Query 024108
Match_columns 272
No_of_seqs 110 out of 331
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 09:02:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024108.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024108hhsearch_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 4E-117 9E-122 809.1 30.4 260 1-267 1-260 (261)
2 PTZ00118 40S ribosomal protein 100.0 8E-117 2E-121 807.7 30.8 260 1-267 1-260 (262)
3 PTZ00223 40S ribosomal protein 100.0 1E-112 3E-117 783.4 30.7 258 5-269 2-260 (273)
4 PRK04313 30S ribosomal protein 100.0 5E-106 1E-110 728.2 28.3 235 5-247 1-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 6E-104 1E-108 710.2 24.3 240 2-249 1-241 (241)
6 KOG0378 40S ribosomal protein 100.0 2E-101 5E-106 696.5 15.3 263 1-270 1-263 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 2.7E-33 5.9E-38 215.7 9.9 77 94-177 1-77 (77)
8 PF08071 RS4NT: RS4NT (NUC023) 99.8 7.2E-21 1.6E-25 129.3 1.6 38 3-40 1-38 (38)
9 PF01479 S4: S4 domain; Inter 98.5 2.5E-07 5.3E-12 63.8 5.1 48 42-90 1-48 (48)
10 cd00165 S4 S4/Hsp/ tRNA synthe 97.5 0.00042 9.1E-09 48.1 6.8 62 43-105 2-63 (70)
11 smart00363 S4 S4 RNA-binding d 97.1 0.0012 2.6E-08 44.6 5.3 50 44-94 3-52 (60)
12 PF00467 KOW: KOW motif; Inte 96.7 0.0017 3.6E-08 42.1 3.1 31 184-217 1-31 (32)
13 COG0522 RpsD Ribosomal protein 96.7 0.0016 3.5E-08 58.9 3.8 43 51-93 102-144 (205)
14 smart00739 KOW KOW (Kyprides, 96.7 0.0017 3.8E-08 39.6 2.8 27 181-207 1-27 (28)
15 TIGR02988 YaaA_near_RecF S4 do 96.6 0.0056 1.2E-07 44.1 5.5 51 42-93 9-59 (59)
16 PF13275 S4_2: S4 domain; PDB: 95.9 0.004 8.7E-08 47.1 1.5 60 40-102 6-65 (65)
17 PRK11507 ribosome-associated p 95.6 0.049 1.1E-06 41.9 6.6 60 40-102 10-69 (70)
18 TIGR01018 rpsD_arch ribosomal 95.2 0.016 3.5E-07 50.9 2.9 44 51-94 112-157 (162)
19 PTZ00155 40S ribosomal protein 95.0 0.019 4.1E-07 51.3 2.8 40 45-84 102-148 (181)
20 PRK04051 rps4p 30S ribosomal p 94.9 0.042 9.1E-07 48.9 4.8 44 52-95 112-157 (177)
21 PLN00189 40S ribosomal protein 94.8 0.023 5E-07 51.3 3.0 43 51-93 117-161 (194)
22 TIGR01017 rpsD_bact ribosomal 94.8 0.046 9.9E-07 49.0 4.8 43 52-94 99-141 (200)
23 TIGR01080 rplX_A_E ribosomal p 94.7 0.067 1.4E-06 44.6 5.3 57 177-236 37-100 (114)
24 TIGR00005 rluA_subfam pseudour 94.6 0.15 3.2E-06 47.2 7.8 52 41-93 5-56 (299)
25 PRK05327 rpsD 30S ribosomal pr 94.5 0.062 1.3E-06 48.3 5.0 42 53-94 103-144 (203)
26 CHL00113 rps4 ribosomal protei 94.3 0.067 1.5E-06 48.3 4.7 43 52-94 98-140 (201)
27 TIGR03069 PS_II_S4 photosystem 94.0 0.17 3.7E-06 47.0 6.8 62 41-115 183-244 (257)
28 TIGR00478 tly hemolysin TlyA f 93.1 0.16 3.6E-06 46.3 5.1 47 47-94 5-51 (228)
29 COG2501 S4-like RNA binding pr 92.3 0.32 7E-06 37.8 5.0 59 40-101 10-68 (73)
30 COG0564 RluA Pseudouridylate s 91.7 0.45 9.8E-06 44.8 6.4 57 40-99 11-67 (289)
31 PRK01191 rpl24p 50S ribosomal 91.6 0.46 9.9E-06 40.1 5.6 55 179-236 43-104 (120)
32 PRK11180 rluD 23S rRNA pseudou 91.6 0.61 1.3E-05 44.1 7.2 52 41-93 17-68 (325)
33 PRK05912 tyrosyl-tRNA syntheta 90.5 0.88 1.9E-05 44.9 7.3 65 41-112 342-406 (408)
34 PRK10700 23S rRNA pseudouridyl 90.4 0.82 1.8E-05 43.0 6.8 55 56-111 15-81 (289)
35 PRK10348 ribosome-associated h 89.8 0.79 1.7E-05 39.2 5.5 59 41-101 8-66 (133)
36 PTZ00194 60S ribosomal protein 89.0 0.99 2.1E-05 39.2 5.6 57 180-236 45-105 (143)
37 COG1187 RsuA 16S rRNA uridine- 88.1 1.1 2.4E-05 41.8 5.8 57 53-110 13-76 (248)
38 PRK10475 23S rRNA pseudouridin 87.9 2 4.3E-05 40.7 7.3 68 40-110 5-80 (290)
39 PRK11025 23S rRNA pseudouridyl 87.7 2.1 4.5E-05 40.4 7.4 51 41-93 19-69 (317)
40 PRK12281 rplX 50S ribosomal pr 87.0 1.1 2.4E-05 34.7 4.3 38 180-220 5-42 (76)
41 PRK10839 16S rRNA pseudouridyl 86.4 3.9 8.4E-05 36.6 8.1 68 44-114 3-76 (232)
42 CHL00141 rpl24 ribosomal prote 86.1 1.4 3E-05 34.7 4.4 37 180-219 7-43 (83)
43 PRK13354 tyrosyl-tRNA syntheta 85.8 2.7 5.8E-05 41.7 7.2 67 41-113 342-408 (410)
44 PRK00004 rplX 50S ribosomal pr 85.1 1.3 2.7E-05 36.2 3.9 29 180-208 3-31 (105)
45 PLN00051 RNA-binding S4 domain 84.4 3.3 7.2E-05 38.9 6.9 62 41-115 191-252 (267)
46 COG1189 Predicted rRNA methyla 84.1 1.5 3.2E-05 41.1 4.4 119 53-172 13-153 (245)
47 COG2302 Uncharacterized conser 82.4 3.1 6.7E-05 39.3 5.7 63 40-115 179-241 (257)
48 PF13051 DUF3912: Protein of u 79.7 4.8 0.0001 30.4 4.9 50 184-237 5-55 (68)
49 TIGR01079 rplX_bact ribosomal 79.3 2.8 6.1E-05 34.3 3.9 28 181-208 3-30 (104)
50 KOG4655 U3 small nucleolar rib 63.3 5.3 0.00012 35.8 2.2 55 30-84 87-148 (181)
51 COG0162 TyrS Tyrosyl-tRNA synt 62.6 16 0.00036 36.4 5.7 61 44-112 338-398 (401)
52 COG2163 RPL14A Ribosomal prote 59.1 9.7 0.00021 32.4 3.0 34 182-219 5-38 (125)
53 COG0198 RplX Ribosomal protein 58.6 15 0.00032 30.4 3.8 29 180-208 3-31 (104)
54 PF03417 AAT: Acyl-coenzyme A: 58.2 44 0.00095 29.3 7.1 29 39-68 69-97 (225)
55 PF14001 YdfZ: YdfZ protein 55.4 19 0.0004 27.6 3.6 42 181-226 9-56 (64)
56 PTZ00065 60S ribosomal protein 53.8 15 0.00032 31.5 3.2 32 182-217 8-39 (130)
57 COG1188 Ribosome-associated he 50.6 38 0.00083 27.9 5.0 45 53-98 19-63 (100)
58 PF12005 DUF3499: Protein of u 48.6 7.5 0.00016 33.1 0.7 23 7-29 46-68 (123)
59 cd04093 HBS1_C HBS1_C: this fa 46.8 1.4E+02 0.0029 23.2 8.0 45 160-205 59-107 (107)
60 PRK04333 50S ribosomal protein 46.4 22 0.00048 28.1 2.9 33 181-217 3-35 (84)
61 PRK02290 3-dehydroquinate synt 45.7 65 0.0014 31.8 6.6 55 129-198 278-335 (344)
62 cd03704 eRF3c_III This family 42.5 69 0.0015 25.1 5.3 48 157-205 56-108 (108)
63 PF01959 DHQS: 3-dehydroquinat 41.9 84 0.0018 31.2 6.8 54 130-198 289-345 (354)
64 TIGR03318 YdfZ_fam putative se 38.4 33 0.0007 26.3 2.6 41 182-226 11-57 (65)
65 cd03706 mtEFTU_III Domain III 38.1 1.8E+02 0.0039 22.1 7.6 40 161-204 52-92 (93)
66 cd01234 PH_CADPS CADPS (Ca2+-d 36.8 22 0.00047 30.0 1.6 42 106-159 21-62 (117)
67 PF01588 tRNA_bind: Putative t 35.8 83 0.0018 24.5 4.7 19 198-216 2-20 (95)
68 PF08828 DSX_dimer: Doublesex 35.0 24 0.00053 26.8 1.5 32 40-74 22-54 (62)
69 PRK08559 nusG transcription an 34.9 63 0.0014 27.6 4.2 29 180-208 93-121 (153)
70 TIGR00405 L26e_arch ribosomal 34.0 72 0.0016 26.5 4.4 26 182-207 87-112 (145)
71 KOG1784 Small Nuclear ribonucl 33.7 73 0.0016 26.1 4.1 60 141-204 10-75 (96)
72 PRK05609 nusG transcription an 33.4 1E+02 0.0022 26.2 5.4 28 180-207 125-152 (181)
73 PTZ00471 60S ribosomal protein 33.4 42 0.00091 29.0 2.9 24 182-205 5-28 (134)
74 TIGR03193 4hydroxCoAred 4-hydr 33.3 35 0.00076 29.7 2.4 53 40-96 17-77 (148)
75 PF09285 Elong-fact-P_C: Elong 32.3 84 0.0018 23.2 3.9 36 141-177 19-54 (56)
76 PF04773 FecR: FecR protein; 31.8 2.1E+02 0.0046 21.1 9.5 67 136-202 3-76 (98)
77 cd03705 EF1_alpha_III Domain I 31.6 97 0.0021 23.9 4.5 35 160-197 59-100 (104)
78 PF07076 DUF1344: Protein of u 31.1 1.1E+02 0.0024 23.2 4.4 36 137-172 10-49 (61)
79 PF11314 DUF3117: Protein of u 31.1 56 0.0012 23.9 2.7 36 85-122 8-43 (51)
80 PRK13922 rod shape-determining 29.6 3.8E+02 0.0082 24.5 8.7 36 198-236 235-271 (276)
81 TIGR00922 nusG transcription t 29.1 1.3E+02 0.0027 25.6 5.2 28 180-207 118-145 (172)
82 TIGR01955 RfaH transcriptional 29.0 1.4E+02 0.0031 24.8 5.4 28 179-206 106-133 (159)
83 PF12961 DUF3850: Domain of Un 27.9 55 0.0012 25.4 2.4 18 153-170 21-38 (72)
84 cd05794 S1_EF-P_repeat_2 S1_EF 27.2 1.1E+02 0.0023 22.7 3.7 36 140-176 18-53 (56)
85 smart00306 HintN Hint (Hedgeho 26.9 2.6E+02 0.0056 20.6 8.5 55 183-237 23-78 (100)
86 KOG3586 TBX1 and related T-box 26.8 87 0.0019 31.7 4.2 118 69-196 114-251 (437)
87 KOG1999 RNA polymerase II tran 26.3 97 0.0021 34.6 4.7 27 181-207 459-485 (1024)
88 COG1792 MreC Cell shape-determ 26.2 5.6E+02 0.012 24.2 11.6 61 157-237 209-270 (284)
89 PF11717 Tudor-knot: RNA bindi 25.7 1.9E+02 0.0041 20.4 4.8 37 182-218 1-38 (55)
90 TIGR02658 TTQ_MADH_Hv methylam 25.3 5.2E+02 0.011 25.4 9.2 94 95-192 45-156 (352)
91 PTZ00141 elongation factor 1- 25.0 3.7E+02 0.008 26.8 8.3 52 160-212 381-436 (446)
92 KOG3513 Neural cell adhesion m 24.9 1.5E+02 0.0033 33.3 6.0 158 66-237 440-614 (1051)
93 PRK14898 DNA-directed RNA poly 24.5 2.9E+02 0.0064 30.3 8.0 77 84-169 112-195 (858)
94 TIGR03198 pucE xanthine dehydr 24.5 29 0.00062 30.2 0.4 52 40-95 19-78 (151)
95 KOG3401 60S ribosomal protein 24.5 60 0.0013 28.5 2.3 51 174-224 41-94 (145)
96 TIGR00739 yajC preprotein tran 24.0 1.9E+02 0.0042 22.5 4.9 33 182-223 38-70 (84)
97 cd02899 PLAT_SR Scavenger rece 23.8 2.8E+02 0.006 22.7 6.0 61 182-255 41-108 (109)
98 TIGR00234 tyrS tyrosyl-tRNA sy 23.1 78 0.0017 31.1 3.1 45 41-86 329-373 (377)
99 PF01063 Aminotran_4: Aminotra 22.8 2.7E+02 0.0059 24.0 6.2 52 212-265 125-176 (231)
100 KOG1999 RNA polymerase II tran 22.2 1.1E+02 0.0023 34.3 4.1 55 182-240 582-638 (1024)
101 smart00841 Elong-fact-P_C Elon 22.1 1.5E+02 0.0033 21.9 3.7 31 145-176 23-53 (56)
102 PF06905 FAIM1: Fas apoptotic 22.0 5.8E+02 0.013 22.9 10.0 51 149-201 82-133 (177)
103 PLN02772 guanylate kinase 21.9 1.9E+02 0.0042 29.0 5.6 63 179-241 28-98 (398)
104 cd05892 Ig_Myotilin_C C-termin 21.5 1.8E+02 0.0038 21.5 4.1 35 95-136 27-63 (75)
105 TIGR01956 NusG_myco NusG famil 21.3 2.6E+02 0.0056 26.7 6.0 32 176-207 200-231 (258)
106 PF02239 Cytochrom_D1: Cytochr 20.8 3.9E+02 0.0085 25.9 7.3 46 136-183 74-119 (369)
107 PRK09014 rfaH transcriptional 20.1 1.1E+02 0.0023 25.9 3.0 26 181-206 109-134 (162)
108 TIGR00432 arcsn_tRNA_tgt tRNA- 20.0 3.4E+02 0.0075 28.3 7.1 96 77-178 399-514 (540)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=4.2e-117 Score=809.14 Aligned_cols=260 Identities=90% Similarity=1.398 Sum_probs=257.4
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccc
Q 024108 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDK 80 (272)
Q Consensus 1 MarG~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~ 80 (272)
||||||+|||||+||+||||+||+++||||||||||++++||||++||||+|+||+|++||++||+||+|+|||+||||+
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 cCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCCC
Q 024108 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPL 160 (272)
Q Consensus 81 k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ 160 (272)
+||||||||||||++||+|||+||++|||.+|+|++|||+ ||||||++|+++++|+|||+|||||||+|+||.
T Consensus 81 ~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~-------~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~ 153 (261)
T PLN00036 81 TYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAK-------FKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPL 153 (261)
T ss_pred CCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHcc-------ceEEEEEEEEEecCCeEEEEecCCceeccCCCc
Confidence 9999999999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred cccCCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCC
Q 024108 161 IKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTK 240 (272)
Q Consensus 161 ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~k 240 (272)
||+||||+||||+++|++||||++||+||||||+|+|++|+|.+|+++++|+++||++|++|++|+|+++||||||++++
T Consensus 154 ~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~k 233 (261)
T PLN00036 154 IKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTK 233 (261)
T ss_pred cccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998899
Q ss_pred ceeeCCCCcceeeehHHHHHHHHHHHh
Q 024108 241 PWVSLPKGKGIKLSIIEEARKRQALAT 267 (272)
Q Consensus 241 p~Islp~~~gi~~~~~e~~~~~~~~~~ 267 (272)
|||+||+++|||+|++|||++++++.+
T Consensus 234 p~isLp~~~gi~~~~~e~r~~~~~~~~ 260 (261)
T PLN00036 234 PWISLPKGKGIKLSIIEEARKRLAAGQ 260 (261)
T ss_pred eeEeCcCCCCcccchHHHHHHhhhhhc
Confidence 999999999999999999999998764
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=8.1e-117 Score=807.65 Aligned_cols=260 Identities=64% Similarity=1.059 Sum_probs=257.8
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccc
Q 024108 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDK 80 (272)
Q Consensus 1 MarG~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~ 80 (272)
|||||++|||||+||+||||+||+++|||+||||||++++||||++||||+|+||+|++||++||+||+|+|||+||||+
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 cCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCCC
Q 024108 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPL 160 (272)
Q Consensus 81 k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ 160 (272)
+||||||||||||+|||||||+||++|+|.+|+|++|||+ ||||||++|+++++|+|||+|||||||+|+||.
T Consensus 81 ~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~-------~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ 153 (262)
T PTZ00118 81 TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAK-------YKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPD 153 (262)
T ss_pred CCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhc-------ceEEEEeEEEECCCCeEEEEecCcceeccCCCc
Confidence 9999999999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred cccCCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCC
Q 024108 161 IKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTK 240 (272)
Q Consensus 161 ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~k 240 (272)
||+||||+||||+++|++||||++||+||||||+|+|++|+|.+++++++|+++||++|++|++|+|+++||||||++++
T Consensus 154 ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~k 233 (262)
T PTZ00118 154 VKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTK 233 (262)
T ss_pred ccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998899
Q ss_pred ceeeCCCCcceeeehHHHHHHHHHHHh
Q 024108 241 PWVSLPKGKGIKLSIIEEARKRQALAT 267 (272)
Q Consensus 241 p~Islp~~~gi~~~~~e~~~~~~~~~~ 267 (272)
|||+||+++|||+|++|||++++++++
T Consensus 234 p~islp~~kgi~~~~~e~~~~~~~~~~ 260 (262)
T PTZ00118 234 PYVSLPRERGIKKDIIEERRNRLAKAL 260 (262)
T ss_pred eeEeCcCCCCccccHHHHHHHHHHHHh
Confidence 999999999999999999999998876
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.3e-112 Score=783.35 Aligned_cols=258 Identities=53% Similarity=0.866 Sum_probs=253.7
Q ss_pred cccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 024108 5 LKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (272)
Q Consensus 5 ~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~Pv 84 (272)
.++|||||+||+||||+||+++|||+||||||++++||||++||||+|+||+|++||++||+||+|+|||+||+|++|||
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 cceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCCCcccC
Q 024108 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKAN 164 (272)
Q Consensus 85 G~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~ 164 (272)
|||||||||++||+|||+||++|+|.+|+|++|||+ ||||||++|++++||+|||+|||||||+|+||+||+|
T Consensus 82 GlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~-------~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~ 154 (273)
T PTZ00223 82 GFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQ-------IKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRG 154 (273)
T ss_pred ceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHcc-------ceEEEEEEEEEecCCeeEEEecCCceeccCCccccCC
Confidence 999999999999999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred CeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccC-CCcee
Q 024108 165 DTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-TKPWV 243 (272)
Q Consensus 165 Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~-~kp~I 243 (272)
|||+|+||+++|++||||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++ ++|||
T Consensus 155 Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~I 234 (273)
T PTZ00223 155 DTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPV 234 (273)
T ss_pred CEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999986 69999
Q ss_pred eCCCCcceeeehHHHHHHHHHHHhhh
Q 024108 244 SLPKGKGIKLSIIEEARKRQALATSA 269 (272)
Q Consensus 244 slp~~~gi~~~~~e~~~~~~~~~~~~ 269 (272)
+||+++|||+|++|||+++++++++.
T Consensus 235 sLp~~kgi~~~~~e~~~~~~~~~~~~ 260 (273)
T PTZ00223 235 TLPKQQGLRINVIQEREEKLIAAEAR 260 (273)
T ss_pred ECcCCCCccccHHHHHHHHHHHHHhh
Confidence 99999999999999999999888754
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=5.4e-106 Score=728.16 Aligned_cols=235 Identities=41% Similarity=0.681 Sum_probs=231.5
Q ss_pred cccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 024108 5 LKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (272)
Q Consensus 5 ~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~Pv 84 (272)
+++|||||+||+||||+||+++||||||||||++++||||+++|||+|+||+|+|||++||+||+|+||||||+|++|||
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 cceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCC-CCccc
Q 024108 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKA 163 (272)
Q Consensus 85 G~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d-~~ik~ 163 (272)
|||||||||++||+|||+||++|||++|+|++|||+ ||||||++|++++||+|||+|||||||+++| ++||+
T Consensus 81 GlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~-------~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~ 153 (237)
T PRK04313 81 GLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAK-------LKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKT 153 (237)
T ss_pred CceeEEEEccCCCeEEEEECCCCcEEEEECChHHcc-------ceEEEEEeEEEecCCEEEEEecCCceEEccCcccccc
Confidence 999999999999999999999999999999999999 9999999999999999999999999999998 99999
Q ss_pred CCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCCce
Q 024108 164 NDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGTKPW 242 (272)
Q Consensus 164 ~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~ 242 (272)
||||+|+||+++|++||+|++||+||||||+|+|++|+|.+|++++ +++++||++|++|++|+|+++||||||+ ++|+
T Consensus 154 ~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~ 232 (237)
T PRK04313 154 GDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPV 232 (237)
T ss_pred CCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcc
Confidence 9999999999999999999999999999999999999999999999 6789999999999999999999999998 9999
Q ss_pred eeCCC
Q 024108 243 VSLPK 247 (272)
Q Consensus 243 Islp~ 247 (272)
|+||.
T Consensus 233 isl~~ 237 (237)
T PRK04313 233 IKLPE 237 (237)
T ss_pred eeCCC
Confidence 99984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-104 Score=710.19 Aligned_cols=240 Identities=49% Similarity=0.774 Sum_probs=236.5
Q ss_pred CCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEecccc
Q 024108 2 ARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKT 81 (272)
Q Consensus 2 arG~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k 81 (272)
||||++|||||+||+||||+||+++|+|+|+||||++++||||++++||+|+||+|+|||++||++|+|+|||+||+|++
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 CCCcceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCCCc
Q 024108 82 YPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLI 161 (272)
Q Consensus 82 ~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~i 161 (272)
||||||||||||+|||+||||||.+|+|.||+|++|||. ||||||++|++++||++|||||||||++++|++|
T Consensus 81 fPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~-------~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~ 153 (241)
T COG1471 81 FPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEAS-------YKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNY 153 (241)
T ss_pred CCcceEEEEEECCCCceEEEEecCCccEEEEecChhhcc-------ceEEEEEeEEEecCCEEEEEecCCceeeccCCcc
Confidence 999999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred ccCCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEEccCCC
Q 024108 162 KANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGTK 240 (272)
Q Consensus 162 k~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~k 240 (272)
++||||++++|+++|++||+|++|++||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++
T Consensus 154 k~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k 232 (241)
T COG1471 154 KTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DK 232 (241)
T ss_pred ccccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CC
Confidence 999999999999999999999999999999999999999999999999 5579999999999999999999999997 99
Q ss_pred ceeeCCCCc
Q 024108 241 PWVSLPKGK 249 (272)
Q Consensus 241 p~Islp~~~ 249 (272)
|||+||+|+
T Consensus 233 ~~i~l~~e~ 241 (241)
T COG1471 233 PVISLPKEK 241 (241)
T ss_pred ceEeCCCCC
Confidence 999999874
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-101 Score=696.51 Aligned_cols=263 Identities=71% Similarity=1.160 Sum_probs=261.2
Q ss_pred CCCCcccccccccCCCceecccccceeccCCCCCCCCCcccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccc
Q 024108 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDK 80 (272)
Q Consensus 1 MarG~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~ 80 (272)
|+|||++||||++||+|||++|++|+|||+||+|||+++||+||++||||+|+||+|.+|+++|++|+.|+|||+||+|.
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 cCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCCC
Q 024108 81 TYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPL 160 (272)
Q Consensus 81 k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ 160 (272)
+||+||||||+|++|||+||++||++|+|.+|.|++|||+ ||||||++++.+.+|+|+|+|||||+||||||.
T Consensus 81 ~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeak-------yKLcKVrk~f~~tkGiP~lvthDg~tIrypDpl 153 (263)
T KOG0378|consen 81 TYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAK-------YKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPL 153 (263)
T ss_pred ccccceeEEEEecccchhhhhhhhcccceEEEEecccccc-------ceeeeeEEEEeeccCcceEEccCCceEecCCcc
Confidence 9999999999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred cccCCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEccCCC
Q 024108 161 IKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTK 240 (272)
Q Consensus 161 ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk~~k 240 (272)
||+|||+++++++++|.++++|++|++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++||||||+|+|
T Consensus 154 Ik~~dtI~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnK 233 (263)
T KOG0378|consen 154 IKVNDTIKIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNK 233 (263)
T ss_pred cCccceeeccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeCCCCcceeeehHHHHHHHHHHHhhhh
Q 024108 241 PWVSLPKGKGIKLSIIEEARKRQALATSAA 270 (272)
Q Consensus 241 p~Islp~~~gi~~~~~e~~~~~~~~~~~~~ 270 (272)
||||||+++||+++++||||+|++++++++
T Consensus 234 pwisLPkgkgi~~siaEe~dkrl~~k~~s~ 263 (263)
T KOG0378|consen 234 PWISLPKGKGIALSIAEERDKRLAAKISSG 263 (263)
T ss_pred ccccCccccCccchhhHHHHHHHhhhccCC
Confidence 999999999999999999999999999863
No 7
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=100.00 E-value=2.7e-33 Score=215.69 Aligned_cols=77 Identities=64% Similarity=1.028 Sum_probs=69.7
Q ss_pred cCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCC
Q 024108 94 KTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLET 173 (272)
Q Consensus 94 kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~ 173 (272)
+|||+|||+||++|+|.+|+|++|||+ ||||||++|++++||+|||+|||||||+|+||.||+||||+|+||+
T Consensus 1 kt~e~yRvl~d~kgr~~l~~I~~eea~-------~KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~ 73 (77)
T PF00900_consen 1 KTGEHYRVLYDTKGRFVLHPISEEEAK-------YKLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPT 73 (77)
T ss_dssp CTTEEEEEEE-TTS-EEEEEE-TTGGG-------EEEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETTT
T ss_pred CCCcEEEEEECCCCcEEEEECCHHHcc-------CeEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECCC
Confidence 689999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred Ccee
Q 024108 174 NKIT 177 (272)
Q Consensus 174 ~kI~ 177 (272)
+||+
T Consensus 74 ~kI~ 77 (77)
T PF00900_consen 74 QKIV 77 (77)
T ss_dssp TEEE
T ss_pred CcCC
Confidence 9986
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=99.80 E-value=7.2e-21 Score=129.28 Aligned_cols=38 Identities=74% Similarity=1.241 Sum_probs=22.2
Q ss_pred CCcccccccccCCCceecccccceeccCCCCCCCCCcc
Q 024108 3 RGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRE 40 (272)
Q Consensus 3 rG~kkHlKRl~AP~~W~i~kk~~~~a~kpspGPH~~~~ 40 (272)
+|+++|||||+||++|||+||+++||++||||||+++|
T Consensus 1 ~G~kkHlKRl~AP~~W~i~kk~~~~a~rpspGPH~~~e 38 (38)
T PF08071_consen 1 RGPKKHLKRLAAPKSWMIDKKTGKFAPRPSPGPHKLRE 38 (38)
T ss_dssp -S-----BCCCS-GGGT--SSSSSB-----SSSS-CCC
T ss_pred CCcccccccccCCcccccccccCccccCCCCCCccCCC
Confidence 69999999999999999999999999999999999975
No 9
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.49 E-value=2.5e-07 Score=63.79 Aligned_cols=48 Identities=31% Similarity=0.323 Sum_probs=44.1
Q ss_pred chHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEE
Q 024108 42 LPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVV 90 (272)
Q Consensus 42 lPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVI 90 (272)
++|..+| ..++++.+..||++.|++|.|+|||++++|+.|++...|+|
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 44899999999999999999999999999999999999987
No 10
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.53 E-value=0.00042 Score=48.11 Aligned_cols=62 Identities=26% Similarity=0.305 Sum_probs=48.0
Q ss_pred hHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcC
Q 024108 43 PLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDT 105 (272)
Q Consensus 43 PL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~ 105 (272)
.|.-+|+.. ..+.+..+|++++.+|.|+|||+..++..+++-..|+|++........++|..
T Consensus 2 rl~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~ed 63 (70)
T cd00165 2 RLDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYED 63 (70)
T ss_pred cHHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceeecc
Confidence 345566654 36789999999999999999999999999999888999997643333444444
No 11
>smart00363 S4 S4 RNA-binding domain.
Probab=97.14 E-value=0.0012 Score=44.58 Aligned_cols=50 Identities=24% Similarity=0.177 Sum_probs=42.1
Q ss_pred HHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 024108 44 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (272)
Q Consensus 44 L~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k 94 (272)
|..+|... ..+.+..++++.+.+|.|+|||++.++..+++--.|.|++..
T Consensus 3 l~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 3 LDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred HHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 45566543 356799999999999999999999999999998889999965
No 12
>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=96.74 E-value=0.0017 Score=42.10 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=25.9
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 024108 184 VGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 217 (272)
Q Consensus 184 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i 217 (272)
+|+.|+|+.|++.|+.|+|.++..+. ..|++
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 13
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=96.68 E-value=0.0016 Score=58.89 Aligned_cols=43 Identities=28% Similarity=0.358 Sum_probs=40.9
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 024108 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (272)
Q Consensus 51 ~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~ 93 (272)
++++|.|.++|++.+..|+|.|||++++++.|=|-.=|+++|.
T Consensus 102 R~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~ 144 (205)
T COG0522 102 RLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVR 144 (205)
T ss_pred HhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEee
Confidence 4689999999999999999999999999999999999999996
No 14
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.68 E-value=0.0017 Score=39.57 Aligned_cols=27 Identities=37% Similarity=0.668 Sum_probs=24.6
Q ss_pred eecCCcEEEEECCCcceeEEEEEeEEE
Q 024108 181 KFDVGNVVMVTGGRNRGRVGIIKNREK 207 (272)
Q Consensus 181 kf~~G~~~~v~gG~n~G~vG~I~~i~~ 207 (272)
+|++|+.++|++|.+.|.+|+|.+++.
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 478999999999999999999999863
No 15
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=96.62 E-value=0.0056 Score=44.12 Aligned_cols=51 Identities=20% Similarity=0.184 Sum_probs=44.3
Q ss_pred chHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 024108 42 LPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (272)
Q Consensus 42 lPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~ 93 (272)
..|--+|... .++.+...+++++.+|.|+|||++++.+.|.+--=|+|+|+
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 5666777776 77779999999999999999999999889999888888874
No 16
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.89 E-value=0.004 Score=47.08 Aligned_cols=60 Identities=25% Similarity=0.281 Sum_probs=41.8
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 102 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl 102 (272)
+.|.|.=+|.- .+++.|.-|||..|.+|.|+|||.+.+...--+--=|+|++ .++.|+++
T Consensus 6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~--~~~~~~Vv 65 (65)
T PF13275_consen 6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI--DGEEYRVV 65 (65)
T ss_dssp S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE--TTEEEEEE
T ss_pred CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE--CCEEEEEC
Confidence 46677777766 58899999999999999999999999988888888899999 67888874
No 17
>PRK11507 ribosome-associated protein; Provisional
Probab=95.63 E-value=0.049 Score=41.93 Aligned_cols=60 Identities=17% Similarity=0.139 Sum_probs=49.0
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL 102 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl 102 (272)
+.|-|.=+|.- .+++.|.-|||..|.+|.|+|||.+.+-..-=+=-=|+|+++ |+.|++.
T Consensus 10 e~I~L~QlLK~-~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~--g~~~~v~ 69 (70)
T PRK11507 10 PHVELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQVV 69 (70)
T ss_pred CeEEHHHHHhh-hCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEEC--CEEEEEe
Confidence 45666667665 588999999999999999999999987777667777999994 5777764
No 18
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=95.16 E-value=0.016 Score=50.87 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=36.2
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCcc--eeEEEecc
Q 024108 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGF--MDVVSIPK 94 (272)
Q Consensus 51 ~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~--mDVIsI~k 94 (272)
++++|.|.++|++.+.+|+|.|||++++++.|-|-. =|-|+...
T Consensus 112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~ 157 (162)
T TIGR01018 112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAP 157 (162)
T ss_pred hccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeec
Confidence 468999999999999999999999999999886633 25555443
No 19
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=94.96 E-value=0.019 Score=51.27 Aligned_cols=40 Identities=20% Similarity=0.286 Sum_probs=34.9
Q ss_pred HHHHHhhh-------cccccHHHHHHHHhCceEEECCEEeccccCCC
Q 024108 45 ILILRNRL-------KYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (272)
Q Consensus 45 ~i~LRd~L-------kyA~t~rEak~Il~~g~V~VDGkvr~D~k~Pv 84 (272)
--+|+.+| ++|.|..+|++.+.+|+|.|||++++|+.|=|
T Consensus 102 ~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V 148 (181)
T PTZ00155 102 EKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLV 148 (181)
T ss_pred HHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEe
Confidence 35666666 99999999999999999999999999997643
No 20
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=94.87 E-value=0.042 Score=48.86 Aligned_cols=44 Identities=18% Similarity=0.211 Sum_probs=37.1
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEeccC
Q 024108 52 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPA--GFMDVVSIPKT 95 (272)
Q Consensus 52 LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~Pv--G~mDVIsI~kt 95 (272)
+++|.|..+|++.+.+|+|.|||++++++.|.| +.=|.|++..+
T Consensus 112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~ 157 (177)
T PRK04051 112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPT 157 (177)
T ss_pred ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCC
Confidence 589999999999999999999999999998876 34456666543
No 21
>PLN00189 40S ribosomal protein S9; Provisional
Probab=94.81 E-value=0.023 Score=51.26 Aligned_cols=43 Identities=12% Similarity=0.181 Sum_probs=35.8
Q ss_pred hhcccccHHHHHHHHhCceEEECCEEeccccCCCc--ceeEEEec
Q 024108 51 RLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAG--FMDVVSIP 93 (272)
Q Consensus 51 ~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG--~mDVIsI~ 93 (272)
+|++|.|..+|++++.+|+|.|||++++++.|-|- .-|-|+..
T Consensus 117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~ 161 (194)
T PLN00189 117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFS 161 (194)
T ss_pred ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEe
Confidence 46899999999999999999999999999988664 34444443
No 22
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=94.78 E-value=0.046 Score=49.00 Aligned_cols=43 Identities=26% Similarity=0.307 Sum_probs=38.6
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 024108 52 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (272)
Q Consensus 52 LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k 94 (272)
++++.|.++|++.+.+|.|.|||++++++.|.+--=|+|++..
T Consensus 99 ~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~ 141 (200)
T TIGR01017 99 LGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKE 141 (200)
T ss_pred cCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEee
Confidence 3567899999999999999999999999999997779999953
No 23
>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=94.73 E-value=0.067 Score=44.59 Aligned_cols=57 Identities=18% Similarity=0.242 Sum_probs=39.7
Q ss_pred eeEEeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCC-----CCeEeEe--eceEEEEc
Q 024108 177 TEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDAL-----GHEFATR--LGNVFTIG 236 (272)
Q Consensus 177 ~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~-----g~~F~T~--~~~vfvIG 236 (272)
.+.+++..|+.+.|++|++-|..|+|.++... ...|.|+.-+ |.+++.. .+||+++.
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 45568889999999999999999999999743 2356565433 4333333 36666543
No 24
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=94.59 E-value=0.15 Score=47.18 Aligned_cols=52 Identities=17% Similarity=0.150 Sum_probs=43.3
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~ 93 (272)
++.|.-+|...+. ..+.+++++.+.+|.|+|||+++++..+.+---|+|++.
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 457999999999999999998888888999777999983
No 25
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=94.51 E-value=0.062 Score=48.29 Aligned_cols=42 Identities=24% Similarity=0.333 Sum_probs=38.8
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 024108 53 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (272)
Q Consensus 53 kyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k 94 (272)
+++.+..+|++++..|.|.|||++++.+.|++--=|+|++..
T Consensus 103 g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 103 GFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred CccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 778899999999999999999999999999997779999964
No 26
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=94.28 E-value=0.067 Score=48.30 Aligned_cols=43 Identities=19% Similarity=0.315 Sum_probs=38.1
Q ss_pred hcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 024108 52 LKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (272)
Q Consensus 52 LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k 94 (272)
+++|.+.++|++++.+|.|.|||++++++.|.+--=|+|++..
T Consensus 98 ~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 98 LGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKD 140 (201)
T ss_pred cCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEcc
Confidence 4678899999999999999999999999999985559999853
No 27
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=93.97 E-value=0.17 Score=47.03 Aligned_cols=62 Identities=15% Similarity=0.209 Sum_probs=50.5
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 115 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 115 (272)
|+=|-.++...+ ..+.+.|++.+.+|.|+|||+++++..+.+--=|+||+. ..|||.+.++.
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 455667787755 558999999999999999999999999988777999884 45777777664
No 28
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=93.11 E-value=0.16 Score=46.33 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=40.0
Q ss_pred HHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc
Q 024108 47 ILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK 94 (272)
Q Consensus 47 ~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k 94 (272)
+|.+ .+++.+.++|++.+++|.|+|||+++++..+.+--=|.|++..
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 4688899999999999999999999999999886559999853
No 29
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=92.25 E-value=0.32 Score=37.80 Aligned_cols=59 Identities=22% Similarity=0.244 Sum_probs=44.3
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEE
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRv 101 (272)
+-|-|.=+|.- ++.+++.-+||..|.+|.|+|||.+-+=..-=+=-=|+|+||. ..|-+
T Consensus 10 e~I~L~qlLK~-~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~--~~~~v 68 (73)
T COG2501 10 EFITLGQLLKL-AGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG--QRYQV 68 (73)
T ss_pred ceEEHHHHHHH-hCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC--EEEEE
Confidence 45566666665 6899999999999999999999998655444455558999964 44443
No 30
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=91.74 E-value=0.45 Score=44.83 Aligned_cols=57 Identities=23% Similarity=0.190 Sum_probs=49.8
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceE
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENF 99 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~y 99 (272)
...-|--+|++ |.- .+..+..+++.+|.|.|||++.+ ..|.+..=|+|+++...+.+
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 666 78999999999999999999999 99999999999999876555
No 31
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=91.65 E-value=0.46 Score=40.09 Aligned_cols=55 Identities=24% Similarity=0.335 Sum_probs=37.5
Q ss_pred EEeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc-----CCCCeEeEe--eceEEEEc
Q 024108 179 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD-----ALGHEFATR--LGNVFTIG 236 (272)
Q Consensus 179 ~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d-----~~g~~F~T~--~~~vfvIG 236 (272)
.+++..|+.+.|+.|..-|..|+|.++....+ .|.|+. .+|.+++-. .+||+++-
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~---~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~ 104 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRG---RIYVEGVTVKKADGTEVPRPIHPSNVMITK 104 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCC---EEEEeCcEEECCCCeEEEcccchhHeEEEe
Confidence 45788999999999999999999999965433 444443 345443332 25665543
No 32
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=91.61 E-value=0.61 Score=44.08 Aligned_cols=52 Identities=17% Similarity=0.099 Sum_probs=41.9
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~ 93 (272)
...|.-+|+..+. ..+.+.+++.+.+|.|+|||+..+...+.+---|+|++.
T Consensus 17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~ 68 (325)
T PRK11180 17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAID 68 (325)
T ss_pred CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEe
Confidence 4678888888654 358899999999999999999987666666555999885
No 33
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=90.50 E-value=0.88 Score=44.91 Aligned_cols=65 Identities=15% Similarity=0.188 Sum_probs=50.3
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 112 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~ 112 (272)
.+|+.-+|-+ .+.|.+..||++.+.+|-|+|||..++|..+-+-- ...+..|-+|---|.+|.+.
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~------~~~~~~~~~lr~GKk~~~~i 406 (408)
T PRK05912 342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA------DDRFGKYTVLQRGKKKFARV 406 (408)
T ss_pred CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccccc------cccCCCEEEEEeCCCceEEE
Confidence 5788888876 69999999999999999999999999999764422 11145566777777776654
No 34
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=90.43 E-value=0.82 Score=43.00 Aligned_cols=55 Identities=18% Similarity=0.096 Sum_probs=42.7
Q ss_pred ccHHHHHHHHhCceEEECCEEeccccCCC--cceeEEEecc----------CCceEEEEEcCCCceEE
Q 024108 56 LTYREVIAILMQRHVLVDAKVRTDKTYPA--GFMDVVSIPK----------TNENFRLLYDTKGRFRL 111 (272)
Q Consensus 56 ~t~rEak~Il~~g~V~VDGkvr~D~k~Pv--G~mDVIsI~k----------t~e~yRvl~d~kgrf~l 111 (272)
.+.++|++++.+|.|+|||++. +..+.| +-.|.|+++. ..++|-+++-+.|..+-
T Consensus 15 ~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~~~~e~~~ylvlnKP~G~~~s 81 (289)
T PRK10700 15 GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCT 81 (289)
T ss_pred CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecccccccCCeEEEEECCCCCEee
Confidence 6899999999999999999987 566666 5557787653 11468899999996643
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=89.80 E-value=0.79 Score=39.20 Aligned_cols=59 Identities=8% Similarity=0.039 Sum_probs=49.9
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEE
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL 101 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRv 101 (272)
++-|-.||=- .+++.|..-|+..|..|.|.|||.. .-....|-.=|+|+|...+..|-+
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 4667777766 5899999999999999999999999 888999999999999776555443
No 36
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.00 E-value=0.99 Score=39.17 Aligned_cols=57 Identities=25% Similarity=0.317 Sum_probs=39.8
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeE--eEeeceEEEEc
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEF--ATRLGNVFTIG 236 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~--~~V~i~d~~g~~F--~T~~~~vfvIG 236 (272)
+++..|+.+.|+.|..-|..|+|..+....+.. +=|.+.-..|..+ --..+||+++.
T Consensus 45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred ceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 477889999999999999999999997644421 2222333556543 34457887776
No 37
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=88.14 E-value=1.1 Score=41.81 Aligned_cols=57 Identities=23% Similarity=0.229 Sum_probs=42.9
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcce-eEEEeccC------CceEEEEEcCCCceE
Q 024108 53 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFM-DVVSIPKT------NENFRLLYDTKGRFR 110 (272)
Q Consensus 53 kyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~m-DVIsI~kt------~e~yRvl~d~kgrf~ 110 (272)
++| +.|||.++|.+|.|.|||++.++...-+=-- |+|.++.. ...|=+++-+.|..+
T Consensus 13 G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~ 76 (248)
T COG1187 13 GVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVS 76 (248)
T ss_pred CCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEe
Confidence 444 7899999999999999999999986555444 46665443 122888899988664
No 38
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=87.87 E-value=2 Score=40.70 Aligned_cols=68 Identities=16% Similarity=0.080 Sum_probs=50.1
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc--------CCceEEEEEcCCCceE
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK--------TNENFRLLYDTKGRFR 110 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k--------t~e~yRvl~d~kgrf~ 110 (272)
.++-|.=+|.+. ++ .+.++|++.+.+|.|+|||++. +..+.|---|+|++.. .+++|-++.-+.|..+
T Consensus 5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~~~ed~~~lvlnKP~G~~~ 80 (290)
T PRK10475 5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80 (290)
T ss_pred hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccccccCCCeEEEEECCCCCCc
Confidence 355666677653 43 4799999999999999999987 4667775559888742 1346888888888654
No 39
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=87.75 E-value=2.1 Score=40.43 Aligned_cols=51 Identities=27% Similarity=0.260 Sum_probs=41.2
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEec
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIP 93 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~ 93 (272)
...|.-+|++.+. ..+.+.+++++.+|.|.|||+++ +..+.+---|+|+++
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 4567778877663 45799999999999999999988 467888666999985
No 40
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=87.01 E-value=1.1 Score=34.68 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=31.2
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcC
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 220 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~ 220 (272)
+++..|+.+.|+.|+.-|.+|+|..+.+. .+.|.+++-
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegv 42 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPK---KNRVIVEGV 42 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCc
Confidence 47889999999999999999999999754 245667653
No 41
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=86.40 E-value=3.9 Score=36.62 Aligned_cols=68 Identities=13% Similarity=0.121 Sum_probs=47.9
Q ss_pred HHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEecc------CCceEEEEEcCCCceEEEEc
Q 024108 44 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPK------TNENFRLLYDTKGRFRLHSI 114 (272)
Q Consensus 44 L~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~k------t~e~yRvl~d~kgrf~l~~I 114 (272)
|--+|...+ ..+.+.+++++.+|.|+|||++.++..+.+---|+|++.. ..++|=++--+.| +..|+-
T Consensus 3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~~~~~~~~lvvnKP~G-~~~~~~ 76 (232)
T PRK10839 3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQG-YVCSTD 76 (232)
T ss_pred HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcccCCCCEEEEEECCCC-eEeccc
Confidence 445666655 3679999999999999999999887777775569999852 1245656655566 444543
No 42
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=86.09 E-value=1.4 Score=34.69 Aligned_cols=37 Identities=16% Similarity=0.499 Sum_probs=30.5
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 219 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d 219 (272)
+++..|+.++|+.|+.-|..|+|.++.... +.|++++
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Veg 43 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKG 43 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence 478899999999999999999999997542 4566654
No 43
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=85.79 E-value=2.7 Score=41.68 Aligned_cols=67 Identities=19% Similarity=0.193 Sum_probs=48.8
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEE
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS 113 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~ 113 (272)
.+||.=+|-. .+.|.+..||++.+.||-|+|||...+|..+-+-.=|. .+..|-+|---|.+|.+..
T Consensus 342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~-----l~~~~~~lr~GKk~~~~i~ 408 (410)
T PRK13354 342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA-----FDGKFVILRRGKKKFFLVK 408 (410)
T ss_pred CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh-----cCCCEEEEEeCCccEEEEE
Confidence 5778777775 79999999999999999999999999998754322111 2344566666666665543
No 44
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=85.14 E-value=1.3 Score=36.22 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=26.0
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEEe
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 208 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~~ 208 (272)
+++..|+.+.|+.|++-|.+|+|..+...
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 37788999999999999999999999654
No 45
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=84.35 E-value=3.3 Score=38.93 Aligned_cols=62 Identities=21% Similarity=0.262 Sum_probs=50.5
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 115 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 115 (272)
|+=|--++-..+ -.+...|+..+.+|+|+|||++.++..|-+--=|+|||-. .|||.+.++.
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 455656666655 4678889999999999999999999999999999999954 4777777664
No 46
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=84.14 E-value=1.5 Score=41.12 Aligned_cols=119 Identities=18% Similarity=0.260 Sum_probs=71.5
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE-------------EEEcCCCceEEEEcChHhH
Q 024108 53 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFR-------------LLYDTKGRFRLHSIRDEEA 119 (272)
Q Consensus 53 kyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yR-------------vl~d~kgrf~l~~I~~eEa 119 (272)
+++.|...|+..++.|+|+|||...+-+.+=|-.-+.|++......|. .=.|.+|+-++- |-+..-
T Consensus 13 gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~yVSRG~~KL~~ale~F~l~~k~kv~LD-iGsSTG 91 (245)
T COG1189 13 GLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFELDVKGKVVLD-IGSSTG 91 (245)
T ss_pred cchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCccccHHHHHHHHHHhcCcCCCCCEEEE-ecCCCc
Confidence 889999999999999999999999999999999999999975444332 113444544332 322222
Q ss_pred hhhhccceeeEEEEEeEEEee-------CCceEEEccCCeeeecCCCC--cccCCeEEEecC
Q 024108 120 KALILLFQFKLCKVRSVQFGQ-------KGIPYINTYDGRTIRYPDPL--IKANDTIKLDLE 172 (272)
Q Consensus 120 ~~~~~~~~~KLcKV~~k~~~~-------~g~~ql~~hDGrni~~~d~~--ik~~Dtv~i~l~ 172 (272)
.-.-.+.|-.--+|-.+-++. ..-|.+....+.|+||-.++ ...-|-+++|+.
T Consensus 92 GFTd~lLq~gAk~VyavDVG~~Ql~~kLR~d~rV~~~E~tN~r~l~~~~~~~~~d~~v~DvS 153 (245)
T COG1189 92 GFTDVLLQRGAKHVYAVDVGYGQLHWKLRNDPRVIVLERTNVRYLTPEDFTEKPDLIVIDVS 153 (245)
T ss_pred cHHHHHHHcCCcEEEEEEccCCccCHhHhcCCcEEEEecCChhhCCHHHcccCCCeEEEEee
Confidence 100011111122444444444 34456666677777665443 223355555553
No 47
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=82.40 E-value=3.1 Score=39.31 Aligned_cols=63 Identities=21% Similarity=0.292 Sum_probs=52.8
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcC
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIR 115 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~ 115 (272)
.||=|-.++-+.++.. ..-|...+..|+|+||.++.++..|-+..=|.|||-. .|||.+-+|.
T Consensus 179 sSlRLD~vis~~~~~S--R~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG-----------~GR~~i~~i~ 241 (257)
T COG2302 179 SSLRLDVVISEGFGLS--RAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG-----------FGRLKILEIN 241 (257)
T ss_pred ehhhHHHHHHHHHhhh--HHHHHHHHHcCceEEeeEEeccccceeccCCEEEEec-----------cccEEEEeec
Confidence 3777888888877764 4458899999999999999999999999999999954 4777776665
No 48
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=79.70 E-value=4.8 Score=30.44 Aligned_cols=50 Identities=28% Similarity=0.521 Sum_probs=38.7
Q ss_pred CCcEEEEECCCcceeEEEEEeEEEecC-CccEEEEEcCCCCeEeEeeceEEEEcc
Q 024108 184 VGNVVMVTGGRNRGRVGIIKNREKHKG-SFETIHIQDALGHEFATRLGNVFTIGK 237 (272)
Q Consensus 184 ~G~~~~v~gG~n~G~vG~I~~i~~~~~-s~~~V~i~d~~g~~F~T~~~~vfvIGk 237 (272)
+|..|+|-.|.+..|+|.++.-|.... +|.+| | ++...+.-+..+..+|-
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 488999999999999999999888774 45655 2 34556777777777774
No 49
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=79.32 E-value=2.8 Score=34.27 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=25.4
Q ss_pred eecCCcEEEEECCCcceeEEEEEeEEEe
Q 024108 181 KFDVGNVVMVTGGRNRGRVGIIKNREKH 208 (272)
Q Consensus 181 kf~~G~~~~v~gG~n~G~vG~I~~i~~~ 208 (272)
++..|+.+.|+.|+.-|.+|+|..+...
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5778999999999999999999999654
No 50
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=63.33 E-value=5.3 Score=35.81 Aligned_cols=55 Identities=27% Similarity=0.344 Sum_probs=40.0
Q ss_pred CCCCCCCCCcccchHHHHHH-------hhhcccccHHHHHHHHhCceEEECCEEeccccCCC
Q 024108 30 KPSSGPHKSRECLPLILILR-------NRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPA 84 (272)
Q Consensus 30 kpspGPH~~~~slPL~i~LR-------d~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~Pv 84 (272)
-|..+.|..-+-+-..-|-| -.|+.|.+-+||-+.+.||.|.|.-++++|+.|=|
T Consensus 87 ipTr~~l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv 148 (181)
T KOG4655|consen 87 IPTRKSLELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV 148 (181)
T ss_pred ecchhhhhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence 44555555444222333333 23789999999999999999999999999998754
No 51
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=62.56 E-value=16 Score=36.41 Aligned_cols=61 Identities=21% Similarity=0.271 Sum_probs=44.7
Q ss_pred HHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEE
Q 024108 44 LILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLH 112 (272)
Q Consensus 44 L~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~ 112 (272)
++-+|-+ .+++.+.+||++.+.+|-|++||....|.+++.+ | .....|.++--.|.+|...
T Consensus 338 ~~~~lv~-~~L~psr~earr~i~~g~v~in~~~v~d~~~~~~--~-----~~~~~~~~l~~GKkk~~~i 398 (401)
T COG0162 338 LVDLLVD-AGLAPSRSEARRLIQQGGVKINGEKVEDENYVLS--D-----LLDNGLLVLRRGKKKFALI 398 (401)
T ss_pred HHHHHHH-hCCcccHHHHHhhcccCCEEECCEeccccccchh--h-----ccCCceEEEecccccEEEE
Confidence 3334444 5899999999999999999999999999998871 1 1234555666566666544
No 52
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=59.12 E-value=9.7 Score=32.37 Aligned_cols=34 Identities=32% Similarity=0.469 Sum_probs=27.6
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEc
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 219 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d 219 (272)
+++|-.|+++.|+.+|+-.+|..+-.. +.+++-+
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd----~~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDD----NFVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccC----CEEEEeC
Confidence 689999999999999999999988553 3555544
No 53
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=58.56 E-value=15 Score=30.42 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=24.8
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEEe
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 208 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~~ 208 (272)
.+...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45667999999999999999999988654
No 54
>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification.; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.
Probab=58.15 E-value=44 Score=29.34 Aligned_cols=29 Identities=34% Similarity=0.429 Sum_probs=25.0
Q ss_pred cccchHHHHHHhhhcccccHHHHHHHHhCc
Q 024108 39 RECLPLILILRNRLKYALTYREVIAILMQR 68 (272)
Q Consensus 39 ~~slPL~i~LRd~LkyA~t~rEak~Il~~g 68 (272)
...+|..+++|..|. |.|..||..+|.+-
T Consensus 69 ~~G~p~~~l~R~iLe-~~t~~eA~~~l~~~ 97 (225)
T PF03417_consen 69 QPGLPRHFLVRKILE-CRTVEEAIAILRSA 97 (225)
T ss_dssp TTSB-HHHHHHHHHC--SSHHHHHHCHHCC
T ss_pred cCCChHHHHHHHHhc-CCCHHHHHHHHHhc
Confidence 679999999999999 99999999999865
No 55
>PF14001 YdfZ: YdfZ protein
Probab=55.36 E-value=19 Score=27.56 Aligned_cols=42 Identities=26% Similarity=0.472 Sum_probs=29.6
Q ss_pred eecCCcEEEEECCCcceeEEEEEeEEEecC------CccEEEEEcCCCCeEe
Q 024108 181 KFDVGNVVMVTGGRNRGRVGIIKNREKHKG------SFETIHIQDALGHEFA 226 (272)
Q Consensus 181 kf~~G~~~~v~gG~n~G~vG~I~~i~~~~~------s~~~V~i~d~~g~~F~ 226 (272)
++.+|+.+|+.| +|.+|+|+.|..... ....|.+++.+| .|+
T Consensus 9 ~i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 9 AITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred cCCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 356799999977 688889999965322 235788887765 354
No 56
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=53.83 E-value=15 Score=31.55 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=27.2
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 217 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i 217 (272)
.|+|-+|+|.-|.+.|+.++|++|-.+ |.|.|
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 57
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=50.57 E-value=38 Score=27.87 Aligned_cols=45 Identities=11% Similarity=0.118 Sum_probs=34.8
Q ss_pred cccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCce
Q 024108 53 KYALTYREVIAILMQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNEN 98 (272)
Q Consensus 53 kyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~ 98 (272)
.+..+.-.|+..+..|.|.|||...+- ..-|=.=|+|+|--.+..
T Consensus 19 R~~KrRslAk~~~~~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 19 RFIKRRSLAKEMIEGGRVKVNGQRAKP-SKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHhhhHHHHHHHHHCCeEEECCEEccc-ccccCCCCEEEEEeCCcE
Confidence 455788999999999999999999854 455667788888654443
No 58
>PF12005 DUF3499: Protein of unknown function (DUF3499); InterPro: IPR021888 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Probab=48.64 E-value=7.5 Score=33.09 Aligned_cols=23 Identities=48% Similarity=0.993 Sum_probs=21.0
Q ss_pred cccccccCCCceecccccceecc
Q 024108 7 KHLKRLNAPKHWMLDKLGGAFAP 29 (272)
Q Consensus 7 kHlKRl~AP~~W~i~kk~~~~a~ 29 (272)
.|-.||+||+-|.+=|....|++
T Consensus 46 ~Ha~rlTaP~GWevvR~~~~~~~ 68 (123)
T PF12005_consen 46 EHAERLTAPRGWEVVRLEGPFAP 68 (123)
T ss_pred HHHhcccCCCCcEEEeccCCCCC
Confidence 58899999999999999998873
No 59
>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=46.79 E-value=1.4e+02 Score=23.21 Aligned_cols=45 Identities=18% Similarity=0.381 Sum_probs=30.0
Q ss_pred CcccCCeEEEecCCCceeeEEee----cCCcEEEEECCCcceeEEEEEeE
Q 024108 160 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNR 205 (272)
Q Consensus 160 ~ik~~Dtv~i~l~~~kI~~~ikf----~~G~~~~v~gG~n~G~vG~I~~i 205 (272)
.++.||...+.+...+-+-.=+| ..|...+-..|..+| .|.|.+|
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 59999999999976553322222 237777766776666 5888654
No 60
>PRK04333 50S ribosomal protein L14e; Validated
Probab=46.36 E-value=22 Score=28.10 Aligned_cols=33 Identities=27% Similarity=0.463 Sum_probs=27.2
Q ss_pred eecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEE
Q 024108 181 KFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI 217 (272)
Q Consensus 181 kf~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i 217 (272)
.++.|-+|++.-|+..|+..+|.++... +.|.|
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 4688999999999999999999998432 45555
No 61
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=45.74 E-value=65 Score=31.79 Aligned_cols=55 Identities=18% Similarity=0.163 Sum_probs=28.8
Q ss_pred eEEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEeecCCcEEEEE---CCCccee
Q 024108 129 KLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVT---GGRNRGR 198 (272)
Q Consensus 129 KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~---gG~n~G~ 198 (272)
=|..|+-.. .|....+.+.|..|||+-.| +|+-+..-.+++|+.+++. +|+|.|.
T Consensus 278 PL~lIeAe~--~g~~~~viLQnaetIrlv~~-------------dG~~vsVt~Lk~GD~VL~~~~~~~RHfG~ 335 (344)
T PRK02290 278 PLLLIEAEY--GGKRIRTILQNAETIRLVTP-------------DGKPVSVVDLKPGDEVLGYLEEAARHFGM 335 (344)
T ss_pred cEEEEEEEe--CCeEEEEEEecCcEEEEECC-------------CCCEeeeeecCCCCEEEEEecCCcccccc
Confidence 344455444 44556666677777765433 3344444444444444332 6778773
No 62
>cd03704 eRF3c_III This family represents eEF1alpha-like C-terminal region of eRF3 homologous to the domain III of EF-Tu. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.
Probab=42.49 E-value=69 Score=25.09 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=30.3
Q ss_pred CCC-CcccCCeEEEecCCCceeeEEeecC----CcEEEEECCCcceeEEEEEeE
Q 024108 157 PDP-LIKANDTIKLDLETNKITEFIKFDV----GNVVMVTGGRNRGRVGIIKNR 205 (272)
Q Consensus 157 ~d~-~ik~~Dtv~i~l~~~kI~~~ikf~~----G~~~~v~gG~n~G~vG~I~~i 205 (272)
.+| .++.||...+.+...+=+-.=+|+. |-.++--+|+.+| +|.|.+|
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 6899999999987554221122322 6666667777766 7887653
No 63
>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=41.93 E-value=84 Score=31.17 Aligned_cols=54 Identities=19% Similarity=0.223 Sum_probs=32.4
Q ss_pred EEEEEeEEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEeecCCcEEEE---ECCCccee
Q 024108 130 LCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMV---TGGRNRGR 198 (272)
Q Consensus 130 LcKV~~k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v---~gG~n~G~ 198 (272)
|..|+-.. .|....+.+.|..|||+-. |+++.+....+++|+.+++ .+|+|.|.
T Consensus 289 LllIeA~~--~g~~~svilQnaetIRlv~-------------p~G~~vsVt~Lk~GD~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 289 LLLIEAEA--DGKRISVILQNAETIRLVG-------------PDGEPVSVTELKPGDEVLVYLEEAGRHFGM 345 (354)
T ss_pred eEEEEEEe--CCeEEEEEEecCcEEEEEC-------------CCCCEeeeeecCCCCEEEEEecCCCcccce
Confidence 44444444 4455566667777776543 3556666666666666555 37888884
No 64
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=38.43 E-value=33 Score=26.31 Aligned_cols=41 Identities=24% Similarity=0.456 Sum_probs=27.9
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEEec------CCccEEEEEcCCCCeEe
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 226 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~~~------~s~~~V~i~d~~g~~F~ 226 (272)
+..|+.+||.| .|++|+|+.|.... .....|.++..+| .|+
T Consensus 11 it~G~rVMia~---tG~tgvikaIh~dglt~~Q~rR~k~Vel~g~e~-~f~ 57 (65)
T TIGR03318 11 ITTGSRVMIAG---TGHTGVIKAIHTEGLTAEQARREKCVELEGCEE-RFA 57 (65)
T ss_pred cCCCcEEEEec---CCccceeehhhhCCCCHHHhhhccEEEEecccc-eec
Confidence 45699999987 68888999986522 1235777776554 454
No 65
>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=38.08 E-value=1.8e+02 Score=22.14 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=24.1
Q ss_pred cccCCeEEEecCCCceeeEEeecCCcEEEE-ECCCcceeEEEEEe
Q 024108 161 IKANDTIKLDLETNKITEFIKFDVGNVVMV-TGGRNRGRVGIIKN 204 (272)
Q Consensus 161 ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v-~gG~n~G~vG~I~~ 204 (272)
+++||+..+.+.-.+ -+..+.|.-.++ .+|+.+| .|+|.+
T Consensus 52 l~~g~~~~v~i~l~~---p~~~~~g~rf~lR~~~~tvg-~G~V~~ 92 (93)
T cd03706 52 VMPGEDTKVTLILRR---PMVLEKGQRFTLRDGNRTIG-TGLVTD 92 (93)
T ss_pred eCCCCEEEEEEEECC---cEEEeeCCEEEEEECCEEEE-EEEEEe
Confidence 788888887775432 224455655555 5555555 676654
No 66
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=36.80 E-value=22 Score=29.96 Aligned_cols=42 Identities=24% Similarity=0.369 Sum_probs=33.8
Q ss_pred CCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceEEEccCCeeeecCCC
Q 024108 106 KGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 159 (272)
Q Consensus 106 kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~ql~~hDGrni~~~d~ 159 (272)
+..|+|+.+|+=. |-+|--+.|..-+....|| ||-|+-|.+|
T Consensus 21 KRwFvL~qvsQYt---------famcsy~ekks~P~e~~ql---dGyTvDy~~~ 62 (117)
T cd01234 21 KRFFVLVQVSQYT---------FAMCSYREKKAEPTEFIQL---DGYTVDYMPE 62 (117)
T ss_pred eeEEEEEchhHHH---------HHHHhhhhhcCCchhheee---cceEEeccCC
Confidence 3458888887655 6789888888888888888 9999988765
No 67
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=35.81 E-value=83 Score=24.52 Aligned_cols=19 Identities=37% Similarity=0.301 Sum_probs=15.3
Q ss_pred eEEEEEeEEEecCCccEEE
Q 024108 198 RVGIIKNREKHKGSFETIH 216 (272)
Q Consensus 198 ~vG~I~~i~~~~~s~~~V~ 216 (272)
++|+|.+.+.|+++..+..
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 6899999999998864433
No 68
>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=35.05 E-value=24 Score=26.76 Aligned_cols=32 Identities=28% Similarity=0.457 Sum_probs=21.6
Q ss_pred ccchHHHHHHhhhcccc-cHHHHHHHHhCceEEECC
Q 024108 40 ECLPLILILRNRLKYAL-TYREVIAILMQRHVLVDA 74 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~-t~rEak~Il~~g~V~VDG 74 (272)
|.|||..++ ||||. +..||-+-+.+|.-.|+-
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 789999886 89999 999999999888766654
No 69
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=34.92 E-value=63 Score=27.57 Aligned_cols=29 Identities=14% Similarity=0.265 Sum_probs=26.6
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEEe
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREKH 208 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~~ 208 (272)
..|.+|+.+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999764
No 70
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=33.95 E-value=72 Score=26.52 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=24.7
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEE
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREK 207 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~ 207 (272)
|.+|+.+.|+.|.=.|..|+|.+++.
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 89999999999999999999999875
No 71
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=33.70 E-value=73 Score=26.08 Aligned_cols=60 Identities=20% Similarity=0.188 Sum_probs=35.0
Q ss_pred CCceEEEccCCeeeecCCCCcccCCeEEEecCC------CceeeEEeecCCcEEEEECCCcceeEEEEEe
Q 024108 141 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLET------NKITEFIKFDVGNVVMVTGGRNRGRVGIIKN 204 (272)
Q Consensus 141 ~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~------~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~ 204 (272)
+-..++.|.|||+|.-.=.-+...--+.|+-.- .+=++.+++. .+++.|-|.+-+|-|-|
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDE 75 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecch
Confidence 345678999999995321112222224444321 1112333333 78999999999998876
No 72
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=33.44 E-value=1e+02 Score=26.20 Aligned_cols=28 Identities=25% Similarity=0.440 Sum_probs=25.6
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEE
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREK 207 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~ 207 (272)
..|.+|+.+-|++|.=.|..|.|.++..
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDY 152 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeC
Confidence 5688999999999999999999999854
No 73
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=33.38 E-value=42 Score=29.02 Aligned_cols=24 Identities=42% Similarity=0.688 Sum_probs=21.2
Q ss_pred ecCCcEEEEECCCcceeEEEEEeE
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNR 205 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i 205 (272)
+.+|..|+|..|+++|+-++|..-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 458999999999999999988765
No 74
>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=33.29 E-value=35 Score=29.70 Aligned_cols=53 Identities=21% Similarity=0.108 Sum_probs=42.6
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEeccCC
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIPKTN 96 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g-----~V~VDGkvr~D~k~PvG~mD---VIsI~kt~ 96 (272)
...+|+-+||+.|++-.+ |.=+.+| .|+|||+++..--+|+.-+| |++|+-..
T Consensus 17 ~~~~Ll~~LR~~lgltg~----K~gC~~G~CGACtVlvdg~~v~SCl~~~~~~~G~~V~TiEgl~ 77 (148)
T TIGR03193 17 DNMLLVDYLRDTVGLTGT----KQGCDGGECGACTVLVDGRPRLACSTLAHRVAGRKVETVEGLA 77 (148)
T ss_pred CCCcHHHHHHHhcCCCCC----CCCCCCCCCCCCEEEECCeEeeccHhhHhhcCCCcEEEeCCCC
Confidence 468999999998876543 4555666 69999999999999998886 89997644
No 75
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=32.27 E-value=84 Score=23.18 Aligned_cols=36 Identities=22% Similarity=0.301 Sum_probs=24.9
Q ss_pred CCceEEEccCCeeeecCCCCcccCCeEEEecCCCcee
Q 024108 141 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT 177 (272)
Q Consensus 141 ~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~ 177 (272)
+..-...+..|-.|.+| +-|+.||.|++|-.+++-+
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 34456778889999887 4799999999999988744
No 76
>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=31.85 E-value=2.1e+02 Score=21.14 Aligned_cols=67 Identities=16% Similarity=0.144 Sum_probs=39.9
Q ss_pred EEEeeCCceEEEccCCeeeecCC-CCc-----ccCCeEEEecCCCceeeEEeecCCc-EEEEECCCcceeEEEE
Q 024108 136 VQFGQKGIPYINTYDGRTIRYPD-PLI-----KANDTIKLDLETNKITEFIKFDVGN-VVMVTGGRNRGRVGII 202 (272)
Q Consensus 136 k~~~~~g~~ql~~hDGrni~~~d-~~i-----k~~Dtv~i~l~~~kI~~~ikf~~G~-~~~v~gG~n~G~vG~I 202 (272)
+.+..++.-+|.+.||..+.... ..+ ...+...+.|..|++.-.++=..+. +.+-|....++-.|+-
T Consensus 3 i~T~~~~~~~i~l~dgs~v~l~~~s~~~~~~~~~~~~~~~~L~~G~~~~~~~~~~~~~~~V~T~~~~i~v~GT~ 76 (98)
T PF04773_consen 3 IRTGAGSRAEIALSDGSRVRLGPNSRVSVDRDSGSEPTRLRLLSGEILFDVSPGKKRPFEVRTPTATIGVRGTR 76 (98)
T ss_pred EEcCCCCEEEEEECCCCEEEECCCcEEEEEcccCCCceEEEEcCCCEEEEEcccCCCCEEEEeCCEEEEEecCE
Confidence 46778999999999999997543 234 3444556666666654333322222 5555555555555543
No 77
>cd03705 EF1_alpha_III Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
Probab=31.58 E-value=97 Score=23.89 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=24.6
Q ss_pred CcccCCeEEEecCCCceeeEEeecC-------CcEEEEECCCcce
Q 024108 160 LIKANDTIKLDLETNKITEFIKFDV-------GNVVMVTGGRNRG 197 (272)
Q Consensus 160 ~ik~~Dtv~i~l~~~kI~~~ikf~~-------G~~~~v~gG~n~G 197 (272)
.++.||...+.|...+ -+.+|+ |..+++-+|..+|
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 7777776666555
No 78
>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=31.14 E-value=1.1e+02 Score=23.18 Aligned_cols=36 Identities=14% Similarity=0.160 Sum_probs=27.4
Q ss_pred EEeeCCceEEEccCCeeeecCC----CCcccCCeEEEecC
Q 024108 137 QFGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 172 (272)
Q Consensus 137 ~~~~~g~~ql~~hDGrni~~~d----~~ik~~Dtv~i~l~ 172 (272)
+.+....-.|.|.||.++..|. +.+++|..|++-..
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 4466677889999999998774 36888888777554
No 79
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.07 E-value=56 Score=23.87 Aligned_cols=36 Identities=25% Similarity=0.378 Sum_probs=26.9
Q ss_pred cceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhh
Q 024108 85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKAL 122 (272)
Q Consensus 85 G~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~ 122 (272)
|-|.|..=. -+-..|+=.|-.||+ +++++++||++|
T Consensus 8 GPlEv~kEg-R~ivmRvPleGGGRL-VvEl~~~Ea~~L 43 (51)
T PF11314_consen 8 GPLEVTKEG-RGIVMRVPLEGGGRL-VVELNPDEAKEL 43 (51)
T ss_pred CCcEEeecC-ceEEEEEecCCCcEE-EEEeCHHHHHHH
Confidence 556665432 356789999999999 567999999865
No 80
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=29.55 E-value=3.8e+02 Score=24.52 Aligned_cols=36 Identities=25% Similarity=0.390 Sum_probs=24.9
Q ss_pred eEEEEEeEEEecCC-ccEEEEEcCCCCeEeEeeceEEEEc
Q 024108 198 RVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIG 236 (272)
Q Consensus 198 ~vG~I~~i~~~~~s-~~~V~i~d~~g~~F~T~~~~vfvIG 236 (272)
.||+|.+++..... +-.+.++-... -..+++|+||-
T Consensus 235 ~VG~V~~v~~~~~~~~~~~~v~p~~d---~~~l~~V~Vi~ 271 (276)
T PRK13922 235 PVGKVTSVERDDYGLFKTVYVKPAAD---LDRLRYVLVVK 271 (276)
T ss_pred EEEEEEEEEeCCCCCeeEEEEEECcc---cCCCcEEEEEe
Confidence 47888888776643 56777775332 45678999985
No 81
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=29.08 E-value=1.3e+02 Score=25.57 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=25.3
Q ss_pred EeecCCcEEEEECCCcceeEEEEEeEEE
Q 024108 180 IKFDVGNVVMVTGGRNRGRVGIIKNREK 207 (272)
Q Consensus 180 ikf~~G~~~~v~gG~n~G~vG~I~~i~~ 207 (272)
..|.+|+.+.|++|.=.|..|+|.++..
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 82
>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=28.98 E-value=1.4e+02 Score=24.79 Aligned_cols=28 Identities=21% Similarity=0.135 Sum_probs=25.4
Q ss_pred EEeecCCcEEEEECCCcceeEEEEEeEE
Q 024108 179 FIKFDVGNVVMVTGGRNRGRVGIIKNRE 206 (272)
Q Consensus 179 ~ikf~~G~~~~v~gG~n~G~vG~I~~i~ 206 (272)
...|.+|+.+.|++|.-.|..|.|.++.
T Consensus 106 ~~~~~~G~~V~V~~GPf~g~~g~v~~~~ 133 (159)
T TIGR01955 106 TTLPYKGDKVRITDGAFAGFEAIFLEPD 133 (159)
T ss_pred ccCCCCCCEEEEeccCCCCcEEEEEEEC
Confidence 3569999999999999999999999985
No 83
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=27.93 E-value=55 Score=25.44 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.2
Q ss_pred eeecCCCCcccCCeEEEe
Q 024108 153 TIRYPDPLIKANDTIKLD 170 (272)
Q Consensus 153 ni~~~d~~ik~~Dtv~i~ 170 (272)
-||..|-+|++||.+.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 357889999999999884
No 84
>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=27.22 E-value=1.1e+02 Score=22.66 Aligned_cols=36 Identities=25% Similarity=0.386 Sum_probs=27.6
Q ss_pred eCCceEEEccCCeeeecCCCCcccCCeEEEecCCCce
Q 024108 140 QKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKI 176 (272)
Q Consensus 140 ~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI 176 (272)
.++.-...+..|-.|.+| +-|+.||.|++|-.+++=
T Consensus 18 ~~~~K~A~letG~~i~VP-~FI~~Gd~I~V~T~~g~Y 53 (56)
T cd05794 18 SSGTKPATLETGAEVQVP-LFIKEGEKIKVDTRTGEY 53 (56)
T ss_pred CCCcceEEECCCCEEEcC-CeecCCCEEEEECCCCcE
Confidence 344344668889999876 468999999999998763
No 85
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=26.91 E-value=2.6e+02 Score=20.55 Aligned_cols=55 Identities=13% Similarity=0.125 Sum_probs=29.7
Q ss_pred cCCcEEEEECCCcceeEE-EEEeEEEecCCccEEEEEcCCCCeEeEeeceEEEEcc
Q 024108 183 DVGNVVMVTGGRNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 237 (272)
Q Consensus 183 ~~G~~~~v~gG~n~G~vG-~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIGk 237 (272)
.+|+.++...+.+..... .+.......+...++.|+..+|.++..-.+.-|.+.+
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 456667766653222211 1122222334557888888888777655555555554
No 86
>KOG3586 consensus TBX1 and related T-box transcription factors [Transcription]
Probab=26.85 E-value=87 Score=31.72 Aligned_cols=118 Identities=21% Similarity=0.287 Sum_probs=71.6
Q ss_pred eEEECCEEeccccCCCcceeEEEeccCCceEEEEEcC-------------CCceEEEEcChHhHhhh---hccceeeEEE
Q 024108 69 HVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDT-------------KGRFRLHSIRDEEAKAL---ILLFQFKLCK 132 (272)
Q Consensus 69 ~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~-------------kgrf~l~~I~~eEa~~~---~~~~~~KLcK 132 (272)
.|++-| +--+-.|= =+||||-++ ++.||-.|.. .+|+.+|+=++---.++ |.-|| =+|
T Consensus 114 rV~~~G-ldP~a~Y~-vlmDvVPvD--~KRYRYayH~S~WlvAGkADp~~p~R~yvHPDSP~sGe~wmkqiVSFd--K~K 187 (437)
T KOG3586|consen 114 RVKFSG-LDPMADYY-VLMDVVPVD--SKRYRYAYHSSSWLVAGKADPAPPPRVYVHPDSPASGEQWMKQIVSFD--KLK 187 (437)
T ss_pred EEEEec-CCcccceE-EEEeEEecc--cceeeeeecccceeeecCCCCCCCCceeeCCCCCCCHHHHHHhhhchh--eee
Confidence 566777 22333443 489999994 6999999974 57888898765444333 33444 478
Q ss_pred EEeEEEeeCCceEEEccCCee----eecCCCCcccCCeEEEecCCCceeeEEeecCCcEEEEECCCcc
Q 024108 133 VRSVQFGQKGIPYINTYDGRT----IRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNR 196 (272)
Q Consensus 133 V~~k~~~~~g~~ql~~hDGrn----i~~~d~~ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~ 196 (272)
.+|-.+-++|.+.||.----- |.+-|+ -+|+.+....+ +=...|-|++=.-.-||.=.|.
T Consensus 188 LTNNelD~nGHIILNSMHkYQPRvHvV~~~~---~~~s~~~~~~~-e~~kTF~FpET~FtAVTAYQNq 251 (437)
T KOG3586|consen 188 LTNNELDDNGHIILNSMHKYQPRVHVVYLDP---GNDSNKYVEKN-EGFKTFVFPETVFTAVTAYQNQ 251 (437)
T ss_pred ccccccccCCcEeeecccccCCceEEEEecC---CCCcccccccc-ccceeEeccceeEEEEeecccc
Confidence 899999999998887532211 111121 11555555443 2245666777665555555543
No 87
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=26.32 E-value=97 Score=34.61 Aligned_cols=27 Identities=33% Similarity=0.602 Sum_probs=25.3
Q ss_pred eecCCcEEEEECCCcceeEEEEEeEEE
Q 024108 181 KFDVGNVVMVTGGRNRGRVGIIKNREK 207 (272)
Q Consensus 181 kf~~G~~~~v~gG~n~G~vG~I~~i~~ 207 (272)
-|++|+.|=|+.|+|-|..|.|+.++.
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeC
Confidence 388999999999999999999999987
No 88
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=26.22 E-value=5.6e+02 Score=24.21 Aligned_cols=61 Identities=23% Similarity=0.310 Sum_probs=39.7
Q ss_pred CCCCcccCCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEEEEeEEEec-CCccEEEEEcCCCCeEeEeeceEEEE
Q 024108 157 PDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTI 235 (272)
Q Consensus 157 ~d~~ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvI 235 (272)
++.+++.||.|+-+=-.|. |..|= -+|+|..++.+. +.+-.|.++-.. -.+++.|||++
T Consensus 209 ~~~~i~~GD~vvTSGlgg~------fP~Gl-----------~Vg~V~~v~~~~~~~~~~v~~~P~a---~~~~l~~v~l~ 268 (284)
T COG1792 209 PNSDIKEGDLVVTSGLGGV------FPAGL-----------PVGEVSSVKLDDYGLFKVVIVKPAA---SLDRLRYVLLV 268 (284)
T ss_pred CCCCccCCCEEEecCCCCc------CCCCc-----------EEEEEEEEEeCCCceeEEEEEeccc---ccccceEEEEE
Confidence 4557888885554433332 22221 378888888766 556777777544 47889999999
Q ss_pred cc
Q 024108 236 GK 237 (272)
Q Consensus 236 Gk 237 (272)
..
T Consensus 269 ~~ 270 (284)
T COG1792 269 KR 270 (284)
T ss_pred ec
Confidence 95
No 89
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=25.75 E-value=1.9e+02 Score=20.44 Aligned_cols=37 Identities=22% Similarity=0.241 Sum_probs=28.8
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEEecCCc-cEEEEE
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 218 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~-~~V~i~ 218 (272)
|++|..|++.-+...-.-++|.+++...+.. =.||-.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEET
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcC
Confidence 6889999999999999999999998866553 366664
No 90
>TIGR02658 TTQ_MADH_Hv methylamine dehydrogenase heavy chain. This family consists of the heavy chain of methylamine dehydrogenase light chain, a periplasmic enzyme. The enzyme contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from two Trp residues in the light subunity. The enzyme forms a complex with the type I blue copper protein amicyanin and a cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome.
Probab=25.32 E-value=5.2e+02 Score=25.38 Aligned_cols=94 Identities=12% Similarity=0.023 Sum_probs=63.6
Q ss_pred CCceEEEEEcCCCceEEEEcC---------hHhHhhhhccceeeEEEEEeEEEeeCC---------ceEEEccCCeeeec
Q 024108 95 TNENFRLLYDTKGRFRLHSIR---------DEEAKALILLFQFKLCKVRSVQFGQKG---------IPYINTYDGRTIRY 156 (272)
Q Consensus 95 t~e~yRvl~d~kgrf~l~~I~---------~eEa~~~~~~~~~KLcKV~~k~~~~~g---------~~ql~~hDGrni~~ 156 (272)
++..=|.+..++|++.++.-+ ..+ .+..||-+-.++...-..... .......||+.+-+
T Consensus 45 ~G~~P~~~~spDg~~lyva~~~~~R~~~G~~~d---~V~v~D~~t~~~~~~i~~p~~p~~~~~~~~~~~~ls~dgk~l~V 121 (352)
T TIGR02658 45 GGFLPNPVVASDGSFFAHASTVYSRIARGKRTD---YVEVIDPQTHLPIADIELPEGPRFLVGTYPWMTSLTPDNKTLLF 121 (352)
T ss_pred ccCCCceeECCCCCEEEEEeccccccccCCCCC---EEEEEECccCcEEeEEccCCCchhhccCccceEEECCCCCEEEE
Confidence 455555568888888888766 333 467788777777764433222 24566788988864
Q ss_pred CCCCcccCCeEEEecCCCceeeEEeecCCcEEEEEC
Q 024108 157 PDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 192 (272)
Q Consensus 157 ~d~~ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~g 192 (272)
.+ .-..+-.-+||+++++++..|+---|..+|+++
T Consensus 122 ~n-~~p~~~V~VvD~~~~kvv~ei~vp~~~~vy~t~ 156 (352)
T TIGR02658 122 YQ-FSPSPAVGVVDLEGKAFVRMMDVPDCYHIFPTA 156 (352)
T ss_pred ec-CCCCCEEEEEECCCCcEEEEEeCCCCcEEEEec
Confidence 42 112444578999999999999987778888763
No 91
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=24.97 E-value=3.7e+02 Score=26.83 Aligned_cols=52 Identities=27% Similarity=0.312 Sum_probs=34.7
Q ss_pred CcccCCeEEEecCCCceeeEEee----cCCcEEEEECCCcceeEEEEEeEEEecCCc
Q 024108 160 LIKANDTIKLDLETNKITEFIKF----DVGNVVMVTGGRNRGRVGIIKNREKHKGSF 212 (272)
Q Consensus 160 ~ik~~Dtv~i~l~~~kI~~~ikf----~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~ 212 (272)
.++.||...+.|...+=+-.-+| .-|-.++.-+|..+| .|.|.++....||.
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 47789998888865443323333 246677777776555 89999988666654
No 92
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=24.86 E-value=1.5e+02 Score=33.34 Aligned_cols=158 Identities=18% Similarity=0.249 Sum_probs=100.8
Q ss_pred hCceEEECCEEeccccCCCcceeEEEeccCCceEEEEEcCCCceEEEEcChHhHhhhhccceeeEEEEEeEEEeeCCceE
Q 024108 66 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKALILLFQFKLCKVRSVQFGQKGIPY 145 (272)
Q Consensus 66 ~~g~V~VDGkvr~D~k~PvG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~~~~~~~~KLcKV~~k~~~~~g~~q 145 (272)
..+.|.++.++.--++.-+--.+.=.+...+++|+++ .+|-|....++.++|. .--|-..|+.=-.....+
T Consensus 440 ~g~~v~i~C~~~asP~p~~~W~k~~~~~~~~~r~~i~--edGtL~I~n~t~~DaG-------~YtC~A~N~~G~a~~~~~ 510 (1051)
T KOG3513|consen 440 VGGTVTIDCKPFASPKPKVSWLKGGEKLLQSGRIRIL--EDGTLEISNVTRSDAG-------KYTCVAENKLGKAESTGN 510 (1051)
T ss_pred eCCeEEEeeccCCCCcceEEEEcCCcccccCceEEEC--CCCcEEecccCcccCc-------EEEEEEEcccCccceEEE
Confidence 3456666666666665544444444444566677765 5589999999999999 788999998766667788
Q ss_pred EEccCCeeeecC--CCCcccCCeEEEecCCC-----ceeeE-------Eee-cCCcEEEEECCCcceeEEEEEeEEE-ec
Q 024108 146 INTYDGRTIRYP--DPLIKANDTIKLDLETN-----KITEF-------IKF-DVGNVVMVTGGRNRGRVGIIKNREK-HK 209 (272)
Q Consensus 146 l~~hDGrni~~~--d~~ik~~Dtv~i~l~~~-----kI~~~-------ikf-~~G~~~~v~gG~n~G~vG~I~~i~~-~~ 209 (272)
|..-|-.-|..+ ...++.|+++.+.-+.. +|.=. |.| ..|.-..+.+|.+.|+. +|.++.- +.
T Consensus 511 L~Vkd~tri~~~P~~~~v~~g~~v~l~Ce~shD~~ld~~f~W~~nG~~id~~~~~~~~~~~~~~~~g~L-~i~nv~l~~~ 589 (1051)
T KOG3513|consen 511 LIVKDATRITLAPSNTDVKVGESVTLTCEASHDPSLDITFTWKKNGRPIDFNPDGDHFEINDGSDSGRL-TIANVSLEDS 589 (1051)
T ss_pred EEEecCceEEeccchhhhccCceEEEEeecccCCCcceEEEEEECCEEhhccCCCCceEEeCCcCccce-EEEeeccccC
Confidence 888898888653 23699999999877632 11111 122 24566778888877765 3355544 34
Q ss_pred CCc-cEEEEEcCCCCeEeEeeceEEEEcc
Q 024108 210 GSF-ETIHIQDALGHEFATRLGNVFTIGK 237 (272)
Q Consensus 210 ~s~-~~V~i~d~~g~~F~T~~~~vfvIGk 237 (272)
|+. -+|.. .- . =.+....++|-|-
T Consensus 590 G~Y~C~aqT--~~-D-s~s~~A~l~V~gp 614 (1051)
T KOG3513|consen 590 GKYTCVAQT--AL-D-SASARADLLVRGP 614 (1051)
T ss_pred ceEEEEEEE--ee-c-chhcccceEEecC
Confidence 655 23322 11 1 1445566777774
No 93
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=24.53 E-value=2.9e+02 Score=30.25 Aligned_cols=77 Identities=19% Similarity=0.243 Sum_probs=51.8
Q ss_pred CcceeEEEeccCCceEEEEEcCCCceEEEEcCh---HhHhhhhccceeeEEEEE----eEEEeeCCceEEEccCCeeeec
Q 024108 84 AGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRD---EEAKALILLFQFKLCKVR----SVQFGQKGIPYINTYDGRTIRY 156 (272)
Q Consensus 84 vG~mDVIsI~kt~e~yRvl~d~kgrf~l~~I~~---eEa~~~~~~~~~KLcKV~----~k~~~~~g~~ql~~hDGrni~~ 156 (272)
+|-++++.++ .+.+=+-+|.+++.+..+++. -++. =||.||+ ....++.++|.++..||.-...
T Consensus 112 ~~~~e~~~~~--~~~~V~s~d~~~k~~~~~v~~v~r~~~~-------~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~ 182 (858)
T PRK14898 112 IGGHEVCDLP--IEIYALSLDQDEKVHWKRIISVIRHKAN-------GKLIKIKTESGRTIRATPYHSFVTRKDNEVIPV 182 (858)
T ss_pred cCCceEEecC--CCcEEEEECCCCcEEEEEeeeEEeccCC-------CcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEe
Confidence 3555555443 234444556667777777664 1222 2788887 3557889999999999987765
Q ss_pred CCCCcccCCeEEE
Q 024108 157 PDPLIKANDTIKL 169 (272)
Q Consensus 157 ~d~~ik~~Dtv~i 169 (272)
....+++||-|.+
T Consensus 183 ~a~~l~~GD~i~~ 195 (858)
T PRK14898 183 EGSELKIGDWLPV 195 (858)
T ss_pred eHHhCCCCCEEee
Confidence 6668999998755
No 94
>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=24.47 E-value=29 Score=30.22 Aligned_cols=52 Identities=23% Similarity=0.118 Sum_probs=40.4
Q ss_pred ccchHHHHHHhhhcccccHHHHHHHHhCc-----eEEECCEEeccccCCCccee---EEEeccC
Q 024108 40 ECLPLILILRNRLKYALTYREVIAILMQR-----HVLVDAKVRTDKTYPAGFMD---VVSIPKT 95 (272)
Q Consensus 40 ~slPL~i~LRd~LkyA~t~rEak~Il~~g-----~V~VDGkvr~D~k~PvG~mD---VIsI~kt 95 (272)
...+|+-+||+.|++-.+..- +.+| .|+|||+.+.---.|+.-+| |.+|+-.
T Consensus 19 ~~~~Ll~~LR~~~~ltgtK~g----C~~G~CGACtVlvdG~~v~SCl~~~~~~~G~~v~TiEgl 78 (151)
T TIGR03198 19 PTTRLSDLLRKELQLTGTKVS----CGIGRCGACSVLIDGKLANACLTMAYQADGHEITTIEGI 78 (151)
T ss_pred CCcHHHHHHHhccCCCCCCCC----CCCCcCCccEEEECCcEEechHHHHHHhcCCEEEecCCc
Confidence 478999999999988765432 6666 69999999998888886554 7777553
No 95
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=24.46 E-value=60 Score=28.46 Aligned_cols=51 Identities=18% Similarity=0.243 Sum_probs=37.4
Q ss_pred CceeeEEeecCCcEEEEECCCcce-eEEEEEeEEEecCC--ccEEEEEcCCCCe
Q 024108 174 NKITEFIKFDVGNVVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 224 (272)
Q Consensus 174 ~kI~~~ikf~~G~~~~v~gG~n~G-~vG~I~~i~~~~~s--~~~V~i~d~~g~~ 224 (272)
.-.+..+|+..++.+-|.+|+..| .+|.|.++-+..-. .+.|.-+-++|..
T Consensus 41 ~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 41 KYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred HhCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 335788999999999999999999 99999998664322 2444444455543
No 96
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=24.02 E-value=1.9e+02 Score=22.53 Aligned_cols=33 Identities=24% Similarity=0.396 Sum_probs=24.3
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEEecCCccEEEEEcCCCC
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGH 223 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~ 223 (272)
+.+|+.++.+|| -+|+|.++.. +.+.++.+.|.
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d-----~~v~vei~~g~ 70 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAE-----NTIVIELNDNT 70 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCCe
Confidence 567888888775 6899999863 46677766653
No 97
>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=23.85 E-value=2.8e+02 Score=22.74 Aligned_cols=61 Identities=16% Similarity=0.352 Sum_probs=38.3
Q ss_pred ecCCcEEEE-ECCCcceeEEEEEeEEEec-----CCc-cEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCCCcceeee
Q 024108 182 FDVGNVVMV-TGGRNRGRVGIIKNREKHK-----GSF-ETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLS 254 (272)
Q Consensus 182 f~~G~~~~v-~gG~n~G~vG~I~~i~~~~-----~s~-~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~Islp~~~gi~~~ 254 (272)
|+.|+.--. +....+ |.|..|+... +-+ +-|.|++.+|. .+.|.+.+ |+.-|-++-|+++
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---GDINAIILSNTALNDPWYCDYVRIKSEDGK------VFAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECcccc---CceEEEEEECCCCCCCceeeEEEEECCCCC------EEEEEcce----eeCCchhceEEEe
Confidence 666655432 124444 4455554421 224 78889886554 35699998 9999999988876
Q ss_pred h
Q 024108 255 I 255 (272)
Q Consensus 255 ~ 255 (272)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 98
>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=23.14 E-value=78 Score=31.07 Aligned_cols=45 Identities=16% Similarity=-0.063 Sum_probs=36.9
Q ss_pred cchHHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcc
Q 024108 41 CLPLILILRNRLKYALTYREVIAILMQRHVLVDAKVRTDKTYPAGF 86 (272)
Q Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~g~V~VDGkvr~D~k~PvG~ 86 (272)
++++.=++.. .+.+.+.+||++.|++|-|+|||...+|..+-.-.
T Consensus 329 ~~~~~~~~~~-~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~ 373 (377)
T TIGR00234 329 DITLADLLVL-SGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRKE 373 (377)
T ss_pred CcCHHHHHHH-cCCCcChHHHHHHHHhCCEEECCEeccCchhhhcc
Confidence 4666666664 58899999999999999999999999998765433
No 99
>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=22.82 E-value=2.7e+02 Score=24.01 Aligned_cols=52 Identities=17% Similarity=0.146 Sum_probs=38.0
Q ss_pred ccEEEEEcCCCCeEeEeeceEEEEccCCCceeeCCCCcceeeehHHHHHHHHHH
Q 024108 212 FETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL 265 (272)
Q Consensus 212 ~~~V~i~d~~g~~F~T~~~~vfvIGk~~kp~Islp~~~gi~~~~~e~~~~~~~~ 265 (272)
++-+.+-|.+|.--|+...|+|++= +.-|++-|.+.|+-..+..+.-.++++
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 3445577899999999999999995 444889998888877776665555544
No 100
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=22.18 E-value=1.1e+02 Score=34.34 Aligned_cols=55 Identities=25% Similarity=0.363 Sum_probs=42.1
Q ss_pred ecCCcEEEEECCCcceeEEEEEeEEEecCCc--cEEEEEcCCCCeEeEeeceEEEEccCCC
Q 024108 182 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFATRLGNVFTIGKGTK 240 (272)
Q Consensus 182 f~~G~~~~v~gG~n~G~vG~I~~i~~~~~s~--~~V~i~d~~g~~F~T~~~~vfvIGk~~k 240 (272)
...++++-+++|.|.|+-|.|.+|-+. .-| +.-++ .++-.|.++..|+..+|. .+
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~-~~F~h~r~~~--En~Gv~vck~k~~~~~g~-~~ 638 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRP-FVFLHSRKNL--ENGGVFVCKEKNLILAGG-KK 638 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecc-eeeeeehhhc--ccCCeEEEecCCceeccc-cC
Confidence 457899999999999999999999652 112 22223 466789999999999995 44
No 101
>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=22.09 E-value=1.5e+02 Score=21.86 Aligned_cols=31 Identities=26% Similarity=0.384 Sum_probs=25.7
Q ss_pred EEEccCCeeeecCCCCcccCCeEEEecCCCce
Q 024108 145 YINTYDGRTIRYPDPLIKANDTIKLDLETNKI 176 (272)
Q Consensus 145 ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI 176 (272)
...+..|-.|.+| +-|+.||.|+||-.+++-
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 4567889999887 479999999999998763
No 102
>PF06905 FAIM1: Fas apoptotic inhibitory molecule (FAIM1); InterPro: IPR010695 This family consists of several fas apoptotic inhibitory molecule (FAIM) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology [].; GO: 0043066 negative regulation of apoptosis; PDB: 3MX7_A 2KW1_A 2KD2_A.
Probab=21.98 E-value=5.8e+02 Score=22.86 Aligned_cols=51 Identities=20% Similarity=0.311 Sum_probs=37.3
Q ss_pred cCCeee-ecCCCCcccCCeEEEecCCCceeeEEeecCCcEEEEECCCcceeEEE
Q 024108 149 YDGRTI-RYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGI 201 (272)
Q Consensus 149 hDGrni-~~~d~~ik~~Dtv~i~l~~~kI~~~ikf~~G~~~~v~gG~n~G~vG~ 201 (272)
=||.++ .|-+...|.-.|..+.+..+ .-.|-|+...+-+=..|......|.
T Consensus 82 VdGksl~ky~e~~~k~~~tW~~~i~G~--~~RIvLdk~t~~vwvnG~~iet~~e 133 (177)
T PF06905_consen 82 VDGKSLKKYKEEQSKKFNTWELNIDGQ--EYRIVLDKDTMDVWVNGEKIETEGE 133 (177)
T ss_dssp ETTEEEEE--SSTTTTEEEEEEEETTE--EEEEEEETTTTEEEETTCEE--EEE
T ss_pred ECCEEHHHHHHHHhhhheeEEEecCCC--EEEEEEEcceEEEEECCEEccccce
Confidence 388888 67788889999999999643 4567788888888889988877664
No 103
>PLN02772 guanylate kinase
Probab=21.88 E-value=1.9e+02 Score=29.04 Aligned_cols=63 Identities=19% Similarity=0.305 Sum_probs=37.9
Q ss_pred EEeecCCcEEEEECCCccee-EEEEEeE-EEecCCccEEEEEc-----CCCCeEeEe-eceEEEEccCCCc
Q 024108 179 FIKFDVGNVVMVTGGRNRGR-VGIIKNR-EKHKGSFETIHIQD-----ALGHEFATR-LGNVFTIGKGTKP 241 (272)
Q Consensus 179 ~ikf~~G~~~~v~gG~n~G~-vG~I~~i-~~~~~s~~~V~i~d-----~~g~~F~T~-~~~vfvIGk~~kp 241 (272)
+--+..|+..+|+||+|-+. .-....| ........+..+.. .+|+++... .+.++||++|..|
T Consensus 28 ~tav~igdk~yv~GG~~d~~~~~~~v~i~D~~t~~W~~P~V~G~~P~~r~GhSa~v~~~~rilv~~~~~~~ 98 (398)
T PLN02772 28 ETSVTIGDKTYVIGGNHEGNTLSIGVQILDKITNNWVSPIVLGTGPKPCKGYSAVVLNKDRILVIKKGSAP 98 (398)
T ss_pred ceeEEECCEEEEEcccCCCccccceEEEEECCCCcEecccccCCCCCCCCcceEEEECCceEEEEeCCCCC
Confidence 44556799999999999864 2222222 22112222333322 467887777 6899999975543
No 104
>cd05892 Ig_Myotilin_C C-terminal immunoglobulin (Ig)-like domain of myotilin. Ig_Myotilin_C: C-terminal immunoglobulin (Ig)-like domain of myotilin. Mytolin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to the latter family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Myotilin is most abundant in skeletal and cardiac muscle, and is involved in maintaining sarcomere integrity. It binds to alpha-actinin, filamin and actin. Mutations in myotilin lead to muscle disorders.
Probab=21.46 E-value=1.8e+02 Score=21.48 Aligned_cols=35 Identities=11% Similarity=0.282 Sum_probs=27.4
Q ss_pred CCceEEEEEcCCC--ceEEEEcChHhHhhhhccceeeEEEEEeE
Q 024108 95 TNENFRLLYDTKG--RFRLHSIRDEEAKALILLFQFKLCKVRSV 136 (272)
Q Consensus 95 t~e~yRvl~d~kg--rf~l~~I~~eEa~~~~~~~~~KLcKV~~k 136 (272)
.+.+|.+..+..| .|.+..+..+++. .-.|...|.
T Consensus 27 ~~~r~~~~~~~~g~~~L~I~~~~~~D~G-------~Y~C~A~N~ 63 (75)
T cd05892 27 NTDRISLYQDNSGRVTLLIKNVNKKDAG-------WYTVSAVNE 63 (75)
T ss_pred CCCeEEEEEcCCCcEEEEECCCChhhCE-------EEEEEEEcC
Confidence 3457888888777 5777799999998 668988873
No 105
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=21.29 E-value=2.6e+02 Score=26.66 Aligned_cols=32 Identities=38% Similarity=0.630 Sum_probs=28.0
Q ss_pred eeeEEeecCCcEEEEECCCcceeEEEEEeEEE
Q 024108 176 ITEFIKFDVGNVVMVTGGRNRGRVGIIKNREK 207 (272)
Q Consensus 176 I~~~ikf~~G~~~~v~gG~n~G~vG~I~~i~~ 207 (272)
....+.|++|+.+-|+.|.=.|..|+|.++..
T Consensus 200 ~~~~~~f~vGd~VrI~dGPF~GfeG~I~eid~ 231 (258)
T TIGR01956 200 VDNLSKFRVGNFVKIVDGPFKGIVGKIKKIDQ 231 (258)
T ss_pred cccccCCCCCCEEEEEecCCCCcEEEEEEEeC
Confidence 33457799999999999999999999999964
No 106
>PF02239 Cytochrom_D1: Cytochrome D1 heme domain; PDB: 1NNO_B 1HZU_A 1N15_B 1N50_A 1GJQ_A 1BL9_B 1NIR_B 1N90_B 1HZV_A 1AOQ_A ....
Probab=20.77 E-value=3.9e+02 Score=25.88 Aligned_cols=46 Identities=15% Similarity=0.117 Sum_probs=29.2
Q ss_pred EEEeeCCceEEEccCCeeeecCCCCcccCCeEEEecCCCceeeEEeec
Q 024108 136 VQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFD 183 (272)
Q Consensus 136 k~~~~~g~~ql~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI~~~ikf~ 183 (272)
+.++.+-.-.-.+.||+-+-.. .+..++..++|..+.+++..|+-.
T Consensus 74 i~~G~~~~~i~~s~DG~~~~v~--n~~~~~v~v~D~~tle~v~~I~~~ 119 (369)
T PF02239_consen 74 IKVGGNPRGIAVSPDGKYVYVA--NYEPGTVSVIDAETLEPVKTIPTG 119 (369)
T ss_dssp EE-SSEEEEEEE--TTTEEEEE--EEETTEEEEEETTT--EEEEEE--
T ss_pred EecCCCcceEEEcCCCCEEEEE--ecCCCceeEeccccccceeecccc
Confidence 3444444445567899988544 578889999999999999988764
No 107
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=20.08 E-value=1.1e+02 Score=25.90 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=24.1
Q ss_pred eecCCcEEEEECCCcceeEEEEEeEE
Q 024108 181 KFDVGNVVMVTGGRNRGRVGIIKNRE 206 (272)
Q Consensus 181 kf~~G~~~~v~gG~n~G~vG~I~~i~ 206 (272)
.|+.|+.+.|++|.=.|..|.|.++.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 58999999999999999999998875
No 108
>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=20.03 E-value=3.4e+02 Score=28.27 Aligned_cols=96 Identities=15% Similarity=0.120 Sum_probs=54.0
Q ss_pred eccccCCCcc----e-eEEEecc--CCceEEEEEcCCCceEEEE-------cChHhHhhhhccceee-EEEEEeEEEeeC
Q 024108 77 RTDKTYPAGF----M-DVVSIPK--TNENFRLLYDTKGRFRLHS-------IRDEEAKALILLFQFK-LCKVRSVQFGQK 141 (272)
Q Consensus 77 r~D~k~PvG~----m-DVIsI~k--t~e~yRvl~d~kgrf~l~~-------I~~eEa~~~~~~~~~K-LcKV~~k~~~~~ 141 (272)
.-||.|..|. + |-+++.. +.-.+|-+++.++.+.... ++.+-|+.|.....+. .+-+.+ ..
T Consensus 399 ia~YQFG~g~g~~l~~~~~~v~~s~~tgr~r~v~~~~~~l~t~r~~dg~l~lt~~Ga~~l~~~~~~p~~rV~v~----~~ 474 (540)
T TIGR00432 399 MKHYQNGPPNGELNVLSDVRIERSRNTGKIRHIYAGDELICTMRASDGLLVLGAEGAVRLHKGTDYPAWRVAVN----EE 474 (540)
T ss_pred HHHhhcCcCchHhhCCCCcEEEEeccCCcceEEEECCEEEEEEEcCCCeEEeCHHHHHHHHhcCCCCceEEEEC----Cc
Confidence 4578887663 2 4455533 2346788887766555443 6777776333332221 111111 11
Q ss_pred CceEEEccCCeee-----ecCCCCcccCCeEEEecCCCceee
Q 024108 142 GIPYINTYDGRTI-----RYPDPLIKANDTIKLDLETNKITE 178 (272)
Q Consensus 142 g~~ql~~hDGrni-----~~~d~~ik~~Dtv~i~l~~~kI~~ 178 (272)
-.+ ..-+|+|+ .-.|+.|.+||-|++-.++++++.
T Consensus 475 ~~~--f~~~g~~vfak~V~~ad~~IR~~dEV~vv~~~~~lla 514 (540)
T TIGR00432 475 SEP--FARKGKSVFAKFIIDCDNNIRANDEVLIVNADDELLA 514 (540)
T ss_pred chh--hccCCCcccCCccccCCCCCCCCCeEEEEcCCCcEEE
Confidence 111 12456666 224899999999998887766553
Done!