Query 024793
Match_columns 262
No_of_seqs 125 out of 393
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:27:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024793.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024793hhsearch_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 7E-115 1E-119 789.6 29.6 260 1-260 1-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 1E-114 3E-119 787.7 29.9 261 1-261 1-261 (262)
3 PTZ00223 40S ribosomal protein 100.0 2E-110 4E-115 763.9 29.8 257 5-261 2-259 (273)
4 PRK04313 30S ribosomal protein 100.0 6E-104 1E-108 710.3 27.6 235 5-240 1-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 5E-102 1E-106 692.0 23.5 240 2-242 1-241 (241)
6 KOG0378 40S ribosomal protein 100.0 1.1E-98 2E-103 673.4 15.7 262 1-262 1-262 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 9.4E-33 2E-37 211.1 9.5 77 94-170 1-77 (77)
8 PF08071 RS4NT: RS4NT (NUC023) 99.8 4.3E-21 9.2E-26 128.8 1.6 38 3-40 1-38 (38)
9 PF01479 S4: S4 domain; Inter 98.9 4.3E-09 9.3E-14 72.2 5.5 48 42-90 1-48 (48)
10 COG0522 RpsD Ribosomal protein 98.9 1.8E-09 3.9E-14 96.4 4.2 44 51-94 102-145 (205)
11 PLN00189 40S ribosomal protein 98.1 2.1E-06 4.6E-11 76.3 3.1 42 51-92 117-158 (194)
12 TIGR01018 rpsD_arch ribosomal 98.1 3.5E-06 7.6E-11 73.1 4.2 46 51-96 112-159 (162)
13 cd00165 S4 S4/Hsp/ tRNA synthe 98.0 3.4E-05 7.3E-10 53.7 7.4 60 43-103 2-61 (70)
14 CHL00113 rps4 ribosomal protei 97.9 5.6E-06 1.2E-10 73.9 2.7 46 51-96 97-142 (201)
15 PTZ00155 40S ribosomal protein 97.9 7.1E-06 1.5E-10 72.3 2.8 43 45-87 102-151 (181)
16 TIGR02988 YaaA_near_RecF S4 do 97.9 4.3E-05 9.4E-10 54.8 5.9 51 42-93 9-59 (59)
17 TIGR01017 rpsD_bact ribosomal 97.8 3.6E-05 7.8E-10 68.4 5.2 44 51-94 98-141 (200)
18 PRK04051 rps4p 30S ribosomal p 97.7 4.3E-05 9.3E-10 67.2 5.1 47 51-97 111-159 (177)
19 PRK05327 rpsD 30S ribosomal pr 97.7 5E-05 1.1E-09 67.7 5.3 44 52-95 102-145 (203)
20 smart00363 S4 S4 RNA-binding d 97.7 9.9E-05 2.2E-09 49.9 5.7 51 43-94 2-52 (60)
21 PF13275 S4_2: S4 domain; PDB: 97.0 0.0003 6.5E-09 52.6 1.2 59 40-101 6-64 (65)
22 PRK11507 ribosome-associated p 96.9 0.0036 7.9E-08 47.6 6.5 60 40-102 10-69 (70)
23 TIGR03069 PS_II_S4 photosystem 96.8 0.004 8.7E-08 57.4 7.4 62 41-115 183-244 (257)
24 smart00739 KOW KOW (Kyprides, 96.7 0.0015 3.2E-08 39.6 2.7 27 174-200 1-27 (28)
25 PF00467 KOW: KOW motif; Inte 96.6 0.0024 5.2E-08 40.9 3.1 26 177-202 1-26 (32)
26 TIGR00478 tly hemolysin TlyA f 96.4 0.0056 1.2E-07 55.5 5.6 48 46-94 4-51 (228)
27 PRK10348 ribosome-associated h 96.4 0.0072 1.6E-07 51.1 5.5 59 41-101 8-66 (133)
28 TIGR00005 rluA_subfam pseudour 96.1 0.023 5E-07 52.3 8.1 52 41-93 5-56 (299)
29 PLN00051 RNA-binding S4 domain 95.7 0.029 6.3E-07 52.2 6.7 62 41-115 191-252 (267)
30 COG2501 S4-like RNA binding pr 95.6 0.028 6E-07 43.1 5.1 60 40-102 10-69 (73)
31 COG2302 Uncharacterized conser 95.4 0.029 6.4E-07 52.0 5.5 53 40-94 179-231 (257)
32 COG0564 RluA Pseudouridylate s 95.3 0.057 1.2E-06 50.6 7.3 57 40-99 11-67 (289)
33 PRK11180 rluD 23S rRNA pseudou 95.2 0.073 1.6E-06 50.1 7.8 53 41-94 17-69 (325)
34 COG1189 Predicted rRNA methyla 95.0 0.051 1.1E-06 50.2 5.7 119 45-165 6-153 (245)
35 COG1188 Ribosome-associated he 94.6 0.067 1.5E-06 43.3 4.9 58 42-101 9-66 (100)
36 TIGR01080 rplX_A_E ribosomal p 94.4 0.092 2E-06 43.4 5.4 56 170-228 37-99 (114)
37 KOG3301 Ribosomal protein S4 [ 94.2 0.029 6.3E-07 49.2 2.1 36 51-86 105-140 (183)
38 PRK10839 16S rRNA pseudouridyl 94.0 0.13 2.7E-06 46.0 5.9 48 44-93 3-50 (232)
39 PRK10475 23S rRNA pseudouridin 93.8 0.13 2.8E-06 48.3 5.8 66 40-108 5-78 (290)
40 PRK11025 23S rRNA pseudouridyl 93.6 0.32 6.8E-06 45.7 8.1 51 41-93 19-69 (317)
41 PRK13354 tyrosyl-tRNA syntheta 92.9 0.34 7.3E-06 47.6 7.4 65 41-111 342-406 (410)
42 PRK05912 tyrosyl-tRNA syntheta 92.9 0.28 6E-06 48.1 6.6 64 41-111 342-405 (408)
43 COG1187 RsuA 16S rRNA uridine- 92.0 0.35 7.5E-06 44.8 5.8 57 52-109 12-75 (248)
44 PRK10700 23S rRNA pseudouridyl 91.5 0.49 1.1E-05 44.3 6.3 63 45-110 6-80 (289)
45 PRK01191 rpl24p 50S ribosomal 91.2 0.69 1.5E-05 38.6 6.2 38 172-212 43-80 (120)
46 KOG4655 U3 small nucleolar rib 88.7 0.27 5.8E-06 43.3 2.0 55 30-84 87-148 (181)
47 PRK12281 rplX 50S ribosomal pr 86.5 1.2 2.5E-05 34.2 4.1 39 173-214 5-43 (76)
48 CHL00141 rpl24 ribosomal prote 85.7 1.4 3E-05 34.3 4.2 38 173-213 7-44 (83)
49 PTZ00194 60S ribosomal protein 84.7 2.4 5.1E-05 36.5 5.5 55 172-229 44-105 (143)
50 PRK00004 rplX 50S ribosomal pr 84.4 1.4 3.1E-05 35.6 3.9 37 173-212 3-39 (105)
51 PF13051 DUF3912: Protein of u 80.2 4.4 9.6E-05 30.1 4.8 50 177-230 5-55 (68)
52 TIGR01079 rplX_bact ribosomal 78.2 3.3 7.1E-05 33.6 3.9 28 174-201 3-30 (104)
53 COG0162 TyrS Tyrosyl-tRNA synt 76.2 5.2 0.00011 39.6 5.4 40 44-84 338-377 (401)
54 COG0198 RplX Ribosomal protein 60.9 13 0.00028 30.4 3.9 29 173-201 3-31 (104)
55 COG2163 RPL14A Ribosomal prote 60.8 8.8 0.00019 32.3 3.0 26 175-200 5-30 (125)
56 KOG1999 RNA polymerase II tran 60.5 53 0.0011 36.2 9.3 55 175-233 582-638 (1024)
57 PTZ00065 60S ribosomal protein 59.6 11 0.00024 32.0 3.3 27 175-201 8-34 (130)
58 PF14001 YdfZ: YdfZ protein 53.9 21 0.00045 26.9 3.6 42 174-219 9-56 (64)
59 PRK04333 50S ribosomal protein 49.8 18 0.00039 28.3 2.9 27 174-200 3-29 (84)
60 PF12005 DUF3499: Protein of u 48.4 7.7 0.00017 32.6 0.7 23 7-29 46-68 (123)
61 TIGR03193 4hydroxCoAred 4-hydr 45.9 17 0.00037 31.3 2.4 51 40-94 17-75 (148)
62 TIGR00234 tyrS tyrosyl-tRNA sy 45.9 20 0.00043 34.9 3.2 46 41-87 329-374 (377)
63 cd04093 HBS1_C HBS1_C: this fa 43.4 1.5E+02 0.0033 22.8 7.9 42 153-198 59-107 (107)
64 cd03704 eRF3c_III This family 42.8 67 0.0015 25.0 5.3 48 150-198 56-108 (108)
65 PF08828 DSX_dimer: Doublesex 41.5 17 0.00037 27.1 1.5 32 40-74 22-54 (62)
66 PF03417 AAT: Acyl-coenzyme A: 40.6 31 0.00067 30.2 3.3 29 39-68 69-97 (225)
67 TIGR01955 RfaH transcriptional 40.1 77 0.0017 26.3 5.5 83 109-199 51-133 (159)
68 KOG2623 Tyrosyl-tRNA synthetas 39.0 35 0.00075 34.3 3.6 40 41-81 398-437 (467)
69 PF11717 Tudor-knot: RNA bindi 38.2 77 0.0017 22.2 4.5 38 175-212 1-39 (55)
70 TIGR03318 YdfZ_fam putative se 37.6 34 0.00074 25.8 2.6 41 175-219 11-57 (65)
71 cd04478 RPA2_DBD_D RPA2_DBD_D: 37.1 1.4E+02 0.003 22.4 6.1 57 89-145 8-75 (95)
72 PF02597 ThiS: ThiS family; I 36.6 58 0.0013 23.3 3.8 27 66-92 42-70 (77)
73 PF01959 DHQS: 3-dehydroquinat 36.1 75 0.0016 31.2 5.4 46 133-191 297-345 (354)
74 KOG1784 Small Nuclear ribonucl 35.6 71 0.0015 25.7 4.3 60 134-197 10-75 (96)
75 PRK02290 3-dehydroquinate synt 35.4 76 0.0016 31.1 5.3 46 133-191 287-335 (344)
76 PF07076 DUF1344: Protein of u 35.2 85 0.0018 23.4 4.4 36 130-165 10-49 (61)
77 PRK08559 nusG transcription an 35.2 58 0.0012 27.6 4.0 29 173-201 93-121 (153)
78 PF01588 tRNA_bind: Putative t 35.0 85 0.0019 24.2 4.7 20 191-210 2-21 (95)
79 PTZ00471 60S ribosomal protein 34.9 39 0.00084 28.9 2.9 24 175-198 5-28 (134)
80 TIGR03198 pucE xanthine dehydr 34.4 13 0.00028 32.0 -0.0 51 40-94 19-77 (151)
81 TIGR00405 L26e_arch ribosomal 33.6 70 0.0015 26.4 4.2 26 175-200 87-112 (145)
82 PF04773 FecR: FecR protein; 33.5 2E+02 0.0042 21.2 9.4 66 129-194 3-75 (98)
83 COG1792 MreC Cell shape-determ 33.0 4.2E+02 0.009 24.9 10.8 61 150-230 209-270 (284)
84 PF09285 Elong-fact-P_C: Elong 32.4 84 0.0018 22.9 3.9 36 134-170 19-54 (56)
85 TIGR01682 moaD molybdopterin c 32.2 1.2E+02 0.0027 22.3 5.0 23 69-92 51-73 (80)
86 PF12961 DUF3850: Domain of Un 31.5 44 0.00094 25.6 2.4 18 146-163 21-38 (72)
87 cd04483 hOBFC1_like hOBFC1_lik 31.3 2.3E+02 0.0049 22.0 6.5 55 88-142 5-87 (92)
88 cd03705 EF1_alpha_III Domain I 31.1 1.1E+02 0.0023 23.5 4.6 35 153-190 59-100 (104)
89 cd03706 mtEFTU_III Domain III 30.2 2.1E+02 0.0046 21.6 6.1 41 153-197 51-92 (93)
90 KOG2404 Fumarate reductase, fl 29.9 88 0.0019 31.2 4.7 79 20-104 117-196 (477)
91 KOG3513 Neural cell adhesion m 28.4 1.8E+02 0.0038 32.6 7.2 159 63-230 437-614 (1051)
92 PRK05609 nusG transcription an 28.3 1.4E+02 0.003 25.3 5.3 29 172-200 124-152 (181)
93 PF01063 Aminotran_4: Aminotra 27.4 2E+02 0.0043 24.7 6.2 52 205-258 125-176 (231)
94 PRK14898 DNA-directed RNA poly 27.2 2.2E+02 0.0048 31.0 7.6 59 104-162 130-195 (858)
95 COG2080 CoxS Aerobic-type carb 27.1 43 0.00094 29.2 1.9 51 39-93 18-76 (156)
96 smart00306 HintN Hint (Hedgeho 26.8 2.6E+02 0.0056 20.4 8.1 55 176-230 23-78 (100)
97 cd05794 S1_EF-P_repeat_2 S1_EF 26.3 1.1E+02 0.0024 22.3 3.6 34 134-168 19-52 (56)
98 PF10781 DSRB: Dextransucrase 25.8 1.4E+02 0.003 22.2 4.1 29 155-183 2-35 (62)
99 PF08529 NusA_N: NusA N-termin 25.8 52 0.0011 26.8 2.1 51 113-166 45-96 (122)
100 TIGR00922 nusG transcription t 25.0 1.6E+02 0.0035 24.8 5.1 28 173-200 118-145 (172)
101 COG5164 SPT5 Transcription elo 24.7 1.2E+02 0.0025 31.4 4.6 42 157-200 124-165 (607)
102 cd04491 SoSSB_OBF SoSSB_OBF: A 24.5 2.9E+02 0.0062 20.2 6.5 52 96-147 22-79 (82)
103 PF02736 Myosin_N: Myosin N-te 24.4 1.7E+02 0.0037 19.5 4.1 36 112-150 4-39 (42)
104 KOG1999 RNA polymerase II tran 23.9 1.1E+02 0.0025 33.8 4.7 39 161-201 448-486 (1024)
105 PLN02799 Molybdopterin synthas 23.6 2E+02 0.0044 21.1 4.9 25 68-93 52-76 (82)
106 PF14505 DUF4438: Domain of un 23.3 75 0.0016 29.8 2.9 32 177-210 60-92 (258)
107 COG1188 Ribosome-associated he 23.0 94 0.002 25.3 3.0 36 129-168 28-63 (100)
108 PTZ00141 elongation factor 1- 22.8 4.3E+02 0.0093 26.2 8.3 53 153-206 381-437 (446)
109 cd00754 MoaD Ubiquitin domain 22.6 1.6E+02 0.0035 21.2 4.1 26 66-92 48-73 (80)
110 smart00841 Elong-fact-P_C Elon 21.7 1.5E+02 0.0033 21.5 3.6 30 138-168 23-52 (56)
111 KOG3401 60S ribosomal protein 21.7 73 0.0016 27.6 2.3 38 164-201 38-76 (145)
112 PRK10708 hypothetical protein; 21.7 1.8E+02 0.004 21.6 4.0 29 155-183 2-35 (62)
113 COG0250 NusG Transcription ant 21.6 91 0.002 27.4 3.0 31 170-200 119-149 (178)
114 PF06905 FAIM1: Fas apoptotic 20.2 6.1E+02 0.013 22.5 10.4 103 66-194 29-133 (177)
115 PF05709 Sipho_tail: Phage tai 20.1 3.7E+02 0.0079 23.1 6.5 53 40-94 40-95 (249)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=6.9e-115 Score=789.57 Aligned_cols=260 Identities=89% Similarity=1.405 Sum_probs=257.3
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEeccc
Q 024793 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDK 80 (262)
Q Consensus 1 MarG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~ 80 (262)
|||||++|||||+||+||||+||+++||||||||||++++||||+|||||+||||+|.|||++||+||+|+|||++|+|+
T Consensus 1 m~~g~kkHlKRl~AP~~W~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~ 80 (261)
T PLN00036 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80 (261)
T ss_pred CCCCcccccccccCccccccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeE
Q 024793 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTI 160 (262)
Q Consensus 81 ~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv 160 (262)
+|||||||||||++++|+||++||++|+|++|+|++|||+||||||++|++++||+|||+|||||||+|+||+||+||||
T Consensus 81 ~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv 160 (261)
T PLN00036 81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160 (261)
T ss_pred CCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 024793 161 KLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 240 (262)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (262)
+||||+++|++||||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++++||||||+
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~ 240 (261)
T PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240 (261)
T ss_pred EEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred CCceeeehHHHHHHHHHHHH
Q 024793 241 GKGIKLSIIEEARKRQAAQA 260 (262)
Q Consensus 241 ~~gi~~~~~~~~~~~~~~~~ 260 (262)
++|||+|++|||++++++.+
T Consensus 241 ~~gi~~~~~e~r~~~~~~~~ 260 (261)
T PLN00036 241 GKGIKLSIIEEARKRLAAGQ 260 (261)
T ss_pred CCCcccchHHHHHHhhhhhc
Confidence 99999999999999998764
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.5e-114 Score=787.75 Aligned_cols=261 Identities=62% Similarity=1.053 Sum_probs=258.2
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEeccc
Q 024793 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDK 80 (262)
Q Consensus 1 MarG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~ 80 (262)
|||||++|||||+||+||||+||+++|||+||||||++++||||+|||||+||||+|.|||++||+||+|+|||++|+|+
T Consensus 1 m~~g~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~ 80 (262)
T PTZ00118 1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDC 80 (262)
T ss_pred CCCCcccccccccCccccccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeE
Q 024793 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTI 160 (262)
Q Consensus 81 ~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv 160 (262)
+|||||||||||++++|+||++||++|+|++|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||
T Consensus 81 ~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dtv 160 (262)
T PTZ00118 81 TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSL 160 (262)
T ss_pred CCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 024793 161 KLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 240 (262)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (262)
+||||+++|++|||||+||+||||||+|+|++|+|.+++++++|+++||++|++|++|+|+++||||||++++||||||+
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~ 240 (262)
T PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPR 240 (262)
T ss_pred EEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred CCceeeehHHHHHHHHHHHHh
Q 024793 241 GKGIKLSIIEEARKRQAAQAA 261 (262)
Q Consensus 241 ~~gi~~~~~~~~~~~~~~~~~ 261 (262)
++|||+|++|||++++++++.
T Consensus 241 ~kgi~~~~~e~~~~~~~~~~~ 261 (262)
T PTZ00118 241 ERGIKKDIIEERRNRLAKALR 261 (262)
T ss_pred CCCccccHHHHHHHHHHHHhc
Confidence 999999999999999988764
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.9e-110 Score=763.94 Aligned_cols=257 Identities=54% Similarity=0.886 Sum_probs=252.8
Q ss_pred cccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024793 5 LKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 84 (262)
Q Consensus 5 ~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypV 84 (262)
.++|||||+||+||||+||+++|||+||||||++++||||+|||||+||||+|.|||++||+||+|+|||++|+|++|||
T Consensus 2 ~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~Pv 81 (273)
T PTZ00223 2 AKKHLKRLYAPKDWMLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPA 81 (273)
T ss_pred ccchhhhhcCccccccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEec
Q 024793 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDL 164 (262)
Q Consensus 85 G~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l 164 (262)
|||||||||+++|+||++||++|+|++|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|||
T Consensus 82 GlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l 161 (273)
T PTZ00223 82 GFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNV 161 (273)
T ss_pred ceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCEEEEEC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccC-CCceEecCCCCc
Q 024793 165 EENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKG 243 (262)
Q Consensus 165 ~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~-~~p~islp~~~g 243 (262)
|+++|++||||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++ ++|||+||+++|
T Consensus 162 ~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kg 241 (273)
T PTZ00223 162 KEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQG 241 (273)
T ss_pred CCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999985 699999999999
Q ss_pred eeeehHHHHHHHHHHHHh
Q 024793 244 IKLSIIEEARKRQAAQAA 261 (262)
Q Consensus 244 i~~~~~~~~~~~~~~~~~ 261 (262)
||+|++|||+++++++++
T Consensus 242 i~~~~~e~~~~~~~~~~~ 259 (273)
T PTZ00223 242 LRINVIQEREEKLIAAEA 259 (273)
T ss_pred ccccHHHHHHHHHHHHHh
Confidence 999999999999987764
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=6.2e-104 Score=710.33 Aligned_cols=235 Identities=43% Similarity=0.699 Sum_probs=231.6
Q ss_pred cccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024793 5 LKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 84 (262)
Q Consensus 5 ~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypV 84 (262)
+++|||||+||++|||+||+++||||||||||++++||||++||||+||||+|+|||++||+||+|+|||++|+|++|||
T Consensus 1 ~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~Pv 80 (237)
T PRK04313 1 MMRHLKRLAAPKSWPIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80 (237)
T ss_pred CCccccceeCCcccccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCC-CCcccCCeEEEe
Q 024793 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKANDTIKLD 163 (262)
Q Consensus 85 G~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d-~~ik~~Dtv~i~ 163 (262)
|||||||||+++|+||++||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| ++||+||||+|+
T Consensus 81 GlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~ 160 (237)
T PRK04313 81 GLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLIS 160 (237)
T ss_pred CceeEEEEccCCCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCCEEEEE
Confidence 9999999999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred cCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 024793 164 LEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 240 (262)
Q Consensus 164 l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (262)
||+++|++||+|++||+||||||+|+|++|+|.+|++++ +++++||++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 161 l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 161 LPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred CCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 999999999999999999999999999999999999999 7789999999999999999999999998 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.4e-102 Score=692.04 Aligned_cols=240 Identities=49% Similarity=0.785 Sum_probs=236.6
Q ss_pred CCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccC
Q 024793 2 ARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKT 81 (262)
Q Consensus 2 arG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ 81 (262)
||||++|||||+||+||||+||+++|||+|+||||++++||||++++||+|+||+|+|||++|+++|+|+|||++|+|++
T Consensus 1 a~g~~~HlKRl~aP~~w~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~k 80 (241)
T COG1471 1 ARGPKRHLKRLAAPKSWPIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYK 80 (241)
T ss_pred CCchhhhhhhccCCceEEeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEecccc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEE
Q 024793 82 YPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIK 161 (262)
Q Consensus 82 ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~ 161 (262)
||||||||||||++||+||++||.+|+|.+|+|++|||.||||||+||++++||++|||||||||++++|++|++||||+
T Consensus 81 fPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dtv~ 160 (241)
T COG1471 81 FPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVK 160 (241)
T ss_pred CCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 024793 162 LDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 240 (262)
Q Consensus 162 i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (262)
+++|+++|++||+|++|++||||||+|+|++|+|.+|+.++ +++++|+++|.+|+.|+|+++||||||+ ++|||+||.
T Consensus 161 i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~ 239 (241)
T COG1471 161 ISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPK 239 (241)
T ss_pred EeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCC
Confidence 99999999999999999999999999999999999999999 6688999999999999999999999998 999999998
Q ss_pred CC
Q 024793 241 GK 242 (262)
Q Consensus 241 ~~ 242 (262)
|+
T Consensus 240 e~ 241 (241)
T COG1471 240 EK 241 (241)
T ss_pred CC
Confidence 74
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-98 Score=673.41 Aligned_cols=262 Identities=71% Similarity=1.175 Sum_probs=260.0
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEeccc
Q 024793 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDK 80 (262)
Q Consensus 1 MarG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~ 80 (262)
|+|||++||||++||+|||++|++|.|||+||+|||+++||+||++||||+|+||+|.+|+++|++|++|+|||++|+|.
T Consensus 1 m~~g~k~hlKr~~ap~~wmldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~ 80 (263)
T KOG0378|consen 1 MARGPKKHLKRLAAPKHWMLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDS 80 (263)
T ss_pred CCcchhhhhhhhcccHhheecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeE
Q 024793 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTI 160 (262)
Q Consensus 81 ~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv 160 (262)
+||+|+||||+|++|+|+||++||++|+|.+|.|++|||+||||||++++.+.+|+|+|+||||++|||+||.||+|||+
T Consensus 81 ~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dtI 160 (263)
T KOG0378|consen 81 TYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDTI 160 (263)
T ss_pred ccccceeEEEEecccchhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCcccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 024793 161 KLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 240 (262)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (262)
++++++++|.++++|+.|++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++|+|+||+|++||||||.
T Consensus 161 ~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPk 240 (263)
T KOG0378|consen 161 KIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPK 240 (263)
T ss_pred eccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeehHHHHHHHHHHHHhC
Q 024793 241 GKGIKLSIIEEARKRQAAQAAA 262 (262)
Q Consensus 241 ~~gi~~~~~~~~~~~~~~~~~~ 262 (262)
++||+++++||||+|++++.++
T Consensus 241 gkgi~~siaEe~dkrl~~k~~s 262 (263)
T KOG0378|consen 241 GKGIALSIAEERDKRLAAKISS 262 (263)
T ss_pred ccCccchhhHHHHHHHhhhccC
Confidence 9999999999999999998764
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=99.98 E-value=9.4e-33 Score=211.13 Aligned_cols=77 Identities=61% Similarity=1.011 Sum_probs=69.6
Q ss_pred ccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCeee
Q 024793 94 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 170 (262)
Q Consensus 94 ~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 170 (262)
+++|+||++||++|+|++|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|+||++||+
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 58999999999999999999999999999999999999999999999999999999999999999999999999986
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=99.81 E-value=4.3e-21 Score=128.77 Aligned_cols=38 Identities=74% Similarity=1.241 Sum_probs=22.2
Q ss_pred CCcccccccccCCCceecccccceeccCCCCCCCCCcc
Q 024793 3 RGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRE 40 (262)
Q Consensus 3 rG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~ 40 (262)
||+++|||||+||++|+|+||+++||++||||||+++|
T Consensus 1 ~G~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 1 RGPKKHLKRLAAPKSWMIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp -S-----BCCCS-GGGT--SSSSSB-----SSSS-CCC
T ss_pred CCcccccccccCCcccccccccCccccCCCCCCccCCC
Confidence 69999999999999999999999999999999999975
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=98.87 E-value=4.3e-09 Score=72.22 Aligned_cols=48 Identities=33% Similarity=0.359 Sum_probs=44.5
Q ss_pred chHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeE
Q 024793 42 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVV 90 (262)
Q Consensus 42 iPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVI 90 (262)
++|..+| ..++++.|..||++++.+|.|+|||++++|++|+|..+|+|
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
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.86 E-value=1.8e-09 Score=96.45 Aligned_cols=44 Identities=30% Similarity=0.405 Sum_probs=42.9
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
|+|||.|.++|||+++||||.|||+++++|+|-|-..|+|+|.+
T Consensus 102 R~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~ 145 (205)
T COG0522 102 RLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVRE 145 (205)
T ss_pred HhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeee
Confidence 57999999999999999999999999999999999999999987
No 11
>PLN00189 40S ribosomal protein S9; Provisional
Probab=98.08 E-value=2.1e-06 Score=76.30 Aligned_cols=42 Identities=14% Similarity=0.168 Sum_probs=39.0
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEe
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSI 92 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI 92 (262)
+||||.|..+|+|++.||||.|||+++++|+|-|-..|++.|
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~I 158 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHI 158 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEE
Confidence 479999999999999999999999999999999988877666
No 12
>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=98.07 E-value=3.5e-06 Score=73.07 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=40.0
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcc--eeEEecccC
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM--DVVSIPKTN 96 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~m--DVIsI~~t~ 96 (262)
++|+|.|.++|+|++.||||.|||+++++|+|-|... |-|+...++
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S 159 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSS 159 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeecCC
Confidence 4799999999999999999999999999999998776 666665443
No 13
>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=98.00 E-value=3.4e-05 Score=53.71 Aligned_cols=60 Identities=27% Similarity=0.329 Sum_probs=48.1
Q ss_pred hHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeee
Q 024793 43 PLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLY 103 (262)
Q Consensus 43 PL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~ 103 (262)
.|.-+|+.. +++.+..+|++++.+|.|+|||+.++++++++..+|+|++........++|
T Consensus 2 rl~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~ 61 (70)
T cd00165 2 RLDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVY 61 (70)
T ss_pred cHHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceee
Confidence 355677664 467899999999999999999999999999999999999976433234444
No 14
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.92 E-value=5.6e-06 Score=73.90 Aligned_cols=46 Identities=22% Similarity=0.378 Sum_probs=42.6
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccC
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTN 96 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~ 96 (262)
++++|.|.++|++++.||+|.|||+++++++|.|...|+|++....
T Consensus 97 r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~~ 142 (201)
T CHL00113 97 RLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQ 142 (201)
T ss_pred HcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEcccc
Confidence 4689999999999999999999999999999999999999997643
No 15
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=97.89 E-value=7.1e-06 Score=72.31 Aligned_cols=43 Identities=19% Similarity=0.223 Sum_probs=38.1
Q ss_pred HHHHHhhh-------ccccCHHHHHHHHhCceEEECCEEecccCCCCCcc
Q 024793 45 ILVLRNRL-------KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 87 (262)
Q Consensus 45 ~i~LRdrL-------g~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~m 87 (262)
--||+-|| |+|.|..+|+|++.||||.|||+++++|+|-|-..
T Consensus 102 ~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~ 151 (181)
T PTZ00155 102 EKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVD 151 (181)
T ss_pred HHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccC
Confidence 35677776 99999999999999999999999999999977554
No 16
>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=97.86 E-value=4.3e-05 Score=54.82 Aligned_cols=51 Identities=22% Similarity=0.217 Sum_probs=46.4
Q ss_pred chHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024793 42 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 93 (262)
Q Consensus 42 iPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~ 93 (262)
..|--+|... +++.++..+++++.+|.|+|||++++.++|.+-.+|+|+|+
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 5676788887 77889999999999999999999999999999999999985
No 17
>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=97.76 E-value=3.6e-05 Score=68.41 Aligned_cols=44 Identities=30% Similarity=0.382 Sum_probs=41.4
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
+++++.|+++|++++.+|+|.|||+++++++|.|...|+|++..
T Consensus 98 ~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 98 RLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKE 141 (200)
T ss_pred HcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEee
Confidence 35788999999999999999999999999999999999999975
No 18
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.73 E-value=4.3e-05 Score=67.16 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=40.7
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcc--eeEEecccCc
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM--DVVSIPKTNE 97 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~m--DVIsI~~t~e 97 (262)
++|||.|..+|++++.||||.|||+++++|+|.|..- |.|+...++.
T Consensus 111 r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~ 159 (177)
T PRK04051 111 RKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSP 159 (177)
T ss_pred HccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCC
Confidence 3699999999999999999999999999999998766 5777766443
No 19
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.72 E-value=5e-05 Score=67.66 Aligned_cols=44 Identities=27% Similarity=0.395 Sum_probs=41.5
Q ss_pred hccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEeccc
Q 024793 52 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT 95 (262)
Q Consensus 52 Lg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t 95 (262)
++++.|..+|++++.+|+|+|||+++++++|++...|+|++...
T Consensus 102 ~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~~ 145 (203)
T PRK05327 102 LGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREK 145 (203)
T ss_pred cCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECCc
Confidence 48899999999999999999999999999999999999999763
No 20
>smart00363 S4 S4 RNA-binding domain.
Probab=97.72 E-value=9.9e-05 Score=49.91 Aligned_cols=51 Identities=27% Similarity=0.242 Sum_probs=43.9
Q ss_pred hHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024793 43 PLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 43 PL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
.|..+|.. .+++.+.+++++++.+|.|+|||++++++.+++..+|.|++..
T Consensus 2 rl~~~l~~-~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 2 RLDKFLAR-LGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred cHHHHHHH-cCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 35566764 3467899999999999999999999999999999999999964
No 21
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=96.97 E-value=0.0003 Score=52.59 Aligned_cols=59 Identities=27% Similarity=0.304 Sum_probs=42.1
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~ 101 (262)
+.|.|.=||.- .+++.|.-|||..+.+|.|+|||.+.+...--+-.+|+|++ .++.|++
T Consensus 6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~--~~~~~~V 64 (65)
T PF13275_consen 6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI--DGEEYRV 64 (65)
T ss_dssp S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE--TTEEEEE
T ss_pred CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE--CCEEEEE
Confidence 56778888877 69999999999999999999999999999999999999999 4677765
No 22
>PRK11507 ribosome-associated protein; Provisional
Probab=96.90 E-value=0.0036 Score=47.55 Aligned_cols=60 Identities=18% Similarity=0.167 Sum_probs=52.1
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeee
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 102 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l 102 (262)
+.|-|.=||.- .+++.|.-|||..+.+|.|+|||.+.+-..--+-.+|+|+++ ++.|++.
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 46777778876 699999999999999999999999999999999999999995 4666653
No 23
>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=96.81 E-value=0.004 Score=57.39 Aligned_cols=62 Identities=15% Similarity=0.208 Sum_probs=51.3
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEEEEeC
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 115 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~ 115 (262)
|+=|-.++...+ ..|++.|++++.+|+|+|||+++++++|.+...|+|++. ..|||.+..+.
T Consensus 183 s~RLD~lls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isvr-----------G~Gr~~i~~~~ 244 (257)
T TIGR03069 183 SLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR-----------GKGRLEILELE 244 (257)
T ss_pred cccHHHHHHhhh--hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEc-----------CCceEEEEEee
Confidence 555667887654 568999999999999999999999999999999999994 45777665553
No 24
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.73 E-value=0.0015 Score=39.56 Aligned_cols=27 Identities=37% Similarity=0.661 Sum_probs=24.6
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 174 KFDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
+|++|+.++|++|.+.|.+|+|.++..
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 25
>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=96.61 E-value=0.0024 Score=40.88 Aligned_cols=26 Identities=35% Similarity=0.618 Sum_probs=23.4
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEec
Q 024793 177 VGNIVMVTGGRNRGRVGIIKNREKHK 202 (262)
Q Consensus 177 ~G~~~~v~gG~n~G~vG~I~~i~~~~ 202 (262)
+|+.++|+.|++.|+.|+|.++..+.
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 58999999999999999999997643
No 26
>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=96.43 E-value=0.0056 Score=55.51 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=43.0
Q ss_pred HHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024793 46 LVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 46 i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
.+|.+ ++++.|+++|++++.+|.|+|||++++.+++.+...|+|++..
T Consensus 4 ~~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 4 ILLVR-RGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred HHHHH-cCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 35555 4789999999999999999999999999999999889999964
No 27
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=96.38 E-value=0.0072 Score=51.06 Aligned_cols=59 Identities=10% Similarity=0.069 Sum_probs=51.1
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~ 101 (262)
++-|-.||=- .+|+.|+..|+.+|..|+|.|||.+ .-++..|...|+|+|...+..|-+
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~v 66 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTV 66 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEEE
Confidence 5677777776 4999999999999999999999999 899999999999999875554443
No 28
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=96.15 E-value=0.023 Score=52.32 Aligned_cols=52 Identities=19% Similarity=0.183 Sum_probs=44.7
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 93 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~ 93 (262)
+..|.-+|...+. ..+.+++++++.+|.|+|||+++.++++.+...|+|++.
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 4667778877653 467999999999999999998888899999999999983
No 29
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=95.69 E-value=0.029 Score=52.24 Aligned_cols=62 Identities=19% Similarity=0.248 Sum_probs=50.5
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEEEEeC
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 115 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~ 115 (262)
|+=|--+|-..+ -.++..|.+.+.+|+|+|||+.+++++|.|...|+|||.. .|||.+..+.
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 555667777765 5677789999999999999999999999999999999964 3666655543
No 30
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=95.61 E-value=0.028 Score=43.14 Aligned_cols=60 Identities=23% Similarity=0.278 Sum_probs=50.3
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeee
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 102 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l 102 (262)
+-|-|.=||.- +|+++|.-+||..+.+|.|+|||.+-+-..--+-..|+|+|+. ..|-+.
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 45667777776 7999999999999999999999999888888889999999974 444443
No 31
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=95.40 E-value=0.029 Score=52.02 Aligned_cols=53 Identities=21% Similarity=0.230 Sum_probs=46.9
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
.||=|-.++-+.+|+.. .-|.+.+..|.|+||.++++.++|-+..+|.|||..
T Consensus 179 sSlRLD~vis~~~~~SR--~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG 231 (257)
T COG2302 179 SSLRLDVVISEGFGLSR--AKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG 231 (257)
T ss_pred ehhhHHHHHHHHHhhhH--HHHHHHHHcCceEEeeEEeccccceeccCCEEEEec
Confidence 47888899999777654 568999999999999999999999999999999954
No 32
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=95.33 E-value=0.057 Score=50.58 Aligned_cols=57 Identities=25% Similarity=0.220 Sum_probs=49.6
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcce
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 99 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~f 99 (262)
...-|--+|++ |.- .+..+..+++.+|.|.|||++++ ++|.+...|+|+++...+.+
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 34567788999 776 78999999999999999999999 99999999999999865454
No 33
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=95.23 E-value=0.073 Score=50.11 Aligned_cols=53 Identities=19% Similarity=0.139 Sum_probs=46.1
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
...|.-+|+.+++ ..+.+++++++.+|.|.|||+.++.+.+.+...|+|++..
T Consensus 17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~ 69 (325)
T PRK11180 17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDA 69 (325)
T ss_pred CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEee
Confidence 4678888888754 4688999999999999999999988999999999999863
No 34
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.95 E-value=0.051 Score=50.23 Aligned_cols=119 Identities=19% Similarity=0.276 Sum_probs=76.4
Q ss_pred HHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee-------------eeecCCceEE
Q 024793 45 ILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRL-------------LYDTKGRFRL 111 (262)
Q Consensus 45 ~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~-------------l~d~kgrf~~ 111 (262)
-.+|=+| |++.|+.+|+..++.|.|+|||..++-|++-|-.-|.|++......|.- -.|.+|+.++
T Consensus 6 D~~Lv~r-gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~yVSRG~~KL~~ale~F~l~~k~kv~L 84 (245)
T COG1189 6 DALLVER-GLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFELDVKGKVVL 84 (245)
T ss_pred HHHHHHc-cchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCccccHHHHHHHHHHhcCcCCCCCEEE
Confidence 3445454 9999999999999999999999999999999999999999853333321 1255555544
Q ss_pred EEeChhhhcceeE-------EEEeEEEee-------CCceEEEccCCeeeecCCCCcc--cCCeEEEecC
Q 024793 112 HSLRDEEAKFKLC-------KVRSVQFGQ-------KGIPYINTYDGRTIRYPDPLIK--ANDTIKLDLE 165 (262)
Q Consensus 112 ~~I~~eea~~KLc-------KV~~k~~~~-------~g~~ql~~hDGrni~~~d~~ik--~~Dtv~i~l~ 165 (262)
-|-+..-.|=.| +|-..-++. ...|.+....+.|+||-.|+.- .-|-+++|+.
T Consensus 85 -DiGsSTGGFTd~lLq~gAk~VyavDVG~~Ql~~kLR~d~rV~~~E~tN~r~l~~~~~~~~~d~~v~DvS 153 (245)
T COG1189 85 -DIGSSTGGFTDVLLQRGAKHVYAVDVGYGQLHWKLRNDPRVIVLERTNVRYLTPEDFTEKPDLIVIDVS 153 (245)
T ss_pred -EecCCCccHHHHHHHcCCcEEEEEEccCCccCHhHhcCCcEEEEecCChhhCCHHHcccCCCeEEEEee
Confidence 343333333222 344444444 2446666677777776544322 3355666553
No 35
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=94.62 E-value=0.067 Score=43.31 Aligned_cols=58 Identities=16% Similarity=0.170 Sum_probs=45.3
Q ss_pred chHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024793 42 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (262)
Q Consensus 42 iPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~ 101 (262)
+=|--||-= -.+..++-.|+.+|..|+|.|||.+. -+++-|.++|+|+|.-.+..|-+
T Consensus 9 mRLDKwL~~-aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~~~v 66 (100)
T COG1188 9 MRLDKWLWA-ARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKEFTV 66 (100)
T ss_pred eehHHHHHH-HHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcEEEE
Confidence 334444432 35668999999999999999999999 78899999999999875555443
No 36
>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=0.092 Score=43.35 Aligned_cols=56 Identities=18% Similarity=0.246 Sum_probs=39.2
Q ss_pred eeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC-----CCeEeEe--eceEEEE
Q 024793 170 TDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL-----GHEFATR--LGNVFTI 228 (262)
Q Consensus 170 ~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~-----g~~F~T~--~~~vfvI 228 (262)
.+.+++..|+.+.|++|++-|..|+|.++... ...|.+++-+ |.+++.. .+||+++
T Consensus 37 ~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~ 99 (114)
T TIGR01080 37 KRALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVTKEKVNGTEVPVPIHPSNVMIT 99 (114)
T ss_pred cccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeEEECCCCeEEEeeechHHeEEE
Confidence 44557888999999999999999999999643 2356666544 4333333 3666554
No 37
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=94.21 E-value=0.029 Score=49.20 Aligned_cols=36 Identities=17% Similarity=0.280 Sum_probs=33.7
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCc
Q 024793 51 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGF 86 (262)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~ 86 (262)
+||+|.|...|+.++.|+||.|++.+++.|+|-|.+
T Consensus 105 klGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 105 KLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 479999999999999999999999999999998873
No 38
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=93.99 E-value=0.13 Score=45.99 Aligned_cols=48 Identities=17% Similarity=0.110 Sum_probs=41.4
Q ss_pred HHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024793 44 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 93 (262)
Q Consensus 44 L~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~ 93 (262)
|--+|...+ ..+++.+++++.+|.|+|||++++++++.+.-.|+|++.
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~ 50 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYD 50 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEEC
Confidence 445676655 367999999999999999999999899999999999986
No 39
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=93.75 E-value=0.13 Score=48.26 Aligned_cols=66 Identities=18% Similarity=0.112 Sum_probs=49.5
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEeccc--------CcceeeeeecCCc
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKT--------NENFRLLYDTKGR 108 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t--------~e~fR~l~d~kgr 108 (262)
.++-|.=+|.+. ++ .+++||++++.+|.|+|||+++ .+.+.|...|+|++... +++|-++.-+.|.
T Consensus 5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~~~ed~~~lvlnKP~G~ 78 (290)
T PRK10475 5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGI 78 (290)
T ss_pred hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccccccCCCeEEEEECCCCC
Confidence 456677777764 54 4799999999999999999988 58899988999998631 1345555556663
No 40
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=93.64 E-value=0.32 Score=45.73 Aligned_cols=51 Identities=27% Similarity=0.249 Sum_probs=43.7
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 93 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~ 93 (262)
...|.-||+..++ ..+.+++++++.+|.|.|||+++ .+++.+...|+|+++
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 3567788887763 46789999999999999999998 589999999999995
No 41
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=92.94 E-value=0.34 Score=47.64 Aligned_cols=65 Identities=22% Similarity=0.246 Sum_probs=48.0
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEE
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRL 111 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~ 111 (262)
.+||.=+|-. .|+|.+..|||+.+.+|-|.|||.+++|+.+-+-.-|.+ +..|-++--.|.+|..
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~l-----~~~~~~lr~GKk~~~~ 406 (410)
T PRK13354 342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDAF-----DGKFVILRRGKKKFFL 406 (410)
T ss_pred CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhhc-----CCCEEEEEeCCccEEE
Confidence 5778777775 799999999999999999999999999997655443321 2345555555555443
No 42
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=92.85 E-value=0.28 Score=48.12 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=47.9
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEE
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRL 111 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~ 111 (262)
.+|+.-+|-+ .|+|.+..|||+++.+|-|.|||.+++|..+-+..-| ....|-++--.|.+|..
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~~~------~~~~~~~lr~GKk~~~~ 405 (408)
T PRK05912 342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTADD------RFGKYTVLQRGKKKFAR 405 (408)
T ss_pred CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccccccc------cCCCEEEEEeCCCceEE
Confidence 4788888876 7999999999999999999999999999987553311 13445555555555544
No 43
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=91.97 E-value=0.35 Score=44.80 Aligned_cols=57 Identities=26% Similarity=0.292 Sum_probs=44.3
Q ss_pred hccccCHHHHHHHHhCceEEECCEEecccCCCCCcc-eeEEeccc-----Ccc-eeeeeecCCce
Q 024793 52 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM-DVVSIPKT-----NEN-FRLLYDTKGRF 109 (262)
Q Consensus 52 Lg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~m-DVIsI~~t-----~e~-fR~l~d~kgrf 109 (262)
+|+| ++|||.+++.+|.|.|||++.++...-+-.- |+|.++.. .+. |-+++-+.|.+
T Consensus 12 ~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v 75 (248)
T COG1187 12 AGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYV 75 (248)
T ss_pred cCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeE
Confidence 4655 6889999999999999999999999888887 47777652 122 66777888843
No 44
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=91.51 E-value=0.49 Score=44.27 Aligned_cols=63 Identities=21% Similarity=0.145 Sum_probs=45.1
Q ss_pred HHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCc--ceeEEecc---c-------CcceeeeeecCCceE
Q 024793 45 ILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGF--MDVVSIPK---T-------NENFRLLYDTKGRFR 110 (262)
Q Consensus 45 ~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~--mDVIsI~~---t-------~e~fR~l~d~kgrf~ 110 (262)
-=||-+ +|+ .++++|++++.+|.|+|||+++ ++.+.|-. .|+|+++. . .++|-++.-+.|..+
T Consensus 6 ~k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~~ 80 (289)
T PRK10700 6 QKVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80 (289)
T ss_pred HHHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCEe
Confidence 344554 454 6899999999999999999987 68888854 47787753 1 134667767777543
No 45
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=91.19 E-value=0.69 Score=38.61 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=30.2
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 024793 172 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 212 (262)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d 212 (262)
.+++..|+.+.|+.|..-|..|+|.++.... ..|+++.
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 4578889999999999999999999996542 2455544
No 46
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=88.72 E-value=0.27 Score=43.32 Aligned_cols=55 Identities=27% Similarity=0.327 Sum_probs=41.0
Q ss_pred CCCCCCCCCcccchHHHHHH-------hhhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024793 30 KPSSGPHKSRECLPLILVLR-------NRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 84 (262)
Q Consensus 30 kpspGPH~~~~siPL~i~LR-------drLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypV 84 (262)
-|..+.|..-+-+-..-|-| -+|++|.+-+||-..+.||||.|.-++++||.|-|
T Consensus 87 ipTr~~l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv 148 (181)
T KOG4655|consen 87 IPTRKSLELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV 148 (181)
T ss_pred ecchhhhhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence 44555555444233333333 24899999999999999999999999999999876
No 47
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=86.53 E-value=1.2 Score=34.25 Aligned_cols=39 Identities=18% Similarity=0.374 Sum_probs=31.6
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC
Q 024793 173 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 214 (262)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~ 214 (262)
+++..|+.+.|+.|+.-|++|+|..+.+. ...|.+++-+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegvn 43 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPK---KNRVIVEGVK 43 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcE
Confidence 47888999999999999999999999654 2356676543
No 48
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=85.66 E-value=1.4 Score=34.30 Aligned_cols=38 Identities=16% Similarity=0.474 Sum_probs=30.9
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcC
Q 024793 173 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 213 (262)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~ 213 (262)
+++..|+.++|+.|+.-|+.|+|.++.... ..|++++.
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv 44 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKGI 44 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence 478889999999999999999999996532 35667654
No 49
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=84.69 E-value=2.4 Score=36.48 Aligned_cols=55 Identities=27% Similarity=0.357 Sum_probs=37.7
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE-----cCCCCeEe--EeeceEEEEc
Q 024793 172 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHEFA--TRLGNVFTIG 229 (262)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~-----d~~g~~F~--T~~~~vfvIG 229 (262)
.+++..|+.++|+.|..-|..|+|..+....+ .|.|+ -.+|..++ --.|||+++-
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 34678899999999999999999999965433 33343 34554433 3346666655
No 50
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=84.39 E-value=1.4 Score=35.56 Aligned_cols=37 Identities=22% Similarity=0.504 Sum_probs=29.4
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 024793 173 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 212 (262)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d 212 (262)
+++..|+.+.|+.|++-|.+|+|..+.... ..|++++
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 39 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKK---NKVIVEG 39 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence 367889999999999999999999996532 2455544
No 51
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=80.17 E-value=4.4 Score=30.11 Aligned_cols=50 Identities=28% Similarity=0.527 Sum_probs=38.7
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEcc
Q 024793 177 VGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 230 (262)
Q Consensus 177 ~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~ 230 (262)
+|..|+|-.|.+.-|+|.++.-|... ++|.+| | ++...+.-+..+..+|-
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~iv-i---~~q~i~velkdivlvgv 55 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIV-I---GEQSIDVELKDIVLVGV 55 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEE-E---CCeEEEEEeeeEEEEEe
Confidence 48899999999999999999988877 446665 2 34566777777777773
No 52
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=78.20 E-value=3.3 Score=33.56 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=25.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024793 174 KFDVGNIVMVTGGRNRGRVGIIKNREKH 201 (262)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (262)
++..|+.+.|+.|+.-|..|+|..+...
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5778999999999999999999999653
No 53
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=76.15 E-value=5.2 Score=39.56 Aligned_cols=40 Identities=23% Similarity=0.283 Sum_probs=35.1
Q ss_pred HHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024793 44 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 84 (262)
Q Consensus 44 L~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypV 84 (262)
++-+|-+ .+++.+.+|||+.+.+|-|++||.++.|..++.
T Consensus 338 ~~~~lv~-~~L~psr~earr~i~~g~v~in~~~v~d~~~~~ 377 (401)
T COG0162 338 LVDLLVD-AGLAPSRSEARRLIQQGGVKINGEKVEDENYVL 377 (401)
T ss_pred HHHHHHH-hCCcccHHHHHhhcccCCEEECCEeccccccch
Confidence 4444555 699999999999999999999999999999887
No 54
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=60.93 E-value=13 Score=30.36 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.6
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024793 173 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 201 (262)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (262)
++...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45667999999999999999999988553
No 55
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=60.76 E-value=8.8 Score=32.28 Aligned_cols=26 Identities=35% Similarity=0.552 Sum_probs=24.1
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
+++|-.|+++.|+.+|+-.+|..+..
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iD 30 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIID 30 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEcc
Confidence 68899999999999999999999865
No 56
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=60.50 E-value=53 Score=36.20 Aligned_cols=55 Identities=27% Similarity=0.387 Sum_probs=41.9
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE--cCCCCeEeEeeceEEEEccCCC
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ--DALGHEFATRLGNVFTIGKGSK 233 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~--d~~g~~F~T~~~~vfvIG~~~~ 233 (262)
...++.+-+++|.|.|+-|.|.+|-+. +--+|-. -.++-.|.+...|+..+|. .+
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~---~~F~h~r~~~En~Gv~vck~k~~~~~g~-~~ 638 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRP---FVFLHSRKNLENGGVFVCKEKNLILAGG-KK 638 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecc---eeeeeehhhcccCCeEEEecCCceeccc-cC
Confidence 456899999999999999999999652 2222211 1566789999999999995 44
No 57
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=59.61 E-value=11 Score=31.98 Aligned_cols=27 Identities=15% Similarity=0.362 Sum_probs=24.6
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEe
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNREKH 201 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (262)
.|+|-+|+|.-|.+.|+.++|++|..+
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~ 34 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP 34 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC
Confidence 378999999999999999999999764
No 58
>PF14001 YdfZ: YdfZ protein
Probab=53.86 E-value=21 Score=26.91 Aligned_cols=42 Identities=26% Similarity=0.496 Sum_probs=29.6
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEec------CCccEEEEEcCCCCeEe
Q 024793 174 KFDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 219 (262)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~~------~s~~~v~i~d~~g~~F~ 219 (262)
++.+|+.+|+.| +|.+|+|+.|...- .....|.+++.+| .|+
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 68888999996532 2234787887776 465
No 59
>PRK04333 50S ribosomal protein L14e; Validated
Probab=49.84 E-value=18 Score=28.26 Aligned_cols=27 Identities=30% Similarity=0.517 Sum_probs=24.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 174 KFDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
.++.|-+|++.-|+..|+..+|.++..
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d 29 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIID 29 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEec
Confidence 468899999999999999999999844
No 60
>PF12005 DUF3499: Protein of unknown function (DUF3499); InterPro: IPR021888 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Probab=48.35 E-value=7.7 Score=32.64 Aligned_cols=23 Identities=48% Similarity=0.993 Sum_probs=21.0
Q ss_pred cccccccCCCceecccccceecc
Q 024793 7 KHLKRLNAPKHWMLDKLGGAFAP 29 (262)
Q Consensus 7 kHlKRl~AP~~W~i~kk~~~~a~ 29 (262)
.|-.||+||+-|.+=|....|++
T Consensus 46 ~Ha~rlTaP~GWevvR~~~~~~~ 68 (123)
T PF12005_consen 46 EHAERLTAPRGWEVVRLEGPFAP 68 (123)
T ss_pred HHHhcccCCCCcEEEeccCCCCC
Confidence 58899999999999999998873
No 61
>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=45.88 E-value=17 Score=31.34 Aligned_cols=51 Identities=24% Similarity=0.159 Sum_probs=41.3
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCc-----eEEECCEEecccCCCCCcce---eEEecc
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPK 94 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g-----~V~VdGkvr~d~~ypVG~mD---VIsI~~ 94 (262)
...+|+-+||++|++-.+ |.=+.+| -|+|||+.++.-.+|+.-+| |++|.-
T Consensus 17 ~~~~Ll~~LR~~lgltg~----K~gC~~G~CGACtVlvdg~~v~SCl~~~~~~~G~~V~TiEg 75 (148)
T TIGR03193 17 DNMLLVDYLRDTVGLTGT----KQGCDGGECGACTVLVDGRPRLACSTLAHRVAGRKVETVEG 75 (148)
T ss_pred CCCcHHHHHHHhcCCCCC----CCCCCCCCCCCCEEEECCeEeeccHhhHhhcCCCcEEEeCC
Confidence 468899999999987654 4556666 69999999999999988776 788865
No 62
>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=45.88 E-value=20 Score=34.89 Aligned_cols=46 Identities=17% Similarity=-0.030 Sum_probs=37.8
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcc
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 87 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~m 87 (262)
++++.=++.. .+++.+.+||++.+++|-|.|||..++|..+-...+
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~~ 374 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKEA 374 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhccc
Confidence 4666666664 699999999999999999999999999987655443
No 63
>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=43.42 E-value=1.5e+02 Score=22.78 Aligned_cols=42 Identities=14% Similarity=0.376 Sum_probs=29.7
Q ss_pred CcccCCeEEEecCCCeeeeEEEeeC-------CcEEEEECCCcceeEEEEEeE
Q 024793 153 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRGRVGIIKNR 198 (262)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f~~-------G~~~~v~gG~n~G~vG~I~~i 198 (262)
.++.||...+.|...+-+ .+|+ |...+-..|..+| .|.|.+|
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 589999999999755533 3443 7777767777766 5888654
No 64
>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=42.82 E-value=67 Score=24.99 Aligned_cols=48 Identities=19% Similarity=0.320 Sum_probs=30.3
Q ss_pred CCC-CcccCCeEEEecCCCeeeeEEEeeC----CcEEEEECCCcceeEEEEEeE
Q 024793 150 PDP-LIKANDTIKLDLEENKITDFIKFDV----GNIVMVTGGRNRGRVGIIKNR 198 (262)
Q Consensus 150 ~d~-~ik~~Dtv~i~l~~~kI~~~i~f~~----G~~~~v~gG~n~G~vG~I~~i 198 (262)
.+| .++.||...+.+...+=+-.=+|+. |-.++--+|+.+| +|.|.+|
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 344 6899999999986554221122322 6666667777766 7887653
No 65
>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=41.46 E-value=17 Score=27.14 Aligned_cols=32 Identities=31% Similarity=0.452 Sum_probs=21.5
Q ss_pred ccchHHHHHHhhhcccc-CHHHHHHHHhCceEEECC
Q 024793 40 ECLPLILVLRNRLKYAL-TYREVIAILMQRHVLVDG 74 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~-t~rEar~Il~~g~V~VdG 74 (262)
|.+||.+++ |++|. +..||-+-+.+|.-.|+-
T Consensus 22 EmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~ 54 (62)
T PF08828_consen 22 EMMPLMYVI---LKYADADVEEASRRIDEAKNVVNE 54 (62)
T ss_dssp GGHHHHHHH---HHHTTT-HHHHHHHHHH-------
T ss_pred HHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHH
Confidence 789999887 88899 899999999888766654
No 66
>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=40.56 E-value=31 Score=30.17 Aligned_cols=29 Identities=34% Similarity=0.417 Sum_probs=24.7
Q ss_pred cccchHHHHHHhhhccccCHHHHHHHHhCc
Q 024793 39 RECLPLILVLRNRLKYALTYREVIAILMQR 68 (262)
Q Consensus 39 ~~siPL~i~LRdrLg~A~t~rEar~Il~~g 68 (262)
...+|..+++|..|. |.|..||..++.+-
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 669999999999999 99999999999854
No 67
>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=40.08 E-value=77 Score=26.26 Aligned_cols=83 Identities=18% Similarity=0.261 Sum_probs=46.5
Q ss_pred eEEEEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCeeeeEEEeeCCcEEEEECCCc
Q 024793 109 FRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRN 188 (262)
Q Consensus 109 f~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n 188 (262)
+++...+.+++.+. .|.+ ..|+..+...+|+....++..+..--... -.+........|++|+.+.|++|.-
T Consensus 51 YvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~~--~~~~~~~~~~~~~~G~~V~V~~GPf 122 (159)
T TIGR01955 51 YLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQYE--PKDSVPPATTLPYKGDKVRITDGAF 122 (159)
T ss_pred eEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhcc--ccccCCccccCCCCCCEEEEeccCC
Confidence 34556665554332 2211 24566665555655555553222111000 0011112335699999999999999
Q ss_pred ceeEEEEEeEE
Q 024793 189 RGRVGIIKNRE 199 (262)
Q Consensus 189 ~G~vG~I~~i~ 199 (262)
.|..|.|.++.
T Consensus 123 ~g~~g~v~~~~ 133 (159)
T TIGR01955 123 AGFEAIFLEPD 133 (159)
T ss_pred CCcEEEEEEEC
Confidence 99999999985
No 68
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.04 E-value=35 Score=34.30 Aligned_cols=40 Identities=15% Similarity=0.166 Sum_probs=34.9
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccC
Q 024793 41 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKT 81 (262)
Q Consensus 41 siPL~i~LRdrLg~A~t~rEar~Il~~g~V~VdGkvr~d~~ 81 (262)
.++++=++|+ ++.-.+..||+++++||-|.+|++.++|++
T Consensus 398 ~~s~~~l~~k-a~~~~s~~~a~r~i~qG~vslnh~~v~~es 437 (467)
T KOG2623|consen 398 GVSILDLLRK-ASRFPSGKEARRMIQQGGVSLNHEKVRDES 437 (467)
T ss_pred CCcHHHHHHH-hhcCCCcHHHHHHHHccceeecCccccCch
Confidence 6788888888 677778889999999999999999999954
No 69
>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=38.23 E-value=77 Score=22.22 Aligned_cols=38 Identities=24% Similarity=0.288 Sum_probs=30.4
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCcc-EEEEEc
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFE-TIHIQD 212 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~-~v~i~d 212 (262)
|++|..+++.-+...-.-++|.+++...+... .||-.+
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~g 39 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQG 39 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEETT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcCC
Confidence 68899999999999999999999988666655 777753
No 70
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=37.60 E-value=34 Score=25.77 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=28.1
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEec------CCccEEEEEcCCCCeEe
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 219 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~~------~s~~~v~i~d~~g~~F~ 219 (262)
+..|+.+||.| +|++|+|+.|...- .....|.++..+| .|+
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 35689999987 68888999986521 2234777876655 465
No 71
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=37.08 E-value=1.4e+02 Score=22.43 Aligned_cols=57 Identities=16% Similarity=0.191 Sum_probs=38.4
Q ss_pred eEEecccCcceeeee-ecCCceEEEEeChhhh----c------ceeEEEEeEEEeeCCceEEEccCCe
Q 024793 89 VVSIPKTNENFRLLY-DTKGRFRLHSLRDEEA----K------FKLCKVRSVQFGQKGIPYINTYDGR 145 (262)
Q Consensus 89 VIsI~~t~e~fR~l~-d~kgrf~~~~I~~eea----~------~KLcKV~~k~~~~~g~~ql~~hDGr 145 (262)
|.++.+.+.++.+.. |..|.+....-..++. . =.+.+|.++...-+|.+||..+.=+
T Consensus 8 V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~ 75 (95)
T cd04478 8 VRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIR 75 (95)
T ss_pred EEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEE
Confidence 556666677777777 8788775443332221 1 2588999988888999999876333
No 72
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=36.61 E-value=58 Score=23.31 Aligned_cols=27 Identities=30% Similarity=0.271 Sum_probs=21.7
Q ss_pred hCceEEECCEEecc--cCCCCCcceeEEe
Q 024793 66 MQRHVLVDGKVRTD--KTYPAGFMDVVSI 92 (262)
Q Consensus 66 ~~g~V~VdGkvr~d--~~ypVG~mDVIsI 92 (262)
..-.|.|||+.+++ ..+++.=.|.|+|
T Consensus 42 ~~~~v~vN~~~v~~~~~~~~l~~gD~V~i 70 (77)
T PF02597_consen 42 DRVAVAVNGEIVPDDGLDTPLKDGDEVAI 70 (77)
T ss_dssp TTEEEEETTEEEGGGTTTSBEETTEEEEE
T ss_pred ccEEEEECCEEcCCccCCcCcCCCCEEEE
Confidence 33469999999999 6778888888876
No 73
>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=36.10 E-value=75 Score=31.20 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=26.7
Q ss_pred eCCceEEEccCCeeeecCCCCcccCCeEEEecCCCeeeeEEEeeCCcEEEE---ECCCccee
Q 024793 133 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMV---TGGRNRGR 191 (262)
Q Consensus 133 ~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v---~gG~n~G~ 191 (262)
.|....+.+.|..|||+- =|+++.+....+++|+.+++ .+|+|.|-
T Consensus 297 ~g~~~svilQnaetIRlv-------------~p~G~~vsVt~Lk~GD~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 297 DGKRISVILQNAETIRLV-------------GPDGEPVSVTELKPGDEVLVYLEEAGRHFGM 345 (354)
T ss_pred CCeEEEEEEecCcEEEEE-------------CCCCCEeeeeecCCCCEEEEEecCCCcccce
Confidence 344445555555555543 34455666666666665554 37888884
No 74
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=35.57 E-value=71 Score=25.74 Aligned_cols=60 Identities=22% Similarity=0.241 Sum_probs=35.6
Q ss_pred CCceEEEccCCeeeecCCCCcccCCeEEEecC------CCeeeeEEEeeCCcEEEEECCCcceeEEEEEe
Q 024793 134 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLE------ENKITDFIKFDVGNIVMVTGGRNRGRVGIIKN 197 (262)
Q Consensus 134 ~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~------~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~ 197 (262)
+...++.|.|||+|.-.=.-+.-.--+.|+-. +.+=++.+++ | .+++.|-|.+-+|-|-|
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~l--G--lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVL--G--LYIIRGENVAVIGEIDE 75 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheee--E--EEEEecCccceeeecch
Confidence 34678899999999522111222222444432 1222334444 3 78999999999998866
No 75
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=35.42 E-value=76 Score=31.07 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=23.5
Q ss_pred eCCceEEEccCCeeeecCCCCcccCCeEEEecCCCeeeeEEEeeCCcEEEEE---CCCccee
Q 024793 133 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVT---GGRNRGR 191 (262)
Q Consensus 133 ~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v~---gG~n~G~ 191 (262)
.|....+.+.|..|||+-. |+|+-+..-.+++|+.+++. +|+|.|.
T Consensus 287 ~g~~~~viLQnaetIrlv~-------------~dG~~vsVt~Lk~GD~VL~~~~~~~RHfG~ 335 (344)
T PRK02290 287 GGKRIRTILQNAETIRLVT-------------PDGKPVSVVDLKPGDEVLGYLEEAARHFGM 335 (344)
T ss_pred CCeEEEEEEecCcEEEEEC-------------CCCCEeeeeecCCCCEEEEEecCCcccccc
Confidence 3445555556666665433 33444444444444444332 6778773
No 76
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=35.23 E-value=85 Score=23.41 Aligned_cols=36 Identities=14% Similarity=0.160 Sum_probs=27.5
Q ss_pred EEeeCCceEEEccCCeeeecCC----CCcccCCeEEEecC
Q 024793 130 QFGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 165 (262)
Q Consensus 130 ~~~~~g~~ql~~hDGrni~~~d----~~ik~~Dtv~i~l~ 165 (262)
+.+......|.|.||.++..|. +.+++|..|++-..
T Consensus 10 ~~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 10 KSIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYD 49 (61)
T ss_pred EEEcCCceEEEecCCCEEECCCcccccccCCCCEEEEEEE
Confidence 4456677889999999998774 36888888877554
No 77
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=35.22 E-value=58 Score=27.57 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=26.6
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024793 173 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 201 (262)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (262)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999764
No 78
>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=35.02 E-value=85 Score=24.23 Aligned_cols=20 Identities=35% Similarity=0.333 Sum_probs=16.1
Q ss_pred eEEEEEeEEEecCCccEEEE
Q 024793 191 RVGIIKNREKHKGSFETIHI 210 (262)
Q Consensus 191 ~vG~I~~i~~~~~s~~~v~i 210 (262)
++|+|.+.+.|+++..+..+
T Consensus 2 ~vg~I~~~~~hp~sdkL~~~ 21 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYVL 21 (95)
T ss_dssp EEEEEEEEEEETTSSSEEEE
T ss_pred EEEEEEEEEECCCCCEEEEE
Confidence 68999999999988664443
No 79
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=34.88 E-value=39 Score=28.88 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=21.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeE
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNR 198 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i 198 (262)
+.+|..++|..|+.+|+-++|...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999998775
No 80
>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=34.40 E-value=13 Score=32.02 Aligned_cols=51 Identities=25% Similarity=0.144 Sum_probs=38.8
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCc-----eEEECCEEecccCCCCCcce---eEEecc
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPK 94 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g-----~V~VdGkvr~d~~ypVG~mD---VIsI~~ 94 (262)
...+|+-+||++|++-.+.. =+.+| .|+|||+.++.--.|+.-+| |.+|.-
T Consensus 19 ~~~~Ll~~LR~~~~ltgtK~----gC~~G~CGACtVlvdG~~v~SCl~~~~~~~G~~v~TiEg 77 (151)
T TIGR03198 19 PTTRLSDLLRKELQLTGTKV----SCGIGRCGACSVLIDGKLANACLTMAYQADGHEITTIEG 77 (151)
T ss_pred CCcHHHHHHHhccCCCCCCC----CCCCCcCCccEEEECCcEEechHHHHHHhcCCEEEecCC
Confidence 47899999999999876653 26666 69999999888777775544 566643
No 81
>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=33.62 E-value=70 Score=26.42 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=24.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 175 FDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
|.+|+.+-|+.|.=.|..|.|.++..
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 82
>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=33.46 E-value=2e+02 Score=21.20 Aligned_cols=66 Identities=17% Similarity=0.168 Sum_probs=38.3
Q ss_pred EEEeeCCceEEEccCCeeeecC-CCCc-----ccCCeEEEecCCCeeeeEEEeeCCc-EEEEECCCcceeEEE
Q 024793 129 VQFGQKGIPYINTYDGRTIRYP-DPLI-----KANDTIKLDLEENKITDFIKFDVGN-IVMVTGGRNRGRVGI 194 (262)
Q Consensus 129 k~~~~~g~~ql~~hDGrni~~~-d~~i-----k~~Dtv~i~l~~~kI~~~i~f~~G~-~~~v~gG~n~G~vG~ 194 (262)
..|..++..+|.+.||..+... +..+ .-.+...+.|..|++.=.++=.... +.+-|....++-.|+
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 4577889999999999999654 3334 3444555666666653222222222 445555444444443
No 83
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=33.03 E-value=4.2e+02 Score=24.87 Aligned_cols=61 Identities=23% Similarity=0.312 Sum_probs=39.4
Q ss_pred CCCCcccCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEE
Q 024793 150 PDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 228 (262)
Q Consensus 150 ~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvI 228 (262)
++.+++.||.|+-+=-.+. |.+|= -||+|..++.+. +.+..+.++-.. ..+.+.|||++
T Consensus 209 ~~~~i~~GD~vvTSGlgg~------fP~Gl-----------~Vg~V~~v~~~~~~~~~~v~~~P~a---~~~~l~~v~l~ 268 (284)
T COG1792 209 PNSDIKEGDLVVTSGLGGV------FPAGL-----------PVGEVSSVKLDDYGLFKVVIVKPAA---SLDRLRYVLLV 268 (284)
T ss_pred CCCCccCCCEEEecCCCCc------CCCCc-----------EEEEEEEEEeCCCceeEEEEEeccc---ccccceEEEEE
Confidence 4557888885554433332 22221 278888888766 556677776544 47889999999
Q ss_pred cc
Q 024793 229 GK 230 (262)
Q Consensus 229 G~ 230 (262)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 85
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=32.44 E-value=84 Score=22.88 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=24.4
Q ss_pred CCceEEEccCCeeeecCCCCcccCCeEEEecCCCeee
Q 024793 134 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 170 (262)
Q Consensus 134 ~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 170 (262)
+..-...+..|-.|.+| +-|+.||.|+||-.+++-+
T Consensus 19 ~~~K~A~letG~~i~VP-~FI~~Gd~I~VdT~~g~Yv 54 (56)
T PF09285_consen 19 SSYKPATLETGAEIQVP-LFIEEGDKIKVDTRDGSYV 54 (56)
T ss_dssp TTEEEEEETTS-EEEEE-TT--TT-EEEEETTTTEEE
T ss_pred CCccEEEEcCCCEEEcc-ceecCCCEEEEECCCCeEe
Confidence 33445677888888877 4799999999999988644
No 85
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=32.18 E-value=1.2e+02 Score=22.29 Aligned_cols=23 Identities=26% Similarity=0.098 Sum_probs=20.0
Q ss_pred eEEECCEEecccCCCCCcceeEEe
Q 024793 69 HVLVDGKVRTDKTYPAGFMDVVSI 92 (262)
Q Consensus 69 ~V~VdGkvr~d~~ypVG~mDVIsI 92 (262)
.|.|||+.+.+ ..++.=.|.|+|
T Consensus 51 ~v~vn~~~v~~-~~~l~dgDevai 73 (80)
T TIGR01682 51 MVAVNEEYVTD-DALLNEGDEVAF 73 (80)
T ss_pred EEEECCEEcCC-CcCcCCCCEEEE
Confidence 58999999886 789999998887
No 86
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=31.45 E-value=44 Score=25.64 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.1
Q ss_pred eeecCCCCcccCCeEEEe
Q 024793 146 TIRYPDPLIKANDTIKLD 163 (262)
Q Consensus 146 ni~~~d~~ik~~Dtv~i~ 163 (262)
-||..|.+|++||.+.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 357789999999999884
No 87
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=31.26 E-value=2.3e+02 Score=22.01 Aligned_cols=55 Identities=20% Similarity=0.048 Sum_probs=35.1
Q ss_pred eeEEecccCcceeeee-ecCCceEE-EEeChhh--------------------------hcceeEEEEeEEEeeCCceEE
Q 024793 88 DVVSIPKTNENFRLLY-DTKGRFRL-HSLRDEE--------------------------AKFKLCKVRSVQFGQKGIPYI 139 (262)
Q Consensus 88 DVIsI~~t~e~fR~l~-d~kgrf~~-~~I~~ee--------------------------a~~KLcKV~~k~~~~~g~~ql 139 (262)
=|+++.+...++.... |..|.+.. .|...+. .--.++||.+.-..-.|..||
T Consensus 5 ~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~frg~~ql 84 (92)
T cd04483 5 TVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGEREI 84 (92)
T ss_pred EEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccCCeeEE
Confidence 4778877766666665 77777633 3333220 112478888877777888888
Q ss_pred Ecc
Q 024793 140 NTY 142 (262)
Q Consensus 140 ~~h 142 (262)
+.+
T Consensus 85 ~i~ 87 (92)
T cd04483 85 NAS 87 (92)
T ss_pred EEE
Confidence 875
No 88
>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=31.09 E-value=1.1e+02 Score=23.51 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=24.7
Q ss_pred CcccCCeEEEecCCCeeeeEEEeeC-------CcEEEEECCCcce
Q 024793 153 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRG 190 (262)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f~~-------G~~~~v~gG~n~G 190 (262)
.++.||...+.|...+ -+.+|+ |..+++-+|..+|
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 5899999999986544 345565 7777777666655
No 89
>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=30.16 E-value=2.1e+02 Score=21.56 Aligned_cols=41 Identities=17% Similarity=0.417 Sum_probs=25.3
Q ss_pred CcccCCeEEEecCCCeeeeEEEeeCCcEEEE-ECCCcceeEEEEEe
Q 024793 153 LIKANDTIKLDLEENKITDFIKFDVGNIVMV-TGGRNRGRVGIIKN 197 (262)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v-~gG~n~G~vG~I~~ 197 (262)
.+++||+..+.+.-.+ -+.++.|.-.++ .+|+.+| .|+|.+
T Consensus 51 ~l~~g~~~~v~i~l~~---p~~~~~g~rf~lR~~~~tvg-~G~V~~ 92 (93)
T cd03706 51 MVMPGEDTKVTLILRR---PMVLEKGQRFTLRDGNRTIG-TGLVTD 92 (93)
T ss_pred EeCCCCEEEEEEEECC---cEEEeeCCEEEEEECCEEEE-EEEEEe
Confidence 3788988887776332 234555666555 5665555 677654
No 90
>KOG2404 consensus Fumarate reductase, flavoprotein subunit [Energy production and conversion]
Probab=29.89 E-value=88 Score=31.18 Aligned_cols=79 Identities=22% Similarity=0.273 Sum_probs=54.1
Q ss_pred cccccceeccCCCCCCCCCcccchHHHHHHhhh-ccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcc
Q 024793 20 LDKLGGAFAPKPSSGPHKSRECLPLILVLRNRL-KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 98 (262)
Q Consensus 20 i~kk~~~~a~kpspGPH~~~~siPL~i~LRdrL-g~A~t~rEar~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~ 98 (262)
+++.+|-=+||+.-+.|++--..|+.-.|+++| ++|.+--|+-||..+-. +++...--=.+.-|.=.++++|.
T Consensus 117 la~lgGHSvpRTHr~s~plppgfei~~~L~~~l~k~as~~pe~~ki~~nsk------vv~il~n~gkVsgVeymd~sgek 190 (477)
T KOG2404|consen 117 LAQLGGHSVPRTHRSSGPLPPGFEIVKALSTRLKKKASENPELVKILLNSK------VVDILRNNGKVSGVEYMDASGEK 190 (477)
T ss_pred HHHhcCCCCCcccccCCCCCCchHHHHHHHHHHHHhhhcChHHHhhhhcce------eeeeecCCCeEEEEEEEcCCCCc
Confidence 456778889999999999999999999999999 47888889999887543 33322211223333333455555
Q ss_pred eeeeee
Q 024793 99 FRLLYD 104 (262)
Q Consensus 99 fR~l~d 104 (262)
-.+++|
T Consensus 191 ~~~~~~ 196 (477)
T KOG2404|consen 191 SKIIGD 196 (477)
T ss_pred cceecC
Confidence 555443
No 91
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=28.43 E-value=1.8e+02 Score=32.62 Aligned_cols=159 Identities=15% Similarity=0.217 Sum_probs=106.4
Q ss_pred HHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEcc
Q 024793 63 AILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTY 142 (262)
Q Consensus 63 ~Il~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~h 142 (262)
+....|.|.+++++.-.|+.-+.-.+.=.+...+++|++. .+|-|....++.+.|..--|-.+|+.=--....+|..-
T Consensus 437 ~a~~g~~v~i~C~~~asP~p~~~W~k~~~~~~~~~r~~i~--edGtL~I~n~t~~DaG~YtC~A~N~~G~a~~~~~L~Vk 514 (1051)
T KOG3513|consen 437 MAVVGGTVTIDCKPFASPKPKVSWLKGGEKLLQSGRIRIL--EDGTLEISNVTRSDAGKYTCVAENKLGKAESTGNLIVK 514 (1051)
T ss_pred EEEeCCeEEEeeccCCCCcceEEEEcCCcccccCceEEEC--CCCcEEecccCcccCcEEEEEEEcccCccceEEEEEEe
Confidence 3445668888888888887766655555544567788775 45788888999999998999999988666778888889
Q ss_pred CCeeeecC--CCCcccCCeEEEecCCC---------------eeeeEEEeeCCcEEEEECCCcceeEEEEEeEEE-ecCC
Q 024793 143 DGRTIRYP--DPLIKANDTIKLDLEEN---------------KITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK-HKGS 204 (262)
Q Consensus 143 DGrni~~~--d~~ik~~Dtv~i~l~~~---------------kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~-~~~s 204 (262)
|-.-|..+ ...++.|+++.+.-+.. ..+|+- ..|.-..+.+|.+.|+.= |.++.- +.|+
T Consensus 515 d~tri~~~P~~~~v~~g~~v~l~Ce~shD~~ld~~f~W~~nG~~id~~--~~~~~~~~~~~~~~g~L~-i~nv~l~~~G~ 591 (1051)
T KOG3513|consen 515 DATRITLAPSNTDVKVGESVTLTCEASHDPSLDITFTWKKNGRPIDFN--PDGDHFEINDGSDSGRLT-IANVSLEDSGK 591 (1051)
T ss_pred cCceEEeccchhhhccCceEEEEeecccCCCcceEEEEEECCEEhhcc--CCCCceEEeCCcCccceE-EEeeccccCce
Confidence 99888653 23689999999876632 222222 246677788888777753 355543 3366
Q ss_pred cc-EEEEEcCCCCeEeEeeceEEEEcc
Q 024793 205 FE-TIHIQDALGHEFATRLGNVFTIGK 230 (262)
Q Consensus 205 ~~-~v~i~d~~g~~F~T~~~~vfvIG~ 230 (262)
.. +|.. ..++ .+....++|-|-
T Consensus 592 Y~C~aqT---~~Ds-~s~~A~l~V~gp 614 (1051)
T KOG3513|consen 592 YTCVAQT---ALDS-ASARADLLVRGP 614 (1051)
T ss_pred EEEEEEE---eecc-hhcccceEEecC
Confidence 55 3322 1111 344456677774
No 92
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=28.35 E-value=1.4e+02 Score=25.28 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=26.2
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 172 FIKFDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
...|.+|+.+-|++|.=.|..|.|.++..
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 93
>PF01063 Aminotran_4: Aminotransferase class IV; InterPro: IPR001544 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the pyridoxal-phosphate-lysine. The D-amino acid transferases (D-AAT), which are among the members of this entry, are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity [, ]. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1EKV_A 2HGX_A 1EKP_A 1KTA_B 1KT8_B 2A1H_B 2HDK_A 2HGW_B 1EKF_B 2HG8_A ....
Probab=27.36 E-value=2e+02 Score=24.75 Aligned_cols=52 Identities=17% Similarity=0.160 Sum_probs=37.9
Q ss_pred ccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHH
Q 024793 205 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAA 258 (262)
Q Consensus 205 ~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~~~gi~~~~~~~~~~~~~~ 258 (262)
++-+.+-|.+|+.-|+..+|+|++= +.-|++-|.+.|+-..+..+.-.++++
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 4445577999999999999999984 455889998888877776665544443
No 94
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=27.18 E-value=2.2e+02 Score=30.98 Aligned_cols=59 Identities=15% Similarity=0.193 Sum_probs=42.9
Q ss_pred ecCCceEEEEeCh---hhhcceeEEEE----eEEEeeCCceEEEccCCeeeecCCCCcccCCeEEE
Q 024793 104 DTKGRFRLHSLRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKL 162 (262)
Q Consensus 104 d~kgrf~~~~I~~---eea~~KLcKV~----~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i 162 (262)
|..++.+..+++. -++.-||.||+ ....++.+++.++..||.-......++++||-|.+
T Consensus 130 d~~~k~~~~~v~~v~r~~~~~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~~a~~l~~GD~i~~ 195 (858)
T PRK14898 130 DQDEKVHWKRIISVIRHKANGKLIKIKTESGRTIRATPYHSFVTRKDNEVIPVEGSELKIGDWLPV 195 (858)
T ss_pred CCCCcEEEEEeeeEEeccCCCcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEeeHHhCCCCCEEee
Confidence 5556666655543 23334888888 45678899999999999877656668999998755
No 95
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=27.11 E-value=43 Score=29.22 Aligned_cols=51 Identities=27% Similarity=0.204 Sum_probs=37.6
Q ss_pred cccchHHHHHHhhhccccCHHHHHHHHhCc-----eEEECCEEecccCCCCCcc---eeEEec
Q 024793 39 RECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFM---DVVSIP 93 (262)
Q Consensus 39 ~~siPL~i~LRdrLg~A~t~rEar~Il~~g-----~V~VdGkvr~d~~ypVG~m---DVIsI~ 93 (262)
+...||+=+|||.|++.-|- .=+.+| -|+|||+.++.--.|+-.. +|.+|.
T Consensus 18 ~p~~~Ll~~LRd~l~ltgtk----~GC~~g~CGACtVlvDG~~v~SCl~~a~~~~G~~ItTiE 76 (156)
T COG2080 18 DPRTPLLDVLRDELGLTGTK----KGCGHGQCGACTVLVDGEAVNSCLTLAVQAEGAEITTIE 76 (156)
T ss_pred CCCChHHHHHHHhcCCCCcC----CCCCCccCCceEEEECCeEehHHHHHHHHhCCCeEEEee
Confidence 34679999999999998764 344444 7999999999887776554 344443
No 96
>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=26.77 E-value=2.6e+02 Score=20.45 Aligned_cols=55 Identities=13% Similarity=0.123 Sum_probs=30.7
Q ss_pred eCCcEEEEECCCcceeEE-EEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEcc
Q 024793 176 DVGNIVMVTGGRNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 230 (262)
Q Consensus 176 ~~G~~~~v~gG~n~G~vG-~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~ 230 (262)
.+|+.++...+.+..... .+.......+..+++.|+..+|.++..-.+.-|.+..
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 456666666553222111 1122222335566888888888887766666666664
No 97
>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=26.30 E-value=1.1e+02 Score=22.27 Aligned_cols=34 Identities=24% Similarity=0.388 Sum_probs=26.2
Q ss_pred CCceEEEccCCeeeecCCCCcccCCeEEEecCCCe
Q 024793 134 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 168 (262)
Q Consensus 134 ~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 168 (262)
++.-...+..|-.|.+| +-|+.||.|++|-.+++
T Consensus 19 ~~~K~A~letG~~i~VP-~FI~~Gd~I~V~T~~g~ 52 (56)
T cd05794 19 SGTKPATLETGAEVQVP-LFIKEGEKIKVDTRTGE 52 (56)
T ss_pred CCcceEEECCCCEEEcC-CeecCCCEEEEECCCCc
Confidence 33334567888888876 46899999999999876
No 98
>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=25.84 E-value=1.4e+02 Score=22.23 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=18.0
Q ss_pred ccCCeEEEecC-----CCeeeeEEEeeCCcEEEE
Q 024793 155 KANDTIKLDLE-----ENKITDFIKFDVGNIVMV 183 (262)
Q Consensus 155 k~~Dtv~i~l~-----~~kI~~~i~f~~G~~~~v 183 (262)
|+||.|.+.-. ++.|+..=+|.+|-+.+|
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 56776666654 455666666666665554
No 99
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=25.77 E-value=52 Score=26.80 Aligned_cols=51 Identities=16% Similarity=0.293 Sum_probs=27.0
Q ss_pred EeChhhhcceeEEEEeEEE-eeCCceEEEccCCeeeecCCCCcccCCeEEEecCC
Q 024793 113 SLRDEEAKFKLCKVRSVQF-GQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEE 166 (262)
Q Consensus 113 ~I~~eea~~KLcKV~~k~~-~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~ 166 (262)
.|+.+...+++++...+.- +.....++.+.|.+.+ +|++++||++.+.++-
T Consensus 45 ~id~~~g~i~v~~~~~VV~d~~d~~~eI~l~eAk~~---~~~~~vGD~i~~~i~~ 96 (122)
T PF08529_consen 45 EIDEDTGEIKVYRKKEVVEDVEDPDTEISLSEAKKI---DPNAEVGDEIEEEIDP 96 (122)
T ss_dssp EEETTTTEEEEEEEEEEETT-S-TTTEEEHHHHHCC---CTT--TTCEEEEE---
T ss_pred EEECCCCeEEEEEEeeecCCccCccceeeHHHHHhh---CCCCccCCEEEecCCh
Confidence 4455555555555322111 2345667777777655 5789999999988863
No 100
>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=25.04 E-value=1.6e+02 Score=24.77 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=25.4
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 173 IKFDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5588999999999999999999999854
No 101
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=24.65 E-value=1.2e+02 Score=31.35 Aligned_cols=42 Identities=17% Similarity=0.196 Sum_probs=32.6
Q ss_pred CCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 157 NDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 157 ~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
+|+..|+.|.+.+-. -|..|+++-|+.|.+.+.+|.|..|+.
T Consensus 124 ~~~~rl~~p~~~lRk--~f~~gD~vkVI~g~~~~d~g~V~rI~~ 165 (607)
T COG5164 124 HFEQRLCGPWGRLRK--GFYKGDLVKVIEGGEMVDIGTVPRIDG 165 (607)
T ss_pred ccCceeecchhhhhc--ccccCCeEEEeccccccccceEEEecC
Confidence 355566666555443 378899999999999999999999965
No 102
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=24.48 E-value=2.9e+02 Score=20.23 Aligned_cols=52 Identities=12% Similarity=0.093 Sum_probs=30.7
Q ss_pred Ccceeeee-ecCCceEEEEeChh-hhc---ceeEEEE-eEEEeeCCceEEEccCCeee
Q 024793 96 NENFRLLY-DTKGRFRLHSLRDE-EAK---FKLCKVR-SVQFGQKGIPYINTYDGRTI 147 (262)
Q Consensus 96 ~e~fR~l~-d~kgrf~~~~I~~e-ea~---~KLcKV~-~k~~~~~g~~ql~~hDGrni 147 (262)
+..+.+.. |..|...+.--+.. ... =+.++++ .+...-+|.+||++.+...|
T Consensus 22 ~~~~~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~~~i 79 (82)
T cd04491 22 GKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEI 79 (82)
T ss_pred eEEEEEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEEecCCcEEEEeCCceEE
Confidence 33444444 77776654433433 111 1477888 56666678899988876665
No 103
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=24.38 E-value=1.7e+02 Score=19.52 Aligned_cols=36 Identities=14% Similarity=0.151 Sum_probs=28.5
Q ss_pred EEeChhhhcceeEEEEeEEEeeCCceEEEccCCeeeecC
Q 024793 112 HSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYP 150 (262)
Q Consensus 112 ~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~ 150 (262)
.|++.++..|=++.|.. ..++...+.+.||++..++
T Consensus 4 vWvpD~~egfv~g~I~~---~~g~~vtV~~~~G~~~tv~ 39 (42)
T PF02736_consen 4 VWVPDPKEGFVKGEIIE---EEGDKVTVKTEDGKEVTVK 39 (42)
T ss_dssp EEEEESSSSEEEEEEEE---EESSEEEEEETTTEEEEEE
T ss_pred EEEeCCcccEEEEEEEE---EcCCEEEEEECCCCEEEeC
Confidence 47777777888899984 5788899999999988543
No 104
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=23.94 E-value=1.1e+02 Score=33.77 Aligned_cols=39 Identities=26% Similarity=0.572 Sum_probs=30.3
Q ss_pred EEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024793 161 KLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 201 (262)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (262)
-|+++..+.-.+ |++|+.|=|+.|+|-|..|.|..++.+
T Consensus 448 pl~~~~~eLrKy--F~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 448 PLEVPASELRKY--FEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccccchHhhhhh--ccCCCeEEEEeccccCCcceEEEEeCC
Confidence 344444444333 778999999999999999999999873
No 105
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=23.64 E-value=2e+02 Score=21.15 Aligned_cols=25 Identities=12% Similarity=-0.003 Sum_probs=20.4
Q ss_pred ceEEECCEEecccCCCCCcceeEEec
Q 024793 68 RHVLVDGKVRTDKTYPAGFMDVVSIP 93 (262)
Q Consensus 68 g~V~VdGkvr~d~~ypVG~mDVIsI~ 93 (262)
-.|.|||+.+. ..+++.=+|.|+|=
T Consensus 52 ~~vavN~~~v~-~~~~l~dgDeVai~ 76 (82)
T PLN02799 52 CVLALNEEYTT-ESAALKDGDELAII 76 (82)
T ss_pred cEEEECCEEcC-CCcCcCCCCEEEEe
Confidence 36899999974 77899999988873
No 106
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=23.27 E-value=75 Score=29.85 Aligned_cols=32 Identities=25% Similarity=0.539 Sum_probs=21.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCcc-EEEE
Q 024793 177 VGNIVMVTGGRNRGRVGIIKNREKHKGSFE-TIHI 210 (262)
Q Consensus 177 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~-~v~i 210 (262)
.||.|.|+.|..-|+.|.++.- |-|..- +|.+
T Consensus 60 iGN~A~VvSG~AKG~~G~VtGk--HGGieHVlV~F 92 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTGK--HGGIEHVLVDF 92 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEEE--ETTTTEEEEE-
T ss_pred cCceeEEeecccCCCcCeEecc--cCCeeeEEEEC
Confidence 5999999999999999999874 656643 4433
No 107
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=22.96 E-value=94 Score=25.30 Aligned_cols=36 Identities=14% Similarity=0.355 Sum_probs=28.2
Q ss_pred EEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCe
Q 024793 129 VQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 168 (262)
Q Consensus 129 k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 168 (262)
+.++.+|+.++ +|.... |...+|+||.|.|.+....
T Consensus 28 k~~~~~GrV~v---NG~~aK-pS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 28 KEMIEGGRVKV---NGQRAK-PSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHHHHCCeEEE---CCEEcc-cccccCCCCEEEEEeCCcE
Confidence 34677899888 566665 7778999999999998654
No 108
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=22.77 E-value=4.3e+02 Score=26.19 Aligned_cols=53 Identities=26% Similarity=0.307 Sum_probs=35.1
Q ss_pred CcccCCeEEEecCCCeeeeEEEe----eCCcEEEEECCCcceeEEEEEeEEEecCCcc
Q 024793 153 LIKANDTIKLDLEENKITDFIKF----DVGNIVMVTGGRNRGRVGIIKNREKHKGSFE 206 (262)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f----~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~ 206 (262)
.++.||...+.|.-.+=+-.-+| .-|..++.-+|.-+| .|.|.++....||..
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 57789998888864443322233 246677777776555 899999886666644
No 109
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=22.61 E-value=1.6e+02 Score=21.17 Aligned_cols=26 Identities=23% Similarity=0.207 Sum_probs=21.9
Q ss_pred hCceEEECCEEecccCCCCCcceeEEe
Q 024793 66 MQRHVLVDGKVRTDKTYPAGFMDVVSI 92 (262)
Q Consensus 66 ~~g~V~VdGkvr~d~~ypVG~mDVIsI 92 (262)
..-.|.|||+.+. ..+++.=.|.|+|
T Consensus 48 ~~~~v~vNg~~v~-~~~~l~~gD~v~i 73 (80)
T cd00754 48 ARVRIAVNGEYVR-LDTPLKDGDEVAI 73 (80)
T ss_pred hcEEEEECCeEcC-CCcccCCCCEEEE
Confidence 3447999999998 6789999999986
No 110
>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=21.67 E-value=1.5e+02 Score=21.54 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=25.0
Q ss_pred EEEccCCeeeecCCCCcccCCeEEEecCCCe
Q 024793 138 YINTYDGRTIRYPDPLIKANDTIKLDLEENK 168 (262)
Q Consensus 138 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 168 (262)
...+..|-.|.+| +-|+.||.|+||-.+++
T Consensus 23 ~A~letG~~i~VP-~FI~~Gd~I~V~T~~g~ 52 (56)
T smart00841 23 PATLETGAVVQVP-LFINEGDKIKVDTRTGE 52 (56)
T ss_pred eEEECCCCEEEcC-CcccCCCEEEEECCCCc
Confidence 4557888889877 47999999999998876
No 111
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=21.67 E-value=73 Score=27.58 Aligned_cols=38 Identities=16% Similarity=0.258 Sum_probs=31.6
Q ss_pred cCCCeeeeEEEeeCCcEEEEECCCcce-eEEEEEeEEEe
Q 024793 164 LEENKITDFIKFDVGNIVMVTGGRNRG-RVGIIKNREKH 201 (262)
Q Consensus 164 l~~~kI~~~i~f~~G~~~~v~gG~n~G-~vG~I~~i~~~ 201 (262)
|-..-.+..+|+..++.+-|.+|+..| .+|.|.++-+.
T Consensus 38 LR~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrK 76 (145)
T KOG3401|consen 38 LRQKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRK 76 (145)
T ss_pred HHHHhCccccceeeccEEEEEeccccccccceehhhhhh
Confidence 333345788999999999999999999 99999998663
No 112
>PRK10708 hypothetical protein; Provisional
Probab=21.66 E-value=1.8e+02 Score=21.59 Aligned_cols=29 Identities=21% Similarity=0.428 Sum_probs=17.4
Q ss_pred ccCCeEEEecC-----CCeeeeEEEeeCCcEEEE
Q 024793 155 KANDTIKLDLE-----ENKITDFIKFDVGNIVMV 183 (262)
Q Consensus 155 k~~Dtv~i~l~-----~~kI~~~i~f~~G~~~~v 183 (262)
|+||.|.+.-. ++.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~iLavE~F~EG~MyLv 35 (62)
T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVEEFSEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCCccccceEEEEeeccCcEEEEE
Confidence 56676666654 445666666666655544
No 113
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=21.61 E-value=91 Score=27.42 Aligned_cols=31 Identities=16% Similarity=0.356 Sum_probs=27.3
Q ss_pred eeEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024793 170 TDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 200 (262)
Q Consensus 170 ~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (262)
.....|++|+.+-|+.|.=+|..|+|.++..
T Consensus 119 ~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ 149 (178)
T COG0250 119 KPKVDFEPGDVVRIIDGPFAGFKAKVEEVDE 149 (178)
T ss_pred cccccCCCCCEEEEeccCCCCccEEEEEEcC
Confidence 3456799999999999999999999999954
No 114
>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=20.22 E-value=6.1e+02 Score=22.46 Aligned_cols=103 Identities=18% Similarity=0.295 Sum_probs=59.7
Q ss_pred hCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEeEEEeeCCceEEEc-cCC
Q 024793 66 MQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT-YDG 144 (262)
Q Consensus 66 ~~g~V~VdGkvr~d~~ypVG~mDVIsI~~t~e~fR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~-hDG 144 (262)
..+.|+||||.+-.. +..|+++ |+..+ .|...+. -|.| ++..+.+..-++.+ =||
T Consensus 29 GkrvI~VDGkei~r~---------------~wmfklv----g~e~F-~ig~~~~---k~~I-~I~~~~g~~YeYsL~VdG 84 (177)
T PF06905_consen 29 GKRVIKVDGKEIVRR---------------DWMFKLV----GKETF-TIGGKNT---KCEI-NIEAVSGFAYEYSLEVDG 84 (177)
T ss_dssp --EEEEETTEEEEEE------------------S-------EEEEE-EETTTTE---EEEE-EEEEETTTEEEEEEEETT
T ss_pred CeEEEEECCcEEEEe---------------cceeeeC----cccEE-EECCCce---EEEE-EEEecCCceEEEEEEECC
Confidence 356899999953322 3344443 22222 3332222 2555 33444554444433 489
Q ss_pred eee-ecCCCCcccCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEE
Q 024793 145 RTI-RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGI 194 (262)
Q Consensus 145 rni-~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~ 194 (262)
.++ .|-+...|.-.|..+.+..+ .-.|-|+...+-+=..|......|.
T Consensus 85 ksl~ky~e~~~k~~~tW~~~i~G~--~~RIvLdk~t~~vwvnG~~iet~~e 133 (177)
T PF06905_consen 85 KSLKKYKEEQSKKFNTWELNIDGQ--EYRIVLDKDTMDVWVNGEKIETEGE 133 (177)
T ss_dssp EEEEE--SSTTTTEEEEEEEETTE--EEEEEEETTTTEEEETTCEE--EEE
T ss_pred EEHHHHHHHHhhhheeEEEecCCC--EEEEEEEcceEEEEECCEEccccce
Confidence 999 77888899999999999743 4667788888999999998877664
No 115
>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=20.11 E-value=3.7e+02 Score=23.13 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=26.9
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCc---eEEECCEEecccCCCCCcceeEEecc
Q 024793 40 ECLPLILVLRNRLKYALTYREVIAILMQR---HVLVDGKVRTDKTYPAGFMDVVSIPK 94 (262)
Q Consensus 40 ~siPL~i~LRdrLg~A~t~rEar~Il~~g---~V~VdGkvr~d~~ypVG~mDVIsI~~ 94 (262)
-.+|+.+.-++.--+..-.++..+.+... .+..+-. .+..|=+.+-+..++++
T Consensus 40 i~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~l~f~d~--p~~~y~~~~~~~~~~~~ 95 (249)
T PF05709_consen 40 ITLTFYIIGEDREDFEQKRRELASWLNPKEPVKLIFDDD--PDKYYYAKVSGSPDPDE 95 (249)
T ss_dssp EEEEEEEE-SSHHHHHHHHHHHHHHH--SS-EEEEETTS--TT-EEEEEEEEEEE--S
T ss_pred EEEEEEEEECCHHHHHHHHHHHHHhhCcCCCEEEEEECC--CCEEEEEEECCcccccc
Confidence 35666666666666777788888888544 3333332 12233444555555544
Done!