Query 026062
Match_columns 244
No_of_seqs 111 out of 337
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:17:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026062.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026062hhsearch_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 8E-107 2E-111 729.9 29.1 242 1-242 19-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 2E-106 4E-111 728.0 29.6 243 1-243 19-261 (262)
3 PTZ00223 40S ribosomal protein 100.0 5E-106 1E-110 728.2 29.8 243 1-243 16-259 (273)
4 PRK04313 30S ribosomal protein 100.0 5.2E-99 1E-103 672.1 27.5 221 1-222 15-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 2.2E-95 5E-100 644.1 23.6 223 1-224 18-241 (241)
6 KOG0378 40S ribosomal protein 100.0 2.8E-93 6.2E-98 633.2 15.2 244 1-244 19-262 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 1.1E-34 2.3E-39 219.9 9.7 77 76-152 1-77 (77)
8 PF08071 RS4NT: RS4NT (NUC023) 98.6 1.2E-08 2.7E-13 68.2 1.4 22 1-22 17-38 (38)
9 PF01479 S4: S4 domain; Inter 98.6 1.1E-07 2.5E-12 64.5 5.2 48 24-72 1-48 (48)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.6 0.00028 6E-09 48.4 6.9 62 25-87 2-63 (70)
11 smart00363 S4 S4 RNA-binding d 97.3 0.00082 1.8E-08 44.8 5.4 51 25-76 2-52 (60)
12 COG0522 RpsD Ribosomal protein 96.9 0.00096 2.1E-08 59.3 3.8 53 23-75 85-144 (205)
13 PF00467 KOW: KOW motif; Inte 96.8 0.0013 2.8E-08 41.8 3.1 31 159-192 1-31 (32)
14 smart00739 KOW KOW (Kyprides, 96.8 0.0012 2.6E-08 39.6 2.7 27 156-182 1-27 (28)
15 TIGR02988 YaaA_near_RecF S4 do 96.8 0.0039 8.4E-08 44.2 5.5 51 24-75 9-59 (59)
16 PF13275 S4_2: S4 domain; PDB: 96.0 0.0036 7.8E-08 46.4 1.5 60 22-84 6-65 (65)
17 TIGR01018 rpsD_arch ribosomal 95.7 0.0082 1.8E-07 51.8 3.0 43 33-75 112-156 (162)
18 PTZ00155 40S ribosomal protein 95.6 0.0096 2.1E-07 52.2 2.9 40 25-64 100-146 (181)
19 PRK11507 ribosome-associated p 95.6 0.058 1.3E-06 40.7 6.6 60 22-84 10-69 (70)
20 PLN00189 40S ribosomal protein 95.5 0.012 2.6E-07 52.2 3.0 40 33-72 117-156 (194)
21 PRK04051 rps4p 30S ribosomal p 95.3 0.019 4.1E-07 50.1 3.7 44 34-77 112-157 (177)
22 TIGR01017 rpsD_bact ribosomal 95.2 0.032 7E-07 49.1 4.9 43 34-76 99-141 (200)
23 PRK05327 rpsD 30S ribosomal pr 94.9 0.044 9.5E-07 48.4 5.0 42 35-76 103-144 (203)
24 TIGR00005 rluA_subfam pseudour 94.9 0.11 2.3E-06 47.3 7.7 53 22-75 4-56 (299)
25 TIGR01080 rplX_A_E ribosomal p 94.8 0.065 1.4E-06 43.8 5.4 57 152-211 37-100 (114)
26 CHL00113 rps4 ribosomal protei 94.8 0.045 9.8E-07 48.5 4.8 43 34-76 98-140 (201)
27 TIGR03069 PS_II_S4 photosystem 94.5 0.13 2.8E-06 47.0 7.1 63 22-97 182-244 (257)
28 TIGR00478 tly hemolysin TlyA f 93.8 0.11 2.5E-06 46.5 5.2 48 28-76 4-51 (228)
29 PRK11180 rluD 23S rRNA pseudou 92.3 0.5 1.1E-05 44.0 7.3 53 22-75 16-68 (325)
30 COG2501 S4-like RNA binding pr 92.0 0.36 7.8E-06 36.8 4.9 59 22-83 10-68 (73)
31 COG0564 RluA Pseudouridylate s 91.8 0.58 1.3E-05 43.4 7.0 57 22-81 11-67 (289)
32 PRK05912 tyrosyl-tRNA syntheta 91.7 0.6 1.3E-05 45.3 7.3 65 23-94 342-406 (408)
33 PRK01191 rpl24p 50S ribosomal 90.9 0.61 1.3E-05 38.6 5.6 55 154-211 43-104 (120)
34 PRK10700 23S rRNA pseudouridyl 90.8 0.77 1.7E-05 42.5 6.8 63 28-93 7-81 (289)
35 PRK10348 ribosome-associated h 90.0 0.78 1.7E-05 38.5 5.6 58 23-82 8-65 (133)
36 COG1187 RsuA 16S rRNA uridine- 89.1 0.93 2E-05 41.6 5.9 59 35-94 13-78 (248)
37 PRK10475 23S rRNA pseudouridin 89.0 1.5 3.3E-05 40.7 7.3 67 22-91 5-79 (290)
38 PRK12281 rplX 50S ribosomal pr 88.7 0.7 1.5E-05 35.1 4.0 39 155-196 5-43 (76)
39 PRK11025 23S rRNA pseudouridyl 88.7 1.8 3.9E-05 40.2 7.6 51 23-75 19-69 (317)
40 CHL00141 rpl24 ribosomal prote 88.1 0.84 1.8E-05 35.2 4.1 39 154-195 6-44 (83)
41 PRK10839 16S rRNA pseudouridyl 87.7 3.1 6.7E-05 36.6 8.1 67 26-95 3-75 (232)
42 PRK13354 tyrosyl-tRNA syntheta 87.5 2 4.2E-05 41.9 7.3 66 23-94 342-407 (410)
43 PLN00051 RNA-binding S4 domain 87.4 2.3 5.1E-05 39.2 7.3 62 23-97 191-252 (267)
44 PRK00004 rplX 50S ribosomal pr 87.2 0.85 1.8E-05 36.5 3.9 37 155-194 3-39 (105)
45 COG2302 Uncharacterized conser 86.8 1.5 3.3E-05 40.5 5.7 63 22-97 179-241 (257)
46 COG1189 Predicted rRNA methyla 86.3 1.5 3.2E-05 40.3 5.3 47 35-81 13-59 (245)
47 PTZ00194 60S ribosomal protein 86.2 1.6 3.5E-05 37.1 5.2 55 154-211 44-105 (143)
48 PF13051 DUF3912: Protein of u 84.8 2.5 5.3E-05 31.2 4.8 50 159-212 5-55 (68)
49 TIGR01079 rplX_bact ribosomal 82.4 1.9 4.2E-05 34.5 3.9 28 156-183 3-30 (104)
50 KOG4655 U3 small nucleolar rib 70.6 3.2 6.9E-05 36.4 2.2 55 12-66 87-148 (181)
51 COG0162 TyrS Tyrosyl-tRNA synt 68.3 11 0.00024 36.9 5.7 62 26-95 338-399 (401)
52 COG2163 RPL14A Ribosomal prote 61.0 8.7 0.00019 32.0 3.0 34 157-194 5-38 (125)
53 COG0198 RplX Ribosomal protein 59.2 15 0.00032 29.7 3.9 29 155-183 3-31 (104)
54 PF03417 AAT: Acyl-coenzyme A: 57.6 45 0.00097 28.8 7.0 29 21-50 69-97 (225)
55 PTZ00065 60S ribosomal protein 56.1 14 0.0003 31.1 3.3 33 157-193 8-40 (130)
56 PF14001 YdfZ: YdfZ protein 54.6 20 0.00043 26.8 3.6 42 156-201 9-56 (64)
57 COG1188 Ribosome-associated he 52.0 37 0.00081 27.3 5.1 45 35-80 19-63 (100)
58 PRK04333 50S ribosomal protein 50.8 17 0.00037 28.1 2.9 33 156-192 3-35 (84)
59 PF08828 DSX_dimer: Doublesex 46.3 13 0.00028 27.6 1.5 33 21-56 21-54 (62)
60 TIGR01955 RfaH transcriptional 44.2 67 0.0015 26.3 5.7 84 90-181 50-133 (159)
61 cd03704 eRF3c_III This family 42.2 76 0.0016 24.4 5.4 48 132-180 56-108 (108)
62 TIGR03193 4hydroxCoAred 4-hydr 40.0 25 0.00053 30.1 2.5 54 21-78 16-77 (148)
63 PRK14898 DNA-directed RNA poly 39.9 1.3E+02 0.0029 32.2 8.4 77 66-144 112-195 (858)
64 PF01959 DHQS: 3-dehydroquinat 38.9 62 0.0013 31.5 5.3 46 115-173 297-345 (354)
65 PTZ00471 60S ribosomal protein 38.9 31 0.00067 29.2 2.9 24 157-180 5-28 (134)
66 PF01588 tRNA_bind: Putative t 38.7 68 0.0015 24.5 4.6 24 173-196 2-27 (95)
67 PRK02290 3-dehydroquinate synt 38.2 62 0.0013 31.3 5.1 45 116-173 288-335 (344)
68 TIGR00405 L26e_arch ribosomal 37.5 58 0.0013 26.6 4.3 26 157-182 87-112 (145)
69 PRK08559 nusG transcription an 36.4 56 0.0012 27.3 4.1 29 155-183 93-121 (153)
70 COG1792 MreC Cell shape-determ 35.6 3.7E+02 0.0079 25.0 11.5 61 132-212 209-270 (284)
71 KOG1999 RNA polymerase II tran 35.5 1.1E+02 0.0025 33.5 7.0 55 157-215 582-638 (1024)
72 cd03706 mtEFTU_III Domain III 35.1 1.8E+02 0.0039 21.7 6.4 41 135-179 51-92 (93)
73 PF12961 DUF3850: Domain of Un 34.6 37 0.0008 25.8 2.4 18 128-145 21-38 (72)
74 PF07076 DUF1344: Protein of u 34.3 90 0.002 23.1 4.4 35 113-147 11-49 (61)
75 PF04773 FecR: FecR protein; 34.3 1.8E+02 0.004 21.1 9.3 68 111-178 3-77 (98)
76 KOG1784 Small Nuclear ribonucl 34.2 78 0.0017 25.3 4.3 61 116-180 10-76 (96)
77 cd04093 HBS1_C HBS1_C: this fa 33.0 2.2E+02 0.0047 21.6 8.7 42 135-180 59-107 (107)
78 PRK05609 nusG transcription an 31.9 53 0.0012 27.5 3.3 29 154-182 124-152 (181)
79 KOG1999 RNA polymerase II tran 31.6 71 0.0015 35.0 4.7 28 156-183 459-486 (1024)
80 TIGR03198 pucE xanthine dehydr 31.0 19 0.00041 30.7 0.4 52 21-76 18-77 (151)
81 cd02899 PLAT_SR Scavenger rece 30.1 1.9E+02 0.0041 23.2 6.0 61 157-230 41-108 (109)
82 cd03705 EF1_alpha_III Domain I 29.6 1.2E+02 0.0027 22.8 4.8 35 135-172 59-100 (104)
83 TIGR00922 nusG transcription t 29.1 60 0.0013 27.1 3.1 28 155-182 118-145 (172)
84 cd01234 PH_CADPS CADPS (Ca2+-d 28.0 48 0.001 27.3 2.2 42 88-134 21-62 (117)
85 PF08942 DUF1919: Domain of un 27.8 16 0.00034 32.8 -0.7 59 26-104 53-111 (201)
86 KOG2404 Fumarate reductase, fl 26.6 52 0.0011 32.4 2.6 51 2-52 117-168 (477)
87 TIGR03318 YdfZ_fam putative se 26.3 44 0.00096 25.0 1.6 41 157-201 11-57 (65)
88 cd05892 Ig_Myotilin_C C-termin 26.2 1.3E+02 0.0029 21.7 4.2 34 78-111 28-63 (75)
89 PF09285 Elong-fact-P_C: Elong 25.6 1.3E+02 0.0029 21.6 3.9 37 115-152 18-54 (56)
90 TIGR00234 tyrS tyrosyl-tRNA sy 25.5 95 0.0021 29.9 4.1 45 23-68 329-373 (377)
91 KOG3401 60S ribosomal protein 25.3 58 0.0013 27.9 2.3 50 150-199 42-94 (145)
92 PF14505 DUF4438: Domain of un 25.2 67 0.0014 29.9 2.9 32 159-192 60-92 (258)
93 PF06905 FAIM1: Fas apoptotic 25.2 4.7E+02 0.01 23.0 10.3 68 106-176 64-133 (177)
94 KOG2623 Tyrosyl-tRNA synthetas 23.9 91 0.002 31.2 3.7 39 22-61 397-435 (467)
95 PTZ00141 elongation factor 1- 23.5 4E+02 0.0087 26.1 8.1 52 135-187 381-436 (446)
96 COG5144 TFB2 RNA polymerase II 23.3 62 0.0013 31.6 2.4 83 17-104 54-138 (447)
97 PF11717 Tudor-knot: RNA bindi 22.8 1.8E+02 0.0039 20.1 4.2 37 157-193 1-38 (55)
98 smart00536 AXH domain in Ataxi 22.6 2.5E+02 0.0054 23.2 5.5 77 120-213 7-84 (116)
99 cd05741 Ig_CEACAM_D1_like Firs 22.0 1.3E+02 0.0028 21.5 3.5 31 82-112 50-80 (92)
100 PRK09014 rfaH transcriptional 21.9 1E+02 0.0022 25.6 3.2 26 156-181 109-134 (162)
101 cd05794 S1_EF-P_repeat_2 S1_EF 21.7 1.6E+02 0.0034 21.3 3.7 35 115-150 18-52 (56)
102 PF01063 Aminotran_4: Aminotra 21.6 2.9E+02 0.0064 23.4 6.1 51 187-239 125-175 (231)
103 TIGR00739 yajC preprotein tran 21.4 2.4E+02 0.0052 21.6 4.9 33 157-198 38-70 (84)
104 COG1188 Ribosome-associated he 21.3 1.1E+02 0.0024 24.7 3.0 35 112-150 29-63 (100)
105 PF07569 Hira: TUP1-like enhan 21.0 2.8E+02 0.006 24.5 5.9 57 77-133 20-94 (219)
106 COG0250 NusG Transcription ant 20.9 97 0.0021 27.0 3.0 30 153-182 120-149 (178)
107 PF10781 DSRB: Dextransucrase 20.9 2.1E+02 0.0044 21.2 4.1 29 137-165 2-35 (62)
108 TIGR01956 NusG_myco NusG famil 20.8 2.6E+02 0.0057 26.1 5.9 30 153-182 202-231 (258)
109 PLN02772 guanylate kinase 20.7 2.3E+02 0.0049 28.0 5.7 63 154-216 28-98 (398)
110 cd04708 BAH_plantDCM_II BAH, o 20.6 1.1E+02 0.0023 27.5 3.2 44 135-184 7-54 (202)
111 COG5164 SPT5 Transcription elo 20.5 1E+02 0.0022 31.4 3.3 42 139-182 124-165 (607)
112 smart00306 HintN Hint (Hedgeho 20.2 3.4E+02 0.0074 19.5 8.2 55 158-212 23-78 (100)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=8e-107 Score=729.88 Aligned_cols=242 Identities=88% Similarity=1.389 Sum_probs=239.2
Q ss_pred CCcccCceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
||+|++++||||||||||+++|||||++||||+|+||+|++||++||+||+|+|||+||||++||||||||||||++|||
T Consensus 19 ~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~ 98 (261)
T PLN00036 19 MLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKTNEN 98 (261)
T ss_pred ccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCC
Q 026062 81 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVG 160 (244)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G 160 (244)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|+||+++|+|||||++|
T Consensus 99 yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G 178 (261)
T PLN00036 99 FRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVG 178 (261)
T ss_pred EEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEEEEeCCCCceeeEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHHHHH
Q 026062 161 NIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAA 240 (244)
Q Consensus 161 ~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (244)
|+||||||+|+|++|+|.+|+++++|+++||++|++|++|+|+++||||||++++|||+||+++|||+|++|||++++++
T Consensus 179 ~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~~e~r~~~~~~ 258 (261)
T PLN00036 179 NLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKRLAA 258 (261)
T ss_pred CEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccchHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999988999999999999999999999999987
Q ss_pred HH
Q 026062 241 QA 242 (244)
Q Consensus 241 ~~ 242 (244)
.+
T Consensus 259 ~~ 260 (261)
T PLN00036 259 GQ 260 (261)
T ss_pred hc
Confidence 65
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.7e-106 Score=728.03 Aligned_cols=243 Identities=62% Similarity=1.026 Sum_probs=240.2
Q ss_pred CCcccCceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
||+|++++||||||||||++++||||++||||+|+||+|++||++||+||+|+|||+||||++||||||||||||++|||
T Consensus 19 ~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~ 98 (262)
T PTZ00118 19 MLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEY 98 (262)
T ss_pred ccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCC
Q 026062 81 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVG 160 (244)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G 160 (244)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|+||+++|++||||++|
T Consensus 99 yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G 178 (262)
T PTZ00118 99 FRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVG 178 (262)
T ss_pred EEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCEEEEECCCCceeeEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHHHHH
Q 026062 161 NIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAA 240 (244)
Q Consensus 161 ~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (244)
|+||||||+|+|++|+|.+++++++|+++||++|++|++|+|+++||||||++++|||+||++||||+|++|||++++++
T Consensus 179 ~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~kgi~~~~~e~~~~~~~~ 258 (262)
T PTZ00118 179 NLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDIIEERRNRLAK 258 (262)
T ss_pred CEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCccccHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999988999999999999999999999999998
Q ss_pred HHh
Q 026062 241 QAA 243 (244)
Q Consensus 241 ~~~ 243 (244)
++.
T Consensus 259 ~~~ 261 (262)
T PTZ00118 259 ALR 261 (262)
T ss_pred Hhc
Confidence 864
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=4.8e-106 Score=728.21 Aligned_cols=243 Identities=52% Similarity=0.863 Sum_probs=239.4
Q ss_pred CCcccCceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
||+|++++||||||||||++++||||++||||+|+||+|++||++||+||+|+|||+||||++||||||||||||++|||
T Consensus 16 ~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~ 95 (273)
T PTZ00223 16 MLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDR 95 (273)
T ss_pred ccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCC
Q 026062 81 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVG 160 (244)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G 160 (244)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+|+||+++|+|||||++|
T Consensus 96 yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G 175 (273)
T PTZ00223 96 FRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNG 175 (273)
T ss_pred EEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCEEEEECCCCeeeEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccC-CCceEecCCCcceeeehHHHHHHHHH
Q 026062 161 NIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEEARKRQA 239 (244)
Q Consensus 161 ~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~-~kp~islp~~~gi~~~~~~~~~~~~~ 239 (244)
|+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++ ++|||+||++||||||++|||+++++
T Consensus 176 ~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~~e~~~~~~~ 255 (273)
T PTZ00223 176 KVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINVIQEREEKLI 255 (273)
T ss_pred CEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999986 69999999999999999999999998
Q ss_pred HHHh
Q 026062 240 AQAA 243 (244)
Q Consensus 240 ~~~~ 243 (244)
++++
T Consensus 256 ~~~~ 259 (273)
T PTZ00223 256 AAEA 259 (273)
T ss_pred HHHh
Confidence 8764
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=5.2e-99 Score=672.07 Aligned_cols=221 Identities=41% Similarity=0.663 Sum_probs=218.0
Q ss_pred CCcccCceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
||+|++++||||||||||++++||||++||||+|+||+|+|||++||+||+|+||||||||++||||||||||||++||+
T Consensus 15 ~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~ 94 (237)
T PRK04313 15 PIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETGEY 94 (237)
T ss_pred ccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCCCe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCC-CCccCCCeEEEecCCCeeeeEEEeeC
Q 026062 81 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKANDTIKLDLEENKITDFIKFDV 159 (244)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d-~~ik~~Dtv~i~l~~~kI~d~i~f~~ 159 (244)
|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| ++||+||||+|+||+++|++||||++
T Consensus 95 yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~ 174 (237)
T PRK04313 95 YRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEE 174 (237)
T ss_pred EEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEecCC
Confidence 99999999999999999999999999999999999999999999999999998 99999999999999999999999999
Q ss_pred CcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCC
Q 026062 160 GNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 222 (244)
Q Consensus 160 G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~ 222 (244)
||+||||||+|+|++|+|.+|++++ +++++||++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 175 G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 175 GNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred CCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 9999999999999999999999999 6789999999999999999999999998 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-95 Score=644.09 Aligned_cols=223 Identities=47% Similarity=0.746 Sum_probs=219.4
Q ss_pred CCcccCceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
|++|++++|||+|+||||++++||||++++||+|+||+|+|||++||++|+|+|||+||+|++||||||||||||+|||+
T Consensus 18 ~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~ 97 (241)
T COG1471 18 PIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEH 97 (241)
T ss_pred EeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCCCce
Confidence 58899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCC
Q 026062 81 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVG 160 (244)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G 160 (244)
||||||.+|+|.||+|++|||+||||||+||++++||++||+||||||++++|+.|++||||++++|+++|++||||++|
T Consensus 98 yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g 177 (241)
T COG1471 98 YRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEG 177 (241)
T ss_pred EEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccEEEEeCCChhheeEeccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCc
Q 026062 161 NIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGK 224 (244)
Q Consensus 161 ~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~ 224 (244)
++||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++|||+||+|+
T Consensus 178 ~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~e~ 241 (241)
T COG1471 178 ALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPKEK 241 (241)
T ss_pred cEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCCCC
Confidence 999999999999999999999999 5579999999999999999999999998 99999999875
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-93 Score=633.25 Aligned_cols=244 Identities=70% Similarity=1.156 Sum_probs=242.1
Q ss_pred CCcccCceeccCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
||||++|.|||+||+|||+++||+||++||||+|+||+|.+|+++|++|+.|+|||+||+|.+||+||||||+|++|||+
T Consensus 19 mldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mDvisiekTge~ 98 (263)
T KOG0378|consen 19 MLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMDVISIEKTGEH 98 (263)
T ss_pred eecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeecccccccceeEEEEecccchh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCC
Q 026062 81 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVG 160 (244)
Q Consensus 81 yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G 160 (244)
||++||++|+|.+|+|++|||+||||||++++.+.+|+|+|+||||++||||||.||++||+++++++++|.++++|++|
T Consensus 99 fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dtI~~~~~t~kit~~ikf~~~ 178 (263)
T KOG0378|consen 99 FRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDTIKIDLETSKITDFIKFDTG 178 (263)
T ss_pred hhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCccceeeccCCCceeeeeeccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHHHHH
Q 026062 161 NIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAA 240 (244)
Q Consensus 161 ~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~~ 240 (244)
++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++||||||+|++||||||+++||+++++||||+|+++
T Consensus 179 ~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPkgkgi~~siaEe~dkrl~~ 258 (263)
T KOG0378|consen 179 NLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPKGKGIALSIAEERDKRLAA 258 (263)
T ss_pred ceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCccccCccchhhHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhC
Q 026062 241 QAAA 244 (244)
Q Consensus 241 ~~~~ 244 (244)
+.++
T Consensus 259 k~~s 262 (263)
T KOG0378|consen 259 KISS 262 (263)
T ss_pred hccC
Confidence 8764
No 7
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=100.00 E-value=1.1e-34 Score=219.86 Aligned_cols=77 Identities=61% Similarity=1.011 Sum_probs=69.7
Q ss_pred cCCceEEEEEcCCCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeee
Q 026062 76 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 152 (244)
Q Consensus 76 kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 152 (244)
+|||+|||+||++|+|.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
T Consensus 1 kt~e~yRvl~d~kgr~~l~~I~~eea~~KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~kI~ 77 (77)
T PF00900_consen 1 KTGEHYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQKIV 77 (77)
T ss_dssp CTTEEEEEEE-TTS-EEEEEE-TTGGGEEEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETTTTEEE
T ss_pred CCCcEEEEEECCCCcEEEEECCHHHccCeEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECCCCcCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the N-terminal region of these proteins.; PDB: 2XZM_W 2XZN_W 3U5G_E 3U5C_E.
Probab=98.62 E-value=1.2e-08 Score=68.16 Aligned_cols=22 Identities=68% Similarity=1.173 Sum_probs=13.0
Q ss_pred CCcccCceeccCCCCCCCCCcc
Q 026062 1 MLDKLGGAFAPKPSSGPHKSRE 22 (244)
Q Consensus 1 ml~K~~~~~a~rpspGPH~~~~ 22 (244)
||+|++++|||+||||||+++|
T Consensus 17 ~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 17 MIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp T--SSSSSB-----SSSS-CCC
T ss_pred ccccccCccccCCCCCCccCCC
Confidence 7999999999999999999986
No 9
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.57 E-value=1.1e-07 Score=64.46 Aligned_cols=48 Identities=33% Similarity=0.359 Sum_probs=44.3
Q ss_pred chhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEE
Q 026062 24 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVV 72 (244)
Q Consensus 24 iPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVI 72 (244)
++|..+| ..++++.+..||++.+++|.|+|||++++|+.|++...|+|
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 4678888 44899999999999999999999999999999999999987
No 10
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.62 E-value=0.00028 Score=48.41 Aligned_cols=62 Identities=26% Similarity=0.333 Sum_probs=47.9
Q ss_pred hhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcC
Q 026062 25 PLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDT 87 (244)
Q Consensus 25 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~ 87 (244)
.|.-+|+.. ..+.+..+|++++.+|.|+|||+..++..+++-..|+|++........++|..
T Consensus 2 rl~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~ed 63 (70)
T cd00165 2 RLDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63 (70)
T ss_pred cHHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceeecc
Confidence 355667654 36789999999999999999999999999999888999997643323444433
No 11
>smart00363 S4 S4 RNA-binding domain.
Probab=97.25 E-value=0.00082 Score=44.79 Aligned_cols=51 Identities=25% Similarity=0.201 Sum_probs=42.8
Q ss_pred hhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 026062 25 PLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 76 (244)
Q Consensus 25 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k 76 (244)
.|..+|... .++.+.+++++.+.+|.|+|||++.++..+++--.|.|++..
T Consensus 2 rl~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 2 RLDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred cHHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 355666643 356789999999999999999999999999998889999965
No 12
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=96.89 E-value=0.00096 Score=59.34 Aligned_cols=53 Identities=30% Similarity=0.412 Sum_probs=45.8
Q ss_pred cchhHHHHHh-------hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 026062 23 CLPLILVLRN-------RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 75 (244)
Q Consensus 23 siPL~i~LRd-------~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~ 75 (244)
++-+.-+|.- ++++|.|.++|++.+..|.|.|||+.++.+-|=|-.=|+++|.
T Consensus 85 ~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~ 144 (205)
T COG0522 85 GLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVR 144 (205)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEee
Confidence 4445555554 4689999999999999999999999999999999999999996
No 13
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=96.83 E-value=0.0013 Score=41.75 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=25.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 026062 159 VGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 192 (244)
Q Consensus 159 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i 192 (244)
+|+.++|+.|++.|+.|+|.++..+. +.|++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence 58999999999999999999997643 45554
No 14
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.81 E-value=0.0012 Score=39.57 Aligned_cols=27 Identities=37% Similarity=0.661 Sum_probs=24.5
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 156 KFDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 156 ~f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
+|++|+.++|++|.+.|.+|+|.++..
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 478999999999999999999999853
No 15
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=96.78 E-value=0.0039 Score=44.19 Aligned_cols=51 Identities=22% Similarity=0.217 Sum_probs=44.7
Q ss_pred chhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 026062 24 LPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 75 (244)
Q Consensus 24 iPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~ 75 (244)
..|--||... .++.+...+++++.+|.|.|||++++.+.|.+--=|+|+|+
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 5676778876 77789999999999999999999999889999888888874
No 16
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.97 E-value=0.0036 Score=46.40 Aligned_cols=60 Identities=27% Similarity=0.309 Sum_probs=41.8
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 84 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl 84 (244)
+.|.|.=||.- .+++.|.-|||..|.+|.|+|||.+.+...--+--=|+|++ .++.|+++
T Consensus 6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~--~~~~~~Vv 65 (65)
T PF13275_consen 6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI--DGEEYRVV 65 (65)
T ss_dssp S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE--TTEEEEEE
T ss_pred CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE--CCEEEEEC
Confidence 56677777766 58899999999999999999999999998888888899999 57888874
No 17
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=95.73 E-value=0.0082 Score=51.76 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=35.8
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcce--eEEEec
Q 026062 33 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM--DVVSIP 75 (244)
Q Consensus 33 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~m--DVIsI~ 75 (244)
++++|.|.++|++.+.+|.|.|||++++++.|-|--= |-|+..
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 156 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA 156 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence 4689999999999999999999999999998766432 555543
No 18
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.57 E-value=0.0096 Score=52.17 Aligned_cols=40 Identities=20% Similarity=0.306 Sum_probs=34.9
Q ss_pred hhHHHHHhhh-------cccccHHHHHHHHhCceEEECCEEeccccC
Q 026062 25 PLILVLRNRL-------KYALTYREVIAILMQRHVLVDGKVRTDKTY 64 (244)
Q Consensus 25 PL~i~LRd~L-------kyA~t~rEak~Il~~~~V~VDGkvr~D~k~ 64 (244)
-.--||+.+| |+|.|..+|++.+.+|.|.|||++++++.|
T Consensus 100 ~~~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~ 146 (181)
T PTZ00155 100 TVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146 (181)
T ss_pred cHHHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCce
Confidence 3345667666 999999999999999999999999999966
No 19
>PRK11507 ribosome-associated protein; Provisional
Probab=95.56 E-value=0.058 Score=40.68 Aligned_cols=60 Identities=18% Similarity=0.167 Sum_probs=48.8
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL 84 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl 84 (244)
+-|-|.=||.- .+++.|.-|||..|.+|.|+|||.+.+-..-=+--=|+|+++ ++.|++.
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 45666666665 588899999999999999999999987777667777999995 5777764
No 20
>PLN00189 40S ribosomal protein S9; Provisional
Probab=95.45 E-value=0.012 Score=52.15 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=34.4
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEE
Q 026062 33 RLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVV 72 (244)
Q Consensus 33 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVI 72 (244)
+|++|.|..+|++++.+|.|.|||++++++.|-|-.=|++
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~ 156 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQK 156 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEE
Confidence 4689999999999999999999999999998866543333
No 21
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=95.26 E-value=0.019 Score=50.12 Aligned_cols=44 Identities=20% Similarity=0.257 Sum_probs=37.1
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEeccC
Q 026062 34 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPA--GFMDVVSIPKT 77 (244)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv--G~mDVIsI~kt 77 (244)
+++|.|..+|++.+.+|.|.|||++++++.|.| +.=|.|+...+
T Consensus 112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~ 157 (177)
T PRK04051 112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPT 157 (177)
T ss_pred ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCC
Confidence 689999999999999999999999999998876 34456666543
No 22
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=95.17 E-value=0.032 Score=49.12 Aligned_cols=43 Identities=28% Similarity=0.354 Sum_probs=39.1
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 026062 34 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 76 (244)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k 76 (244)
++++.|.++|++.+.+|.|.|||++++++.|.+--=|+|++..
T Consensus 99 ~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 99 LGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKE 141 (200)
T ss_pred cCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEee
Confidence 4678899999999999999999999999999997779999964
No 23
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=94.93 E-value=0.044 Score=48.42 Aligned_cols=42 Identities=26% Similarity=0.381 Sum_probs=39.1
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 026062 35 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 76 (244)
Q Consensus 35 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k 76 (244)
+++.+..+|++.+..|.|.|||++++.+.|++--=|+|++..
T Consensus 103 g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 103 GFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred CccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 788999999999999999999999999999997779999964
No 24
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=94.90 E-value=0.11 Score=47.33 Aligned_cols=53 Identities=19% Similarity=0.180 Sum_probs=44.0
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 75 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~ 75 (244)
.++.|.-+|...+. ..+.+++++.+.+|.|+|||+++++..+.+---|+|++.
T Consensus 4 ~g~rLd~~L~~~~~-~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~ 56 (299)
T TIGR00005 4 AGQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVR 56 (299)
T ss_pred cchhHHHHHHHhcc-cCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEe
Confidence 34667778877664 357899999999999999998888888999878999983
No 25
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=94.83 E-value=0.065 Score=43.82 Aligned_cols=57 Identities=18% Similarity=0.241 Sum_probs=40.0
Q ss_pred eeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC-----CCeEe--EeeceEEEEc
Q 026062 152 TDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL-----GHEFA--TRLGNVFTIG 211 (244)
Q Consensus 152 ~d~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~-----g~~F~--T~~~~vfvIG 211 (244)
.+.+++..|+.+.|++|++-|..|+|.++... ...|.|+.-+ |.+++ -..|||.++.
T Consensus 37 ~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~ 100 (114)
T TIGR01080 37 KRALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVTKEKVNGTEVPVPIHPSNVMITK 100 (114)
T ss_pred cccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeEEECCCCeEEEeeechHHeEEEe
Confidence 35568889999999999999999999999643 2456666543 33333 3346666543
No 26
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=94.81 E-value=0.045 Score=48.52 Aligned_cols=43 Identities=21% Similarity=0.362 Sum_probs=38.5
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 026062 34 LKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 76 (244)
Q Consensus 34 LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k 76 (244)
+++|.+.++|++++.+|.|.|||++++.+.|.+--=|+|++..
T Consensus 98 ~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 98 LGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKD 140 (201)
T ss_pred cCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEcc
Confidence 5788999999999999999999999999999985559999953
No 27
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=94.47 E-value=0.13 Score=46.96 Aligned_cols=63 Identities=14% Similarity=0.205 Sum_probs=51.5
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 97 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 97 (244)
.|+=|-.++...+ ..+.+.|++.+.+|.|+|||++++++.+.+--=|+||+. ..|||.+.++.
T Consensus 182 ~s~RLD~lls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isvr-----------G~Gr~~i~~~~ 244 (257)
T TIGR03069 182 ASLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR-----------GKGRLEILELE 244 (257)
T ss_pred ccccHHHHHHhhh--hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEc-----------CCceEEEEEee
Confidence 4556777887755 558899999999999999999999999988777999884 46788777664
No 28
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=93.77 E-value=0.11 Score=46.54 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=40.7
Q ss_pred HHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 026062 28 LVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK 76 (244)
Q Consensus 28 i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k 76 (244)
.+|.+ .+++.+.++|++.+++|.|.|||++++++.+.+--=|.|++..
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 34444 4688899999999999999999999999999886559999964
No 29
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=92.29 E-value=0.5 Score=44.00 Aligned_cols=53 Identities=19% Similarity=0.124 Sum_probs=42.7
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 75 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~ 75 (244)
..+.|.-+|+..+. ..+.+.+++.+.+|.|+|||+.++...+.+---|+|++.
T Consensus 16 ~g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~ 68 (325)
T PRK11180 16 LGQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAID 68 (325)
T ss_pred CCccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEe
Confidence 34678888888654 357899999999999999999987666666555999885
No 30
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=92.04 E-value=0.36 Score=36.75 Aligned_cols=59 Identities=24% Similarity=0.273 Sum_probs=44.5
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEE
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRL 83 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRv 83 (244)
+-|-|.=||.- ++.+++.-+||..|.++.|+|||.+-+=..-=+=-=|+|+||. ..|-+
T Consensus 10 e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~--~~~~v 68 (73)
T COG2501 10 EFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG--QRYQV 68 (73)
T ss_pred ceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC--EEEEE
Confidence 44566666665 7899999999999999999999998555544455568999964 44443
No 31
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=91.77 E-value=0.58 Score=43.38 Aligned_cols=57 Identities=25% Similarity=0.220 Sum_probs=50.0
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 81 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~y 81 (244)
...-|--||++ |.- .+..+..+++.+|.|.|||++++ ..|.+..=|+|+++...+.+
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 35567888999 665 78899999999999999999999 99999999999999876565
No 32
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=91.70 E-value=0.6 Score=45.30 Aligned_cols=65 Identities=17% Similarity=0.214 Sum_probs=49.6
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 026062 23 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 94 (244)
Q Consensus 23 siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~ 94 (244)
.+|+.-+|.+ .+.|.+..|||+.+.||-|+|||..++|..+-+-- ......|-+|---|.+|.+.
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~------~~~~~~~~~lr~GKk~~~~i 406 (408)
T PRK05912 342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA------DDRFGKYTVLQRGKKKFARV 406 (408)
T ss_pred CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccccc------cccCCCEEEEEeCCCceEEE
Confidence 5788888876 69999999999999999999999999999764322 11134566666666666554
No 33
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=90.94 E-value=0.61 Score=38.57 Aligned_cols=55 Identities=22% Similarity=0.296 Sum_probs=37.6
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc-----CCCCeEeE--eeceEEEEc
Q 026062 154 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD-----ALGHEFAT--RLGNVFTIG 211 (244)
Q Consensus 154 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d-----~~g~~F~T--~~~~vfvIG 211 (244)
.+++..|+.+.|+.|..-|..|+|.++.... +.|+|+. .+|.+++- ..|||+++.
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~---~~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~ 104 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKR---GRIYVEGVTVKKADGTEVPRPIHPSNVMITK 104 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCC---CEEEEeCcEEECCCCeEEEcccchhHeEEEe
Confidence 4578899999999999999999999996543 3455543 33533332 235665543
No 34
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=90.78 E-value=0.77 Score=42.50 Aligned_cols=63 Identities=21% Similarity=0.119 Sum_probs=45.5
Q ss_pred HHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEecc----------CCceEEEEEcCCCceEE
Q 026062 28 LVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA--GFMDVVSIPK----------TNENFRLLYDTKGRFRL 93 (244)
Q Consensus 28 i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv--G~mDVIsI~k----------t~e~yRvl~d~kgrf~l 93 (244)
=||-+ +++ .+.++|++++.+|.|+|||++. +..+.| +-.|.|+++. ..++|-+++-+.|..+-
T Consensus 7 k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~~s 81 (289)
T PRK10700 7 KVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCT 81 (289)
T ss_pred HHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCEee
Confidence 34443 343 5899999999999999999987 566666 4557787753 11468889999986543
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=90.01 E-value=0.78 Score=38.48 Aligned_cols=58 Identities=10% Similarity=0.060 Sum_probs=49.7
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 026062 23 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR 82 (244)
Q Consensus 23 siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yR 82 (244)
++-|-.||=. .+++.|..-|+..|..|.|.|||.+ .-+-..|-.=|+|+|...+..|-
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~ 65 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERT 65 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEE
Confidence 5677777766 5999999999999999999999999 88899999999999977555443
No 36
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=89.13 E-value=0.93 Score=41.56 Aligned_cols=59 Identities=24% Similarity=0.239 Sum_probs=43.6
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcce-eEEEeccCC------ceEEEEEcCCCceEEE
Q 026062 35 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM-DVVSIPKTN------ENFRLLYDTKGRFRLH 94 (244)
Q Consensus 35 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~m-DVIsI~kt~------e~yRvl~d~kgrf~l~ 94 (244)
++| +.|||.+.|.+|.|.|||++.++...-+=-- |+|.++..- ..|-|++-+.|..+-+
T Consensus 13 G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~ 78 (248)
T COG1187 13 GVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSST 78 (248)
T ss_pred CCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEecc
Confidence 555 6899999999999999999999986555444 466655431 2288888888865433
No 37
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=89.02 E-value=1.5 Score=40.69 Aligned_cols=67 Identities=18% Similarity=0.110 Sum_probs=49.4
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc--------CCceEEEEEcCCCce
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK--------TNENFRLLYDTKGRF 91 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k--------t~e~yRvl~d~kgrf 91 (244)
+++-|.=+|.+. ++ .+.++|++.+.+|.|+|||++. +..+.|---|+|+++- .+++|-++.-+.|..
T Consensus 5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~~~ed~~~lvlnKP~G~~ 79 (290)
T PRK10475 5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGIV 79 (290)
T ss_pred hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccccccCCCeEEEEECCCCCC
Confidence 456677777663 43 4799999999999999999987 4667775559888852 134677777778754
No 38
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=88.70 E-value=0.7 Score=35.10 Aligned_cols=39 Identities=21% Similarity=0.429 Sum_probs=31.8
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC
Q 026062 155 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 196 (244)
Q Consensus 155 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~ 196 (244)
+++..|+.+.|+.|+.-|.+|+|.++.+.. +.|.+++-+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegvn 43 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKK---NRVIVEGVK 43 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCcE
Confidence 478899999999999999999999996543 467776543
No 39
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=88.67 E-value=1.8 Score=40.20 Aligned_cols=51 Identities=27% Similarity=0.249 Sum_probs=41.7
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 026062 23 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIP 75 (244)
Q Consensus 23 siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~ 75 (244)
...|.-||++.+. ..+.+.+++.+.+|.|.|||+++ +..+.+---|+|+++
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 4677788887663 35789999999999999999988 467888666999985
No 40
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=88.11 E-value=0.84 Score=35.20 Aligned_cols=39 Identities=15% Similarity=0.434 Sum_probs=31.5
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcC
Q 026062 154 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 195 (244)
Q Consensus 154 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~ 195 (244)
.+++..|+.++|+.|+.-|.+|+|.++.... +.|++++-
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence 3478899999999999999999999996542 46666643
No 41
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=87.75 E-value=3.1 Score=36.63 Aligned_cols=67 Identities=15% Similarity=0.168 Sum_probs=47.7
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc------CCceEEEEEcCCCceEEEE
Q 026062 26 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPK------TNENFRLLYDTKGRFRLHS 95 (244)
Q Consensus 26 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~k------t~e~yRvl~d~kgrf~l~~ 95 (244)
|--+|...+ ..+.+.+++++.+|.|.|||+++++..+.+---|.|++.. ..++|=++--+.| +..|+
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~~~~~~~~lvvnKP~G-~~~~~ 75 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQG-YVCST 75 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcccCCCCEEEEEECCCC-eEecc
Confidence 445666655 3578999999999999999999887777775569999852 1235655555566 44454
No 42
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=87.53 E-value=2 Score=41.89 Aligned_cols=66 Identities=21% Similarity=0.221 Sum_probs=48.1
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 026062 23 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 94 (244)
Q Consensus 23 siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~ 94 (244)
.+||.=+|-. .+.|.+..||++.+.||-|+|||..++|..+-+-.=|. .+..|-+|---|.+|.+.
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~-----l~~~~~~lr~GKk~~~~i 407 (410)
T PRK13354 342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA-----FDGKFVILRRGKKKFFLV 407 (410)
T ss_pred CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh-----cCCCEEEEEeCCccEEEE
Confidence 5788887775 79999999999999999999999999998653322111 233455666556565544
No 43
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=87.38 E-value=2.3 Score=39.23 Aligned_cols=62 Identities=19% Similarity=0.248 Sum_probs=50.6
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 026062 23 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 97 (244)
Q Consensus 23 siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 97 (244)
|+=|--++-..+ -.+...|+..+.+|+|+|||++.++..|-+--=|+|||-. .|||.+.++.
T Consensus 191 s~RLD~vla~~~--~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG-----------~GR~~i~~~~ 252 (267)
T PLN00051 191 SLRLDALASAGF--RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSG-----------KGRLEVGEIN 252 (267)
T ss_pred cccHHHHHHHHh--ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEee-----------CCEEEEEEEe
Confidence 455666666655 4577889999999999999999999999999999999954 5677777664
No 44
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=87.22 E-value=0.85 Score=36.52 Aligned_cols=37 Identities=22% Similarity=0.504 Sum_probs=29.5
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 026062 155 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 194 (244)
Q Consensus 155 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d 194 (244)
+++..|+.+.|+.|++-|.+|+|.++.... +.|+|++
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 377889999999999999999999996533 3455543
No 45
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=86.76 E-value=1.5 Score=40.49 Aligned_cols=63 Identities=21% Similarity=0.283 Sum_probs=53.2
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLR 97 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 97 (244)
.||=|-.++-+.++... .-|...+.+|+|+||.+++++..|-+..=|.|||-. .|||.+-++.
T Consensus 179 sSlRLD~vis~~~~~SR--~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG-----------~GR~~i~~i~ 241 (257)
T COG2302 179 SSLRLDVVISEGFGLSR--AKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG-----------FGRLKILEIN 241 (257)
T ss_pred ehhhHHHHHHHHHhhhH--HHHHHHHHcCceEEeeEEeccccceeccCCEEEEec-----------cccEEEEeec
Confidence 47778888888777654 678999999999999999999999999999999954 5777666654
No 46
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=86.26 E-value=1.5 Score=40.34 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=42.1
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 026062 35 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENF 81 (244)
Q Consensus 35 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~y 81 (244)
+++.|...|+..++.|+|+|||...+-+.+=|-.-+.|++......|
T Consensus 13 gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~y 59 (245)
T COG1189 13 GLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPY 59 (245)
T ss_pred cchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCc
Confidence 89999999999999999999999999999999999999997544433
No 47
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=86.21 E-value=1.6 Score=37.13 Aligned_cols=55 Identities=27% Similarity=0.366 Sum_probs=39.3
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE-----cCCCCe--EeEeeceEEEEc
Q 026062 154 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHE--FATRLGNVFTIG 211 (244)
Q Consensus 154 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~-----d~~g~~--F~T~~~~vfvIG 211 (244)
.+++..|+.+.|+.|.+-|..|+|..+....+ .|.|+ -..|.. +--..|||+++.
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 34778899999999999999999999966443 33333 345544 344567777776
No 48
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=84.77 E-value=2.5 Score=31.23 Aligned_cols=50 Identities=28% Similarity=0.494 Sum_probs=38.3
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCC-ccEEEEEcCCCCeEeEeeceEEEEcc
Q 026062 159 VGNIVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGK 212 (244)
Q Consensus 159 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s-~~~v~i~d~~g~~F~T~~~~vfvIG~ 212 (244)
+|..|+|-.|.+.-|+|+++.-|....| |.+|. ++...+.-+..+..+|-
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi----~~q~i~velkdivlvgv 55 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVI----GEQSIDVELKDIVLVGV 55 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEEE----CCeEEEEEeeeEEEEEe
Confidence 4889999999999999999998887744 55552 33456777777777774
No 49
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=82.39 E-value=1.9 Score=34.55 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=25.3
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEe
Q 026062 156 KFDVGNIVMVTGGRNRGRVGIIKNREKH 183 (244)
Q Consensus 156 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 183 (244)
++..|+.+.|+.|+.-|.+|+|.++...
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5778999999999999999999999654
No 50
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=70.58 E-value=3.2 Score=36.43 Aligned_cols=55 Identities=27% Similarity=0.327 Sum_probs=40.8
Q ss_pred CCCCCCCCCcccchhHHHHH-------hhhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 026062 12 KPSSGPHKSRECLPLILVLR-------NRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 66 (244)
Q Consensus 12 rpspGPH~~~~siPL~i~LR-------d~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~Pv 66 (244)
-|..+.|..-+-+...-|-| -.|+.|.+-+||.+.+.||.|.|.-++++|+.|=|
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 55666665544233333333 24789999999999999999999999999997754
No 51
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=68.33 E-value=11 Score=36.85 Aligned_cols=62 Identities=23% Similarity=0.289 Sum_probs=45.0
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEE
Q 026062 26 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS 95 (244)
Q Consensus 26 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~ 95 (244)
++-+|-+ .+++...+||++.+.+|-|++||..+.|.+++.+ | .....|.++--.|.+|....
T Consensus 338 ~~~~lv~-~~L~psr~earr~i~~g~v~in~~~v~d~~~~~~--~-----~~~~~~~~l~~GKkk~~~i~ 399 (401)
T COG0162 338 LVDLLVD-AGLAPSRSEARRLIQQGGVKINGEKVEDENYVLS--D-----LLDNGLLVLRRGKKKFALIV 399 (401)
T ss_pred HHHHHHH-hCCcccHHHHHhhcccCCEEECCEeccccccchh--h-----ccCCceEEEecccccEEEEe
Confidence 3334444 5899999999999999999999999999998871 1 22345555555565665443
No 52
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=60.98 E-value=8.7 Score=31.98 Aligned_cols=34 Identities=29% Similarity=0.466 Sum_probs=27.5
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 194 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d 194 (244)
+++|-.|+++.|+.+|+-.+|..+-.. +.+++-+
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd----~~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDD----NFVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccC----CEEEEeC
Confidence 689999999999999999999988553 3555543
No 53
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=59.16 E-value=15 Score=29.75 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.6
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 026062 155 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 183 (244)
Q Consensus 155 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 183 (244)
++...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45677999999999999999999888543
No 54
>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification.; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.
Probab=57.62 E-value=45 Score=28.81 Aligned_cols=29 Identities=34% Similarity=0.417 Sum_probs=25.0
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc
Q 026062 21 RECLPLILVLRNRLKYALTYREVIAILMQR 50 (244)
Q Consensus 21 ~~siPL~i~LRd~LkyA~t~rEak~Il~~~ 50 (244)
...+|..+++|..|. |.|..||..+|.+-
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 99999999999865
No 55
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=56.10 E-value=14 Score=31.10 Aligned_cols=33 Identities=12% Similarity=0.346 Sum_probs=28.0
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEE
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ 193 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~ 193 (244)
.|+|-+|+|.-|.+.|+.++|.+|-.+ +.|.|.
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~----nRvLVD 40 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLVD 40 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC----CeEEEe
Confidence 378999999999999999999999764 566553
No 56
>PF14001 YdfZ: YdfZ protein
Probab=54.61 E-value=20 Score=26.77 Aligned_cols=42 Identities=26% Similarity=0.483 Sum_probs=29.1
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEecCC------ccEEEEEcCCCCeEe
Q 026062 156 KFDVGNIVMVTGGRNRGRVGIIKNREKHKGS------FETIHIQDALGHEFA 201 (244)
Q Consensus 156 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s------~~~v~i~d~~g~~F~ 201 (244)
++.+|+.+|+.| +|.+|+|+.|...-.+ ...|.+++.+| .|+
T Consensus 9 ~i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 9 AITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred cCCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 356799999977 6788899998653222 25788886665 354
No 57
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=51.98 E-value=37 Score=27.33 Aligned_cols=45 Identities=13% Similarity=0.153 Sum_probs=34.7
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 026062 35 KYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNEN 80 (244)
Q Consensus 35 kyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 80 (244)
.+..+...|+..+..|.|.|||...+-. .-|=.=|+|+|--.+..
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~aKpS-~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRAKPS-KEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEcccc-cccCCCCEEEEEeCCcE
Confidence 4557889999999999999999998543 55667788888554433
No 58
>PRK04333 50S ribosomal protein L14e; Validated
Probab=50.80 E-value=17 Score=28.10 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=27.4
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 026062 156 KFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 192 (244)
Q Consensus 156 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i 192 (244)
.+++|.+|++.-|+..|+..+|.++... +.|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~----~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK----NFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC----CEEEE
Confidence 4688999999999999999999998442 45655
No 59
>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=46.31 E-value=13 Score=27.58 Aligned_cols=33 Identities=30% Similarity=0.422 Sum_probs=22.2
Q ss_pred cccchhHHHHHhhhcccc-cHHHHHHHHhCceEEECC
Q 026062 21 RECLPLILVLRNRLKYAL-TYREVIAILMQRHVLVDG 56 (244)
Q Consensus 21 ~~siPL~i~LRd~LkyA~-t~rEak~Il~~~~V~VDG 56 (244)
.|.|||..++ ||||. +..||-+-+.+++-.|+-
T Consensus 21 WEmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~ 54 (62)
T PF08828_consen 21 WEMMPLMYVI---LKYADADVEEASRRIDEAKNVVNE 54 (62)
T ss_dssp GGGHHHHHHH---HHHTTT-HHHHHHHHHH-------
T ss_pred HHHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHH
Confidence 4789999986 89999 999999998888766654
No 60
>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=44.17 E-value=67 Score=26.31 Aligned_cols=84 Identities=18% Similarity=0.259 Sum_probs=47.5
Q ss_pred ceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCC
Q 026062 90 RFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGR 169 (244)
Q Consensus 90 rf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v~gG~ 169 (244)
.+.+++.+.++..+. .|.+ ..|...+...+|+....|+..+..--... -..........|.+|+.+.|++|.
T Consensus 50 gYvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~~--~~~~~~~~~~~~~~G~~V~V~~GP 121 (159)
T TIGR01955 50 NYLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQYE--PKDSVPPATTLPYKGDKVRITDGA 121 (159)
T ss_pred CeEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhcc--ccccCCccccCCCCCCEEEEeccC
Confidence 356777766554332 2211 24566665555655555554222110000 001011233569999999999999
Q ss_pred cceeEEEEEeEE
Q 026062 170 NRGRVGIIKNRE 181 (244)
Q Consensus 170 n~G~vG~I~~i~ 181 (244)
-.|..|.|.++.
T Consensus 122 f~g~~g~v~~~~ 133 (159)
T TIGR01955 122 FAGFEAIFLEPD 133 (159)
T ss_pred CCCcEEEEEEEC
Confidence 999999999985
No 61
>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=42.24 E-value=76 Score=24.41 Aligned_cols=48 Identities=19% Similarity=0.320 Sum_probs=30.2
Q ss_pred CCC-CccCCCeEEEecCCCeeeeEEEeeC----CcEEEEECCCcceeEEEEEeE
Q 026062 132 PDP-LIKANDTIKLDLEENKITDFIKFDV----GNIVMVTGGRNRGRVGIIKNR 180 (244)
Q Consensus 132 ~d~-~ik~~Dtv~i~l~~~kI~d~i~f~~----G~~~~v~gG~n~G~vG~I~~i 180 (244)
.+| .++.||...+.+...+=+-.=+|+. |..++--+|+.+| .|.|.+|
T Consensus 56 ~~p~~l~~g~~a~v~i~~~~pi~~e~~~~~~~lGRf~lR~~g~Tva-~G~V~~~ 108 (108)
T cd03704 56 KRPRFVKSGMKVIARLETTGPICLEKFEDFPQLGRFTLRDEGKTIA-IGKVLKL 108 (108)
T ss_pred cCCcEeCCCCEEEEEEEeCCcEEEEEcccCCCcccEEEEeCCCEEE-EEEEEEC
Confidence 444 6899999999987655221122222 5666666777665 7887653
No 62
>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=39.98 E-value=25 Score=30.06 Aligned_cols=54 Identities=22% Similarity=0.137 Sum_probs=43.1
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEeccCC
Q 026062 21 RECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPKTN 78 (244)
Q Consensus 21 ~~siPL~i~LRd~LkyA~t~rEak~Il~~~-----~V~VDGkvr~D~k~PvG~mD---VIsI~kt~ 78 (244)
+...+|+-+||+.|++-.+ |.=+.+| .|+|||+++..--+|+.-+| |++|+-..
T Consensus 16 ~~~~~Ll~~LR~~lgltg~----K~gC~~G~CGACtVlvdg~~v~SCl~~~~~~~G~~V~TiEgl~ 77 (148)
T TIGR03193 16 ADNMLLVDYLRDTVGLTGT----KQGCDGGECGACTVLVDGRPRLACSTLAHRVAGRKVETVEGLA 77 (148)
T ss_pred CCCCcHHHHHHHhcCCCCC----CCCCCCCCCCCCEEEECCeEeeccHhhHhhcCCCcEEEeCCCC
Confidence 4468999999999876554 5556666 69999999999999998876 89987644
No 63
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=39.92 E-value=1.3e+02 Score=32.24 Aligned_cols=77 Identities=18% Similarity=0.238 Sum_probs=51.8
Q ss_pred CcceeEEEeccCCceEEEEEcCCCceEEEEcCh---hhhcceeEEEe----eeEEeeCCceEEEccCceeEecCCCCccC
Q 026062 66 AGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIKA 138 (244)
Q Consensus 66 vG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~---eEa~~KLcKV~----~k~~~~gg~~ql~~hDGrni~~~d~~ik~ 138 (244)
.|-++++..+ .+.+=+-+|.+++....+++. -++.-||.||+ ....++.++|.++..||.-.......+++
T Consensus 112 ~~~~e~~~~~--~~~~V~s~d~~~k~~~~~v~~v~r~~~~~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~~a~~l~~ 189 (858)
T PRK14898 112 IGGHEVCDLP--IEIYALSLDQDEKVHWKRIISVIRHKANGKLIKIKTESGRTIRATPYHSFVTRKDNEVIPVEGSELKI 189 (858)
T ss_pred cCCceEEecC--CCcEEEEECCCCcEEEEEeeeEEeccCCCcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEeeHHhCCC
Confidence 3445555443 234444456666777776654 23344888888 44567899999999999877656668999
Q ss_pred CCeEEE
Q 026062 139 NDTIKL 144 (244)
Q Consensus 139 ~Dtv~i 144 (244)
||-|.+
T Consensus 190 GD~i~~ 195 (858)
T PRK14898 190 GDWLPV 195 (858)
T ss_pred CCEEee
Confidence 998765
No 64
>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=38.91 E-value=62 Score=31.47 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=29.3
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEE---ECCCccee
Q 026062 115 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMV---TGGRNRGR 173 (244)
Q Consensus 115 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v---~gG~n~G~ 173 (244)
.|....+.+.|..|||+- =|+|+.+..-.+++|+.+++ .+|+|.|-
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 345555555666666543 34667777777777776655 47888884
No 65
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=38.90 E-value=31 Score=29.20 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=21.2
Q ss_pred eeCCcEEEEECCCcceeEEEEEeE
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNR 180 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i 180 (244)
+.+|..|+|..|+++|+-++|...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999998765
No 66
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=38.73 E-value=68 Score=24.53 Aligned_cols=24 Identities=29% Similarity=0.313 Sum_probs=17.5
Q ss_pred eEEEEEeEEEecCCcc--EEEEEcCC
Q 026062 173 RVGIIKNREKHKGSFE--TIHIQDAL 196 (244)
Q Consensus 173 ~vG~I~~i~~~~~s~~--~v~i~d~~ 196 (244)
++|+|.+.+.||++.. +..+...+
T Consensus 2 ~vg~I~~~~~hp~sdkL~~~~Vd~G~ 27 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYVLKVDIGE 27 (95)
T ss_dssp EEEEEEEEEEETTSSSEEEEEEESSS
T ss_pred EEEEEEEEEECCCCCEEEEEEEEeCC
Confidence 6899999999998864 44454333
No 67
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=38.21 E-value=62 Score=31.33 Aligned_cols=45 Identities=18% Similarity=0.147 Sum_probs=25.4
Q ss_pred CCceEEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEE---CCCccee
Q 026062 116 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVT---GGRNRGR 173 (244)
Q Consensus 116 gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v~---gG~n~G~ 173 (244)
|....+.+.|..|||+- -|+|+-+..-.+++|+.+++. +|+|.|.
T Consensus 288 g~~~~viLQnaetIrlv-------------~~dG~~vsVt~Lk~GD~VL~~~~~~~RHfG~ 335 (344)
T PRK02290 288 GKRIRTILQNAETIRLV-------------TPDGKPVSVVDLKPGDEVLGYLEEAARHFGM 335 (344)
T ss_pred CeEEEEEEecCcEEEEE-------------CCCCCEeeeeecCCCCEEEEEecCCcccccc
Confidence 44555555566665543 344555555556666655542 6778773
No 68
>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=37.48 E-value=58 Score=26.59 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=24.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
|.+|+.+.|+.|.=.|..|.|.++..
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 69
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=36.42 E-value=56 Score=27.34 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=26.5
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 026062 155 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 183 (244)
Q Consensus 155 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 183 (244)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999654
No 70
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=35.57 E-value=3.7e+02 Score=24.97 Aligned_cols=61 Identities=23% Similarity=0.312 Sum_probs=40.7
Q ss_pred CCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEE
Q 026062 132 PDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 210 (244)
Q Consensus 132 ~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvI 210 (244)
++.+++.||.|+-+=-.|. |.+|= -||+|..++.+. +.+..+.++-.. -.+++.|||++
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 4667888886555433332 22221 278888888766 556778787543 47889999999
Q ss_pred cc
Q 026062 211 GK 212 (244)
Q Consensus 211 G~ 212 (244)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 85
No 71
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=35.46 E-value=1.1e+02 Score=33.45 Aligned_cols=55 Identities=25% Similarity=0.359 Sum_probs=42.2
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeEeEeeceEEEEccCCC
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFATRLGNVFTIGKGSK 215 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~--~~v~i~d~~g~~F~T~~~~vfvIG~~~k 215 (244)
...++.+-+++|.|.|+-|.|.+|.+. .-| +.-++ .++-.|.++..|+..+|. .+
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~-~~F~h~r~~~--En~Gv~vck~k~~~~~g~-~~ 638 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRP-FVFLHSRKNL--ENGGVFVCKEKNLILAGG-KK 638 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecc-eeeeeehhhc--ccCCeEEEecCCceeccc-cC
Confidence 467899999999999999999999652 112 22234 456689999999999995 44
No 72
>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=35.07 E-value=1.8e+02 Score=21.72 Aligned_cols=41 Identities=17% Similarity=0.417 Sum_probs=25.6
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeCCcEEEE-ECCCcceeEEEEEe
Q 026062 135 LIKANDTIKLDLEENKITDFIKFDVGNIVMV-TGGRNRGRVGIIKN 179 (244)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v-~gG~n~G~vG~I~~ 179 (244)
.+++||+..+.+.-.+ -+.++.|.-.++ .+|+.+| .|.|.+
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 3788988888776433 224555666666 5665555 677654
No 73
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=34.60 E-value=37 Score=25.79 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.2
Q ss_pred eEecCCCCccCCCeEEEe
Q 026062 128 TIRYPDPLIKANDTIKLD 145 (244)
Q Consensus 128 ni~~~d~~ik~~Dtv~i~ 145 (244)
-||..|.+|++||.+.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 357889999999999884
No 74
>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=34.34 E-value=90 Score=23.06 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=26.8
Q ss_pred EeeCCceEEEccCceeEecCC----CCccCCCeEEEecC
Q 026062 113 FGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 147 (244)
Q Consensus 113 ~~~gg~~ql~~hDGrni~~~d----~~ik~~Dtv~i~l~ 147 (244)
.+....-.|.|.||.++..|. +.+++|..|++-..
T Consensus 11 ~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 11 SIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYD 49 (61)
T ss_pred EEcCCceEEEecCCCEEECCCcccccccCCCCEEEEEEE
Confidence 345667789999999998774 36888888877554
No 75
>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=34.31 E-value=1.8e+02 Score=21.12 Aligned_cols=68 Identities=16% Similarity=0.121 Sum_probs=40.9
Q ss_pred eEEeeCCceEEEccCceeEecCC-CCc-----cCCCeEEEecCCCeeeeEEEeeCCc-EEEEECCCcceeEEEEE
Q 026062 111 VQFGQKGIPYINTYDGRTIRYPD-PLI-----KANDTIKLDLEENKITDFIKFDVGN-IVMVTGGRNRGRVGIIK 178 (244)
Q Consensus 111 k~~~~gg~~ql~~hDGrni~~~d-~~i-----k~~Dtv~i~l~~~kI~d~i~f~~G~-~~~v~gG~n~G~vG~I~ 178 (244)
+.+..++.-+|.+.||..+.... ..+ .-.+...+.|..|++.-.++=.... +.+-|....++-.|+--
T Consensus 3 i~T~~~~~~~i~l~dgs~v~l~~~s~~~~~~~~~~~~~~~~L~~G~~~~~~~~~~~~~~~V~T~~~~i~v~GT~f 77 (98)
T PF04773_consen 3 IRTGAGSRAEIALSDGSRVRLGPNSRVSVDRDSGSEPTRLRLLSGEILFDVSPGKKRPFEVRTPTATIGVRGTRF 77 (98)
T ss_pred EEcCCCCEEEEEECCCCEEEECCCcEEEEEcccCCCceEEEEcCCCEEEEEcccCCCCEEEEeCCEEEEEecCEE
Confidence 45678899999999999997543 334 4445556666666664333222222 55555555555555433
No 76
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=34.22 E-value=78 Score=25.32 Aligned_cols=61 Identities=20% Similarity=0.204 Sum_probs=35.6
Q ss_pred CCceEEEccCceeEecCCCCccCCCeEEEecC------CCeeeeEEEeeCCcEEEEECCCcceeEEEEEeE
Q 026062 116 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLE------ENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNR 180 (244)
Q Consensus 116 gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~------~~kI~d~i~f~~G~~~~v~gG~n~G~vG~I~~i 180 (244)
+.+.++.|.|||++.-.=.-+.-.--+.|+-. +.+=++.+++- .+++.|-|.+-+|-|.|=
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDEe 76 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDEE 76 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecchh
Confidence 45678899999999532111222222444332 11112333333 789999999999988763
No 77
>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=32.97 E-value=2.2e+02 Score=21.60 Aligned_cols=42 Identities=14% Similarity=0.376 Sum_probs=29.8
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeC-------CcEEEEECCCcceeEEEEEeE
Q 026062 135 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRGRVGIIKNR 180 (244)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~i~f~~-------G~~~~v~gG~n~G~vG~I~~i 180 (244)
.++.||...+.+...+-+ .+|+ |...+-..|..+| .|.|.+|
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 589999999999765533 3444 7777766776666 5887654
No 78
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=31.94 E-value=53 Score=27.50 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=26.1
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 154 FIKFDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 154 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
...|.+|+.+-|++|.=.|..|+|.++..
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 79
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=31.60 E-value=71 Score=34.95 Aligned_cols=28 Identities=32% Similarity=0.561 Sum_probs=25.8
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEe
Q 026062 156 KFDVGNIVMVTGGRNRGRVGIIKNREKH 183 (244)
Q Consensus 156 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 183 (244)
-|++|+.|=|+.|+|-|..|.|..++.+
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeCC
Confidence 3889999999999999999999999874
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=30.96 E-value=19 Score=30.71 Aligned_cols=52 Identities=25% Similarity=0.141 Sum_probs=40.2
Q ss_pred cccchhHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEecc
Q 026062 21 RECLPLILVLRNRLKYALTYREVIAILMQR-----HVLVDGKVRTDKTYPAGFMD---VVSIPK 76 (244)
Q Consensus 21 ~~siPL~i~LRd~LkyA~t~rEak~Il~~~-----~V~VDGkvr~D~k~PvG~mD---VIsI~k 76 (244)
....+|+-+||+.|++-.+..- +.+| .|.|||+.+.---.|+.-+| |.+|+-
T Consensus 18 ~~~~~Ll~~LR~~~~ltgtK~g----C~~G~CGACtVlvdG~~v~SCl~~~~~~~G~~v~TiEg 77 (151)
T TIGR03198 18 VPTTRLSDLLRKELQLTGTKVS----CGIGRCGACSVLIDGKLANACLTMAYQADGHEITTIEG 77 (151)
T ss_pred CCCcHHHHHHHhccCCCCCCCC----CCCCcCCccEEEECCcEEechHHHHHHhcCCEEEecCC
Confidence 3478999999999998765433 6666 69999999998888876554 677754
No 81
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=30.14 E-value=1.9e+02 Score=23.22 Aligned_cols=61 Identities=18% Similarity=0.406 Sum_probs=38.1
Q ss_pred eeCCcEEEEE-CCCcceeEEEEEeEEEec-----CCc-cEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeee
Q 026062 157 FDVGNIVMVT-GGRNRGRVGIIKNREKHK-----GSF-ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLS 229 (244)
Q Consensus 157 f~~G~~~~v~-gG~n~G~vG~I~~i~~~~-----~s~-~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~ 229 (244)
|+.|+.--.. .... +|.|..|+... +-+ +-|.|++.+|+. +.|...+ |+.-|-++-|+++
T Consensus 41 F~~G~~d~F~v~~~d---LG~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~ 107 (109)
T cd02899 41 FYPGSLKRIRFRAAD---VGDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECccc---cCceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEe
Confidence 5556543321 2333 44555554421 223 788898866544 4599988 9999999988876
Q ss_pred h
Q 026062 230 I 230 (244)
Q Consensus 230 ~ 230 (244)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 82
>cd03705 EF1_alpha_III Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
Probab=29.62 E-value=1.2e+02 Score=22.85 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=24.9
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeC-------CcEEEEECCCcce
Q 026062 135 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRG 172 (244)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~i~f~~-------G~~~~v~gG~n~G 172 (244)
.++.||...+.|...+ -+.+|+ |..+++-+|..+|
T Consensus 59 ~l~~n~~a~v~l~~~~---pi~~e~~~~~~~lgrf~lrd~~~Tva 100 (104)
T cd03705 59 FLKSGDAAIVKIVPQK---PLVVETFSEYPPLGRFAVRDMGQTVA 100 (104)
T ss_pred ccCCCCEEEEEEEECC---eeEEEEcccCCCccCEEEEeCCCEEE
Confidence 5899999999997554 345565 7777776666555
No 83
>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=29.12 E-value=60 Score=27.09 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=25.3
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 155 IKFDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 155 i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5588999999999999999999999853
No 84
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=28.05 E-value=48 Score=27.35 Aligned_cols=42 Identities=24% Similarity=0.360 Sum_probs=33.1
Q ss_pred CCceEEEEcChhhhcceeEEEeeeEEeeCCceEEEccCceeEecCCC
Q 026062 88 KGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 134 (244)
Q Consensus 88 kgrf~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~ 134 (244)
+..|+|+.+|+= .|-+|--+.|..-+...+|| ||-|+-|.+|
T Consensus 21 KRwFvL~qvsQY--tfamcsy~ekks~P~e~~ql---dGyTvDy~~~ 62 (117)
T cd01234 21 KRFFVLVQVSQY--TFAMCSYREKKAEPTEFIQL---DGYTVDYMPE 62 (117)
T ss_pred eeEEEEEchhHH--HHHHHhhhhhcCCchhheee---cceEEeccCC
Confidence 345788877654 45789888888889999998 9999988765
No 85
>PF08942 DUF1919: Domain of unknown function (DUF1919); InterPro: IPR015037 This protein has no known function. It is found in various hypothetical and putative bacterial proteins. ; PDB: 2G6T_B.
Probab=27.84 E-value=16 Score=32.81 Aligned_cols=59 Identities=29% Similarity=0.412 Sum_probs=36.2
Q ss_pred hHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChhhhcce
Q 026062 26 LILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFK 104 (244)
Q Consensus 26 L~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~K 104 (244)
|-+.-+|+++|-.|.+. -+.+....++-.-..+ .||||..|-|+| | | +|==|.+||+-|
T Consensus 53 L~i~~~Dyik~l~nl~~---y~~~~l~~~~~~~~~~-~YPvG~L~dIei-----h----------F-~HY~s~~eA~~K 111 (201)
T PF08942_consen 53 LFIFPPDYIKFLENLDY---YLSQELEFIDESKSYD-DYPVGLLGDIEI-----H----------F-MHYKSFEEAKEK 111 (201)
T ss_dssp EE--HHHHHHHHHSHHH---HHCS--EECE--BGGG-B--EEEEC-EEE-----E----------E-SS-SSHHHHHHH
T ss_pred eEECcHHHHHHHHCHHH---HhcCCeEEeecCcccC-CcceEeECCEEE-----E----------E-EecCCHHHHHHH
Confidence 45666899999888865 4666666665555456 899999999999 2 3 565689999755
No 86
>KOG2404 consensus Fumarate reductase, flavoprotein subunit [Energy production and conversion]
Probab=26.64 E-value=52 Score=32.44 Aligned_cols=51 Identities=27% Similarity=0.413 Sum_probs=44.6
Q ss_pred CcccCceeccCCCCCCCCCcccchhHHHHHhhh-cccccHHHHHHHHhCceE
Q 026062 2 LDKLGGAFAPKPSSGPHKSRECLPLILVLRNRL-KYALTYREVIAILMQRHV 52 (244)
Q Consensus 2 l~K~~~~~a~rpspGPH~~~~siPL~i~LRd~L-kyA~t~rEak~Il~~~~V 52 (244)
|+.++|.-.||+.-+.|++--..|+.-.|+++| +.|.+.-|+-+|+.|-.|
T Consensus 117 la~lgGHSvpRTHr~s~plppgfei~~~L~~~l~k~as~~pe~~ki~~nskv 168 (477)
T KOG2404|consen 117 LAQLGGHSVPRTHRSSGPLPPGFEIVKALSTRLKKKASENPELVKILLNSKV 168 (477)
T ss_pred HHHhcCCCCCcccccCCCCCCchHHHHHHHHHHHHhhhcChHHHhhhhccee
Confidence 566788899999999999999999999999999 478888899999887654
No 87
>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=26.35 E-value=44 Score=24.98 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=27.0
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEec------CCccEEEEEcCCCCeEe
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 201 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~~~------~s~~~v~i~d~~g~~F~ 201 (244)
+.+|+.+||.| +|++|+|+.|.-.- .....|.++..+| .|+
T Consensus 11 it~G~rVMia~---tG~tgvikaIh~dglt~~Q~rR~k~Vel~g~e~-~f~ 57 (65)
T TIGR03318 11 ITTGSRVMIAG---TGHTGVIKAIHTEGLTAEQARREKCVELEGCEE-RFA 57 (65)
T ss_pred cCCCcEEEEec---CCccceeehhhhCCCCHHHhhhccEEEEecccc-eec
Confidence 45799999987 67888898885422 1125777775444 454
No 88
>cd05892 Ig_Myotilin_C C-terminal immunoglobulin (Ig)-like domain of myotilin. Ig_Myotilin_C: C-terminal immunoglobulin (Ig)-like domain of myotilin. Mytolin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to the latter family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Myotilin is most abundant in skeletal and cardiac muscle, and is involved in maintaining sarcomere integrity. It binds to alpha-actinin, filamin and actin. Mutations in myotilin lead to muscle disorders.
Probab=26.16 E-value=1.3e+02 Score=21.68 Aligned_cols=34 Identities=12% Similarity=0.272 Sum_probs=27.8
Q ss_pred CceEEEEEcCCC--ceEEEEcChhhhcceeEEEeee
Q 026062 78 NENFRLLYDTKG--RFRLHSLRDEEAKFKLCKVRSV 111 (244)
Q Consensus 78 ~e~yRvl~d~kg--rf~l~~I~~eEa~~KLcKV~~k 111 (244)
+.+|.+..+..| .|.+..+..++++.-.|...|.
T Consensus 28 ~~r~~~~~~~~g~~~L~I~~~~~~D~G~Y~C~A~N~ 63 (75)
T cd05892 28 TDRISLYQDNSGRVTLLIKNVNKKDAGWYTVSAVNE 63 (75)
T ss_pred CCeEEEEEcCCCcEEEEECCCChhhCEEEEEEEEcC
Confidence 457888888777 5777799999999889998873
No 89
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=25.61 E-value=1.3e+02 Score=21.62 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=24.9
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCeee
Q 026062 115 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 152 (244)
Q Consensus 115 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 152 (244)
.+..-...+..|-.+.+|. -|+.||.|++|-.+++=+
T Consensus 18 ~~~~K~A~letG~~i~VP~-FI~~Gd~I~VdT~~g~Yv 54 (56)
T PF09285_consen 18 SSSYKPATLETGAEIQVPL-FIEEGDKIKVDTRDGSYV 54 (56)
T ss_dssp STTEEEEEETTS-EEEEET-T--TT-EEEEETTTTEEE
T ss_pred CCCccEEEEcCCCEEEccc-eecCCCEEEEECCCCeEe
Confidence 3444566778888888665 699999999999998643
No 90
>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=25.51 E-value=95 Score=29.94 Aligned_cols=45 Identities=18% Similarity=-0.026 Sum_probs=36.9
Q ss_pred cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcc
Q 026062 23 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGF 68 (244)
Q Consensus 23 siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~k~PvG~ 68 (244)
++++.=++.. .+.+.+.+||++.|++|-|+|||...+|..+-.-.
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~ 373 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKE 373 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhcc
Confidence 4666666664 58899999999999999999999999998765443
No 91
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=25.29 E-value=58 Score=27.93 Aligned_cols=50 Identities=18% Similarity=0.232 Sum_probs=36.6
Q ss_pred eeeeEEEeeCCcEEEEECCCcce-eEEEEEeEEEecCC--ccEEEEEcCCCCe
Q 026062 150 KITDFIKFDVGNIVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 199 (244)
Q Consensus 150 kI~d~i~f~~G~~~~v~gG~n~G-~vG~I~~i~~~~~s--~~~v~i~d~~g~~ 199 (244)
=.+..+|+..++.+-|.+|+..| .+|.|.++-+..-. .+.|.-+-.+|..
T Consensus 42 y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 42 YNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred hCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 35788999999999999999999 99999998664322 2344444455543
No 92
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=25.22 E-value=67 Score=29.91 Aligned_cols=32 Identities=25% Similarity=0.515 Sum_probs=22.0
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEE
Q 026062 159 VGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHI 192 (244)
Q Consensus 159 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~-~~v~i 192 (244)
.||.|.|+.|...|+.|.+..- |-|.. -+|++
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 4999999999999999999874 66664 34444
No 93
>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=25.17 E-value=4.7e+02 Score=22.95 Aligned_cols=68 Identities=16% Similarity=0.256 Sum_probs=46.1
Q ss_pred EEEeeeEEeeCCceEEEc-cCceeE-ecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEE
Q 026062 106 CKVRSVQFGQKGIPYINT-YDGRTI-RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGI 176 (244)
Q Consensus 106 cKV~~k~~~~gg~~ql~~-hDGrni-~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v~gG~n~G~vG~ 176 (244)
|.| ++..+.+..-++.+ =||.++ .|-+...|.-.|..+.+..++ -.|-|+...+-+=..|......|.
T Consensus 64 ~~I-~I~~~~g~~YeYsL~VdGksl~ky~e~~~k~~~tW~~~i~G~~--~RIvLdk~t~~vwvnG~~iet~~e 133 (177)
T PF06905_consen 64 CEI-NIEAVSGFAYEYSLEVDGKSLKKYKEEQSKKFNTWELNIDGQE--YRIVLDKDTMDVWVNGEKIETEGE 133 (177)
T ss_dssp EEE-EEEEETTTEEEEEEEETTEEEEE--SSTTTTEEEEEEEETTEE--EEEEEETTTTEEEETTCEE--EEE
T ss_pred EEE-EEEecCCceEEEEEEECCEEHHHHHHHHhhhheeEEEecCCCE--EEEEEEcceEEEEECCEEccccce
Confidence 444 33444555444443 388888 677888899999999997644 667888888888899998877664
No 94
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.95 E-value=91 Score=31.17 Aligned_cols=39 Identities=15% Similarity=0.143 Sum_probs=34.0
Q ss_pred ccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEecc
Q 026062 22 ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTD 61 (244)
Q Consensus 22 ~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D 61 (244)
..+|++=++|+ ++.-.+..||++++.||-|.+|++.++|
T Consensus 397 ~~~s~~~l~~k-a~~~~s~~~a~r~i~qG~vslnh~~v~~ 435 (467)
T KOG2623|consen 397 PGVSILDLLRK-ASRFPSGKEARRMIQQGGVSLNHEKVRD 435 (467)
T ss_pred CCCcHHHHHHH-hhcCCCcHHHHHHHHccceeecCccccC
Confidence 36788888888 5666778899999999999999999999
No 95
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=23.52 E-value=4e+02 Score=26.10 Aligned_cols=52 Identities=27% Similarity=0.313 Sum_probs=34.8
Q ss_pred CccCCCeEEEecCCCeeeeEEEe----eCCcEEEEECCCcceeEEEEEeEEEecCCc
Q 026062 135 LIKANDTIKLDLEENKITDFIKF----DVGNIVMVTGGRNRGRVGIIKNREKHKGSF 187 (244)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~i~f----~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~ 187 (244)
.++.||...+.|...+=+-.-+| .-|..++.-+|.-+| .|.|.++....||-
T Consensus 381 ~l~~g~~a~v~l~~~~pi~~e~~~~~~~lgrfilrd~g~tva-~G~I~~v~~~~~~~ 436 (446)
T PTZ00141 381 AIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRDMKQTVA-VGVIKSVEKKEGSG 436 (446)
T ss_pred EECCCCEEEEEEEECCceEEeecccCCCCccEEEEECCCEEE-EEEEEEEecCCCcc
Confidence 57789999888875543322333 246677777776555 89999988666664
No 96
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=23.26 E-value=62 Score=31.63 Aligned_cols=83 Identities=18% Similarity=0.203 Sum_probs=62.3
Q ss_pred CCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCE--EeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 026062 17 PHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGK--VRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 94 (244)
Q Consensus 17 PH~~~~siPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGk--vr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~ 94 (244)
||+.. ++-+.-|+..-+|.-. +++-.=.+.-+|+.|.. .+.++.|-+.|||-.+-.....+|++.-+++ ++.+
T Consensus 54 ~~~v~-lld~d~wik~~~Ki~~--~~~v~~~k~~hi~~~~g~~i~ln~~fk~sl~~altgg~~~nsfgv~i~E~--lvsv 128 (447)
T COG5144 54 SHSVS-LLDEDEWIKETLKILL--RIQVIGKKGNHIYLDEGLMIRLNPEFKISLMDALTGGTMENSFGVCIGEK--LVSV 128 (447)
T ss_pred CCCcc-hhhHHHHHhhhhHHHH--HHHHhhhccceEEecCCceEEeChHHHHHHHHHhhccccccccceeeccc--eeee
Confidence 44432 4445556665555543 55555566668999988 9999999999999999999999999999988 7777
Q ss_pred EcChhhhcce
Q 026062 95 SLRDEEAKFK 104 (244)
Q Consensus 95 ~I~~eEa~~K 104 (244)
...+++|+.|
T Consensus 129 d~ld~ys~~k 138 (447)
T COG5144 129 DMLDSYSSRK 138 (447)
T ss_pred ehhhhhhhhh
Confidence 7777777654
No 97
>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=22.83 E-value=1.8e+02 Score=20.09 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=28.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEE
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 193 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~-~~v~i~ 193 (244)
|++|..+++.-+...-.-++|.+++..++.. =.||-.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEET
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcC
Confidence 6789999999999999999999998865553 356654
No 98
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=22.63 E-value=2.5e+02 Score=23.23 Aligned_cols=77 Identities=16% Similarity=0.201 Sum_probs=45.1
Q ss_pred EEEccCceeEecCCCCccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEEcCCCC
Q 026062 120 YINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQDALGH 198 (244)
Q Consensus 120 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~-~~v~i~d~~g~ 198 (244)
+|.+|+|++-++.| +++.|.+.-...+ +-++++..-..+|......|- ..|.=.++.. ..++++=.-++
T Consensus 7 ~I~l~~G~~krvED--l~teDfi~sa~~s----~~~~l~~stv~~i~~~~~~~~----v~itF~~g~~~~~v~~ev~~eH 76 (116)
T smart00536 7 RLCLANGSNKKVED--LKTEDFIRSAECS----NDEEIQMSTVKRIGSSGLPSV----VTLTFDPGVEDALLTVECQVEH 76 (116)
T ss_pred EEEecCCCeeeeec--cchhhhHhhhccC----CcccccceeEEEeCCCCCcce----EEEEEEecCccceEEEEEecCC
Confidence 56679999888766 7888888776655 445555555555554433322 2233333332 46666544444
Q ss_pred eEeEeeceEEEEccC
Q 026062 199 EFATRLGNVFTIGKG 213 (244)
Q Consensus 199 ~F~T~~~~vfvIG~~ 213 (244)
-| ||-|+|
T Consensus 77 Pf-------FV~gqG 84 (116)
T smart00536 77 PF-------FVKGKG 84 (116)
T ss_pred Ce-------EEcCcc
Confidence 44 777765
No 99
>cd05741 Ig_CEACAM_D1_like First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins. Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily-like. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surf
Probab=21.99 E-value=1.3e+02 Score=21.51 Aligned_cols=31 Identities=16% Similarity=0.192 Sum_probs=25.3
Q ss_pred EEEEcCCCceEEEEcChhhhcceeEEEeeeE
Q 026062 82 RLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQ 112 (244)
Q Consensus 82 Rvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~ 112 (244)
|+-.+..+.|.+..+.++++..-.|.|....
T Consensus 50 R~~~~~~~sL~I~~l~~~DsG~Y~c~v~~~~ 80 (92)
T cd05741 50 RETIYPNGSLLIQNLTKEDSGTYTLQIISTN 80 (92)
T ss_pred eEEEcCCceEEEccCCchhcEEEEEEEEcCC
Confidence 3444555899999999999999999998754
No 100
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=21.93 E-value=1e+02 Score=25.57 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=24.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEE
Q 026062 156 KFDVGNIVMVTGGRNRGRVGIIKNRE 181 (244)
Q Consensus 156 ~f~~G~~~~v~gG~n~G~vG~I~~i~ 181 (244)
.|.+|+.+.|++|.=.|..|.|.++.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 58999999999999999999998874
No 101
>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=21.70 E-value=1.6e+02 Score=21.26 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=26.6
Q ss_pred eCCceEEEccCceeEecCCCCccCCCeEEEecCCCe
Q 026062 115 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 150 (244)
Q Consensus 115 ~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 150 (244)
.++.-...+..|-.+.+|. -|+.||.|++|-.+++
T Consensus 18 ~~~~K~A~letG~~i~VP~-FI~~Gd~I~V~T~~g~ 52 (56)
T cd05794 18 SSGTKPATLETGAEVQVPL-FIKEGEKIKVDTRTGE 52 (56)
T ss_pred CCCcceEEECCCCEEEcCC-eecCCCEEEEECCCCc
Confidence 3444445678888887554 6899999999999876
No 102
>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=21.56 E-value=2.9e+02 Score=23.39 Aligned_cols=51 Identities=18% Similarity=0.166 Sum_probs=35.6
Q ss_pred ccEEEEEcCCCCeEeEeeceEEEEccCCCceEecCCCcceeeehHHHHHHHHH
Q 026062 187 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQA 239 (244)
Q Consensus 187 ~~~v~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~~gi~~~~~~~~~~~~~ 239 (244)
++-+.+-|.+|+--|+..+|+|++= +.-|++-|.+.|+-..+..+.-.+++
T Consensus 125 ~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~giL~Gitr~~ll~~~ 175 (231)
T PF01063_consen 125 ADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGILPGITRQLLLELA 175 (231)
T ss_dssp SSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSSB--HHHHHHHHHH
T ss_pred cchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhhccHHHHHHHHHHH
Confidence 4445667899999999999999994 34488888888876666554444333
No 103
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=21.35 E-value=2.4e+02 Score=21.55 Aligned_cols=33 Identities=24% Similarity=0.392 Sum_probs=24.1
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCC
Q 026062 157 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGH 198 (244)
Q Consensus 157 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~ 198 (244)
+.+|+.++-+|| -+|+|.++.. +.+.++.+.|.
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d-----~~v~vei~~g~ 70 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAE-----NTIVIELNDNT 70 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCCe
Confidence 567888888775 6899999863 46677766653
No 104
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=21.26 E-value=1.1e+02 Score=24.71 Aligned_cols=35 Identities=14% Similarity=0.381 Sum_probs=27.9
Q ss_pred EEeeCCceEEEccCceeEecCCCCccCCCeEEEecCCCe
Q 026062 112 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 150 (244)
Q Consensus 112 ~~~~gg~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 150 (244)
.++.+|+.++ +|.... |...+|+||.|.|.+....
T Consensus 29 ~~~~~GrV~v---NG~~aK-pS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 29 EMIEGGRVKV---NGQRAK-PSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHHHCCeEEE---CCEEcc-cccccCCCCEEEEEeCCcE
Confidence 3567888888 577775 7889999999999997744
No 105
>PF07569 Hira: TUP1-like enhancer of split; InterPro: IPR011494 The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain IPR001680 from INTERPRO.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.02 E-value=2.8e+02 Score=24.53 Aligned_cols=57 Identities=18% Similarity=0.366 Sum_probs=40.8
Q ss_pred CCceEEEEEcCCCceEEEEcChhhhccee------------------EEEeeeEEeeCCceEEEccCceeEecCC
Q 026062 77 TNENFRLLYDTKGRFRLHSLRDEEAKFKL------------------CKVRSVQFGQKGIPYINTYDGRTIRYPD 133 (244)
Q Consensus 77 t~e~yRvl~d~kgrf~l~~I~~eEa~~KL------------------cKV~~k~~~~gg~~ql~~hDGrni~~~d 133 (244)
...+|-+.....|.|..=.+....+-++- ..|+..++-+.|.|.+.+.+|..+.|..
T Consensus 20 ~~~~~Ll~iT~~G~l~vWnl~~~k~~~~~~Si~pll~~~~~~~~~~~~~i~~~~lt~~G~PiV~lsng~~y~y~~ 94 (219)
T PF07569_consen 20 CNGSYLLAITSSGLLYVWNLKKGKAVLPPVSIAPLLNSSPVSDKSSSPNITSCSLTSNGVPIVTLSNGDSYSYSP 94 (219)
T ss_pred eCCCEEEEEeCCCeEEEEECCCCeeccCCccHHHHhcccccccCCCCCcEEEEEEcCCCCEEEEEeCCCEEEecc
Confidence 45667777777777766665554444333 5667777778999999999999988753
No 106
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=20.89 E-value=97 Score=26.96 Aligned_cols=30 Identities=17% Similarity=0.367 Sum_probs=26.5
Q ss_pred eEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 153 DFIKFDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 153 d~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
....|++|+.+-|+.|.=+|..|+|.++..
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ 149 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDE 149 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEcC
Confidence 446789999999999999999999999853
No 107
>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=20.86 E-value=2.1e+02 Score=21.17 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=16.6
Q ss_pred cCCCeEEEecC-----CCeeeeEEEeeCCcEEEE
Q 026062 137 KANDTIKLDLE-----ENKITDFIKFDVGNIVMV 165 (244)
Q Consensus 137 k~~Dtv~i~l~-----~~kI~d~i~f~~G~~~~v 165 (244)
|+||.|.+.-. +|.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG~MYLv 35 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCcEEEEE
Confidence 55666655544 345666666666655444
No 108
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=20.83 E-value=2.6e+02 Score=26.05 Aligned_cols=30 Identities=40% Similarity=0.661 Sum_probs=27.1
Q ss_pred eEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 153 DFIKFDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 153 d~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
..+.|++|+.+-|+.|.=.|..|+|.++..
T Consensus 202 ~~~~f~vGd~VrI~dGPF~GfeG~I~eid~ 231 (258)
T TIGR01956 202 NLSKFRVGNFVKIVDGPFKGIVGKIKKIDQ 231 (258)
T ss_pred cccCCCCCCEEEEEecCCCCcEEEEEEEeC
Confidence 457799999999999999999999999953
No 109
>PLN02772 guanylate kinase
Probab=20.73 E-value=2.3e+02 Score=28.01 Aligned_cols=63 Identities=19% Similarity=0.263 Sum_probs=37.5
Q ss_pred EEEeeCCcEEEEECCCccee-EEEEEeEEE-ecCCccEEEEEc-----CCCCeEeEe-eceEEEEccCCCc
Q 026062 154 FIKFDVGNIVMVTGGRNRGR-VGIIKNREK-HKGSFETIHIQD-----ALGHEFATR-LGNVFTIGKGSKP 216 (244)
Q Consensus 154 ~i~f~~G~~~~v~gG~n~G~-vG~I~~i~~-~~~s~~~v~i~d-----~~g~~F~T~-~~~vfvIG~~~kp 216 (244)
+--+..|+..+|+||+|-+. .-....|-. .........+.. .+|+++... .+.++||+++..|
T Consensus 28 ~tav~igdk~yv~GG~~d~~~~~~~v~i~D~~t~~W~~P~V~G~~P~~r~GhSa~v~~~~rilv~~~~~~~ 98 (398)
T PLN02772 28 ETSVTIGDKTYVIGGNHEGNTLSIGVQILDKITNNWVSPIVLGTGPKPCKGYSAVVLNKDRILVIKKGSAP 98 (398)
T ss_pred ceeEEECCEEEEEcccCCCccccceEEEEECCCCcEecccccCCCCCCCCcceEEEECCceEEEEeCCCCC
Confidence 34456699999999999864 222222211 112223333332 467887777 6899999976443
No 110
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.63 E-value=1.1e+02 Score=27.52 Aligned_cols=44 Identities=18% Similarity=0.124 Sum_probs=31.2
Q ss_pred CccCCCeEEEecCCCeeeeEEEeeCCcEEEEECCCcce----eEEEEEeEEEec
Q 026062 135 LIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRG----RVGIIKNREKHK 184 (244)
Q Consensus 135 ~ik~~Dtv~i~l~~~kI~d~i~f~~G~~~~v~gG~n~G----~vG~I~~i~~~~ 184 (244)
.|++||.|-+.= ++|.|+.....--++|+|+| +||.|.+|....
T Consensus 7 ~Y~vgD~VYv~p------~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k 54 (202)
T cd04708 7 TYSVGDFLYVSP------DAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEK 54 (202)
T ss_pred EEecCCeEEECc------ccccccccccccccccccCCCCCcEEEEEEEEEecc
Confidence 467777777765 44555556677778888976 799999986533
No 111
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=20.52 E-value=1e+02 Score=31.41 Aligned_cols=42 Identities=17% Similarity=0.196 Sum_probs=32.1
Q ss_pred CCeEEEecCCCeeeeEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 026062 139 NDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 182 (244)
Q Consensus 139 ~Dtv~i~l~~~kI~d~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 182 (244)
+|+..|+.|.+.+-. -|..|+++-|+-|.+.+.+|.|..|+.
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 345555555544432 378899999999999999999999865
No 112
>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=20.19 E-value=3.4e+02 Score=19.51 Aligned_cols=55 Identities=13% Similarity=0.123 Sum_probs=29.4
Q ss_pred eCCcEEEEECCCcceeEE-EEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEcc
Q 026062 158 DVGNIVMVTGGRNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 212 (244)
Q Consensus 158 ~~G~~~~v~gG~n~G~vG-~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~ 212 (244)
.+|+.++...+.+..... .+.......+...++.|+..+|.++..-.+.-|.+..
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 456666666653222111 1122222334457888887778777655555555554
Done!