Query 023289
Match_columns 284
No_of_seqs 109 out of 335
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 02:54:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023289.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023289hhsearch_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 2E-103 5E-108 722.8 29.2 240 43-282 21-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 4E-103 9E-108 721.4 29.6 241 43-283 21-261 (262)
3 PTZ00223 40S ribosomal protein 100.0 1E-102 2E-107 721.7 29.9 241 43-283 18-259 (273)
4 PRK04313 30S ribosomal protein 100.0 1E-95 2E-100 664.8 27.6 219 43-262 17-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 2E-92 4.3E-97 639.5 24.0 221 43-264 20-241 (241)
6 KOG0378 40S ribosomal protein 100.0 2.2E-90 4.8E-95 629.1 15.5 242 43-284 21-262 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 5.4E-34 1.2E-38 220.9 10.0 77 116-192 1-77 (77)
8 PF01479 S4: S4 domain; Inter 98.5 2.2E-07 4.8E-12 64.4 5.3 48 64-112 1-48 (48)
9 PF08071 RS4NT: RS4NT (NUC023) 98.1 1.2E-06 2.6E-11 60.3 1.2 20 43-62 19-38 (38)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.5 0.00053 1.2E-08 47.8 7.3 61 65-126 2-62 (70)
11 smart00363 S4 S4 RNA-binding d 97.2 0.0011 2.4E-08 44.9 5.5 50 66-116 3-52 (60)
12 PF00467 KOW: KOW motif; Inte 96.7 0.0017 3.7E-08 42.3 3.1 31 199-232 1-31 (32)
13 smart00739 KOW KOW (Kyprides, 96.7 0.0016 3.6E-08 40.0 2.7 27 196-222 1-27 (28)
14 COG0522 RpsD Ribosomal protein 96.7 0.0017 3.7E-08 59.1 3.9 43 73-115 102-144 (205)
15 TIGR02988 YaaA_near_RecF S4 do 96.6 0.0055 1.2E-07 44.4 5.7 51 64-115 9-59 (59)
16 PF13275 S4_2: S4 domain; PDB: 95.7 0.0056 1.2E-07 46.6 1.7 60 62-124 6-65 (65)
17 TIGR01018 rpsD_arch ribosomal 95.3 0.014 3E-07 51.6 3.0 43 73-115 112-156 (162)
18 PRK11507 ribosome-associated p 95.2 0.088 1.9E-06 40.8 6.7 60 62-124 10-69 (70)
19 PTZ00155 40S ribosomal protein 95.1 0.016 3.6E-07 52.0 2.9 38 68-105 103-147 (181)
20 PLN00189 40S ribosomal protein 95.0 0.02 4.3E-07 52.0 3.1 41 73-113 117-157 (194)
21 TIGR01017 rpsD_bact ribosomal 94.8 0.048 1E-06 49.2 5.0 43 74-116 99-141 (200)
22 TIGR00005 rluA_subfam pseudour 94.7 0.14 3E-06 47.6 8.0 53 62-115 4-56 (299)
23 PRK04051 rps4p 30S ribosomal p 94.7 0.033 7E-07 49.9 3.7 44 74-117 112-157 (177)
24 PRK05327 rpsD 30S ribosomal pr 94.6 0.062 1.3E-06 48.6 5.1 43 74-116 102-144 (203)
25 TIGR01080 rplX_A_E ribosomal p 94.5 0.084 1.8E-06 44.3 5.3 55 193-250 38-99 (114)
26 CHL00113 rps4 ribosomal protei 94.4 0.064 1.4E-06 48.7 4.9 43 74-116 98-140 (201)
27 TIGR03069 PS_II_S4 photosystem 94.1 0.18 3.8E-06 47.2 7.2 63 62-137 182-244 (257)
28 TIGR00478 tly hemolysin TlyA f 93.0 0.18 3.9E-06 46.4 5.3 47 69-116 5-51 (228)
29 COG2501 S4-like RNA binding pr 91.8 0.67 1.4E-05 36.3 6.3 60 62-124 10-69 (73)
30 PRK11180 rluD 23S rRNA pseudou 91.7 0.63 1.4E-05 44.3 7.4 52 63-115 17-68 (325)
31 COG0564 RluA Pseudouridylate s 91.6 0.51 1.1E-05 44.8 6.6 57 62-121 11-67 (289)
32 PRK01191 rpl24p 50S ribosomal 90.5 0.65 1.4E-05 39.5 5.5 38 194-234 43-80 (120)
33 PRK05912 tyrosyl-tRNA syntheta 90.3 0.97 2.1E-05 44.9 7.4 65 63-134 342-406 (408)
34 PRK10700 23S rRNA pseudouridyl 90.0 0.93 2E-05 42.9 6.8 65 66-133 5-81 (289)
35 PRK10348 ribosome-associated h 89.0 1 2.2E-05 38.8 5.7 59 63-123 8-66 (133)
36 PRK12281 rplX 50S ribosomal pr 88.6 0.7 1.5E-05 36.1 4.0 39 195-236 5-43 (76)
37 COG1187 RsuA 16S rRNA uridine- 88.5 1.1 2.3E-05 42.2 5.9 59 75-134 13-78 (248)
38 PRK10475 23S rRNA pseudouridin 88.2 2 4.2E-05 41.0 7.5 68 62-132 5-80 (290)
39 CHL00141 rpl24 ribosomal prote 88.0 0.85 1.8E-05 36.1 4.2 39 194-235 6-44 (83)
40 PRK11025 23S rRNA pseudouridyl 87.7 2.3 4.9E-05 40.4 7.7 51 63-115 19-69 (317)
41 PRK00004 rplX 50S ribosomal pr 87.0 0.89 1.9E-05 37.4 3.9 37 195-234 3-39 (105)
42 PRK10839 16S rRNA pseudouridyl 86.9 3.1 6.8E-05 37.4 7.8 67 66-135 3-75 (232)
43 PLN00051 RNA-binding S4 domain 85.3 3.5 7.5E-05 39.1 7.5 62 63-137 191-252 (267)
44 PRK13354 tyrosyl-tRNA syntheta 85.0 3.1 6.8E-05 41.4 7.3 66 63-134 342-407 (410)
45 COG2302 Uncharacterized conser 84.8 2.2 4.7E-05 40.6 5.8 63 62-137 179-241 (257)
46 COG1189 Predicted rRNA methyla 84.6 2 4.3E-05 40.6 5.4 111 75-186 13-152 (245)
47 PTZ00194 60S ribosomal protein 84.0 2.5 5.5E-05 36.9 5.5 54 195-251 45-105 (143)
48 TIGR01079 rplX_bact ribosomal 82.4 1.9 4.1E-05 35.5 3.9 28 196-223 3-30 (104)
49 PF13051 DUF3912: Protein of u 79.4 4.8 0.0001 30.7 4.8 50 199-252 5-55 (68)
50 COG0162 TyrS Tyrosyl-tRNA synt 63.7 15 0.00033 36.9 5.7 62 66-135 338-399 (401)
51 KOG4655 U3 small nucleolar rib 63.5 5.3 0.00011 36.1 2.2 55 52-106 87-148 (181)
52 COG0198 RplX Ribosomal protein 60.9 12 0.00027 31.1 3.8 29 195-223 3-31 (104)
53 COG2163 RPL14A Ribosomal prote 59.0 9.8 0.00021 32.6 3.0 34 197-234 5-38 (125)
54 PF03417 AAT: Acyl-coenzyme A: 57.4 27 0.00058 30.9 5.7 29 61-90 69-97 (225)
55 PF14001 YdfZ: YdfZ protein 55.0 19 0.00041 27.8 3.6 42 196-241 9-56 (64)
56 PTZ00065 60S ribosomal protein 52.9 16 0.00034 31.6 3.3 32 197-232 8-39 (130)
57 COG1188 Ribosome-associated he 48.9 43 0.00093 27.8 5.1 46 75-121 19-64 (100)
58 PRK04333 50S ribosomal protein 45.5 23 0.0005 28.2 3.0 33 196-232 3-35 (84)
59 PF04773 FecR: FecR protein; 45.5 1.3E+02 0.0028 22.5 8.8 66 151-216 3-75 (98)
60 PRK02290 3-dehydroquinate synt 42.6 98 0.0021 30.8 7.3 43 144-188 278-328 (344)
61 PF08828 DSX_dimer: Doublesex 42.3 16 0.00034 28.0 1.5 34 61-97 21-55 (62)
62 PF06905 FAIM1: Fas apoptotic 42.0 2.6E+02 0.0057 25.2 9.5 63 152-216 69-133 (177)
63 cd03704 eRF3c_III This family 41.5 74 0.0016 25.1 5.4 48 172-220 56-108 (108)
64 cd03706 mtEFTU_III Domain III 40.0 1.5E+02 0.0032 22.8 6.7 40 176-219 52-92 (93)
65 PRK14898 DNA-directed RNA poly 38.9 1.4E+02 0.003 32.9 8.5 77 106-184 112-195 (858)
66 PF01588 tRNA_bind: Putative t 37.9 71 0.0015 25.1 4.7 19 213-231 2-20 (95)
67 TIGR00405 L26e_arch ribosomal 36.5 61 0.0013 27.1 4.3 26 197-222 87-112 (145)
68 PRK08559 nusG transcription an 36.2 56 0.0012 28.1 4.2 29 195-223 93-121 (153)
69 PF01959 DHQS: 3-dehydroquinat 35.9 79 0.0017 31.6 5.6 55 144-213 288-345 (354)
70 PTZ00471 60S ribosomal protein 35.7 37 0.0008 29.6 2.9 24 197-220 5-28 (134)
71 KOG1784 Small Nuclear ribonucl 35.5 69 0.0015 26.4 4.3 60 156-219 10-75 (96)
72 cd04478 RPA2_DBD_D RPA2_DBD_D: 33.6 2.1E+02 0.0046 21.7 6.7 57 111-167 8-75 (95)
73 cd04093 HBS1_C HBS1_C: this fa 33.3 2.3E+02 0.005 22.0 9.0 42 175-220 59-107 (107)
74 COG1792 MreC Cell shape-determ 32.3 4.5E+02 0.0098 25.0 11.8 61 172-252 209-270 (284)
75 PF07076 DUF1344: Protein of u 31.9 1E+02 0.0022 23.5 4.4 35 153-187 11-49 (61)
76 TIGR03193 4hydroxCoAred 4-hydr 31.7 40 0.00086 29.6 2.5 54 61-118 16-77 (148)
77 PRK05609 nusG transcription an 31.1 54 0.0012 28.2 3.2 29 194-222 124-152 (181)
78 cd02899 PLAT_SR Scavenger rece 30.8 1.7E+02 0.0037 24.2 6.0 61 197-270 41-108 (109)
79 KOG1999 RNA polymerase II tran 30.4 74 0.0016 35.7 4.7 27 197-223 460-486 (1024)
80 TIGR03318 YdfZ_fam putative se 29.0 54 0.0012 25.4 2.5 41 197-241 11-57 (65)
81 TIGR00922 nusG transcription t 28.9 58 0.0012 27.8 3.0 28 195-222 118-145 (172)
82 cd03705 EF1_alpha_III Domain I 28.9 1.2E+02 0.0026 23.5 4.6 35 175-212 59-100 (104)
83 KOG1999 RNA polymerase II tran 28.6 1.3E+02 0.0028 34.0 6.1 55 197-255 582-638 (1024)
84 PF12961 DUF3850: Domain of Un 26.5 60 0.0013 25.4 2.4 17 169-185 22-38 (72)
85 TIGR01955 RfaH transcriptional 25.7 1.8E+02 0.0038 24.4 5.4 84 130-221 50-133 (159)
86 KOG3401 60S ribosomal protein 25.7 53 0.0012 29.0 2.2 50 190-239 42-94 (145)
87 cd01234 PH_CADPS CADPS (Ca2+-d 25.6 44 0.00096 28.4 1.7 42 128-174 21-62 (117)
88 PF01063 Aminotran_4: Aminotra 25.5 2.2E+02 0.0048 24.7 6.2 52 227-280 125-176 (231)
89 PF09285 Elong-fact-P_C: Elong 25.1 1.4E+02 0.003 22.2 4.0 37 155-192 18-54 (56)
90 smart00306 HintN Hint (Hedgeho 25.0 2.9E+02 0.0063 20.4 8.3 55 198-252 23-78 (100)
91 cd05892 Ig_Myotilin_C C-termin 24.2 1.5E+02 0.0032 22.1 4.2 34 118-151 28-63 (75)
92 PF08942 DUF1919: Domain of un 24.1 19 0.00042 33.1 -0.8 59 66-144 53-111 (201)
93 TIGR00234 tyrS tyrosyl-tRNA sy 24.1 74 0.0016 31.4 3.2 45 63-108 329-373 (377)
94 PF11717 Tudor-knot: RNA bindi 23.1 1.7E+02 0.0037 20.8 4.2 37 197-233 1-38 (55)
95 PF08529 NusA_N: NusA N-termin 23.0 81 0.0018 26.1 2.8 30 156-188 67-96 (122)
96 TIGR02888 spore_YlmC_YmxH spor 22.9 3.5E+02 0.0076 21.0 6.1 41 156-201 6-46 (76)
97 PF14505 DUF4438: Domain of un 22.7 79 0.0017 30.3 2.9 32 199-232 60-92 (258)
98 PTZ00141 elongation factor 1- 22.1 4.6E+02 0.01 26.3 8.4 52 175-227 381-436 (446)
99 KOG1708 Mitochondrial/chloropl 21.8 1.5E+02 0.0032 28.0 4.4 11 176-186 73-83 (236)
100 cd03707 EFTU_III Domain III of 21.6 3.6E+02 0.0078 20.3 6.4 27 176-205 52-78 (90)
101 PF02239 Cytochrom_D1: Cytochr 21.6 4.6E+02 0.01 25.5 8.1 71 120-198 49-119 (369)
102 PLN02772 guanylate kinase 21.4 2E+02 0.0042 29.2 5.5 63 194-256 28-98 (398)
103 smart00536 AXH domain in Ataxi 21.1 2.8E+02 0.006 23.7 5.6 77 160-253 7-84 (116)
104 PF03143 GTP_EFTU_D3: Elongati 21.1 2.3E+02 0.0051 22.2 5.0 43 175-220 56-98 (99)
105 PRK09014 rfaH transcriptional 20.6 1E+02 0.0022 26.2 3.0 26 196-221 109-134 (162)
106 TIGR00739 yajC preprotein tran 20.5 2.5E+02 0.0054 22.1 4.9 33 197-238 38-70 (84)
107 COG0250 NusG Transcription ant 20.2 1E+02 0.0022 27.6 3.0 30 193-222 120-149 (178)
108 cd05794 S1_EF-P_repeat_2 S1_EF 20.1 1.7E+02 0.0037 21.8 3.7 35 155-190 18-52 (56)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=2.2e-103 Score=722.82 Aligned_cols=240 Identities=86% Similarity=1.333 Sum_probs=236.7
Q ss_pred ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289 43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 122 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR 122 (284)
+|++++||||||||||+++|||||++||||+||||+|+|||++||+||+|+||||||||++||||||||||||++|||||
T Consensus 21 ~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yR 100 (261)
T PLN00036 21 DKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFR 100 (261)
T ss_pred ccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCCCCeEE
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289 123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI 202 (284)
Q Consensus 123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~ 202 (284)
|+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||+||+||||+||+|+|||+||+|||+||+
T Consensus 101 vl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l 180 (261)
T PLN00036 101 LLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNL 180 (261)
T ss_pred EEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEEEEeCCCCceeeEEecCCCCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHHHH
Q 023289 203 VMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 282 (284)
Q Consensus 203 ~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~~~e~r~~~~~~~~ 282 (284)
||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++++||||||++||||++++|||++++++.+
T Consensus 181 ~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~~e~r~~~~~~~~ 260 (261)
T PLN00036 181 VMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKRLAAGQ 260 (261)
T ss_pred EEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccchHHHHHHhhhhhc
Confidence 99999999999999999999999999999999999999999999999998899999999999999999999999998764
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=4e-103 Score=721.39 Aligned_cols=241 Identities=60% Similarity=0.975 Sum_probs=237.7
Q ss_pred ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289 43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 122 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR 122 (284)
+|++++||||||||||+++|||||++||||+|+||+|+|||++||+||+|+||||||||++||||||||||||++|||||
T Consensus 21 ~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yR 100 (262)
T PTZ00118 21 DKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFR 100 (262)
T ss_pred ccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCCCCeEE
Confidence 68889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289 123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI 202 (284)
Q Consensus 123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~ 202 (284)
|+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+||+|+|||+||+|||+||+
T Consensus 101 vl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l 180 (262)
T PTZ00118 101 LLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNL 180 (262)
T ss_pred EEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCEEEEECCCCceeeEEecCCCCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHHHH
Q 023289 203 VMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 282 (284)
Q Consensus 203 ~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~~~e~r~~~~~~~~ 282 (284)
||||||+|+|++|+|.++++++|++++||++|++|++|+|+++||||||++++||||||++||||+|++|||++++++++
T Consensus 181 ~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~kgi~~~~~e~~~~~~~~~~ 260 (262)
T PTZ00118 181 VMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDIIEERRNRLAKAL 260 (262)
T ss_pred EEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCccccHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999998899999999999999999999999999876
Q ss_pred h
Q 023289 283 A 283 (284)
Q Consensus 283 ~ 283 (284)
.
T Consensus 261 ~ 261 (262)
T PTZ00118 261 R 261 (262)
T ss_pred c
Confidence 4
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.1e-102 Score=721.67 Aligned_cols=241 Identities=51% Similarity=0.833 Sum_probs=237.0
Q ss_pred ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289 43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 122 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR 122 (284)
+|++++||||||||||++++||||++||||+||||+|+|||++||+||+|+||||||||++||||||||||||++||+||
T Consensus 18 ~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~yR 97 (273)
T PTZ00223 18 SKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFR 97 (273)
T ss_pred ccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCCCeEE
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289 123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI 202 (284)
Q Consensus 123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~ 202 (284)
|+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||+||+||||+||+|+|||+||+|||+||+
T Consensus 98 vl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l 177 (273)
T PTZ00223 98 ILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKV 177 (273)
T ss_pred EEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCEEEEECCCCeeeEEEecCCCCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEccC-CCceEecCCCCceeeehHHHHHHHHHHH
Q 023289 203 VMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEEARKRQAAQ 281 (284)
Q Consensus 203 ~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk~-~kp~IsLp~~kGi~~~~~e~r~~~~~~~ 281 (284)
||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++ ++|||+||++||||++++|||+++++++
T Consensus 178 ~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~~e~~~~~~~~~ 257 (273)
T PTZ00223 178 VMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINVIQEREEKLIAA 257 (273)
T ss_pred EEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999986 6999999999999999999999999887
Q ss_pred Hh
Q 023289 282 AA 283 (284)
Q Consensus 282 ~~ 283 (284)
++
T Consensus 258 ~~ 259 (273)
T PTZ00223 258 EA 259 (273)
T ss_pred Hh
Confidence 64
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=1e-95 Score=664.84 Aligned_cols=219 Identities=42% Similarity=0.650 Sum_probs=215.5
Q ss_pred ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289 43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 122 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR 122 (284)
+|++++||||||||||+++|||||+++|||+||||+|+|||++||+||+|+||||||||++||||||||||||++||+||
T Consensus 17 ~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~yR 96 (237)
T PRK04313 17 PRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYR 96 (237)
T ss_pred ccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCCCeEE
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCC-CCCcCCCeEEEecCCceeeeEEeecCCc
Q 023289 123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKANDTIKLDLEENKITDFIKFDVGN 201 (284)
Q Consensus 123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~d-p~ik~~DTv~i~l~~~kI~d~ikfe~G~ 201 (284)
|+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| ++||+||||+|++|+|||+||+|||+||
T Consensus 97 vl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~ 176 (237)
T PRK04313 97 VLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGN 176 (237)
T ss_pred EEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEecCCCC
Confidence 999999999999999999999999999999999999999999999999998 9999999999999999999999999999
Q ss_pred EEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCC
Q 023289 202 IVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 262 (284)
Q Consensus 202 ~~~VtgG~n~GrvG~I~~I~~~~-gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~ 262 (284)
+||||||+|+||+|+|.+|++++ +++++|+++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 177 l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 177 LAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred EEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 99999999999999999999999 6789999999999999999999999998 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-92 Score=639.53 Aligned_cols=221 Identities=47% Similarity=0.736 Sum_probs=216.8
Q ss_pred ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289 43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 122 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR 122 (284)
++.+++|||||+||||++++|+||++++||+|+||+|+|||++||++|+|+|||+||+|++||||||||||||+|||+||
T Consensus 20 ~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~yR 99 (241)
T COG1471 20 PRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYR 99 (241)
T ss_pred ccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCCCceEE
Confidence 56778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289 123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI 202 (284)
Q Consensus 123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~ 202 (284)
|+||.+|+|.+|+|++|||.||||||+||++++||++|||+|||||++++|+.|++||||++++|+++|++||||++|++
T Consensus 100 vl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g~~ 179 (241)
T COG1471 100 VLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGAL 179 (241)
T ss_pred EEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccEEEEeCCChhheeEeccCCCcE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCC
Q 023289 203 VMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGK 264 (284)
Q Consensus 203 ~~VtgG~n~GrvG~I~~I~~~~-gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~k 264 (284)
||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++|||+||+|+
T Consensus 180 ~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~e~ 241 (241)
T COG1471 180 VYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPKEK 241 (241)
T ss_pred EEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCCCC
Confidence 9999999999999999999999 5579999999999999999999999998 99999999885
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-90 Score=629.08 Aligned_cols=242 Identities=68% Similarity=1.106 Sum_probs=239.9
Q ss_pred ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289 43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 122 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR 122 (284)
||++|.|||+||+|||+++||+||++||||+|+||+|.+|+++|++|+.|+|||+||+|.+||+||||||+|++|||+||
T Consensus 21 dk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisiekTge~fr 100 (263)
T KOG0378|consen 21 DKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIEKTGEHFR 100 (263)
T ss_pred cccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeecccccccceeEEEEecccchhhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289 123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI 202 (284)
Q Consensus 123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~ 202 (284)
++||++|||.+|+|++|||+||||||++++.+++|+|+|+|||||+||||||.||+|||+++++++++|.++++|++|++
T Consensus 101 ~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dtI~~~~~t~kit~~ikf~~~~~ 180 (263)
T KOG0378|consen 101 LIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDTIKIDLETSKITDFIKFDTGNL 180 (263)
T ss_pred hhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCccceeeccCCCceeeeeeccCccce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHHHH
Q 023289 203 VMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 282 (284)
Q Consensus 203 ~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~~~e~r~~~~~~~~ 282 (284)
||++||+|.||+|+|.+.|+|+|+|++||++|++|++|+|+++|+|+||+|+|||||||+++||+++++||||+|++++.
T Consensus 181 ~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPkgkgi~~siaEe~dkrl~~k~ 260 (263)
T KOG0378|consen 181 CMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPKGKGIALSIAEERDKRLAAKI 260 (263)
T ss_pred eeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCccccCccchhhHHHHHHHhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred hC
Q 023289 283 AA 284 (284)
Q Consensus 283 ~~ 284 (284)
++
T Consensus 261 ~s 262 (263)
T KOG0378|consen 261 SS 262 (263)
T ss_pred cC
Confidence 64
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=5.4e-34 Score=220.88 Aligned_cols=77 Identities=61% Similarity=1.011 Sum_probs=69.8
Q ss_pred cCCceEEEEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceee
Q 023289 116 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 192 (284)
Q Consensus 116 kt~e~yRvl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~ 192 (284)
||||+|||+||++|+|.+|+|++|||+||||||++|++++||+|||+|||||||+|+||+||+||||+|++|++||+
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 68999999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>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=98.51 E-value=2.2e-07 Score=64.37 Aligned_cols=48 Identities=33% Similarity=0.359 Sum_probs=44.1
Q ss_pred chhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEE
Q 023289 64 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVV 112 (284)
Q Consensus 64 lPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVI 112 (284)
++|..+| ..++++.+..||++.+++|.|+|||++++|+.|++...|+|
T Consensus 1 ~RLd~~L-~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFL-SRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHH-HHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCHHHHH-HHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 4677888 44899999999999999999999999999999999999987
No 9
>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 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 N-terminal region of these proteins.; PDB: 2XZM_W 2XZN_W 3U5G_E 3U5C_E.
Probab=98.09 E-value=1.2e-06 Score=60.34 Aligned_cols=20 Identities=55% Similarity=0.853 Sum_probs=11.9
Q ss_pred ecccceeecCCCCCCCCCcc
Q 023289 43 YNSLGLQAPKPSSGPHKSRE 62 (284)
Q Consensus 43 ~k~~g~~a~rpspGPH~~~e 62 (284)
+|++++|||+||||||+++|
T Consensus 19 ~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 19 DKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp -SSSSSB-----SSSS-CCC
T ss_pred ccccCccccCCCCCCccCCC
Confidence 68889999999999999986
No 10
>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=97.52 E-value=0.00053 Score=47.80 Aligned_cols=61 Identities=26% Similarity=0.338 Sum_probs=47.0
Q ss_pred hhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEc
Q 023289 65 PLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYD 126 (284)
Q Consensus 65 PL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D 126 (284)
.|.-+|+.. ..+.+.++|++++.+|.|+|||+..++..+++-..|+|++........++|.
T Consensus 2 rl~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~e 62 (70)
T cd00165 2 RLDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYE 62 (70)
T ss_pred cHHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceeec
Confidence 345566654 3678999999999999999999999999999988899999764322234443
No 11
>smart00363 S4 S4 RNA-binding domain.
Probab=97.18 E-value=0.0011 Score=44.93 Aligned_cols=50 Identities=26% Similarity=0.211 Sum_probs=42.2
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 023289 66 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 116 (284)
Q Consensus 66 L~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k 116 (284)
|..+|+.. ..+.+.+++++.+.+|.|+|||++.++..+++--.|.|+++.
T Consensus 3 l~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 3 LDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred HHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 45566543 356789999999999999999999999999998889999964
No 12
>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=96.72 E-value=0.0017 Score=42.33 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=25.8
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 023289 199 VGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 232 (284)
Q Consensus 199 ~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~i 232 (284)
+|+.++|+.|++.|+.|+|.+|.++. +.|++
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 58999999999999999999997643 44544
No 13
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.70 E-value=0.0016 Score=39.95 Aligned_cols=27 Identities=37% Similarity=0.661 Sum_probs=24.6
Q ss_pred eecCCcEEEEECCCcceeEEEEEEEEE
Q 023289 196 KFDVGNIVMVTGGRNRGRVGIIKNREK 222 (284)
Q Consensus 196 kfe~G~~~~VtgG~n~GrvG~I~~I~~ 222 (284)
+|++|+.++|++|.+.|++|+|.++..
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 478999999999999999999999853
No 14
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=96.68 E-value=0.0017 Score=59.13 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=41.1
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 023289 73 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 115 (284)
Q Consensus 73 ~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~ 115 (284)
++++|.|.++|++.+..|.|.|||++++++.|=|-.=|+++|.
T Consensus 102 R~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~ 144 (205)
T COG0522 102 RLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVR 144 (205)
T ss_pred HhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEee
Confidence 4799999999999999999999999999999999999999996
No 15
>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=96.64 E-value=0.0055 Score=44.42 Aligned_cols=51 Identities=22% Similarity=0.217 Sum_probs=44.6
Q ss_pred chhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 023289 64 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 115 (284)
Q Consensus 64 lPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~ 115 (284)
..|--+|+.. .++.+...+++++.+|.|.|||++++.+.|.+--=|+|+|+
T Consensus 9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59 (59)
T ss_pred HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEeC
Confidence 5666778877 77779999999999999999999999889999888888874
No 16
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.71 E-value=0.0056 Score=46.63 Aligned_cols=60 Identities=27% Similarity=0.309 Sum_probs=41.7
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 124 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl 124 (284)
+.|.|.=+|.- .+++.|.-|||..+.+|.|+|||.+.+...--+--=|+|++ .++.|+++
T Consensus 6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~--~~~~~~Vv 65 (65)
T PF13275_consen 6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI--DGEEYRVV 65 (65)
T ss_dssp S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE--TTEEEEEE
T ss_pred CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE--CCEEEEEC
Confidence 56677777765 58899999999999999999999999998888888899999 57888874
No 17
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=95.32 E-value=0.014 Score=51.61 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=35.9
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcce--eEEEec
Q 023289 73 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM--DVVSIP 115 (284)
Q Consensus 73 ~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~M--DVIsI~ 115 (284)
++++|.|.++|++.+.+|.|.|||++++++.|-|--= |-|+..
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 156 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA 156 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence 3699999999999999999999999999998866432 555543
No 18
>PRK11507 ribosome-associated protein; Provisional
Probab=95.20 E-value=0.088 Score=40.84 Aligned_cols=60 Identities=18% Similarity=0.167 Sum_probs=49.3
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 124 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl 124 (284)
+-|-|.=+|.- .+++.|.-|||..|.+|.|+|||.+.+-..-=+--=|+|+++ ++.|++.
T Consensus 10 e~I~L~QlLK~-~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~--g~~~~v~ 69 (70)
T PRK11507 10 PHVELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQVV 69 (70)
T ss_pred CeEEHHHHHhh-hCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEEC--CEEEEEe
Confidence 45666667664 588999999999999999999999988777777778999996 5777764
No 19
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.12 E-value=0.016 Score=51.97 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=33.4
Q ss_pred HHHHhhh-------cccccHHHHHHHHhCceEEECCEEeccccCC
Q 023289 68 LVLRNRL-------KYALTYREVIAILMQRHVLVDGKVRTDKTYP 105 (284)
Q Consensus 68 i~LRd~L-------kyA~t~rEakkIl~~g~VkVDGkvrtD~kfP 105 (284)
-+|+.+| |+|.|..+|++.+.+|.|.|||++++|+.|=
T Consensus 103 ~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~ 147 (181)
T PTZ00155 103 KLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFL 147 (181)
T ss_pred HHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceE
Confidence 4555555 9999999999999999999999999999763
No 20
>PLN00189 40S ribosomal protein S9; Provisional
Probab=95.00 E-value=0.02 Score=52.03 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=34.8
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEE
Q 023289 73 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVS 113 (284)
Q Consensus 73 ~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIs 113 (284)
++++|.|..+|++++.+|.|.|||++++++.|-|--=|++.
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~ 157 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKH 157 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEE
Confidence 46899999999999999999999999999988665443333
No 21
>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=94.78 E-value=0.048 Score=49.16 Aligned_cols=43 Identities=28% Similarity=0.354 Sum_probs=39.3
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 023289 74 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 116 (284)
Q Consensus 74 LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k 116 (284)
++++.|.++|++.+.+|.|.|||++++++.|.+--=|+|++..
T Consensus 99 ~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 99 LGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKE 141 (200)
T ss_pred cCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEee
Confidence 4778899999999999999999999999999997779999963
No 22
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=94.73 E-value=0.14 Score=47.60 Aligned_cols=53 Identities=19% Similarity=0.180 Sum_probs=43.9
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 115 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~ 115 (284)
.++.|.-+|+..+. ..+.+++++.+.+|.|+|||+++++..+.+---|+|++.
T Consensus 4 ~g~rLd~~L~~~~~-~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~ 56 (299)
T TIGR00005 4 AGQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVR 56 (299)
T ss_pred cchhHHHHHHHhcc-cCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEe
Confidence 34667778877664 357899999999999999998888888999878999984
No 23
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=94.73 E-value=0.033 Score=49.89 Aligned_cols=44 Identities=20% Similarity=0.257 Sum_probs=37.1
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEeccC
Q 023289 74 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPA--GFMDVVSIPKT 117 (284)
Q Consensus 74 LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPV--G~MDVIsI~kt 117 (284)
+++|.|..+|++.+.+|.|.|||++++++.|.| +.=|.|+...+
T Consensus 112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~ 157 (177)
T PRK04051 112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPT 157 (177)
T ss_pred ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCC
Confidence 699999999999999999999999999998876 34456666443
No 24
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=94.55 E-value=0.062 Score=48.56 Aligned_cols=43 Identities=28% Similarity=0.404 Sum_probs=39.5
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 023289 74 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 116 (284)
Q Consensus 74 LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k 116 (284)
++++.+..+|++.+.+|.|.|||++++.+.|++--=|+|++..
T Consensus 102 ~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 102 LGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred cCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 3788999999999999999999999999999997779999964
No 25
>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=94.47 E-value=0.084 Score=44.32 Aligned_cols=55 Identities=18% Similarity=0.250 Sum_probs=38.8
Q ss_pred eEEeecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCC-----CCeeeEe--eceEEEE
Q 023289 193 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL-----GHEFATR--LGNVFTI 250 (284)
Q Consensus 193 d~ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~-----g~~F~T~--~~nVfvI 250 (284)
+.+++..|+.+.|++|++-|..|+|.++... ...|.|++-+ |.+++.. .+||.++
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~ 99 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVTKEKVNGTEVPVPIHPSNVMIT 99 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeEEECCCCeEEEeeechHHeEEE
Confidence 5568889999999999999999999999643 2456666543 4333333 3566553
No 26
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=94.42 E-value=0.064 Score=48.74 Aligned_cols=43 Identities=21% Similarity=0.362 Sum_probs=38.5
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 023289 74 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 116 (284)
Q Consensus 74 LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k 116 (284)
+++|.+.++|++++.+|.|.|||++++++.|.+--=|+|++..
T Consensus 98 ~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 98 LGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKD 140 (201)
T ss_pred cCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEcc
Confidence 5788999999999999999999999999999985559999953
No 27
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=94.08 E-value=0.18 Score=47.18 Aligned_cols=63 Identities=14% Similarity=0.205 Sum_probs=51.3
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 137 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~~I~ 137 (284)
.|+=|-.+++..+ ..+.+.|++.+.+|.|+|||++++++.+.+--=|+|++. ..|||.+.++.
T Consensus 182 ~s~RLD~lls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isvr-----------G~Gr~~i~~~~ 244 (257)
T TIGR03069 182 ASLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR-----------GKGRLEILELE 244 (257)
T ss_pred ccccHHHHHHhhh--hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEc-----------CCceEEEEEee
Confidence 3555777887655 558899999999999999999999999988777999984 56788777664
No 28
>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=93.03 E-value=0.18 Score=46.37 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=40.2
Q ss_pred HHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 023289 69 VLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 116 (284)
Q Consensus 69 ~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k 116 (284)
+|.+ .+++.+.++|++.+++|.|.|||++++++.+.+--=|.|++..
T Consensus 5 ~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 5 LLVR-RGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred HHHH-cCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 4444 4688899999999999999999999999999886559999963
No 29
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=91.84 E-value=0.67 Score=36.35 Aligned_cols=60 Identities=23% Similarity=0.287 Sum_probs=45.3
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 124 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl 124 (284)
|=|-|.=+|.- ++.+++.-+||..|.++.|+|||.+-+=..-=+--=|+|+|| +..|-+.
T Consensus 10 e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~--~~~~~v~ 69 (73)
T COG2501 10 EFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIP--GQRYQVV 69 (73)
T ss_pred ceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEEC--CEEEEEE
Confidence 44556666664 689999999999999999999999866554445566899997 4555443
No 30
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=91.74 E-value=0.63 Score=44.27 Aligned_cols=52 Identities=19% Similarity=0.144 Sum_probs=42.2
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 115 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~ 115 (284)
...|.-+|+..+. ..+.+++++.+.+|.|+|||+.++...+.+---|+|++.
T Consensus 17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~ 68 (325)
T PRK11180 17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAID 68 (325)
T ss_pred CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEe
Confidence 4678888887654 357899999999999999999987666666555999985
No 31
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=91.61 E-value=0.51 Score=44.75 Aligned_cols=57 Identities=25% Similarity=0.220 Sum_probs=50.0
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 121 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~y 121 (284)
...-|--+|++ |.- .+..+..+++.+|.|.|||++.+ ..|.+.-=|+|+++...+.+
T Consensus 11 ~g~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~ 67 (289)
T COG0564 11 AGQRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPE 67 (289)
T ss_pred cCCCHHHHHHH-ccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecccccc
Confidence 45567888998 665 78899999999999999999999 99999999999999876665
No 32
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=90.48 E-value=0.65 Score=39.45 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=30.4
Q ss_pred EEeecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 023289 194 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 234 (284)
Q Consensus 194 ~ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd 234 (284)
.+++..|+.+.|+.|+.-|..|+|.++.... +.|.|+.
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~---~~V~VeG 80 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKR---GRIYVEG 80 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCC---CEEEEeC
Confidence 4578899999999999999999999996542 3455554
No 33
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=90.26 E-value=0.97 Score=44.87 Aligned_cols=65 Identities=17% Similarity=0.214 Sum_probs=49.7
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 134 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~ 134 (284)
.+|+.-+|.+ .+.|.+..|||+.+.||-|+|||..++|..+-+-- ...+..|-++---|.+|.+.
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~------~~~~~~~~~lr~GKk~~~~i 406 (408)
T PRK05912 342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA------DDRFGKYTVLQRGKKKFARV 406 (408)
T ss_pred CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccccc------cccCCCEEEEEeCCCceEEE
Confidence 5788888875 69999999999999999999999999999764322 11145566666666666554
No 34
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=90.05 E-value=0.93 Score=42.90 Aligned_cols=65 Identities=22% Similarity=0.126 Sum_probs=46.6
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEecc----------CCceEEEEEcCCCceEE
Q 023289 66 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA--GFMDVVSIPK----------TNENFRLLYDTKGRFRL 133 (284)
Q Consensus 66 L~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPV--G~MDVIsI~k----------t~e~yRvl~D~kGrf~l 133 (284)
|.=+|.+ +++ .+.++|++++.+|.|+|||++. +..+.| +-.|.|+++. ..++|-+++-+.|..+-
T Consensus 5 L~k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~~s 81 (289)
T PRK10700 5 LQKVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCT 81 (289)
T ss_pred HHHHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCEee
Confidence 3334443 333 6789999999999999999987 676666 4557787753 11468888888887654
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=89.03 E-value=1 Score=38.79 Aligned_cols=59 Identities=10% Similarity=0.069 Sum_probs=50.4
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEE
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRL 123 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRv 123 (284)
++-|-.||=- .+++.|..-|+..|..|.|.|||.+ .-+...|-.=|+|+|...+..+-+
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~v 66 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTV 66 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEEE
Confidence 4677777765 4999999999999999999999999 889999999999999876655544
No 36
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=88.62 E-value=0.7 Score=36.07 Aligned_cols=39 Identities=18% Similarity=0.374 Sum_probs=32.0
Q ss_pred EeecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCC
Q 023289 195 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 236 (284)
Q Consensus 195 ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~ 236 (284)
+++..|+.+.|+.|+.-|++|+|.++.+. .+.|.+++-+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegvn 43 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPK---KNRVIVEGVK 43 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcE
Confidence 47889999999999999999999999753 3467776543
No 37
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=88.54 E-value=1.1 Score=42.23 Aligned_cols=59 Identities=24% Similarity=0.239 Sum_probs=43.9
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcce-eEEEeccCC------ceEEEEEcCCCceEEE
Q 023289 75 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM-DVVSIPKTN------ENFRLLYDTKGRFRLH 134 (284)
Q Consensus 75 kyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~M-DVIsI~kt~------e~yRvl~D~kGrf~l~ 134 (284)
++| +.|||++.|.+|.|.|||++.++...-+=-- |+|.++..- ..|-+++.+.|..+-+
T Consensus 13 G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~ 78 (248)
T COG1187 13 GVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSST 78 (248)
T ss_pred CCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEecc
Confidence 554 5899999999999999999999987555444 466665431 2278888888876544
No 38
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=88.17 E-value=2 Score=40.97 Aligned_cols=68 Identities=18% Similarity=0.108 Sum_probs=49.6
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc--------CCceEEEEEcCCCceE
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK--------TNENFRLLYDTKGRFR 132 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k--------t~e~yRvl~D~kGrf~ 132 (284)
.++-|.-+|.+. ++ .+.+||++.+.+|.|+|||++. +..+.|---|+|+++- .+++|-++.-+.|-.+
T Consensus 5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~~~ed~~~lvlnKP~G~~~ 80 (290)
T PRK10475 5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80 (290)
T ss_pred hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccccccCCCeEEEEECCCCCCc
Confidence 456677777654 43 4799999999999999999987 5667775559898852 1245777777777653
No 39
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=87.98 E-value=0.85 Score=36.12 Aligned_cols=39 Identities=15% Similarity=0.409 Sum_probs=31.7
Q ss_pred EEeecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 023289 194 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 235 (284)
Q Consensus 194 ~ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~ 235 (284)
.+++..|+.+.|+.|+.-|++|+|.++.+. .+.|++++-
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKK---SNKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCc
Confidence 347889999999999999999999999753 246777654
No 40
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=87.74 E-value=2.3 Score=40.44 Aligned_cols=51 Identities=27% Similarity=0.249 Sum_probs=41.4
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 115 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~ 115 (284)
...|.-+|++.+. ..+.+.+++.+.+|.|.|||+++ +..+.+---|+|+++
T Consensus 19 g~RLd~~L~~~~~-~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~ 69 (317)
T PRK11025 19 GQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIP 69 (317)
T ss_pred CchHHHHHHHhcc-cCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeC
Confidence 4567788887663 35789999999999999999988 467888666999985
No 41
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=87.02 E-value=0.89 Score=37.38 Aligned_cols=37 Identities=22% Similarity=0.504 Sum_probs=29.6
Q ss_pred EeecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 023289 195 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 234 (284)
Q Consensus 195 ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd 234 (284)
.++..|+.+.|+.|++-|.+|+|.++.+.. +.|.|++
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 39 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKK---NKVIVEG 39 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence 377889999999999999999999996532 3455544
No 42
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=86.90 E-value=3.1 Score=37.42 Aligned_cols=67 Identities=15% Similarity=0.133 Sum_probs=46.6
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc------CCceEEEEEcCCCceEEEE
Q 023289 66 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK------TNENFRLLYDTKGRFRLHS 135 (284)
Q Consensus 66 L~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~k------t~e~yRvl~D~kGrf~l~~ 135 (284)
|--+|...+ ..+.+.+++++.+|.|.|||++.++..+.+---|.|++.. ..++|=++--+.|- ..|+
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~~~~~~~~lvvnKP~G~-~~~~ 75 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGY-VCST 75 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcccCCCCEEEEEECCCCe-Eecc
Confidence 445666655 3678999999999999999999887777775569999852 12345555555553 3454
No 43
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=85.31 E-value=3.5 Score=39.06 Aligned_cols=62 Identities=19% Similarity=0.248 Sum_probs=50.7
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 137 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~~I~ 137 (284)
|+=|--++-..+ -.+...|+..+.+|+|+|||++.++..|-+--=|+|||-. .|||.+.++.
T Consensus 191 s~RLD~vla~~~--~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG-----------~GR~~i~~~~ 252 (267)
T PLN00051 191 SLRLDALASAGF--RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSG-----------KGRLEVGEIN 252 (267)
T ss_pred cccHHHHHHHHh--ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEee-----------CCEEEEEEEe
Confidence 455666777655 4677889999999999999999999999999999999953 5677777664
No 44
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=84.98 E-value=3.1 Score=41.45 Aligned_cols=66 Identities=21% Similarity=0.221 Sum_probs=47.8
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 134 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~ 134 (284)
.+|+.-+|-. .+.|.+..|||+.+.||-|+|||...+|..+-+--=|. .+..|-++---|.+|...
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~-----l~~~~~~lr~GKk~~~~i 407 (410)
T PRK13354 342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA-----FDGKFVILRRGKKKFFLV 407 (410)
T ss_pred CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh-----cCCCEEEEEeCCccEEEE
Confidence 5778777775 79999999999999999999999999999653322111 133455565555555544
No 45
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=84.79 E-value=2.2 Score=40.61 Aligned_cols=63 Identities=21% Similarity=0.283 Sum_probs=53.6
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 023289 62 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 137 (284)
Q Consensus 62 eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~~I~ 137 (284)
.|+=|-.++-+.++... .-|...+..|+|+||.+++++..|-+..=|.|||-. .||+.+-+|.
T Consensus 179 sSlRLD~vis~~~~~SR--~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG-----------~GR~~i~~i~ 241 (257)
T COG2302 179 SSLRLDVVISEGFGLSR--AKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG-----------FGRLKILEIN 241 (257)
T ss_pred ehhhHHHHHHHHHhhhH--HHHHHHHHcCceEEeeEEeccccceeccCCEEEEec-----------cccEEEEeec
Confidence 47888899999888655 567899999999999999999999999999999953 5777776664
No 46
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=84.59 E-value=2 Score=40.62 Aligned_cols=111 Identities=19% Similarity=0.317 Sum_probs=70.4
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE-------------EEEcCCCceEEEEcChhhh
Q 023289 75 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR-------------LLYDTKGRFRLHSLRDEEA 141 (284)
Q Consensus 75 kyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR-------------vl~D~kGrf~l~~I~~eEA 141 (284)
+++.|..+|+..++.|+|+|||...+-+.+=|-.-+.|++......|. .=.|.+|+-++- |-+.--
T Consensus 13 gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~yVSRG~~KL~~ale~F~l~~k~kv~LD-iGsSTG 91 (245)
T COG1189 13 GLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFELDVKGKVVLD-IGSSTG 91 (245)
T ss_pred cchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCccccHHHHHHHHHHhcCcCCCCCEEEE-ecCCCc
Confidence 889999999999999999999999999999999999999975343332 113455554332 433333
Q ss_pred cceeE-------EEEeEEEee-------CCeeEEEccCCeeeecCCCC--CcCCCeEEEec
Q 023289 142 KFKLC-------KVRSVQFGQ-------KGIPYINTYDGRTIRYPDPL--IKANDTIKLDL 186 (284)
Q Consensus 142 ~~KLc-------KV~~Kt~~k-------gG~~ql~thDGrni~~~dp~--ik~~DTv~i~l 186 (284)
.|=.| +|-.+-++. ...|.+....+.|+||-.|+ ...-|-+++|+
T Consensus 92 GFTd~lLq~gAk~VyavDVG~~Ql~~kLR~d~rV~~~E~tN~r~l~~~~~~~~~d~~v~Dv 152 (245)
T COG1189 92 GFTDVLLQRGAKHVYAVDVGYGQLHWKLRNDPRVIVLERTNVRYLTPEDFTEKPDLIVIDV 152 (245)
T ss_pred cHHHHHHHcCCcEEEEEEccCCccCHhHhcCCcEEEEecCChhhCCHHHcccCCCeEEEEe
Confidence 22222 344444443 23455666666676664443 22235555555
No 47
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=84.01 E-value=2.5 Score=36.95 Aligned_cols=54 Identities=28% Similarity=0.380 Sum_probs=38.0
Q ss_pred EeecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEE-----cCCCCeee--EeeceEEEEc
Q 023289 195 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHEFA--TRLGNVFTIG 251 (284)
Q Consensus 195 ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ik-----d~~g~~F~--T~~~nVfvIG 251 (284)
+++..|+.+.|+.|+.-|..|+|..+....+ .|.|+ -.+|..++ .-.|||+++-
T Consensus 45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~---~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKW---VIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred ceeecCCEEEEecCCCCCCceEEEEEEcCCC---EEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 4778899999999999999999999966433 33333 35554433 3456776655
No 48
>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=82.35 E-value=1.9 Score=35.50 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=25.3
Q ss_pred eecCCcEEEEECCCcceeEEEEEEEEEe
Q 023289 196 KFDVGNIVMVTGGRNRGRVGIIKNREKH 223 (284)
Q Consensus 196 kfe~G~~~~VtgG~n~GrvG~I~~I~~~ 223 (284)
++..|+.+.|+.|+.-|.+|+|.++.+.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6778999999999999999999999654
No 49
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=79.41 E-value=4.8 Score=30.74 Aligned_cols=50 Identities=28% Similarity=0.494 Sum_probs=38.3
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEecCC-ccEEEEEcCCCCeeeEeeceEEEEcc
Q 023289 199 VGNIVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGK 252 (284)
Q Consensus 199 ~G~~~~VtgG~n~GrvG~I~~I~~~~gs-~~iV~ikd~~g~~F~T~~~nVfvIGk 252 (284)
.|..|+|-.|.+.-|+|.++.-|+...| |.+|. ++...+.-+..+..+|-
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi----~~q~i~velkdivlvgv 55 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVI----GEQSIDVELKDIVLVGV 55 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEEE----CCeEEEEEeeeEEEEEe
Confidence 4889999999999999999998887744 55552 33456777777777773
No 50
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=63.71 E-value=15 Score=36.85 Aligned_cols=62 Identities=21% Similarity=0.260 Sum_probs=45.2
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEE
Q 023289 66 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS 135 (284)
Q Consensus 66 L~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~~ 135 (284)
++-+|-+ .+++...+||++.+.+|-|++||....|.+++.+ +.....|.++--.|.+|....
T Consensus 338 ~~~~lv~-~~L~psr~earr~i~~g~v~in~~~v~d~~~~~~-------~~~~~~~~~l~~GKkk~~~i~ 399 (401)
T COG0162 338 LVDLLVD-AGLAPSRSEARRLIQQGGVKINGEKVEDENYVLS-------DLLDNGLLVLRRGKKKFALIV 399 (401)
T ss_pred HHHHHHH-hCCcccHHHHHhhcccCCEEECCEeccccccchh-------hccCCceEEEecccccEEEEe
Confidence 3334444 5899999999999999999999999999998871 123345566665666665543
No 51
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=63.49 E-value=5.3 Score=36.11 Aligned_cols=55 Identities=27% Similarity=0.327 Sum_probs=41.2
Q ss_pred CCCCCCCCCcccchhHHHHHh-------hhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 023289 52 KPSSGPHKSRECLPLILVLRN-------RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106 (284)
Q Consensus 52 rpspGPH~~~eslPL~i~LRd-------~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPV 106 (284)
-|..+.|..-+-+.-.-|-|. .|+.|.+-+||-+.+.||.|.|.-++++|+.|=|
T Consensus 87 ipTr~~l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv 148 (181)
T KOG4655|consen 87 IPTRKSLELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV 148 (181)
T ss_pred ecchhhhhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence 566666665542333333332 3789999999999999999999999999997754
No 52
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=60.90 E-value=12 Score=31.06 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.6
Q ss_pred EeecCCcEEEEECCCcceeEEEEEEEEEe
Q 023289 195 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 223 (284)
Q Consensus 195 ikfe~G~~~~VtgG~n~GrvG~I~~I~~~ 223 (284)
.+...|+.+.|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45677999999999999999999988543
No 53
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=59.01 E-value=9.8 Score=32.60 Aligned_cols=34 Identities=29% Similarity=0.466 Sum_probs=27.7
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 234 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd 234 (284)
+++|-.|+++.|+.+|+-.+|..+... +.+++-+
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd----~~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDD----NFVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccC----CEEEEeC
Confidence 689999999999999999999998653 3555544
No 54
>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification.; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.
Probab=57.40 E-value=27 Score=30.87 Aligned_cols=29 Identities=34% Similarity=0.417 Sum_probs=25.0
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc
Q 023289 61 RECLPLILVLRNRLKYALTYREVIAILMQR 90 (284)
Q Consensus 61 ~eslPL~i~LRd~LkyA~t~rEakkIl~~g 90 (284)
...+|..+++|..|. |.|..||..+|.+-
T Consensus 69 ~~G~p~~~l~R~iLe-~~t~~eA~~~l~~~ 97 (225)
T PF03417_consen 69 QPGLPRHFLVRKILE-CRTVEEAIAILRSA 97 (225)
T ss_dssp TTSB-HHHHHHHHHC--SSHHHHHHCHHCC
T ss_pred cCCChHHHHHHHHhc-CCCHHHHHHHHHhc
Confidence 679999999999999 99999999999865
No 55
>PF14001 YdfZ: YdfZ protein
Probab=55.01 E-value=19 Score=27.78 Aligned_cols=42 Identities=26% Similarity=0.469 Sum_probs=29.6
Q ss_pred eecCCcEEEEECCCcceeEEEEEEEEEecC------CccEEEEEcCCCCeee
Q 023289 196 KFDVGNIVMVTGGRNRGRVGIIKNREKHKG------SFETIHIQDALGHEFA 241 (284)
Q Consensus 196 kfe~G~~~~VtgG~n~GrvG~I~~I~~~~g------s~~iV~ikd~~g~~F~ 241 (284)
++.+|+.+|+.| +|.+|+|+.|....- ....|.+++.+| .|+
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 356799999977 688889999865321 235788887776 354
No 56
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=52.92 E-value=16 Score=31.65 Aligned_cols=32 Identities=13% Similarity=0.347 Sum_probs=27.4
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 232 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~i 232 (284)
.|+|-.|+|.-|.+.|+.++|.+|..+ |.|-|
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~----nRvLV 39 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLV 39 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC----CeEEE
Confidence 378999999999999999999999764 55555
No 57
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=48.91 E-value=43 Score=27.81 Aligned_cols=46 Identities=15% Similarity=0.211 Sum_probs=35.4
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 023289 75 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 121 (284)
Q Consensus 75 kyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~y 121 (284)
.+..+...|+..+..|.|.|||...+- ..-|=.=|+|+|--.+..+
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~~~~ 64 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRAKP-SKEVKVGDILTIRFGNKEF 64 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEccc-ccccCCCCEEEEEeCCcEE
Confidence 455788999999999999999999854 4556677888886544443
No 58
>PRK04333 50S ribosomal protein L14e; Validated
Probab=45.53 E-value=23 Score=28.20 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=27.1
Q ss_pred eecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 023289 196 KFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 232 (284)
Q Consensus 196 kfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~i 232 (284)
.++.|.+|++.-|+..|+..+|.++... +.|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~----~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK----NFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC----CEEEE
Confidence 4688999999999999999999998442 45555
No 59
>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=45.49 E-value=1.3e+02 Score=22.54 Aligned_cols=66 Identities=17% Similarity=0.153 Sum_probs=38.4
Q ss_pred EEEeeCCeeEEEccCCeeeecCC-CCC-----cCCCeEEEecCCceeeeEEeecCCc-EEEEECCCcceeEEE
Q 023289 151 VQFGQKGIPYINTYDGRTIRYPD-PLI-----KANDTIKLDLEENKITDFIKFDVGN-IVMVTGGRNRGRVGI 216 (284)
Q Consensus 151 Kt~~kgG~~ql~thDGrni~~~d-p~i-----k~~DTv~i~l~~~kI~d~ikfe~G~-~~~VtgG~n~GrvG~ 216 (284)
+.+..++.-++.+.||..++... ..+ ...+...+.|..|++.-.++=..+. ..+-|....++-.|+
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 45678999999999999987643 234 3444555666666654222222222 445555544444443
No 60
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=42.60 E-value=98 Score=30.83 Aligned_cols=43 Identities=23% Similarity=0.132 Sum_probs=26.0
Q ss_pred eeEEEEeEEEeeCCeeEEEccCCeeeecCCC--------CCcCCCeEEEecCC
Q 023289 144 KLCKVRSVQFGQKGIPYINTYDGRTIRYPDP--------LIKANDTIKLDLEE 188 (284)
Q Consensus 144 KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp--------~ik~~DTv~i~l~~ 188 (284)
=|..|+-+. .|....+.+.|..|||+-.| +.|+||.|+.-+++
T Consensus 278 PL~lIeAe~--~g~~~~viLQnaetIrlv~~dG~~vsVt~Lk~GD~VL~~~~~ 328 (344)
T PRK02290 278 PLLLIEAEY--GGKRIRTILQNAETIRLVTPDGKPVSVVDLKPGDEVLGYLEE 328 (344)
T ss_pred cEEEEEEEe--CCeEEEEEEecCcEEEEECCCCCEeeeeecCCCCEEEEEecC
Confidence 455666555 55666677777777776433 45666666655543
No 61
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=42.27 E-value=16 Score=27.99 Aligned_cols=34 Identities=29% Similarity=0.389 Sum_probs=22.3
Q ss_pred cccchhHHHHHhhhcccc-cHHHHHHHHhCceEEECCE
Q 023289 61 RECLPLILVLRNRLKYAL-TYREVIAILMQRHVLVDGK 97 (284)
Q Consensus 61 ~eslPL~i~LRd~LkyA~-t~rEakkIl~~g~VkVDGk 97 (284)
.|.|||.+++ ||||. +..||.+-+.+++-.|+--
T Consensus 21 WEmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~~ 55 (62)
T PF08828_consen 21 WEMMPLMYVI---LKYADADVEEASRRIDEAKNVVNEY 55 (62)
T ss_dssp GGGHHHHHHH---HHHTTT-HHHHHHHHHH--------
T ss_pred HHHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 4789999986 89999 9999999998887666543
No 62
>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=42.02 E-value=2.6e+02 Score=25.22 Aligned_cols=63 Identities=16% Similarity=0.172 Sum_probs=40.4
Q ss_pred EEeeCCeeEEEc-cCCeee-ecCCCCCcCCCeEEEecCCceeeeEEeecCCcEEEEECCCcceeEEE
Q 023289 152 QFGQKGIPYINT-YDGRTI-RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGI 216 (284)
Q Consensus 152 t~~kgG~~ql~t-hDGrni-~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~~~VtgG~n~GrvG~ 216 (284)
..+.+..-+..+ =||.++ .|-+...|.-.|..+.+..++ -.|-|+...+-+=..|......|.
T Consensus 69 ~~~~g~~YeYsL~VdGksl~ky~e~~~k~~~tW~~~i~G~~--~RIvLdk~t~~vwvnG~~iet~~e 133 (177)
T PF06905_consen 69 EAVSGFAYEYSLEVDGKSLKKYKEEQSKKFNTWELNIDGQE--YRIVLDKDTMDVWVNGEKIETEGE 133 (177)
T ss_dssp EEETTTEEEEEEEETTEEEEE--SSTTTTEEEEEEEETTEE--EEEEEETTTTEEEETTCEE--EEE
T ss_pred EecCCceEEEEEEECCEEHHHHHHHHhhhheeEEEecCCCE--EEEEEEcceEEEEECCEEccccce
Confidence 333444433333 377775 345667788889998887644 667788888888889988876664
No 63
>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=41.50 E-value=74 Score=25.10 Aligned_cols=48 Identities=19% Similarity=0.320 Sum_probs=30.3
Q ss_pred CCC-CCcCCCeEEEecCCceeeeEEeecC----CcEEEEECCCcceeEEEEEEE
Q 023289 172 PDP-LIKANDTIKLDLEENKITDFIKFDV----GNIVMVTGGRNRGRVGIIKNR 220 (284)
Q Consensus 172 ~dp-~ik~~DTv~i~l~~~kI~d~ikfe~----G~~~~VtgG~n~GrvG~I~~I 220 (284)
++| .++.||...+.+...+=+-.=+|+. |..++--+|+.+| .|.|++|
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 6899999999987655221122322 6666666776665 7887653
No 64
>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=40.04 E-value=1.5e+02 Score=22.78 Aligned_cols=40 Identities=18% Similarity=0.404 Sum_probs=25.4
Q ss_pred CcCCCeEEEecCCceeeeEEeecCCcEEEE-ECCCcceeEEEEEE
Q 023289 176 IKANDTIKLDLEENKITDFIKFDVGNIVMV-TGGRNRGRVGIIKN 219 (284)
Q Consensus 176 ik~~DTv~i~l~~~kI~d~ikfe~G~~~~V-tgG~n~GrvG~I~~ 219 (284)
+++||+..+.+.-.+ -+..++|.-.++ .+|+..| .|+|.+
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 788888888776443 235566666666 5565555 677654
No 65
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=38.85 E-value=1.4e+02 Score=32.87 Aligned_cols=77 Identities=18% Similarity=0.238 Sum_probs=51.7
Q ss_pred CcceeEEEeccCCceEEEEEcCCCceEEEEcCh---hhhcceeEEEE----eEEEeeCCeeEEEccCCeeeecCCCCCcC
Q 023289 106 AGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIKA 178 (284)
Q Consensus 106 VG~MDVIsI~kt~e~yRvl~D~kGrf~l~~I~~---eEA~~KLcKV~----~Kt~~kgG~~ql~thDGrni~~~dp~ik~ 178 (284)
+|-++++..+ .+.+=+-+|.+++....+++. -++.-||.||+ ....++.++|.++..||+-....-.++++
T Consensus 112 ~~~~e~~~~~--~~~~V~s~d~~~k~~~~~v~~v~r~~~~~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~~a~~l~~ 189 (858)
T PRK14898 112 IGGHEVCDLP--IEIYALSLDQDEKVHWKRIISVIRHKANGKLIKIKTESGRTIRATPYHSFVTRKDNEVIPVEGSELKI 189 (858)
T ss_pred cCCceEEecC--CCcEEEEECCCCcEEEEEeeeEEeccCCCcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEeeHHhCCC
Confidence 3445555443 233334456667777777654 23345889888 44567899999999999877666668999
Q ss_pred CCeEEE
Q 023289 179 NDTIKL 184 (284)
Q Consensus 179 ~DTv~i 184 (284)
||-+.+
T Consensus 190 GD~i~~ 195 (858)
T PRK14898 190 GDWLPV 195 (858)
T ss_pred CCEEee
Confidence 998755
No 66
>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=37.90 E-value=71 Score=25.07 Aligned_cols=19 Identities=37% Similarity=0.301 Sum_probs=15.4
Q ss_pred eEEEEEEEEEecCCccEEE
Q 023289 213 RVGIIKNREKHKGSFETIH 231 (284)
Q Consensus 213 rvG~I~~I~~~~gs~~iV~ 231 (284)
++|+|.+.+.||++..+..
T Consensus 2 ~vg~I~~~~~hp~sdkL~~ 20 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYV 20 (95)
T ss_dssp EEEEEEEEEEETTSSSEEE
T ss_pred EEEEEEEEEECCCCCEEEE
Confidence 6899999999998864443
No 67
>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=36.48 E-value=61 Score=27.15 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=24.7
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEE
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREK 222 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~ 222 (284)
|.+|+.+-|++|.=.|..|+|.++..
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 89999999999999999999999865
No 68
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=36.19 E-value=56 Score=28.05 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=26.5
Q ss_pred EeecCCcEEEEECCCcceeEEEEEEEEEe
Q 023289 195 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 223 (284)
Q Consensus 195 ikfe~G~~~~VtgG~n~GrvG~I~~I~~~ 223 (284)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999654
No 69
>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=35.93 E-value=79 Score=31.58 Aligned_cols=55 Identities=20% Similarity=0.277 Sum_probs=32.6
Q ss_pred eeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcEEEE---ECCCccee
Q 023289 144 KLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMV---TGGRNRGR 213 (284)
Q Consensus 144 KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~~~V---tgG~n~Gr 213 (284)
=|..|+-.. .|....+.+.|..|||.-.| +|+.+..-.+++|+.+++ .+|+|.|.
T Consensus 288 PLllIeA~~--~g~~~svilQnaetIRlv~p-------------~G~~vsVt~Lk~GD~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 288 PLLLIEAEA--DGKRISVILQNAETIRLVGP-------------DGEPVSVTELKPGDEVLVYLEEAGRHFGM 345 (354)
T ss_pred ceEEEEEEe--CCeEEEEEEecCcEEEEECC-------------CCCEeeeeecCCCCEEEEEecCCCcccce
Confidence 455565555 55666667777777775433 344445555555555444 37888884
No 70
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=35.69 E-value=37 Score=29.61 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=21.4
Q ss_pred ecCCcEEEEECCCcceeEEEEEEE
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNR 220 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I 220 (284)
+.+|..++|..|+.+|+-++|...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999998775
No 71
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=35.54 E-value=69 Score=26.44 Aligned_cols=60 Identities=18% Similarity=0.197 Sum_probs=36.2
Q ss_pred CCeeEEEccCCeeeecCCCCCcCCCeEEEecCCce------eeeEEeecCCcEEEEECCCcceeEEEEEE
Q 023289 156 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK------ITDFIKFDVGNIVMVTGGRNRGRVGIIKN 219 (284)
Q Consensus 156 gG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~k------I~d~ikfe~G~~~~VtgG~n~GrvG~I~~ 219 (284)
+.+.++.|.|||++.-.=.-+.-.--+.|+-.-.+ =++.+++- .++++|.|.+-+|-|-|
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDE 75 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecch
Confidence 34678889999998643222333323444433111 12333333 78999999999998876
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=33.55 E-value=2.1e+02 Score=21.67 Aligned_cols=57 Identities=16% Similarity=0.202 Sum_probs=40.9
Q ss_pred EEEeccCCceEEE-EEcCCCceEEEEcChhhh----c------ceeEEEEeEEEeeCCeeEEEccCCe
Q 023289 111 VVSIPKTNENFRL-LYDTKGRFRLHSLRDEEA----K------FKLCKVRSVQFGQKGIPYINTYDGR 167 (284)
Q Consensus 111 VIsI~kt~e~yRv-l~D~kGrf~l~~I~~eEA----~------~KLcKV~~Kt~~kgG~~ql~thDGr 167 (284)
|.++...+.++++ +-|..|......-...+. . =.+.||.++...-+|.+|+..+.=+
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 5667777778877 677788877665543331 1 2589999999888999999976433
No 73
>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=33.29 E-value=2.3e+02 Score=22.02 Aligned_cols=42 Identities=14% Similarity=0.376 Sum_probs=29.9
Q ss_pred CCcCCCeEEEecCCceeeeEEeecC-------CcEEEEECCCcceeEEEEEEE
Q 023289 175 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRGRVGIIKNR 220 (284)
Q Consensus 175 ~ik~~DTv~i~l~~~kI~d~ikfe~-------G~~~~VtgG~n~GrvG~I~~I 220 (284)
.++.||...+.+...+-+ .+|+ |...+-.+|+.+| .|.|.+|
T Consensus 59 ~l~~~~~a~v~l~~~~pi---~~e~~~~~~~~Grfilr~~~~Tva-~G~I~~i 107 (107)
T cd04093 59 CLTKGQTAIVEIELERPI---PLELFKDNKELGRVVLRRDGETIA-AGLVTEI 107 (107)
T ss_pred CcCCCCEEEEEEEECCeE---EEEEcccCCCcceEEEEcCCCEEE-EEEEEeC
Confidence 589999999999766533 3444 7777766776666 5888654
No 74
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=32.27 E-value=4.5e+02 Score=25.03 Aligned_cols=61 Identities=23% Similarity=0.312 Sum_probs=39.8
Q ss_pred CCCCCcCCCeEEEecCCceeeeEEeecCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeeeEeeceEEEE
Q 023289 172 PDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 250 (284)
Q Consensus 172 ~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~-gs~~iV~ikd~~g~~F~T~~~nVfvI 250 (284)
++.+++.||.++-+=-.|. |.+|= -+|+|..++.+. +.+..+.++-.. -.+++.||+++
T Consensus 209 ~~~~i~~GD~vvTSGlgg~------fP~Gl-----------~Vg~V~~v~~~~~~~~~~v~~~P~a---~~~~l~~v~l~ 268 (284)
T COG1792 209 PNSDIKEGDLVVTSGLGGV------FPAGL-----------PVGEVSSVKLDDYGLFKVVIVKPAA---SLDRLRYVLLV 268 (284)
T ss_pred CCCCccCCCEEEecCCCCc------CCCCc-----------EEEEEEEEEeCCCceeEEEEEeccc---ccccceEEEEE
Confidence 4557788875544433322 22231 378888888766 556778887654 37899999999
Q ss_pred cc
Q 023289 251 GK 252 (284)
Q Consensus 251 Gk 252 (284)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 85
No 75
>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=31.92 E-value=1e+02 Score=23.54 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=27.2
Q ss_pred EeeCCeeEEEccCCeeeecCC----CCCcCCCeEEEecC
Q 023289 153 FGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 187 (284)
Q Consensus 153 ~~kgG~~ql~thDGrni~~~d----p~ik~~DTv~i~l~ 187 (284)
.+......|.+.||.++..|. +.+++|..|++-..
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 356677899999999998875 36888888777554
No 76
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=31.65 E-value=40 Score=29.60 Aligned_cols=54 Identities=22% Similarity=0.137 Sum_probs=42.7
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEeccCC
Q 023289 61 RECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPKTN 118 (284)
Q Consensus 61 ~eslPL~i~LRd~LkyA~t~rEakkIl~~g-----~VkVDGkvrtD~kfPVG~MD---VIsI~kt~ 118 (284)
+...+|+-+||+.|++-.+ |.=+.+| .|+|||+++..--.|+.-+| |++|+--.
T Consensus 16 ~~~~~Ll~~LR~~lgltg~----K~gC~~G~CGACtVlvdg~~v~SCl~~~~~~~G~~V~TiEgl~ 77 (148)
T TIGR03193 16 ADNMLLVDYLRDTVGLTGT----KQGCDGGECGACTVLVDGRPRLACSTLAHRVAGRKVETVEGLA 77 (148)
T ss_pred CCCCcHHHHHHHhcCCCCC----CCCCCCCCCCCCEEEECCeEeeccHhhHhhcCCCcEEEeCCCC
Confidence 3467899999999876543 4556666 69999999999999998876 89987644
No 77
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=31.14 E-value=54 Score=28.15 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=25.9
Q ss_pred EEeecCCcEEEEECCCcceeEEEEEEEEE
Q 023289 194 FIKFDVGNIVMVTGGRNRGRVGIIKNREK 222 (284)
Q Consensus 194 ~ikfe~G~~~~VtgG~n~GrvG~I~~I~~ 222 (284)
...|++|+.+-|++|.=.|..|.|.++.+
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDY 152 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeC
Confidence 35688999999999999999999999854
No 78
>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=30.81 E-value=1.7e+02 Score=24.17 Aligned_cols=61 Identities=18% Similarity=0.393 Sum_probs=38.2
Q ss_pred ecCCcEEEE-ECCCcceeEEEEEEEEEe-----cCCc-cEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeee
Q 023289 197 FDVGNIVMV-TGGRNRGRVGIIKNREKH-----KGSF-ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLS 269 (284)
Q Consensus 197 fe~G~~~~V-tgG~n~GrvG~I~~I~~~-----~gs~-~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~ 269 (284)
|+.|+.--. +.... +|.|..|+.. ++-+ +-|.|+|.+|+. +.|...+ |+.-|-++-|+++
T Consensus 41 F~~G~~d~F~v~~~d---LG~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~ 107 (109)
T cd02899 41 FYPGSLKRIRFRAAD---VGDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECccc---cCceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEe
Confidence 555554322 12333 4445555442 1224 788898866644 4599988 9999999988876
Q ss_pred h
Q 023289 270 I 270 (284)
Q Consensus 270 ~ 270 (284)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 79
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=30.37 E-value=74 Score=35.72 Aligned_cols=27 Identities=33% Similarity=0.608 Sum_probs=25.4
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEe
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKH 223 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~ 223 (284)
|++|+.|=|+.|+|-|..|.|..++.+
T Consensus 460 F~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 460 FEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccCCCeEEEEeccccCCcceEEEEeCC
Confidence 889999999999999999999999873
No 80
>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=29.00 E-value=54 Score=25.37 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=27.8
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEec------CCccEEEEEcCCCCeee
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 241 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~~------gs~~iV~ikd~~g~~F~ 241 (284)
+.+|+.+||.| +|++|+|+.|.... .....|.++..+| .|+
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 45699999987 68888999986522 2235777776555 354
No 81
>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=28.91 E-value=58 Score=27.84 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=25.3
Q ss_pred EeecCCcEEEEECCCcceeEEEEEEEEE
Q 023289 195 IKFDVGNIVMVTGGRNRGRVGIIKNREK 222 (284)
Q Consensus 195 ikfe~G~~~~VtgG~n~GrvG~I~~I~~ 222 (284)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5588999999999999999999999853
No 82
>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=28.86 E-value=1.2e+02 Score=23.54 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=24.7
Q ss_pred CCcCCCeEEEecCCceeeeEEeecC-------CcEEEEECCCcce
Q 023289 175 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRG 212 (284)
Q Consensus 175 ~ik~~DTv~i~l~~~kI~d~ikfe~-------G~~~~VtgG~n~G 212 (284)
.++.||...+.+..++ -+.+|+ |..+++-+|+.+|
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 5899999999997554 345565 6777766665554
No 83
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=28.59 E-value=1.3e+02 Score=33.96 Aligned_cols=55 Identities=25% Similarity=0.359 Sum_probs=42.0
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCc--cEEEEEcCCCCeeeEeeceEEEEccCCC
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFATRLGNVFTIGKGSK 255 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~--~iV~ikd~~g~~F~T~~~nVfvIGk~~k 255 (284)
...++.+-+++|.|.|+-|.|.+|-+. .-| +.-.+ .++-.|.++.+|+..+|. .+
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~-~~F~h~r~~~--En~Gv~vck~k~~~~~g~-~~ 638 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRP-FVFLHSRKNL--ENGGVFVCKEKNLILAGG-KK 638 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecc-eeeeeehhhc--ccCCeEEEecCCceeccc-cC
Confidence 457899999999999999999999652 111 22223 466689999999999995 44
No 84
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=26.51 E-value=60 Score=25.43 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=15.2
Q ss_pred eecCCCCCcCCCeEEEe
Q 023289 169 IRYPDPLIKANDTIKLD 185 (284)
Q Consensus 169 i~~~dp~ik~~DTv~i~ 185 (284)
||..|.+|++||.+.+.
T Consensus 22 iRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 22 IRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEecCCCCCCCCEEEEE
Confidence 88899999999998874
No 85
>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=25.71 E-value=1.8e+02 Score=24.40 Aligned_cols=84 Identities=18% Similarity=0.265 Sum_probs=46.6
Q ss_pred ceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcEEEEECCC
Q 023289 130 RFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGR 209 (284)
Q Consensus 130 rf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~~~VtgG~ 209 (284)
.+.+.+.+.++..+. .|.+ ..|...+.-.+|+....|+..+..--.. .-+.........|++|+.+.|++|.
T Consensus 50 gYvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~--~~~~~~~~~~~~~~~G~~V~V~~GP 121 (159)
T TIGR01955 50 NYLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQY--EPKDSVPPATTLPYKGDKVRITDGA 121 (159)
T ss_pred CeEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhc--cccccCCccccCCCCCCEEEEeccC
Confidence 344666665543322 2211 2456666555565555555322211000 0001111233569999999999999
Q ss_pred cceeEEEEEEEE
Q 023289 210 NRGRVGIIKNRE 221 (284)
Q Consensus 210 n~GrvG~I~~I~ 221 (284)
-.|..|.|.++.
T Consensus 122 f~g~~g~v~~~~ 133 (159)
T TIGR01955 122 FAGFEAIFLEPD 133 (159)
T ss_pred CCCcEEEEEEEC
Confidence 999999999985
No 86
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=25.70 E-value=53 Score=28.98 Aligned_cols=50 Identities=18% Similarity=0.232 Sum_probs=36.7
Q ss_pred eeeeEEeecCCcEEEEECCCcce-eEEEEEEEEEecCC--ccEEEEEcCCCCe
Q 023289 190 KITDFIKFDVGNIVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 239 (284)
Q Consensus 190 kI~d~ikfe~G~~~~VtgG~n~G-rvG~I~~I~~~~gs--~~iV~ikd~~g~~ 239 (284)
-.+..+|+..++.+-|.+|+..| ++|+|.++-+..-. .+.|.-+-++|..
T Consensus 42 y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 42 YNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred hCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 35788999999999999999999 99999998663322 2344444455543
No 87
>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=25.60 E-value=44 Score=28.41 Aligned_cols=42 Identities=24% Similarity=0.360 Sum_probs=32.9
Q ss_pred CCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCC
Q 023289 128 KGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 174 (284)
Q Consensus 128 kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp 174 (284)
+..|+++.+|+= .+-+|--+.|..-+...+|| ||-|+-|.||
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 345777777654 45788888888888899998 9999999765
No 88
>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=25.47 E-value=2.2e+02 Score=24.72 Aligned_cols=52 Identities=17% Similarity=0.160 Sum_probs=38.2
Q ss_pred ccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHH
Q 023289 227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAA 280 (284)
Q Consensus 227 ~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~~~e~r~~~~~~ 280 (284)
++-+.+-|.+|+-=|+..+|+|++= +.-|++-|.+.|+-..+..+.-.++++
T Consensus 125 ~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~giL~Gitr~~ll~~~~ 176 (231)
T PF01063_consen 125 ADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGILPGITRQLLLELAK 176 (231)
T ss_dssp SSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSSB--HHHHHHHHHHH
T ss_pred cchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhhccHHHHHHHHHHHH
Confidence 4445667899999999999999984 445889999988877776665555444
No 89
>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=25.08 E-value=1.4e+02 Score=22.25 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=24.8
Q ss_pred eCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceee
Q 023289 155 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 192 (284)
Q Consensus 155 kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~ 192 (284)
.+..-...+..|-.|.+|. -|+.||.|+||-.+++=+
T Consensus 18 ~~~~K~A~letG~~i~VP~-FI~~Gd~I~VdT~~g~Yv 54 (56)
T PF09285_consen 18 SSSYKPATLETGAEIQVPL-FIEEGDKIKVDTRDGSYV 54 (56)
T ss_dssp STTEEEEEETTS-EEEEET-T--TT-EEEEETTTTEEE
T ss_pred CCCccEEEEcCCCEEEccc-eecCCCEEEEECCCCeEe
Confidence 3444566778888888764 799999999999998643
No 90
>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=24.99 E-value=2.9e+02 Score=20.44 Aligned_cols=55 Identities=13% Similarity=0.123 Sum_probs=29.4
Q ss_pred cCCcEEEEECCCcceeEE-EEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEcc
Q 023289 198 DVGNIVMVTGGRNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 252 (284)
Q Consensus 198 e~G~~~~VtgG~n~GrvG-~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk 252 (284)
.+|+.++...+.+..... .+.......+...++.++..+|.++..-.+.-|.+.+
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 456666666653222211 1122222334557888888888877655555555554
No 91
>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=24.20 E-value=1.5e+02 Score=22.09 Aligned_cols=34 Identities=12% Similarity=0.272 Sum_probs=27.8
Q ss_pred CceEEEEEcCCC--ceEEEEcChhhhcceeEEEEeE
Q 023289 118 NENFRLLYDTKG--RFRLHSLRDEEAKFKLCKVRSV 151 (284)
Q Consensus 118 ~e~yRvl~D~kG--rf~l~~I~~eEA~~KLcKV~~K 151 (284)
+++|++..+..| .|.+..+..++++.-.|...|.
T Consensus 28 ~~r~~~~~~~~g~~~L~I~~~~~~D~G~Y~C~A~N~ 63 (75)
T cd05892 28 TDRISLYQDNSGRVTLLIKNVNKKDAGWYTVSAVNE 63 (75)
T ss_pred CCeEEEEEcCCCcEEEEECCCChhhCEEEEEEEEcC
Confidence 467888888777 5777799999999889998873
No 92
>PF08942 DUF1919: Domain of unknown function (DUF1919); InterPro: IPR015037 This protein has no known function. It is found in various hypothetical and putative bacterial proteins. ; PDB: 2G6T_B.
Probab=24.12 E-value=19 Score=33.13 Aligned_cols=59 Identities=29% Similarity=0.408 Sum_probs=36.3
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChhhhcce
Q 023289 66 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFK 144 (284)
Q Consensus 66 L~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eEA~~K 144 (284)
|-+.-+|++++-.|.+. -+.+....++-.-..+ .||||..|-|+| .| +|==|.+||+-|
T Consensus 53 L~i~~~Dyik~l~nl~~---y~~~~l~~~~~~~~~~-~YPvG~L~dIei---------------hF-~HY~s~~eA~~K 111 (201)
T PF08942_consen 53 LFIFPPDYIKFLENLDY---YLSQELEFIDESKSYD-DYPVGLLGDIEI---------------HF-MHYKSFEEAKEK 111 (201)
T ss_dssp EE--HHHHHHHHHSHHH---HHCS--EECE--BGGG-B--EEEEC-EEE---------------EE-SS-SSHHHHHHH
T ss_pred eEECcHHHHHHHHCHHH---HhcCCeEEeecCcccC-CcceEeECCEEE---------------EE-EecCCHHHHHHH
Confidence 55666899999999875 3666655555444456 899999999998 34 455589999755
No 93
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=24.12 E-value=74 Score=31.43 Aligned_cols=45 Identities=18% Similarity=-0.026 Sum_probs=36.9
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcc
Q 023289 63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGF 108 (284)
Q Consensus 63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~ 108 (284)
.+++.=++.. .+.+.+.+||++-|++|-|+|||...+|..+-.-.
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~ 373 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKE 373 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhcc
Confidence 4666666664 58899999999999999999999999998764433
No 94
>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=23.11 E-value=1.7e+02 Score=20.83 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=28.7
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCc-cEEEEE
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 233 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~-~iV~ik 233 (284)
|++|..+++.-+...-.-++|.+++..++.. =.||-.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEET
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcC
Confidence 6789999999999999999999998866553 366664
No 95
>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=23.03 E-value=81 Score=26.05 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=18.7
Q ss_pred CCeeEEEccCCeeeecCCCCCcCCCeEEEecCC
Q 023289 156 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEE 188 (284)
Q Consensus 156 gG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~ 188 (284)
....++.+.|.+.+ +|++++||++.+.++-
T Consensus 67 d~~~eI~l~eAk~~---~~~~~vGD~i~~~i~~ 96 (122)
T PF08529_consen 67 DPDTEISLSEAKKI---DPNAEVGDEIEEEIDP 96 (122)
T ss_dssp -TTTEEEHHHHHCC---CTT--TTCEEEEE---
T ss_pred CccceeeHHHHHhh---CCCCccCCEEEecCCh
Confidence 45667777777655 6889999999888864
No 96
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family. Members of this family belong to the broader family of PRC-barrel domain proteins (see Pfam model pfam05239), but are found only in endospore-forming bacteria of the Firmicutes lineage. Most such species have exactly two members of this family and all have at least one; the function is unknown. One of two members from Bacillus subtilis, YmxH, is strongly induced by the mother cell-specific sigma-E factor.
Probab=22.91 E-value=3.5e+02 Score=21.00 Aligned_cols=41 Identities=29% Similarity=0.459 Sum_probs=28.5
Q ss_pred CCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCc
Q 023289 156 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGN 201 (284)
Q Consensus 156 gG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~ 201 (284)
.++..+|.+||+.+-+ +.-.| +.||..+|+|...+-...|.
T Consensus 6 ~~keVIni~~G~~lG~----v~~~D-l~iD~~~G~I~aiIi~~~~~ 46 (76)
T TIGR02888 6 RGKEIINVNDGERLGV----IGNID-LEIDEEDGRILSLIIPGKGK 46 (76)
T ss_pred cCCCEEECCCCcEeec----cccce-EEEECCCCEEEEEEEeCCCc
Confidence 3567789999999863 22234 78888899987666554443
No 97
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=22.70 E-value=79 Score=30.28 Aligned_cols=32 Identities=28% Similarity=0.521 Sum_probs=22.1
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEecCCc-cEEEE
Q 023289 199 VGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHI 232 (284)
Q Consensus 199 ~G~~~~VtgG~n~GrvG~I~~I~~~~gs~-~iV~i 232 (284)
.||.|.|+.|...|+.|.++. +|-|.. -+|.+
T Consensus 60 iGN~A~VvSG~AKG~~G~VtG--kHGGieHVlV~F 92 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTG--KHGGIEHVLVDF 92 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEE--EETTTTEEEEE-
T ss_pred cCceeEEeecccCCCcCeEec--ccCCeeeEEEEC
Confidence 499999999999999999987 366664 34444
No 98
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=22.05 E-value=4.6e+02 Score=26.34 Aligned_cols=52 Identities=27% Similarity=0.313 Sum_probs=34.8
Q ss_pred CCcCCCeEEEecCCceeeeEEee----cCCcEEEEECCCcceeEEEEEEEEEecCCc
Q 023289 175 LIKANDTIKLDLEENKITDFIKF----DVGNIVMVTGGRNRGRVGIIKNREKHKGSF 227 (284)
Q Consensus 175 ~ik~~DTv~i~l~~~kI~d~ikf----e~G~~~~VtgG~n~GrvG~I~~I~~~~gs~ 227 (284)
.++.||...+.+...+=+-.-+| .-|..++.-+|+-+| .|.|.++....||.
T Consensus 381 ~l~~g~~a~v~l~~~~pi~~e~~~~~~~lgrfilrd~g~tva-~G~I~~v~~~~~~~ 436 (446)
T PTZ00141 381 AIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRDMKQTVA-VGVIKSVEKKEGSG 436 (446)
T ss_pred EECCCCEEEEEEEECCceEEeecccCCCCccEEEEECCCEEE-EEEEEEEecCCCcc
Confidence 47789999888875543322333 246677777776555 89999988666664
No 99
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=21.83 E-value=1.5e+02 Score=28.01 Aligned_cols=11 Identities=18% Similarity=0.211 Sum_probs=5.9
Q ss_pred CcCCCeEEEec
Q 023289 176 IKANDTIKLDL 186 (284)
Q Consensus 176 ik~~DTv~i~l 186 (284)
+..||+|.+=.
T Consensus 73 ff~GDtVeVlv 83 (236)
T KOG1708|consen 73 FFFGDTVEVLV 83 (236)
T ss_pred EecCCEEEEEe
Confidence 55566655543
No 100
>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=21.62 E-value=3.6e+02 Score=20.34 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=16.5
Q ss_pred CcCCCeEEEecCCceeeeEEeecCCcEEEE
Q 023289 176 IKANDTIKLDLEENKITDFIKFDVGNIVMV 205 (284)
Q Consensus 176 ik~~DTv~i~l~~~kI~d~ikfe~G~~~~V 205 (284)
+++||+..+.+.-.+ -+.+++|.-.++
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 888888887776443 234555544444
No 101
>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=21.56 E-value=4.6e+02 Score=25.54 Aligned_cols=71 Identities=14% Similarity=0.155 Sum_probs=40.4
Q ss_pred eEEEEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeec
Q 023289 120 NFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFD 198 (284)
Q Consensus 120 ~yRvl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe 198 (284)
.|=.+-+.+|.+...-+... | .|..+.++.+-.-.-...|||-+-.. .+..++..++|.++.+++..|+-.
T Consensus 49 r~~yv~~rdg~vsviD~~~~----~--~v~~i~~G~~~~~i~~s~DG~~~~v~--n~~~~~v~v~D~~tle~v~~I~~~ 119 (369)
T PF02239_consen 49 RYLYVANRDGTVSVIDLATG----K--VVATIKVGGNPRGIAVSPDGKYVYVA--NYEPGTVSVIDAETLEPVKTIPTG 119 (369)
T ss_dssp SEEEEEETTSEEEEEETTSS----S--EEEEEE-SSEEEEEEE--TTTEEEEE--EEETTEEEEEETTT--EEEEEE--
T ss_pred CEEEEEcCCCeEEEEECCcc----c--EEEEEecCCCcceEEEcCCCCEEEEE--ecCCCceeEeccccccceeecccc
Confidence 34444566676555544222 2 23344455555555567899987543 377888899999999999988754
No 102
>PLN02772 guanylate kinase
Probab=21.40 E-value=2e+02 Score=29.21 Aligned_cols=63 Identities=21% Similarity=0.306 Sum_probs=38.4
Q ss_pred EEeecCCcEEEEECCCccee-EEEEEEE-EEecCCccEEEEEc-----CCCCeeeEe-eceEEEEccCCCc
Q 023289 194 FIKFDVGNIVMVTGGRNRGR-VGIIKNR-EKHKGSFETIHIQD-----ALGHEFATR-LGNVFTIGKGSKP 256 (284)
Q Consensus 194 ~ikfe~G~~~~VtgG~n~Gr-vG~I~~I-~~~~gs~~iV~ikd-----~~g~~F~T~-~~nVfvIGk~~kp 256 (284)
+--+..|+..+|+||+|-+. .-....| ...........+.. .+|+++... .+.+.||+++..|
T Consensus 28 ~tav~igdk~yv~GG~~d~~~~~~~v~i~D~~t~~W~~P~V~G~~P~~r~GhSa~v~~~~rilv~~~~~~~ 98 (398)
T PLN02772 28 ETSVTIGDKTYVIGGNHEGNTLSIGVQILDKITNNWVSPIVLGTGPKPCKGYSAVVLNKDRILVIKKGSAP 98 (398)
T ss_pred ceeEEECCEEEEEcccCCCccccceEEEEECCCCcEecccccCCCCCCCCcceEEEECCceEEEEeCCCCC
Confidence 34456689999999999864 2222222 22112233333332 468887777 6899999976543
No 103
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=21.12 E-value=2.8e+02 Score=23.71 Aligned_cols=77 Identities=16% Similarity=0.201 Sum_probs=45.3
Q ss_pred EEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcEEEEECCCcceeEEEEEEEEEecCCc-cEEEEEcCCCC
Q 023289 160 YINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQDALGH 238 (284)
Q Consensus 160 ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~-~iV~ikd~~g~ 238 (284)
+|.+|+|++-++.| +++.|.++-...+ +-+++++.-...|......|. ..|.=.++.. ..++++-.-++
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 56679999988765 7888887766555 445555555555554433322 2233333432 56666655555
Q ss_pred eeeEeeceEEEEccC
Q 023289 239 EFATRLGNVFTIGKG 253 (284)
Q Consensus 239 ~F~T~~~nVfvIGk~ 253 (284)
-| ||-|+|
T Consensus 77 Pf-------FV~gqG 84 (116)
T smart00536 77 PF-------FVKGKG 84 (116)
T ss_pred Ce-------EEcCcc
Confidence 54 777764
No 104
>PF03143 GTP_EFTU_D3: Elongation factor Tu C-terminal domain; InterPro: IPR004160 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents the C-terminal domain, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA and to EF1B (or EF-Ts, IPR001816 from INTERPRO) []. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1TUI_C 1OB5_E 1TTT_B 1B23_P 1EFT_A 3E20_E 1R5B_A 1R5O_A 1R5N_A 3AGJ_C ....
Probab=21.11 E-value=2.3e+02 Score=22.19 Aligned_cols=43 Identities=21% Similarity=0.273 Sum_probs=33.6
Q ss_pred CCcCCCeEEEecCCceeeeEEeecCCcEEEEECCCcceeEEEEEEE
Q 023289 175 LIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNR 220 (284)
Q Consensus 175 ~ik~~DTv~i~l~~~kI~d~ikfe~G~~~~VtgG~n~GrvG~I~~I 220 (284)
.++.||...+.+.-.+ -+..|+++..++=.|.++--+|+|+++
T Consensus 56 ~l~~g~~a~v~l~~~~---pi~ve~~~Rf~lR~~~~Tia~G~V~~v 98 (99)
T PF03143_consen 56 FLKPGDRAVVELEFQK---PICVEPFSRFILRDGGKTIAVGVVTKV 98 (99)
T ss_dssp EB-TTEEEEEEEEEEE---EEEETTTTEEEEEETTEEEEEEEEEEE
T ss_pred ccccccccccceeecc---ceeeecCceEEEccCCeEEEEEEEEEe
Confidence 4899999999986654 678899997777777766669999886
No 105
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=20.56 E-value=1e+02 Score=26.19 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=24.2
Q ss_pred eecCCcEEEEECCCcceeEEEEEEEE
Q 023289 196 KFDVGNIVMVTGGRNRGRVGIIKNRE 221 (284)
Q Consensus 196 kfe~G~~~~VtgG~n~GrvG~I~~I~ 221 (284)
.|++|+.+.|++|.=.|..|.|.++.
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 106
>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=20.48 E-value=2.5e+02 Score=22.09 Aligned_cols=33 Identities=24% Similarity=0.392 Sum_probs=24.2
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCC
Q 023289 197 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGH 238 (284)
Q Consensus 197 fe~G~~~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~ 238 (284)
+.+|+.++-+|| -+|+|.++.. +.+.++.++|.
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d-----~~v~vei~~g~ 70 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAE-----NTIVIELNDNT 70 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCCe
Confidence 567888888775 6899999863 56777776653
No 107
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=20.18 E-value=1e+02 Score=27.58 Aligned_cols=30 Identities=17% Similarity=0.367 Sum_probs=26.4
Q ss_pred eEEeecCCcEEEEECCCcceeEEEEEEEEE
Q 023289 193 DFIKFDVGNIVMVTGGRNRGRVGIIKNREK 222 (284)
Q Consensus 193 d~ikfe~G~~~~VtgG~n~GrvG~I~~I~~ 222 (284)
....|++|+.+-|+.|.=+|..|+|.++..
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ 149 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDE 149 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEcC
Confidence 445689999999999999999999999854
No 108
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=20.08 E-value=1.7e+02 Score=21.77 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=26.3
Q ss_pred eCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCce
Q 023289 155 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 190 (284)
Q Consensus 155 kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~k 190 (284)
.++.-...+..|-.|.+|. -|+.||.|++|-.+++
T Consensus 18 ~~~~K~A~letG~~i~VP~-FI~~Gd~I~V~T~~g~ 52 (56)
T cd05794 18 SSGTKPATLETGAEVQVPL-FIKEGEKIKVDTRTGE 52 (56)
T ss_pred CCCcceEEECCCCEEEcCC-eecCCCEEEEECCCCc
Confidence 3343445578888887653 6899999999999876
Done!