Query 025354
Match_columns 254
No_of_seqs 114 out of 336
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:58:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025354.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025354hhsearch_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 9E-108 2E-112 740.5 29.2 245 8-252 16-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 2E-107 4E-112 738.9 29.6 246 8-253 16-261 (262)
3 PTZ00223 40S ribosomal protein 100.0 6E-107 1E-111 738.7 29.9 246 8-253 13-259 (273)
4 PRK04313 30S ribosomal protein 100.0 3E-100 7E-105 684.0 27.6 224 8-232 12-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 2.3E-97 5E-102 660.8 24.3 226 8-234 15-241 (241)
6 KOG0378 40S ribosomal protein 100.0 2.5E-93 5.4E-98 637.6 15.5 247 8-254 16-262 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 1.3E-34 2.8E-39 220.7 10.0 77 86-162 1-77 (77)
8 PF08071 RS4NT: RS4NT (NUC023) 98.9 3.1E-10 6.7E-15 76.4 0.8 25 8-32 14-38 (38)
9 PF01479 S4: S4 domain; Inter 98.5 1.7E-07 3.7E-12 64.0 5.2 48 34-82 1-48 (48)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.6 0.00037 8E-09 48.0 6.9 62 35-97 2-63 (70)
11 smart00363 S4 S4 RNA-binding d 97.2 0.00097 2.1E-08 44.7 5.4 50 36-86 3-52 (60)
12 COG0522 RpsD Ribosomal protein 96.9 0.0009 1.9E-08 59.9 3.8 43 43-85 102-144 (205)
13 smart00739 KOW KOW (Kyprides, 96.7 0.0015 3.3E-08 39.4 2.7 27 166-192 1-27 (28)
14 TIGR02988 YaaA_near_RecF S4 do 96.7 0.0046 1E-07 44.1 5.6 51 34-85 9-59 (59)
15 PF00467 KOW: KOW motif; Inte 96.7 0.0018 4E-08 41.3 3.1 31 169-202 1-31 (32)
16 TIGR01018 rpsD_arch ribosomal 95.7 0.008 1.7E-07 52.2 3.0 44 43-86 112-157 (162)
17 PF13275 S4_2: S4 domain; PDB: 95.7 0.0056 1.2E-07 45.7 1.5 60 32-94 6-65 (65)
18 PTZ00155 40S ribosomal protein 95.6 0.0095 2.1E-07 52.5 2.9 38 38-75 103-147 (181)
19 PLN00189 40S ribosomal protein 95.5 0.011 2.5E-07 52.6 3.1 42 43-84 117-160 (194)
20 PRK11507 ribosome-associated p 95.3 0.082 1.8E-06 40.2 6.6 60 32-94 10-69 (70)
21 PRK04051 rps4p 30S ribosomal p 95.2 0.021 4.5E-07 50.2 3.7 44 44-87 112-157 (177)
22 TIGR01017 rpsD_bact ribosomal 95.1 0.036 7.8E-07 49.2 4.9 43 44-86 99-141 (200)
23 PRK05327 rpsD 30S ribosomal pr 94.8 0.049 1.1E-06 48.4 5.0 43 44-86 102-144 (203)
24 TIGR00005 rluA_subfam pseudour 94.8 0.12 2.7E-06 47.2 7.7 52 33-85 5-56 (299)
25 CHL00113 rps4 ribosomal protei 94.7 0.049 1.1E-06 48.6 4.8 43 44-86 98-140 (201)
26 TIGR01080 rplX_A_E ribosomal p 94.4 0.093 2E-06 43.2 5.4 41 163-206 38-78 (114)
27 TIGR03069 PS_II_S4 photosystem 94.1 0.18 3.8E-06 46.4 7.1 63 32-107 182-244 (257)
28 TIGR00478 tly hemolysin TlyA f 93.2 0.16 3.5E-06 45.9 5.2 47 39-86 5-51 (228)
29 COG2501 S4-like RNA binding pr 92.1 0.23 5E-06 38.1 4.0 60 32-94 10-69 (73)
30 PRK11180 rluD 23S rRNA pseudou 91.9 0.58 1.3E-05 43.8 7.3 52 33-85 17-68 (325)
31 PRK05912 tyrosyl-tRNA syntheta 91.4 0.68 1.5E-05 45.2 7.4 65 33-104 342-406 (408)
32 COG0564 RluA Pseudouridylate s 91.3 0.67 1.5E-05 43.2 6.9 57 32-91 11-67 (289)
33 PRK10700 23S rRNA pseudouridyl 90.8 0.75 1.6E-05 42.8 6.8 64 37-103 6-81 (289)
34 PRK01191 rpl24p 50S ribosomal 90.3 0.75 1.6E-05 38.3 5.6 38 164-204 43-80 (120)
35 PRK10348 ribosome-associated h 89.6 0.88 1.9E-05 38.4 5.6 58 33-92 8-65 (133)
36 COG1187 RsuA 16S rRNA uridine- 89.4 0.86 1.9E-05 42.1 5.9 59 45-104 13-78 (248)
37 PRK12281 rplX 50S ribosomal pr 89.1 0.64 1.4E-05 35.6 4.0 39 165-206 5-43 (76)
38 PRK10475 23S rRNA pseudouridin 88.9 1.6 3.4E-05 40.9 7.3 68 32-102 5-80 (290)
39 CHL00141 rpl24 ribosomal prote 88.4 0.78 1.7E-05 35.6 4.2 39 164-205 6-44 (83)
40 PRK11025 23S rRNA pseudouridyl 88.1 2.1 4.5E-05 40.1 7.6 51 33-85 19-69 (317)
41 PRK10839 16S rRNA pseudouridyl 87.4 3.3 7.2E-05 36.7 8.1 67 36-105 3-75 (232)
42 PRK00004 rplX 50S ribosomal pr 87.3 0.82 1.8E-05 36.9 3.9 37 165-204 3-39 (105)
43 PRK13354 tyrosyl-tRNA syntheta 87.1 2.1 4.6E-05 41.9 7.3 66 33-104 342-407 (410)
44 PLN00051 RNA-binding S4 domain 85.4 3.4 7.4E-05 38.4 7.4 62 33-107 191-252 (267)
45 COG2302 Uncharacterized conser 85.1 2.1 4.5E-05 39.9 5.7 63 32-107 179-241 (257)
46 COG1189 Predicted rRNA methyla 84.9 1.9 4.1E-05 40.0 5.3 47 45-91 13-59 (245)
47 TIGR01079 rplX_bact ribosomal 82.5 1.9 4.1E-05 34.9 3.9 28 166-193 3-30 (104)
48 PTZ00194 60S ribosomal protein 81.1 4 8.7E-05 35.0 5.5 55 164-221 44-105 (143)
49 PF13051 DUF3912: Protein of u 81.0 4.2 9.1E-05 30.3 4.9 50 169-222 5-55 (68)
50 KOG4655 U3 small nucleolar rib 72.0 2.8 6.1E-05 37.0 2.2 56 21-76 86-148 (181)
51 COG0162 TyrS Tyrosyl-tRNA synt 66.6 13 0.00028 36.7 5.7 54 44-104 345-398 (401)
52 COG0198 RplX Ribosomal protein 62.3 12 0.00026 30.5 3.9 29 165-193 3-31 (104)
53 COG2163 RPL14A Ribosomal prote 61.9 8.2 0.00018 32.4 3.0 34 167-204 5-38 (125)
54 PF03417 AAT: Acyl-coenzyme A: 57.2 46 0.00099 28.9 7.0 29 31-60 69-97 (225)
55 PTZ00065 60S ribosomal protein 55.6 14 0.00031 31.3 3.3 33 167-203 8-40 (130)
56 PF14001 YdfZ: YdfZ protein 54.7 20 0.00043 27.0 3.6 42 166-211 9-56 (64)
57 PRK04333 50S ribosomal protein 52.0 16 0.00035 28.5 2.9 33 166-202 3-35 (84)
58 COG1188 Ribosome-associated he 50.7 40 0.00086 27.4 5.1 45 45-90 19-63 (100)
59 cd03704 eRF3c_III This family 46.6 56 0.0012 25.3 5.3 48 142-190 56-108 (108)
60 PF08828 DSX_dimer: Doublesex 45.4 14 0.0003 27.7 1.5 45 8-67 10-55 (62)
61 PRK14898 DNA-directed RNA poly 45.4 99 0.0021 33.4 8.5 77 76-154 112-195 (858)
62 PF04773 FecR: FecR protein; 44.8 1.2E+02 0.0027 22.2 9.5 66 121-186 3-75 (98)
63 cd03706 mtEFTU_III Domain III 43.3 1.2E+02 0.0025 22.9 6.5 40 146-189 52-92 (93)
64 TIGR01955 RfaH transcriptional 42.9 66 0.0014 26.5 5.5 84 100-191 50-133 (159)
65 PF01959 DHQS: 3-dehydroquinat 42.3 54 0.0012 32.1 5.5 54 115-183 289-345 (354)
66 KOG1784 Small Nuclear ribonucl 41.9 49 0.0011 26.6 4.3 60 126-189 10-75 (96)
67 PRK02290 3-dehydroquinate synt 40.1 59 0.0013 31.7 5.4 46 125-183 287-335 (344)
68 cd04093 HBS1_C HBS1_C: this fa 39.7 1.7E+02 0.0037 22.4 9.0 42 145-190 59-107 (107)
69 PTZ00471 60S ribosomal protein 39.5 30 0.00064 29.5 2.9 24 167-190 5-28 (134)
70 TIGR03193 4hydroxCoAred 4-hydr 38.6 26 0.00057 30.1 2.5 54 31-88 16-77 (148)
71 PF01588 tRNA_bind: Putative t 37.4 72 0.0016 24.6 4.6 24 183-206 2-27 (95)
72 PF07076 DUF1344: Protein of u 37.1 78 0.0017 23.6 4.4 35 123-157 11-49 (61)
73 TIGR03318 YdfZ_fam putative se 35.9 40 0.00086 25.4 2.7 41 167-211 11-57 (65)
74 TIGR00405 L26e_arch ribosomal 35.5 65 0.0014 26.5 4.3 26 167-192 87-112 (145)
75 PRK08559 nusG transcription an 35.4 59 0.0013 27.4 4.1 29 165-193 93-121 (153)
76 cd02899 PLAT_SR Scavenger rece 35.0 1.4E+02 0.003 24.2 6.0 61 167-240 41-108 (109)
77 KOG1999 RNA polymerase II tran 34.9 57 0.0012 35.8 4.7 27 167-193 460-486 (1024)
78 cd03705 EF1_alpha_III Domain I 33.6 94 0.002 23.7 4.7 35 145-182 59-100 (104)
79 PF06905 FAIM1: Fas apoptotic 32.0 3.6E+02 0.0079 23.8 10.1 101 58-186 29-133 (177)
80 PRK05609 nusG transcription an 31.4 55 0.0012 27.6 3.3 29 164-192 124-152 (181)
81 PF12961 DUF3850: Domain of Un 30.8 46 0.001 25.5 2.4 18 138-155 21-38 (72)
82 PF08942 DUF1919: Domain of un 30.7 13 0.00028 33.6 -0.7 59 36-114 53-111 (201)
83 KOG3401 60S ribosomal protein 30.1 42 0.00091 29.0 2.3 52 158-209 40-94 (145)
84 PF09285 Elong-fact-P_C: Elong 29.5 1E+02 0.0022 22.4 4.0 37 125-162 18-54 (56)
85 TIGR00922 nusG transcription t 28.6 61 0.0013 27.2 3.1 28 165-192 118-145 (172)
86 KOG1999 RNA polymerase II tran 28.4 1.9E+02 0.0041 32.1 7.2 55 167-225 582-638 (1024)
87 COG1792 MreC Cell shape-determ 27.1 5.2E+02 0.011 24.1 11.8 61 142-222 209-270 (284)
88 TIGR00234 tyrS tyrosyl-tRNA sy 26.9 61 0.0013 31.4 3.1 45 33-78 329-373 (377)
89 PTZ00141 elongation factor 1- 26.8 3.4E+02 0.0074 26.8 8.3 53 145-198 381-437 (446)
90 PF02239 Cytochrom_D1: Cytochr 26.5 3.4E+02 0.0073 26.0 8.1 90 90-187 49-155 (369)
91 TIGR03198 pucE xanthine dehydr 26.2 26 0.00056 30.1 0.4 53 31-87 18-78 (151)
92 PF01063 Aminotran_4: Aminotra 25.9 2.2E+02 0.0047 24.4 6.1 52 197-250 125-176 (231)
93 PF11717 Tudor-knot: RNA bindi 25.3 2E+02 0.0044 20.0 4.8 37 167-203 1-38 (55)
94 cd04708 BAH_plantDCM_II BAH, o 24.8 78 0.0017 28.6 3.2 44 145-194 7-54 (202)
95 cd01234 PH_CADPS CADPS (Ca2+-d 24.6 49 0.0011 27.5 1.7 41 99-144 22-62 (117)
96 cd05892 Ig_Myotilin_C C-termin 24.5 1.5E+02 0.0033 21.6 4.2 34 88-121 28-63 (75)
97 smart00536 AXH domain in Ataxi 23.6 2.3E+02 0.005 23.6 5.5 77 130-223 7-84 (116)
98 cd03707 EFTU_III Domain III of 23.3 3.1E+02 0.0068 20.3 6.4 27 146-175 52-78 (90)
99 cd05794 S1_EF-P_repeat_2 S1_EF 23.1 1.4E+02 0.003 21.7 3.7 35 125-160 18-52 (56)
100 PF10781 DSRB: Dextransucrase 22.5 1.8E+02 0.0039 21.7 4.1 29 147-175 2-35 (62)
101 COG5144 TFB2 RNA polymerase II 22.1 66 0.0014 31.7 2.3 96 14-114 41-138 (447)
102 COG1188 Ribosome-associated he 21.9 1E+02 0.0022 25.0 3.1 35 122-160 29-63 (100)
103 KOG2623 Tyrosyl-tRNA synthetas 21.9 1.1E+02 0.0023 31.0 3.7 39 32-71 397-435 (467)
104 KOG1708 Mitochondrial/chloropl 21.8 1.5E+02 0.0033 27.3 4.4 23 169-191 75-97 (236)
105 PF07569 Hira: TUP1-like enhan 21.7 2.9E+02 0.0062 24.6 6.2 57 87-143 20-94 (219)
106 smart00841 Elong-fact-P_C Elon 21.7 1.6E+02 0.0034 21.4 3.7 30 130-160 23-52 (56)
107 PF05709 Sipho_tail: Phage tai 21.6 3.4E+02 0.0074 23.2 6.5 54 32-87 40-96 (249)
108 smart00306 HintN Hint (Hedgeho 21.4 3.3E+02 0.0071 19.8 8.2 55 168-222 23-78 (100)
109 KOG2404 Fumarate reductase, fl 21.0 75 0.0016 31.6 2.5 51 12-62 117-168 (477)
110 PRK09014 rfaH transcriptional 21.0 1.1E+02 0.0023 25.6 3.2 26 166-191 109-134 (162)
111 PF03143 GTP_EFTU_D3: Elongati 20.7 2.3E+02 0.005 21.8 4.8 43 145-190 56-98 (99)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=9.1e-108 Score=740.47 Aligned_cols=245 Identities=84% Similarity=1.302 Sum_probs=241.6
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccC
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
=+|||+||+++||||||||||++++||||++||||+|+||+|+|||++||+||+|+|||+||+|++||||||||||||++
T Consensus 16 ~~W~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt 95 (261)
T PLN00036 16 KHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKT 95 (261)
T ss_pred cccccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCC
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEe
Q 025354 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKF 167 (254)
Q Consensus 88 ~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f 167 (254)
||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||+||+||||+||||+++|++|+||
T Consensus 96 ~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~kI~~~ikf 175 (261)
T PLN00036 96 NENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKF 175 (261)
T ss_pred CCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEEEEeCCCCceeeEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHH
Q 025354 168 DVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR 247 (254)
Q Consensus 168 e~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~~kgi~~~~~e~~~~~ 247 (254)
++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++++||||||++||||++++|||+++
T Consensus 176 e~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~~e~r~~~ 255 (261)
T PLN00036 176 DVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKR 255 (261)
T ss_pred CCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccchHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999988999999999999999999999999
Q ss_pred HHHHH
Q 025354 248 QAAQA 252 (254)
Q Consensus 248 ~~~~~ 252 (254)
+++.+
T Consensus 256 ~~~~~ 260 (261)
T PLN00036 256 LAAGQ 260 (261)
T ss_pred hhhhc
Confidence 98764
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.8e-107 Score=738.87 Aligned_cols=246 Identities=59% Similarity=0.947 Sum_probs=242.6
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccC
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
=+|||+||+++||||||||||++++||||++||||+|+||+|+|||++||+||+|+|||+||+|++||||||||||||++
T Consensus 16 ~~W~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt 95 (262)
T PTZ00118 16 SHWMLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKT 95 (262)
T ss_pred cccccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCC
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEe
Q 025354 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKF 167 (254)
Q Consensus 88 ~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f 167 (254)
||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+||||+++|++|+||
T Consensus 96 ~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikf 175 (262)
T PTZ00118 96 NEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSLRLDLETGKVLEFLKF 175 (262)
T ss_pred CCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCEEEEECCCCceeeEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHH
Q 025354 168 DVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR 247 (254)
Q Consensus 168 e~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~~kgi~~~~~e~~~~~ 247 (254)
|+||+||||||+|+|++|+|.+++++++|+++||++|++|++|+|+++||||||++++||||||++||||+|++|||+++
T Consensus 176 e~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~kgi~~~~~e~~~~~ 255 (262)
T PTZ00118 176 EVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDIIEERRNR 255 (262)
T ss_pred CCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCccccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999988999999999999999999999999
Q ss_pred HHHHHh
Q 025354 248 QAAQAA 253 (254)
Q Consensus 248 ~~~~~~ 253 (254)
+++++.
T Consensus 256 ~~~~~~ 261 (262)
T PTZ00118 256 LAKALR 261 (262)
T ss_pred HHHHhc
Confidence 988764
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=5.6e-107 Score=738.75 Aligned_cols=246 Identities=50% Similarity=0.807 Sum_probs=241.9
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccC
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
=+|||+||+++||||||||||++++||||++||||+|+||+|+|||++||+||+|+|||+||+|++||||||||||||++
T Consensus 13 ~~W~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt 92 (273)
T PTZ00223 13 KDWMLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKT 92 (273)
T ss_pred cccccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCC
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEe
Q 025354 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKF 167 (254)
Q Consensus 88 ~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f 167 (254)
||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|+||+++|++|+||
T Consensus 93 ~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l~~~kI~~~ikf 172 (273)
T PTZ00223 93 GDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVKEKKVVDLIKN 172 (273)
T ss_pred CCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCEEEEECCCCeeeEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccC-CCceEecCCCcceeeehHHHHHH
Q 025354 168 DVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEEARK 246 (254)
Q Consensus 168 e~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~-~kp~islp~~kgi~~~~~e~~~~ 246 (254)
++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++ ++||||||++||||++++|||++
T Consensus 173 e~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~~e~~~~ 252 (273)
T PTZ00223 173 RNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINVIQEREE 252 (273)
T ss_pred CCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999986 69999999999999999999999
Q ss_pred HHHHHHh
Q 025354 247 RQAAQAA 253 (254)
Q Consensus 247 ~~~~~~~ 253 (254)
+++++++
T Consensus 253 ~~~~~~~ 259 (273)
T PTZ00223 253 KLIAAEA 259 (273)
T ss_pred HHHHHHh
Confidence 9988764
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=3.1e-100 Score=683.99 Aligned_cols=224 Identities=41% Similarity=0.633 Sum_probs=220.7
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccC
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
-+|||+||+++||||||||||++++||||+++|||+|+||+|+|||++||+||+|+|||+||+|++||||||||||||++
T Consensus 12 ~~W~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~ 91 (237)
T PRK04313 12 KSWPIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPET 91 (237)
T ss_pred cccccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccC
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCC-CCccCCCeEEEecCCCeeeeEEE
Q 025354 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKANDTIKLDLEENKITDFIK 166 (254)
Q Consensus 88 ~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d-~~ik~~Dtv~i~l~~~kI~d~i~ 166 (254)
||+|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| ++||+||||+|+||+++|++|||
T Consensus 92 ~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~ 171 (237)
T PRK04313 92 GEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIP 171 (237)
T ss_pred CCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEe
Confidence 99999999999999999999999999999999999999999999999999999998 99999999999999999999999
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 232 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~ 232 (254)
|++||+||||||+|+||+|+|.+|++++ +++|+||++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 9999999999999999999999999999 7789999999999999999999999998 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-97 Score=660.81 Aligned_cols=226 Identities=46% Similarity=0.698 Sum_probs=222.6
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccC
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
-+||++||+++|||+|+||||++++||||++++||+|+||+|+|||++||++|+|+|||+||+|++||||||||||||+|
T Consensus 15 ~~w~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~t 94 (241)
T COG1471 15 KSWPIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKT 94 (241)
T ss_pred ceEEeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEe
Q 025354 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKF 167 (254)
Q Consensus 88 ~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f 167 (254)
||+||||||.+|+|.||+|++|||.||||||+|||+++||++|||||||||++++|++|++||||++++|+++|++||||
T Consensus 95 gE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dtv~i~lp~~~I~~~i~f 174 (241)
T COG1471 95 GEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVKISLPEQKIVEHIKF 174 (241)
T ss_pred CceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccEEEEeCCChhheeEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCc
Q 025354 168 DVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGK 234 (254)
Q Consensus 168 e~G~~~~i~gG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~~k 234 (254)
++|++||||||+|+|++|+|.+|+.++ +++|+||++|.+|+.|+|+++||||||+ ++|||+||.|+
T Consensus 175 e~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~e~ 241 (241)
T COG1471 175 EEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPKEK 241 (241)
T ss_pred CCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCCCC
Confidence 999999999999999999999999999 5679999999999999999999999998 99999999875
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-93 Score=637.64 Aligned_cols=247 Identities=66% Similarity=1.075 Sum_probs=244.3
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccC
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
=.|||||++|.|||+||+|||+++||+||++||||+|+||+|.+|+++|++|+.|+|||+||+|.+||+||||||+|++|
T Consensus 16 ~~wmldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisiekT 95 (263)
T KOG0378|consen 16 KHWMLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIEKT 95 (263)
T ss_pred HhheecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeecccccccceeEEEEeccc
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEe
Q 025354 88 NENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKF 167 (254)
Q Consensus 88 ~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f 167 (254)
||+||++||++|+|.+|+|++|||+||||||++++.+.+|+|+|+|||||+||||||.||+|||+++++++++|.++++|
T Consensus 96 ge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dtI~~~~~t~kit~~ikf 175 (263)
T KOG0378|consen 96 GEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDTIKIDLETSKITDFIKF 175 (263)
T ss_pred chhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCccceeeccCCCceeeeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHH
Q 025354 168 DVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR 247 (254)
Q Consensus 168 e~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~~kgi~~~~~e~~~~~ 247 (254)
++|++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++|+||||+|++||||||+++||+++++||||+|
T Consensus 176 ~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPkgkgi~~siaEe~dkr 255 (263)
T KOG0378|consen 176 DTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPKGKGIALSIAEERDKR 255 (263)
T ss_pred CccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCccccCccchhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhC
Q 025354 248 QAAQAAA 254 (254)
Q Consensus 248 ~~~~~~~ 254 (254)
++++.++
T Consensus 256 l~~k~~s 262 (263)
T KOG0378|consen 256 LAAKISS 262 (263)
T ss_pred HhhhccC
Confidence 9998764
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=1.3e-34 Score=220.73 Aligned_cols=77 Identities=61% Similarity=1.011 Sum_probs=69.8
Q ss_pred cCCceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeee
Q 025354 86 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 162 (254)
Q Consensus 86 kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 162 (254)
||||+|||+||++|+|.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
T Consensus 1 kt~e~yRvl~d~kgr~~l~~I~~eea~~KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~kI~ 77 (77)
T PF00900_consen 1 KTGEHYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQKIV 77 (77)
T ss_dssp CTTEEEEEEE-TTS-EEEEEE-TTGGGEEEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETTTTEEE
T ss_pred CCCcEEEEEECCCCcEEEEECCHHHccCeEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECCCCcCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999986
No 8
>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=98.91 E-value=3.1e-10 Score=76.38 Aligned_cols=25 Identities=40% Similarity=0.527 Sum_probs=15.4
Q ss_pred eeeeeecccceeccCCCCCCCCCcc
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRE 32 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~ 32 (254)
-+|||+|++++|||+||||||+++|
T Consensus 14 ~~W~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 14 KSWMIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp GGGT--SSSSSB-----SSSS-CCC
T ss_pred cccccccccCccccCCCCCCccCCC
Confidence 3799999999999999999999986
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=98.53 E-value=1.7e-07 Score=63.98 Aligned_cols=48 Identities=33% Similarity=0.359 Sum_probs=44.1
Q ss_pred chhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEE
Q 025354 34 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVV 82 (254)
Q Consensus 34 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVI 82 (254)
++|..+| ..++++.+..||++.+++|.|+|||++++|+.|++...|+|
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 3677888 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=97.57 E-value=0.00037 Score=48.03 Aligned_cols=62 Identities=26% Similarity=0.333 Sum_probs=47.5
Q ss_pred hhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcC
Q 025354 35 PLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDT 97 (254)
Q Consensus 35 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~ 97 (254)
.|.-+|+.. ..+.+.++|++++.+|.|+|||+..++..+++-..|+|++........++|..
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 345566654 36789999999999999999999999999999888999997643223444433
No 11
>smart00363 S4 S4 RNA-binding domain.
Probab=97.21 E-value=0.00097 Score=44.66 Aligned_cols=50 Identities=26% Similarity=0.211 Sum_probs=42.2
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 025354 36 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 86 (254)
Q Consensus 36 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 86 (254)
|..+|... ..+.+.+++++.+.+|.|+|||++.++..+++--.|.|++..
T Consensus 3 l~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 3 LDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred HHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 45566543 356789999999999999999999999999998889999965
No 12
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=96.90 E-value=0.0009 Score=59.90 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=41.0
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 025354 43 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 85 (254)
Q Consensus 43 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 85 (254)
++++|.|.++|++.+..|+|.|||+.++++.|=|-.=|+|+|.
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 3799999999999999999999999999999999999999996
No 13
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.73 E-value=0.0015 Score=39.39 Aligned_cols=27 Identities=37% Similarity=0.661 Sum_probs=24.5
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEE
Q 025354 166 KFDVGNIVMVTGGRNRGRVGIIKNREK 192 (254)
Q Consensus 166 ~fe~G~~~~i~gG~n~G~vG~I~~i~~ 192 (254)
+|++|+.++|++|.+.|.+|+|.++..
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 478999999999999999999999853
No 14
>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=96.71 E-value=0.0046 Score=44.07 Aligned_cols=51 Identities=22% Similarity=0.217 Sum_probs=44.4
Q ss_pred chhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 025354 34 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 85 (254)
Q Consensus 34 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 85 (254)
..|--+|... .++.+...+++++.+|.|.|||++++.+.|.+--=|+|+|+
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 5566777776 77779999999999999999999999889999888888874
No 15
>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=96.71 E-value=0.0018 Score=41.35 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=25.8
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 025354 169 VGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 202 (254)
Q Consensus 169 ~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i 202 (254)
+|+.++|+.|++.|+.|+|.++..+. +.|++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence 58999999999999999999997543 45554
No 16
>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=95.75 E-value=0.008 Score=52.18 Aligned_cols=44 Identities=18% Similarity=0.275 Sum_probs=36.3
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcce--eEEEecc
Q 025354 43 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM--DVVSIPK 86 (254)
Q Consensus 43 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~M--DVIsI~k 86 (254)
++++|.|.++|++.+.+|+|.|||++++++.|-|--= |-|+...
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~ 157 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAP 157 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeec
Confidence 3799999999999999999999999999998866432 5555543
No 17
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.69 E-value=0.0056 Score=45.74 Aligned_cols=60 Identities=27% Similarity=0.309 Sum_probs=41.4
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 94 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 94 (254)
+.|.|.=+|.- .+++.|.-|||..|.+|.|+|||.+.+...--+--=|+|++ .++.|+++
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 45667777765 58899999999999999999999999988888888899999 57888874
No 18
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.58 E-value=0.0095 Score=52.54 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=33.5
Q ss_pred HHHHhhh-------cccccHHHHHHHHhCceEEECCEEeccccCC
Q 025354 38 LVLRNRL-------KYALTYREVIAILMQRHVLVDGKVRTDKTYP 75 (254)
Q Consensus 38 i~LRd~L-------kyA~t~rEak~Il~~~~V~VDGkvr~D~k~P 75 (254)
-+|+.+| |+|.|..+|++.+.+|+|.|||++++|+.|=
T Consensus 103 ~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~ 147 (181)
T PTZ00155 103 KLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFL 147 (181)
T ss_pred HHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceE
Confidence 4556555 9999999999999999999999999999763
No 19
>PLN00189 40S ribosomal protein S9; Provisional
Probab=95.49 E-value=0.011 Score=52.64 Aligned_cols=42 Identities=12% Similarity=0.184 Sum_probs=35.4
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcce--eEEEe
Q 025354 43 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM--DVVSI 84 (254)
Q Consensus 43 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~M--DVIsI 84 (254)
+|++|.|..+|++++.+|+|.|||++++++.|-|-.= |-|+.
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw 160 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDF 160 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEE
Confidence 4789999999999999999999999999998866543 44444
No 20
>PRK11507 ribosome-associated protein; Provisional
Probab=95.27 E-value=0.082 Score=40.19 Aligned_cols=60 Identities=18% Similarity=0.167 Sum_probs=48.3
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 94 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 94 (254)
+-|-|.=+|.- .+++.|.-|||..|.+|.|+|||.+.+-..-=+--=|+|+++ ++.|++.
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 44666666654 588899999999999999999999987776667777999995 5777764
No 21
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=95.18 E-value=0.021 Score=50.20 Aligned_cols=44 Identities=20% Similarity=0.257 Sum_probs=37.2
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEeccC
Q 025354 44 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPA--GFMDVVSIPKT 87 (254)
Q Consensus 44 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv--G~MDVIsI~kt 87 (254)
+++|.|..+|++.+.+|+|.|||++++++.|.| +.=|.|+...+
T Consensus 112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~ 157 (177)
T PRK04051 112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPT 157 (177)
T ss_pred ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCC
Confidence 699999999999999999999999999998876 44466666543
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=95.07 E-value=0.036 Score=49.17 Aligned_cols=43 Identities=28% Similarity=0.354 Sum_probs=39.0
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 025354 44 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 86 (254)
Q Consensus 44 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 86 (254)
++++.|.++|++.+.+|.|.|||++++++.|.+--=|+|++..
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
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=94.81 E-value=0.049 Score=48.44 Aligned_cols=43 Identities=28% Similarity=0.404 Sum_probs=39.4
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 025354 44 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 86 (254)
Q Consensus 44 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 86 (254)
++++.+..+|++++..|.|.|||++++.+.|++--=|+|++..
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 24
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=94.75 E-value=0.12 Score=47.23 Aligned_cols=52 Identities=19% Similarity=0.183 Sum_probs=43.3
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 85 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 85 (254)
+..|.-+|...+. ..+.+++++.+.+|.|+|||+++++..+.+---|+|++.
T Consensus 5 g~rLd~~L~~~~~-~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~ 56 (299)
T TIGR00005 5 GQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVR 56 (299)
T ss_pred chhHHHHHHHhcc-cCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEe
Confidence 4567778877663 357899999999999999998888888999777999983
No 25
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=94.72 E-value=0.049 Score=48.63 Aligned_cols=43 Identities=21% Similarity=0.362 Sum_probs=38.4
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 025354 44 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 86 (254)
Q Consensus 44 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 86 (254)
+++|.+.++|++++.+|.|.|||++++++.|.+--=|+|++..
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=94.43 E-value=0.093 Score=43.22 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=32.8
Q ss_pred eEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC
Q 025354 163 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 206 (254)
Q Consensus 163 d~i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~ 206 (254)
+.+++..|+.+.|++|++-|..|+|.+|... .+.|.|+.-+
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn 78 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVT 78 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeE
Confidence 5568889999999999999999999999633 2466666543
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=94.09 E-value=0.18 Score=46.44 Aligned_cols=63 Identities=14% Similarity=0.205 Sum_probs=51.0
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 107 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 107 (254)
.|+=|-.++...+ ..+.+.|++.+.+|.|+|||++++++.+.+--=|+|+|. ..|||.+..+.
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 3555667887655 568899999999999999999999999988777999984 46788777664
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=93.22 E-value=0.16 Score=45.92 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=40.2
Q ss_pred HHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 025354 39 VLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 86 (254)
Q Consensus 39 ~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k 86 (254)
+|.+ .+++.+.++|++.+++|.|.|||++++++.+.+--=|.|++..
T Consensus 5 ~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 5 LLVR-RGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred HHHH-cCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 4444 4688899999999999999999999999999886559999964
No 29
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=92.11 E-value=0.23 Score=38.07 Aligned_cols=60 Identities=23% Similarity=0.278 Sum_probs=44.2
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 94 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl 94 (254)
+-|-|.=+|.- ++.+++.-+||..|+++.|+|||.+-+=..-=+=-=|+|+||. ..|-+.
T Consensus 10 e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~--~~~~v~ 69 (73)
T COG2501 10 EFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG--QRYQVV 69 (73)
T ss_pred ceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC--EEEEEE
Confidence 34556666654 6899999999999999999999998554444455568999964 444443
No 30
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=91.90 E-value=0.58 Score=43.80 Aligned_cols=52 Identities=19% Similarity=0.144 Sum_probs=42.1
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 85 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 85 (254)
...|.-+|+..+. ..+.+.+++.+.+|.|+|||+.++...+.+---|+|++.
T Consensus 17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~ 68 (325)
T PRK11180 17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAID 68 (325)
T ss_pred CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEe
Confidence 4678888888654 357899999999999999999987666666555999885
No 31
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=91.37 E-value=0.68 Score=45.21 Aligned_cols=65 Identities=17% Similarity=0.214 Sum_probs=49.2
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 104 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~ 104 (254)
.+|+.-+|.+ .+.|.+..|||+.+.||-|+|||..++|..+-+-- ......|-+|---|.+|.+.
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 69999999999999999999999999999763322 11135566666666666554
No 32
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=91.26 E-value=0.67 Score=43.24 Aligned_cols=57 Identities=25% Similarity=0.220 Sum_probs=50.0
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 91 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~y 91 (254)
...-|--+|++ |.- .+..+..+++.+|.|.|||++++ ..|.+..=|+|+++...+.+
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 35567788998 665 78899999999999999999999 99999999999999876665
No 33
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=90.82 E-value=0.75 Score=42.83 Aligned_cols=64 Identities=20% Similarity=0.107 Sum_probs=46.1
Q ss_pred HHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEecc----------CCceEEEEEcCCCceEE
Q 025354 37 ILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA--GFMDVVSIPK----------TNENFRLLYDTKGRFRL 103 (254)
Q Consensus 37 ~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv--G~MDVIsI~k----------t~e~yRvl~d~kgrf~l 103 (254)
-=||-+ +++ .+.++|++++.+|.|+|||++. +..+.| +-.|.|+++. ..++|-+++-+.|..+-
T Consensus 6 ~k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~~s 81 (289)
T PRK10700 6 QKVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCT 81 (289)
T ss_pred HHHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCEee
Confidence 334443 343 6789999999999999999987 566666 5557787753 11468888989986643
No 34
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=90.28 E-value=0.75 Score=38.32 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=30.5
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 025354 164 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 204 (254)
Q Consensus 164 ~i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d 204 (254)
.+++..|+.+.|+.|+.-|..|+|.++.... +.|+|+.
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 4578899999999999999999999996533 3555554
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=89.58 E-value=0.88 Score=38.45 Aligned_cols=58 Identities=10% Similarity=0.060 Sum_probs=48.9
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 92 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yR 92 (254)
++-|-.||=- .+++.|..-|+..|..|.|.|||.+ .-+...|-.=|+|+|...+..|-
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~ 65 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERT 65 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEE
Confidence 4566666655 4999999999999999999999999 88999999999999977555443
No 36
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=89.44 E-value=0.86 Score=42.09 Aligned_cols=59 Identities=24% Similarity=0.239 Sum_probs=43.8
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcce-eEEEeccCC------ceEEEEEcCCCceEEE
Q 025354 45 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM-DVVSIPKTN------ENFRLLYDTKGRFRLH 104 (254)
Q Consensus 45 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~M-DVIsI~kt~------e~yRvl~d~kgrf~l~ 104 (254)
++| +.|||.++|.+|.|.|||++.++...-+=-- |+|.++..- ..|-|++-+.|..+-+
T Consensus 13 G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~ 78 (248)
T COG1187 13 GVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSST 78 (248)
T ss_pred CCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEecc
Confidence 554 5899999999999999999999986555444 466665431 2288888888866444
No 37
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=89.08 E-value=0.64 Score=35.60 Aligned_cols=39 Identities=21% Similarity=0.429 Sum_probs=32.0
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC
Q 025354 165 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 206 (254)
Q Consensus 165 i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~ 206 (254)
+++..|+.+.|+.|+.-|++|+|.++.... +.|.|++-+
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 478899999999999999999999996533 467777543
No 38
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=88.88 E-value=1.6 Score=40.88 Aligned_cols=68 Identities=18% Similarity=0.108 Sum_probs=49.7
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc--------CCceEEEEEcCCCceE
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK--------TNENFRLLYDTKGRFR 102 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k--------t~e~yRvl~d~kgrf~ 102 (254)
.++-|.-+|.+. ++ .+.++|++.+.+|.|+|||++. +..+.|---|+|+++. .+++|-++.-+.|..+
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 356676777653 43 4799999999999999999987 4666675559898852 1346777877787543
No 39
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=88.42 E-value=0.78 Score=35.64 Aligned_cols=39 Identities=15% Similarity=0.409 Sum_probs=31.8
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcC
Q 025354 164 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 205 (254)
Q Consensus 164 ~i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~ 205 (254)
.+++..|+.+.|+.|+.-|+.|+|.++... .+.|+|++.
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKK---SNKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCc
Confidence 347889999999999999999999999653 246777654
No 40
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=88.08 E-value=2.1 Score=40.06 Aligned_cols=51 Identities=27% Similarity=0.249 Sum_probs=41.5
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 85 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~ 85 (254)
...|.-+|++.+. ..+.+.+++++.+|.|.|||+++ +..+.+--=|+|+++
T Consensus 19 g~RLd~~L~~~~~-~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~ 69 (317)
T PRK11025 19 GQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIP 69 (317)
T ss_pred CchHHHHHHHhcc-cCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeC
Confidence 4567788887663 35789999999999999999988 467888666999985
No 41
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=87.35 E-value=3.3 Score=36.66 Aligned_cols=67 Identities=15% Similarity=0.168 Sum_probs=47.4
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc------CCceEEEEEcCCCceEEEE
Q 025354 36 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK------TNENFRLLYDTKGRFRLHS 105 (254)
Q Consensus 36 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~k------t~e~yRvl~d~kgrf~l~~ 105 (254)
|--+|...+ ..+.+.+++++.+|.|.|||++.++..+.+---|+|++.. ..++|-++--+.| +..|+
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 3678999999999999999999887777775569999852 1245655555565 44454
No 42
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=87.34 E-value=0.82 Score=36.86 Aligned_cols=37 Identities=22% Similarity=0.504 Sum_probs=29.7
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 025354 165 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 204 (254)
Q Consensus 165 i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d 204 (254)
+++..|+.+.|+.|++-|.+|+|.++.... +.|+|++
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 39 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKK---NKVIVEG 39 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence 377889999999999999999999996532 3455554
No 43
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=87.10 E-value=2.1 Score=41.90 Aligned_cols=66 Identities=21% Similarity=0.221 Sum_probs=47.4
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 104 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~ 104 (254)
.+||.-+|-. .+.|.+..|||+.+.||-|+|||..++|..+-+-.=|. .+..|-+|---|.+|.+.
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 79999999999999999999999999998653322111 233455555555555443
No 44
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=85.44 E-value=3.4 Score=38.43 Aligned_cols=62 Identities=19% Similarity=0.248 Sum_probs=50.4
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 107 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 107 (254)
|+=|--++-..+ -.+...|+..+.+|+|+|||++.++..|-+--=|+|||-. .|||.+.++.
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 455666666655 4677889999999999999999999999999999999954 5677777664
No 45
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=85.13 E-value=2.1 Score=39.94 Aligned_cols=63 Identities=21% Similarity=0.283 Sum_probs=53.1
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 107 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 107 (254)
.||=|-.++-+.++... .-|...+..|+|+||.+++++..|-+..=|.|||-. .|||.+-++.
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 47778888888877655 568899999999999999999999999999999954 5777776664
No 46
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=84.90 E-value=1.9 Score=39.98 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=42.0
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 025354 45 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 91 (254)
Q Consensus 45 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~y 91 (254)
+++.|...|+..++.|+|+|||...+-+.+=|-.-+.|++......|
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
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=82.51 E-value=1.9 Score=34.85 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=25.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEe
Q 025354 166 KFDVGNIVMVTGGRNRGRVGIIKNREKH 193 (254)
Q Consensus 166 ~fe~G~~~~i~gG~n~G~vG~I~~i~~~ 193 (254)
++..|+.+.|+.|+.-|.+|+|.++...
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 48
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=81.15 E-value=4 Score=35.02 Aligned_cols=55 Identities=27% Similarity=0.357 Sum_probs=38.0
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE-----cCCCCeEe--EeeceEEEEc
Q 025354 164 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHEFA--TRLGNVFTIG 221 (254)
Q Consensus 164 ~i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~-----d~~g~~F~--T~~~~vfvIG 221 (254)
.+++..|+.+.|+.|.+-|..|+|..+....+ .|.|+ -.+|..++ --.|||+++-
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~---~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKW---VIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCCC---EEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 34778899999999999999999999965433 34443 35554433 3346666655
No 49
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=81.01 E-value=4.2 Score=30.28 Aligned_cols=50 Identities=28% Similarity=0.494 Sum_probs=37.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCC-ccEEEEEcCCCCeEeEeeceEEEEcc
Q 025354 169 VGNIVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGK 222 (254)
Q Consensus 169 ~G~~~~i~gG~n~G~vG~I~~i~~~~~s-~~~V~i~d~~g~~F~T~~~~vfvIGk 222 (254)
+|..|+|-.|.+.-|+|.++.-|+...| |.+|. ++...+.-+..+..+|-
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 4889999999999999999988877644 55552 33456666777777774
No 50
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=71.95 E-value=2.8 Score=37.00 Aligned_cols=56 Identities=27% Similarity=0.311 Sum_probs=40.8
Q ss_pred cCCCCCCCCCcccchhHHHHH-------hhhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 025354 21 PKPSSGPHKSRECLPLILVLR-------NRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 76 (254)
Q Consensus 21 ~rpspGPH~~~~slPL~i~LR-------d~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv 76 (254)
+-|..+.|..-+-+...-|-| -.|+.|.+-+||.+.+.||.|.|.-++++|+.|=|
T Consensus 86 vipTr~~l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv 148 (181)
T KOG4655|consen 86 VIPTRKSLELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV 148 (181)
T ss_pred eecchhhhhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence 355566665544222223333 24799999999999999999999999999998754
No 51
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=66.62 E-value=13 Score=36.74 Aligned_cols=54 Identities=22% Similarity=0.281 Sum_probs=41.6
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 025354 44 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 104 (254)
Q Consensus 44 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~ 104 (254)
.+++...+||++.+.+|-|++||..+.|.+++.+ | .....|.++--.|.+|...
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 5899999999999999999999999999998871 1 2234555555555555544
No 52
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=62.30 E-value=12 Score=30.50 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.4
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 025354 165 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 193 (254)
Q Consensus 165 i~fe~G~~~~i~gG~n~G~vG~I~~i~~~ 193 (254)
++...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45677999999999999999999887543
No 53
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=61.86 E-value=8.2 Score=32.38 Aligned_cols=34 Identities=29% Similarity=0.466 Sum_probs=27.6
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 204 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~d 204 (254)
+++|-.|+++.|+.+|+-.+|..+... +.+++-+
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd----~~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDD----NFVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccC----CEEEEeC
Confidence 689999999999999999999988553 3555544
No 54
>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification.; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.
Probab=57.21 E-value=46 Score=28.93 Aligned_cols=29 Identities=34% Similarity=0.417 Sum_probs=25.0
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc
Q 025354 31 RECLPLILVLRNRLKYALTYREVIAILMQR 60 (254)
Q Consensus 31 ~~slPL~i~LRd~LkyA~t~rEak~Il~~~ 60 (254)
...+|..+++|..|. |.|..||..+|.+-
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=55.58 E-value=14 Score=31.26 Aligned_cols=33 Identities=12% Similarity=0.346 Sum_probs=27.9
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ 203 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i~ 203 (254)
.|+|-.|+|.-|.+.|+.++|.+|..+ |.|.|.
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~----nRvLVD 40 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLVD 40 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC----CeEEEe
Confidence 378999999999999999999999764 556553
No 56
>PF14001 YdfZ: YdfZ protein
Probab=54.68 E-value=20 Score=27.02 Aligned_cols=42 Identities=26% Similarity=0.469 Sum_probs=29.4
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEecC------CccEEEEEcCCCCeEe
Q 025354 166 KFDVGNIVMVTGGRNRGRVGIIKNREKHKG------SFETIHIQDALGHEFA 211 (254)
Q Consensus 166 ~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~------s~~~V~i~d~~g~~F~ 211 (254)
++.+|+.+|+-| +|.+|+|+.|..... ....|.+++.+| .|+
T Consensus 9 ~i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 9 AITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred cCCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 346799999977 678889999865322 236788887776 354
No 57
>PRK04333 50S ribosomal protein L14e; Validated
Probab=52.01 E-value=16 Score=28.50 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=27.1
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 025354 166 KFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 202 (254)
Q Consensus 166 ~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~~V~i 202 (254)
.+++|.+|++.-|+..|+..+|.++... +.|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~----~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK----NFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC----CEEEE
Confidence 4688999999999999999999998442 45555
No 58
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=50.71 E-value=40 Score=27.41 Aligned_cols=45 Identities=13% Similarity=0.163 Sum_probs=34.7
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 025354 45 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 90 (254)
Q Consensus 45 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~ 90 (254)
.+..+.-.|+..+..|.|.|||...+- ..-|=.=|+|+|--.+..
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRAKP-SKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEccc-ccccCCCCEEEEEeCCcE
Confidence 455788999999999999999999854 455667788888554443
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=46.62 E-value=56 Score=25.32 Aligned_cols=48 Identities=19% Similarity=0.320 Sum_probs=30.5
Q ss_pred CCC-CccCCCeEEEecCCCeeeeEEEeeC----CcEEEEECCCcceeEEEEEeE
Q 025354 142 PDP-LIKANDTIKLDLEENKITDFIKFDV----GNIVMVTGGRNRGRVGIIKNR 190 (254)
Q Consensus 142 ~d~-~ik~~Dtv~i~l~~~kI~d~i~fe~----G~~~~i~gG~n~G~vG~I~~i 190 (254)
.+| .++.||...+.+...+=+-.=+|+. |..++--+|+.+| +|.|++|
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 7887653
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=45.43 E-value=14 Score=27.66 Aligned_cols=45 Identities=24% Similarity=0.280 Sum_probs=27.4
Q ss_pred eeeeeecccceeccCCCCCCCCCcccchhHHHHHhhhcccc-cHHHHHHHHhCceEEECCE
Q 025354 8 LTSLVVHLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYAL-TYREVIAILMQRHVLVDGK 67 (254)
Q Consensus 8 ~~~~l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~-t~rEak~Il~~~~V~VDGk 67 (254)
-.|-|.|..+.| |.+||.+++ ||||. +..||.+-+.+++-.|+--
T Consensus 10 cqkLlEkf~YpW------------EmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~~ 55 (62)
T PF08828_consen 10 CQKLLEKFRYPW------------EMMPLMYVI---LKYADADVEEASRRIDEAKNVVNEY 55 (62)
T ss_dssp HHHHHHHTT--G------------GGHHHHHHH---HHHTTT-HHHHHHHHHH--------
T ss_pred HHHHHHHhCCCH------------HHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 345666666554 789999886 89999 9999999999887666543
No 61
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=45.39 E-value=99 Score=33.42 Aligned_cols=77 Identities=18% Similarity=0.238 Sum_probs=52.8
Q ss_pred CcceeEEEeccCCceEEEEEcCCCceEEEEcCh---hhhcceeEEEE----EEEEeeCCceEEEccCceeEecCCCCccC
Q 025354 76 AGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIKA 148 (254)
Q Consensus 76 vG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~---eEa~~KLcKV~----~k~~~~gg~~ql~~hDGrni~~~d~~ik~ 148 (254)
+|-++++..+ .+.+=+-+|.+++....+++. -++.-||.||+ ....++.++|.++..||.-.......+++
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 3555555443 244444556667777777754 23345889888 45567899999999999877656668999
Q ss_pred CCeEEE
Q 025354 149 NDTIKL 154 (254)
Q Consensus 149 ~Dtv~i 154 (254)
||-|.+
T Consensus 190 GD~i~~ 195 (858)
T PRK14898 190 GDWLPV 195 (858)
T ss_pred CCEEee
Confidence 998755
No 62
>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=44.79 E-value=1.2e+02 Score=22.20 Aligned_cols=66 Identities=17% Similarity=0.168 Sum_probs=38.8
Q ss_pred EEEeeCCceEEEccCceeEecC-CCCc-----cCCCeEEEecCCCeeeeEEEeeCCc-EEEEECCCcceeEEE
Q 025354 121 VQFGQKGIPYINTYDGRTIRYP-DPLI-----KANDTIKLDLEENKITDFIKFDVGN-IVMVTGGRNRGRVGI 186 (254)
Q Consensus 121 k~~~~gg~~ql~~hDGrni~~~-d~~i-----k~~Dtv~i~l~~~kI~d~i~fe~G~-~~~i~gG~n~G~vG~ 186 (254)
+.+..++.-+|.+.||..+... +..+ .-.+...+.|..|++.-.++=..+. +.+-|....++-.|+
T Consensus 3 i~T~~~~~~~i~l~dgs~v~l~~~s~~~~~~~~~~~~~~~~L~~G~~~~~~~~~~~~~~~V~T~~~~i~v~GT 75 (98)
T PF04773_consen 3 IRTGAGSRAEIALSDGSRVRLGPNSRVSVDRDSGSEPTRLRLLSGEILFDVSPGKKRPFEVRTPTATIGVRGT 75 (98)
T ss_pred EEcCCCCEEEEEECCCCEEEECCCcEEEEEcccCCCceEEEEcCCCEEEEEcccCCCCEEEEeCCEEEEEecC
Confidence 4567889999999999999753 3334 3444556666666653222222222 455555555554444
No 63
>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=43.28 E-value=1.2e+02 Score=22.90 Aligned_cols=40 Identities=18% Similarity=0.404 Sum_probs=25.4
Q ss_pred ccCCCeEEEecCCCeeeeEEEeeCCcEEEE-ECCCcceeEEEEEe
Q 025354 146 IKANDTIKLDLEENKITDFIKFDVGNIVMV-TGGRNRGRVGIIKN 189 (254)
Q Consensus 146 ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i-~gG~n~G~vG~I~~ 189 (254)
+++||+..+.+.-.+ -+.++.|.-.++ .+|+.+| .|+|.+
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 788998888776433 235566666666 5665555 677654
No 64
>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=42.94 E-value=66 Score=26.54 Aligned_cols=84 Identities=18% Similarity=0.265 Sum_probs=47.9
Q ss_pred ceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCC
Q 025354 100 RFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGR 179 (254)
Q Consensus 100 rf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~gG~ 179 (254)
.+.+++.+.++..+. .|.+ ..|...+.-.+|+....++..+..--.. .-..........|++|+.+.|++|.
T Consensus 50 gYvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~--~~~~~~~~~~~~~~~G~~V~V~~GP 121 (159)
T TIGR01955 50 NYLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQY--EPKDSVPPATTLPYKGDKVRITDGA 121 (159)
T ss_pred CeEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhc--cccccCCccccCCCCCCEEEEeccC
Confidence 355677766554332 2211 2466666655665555555422211000 0001011233569999999999999
Q ss_pred cceeEEEEEeEE
Q 025354 180 NRGRVGIIKNRE 191 (254)
Q Consensus 180 n~G~vG~I~~i~ 191 (254)
-.|..|.|.++.
T Consensus 122 f~g~~g~v~~~~ 133 (159)
T TIGR01955 122 FAGFEAIFLEPD 133 (159)
T ss_pred CCCcEEEEEEEC
Confidence 999999999974
No 65
>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=42.25 E-value=54 Score=32.07 Aligned_cols=54 Identities=19% Similarity=0.209 Sum_probs=29.9
Q ss_pred eEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEE---ECCCccee
Q 025354 115 LCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMV---TGGRNRGR 183 (254)
Q Consensus 115 LcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i---~gG~n~G~ 183 (254)
|..|+-.. .|....+.+.|..|||.- =|+|+.+....+++|+.+++ .+|+|.|-
T Consensus 289 LllIeA~~--~g~~~svilQnaetIRlv-------------~p~G~~vsVt~Lk~GD~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 289 LLLIEAEA--DGKRISVILQNAETIRLV-------------GPDGEPVSVTELKPGDEVLVYLEEAGRHFGM 345 (354)
T ss_pred eEEEEEEe--CCeEEEEEEecCcEEEEE-------------CCCCCEeeeeecCCCCEEEEEecCCCcccce
Confidence 34444433 445555566666666543 33455555555666665544 37888884
No 66
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=41.86 E-value=49 Score=26.64 Aligned_cols=60 Identities=20% Similarity=0.205 Sum_probs=35.8
Q ss_pred CCceEEEccCceeEecCCCCccCCCeEEEecC------CCeeeeEEEeeCCcEEEEECCCcceeEEEEEe
Q 025354 126 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLE------ENKITDFIKFDVGNIVMVTGGRNRGRVGIIKN 189 (254)
Q Consensus 126 gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~------~~kI~d~i~fe~G~~~~i~gG~n~G~vG~I~~ 189 (254)
+.+.++.|.|||++.-.=.-+.-.--+.|+-. +.+=++.+++- .+++.|-|.+-+|-|.|
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDE 75 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecch
Confidence 35678899999999532111222222444332 22222334443 78999999999999876
No 67
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=40.15 E-value=59 Score=31.70 Aligned_cols=46 Identities=17% Similarity=0.137 Sum_probs=23.6
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEE---CCCccee
Q 025354 125 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVT---GGRNRGR 183 (254)
Q Consensus 125 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~---gG~n~G~ 183 (254)
.|....+.+.|..|||+- -|+|+-+..-.+++|+.+++. +|+|.|.
T Consensus 287 ~g~~~~viLQnaetIrlv-------------~~dG~~vsVt~Lk~GD~VL~~~~~~~RHfG~ 335 (344)
T PRK02290 287 GGKRIRTILQNAETIRLV-------------TPDGKPVSVVDLKPGDEVLGYLEEAARHFGM 335 (344)
T ss_pred CCeEEEEEEecCcEEEEE-------------CCCCCEeeeeecCCCCEEEEEecCCcccccc
Confidence 345555555666666543 333444444444444444432 6788773
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=39.67 E-value=1.7e+02 Score=22.36 Aligned_cols=42 Identities=14% Similarity=0.376 Sum_probs=30.0
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeC-------CcEEEEECCCcceeEEEEEeE
Q 025354 145 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRGRVGIIKNR 190 (254)
Q Consensus 145 ~ik~~Dtv~i~l~~~kI~d~i~fe~-------G~~~~i~gG~n~G~vG~I~~i 190 (254)
.++.||...+.+...+-+ .+|+ |...+-..|..+| +|.|.+|
T Consensus 59 ~l~~~~~a~v~l~~~~pi---~~e~~~~~~~~Grfilr~~~~Tva-~G~I~~i 107 (107)
T cd04093 59 CLTKGQTAIVEIELERPI---PLELFKDNKELGRVVLRRDGETIA-AGLVTEI 107 (107)
T ss_pred CcCCCCEEEEEEEECCeE---EEEEcccCCCcceEEEEcCCCEEE-EEEEEeC
Confidence 689999999999765533 3444 7777766776666 5888654
No 69
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=39.55 E-value=30 Score=29.53 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=21.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeE
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNR 190 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i 190 (254)
+.+|..++|..|+++|+-++|...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999998764
No 70
>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=38.62 E-value=26 Score=30.11 Aligned_cols=54 Identities=22% Similarity=0.137 Sum_probs=43.1
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEeccCC
Q 025354 31 RECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPKTN 88 (254)
Q Consensus 31 ~~slPL~i~LRd~LkyA~t~rEak~Il~~~-----~V~VDGkvr~D~k~PvG~MD---VIsI~kt~ 88 (254)
+...+|+-+||+.|++-.+ |.=+.+| .|+|||+++..--+|+.-+| |++|+-..
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 3467899999999876553 4556666 69999999999999998886 89997644
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=37.36 E-value=72 Score=24.56 Aligned_cols=24 Identities=29% Similarity=0.313 Sum_probs=17.5
Q ss_pred eEEEEEeEEEecCCcc--EEEEEcCC
Q 025354 183 RVGIIKNREKHKGSFE--TIHIQDAL 206 (254)
Q Consensus 183 ~vG~I~~i~~~~~s~~--~V~i~d~~ 206 (254)
++|+|.+.+.||++.. +..+...+
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
>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=37.14 E-value=78 Score=23.61 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=26.8
Q ss_pred EeeCCceEEEccCceeEecCC----CCccCCCeEEEecC
Q 025354 123 FGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 157 (254)
Q Consensus 123 ~~~gg~~ql~~hDGrni~~~d----~~ik~~Dtv~i~l~ 157 (254)
.+......|.|.||.++..|. +.+++|..|++-..
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 355677899999999998774 36888888777554
No 73
>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=35.88 E-value=40 Score=25.44 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=27.6
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEec------CCccEEEEEcCCCCeEe
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 211 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~~------~s~~~V~i~d~~g~~F~ 211 (254)
+.+|+.+||.| +|++|+|+.|.... .....|.++..+| .|+
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 67888898886422 2235777876554 454
No 74
>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=35.51 E-value=65 Score=26.49 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=24.6
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREK 192 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~ 192 (254)
|.+|+.+-|+.|.=.|..|+|.++..
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 75
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=35.44 E-value=59 Score=27.40 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=26.4
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 025354 165 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 193 (254)
Q Consensus 165 i~fe~G~~~~i~gG~n~G~vG~I~~i~~~ 193 (254)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999998654
No 76
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=35.03 E-value=1.4e+02 Score=24.19 Aligned_cols=61 Identities=18% Similarity=0.393 Sum_probs=38.3
Q ss_pred eeCCcEEEE-ECCCcceeEEEEEeEEEe-----cCCc-cEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeee
Q 025354 167 FDVGNIVMV-TGGRNRGRVGIIKNREKH-----KGSF-ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLS 239 (254)
Q Consensus 167 fe~G~~~~i-~gG~n~G~vG~I~~i~~~-----~~s~-~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~~kgi~~~ 239 (254)
|+.|+.--. +.... +|.|..|+.. ++.+ +-|.|+|.+|+. +.|...+ |+.-|-++-|+++
T Consensus 41 F~~G~~d~F~v~~~d---LG~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~ 107 (109)
T cd02899 41 FYPGSLKRIRFRAAD---VGDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECccc---cCceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEe
Confidence 666654432 12344 4445555442 2334 788898866644 4599888 9999999988876
Q ss_pred h
Q 025354 240 I 240 (254)
Q Consensus 240 ~ 240 (254)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 77
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=34.91 E-value=57 Score=35.85 Aligned_cols=27 Identities=33% Similarity=0.608 Sum_probs=25.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEe
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKH 193 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~ 193 (254)
|++|+.|=|+.|+|-|..|.|..++.+
T Consensus 460 F~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 460 FEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccCCCeEEEEeccccCCcceEEEEeCC
Confidence 789999999999999999999999874
No 78
>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=33.62 E-value=94 Score=23.70 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=25.0
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeC-------CcEEEEECCCcce
Q 025354 145 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRG 182 (254)
Q Consensus 145 ~ik~~Dtv~i~l~~~kI~d~i~fe~-------G~~~~i~gG~n~G 182 (254)
.++.||...+.|...+ -+.+|+ |..+++-+|+.+|
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 6899999999997554 345565 7777777666655
No 79
>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=31.97 E-value=3.6e+02 Score=23.84 Aligned_cols=101 Identities=21% Similarity=0.347 Sum_probs=59.5
Q ss_pred hCceEEECCE--EeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEc-c
Q 025354 58 MQRHVLVDGK--VRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT-Y 134 (254)
Q Consensus 58 ~~~~V~VDGk--vr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~-h 134 (254)
..+.|+|||+ +|+|--| +++ |+..+ .|...+. -|.| ++..+.+..-++.+ =
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 5555433 322 22222 2332222 2544 34444555444443 4
Q ss_pred CceeE-ecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEE
Q 025354 135 DGRTI-RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGI 186 (254)
Q Consensus 135 DGrni-~~~d~~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~gG~n~G~vG~ 186 (254)
||.++ .|-+...|.-.|..+.+..++ -.|-|+...+-+=..|......|.
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 677778899999999997644 677888888888899998877764
No 80
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=31.41 E-value=55 Score=27.60 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=26.0
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 025354 164 FIKFDVGNIVMVTGGRNRGRVGIIKNREK 192 (254)
Q Consensus 164 ~i~fe~G~~~~i~gG~n~G~vG~I~~i~~ 192 (254)
...|.+|+.+-|++|.=.|..|.|.++..
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDY 152 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeC
Confidence 46789999999999999999999999854
No 81
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=30.77 E-value=46 Score=25.47 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.0
Q ss_pred eEecCCCCccCCCeEEEe
Q 025354 138 TIRYPDPLIKANDTIKLD 155 (254)
Q Consensus 138 ni~~~d~~ik~~Dtv~i~ 155 (254)
-||..|.+|++||.+.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 357889999999998873
No 82
>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=30.66 E-value=13 Score=33.58 Aligned_cols=59 Identities=29% Similarity=0.408 Sum_probs=36.8
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChhhhcce
Q 025354 36 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFK 114 (254)
Q Consensus 36 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~K 114 (254)
|-+.-+|++++-.|.+. -+.+....++-.-..+ .||||..|-|+| +| +|==|.+||+-|
T Consensus 53 L~i~~~Dyik~l~nl~~---y~~~~l~~~~~~~~~~-~YPvG~L~dIei---------------hF-~HY~s~~eA~~K 111 (201)
T PF08942_consen 53 LFIFPPDYIKFLENLDY---YLSQELEFIDESKSYD-DYPVGLLGDIEI---------------HF-MHYKSFEEAKEK 111 (201)
T ss_dssp EE--HHHHHHHHHSHHH---HHCS--EECE--BGGG-B--EEEEC-EEE---------------EE-SS-SSHHHHHHH
T ss_pred eEECcHHHHHHHHCHHH---HhcCCeEEeecCcccC-CcceEeECCEEE---------------EE-EecCCHHHHHHH
Confidence 55666899999998875 4666666655554456 899999999998 34 566689999755
No 83
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=30.09 E-value=42 Score=28.99 Aligned_cols=52 Identities=17% Similarity=0.240 Sum_probs=37.5
Q ss_pred CCeeeeEEEeeCCcEEEEECCCcce-eEEEEEeEEEecCC--ccEEEEEcCCCCe
Q 025354 158 ENKITDFIKFDVGNIVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 209 (254)
Q Consensus 158 ~~kI~d~i~fe~G~~~~i~gG~n~G-~vG~I~~i~~~~~s--~~~V~i~d~~g~~ 209 (254)
..=.+..+|+..++.+-|.+|+..| ++|.|.++-+..-. .+.|.-+-++|..
T Consensus 40 ~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 40 QKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred HHhCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 3335788999999999999999999 99999998653321 2344444455543
No 84
>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=29.49 E-value=1e+02 Score=22.38 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=24.8
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCeee
Q 025354 125 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 162 (254)
Q Consensus 125 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 162 (254)
.+..-...+..|-.+.+|. -|+.||.|++|-.+++=+
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 3344566778888888765 799999999999998643
No 85
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=28.63 E-value=61 Score=27.20 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=25.2
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEE
Q 025354 165 IKFDVGNIVMVTGGRNRGRVGIIKNREK 192 (254)
Q Consensus 165 i~fe~G~~~~i~gG~n~G~vG~I~~i~~ 192 (254)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5588999999999999999999999853
No 86
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=28.35 E-value=1.9e+02 Score=32.07 Aligned_cols=55 Identities=25% Similarity=0.370 Sum_probs=41.9
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeEeEeeceEEEEccCCC
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFATRLGNVFTIGKGSK 225 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~--~~V~i~d~~g~~F~T~~~~vfvIGk~~k 225 (254)
...++.+-+++|.|.|+-|.|.+|.+.. -| +.-++ .++-.|.++..|+..+|. .+
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 466689999999999996 44
No 87
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=27.14 E-value=5.2e+02 Score=24.13 Aligned_cols=61 Identities=23% Similarity=0.312 Sum_probs=40.3
Q ss_pred CCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEE
Q 025354 142 PDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 220 (254)
Q Consensus 142 ~d~~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvI 220 (254)
++.+++.||.|+-+=-.|. |.+|= -||+|..++.+. +.+..+.++-.. -.+++.|||++
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 4567888885554433322 22332 278888887766 556778887544 47899999999
Q ss_pred cc
Q 025354 221 GK 222 (254)
Q Consensus 221 Gk 222 (254)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 86
No 88
>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=26.87 E-value=61 Score=31.44 Aligned_cols=45 Identities=18% Similarity=-0.026 Sum_probs=36.7
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcc
Q 025354 33 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGF 78 (254)
Q Consensus 33 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~ 78 (254)
++++.=++.. .+.+.+.+||++.|++|-|+|||...+|..+-.-.
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~ 373 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKE 373 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhcc
Confidence 4666666654 58899999999999999999999999998764433
No 89
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=26.76 E-value=3.4e+02 Score=26.80 Aligned_cols=53 Identities=26% Similarity=0.307 Sum_probs=35.5
Q ss_pred CccCCCeEEEecCCCeeeeEEEe----eCCcEEEEECCCcceeEEEEEeEEEecCCcc
Q 025354 145 LIKANDTIKLDLEENKITDFIKF----DVGNIVMVTGGRNRGRVGIIKNREKHKGSFE 198 (254)
Q Consensus 145 ~ik~~Dtv~i~l~~~kI~d~i~f----e~G~~~~i~gG~n~G~vG~I~~i~~~~~s~~ 198 (254)
.++.||...+.|...+=+-.-+| .-|..++.-+|.-+| .|.|.++....||..
T Consensus 381 ~l~~g~~a~v~l~~~~pi~~e~~~~~~~lgrfilrd~g~tva-~G~I~~v~~~~~~~~ 437 (446)
T PTZ00141 381 AIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRDMKQTVA-VGVIKSVEKKEGSGT 437 (446)
T ss_pred EECCCCEEEEEEEECCceEEeecccCCCCccEEEEECCCEEE-EEEEEEEecCCCcce
Confidence 57789999888875543322333 246677777776555 899999887666643
No 90
>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=26.49 E-value=3.4e+02 Score=26.03 Aligned_cols=90 Identities=14% Similarity=0.211 Sum_probs=50.0
Q ss_pred eEEEEEcCCCceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEee-
Q 025354 90 NFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFD- 168 (254)
Q Consensus 90 ~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~fe- 168 (254)
.|-.+.+.+|.+.+.-+... | .|..+.++.+-.-.-...||+-+-..+ +..++..++|..+.+++..|+..
T Consensus 49 r~~yv~~rdg~vsviD~~~~----~--~v~~i~~G~~~~~i~~s~DG~~~~v~n--~~~~~v~v~D~~tle~v~~I~~~~ 120 (369)
T PF02239_consen 49 RYLYVANRDGTVSVIDLATG----K--VVATIKVGGNPRGIAVSPDGKYVYVAN--YEPGTVSVIDAETLEPVKTIPTGG 120 (369)
T ss_dssp SEEEEEETTSEEEEEETTSS----S--EEEEEE-SSEEEEEEE--TTTEEEEEE--EETTEEEEEETTT--EEEEEE--E
T ss_pred CEEEEEcCCCeEEEEECCcc----c--EEEEEecCCCcceEEEcCCCCEEEEEe--cCCCceeEeccccccceeeccccc
Confidence 34444566666555444222 2 233344455544455667999885443 77888999999999999988764
Q ss_pred ----------------CCcEEEEECCCcceeEEEE
Q 025354 169 ----------------VGNIVMVTGGRNRGRVGII 187 (254)
Q Consensus 169 ----------------~G~~~~i~gG~n~G~vG~I 187 (254)
.++..+|+.=+..|++..+
T Consensus 121 ~~~~~~~~Rv~aIv~s~~~~~fVv~lkd~~~I~vV 155 (369)
T PF02239_consen 121 MPVDGPESRVAAIVASPGRPEFVVNLKDTGEIWVV 155 (369)
T ss_dssp E-TTTS---EEEEEE-SSSSEEEEEETTTTEEEEE
T ss_pred ccccccCCCceeEEecCCCCEEEEEEccCCeEEEE
Confidence 2223344455556777766
No 91
>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=26.22 E-value=26 Score=30.14 Aligned_cols=53 Identities=25% Similarity=0.135 Sum_probs=40.5
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEeccC
Q 025354 31 RECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPKT 87 (254)
Q Consensus 31 ~~slPL~i~LRd~LkyA~t~rEak~Il~~~-----~V~VDGkvr~D~k~PvG~MD---VIsI~kt 87 (254)
+...+|+-+||+.|++-.+. .=+.+| .|.|||+.+.---.|+.-+| |.+|+-.
T Consensus 18 ~~~~~Ll~~LR~~~~ltgtK----~gC~~G~CGACtVlvdG~~v~SCl~~~~~~~G~~v~TiEgl 78 (151)
T TIGR03198 18 VPTTRLSDLLRKELQLTGTK----VSCGIGRCGACSVLIDGKLANACLTMAYQADGHEITTIEGI 78 (151)
T ss_pred CCCcHHHHHHHhccCCCCCC----CCCCCCcCCccEEEECCcEEechHHHHHHhcCCEEEecCCc
Confidence 34789999999998886654 336666 69999999998888886554 7777543
No 92
>PF01063 Aminotran_4: Aminotransferase class IV; InterPro: IPR001544 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the pyridoxal-phosphate-lysine. The D-amino acid transferases (D-AAT), which are among the members of this entry, are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity [, ]. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1EKV_A 2HGX_A 1EKP_A 1KTA_B 1KT8_B 2A1H_B 2HDK_A 2HGW_B 1EKF_B 2HG8_A ....
Probab=25.87 E-value=2.2e+02 Score=24.39 Aligned_cols=52 Identities=17% Similarity=0.160 Sum_probs=37.7
Q ss_pred ccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHHHHH
Q 025354 197 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAA 250 (254)
Q Consensus 197 ~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~islp~~kgi~~~~~e~~~~~~~~ 250 (254)
++-+.+-|.+|+--++..+|+|++= +.-|++-|.+.|+-..+..+.-.++++
T Consensus 125 ~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~giL~Gitr~~ll~~~~ 176 (231)
T PF01063_consen 125 ADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGILPGITRQLLLELAK 176 (231)
T ss_dssp SSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSSB--HHHHHHHHHHH
T ss_pred cchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhhccHHHHHHHHHHHH
Confidence 3445667899999999999999984 455889998988877776665544443
No 93
>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=25.34 E-value=2e+02 Score=20.03 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=28.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEE
Q 025354 167 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 203 (254)
Q Consensus 167 fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~-~~V~i~ 203 (254)
|++|..+++.-+...-.-++|.+++...+.. =.||-.
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 356654
No 94
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=24.82 E-value=78 Score=28.60 Aligned_cols=44 Identities=18% Similarity=0.124 Sum_probs=32.0
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcce----eEEEEEeEEEec
Q 025354 145 LIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRG----RVGIIKNREKHK 194 (254)
Q Consensus 145 ~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~gG~n~G----~vG~I~~i~~~~ 194 (254)
.|++||.|-+.= ++|.|+.....--++|+|+| +||.|.+|....
T Consensus 7 ~Y~vgD~VYv~p------~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k 54 (202)
T cd04708 7 TYSVGDFLYVSP------DAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEK 54 (202)
T ss_pred EEecCCeEEECc------ccccccccccccccccccCCCCCcEEEEEEEEEecc
Confidence 477888877765 44556666777778899976 799999986533
No 95
>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=24.59 E-value=49 Score=27.50 Aligned_cols=41 Identities=22% Similarity=0.343 Sum_probs=32.2
Q ss_pred CceEEEEcChhhhcceeEEEEEEEEeeCCceEEEccCceeEecCCC
Q 025354 99 GRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 144 (254)
Q Consensus 99 grf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~ 144 (254)
..|+|+.+|+= -+-+|--+.|..-+...+|| ||-|+-|.+|
T Consensus 22 RwFvL~qvsQY--tfamcsy~ekks~P~e~~ql---dGyTvDy~~~ 62 (117)
T cd01234 22 RFFVLVQVSQY--TFAMCSYREKKAEPTEFIQL---DGYTVDYMPE 62 (117)
T ss_pred eEEEEEchhHH--HHHHHhhhhhcCCchhheee---cceEEeccCC
Confidence 45778877654 34678888888888899998 9999988765
No 96
>cd05892 Ig_Myotilin_C C-terminal immunoglobulin (Ig)-like domain of myotilin. Ig_Myotilin_C: C-terminal immunoglobulin (Ig)-like domain of myotilin. Mytolin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to the latter family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Myotilin is most abundant in skeletal and cardiac muscle, and is involved in maintaining sarcomere integrity. It binds to alpha-actinin, filamin and actin. Mutations in myotilin lead to muscle disorders.
Probab=24.52 E-value=1.5e+02 Score=21.58 Aligned_cols=34 Identities=12% Similarity=0.272 Sum_probs=27.7
Q ss_pred CceEEEEEcCCC--ceEEEEcChhhhcceeEEEEEE
Q 025354 88 NENFRLLYDTKG--RFRLHSLRDEEAKFKLCKVRSV 121 (254)
Q Consensus 88 ~e~yRvl~d~kg--rf~l~~I~~eEa~~KLcKV~~k 121 (254)
+++|++..+..| .|.+..+..+++..-.|...|.
T Consensus 28 ~~r~~~~~~~~g~~~L~I~~~~~~D~G~Y~C~A~N~ 63 (75)
T cd05892 28 TDRISLYQDNSGRVTLLIKNVNKKDAGWYTVSAVNE 63 (75)
T ss_pred CCeEEEEEcCCCcEEEEECCCChhhCEEEEEEEEcC
Confidence 467888888777 5777789999999889998884
No 97
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=23.58 E-value=2.3e+02 Score=23.63 Aligned_cols=77 Identities=16% Similarity=0.193 Sum_probs=43.9
Q ss_pred EEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEEcCCCC
Q 025354 130 YINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQDALGH 208 (254)
Q Consensus 130 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~gG~n~G~vG~I~~i~~~~~s~-~~V~i~d~~g~ 208 (254)
+|.+|+|++-++.| +++.|.+.-...+ +-++++..-...|......|-+ .|.=.++.. ..++++=.-++
T Consensus 7 ~I~l~~G~~krvED--l~teDfi~sa~~s----~~~~l~~stv~~i~~~~~~~~v----~itF~~g~~~~~v~~ev~~eH 76 (116)
T smart00536 7 RLCLANGSNKKVED--LKTEDFIRSAECS----NDEEIQMSTVKRIGSSGLPSVV----TLTFDPGVEDALLTVECQVEH 76 (116)
T ss_pred EEEecCCCeeeeec--cchhhhHhhhccC----CcccccceeEEEeCCCCCcceE----EEEEEecCccceEEEEEecCC
Confidence 56679999998877 8888888776655 3445555544555443332221 222233332 46666544444
Q ss_pred eEeEeeceEEEEccC
Q 025354 209 EFATRLGNVFTIGKG 223 (254)
Q Consensus 209 ~F~T~~~~vfvIGk~ 223 (254)
- .||-|+|
T Consensus 77 P-------fFV~gqG 84 (116)
T smart00536 77 P-------FFVKGKG 84 (116)
T ss_pred C-------eEEcCcc
Confidence 4 3777765
No 98
>cd03707 EFTU_III Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix
Probab=23.33 E-value=3.1e+02 Score=20.27 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=16.4
Q ss_pred ccCCCeEEEecCCCeeeeEEEeeCCcEEEE
Q 025354 146 IKANDTIKLDLEENKITDFIKFDVGNIVMV 175 (254)
Q Consensus 146 ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i 175 (254)
+++||+..+.|.-.+ -+.+++|.-.++
T Consensus 52 i~~g~~~~v~l~l~~---pv~~~~~~rf~l 78 (90)
T cd03707 52 VMPGDNVKMTVELIH---PIALEKGLRFAI 78 (90)
T ss_pred cCCCCEEEEEEEECC---cEEEecCCEEEE
Confidence 888888887775433 234555544444
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=23.14 E-value=1.4e+02 Score=21.69 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=26.7
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCe
Q 025354 125 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 160 (254)
Q Consensus 125 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 160 (254)
.++.-...+..|-.+.+|- -|+.||.|++|-.+++
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 3444445678888888654 6899999999999876
No 100
>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=22.54 E-value=1.8e+02 Score=21.66 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=16.7
Q ss_pred cCCCeEEEecC-----CCeeeeEEEeeCCcEEEE
Q 025354 147 KANDTIKLDLE-----ENKITDFIKFDVGNIVMV 175 (254)
Q Consensus 147 k~~Dtv~i~l~-----~~kI~d~i~fe~G~~~~i 175 (254)
|+||.|.+.-. +|.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG~MYLv 35 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCcEEEEE
Confidence 56666666554 445666666666655444
No 101
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=22.14 E-value=66 Score=31.67 Aligned_cols=96 Identities=17% Similarity=0.135 Sum_probs=68.3
Q ss_pred cccceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCE--EeccccCCCcceeEEEeccCCceE
Q 025354 14 HLYVCQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGK--VRTDKTYPAGFMDVVSIPKTNENF 91 (254)
Q Consensus 14 Kk~~~~a~rpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGk--vr~D~k~PvG~MDVIsI~kt~e~y 91 (254)
-+..+|+----=-||+.. ++-+.-|+..-+|.-. +++-.-.+.-+|+.|.. .+.++.|-+.|||-.+-.....+|
T Consensus 41 ~la~~fvm~mlfn~~~v~-lld~d~wik~~~Ki~~--~~~v~~~k~~hi~~~~g~~i~ln~~fk~sl~~altgg~~~nsf 117 (447)
T COG5144 41 ELATKFVMDMLFNSHSVS-LLDEDEWIKETLKILL--RIQVIGKKGNHIYLDEGLMIRLNPEFKISLMDALTGGTMENSF 117 (447)
T ss_pred HHHHHHHHHHHcCCCCcc-hhhHHHHHhhhhHHHH--HHHHhhhccceEEecCCceEEeChHHHHHHHHHhhcccccccc
Confidence 333344333333456543 5555566666555543 56555566668999988 999999999999999999999999
Q ss_pred EEEEcCCCceEEEEcChhhhcce
Q 025354 92 RLLYDTKGRFRLHSLRDEEAKFK 114 (254)
Q Consensus 92 Rvl~d~kgrf~l~~I~~eEa~~K 114 (254)
++.-+++ ++.+...+++|+.|
T Consensus 118 gv~i~E~--lvsvd~ld~ys~~k 138 (447)
T COG5144 118 GVCIGEK--LVSVDMLDSYSSRK 138 (447)
T ss_pred ceeeccc--eeeeehhhhhhhhh
Confidence 9999988 77777777777654
No 102
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=21.93 E-value=1e+02 Score=25.04 Aligned_cols=35 Identities=14% Similarity=0.381 Sum_probs=27.6
Q ss_pred EEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCe
Q 025354 122 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 160 (254)
Q Consensus 122 ~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 160 (254)
.++.+|+.++ +|.... |...+|+||.|.|.+....
T Consensus 29 ~~~~~GrV~v---NG~~aK-pS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 29 EMIEGGRVKV---NGQRAK-PSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHHHCCeEEE---CCEEcc-cccccCCCCEEEEEeCCcE
Confidence 3467888888 577665 7778999999999997744
No 103
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.91 E-value=1.1e+02 Score=30.96 Aligned_cols=39 Identities=15% Similarity=0.143 Sum_probs=33.9
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEecc
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTD 71 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D 71 (254)
..++++=++|+ ++.-.+..||++++.||-|.+|++.++|
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 36788888887 5666788899999999999999999999
No 104
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=21.81 E-value=1.5e+02 Score=27.26 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=10.5
Q ss_pred CCcEEEEECCCcceeEEEEEeEE
Q 025354 169 VGNIVMVTGGRNRGRVGIIKNRE 191 (254)
Q Consensus 169 ~G~~~~i~gG~n~G~vG~I~~i~ 191 (254)
.|+.+=|.-|+..|+.|.++.+.
T Consensus 75 ~GDtVeVlvGkDkGkqG~Vtqv~ 97 (236)
T KOG1708|consen 75 FGDTVEVLVGKDKGKQGEVTQVI 97 (236)
T ss_pred cCCEEEEEecccCCccceEEEEe
Confidence 34444444444444444444443
No 105
>PF07569 Hira: TUP1-like enhancer of split; InterPro: IPR011494 The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain IPR001680 from INTERPRO.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.69 E-value=2.9e+02 Score=24.62 Aligned_cols=57 Identities=18% Similarity=0.366 Sum_probs=41.4
Q ss_pred CCceEEEEEcCCCceEEEEcChhhhccee------------------EEEEEEEEeeCCceEEEccCceeEecCC
Q 025354 87 TNENFRLLYDTKGRFRLHSLRDEEAKFKL------------------CKVRSVQFGQKGIPYINTYDGRTIRYPD 143 (254)
Q Consensus 87 t~e~yRvl~d~kgrf~l~~I~~eEa~~KL------------------cKV~~k~~~~gg~~ql~~hDGrni~~~d 143 (254)
..++|-+.....|.|.+=.+....+-++- ..|+...+-+.|.|.+.+.+|..+.|..
T Consensus 20 ~~~~~Ll~iT~~G~l~vWnl~~~k~~~~~~Si~pll~~~~~~~~~~~~~i~~~~lt~~G~PiV~lsng~~y~y~~ 94 (219)
T PF07569_consen 20 CNGSYLLAITSSGLLYVWNLKKGKAVLPPVSIAPLLNSSPVSDKSSSPNITSCSLTSNGVPIVTLSNGDSYSYSP 94 (219)
T ss_pred eCCCEEEEEeCCCeEEEEECCCCeeccCCccHHHHhcccccccCCCCCcEEEEEEcCCCCEEEEEeCCCEEEecc
Confidence 45677777777777766666554444433 5677777778999999999999998743
No 106
>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=21.66 E-value=1.6e+02 Score=21.44 Aligned_cols=30 Identities=23% Similarity=0.357 Sum_probs=25.0
Q ss_pred EEEccCceeEecCCCCccCCCeEEEecCCCe
Q 025354 130 YINTYDGRTIRYPDPLIKANDTIKLDLEENK 160 (254)
Q Consensus 130 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 160 (254)
...+..|-.|.+|. -|+.||.|+||-.+++
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 45678898998765 7999999999999875
No 107
>PF05709 Sipho_tail: Phage tail protein; InterPro: IPR008841 This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 4DIV_X 2X8K_C.
Probab=21.63 E-value=3.4e+02 Score=23.20 Aligned_cols=54 Identities=19% Similarity=0.245 Sum_probs=27.5
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCc---eEEECCEEeccccCCCcceeEEEeccC
Q 025354 32 ECLPLILVLRNRLKYALTYREVIAILMQR---HVLVDGKVRTDKTYPAGFMDVVSIPKT 87 (254)
Q Consensus 32 ~slPL~i~LRd~LkyA~t~rEak~Il~~~---~V~VDGkvr~D~k~PvG~MDVIsI~kt 87 (254)
-.+|+.+.-++.-.+..-.++..+.|... .+..+-. -|..|=+.+-+..+++..
T Consensus 40 i~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~l~f~d~--p~~~y~~~~~~~~~~~~~ 96 (249)
T PF05709_consen 40 ITLTFYIIGEDREDFEQKRRELASWLNPKEPVKLIFDDD--PDKYYYAKVSGSPDPDEG 96 (249)
T ss_dssp EEEEEEEE-SSHHHHHHHHHHHHHHH--SS-EEEEETTS--TT-EEEEEEEEEEE--SS
T ss_pred EEEEEEEEECCHHHHHHHHHHHHHhhCcCCCEEEEEECC--CCEEEEEEECCccccccc
Confidence 35666666666666777788888888654 3333332 223333444455555443
No 108
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=21.36 E-value=3.3e+02 Score=19.76 Aligned_cols=55 Identities=13% Similarity=0.123 Sum_probs=28.4
Q ss_pred eCCcEEEEECCCcceeEE-EEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEcc
Q 025354 168 DVGNIVMVTGGRNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 222 (254)
Q Consensus 168 e~G~~~~i~gG~n~G~vG-~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk 222 (254)
.+|+.++...+.+..... .+.......+...++.|+..+|.++..-.++-|.+..
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 356666666552222111 1122222334557888887778777655555555554
No 109
>KOG2404 consensus Fumarate reductase, flavoprotein subunit [Energy production and conversion]
Probab=21.05 E-value=75 Score=31.59 Aligned_cols=51 Identities=22% Similarity=0.282 Sum_probs=44.6
Q ss_pred eecccceeccCCCCCCCCCcccchhHHHHHhhh-cccccHHHHHHHHhCceE
Q 025354 12 VVHLYVCQAPKPSSGPHKSRECLPLILVLRNRL-KYALTYREVIAILMQRHV 62 (254)
Q Consensus 12 l~Kk~~~~a~rpspGPH~~~~slPL~i~LRd~L-kyA~t~rEak~Il~~~~V 62 (254)
|..++|-=+||+.-+.|++--..|+.-.|+++| +.|.+.-|+-+|+.|-+|
T Consensus 117 la~lgGHSvpRTHr~s~plppgfei~~~L~~~l~k~as~~pe~~ki~~nskv 168 (477)
T KOG2404|consen 117 LAQLGGHSVPRTHRSSGPLPPGFEIVKALSTRLKKKASENPELVKILLNSKV 168 (477)
T ss_pred HHHhcCCCCCcccccCCCCCCchHHHHHHHHHHHHhhhcChHHHhhhhccee
Confidence 567788899999999999999999999999999 478888899999887654
No 110
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=20.98 E-value=1.1e+02 Score=25.57 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=24.1
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEE
Q 025354 166 KFDVGNIVMVTGGRNRGRVGIIKNRE 191 (254)
Q Consensus 166 ~fe~G~~~~i~gG~n~G~vG~I~~i~ 191 (254)
.|++|+.+.|++|.=.|..|.|.++.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 58999999999999999999998874
No 111
>PF03143 GTP_EFTU_D3: Elongation factor Tu C-terminal domain; InterPro: IPR004160 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents the C-terminal domain, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA and to EF1B (or EF-Ts, IPR001816 from INTERPRO) []. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1TUI_C 1OB5_E 1TTT_B 1B23_P 1EFT_A 3E20_E 1R5B_A 1R5O_A 1R5N_A 3AGJ_C ....
Probab=20.71 E-value=2.3e+02 Score=21.80 Aligned_cols=43 Identities=21% Similarity=0.273 Sum_probs=33.1
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeE
Q 025354 145 LIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNR 190 (254)
Q Consensus 145 ~ik~~Dtv~i~l~~~kI~d~i~fe~G~~~~i~gG~n~G~vG~I~~i 190 (254)
.++.||...+.+.-.+ -+.+|+++..++=.|.++=-+|+|+++
T Consensus 56 ~l~~g~~a~v~l~~~~---pi~ve~~~Rf~lR~~~~Tia~G~V~~v 98 (99)
T PF03143_consen 56 FLKPGDRAVVELEFQK---PICVEPFSRFILRDGGKTIAVGVVTKV 98 (99)
T ss_dssp EB-TTEEEEEEEEEEE---EEEETTTTEEEEEETTEEEEEEEEEEE
T ss_pred ccccccccccceeecc---ceeeecCceEEEccCCeEEEEEEEEEe
Confidence 5899999999986544 678899997777666666668999886
Done!