Query 029038
Match_columns 200
No_of_seqs 110 out of 329
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:29:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029038.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029038hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00036 40S ribosomal protein 100.0 3.1E-84 6.8E-89 566.9 24.8 195 1-196 66-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 1.2E-83 2.7E-88 563.4 24.8 194 1-195 66-259 (262)
3 PTZ00223 40S ribosomal protein 100.0 2.7E-83 5.8E-88 563.7 25.0 196 1-197 63-259 (273)
4 PRK04313 30S ribosomal protein 100.0 2.1E-76 4.6E-81 512.0 23.3 174 1-175 62-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 4.5E-74 9.8E-79 494.5 22.1 176 1-177 65-241 (241)
6 KOG0378 40S ribosomal protein 100.0 6.2E-73 1.4E-77 489.8 14.7 195 1-196 66-260 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 2.7E-36 5.9E-41 222.2 10.1 77 29-105 1-77 (77)
8 PF00467 KOW: KOW motif; Inte 97.0 0.001 2.3E-08 41.0 3.4 31 112-145 1-31 (32)
9 smart00739 KOW KOW (Kyprides, 96.9 0.00089 1.9E-08 39.0 2.7 27 109-135 1-27 (28)
10 PF01479 S4: S4 domain; Inter 96.6 0.0015 3.2E-08 42.8 2.0 25 1-25 24-48 (48)
11 TIGR01080 rplX_A_E ribosomal p 94.2 0.12 2.6E-06 41.1 5.5 40 106-148 38-77 (114)
12 cd00165 S4 S4/Hsp/ tRNA synthe 93.6 0.12 2.6E-06 33.9 3.9 39 1-39 24-62 (70)
13 smart00363 S4 S4 RNA-binding d 92.8 0.1 2.2E-06 33.3 2.4 28 2-29 25-52 (60)
14 PRK01191 rpl24p 50S ribosomal 92.3 0.42 9.2E-06 38.3 5.8 38 107-147 43-80 (120)
15 PRK12281 rplX 50S ribosomal pr 91.2 0.34 7.4E-06 35.7 3.9 38 108-148 5-42 (76)
16 CHL00141 rpl24 ribosomal prote 90.5 0.42 9.2E-06 35.7 4.0 38 107-147 6-43 (83)
17 PRK00004 rplX 50S ribosomal pr 89.5 0.49 1.1E-05 36.8 3.7 37 108-147 3-39 (105)
18 TIGR02988 YaaA_near_RecF S4 do 86.4 0.77 1.7E-05 31.3 2.8 27 2-28 33-59 (59)
19 TIGR01079 rplX_bact ribosomal 84.8 1.3 2.9E-05 34.3 3.8 29 109-137 3-31 (104)
20 PTZ00194 60S ribosomal protein 82.5 2.3 5E-05 35.1 4.4 55 107-164 44-105 (143)
21 TIGR00005 rluA_subfam pseudour 75.6 4.9 0.00011 35.4 4.6 27 2-28 30-56 (299)
22 PF13051 DUF3912: Protein of u 73.8 13 0.00029 26.6 5.6 50 112-165 5-55 (68)
23 PF13275 S4_2: S4 domain; PDB: 69.4 3.5 7.7E-05 29.6 1.9 34 2-37 32-65 (65)
24 PRK11507 ribosome-associated p 66.6 9.6 0.00021 27.9 3.7 34 2-37 36-69 (70)
25 COG0198 RplX Ribosomal protein 66.0 10 0.00022 29.7 4.0 29 108-136 3-31 (104)
26 TIGR01017 rpsD_bact ribosomal 63.4 6.2 0.00014 33.7 2.6 28 2-29 114-141 (200)
27 COG2163 RPL14A Ribosomal prote 63.4 7.8 0.00017 31.3 3.0 26 110-135 5-30 (125)
28 PRK05327 rpsD 30S ribosomal pr 63.1 6.9 0.00015 33.5 2.8 28 2-29 117-144 (203)
29 PRK02290 3-dehydroquinate synt 62.9 38 0.00081 31.8 7.7 63 36-101 256-328 (344)
30 COG0564 RluA Pseudouridylate s 60.6 12 0.00026 33.7 4.0 32 2-34 36-67 (289)
31 PF01959 DHQS: 3-dehydroquinat 59.6 48 0.001 31.2 7.8 75 36-126 266-345 (354)
32 PRK10700 23S rRNA pseudouridyl 58.7 20 0.00044 32.1 5.1 44 2-46 26-81 (289)
33 PTZ00065 60S ribosomal protein 57.7 12 0.00026 30.5 3.2 26 111-136 9-34 (130)
34 PRK11180 rluD 23S rRNA pseudou 57.7 15 0.00032 33.1 4.1 28 1-28 41-68 (325)
35 PF14001 YdfZ: YdfZ protein 57.5 17 0.00038 26.3 3.6 42 109-154 9-56 (64)
36 COG0522 RpsD Ribosomal protein 56.7 8.3 0.00018 33.4 2.2 27 2-28 118-144 (205)
37 PRK04333 50S ribosomal protein 54.7 14 0.00031 27.7 2.9 26 109-134 3-28 (84)
38 PRK14898 DNA-directed RNA poly 54.3 69 0.0015 33.2 8.7 78 18-97 111-195 (858)
39 TIGR00478 tly hemolysin TlyA f 52.5 11 0.00025 32.7 2.4 29 1-29 23-51 (228)
40 PF11717 Tudor-knot: RNA bindi 48.8 55 0.0012 22.0 4.9 38 110-147 1-39 (55)
41 CHL00113 rps4 ribosomal protei 48.7 16 0.00036 31.4 2.8 28 2-29 113-140 (201)
42 cd03706 mtEFTU_III Domain III 47.6 1.1E+02 0.0023 22.2 7.3 40 89-132 52-92 (93)
43 KOG1784 Small Nuclear ribonucl 47.3 42 0.0009 26.1 4.4 59 70-132 11-75 (96)
44 cd03704 eRF3c_III This family 46.6 1.1E+02 0.0023 22.8 6.7 48 85-133 56-108 (108)
45 COG2501 S4-like RNA binding pr 44.8 37 0.00081 25.1 3.8 34 2-37 36-69 (73)
46 PF01588 tRNA_bind: Putative t 43.5 55 0.0012 24.2 4.6 22 126-147 2-25 (95)
47 PF07076 DUF1344: Protein of u 42.6 60 0.0013 23.3 4.4 35 66-100 11-49 (61)
48 PTZ00471 60S ribosomal protein 42.5 26 0.00057 28.7 2.9 24 110-133 5-28 (134)
49 PF08940 DUF1918: Domain of un 42.2 31 0.00067 24.5 2.8 34 117-151 9-46 (58)
50 PRK10348 ribosome-associated h 41.4 33 0.00071 27.9 3.3 34 1-35 32-65 (133)
51 PF04773 FecR: FecR protein; 40.9 1.3E+02 0.0028 21.2 9.9 66 64-129 3-75 (98)
52 TIGR00405 L26e_arch ribosomal 39.9 54 0.0012 25.9 4.3 26 110-135 87-112 (145)
53 PRK10475 23S rRNA pseudouridin 39.5 55 0.0012 29.5 4.8 43 2-45 30-80 (290)
54 PF06905 FAIM1: Fas apoptotic 39.0 2.4E+02 0.0053 23.9 9.4 68 59-129 64-133 (177)
55 PRK08559 nusG transcription an 38.8 52 0.0011 26.6 4.2 29 108-136 93-121 (153)
56 COG1187 RsuA 16S rRNA uridine- 38.3 50 0.0011 29.4 4.2 48 1-48 25-79 (248)
57 cd05741 Ig_CEACAM_D1_like Firs 38.0 51 0.0011 22.9 3.6 31 35-65 50-80 (92)
58 TIGR03318 YdfZ_fam putative se 38.0 34 0.00075 24.8 2.6 41 110-154 11-57 (65)
59 cd05892 Ig_Myotilin_C C-termin 37.9 72 0.0015 22.4 4.3 35 30-64 27-63 (75)
60 PRK10839 16S rRNA pseudouridyl 37.9 80 0.0017 26.8 5.4 46 2-48 24-75 (232)
61 PRK11025 23S rRNA pseudouridyl 37.4 54 0.0012 29.4 4.4 26 2-28 44-69 (317)
62 PF12961 DUF3850: Domain of Un 37.2 34 0.00074 25.2 2.5 17 82-98 22-38 (72)
63 KOG3513 Neural cell adhesion m 37.0 1.1E+02 0.0023 32.9 7.0 156 3-165 442-614 (1051)
64 PRK05609 nusG transcription an 35.9 42 0.00092 27.2 3.2 29 107-135 124-152 (181)
65 cd02899 PLAT_SR Scavenger rece 35.2 1.6E+02 0.0034 23.0 6.1 33 141-183 76-108 (109)
66 cd03705 EF1_alpha_III Domain I 33.5 97 0.0021 22.7 4.6 35 88-125 59-100 (104)
67 cd01234 PH_CADPS CADPS (Ca2+-d 32.8 23 0.00049 28.4 1.1 42 41-87 21-62 (117)
68 TIGR00922 nusG transcription t 32.6 48 0.001 26.7 3.0 28 108-135 118-145 (172)
69 KOG3401 60S ribosomal protein 32.1 37 0.00081 28.2 2.3 52 101-152 40-94 (145)
70 cd04093 HBS1_C HBS1_C: this fa 30.9 2.1E+02 0.0047 20.9 9.4 45 88-133 59-107 (107)
71 COG1792 MreC Cell shape-determ 30.3 4E+02 0.0088 23.9 11.7 104 24-165 160-270 (284)
72 cd04478 RPA2_DBD_D RPA2_DBD_D: 30.3 2.1E+02 0.0044 20.5 7.0 57 24-80 8-75 (95)
73 PF10781 DSRB: Dextransucrase 29.8 1.2E+02 0.0025 21.8 4.1 29 90-118 2-35 (62)
74 TIGR01955 RfaH transcriptional 29.7 85 0.0019 24.8 4.0 28 107-134 106-133 (159)
75 PLN00189 40S ribosomal protein 29.5 43 0.00094 28.9 2.4 20 2-21 133-152 (194)
76 PF08529 NusA_N: NusA N-termin 29.0 60 0.0013 25.3 2.9 48 49-101 46-96 (122)
77 COG1188 Ribosome-associated he 28.8 69 0.0015 25.1 3.1 35 65-103 29-63 (100)
78 COG5164 SPT5 Transcription elo 28.8 73 0.0016 31.5 3.9 43 91-135 123-165 (607)
79 KOG3586 TBX1 and related T-box 28.8 79 0.0017 30.4 4.1 99 20-124 128-251 (437)
80 PF13620 CarboxypepD_reg: Carb 28.4 1.2E+02 0.0026 20.8 4.1 45 7-51 2-47 (82)
81 PTZ00141 elongation factor 1- 28.4 3.4E+02 0.0074 25.7 8.3 53 88-141 381-437 (446)
82 PF09285 Elong-fact-P_C: Elong 28.1 1.4E+02 0.0031 20.8 4.4 36 69-105 19-54 (56)
83 PF01063 Aminotran_4: Aminotra 27.6 1.4E+02 0.003 24.6 5.0 45 140-186 125-169 (231)
84 cd04708 BAH_plantDCM_II BAH, o 27.5 1.1E+02 0.0023 26.7 4.4 44 88-137 7-54 (202)
85 KOG1999 RNA polymerase II tran 27.2 1E+02 0.0022 32.9 4.8 27 109-135 459-485 (1024)
86 PF02239 Cytochrom_D1: Cytochr 27.0 4.4E+02 0.0096 24.2 8.7 70 34-111 50-119 (369)
87 KOG1999 RNA polymerase II tran 27.0 3.4E+02 0.0073 29.2 8.5 54 110-165 582-636 (1024)
88 cd03707 EFTU_III Domain III of 26.8 2.4E+02 0.0051 20.1 6.8 27 89-118 52-78 (90)
89 PF07569 Hira: TUP1-like enhan 26.8 2.2E+02 0.0048 24.3 6.3 57 30-86 20-94 (219)
90 PRK10708 hypothetical protein; 26.6 1.3E+02 0.0028 21.6 3.9 29 90-118 2-35 (62)
91 cd01723 LSm4 The eukaryotic Sm 25.6 1.3E+02 0.0028 21.6 3.9 49 126-176 24-73 (76)
92 PF00924 MS_channel: Mechanose 25.3 81 0.0018 25.6 3.2 34 109-152 60-93 (206)
93 PF00181 Ribosomal_L2: Ribosom 25.2 1.3E+02 0.0029 21.6 4.0 32 126-157 33-65 (77)
94 smart00536 AXH domain in Ataxi 25.1 2.2E+02 0.0048 22.8 5.5 77 73-166 7-84 (116)
95 KOG1708 Mitochondrial/chloropl 23.4 1.3E+02 0.0029 26.6 4.3 26 110-135 73-98 (236)
96 PF01176 eIF-1a: Translation i 23.3 2.6E+02 0.0057 19.3 5.1 42 58-101 6-54 (65)
97 TIGR01956 NusG_myco NusG famil 22.6 98 0.0021 27.9 3.4 30 106-135 202-231 (258)
98 smart00306 HintN Hint (Hedgeho 22.6 2.7E+02 0.006 19.3 8.4 55 111-165 23-78 (100)
99 COG1917 Uncharacterized conser 22.2 1.5E+02 0.0032 22.6 3.9 56 57-122 41-98 (131)
100 PF05709 Sipho_tail: Phage tai 22.1 3.8E+02 0.0083 21.9 6.7 34 69-103 161-197 (249)
101 PRK09014 rfaH transcriptional 21.9 97 0.0021 24.8 3.0 26 109-134 109-134 (162)
102 COG0250 NusG Transcription ant 21.8 95 0.0021 26.2 3.0 29 106-134 120-148 (178)
103 cd05774 Ig_CEACAM_D1 First imm 21.3 1.5E+02 0.0032 22.5 3.8 32 34-65 62-93 (105)
104 PF08269 Cache_2: Cache domain 21.1 83 0.0018 22.7 2.2 22 31-52 55-76 (95)
105 TIGR00739 yajC preprotein tran 20.6 2.4E+02 0.0052 20.8 4.6 32 110-150 38-69 (84)
106 COG1189 Predicted rRNA methyla 20.4 88 0.0019 28.1 2.6 98 1-99 26-152 (245)
107 PRK09790 hypothetical protein; 20.2 2.1E+02 0.0045 21.5 4.1 48 120-177 22-74 (91)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=3.1e-84 Score=566.87 Aligned_cols=195 Identities=86% Similarity=1.345 Sum_probs=191.6
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
+||+|+|||+||+|++||||||||||||++||||||+||++|||++|+|++|||+||||||++|++++||+|||+|||||
T Consensus 66 ~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGr 145 (261)
T PLN00036 66 MQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGR 145 (261)
T ss_pred hCCeEEECCEEeccCCCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038 81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV 160 (200)
Q Consensus 81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v 160 (200)
||+|+||.||+||||+|+||+++|++|+||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||
T Consensus 146 ni~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~v 225 (261)
T PLN00036 146 TIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNV 225 (261)
T ss_pred eeccCCCccccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhhh
Q 029038 161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATS 196 (200)
Q Consensus 161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~~ 196 (200)
||||++++||||||+++|||++++|| |++||.+-+
T Consensus 226 fvIG~~~kp~isLp~~~gi~~~~~e~-r~~~~~~~~ 260 (261)
T PLN00036 226 FVIGKGTKPWISLPKGKGIKLSIIEE-ARKRLAAGQ 260 (261)
T ss_pred EEEccCCCeeEeCcCCCCcccchHHH-HHHhhhhhc
Confidence 99999899999999999999999999 999997654
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.2e-83 Score=563.37 Aligned_cols=194 Identities=60% Similarity=0.978 Sum_probs=191.0
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
+||+|+||||||+|++||||||||||||++||||||+||++|||++|+|++|||+||||||++|++++||+|||+|||||
T Consensus 66 ~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGr 145 (262)
T PTZ00118 66 IQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGR 145 (262)
T ss_pred HCCcEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038 81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV 160 (200)
Q Consensus 81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v 160 (200)
||+|+||.||+||||+|+||+++|++|+||++||+||||||+|+|++|+|.+++++++|+++|||+|++|++|+|+++||
T Consensus 146 ni~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~v 225 (262)
T PTZ00118 146 TIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNV 225 (262)
T ss_pred eeccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhh
Q 029038 161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALAT 195 (200)
Q Consensus 161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~ 195 (200)
||||++++||||||++||||||++|| |+++|.+.
T Consensus 226 fvIG~~~kp~islp~~kgi~~~~~e~-~~~~~~~~ 259 (262)
T PTZ00118 226 FVIGVGTKPYVSLPRERGIKKDIIEE-RRNRLAKA 259 (262)
T ss_pred EEEccCCCeeEeCcCCCCccccHHHH-HHHHHHHH
Confidence 99999899999999999999999999 99998764
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=2.7e-83 Score=563.66 Aligned_cols=196 Identities=48% Similarity=0.788 Sum_probs=191.7
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
+||+|+||||||+|++||||||||||||++||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||
T Consensus 63 ~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGr 142 (273)
T PTZ00223 63 RQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGH 142 (273)
T ss_pred hCCeEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038 81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV 160 (200)
Q Consensus 81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v 160 (200)
||+|+||.||+||||+|+||+++|++|+||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||
T Consensus 143 nI~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~V 222 (273)
T PTZ00223 143 RIRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANI 222 (273)
T ss_pred eeccCCccccCCCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccC-CCceEeCcCCCceeeehhHHHHHHHHhhhhh
Q 029038 161 FTIGKG-TKPWVSLPKGKGIKLSIIEEARKRQALATSA 197 (200)
Q Consensus 161 fvIG~~-~~p~isLp~~~gi~~~~~e~~~~~~~~~~~~ 197 (200)
||||++ ++||||||++||||||++|| |+++|.+..+
T Consensus 223 fvIG~~~~kp~IsLp~~kgi~~~~~e~-~~~~~~~~~~ 259 (273)
T PTZ00223 223 FVIGKDMNSVPVTLPKQQGLRINVIQE-REEKLIAAEA 259 (273)
T ss_pred EEEeCCCCCcceECcCCCCccccHHHH-HHHHHHHHHh
Confidence 999996 69999999999999999999 9999877654
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=2.1e-76 Score=511.99 Aligned_cols=174 Identities=40% Similarity=0.653 Sum_probs=170.9
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
+||+|+||||||+|++||||||||||||++||||||+||++|||++|+|++|||+||||||++|++++||+|||+|||||
T Consensus 62 ~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGr 141 (237)
T PRK04313 62 NEGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGR 141 (237)
T ss_pred hCCcEEECCEEEcccccCcCceeEEEEccCCCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCC-CCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeec
Q 029038 81 TIRYPD-PLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLG 158 (200)
Q Consensus 81 ni~~~d-~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~ 158 (200)
||+++| |.||+||||+|+||+++|++|+||++||+||||||+|+||+|+|.+|++++ +++++||++|++|++|+|+++
T Consensus 142 ni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~ 221 (237)
T PRK04313 142 NILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILD 221 (237)
T ss_pred eEEccCccccccCCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEee
Confidence 999998 999999999999999999999999999999999999999999999999999 678999999999999999999
Q ss_pred cEEEEccCCCceEeCcC
Q 029038 159 NVFTIGKGTKPWVSLPK 175 (200)
Q Consensus 159 ~vfvIG~~~~p~isLp~ 175 (200)
||||||+ ++|||+||.
T Consensus 222 ~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 222 YVFVIGK-EKPVIKLPE 237 (237)
T ss_pred eEEEEcC-CCcceeCCC
Confidence 9999999 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.5e-74 Score=494.53 Aligned_cols=176 Identities=47% Similarity=0.724 Sum_probs=172.4
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
++|+|+|||+||+|++||||||||||||+|||+||||||.+|||.||+|++|||.||||||++|++++||++||||||||
T Consensus 65 ~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGr 144 (241)
T COG1471 65 SEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGR 144 (241)
T ss_pred hcCcEEECCEEeccccCCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeecc
Q 029038 81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGN 159 (200)
Q Consensus 81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~~ 159 (200)
|++++|+.|+++|||++++|+++|++||||++|++|||+||+|+|++|+|.+|+.++ +++++||++|.+|+.|+|+++|
T Consensus 145 ni~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~y 224 (241)
T COG1471 145 NIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDY 224 (241)
T ss_pred eeeccCCccccccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeE
Confidence 999999999999999999999999999999999999999999999999999999999 5578999999999999999999
Q ss_pred EEEEccCCCceEeCcCCC
Q 029038 160 VFTIGKGTKPWVSLPKGK 177 (200)
Q Consensus 160 vfvIG~~~~p~isLp~~~ 177 (200)
|||||+ ++|||+||.|+
T Consensus 225 VfvIG~-~k~~i~l~~e~ 241 (241)
T COG1471 225 VFVIGE-DKPVISLPKEK 241 (241)
T ss_pred EEEEcC-CCceEeCCCCC
Confidence 999999 99999999874
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.2e-73 Score=489.80 Aligned_cols=195 Identities=68% Similarity=1.131 Sum_probs=192.4
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
||+.|+|||+||+|.+||+|||||++|++|||+||++||++|||.+|+|++|||+||||||++++.+.+|+|+|++||||
T Consensus 66 ~qr~i~v~gkvrt~~~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~ 145 (263)
T KOG0378|consen 66 MQREIKVDGKVRTDSTYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGR 145 (263)
T ss_pred HHhhhhccceeecccccccceeEEEEecccchhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038 81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV 160 (200)
Q Consensus 81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v 160 (200)
+||||||.+|+|||+++++++++|.++++|++|++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++|+
T Consensus 146 tIrypDplIk~~dtI~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNi 225 (263)
T KOG0378|consen 146 TIRYPDPLIKVNDTIKIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNI 225 (263)
T ss_pred eEecCCcccCccceeeccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhhh
Q 029038 161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATS 196 (200)
Q Consensus 161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~~ 196 (200)
|+||+|++||||||+++||+++++|| |++||+|--
T Consensus 226 fvIgkgnKpwisLPkgkgi~~siaEe-~dkrl~~k~ 260 (263)
T KOG0378|consen 226 FVIGEGNKPWISLPKGKGIALSIAEE-RDKRLAAKI 260 (263)
T ss_pred EEEecCCCccccCccccCccchhhHH-HHHHHhhhc
Confidence 99999999999999999999999999 999998754
No 7
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=100.00 E-value=2.7e-36 Score=222.17 Aligned_cols=77 Identities=64% Similarity=1.028 Sum_probs=69.8
Q ss_pred CCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCceEEeeCCCCccCCCeEEEecCCCcee
Q 029038 29 KTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 105 (200)
Q Consensus 29 kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~ 105 (200)
||||+|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
T Consensus 1 kt~e~yRvl~d~kgr~~l~~I~~eea~~KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~kI~ 77 (77)
T PF00900_consen 1 KTGEHYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQKIV 77 (77)
T ss_dssp CTTEEEEEEE-TTS-EEEEEE-TTGGGEEEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETTTTEEE
T ss_pred CCCcEEEEEECCCCcEEEEECCHHHccCeEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECCCCcCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999986
No 8
>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=96.96 E-value=0.001 Score=40.96 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=25.9
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 029038 112 VGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 145 (200)
Q Consensus 112 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v 145 (200)
+|+.|+|+.|++.|+.|+|.++..+. ..|++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence 58999999999999999999997543 44554
No 9
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.93 E-value=0.00089 Score=38.96 Aligned_cols=27 Identities=37% Similarity=0.668 Sum_probs=24.6
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
+|++|+.++|++|.+.|..|+|.++..
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 478999999999999999999999863
No 10
>PF01479 S4: S4 domain; InterPro: IPR002942 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 S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=96.57 E-value=0.0015 Score=42.75 Aligned_cols=25 Identities=36% Similarity=0.357 Sum_probs=23.4
Q ss_pred CCccEEECCEEeccCCCCceeeEEE
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVV 25 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVI 25 (200)
++|.|+|||++++|+.|++...|+|
T Consensus 24 ~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 24 KQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp HTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCCEEEECCEEEcCCCCCCCCcCCC
Confidence 4799999999999999999999987
No 11
>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=94.24 E-value=0.12 Score=41.05 Aligned_cols=40 Identities=15% Similarity=0.287 Sum_probs=32.2
Q ss_pred EEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029038 106 EFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 148 (200)
Q Consensus 106 ~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~ 148 (200)
+.+++..|+.+.|++|++-|..|+|.++.... ..|.|+.-
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~---~~V~Vegv 77 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLKR---YRIYVEGV 77 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcCC---CEEEEcCe
Confidence 55688999999999999999999999997333 35666653
No 12
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=93.59 E-value=0.12 Score=33.88 Aligned_cols=39 Identities=28% Similarity=0.416 Sum_probs=29.5
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEc
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYD 39 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d 39 (200)
++|.|+|||+..++..+++-..|+|++........++|.
T Consensus 24 ~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~e 62 (70)
T cd00165 24 KHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYE 62 (70)
T ss_pred HcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceeec
Confidence 368999999999999999988899999764322234443
No 13
>smart00363 S4 S4 RNA-binding domain.
Probab=92.78 E-value=0.1 Score=33.32 Aligned_cols=28 Identities=32% Similarity=0.293 Sum_probs=25.3
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecC
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK 29 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k 29 (200)
+|.|+|||++.++..+++--.|.|+++.
T Consensus 25 ~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 25 QGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred cCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 6889999999999999998889999975
No 14
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=92.26 E-value=0.42 Score=38.33 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=30.7
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038 107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 147 (200)
Q Consensus 107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d 147 (200)
.+++..|+.+.|+.|+.-|..|+|.++....+ .|+|+.
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~---~V~VeG 80 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRG---RIYVEG 80 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCC---EEEEeC
Confidence 45788999999999999999999999965433 465654
No 15
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=91.15 E-value=0.34 Score=35.69 Aligned_cols=38 Identities=21% Similarity=0.451 Sum_probs=31.7
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029038 108 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 148 (200)
Q Consensus 108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~ 148 (200)
+++..|+.+.|+.|+.-|++|+|.++.+.. ..|.||+-
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv 42 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKK---NRVIVEGV 42 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence 478899999999999999999999997544 35777653
No 16
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=90.53 E-value=0.42 Score=35.73 Aligned_cols=38 Identities=16% Similarity=0.457 Sum_probs=31.4
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038 107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 147 (200)
Q Consensus 107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d 147 (200)
.+++..|+.+.|+.|+.-|+.|+|.++.+.. ..|+|++
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Veg 43 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKG 43 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence 3578899999999999999999999997543 3577765
No 17
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=89.53 E-value=0.49 Score=36.75 Aligned_cols=37 Identities=22% Similarity=0.505 Sum_probs=29.8
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038 108 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 147 (200)
Q Consensus 108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d 147 (200)
+++..|+.+.|+.|++-|++|+|.++..... .|+|++
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~---~V~Veg 39 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKN---KVIVEG 39 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCC---EEEEcC
Confidence 4788999999999999999999999975432 355554
No 18
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=86.36 E-value=0.77 Score=31.29 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=23.7
Q ss_pred CccEEECCEEeccCCCCceeeEEEEec
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIP 28 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~ 28 (200)
+|.|+|||++++.+.|.+--=|+|+|+
T Consensus 33 ~G~V~VNg~~~~~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 33 ENEVLVNGELENRRGKKLYPGDVIEIP 59 (59)
T ss_pred cCCEEECCEEccCCCCCCCCCCEEEeC
Confidence 689999999999888988888888874
No 19
>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=84.79 E-value=1.3 Score=34.34 Aligned_cols=29 Identities=24% Similarity=0.462 Sum_probs=25.7
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEEEec
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNREKHK 137 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~~~ 137 (200)
++..|+.+.|+.|+.-|..|+|.++.+..
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~ 31 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKT 31 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCC
Confidence 67789999999999999999999996543
No 20
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=82.48 E-value=2.3 Score=35.14 Aligned_cols=55 Identities=27% Similarity=0.361 Sum_probs=38.6
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEE-----cCCCCeEe--EeeccEEEEc
Q 029038 107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHEFA--TRLGNVFTIG 164 (200)
Q Consensus 107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~-----d~~g~~F~--T~~~~vfvIG 164 (200)
.+++..|+.+.|+.|++-|..|+|.++....+ .|.|+ ..+|..++ --.|||+++-
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~---~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKW---VIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCCC---EEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 34788899999999999999999999975443 34443 35554433 3346676664
No 21
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=75.56 E-value=4.9 Score=35.35 Aligned_cols=27 Identities=19% Similarity=0.210 Sum_probs=23.5
Q ss_pred CccEEECCEEeccCCCCceeeEEEEec
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIP 28 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~ 28 (200)
+|.|+|||+++++..+++---|+|++.
T Consensus 30 ~G~V~VNg~~~~~~~~~v~~gd~I~i~ 56 (299)
T TIGR00005 30 NGQVKVNGKVTANPKLKVKDGDRITVR 56 (299)
T ss_pred CCcEEECCEeccCcccCCCCCCEEEEe
Confidence 689999998888888999777999983
No 22
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=73.82 E-value=13 Score=26.65 Aligned_cols=50 Identities=28% Similarity=0.529 Sum_probs=38.3
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeeccEEEEcc
Q 029038 112 VGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 165 (200)
Q Consensus 112 ~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~~vfvIG~ 165 (200)
+|..|+|-.|.+.-|+|.++.-|... ++|.+| + ++...+--+..+..+|-
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~iv-i---~~q~i~velkdivlvgv 55 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIV-I---GEQSIDVELKDIVLVGV 55 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEE-E---CCeEEEEEeeeEEEEEe
Confidence 48899999999999999999888766 445555 2 34566777777777774
No 23
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=69.41 E-value=3.5 Score=29.62 Aligned_cols=34 Identities=29% Similarity=0.385 Sum_probs=22.1
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecCCCceEEEE
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 37 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 37 (200)
+|.|+|||.+.+...--+--=|+|++ .++.|+++
T Consensus 32 ~g~V~VNGe~e~rrg~Kl~~GD~V~~--~~~~~~Vv 65 (65)
T PF13275_consen 32 EGEVKVNGEVETRRGKKLRPGDVVEI--DGEEYRVV 65 (65)
T ss_dssp HHHHEETTB----SS----SSEEEEE--TTEEEEEE
T ss_pred cCceEECCEEccccCCcCCCCCEEEE--CCEEEEEC
Confidence 57899999999988888888899999 47888874
No 24
>PRK11507 ribosome-associated protein; Provisional
Probab=66.57 E-value=9.6 Score=27.91 Aligned_cols=34 Identities=24% Similarity=0.238 Sum_probs=27.0
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecCCCceEEEE
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 37 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 37 (200)
+|.|+|||.+.+=..--+--=|+|+++ ++.|++.
T Consensus 36 eg~V~VNGeve~rRgkKl~~GD~V~~~--g~~~~v~ 69 (70)
T PRK11507 36 EGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQVV 69 (70)
T ss_pred cCceEECCEEecccCCCCCCCCEEEEC--CEEEEEe
Confidence 689999999977776666677999996 5777764
No 25
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=65.97 E-value=10 Score=29.74 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=24.7
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEEEEEe
Q 029038 108 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 136 (200)
Q Consensus 108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~~ 136 (200)
++...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 46677999999999999999999988543
No 26
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=63.44 E-value=6.2 Score=33.66 Aligned_cols=28 Identities=29% Similarity=0.395 Sum_probs=24.9
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecC
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK 29 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k 29 (200)
+|.|.|||++++++.|.+--=|+|++..
T Consensus 114 ~G~V~VNgk~v~~ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 114 HGHILVNGKKVDIPSYQVRPGDIISIKE 141 (200)
T ss_pred CCCEEECCEEeCCCCCCCCCCCEEEEee
Confidence 6899999999999999997779999963
No 27
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=63.44 E-value=7.8 Score=31.29 Aligned_cols=26 Identities=38% Similarity=0.556 Sum_probs=23.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
+++|-.|+++.|+.+|+-.+|..+-.
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iD 30 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIID 30 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEcc
Confidence 68999999999999999999998853
No 28
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=63.13 E-value=6.9 Score=33.49 Aligned_cols=28 Identities=25% Similarity=0.357 Sum_probs=25.0
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecC
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK 29 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k 29 (200)
.|.|.|||++++.+.|++--=|+|++..
T Consensus 117 ~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 117 HGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred CCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 6899999999999999997779999974
No 29
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=62.94 E-value=38 Score=31.79 Aligned_cols=63 Identities=22% Similarity=0.148 Sum_probs=37.6
Q ss_pred EEEcCCCceEEEEcC--ccccceeeEEEEEEEEeeCCeeEEEccCceEEeeCCC--------CccCCCeEEEecCC
Q 029038 36 LLYDTKGRFRLHSIR--DEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP--------LIKANDTIKLDLET 101 (200)
Q Consensus 36 vl~d~kgrf~l~~I~--~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~--------~ik~~DTv~i~l~~ 101 (200)
++.|.+|+-....+- +=|. .=|..|+-+. .|....+.+.|..|||+-.| +.|+||.|+..+++
T Consensus 256 lvVd~~G~tR~~~VGRvKIE~-RPL~lIeAe~--~g~~~~viLQnaetIrlv~~dG~~vsVt~Lk~GD~VL~~~~~ 328 (344)
T PRK02290 256 LVVDADGNTREAIVGRVKIEK-RPLLLIEAEY--GGKRIRTILQNAETIRLVTPDGKPVSVVDLKPGDEVLGYLEE 328 (344)
T ss_pred EEEeCCCCEEEEEeeEEEEee-ccEEEEEEEe--CCeEEEEEEecCcEEEEECCCCCEeeeeecCCCCEEEEEecC
Confidence 456777776554331 1132 2456666655 55677777888888887544 45666666666554
No 30
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=60.65 E-value=12 Score=33.67 Aligned_cols=32 Identities=31% Similarity=0.284 Sum_probs=29.1
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecCCCceE
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENF 34 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~y 34 (200)
+|.|+|||++.+ ..|.+..=|+|+++...+.+
T Consensus 36 ~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~ 67 (289)
T COG0564 36 KGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPE 67 (289)
T ss_pred CCCEEECCEEcc-CCeeeCCCCEEEEecccccc
Confidence 689999999999 99999999999999877665
No 31
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=59.62 E-value=48 Score=31.22 Aligned_cols=75 Identities=23% Similarity=0.298 Sum_probs=41.6
Q ss_pred EEEcCCCceEEEEcC--ccccceeeEEEEEEEEeeCCeeEEEccCceEEeeCCCCccCCCeEEEecCCCceeEEEEeeCC
Q 029038 36 LLYDTKGRFRLHSIR--DEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVG 113 (200)
Q Consensus 36 vl~d~kgrf~l~~I~--~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G 113 (200)
|+.|.+|+-....+- +=| +.=|..|+-.. .|....+.+.|..|||+-.| +++.+....+++|
T Consensus 266 lvVd~~G~tR~~~VGRvKIE-~RPLllIeA~~--~g~~~svilQnaetIRlv~p-------------~G~~vsVt~Lk~G 329 (354)
T PF01959_consen 266 LVVDADGRTRTAIVGRVKIE-RRPLLLIEAEA--DGKRISVILQNAETIRLVGP-------------DGEPVSVTELKPG 329 (354)
T ss_pred EEEeCCCCEEEEEeeEEEEe-ecceEEEEEEe--CCeEEEEEEecCcEEEEECC-------------CCCEeeeeecCCC
Confidence 345666665443321 113 22456666655 55677777888888886544 2344444444444
Q ss_pred cEEEE---ECCCccee
Q 029038 114 NVVMV---TGGRNRGR 126 (200)
Q Consensus 114 ~~~~v---~gG~n~G~ 126 (200)
+.+++ .+|||.|-
T Consensus 330 D~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 330 DEVLVYLEEAGRHFGM 345 (354)
T ss_pred CEEEEEecCCCcccce
Confidence 44433 27888884
No 32
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=58.74 E-value=20 Score=32.10 Aligned_cols=44 Identities=16% Similarity=0.044 Sum_probs=32.1
Q ss_pred CccEEECCEEeccCCCCc--eeeEEEEecC----------CCceEEEEEcCCCceEE
Q 029038 2 QRHVLVDAKVRTDKTYPA--GFMDVVSIPK----------TNENFRLLYDTKGRFRL 46 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~Pv--G~MDVIsI~k----------t~e~yRvl~d~kgrf~l 46 (200)
+|.|+|||++. +..+.| +-.|.|+++. ..++|-+++-+.|..+-
T Consensus 26 ~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~~s 81 (289)
T PRK10700 26 AGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCT 81 (289)
T ss_pred cCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCEee
Confidence 68999999987 666666 4557787653 11468888999988754
No 33
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=57.75 E-value=12 Score=30.50 Aligned_cols=26 Identities=15% Similarity=0.362 Sum_probs=23.9
Q ss_pred eCCcEEEEECCCcceeEEEEEEEEEe
Q 029038 111 DVGNVVMVTGGRNRGRVGIIKNREKH 136 (200)
Q Consensus 111 e~G~~~~v~gG~n~G~vG~I~~i~~~ 136 (200)
|+|-.|++.-|.+.|+.++|++|-.+
T Consensus 9 EiGRVvli~~Gp~~GKL~vIVDIID~ 34 (130)
T PTZ00065 9 EPGRLCLIQYGPDAGKLCFIVDIVTP 34 (130)
T ss_pred eeceEEEEecCCCCCCEEEEEEEEcC
Confidence 78999999999999999999999643
No 34
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=57.72 E-value=15 Score=33.12 Aligned_cols=28 Identities=25% Similarity=0.201 Sum_probs=21.6
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEec
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIP 28 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~ 28 (200)
++|.|+|||++++...+.+---|+|++.
T Consensus 41 ~~G~V~VNg~~v~~~~~~v~~gD~I~v~ 68 (325)
T PRK11180 41 LDQRVLVNGKVINKPKEKVLGGEQVAID 68 (325)
T ss_pred HCCCEEECCEEccCCCcCcCCCCEEEEe
Confidence 3689999999987666666555888885
No 35
>PF14001 YdfZ: YdfZ protein
Probab=57.48 E-value=17 Score=26.26 Aligned_cols=42 Identities=26% Similarity=0.499 Sum_probs=29.7
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEEEec------CCccEEEEEcCCCCeEe
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 154 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~~~------~s~~iV~v~d~~g~~F~ 154 (200)
++.+|+.+|+-| +|.+|+|+.|.-.. .....|.++..+| .|+
T Consensus 9 ~i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 9 AITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred cCCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 456799999977 67888899886532 2234788888665 465
No 36
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=56.70 E-value=8.3 Score=33.39 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=25.1
Q ss_pred CccEEECCEEeccCCCCceeeEEEEec
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIP 28 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~ 28 (200)
.|+|.|||+.++.+-|=|-.=|+++|.
T Consensus 118 HGHI~VnGk~V~iPSy~V~~gdei~V~ 144 (205)
T COG0522 118 HGHILVNGKRVNIPSYLVSPGDEISVR 144 (205)
T ss_pred cceEEECCEEeccCcEEecCCCEEEee
Confidence 589999999999999999999999996
No 37
>PRK04333 50S ribosomal protein L14e; Validated
Probab=54.74 E-value=14 Score=27.67 Aligned_cols=26 Identities=35% Similarity=0.534 Sum_probs=23.7
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEE
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNRE 134 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~ 134 (200)
.++.|-+|++.-|+..|+..+|.++.
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~ 28 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDII 28 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEe
Confidence 46889999999999999999999884
No 38
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=54.32 E-value=69 Score=33.23 Aligned_cols=78 Identities=19% Similarity=0.237 Sum_probs=56.2
Q ss_pred CceeeEEEEecCCCceEEEEEcCCCceEEEEcCc---cccceeeEEEE----EEEEeeCCeeEEEccCceEEeeCCCCcc
Q 029038 18 PAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIK 90 (200)
Q Consensus 18 PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~---eEa~~KLcKV~----~k~~~~gG~~ql~~hDGrni~~~d~~ik 90 (200)
+.|-++++..+ .+.+=+-+|++++....+++. -++.-||.||+ ....++.++|.++..||+-....-..++
T Consensus 111 ~~~~~e~~~~~--~~~~V~s~d~~~k~~~~~v~~v~r~~~~~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~~a~~l~ 188 (858)
T PRK14898 111 KIGGHEVCDLP--IEIYALSLDQDEKVHWKRIISVIRHKANGKLIKIKTESGRTIRATPYHSFVTRKDNEVIPVEGSELK 188 (858)
T ss_pred ccCCceEEecC--CCcEEEEECCCCcEEEEEeeeEEeccCCCcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEeeHHhCC
Confidence 34666666554 244444578888888888865 23334889888 4557788999999999987665666899
Q ss_pred CCCeEEE
Q 029038 91 ANDTIKL 97 (200)
Q Consensus 91 ~~DTv~i 97 (200)
+||-|.+
T Consensus 189 ~GD~i~~ 195 (858)
T PRK14898 189 IGDWLPV 195 (858)
T ss_pred CCCEEee
Confidence 9998755
No 39
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=52.52 E-value=11 Score=32.72 Aligned_cols=29 Identities=17% Similarity=0.238 Sum_probs=24.8
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecC
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPK 29 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~k 29 (200)
++|.|+|||++++++.+.+--=|.|++..
T Consensus 23 ~~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 23 LKGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred HCCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 47999999999999998886559999964
No 40
>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=48.75 E-value=55 Score=22.02 Aligned_cols=38 Identities=24% Similarity=0.291 Sum_probs=30.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEEecCCcc-EEEEEc
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFE-TIHIQD 147 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~-iV~v~d 147 (200)
|++|..+++.-+...-.-++|.+++..++... .||-..
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~g 39 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQG 39 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEETT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcCC
Confidence 68899999999999999999999988766655 788753
No 41
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=48.75 E-value=16 Score=31.38 Aligned_cols=28 Identities=18% Similarity=0.439 Sum_probs=24.0
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecC
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK 29 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k 29 (200)
+|.|.|||++++.+.|.+--=|+|++..
T Consensus 113 ~G~V~VNGk~v~~ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 113 HGHILVNGRIVDIPSYRCKPKDIITVKD 140 (201)
T ss_pred CCcEEECCEEecCccccCCCCCEEEEcc
Confidence 6899999999999999885559999853
No 42
>cd03706 mtEFTU_III Domain III of mitochondrial EF-TU (mtEF-TU). mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU the nucleotide-binding domain (domain I) of EF-TUmt is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors.
Probab=47.62 E-value=1.1e+02 Score=22.21 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=24.8
Q ss_pred ccCCCeEEEecCCCceeEEEEeeCCcEEEE-ECCCcceeEEEEEE
Q 029038 89 IKANDTIKLDLETNKITEFIKFDVGNVVMV-TGGRNRGRVGIIKN 132 (200)
Q Consensus 89 ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v-~gG~n~G~vG~I~~ 132 (200)
+++||+..+.+.-.+ -+..+.|.-.++ -+|+.+| .|.|.+
T Consensus 52 l~~g~~~~v~i~l~~---p~~~~~g~rf~lR~~~~tvg-~G~V~~ 92 (93)
T cd03706 52 VMPGEDTKVTLILRR---PMVLEKGQRFTLRDGNRTIG-TGLVTD 92 (93)
T ss_pred eCCCCEEEEEEEECC---cEEEeeCCEEEEEECCEEEE-EEEEEe
Confidence 788888887776433 224555655555 5565555 677654
No 43
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=47.26 E-value=42 Score=26.05 Aligned_cols=59 Identities=20% Similarity=0.188 Sum_probs=36.1
Q ss_pred CeeEEEccCceEEeeCCCCccCCCeEEEecC------CCceeEEEEeeCCcEEEEECCCcceeEEEEEE
Q 029038 70 GIPYINTYDGRTIRYPDPLIKANDTIKLDLE------TNKITEFIKFDVGNVVMVTGGRNRGRVGIIKN 132 (200)
Q Consensus 70 G~~ql~~hDGrni~~~d~~ik~~DTv~i~l~------~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~ 132 (200)
...++.|.|||++.-.=.-+...--+.|+-. +.+=++.+++- .+++.|.|.+-+|.|-|
T Consensus 11 ~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 11 QRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDE 75 (96)
T ss_pred ceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecch
Confidence 4678889999997633122222222444432 22223344443 78999999999998875
No 44
>cd03704 eRF3c_III This family represents eEF1alpha-like C-terminal region of eRF3 homologous to the domain III of EF-Tu. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.
Probab=46.57 E-value=1.1e+02 Score=22.78 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=30.2
Q ss_pred CCC-CccCCCeEEEecCCCceeEEEEeeC----CcEEEEECCCcceeEEEEEEE
Q 029038 85 PDP-LIKANDTIKLDLETNKITEFIKFDV----GNVVMVTGGRNRGRVGIIKNR 133 (200)
Q Consensus 85 ~d~-~ik~~DTv~i~l~~~kI~~~i~fe~----G~~~~v~gG~n~G~vG~I~~i 133 (200)
.+| .++.||...+.+...+-+-.=+|+. |-.++--+|+.+| .|.|.+|
T Consensus 56 ~~p~~l~~g~~a~v~i~~~~pi~~e~~~~~~~lGRf~lR~~g~Tva-~G~V~~~ 108 (108)
T cd03704 56 KRPRFVKSGMKVIARLETTGPICLEKFEDFPQLGRFTLRDEGKTIA-IGKVLKL 108 (108)
T ss_pred cCCcEeCCCCEEEEEEEeCCcEEEEEcccCCCcccEEEEeCCCEEE-EEEEEEC
Confidence 444 6899999999987555221122322 6666666777665 7877653
No 45
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=44.82 E-value=37 Score=25.08 Aligned_cols=34 Identities=26% Similarity=0.396 Sum_probs=23.5
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecCCCceEEEE
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 37 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 37 (200)
++.|+|||.+-+=..--+--=|+|+|| +..|-+.
T Consensus 36 eg~V~vNGe~EtRRgkKlr~gd~V~i~--~~~~~v~ 69 (73)
T COG2501 36 EGEVKVNGEVETRRGKKLRDGDVVEIP--GQRYQVV 69 (73)
T ss_pred CCeEEECCeeeeccCCEeecCCEEEEC--CEEEEEE
Confidence 689999999865554444556899997 4555443
No 46
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=43.53 E-value=55 Score=24.21 Aligned_cols=22 Identities=32% Similarity=0.376 Sum_probs=16.8
Q ss_pred eEEEEEEEEEecCCcc--EEEEEc
Q 029038 126 RVGIIKNREKHKGSFE--TIHIQD 147 (200)
Q Consensus 126 ~vG~I~~i~~~~~s~~--iV~v~d 147 (200)
++|+|.+.+.||++.. +..+..
T Consensus 2 ~vg~I~~~~~hp~sdkL~~~~Vd~ 25 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYVLKVDI 25 (95)
T ss_dssp EEEEEEEEEEETTSSSEEEEEEES
T ss_pred EEEEEEEEEECCCCCEEEEEEEEe
Confidence 6899999999998865 444433
No 47
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=42.64 E-value=60 Score=23.27 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=27.2
Q ss_pred EeeCCeeEEEccCceEEeeCC----CCccCCCeEEEecC
Q 029038 66 FGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 100 (200)
Q Consensus 66 ~~~gG~~ql~~hDGrni~~~d----~~ik~~DTv~i~l~ 100 (200)
.+......|.|.||.++..|. +.+++|..|++-..
T Consensus 11 ~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 11 SIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYD 49 (61)
T ss_pred EEcCCceEEEecCCCEEECCCcccccccCCCCEEEEEEE
Confidence 355567899999999999874 36889988877654
No 48
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=42.47 E-value=26 Score=28.72 Aligned_cols=24 Identities=42% Similarity=0.688 Sum_probs=21.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEEE
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNR 133 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i 133 (200)
+.+|..|++..|+++|+-++|..-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999988864
No 49
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=42.15 E-value=31 Score=24.53 Aligned_cols=34 Identities=35% Similarity=0.488 Sum_probs=20.4
Q ss_pred EEECCCcce---eEEEEEEEEEecCCcc-EEEEEcCCCC
Q 029038 117 MVTGGRNRG---RVGIIKNREKHKGSFE-TIHIQDALGH 151 (200)
Q Consensus 117 ~v~gG~n~G---~vG~I~~i~~~~~s~~-iV~v~d~~g~ 151 (200)
+++.|+++| |.|.|.|+.-..|+.+ +|.-.| +|+
T Consensus 9 lvv~g~~vg~~~r~GeIveV~g~dG~PPY~VRw~D-~Gh 46 (58)
T PF08940_consen 9 LVVHGRTVGQPDRHGEIVEVRGPDGSPPYLVRWDD-TGH 46 (58)
T ss_dssp EEES-TTTS--EEEEEEEE-S-SSS-S-EEEEETT-TTE
T ss_pred EEEcCCcCCCCCcEeEEEEEECCCCCCCEEEEecC-CCc
Confidence 456677765 6788888876668888 888765 454
No 50
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=41.37 E-value=33 Score=27.92 Aligned_cols=34 Identities=6% Similarity=0.059 Sum_probs=28.2
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEE
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFR 35 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yR 35 (200)
++|.|.|||.+ .-+-.+|-.=|+|+|...+..|-
T Consensus 32 ~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~ 65 (133)
T PRK10348 32 EGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERT 65 (133)
T ss_pred HCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEE
Confidence 46999999999 88999999999999976555443
No 51
>PF04773 FecR: FecR protein; InterPro: IPR006860 FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Probab=40.90 E-value=1.3e+02 Score=21.22 Aligned_cols=66 Identities=17% Similarity=0.158 Sum_probs=37.1
Q ss_pred EEEeeCCeeEEEccCceEEeeCC-CCc-----cCCCeEEEecCCCceeEEEEeeCCc-EEEEECCCcceeEEE
Q 029038 64 VQFGQKGIPYINTYDGRTIRYPD-PLI-----KANDTIKLDLETNKITEFIKFDVGN-VVMVTGGRNRGRVGI 129 (200)
Q Consensus 64 k~~~~gG~~ql~~hDGrni~~~d-~~i-----k~~DTv~i~l~~~kI~~~i~fe~G~-~~~v~gG~n~G~vG~ 129 (200)
..+..++.-+|.+.||..++... ..+ .-.+...+.|..|++.-.++=.... +.+-|....++-.|+
T Consensus 3 i~T~~~~~~~i~l~dgs~v~l~~~s~~~~~~~~~~~~~~~~L~~G~~~~~~~~~~~~~~~V~T~~~~i~v~GT 75 (98)
T PF04773_consen 3 IRTGAGSRAEIALSDGSRVRLGPNSRVSVDRDSGSEPTRLRLLSGEILFDVSPGKKRPFEVRTPTATIGVRGT 75 (98)
T ss_pred EEcCCCCEEEEEECCCCEEEECCCcEEEEEcccCCCceEEEEcCCCEEEEEcccCCCCEEEEeCCEEEEEecC
Confidence 45678899999999999987643 234 3444455666666553222222222 444444444444443
No 52
>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=39.85 E-value=54 Score=25.89 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=24.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
|.+|+.+.|+.|.=.|..|.|.++..
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 89999999999999999999999875
No 53
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=39.46 E-value=55 Score=29.48 Aligned_cols=43 Identities=19% Similarity=0.122 Sum_probs=31.1
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecC--------CCceEEEEEcCCCceE
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK--------TNENFRLLYDTKGRFR 45 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k--------t~e~yRvl~d~kgrf~ 45 (200)
+|.|+|||++. ...+.+---|+|++.. .+++|-++.-+.|..+
T Consensus 30 ~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~~~ed~~~lvlnKP~G~~~ 80 (290)
T PRK10475 30 QGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80 (290)
T ss_pred CCcEEECCEEc-cCCCCcCCCCEEEECCEEccccccCCCeEEEEECCCCCCc
Confidence 68999999987 4666665558888752 1346778888888654
No 54
>PF06905 FAIM1: Fas apoptotic inhibitory molecule (FAIM1); InterPro: IPR010695 This family consists of several fas apoptotic inhibitory molecule (FAIM) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology [].; GO: 0043066 negative regulation of apoptosis; PDB: 3MX7_A 2KW1_A 2KD2_A.
Probab=38.97 E-value=2.4e+02 Score=23.94 Aligned_cols=68 Identities=16% Similarity=0.251 Sum_probs=44.4
Q ss_pred EEEEEEEEeeCCeeEEEc-cCceEE-eeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEE
Q 029038 59 CKVRSVQFGQKGIPYINT-YDGRTI-RYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGI 129 (200)
Q Consensus 59 cKV~~k~~~~gG~~ql~~-hDGrni-~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~ 129 (200)
|.| ++..+.+..-++.| =||.++ .|-+...|.-.|..+.+..++ -.|-|+...+-+=..|......|.
T Consensus 64 ~~I-~I~~~~g~~YeYsL~VdGksl~ky~e~~~k~~~tW~~~i~G~~--~RIvLdk~t~~vwvnG~~iet~~e 133 (177)
T PF06905_consen 64 CEI-NIEAVSGFAYEYSLEVDGKSLKKYKEEQSKKFNTWELNIDGQE--YRIVLDKDTMDVWVNGEKIETEGE 133 (177)
T ss_dssp EEE-EEEEETTTEEEEEEEETTEEEEE--SSTTTTEEEEEEEETTEE--EEEEEETTTTEEEETTCEE--EEE
T ss_pred EEE-EEEecCCceEEEEEEECCEEHHHHHHHHhhhheeEEEecCCCE--EEEEEEcceEEEEECCEEccccce
Confidence 444 33444555544444 378775 355777889999999997544 567788888888899998877664
No 55
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=38.77 E-value=52 Score=26.63 Aligned_cols=29 Identities=14% Similarity=0.265 Sum_probs=26.6
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEEEEEe
Q 029038 108 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 136 (200)
Q Consensus 108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~~ 136 (200)
..|.+|..+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999754
No 56
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=38.27 E-value=50 Score=29.44 Aligned_cols=48 Identities=23% Similarity=0.191 Sum_probs=33.7
Q ss_pred CCccEEECCEEeccCCCCceee-EEEEecCCC------ceEEEEEcCCCceEEEE
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFM-DVVSIPKTN------ENFRLLYDTKGRFRLHS 48 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~M-DVIsI~kt~------e~yRvl~d~kgrf~l~~ 48 (200)
.+|.|.|||++.++...-+=-- |+|.++..- ..|-|++-+.|.++-+.
T Consensus 25 ~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~~ 79 (248)
T COG1187 25 EEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSSTE 79 (248)
T ss_pred HcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEeccc
Confidence 3789999999999986555444 466655431 22888898888776553
No 57
>cd05741 Ig_CEACAM_D1_like First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins. Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily-like. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surf
Probab=37.98 E-value=51 Score=22.90 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=25.6
Q ss_pred EEEEcCCCceEEEEcCccccceeeEEEEEEE
Q 029038 35 RLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQ 65 (200)
Q Consensus 35 Rvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~ 65 (200)
|+-.+..+.|.+..+.++++..-.|.|....
T Consensus 50 R~~~~~~~sL~I~~l~~~DsG~Y~c~v~~~~ 80 (92)
T cd05741 50 RETIYPNGSLLIQNLTKEDSGTYTLQIISTN 80 (92)
T ss_pred eEEEcCCceEEEccCCchhcEEEEEEEEcCC
Confidence 4445556999999999999999999998764
No 58
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=37.98 E-value=34 Score=24.81 Aligned_cols=41 Identities=24% Similarity=0.456 Sum_probs=28.0
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEEec------CCccEEEEEcCCCCeEe
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 154 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~~~------~s~~iV~v~d~~g~~F~ 154 (200)
+..|+.+||.| .|++|+|+.|.-.. .....|.++-.+| .|+
T Consensus 11 it~G~rVMia~---tG~tgvikaIh~dglt~~Q~rR~k~Vel~g~e~-~f~ 57 (65)
T TIGR03318 11 ITTGSRVMIAG---TGHTGVIKAIHTEGLTAEQARREKCVELEGCEE-RFA 57 (65)
T ss_pred cCCCcEEEEec---CCccceeehhhhCCCCHHHhhhccEEEEecccc-eec
Confidence 45799999987 67888888886422 2234788876554 465
No 59
>cd05892 Ig_Myotilin_C C-terminal immunoglobulin (Ig)-like domain of myotilin. Ig_Myotilin_C: C-terminal immunoglobulin (Ig)-like domain of myotilin. Mytolin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to the latter family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Myotilin is most abundant in skeletal and cardiac muscle, and is involved in maintaining sarcomere integrity. It binds to alpha-actinin, filamin and actin. Mutations in myotilin lead to muscle disorders.
Probab=37.92 E-value=72 Score=22.39 Aligned_cols=35 Identities=11% Similarity=0.282 Sum_probs=28.5
Q ss_pred CCceEEEEEcCCC--ceEEEEcCccccceeeEEEEEE
Q 029038 30 TNENFRLLYDTKG--RFRLHSIRDEEAKFKLCKVRSV 64 (200)
Q Consensus 30 t~e~yRvl~d~kg--rf~l~~I~~eEa~~KLcKV~~k 64 (200)
.+.+|++..+..| .|.+..+.++++..-.|...|.
T Consensus 27 ~~~r~~~~~~~~g~~~L~I~~~~~~D~G~Y~C~A~N~ 63 (75)
T cd05892 27 NTDRISLYQDNSGRVTLLIKNVNKKDAGWYTVSAVNE 63 (75)
T ss_pred CCCeEEEEEcCCCcEEEEECCCChhhCEEEEEEEEcC
Confidence 3467888888777 5777899999999889998874
No 60
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=37.88 E-value=80 Score=26.76 Aligned_cols=46 Identities=13% Similarity=0.162 Sum_probs=31.0
Q ss_pred CccEEECCEEeccCCCCceeeEEEEecC------CCceEEEEEcCCCceEEEE
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK------TNENFRLLYDTKGRFRLHS 48 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k------t~e~yRvl~d~kgrf~l~~ 48 (200)
+|.|+|||++.++..+.+---|.|++.. ..++|-++--+.|-. .|+
T Consensus 24 ~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~~~~~~~~lvvnKP~G~~-~~~ 75 (232)
T PRK10839 24 ANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYV-CST 75 (232)
T ss_pred cCeEEECCEEeccCCcCcCCCCEEEECCEEcccCCCCEEEEEECCCCeE-ecc
Confidence 6899999999887767665558998852 124565555556543 454
No 61
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=37.35 E-value=54 Score=29.43 Aligned_cols=26 Identities=31% Similarity=0.295 Sum_probs=21.3
Q ss_pred CccEEECCEEeccCCCCceeeEEEEec
Q 029038 2 QRHVLVDAKVRTDKTYPAGFMDVVSIP 28 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~MDVIsI~ 28 (200)
+|.|.|||+++ ...+.+--=|+|+++
T Consensus 44 ~G~V~VNg~~v-~~~~~v~~GD~I~i~ 69 (317)
T PRK11025 44 KGEVRVNKKRI-KPEYKLEAGDEVRIP 69 (317)
T ss_pred cCCEEECCEEc-CcccccCCCCEEEeC
Confidence 68999999988 467877555999985
No 62
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=37.24 E-value=34 Score=25.19 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=15.4
Q ss_pred EeeCCCCccCCCeEEEe
Q 029038 82 IRYPDPLIKANDTIKLD 98 (200)
Q Consensus 82 i~~~d~~ik~~DTv~i~ 98 (200)
||..|.+|++||.|.+.
T Consensus 22 iRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 22 IRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEecCCCCCCCCEEEEE
Confidence 88899999999999884
No 63
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=36.98 E-value=1.1e+02 Score=32.88 Aligned_cols=156 Identities=17% Similarity=0.235 Sum_probs=100.7
Q ss_pred ccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCceEE
Q 029038 3 RHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 82 (200)
Q Consensus 3 ~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni 82 (200)
+.|.++.++.--++.=+--.+-=.+...+++|+++ .+|-|....++.++|..--|-..|+.=--....+|..-|..-|
T Consensus 442 ~~v~i~C~~~asP~p~~~W~k~~~~~~~~~r~~i~--edGtL~I~n~t~~DaG~YtC~A~N~~G~a~~~~~L~Vkd~tri 519 (1051)
T KOG3513|consen 442 GTVTIDCKPFASPKPKVSWLKGGEKLLQSGRIRIL--EDGTLEISNVTRSDAGKYTCVAENKLGKAESTGNLIVKDATRI 519 (1051)
T ss_pred CeEEEeeccCCCCcceEEEEcCCcccccCceEEEC--CCCcEEecccCcccCcEEEEEEEcccCccceEEEEEEecCceE
Confidence 45566666666665544444444445566777765 5688999999999999999999998866677788888888887
Q ss_pred eeC--CCCccCCCeEEEecCCC-----ceeE-------EEEe-eCCcEEEEECCCcceeEEEEEEEEE-ecCCcc-EEEE
Q 029038 83 RYP--DPLIKANDTIKLDLETN-----KITE-------FIKF-DVGNVVMVTGGRNRGRVGIIKNREK-HKGSFE-TIHI 145 (200)
Q Consensus 83 ~~~--d~~ik~~DTv~i~l~~~-----kI~~-------~i~f-e~G~~~~v~gG~n~G~vG~I~~i~~-~~~s~~-iV~v 145 (200)
..+ ...++.|+++.+.-+.. +|.= .+.| ..|.-..+.+|.+.|+. +|.++.- +.|++. +|.-
T Consensus 520 ~~~P~~~~v~~g~~v~l~Ce~shD~~ld~~f~W~~nG~~id~~~~~~~~~~~~~~~~g~L-~i~nv~l~~~G~Y~C~aqT 598 (1051)
T KOG3513|consen 520 TLAPSNTDVKVGESVTLTCEASHDPSLDITFTWKKNGRPIDFNPDGDHFEINDGSDSGRL-TIANVSLEDSGKYTCVAQT 598 (1051)
T ss_pred EeccchhhhccCceEEEEeecccCCCcceEEEEEECCEEhhccCCCCceEEeCCcCccce-EEEeeccccCceEEEEEEE
Confidence 663 23689999999876633 1111 1222 24666778888877765 3355543 446654 3322
Q ss_pred EcCCCCeEeEeeccEEEEcc
Q 029038 146 QDALGHEFATRLGNVFTIGK 165 (200)
Q Consensus 146 ~d~~g~~F~T~~~~vfvIG~ 165 (200)
...+ .+....++|-|-
T Consensus 599 ---~~Ds-~s~~A~l~V~gp 614 (1051)
T KOG3513|consen 599 ---ALDS-ASARADLLVRGP 614 (1051)
T ss_pred ---eecc-hhcccceEEecC
Confidence 1111 445566777775
No 64
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=35.90 E-value=42 Score=27.17 Aligned_cols=29 Identities=24% Similarity=0.388 Sum_probs=26.2
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 107 FIKFDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
...|.+|+.+-|++|.=.|..|.|.++..
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDY 152 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeC
Confidence 46799999999999999999999999853
No 65
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=35.23 E-value=1.6e+02 Score=22.96 Aligned_cols=33 Identities=18% Similarity=0.570 Sum_probs=26.2
Q ss_pred cEEEEEcCCCCeEeEeeccEEEEccCCCceEeCcCCCceeeeh
Q 029038 141 ETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSI 183 (200)
Q Consensus 141 ~iV~v~d~~g~~F~T~~~~vfvIG~~~~p~isLp~~~gi~~~~ 183 (200)
+-|.|++.+|+. |.|...+ |+.-|-++-|++++
T Consensus 76 ~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~~ 108 (109)
T cd02899 76 DYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVSL 108 (109)
T ss_pred eEEEEECCCCCE------EEEEcce----eeCCchhceEEEec
Confidence 478888866654 4599988 99999999888774
No 66
>cd03705 EF1_alpha_III Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
Probab=33.48 E-value=97 Score=22.66 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=24.5
Q ss_pred CccCCCeEEEecCCCceeEEEEeeC-------CcEEEEECCCcce
Q 029038 88 LIKANDTIKLDLETNKITEFIKFDV-------GNVVMVTGGRNRG 125 (200)
Q Consensus 88 ~ik~~DTv~i~l~~~kI~~~i~fe~-------G~~~~v~gG~n~G 125 (200)
.++.||...+.|..++ -+.+|+ |..+++-+|+.+|
T Consensus 59 ~l~~n~~a~v~l~~~~---pi~~e~~~~~~~lgrf~lrd~~~Tva 100 (104)
T cd03705 59 FLKSGDAAIVKIVPQK---PLVVETFSEYPPLGRFAVRDMGQTVA 100 (104)
T ss_pred ccCCCCEEEEEEEECC---eeEEEEcccCCCccCEEEEeCCCEEE
Confidence 5899999999987554 345555 6777766665554
No 67
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=32.79 E-value=23 Score=28.36 Aligned_cols=42 Identities=24% Similarity=0.370 Sum_probs=33.0
Q ss_pred CCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCceEEeeCCC
Q 029038 41 KGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 87 (200)
Q Consensus 41 kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~ 87 (200)
++.|+|+.+|+= -|-+|--+.|..-+...+|| ||-|+-|.+|
T Consensus 21 KRwFvL~qvsQY--tfamcsy~ekks~P~e~~ql---dGyTvDy~~~ 62 (117)
T cd01234 21 KRFFVLVQVSQY--TFAMCSYREKKAEPTEFIQL---DGYTVDYMPE 62 (117)
T ss_pred eeEEEEEchhHH--HHHHHhhhhhcCCchhheee---cceEEeccCC
Confidence 445788877654 34688888888888889998 9999999865
No 68
>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=32.63 E-value=48 Score=26.74 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=25.3
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 108 IKFDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
..|.+|+.+.|++|.=.|..|.|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5589999999999999999999999853
No 69
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=32.13 E-value=37 Score=28.20 Aligned_cols=52 Identities=17% Similarity=0.238 Sum_probs=37.5
Q ss_pred CCceeEEEEeeCCcEEEEECCCcce-eEEEEEEEEEecCC--ccEEEEEcCCCCe
Q 029038 101 TNKITEFIKFDVGNVVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 152 (200)
Q Consensus 101 ~~kI~~~i~fe~G~~~~v~gG~n~G-~vG~I~~i~~~~~s--~~iV~v~d~~g~~ 152 (200)
..=.+..+|+..++.+-|.+|+..| .+|.|.++-+..-. .+.|.-+-++|..
T Consensus 40 ~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 40 QKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred HHhCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 3345788999999999999999999 99999998664322 2334444455543
No 70
>cd04093 HBS1_C HBS1_C: this family represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1) which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and, to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.
Probab=30.92 E-value=2.1e+02 Score=20.90 Aligned_cols=45 Identities=18% Similarity=0.381 Sum_probs=29.7
Q ss_pred CccCCCeEEEecCCCceeEEEEe----eCCcEEEEECCCcceeEEEEEEE
Q 029038 88 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNR 133 (200)
Q Consensus 88 ~ik~~DTv~i~l~~~kI~~~i~f----e~G~~~~v~gG~n~G~vG~I~~i 133 (200)
.++.||...+.+...+-+-.=+| ..|...+-..|+.+| .|.|.+|
T Consensus 59 ~l~~~~~a~v~l~~~~pi~~e~~~~~~~~Grfilr~~~~Tva-~G~I~~i 107 (107)
T cd04093 59 CLTKGQTAIVEIELERPIPLELFKDNKELGRVVLRRDGETIA-AGLVTEI 107 (107)
T ss_pred CcCCCCEEEEEEEECCeEEEEEcccCCCcceEEEEcCCCEEE-EEEEEeC
Confidence 68999999999976653322222 227777766676666 5887653
No 71
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=30.33 E-value=4e+02 Score=23.88 Aligned_cols=104 Identities=24% Similarity=0.273 Sum_probs=60.3
Q ss_pred EEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCceE----E--eeCCCCccCCCeEEE
Q 029038 24 VVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRT----I--RYPDPLIKANDTIKL 97 (200)
Q Consensus 24 VIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrn----i--~~~d~~ik~~DTv~i 97 (200)
|++..+.--...++.|.. ...++.|.... .--+..+||.+ + .-++.+++.||.|+-
T Consensus 160 V~~V~~~tS~V~Lltd~~-~~i~v~i~r~~-----------------~~~i~~~d~~~~~l~~~~~~~~~~i~~GD~vvT 221 (284)
T COG1792 160 VVEVSKNTSRVLLLTDVN-SKIPVKINRGD-----------------IGVIVGGDGENDLLLLVYLPPNSDIKEGDLVVT 221 (284)
T ss_pred EEEEcCceeEEEEeeccc-cceeEEeccCc-----------------eeEEEecCCCCCceeeeeccCCCCccCCCEEEe
Confidence 666666666667777744 22233332222 22233344443 1 114668899985554
Q ss_pred ecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeeccEEEEcc
Q 029038 98 DLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 165 (200)
Q Consensus 98 ~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~~vfvIG~ 165 (200)
+=-.+. |.+|= -+|+|..++.+. +.+..+.++-.. -.+++.|||++..
T Consensus 222 SGlgg~------fP~Gl-----------~Vg~V~~v~~~~~~~~~~v~~~P~a---~~~~l~~v~l~~~ 270 (284)
T COG1792 222 SGLGGV------FPAGL-----------PVGEVSSVKLDDYGLFKVVIVKPAA---SLDRLRYVLLVKR 270 (284)
T ss_pred cCCCCc------CCCCc-----------EEEEEEEEEeCCCceeEEEEEeccc---ccccceEEEEEec
Confidence 433332 33332 278888888766 556678887533 4789999999987
No 72
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=30.29 E-value=2.1e+02 Score=20.47 Aligned_cols=57 Identities=16% Similarity=0.172 Sum_probs=39.3
Q ss_pred EEEecCCCceEEEE-EcCCCceEEEEcCcccc----c------eeeEEEEEEEEeeCCeeEEEccCce
Q 029038 24 VVSIPKTNENFRLL-YDTKGRFRLHSIRDEEA----K------FKLCKVRSVQFGQKGIPYINTYDGR 80 (200)
Q Consensus 24 VIsI~kt~e~yRvl-~d~kgrf~l~~I~~eEa----~------~KLcKV~~k~~~~gG~~ql~~hDGr 80 (200)
|.++...+.++++. -|..|.+....-...+. . =.+.||.++...-+|.+||..+.=+
T Consensus 8 V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~ 75 (95)
T cd04478 8 VRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIR 75 (95)
T ss_pred EEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEE
Confidence 56666666777665 56678877665543331 1 1589999999998999999876333
No 73
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=29.81 E-value=1.2e+02 Score=21.77 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=17.2
Q ss_pred cCCCeEEEecC-----CCceeEEEEeeCCcEEEE
Q 029038 90 KANDTIKLDLE-----TNKITEFIKFDVGNVVMV 118 (200)
Q Consensus 90 k~~DTv~i~l~-----~~kI~~~i~fe~G~~~~v 118 (200)
|+||.|.+.-. ++.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG~MYLv 35 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCcEEEEE
Confidence 56666666554 445666666666655544
No 74
>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=29.74 E-value=85 Score=24.81 Aligned_cols=28 Identities=21% Similarity=0.135 Sum_probs=25.4
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEEEE
Q 029038 107 FIKFDVGNVVMVTGGRNRGRVGIIKNRE 134 (200)
Q Consensus 107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~ 134 (200)
...|.+|+.+.|++|.-.|..|.|.++.
T Consensus 106 ~~~~~~G~~V~V~~GPf~g~~g~v~~~~ 133 (159)
T TIGR01955 106 TTLPYKGDKVRITDGAFAGFEAIFLEPD 133 (159)
T ss_pred ccCCCCCCEEEEeccCCCCcEEEEEEEC
Confidence 3569999999999999999999999985
No 75
>PLN00189 40S ribosomal protein S9; Provisional
Probab=29.52 E-value=43 Score=28.95 Aligned_cols=20 Identities=20% Similarity=0.341 Sum_probs=17.3
Q ss_pred CccEEECCEEeccCCCCcee
Q 029038 2 QRHVLVDAKVRTDKTYPAGF 21 (200)
Q Consensus 2 q~~V~VDGkvr~D~k~PvG~ 21 (200)
+|+|.|||++++++.|-|-.
T Consensus 133 hgHI~V~~~~V~~Ps~~V~~ 152 (194)
T PLN00189 133 QRHIRVGKQIVNVPSFMVRV 152 (194)
T ss_pred CCCEeECCEEEecCcEEEec
Confidence 79999999999999886543
No 76
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=29.02 E-value=60 Score=25.27 Aligned_cols=48 Identities=17% Similarity=0.317 Sum_probs=26.0
Q ss_pred cCccccceeeEEEEEEEEee---CCeeEEEccCceEEeeCCCCccCCCeEEEecCC
Q 029038 49 IRDEEAKFKLCKVRSVQFGQ---KGIPYINTYDGRTIRYPDPLIKANDTIKLDLET 101 (200)
Q Consensus 49 I~~eEa~~KLcKV~~k~~~~---gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~ 101 (200)
|+++...+++++. +.++. ....++.+.|.+.+ +|++++||++.+.++-
T Consensus 46 id~~~g~i~v~~~--~~VV~d~~d~~~eI~l~eAk~~---~~~~~vGD~i~~~i~~ 96 (122)
T PF08529_consen 46 IDEDTGEIKVYRK--KEVVEDVEDPDTEISLSEAKKI---DPNAEVGDEIEEEIDP 96 (122)
T ss_dssp EETTTTEEEEEEE--EEEETT-S-TTTEEEHHHHHCC---CTT--TTCEEEEE---
T ss_pred EECCCCeEEEEEE--eeecCCccCccceeeHHHHHhh---CCCCccCCEEEecCCh
Confidence 4444555566553 23333 34556666666544 6889999999988864
No 77
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=28.85 E-value=69 Score=25.05 Aligned_cols=35 Identities=14% Similarity=0.377 Sum_probs=27.9
Q ss_pred EEeeCCeeEEEccCceEEeeCCCCccCCCeEEEecCCCc
Q 029038 65 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNK 103 (200)
Q Consensus 65 ~~~~gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~k 103 (200)
.++.+|+.++ +|.... |...+|+||.|.|.+....
T Consensus 29 ~~~~~GrV~v---NG~~aK-pS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 29 EMIEGGRVKV---NGQRAK-PSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHHHCCeEEE---CCEEcc-cccccCCCCEEEEEeCCcE
Confidence 3467888888 577775 7789999999999998744
No 78
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=28.81 E-value=73 Score=31.55 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=33.4
Q ss_pred CCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 91 ANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 91 ~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
-+|+.-|+.|.+.+-. -|..|+++-|+.|.+.+.+|.|..|+.
T Consensus 123 ~~~~~rl~~p~~~lRk--~f~~gD~vkVI~g~~~~d~g~V~rI~~ 165 (607)
T COG5164 123 YHFEQRLCGPWGRLRK--GFYKGDLVKVIEGGEMVDIGTVPRIDG 165 (607)
T ss_pred eccCceeecchhhhhc--ccccCCeEEEeccccccccceEEEecC
Confidence 3456666666555433 478999999999999999999999975
No 79
>KOG3586 consensus TBX1 and related T-box transcription factors [Transcription]
Probab=28.75 E-value=79 Score=30.45 Aligned_cols=99 Identities=22% Similarity=0.289 Sum_probs=65.6
Q ss_pred eeeEEEEecCCCceEEEEEcC-------------CCceEEEEcCccc--------cceeeEEEEEEEEeeCCeeEEEccC
Q 029038 20 GFMDVVSIPKTNENFRLLYDT-------------KGRFRLHSIRDEE--------AKFKLCKVRSVQFGQKGIPYINTYD 78 (200)
Q Consensus 20 G~MDVIsI~kt~e~yRvl~d~-------------kgrf~l~~I~~eE--------a~~KLcKV~~k~~~~gG~~ql~~hD 78 (200)
=+|||+-++ ++.||-.|.. .+|+.+|+=++-. .+|-=+|.+|..+-++|++.||.-.
T Consensus 128 vlmDvVPvD--~KRYRYayH~S~WlvAGkADp~~p~R~yvHPDSP~sGe~wmkqiVSFdK~KLTNNelD~nGHIILNSMH 205 (437)
T KOG3586|consen 128 VLMDVVPVD--SKRYRYAYHSSSWLVAGKADPAPPPRVYVHPDSPASGEQWMKQIVSFDKLKLTNNELDDNGHIILNSMH 205 (437)
T ss_pred EEEeEEecc--cceeeeeecccceeeecCCCCCCCCceeeCCCCCCCHHHHHHhhhchheeeccccccccCCcEeeeccc
Confidence 489999996 7999999974 5788888755432 1344478899999999999998654
Q ss_pred ceE----EeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcc
Q 029038 79 GRT----IRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNR 124 (200)
Q Consensus 79 Grn----i~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~ 124 (200)
--- |.+-|+. +|+.+....+ +=...|-|+|=..--||.=.|.
T Consensus 206 kYQPRvHvV~~~~~---~~s~~~~~~~-e~~kTF~FpET~FtAVTAYQNq 251 (437)
T KOG3586|consen 206 KYQPRVHVVYLDPG---NDSNKYVEKN-EGFKTFVFPETVFTAVTAYQNQ 251 (437)
T ss_pred ccCCceEEEEecCC---CCcccccccc-ccceeEeccceeEEEEeecccc
Confidence 322 3333332 1666655543 2235667777666666665554
No 80
>PF13620 CarboxypepD_reg: Carboxypeptidase regulatory-like domain; PDB: 3MN8_D 3P0D_I 3KCP_A 2B59_B 1UWY_A 1H8L_A 1QMU_A 2NSM_A.
Probab=28.38 E-value=1.2e+02 Score=20.75 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=30.7
Q ss_pred ECCEEeccCCCCceeeEEEEe-cCCCceEEEEEcCCCceEEEEcCc
Q 029038 7 VDAKVRTDKTYPAGFMDVVSI-PKTNENFRLLYDTKGRFRLHSIRD 51 (200)
Q Consensus 7 VDGkvr~D~k~PvG~MDVIsI-~kt~e~yRvl~d~kgrf~l~~I~~ 51 (200)
|-|+|+..-.-|+--..|.-. ...+..+...-|.+|+|.+-.+++
T Consensus 2 I~G~V~d~~g~pv~~a~V~l~~~~~~~~~~~~Td~~G~f~~~~l~~ 47 (82)
T PF13620_consen 2 ISGTVTDATGQPVPGATVTLTDQDGGTVYTTTTDSDGRFSFEGLPP 47 (82)
T ss_dssp EEEEEEETTSCBHTT-EEEET--TTTECCEEE--TTSEEEEEEE-S
T ss_pred EEEEEEcCCCCCcCCEEEEEEEeeCCCEEEEEECCCceEEEEccCC
Confidence 456777666677776666544 256788999999999999998877
No 81
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=28.36 E-value=3.4e+02 Score=25.72 Aligned_cols=53 Identities=26% Similarity=0.306 Sum_probs=36.0
Q ss_pred CccCCCeEEEecCCCceeEEEEe----eCCcEEEEECCCcceeEEEEEEEEEecCCcc
Q 029038 88 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNREKHKGSFE 141 (200)
Q Consensus 88 ~ik~~DTv~i~l~~~kI~~~i~f----e~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~ 141 (200)
.++.||...+.|...+-+-.-+| .-|..++.-+|+-+| .|.|.++....||..
T Consensus 381 ~l~~g~~a~v~l~~~~pi~~e~~~~~~~lgrfilrd~g~tva-~G~I~~v~~~~~~~~ 437 (446)
T PTZ00141 381 AIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRDMKQTVA-VGVIKSVEKKEGSGT 437 (446)
T ss_pred EECCCCEEEEEEEECCceEEeecccCCCCccEEEEECCCEEE-EEEEEEEecCCCcce
Confidence 57889999998875553333333 246677777776555 899999886666643
No 82
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=28.12 E-value=1.4e+02 Score=20.78 Aligned_cols=36 Identities=22% Similarity=0.286 Sum_probs=23.9
Q ss_pred CCeeEEEccCceEEeeCCCCccCCCeEEEecCCCcee
Q 029038 69 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 105 (200)
Q Consensus 69 gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~ 105 (200)
+..-...|..|-.|.+|. -++.||.|++|-.+++-+
T Consensus 19 ~~~K~A~letG~~i~VP~-FI~~Gd~I~VdT~~g~Yv 54 (56)
T PF09285_consen 19 SSYKPATLETGAEIQVPL-FIEEGDKIKVDTRDGSYV 54 (56)
T ss_dssp TTEEEEEETTS-EEEEET-T--TT-EEEEETTTTEEE
T ss_pred CCccEEEEcCCCEEEccc-eecCCCEEEEECCCCeEe
Confidence 334556677888888664 799999999999997643
No 83
>PF01063 Aminotran_4: Aminotransferase class IV; InterPro: IPR001544 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the pyridoxal-phosphate-lysine. The D-amino acid transferases (D-AAT), which are among the members of this entry, are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity [, ]. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1EKV_A 2HGX_A 1EKP_A 1KTA_B 1KT8_B 2A1H_B 2HDK_A 2HGW_B 1EKF_B 2HG8_A ....
Probab=27.57 E-value=1.4e+02 Score=24.56 Aligned_cols=45 Identities=18% Similarity=0.216 Sum_probs=33.9
Q ss_pred ccEEEEEcCCCCeEeEeeccEEEEccCCCceEeCcCCCceeeehhHH
Q 029038 140 FETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEE 186 (200)
Q Consensus 140 ~~iV~v~d~~g~~F~T~~~~vfvIG~~~~p~isLp~~~gi~~~~~e~ 186 (200)
++-+.+-|.+|+.-|+..+|+|++= +.-|++-|.+.|+-..+..+
T Consensus 125 ~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~giL~Gitr~ 169 (231)
T PF01063_consen 125 ADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGILPGITRQ 169 (231)
T ss_dssp SSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSSB--HHHH
T ss_pred cchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhhccHHHHH
Confidence 3435566889999999999999993 33488989898888887666
No 84
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=27.46 E-value=1.1e+02 Score=26.70 Aligned_cols=44 Identities=16% Similarity=0.112 Sum_probs=32.4
Q ss_pred CccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcce----eEEEEEEEEEec
Q 029038 88 LIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRG----RVGIIKNREKHK 137 (200)
Q Consensus 88 ~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G----~vG~I~~i~~~~ 137 (200)
.|++||.|-+.= ++|.|+.....--++|+|+| +||.|.+|....
T Consensus 7 ~Y~vgD~VYv~p------~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k 54 (202)
T cd04708 7 TYSVGDFLYVSP------DAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEK 54 (202)
T ss_pred EEecCCeEEECc------ccccccccccccccccccCCCCCcEEEEEEEEEecc
Confidence 477788877765 45566666777788899976 799999996544
No 85
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=27.20 E-value=1e+02 Score=32.88 Aligned_cols=27 Identities=33% Similarity=0.602 Sum_probs=25.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
-|++|+.|=|+.|+|-|..|.|+.++.
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeC
Confidence 389999999999999999999999986
No 86
>PF02239 Cytochrom_D1: Cytochrome D1 heme domain; PDB: 1NNO_B 1HZU_A 1N15_B 1N50_A 1GJQ_A 1BL9_B 1NIR_B 1N90_B 1HZV_A 1AOQ_A ....
Probab=27.04 E-value=4.4e+02 Score=24.20 Aligned_cols=70 Identities=14% Similarity=0.166 Sum_probs=39.0
Q ss_pred EEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCceEEeeCCCCccCCCeEEEecCCCceeEEEEee
Q 029038 34 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFD 111 (200)
Q Consensus 34 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe 111 (200)
|-.+.+..|.+.+.-+... | .|..+.++.+..-.-...|||-+-.. .+..++..++|..+.+++..|+-.
T Consensus 50 ~~yv~~rdg~vsviD~~~~----~--~v~~i~~G~~~~~i~~s~DG~~~~v~--n~~~~~v~v~D~~tle~v~~I~~~ 119 (369)
T PF02239_consen 50 YLYVANRDGTVSVIDLATG----K--VVATIKVGGNPRGIAVSPDGKYVYVA--NYEPGTVSVIDAETLEPVKTIPTG 119 (369)
T ss_dssp EEEEEETTSEEEEEETTSS----S--EEEEEE-SSEEEEEEE--TTTEEEEE--EEETTEEEEEETTT--EEEEEE--
T ss_pred EEEEEcCCCeEEEEECCcc----c--EEEEEecCCCcceEEEcCCCCEEEEE--ecCCCceeEeccccccceeecccc
Confidence 3344455665554444222 2 23334445554445567799987544 377889999999999999988764
No 87
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=27.03 E-value=3.4e+02 Score=29.16 Aligned_cols=54 Identities=22% Similarity=0.289 Sum_probs=41.6
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeeccEEEEcc
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 165 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~~vfvIG~ 165 (200)
...++.+-+++|.|.|+-|.|.+|.+.. =..+.-++| ++-.|.++..|+..+|.
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~E--n~Gv~vck~k~~~~~g~ 636 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLE--NGGVFVCKEKNLILAGG 636 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecceeeeeehhhcc--cCCeEEEecCCceeccc
Confidence 4578999999999999999999996422 111233344 56689999999999997
No 88
>cd03707 EFTU_III Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix
Probab=26.83 E-value=2.4e+02 Score=20.08 Aligned_cols=27 Identities=19% Similarity=0.316 Sum_probs=16.3
Q ss_pred ccCCCeEEEecCCCceeEEEEeeCCcEEEE
Q 029038 89 IKANDTIKLDLETNKITEFIKFDVGNVVMV 118 (200)
Q Consensus 89 ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v 118 (200)
+++||+..+.|.-.+ -+.+++|.-.++
T Consensus 52 i~~g~~~~v~l~l~~---pv~~~~~~rf~l 78 (90)
T cd03707 52 VMPGDNVKMTVELIH---PIALEKGLRFAI 78 (90)
T ss_pred cCCCCEEEEEEEECC---cEEEecCCEEEE
Confidence 888888888776433 234455544444
No 89
>PF07569 Hira: TUP1-like enhancer of split; InterPro: IPR011494 The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain IPR001680 from INTERPRO.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.78 E-value=2.2e+02 Score=24.30 Aligned_cols=57 Identities=16% Similarity=0.359 Sum_probs=42.8
Q ss_pred CCceEEEEEcCCCceEEEEcCccccceee------------------EEEEEEEEeeCCeeEEEccCceEEeeCC
Q 029038 30 TNENFRLLYDTKGRFRLHSIRDEEAKFKL------------------CKVRSVQFGQKGIPYINTYDGRTIRYPD 86 (200)
Q Consensus 30 t~e~yRvl~d~kgrf~l~~I~~eEa~~KL------------------cKV~~k~~~~gG~~ql~~hDGrni~~~d 86 (200)
...+|-+.....|.|.+=.+....+-++- ..|+...+-+.|.|.+.+.+|..+.|..
T Consensus 20 ~~~~~Ll~iT~~G~l~vWnl~~~k~~~~~~Si~pll~~~~~~~~~~~~~i~~~~lt~~G~PiV~lsng~~y~y~~ 94 (219)
T PF07569_consen 20 CNGSYLLAITSSGLLYVWNLKKGKAVLPPVSIAPLLNSSPVSDKSSSPNITSCSLTSNGVPIVTLSNGDSYSYSP 94 (219)
T ss_pred eCCCEEEEEeCCCeEEEEECCCCeeccCCccHHHHhcccccccCCCCCcEEEEEEcCCCCEEEEEeCCCEEEecc
Confidence 46777777888888877766655554444 5677777778999999999999988753
No 90
>PRK10708 hypothetical protein; Provisional
Probab=26.63 E-value=1.3e+02 Score=21.57 Aligned_cols=29 Identities=21% Similarity=0.428 Sum_probs=16.8
Q ss_pred cCCCeEEEecC-----CCceeEEEEeeCCcEEEE
Q 029038 90 KANDTIKLDLE-----TNKITEFIKFDVGNVVMV 118 (200)
Q Consensus 90 k~~DTv~i~l~-----~~kI~~~i~fe~G~~~~v 118 (200)
|+||.|.+.-. ++.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~iLavE~F~EG~MyLv 35 (62)
T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVEEFSEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCCccccceEEEEeeccCcEEEEE
Confidence 56666666554 344666666666655544
No 91
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=25.60 E-value=1.3e+02 Score=21.58 Aligned_cols=49 Identities=14% Similarity=0.286 Sum_probs=31.5
Q ss_pred eEEEEEEEEEecCC-ccEEEEEcCCCCeEeEeeccEEEEccCCCceEeCcCC
Q 029038 126 RVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKG 176 (200)
Q Consensus 126 ~vG~I~~i~~~~~s-~~iV~v~d~~g~~F~T~~~~vfvIG~~~~p~isLp~~ 176 (200)
-.|++.....++.= -.=++..+.+|+.| +..+.+|+=|. +=-+|++|.+
T Consensus 24 ~~G~L~~~D~~mNi~L~~~~~~~~~g~~~-~~~~~v~IRG~-~I~~i~~p~~ 73 (76)
T cd01723 24 YNGHLVNCDNWMNIHLREVICTSKDGDKF-WKMPECYIRGN-TIKYLRVPDE 73 (76)
T ss_pred EEEEEEEEcCCCceEEEeEEEECCCCcEe-eeCCcEEEeCC-EEEEEEcCHH
Confidence 46888888776522 12234455677664 35688999997 5556777753
No 92
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=25.34 E-value=81 Score=25.58 Aligned_cols=34 Identities=18% Similarity=0.281 Sum_probs=17.0
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCe
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHE 152 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~ 152 (200)
||++|+.+.+- |..|+|.+|.. . ..++++.+|+.
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l--~---~t~l~~~~g~~ 93 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGL--R---STRLRTWDGEI 93 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-S--S---EEEEEETTS-E
T ss_pred CccCCCEEEEE-----EeehHHHhcCc--c---eeeeecCCCCE
Confidence 45555553332 77888888842 1 25566667654
No 93
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=25.17 E-value=1.3e+02 Score=21.64 Aligned_cols=32 Identities=16% Similarity=0.004 Sum_probs=24.2
Q ss_pred eEEEEEEEEEec-CCccEEEEEcCCCCeEeEee
Q 029038 126 RVGIIKNREKHK-GSFETIHIQDALGHEFATRL 157 (200)
Q Consensus 126 ~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~ 157 (200)
-.|+|.+|+-.| .|.+++.|+..+|..|-.+.
T Consensus 33 ~~g~V~~i~~DP~Rsa~iAlV~~~~g~~~yiiA 65 (77)
T PF00181_consen 33 IKGIVIDIEYDPNRSAPIALVKYEDGEKRYIIA 65 (77)
T ss_dssp EEEEEEEEEEETTTSSEEEEEEETTSEEEEEEE
T ss_pred CcEEEEEEEecCCcCccEEEEEecCCcEEEEEe
Confidence 469999999888 55678888887877664443
No 94
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=25.07 E-value=2.2e+02 Score=22.81 Aligned_cols=77 Identities=17% Similarity=0.202 Sum_probs=44.6
Q ss_pred EEEccCceEEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCc-cEEEEEcCCCC
Q 029038 73 YINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQDALGH 151 (200)
Q Consensus 73 ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~-~iV~v~d~~g~ 151 (200)
+|.+|+|++-++.| +++.|.+.-...+ +.+++++.....|......|- ..|.=.++.. ..|+++=.-++
T Consensus 7 ~I~l~~G~~krvED--l~teDfi~sa~~s----~~~~l~~stv~~i~~~~~~~~----v~itF~~g~~~~~v~~ev~~eH 76 (116)
T smart00536 7 RLCLANGSNKKVED--LKTEDFIRSAECS----NDEEIQMSTVKRIGSSGLPSV----VTLTFDPGVEDALLTVECQVEH 76 (116)
T ss_pred EEEecCCCeeeeec--cchhhhHhhhccC----CcccccceeEEEeCCCCCcce----EEEEEEecCccceEEEEEecCC
Confidence 56679999887665 7888888776655 344555555555544332221 2233334433 36666644444
Q ss_pred eEeEeeccEEEEccC
Q 029038 152 EFATRLGNVFTIGKG 166 (200)
Q Consensus 152 ~F~T~~~~vfvIG~~ 166 (200)
.| ||-|+|
T Consensus 77 Pf-------FV~gqG 84 (116)
T smart00536 77 PF-------FVKGKG 84 (116)
T ss_pred Ce-------EEcCcc
Confidence 44 777875
No 95
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=23.44 E-value=1.3e+02 Score=26.61 Aligned_cols=26 Identities=27% Similarity=0.506 Sum_probs=12.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
|--|+.+=|.-|+..|+.|.+..+-+
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r 98 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIR 98 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEee
Confidence 33344444444555555555544443
No 96
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=23.30 E-value=2.6e+02 Score=19.35 Aligned_cols=42 Identities=17% Similarity=0.172 Sum_probs=25.5
Q ss_pred eEEEEEEEEeeCCeeEEEccCceEEeeCCC-------CccCCCeEEEecCC
Q 029038 58 LCKVRSVQFGQKGIPYINTYDGRTIRYPDP-------LIKANDTIKLDLET 101 (200)
Q Consensus 58 LcKV~~k~~~~gG~~ql~~hDGrni~~~d~-------~ik~~DTv~i~l~~ 101 (200)
+|+|.. ...++...+.+.||.+++..=| -++.||.|++++..
T Consensus 6 ~~~V~~--~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~ 54 (65)
T PF01176_consen 6 IGRVTE--MLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSP 54 (65)
T ss_dssp EEEEEE--EESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEEST
T ss_pred EEEEEE--ECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecc
Confidence 466654 3455577777788887554322 57899999998764
No 97
>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=22.62 E-value=98 Score=27.94 Aligned_cols=30 Identities=40% Similarity=0.637 Sum_probs=27.1
Q ss_pred EEEEeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038 106 EFIKFDVGNVVMVTGGRNRGRVGIIKNREK 135 (200)
Q Consensus 106 ~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~ 135 (200)
..+.|++|..+-|+.|.=.|..|+|.++..
T Consensus 202 ~~~~f~vGd~VrI~dGPF~GfeG~I~eid~ 231 (258)
T TIGR01956 202 NLSKFRVGNFVKIVDGPFKGIVGKIKKIDQ 231 (258)
T ss_pred cccCCCCCCEEEEEecCCCCcEEEEEEEeC
Confidence 457799999999999999999999999863
No 98
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=22.61 E-value=2.7e+02 Score=19.34 Aligned_cols=55 Identities=13% Similarity=0.125 Sum_probs=29.4
Q ss_pred eCCcEEEEECCCcceeEE-EEEEEEEecCCccEEEEEcCCCCeEeEeeccEEEEcc
Q 029038 111 DVGNVVMVTGGRNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 165 (200)
Q Consensus 111 e~G~~~~v~gG~n~G~vG-~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~vfvIG~ 165 (200)
.+|+.++...+.+..... .+.......+..+++.|+..+|.++..-.+.-|.+.+
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 456666666653222111 1122222345567888888888777655555555444
No 99
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=22.23 E-value=1.5e+02 Score=22.60 Aligned_cols=56 Identities=23% Similarity=0.265 Sum_probs=36.1
Q ss_pred eeEEEEEEEEeeCCeeEEEccC-c-eEEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCC
Q 029038 57 KLCKVRSVQFGQKGIPYINTYD-G-RTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGR 122 (200)
Q Consensus 57 KLcKV~~k~~~~gG~~ql~~hD-G-rni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~ 122 (200)
.-|.+...+.-+|+....++|+ + .++-+-+ -.+.+.+.. +...+.+|+...+=-|.
T Consensus 41 ~~~~~~~v~~~~G~~~~~H~hp~~~~~~~Vl~------G~~~~~~~g----~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 41 ENLSVVLVTFEPGAVIPWHTHPLGEQTIYVLE------GEGTVQLEG----EKKELKAGDVIIIPPGV 98 (131)
T ss_pred ceEEEEEEEECCCcccccccCCCcceEEEEEe------cEEEEEecC----CceEecCCCEEEECCCC
Confidence 4588899999999999999998 6 4443222 234444442 44556667666665543
No 100
>PF05709 Sipho_tail: Phage tail protein; InterPro: IPR008841 This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 4DIV_X 2X8K_C.
Probab=22.06 E-value=3.8e+02 Score=21.94 Aligned_cols=34 Identities=26% Similarity=0.351 Sum_probs=18.8
Q ss_pred CCeeEEEccCceEEeeCCC---CccCCCeEEEecCCCc
Q 029038 69 KGIPYINTYDGRTIRYPDP---LIKANDTIKLDLETNK 103 (200)
Q Consensus 69 gG~~ql~~hDGrni~~~d~---~ik~~DTv~i~l~~~k 103 (200)
...++++..++ .+.+.++ ++..||+++||-+.+.
T Consensus 161 ~~~~~i~~~~~-~~~~~~~~~~~~~~gd~i~Id~~~~~ 197 (249)
T PF05709_consen 161 SSNITINNGQT-VFQFGNPKEIDLTAGDTIVIDSEKDT 197 (249)
T ss_dssp SSSEEEEECCT-EEEEE-EE----STSCEEEECCTTCE
T ss_pred ccEEEEecCce-eEEecCccccccCCCcEEEEECCCCE
Confidence 33456666555 4443332 3788899999865443
No 101
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=21.89 E-value=97 Score=24.80 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=24.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEEEE
Q 029038 109 KFDVGNVVMVTGGRNRGRVGIIKNRE 134 (200)
Q Consensus 109 ~fe~G~~~~v~gG~n~G~vG~I~~i~ 134 (200)
.|++|..+.|++|.=.|..|.|.++.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 58999999999999999999999874
No 102
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=21.83 E-value=95 Score=26.16 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=26.3
Q ss_pred EEEEeeCCcEEEEECCCcceeEEEEEEEE
Q 029038 106 EFIKFDVGNVVMVTGGRNRGRVGIIKNRE 134 (200)
Q Consensus 106 ~~i~fe~G~~~~v~gG~n~G~vG~I~~i~ 134 (200)
....|++|+.+-|+.|.=.|..|+|.++.
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd 148 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVD 148 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEc
Confidence 45679999999999999999999999986
No 103
>cd05774 Ig_CEACAM_D1 First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM). IG_CEACAM_D1: immunoglobulin (Ig)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surface. This family corresponds to the D
Probab=21.34 E-value=1.5e+02 Score=22.46 Aligned_cols=32 Identities=9% Similarity=0.153 Sum_probs=27.0
Q ss_pred EEEEEcCCCceEEEEcCccccceeeEEEEEEE
Q 029038 34 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQ 65 (200)
Q Consensus 34 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~ 65 (200)
-|.....+|.|.++.++.+++.+-.|.+.+..
T Consensus 62 gR~~~~~ngSL~I~~v~~~D~G~Y~~~v~~~~ 93 (105)
T cd05774 62 GRETIYPNGSLLIQNVTQKDTGFYTLQTITTN 93 (105)
T ss_pred CcEEEeCCCcEEEecCCcccCEEEEEEEEeCC
Confidence 36666778999999999999999999997754
No 104
>PF08269 Cache_2: Cache domain; InterPro: IPR013163 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions []. This entry is composed of the type 2 Cache domain.; PDB: 2QHK_A 4EXO_A.
Probab=21.11 E-value=83 Score=22.69 Aligned_cols=22 Identities=23% Similarity=0.481 Sum_probs=15.3
Q ss_pred CceEEEEEcCCCceEEEEcCcc
Q 029038 31 NENFRLLYDTKGRFRLHSIRDE 52 (200)
Q Consensus 31 ~e~yRvl~d~kgrf~l~~I~~e 52 (200)
+..|-.+||.+|.+.+||..++
T Consensus 55 ~~gY~fi~d~~g~~l~hp~~p~ 76 (95)
T PF08269_consen 55 GDGYFFIYDMDGVVLAHPSNPE 76 (95)
T ss_dssp TTB--EEE-TTSBEEEESS-GG
T ss_pred CCCeEEEEeCCCeEEEcCCCcc
Confidence 4678899999999999998554
No 105
>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=20.56 E-value=2.4e+02 Score=20.84 Aligned_cols=32 Identities=25% Similarity=0.412 Sum_probs=23.5
Q ss_pred eeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCC
Q 029038 110 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALG 150 (200)
Q Consensus 110 fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g 150 (200)
+.+|+.++.+|| -+|+|.++.. +.+.++.+.|
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d-----~~v~vei~~g 69 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAE-----NTIVIELNDN 69 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCC
Confidence 567888888775 5799998862 4577777665
No 106
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=20.43 E-value=88 Score=28.10 Aligned_cols=98 Identities=21% Similarity=0.347 Sum_probs=57.2
Q ss_pred CCccEEECCEEeccCCCCceeeEEEEecCCCceEE-------------EEEcCCCceEEEEcCccccceeeE-------E
Q 029038 1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFR-------------LLYDTKGRFRLHSIRDEEAKFKLC-------K 60 (200)
Q Consensus 1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yR-------------vl~d~kgrf~l~~I~~eEa~~KLc-------K 60 (200)
|.|+|+|||...+-+.+=|-.-+.|++......|. .=.|.+|+-++- |-+....|=.| +
T Consensus 26 ~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~yVSRG~~KL~~ale~F~l~~k~kv~LD-iGsSTGGFTd~lLq~gAk~ 104 (245)
T COG1189 26 LAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFELDVKGKVVLD-IGSSTGGFTDVLLQRGAKH 104 (245)
T ss_pred HcCeEEECCEEecCcceecCCCceEEEcccCcCccccHHHHHHHHHHhcCcCCCCCEEEE-ecCCCccHHHHHHHcCCcE
Confidence 57999999999999999999999999975444432 113555554432 33333222222 3
Q ss_pred EEEEEEee-------CCeeEEEccCceEEeeCCCC--ccCCCeEEEec
Q 029038 61 VRSVQFGQ-------KGIPYINTYDGRTIRYPDPL--IKANDTIKLDL 99 (200)
Q Consensus 61 V~~k~~~~-------gG~~ql~~hDGrni~~~d~~--ik~~DTv~i~l 99 (200)
|-..-++. ...|.+......|+||-.|. ...-|-+++|+
T Consensus 105 VyavDVG~~Ql~~kLR~d~rV~~~E~tN~r~l~~~~~~~~~d~~v~Dv 152 (245)
T COG1189 105 VYAVDVGYGQLHWKLRNDPRVIVLERTNVRYLTPEDFTEKPDLIVIDV 152 (245)
T ss_pred EEEEEccCCccCHhHhcCCcEEEEecCChhhCCHHHcccCCCeEEEEe
Confidence 33444444 23455566666777765443 22335555555
No 107
>PRK09790 hypothetical protein; Reviewed
Probab=20.22 E-value=2.1e+02 Score=21.53 Aligned_cols=48 Identities=27% Similarity=0.454 Sum_probs=28.8
Q ss_pred CCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeecc-----EEEEccCCCceEeCcCCC
Q 029038 120 GGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGN-----VFTIGKGTKPWVSLPKGK 177 (200)
Q Consensus 120 gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~-----vfvIG~~~~p~isLp~~~ 177 (200)
.|+|.|- +..-|-..-.|.+|-+...+|+ |.|..+- +.-||+ .||.+|
T Consensus 22 egk~igy---viktenketpftvvdidg~sgn-~ktl~eg~~kmclv~ig~------nlpaek 74 (91)
T PRK09790 22 EGKRIGY---VIKTENKETPFTVVDIDGPSGN-VKTLDEGVKKMCLVHIGK------NLPAEK 74 (91)
T ss_pred cCcEEEE---EEEecCCCCCeEEEeccCCCCc-eeEhhhccceEEEEEecC------CCCccc
Confidence 4666554 3444444456777777666665 8887543 345777 677664
Done!