Query 024598
Match_columns 265
No_of_seqs 134 out of 392
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:54:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024598.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024598hhsearch_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 3E-115 6E-120 793.7 29.6 260 1-260 1-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 5E-115 1E-119 792.3 29.9 260 1-260 1-260 (262)
3 PTZ00223 40S ribosomal protein 100.0 9E-111 2E-115 767.6 29.8 258 5-262 2-260 (273)
4 PRK04313 30S ribosomal protein 100.0 3E-104 7E-109 713.6 27.5 235 5-240 1-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 6E-102 1E-106 693.3 23.4 240 2-242 1-241 (241)
6 KOG0378 40S ribosomal protein 100.0 1.3E-99 3E-104 680.6 15.6 263 1-263 1-263 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 9.2E-33 2E-37 211.6 9.4 77 94-170 1-77 (77)
8 PF08071 RS4NT: RS4NT (NUC023) 99.8 2.9E-21 6.2E-26 129.9 1.6 38 3-40 1-38 (38)
9 PF01479 S4: S4 domain; Inter 98.8 5.9E-09 1.3E-13 71.7 5.4 48 42-90 1-48 (48)
10 COG0522 RpsD Ribosomal protein 98.8 3.1E-09 6.7E-14 95.1 4.1 44 51-94 102-145 (205)
11 TIGR01018 rpsD_arch ribosomal 98.1 2.7E-06 5.9E-11 73.9 3.8 45 51-95 112-158 (162)
12 PLN00189 40S ribosomal protein 98.0 3.1E-06 6.8E-11 75.4 3.1 43 51-93 117-159 (194)
13 cd00165 S4 S4/Hsp/ tRNA synthe 97.9 4.8E-05 1E-09 53.0 7.4 60 43-103 2-61 (70)
14 CHL00113 rps4 ribosomal protei 97.8 9.5E-06 2.1E-10 72.6 2.7 46 51-96 97-142 (201)
15 PTZ00155 40S ribosomal protein 97.8 1E-05 2.3E-10 71.4 2.8 44 45-88 102-152 (181)
16 TIGR02988 YaaA_near_RecF S4 do 97.8 6E-05 1.3E-09 54.2 5.9 51 42-93 9-59 (59)
17 PRK04051 rps4p 30S ribosomal p 97.7 4.4E-05 9.5E-10 67.2 5.1 47 51-97 111-159 (177)
18 TIGR01017 rpsD_bact ribosomal 97.7 5E-05 1.1E-09 67.6 5.1 44 51-94 98-141 (200)
19 smart00363 S4 S4 RNA-binding d 97.7 0.00012 2.7E-09 49.5 5.6 51 43-94 2-52 (60)
20 PRK05327 rpsD 30S ribosomal pr 97.7 6.9E-05 1.5E-09 66.9 5.2 43 52-94 102-144 (203)
21 PF13275 S4_2: S4 domain; PDB: 96.8 0.00047 1E-08 51.7 1.3 59 40-101 6-64 (65)
22 TIGR03069 PS_II_S4 photosystem 96.7 0.0052 1.1E-07 56.8 7.4 62 41-115 183-244 (257)
23 PF00467 KOW: KOW motif; Inte 96.7 0.002 4.4E-08 41.3 3.1 31 177-210 1-31 (32)
24 PRK11507 ribosome-associated p 96.7 0.007 1.5E-07 46.1 6.4 59 40-101 10-68 (70)
25 smart00739 KOW KOW (Kyprides, 96.6 0.0019 4.2E-08 39.1 2.7 27 174-200 1-27 (28)
26 PRK10348 ribosome-associated h 96.3 0.0086 1.9E-07 50.7 5.5 59 41-101 8-66 (133)
27 TIGR00478 tly hemolysin TlyA f 96.2 0.0083 1.8E-07 54.5 5.5 47 47-94 5-51 (228)
28 TIGR00005 rluA_subfam pseudour 96.0 0.031 6.8E-07 51.5 8.1 52 41-93 5-56 (299)
29 PLN00051 RNA-binding S4 domain 95.5 0.038 8.1E-07 51.6 6.7 62 41-115 191-252 (267)
30 COG2501 S4-like RNA binding pr 95.3 0.04 8.6E-07 42.4 5.1 60 40-102 10-69 (73)
31 COG0564 RluA Pseudouridylate s 95.1 0.06 1.3E-06 50.5 6.8 57 40-99 11-67 (289)
32 PRK11180 rluD 23S rRNA pseudou 95.0 0.092 2E-06 49.5 7.7 53 41-94 17-69 (325)
33 COG2302 Uncharacterized conser 94.8 0.066 1.4E-06 49.8 6.0 53 40-94 179-231 (257)
34 TIGR01080 rplX_A_E ribosomal p 94.5 0.08 1.7E-06 43.8 5.3 57 170-229 37-100 (114)
35 COG1188 Ribosome-associated he 94.3 0.084 1.8E-06 42.9 4.9 48 53-101 19-66 (100)
36 COG1189 Predicted rRNA methyla 94.1 0.072 1.6E-06 49.4 4.7 112 52-164 12-152 (245)
37 KOG3301 Ribosomal protein S4 [ 93.7 0.04 8.7E-07 48.4 2.1 36 51-86 105-140 (183)
38 PRK10839 16S rRNA pseudouridyl 93.7 0.15 3.4E-06 45.5 5.8 48 44-93 3-50 (232)
39 PRK10475 23S rRNA pseudouridin 93.4 0.16 3.4E-06 47.8 5.7 66 40-108 5-78 (290)
40 PRK11025 23S rRNA pseudouridyl 93.1 0.43 9.3E-06 44.9 8.1 51 41-93 19-69 (317)
41 PRK13354 tyrosyl-tRNA syntheta 92.3 0.46 1E-05 46.8 7.4 65 41-111 342-406 (410)
42 PRK05912 tyrosyl-tRNA syntheta 92.3 0.36 7.9E-06 47.4 6.6 64 41-111 342-405 (408)
43 COG1187 RsuA 16S rRNA uridine- 92.0 0.42 9.1E-06 44.3 6.3 55 52-107 12-73 (248)
44 PRK10700 23S rRNA pseudouridyl 91.0 0.58 1.2E-05 43.9 6.3 61 46-109 7-79 (289)
45 PRK01191 rpl24p 50S ribosomal 90.8 0.64 1.4E-05 38.9 5.7 55 172-229 43-104 (120)
46 KOG4655 U3 small nucleolar rib 88.2 0.3 6.5E-06 43.1 2.0 34 51-84 115-148 (181)
47 PTZ00194 60S ribosomal protein 87.8 1.4 3E-05 38.0 5.7 58 172-229 44-105 (143)
48 PRK12281 rplX 50S ribosomal pr 86.7 1.1 2.4E-05 34.5 4.0 39 173-214 5-43 (76)
49 CHL00141 rpl24 ribosomal prote 85.8 1.3 2.9E-05 34.5 4.2 39 172-213 6-44 (83)
50 PRK00004 rplX 50S ribosomal pr 84.3 1.4 3.1E-05 35.7 3.9 29 173-201 3-31 (105)
51 TIGR01079 rplX_bact ribosomal 78.7 2.9 6.3E-05 33.9 3.8 28 174-201 3-30 (104)
52 COG0162 TyrS Tyrosyl-tRNA synt 76.0 5.2 0.00011 39.6 5.4 60 44-111 338-397 (401)
53 PF13051 DUF3912: Protein of u 75.7 7.5 0.00016 29.0 4.9 50 177-230 5-55 (68)
54 PTZ00065 60S ribosomal protein 59.8 11 0.00023 32.1 3.3 32 175-210 8-39 (130)
55 COG2163 RPL14A Ribosomal prote 59.2 9.7 0.00021 32.1 3.0 26 175-200 5-30 (125)
56 KOG1999 RNA polymerase II tran 56.4 65 0.0014 35.6 9.1 55 175-233 582-638 (1024)
57 COG0198 RplX Ribosomal protein 56.0 18 0.00038 29.7 3.9 29 173-201 3-31 (104)
58 PF14001 YdfZ: YdfZ protein 55.7 19 0.00041 27.2 3.7 41 175-219 10-56 (64)
59 PF12005 DUF3499: Protein of u 49.6 7.1 0.00015 32.9 0.7 23 7-29 46-68 (123)
60 TIGR03193 4hydroxCoAred 4-hydr 48.7 14 0.00031 31.9 2.4 52 39-94 16-75 (148)
61 PRK04333 50S ribosomal protein 47.3 21 0.00045 28.0 2.9 33 174-210 3-35 (84)
62 PF04773 FecR: FecR protein; 46.6 1.2E+02 0.0026 22.5 9.4 68 129-196 3-77 (98)
63 cd04093 HBS1_C HBS1_C: this fa 44.9 1.4E+02 0.0031 22.9 8.0 45 153-198 59-107 (107)
64 cd03704 eRF3c_III This family 43.7 91 0.002 24.3 6.2 48 150-198 56-108 (108)
65 PF03417 AAT: Acyl-coenzyme A: 43.3 26 0.00057 30.6 3.3 29 39-68 69-97 (225)
66 TIGR00234 tyrS tyrosyl-tRNA sy 43.2 23 0.0005 34.5 3.2 46 41-87 329-374 (377)
67 cd04478 RPA2_DBD_D RPA2_DBD_D: 42.0 1E+02 0.0023 23.1 6.1 57 89-145 8-75 (95)
68 TIGR01955 RfaH transcriptional 39.2 84 0.0018 26.1 5.6 83 109-199 51-133 (159)
69 PF08828 DSX_dimer: Doublesex 37.7 22 0.00047 26.7 1.6 32 40-74 22-54 (62)
70 KOG2623 Tyrosyl-tRNA synthetas 37.1 39 0.00084 34.0 3.7 40 41-81 398-437 (467)
71 PF01588 tRNA_bind: Putative t 36.2 78 0.0017 24.5 4.6 19 191-209 2-20 (95)
72 TIGR03198 pucE xanthine dehydr 36.0 12 0.00025 32.4 -0.1 51 40-94 19-77 (151)
73 cd04483 hOBFC1_like hOBFC1_lik 35.2 1.8E+02 0.0039 22.6 6.6 55 88-142 5-87 (92)
74 PF02597 ThiS: ThiS family; I 34.9 66 0.0014 23.1 3.8 25 68-92 44-70 (77)
75 PTZ00471 60S ribosomal protein 33.8 41 0.00089 28.8 2.9 24 175-198 5-28 (134)
76 COG2080 CoxS Aerobic-type carb 32.0 30 0.00066 30.2 1.8 51 39-93 18-76 (156)
77 TIGR00405 L26e_arch ribosomal 32.0 81 0.0018 26.1 4.4 26 175-200 87-112 (145)
78 PF01959 DHQS: 3-dehydroquinat 31.9 97 0.0021 30.5 5.4 46 133-191 297-345 (354)
79 PRK08559 nusG transcription an 31.5 75 0.0016 26.9 4.2 29 173-201 93-121 (153)
80 PF12961 DUF3850: Domain of Un 31.2 45 0.00097 25.7 2.4 18 146-163 21-38 (72)
81 cd03706 mtEFTU_III Domain III 31.1 1.9E+02 0.0042 21.8 6.1 41 153-197 51-92 (93)
82 PF09285 Elong-fact-P_C: Elong 30.5 93 0.002 22.7 3.9 36 134-170 19-54 (56)
83 TIGR01682 moaD molybdopterin c 30.4 1.4E+02 0.003 22.1 5.0 23 69-92 51-73 (80)
84 PF07076 DUF1344: Protein of u 29.9 1.2E+02 0.0026 22.7 4.4 36 130-165 10-49 (61)
85 cd03705 EF1_alpha_III Domain I 29.5 1.2E+02 0.0025 23.4 4.6 35 153-190 59-100 (104)
86 KOG1784 Small Nuclear ribonucl 29.1 1E+02 0.0022 24.9 4.2 59 135-197 11-75 (96)
87 COG1792 MreC Cell shape-determ 28.8 4.9E+02 0.011 24.4 10.7 61 150-230 209-270 (284)
88 cd02899 PLAT_SR Scavenger rece 28.8 2E+02 0.0044 23.4 6.0 61 175-248 41-108 (109)
89 KOG1999 RNA polymerase II tran 28.1 87 0.0019 34.7 4.7 38 162-201 449-486 (1024)
90 cd04491 SoSSB_OBF SoSSB_OBF: A 27.9 2.5E+02 0.0054 20.6 6.6 52 96-147 22-79 (82)
91 PRK05609 nusG transcription an 27.1 1.5E+02 0.0033 25.0 5.4 29 172-200 124-152 (181)
92 KOG2404 Fumarate reductase, fl 26.9 1.1E+02 0.0023 30.7 4.7 79 20-104 117-196 (477)
93 PRK14898 DNA-directed RNA poly 26.5 2.3E+02 0.0051 30.8 7.7 59 104-162 130-195 (858)
94 TIGR00922 nusG transcription t 25.3 76 0.0016 26.8 3.1 28 173-200 118-145 (172)
95 cd05794 S1_EF-P_repeat_2 S1_EF 25.2 1.2E+02 0.0026 22.1 3.7 32 137-169 22-53 (56)
96 PF01063 Aminotran_4: Aminotra 24.8 2.2E+02 0.0048 24.5 6.0 52 205-258 125-176 (231)
97 PF02736 Myosin_N: Myosin N-te 24.2 1.8E+02 0.0039 19.5 4.2 36 111-149 3-38 (42)
98 PTZ00141 elongation factor 1- 23.5 4.1E+02 0.0089 26.4 8.3 52 153-205 381-436 (446)
99 PF08529 NusA_N: NusA N-termin 23.3 62 0.0013 26.4 2.1 49 113-166 45-96 (122)
100 PF14451 Ub-Mut7C: Mut7-C ubiq 23.0 93 0.002 24.0 2.9 26 68-94 50-75 (81)
101 PRK02290 3-dehydroquinate synt 22.8 2.8E+02 0.0061 27.3 6.8 54 123-191 279-335 (344)
102 PF10781 DSRB: Dextransucrase 22.6 1.7E+02 0.0038 21.8 4.1 29 155-183 2-35 (62)
103 COG5164 SPT5 Transcription elo 22.1 1.4E+02 0.003 30.9 4.6 42 157-200 124-165 (607)
104 PLN02799 Molybdopterin synthas 21.8 2.3E+02 0.005 20.9 4.9 25 68-93 52-76 (82)
105 KOG3401 60S ribosomal protein 21.4 76 0.0016 27.5 2.3 54 164-217 38-94 (145)
106 smart00841 Elong-fact-P_C Elon 20.8 1.6E+02 0.0036 21.4 3.7 31 138-169 23-53 (56)
107 COG0090 RplB Ribosomal protein 20.8 5.6E+02 0.012 24.5 8.1 71 144-225 113-188 (275)
108 cd00754 MoaD Ubiquitin domain 20.7 1.8E+02 0.0038 21.0 4.0 26 66-92 48-73 (80)
109 TIGR00432 arcsn_tRNA_tgt tRNA- 20.4 1.9E+02 0.0041 30.0 5.3 93 77-171 399-514 (540)
110 TIGR02888 spore_YlmC_YmxH spor 20.1 4E+02 0.0087 20.3 6.0 40 135-179 7-46 (76)
111 cd01903 Ntn_AC_NAAA AC_NAAA Th 20.0 1.9E+02 0.0041 26.0 4.8 30 40-69 97-126 (231)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=2.6e-115 Score=793.72 Aligned_cols=260 Identities=90% Similarity=1.398 Sum_probs=257.3
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEeccc
Q 024598 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDK 80 (265)
Q Consensus 1 MarG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~ 80 (265)
|||||++|||||+||+||||+||+++|||+||||||+++|||||+|||||+||||+|.|||++||+||+|+|||++|+|+
T Consensus 1 m~~g~kkHlKRl~AP~~W~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~ 80 (261)
T PLN00036 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDK 80 (261)
T ss_pred CCCCcccccccccCccccccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeE
Q 024598 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTI 160 (265)
Q Consensus 81 ~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv 160 (265)
+|||||||||||++++|+||++||++|||++|+|++|||+||||||++|++++||+|||+|||||||+|+||+|++||||
T Consensus 81 ~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv 160 (261)
T PLN00036 81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTI 160 (261)
T ss_pred CCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCC
Q 024598 161 KLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 240 (265)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (265)
+||||+++|++||||++||+||||||+|+|++|+|.+|+++++|+++||++|++|++|+|+++||||||++++|||+||+
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~ 240 (261)
T PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPK 240 (261)
T ss_pred EEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred CcceeeehHHHHHHHHHHHH
Q 024598 241 GKGIKLSIIEEARKRQALAT 260 (265)
Q Consensus 241 ~~gi~~~~~~~~~~~~~~~~ 260 (265)
++|||+|++|||++++++.+
T Consensus 241 ~~gi~~~~~e~r~~~~~~~~ 260 (261)
T PLN00036 241 GKGIKLSIIEEARKRLAAGQ 260 (261)
T ss_pred CCCcccchHHHHHHhhhhhc
Confidence 99999999999999998764
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=4.9e-115 Score=792.29 Aligned_cols=260 Identities=64% Similarity=1.059 Sum_probs=257.7
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEeccc
Q 024598 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDK 80 (265)
Q Consensus 1 MarG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~ 80 (265)
|||||++|||||+||+||||+||+++|||+||||||++++||||+|||||+||||+|.|||++||+||+|+|||++|+|+
T Consensus 1 m~~g~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~ 80 (262)
T PTZ00118 1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDC 80 (262)
T ss_pred CCCCcccccccccCccccccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeE
Q 024598 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTI 160 (265)
Q Consensus 81 ~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv 160 (265)
+|||||||||||++++|+||++||++|||++|+|++|||+||||||++|++++||+|||+|||||||+|+||+|++||||
T Consensus 81 ~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dtv 160 (262)
T PTZ00118 81 TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSL 160 (262)
T ss_pred CCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCC
Q 024598 161 KLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 240 (265)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (265)
+||||+++|++|||||+||+||||||+|+|++|+|.+++++++|+++|+|+|++|++|+|+++||||||++++|||+||+
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~ 240 (262)
T PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPR 240 (262)
T ss_pred EEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred CcceeeehHHHHHHHHHHHH
Q 024598 241 GKGIKLSIIEEARKRQALAT 260 (265)
Q Consensus 241 ~~gi~~~~~~~~~~~~~~~~ 260 (265)
+||||+|++|||++++++++
T Consensus 241 ~kgi~~~~~e~~~~~~~~~~ 260 (262)
T PTZ00118 241 ERGIKKDIIEERRNRLAKAL 260 (262)
T ss_pred CCCccccHHHHHHHHHHHHh
Confidence 99999999999999998876
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=8.9e-111 Score=767.56 Aligned_cols=258 Identities=53% Similarity=0.866 Sum_probs=253.6
Q ss_pred cccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024598 5 LKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (265)
Q Consensus 5 ~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypV 84 (265)
.++|||||+||+||||+||+++|||+||||||++++||||+|||||+||||+|.|||++||+||+|+|||++|+|++|||
T Consensus 2 ~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~Pv 81 (273)
T PTZ00223 2 AKKHLKRLYAPKDWMLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPA 81 (273)
T ss_pred ccchhhhhcCccccccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEec
Q 024598 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDL 164 (265)
Q Consensus 85 G~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l 164 (265)
|||||||||+++|+||++||++|||++|+|++|||+||||||++|++++||+|||+|||||||+|+||+|++||||+|||
T Consensus 82 GlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l 161 (273)
T PTZ00223 82 GFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNV 161 (273)
T ss_pred ceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCEEEEEC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccC-CCceeeCCCCcc
Q 024598 165 ETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-TKPWVSLPKGKG 243 (265)
Q Consensus 165 ~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~-~~p~islp~~~g 243 (265)
|+++|++||||++||+||||||+|+|++|+|.+|+++++++++|+++|++|++|+|+++||||||++ ++|||+||++||
T Consensus 162 ~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kg 241 (273)
T PTZ00223 162 KEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQG 241 (273)
T ss_pred CCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999986 699999999999
Q ss_pred eeeehHHHHHHHHHHHHhc
Q 024598 244 IKLSIIEEARKRQALATSA 262 (265)
Q Consensus 244 i~~~~~~~~~~~~~~~~~~ 262 (265)
||+|++|||++++++++..
T Consensus 242 i~~~~~e~~~~~~~~~~~~ 260 (273)
T PTZ00223 242 LRINVIQEREEKLIAAEAR 260 (273)
T ss_pred ccccHHHHHHHHHHHHHhh
Confidence 9999999999999887753
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=3.1e-104 Score=713.57 Aligned_cols=235 Identities=41% Similarity=0.681 Sum_probs=231.6
Q ss_pred cccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024598 5 LKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (265)
Q Consensus 5 ~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypV 84 (265)
+++|||||+||+||||+||+++||||||||||++++||||+|||||+||||+|+|||++||+||+|+|||++|+|++|||
T Consensus 1 ~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~Pv 80 (237)
T PRK04313 1 MMRHLKRLAAPKSWPIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80 (237)
T ss_pred CCccccceeCCcccccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCC-CCcccCCeEEEe
Q 024598 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKANDTIKLD 163 (265)
Q Consensus 85 G~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d-~~ik~~Dtv~i~ 163 (265)
|||||||||+++|+||++||++|||++|+|++|||+||||||++|++++||+|||+|||||||+++| ++|++||||+|+
T Consensus 81 GlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~ 160 (237)
T PRK04313 81 GLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLIS 160 (237)
T ss_pred CceeEEEEccCCCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCCEEEEE
Confidence 9999999999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred cCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCC
Q 024598 164 LETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 240 (265)
Q Consensus 164 l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (265)
||+++|++||+|++||+||||||+|+|++|+|.+|++++ +++|+|+++|++|++|+|+++||||||+ ++|+|+||.
T Consensus 161 l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~ 237 (237)
T PRK04313 161 LPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE 237 (237)
T ss_pred CCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence 999999999999999999999999999999999999999 6789999999999999999999999998 999999984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-102 Score=693.28 Aligned_cols=240 Identities=49% Similarity=0.774 Sum_probs=236.6
Q ss_pred CCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccC
Q 024598 2 ARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKT 81 (265)
Q Consensus 2 arG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ 81 (265)
||||++|||||+||+||||+||+++|||+|+||||++++||||++++||+|+||+|.|||++|+++|+|+|||++|+|++
T Consensus 1 a~g~~~HlKRl~aP~~w~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~k 80 (241)
T COG1471 1 ARGPKRHLKRLAAPKSWPIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYK 80 (241)
T ss_pred CCchhhhhhhccCCceEEeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEecccc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeEE
Q 024598 82 YPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIK 161 (265)
Q Consensus 82 ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~ 161 (265)
||||||||||||+++|+||++||.+|+|.+|+|++|||.||||||+||++++||++|||||||||++++|++|++||||+
T Consensus 81 fPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dtv~ 160 (241)
T COG1471 81 FPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVK 160 (241)
T ss_pred CCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCC
Q 024598 162 LDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 240 (265)
Q Consensus 162 i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (265)
+++|+++|++||+|++|++||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++|||+||.
T Consensus 161 i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~ 239 (241)
T COG1471 161 ISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPK 239 (241)
T ss_pred EeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCC
Confidence 99999999999999999999999999999999999999999 5679999999999999999999999998 999999998
Q ss_pred Cc
Q 024598 241 GK 242 (265)
Q Consensus 241 ~~ 242 (265)
|+
T Consensus 240 e~ 241 (241)
T COG1471 240 EK 241 (241)
T ss_pred CC
Confidence 74
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-99 Score=680.64 Aligned_cols=263 Identities=71% Similarity=1.160 Sum_probs=261.4
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEeccc
Q 024598 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDK 80 (265)
Q Consensus 1 MarG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~ 80 (265)
|+|||++||||++||+|||++|++|.|||+||+|||+++||+||++||||+|+||+|.+|+++|++|++|+|||++|+|.
T Consensus 1 m~~g~k~hlKr~~ap~~wmldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~ 80 (263)
T KOG0378|consen 1 MARGPKKHLKRLAAPKHWMLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDS 80 (263)
T ss_pred CCcchhhhhhhhcccHhheecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcceeEEecccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeE
Q 024598 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTI 160 (265)
Q Consensus 81 ~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv 160 (265)
+||+||||||+|++|+|+||++||++|+|.+|.|++|||+||||||++++.+++|+|+|++|||++|||+||.|++|||+
T Consensus 81 ~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dtI 160 (263)
T KOG0378|consen 81 TYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDTI 160 (263)
T ss_pred ccccceeEEEEecccchhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCcccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCC
Q 024598 161 KLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 240 (265)
Q Consensus 161 ~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~ 240 (265)
++++++++|.++++|++|++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++||||||+|++||||||+
T Consensus 161 ~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPk 240 (263)
T KOG0378|consen 161 KIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPK 240 (263)
T ss_pred eccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeehHHHHHHHHHHHHhcc
Q 024598 241 GKGIKLSIIEEARKRQALATSAA 263 (265)
Q Consensus 241 ~~gi~~~~~~~~~~~~~~~~~~~ 263 (265)
++||+++++||||+|+++++++|
T Consensus 241 gkgi~~siaEe~dkrl~~k~~s~ 263 (263)
T KOG0378|consen 241 GKGIALSIAEERDKRLAAKISSG 263 (263)
T ss_pred ccCccchhhHHHHHHHhhhccCC
Confidence 99999999999999999999875
No 7
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=99.98 E-value=9.2e-33 Score=211.57 Aligned_cols=77 Identities=64% Similarity=1.028 Sum_probs=69.6
Q ss_pred ccCcceeeeeecCCceEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCcee
Q 024598 94 KTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 170 (265)
Q Consensus 94 kt~e~yR~l~d~kgrf~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 170 (265)
+++|+||++||++|+|++|+|++|||+||||||++|++++||+|||+|||||||+|+||+|++||||+|+||++||+
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 58999999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the N-terminal region of these proteins.; PDB: 2XZM_W 2XZN_W 3U5G_E 3U5C_E.
Probab=99.82 E-value=2.9e-21 Score=129.91 Aligned_cols=38 Identities=74% Similarity=1.241 Sum_probs=22.2
Q ss_pred CCcccccccccCCCceecccccceeccCCCCCCCCCcc
Q 024598 3 RGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRE 40 (265)
Q Consensus 3 rG~~kHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~ 40 (265)
+|+++|||||+||++|||+||+++|||+||||||+++|
T Consensus 1 ~G~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 1 RGPKKHLKRLAAPKSWMIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp -S-----BCCCS-GGGT--SSSSSB-----SSSS-CCC
T ss_pred CCcccccccccCCcccccccccCccccCCCCCCccCCC
Confidence 69999999999999999999999999999999999986
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=98.84 E-value=5.9e-09 Score=71.67 Aligned_cols=48 Identities=31% Similarity=0.323 Sum_probs=44.5
Q ss_pred chHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeE
Q 024598 42 LPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVV 90 (265)
Q Consensus 42 lPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVI 90 (265)
++|..+| ..++++.|+.||++++.+|.|+|||++++|++|+|..+|+|
T Consensus 1 ~RLd~~L-~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFL-SRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHH-HHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCHHHHH-HHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 4677888 45899999999999999999999999999999999999987
No 10
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.81 E-value=3.1e-09 Score=95.11 Aligned_cols=44 Identities=27% Similarity=0.359 Sum_probs=42.8
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
|+|||.|.++|||+++||||.|||+++++|+|-|-..|+|+|.+
T Consensus 102 R~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~ 145 (205)
T COG0522 102 RLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVRE 145 (205)
T ss_pred HhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeee
Confidence 57999999999999999999999999999999999999999987
No 11
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=98.09 E-value=2.7e-06 Score=73.87 Aligned_cols=45 Identities=16% Similarity=0.235 Sum_probs=39.7
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcc--eeEEeccc
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM--DVVSIPKT 95 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~m--DVIsI~kt 95 (265)
++|+|.|..+|+|++.||||.|||+++++|+|-|... |-|+...+
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~ 158 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPS 158 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeecC
Confidence 5799999999999999999999999999999998776 66666543
No 12
>PLN00189 40S ribosomal protein S9; Provisional
Probab=98.03 E-value=3.1e-06 Score=75.43 Aligned_cols=43 Identities=14% Similarity=0.164 Sum_probs=39.4
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~ 93 (265)
+||||.|..+|+|++.||||.|||+++++|+|-|-..|++.|.
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~It 159 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHID 159 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEE
Confidence 4799999999999999999999999999999999888777663
No 13
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.95 E-value=4.8e-05 Score=52.97 Aligned_cols=60 Identities=27% Similarity=0.300 Sum_probs=47.8
Q ss_pred hHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeee
Q 024598 43 PLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLY 103 (265)
Q Consensus 43 PL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l~ 103 (265)
.|.-+|+.. +++.+..+|++++.+|.|+|||+.++++++++..+|+|++........++|
T Consensus 2 rl~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~ 61 (70)
T cd00165 2 RLDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVY 61 (70)
T ss_pred cHHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceee
Confidence 355667654 467899999999999999999999999999999999999976432234444
No 14
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.84 E-value=9.5e-06 Score=72.57 Aligned_cols=46 Identities=20% Similarity=0.334 Sum_probs=42.5
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccC
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTN 96 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~ 96 (265)
++++|.|+++|++++.+|+|.|||+++++++|.|...|+|++....
T Consensus 97 r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~~ 142 (201)
T CHL00113 97 RLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQ 142 (201)
T ss_pred HcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEcccc
Confidence 4688999999999999999999999999999999999999997633
No 15
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=97.83 E-value=1e-05 Score=71.39 Aligned_cols=44 Identities=18% Similarity=0.234 Sum_probs=37.8
Q ss_pred HHHHHhhh-------ccccCHHHHHHHHhCceEEECCEEecccCCCCCcce
Q 024598 45 ILILRNRL-------KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMD 88 (265)
Q Consensus 45 ~i~LRdrL-------g~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mD 88 (265)
--||+-|| |+|.|..+|+|++.||||.|||+++++|+|-|-..|
T Consensus 102 ~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~ 152 (181)
T PTZ00155 102 EKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDS 152 (181)
T ss_pred HHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCc
Confidence 34566666 999999999999999999999999999999775543
No 16
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=97.80 E-value=6e-05 Score=54.17 Aligned_cols=51 Identities=20% Similarity=0.184 Sum_probs=46.4
Q ss_pred chHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024598 42 LPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (265)
Q Consensus 42 lPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~ 93 (265)
..|--+|... +++.++..+++++.+|.|+|||++++.++|.+--+|+|+|+
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 5676788877 77889999999999999999999999999999999999985
No 17
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.73 E-value=4.4e-05 Score=67.25 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=40.7
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcc--eeEEecccCc
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM--DVVSIPKTNE 97 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~m--DVIsI~kt~e 97 (265)
++|||.|..+|++++.||||.|||+++++|+|.|..- |.|+...++.
T Consensus 111 r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~ 159 (177)
T PRK04051 111 RKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSP 159 (177)
T ss_pred HccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCC
Confidence 4799999999999999999999999999999998766 5777765443
No 18
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=97.70 E-value=5e-05 Score=67.60 Aligned_cols=44 Identities=27% Similarity=0.335 Sum_probs=41.4
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
+++++.|+++|++++.+|+|.|||+++++++|.|...|+|++..
T Consensus 98 ~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 98 RLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKE 141 (200)
T ss_pred HcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEee
Confidence 35788999999999999999999999999999999999999975
No 19
>smart00363 S4 S4 RNA-binding domain.
Probab=97.67 E-value=0.00012 Score=49.50 Aligned_cols=51 Identities=25% Similarity=0.208 Sum_probs=43.7
Q ss_pred hHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 43 PLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 43 PL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
.|..+|.. .+++.+.+++++++.+|.|.|||++++++.+++..+|.|++..
T Consensus 2 rl~~~l~~-~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 2 RLDKFLAR-LGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred cHHHHHHH-cCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 34566664 3467899999999999999999999999999999999999964
No 20
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.65 E-value=6.9e-05 Score=66.89 Aligned_cols=43 Identities=26% Similarity=0.356 Sum_probs=41.2
Q ss_pred hccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 52 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 52 Lg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
++++.|+.+|++++.+|+|+|||+++++++|++...|+|+|..
T Consensus 102 ~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 102 LGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred cCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 4889999999999999999999999999999999999999986
No 21
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=96.84 E-value=0.00047 Score=51.66 Aligned_cols=59 Identities=25% Similarity=0.276 Sum_probs=41.6
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~ 101 (265)
+.|.|.=||.- .+++.|.-|||..+.+|.|+|||.+.+...--+-..|+|++ .++.|++
T Consensus 6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~--~~~~~~V 64 (65)
T PF13275_consen 6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI--DGEEYRV 64 (65)
T ss_dssp S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE--TTEEEEE
T ss_pred CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE--CCEEEEE
Confidence 56777777775 69999999999999999999999999999999999999999 4677765
No 22
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=96.72 E-value=0.0052 Score=56.77 Aligned_cols=62 Identities=15% Similarity=0.209 Sum_probs=51.4
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEEEEeC
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 115 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~ 115 (265)
|+=|-.++...+ ..++++|++++.+|+|+|||+++++++|.+...|+|++. ..|||.+..+.
T Consensus 183 s~RLD~lls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isvr-----------G~Gr~~i~~~~ 244 (257)
T TIGR03069 183 SLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR-----------GKGRLEILELE 244 (257)
T ss_pred cccHHHHHHhhh--hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEc-----------CCceEEEEEee
Confidence 555667887644 569999999999999999999999999999999999984 45777665553
No 23
>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=96.66 E-value=0.002 Score=41.32 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=25.7
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 024598 177 VGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 210 (265)
Q Consensus 177 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i 210 (265)
+|+.++|+.|++.|+.|+|.+|..+. +.|++
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 45544
No 24
>PRK11507 ribosome-associated protein; Provisional
Probab=96.66 E-value=0.007 Score=46.13 Aligned_cols=59 Identities=17% Similarity=0.131 Sum_probs=51.2
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~ 101 (265)
+-|-|.=||.- .+++.|+-|||..+.+|.|+|||.+.+-..--+-.+|+|+++ ++.|++
T Consensus 10 e~I~L~QlLK~-~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~--g~~~~v 68 (70)
T PRK11507 10 PHVELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQV 68 (70)
T ss_pred CeEEHHHHHhh-hCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEEC--CEEEEE
Confidence 45677777774 799999999999999999999999999999999999999996 455655
No 25
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.62 E-value=0.0019 Score=39.13 Aligned_cols=27 Identities=37% Similarity=0.668 Sum_probs=24.5
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEE
Q 024598 174 KFDVGNVVMVTGGRNRGRVGIIKNREK 200 (265)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (265)
+|++|+.++|++|.+.|.+|+|.++..
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 26
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=96.28 E-value=0.0086 Score=50.70 Aligned_cols=59 Identities=8% Similarity=0.039 Sum_probs=50.1
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~ 101 (265)
++-|-.||=- .+|+.|+..|+.+|..|+|.|||.+ .-++..|...|+|+|...+..|-+
T Consensus 8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~v 66 (133)
T PRK10348 8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTV 66 (133)
T ss_pred cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEEE
Confidence 4566666664 5999999999999999999999999 899999999999999875554444
No 27
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=96.24 E-value=0.0083 Score=54.53 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=42.3
Q ss_pred HHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 47 ILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 47 ~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
+|.+ ++++.|+++|++++.+|.|+|||++++.+++.+.-.|+|++..
T Consensus 5 ~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 5 LLVR-RGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred HHHH-cCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 4444 5789999999999999999999999999999999889999974
No 28
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=95.96 E-value=0.031 Score=51.54 Aligned_cols=52 Identities=17% Similarity=0.150 Sum_probs=44.7
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~ 93 (265)
++.|.-+|...+. ..+.+++++++.+|.|+|||+++.++++.+...|+|++.
T Consensus 5 g~rLd~~L~~~~~-~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~ 56 (299)
T TIGR00005 5 GQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVR 56 (299)
T ss_pred chhHHHHHHHhcc-cCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEe
Confidence 4667778877653 468999999999999999998888999999999999984
No 29
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=95.50 E-value=0.038 Score=51.58 Aligned_cols=62 Identities=21% Similarity=0.262 Sum_probs=50.1
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEEEEeC
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 115 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~~~I~ 115 (265)
|+=|=-++-..+ -.++..|.+.+.+|+|+|||+.+++++|.|...|+|||.. .|||.+..+.
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 5688889999999999999999999999999999999964 4666665553
No 30
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=95.30 E-value=0.04 Score=42.37 Aligned_cols=60 Identities=22% Similarity=0.250 Sum_probs=49.8
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeee
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 102 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l 102 (265)
+-|-|.=||.- +|+++|+-+||..+.+|.|+|||.+-+-..--+-..|+|+|+. ..|-+.
T Consensus 10 e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~--~~~~v~ 69 (73)
T COG2501 10 EFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG--QRYQVV 69 (73)
T ss_pred ceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC--EEEEEE
Confidence 45566667764 7999999999999999999999999988888899999999974 444443
No 31
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=95.13 E-value=0.06 Score=50.53 Aligned_cols=57 Identities=23% Similarity=0.190 Sum_probs=49.9
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcce
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENF 99 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~y 99 (265)
...-|--+|++ |.- .+..+..+++.+|.|+|||++++ ++|.+...|+|+++...+.+
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 45567788999 776 78999999999999999999999 99999999999999865554
No 32
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=95.00 E-value=0.092 Score=49.51 Aligned_cols=53 Identities=17% Similarity=0.095 Sum_probs=46.2
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
...|.-+|+.+++ ..+.+++++++.+|.|.|||+.++.+.+.+...|+|++..
T Consensus 17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~ 69 (325)
T PRK11180 17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDA 69 (325)
T ss_pred CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEee
Confidence 4678888888764 3589999999999999999999988999999999999863
No 33
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=94.81 E-value=0.066 Score=49.84 Aligned_cols=53 Identities=19% Similarity=0.236 Sum_probs=46.8
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecc
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
.||=|-.++-+.+++ ++..|.+.+..|.|+||.++++.++|-+..+|.|||..
T Consensus 179 sSlRLD~vis~~~~~--SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG 231 (257)
T COG2302 179 SSLRLDVVISEGFGL--SRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG 231 (257)
T ss_pred ehhhHHHHHHHHHhh--hHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEec
Confidence 377888888886665 56678999999999999999999999999999999954
No 34
>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=94.54 E-value=0.08 Score=43.78 Aligned_cols=57 Identities=18% Similarity=0.242 Sum_probs=39.7
Q ss_pred eeEEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC-----CCeEeEe--eceEEEEc
Q 024598 170 TEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL-----GHEFATR--LGNVFTIG 229 (265)
Q Consensus 170 ~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~-----g~~F~T~--~~~vfvIG 229 (265)
.+.+++..|+.+.|++|++-|..|+|.++... ...|.|+.-+ |.+++.. .+||.++.
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 35568889999999999999999999999633 2456665543 4333333 36666543
No 35
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=94.34 E-value=0.084 Score=42.86 Aligned_cols=48 Identities=13% Similarity=0.174 Sum_probs=41.5
Q ss_pred ccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee
Q 024598 53 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (265)
Q Consensus 53 g~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~ 101 (265)
.+..++-.|+.+|..|+|.|||... -+++-|.++|+|+|.-.+..|-+
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~~~v 66 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKEFTV 66 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcEEEE
Confidence 4667999999999999999999999 78899999999999875555444
No 36
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.15 E-value=0.072 Score=49.36 Aligned_cols=112 Identities=19% Similarity=0.281 Sum_probs=71.9
Q ss_pred hccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceee-------------eeecCCceEEEEeChhh
Q 024598 52 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL-------------LYDTKGRFRLHSIRDEE 118 (265)
Q Consensus 52 Lg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~-------------l~d~kgrf~~~~I~~ee 118 (265)
.|++.|+.+|+..++.|.|+|||..++-|++-|-.-|.|++......|.- -.|.+|+-++ -|-+..
T Consensus 12 rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~yVSRG~~KL~~ale~F~l~~k~kv~L-DiGsST 90 (245)
T COG1189 12 RGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFELDVKGKVVL-DIGSST 90 (245)
T ss_pred ccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCccccHHHHHHHHHHhcCcCCCCCEEE-EecCCC
Confidence 39999999999999999999999999999999999999999853333321 1255555444 333333
Q ss_pred hcceeE-------EEEEEEEee-------CCceEEEccCCeeeecCCCC--cccCCeEEEec
Q 024598 119 AKFKLC-------KVRSVQFGQ-------KGIPYINTYDGRTIRYPDPL--IKANDTIKLDL 164 (265)
Q Consensus 119 a~~KLc-------KV~~k~~~~-------~g~~ql~~hDGrni~~~d~~--ik~~Dtv~i~l 164 (265)
-.|=.| +|-.+-++. ...|.+....+.|+||-.|+ ...-|-+++|+
T Consensus 91 GGFTd~lLq~gAk~VyavDVG~~Ql~~kLR~d~rV~~~E~tN~r~l~~~~~~~~~d~~v~Dv 152 (245)
T COG1189 91 GGFTDVLLQRGAKHVYAVDVGYGQLHWKLRNDPRVIVLERTNVRYLTPEDFTEKPDLIVIDV 152 (245)
T ss_pred ccHHHHHHHcCCcEEEEEEccCCccCHhHhcCCcEEEEecCChhhCCHHHcccCCCeEEEEe
Confidence 222222 344444444 23455666677777765443 22335555554
No 37
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=93.73 E-value=0.04 Score=48.44 Aligned_cols=36 Identities=17% Similarity=0.287 Sum_probs=33.7
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCCCc
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGF 86 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~ 86 (265)
+||+|.|...|+.++.|+||.|++.+++.|+|-|.+
T Consensus 105 klGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 105 KLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 479999999999999999999999999999998873
No 38
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=93.66 E-value=0.15 Score=45.48 Aligned_cols=48 Identities=15% Similarity=0.075 Sum_probs=41.3
Q ss_pred HHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024598 44 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (265)
Q Consensus 44 L~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~ 93 (265)
|--+|...+ ..+++.+++++.+|.|+|||++++++++.+.-.|+|++.
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~ 50 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYD 50 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEEC
Confidence 445666655 368999999999999999999999899999999999986
No 39
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=93.42 E-value=0.16 Score=47.81 Aligned_cols=66 Identities=17% Similarity=0.083 Sum_probs=49.7
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEeccc--------CcceeeeeecCCc
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKT--------NENFRLLYDTKGR 108 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt--------~e~yR~l~d~kgr 108 (265)
.++-|.=+|.+. ++ .++++|++++.+|.|+|||+++ .+.+.|...|+|+++.. ++.|-++.-+.|.
T Consensus 5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~~~ed~~~lvlnKP~G~ 78 (290)
T PRK10475 5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGI 78 (290)
T ss_pred hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccccccCCCeEEEEECCCCC
Confidence 456677777753 54 4799999999999999999988 58899988999998631 2345555566663
No 40
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=93.11 E-value=0.43 Score=44.94 Aligned_cols=51 Identities=27% Similarity=0.260 Sum_probs=43.9
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEec
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~ 93 (265)
...|.-||++.++ ..+.+.+++++.+|.|.|||+++ .+++.+...|+|++.
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 4667788887763 46799999999999999999998 589999999999995
No 41
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=92.30 E-value=0.46 Score=46.78 Aligned_cols=65 Identities=20% Similarity=0.220 Sum_probs=47.9
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEE
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRL 111 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~ 111 (265)
.+||.=+|-. .|+|.+..|||+.+.+|-|.|||.+++|+.+-+-.-|.+ ...|-++--.|.+|..
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~l-----~~~~~~lr~GKk~~~~ 406 (410)
T PRK13354 342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDAF-----DGKFVILRRGKKKFFL 406 (410)
T ss_pred CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhhc-----CCCEEEEEeCCccEEE
Confidence 5777777775 799999999999999999999999999997655433321 2345555555555544
No 42
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=92.26 E-value=0.36 Score=47.39 Aligned_cols=64 Identities=17% Similarity=0.211 Sum_probs=47.9
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEE
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRL 111 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~ 111 (265)
.+|++-+|-+ .|+|.+..|||+.+.+|-|.|||.+++|..+-+..-| ....|-++.-.|.+|..
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~~~------~~~~~~~lr~GKk~~~~ 405 (408)
T PRK05912 342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTADD------RFGKYTVLQRGKKKFAR 405 (408)
T ss_pred CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccccccc------cCCCEEEEEeCCCceEE
Confidence 5788888875 7999999999999999999999999999987553311 13445555555555544
No 43
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=91.98 E-value=0.42 Score=44.33 Aligned_cols=55 Identities=25% Similarity=0.273 Sum_probs=44.0
Q ss_pred hccccCHHHHHHHHhCceEEECCEEecccCCCCCcc-eeEEecccC-----cc-eeeeeecCC
Q 024598 52 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM-DVVSIPKTN-----EN-FRLLYDTKG 107 (265)
Q Consensus 52 Lg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~m-DVIsI~kt~-----e~-yR~l~d~kg 107 (265)
+|+| ++|||.+++.+|.|.|||++.++...-+-.- |+|.++..- +. |-+++-+.|
T Consensus 12 ~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G 73 (248)
T COG1187 12 AGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRG 73 (248)
T ss_pred cCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCC
Confidence 4665 7999999999999999999999999888887 477776621 22 667778888
No 44
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=91.00 E-value=0.58 Score=43.87 Aligned_cols=61 Identities=18% Similarity=0.138 Sum_probs=44.3
Q ss_pred HHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCc--ceeEEecc---c-------CcceeeeeecCCce
Q 024598 46 LILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGF--MDVVSIPK---T-------NENFRLLYDTKGRF 109 (265)
Q Consensus 46 i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~--mDVIsI~k---t-------~e~yR~l~d~kgrf 109 (265)
=||-+ +|+ .++++|++++.+|.|+|||+++ ++.+.|-. .|+|+++. . .++|-++.-+.|..
T Consensus 7 k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~ 79 (289)
T PRK10700 7 KVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGEL 79 (289)
T ss_pred HHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCE
Confidence 34443 454 6899999999999999999987 68888854 47787753 1 13466777787844
No 45
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=90.84 E-value=0.64 Score=38.91 Aligned_cols=55 Identities=22% Similarity=0.291 Sum_probs=37.3
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc-----CCCCeEeEe--eceEEEEc
Q 024598 172 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD-----ALGHEFATR--LGNVFTIG 229 (265)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d-----~~g~~F~T~--~~~vfvIG 229 (265)
.+++..|+.+.|+.|..-|..|+|.++.... +.|+|+. .+|.+++-. .+||+++-
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 3444443 345443332 25555543
No 46
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=88.23 E-value=0.3 Score=43.12 Aligned_cols=34 Identities=35% Similarity=0.474 Sum_probs=32.3
Q ss_pred hhccccCHHHHHHHHhCceEEECCEEecccCCCC
Q 024598 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (265)
Q Consensus 51 rLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypV 84 (265)
+|++|.+-+||-..+.||||-|.-++++||.|-|
T Consensus 115 ~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv 148 (181)
T KOG4655|consen 115 RLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV 148 (181)
T ss_pred echhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence 5899999999999999999999999999999876
No 47
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=87.82 E-value=1.4 Score=37.99 Aligned_cols=58 Identities=24% Similarity=0.291 Sum_probs=39.7
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeEe--EeeceEEEEc
Q 024598 172 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFA--TRLGNVFTIG 229 (265)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~--~~v~i~d~~g~~F~--T~~~~vfvIG 229 (265)
.+++..|+.++|+.|..-|..|+|..+....+.. +=|.+.-.+|..++ -..+||+++-
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 3477889999999999999999999997644321 22223335555433 4457777766
No 48
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=86.68 E-value=1.1 Score=34.48 Aligned_cols=39 Identities=18% Similarity=0.366 Sum_probs=31.5
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC
Q 024598 173 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL 214 (265)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~~ 214 (265)
+++..|+.+.|+.|+.-|++|+|..+... .+.|.+++-+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegvn 43 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPK---KNRVIVEGVK 43 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcE
Confidence 47889999999999999999999999653 3456676543
No 49
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=85.82 E-value=1.3 Score=34.51 Aligned_cols=39 Identities=15% Similarity=0.414 Sum_probs=31.2
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcC
Q 024598 172 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 213 (265)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i~d~ 213 (265)
.+++..|+.++|+.|+.-|+.|+|.++... .+.|++++-
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKK---SNKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCc
Confidence 347889999999999999999999999653 245666543
No 50
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=84.35 E-value=1.4 Score=35.69 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=25.9
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024598 173 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 201 (265)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (265)
+++..|+.+.|+.|++-|.+|+|..+...
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 31 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPK 31 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 36788999999999999999999999653
No 51
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=78.71 E-value=2.9 Score=33.92 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=25.3
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024598 174 KFDVGNVVMVTGGRNRGRVGIIKNREKH 201 (265)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (265)
++..|+.+.|+.|+.-|..|+|..+...
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5778999999999999999999999653
No 52
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=75.98 E-value=5.2 Score=39.61 Aligned_cols=60 Identities=22% Similarity=0.299 Sum_probs=43.2
Q ss_pred HHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcceeeeeecCCceEE
Q 024598 44 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRL 111 (265)
Q Consensus 44 L~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~yR~l~d~kgrf~~ 111 (265)
++-+|-+ .+++.+.+|||+.+.+|-|++||.++.|..++. .|. ....|.++--.|.+|..
T Consensus 338 ~~~~lv~-~~L~psr~earr~i~~g~v~in~~~v~d~~~~~--~~~-----~~~~~~~l~~GKkk~~~ 397 (401)
T COG0162 338 LVDLLVD-AGLAPSRSEARRLIQQGGVKINGEKVEDENYVL--SDL-----LDNGLLVLRRGKKKFAL 397 (401)
T ss_pred HHHHHHH-hCCcccHHHHHhhcccCCEEECCEeccccccch--hhc-----cCCceEEEecccccEEE
Confidence 3334443 699999999999999999999999999999887 221 22345555555555544
No 53
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=75.69 E-value=7.5 Score=29.00 Aligned_cols=50 Identities=28% Similarity=0.529 Sum_probs=38.2
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEcc
Q 024598 177 VGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 230 (265)
Q Consensus 177 ~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvIG~ 230 (265)
+|..|+|-.|.+.-|+|.++.-|... ++|.+| | ++...+.-+..+..+|-
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~iv-i---~~q~i~velkdivlvgv 55 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIV-I---GEQSIDVELKDIVLVGV 55 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEE-E---CCeEEEEEeeeEEEEEe
Confidence 48889999999999999999988876 445655 2 34456667777777774
No 54
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=59.81 E-value=11 Score=32.10 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=27.4
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 024598 175 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 210 (265)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i 210 (265)
.|+|-+|+|.-|.+.|+.++|++|..+ |.|.|
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~----nRvLV 39 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLV 39 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC----CeEEE
Confidence 378999999999999999999999764 55544
No 55
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=59.17 E-value=9.7 Score=32.09 Aligned_cols=26 Identities=38% Similarity=0.556 Sum_probs=24.1
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 024598 175 FDVGNVVMVTGGRNRGRVGIIKNREK 200 (265)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (265)
+++|-.|+++.|+.+|+-.+|..+..
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iD 30 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIID 30 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEcc
Confidence 68899999999999999999999865
No 56
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=56.37 E-value=65 Score=35.63 Aligned_cols=55 Identities=25% Similarity=0.374 Sum_probs=41.8
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeEeEeeceEEEEccCCC
Q 024598 175 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFATRLGNVFTIGKGTK 233 (265)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~--~~v~i~d~~g~~F~T~~~~vfvIG~~~~ 233 (265)
...++++-+++|.|.|+-|.|.+|-+.. -| +.-++ .++-.|.+...|+..+|. .+
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~-~F~h~r~~~--En~Gv~vck~k~~~~~g~-~~ 638 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRPF-VFLHSRKNL--ENGGVFVCKEKNLILAGG-KK 638 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecce-eeeeehhhc--ccCCeEEEecCCceeccc-cC
Confidence 4568999999999999999999996521 12 22223 466689999999999995 44
No 57
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=56.02 E-value=18 Score=29.67 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=24.7
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024598 173 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 201 (265)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (265)
++...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45677999999999999999999988553
No 58
>PF14001 YdfZ: YdfZ protein
Probab=55.73 E-value=19 Score=27.15 Aligned_cols=41 Identities=27% Similarity=0.487 Sum_probs=29.0
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEEecC------CccEEEEEcCCCCeEe
Q 024598 175 FDVGNVVMVTGGRNRGRVGIIKNREKHKG------SFETIHIQDALGHEFA 219 (265)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~------s~~~v~i~d~~g~~F~ 219 (265)
+.+|+.+|+.| +|.+|+|+.|...-. ....|.+++.+| .|+
T Consensus 10 i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 10 ITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred CCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 46799999977 688899999976332 235787887665 354
No 59
>PF12005 DUF3499: Protein of unknown function (DUF3499); InterPro: IPR021888 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Probab=49.63 E-value=7.1 Score=32.91 Aligned_cols=23 Identities=48% Similarity=0.993 Sum_probs=21.0
Q ss_pred cccccccCCCceecccccceecc
Q 024598 7 KHLKRLNAPKHWMLDKLGGAFAP 29 (265)
Q Consensus 7 kHlKRl~AP~~W~i~kk~~~~a~ 29 (265)
.|-.||+||+-|.+=|...-|++
T Consensus 46 ~Ha~rlTaP~GWevvR~~~~~~~ 68 (123)
T PF12005_consen 46 EHAERLTAPRGWEVVRLEGPFAP 68 (123)
T ss_pred HHHhcccCCCCcEEEeccCCCCC
Confidence 58899999999999999999873
No 60
>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=48.69 E-value=14 Score=31.88 Aligned_cols=52 Identities=21% Similarity=0.116 Sum_probs=41.9
Q ss_pred cccchHHHHHHhhhccccCHHHHHHHHhCc-----eEEECCEEecccCCCCCcce---eEEecc
Q 024598 39 RECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIPK 94 (265)
Q Consensus 39 ~~slPL~i~LRdrLg~A~t~rEar~Il~~g-----~V~VDGkvr~d~~ypVG~mD---VIsI~k 94 (265)
+...+|+-+||++|++-.+ |.=+.+| -|+|||+.++.-.+|+.-+| |++|.-
T Consensus 16 ~~~~~Ll~~LR~~lgltg~----K~gC~~G~CGACtVlvdg~~v~SCl~~~~~~~G~~V~TiEg 75 (148)
T TIGR03193 16 ADNMLLVDYLRDTVGLTGT----KQGCDGGECGACTVLVDGRPRLACSTLAHRVAGRKVETVEG 75 (148)
T ss_pred CCCCcHHHHHHHhcCCCCC----CCCCCCCCCCCCEEEECCeEeeccHhhHhhcCCCcEEEeCC
Confidence 3478999999999987655 4446666 69999999999999998776 888865
No 61
>PRK04333 50S ribosomal protein L14e; Validated
Probab=47.28 E-value=21 Score=27.99 Aligned_cols=33 Identities=27% Similarity=0.463 Sum_probs=27.2
Q ss_pred EeeCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 024598 174 KFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 210 (265)
Q Consensus 174 ~f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~v~i 210 (265)
.++.|-+|++.-|+..|+..+|.++... +.|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~----~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK----NFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC----CEEEE
Confidence 4688999999999999999999998442 45555
No 62
>PF04773 FecR: FecR protein; InterPro: IPR006860 FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Probab=46.56 E-value=1.2e+02 Score=22.47 Aligned_cols=68 Identities=16% Similarity=0.140 Sum_probs=40.4
Q ss_pred EEEeeCCceEEEccCCeeeecC-CCCc-----ccCCeEEEecCCCceeeEEEeeCCc-EEEEECCCcceeEEEEE
Q 024598 129 VQFGQKGIPYINTYDGRTIRYP-DPLI-----KANDTIKLDLETNKITEFIKFDVGN-VVMVTGGRNRGRVGIIK 196 (265)
Q Consensus 129 k~~~~~g~~ql~~hDGrni~~~-d~~i-----k~~Dtv~i~l~~~kI~~~i~f~~G~-~~~v~gG~n~G~vG~I~ 196 (265)
..|..++..+|.+.||..+... +..+ .-.+...+.|..|++.-.++=.... +.+-|....++-.|+--
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 4577889999999999999654 3334 3445556666666654333222222 55555555555555433
No 63
>cd04093 HBS1_C HBS1_C: this family represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1) which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and, to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.
Probab=44.89 E-value=1.4e+02 Score=22.95 Aligned_cols=45 Identities=18% Similarity=0.381 Sum_probs=30.2
Q ss_pred CcccCCeEEEecCCCceeeEEEe----eCCcEEEEECCCcceeEEEEEeE
Q 024598 153 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNR 198 (265)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f----~~G~~~~v~gG~n~G~vG~I~~i 198 (265)
.++.||...+.|...+-+-.=+| ..|...+-..|..+| .|.|.+|
T Consensus 59 ~l~~~~~a~v~l~~~~pi~~e~~~~~~~~Grfilr~~~~Tva-~G~I~~i 107 (107)
T cd04093 59 CLTKGQTAIVEIELERPIPLELFKDNKELGRVVLRRDGETIA-AGLVTEI 107 (107)
T ss_pred CcCCCCEEEEEEEECCeEEEEEcccCCCcceEEEEcCCCEEE-EEEEEeC
Confidence 59999999999976553322223 227777767777777 5888654
No 64
>cd03704 eRF3c_III This family represents eEF1alpha-like C-terminal region of eRF3 homologous to the domain III of EF-Tu. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.
Probab=43.72 E-value=91 Score=24.29 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=30.6
Q ss_pred CCC-CcccCCeEEEecCCCceeeEEEeeC----CcEEEEECCCcceeEEEEEeE
Q 024598 150 PDP-LIKANDTIKLDLETNKITEFIKFDV----GNVVMVTGGRNRGRVGIIKNR 198 (265)
Q Consensus 150 ~d~-~ik~~Dtv~i~l~~~kI~~~i~f~~----G~~~~v~gG~n~G~vG~I~~i 198 (265)
.+| .++.||...+.+...+=+-.=+|+. |-.++--+|+.+| .|.|.+|
T Consensus 56 ~~p~~l~~g~~a~v~i~~~~pi~~e~~~~~~~lGRf~lR~~g~Tva-~G~V~~~ 108 (108)
T cd03704 56 KRPRFVKSGMKVIARLETTGPICLEKFEDFPQLGRFTLRDEGKTIA-IGKVLKL 108 (108)
T ss_pred cCCcEeCCCCEEEEEEEeCCcEEEEEcccCCCcccEEEEeCCCEEE-EEEEEEC
Confidence 344 6899999999987555221122322 6666667777766 7887653
No 65
>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=43.32 E-value=26 Score=30.65 Aligned_cols=29 Identities=34% Similarity=0.429 Sum_probs=24.7
Q ss_pred cccchHHHHHHhhhccccCHHHHHHHHhCc
Q 024598 39 RECLPLILILRNRLKYALTYREVIAILMQR 68 (265)
Q Consensus 39 ~~slPL~i~LRdrLg~A~t~rEar~Il~~g 68 (265)
...+|..+++|..|. |.|..||..+|.+-
T Consensus 69 ~~G~p~~~l~R~iLe-~~t~~eA~~~l~~~ 97 (225)
T PF03417_consen 69 QPGLPRHFLVRKILE-CRTVEEAIAILRSA 97 (225)
T ss_dssp TTSB-HHHHHHHHHC--SSHHHHHHCHHCC
T ss_pred cCCChHHHHHHHHhc-CCCHHHHHHHHHhc
Confidence 679999999999999 99999999999754
No 66
>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=43.24 E-value=23 Score=34.53 Aligned_cols=46 Identities=15% Similarity=-0.067 Sum_probs=37.6
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccCCCCCcc
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM 87 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~m 87 (265)
++++.=++.. .+++.+.+||++.+.+|-|.|||..++|..+-...+
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~~ 374 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKEA 374 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhccc
Confidence 4666656654 699999999999999999999999999987655443
No 67
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=41.98 E-value=1e+02 Score=23.12 Aligned_cols=57 Identities=16% Similarity=0.184 Sum_probs=38.9
Q ss_pred eEEecccCcceeeee-ecCCceEEEEeChhhh----c------ceeEEEEEEEEeeCCceEEEccCCe
Q 024598 89 VVSIPKTNENFRLLY-DTKGRFRLHSIRDEEA----K------FKLCKVRSVQFGQKGIPYINTYDGR 145 (265)
Q Consensus 89 VIsI~kt~e~yR~l~-d~kgrf~~~~I~~eea----~------~KLcKV~~k~~~~~g~~ql~~hDGr 145 (265)
|.++.+.+.++.+.. |..|.+....-..++. . =.+.+|.++...-+|.+||..+.=+
T Consensus 8 V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~ 75 (95)
T cd04478 8 VRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIR 75 (95)
T ss_pred EEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEE
Confidence 556666677777777 8888875443333321 1 2588999988888999999976333
No 68
>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=39.20 E-value=84 Score=26.08 Aligned_cols=83 Identities=18% Similarity=0.249 Sum_probs=46.9
Q ss_pred eEEEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEEeeCCcEEEEECCCc
Q 024598 109 FRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRN 188 (265)
Q Consensus 109 f~~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n 188 (265)
+++...+.+++.+. .|.+ ..|+..+.-.+|+....++..+..--... -.+........|.+|+.+.|++|.-
T Consensus 51 YvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~~--~~~~~~~~~~~~~~G~~V~V~~GPf 122 (159)
T TIGR01955 51 YLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQYE--PKDSVPPATTLPYKGDKVRITDGAF 122 (159)
T ss_pred eEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhcc--ccccCCccccCCCCCCEEEEeccCC
Confidence 44556666554332 2221 24666665556655555554222111000 0011112335699999999999999
Q ss_pred ceeEEEEEeEE
Q 024598 189 RGRVGIIKNRE 199 (265)
Q Consensus 189 ~G~vG~I~~i~ 199 (265)
.|-.|.|.++.
T Consensus 123 ~g~~g~v~~~~ 133 (159)
T TIGR01955 123 AGFEAIFLEPD 133 (159)
T ss_pred CCcEEEEEEEC
Confidence 99999999985
No 69
>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=37.73 E-value=22 Score=26.66 Aligned_cols=32 Identities=28% Similarity=0.457 Sum_probs=21.6
Q ss_pred ccchHHHHHHhhhcccc-CHHHHHHHHhCceEEECC
Q 024598 40 ECLPLILILRNRLKYAL-TYREVIAILMQRHVLVDA 74 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~-t~rEar~Il~~g~V~VDG 74 (265)
|.|||..++ |++|. +..||-+-+.+|.-.|+-
T Consensus 22 EmmpLmyVI---LK~A~~D~eeA~rrI~E~~~~v~~ 54 (62)
T PF08828_consen 22 EMMPLMYVI---LKYADADVEEASRRIDEAKNVVNE 54 (62)
T ss_dssp GGHHHHHHH---HHHTTT-HHHHHHHHHH-------
T ss_pred HHHHHHHHH---HHhcCCCHHHHHHHHHHHHHHHHH
Confidence 789999984 89999 999999999988776664
No 70
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.07 E-value=39 Score=34.02 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=34.9
Q ss_pred cchHHHHHHhhhccccCHHHHHHHHhCceEEECCEEecccC
Q 024598 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKT 81 (265)
Q Consensus 41 slPL~i~LRdrLg~A~t~rEar~Il~~g~V~VDGkvr~d~~ 81 (265)
.++++=++|+ ++.-.+..||++++.||-|.+|++.++|++
T Consensus 398 ~~s~~~l~~k-a~~~~s~~~a~r~i~qG~vslnh~~v~~es 437 (467)
T KOG2623|consen 398 GVSILDLLRK-ASRFPSGKEARRMIQQGGVSLNHEKVRDES 437 (467)
T ss_pred CCcHHHHHHH-hhcCCCcHHHHHHHHccceeecCccccCch
Confidence 6788888887 677778889999999999999999999954
No 71
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=36.17 E-value=78 Score=24.49 Aligned_cols=19 Identities=37% Similarity=0.301 Sum_probs=15.1
Q ss_pred eEEEEEeEEEecCCccEEE
Q 024598 191 RVGIIKNREKHKGSFETIH 209 (265)
Q Consensus 191 ~vG~I~~i~~~~~s~~~v~ 209 (265)
++|+|.+.+.|+++..+..
T Consensus 2 ~vg~I~~~~~hp~sdkL~~ 20 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYV 20 (95)
T ss_dssp EEEEEEEEEEETTSSSEEE
T ss_pred EEEEEEEEEECCCCCEEEE
Confidence 6899999999998764333
No 72
>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=35.99 E-value=12 Score=32.39 Aligned_cols=51 Identities=24% Similarity=0.124 Sum_probs=39.1
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCc-----eEEECCEEecccCCCCCcce---eEEecc
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIPK 94 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g-----~V~VDGkvr~d~~ypVG~mD---VIsI~k 94 (265)
...+|+-+||++|++-.+..- +.+| .|+|||+.++.--.|+.-+| |.+|.-
T Consensus 19 ~~~~Ll~~LR~~~~ltgtK~g----C~~G~CGACtVlvdG~~v~SCl~~~~~~~G~~v~TiEg 77 (151)
T TIGR03198 19 PTTRLSDLLRKELQLTGTKVS----CGIGRCGACSVLIDGKLANACLTMAYQADGHEITTIEG 77 (151)
T ss_pred CCcHHHHHHHhccCCCCCCCC----CCCCcCCccEEEECCcEEechHHHHHHhcCCEEEecCC
Confidence 478999999999998776543 6666 69999999888777775544 566643
No 73
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=35.23 E-value=1.8e+02 Score=22.61 Aligned_cols=55 Identities=20% Similarity=0.048 Sum_probs=35.6
Q ss_pred eeEEecccCcceeeee-ecCCceEE-EEeChhh--------------------------hcceeEEEEEEEEeeCCceEE
Q 024598 88 DVVSIPKTNENFRLLY-DTKGRFRL-HSIRDEE--------------------------AKFKLCKVRSVQFGQKGIPYI 139 (265)
Q Consensus 88 DVIsI~kt~e~yR~l~-d~kgrf~~-~~I~~ee--------------------------a~~KLcKV~~k~~~~~g~~ql 139 (265)
=|+++.+...++.... |..|.+.. .|...+. .--.++||.+.-..-.|..||
T Consensus 5 ~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~frg~~ql 84 (92)
T cd04483 5 TVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGEREI 84 (92)
T ss_pred EEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccCCeeEE
Confidence 4778887776666666 77787633 2332220 112478888877777888888
Q ss_pred Ecc
Q 024598 140 NTY 142 (265)
Q Consensus 140 ~~h 142 (265)
+.+
T Consensus 85 ~i~ 87 (92)
T cd04483 85 NAS 87 (92)
T ss_pred EEE
Confidence 875
No 74
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=34.90 E-value=66 Score=23.08 Aligned_cols=25 Identities=28% Similarity=0.231 Sum_probs=20.6
Q ss_pred ceEEECCEEecc--cCCCCCcceeEEe
Q 024598 68 RHVLVDAKVRTD--KTYPAGFMDVVSI 92 (265)
Q Consensus 68 g~V~VDGkvr~d--~~ypVG~mDVIsI 92 (265)
-.|.|||+.+++ ..+++.=.|.|+|
T Consensus 44 ~~v~vN~~~v~~~~~~~~l~~gD~V~i 70 (77)
T PF02597_consen 44 VAVAVNGEIVPDDGLDTPLKDGDEVAI 70 (77)
T ss_dssp EEEEETTEEEGGGTTTSBEETTEEEEE
T ss_pred EEEEECCEEcCCccCCcCcCCCCEEEE
Confidence 359999999999 6678888888876
No 75
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=33.81 E-value=41 Score=28.79 Aligned_cols=24 Identities=42% Similarity=0.688 Sum_probs=21.3
Q ss_pred eeCCcEEEEECCCcceeEEEEEeE
Q 024598 175 FDVGNVVMVTGGRNRGRVGIIKNR 198 (265)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i 198 (265)
+.+|..++|..|+++|+-++|...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999998775
No 76
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=32.01 E-value=30 Score=30.25 Aligned_cols=51 Identities=24% Similarity=0.183 Sum_probs=37.9
Q ss_pred cccchHHHHHHhhhccccCHHHHHHHHhCc-----eEEECCEEecccCCCCCcce---eEEec
Q 024598 39 RECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIP 93 (265)
Q Consensus 39 ~~slPL~i~LRdrLg~A~t~rEar~Il~~g-----~V~VDGkvr~d~~ypVG~mD---VIsI~ 93 (265)
+...||+=+|||.|++.-|.. =+.+| -|+|||+.++.--.|+-..| |.+|.
T Consensus 18 ~p~~~Ll~~LRd~l~ltgtk~----GC~~g~CGACtVlvDG~~v~SCl~~a~~~~G~~ItTiE 76 (156)
T COG2080 18 DPRTPLLDVLRDELGLTGTKK----GCGHGQCGACTVLVDGEAVNSCLTLAVQAEGAEITTIE 76 (156)
T ss_pred CCCChHHHHHHHhcCCCCcCC----CCCCccCCceEEEECCeEehHHHHHHHHhCCCeEEEee
Confidence 346799999999999988754 34444 79999999998877765543 45554
No 77
>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=31.97 E-value=81 Score=26.09 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=24.7
Q ss_pred eeCCcEEEEECCCcceeEEEEEeEEE
Q 024598 175 FDVGNVVMVTGGRNRGRVGIIKNREK 200 (265)
Q Consensus 175 f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (265)
|.+|+.+.|+.|.=.|..|.|.++..
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 78
>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=31.94 E-value=97 Score=30.51 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=28.8
Q ss_pred eCCceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEEeeCCcEEEE---ECCCccee
Q 024598 133 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMV---TGGRNRGR 191 (265)
Q Consensus 133 ~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v---~gG~n~G~ 191 (265)
.|....+.+.|..|||+- =|+|+.+....+++|+.+++ .+|+|.|-
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 344455555666666543 34567777777777775554 47888884
No 79
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=31.54 E-value=75 Score=26.93 Aligned_cols=29 Identities=14% Similarity=0.265 Sum_probs=26.5
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024598 173 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 201 (265)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (265)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999754
No 80
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=31.17 E-value=45 Score=25.65 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.0
Q ss_pred eeecCCCCcccCCeEEEe
Q 024598 146 TIRYPDPLIKANDTIKLD 163 (265)
Q Consensus 146 ni~~~d~~ik~~Dtv~i~ 163 (265)
-||..|.+|++||.|.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 357789999999998883
No 81
>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=31.09 E-value=1.9e+02 Score=21.81 Aligned_cols=41 Identities=17% Similarity=0.433 Sum_probs=25.7
Q ss_pred CcccCCeEEEecCCCceeeEEEeeCCcEEEE-ECCCcceeEEEEEe
Q 024598 153 LIKANDTIKLDLETNKITEFIKFDVGNVVMV-TGGRNRGRVGIIKN 197 (265)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v-~gG~n~G~vG~I~~ 197 (265)
.+++||+..+.+.-.+ -+.++.|.-.++ .+|+.+| .|+|.+
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 3888998887776433 234555665555 6665555 677754
No 82
>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=30.53 E-value=93 Score=22.71 Aligned_cols=36 Identities=22% Similarity=0.301 Sum_probs=24.3
Q ss_pred CCceEEEccCCeeeecCCCCcccCCeEEEecCCCcee
Q 024598 134 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 170 (265)
Q Consensus 134 ~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 170 (265)
+..-...|..|-.|.+| +-|+.||.|++|-.+++-+
T Consensus 19 ~~~K~A~letG~~i~VP-~FI~~Gd~I~VdT~~g~Yv 54 (56)
T PF09285_consen 19 SSYKPATLETGAEIQVP-LFIEEGDKIKVDTRDGSYV 54 (56)
T ss_dssp TTEEEEEETTS-EEEEE-TT--TT-EEEEETTTTEEE
T ss_pred CCccEEEEcCCCEEEcc-ceecCCCEEEEECCCCeEe
Confidence 33445667888888877 4799999999999988644
No 83
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=30.38 E-value=1.4e+02 Score=22.10 Aligned_cols=23 Identities=26% Similarity=0.109 Sum_probs=19.8
Q ss_pred eEEECCEEecccCCCCCcceeEEe
Q 024598 69 HVLVDAKVRTDKTYPAGFMDVVSI 92 (265)
Q Consensus 69 ~V~VDGkvr~d~~ypVG~mDVIsI 92 (265)
.|.|||+...+ ..++.=.|.|+|
T Consensus 51 ~v~vn~~~v~~-~~~l~dgDevai 73 (80)
T TIGR01682 51 MVAVNEEYVTD-DALLNEGDEVAF 73 (80)
T ss_pred EEEECCEEcCC-CcCcCCCCEEEE
Confidence 58999999886 788998998887
No 84
>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=29.86 E-value=1.2e+02 Score=22.71 Aligned_cols=36 Identities=14% Similarity=0.160 Sum_probs=26.8
Q ss_pred EEeeCCceEEEccCCeeeecCC----CCcccCCeEEEecC
Q 024598 130 QFGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 165 (265)
Q Consensus 130 ~~~~~g~~ql~~hDGrni~~~d----~~ik~~Dtv~i~l~ 165 (265)
+.+......|.|.||.++..|. +.+++|..|++-..
T Consensus 10 ~~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 10 KSIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYD 49 (61)
T ss_pred EEEcCCceEEEecCCCEEECCCcccccccCCCCEEEEEEE
Confidence 4456677889999999998774 36788887776544
No 85
>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=29.52 E-value=1.2e+02 Score=23.36 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=24.8
Q ss_pred CcccCCeEEEecCCCceeeEEEeeC-------CcEEEEECCCcce
Q 024598 153 LIKANDTIKLDLETNKITEFIKFDV-------GNVVMVTGGRNRG 190 (265)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f~~-------G~~~~v~gG~n~G 190 (265)
.++.||...+.|...+ -+.+|+ |..+++-+|..+|
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 5899999999986554 345555 7777777666655
No 86
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=29.08 E-value=1e+02 Score=24.91 Aligned_cols=59 Identities=20% Similarity=0.188 Sum_probs=33.9
Q ss_pred CceEEEccCCeeeecCCCCcccCCeEEEecC------CCceeeEEEeeCCcEEEEECCCcceeEEEEEe
Q 024598 135 GIPYINTYDGRTIRYPDPLIKANDTIKLDLE------TNKITEFIKFDVGNVVMVTGGRNRGRVGIIKN 197 (265)
Q Consensus 135 g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~------~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~ 197 (265)
...++.+.|||+|.-.=.-+.-.--+.|+-. +.+=++.+++. .+++.|-|.+-+|-|-|
T Consensus 11 ~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 11 QRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDE 75 (96)
T ss_pred ceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecch
Confidence 4578899999999522111222222344322 11112333333 78999999999998876
No 87
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=28.83 E-value=4.9e+02 Score=24.42 Aligned_cols=61 Identities=23% Similarity=0.310 Sum_probs=39.4
Q ss_pred CCCCcccCCeEEEecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEE
Q 024598 150 PDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 228 (265)
Q Consensus 150 ~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~v~i~d~~g~~F~T~~~~vfvI 228 (265)
++.+++.||.|+-+=-.|. |..|= -+|+|..++.+. +.+..+.++-.. ..+...|||++
T Consensus 209 ~~~~i~~GD~vvTSGlgg~------fP~Gl-----------~Vg~V~~v~~~~~~~~~~v~~~P~a---~~~~l~~v~l~ 268 (284)
T COG1792 209 PNSDIKEGDLVVTSGLGGV------FPAGL-----------PVGEVSSVKLDDYGLFKVVIVKPAA---SLDRLRYVLLV 268 (284)
T ss_pred CCCCccCCCEEEecCCCCc------CCCCc-----------EEEEEEEEEeCCCceeEEEEEeccc---ccccceEEEEE
Confidence 4557888885554433332 22222 278888888766 556777776543 47889999999
Q ss_pred cc
Q 024598 229 GK 230 (265)
Q Consensus 229 G~ 230 (265)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 96
No 88
>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=28.83 E-value=2e+02 Score=23.37 Aligned_cols=61 Identities=16% Similarity=0.332 Sum_probs=38.7
Q ss_pred eeCCcEEE-EECCCcceeEEEEEeEEEec-----CCc-cEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCCCcceeee
Q 024598 175 FDVGNVVM-VTGGRNRGRVGIIKNREKHK-----GSF-ETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLS 247 (265)
Q Consensus 175 f~~G~~~~-v~gG~n~G~vG~I~~i~~~~-----~s~-~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~~~gi~~~ 247 (265)
|+.|+.-- .+....+ |.|..|+... +-+ +-|.|++.+|+. |.|...+ |+.-|-++-|+++
T Consensus 41 F~~G~~d~F~v~~~dL---G~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~ 107 (109)
T cd02899 41 FYPGSLKRIRFRAADV---GDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECcccc---CceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEe
Confidence 66666433 2224444 4455554421 223 778888866544 4599998 9999999988876
Q ss_pred h
Q 024598 248 I 248 (265)
Q Consensus 248 ~ 248 (265)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 89
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=28.09 E-value=87 Score=34.70 Aligned_cols=38 Identities=26% Similarity=0.543 Sum_probs=29.6
Q ss_pred EecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEEe
Q 024598 162 LDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKH 201 (265)
Q Consensus 162 i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~~ 201 (265)
|+++..+.-. -|++|+.|=|+.|+|-|..|.|..++.+
T Consensus 449 l~~~~~eLrK--yF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 449 LEVPASELRK--YFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred cccchHhhhh--hccCCCeEEEEeccccCCcceEEEEeCC
Confidence 3444444433 3789999999999999999999999873
No 90
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=27.94 E-value=2.5e+02 Score=20.64 Aligned_cols=52 Identities=12% Similarity=0.086 Sum_probs=31.0
Q ss_pred Ccceeeee-ecCCceEEEEeChh-hhc---ceeEEEE-EEEEeeCCceEEEccCCeee
Q 024598 96 NENFRLLY-DTKGRFRLHSIRDE-EAK---FKLCKVR-SVQFGQKGIPYINTYDGRTI 147 (265)
Q Consensus 96 ~e~yR~l~-d~kgrf~~~~I~~e-ea~---~KLcKV~-~k~~~~~g~~ql~~hDGrni 147 (265)
+..+.+.. |..|...+.--++. ... =+.++++ .+...-+|.+||++.+...|
T Consensus 22 ~~~~~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~~~i 79 (82)
T cd04491 22 GKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEI 79 (82)
T ss_pred eEEEEEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEEecCCcEEEEeCCceEE
Confidence 33444444 77776655433433 111 1478888 56666678899988876665
No 91
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=27.12 E-value=1.5e+02 Score=25.04 Aligned_cols=29 Identities=24% Similarity=0.388 Sum_probs=26.1
Q ss_pred EEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024598 172 FIKFDVGNVVMVTGGRNRGRVGIIKNREK 200 (265)
Q Consensus 172 ~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (265)
...|.+|+.+-|++|.=.|..|.|.++..
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 92
>KOG2404 consensus Fumarate reductase, flavoprotein subunit [Energy production and conversion]
Probab=26.86 E-value=1.1e+02 Score=30.70 Aligned_cols=79 Identities=23% Similarity=0.280 Sum_probs=54.7
Q ss_pred cccccceeccCCCCCCCCCcccchHHHHHHhhh-ccccCHHHHHHHHhCceEEECCEEecccCCCCCcceeEEecccCcc
Q 024598 20 LDKLGGAFAPKPSSGPHKSRECLPLILILRNRL-KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 98 (265)
Q Consensus 20 i~kk~~~~a~kpspGPH~~~~slPL~i~LRdrL-g~A~t~rEar~Il~~g~V~VDGkvr~d~~ypVG~mDVIsI~kt~e~ 98 (265)
+.+.+|-=+||+.-+.|++--..|+.-.|+++| ++|.+--|+-||..+- |+++...--=.+.-|.-.++++|.
T Consensus 117 la~lgGHSvpRTHr~s~plppgfei~~~L~~~l~k~as~~pe~~ki~~ns------kvv~il~n~gkVsgVeymd~sgek 190 (477)
T KOG2404|consen 117 LAQLGGHSVPRTHRSSGPLPPGFEIVKALSTRLKKKASENPELVKILLNS------KVVDILRNNGKVSGVEYMDASGEK 190 (477)
T ss_pred HHHhcCCCCCcccccCCCCCCchHHHHHHHHHHHHhhhcChHHHhhhhcc------eeeeeecCCCeEEEEEEEcCCCCc
Confidence 456778889999999999999999999999999 4788888888888754 333333222233344444556665
Q ss_pred eeeeee
Q 024598 99 FRLLYD 104 (265)
Q Consensus 99 yR~l~d 104 (265)
-.+++|
T Consensus 191 ~~~~~~ 196 (477)
T KOG2404|consen 191 SKIIGD 196 (477)
T ss_pred cceecC
Confidence 555543
No 93
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=26.54 E-value=2.3e+02 Score=30.84 Aligned_cols=59 Identities=17% Similarity=0.200 Sum_probs=43.1
Q ss_pred ecCCceEEEEeCh---hhhcceeEEEE----EEEEeeCCceEEEccCCeeeecCCCCcccCCeEEE
Q 024598 104 DTKGRFRLHSIRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKL 162 (265)
Q Consensus 104 d~kgrf~~~~I~~---eea~~KLcKV~----~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i 162 (265)
|.+++.+..+++. -++.-||.||+ ....++.++|.++..||.-......++++||-|.+
T Consensus 130 d~~~k~~~~~v~~v~r~~~~~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~~a~~l~~GD~i~~ 195 (858)
T PRK14898 130 DQDEKVHWKRIISVIRHKANGKLIKIKTESGRTIRATPYHSFVTRKDNEVIPVEGSELKIGDWLPV 195 (858)
T ss_pred CCCCcEEEEEeeeEEeccCCCcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEeeHHhCCCCCEEee
Confidence 6666666666653 22334888888 45678899999999999877666668999998755
No 94
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=25.29 E-value=76 Score=26.81 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=25.3
Q ss_pred EEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024598 173 IKFDVGNVVMVTGGRNRGRVGIIKNREK 200 (265)
Q Consensus 173 i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (265)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5588999999999999999999999854
No 95
>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=25.24 E-value=1.2e+02 Score=22.12 Aligned_cols=32 Identities=25% Similarity=0.369 Sum_probs=25.4
Q ss_pred eEEEccCCeeeecCCCCcccCCeEEEecCCCce
Q 024598 137 PYINTYDGRTIRYPDPLIKANDTIKLDLETNKI 169 (265)
Q Consensus 137 ~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI 169 (265)
-...+..|-.|.+| +-|+.||.|++|-.+++=
T Consensus 22 K~A~letG~~i~VP-~FI~~Gd~I~V~T~~g~Y 53 (56)
T cd05794 22 KPATLETGAEVQVP-LFIKEGEKIKVDTRTGEY 53 (56)
T ss_pred ceEEECCCCEEEcC-CeecCCCEEEEECCCCcE
Confidence 34557888888876 468999999999998763
No 96
>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=24.77 E-value=2.2e+02 Score=24.47 Aligned_cols=52 Identities=17% Similarity=0.146 Sum_probs=37.7
Q ss_pred ccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCCCcceeeehHHHHHHHHHH
Q 024598 205 FETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL 258 (265)
Q Consensus 205 ~~~v~i~d~~g~~F~T~~~~vfvIG~~~~p~islp~~~gi~~~~~~~~~~~~~~ 258 (265)
++-+.+-|.+|+--|+..+|+|++= +.-|++-|.+.|+-..+..+.-.++++
T Consensus 125 ~de~ll~d~~G~v~E~~~sNif~~~--~~~~~TP~~~~giL~Gitr~~ll~~~~ 176 (231)
T PF01063_consen 125 ADEALLLDEDGNVTEGSTSNIFFVK--DGTLYTPPLDSGILPGITRQLLLELAK 176 (231)
T ss_dssp SSEEEEEETTSBEEEESSSEEEEEE--TTEEEEESGSSSSB--HHHHHHHHHHH
T ss_pred cchhheecCCCCcCCCCCccccccc--CCEEEcCChhhhhccHHHHHHHHHHHH
Confidence 3444577899999999999999994 455889998888877776665554444
No 97
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=24.24 E-value=1.8e+02 Score=19.46 Aligned_cols=36 Identities=14% Similarity=0.162 Sum_probs=28.6
Q ss_pred EEEeChhhhcceeEEEEEEEEeeCCceEEEccCCeeeec
Q 024598 111 LHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRY 149 (265)
Q Consensus 111 ~~~I~~eea~~KLcKV~~k~~~~~g~~ql~~hDGrni~~ 149 (265)
..|++.++..|=++.|.. ..++...+.+.||++..+
T Consensus 3 ~vWvpD~~egfv~g~I~~---~~g~~vtV~~~~G~~~tv 38 (42)
T PF02736_consen 3 WVWVPDPKEGFVKGEIIE---EEGDKVTVKTEDGKEVTV 38 (42)
T ss_dssp EEEEEESSSSEEEEEEEE---EESSEEEEEETTTEEEEE
T ss_pred EEEEeCCcccEEEEEEEE---EcCCEEEEEECCCCEEEe
Confidence 357777777888899884 578889999999998754
No 98
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=23.53 E-value=4.1e+02 Score=26.40 Aligned_cols=52 Identities=27% Similarity=0.312 Sum_probs=35.2
Q ss_pred CcccCCeEEEecCCCceeeEEEe----eCCcEEEEECCCcceeEEEEEeEEEecCCc
Q 024598 153 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNREKHKGSF 205 (265)
Q Consensus 153 ~ik~~Dtv~i~l~~~kI~~~i~f----~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~ 205 (265)
.++.||...+.|...+=+-.-+| .-|-.++.-+|..+| .|.|.++....||.
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 57789998888875443323333 246677777886666 89999988666664
No 99
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=23.26 E-value=62 Score=26.41 Aligned_cols=49 Identities=16% Similarity=0.342 Sum_probs=26.8
Q ss_pred EeChhhhcceeEEEEEEEEee---CCceEEEccCCeeeecCCCCcccCCeEEEecCC
Q 024598 113 SIRDEEAKFKLCKVRSVQFGQ---KGIPYINTYDGRTIRYPDPLIKANDTIKLDLET 166 (265)
Q Consensus 113 ~I~~eea~~KLcKV~~k~~~~---~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~ 166 (265)
.|+.+.-.+++++.. .++. ....++.+.|.+.+ +|++++||++.+.++-
T Consensus 45 ~id~~~g~i~v~~~~--~VV~d~~d~~~eI~l~eAk~~---~~~~~vGD~i~~~i~~ 96 (122)
T PF08529_consen 45 EIDEDTGEIKVYRKK--EVVEDVEDPDTEISLSEAKKI---DPNAEVGDEIEEEIDP 96 (122)
T ss_dssp EEETTTTEEEEEEEE--EEETT-S-TTTEEEHHHHHCC---CTT--TTCEEEEE---
T ss_pred EEECCCCeEEEEEEe--eecCCccCccceeeHHHHHhh---CCCCccCCEEEecCCh
Confidence 455555555555532 2232 45566777777655 5789999999888863
No 100
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=22.98 E-value=93 Score=24.05 Aligned_cols=26 Identities=19% Similarity=0.119 Sum_probs=21.5
Q ss_pred ceEEECCEEecccCCCCCcceeEEecc
Q 024598 68 RHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (265)
Q Consensus 68 g~V~VDGkvr~d~~ypVG~mDVIsI~k 94 (265)
|.|+|||+.+. ..|.+.-+|.|++-.
T Consensus 50 ~~i~vNG~~v~-~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 50 GLILVNGRPVD-FDYRLKDGDRVAVYP 75 (81)
T ss_pred EEEEECCEECC-CcccCCCCCEEEEEe
Confidence 68999999884 578999999988743
No 101
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=22.79 E-value=2.8e+02 Score=27.27 Aligned_cols=54 Identities=17% Similarity=0.131 Sum_probs=28.4
Q ss_pred eEEEEEEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEEeeCCcEEEE---ECCCccee
Q 024598 123 LCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMV---TGGRNRGR 191 (265)
Q Consensus 123 LcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~~~~v---~gG~n~G~ 191 (265)
|..|+-.. .|....+.+.|..|||+-. |+|+-+..-.+++|+.+++ .+|+|.|.
T Consensus 279 L~lIeAe~--~g~~~~viLQnaetIrlv~-------------~dG~~vsVt~Lk~GD~VL~~~~~~~RHfG~ 335 (344)
T PRK02290 279 LLLIEAEY--GGKRIRTILQNAETIRLVT-------------PDGKPVSVVDLKPGDEVLGYLEEAARHFGM 335 (344)
T ss_pred EEEEEEEe--CCeEEEEEEecCcEEEEEC-------------CCCCEeeeeecCCCCEEEEEecCCcccccc
Confidence 33444433 4455556666666665533 3344455555555554433 26778773
No 102
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=22.64 E-value=1.7e+02 Score=21.77 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=17.8
Q ss_pred ccCCeEEEecC-----CCceeeEEEeeCCcEEEE
Q 024598 155 KANDTIKLDLE-----TNKITEFIKFDVGNVVMV 183 (265)
Q Consensus 155 k~~Dtv~i~l~-----~~kI~~~i~f~~G~~~~v 183 (265)
|+||.|.+.-. +|.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG~MYLv 35 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCcEEEEE
Confidence 56666666554 455666667777765554
No 103
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=22.12 E-value=1.4e+02 Score=30.89 Aligned_cols=42 Identities=17% Similarity=0.200 Sum_probs=32.6
Q ss_pred CCeEEEecCCCceeeEEEeeCCcEEEEECCCcceeEEEEEeEEE
Q 024598 157 NDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREK 200 (265)
Q Consensus 157 ~Dtv~i~l~~~kI~~~i~f~~G~~~~v~gG~n~G~vG~I~~i~~ 200 (265)
+|+.-|+.|.+.+-. -|..|+++-|+-|.+.+.+|.|..|+.
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 355555666555433 378899999999999999999999976
No 104
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=21.78 E-value=2.3e+02 Score=20.90 Aligned_cols=25 Identities=12% Similarity=0.008 Sum_probs=20.3
Q ss_pred ceEEECCEEecccCCCCCcceeEEec
Q 024598 68 RHVLVDAKVRTDKTYPAGFMDVVSIP 93 (265)
Q Consensus 68 g~V~VDGkvr~d~~ypVG~mDVIsI~ 93 (265)
=.|.|||+.+. ..+++.=+|.|+|=
T Consensus 52 ~~vavN~~~v~-~~~~l~dgDeVai~ 76 (82)
T PLN02799 52 CVLALNEEYTT-ESAALKDGDELAII 76 (82)
T ss_pred cEEEECCEEcC-CCcCcCCCCEEEEe
Confidence 35899999974 77899999988873
No 105
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=21.39 E-value=76 Score=27.54 Aligned_cols=54 Identities=19% Similarity=0.257 Sum_probs=38.1
Q ss_pred cCCCceeeEEEeeCCcEEEEECCCcce-eEEEEEeEEEecCC--ccEEEEEcCCCCe
Q 024598 164 LETNKITEFIKFDVGNVVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 217 (265)
Q Consensus 164 l~~~kI~~~i~f~~G~~~~v~gG~n~G-~vG~I~~i~~~~~s--~~~v~i~d~~g~~ 217 (265)
|-..-.+..+|+..++.+.|.+|+.-| .+|.|.++-+..-. .+.|.-+-.+|..
T Consensus 38 LR~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 38 LRQKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred HHHHhCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 333345788999999999999999999 99999998663322 2344444455543
No 106
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=20.80 E-value=1.6e+02 Score=21.40 Aligned_cols=31 Identities=26% Similarity=0.384 Sum_probs=25.3
Q ss_pred EEEccCCeeeecCCCCcccCCeEEEecCCCce
Q 024598 138 YINTYDGRTIRYPDPLIKANDTIKLDLETNKI 169 (265)
Q Consensus 138 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI 169 (265)
...+..|-.|.+| +-|+.||.|+||-.+++-
T Consensus 23 ~A~letG~~i~VP-~FI~~Gd~I~V~T~~g~Y 53 (56)
T smart00841 23 PATLETGAVVQVP-LFINEGDKIKVDTRTGEY 53 (56)
T ss_pred eEEECCCCEEEcC-CcccCCCEEEEECCCCcE
Confidence 4557888889877 479999999999998763
No 107
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=20.76 E-value=5.6e+02 Score=24.52 Aligned_cols=71 Identities=21% Similarity=0.463 Sum_probs=41.2
Q ss_pred CeeeecC-CCCcccCCeEEE-ecCCCceeeEEEeeCCcEEEEECCC---cceeEEEEEeEEEecCCccEEEEEcCCCCeE
Q 024598 144 GRTIRYP-DPLIKANDTIKL-DLETNKITEFIKFDVGNVVMVTGGR---NRGRVGIIKNREKHKGSFETIHIQDALGHEF 218 (265)
Q Consensus 144 Grni~~~-d~~ik~~Dtv~i-~l~~~kI~~~i~f~~G~~~~v~gG~---n~G~vG~I~~i~~~~~s~~~v~i~d~~g~~F 218 (265)
|-.|... +.+|++|.++-| ++|.+.++--|.+.+|+ ||+ .+|....|...+ +...+|.| .+|+ +
T Consensus 113 Gd~I~sG~~a~ik~GN~lpL~~IP~Gt~VhNVE~~pG~-----GGq~aRSaGtyA~vv~~~---~~y~~vrL--pSGe-~ 181 (275)
T COG0090 113 GDVIESGKDADIKPGNALPLGNIPEGTIVHNVELKPGD-----GGQLARSAGTYAQVVGKE---GNYVIVRL--PSGE-M 181 (275)
T ss_pred CCEEEeCCCCCcCCcceeeeccCCCCceEEeeeeccCC-----CceEEEeCCceEEEEEcc---CCEEEEEC--CCCC-e
Confidence 4444333 557888877766 58899999999998887 553 445444444432 33344433 4554 3
Q ss_pred eEeeceE
Q 024598 219 ATRLGNV 225 (265)
Q Consensus 219 ~T~~~~v 225 (265)
..+.+.+
T Consensus 182 r~v~~~C 188 (275)
T COG0090 182 RKVLSEC 188 (275)
T ss_pred Eeecccc
Confidence 3333333
No 108
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=20.72 E-value=1.8e+02 Score=20.98 Aligned_cols=26 Identities=19% Similarity=0.129 Sum_probs=21.8
Q ss_pred hCceEEECCEEecccCCCCCcceeEEe
Q 024598 66 MQRHVLVDAKVRTDKTYPAGFMDVVSI 92 (265)
Q Consensus 66 ~~g~V~VDGkvr~d~~ypVG~mDVIsI 92 (265)
..-.|.|||+.+. ..+++.=.|.|+|
T Consensus 48 ~~~~v~vNg~~v~-~~~~l~~gD~v~i 73 (80)
T cd00754 48 ARVRIAVNGEYVR-LDTPLKDGDEVAI 73 (80)
T ss_pred hcEEEEECCeEcC-CCcccCCCCEEEE
Confidence 3447999999998 7789999999886
No 109
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=20.41 E-value=1.9e+02 Score=29.98 Aligned_cols=93 Identities=15% Similarity=0.067 Sum_probs=50.8
Q ss_pred ecccCCCCCcce-----eEEecc--cCcceeeeeecCCceEEEE-------eChhhhcceeEEEE----EEEEeeCCceE
Q 024598 77 RTDKTYPAGFMD-----VVSIPK--TNENFRLLYDTKGRFRLHS-------IRDEEAKFKLCKVR----SVQFGQKGIPY 138 (265)
Q Consensus 77 r~d~~ypVG~mD-----VIsI~k--t~e~yR~l~d~kgrf~~~~-------I~~eea~~KLcKV~----~k~~~~~g~~q 138 (265)
+-|+.|+.|..| -+++.. +.-.+|-+++.++++.... ++.+-|+ .|.+-. ...++......
T Consensus 399 ia~YQFG~g~g~~l~~~~~~v~~s~~tgr~r~v~~~~~~l~t~r~~dg~l~lt~~Ga~-~l~~~~~~p~~rV~v~~~~~~ 477 (540)
T TIGR00432 399 MKHYQNGPPNGELNVLSDVRIERSRNTGKIRHIYAGDELICTMRASDGLLVLGAEGAV-RLHKGTDYPAWRVAVNEESEP 477 (540)
T ss_pred HHHhhcCcCchHhhCCCCcEEEEeccCCcceEEEECCEEEEEEEcCCCeEEeCHHHHH-HHHhcCCCCceEEEECCcchh
Confidence 346677766543 355533 2346788886655544432 5666663 332211 11112221111
Q ss_pred EEccCCeeee-----cCCCCcccCCeEEEecCCCceee
Q 024598 139 INTYDGRTIR-----YPDPLIKANDTIKLDLETNKITE 171 (265)
Q Consensus 139 l~~hDGrni~-----~~d~~ik~~Dtv~i~l~~~kI~~ 171 (265)
.+-+|+|+- -.|+.|.+||-|++-.++++++.
T Consensus 478 -f~~~g~~vfak~V~~ad~~IR~~dEV~vv~~~~~lla 514 (540)
T TIGR00432 478 -FARKGKSVFAKFIIDCDNNIRANDEVLIVNADDELLA 514 (540)
T ss_pred -hccCCCcccCCccccCCCCCCCCCeEEEEcCCCcEEE
Confidence 235677772 24899999999998887777653
No 110
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family. Members of this family belong to the broader family of PRC-barrel domain proteins (see Pfam model pfam05239), but are found only in endospore-forming bacteria of the Firmicutes lineage. Most such species have exactly two members of this family and all have at least one; the function is unknown. One of two members from Bacillus subtilis, YmxH, is strongly induced by the mother cell-specific sigma-E factor.
Probab=20.10 E-value=4e+02 Score=20.28 Aligned_cols=40 Identities=28% Similarity=0.368 Sum_probs=27.2
Q ss_pred CceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEEeeCCc
Q 024598 135 GIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGN 179 (265)
Q Consensus 135 g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~i~f~~G~ 179 (265)
++.-+|.+||+.+-+- .-.| +.||..+++|...+--..|.
T Consensus 7 ~keVIni~~G~~lG~v----~~~D-l~iD~~~G~I~aiIi~~~~~ 46 (76)
T TIGR02888 7 GKEIINVNDGERLGVI----GNID-LEIDEEDGRILSLIIPGKGK 46 (76)
T ss_pred CCCEEECCCCcEeecc----ccce-EEEECCCCEEEEEEEeCCCc
Confidence 5667899999999532 1123 78888899987666554444
No 111
>cd01903 Ntn_AC_NAAA AC_NAAA This conserved domain includes two closely related proteins, acid ceramidase (AC, also known as N-acylsphingosine amidohydrolase), and N-acylethanolamine-hydrolyzing acid amidase (NAAA). AC catalyzes the hydrolysis of ceramide to sphingosine and fatty acid. Ceramide is required for the biosynthesis of most sphingolipids and plays an important role in many signal transduction pathways by inducing apoptosis and/or arresting cell growth. An inherited deficiency of AC activity leads to the lysosomal storage disorder known as Farber disease. AC is considered a "rheostat" important for maintaining the proper intracellular levels of these lipids since hydrolysis of ceramide is the only source of sphingosine in cells. NAAA is a eukaryotic glycoprotein that hydrolyzes bioactive N-acylethanolamines, including anandamide (an endocannabinoid) and N-palmitoylethanolamine (an anti-inflammatory and neuroprotective substance), to fatty acids and ethanolamine at acidic pH
Probab=20.03 E-value=1.9e+02 Score=26.01 Aligned_cols=30 Identities=20% Similarity=0.458 Sum_probs=26.6
Q ss_pred ccchHHHHHHhhhccccCHHHHHHHHhCce
Q 024598 40 ECLPLILILRNRLKYALTYREVIAILMQRH 69 (265)
Q Consensus 40 ~slPL~i~LRdrLg~A~t~rEar~Il~~g~ 69 (265)
..+|..+++|..|.-+.|..||++.+.+-.
T Consensus 97 ~g~p~~~liR~vLe~~~s~~eA~~~L~~~~ 126 (231)
T cd01903 97 DGIPVSWLIRETLENATSYEDAVEKLSTTP 126 (231)
T ss_pred CCCchhhhHHHHHhccCCHHHHHHHhccCc
Confidence 588999999999998899999999997543
Done!