Query 025838
Match_columns 247
No_of_seqs 122 out of 333
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 10:07:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025838.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025838hhsearch_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-107 4E-112 735.4 29.2 242 1-242 19-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 4E-107 8E-112 733.9 29.6 243 1-243 19-261 (262)
3 PTZ00223 40S ribosomal protein 100.0 1E-106 2E-111 734.1 29.9 245 1-245 16-261 (273)
4 PRK04313 30S ribosomal protein 100.0 1.8E-99 4E-104 676.2 27.4 221 1-222 15-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 2.8E-96 6E-101 651.0 23.6 223 1-224 18-241 (241)
6 KOG0378 40S ribosomal protein 100.0 2.6E-94 5.6E-99 641.2 15.1 245 1-245 19-263 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 4.9E-35 1.1E-39 222.1 9.7 77 76-152 1-77 (77)
8 PF08071 RS4NT: RS4NT (NUC023) 98.6 1.2E-08 2.6E-13 68.3 1.4 22 1-22 17-38 (38)
9 PF01479 S4: S4 domain; Inter 98.6 1.2E-07 2.6E-12 64.4 5.2 48 24-72 1-48 (48)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.6 0.00031 6.8E-09 48.2 6.9 62 25-87 2-63 (70)
11 smart00363 S4 S4 RNA-binding d 97.2 0.00084 1.8E-08 44.8 5.4 51 25-76 2-52 (60)
12 COG0522 RpsD Ribosomal protein 96.8 0.0012 2.6E-08 58.8 3.8 43 33-75 102-144 (205)
13 PF00467 KOW: KOW motif; Inte 96.8 0.0015 3.2E-08 41.6 3.1 31 159-192 1-31 (32)
14 smart00739 KOW KOW (Kyprides, 96.7 0.0014 3.1E-08 39.3 2.7 27 156-182 1-27 (28)
15 TIGR02988 YaaA_near_RecF S4 do 96.7 0.0043 9.4E-08 44.0 5.6 51 24-75 9-59 (59)
16 PF13275 S4_2: S4 domain; PDB: 95.9 0.004 8.7E-08 46.3 1.6 60 22-84 6-65 (65)
17 TIGR01018 rpsD_arch ribosomal 95.6 0.01 2.2E-07 51.3 3.0 43 33-75 112-156 (162)
18 PRK11507 ribosome-associated p 95.5 0.06 1.3E-06 40.7 6.7 60 22-84 10-69 (70)
19 PTZ00155 40S ribosomal protein 95.4 0.011 2.5E-07 51.8 2.9 38 27-64 102-146 (181)
20 PLN00189 40S ribosomal protein 95.3 0.015 3.2E-07 51.7 3.0 40 33-72 117-156 (194)
21 PRK04051 rps4p 30S ribosomal p 95.1 0.022 4.8E-07 49.8 3.7 43 34-76 112-156 (177)
22 TIGR01017 rpsD_bact ribosomal 95.0 0.04 8.6E-07 48.7 4.9 43 34-76 99-141 (200)
23 TIGR00005 rluA_subfam pseudour 95.0 0.1 2.2E-06 47.6 7.7 53 22-75 4-56 (299)
24 PRK05327 rpsD 30S ribosomal pr 94.8 0.052 1.1E-06 48.1 5.0 43 34-76 102-144 (203)
25 CHL00113 rps4 ribosomal protei 94.6 0.055 1.2E-06 48.1 4.8 43 34-76 98-140 (201)
26 TIGR01080 rplX_A_E ribosomal p 94.6 0.082 1.8E-06 43.3 5.4 56 153-211 38-100 (114)
27 TIGR03069 PS_II_S4 photosystem 94.4 0.14 3.1E-06 46.8 7.1 63 22-97 182-244 (257)
28 TIGR00478 tly hemolysin TlyA f 93.2 0.16 3.5E-06 45.7 5.2 47 29-76 5-51 (228)
29 COG2501 S4-like RNA binding pr 92.7 0.17 3.6E-06 38.6 3.9 54 22-76 10-63 (73)
30 PRK11180 rluD 23S rRNA pseudou 92.4 0.48 1E-05 44.2 7.3 53 22-75 16-68 (325)
31 PRK05912 tyrosyl-tRNA syntheta 90.9 0.8 1.7E-05 44.5 7.4 65 23-94 342-406 (408)
32 COG0564 RluA Pseudouridylate s 90.9 0.81 1.8E-05 42.5 7.1 57 22-81 11-67 (289)
33 PRK10700 23S rRNA pseudouridyl 90.8 0.76 1.6E-05 42.6 6.8 65 26-93 5-81 (289)
34 PRK01191 rpl24p 50S ribosomal 90.0 0.83 1.8E-05 37.9 5.6 38 154-194 43-80 (120)
35 PRK10348 ribosome-associated h 89.5 0.9 2E-05 38.2 5.6 57 23-81 8-64 (133)
36 COG1187 RsuA 16S rRNA uridine- 89.2 0.91 2E-05 41.7 5.8 60 34-94 12-78 (248)
37 PRK10475 23S rRNA pseudouridin 89.0 1.5 3.3E-05 40.8 7.3 68 22-92 5-80 (290)
38 PRK11025 23S rRNA pseudouridyl 88.5 1.9 4.2E-05 40.1 7.6 51 23-75 19-69 (317)
39 PRK10839 16S rRNA pseudouridyl 87.0 3.6 7.8E-05 36.3 8.1 67 26-95 3-75 (232)
40 PLN00051 RNA-binding S4 domain 86.9 2.6 5.6E-05 39.0 7.4 62 23-97 191-252 (267)
41 PRK12281 rplX 50S ribosomal pr 86.8 1.1 2.4E-05 34.1 4.1 39 155-196 5-43 (76)
42 CHL00141 rpl24 ribosomal prote 86.4 1.2 2.7E-05 34.3 4.2 39 154-195 6-44 (83)
43 COG2302 Uncharacterized conser 86.0 1.8 3.9E-05 40.2 5.8 63 22-97 179-241 (257)
44 PRK13354 tyrosyl-tRNA syntheta 85.7 2.8 6.1E-05 40.9 7.3 66 23-94 342-407 (410)
45 PRK00004 rplX 50S ribosomal pr 85.4 1.2 2.6E-05 35.8 3.8 37 155-194 3-39 (105)
46 COG1189 Predicted rRNA methyla 84.8 1.4 3E-05 40.6 4.4 47 35-81 13-59 (245)
47 PTZ00194 60S ribosomal protein 84.5 2.2 4.7E-05 36.5 5.2 57 155-211 45-105 (143)
48 TIGR01079 rplX_bact ribosomal 78.7 3.1 6.7E-05 33.4 3.9 28 156-183 3-30 (104)
49 PF13051 DUF3912: Protein of u 78.6 5.6 0.00012 29.5 4.8 50 159-212 5-55 (68)
50 KOG4655 U3 small nucleolar rib 68.7 3.7 8E-05 36.1 2.2 55 12-66 87-148 (181)
51 COG0162 TyrS Tyrosyl-tRNA synt 65.9 13 0.00029 36.4 5.7 54 34-94 345-398 (401)
52 COG2163 RPL14A Ribosomal prote 61.1 8.7 0.00019 32.1 3.0 26 157-182 5-30 (125)
53 COG0198 RplX Ribosomal protein 60.4 14 0.0003 30.0 3.9 29 155-183 3-31 (104)
54 PF03417 AAT: Acyl-coenzyme A: 59.7 43 0.00092 29.0 7.2 29 21-50 69-97 (225)
55 PTZ00065 60S ribosomal protein 53.3 16 0.00035 30.7 3.3 33 157-193 8-40 (130)
56 PF14001 YdfZ: YdfZ protein 52.1 23 0.0005 26.5 3.6 41 157-201 10-56 (64)
57 PRK04333 50S ribosomal protein 49.9 18 0.00039 28.1 2.9 33 156-192 3-35 (84)
58 COG1188 Ribosome-associated he 48.9 44 0.00095 27.0 5.0 44 35-79 19-62 (100)
59 cd03704 eRF3c_III This family 44.8 65 0.0014 24.8 5.4 48 132-180 56-108 (108)
60 PF08828 DSX_dimer: Doublesex 44.1 14 0.00031 27.4 1.5 33 21-56 21-54 (62)
61 PRK14898 DNA-directed RNA poly 43.6 1.1E+02 0.0023 33.0 8.4 77 66-144 112-195 (858)
62 PF01959 DHQS: 3-dehydroquinat 42.8 49 0.0011 32.2 5.2 54 105-173 289-345 (354)
63 PRK02290 3-dehydroquinate synt 42.3 49 0.0011 32.1 5.1 54 105-173 279-335 (344)
64 PF04773 FecR: FecR protein; 42.0 1.4E+02 0.0029 21.9 9.4 68 111-178 3-77 (98)
65 TIGR03193 4hydroxCoAred 4-hydr 40.6 23 0.00051 30.3 2.4 54 21-78 16-77 (148)
66 PTZ00471 60S ribosomal protein 39.5 30 0.00064 29.4 2.9 24 157-180 5-28 (134)
67 cd02899 PLAT_SR Scavenger rece 38.0 1.2E+02 0.0026 24.4 6.1 61 157-230 41-108 (109)
68 cd04093 HBS1_C HBS1_C: this fa 37.6 1.8E+02 0.004 22.1 8.8 45 135-180 59-107 (107)
69 cd03706 mtEFTU_III Domain III 36.2 1.6E+02 0.0035 22.0 6.3 40 136-179 52-92 (93)
70 COG1792 MreC Cell shape-determ 35.1 3.8E+02 0.0081 25.0 11.4 61 132-212 209-270 (284)
71 PF01588 tRNA_bind: Putative t 34.6 86 0.0019 24.0 4.6 24 173-196 2-27 (95)
72 TIGR00405 L26e_arch ribosomal 34.3 70 0.0015 26.2 4.3 26 157-182 87-112 (145)
73 PRK08559 nusG transcription an 34.1 64 0.0014 27.1 4.1 29 155-183 93-121 (153)
74 cd03705 EF1_alpha_III Domain I 33.1 98 0.0021 23.5 4.7 35 135-172 59-100 (104)
75 PF12961 DUF3850: Domain of Un 32.6 42 0.0009 25.6 2.4 18 128-145 21-38 (72)
76 PF07076 DUF1344: Protein of u 32.4 1E+02 0.0022 22.9 4.3 35 113-147 11-49 (61)
77 KOG1999 RNA polymerase II tran 31.3 72 0.0016 35.0 4.7 27 157-183 460-486 (1024)
78 PRK05609 nusG transcription an 30.3 59 0.0013 27.3 3.3 29 154-182 124-152 (181)
79 TIGR03198 pucE xanthine dehydr 29.9 20 0.00043 30.7 0.4 53 21-77 18-78 (151)
80 PF08942 DUF1919: Domain of un 28.6 14 0.00031 33.1 -0.7 60 26-105 53-112 (201)
81 KOG1999 RNA polymerase II tran 28.4 1.3E+02 0.0029 33.1 6.1 55 157-215 582-638 (1024)
82 cd01234 PH_CADPS CADPS (Ca2+-d 28.3 41 0.00089 27.8 1.9 42 88-134 21-62 (117)
83 TIGR00234 tyrS tyrosyl-tRNA sy 27.8 58 0.0013 31.4 3.1 46 23-69 329-374 (377)
84 TIGR00922 nusG transcription t 27.4 67 0.0014 26.8 3.1 28 155-182 118-145 (172)
85 cd05892 Ig_Myotilin_C C-termin 27.3 1.2E+02 0.0026 22.0 4.1 34 78-111 28-63 (75)
86 KOG3401 60S ribosomal protein 26.8 52 0.0011 28.3 2.3 50 150-199 42-94 (145)
87 PF11717 Tudor-knot: RNA bindi 26.8 1.8E+02 0.004 20.1 4.8 37 157-193 1-38 (55)
88 PF09285 Elong-fact-P_C: Elong 26.2 1.2E+02 0.0027 21.8 3.9 37 115-152 18-54 (56)
89 PTZ00141 elongation factor 1- 26.1 3.3E+02 0.0072 26.7 8.1 52 135-187 381-436 (446)
90 TIGR00432 arcsn_tRNA_tgt tRNA- 25.5 1.4E+02 0.003 30.5 5.5 93 59-153 399-514 (540)
91 KOG1784 Small Nuclear ribonucl 25.0 1.4E+02 0.003 24.0 4.2 60 116-179 10-75 (96)
92 cd05741 Ig_CEACAM_D1_like Firs 24.0 1.1E+02 0.0024 21.9 3.4 31 82-112 50-80 (92)
93 PF10781 DSRB: Dextransucrase 23.5 1.7E+02 0.0036 21.7 4.1 29 137-165 2-35 (62)
94 PF01063 Aminotran_4: Aminotra 23.3 2.1E+02 0.0046 24.3 5.5 53 186-240 124-176 (231)
95 PF06905 FAIM1: Fas apoptotic 23.0 5.2E+02 0.011 22.7 10.3 101 48-176 29-133 (177)
96 TIGR02888 spore_YlmC_YmxH spor 22.8 3.4E+02 0.0074 20.5 6.1 40 117-161 7-46 (76)
97 PF08529 NusA_N: NusA N-termin 22.5 86 0.0019 25.3 2.8 31 115-148 66-96 (122)
98 PF14505 DUF4438: Domain of un 22.2 66 0.0014 30.0 2.3 33 159-193 60-93 (258)
99 cd05794 S1_EF-P_repeat_2 S1_EF 22.2 1.5E+02 0.0033 21.4 3.7 35 115-150 18-52 (56)
100 TIGR01955 RfaH transcriptional 21.9 2.5E+02 0.0054 22.9 5.5 83 91-181 51-133 (159)
101 KOG2623 Tyrosyl-tRNA synthetas 21.7 1.1E+02 0.0023 30.7 3.7 39 22-61 397-435 (467)
102 TIGR03318 YdfZ_fam putative se 21.5 64 0.0014 24.2 1.7 41 157-201 11-57 (65)
103 PF13620 CarboxypepD_reg: Carb 21.3 1.4E+02 0.0031 21.1 3.5 45 54-98 2-47 (82)
104 COG1188 Ribosome-associated he 20.9 1.1E+02 0.0023 24.8 2.9 35 112-150 29-63 (100)
105 smart00841 Elong-fact-P_C Elon 20.6 1.7E+02 0.0037 21.1 3.7 30 120-150 23-52 (56)
106 TIGR01956 NusG_myco NusG famil 20.5 1.1E+02 0.0023 28.6 3.3 30 153-182 202-231 (258)
107 PF02239 Cytochrom_D1: Cytochr 20.2 5.7E+02 0.012 24.4 8.2 71 80-158 49-119 (369)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.9e-107 Score=735.36 Aligned_cols=242 Identities=89% Similarity=1.381 Sum_probs=239.2
Q ss_pred CCcccCceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCce
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 80 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 80 (247)
||+|++++||||||||||+++|||||++||||+|+||+|++||++||+||+|+|||+||||++||||||||||||++||+
T Consensus 19 ~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~ 98 (261)
T PLN00036 19 MLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKTNEN 98 (261)
T ss_pred ccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCC
Q 025838 81 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVG 160 (247)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G 160 (247)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+||||+|+|++|+||++|
T Consensus 99 yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G 178 (261)
T PLN00036 99 FRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVG 178 (261)
T ss_pred EEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEEEEeCCCCceeeEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCCCCceeeehHHHHHHHHHH
Q 025838 161 NVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL 240 (247)
Q Consensus 161 ~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (247)
|+||||||+|+|++|+|.+|+++++|+++||++|++|++|+|+++||||||++++||||||+++|||+|++|||++++++
T Consensus 179 ~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~~e~r~~~~~~ 258 (261)
T PLN00036 179 NLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKRLAA 258 (261)
T ss_pred CEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccchHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999988999999999999999999999999987
Q ss_pred Hh
Q 025838 241 AT 242 (247)
Q Consensus 241 ~~ 242 (247)
.+
T Consensus 259 ~~ 260 (261)
T PLN00036 259 GQ 260 (261)
T ss_pred hc
Confidence 64
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=3.5e-107 Score=733.87 Aligned_cols=243 Identities=64% Similarity=1.027 Sum_probs=240.0
Q ss_pred CCcccCceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCce
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 80 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 80 (247)
||+|++++||||||||||++++||||++||||+|+||+|++||++||+||+|+|||+||||++||||||||||||++|||
T Consensus 19 ~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~ 98 (262)
T PTZ00118 19 MLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEY 98 (262)
T ss_pred ccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCC
Q 025838 81 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVG 160 (247)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G 160 (247)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+||||+|+|++||||++|
T Consensus 99 yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G 178 (262)
T PTZ00118 99 FRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVG 178 (262)
T ss_pred EEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCEEEEECCCCceeeEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCCCCceeeehHHHHHHHHHH
Q 025838 161 NVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL 240 (247)
Q Consensus 161 ~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (247)
|+||||||+|+|++|+|.++++++||+++||++|++|++|+|+++||||||++++||||||++||||||++|||++++++
T Consensus 179 ~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~kgi~~~~~e~~~~~~~~ 258 (262)
T PTZ00118 179 NLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDIIEERRNRLAK 258 (262)
T ss_pred CEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCccccHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999988999999999999999999999999988
Q ss_pred Hhh
Q 025838 241 ATS 243 (247)
Q Consensus 241 ~~~ 243 (247)
++.
T Consensus 259 ~~~ 261 (262)
T PTZ00118 259 ALR 261 (262)
T ss_pred Hhc
Confidence 763
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=9.9e-107 Score=734.06 Aligned_cols=245 Identities=51% Similarity=0.839 Sum_probs=240.7
Q ss_pred CCcccCceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCce
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 80 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 80 (247)
||+|++++||||||||||++++||||++||||+|+||+|++||++||+||+|+|||+||||++||||||||||||++||+
T Consensus 16 ~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~ 95 (273)
T PTZ00223 16 MLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDR 95 (273)
T ss_pred ccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCC
Q 025838 81 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVG 160 (247)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G 160 (247)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|+||+|+|++||||++|
T Consensus 96 yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G 175 (273)
T PTZ00223 96 FRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNG 175 (273)
T ss_pred EEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCEEEEECCCCeeeEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccC-CCceEeCCCCCceeeehHHHHHHHHH
Q 025838 161 NVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-TKPWVSLPKGKGIKLSIIEEARKRQA 239 (247)
Q Consensus 161 ~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~~g~~F~T~~~~vfvIG~~-~kp~islp~~~gi~~~~~~~~~~~~~ 239 (247)
|+||||||+|+|++|+|.+|++++|++++||++|++|++|+|+++||||||++ ++|||+||++||||||++|||+++++
T Consensus 176 ~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~~e~~~~~~~ 255 (273)
T PTZ00223 176 KVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINVIQEREEKLI 255 (273)
T ss_pred CEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999986 69999999999999999999999998
Q ss_pred HHhhhh
Q 025838 240 LATSAA 245 (247)
Q Consensus 240 ~~~~~~ 245 (247)
++++++
T Consensus 256 ~~~~~~ 261 (273)
T PTZ00223 256 AAEARK 261 (273)
T ss_pred HHHhhh
Confidence 887643
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=1.8e-99 Score=676.19 Aligned_cols=221 Identities=40% Similarity=0.645 Sum_probs=218.1
Q ss_pred CCcccCceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCce
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 80 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 80 (247)
||+|++++||||||||||++++||||++||||+|+||+|+|||++||+||+|+||||||+|++||||||||||||++||+
T Consensus 15 ~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~ 94 (237)
T PRK04313 15 PIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETGEY 94 (237)
T ss_pred ccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCC-CCccCCCeEEEecCCCceeeEEEeeC
Q 025838 81 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKANDTIKLDLETNKITEFIKFDV 159 (247)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d-~~ik~~Dtv~i~l~~~kI~d~ikfe~ 159 (247)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| ++||+||||+|+||+|+|++||||++
T Consensus 95 yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~ 174 (237)
T PRK04313 95 YRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEE 174 (237)
T ss_pred EEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEecCC
Confidence 99999999999999999999999999999999999999999999999999998 99999999999999999999999999
Q ss_pred CcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCC
Q 025838 160 GNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 222 (247)
Q Consensus 160 G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~ 222 (247)
||+||||||+|+|++|+|.+|++++ +++++|+++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 175 G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 175 GNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred CCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 9999999999999999999999999 7789999999999999999999999998 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-96 Score=651.02 Aligned_cols=223 Identities=47% Similarity=0.734 Sum_probs=219.5
Q ss_pred CCcccCceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCce
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 80 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 80 (247)
|++||+++|||+|+||||++++||||++++||+|+||+|+|||++||++|+|+|||+||+|++||||||||||||+|||+
T Consensus 18 ~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~ 97 (241)
T COG1471 18 PIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEH 97 (241)
T ss_pred EeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCCCce
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCC
Q 025838 81 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVG 160 (247)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G 160 (247)
||||||.+|+|.||+|++|||.||||||+||++++||++|||||||||++++|+.|++||||++++|+++|++||||++|
T Consensus 98 yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g 177 (241)
T COG1471 98 YRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEG 177 (241)
T ss_pred EEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccEEEEeCCChhheeEeccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCCCC
Q 025838 161 NVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGK 224 (247)
Q Consensus 161 ~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~ 224 (247)
++||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++|||+||+|+
T Consensus 178 ~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~e~ 241 (241)
T COG1471 178 ALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPKEK 241 (241)
T ss_pred cEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCCCC
Confidence 999999999999999999999999 5579999999999999999999999998 99999999875
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-94 Score=641.16 Aligned_cols=245 Identities=70% Similarity=1.140 Sum_probs=243.0
Q ss_pred CCcccCceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCce
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 80 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 80 (247)
||||++|.|||+||+|||+++||+||++||||+|+||+|.+|+++|++|+.|+|||+||+|.+||+||||||+|++|||+
T Consensus 19 mldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisiekTge~ 98 (263)
T KOG0378|consen 19 MLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIEKTGEH 98 (263)
T ss_pred eecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeecccccccceeEEEEecccchh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCC
Q 025838 81 FRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVG 160 (247)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G 160 (247)
||++||++|+|.+|+|++|||+||||||++++.+++|+|+|+|||||+||||||.||+|||+++++++++|.++++|++|
T Consensus 99 fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dtI~~~~~t~kit~~ikf~~~ 178 (263)
T KOG0378|consen 99 FRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDTIKIDLETSKITDFIKFDTG 178 (263)
T ss_pred hhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCccceeeccCCCceeeeeeccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCCCCceeeehHHHHHHHHHH
Q 025838 161 NVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL 240 (247)
Q Consensus 161 ~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (247)
++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++|+||||++++||||||+++||+++++||||+|+++
T Consensus 179 ~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPkgkgi~~siaEe~dkrl~~ 258 (263)
T KOG0378|consen 179 NLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPKGKGIALSIAEERDKRLAA 258 (263)
T ss_pred ceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCccccCccchhhHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhh
Q 025838 241 ATSAA 245 (247)
Q Consensus 241 ~~~~~ 245 (247)
+.+++
T Consensus 259 k~~s~ 263 (263)
T KOG0378|consen 259 KISSG 263 (263)
T ss_pred hccCC
Confidence 98763
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=4.9e-35 Score=222.13 Aligned_cols=77 Identities=64% Similarity=1.028 Sum_probs=69.7
Q ss_pred cCCceEEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCcee
Q 025838 76 KTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 152 (247)
Q Consensus 76 kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 152 (247)
+|||+|||+||++|+|.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
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
>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=98.62 E-value=1.2e-08 Score=68.34 Aligned_cols=22 Identities=68% Similarity=1.173 Sum_probs=13.0
Q ss_pred CCcccCceeccCCCCCCCCCcc
Q 025838 1 MLDKLGGAFAPKPSSGPHKSRE 22 (247)
Q Consensus 1 ml~K~~~~~a~kpspGPH~~~e 22 (247)
||+|++++|||+||||||+++|
T Consensus 17 ~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 17 MIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp T--SSSSSB-----SSSS-CCC
T ss_pred ccccccCccccCCCCCCccCCC
Confidence 7999999999999999999986
No 9
>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=98.57 E-value=1.2e-07 Score=64.41 Aligned_cols=48 Identities=31% Similarity=0.323 Sum_probs=44.3
Q ss_pred chHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeE
Q 025838 24 LPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVV 72 (247)
Q Consensus 24 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVI 72 (247)
++|..|| ..++++.+..||++++++|.|+|||++++|+.|++...|+|
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 45899999999999999999999999999999999999987
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=97.60 E-value=0.00031 Score=48.23 Aligned_cols=62 Identities=26% Similarity=0.305 Sum_probs=47.6
Q ss_pred hHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcC
Q 025838 25 PLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDT 87 (247)
Q Consensus 25 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~ 87 (247)
.|.-+|+.. ..+.+..+|++++.+|.|+|||+..++..+++-..|+|++........++|..
T Consensus 2 rl~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~ed 63 (70)
T cd00165 2 RLDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63 (70)
T ss_pred cHHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceeecc
Confidence 355566654 35789999999999999999999999999999888999997643223444433
No 11
>smart00363 S4 S4 RNA-binding domain.
Probab=97.25 E-value=0.00084 Score=44.80 Aligned_cols=51 Identities=24% Similarity=0.167 Sum_probs=42.6
Q ss_pred hHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc
Q 025838 25 PLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 76 (247)
Q Consensus 25 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 76 (247)
.|..+|... ..+.+.+++++++.+|.|+|||++.++..+++--.|.|++..
T Consensus 2 rl~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 2 RLDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred cHHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 345566543 346789999999999999999999999999998889999965
No 12
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=96.80 E-value=0.0012 Score=58.79 Aligned_cols=43 Identities=28% Similarity=0.358 Sum_probs=41.0
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEec
Q 025838 33 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 75 (247)
Q Consensus 33 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 75 (247)
++|+|.|.++|++.+..|+|.|||+.++.+-|=|--=|+|+|.
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 13
>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=96.78 E-value=0.0015 Score=41.56 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=25.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 025838 159 VGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 192 (247)
Q Consensus 159 ~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v 192 (247)
+|+.++|+.|++.|+.|+|.++..+. ..|++
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 45554
No 14
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.74 E-value=0.0014 Score=39.32 Aligned_cols=27 Identities=37% Similarity=0.668 Sum_probs=24.5
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEE
Q 025838 156 KFDVGNVVMVTGGRNRGRVGIIKNREK 182 (247)
Q Consensus 156 kfe~G~~~~vtgG~n~G~vG~I~~i~~ 182 (247)
+|++|+.++|++|.+.|.+|+|.++..
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 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=96.74 E-value=0.0043 Score=44.02 Aligned_cols=51 Identities=20% Similarity=0.184 Sum_probs=44.5
Q ss_pred chHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEec
Q 025838 24 LPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 75 (247)
Q Consensus 24 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 75 (247)
..|--||... .++.+...+++++.+|.|+|||++++.+.|.+--=|+|+|+
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 5676777777 77779999999999999999999999889998888888874
No 16
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.93 E-value=0.004 Score=46.27 Aligned_cols=60 Identities=25% Similarity=0.281 Sum_probs=41.6
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEE
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 84 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 84 (247)
+.|.|.=||.- .+++.|.-|||..|.+|.|+|||.+.+...--+--=|+|++ .++.|+++
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 56677777764 68899999999999999999999999998888888899999 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=95.58 E-value=0.01 Score=51.34 Aligned_cols=43 Identities=16% Similarity=0.239 Sum_probs=35.8
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcce--eeEEec
Q 025838 33 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM--DVVSIP 75 (247)
Q Consensus 33 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~M--DVIsI~ 75 (247)
++++|.|.++|++.+.+|.|.|||++++++-|-|--= |-|+..
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 3799999999999999999999999999998765432 555543
No 18
>PRK11507 ribosome-associated protein; Provisional
Probab=95.55 E-value=0.06 Score=40.71 Aligned_cols=60 Identities=17% Similarity=0.139 Sum_probs=48.8
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEE
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 84 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 84 (247)
+-|-|.=||.- .+++.|+-|||..|.+|.|+|||.+.+-..-=+--=|+|+++ ++.|++.
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 45666666653 688999999999999999999999988777667778999995 5777764
No 19
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.43 E-value=0.011 Score=51.81 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=33.4
Q ss_pred HHHHHhhh-------cccccHHHHHHHHhCceEEECCEEeccccC
Q 025838 27 ILILRNRL-------KYALTYREVIAILMQRHVLVDAKVRTDKTY 64 (247)
Q Consensus 27 ~i~LRd~L-------kyA~t~rEak~Il~~~~V~VDGkvr~D~k~ 64 (247)
--||+.+| |+|.|..+|++++.+|.|.|||++++++-|
T Consensus 102 ~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~ 146 (181)
T PTZ00155 102 EKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146 (181)
T ss_pred HHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCce
Confidence 34556655 999999999999999999999999999965
No 20
>PLN00189 40S ribosomal protein S9; Provisional
Probab=95.28 E-value=0.015 Score=51.68 Aligned_cols=40 Identities=13% Similarity=0.150 Sum_probs=34.3
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeE
Q 025838 33 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVV 72 (247)
Q Consensus 33 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVI 72 (247)
+||+|.|..+|++++.+|.|.|||++++++.|-|--=|++
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~ 156 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQK 156 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEE
Confidence 4789999999999999999999999999998866543333
No 21
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=95.12 E-value=0.022 Score=49.80 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=36.7
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeeEEecc
Q 025838 34 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPA--GFMDVVSIPK 76 (247)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv--G~MDVIsI~k 76 (247)
+++|.|..+|++.+.+|.|.|||++++++.|.| +.=|.|+...
T Consensus 112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~ 156 (177)
T PRK04051 112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYP 156 (177)
T ss_pred ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeC
Confidence 699999999999999999999999999998866 3345666644
No 22
>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=94.98 E-value=0.04 Score=48.66 Aligned_cols=43 Identities=26% Similarity=0.307 Sum_probs=39.1
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc
Q 025838 34 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 76 (247)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 76 (247)
++++.|.++|++.+.+|.|.|||++++++.|.+--=|+|++..
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 4678899999999999999999999999999997779999964
No 23
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=94.96 E-value=0.1 Score=47.55 Aligned_cols=53 Identities=17% Similarity=0.147 Sum_probs=43.9
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEec
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 75 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 75 (247)
.++.|.-||...+. ..+.+++++.+.+|.|+|||+++++..+.+---|+|++.
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 357899999999999999998888888999878999983
No 24
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=94.76 E-value=0.052 Score=48.05 Aligned_cols=43 Identities=26% Similarity=0.356 Sum_probs=39.4
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc
Q 025838 34 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 76 (247)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 76 (247)
++++.+..+|++++..|.|.|||++++.+.|++--=|+|++..
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
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=94.60 E-value=0.055 Score=48.09 Aligned_cols=43 Identities=19% Similarity=0.315 Sum_probs=38.4
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc
Q 025838 34 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 76 (247)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 76 (247)
+++|.+.++|++++.+|.|.|||++++++.|.+--=|+|++..
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 5788999999999999999999999999999885559999953
No 26
>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=94.55 E-value=0.082 Score=43.32 Aligned_cols=56 Identities=18% Similarity=0.255 Sum_probs=39.3
Q ss_pred eEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC-----CCeEeE--eeceEEEEc
Q 025838 153 EFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL-----GHEFAT--RLGNVFTIG 211 (247)
Q Consensus 153 d~ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~~-----g~~F~T--~~~~vfvIG 211 (247)
+.+++..|+.+.|++|++-|..|+|.++... ...|.|+.-+ |.+++. ..+||.++.
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~ 100 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVTKEKVNGTEVPVPIHPSNVMITK 100 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeEEECCCCeEEEeeechHHeEEEe
Confidence 5568889999999999999999999999643 2466666544 333333 336665543
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=94.36 E-value=0.14 Score=46.77 Aligned_cols=63 Identities=14% Similarity=0.206 Sum_probs=51.2
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEEEcC
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 97 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 97 (247)
.|+=|-.++...+ ..+.+.|++.+.+|.|+|||+++++..+.+--=|+|++. ..|||.+..+.
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 4556777887655 558899999999999999999999999988777999984 46778777664
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=93.23 E-value=0.16 Score=45.70 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=40.0
Q ss_pred HHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc
Q 025838 29 ILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 76 (247)
Q Consensus 29 ~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 76 (247)
+|.+ ++++.+.++|++.+++|.|.|||++++++.+.+--=|.|++..
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 4443 4688899999999999999999999999999886559999964
No 29
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=92.75 E-value=0.17 Score=38.64 Aligned_cols=54 Identities=24% Similarity=0.202 Sum_probs=42.3
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 76 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 76 (247)
+-|-|.=||.- ++.++++-+||..|.++.|+|||.+-+=..-=+--=|+|+||.
T Consensus 10 e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 10 EFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred ceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 44556666654 7899999999999999999999998655544455568999964
No 30
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=92.37 E-value=0.48 Score=44.16 Aligned_cols=53 Identities=17% Similarity=0.080 Sum_probs=42.5
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEec
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 75 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 75 (247)
..+.|.-+|+..+. ..+.+.+++.+.+|.|+|||+.++...+.+---|+|++.
T Consensus 16 ~g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~ 68 (325)
T PRK11180 16 LGQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAID 68 (325)
T ss_pred CCccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEe
Confidence 34678888887654 357899999999999999999987666666555999885
No 31
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=90.93 E-value=0.8 Score=44.51 Aligned_cols=65 Identities=15% Similarity=0.188 Sum_probs=48.6
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEE
Q 025838 23 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 94 (247)
Q Consensus 23 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~ 94 (247)
.+|+.-+|.+ .+.|.+..|||+.+.||-|+|||..++|..+-+-- ......|-+|---|.+|.+.
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 69999999999999999999999999999763321 11134556666666666544
No 32
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=90.92 E-value=0.81 Score=42.52 Aligned_cols=57 Identities=23% Similarity=0.190 Sum_probs=49.9
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceE
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENF 81 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~y 81 (247)
...-|--||++ |.- .+..+..+++.+|.|.|||++.+ ..|.+.-=|+|+++...+.+
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 68899999999999999999999 99999999999999876565
No 33
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=90.79 E-value=0.76 Score=42.61 Aligned_cols=65 Identities=18% Similarity=0.093 Sum_probs=46.5
Q ss_pred HHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeeEEecc----------CCceEEEEEcCCCceEE
Q 025838 26 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA--GFMDVVSIPK----------TNENFRLLYDTKGRFRL 93 (247)
Q Consensus 26 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv--G~MDVIsI~k----------t~e~yRvl~d~kgrf~l 93 (247)
|-=||-+ +++ .+.++|++++.+|.|+|||++. +..+.| +-.|.|+++. ..++|-+++-+.|..+-
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 3344443 343 6789999999999999999987 666666 4557787753 11468888999986543
No 34
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=89.96 E-value=0.83 Score=37.88 Aligned_cols=38 Identities=18% Similarity=0.313 Sum_probs=30.4
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 025838 154 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 194 (247)
Q Consensus 154 ~ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d 194 (247)
.+++..|+.+.|+.|..-|..|+|.++.... +.|+|+.
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 4578899999999999999999999996543 3455543
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=89.55 E-value=0.9 Score=38.19 Aligned_cols=57 Identities=9% Similarity=0.031 Sum_probs=48.3
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceE
Q 025838 23 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENF 81 (247)
Q Consensus 23 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~y 81 (247)
++-|-.||=. .+++.|..-|+..|..|.|.|||.+ .-+-..|-.=|+|+|...+..|
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~ 64 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDER 64 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEE
Confidence 4566666654 5899999999999999999999999 8889999999999997755444
No 36
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=89.22 E-value=0.91 Score=41.73 Aligned_cols=60 Identities=22% Similarity=0.195 Sum_probs=44.0
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcce-eeEEeccCC------ceEEEEEcCCCceEEE
Q 025838 34 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM-DVVSIPKTN------ENFRLLYDTKGRFRLH 94 (247)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~M-DVIsI~kt~------e~yRvl~d~kgrf~l~ 94 (247)
+++| +.|||.++|.+|.|.|||++.++...-+=-- |+|.++..- ..|=|++-+.|..+-+
T Consensus 12 ~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~ 78 (248)
T COG1187 12 AGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSST 78 (248)
T ss_pred cCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEecc
Confidence 3555 6899999999999999999999986555444 466655431 2288888888866444
No 37
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=89.01 E-value=1.5 Score=40.77 Aligned_cols=68 Identities=16% Similarity=0.080 Sum_probs=49.9
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc--------CCceEEEEEcCCCceE
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK--------TNENFRLLYDTKGRFR 92 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k--------t~e~yRvl~d~kgrf~ 92 (247)
.++-|.-+|.+. ++ .+.++|++.+.+|.|+|||++. +..+.|---|+|+++. .+++|-++.-+.|..+
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 456677777754 43 4799999999999999999987 4667775559888852 1246777777887543
No 38
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=88.45 E-value=1.9 Score=40.09 Aligned_cols=51 Identities=27% Similarity=0.260 Sum_probs=41.6
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEec
Q 025838 23 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 75 (247)
Q Consensus 23 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 75 (247)
...|.-||+..+. ..+.+.+++++.+|.|.|||+++ +..+.+-.=|+|+++
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 4678888887663 35789999999999999999988 467888666999985
No 39
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=86.99 E-value=3.6 Score=36.28 Aligned_cols=67 Identities=13% Similarity=0.142 Sum_probs=47.3
Q ss_pred HHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEecc------CCceEEEEEcCCCceEEEE
Q 025838 26 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK------TNENFRLLYDTKGRFRLHS 95 (247)
Q Consensus 26 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k------t~e~yRvl~d~kgrf~l~~ 95 (247)
|--||...+ ..+.+.+++++.+|.|+|||++.++..+.+---|.|++.. ..++|=++--+.| +..|+
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~~~~~~~~lvvnKP~G-~~~~~ 75 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQG-YVCST 75 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcccCCCCEEEEEECCCC-eEecc
Confidence 445666655 3578999999999999999999887777775569999852 1235555555565 44454
No 40
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=86.94 E-value=2.6 Score=39.02 Aligned_cols=62 Identities=21% Similarity=0.262 Sum_probs=50.0
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEEEcC
Q 025838 23 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 97 (247)
Q Consensus 23 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 97 (247)
|+=|--++-..+ -.+...|+..+.+|+|+|||++.++..|-+--=|+|||-. .|||.+.++.
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 445556666655 4577889999999999999999999999999999999954 5677777664
No 41
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=86.77 E-value=1.1 Score=34.07 Aligned_cols=39 Identities=21% Similarity=0.422 Sum_probs=31.9
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC
Q 025838 155 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 196 (247)
Q Consensus 155 ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~~ 196 (247)
+++..|+.+.|+.|+.-|.+|+|..+.+.. +.|.|++-+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegvn 43 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKK---NRVIVEGVK 43 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCcE
Confidence 478889999999999999999999996543 467776543
No 42
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=86.45 E-value=1.2 Score=34.35 Aligned_cols=39 Identities=15% Similarity=0.439 Sum_probs=31.6
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcC
Q 025838 154 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 195 (247)
Q Consensus 154 ~ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d~ 195 (247)
.+++..|+.++|+.|+.-|..|+|.++.+.. +.|+|++-
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence 3478889999999999999999999996532 46777644
No 43
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=86.04 E-value=1.8 Score=40.16 Aligned_cols=63 Identities=21% Similarity=0.290 Sum_probs=52.9
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEEEcC
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 97 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 97 (247)
.||=|-.++-..++... .-|...+..|+|+||.+++++..|-+..=|.|||-. .|||.+-+|.
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 47778888888777654 568899999999999999999999999999999954 5777776664
No 44
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=85.74 E-value=2.8 Score=40.87 Aligned_cols=66 Identities=20% Similarity=0.195 Sum_probs=46.7
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEE
Q 025838 23 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 94 (247)
Q Consensus 23 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~ 94 (247)
.+||.-+|-. .+.|.+..|||+.+.||-|+|||..++|..+=+--=|. .+..|-+|---|.+|.+.
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 79999999999999999999999999998653321111 123345555555555443
No 45
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=85.43 E-value=1.2 Score=35.76 Aligned_cols=37 Identities=22% Similarity=0.510 Sum_probs=29.5
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 025838 155 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 194 (247)
Q Consensus 155 ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~d 194 (247)
+++..|+.+.|+.|++-|.+|+|.++.... +.|+|++
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 367889999999999999999999996532 3455544
No 46
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=84.81 E-value=1.4 Score=40.63 Aligned_cols=47 Identities=11% Similarity=0.178 Sum_probs=41.9
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceE
Q 025838 35 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENF 81 (247)
Q Consensus 35 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~y 81 (247)
+++.|...|+..++.|+|+|||...+-+.+=|-.-+.|++......|
T Consensus 13 gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~y 59 (245)
T COG1189 13 GLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPY 59 (245)
T ss_pred cchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCc
Confidence 88999999999999999999999999999999999999997533333
No 47
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=84.52 E-value=2.2 Score=36.46 Aligned_cols=57 Identities=25% Similarity=0.317 Sum_probs=38.8
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeE--eEeeceEEEEc
Q 025838 155 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEF--ATRLGNVFTIG 211 (247)
Q Consensus 155 ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~--~~V~v~d~~g~~F--~T~~~~vfvIG 211 (247)
+++..|+.++|+.|.+-|..|+|..+....+.. +=|.+.-.+|..+ --..+||+++.
T Consensus 45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred ceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 477889999999999999999999996644321 1122333555443 34457777765
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=78.75 E-value=3.1 Score=33.43 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=25.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEe
Q 025838 156 KFDVGNVVMVTGGRNRGRVGIIKNREKH 183 (247)
Q Consensus 156 kfe~G~~~~vtgG~n~G~vG~I~~i~~~ 183 (247)
++..|+.+.|+.|+.-|.+|+|.++.+.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5778999999999999999999999654
No 49
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=78.62 E-value=5.6 Score=29.46 Aligned_cols=50 Identities=26% Similarity=0.488 Sum_probs=37.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEcc
Q 025838 159 VGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 212 (247)
Q Consensus 159 ~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~v~d~~g~~F~T~~~~vfvIG~ 212 (247)
+|..|+|-.|.+.-|+|.++.-|... ++|.+|. ++...+.-+..+..+|-
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 48899999999999999999988776 4456552 33456666777777773
No 50
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=68.67 E-value=3.7 Score=36.12 Aligned_cols=55 Identities=27% Similarity=0.344 Sum_probs=40.0
Q ss_pred CCCCCCCCCcccchHHHHHH-------hhhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 025838 12 KPSSGPHKSRECLPLILILR-------NRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 66 (247)
Q Consensus 12 kpspGPH~~~eslPL~i~LR-------d~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv 66 (247)
-|..+.|..-+-+...-|-| -.|+.|.+-+||-+.+.||.|.|.-++++|+-|=|
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 45555555444222333333 24789999999999999999999999999997754
No 51
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=65.94 E-value=13 Score=36.41 Aligned_cols=54 Identities=20% Similarity=0.244 Sum_probs=41.0
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEE
Q 025838 34 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 94 (247)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~ 94 (247)
.+++...+||++.+.+|-|++||..+.|.+++.+ | .....|.++--.|.+|...
T Consensus 345 ~~L~psr~earr~i~~g~v~in~~~v~d~~~~~~--~-----~~~~~~~~l~~GKkk~~~i 398 (401)
T COG0162 345 AGLAPSRSEARRLIQQGGVKINGEKVEDENYVLS--D-----LLDNGLLVLRRGKKKFALI 398 (401)
T ss_pred hCCcccHHHHHhhcccCCEEECCEeccccccchh--h-----ccCCceEEEecccccEEEE
Confidence 6899999999999999999999999999998872 1 1234455555555555544
No 52
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=61.11 E-value=8.7 Score=32.08 Aligned_cols=26 Identities=38% Similarity=0.556 Sum_probs=23.9
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREK 182 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~ 182 (247)
+++|-.|+++.|+.+|+-.+|..+..
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iD 30 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIID 30 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEcc
Confidence 68899999999999999999998854
No 53
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=60.38 E-value=14 Score=30.03 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=24.7
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 025838 155 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 183 (247)
Q Consensus 155 ikfe~G~~~~vtgG~n~G~vG~I~~i~~~ 183 (247)
++...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45677999999999999999999988544
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=59.74 E-value=43 Score=28.99 Aligned_cols=29 Identities=34% Similarity=0.429 Sum_probs=25.0
Q ss_pred cccchHHHHHHhhhcccccHHHHHHHHhCc
Q 025838 21 RECLPLILILRNRLKYALTYREVIAILMQR 50 (247)
Q Consensus 21 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~ 50 (247)
...+|..+++|..|. |.|..||..+|.+-
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
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=53.29 E-value=16 Score=30.74 Aligned_cols=33 Identities=12% Similarity=0.336 Sum_probs=27.6
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ 193 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v~ 193 (247)
.|+|-+|+|.-|.+.|..++|.+|..+ +.|.|.
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~----nRvLVD 40 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLVD 40 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC----CeEEEe
Confidence 378999999999999999999999764 455553
No 56
>PF14001 YdfZ: YdfZ protein
Probab=52.05 E-value=23 Score=26.50 Aligned_cols=41 Identities=27% Similarity=0.487 Sum_probs=28.8
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecC------CccEEEEEcCCCCeEe
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREKHKG------SFETIHIQDALGHEFA 201 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~------s~~~V~v~d~~g~~F~ 201 (247)
+.+|+.+|+.| +|.+|+|+.|.-..- ....|.+++.+| .|+
T Consensus 10 i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 10 ITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred CCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 46799999977 678889998865322 235788887765 354
No 57
>PRK04333 50S ribosomal protein L14e; Validated
Probab=49.89 E-value=18 Score=28.06 Aligned_cols=33 Identities=27% Similarity=0.463 Sum_probs=26.9
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 025838 156 KFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 192 (247)
Q Consensus 156 kfe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~v 192 (247)
.++.|-+|++.-|+..|+..+|.++... +.|.|
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 4678999999999999999999998432 45555
No 58
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=48.93 E-value=44 Score=27.00 Aligned_cols=44 Identities=11% Similarity=0.114 Sum_probs=33.8
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCc
Q 025838 35 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNE 79 (247)
Q Consensus 35 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e 79 (247)
.+..+...|+..|..|.|.|||...+- ..-|=.=|+|+|--.+.
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRAKP-SKEVKVGDILTIRFGNK 62 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEccc-ccccCCCCEEEEEeCCc
Confidence 455788999999999999999999854 34566678888754433
No 59
>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=44.75 E-value=65 Score=24.84 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=30.5
Q ss_pred CCC-CccCCCeEEEecCCCceeeEEEeeC----CcEEEEECCCcceeEEEEEeE
Q 025838 132 PDP-LIKANDTIKLDLETNKITEFIKFDV----GNVVMVTGGRNRGRVGIIKNR 180 (247)
Q Consensus 132 ~d~-~ik~~Dtv~i~l~~~kI~d~ikfe~----G~~~~vtgG~n~G~vG~I~~i 180 (247)
.+| .++.||...+.+...+=+-.=+|+. |-.++--+|+.+| .|.|.+|
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 6666667777766 7877653
No 60
>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=44.14 E-value=14 Score=27.40 Aligned_cols=33 Identities=27% Similarity=0.427 Sum_probs=22.1
Q ss_pred cccchHHHHHHhhhcccc-cHHHHHHHHhCceEEECC
Q 025838 21 RECLPLILILRNRLKYAL-TYREVIAILMQRHVLVDA 56 (247)
Q Consensus 21 ~eslPL~i~LRd~LkyA~-t~rEak~Il~~~~V~VDG 56 (247)
.|.|||..++ ||||. +..||-+-+.+++-.|+-
T Consensus 21 WEmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~ 54 (62)
T PF08828_consen 21 WEMMPLMYVI---LKYADADVEEASRRIDEAKNVVNE 54 (62)
T ss_dssp GGGHHHHHHH---HHHTTT-HHHHHHHHHH-------
T ss_pred HHHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHH
Confidence 4789999885 89999 999999999888766654
No 61
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=43.62 E-value=1.1e+02 Score=32.98 Aligned_cols=77 Identities=19% Similarity=0.243 Sum_probs=52.4
Q ss_pred CcceeeEEeccCCceEEEEEcCCCceEEEEcCh---hhhcceeEEEe----eeEEeeCCceEEEccCceeEecCCCCccC
Q 025838 66 AGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIKA 138 (247)
Q Consensus 66 vG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~---eEa~~KLcKV~----~k~~~~gg~~ql~~hDGrni~~~d~~ik~ 138 (247)
.|-++++..+ .+.+=+-+|.+++....+++. -++.-||.||+ ....++.++|.++..||.-.......+++
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 234444456667777777654 23345889888 45567899999999999877666668999
Q ss_pred CCeEEE
Q 025838 139 NDTIKL 144 (247)
Q Consensus 139 ~Dtv~i 144 (247)
||-|.+
T Consensus 190 GD~i~~ 195 (858)
T PRK14898 190 GDWLPV 195 (858)
T ss_pred CCEEee
Confidence 998755
No 62
>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=42.78 E-value=49 Score=32.21 Aligned_cols=54 Identities=19% Similarity=0.223 Sum_probs=33.1
Q ss_pred eEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCCcEEEE---ECCCccee
Q 025838 105 LCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMV---TGGRNRGR 173 (247)
Q Consensus 105 LcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G~~~~v---tgG~n~G~ 173 (247)
|..|+-.. .|....+.++|..|||+-. |+|+.+..-.+++|+.+++ .+|+|.|-
T Consensus 289 LllIeA~~--~g~~~svilQnaetIRlv~-------------p~G~~vsVt~Lk~GD~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 289 LLLIEAEA--DGKRISVILQNAETIRLVG-------------PDGEPVSVTELKPGDEVLVYLEEAGRHFGM 345 (354)
T ss_pred eEEEEEEe--CCeEEEEEEecCcEEEEEC-------------CCCCEeeeeecCCCCEEEEEecCCCcccce
Confidence 44444444 4556666667777776543 3566666666666666554 47889884
No 63
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=42.26 E-value=49 Score=32.10 Aligned_cols=54 Identities=19% Similarity=0.181 Sum_probs=28.8
Q ss_pred eEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCCcEEEE---ECCCccee
Q 025838 105 LCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMV---TGGRNRGR 173 (247)
Q Consensus 105 LcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G~~~~v---tgG~n~G~ 173 (247)
|..|+-.. .|....+.++|..|||+-.| +|+-+..-.+++|+.+++ .+|+|.|.
T Consensus 279 L~lIeAe~--~g~~~~viLQnaetIrlv~~-------------dG~~vsVt~Lk~GD~VL~~~~~~~RHfG~ 335 (344)
T PRK02290 279 LLLIEAEY--GGKRIRTILQNAETIRLVTP-------------DGKPVSVVDLKPGDEVLGYLEEAARHFGM 335 (344)
T ss_pred EEEEEEEe--CCeEEEEEEecCcEEEEECC-------------CCCEeeeeecCCCCEEEEEecCCcccccc
Confidence 34444433 45556666677777755433 344444444555554443 26788873
No 64
>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=42.02 E-value=1.4e+02 Score=21.87 Aligned_cols=68 Identities=16% Similarity=0.126 Sum_probs=40.1
Q ss_pred eEEeeCCceEEEccCceeEecCC-CCc-----cCCCeEEEecCCCceeeEEEeeCCc-EEEEECCCcceeEEEEE
Q 025838 111 VQFGQKGIPYINTYDGRTIRYPD-PLI-----KANDTIKLDLETNKITEFIKFDVGN-VVMVTGGRNRGRVGIIK 178 (247)
Q Consensus 111 k~~~~gg~~ql~~hDGrni~~~d-~~i-----k~~Dtv~i~l~~~kI~d~ikfe~G~-~~~vtgG~n~G~vG~I~ 178 (247)
+.+..++..+|.+.||..+.... ..+ .-.+...+.|..|++.-.++=.... +.+-|....++-.|+--
T Consensus 3 i~T~~~~~~~i~l~dgs~v~l~~~s~~~~~~~~~~~~~~~~L~~G~~~~~~~~~~~~~~~V~T~~~~i~v~GT~f 77 (98)
T PF04773_consen 3 IRTGAGSRAEIALSDGSRVRLGPNSRVSVDRDSGSEPTRLRLLSGEILFDVSPGKKRPFEVRTPTATIGVRGTRF 77 (98)
T ss_pred EEcCCCCEEEEEECCCCEEEECCCcEEEEEcccCCCceEEEEcCCCEEEEEcccCCCCEEEEeCCEEEEEecCEE
Confidence 45678999999999999996543 334 3444555666666654322222222 55555555555555433
No 65
>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=40.58 E-value=23 Score=30.25 Aligned_cols=54 Identities=20% Similarity=0.102 Sum_probs=43.2
Q ss_pred cccchHHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---eEEeccCC
Q 025838 21 RECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIPKTN 78 (247)
Q Consensus 21 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~-----~V~VDGkvr~D~k~PvG~MD---VIsI~kt~ 78 (247)
+...+|+-+||+.|++-.+ |.=+.+| .|+|||+++..--+|+.-+| |++|+--.
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 4568999999999876543 4556666 69999999999999998886 89997644
No 66
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=39.54 E-value=30 Score=29.37 Aligned_cols=24 Identities=42% Similarity=0.688 Sum_probs=21.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeE
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNR 180 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i 180 (247)
+.+|..++|..|+++|+-++|..-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999998774
No 67
>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=37.97 E-value=1.2e+02 Score=24.45 Aligned_cols=61 Identities=16% Similarity=0.369 Sum_probs=38.8
Q ss_pred eeCCcEEEEE-CCCcceeEEEEEeEEEe-----cCCc-cEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCCCCceeee
Q 025838 157 FDVGNVVMVT-GGRNRGRVGIIKNREKH-----KGSF-ETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLS 229 (247)
Q Consensus 157 fe~G~~~~vt-gG~n~G~vG~I~~i~~~-----~~s~-~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~ 229 (247)
|+.|+.--.. ....+ |.|..|+.. ++.| +-|.|++.+|+. +.|...+ |+.-|-++-|+++
T Consensus 41 F~~G~~d~F~v~~~dL---G~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~ 107 (109)
T cd02899 41 FYPGSLKRIRFRAADV---GDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECcccc---CceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEe
Confidence 6666654321 24444 445555442 2334 788898866544 4599988 9999999998876
Q ss_pred h
Q 025838 230 I 230 (247)
Q Consensus 230 ~ 230 (247)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 68
>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=37.64 E-value=1.8e+02 Score=22.09 Aligned_cols=45 Identities=18% Similarity=0.381 Sum_probs=29.9
Q ss_pred CccCCCeEEEecCCCceeeEEEe----eCCcEEEEECCCcceeEEEEEeE
Q 025838 135 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNR 180 (247)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~ikf----e~G~~~~vtgG~n~G~vG~I~~i 180 (247)
.++.||...+.+...+-+-.=+| ..|...+-..|..+| .|.|.+|
T Consensus 59 ~l~~~~~a~v~l~~~~pi~~e~~~~~~~~Grfilr~~~~Tva-~G~I~~i 107 (107)
T cd04093 59 CLTKGQTAIVEIELERPIPLELFKDNKELGRVVLRRDGETIA-AGLVTEI 107 (107)
T ss_pred CcCCCCEEEEEEEECCeEEEEEcccCCCcceEEEEcCCCEEE-EEEEEeC
Confidence 59999999999976653322222 227777767777766 5887653
No 69
>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=36.16 E-value=1.6e+02 Score=21.98 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=25.1
Q ss_pred ccCCCeEEEecCCCceeeEEEeeCCcEEEE-ECCCcceeEEEEEe
Q 025838 136 IKANDTIKLDLETNKITEFIKFDVGNVVMV-TGGRNRGRVGIIKN 179 (247)
Q Consensus 136 ik~~Dtv~i~l~~~kI~d~ikfe~G~~~~v-tgG~n~G~vG~I~~ 179 (247)
+++||+..+.+.-.+ -+.++.|.-.++ .+|+.+| .|.|.+
T Consensus 52 l~~g~~~~v~i~l~~---p~~~~~g~rf~lR~~~~tvg-~G~V~~ 92 (93)
T cd03706 52 VMPGEDTKVTLILRR---PMVLEKGQRFTLRDGNRTIG-TGLVTD 92 (93)
T ss_pred eCCCCEEEEEEEECC---cEEEeeCCEEEEEECCEEEE-EEEEEe
Confidence 788888887776433 224555665555 6665555 677654
No 70
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=35.07 E-value=3.8e+02 Score=24.95 Aligned_cols=61 Identities=23% Similarity=0.310 Sum_probs=40.5
Q ss_pred CCCCccCCCeEEEecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEE
Q 025838 132 PDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 210 (247)
Q Consensus 132 ~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~v~d~~g~~F~T~~~~vfvI 210 (247)
++.+++.||.|+-+=-.|. |.+|= -+|+|..++.+. +.+..+.++-.. -.+++.|||++
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 4557888885554433332 23332 378888888776 556778887544 47899999999
Q ss_pred cc
Q 025838 211 GK 212 (247)
Q Consensus 211 G~ 212 (247)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 85
No 71
>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=34.63 E-value=86 Score=24.01 Aligned_cols=24 Identities=29% Similarity=0.313 Sum_probs=17.5
Q ss_pred eEEEEEeEEEecCCcc--EEEEEcCC
Q 025838 173 RVGIIKNREKHKGSFE--TIHIQDAL 196 (247)
Q Consensus 173 ~vG~I~~i~~~~~s~~--~V~v~d~~ 196 (247)
++|+|.+.+.|+++.. +..+...+
T Consensus 2 ~vg~I~~~~~hp~sdkL~~~~Vd~G~ 27 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYVLKVDIGE 27 (95)
T ss_dssp EEEEEEEEEEETTSSSEEEEEEESSS
T ss_pred EEEEEEEEEECCCCCEEEEEEEEeCC
Confidence 6899999999998864 44454333
No 72
>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=34.28 E-value=70 Score=26.16 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=24.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREK 182 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~ 182 (247)
|.+|+.+.|+.|.=.|..|.|.++..
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 73
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=34.06 E-value=64 Score=27.05 Aligned_cols=29 Identities=14% Similarity=0.265 Sum_probs=26.5
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 025838 155 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 183 (247)
Q Consensus 155 ikfe~G~~~~vtgG~n~G~vG~I~~i~~~ 183 (247)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999998764
No 74
>cd03705 EF1_alpha_III Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
Probab=33.09 E-value=98 Score=23.48 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=25.0
Q ss_pred CccCCCeEEEecCCCceeeEEEeeC-------CcEEEEECCCcce
Q 025838 135 LIKANDTIKLDLETNKITEFIKFDV-------GNVVMVTGGRNRG 172 (247)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~ikfe~-------G~~~~vtgG~n~G 172 (247)
.++.||...+.|...+ -+.+|+ |..+++-+|..+|
T Consensus 59 ~l~~n~~a~v~l~~~~---pi~~e~~~~~~~lgrf~lrd~~~Tva 100 (104)
T cd03705 59 FLKSGDAAIVKIVPQK---PLVVETFSEYPPLGRFAVRDMGQTVA 100 (104)
T ss_pred ccCCCCEEEEEEEECC---eeEEEEcccCCCccCEEEEeCCCEEE
Confidence 5899999999987554 345565 7777777666655
No 75
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=32.63 E-value=42 Score=25.58 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.1
Q ss_pred eEecCCCCccCCCeEEEe
Q 025838 128 TIRYPDPLIKANDTIKLD 145 (247)
Q Consensus 128 ni~~~d~~ik~~Dtv~i~ 145 (247)
-||..|.+|++||.+.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 358889999999998874
No 76
>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=32.44 E-value=1e+02 Score=22.88 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=26.5
Q ss_pred EeeCCceEEEccCceeEecCC----CCccCCCeEEEecC
Q 025838 113 FGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 147 (247)
Q Consensus 113 ~~~gg~~ql~~hDGrni~~~d----~~ik~~Dtv~i~l~ 147 (247)
.+......|.|.||.++..|. +.+++|..|++-..
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 345667889999999998774 36888887777554
No 77
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=31.31 E-value=72 Score=34.98 Aligned_cols=27 Identities=33% Similarity=0.610 Sum_probs=25.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEe
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREKH 183 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~~ 183 (247)
|++|+.|=|+.|+|-|..|.|..++.+
T Consensus 460 F~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 460 FEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccCCCeEEEEeccccCCcceEEEEeCC
Confidence 889999999999999999999999873
No 78
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=30.26 E-value=59 Score=27.27 Aligned_cols=29 Identities=24% Similarity=0.388 Sum_probs=26.1
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 025838 154 FIKFDVGNVVMVTGGRNRGRVGIIKNREK 182 (247)
Q Consensus 154 ~ikfe~G~~~~vtgG~n~G~vG~I~~i~~ 182 (247)
...|.+|+.+-|++|.=.|..|.|.++..
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDY 152 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeC
Confidence 36789999999999999999999999854
No 79
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=29.93 E-value=20 Score=30.67 Aligned_cols=53 Identities=23% Similarity=0.090 Sum_probs=40.6
Q ss_pred cccchHHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---eEEeccC
Q 025838 21 RECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIPKT 77 (247)
Q Consensus 21 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~-----~V~VDGkvr~D~k~PvG~MD---VIsI~kt 77 (247)
....+|+-+||+.|++-.+.. =+.+| .|.|||+.+.---.|+.-+| |.+|+-.
T Consensus 18 ~~~~~Ll~~LR~~~~ltgtK~----gC~~G~CGACtVlvdG~~v~SCl~~~~~~~G~~v~TiEgl 78 (151)
T TIGR03198 18 VPTTRLSDLLRKELQLTGTKV----SCGIGRCGACSVLIDGKLANACLTMAYQADGHEITTIEGI 78 (151)
T ss_pred CCCcHHHHHHHhccCCCCCCC----CCCCCcCCccEEEECCcEEechHHHHHHhcCCEEEecCCc
Confidence 357899999999998876543 36666 69999999988888876554 7777553
No 80
>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=28.60 E-value=14 Score=33.11 Aligned_cols=60 Identities=28% Similarity=0.407 Sum_probs=36.6
Q ss_pred HHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeeEEeccCCceEEEEEcCCCceEEEEcChhhhccee
Q 025838 26 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKL 105 (247)
Q Consensus 26 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KL 105 (247)
|-+.-+|++++-.|.+. -+.+....++-.-..+ .||||..|-|+| .| +|==|.+||+-|=
T Consensus 53 L~i~~~Dyik~l~nl~~---y~~~~l~~~~~~~~~~-~YPvG~L~dIei---------------hF-~HY~s~~eA~~KW 112 (201)
T PF08942_consen 53 LFIFPPDYIKFLENLDY---YLSQELEFIDESKSYD-DYPVGLLGDIEI---------------HF-MHYKSFEEAKEKW 112 (201)
T ss_dssp EE--HHHHHHHHHSHHH---HHCS--EECE--BGGG-B--EEEEC-EEE---------------EE-SS-SSHHHHHHHH
T ss_pred eEECcHHHHHHHHCHHH---HhcCCeEEeecCcccC-CcceEeECCEEE---------------EE-EecCCHHHHHHHH
Confidence 45566899999988875 3666665555544456 899999999999 23 5666899998653
No 81
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=28.39 E-value=1.3e+02 Score=33.07 Aligned_cols=55 Identities=25% Similarity=0.374 Sum_probs=41.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeEeEeeceEEEEccCCC
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFATRLGNVFTIGKGTK 215 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~--~~V~v~d~~g~~F~T~~~~vfvIG~~~k 215 (247)
...++.+-+++|.|.|+-|.|.+|-+.. -| +.-++ .++-.|.++..|+..+|. .+
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 IRVKDTVKVIGGPSKGREGEVLHIYRPF-VFLHSRKNL--ENGGVFVCKEKNLILAGG-KK 638 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecce-eeeeehhhc--ccCCeEEEecCCceeccc-cC
Confidence 3568999999999999999999996521 11 22223 466689999999999995 44
No 82
>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=28.26 E-value=41 Score=27.79 Aligned_cols=42 Identities=24% Similarity=0.370 Sum_probs=33.0
Q ss_pred CCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCC
Q 025838 88 KGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 134 (247)
Q Consensus 88 kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~ 134 (247)
+..|+|+.+|+= -+-+|--+.|..-+....|| ||-|+-|.+|
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 345788877654 34688888888888899998 9999988765
No 83
>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=27.77 E-value=58 Score=31.45 Aligned_cols=46 Identities=15% Similarity=-0.067 Sum_probs=37.0
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcce
Q 025838 23 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM 69 (247)
Q Consensus 23 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~M 69 (247)
++++.=++.. .+.+.+.+||++.|++|-|+|||...+|..+-.-.+
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~~ 374 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKEA 374 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhccc
Confidence 4666666553 588999999999999999999999999987654433
No 84
>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=27.41 E-value=67 Score=26.85 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=25.3
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEE
Q 025838 155 IKFDVGNVVMVTGGRNRGRVGIIKNREK 182 (247)
Q Consensus 155 ikfe~G~~~~vtgG~n~G~vG~I~~i~~ 182 (247)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5588999999999999999999999854
No 85
>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=27.25 E-value=1.2e+02 Score=21.98 Aligned_cols=34 Identities=12% Similarity=0.285 Sum_probs=27.9
Q ss_pred CceEEEEEcCCC--ceEEEEcChhhhcceeEEEeee
Q 025838 78 NENFRLLYDTKG--RFRLHSIRDEEAKFKLCKVRSV 111 (247)
Q Consensus 78 ~e~yRvl~d~kg--rf~l~~I~~eEa~~KLcKV~~k 111 (247)
+.+|++..+..| .|.+..+..+++..-.|...|.
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 457888888777 5777799999999889998884
No 86
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=26.82 E-value=52 Score=28.29 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=36.9
Q ss_pred ceeeEEEeeCCcEEEEECCCcce-eEEEEEeEEEecCC--ccEEEEEcCCCCe
Q 025838 150 KITEFIKFDVGNVVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 199 (247)
Q Consensus 150 kI~d~ikfe~G~~~~vtgG~n~G-~vG~I~~i~~~~~s--~~~V~v~d~~g~~ 199 (247)
-.+..+|+..++.+-|.+|+..| .+|.|.++-+..-. .+.|.-+-++|..
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 2444444455543
No 87
>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=26.80 E-value=1.8e+02 Score=20.13 Aligned_cols=37 Identities=22% Similarity=0.241 Sum_probs=28.4
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEE
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 193 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~-~~V~v~ 193 (247)
|++|..+++.-+...-.-++|.+++..++.. =.||-.
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 6889999999999999999999998865553 366654
No 88
>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=26.23 E-value=1.2e+02 Score=21.83 Aligned_cols=37 Identities=22% Similarity=0.280 Sum_probs=25.0
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCcee
Q 025838 115 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 152 (247)
Q Consensus 115 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 152 (247)
.+..-...|..|-.|.+|. -|+.||.|++|-.+++=+
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 3444566778888898766 699999999999998643
No 89
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=26.12 E-value=3.3e+02 Score=26.73 Aligned_cols=52 Identities=27% Similarity=0.312 Sum_probs=35.3
Q ss_pred CccCCCeEEEecCCCceeeEEEe----eCCcEEEEECCCcceeEEEEEeEEEecCCc
Q 025838 135 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNREKHKGSF 187 (247)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~ikf----e~G~~~~vtgG~n~G~vG~I~~i~~~~~s~ 187 (247)
.++.||...+.|...+=+-.-+| .-|..++.-+|..+| .|.|.++....||-
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 57789998888875543323333 246677778886655 89999988766664
No 90
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=25.54 E-value=1.4e+02 Score=30.55 Aligned_cols=93 Identities=15% Similarity=0.081 Sum_probs=51.8
Q ss_pred eccccCCCcc----e-eeEEeccC--CceEEEEEcCCCceEEEE-------cChhhhcceeEEEe----eeEEeeCCceE
Q 025838 59 RTDKTYPAGF----M-DVVSIPKT--NENFRLLYDTKGRFRLHS-------IRDEEAKFKLCKVR----SVQFGQKGIPY 120 (247)
Q Consensus 59 r~D~k~PvG~----M-DVIsI~kt--~e~yRvl~d~kgrf~l~~-------I~~eEa~~KLcKV~----~k~~~~gg~~q 120 (247)
.-||.|+.|. | |=+++..+ .-.+|-+++.++++.... ++.+=|+ +|.+-. .-.++......
T Consensus 399 ia~YQFG~g~g~~l~~~~~~v~~s~~tgr~r~v~~~~~~l~t~r~~dg~l~lt~~Ga~-~l~~~~~~p~~rV~v~~~~~~ 477 (540)
T TIGR00432 399 MKHYQNGPPNGELNVLSDVRIERSRNTGKIRHIYAGDELICTMRASDGLLVLGAEGAV-RLHKGTDYPAWRVAVNEESEP 477 (540)
T ss_pred HHHhhcCcCchHhhCCCCcEEEEeccCCcceEEEECCEEEEEEEcCCCeEEeCHHHHH-HHHhcCCCCceEEEECCcchh
Confidence 4488898663 2 44555332 346788888776665543 4555443 332211 11111111111
Q ss_pred EEccCceeEe-----cCCCCccCCCeEEEecCCCceee
Q 025838 121 INTYDGRTIR-----YPDPLIKANDTIKLDLETNKITE 153 (247)
Q Consensus 121 l~~hDGrni~-----~~d~~ik~~Dtv~i~l~~~kI~d 153 (247)
..-+|+|+- -.|+.|.+||-|++-.++++++.
T Consensus 478 -f~~~g~~vfak~V~~ad~~IR~~dEV~vv~~~~~lla 514 (540)
T TIGR00432 478 -FARKGKSVFAKFIIDCDNNIRANDEVLIVNADDELLA 514 (540)
T ss_pred -hccCCCcccCCccccCCCCCCCCCeEEEEcCCCcEEE
Confidence 235677763 24899999999998877766543
No 91
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=24.98 E-value=1.4e+02 Score=24.02 Aligned_cols=60 Identities=22% Similarity=0.224 Sum_probs=34.0
Q ss_pred CCceEEEccCceeEecCCCCccCCCeEEEecCC------CceeeEEEeeCCcEEEEECCCcceeEEEEEe
Q 025838 116 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLET------NKITEFIKFDVGNVVMVTGGRNRGRVGIIKN 179 (247)
Q Consensus 116 gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~------~kI~d~ikfe~G~~~~vtgG~n~G~vG~I~~ 179 (247)
+.+.++.|.|||+|.-.=.-+.-.--+.|+-.- .+=++.+++ | .+++.|-|.+-+|-|-|
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~l--G--lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVL--G--LYIIRGENVAVIGEIDE 75 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheee--E--EEEEecCccceeeecch
Confidence 346788999999995321112222223333221 111223333 3 78999999999998866
No 92
>cd05741 Ig_CEACAM_D1_like First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins. Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily-like. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surf
Probab=23.99 E-value=1.1e+02 Score=21.94 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=25.3
Q ss_pred EEEEcCCCceEEEEcChhhhcceeEEEeeeE
Q 025838 82 RLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQ 112 (247)
Q Consensus 82 Rvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~ 112 (247)
|+-.+..+.|.+..++++++..-.|.|....
T Consensus 50 R~~~~~~~sL~I~~l~~~DsG~Y~c~v~~~~ 80 (92)
T cd05741 50 RETIYPNGSLLIQNLTKEDSGTYTLQIISTN 80 (92)
T ss_pred eEEEcCCceEEEccCCchhcEEEEEEEEcCC
Confidence 3444555999999999999999999998754
No 93
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=23.48 E-value=1.7e+02 Score=21.69 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=17.3
Q ss_pred cCCCeEEEecC-----CCceeeEEEeeCCcEEEE
Q 025838 137 KANDTIKLDLE-----TNKITEFIKFDVGNVVMV 165 (247)
Q Consensus 137 k~~Dtv~i~l~-----~~kI~d~ikfe~G~~~~v 165 (247)
|+||.|.+.-. +|.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG~MYLv 35 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCcEEEEE
Confidence 55666655544 455666666766665554
No 94
>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=23.26 E-value=2.1e+02 Score=24.34 Aligned_cols=53 Identities=17% Similarity=0.146 Sum_probs=37.8
Q ss_pred CccEEEEEcCCCCeEeEeeceEEEEccCCCceEeCCCCCceeeehHHHHHHHHHH
Q 025838 186 SFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL 240 (247)
Q Consensus 186 s~~~V~v~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (247)
.++-+.+-|.+|+--++...|+|++= +.-|++-|.+.|+-..+..+.-.++++
T Consensus 124 g~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~giL~Gitr~~ll~~~~ 176 (231)
T PF01063_consen 124 GADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGILPGITRQLLLELAK 176 (231)
T ss_dssp TSSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSSB--HHHHHHHHHHH
T ss_pred CcchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhhccHHHHHHHHHHHH
Confidence 34445667899999999999999994 344889998888877776655555544
No 95
>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=23.02 E-value=5.2e+02 Score=22.72 Aligned_cols=101 Identities=21% Similarity=0.328 Sum_probs=58.6
Q ss_pred hCceEEECCE--EeccccCCCcceeeEEeccCCceEEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEc-c
Q 025838 48 MQRHVLVDAK--VRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINT-Y 124 (247)
Q Consensus 48 ~~~~V~VDGk--vr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~-h 124 (247)
..+.|+|||+ +|+|--| +++ |+..+ .|...+. -|.| ++..+.+..-+..| =
T Consensus 29 GkrvI~VDGkei~r~~wmf-----------------klv----g~e~F-~ig~~~~---k~~I-~I~~~~g~~YeYsL~V 82 (177)
T PF06905_consen 29 GKRVIKVDGKEIVRRDWMF-----------------KLV----GKETF-TIGGKNT---KCEI-NIEAVSGFAYEYSLEV 82 (177)
T ss_dssp --EEEEETTEEEEEE---S------------------------EEEEE-EETTTTE---EEEE-EEEEETTTEEEEEEEE
T ss_pred CeEEEEECCcEEEEeccee-----------------eeC----cccEE-EECCCce---EEEE-EEEecCCceEEEEEEE
Confidence 4578999999 5655433 332 22222 2332222 2544 33444444443333 4
Q ss_pred CceeE-ecCCCCccCCCeEEEecCCCceeeEEEeeCCcEEEEECCCcceeEEE
Q 025838 125 DGRTI-RYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGI 176 (247)
Q Consensus 125 DGrni-~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G~~~~vtgG~n~G~vG~ 176 (247)
||.++ .|-+...|.-.|..+.+..++ -.|-|+...+-+=..|......|.
T Consensus 83 dGksl~ky~e~~~k~~~tW~~~i~G~~--~RIvLdk~t~~vwvnG~~iet~~e 133 (177)
T PF06905_consen 83 DGKSLKKYKEEQSKKFNTWELNIDGQE--YRIVLDKDTMDVWVNGEKIETEGE 133 (177)
T ss_dssp TTEEEEE--SSTTTTEEEEEEEETTEE--EEEEEETTTTEEEETTCEE--EEE
T ss_pred CCEEHHHHHHHHhhhheeEEEecCCCE--EEEEEEcceEEEEECCEEccccce
Confidence 88888 677778899999999997543 677888888888899998877664
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=22.77 E-value=3.4e+02 Score=20.47 Aligned_cols=40 Identities=28% Similarity=0.368 Sum_probs=27.5
Q ss_pred CceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCCc
Q 025838 117 GIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGN 161 (247)
Q Consensus 117 g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G~ 161 (247)
++..+|.+||+.+-+- .-.| +.+|..+|+|...+=-..|.
T Consensus 7 ~keVIni~~G~~lG~v----~~~D-l~iD~~~G~I~aiIi~~~~~ 46 (76)
T TIGR02888 7 GKEIINVNDGERLGVI----GNID-LEIDEEDGRILSLIIPGKGK 46 (76)
T ss_pred CCCEEECCCCcEeecc----ccce-EEEECCCCEEEEEEEeCCCc
Confidence 5677899999999532 1123 78888899987666544443
No 97
>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=22.52 E-value=86 Score=25.27 Aligned_cols=31 Identities=19% Similarity=0.339 Sum_probs=19.2
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCC
Q 025838 115 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLET 148 (247)
Q Consensus 115 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~ 148 (247)
.....++.+.|.+.+ +|.+++||++.+.++-
T Consensus 66 ~d~~~eI~l~eAk~~---~~~~~vGD~i~~~i~~ 96 (122)
T PF08529_consen 66 EDPDTEISLSEAKKI---DPNAEVGDEIEEEIDP 96 (122)
T ss_dssp S-TTTEEEHHHHHCC---CTT--TTCEEEEE---
T ss_pred cCccceeeHHHHHhh---CCCCccCCEEEecCCh
Confidence 355667777777655 6789999999888864
No 98
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=22.25 E-value=66 Score=30.01 Aligned_cols=33 Identities=27% Similarity=0.511 Sum_probs=21.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEE
Q 025838 159 VGNVVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 193 (247)
Q Consensus 159 ~G~~~~vtgG~n~G~vG~I~~i~~~~~s~-~~V~v~ 193 (247)
.||.|.|+.|..-|+.|.++. +|-|.. -+|++.
T Consensus 60 iGN~A~VvSG~AKG~~G~VtG--kHGGieHVlV~F~ 93 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTG--KHGGIEHVLVDFP 93 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEE--EETTTTEEEEE--
T ss_pred cCceeEEeecccCCCcCeEec--ccCCeeeEEEECC
Confidence 499999999999999999987 365664 344443
No 99
>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=22.17 E-value=1.5e+02 Score=21.37 Aligned_cols=35 Identities=26% Similarity=0.388 Sum_probs=26.7
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCc
Q 025838 115 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNK 150 (247)
Q Consensus 115 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 150 (247)
.++.-...+..|-.|.+|- -|+.||.|++|-.+++
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 3443445678888888655 6899999999999876
No 100
>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=21.87 E-value=2.5e+02 Score=22.94 Aligned_cols=83 Identities=18% Similarity=0.255 Sum_probs=46.2
Q ss_pred eEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEeeCCcEEEEECCCc
Q 025838 91 FRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRN 170 (247)
Q Consensus 91 f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe~G~~~~vtgG~n 170 (247)
+.+.+.+.++..+. .|.+ ..|...+.-.+|+....|+..+..--.. .-..........|.+|+.+.|++|.-
T Consensus 51 YvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~--~~~~~~~~~~~~~~~G~~V~V~~GPf 122 (159)
T TIGR01955 51 YLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQY--EPKDSVPPATTLPYKGDKVRITDGAF 122 (159)
T ss_pred eEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhc--cccccCCccccCCCCCCEEEEeccCC
Confidence 45666665543322 2211 2466666555555555555322211000 00010112335699999999999999
Q ss_pred ceeEEEEEeEE
Q 025838 171 RGRVGIIKNRE 181 (247)
Q Consensus 171 ~G~vG~I~~i~ 181 (247)
.|..|.|.++.
T Consensus 123 ~g~~g~v~~~~ 133 (159)
T TIGR01955 123 AGFEAIFLEPD 133 (159)
T ss_pred CCcEEEEEEEC
Confidence 99999999975
No 101
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.72 E-value=1.1e+02 Score=30.74 Aligned_cols=39 Identities=15% Similarity=0.157 Sum_probs=33.4
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEecc
Q 025838 22 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTD 61 (247)
Q Consensus 22 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D 61 (247)
..++++=++|+ ++.-.+..||++++.||-|.+|++.++|
T Consensus 397 ~~~s~~~l~~k-a~~~~s~~~a~r~i~qG~vslnh~~v~~ 435 (467)
T KOG2623|consen 397 PGVSILDLLRK-ASRFPSGKEARRMIQQGGVSLNHEKVRD 435 (467)
T ss_pred CCCcHHHHHHH-hhcCCCcHHHHHHHHccceeecCccccC
Confidence 36778878887 5666678899999999999999999999
No 102
>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=21.55 E-value=64 Score=24.21 Aligned_cols=41 Identities=24% Similarity=0.456 Sum_probs=27.2
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEec------CCccEEEEEcCCCCeEe
Q 025838 157 FDVGNVVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 201 (247)
Q Consensus 157 fe~G~~~~vtgG~n~G~vG~I~~i~~~~------~s~~~V~v~d~~g~~F~ 201 (247)
+.+|+.+||.| +|++|+|+.|.-.- .....|.++..+| .|+
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 35699999987 67888888885422 1225777775554 454
No 103
>PF13620 CarboxypepD_reg: Carboxypeptidase regulatory-like domain; PDB: 3MN8_D 3P0D_I 3KCP_A 2B59_B 1UWY_A 1H8L_A 1QMU_A 2NSM_A.
Probab=21.34 E-value=1.4e+02 Score=21.12 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=30.8
Q ss_pred ECCEEeccccCCCcceeeEEe-ccCCceEEEEEcCCCceEEEEcCh
Q 025838 54 VDAKVRTDKTYPAGFMDVVSI-PKTNENFRLLYDTKGRFRLHSIRD 98 (247)
Q Consensus 54 VDGkvr~D~k~PvG~MDVIsI-~kt~e~yRvl~d~kgrf~l~~I~~ 98 (247)
|-|+|+..-.-|+.-..|.=. ...+..+...-|.+|+|.+-.+.+
T Consensus 2 I~G~V~d~~g~pv~~a~V~l~~~~~~~~~~~~Td~~G~f~~~~l~~ 47 (82)
T PF13620_consen 2 ISGTVTDATGQPVPGATVTLTDQDGGTVYTTTTDSDGRFSFEGLPP 47 (82)
T ss_dssp EEEEEEETTSCBHTT-EEEET--TTTECCEEE--TTSEEEEEEE-S
T ss_pred EEEEEEcCCCCCcCCEEEEEEEeeCCCEEEEEECCCceEEEEccCC
Confidence 457777666777777666544 246778999999999999998877
No 104
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=20.85 E-value=1.1e+02 Score=24.79 Aligned_cols=35 Identities=14% Similarity=0.377 Sum_probs=27.5
Q ss_pred EEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCc
Q 025838 112 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNK 150 (247)
Q Consensus 112 ~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 150 (247)
.++.+|+.++ +|.... |...+|+||.|.|.+....
T Consensus 29 ~~~~~GrV~v---NG~~aK-pS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 29 EMIEGGRVKV---NGQRAK-PSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHHHCCeEEE---CCEEcc-cccccCCCCEEEEEeCCcE
Confidence 4567888888 566665 7778999999999997643
No 105
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. 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 PUBMED:15210970.
Probab=20.61 E-value=1.7e+02 Score=21.10 Aligned_cols=30 Identities=27% Similarity=0.386 Sum_probs=25.1
Q ss_pred EEEccCceeEecCCCCccCCCeEEEecCCCc
Q 025838 120 YINTYDGRTIRYPDPLIKANDTIKLDLETNK 150 (247)
Q Consensus 120 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 150 (247)
...+..|-.|.+|. -|+.||.|++|-.+++
T Consensus 23 ~A~letG~~i~VP~-FI~~Gd~I~V~T~~g~ 52 (56)
T smart00841 23 PATLETGAVVQVPL-FINEGDKIKVDTRTGE 52 (56)
T ss_pred eEEECCCCEEEcCC-cccCCCEEEEECCCCc
Confidence 45578898998766 6999999999999875
No 106
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=20.49 E-value=1.1e+02 Score=28.63 Aligned_cols=30 Identities=40% Similarity=0.637 Sum_probs=27.1
Q ss_pred eEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 025838 153 EFIKFDVGNVVMVTGGRNRGRVGIIKNREK 182 (247)
Q Consensus 153 d~ikfe~G~~~~vtgG~n~G~vG~I~~i~~ 182 (247)
..+.|++|+.+-|+.|.=.|..|+|.++..
T Consensus 202 ~~~~f~vGd~VrI~dGPF~GfeG~I~eid~ 231 (258)
T TIGR01956 202 NLSKFRVGNFVKIVDGPFKGIVGKIKKIDQ 231 (258)
T ss_pred cccCCCCCCEEEEEecCCCCcEEEEEEEeC
Confidence 457799999999999999999999999864
No 107
>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=20.22 E-value=5.7e+02 Score=24.37 Aligned_cols=71 Identities=14% Similarity=0.165 Sum_probs=39.5
Q ss_pred eEEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCceeeEEEee
Q 025838 80 NFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFD 158 (247)
Q Consensus 80 ~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~ikfe 158 (247)
.|=.+.+..|.+.+.-+... | .|..+.++.+-.-.-...||+-+-.. .+..++..++|..+.+++..|+..
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 34444566665555444222 2 23334444444445556799988543 377888899999999999988764
Done!