGLFN 203 (229)
T ss_pred hHHHcC
Confidence 76 887
No 80
>cd00564 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions.
Probab=35.33 E-value=29 Score=29.30 Aligned_cols=31 Identities=19% Similarity=0.279 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 240 EGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 240 EGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
.||.+.+.+..+.+.|+..+.+|..+++.+.
T Consensus 156 ~GGi~~~~i~~~~~~Ga~~i~~g~~i~~~~~ 186 (196)
T cd00564 156 IGGITPENAAEVLAAGADGVAVISAITGADD 186 (196)
T ss_pred ECCCCHHHHHHHHHcCCCEEEEehHhhcCCC
Confidence 3899999999999999999999999998776
No 81
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=35.23 E-value=80 Score=24.22 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=23.6
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
=.+++||.|....| . .|+|.+++++.+.+++
T Consensus 36 ~~L~~Gd~VvT~gG---i-~G~V~~i~d~~v~vei 66 (84)
T TIGR00739 36 ESLKKGDKVLTIGG---I-IGTVTKIAENTIVIEL 66 (84)
T ss_pred HhCCCCCEEEECCC---e-EEEEEEEeCCEEEEEE
Confidence 34899999987543 3 6899999998876654
No 82
>CHL00200 trpA tryptophan synthase alpha subunit; Provisional
Probab=35.20 E-value=1.2e+02 Score=28.12 Aligned_cols=120 Identities=8% Similarity=0.146 Sum_probs=71.8
Q ss_pred cHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhccccCCCc
Q 045537 129 RADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLVSQSK 208 (291)
Q Consensus 129 r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~~~~~ 208 (291)
-+|..+++|.+.||+.++.---. .+.-. -. .++|++.+-..++-+.+-.+.+.+.......+
T Consensus 107 G~e~F~~~~~~aGvdgviipDLP------------~ee~~----~~--~~~~~~~gi~~I~lv~PtT~~eri~~i~~~a~ 168 (263)
T CHL00200 107 GINKFIKKISQAGVKGLIIPDLP------------YEESD----YL--ISVCNLYNIELILLIAPTSSKSRIQKIARAAP 168 (263)
T ss_pred CHHHHHHHHHHcCCeEEEecCCC------------HHHHH----HH--HHHHHHcCCCEEEEECCCCCHHHHHHHHHhCC
Confidence 47889999999999999743322 12222 23 46778888888888877666555433222222
Q ss_pred -eEEE-EeCCCC----C----hhhhhccCCCCCceEEEEcCCCCCC-HHHHHHHHHcCCeEEecCCCcccc
Q 045537 209 -LAFV-AIAEAT----P----LVTALSSSRNESSGLIIVGPEGDFT-EKEVNKIVEAGATAVGLGPHRLRV 268 (291)
Q Consensus 209 -~~lv-~~~~~~----~----~~~~l~~~~~~~~i~lvIGPEGGfs-~~Ei~~l~~~Gf~~vsLG~rILRt 268 (291)
..++ .....+ . +.+.+.......+.-++| .+|.+ ++.+..+.+.|+.-|-.|+.++|.
T Consensus 169 gFIY~vS~~GvTG~~~~~~~~~~~~i~~ir~~t~~Pi~v--GFGI~~~e~~~~~~~~GADGvVVGSalv~~ 237 (263)
T CHL00200 169 GCIYLVSTTGVTGLKTELDKKLKKLIETIKKMTNKPIIL--GFGISTSEQIKQIKGWNINGIVIGSACVQI 237 (263)
T ss_pred CcEEEEcCCCCCCCCccccHHHHHHHHHHHHhcCCCEEE--ECCcCCHHHHHHHHhcCCCEEEECHHHHHH
Confidence 3332 222211 1 111111100111223455 58999 889999999999999999998654
No 83
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=34.68 E-value=1.1e+02 Score=22.39 Aligned_cols=31 Identities=23% Similarity=0.295 Sum_probs=19.5
Q ss_pred CCCCCEEEE--EeCCCC--EEEEEEEEeeCC-ceEE
Q 045537 70 LSTNDRVEL--FNGKGG--LIEGCIQRIDRT-GLDV 100 (291)
Q Consensus 70 lk~Gd~i~v--~dG~g~--~~~a~I~~i~k~-~~~v 100 (291)
+++|+.|.+ .++.|. .|.++|.+++.+ .+.+
T Consensus 1 L~iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i 36 (87)
T PF12945_consen 1 LKIGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLII 36 (87)
T ss_dssp --TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEE
T ss_pred CCCCCEEEEEEECCCCceEEEEEEEEEECCCCEEEE
Confidence 578998876 466654 499999999887 5444
No 84
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=33.19 E-value=69 Score=26.32 Aligned_cols=26 Identities=27% Similarity=0.330 Sum_probs=21.4
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEee
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRID 94 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~ 94 (291)
+.+.+||.|.|.+. +..+.++|++|+
T Consensus 138 ~~l~pGDvi~l~~~-~~~~~~RI~~i~ 163 (164)
T PF13550_consen 138 LALEPGDVIALSDD-GRDMRFRITEIE 163 (164)
T ss_pred ccCCCCCEEEEEeC-CCceEEEEEEEe
Confidence 44889999999887 778889998774
No 85
>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed
Probab=33.02 E-value=53 Score=28.42 Aligned_cols=35 Identities=23% Similarity=0.300 Sum_probs=31.2
Q ss_pred EcCCCCCCHHHHHHHHHcCCeEEecCCCccccchH
Q 045537 237 VGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETA 271 (291)
Q Consensus 237 IGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETA 271 (291)
|-+.||.+++.+..+.+.|+..|.+|..|.+++.-
T Consensus 163 v~a~GGI~~~~i~~~~~~Ga~gv~~gs~i~~~~d~ 197 (212)
T PRK00043 163 IVAIGGITPENAPEVLEAGADGVAVVSAITGAEDP 197 (212)
T ss_pred EEEECCcCHHHHHHHHHcCCCEEEEeHHhhcCCCH
Confidence 44669999999999999999999999999998773
No 86
>cd04727 pdxS PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some metazoa. Together with PdxT, PdxS forms the PLP synthase, a heteromeric glutamine amidotransferase (GATase), whereby PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. PLP is the biologically active form of vitamin B6, an essential cofactor in many biochemical processes. PdxS subunits form two hexameric rings.
Probab=32.94 E-value=61 Score=30.68 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=28.3
Q ss_pred CCCCC-CHHHHHHHHHcCCeEEecCCCccccc
Q 045537 239 PEGDF-TEKEVNKIVEAGATAVGLGPHRLRVE 269 (291)
Q Consensus 239 PEGGf-s~~Ei~~l~~~Gf~~vsLG~rILRtE 269 (291)
.|||. +++.+..+.+.|+..|..|.-|.+++
T Consensus 201 AeGGI~Tpena~~v~e~GAdgVaVGSAI~~a~ 232 (283)
T cd04727 201 AAGGVATPADAALMMQLGADGVFVGSGIFKSE 232 (283)
T ss_pred EeCCCCCHHHHHHHHHcCCCEEEEcHHhhcCC
Confidence 68999 99999999999999999999999743
No 87
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=32.43 E-value=85 Score=25.34 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=26.3
Q ss_pred cccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEE
Q 045537 67 VLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDV 100 (291)
Q Consensus 67 VLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v 100 (291)
-++++.||.|.|.-|+..=-.++|.++..+.+.+
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~V~V 35 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKKVVV 35 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCeEEE
Confidence 3688999999999995433478999998887443
No 88
>PTZ00066 pyruvate kinase; Provisional
Probab=32.34 E-value=1.5e+02 Score=30.39 Aligned_cols=72 Identities=6% Similarity=0.023 Sum_probs=41.4
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCC--C-ccceEEEEeeccCCCcHHHHHHHHHhcCccEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQ--H-TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVT 146 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~--~-~~i~l~la~~l~K~~r~d~iiekatELGV~~I~ 146 (291)
+++||.|.+=|| .-..+|.+++.+.+.+++...-...... . +...+.+ -++...| .+.+++.+.+.||+-|-
T Consensus 154 v~~Gd~IlidDG---~i~l~V~~~~~~~v~~~v~~gG~l~~~Kgvnlpg~~~~l-p~ltekD-~~dI~~f~~~~~vD~Ia 228 (513)
T PTZ00066 154 VKVGNIILIADG---SLSCKVLEVHDDYIITKVLNNATIGERKNMNLPGVKVEL-PVIGEKD-KNDILNFAIPMGCDFIA 228 (513)
T ss_pred ccCCCEEEEeCC---EEEEEEEEEECCEEEEEEEeCcEEcCCcccccCCCccCC-CCCCHHH-HHHHHHHHHhcCCCEEE
Confidence 789999988665 3466888888888877765421111000 0 0111111 1233333 34445899999999764
No 89
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=32.10 E-value=88 Score=25.15 Aligned_cols=40 Identities=15% Similarity=0.151 Sum_probs=28.7
Q ss_pred hhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 59 DEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 59 ~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
.+-.|-.-.=-+++||+|.-..| . .|+|.+++++.+.+++
T Consensus 42 ~~k~~~~~~~~Lk~Gd~VvT~gG---i-~G~Vv~i~~~~v~lei 81 (106)
T PRK05585 42 RQKEHKKMLSSLAKGDEVVTNGG---I-IGKVTKVSEDFVIIEL 81 (106)
T ss_pred HHHHHHHHHHhcCCCCEEEECCC---e-EEEEEEEeCCEEEEEE
Confidence 34455555556899999987543 3 6899999988777765
No 90
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=31.85 E-value=72 Score=25.68 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=23.4
Q ss_pred HHHcccCCCCCEEEEEeCCCCEEEEEEEEe
Q 045537 64 MTKVLRLSTNDRVELFNGKGGLIEGCIQRI 93 (291)
Q Consensus 64 l~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i 93 (291)
..+.-+++.||.|.+.+. ++.|..+|.+.
T Consensus 59 F~~L~~l~~Gd~v~v~~~-~~~~~Y~V~~~ 87 (128)
T cd00004 59 FSDLDNLKKGDKIYLTDG-GKTYVYKVTSI 87 (128)
T ss_pred cCCHHHCCCCCEEEEEEC-CEEEEEEEEEE
Confidence 334456788999999997 88999999865
No 91
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.66 E-value=1.6e+02 Score=22.92 Aligned_cols=30 Identities=27% Similarity=0.401 Sum_probs=24.6
Q ss_pred CcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCC
Q 045537 51 GGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGG 84 (291)
Q Consensus 51 ~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~ 84 (291)
...+.+..+++.-+ -++.||.|+|.+..|.
T Consensus 30 ~~~v~i~p~dA~~l----gI~dGd~V~v~s~~G~ 59 (112)
T cd02787 30 RDVVFMNPDDIARL----GLKAGDRVDLESAFGD 59 (112)
T ss_pred ccEEEECHHHHHHh----CCCCCCEEEEEecCCC
Confidence 35688999887654 5899999999999875
No 92
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=31.26 E-value=66 Score=26.54 Aligned_cols=29 Identities=10% Similarity=0.221 Sum_probs=22.5
Q ss_pred HHHcccCCCCCEEEEEeCCCCEEEEEEEEe
Q 045537 64 MTKVLRLSTNDRVELFNGKGGLIEGCIQRI 93 (291)
Q Consensus 64 l~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i 93 (291)
..+.-++++||.|.+.++++ .|..+|.++
T Consensus 60 F~~L~~l~~Gd~i~v~~~~~-~~~Y~V~~~ 88 (137)
T cd05830 60 FNDLDKLRPGDKIVVETADG-WYTYVVRSS 88 (137)
T ss_pred cccHhhCCCCCEEEEEECCe-EEEEEEeEE
Confidence 33344589999999999754 799999876
No 93
>TIGR03128 RuMP_HxlA 3-hexulose-6-phosphate synthase. at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase.
Probab=30.96 E-value=41 Score=29.24 Aligned_cols=117 Identities=13% Similarity=0.071 Sum_probs=68.1
Q ss_pred HHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCC-CHhhhccccC-CCce
Q 045537 132 WLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPM-KIDGLLPLVS-QSKL 209 (291)
Q Consensus 132 ~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~-~l~~~l~~~~-~~~~ 209 (291)
+.++++.+.|++-|+ +..+ -+ ..... ++ ++.+++.+-...+.+..|. .++++....+ +-+.
T Consensus 67 ~~~~~~~~~Gad~i~-vh~~---~~-------~~~~~---~~---i~~~~~~g~~~~~~~~~~~t~~~~~~~~~~~g~d~ 129 (206)
T TIGR03128 67 YEAEQAFAAGADIVT-VLGV---AD-------DATIK---GA---VKAAKKHGKEVQVDLINVKDKVKRAKELKELGADY 129 (206)
T ss_pred HHHHHHHHcCCCEEE-Eecc---CC-------HHHHH---HH---HHHHHHcCCEEEEEecCCCChHHHHHHHHHcCCCE
Confidence 579999999999887 4444 11 01122 33 4557777776666654443 3444432221 2333
Q ss_pred EEEEeCCC---C---Chh---hhhccCCCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 210 AFVAIAEA---T---PLV---TALSSSRNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 210 ~lv~~~~~---~---~~~---~~l~~~~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
. -.++.. . ... ..+.... .. ..|-+.||.+.+.+..+.++|+..+.+|.-+.+++-
T Consensus 130 v-~~~pg~~~~~~~~~~~~~i~~l~~~~-~~---~~i~v~GGI~~~n~~~~~~~Ga~~v~vGsai~~~~d 194 (206)
T TIGR03128 130 I-GVHTGLDEQAKGQNPFEDLQTILKLV-KE---ARVAVAGGINLDTIPDVIKLGPDIVIVGGAITKAAD 194 (206)
T ss_pred E-EEcCCcCcccCCCCCHHHHHHHHHhc-CC---CcEEEECCcCHHHHHHHHHcCCCEEEEeehhcCCCC
Confidence 2 222211 0 111 1121111 11 245667999999999999999999999999998765
No 94
>PLN02623 pyruvate kinase
Probab=29.97 E-value=3.2e+02 Score=28.58 Aligned_cols=71 Identities=7% Similarity=-0.018 Sum_probs=41.6
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCCC---ccceEEEEeeccCCCcHHHHHHHHHhcCccEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQH---TQWNVFAAFGTLKGGRADWLVEKCTELGAQSVT 146 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~---~~i~l~la~~l~K~~r~d~iiekatELGV~~I~ 146 (291)
+++||.|.+=|| .-..+|.+++.+.+.+++...-....... +...+.+ -++...|+ .-|+.+.+.||+-|-
T Consensus 223 v~~Gd~IlidDG---~i~l~V~~~~~~~v~~~V~~gG~L~s~KgvNlpg~~~~l-p~lTekD~--~di~f~~~~~vD~ia 296 (581)
T PLN02623 223 VEVGDMLLVDGG---MMSLAVKSKTSDSVKCEVVDGGELKSRRHLNVRGKSATL-PSITEKDW--EDIKFGVENKVDFYA 296 (581)
T ss_pred CCCCCEEEEeCC---eEEEEEEEEECCEEEEEEEeceEecCCCCCCCCCCcCCC-CCCCHHHH--HHHHHHHHcCCCEEE
Confidence 789999988554 34567888888887777654211110000 0111111 12334444 458899999999875
No 95
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=29.41 E-value=66 Score=25.81 Aligned_cols=53 Identities=15% Similarity=0.214 Sum_probs=39.2
Q ss_pred CccccccEEEe---------------CCcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeC
Q 045537 39 QSRGGIPRFFS---------------QGGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDR 95 (291)
Q Consensus 39 ~~~~~~~rff~---------------~~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k 95 (291)
..||++..|.. .++.+.+++..++-- -=+++||.|.+.-|+ .++..+|..+..
T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~aKpS---~~VK~GD~l~i~~~~-~~~~v~Vl~~~~ 73 (100)
T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRAKPS---KEVKVGDILTIRFGN-KEFTVKVLALGE 73 (100)
T ss_pred ccceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEcccc---cccCCCCEEEEEeCC-cEEEEEEEeccc
Confidence 56788776632 678999999777433 236999999998874 577888877654
No 96
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=29.29 E-value=1e+02 Score=22.70 Aligned_cols=39 Identities=21% Similarity=0.118 Sum_probs=26.2
Q ss_pred cEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEee
Q 045537 52 GIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRID 94 (291)
Q Consensus 52 ~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~ 94 (291)
+.+.....-.. ..|-.++||.|.+-.+.| ....+|.+|.
T Consensus 38 ~~IS~~SPLG~---ALlG~~~Gd~v~~~~~~g-~~~~~I~~I~ 76 (77)
T PF01272_consen 38 GKISIDSPLGK---ALLGKKVGDEVEVELPGG-ERKYEILEIE 76 (77)
T ss_dssp TEEETTSHHHH---HHTT-BTT-EEEEEETTB-EEEEEEEEEE
T ss_pred eEEEecCHHHH---HhcCCCCCCEEEEEeCCc-eEEEEEEEEE
Confidence 34554444443 458899999999988876 7888988763
No 97
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=29.07 E-value=93 Score=25.60 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=23.9
Q ss_pred hHHHHcccCCCCCEEEEEeCCCCEEEEEEEEe
Q 045537 62 WHMTKVLRLSTNDRVELFNGKGGLIEGCIQRI 93 (291)
Q Consensus 62 ~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i 93 (291)
.|..+.-+++.||.|.+-+++ +.|..+|.++
T Consensus 56 ~~F~~L~~l~~GD~i~v~~~~-~~~~Y~V~~~ 86 (136)
T TIGR01076 56 TMFTNLDKLKKGDMLYLHVGN-EVLTYQVTST 86 (136)
T ss_pred CccCCHHHCCCCCEEEEEECC-cEEEEEEEEE
Confidence 344555668999999998865 6899999765
No 98
>PRK04171 ribosome biogenesis protein; Provisional
Probab=28.86 E-value=1.9e+02 Score=26.40 Aligned_cols=77 Identities=16% Similarity=0.176 Sum_probs=48.4
Q ss_pred CCHhhhccccCCCceEEEEeCCCC--ChhhhhccCCCCCceEEEEc--CCCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 195 MKIDGLLPLVSQSKLAFVAIAEAT--PLVTALSSSRNESSGLIIVG--PEGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 195 ~~l~~~l~~~~~~~~~lv~~~~~~--~~~~~l~~~~~~~~i~lvIG--PEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
.++.+.++.... ..++.+++.+. ...+... ...+++++|| |.|.|+.+=.+... ..+|++..-|-|=|
T Consensus 135 ~~l~~~l~~~~~-~~~i~lS~~g~~~~~~~~~~---~~~~~~~vIGaf~hG~f~~~~~~~~~----~~iSIs~~pLsa~~ 206 (222)
T PRK04171 135 KSLEELLEEIGP-DRIILLSEKGELVKPKELGK---ENENIAVGIGGFPHGDFSEKVLELAK----KKYSIYGEPLTAWT 206 (222)
T ss_pred CcHHHhccccCC-CcEEEECCCCcccCHHHHhh---ccCCcEEEEccccCCCcchhhHhhcC----eEEEEeCCChHHHH
Confidence 468888765421 34566665543 2222222 2457899999 89999987333222 46889999998777
Q ss_pred HHHHHHHHH
Q 045537 271 ATIALLATL 279 (291)
Q Consensus 271 Aai~ala~l 279 (291)
++--.++.+
T Consensus 207 v~~ri~~a~ 215 (222)
T PRK04171 207 VVCRVIAAY 215 (222)
T ss_pred HHHHHHHHH
Confidence 666555554
No 99
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=28.38 E-value=1e+02 Score=25.70 Aligned_cols=29 Identities=14% Similarity=0.118 Sum_probs=24.2
Q ss_pred HcccCCCCCEEEEEeCCCCEEEEEEEEee
Q 045537 66 KVLRLSTNDRVELFNGKGGLIEGCIQRID 94 (291)
Q Consensus 66 kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~ 94 (291)
-.|-.++||.|.+-..+|..+..+|.+|.
T Consensus 98 ALlG~~~Gd~v~v~~p~G~~~~~~I~~I~ 126 (137)
T PRK05753 98 ALLGLSVGQSIDWPLPGGKETHLEVLEVE 126 (137)
T ss_pred HHcCCCCCCEEEEECCCCCEEEEEEEEEE
Confidence 36889999999999888877788887764
No 100
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=28.03 E-value=57 Score=25.28 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=23.2
Q ss_pred EEEcchhhhHHHHcccCCCCCEEEE-EeCCCCEEEEE
Q 045537 54 VRVEGDEFWHMTKVLRLSTNDRVEL-FNGKGGLIEGC 89 (291)
Q Consensus 54 v~L~~~~~~Hl~kVLRlk~Gd~i~v-~dG~g~~~~a~ 89 (291)
+.+-+|...- .-.+++||.|.| ||-+|++|.++
T Consensus 40 f~~~~dk~~~---l~~~~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 40 FEFWGDKIDL---LDNFQVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred EEEEcchhhh---hccCCCCCEEEEEEEeeccEecce
Confidence 4444544433 346789999998 88899999854
No 101
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=27.40 E-value=1.9e+02 Score=30.40 Aligned_cols=71 Identities=15% Similarity=0.079 Sum_probs=45.9
Q ss_pred cCCCCCEEEEEeCCC--CEEEEEEEEeeCCceEEEeeecccccCCCCccceEEEEeeccCCCcHHHHHHHHHhcC
Q 045537 69 RLSTNDRVELFNGKG--GLIEGCIQRIDRTGLDVVALEDLKLVLPQHTQWNVFAAFGTLKGGRADWLVEKCTELG 141 (291)
Q Consensus 69 Rlk~Gd~i~v~dG~g--~~~~a~I~~i~k~~~~v~i~~~~~~~~~~~~~i~l~la~~l~K~~r~d~iiekatELG 141 (291)
++.+||.|.+..+++ ..+.|.|..++++.+++.+.+...... ...+.|.....-.--+||...|.+..+.+
T Consensus 57 ~~~~GD~v~i~~~~~~~~~~~g~V~~v~~~~i~v~~~~~~~~~~--~~~~~i~~~~~~~t~~rm~~aL~~l~~~~ 129 (637)
T TIGR00376 57 EISVGDIVLVSRGNPLQSDLTGVVTRVGKRFITVALEESVPQWS--LKRVRIDLYANDVTFKRMKEALRALTENH 129 (637)
T ss_pred cCCCCCEEEEecCCCCCCCcEEEEEEEcCcEEEEEECCCCCccc--CceEEEEEecCccHHHHHHHHHHHHHhch
Confidence 778999999987654 356899999999988887755321111 11245544332222357777888877654
No 102
>PF07680 DoxA: TQO small subunit DoxA; InterPro: IPR011636 Thiosulphate:quinone oxidoreductase (TQO) catalyses one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Q8AAF0 from SWISSPROT.
Probab=27.07 E-value=1.5e+02 Score=25.00 Aligned_cols=53 Identities=13% Similarity=0.179 Sum_probs=38.9
Q ss_pred ccCccccCCccccccEEEe---CCcEEEEcchhhhHHHHcccCCCCC-EEEEEeCCCCEEEEEEE
Q 045537 31 SSSSDYANQSRGGIPRFFS---QGGIVRVEGDEFWHMTKVLRLSTND-RVELFNGKGGLIEGCIQ 91 (291)
Q Consensus 31 ~~~~~~~~~~~~~~~rff~---~~~~v~L~~~~~~Hl~kVLRlk~Gd-~i~v~dG~g~~~~a~I~ 91 (291)
+-..||.|+-..+-.-+.+ ...++.|+.. +++..|. .+.+.|-+|..|.+.|+
T Consensus 76 ~i~N~Yv~~~~~g~~gl~vpLGakA~i~L~~~--------~~l~~g~Y~l~L~disG~~w~~~~~ 132 (133)
T PF07680_consen 76 NIKNDYVAKVKPGKHGLVVPLGAKATITLPLP--------DHLPPGTYTLKLYDISGITWSAGIT 132 (133)
T ss_pred HcCccEEccccCCceeEEEEcCCcEEEEecCC--------CccCCCcEEEEEEcCCCCeeeeccc
Confidence 3457888887766556665 4456777755 6778898 57899999999988774
No 103
>PRK06247 pyruvate kinase; Provisional
Probab=26.79 E-value=3.6e+02 Score=27.46 Aligned_cols=71 Identities=17% Similarity=0.089 Sum_probs=42.2
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeeecccccCCC--Cc-cceEEEEeeccCCCcHHHHHHHHHhcCccEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALEDLKLVLPQ--HT-QWNVFAAFGTLKGGRADWLVEKCTELGAQSVT 146 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~~~~~~~~~--~~-~i~l~la~~l~K~~r~d~iiekatELGV~~I~ 146 (291)
+++||.|.+=|| .-..+|.+++.+.+.+++...-...... .+ ...+.+ -++...|+ .-|+.+.+.||+-|-
T Consensus 118 v~~G~~I~idDG---~i~l~V~~~~~~~i~~~v~~~G~l~~~Kgvn~p~~~~~~-p~ltekD~--~di~f~~~~~vD~ia 191 (476)
T PRK06247 118 LKPGDRLLVDDG---KVRLVVEACDGDDVVCRVVEGGPVSDRKGVSLPGTVLSV-SALTEKDR--ADLEFALELGVDWVA 191 (476)
T ss_pred cCCCCEEEEeCC---eEEEEEEEEECCEEEEEEEeCcEEcCCCccccCCcccCC-CCCCHHHH--HHHHHHHHcCCCEEE
Confidence 799999988665 3467888888888877765421111000 00 111111 12333344 557899999999885
No 104
>KOG4201 consensus Anthranilate synthase component II [Amino acid transport and metabolism]
Probab=25.92 E-value=78 Score=29.19 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=34.9
Q ss_pred eEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchH
Q 045537 233 GLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETA 271 (291)
Q Consensus 233 i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETA 271 (291)
=+++||--|=||+++++..+++|...|-.|..++|.---
T Consensus 237 Dvilva~SGi~tpdDia~~q~~GV~avLVGEslmk~sDp 275 (289)
T KOG4201|consen 237 DVILVALSGIFTPDDIAKYQKAGVKAVLVGESLMKQSDP 275 (289)
T ss_pred ceEEEeccCCCCHHHHHHHHHcCceEEEecHHHHhccCH
Confidence 348899999999999999999999999999999987553
No 105
>PRK10039 hypothetical protein; Provisional
Probab=25.90 E-value=50 Score=27.60 Aligned_cols=17 Identities=24% Similarity=0.346 Sum_probs=15.1
Q ss_pred cCCCCCCHHHHHHHHHc
Q 045537 238 GPEGDFTEKEVNKIVEA 254 (291)
Q Consensus 238 GPEGGfs~~Ei~~l~~~ 254 (291)
=+|||+|+=|...+.+.
T Consensus 78 ~~EGGlS~VE~R~l~El 94 (127)
T PRK10039 78 MNEGGLSQVEERILIEL 94 (127)
T ss_pred cCCCCccHHHHHHHHHH
Confidence 37999999999999985
No 106
>PF09671 Spore_GerQ: Spore coat protein (Spore_GerQ); InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=25.64 E-value=1.3e+02 Score=23.13 Aligned_cols=41 Identities=17% Similarity=0.199 Sum_probs=28.1
Q ss_pred hhhhHHHHcccCCCCCEEEE--EeCC-----CCEEEEEEEEeeCCceE
Q 045537 59 DEFWHMTKVLRLSTNDRVEL--FNGK-----GGLIEGCIQRIDRTGLD 99 (291)
Q Consensus 59 ~~~~Hl~kVLRlk~Gd~i~v--~dG~-----g~~~~a~I~~i~k~~~~ 99 (291)
-+..++-++||+..|....+ .-.+ -..|.+.|++.+++.+.
T Consensus 5 ~eqsYiENILRlN~GK~~T~Y~Tyenn~ewnakvf~GviE~aGRDhii 52 (81)
T PF09671_consen 5 LEQSYIENILRLNRGKLATFYMTYENNSEWNAKVFRGVIEAAGRDHII 52 (81)
T ss_pred chHHHHHHHHHhcCCceEEEEEEecCchhhhheeeEEEehhcCcceEE
Confidence 35678999999999998765 2223 34566667776666553
No 107
>PRK11320 prpB 2-methylisocitrate lyase; Provisional
Probab=25.53 E-value=5.4e+02 Score=24.33 Aligned_cols=145 Identities=10% Similarity=0.020 Sum_probs=73.3
Q ss_pred CCCcHHHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCC-cceeEc--C---CCCHhh
Q 045537 126 KGGRADWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRL-HEMVLN--P---PMKIDG 199 (291)
Q Consensus 126 K~~r~d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~-~lP~I~--~---p~~l~~ 199 (291)
........+++..+.||.-|..=-...-.|+-....+.+-..+ ..++|+.|+.++.+. .+--+. + ...+++
T Consensus 91 ~~~~v~r~V~~~~~aGaagi~IEDq~~pK~cg~~~~~~lv~~e---e~~~kI~Aa~~a~~~~d~~IiARTDa~~~~g~de 167 (292)
T PRK11320 91 GAFNIARTVKSMIKAGAAAVHIEDQVGAKRCGHRPNKEIVSQE---EMVDRIKAAVDARTDPDFVIMARTDALAVEGLDA 167 (292)
T ss_pred CHHHHHHHHHHHHHcCCeEEEEecCCCccccCCCCCCcccCHH---HHHHHHHHHHHhccCCCeEEEEecCcccccCHHH
Confidence 4455678899999999988763211100022211112222223 334455677776542 122221 1 224777
Q ss_pred hcccc-----CCCceEEEEeCCCCChhhhhccCCCCCceEE--EEcCC-CCCCHHHHHHHHHcCCeEEecCCCccccchH
Q 045537 200 LLPLV-----SQSKLAFVAIAEATPLVTALSSSRNESSGLI--IVGPE-GDFTEKEVNKIVEAGATAVGLGPHRLRVETA 271 (291)
Q Consensus 200 ~l~~~-----~~~~~~lv~~~~~~~~~~~l~~~~~~~~i~l--vIGPE-GGfs~~Ei~~l~~~Gf~~vsLG~rILRtETA 271 (291)
.+... .+.|..++.-.....-...+... ...|+.+ +.||. +-+|.+| |.+.||..|+.|+..+|+-+.
T Consensus 168 AI~Ra~aY~eAGAD~ifi~~~~~~~~i~~~~~~-~~~Pl~~n~~~~~~~p~~s~~~---L~~lGv~~v~~~~~~~~aa~~ 243 (292)
T PRK11320 168 AIERAQAYVEAGADMIFPEAMTELEMYRRFADA-VKVPILANITEFGATPLFTTEE---LASAGVAMVLYPLSAFRAMNK 243 (292)
T ss_pred HHHHHHHHHHcCCCEEEecCCCCHHHHHHHHHh-cCCCEEEEeccCCCCCCCCHHH---HHHcCCcEEEEChHHHHHHHH
Confidence 77543 13454444222111111112211 1245533 32332 2256665 777899999999999998888
Q ss_pred HHHHHH
Q 045537 272 TIALLA 277 (291)
Q Consensus 272 ai~ala 277 (291)
++....
T Consensus 244 a~~~~~ 249 (292)
T PRK11320 244 AAENVY 249 (292)
T ss_pred HHHHHH
Confidence 775444
No 108
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=25.42 E-value=1.3e+02 Score=23.64 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=19.0
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEee
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRID 94 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~ 94 (291)
-..++||.+.+.||+...+.++++++.
T Consensus 29 ~~~k~Gd~~i~~~~~~~~~~i~v~~V~ 55 (105)
T cd06541 29 QLPKAGDYLIILDGQQPLAIAEVVKVE 55 (105)
T ss_pred cCCCCCCEEEEecCCCcEEEEEEEEEE
Confidence 458999999999997444455555543
No 109
>cd00288 Pyruvate_Kinase Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer.
Probab=25.27 E-value=4.8e+02 Score=26.56 Aligned_cols=72 Identities=14% Similarity=0.051 Sum_probs=41.4
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeCC-ceEEEeeecccccCCCCccceEEE-EeeccC-CCcHHHHHHHHHhcCccEEE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDRT-GLDVVALEDLKLVLPQHTQWNVFA-AFGTLK-GGRADWLVEKCTELGAQSVT 146 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k~-~~~v~i~~~~~~~~~~~~~i~l~l-a~~l~K-~~r~d~iiekatELGV~~I~ 146 (291)
+++||.|.+=|| .-..+|.+++.+ .+.+++...-... +...+++-= .+.+|- .++-..-|+.+.+.||+-|-
T Consensus 118 v~~Gd~i~idDG---~i~l~V~~~~~~~~i~~~v~~~G~l~--~~kgin~p~~~~~~p~ltekD~~di~f~~~~~vD~ia 192 (480)
T cd00288 118 VSPGNTILVDDG---LLSLKVLSKDDDKTLVCEVLNGGVLG--SRKGVNLPGTDVDLPALSEKDKADLRFGVEQGVDMIF 192 (480)
T ss_pred cCCCCEEEEeCC---EEEEEEEEEcCCceEEEEEEeCeEEc--CCCceEeeCcccCCCCCCHHHHHHHHHHHHcCCCEEE
Confidence 789999988765 346778888777 6776665432111 111122100 001111 23334668899999999886
No 110
>PRK06354 pyruvate kinase; Provisional
Probab=25.18 E-value=4.4e+02 Score=27.57 Aligned_cols=71 Identities=18% Similarity=0.092 Sum_probs=40.4
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEee--CCceEEEeeecccccCCC--Cc-cceEEEEeeccCCCcHHHHHHHHHhcCccE
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRID--RTGLDVVALEDLKLVLPQ--HT-QWNVFAAFGTLKGGRADWLVEKCTELGAQS 144 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~--k~~~~v~i~~~~~~~~~~--~~-~i~l~la~~l~K~~r~d~iiekatELGV~~ 144 (291)
+++||.|.+-|| .-..+|.+++ .+.+.+++...-...... .+ ...+.+ -++...|+ .-|+.+.+.||+-
T Consensus 121 v~~Gd~i~idDG---~i~l~V~~~~~~~~~v~~~v~~~g~l~~~Kgvn~p~~~~~~-p~ltekD~--~di~f~~~~~vD~ 194 (590)
T PRK06354 121 VPVGSRILLDDG---LIELEVEEVDKADGELHCKVLVGGVLSNKKGVNFPGVSLSL-PAITEKDR--EDLIFGLEQGVDW 194 (590)
T ss_pred cCCCCEEEEeCC---eEEEEEEEEEcCCCEEEEEEEeCeEECCCCcccccCCccCC-CCCCHHHH--HHHHHHHHcCCCE
Confidence 789999988665 3456777777 667776665421110000 00 011111 12333444 4478999999998
Q ss_pred EE
Q 045537 145 VT 146 (291)
Q Consensus 145 I~ 146 (291)
|-
T Consensus 195 ia 196 (590)
T PRK06354 195 IA 196 (590)
T ss_pred EE
Confidence 85
No 111
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=24.81 E-value=1.6e+02 Score=21.48 Aligned_cols=39 Identities=23% Similarity=0.305 Sum_probs=21.1
Q ss_pred HHcccCCCCCEEE----------EEeCCCCEEEEEEEEeeCCceEEEeee
Q 045537 65 TKVLRLSTNDRVE----------LFNGKGGLIEGCIQRIDRTGLDVVALE 104 (291)
Q Consensus 65 ~kVLRlk~Gd~i~----------v~dG~g~~~~a~I~~i~k~~~~v~i~~ 104 (291)
..++++++||.|. +.-++-..|.|++...+. ...+++.+
T Consensus 24 ~el~~L~~Gdvi~l~~~~~~~v~l~v~g~~~~~g~lg~~~~-~~av~I~~ 72 (77)
T PF01052_consen 24 GELLNLKVGDVIPLDKPADEPVELRVNGQPIFRGELGRVNG-RLAVRITE 72 (77)
T ss_dssp HHHHC--TT-EEEECCESSTEEEEEETTEEEEEEEEEEETT-EEEEEEEE
T ss_pred HHHhcCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECC-EEEEEEEE
Confidence 4567777777654 444445677777776654 34455544
No 112
>PTZ00300 pyruvate kinase; Provisional
Probab=24.70 E-value=3.1e+02 Score=27.77 Aligned_cols=68 Identities=10% Similarity=0.082 Sum_probs=39.6
Q ss_pred CCCCCEEEEEeCCCCEEEEEEEEeeC-CceEEEeeecccc------cCCCCccceEEEEeeccCCCcHHHHHHHHHhcCc
Q 045537 70 LSTNDRVELFNGKGGLIEGCIQRIDR-TGLDVVALEDLKL------VLPQHTQWNVFAAFGTLKGGRADWLVEKCTELGA 142 (291)
Q Consensus 70 lk~Gd~i~v~dG~g~~~~a~I~~i~k-~~~~v~i~~~~~~------~~~~~~~i~l~la~~l~K~~r~d~iiekatELGV 142 (291)
+++||.|.+-|| .-..+|.+++. +.+.+++...-.. +.| ...+. +. .++..|+ ..|+.+.++|+
T Consensus 91 v~~G~~ilidDG---~i~l~V~~~~~~~~v~~~v~~gG~l~~~kgvnlp-~~~~~--l~-~ltekD~--~dI~~ald~gv 161 (454)
T PTZ00300 91 VRPGGYIYIDDG---ILILHVQSHEDEQTLKCTVTNAHTISDRRGVNLP-GCDVD--LP-AVSAKDC--ADLQFGVEQGV 161 (454)
T ss_pred cCCCCEEEEeCC---eEEEEEEEEcCCceEEEEEecCcEecCCCccccC-CCccC--CC-CCChhhH--HHHHHHHHCCC
Confidence 789999988665 33567777764 4666655432111 111 11111 11 2334444 56789999999
Q ss_pred cEEE
Q 045537 143 QSVT 146 (291)
Q Consensus 143 ~~I~ 146 (291)
+-|.
T Consensus 162 d~I~ 165 (454)
T PTZ00300 162 DMIF 165 (454)
T ss_pred CEEE
Confidence 9986
No 113
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=24.59 E-value=1.6e+02 Score=27.63 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=27.4
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEee--CCceEEEe
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRID--RTGLDVVA 102 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~--k~~~~v~i 102 (291)
....+||.|.|.+|--.-+.|+|.+++ ++.+.+.+
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV 240 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEE
Confidence 558899999999997666799999997 45554443
No 114
>PF09846 DUF2073: Uncharacterized protein conserved in archaea (DUF2073); InterPro: IPR012017 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.45 E-value=55 Score=26.39 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=16.7
Q ss_pred CCceEEEEcCCCCCCHHHHHHHHH
Q 045537 230 ESSGLIIVGPEGDFTEKEVNKIVE 253 (291)
Q Consensus 230 ~~~i~lvIGPEGGfs~~Ei~~l~~ 253 (291)
.+.|+++ |+||||+|-..|.+
T Consensus 19 ~G~IvVL---E~GLtPeEe~~LIE 39 (104)
T PF09846_consen 19 DGNIVVL---EEGLTPEEESKLIE 39 (104)
T ss_pred cCcEEEE---cCCCChHHHHHHHH
Confidence 3456555 99999999988877
No 115
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=24.23 E-value=1.5e+02 Score=24.10 Aligned_cols=37 Identities=24% Similarity=0.257 Sum_probs=26.2
Q ss_pred hHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEe
Q 045537 62 WHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVA 102 (291)
Q Consensus 62 ~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i 102 (291)
.|-.-.=.+++||.|.-. |+. .++|.+++++.+.+++
T Consensus 31 ~~~~m~~~Lk~GD~VvT~---gGi-~G~V~~I~d~~v~lei 67 (109)
T PRK05886 31 ATIDLHESLQPGDRVHTT---SGL-QATIVGITDDTVDLEI 67 (109)
T ss_pred HHHHHHHhcCCCCEEEEC---CCe-EEEEEEEeCCEEEEEE
Confidence 343334568999998764 333 6889999988777765
No 116
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.10 E-value=1e+02 Score=24.17 Aligned_cols=30 Identities=13% Similarity=0.072 Sum_probs=24.0
Q ss_pred CcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCC
Q 045537 51 GGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGG 84 (291)
Q Consensus 51 ~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~ 84 (291)
...+.+..+++..+ -++.||.|.|.+..|.
T Consensus 34 ~~~v~i~p~dA~~l----gi~~Gd~V~v~s~~G~ 63 (122)
T cd02792 34 EMFVEISPELAAER----GIKNGDMVWVSSPRGK 63 (122)
T ss_pred CcEEEECHHHHHHc----CCCCCCEEEEEcCCce
Confidence 45688888887665 5899999999998774
No 117
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=24.06 E-value=2e+02 Score=20.63 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=20.5
Q ss_pred ccCCCCCEEEEEeCCCCEE-EEEEEEeeCCc
Q 045537 68 LRLSTNDRVELFNGKGGLI-EGCIQRIDRTG 97 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~-~a~I~~i~k~~ 97 (291)
.+...|+.|.+.-.....| .++|++.+.++
T Consensus 4 ~k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 4 RKFAIGEVVMVRWPGSSLYYEGKVLSYDSKS 34 (55)
T ss_dssp SSS-SS-EEEEE-TTTS-EEEEEEEEEETTT
T ss_pred ccccCCCEEEEECCCCCcEEEEEEEEecccC
Confidence 4677899999988866665 99999977543
No 118
>PLN02334 ribulose-phosphate 3-epimerase
Probab=23.63 E-value=64 Score=28.87 Aligned_cols=34 Identities=21% Similarity=0.347 Sum_probs=30.9
Q ss_pred EcCCCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 237 VGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 237 IGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
|-.-||++++.+..+.+.|+..+-.|.-|.+++.
T Consensus 177 I~a~GGI~~e~i~~l~~aGad~vvvgsai~~~~d 210 (229)
T PLN02334 177 IEVDGGVGPSTIDKAAEAGANVIVAGSAVFGAPD 210 (229)
T ss_pred EEEeCCCCHHHHHHHHHcCCCEEEEChHHhCCCC
Confidence 5567999999999999999999999999999876
No 119
>TIGR00246 tRNA_RlmH_YbeA rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA.
Probab=23.55 E-value=4.2e+02 Score=22.57 Aligned_cols=69 Identities=10% Similarity=0.090 Sum_probs=46.8
Q ss_pred ceEEEEeCCCCChh-----hhhccC-CCCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccchHHHHHHHHHH
Q 045537 208 KLAFVAIAEATPLV-----TALSSS-RNESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVETATIALLATLM 280 (291)
Q Consensus 208 ~~~lv~~~~~~~~~-----~~l~~~-~~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtETAai~ala~l~ 280 (291)
+..+++++.++.+. ..+..- .....++++||-=-||+++-.+. + -..+|||+-.+-=+-|-++.+=++.
T Consensus 66 ~~~i~LDe~Gk~~sS~~fA~~l~~~~~~g~~i~FvIGGa~G~~~~v~~~---a-~~~lSLS~mTfpH~larlvL~EQiY 140 (153)
T TIGR00246 66 AHVVTLDIPGKPWTTPQLADTLEKWKTDGRDVTLLIGGPEGLSPTCKAA---A-EQSWSLSKLTLPHPLVRVIVAESLY 140 (153)
T ss_pred CeEEEEcCCCCcCCHHHHHHHHHHHhccCCeEEEEEcCCCcCCHHHHHh---c-CceEEeecCCCcHHHHHHHHHHHHH
Confidence 45667777665432 222210 12346999999889999984443 2 3469999999999999888877663
No 120
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=23.16 E-value=1.7e+02 Score=24.29 Aligned_cols=29 Identities=17% Similarity=0.102 Sum_probs=23.5
Q ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEeeCC
Q 045537 68 LRLSTNDRVELFNGKGGLIEGCIQRIDRT 96 (291)
Q Consensus 68 LRlk~Gd~i~v~dG~g~~~~a~I~~i~k~ 96 (291)
..+++||.|.|.+|--.-+.|.|.+++.+
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~~ 135 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDGE 135 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECCC
Confidence 34789999999999766678999998744
No 121
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=23.14 E-value=1.1e+02 Score=21.77 Aligned_cols=24 Identities=25% Similarity=0.673 Sum_probs=19.0
Q ss_pred CCceEEEEcCCCCCCH-HHHHHHHH
Q 045537 230 ESSGLIIVGPEGDFTE-KEVNKIVE 253 (291)
Q Consensus 230 ~~~i~lvIGPEGGfs~-~Ei~~l~~ 253 (291)
....+++|+|.+-+++ +|++.+.+
T Consensus 34 ~~~tll~i~~~~~~~~~~~~~~l~~ 58 (70)
T PF14258_consen 34 DDGTLLVIGPDLRLSEPEEAEALLE 58 (70)
T ss_pred CCCEEEEEeCCCCCCchHHHHHHHH
Confidence 4467899999999995 87777754
No 122
>PRK13307 bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase; Provisional
Probab=22.86 E-value=1.9e+02 Score=28.68 Aligned_cols=121 Identities=11% Similarity=0.031 Sum_probs=66.3
Q ss_pred HHHHHHHHhcCccEEEEeecccccccccccccccccccchhhchhchhhhhcCCCCcceeEcCCCCHhhhcccc-CCCce
Q 045537 131 DWLVEKCTELGAQSVTPLLTELHLQSRKIGDNGFLSCNFYYGFIANSAFVYGGQRLHEMVLNPPMKIDGLLPLV-SQSKL 209 (291)
Q Consensus 131 d~iiekatELGV~~I~P~~se~~~RS~~~~~~k~eRw~~~~kIi~~~eA~kQs~r~~lP~I~~p~~l~~~l~~~-~~~~~ 209 (291)
.++++.+.+.|++-++.-... -.+... + + +++++++|.-..-....|.+..+.+..+ ..-+.
T Consensus 240 ~~vv~~~a~aGAD~vTVH~ea-----------~~~ti~---~-a--i~~akk~GikvgVD~lnp~tp~e~i~~l~~~vD~ 302 (391)
T PRK13307 240 NLEARMAADATADAVVISGLA-----------PISTIE---K-A--IHEAQKTGIYSILDMLNVEDPVKLLESLKVKPDV 302 (391)
T ss_pred hHHHHHHHhcCCCEEEEeccC-----------CHHHHH---H-H--HHHHHHcCCEEEEEEcCCCCHHHHHHHhhCCCCE
Confidence 366999999999999854432 011233 2 2 4566666644333222233333333322 12243
Q ss_pred EEEEe---CCC-CChhhhhccCC-CCCceEEEEcCCCCCCHHHHHHHHHcCCeEEecCCCccccch
Q 045537 210 AFVAI---AEA-TPLVTALSSSR-NESSGLIIVGPEGDFTEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 210 ~lv~~---~~~-~~~~~~l~~~~-~~~~i~lvIGPEGGfs~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
.++.. ++. .+....+.... .... +.|.--||.+.+.+..+.++|+..+=.|.-|.+++-
T Consensus 303 Vllht~vdp~~~~~~~~kI~~ikk~~~~--~~I~VdGGI~~eti~~l~~aGADivVVGsaIf~a~D 366 (391)
T PRK13307 303 VELHRGIDEEGTEHAWGNIKEIKKAGGK--ILVAVAGGVRVENVEEALKAGADILVVGRAITKSKD 366 (391)
T ss_pred EEEccccCCCcccchHHHHHHHHHhCCC--CcEEEECCcCHHHHHHHHHcCCCEEEEeHHHhCCCC
Confidence 33321 111 12111111100 0112 334556899999999999999999999999999876
No 123
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=22.09 E-value=3e+02 Score=19.50 Aligned_cols=51 Identities=14% Similarity=0.123 Sum_probs=32.9
Q ss_pred cccEEEeCCcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeC-CceEE
Q 045537 43 GIPRFFSQGGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDR-TGLDV 100 (291)
Q Consensus 43 ~~~rff~~~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k-~~~~v 100 (291)
+|...+..|+.+.++.... +++.||.+.+..+.+..+.-++..... ..+.+
T Consensus 9 SM~P~i~~gd~v~i~~~~~-------~~~~G~iv~~~~~~~~~~ikrl~~~~~~~~~~l 60 (84)
T cd06462 9 SMEPTIPDGDLVLVDKSSY-------EPKRGDIVVFRLPGGELTVKRVIGLPGEGHYFL 60 (84)
T ss_pred CccCcccCCCEEEEEecCC-------CCcCCEEEEEEcCCCcEEEEEEEEECCCCEEEE
Confidence 3444466788888876443 789999998877654666566655543 44433
No 124
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=21.82 E-value=1.8e+02 Score=24.43 Aligned_cols=45 Identities=13% Similarity=0.106 Sum_probs=31.1
Q ss_pred cEEEEcchhhhHHHHcc--------cCCCCCEEEEEeCCCCEEEEEEEEeeCC
Q 045537 52 GIVRVEGDEFWHMTKVL--------RLSTNDRVELFNGKGGLIEGCIQRIDRT 96 (291)
Q Consensus 52 ~~v~L~~~~~~Hl~kVL--------Rlk~Gd~i~v~dG~g~~~~a~I~~i~k~ 96 (291)
....+++++...+.... -+++||.|.|.+|--.-+.|.|.+++.+
T Consensus 84 ~p~~I~~~ei~~l~~~~~~~~~~~~~~~~G~~V~I~~Gp~~g~eg~v~~~~~~ 136 (162)
T PRK09014 84 QPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGE 136 (162)
T ss_pred CccccCHHHHHHHHhhcccccccccCCCCCCEEEEecCCCCCcEEEEEEeCCC
Confidence 34556666665554321 2568999999999766678999888744
No 125
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=21.75 E-value=2.7e+02 Score=21.72 Aligned_cols=37 Identities=5% Similarity=-0.042 Sum_probs=28.8
Q ss_pred cccCCCCCEEEEEeCC--CCEEEEEEEEeeCCceEEEee
Q 045537 67 VLRLSTNDRVELFNGK--GGLIEGCIQRIDRTGLDVVAL 103 (291)
Q Consensus 67 VLRlk~Gd~i~v~dG~--g~~~~a~I~~i~k~~~~v~i~ 103 (291)
--..++|.++++.|.. ...+-|+|.++....+.+...
T Consensus 25 ~~~F~vGmkLEavD~~~~~~i~vAtV~~v~g~~l~v~~d 63 (96)
T smart00561 25 PNGFKVGMKLEAVDPRNPSLICVATVVEVKGYRLLLHFD 63 (96)
T ss_pred cCcccCCCEEEEECCCCCceEEEEEEEEEECCEEEEEEc
Confidence 3457899999999986 567889999988777766554
No 126
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=20.86 E-value=1.9e+02 Score=23.37 Aligned_cols=36 Identities=11% Similarity=0.183 Sum_probs=24.1
Q ss_pred EEEEcchhhhHHHHcccCCCCCEEEEEeCC-CCEEEEEEEEee
Q 045537 53 IVRVEGDEFWHMTKVLRLSTNDRVELFNGK-GGLIEGCIQRID 94 (291)
Q Consensus 53 ~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~-g~~~~a~I~~i~ 94 (291)
++++.++.. -++++||.|.+.+.+ |....++|+.+.
T Consensus 21 EiRlnD~kr------~~ikvGD~I~f~~~~~~~~l~v~V~~i~ 57 (109)
T cd06555 21 EIRLNDEKR------QQIKVGDKILFNDLDTGQQLLVKVVDIR 57 (109)
T ss_pred EEEecccch------hcCCCCCEEEEEEcCCCcEEEEEEEEEE
Confidence 456665443 568999999997764 455666666554
No 127
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.46 E-value=1.1e+02 Score=32.84 Aligned_cols=33 Identities=24% Similarity=0.161 Sum_probs=26.6
Q ss_pred hHHHHcccCCCCCEEEEEeCCCCEEEEEEEEeeC
Q 045537 62 WHMTKVLRLSTNDRVELFNGKGGLIEGCIQRIDR 95 (291)
Q Consensus 62 ~Hl~kVLRlk~Gd~i~v~dG~g~~~~a~I~~i~k 95 (291)
.++-+-|.+|.||++.+ ++.|+...|+|+++-+
T Consensus 603 ~~~A~~LglKLGDtvTf-~v~gq~i~A~I~slR~ 635 (829)
T COG3127 603 EGEAKRLGLKLGDTVTF-MVLGQNITAKITSLRK 635 (829)
T ss_pred HhHHHHhCCccCCEEEE-EeccceEEeeeceeee
Confidence 34556778999999997 6779999999987643
No 128
>PRK04302 triosephosphate isomerase; Provisional
Probab=20.29 E-value=1.1e+02 Score=27.35 Aligned_cols=37 Identities=22% Similarity=0.342 Sum_probs=30.2
Q ss_pred ceEEEEcCCCCC-CHHHHHHHHHcCCeEEecCCCccccch
Q 045537 232 SGLIIVGPEGDF-TEKEVNKIVEAGATAVGLGPHRLRVET 270 (291)
Q Consensus 232 ~i~lvIGPEGGf-s~~Ei~~l~~~Gf~~vsLG~rILRtET 270 (291)
.+-++.| ||. +++++..+.+.|+..|-.|.-+++++-
T Consensus 173 ~~pvi~G--ggI~~~e~~~~~~~~gadGvlVGsa~l~~~~ 210 (223)
T PRK04302 173 DVKVLCG--AGISTGEDVKAALELGADGVLLASGVVKAKD 210 (223)
T ss_pred CCEEEEE--CCCCCHHHHHHHHcCCCCEEEEehHHhCCcC
Confidence 3455655 999 677888888899999999999999874
No 129
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=20.17 E-value=1.4e+02 Score=20.20 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=16.4
Q ss_pred ccCCCCCEEEEE-e-CCCCEEEEEE
Q 045537 68 LRLSTNDRVELF-N-GKGGLIEGCI 90 (291)
Q Consensus 68 LRlk~Gd~i~v~-d-G~g~~~~a~I 90 (291)
|.++.||.|.|+ + ..++-|.|+.
T Consensus 16 Ls~~~Gd~i~v~~~~~~~~ww~~~~ 40 (55)
T PF07653_consen 16 LSFKKGDVIEVLGEKDDDGWWLGEN 40 (55)
T ss_dssp -EB-TTEEEEEEEEECSTSEEEEEE
T ss_pred eEEecCCEEEEEEeecCCCEEEEEE
Confidence 889999999998 3 3566677766
No 130
>PRK04950 ProP expression regulator; Provisional
Probab=20.17 E-value=1.5e+02 Score=26.89 Aligned_cols=35 Identities=17% Similarity=0.310 Sum_probs=28.7
Q ss_pred cCCCCCEEEEEeCCCCEEEEEEEEeeCCceEEEeee
Q 045537 69 RLSTNDRVELFNGKGGLIEGCIQRIDRTGLDVVALE 104 (291)
Q Consensus 69 Rlk~Gd~i~v~dG~g~~~~a~I~~i~k~~~~v~i~~ 104 (291)
-+++|+.|.|--|++. -.|+|++|+++.+.+.+..
T Consensus 166 ~l~~gq~v~vk~g~~~-~~a~i~ei~kd~v~vql~~ 200 (213)
T PRK04950 166 ELTVGQAVKVKAGKSA-MDATVLEITKDDVRVQLDS 200 (213)
T ss_pred HhccCCEEEEeccCCC-CceEEEEEecCcEEEEcCC
Confidence 3678999999988775 4899999999999886544
No 131
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=20.16 E-value=1.1e+02 Score=23.89 Aligned_cols=30 Identities=20% Similarity=0.273 Sum_probs=23.5
Q ss_pred CcEEEEcchhhhHHHHcccCCCCCEEEEEeCCCC
Q 045537 51 GGIVRVEGDEFWHMTKVLRLSTNDRVELFNGKGG 84 (291)
Q Consensus 51 ~~~v~L~~~~~~Hl~kVLRlk~Gd~i~v~dG~g~ 84 (291)
...+.+..+++.- +-++.||.|.|.++.|.
T Consensus 34 ~~~v~in~~dA~~----lgi~~Gd~V~v~~~~G~ 63 (122)
T cd02791 34 EPYVEIHPEDAAR----LGLKEGDLVRVTSRRGE 63 (122)
T ss_pred CCEEEECHHHHHH----cCCCCCCEEEEEcCCEE
Confidence 4568888887655 45799999999999774
Done!