Query psy5495
Match_columns 273
No_of_seqs 277 out of 1285
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 18:56:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5495.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5495hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1708|consensus 100.0 1.2E-43 2.6E-48 315.8 12.4 163 95-272 22-193 (236)
2 TIGR01079 rplX_bact ribosomal 100.0 4.3E-33 9.3E-38 225.5 12.1 97 153-250 2-104 (104)
3 PRK00004 rplX 50S ribosomal pr 100.0 7.3E-33 1.6E-37 224.1 12.0 99 152-251 2-105 (105)
4 KOG1708|consensus 100.0 4.6E-34 9.9E-39 254.6 5.3 100 1-100 71-235 (236)
5 COG0198 RplX Ribosomal protein 100.0 1.7E-29 3.8E-34 204.9 11.0 97 152-251 2-104 (104)
6 CHL00141 rpl24 ribosomal prote 99.9 3.2E-24 6.9E-29 167.6 8.3 72 152-224 6-82 (83)
7 PRK12281 rplX 50S ribosomal pr 99.9 9.9E-23 2.1E-27 157.0 7.5 67 152-219 4-75 (76)
8 PRK01191 rpl24p 50S ribosomal 99.8 2.1E-19 4.6E-24 149.3 7.7 72 150-228 41-112 (120)
9 PTZ00194 60S ribosomal protein 99.8 6.6E-19 1.4E-23 150.2 7.2 70 150-226 42-111 (143)
10 TIGR01080 rplX_A_E ribosomal p 99.7 7.4E-18 1.6E-22 139.0 7.7 70 150-226 37-106 (114)
11 PF00467 KOW: KOW motif; Inte 98.6 1.2E-07 2.6E-12 61.7 4.7 32 157-188 1-32 (32)
12 PRK12281 rplX 50S ribosomal pr 98.5 8E-08 1.7E-12 74.4 4.4 51 1-51 5-70 (76)
13 CHL00141 rpl24 ribosomal prote 98.5 9.2E-08 2E-12 75.1 4.4 58 1-58 7-81 (83)
14 TIGR01079 rplX_bact ribosomal 98.4 3.8E-07 8.2E-12 74.3 4.5 58 1-58 2-77 (104)
15 PRK00004 rplX 50S ribosomal pr 98.2 2.2E-06 4.7E-11 69.9 4.8 58 1-58 3-77 (105)
16 KOG3401|consensus 97.8 1.7E-05 3.7E-10 68.4 3.8 66 150-222 44-110 (145)
17 smart00739 KOW KOW (Kyprides, 97.4 0.0002 4.3E-09 43.9 3.8 26 155-180 2-27 (28)
18 COG0198 RplX Ribosomal protein 97.3 0.00034 7.4E-09 57.5 4.3 56 2-57 4-74 (104)
19 PRK01191 rpl24p 50S ribosomal 96.5 0.0024 5.2E-08 53.8 3.5 52 4-58 47-107 (120)
20 PRK08559 nusG transcription an 96.5 0.0077 1.7E-07 51.5 6.3 41 153-193 93-133 (153)
21 TIGR00405 L26e_arch ribosomal 96.4 0.0058 1.3E-07 51.1 4.9 38 155-192 87-124 (145)
22 PRK05609 nusG transcription an 96.1 0.0094 2E-07 51.0 4.8 36 153-188 125-160 (181)
23 TIGR00922 nusG transcription t 96.0 0.011 2.4E-07 50.3 4.8 36 153-188 118-153 (172)
24 COG0250 NusG Transcription ant 95.8 0.015 3.2E-07 51.5 4.8 40 149-188 118-157 (178)
25 PTZ00194 60S ribosomal protein 95.6 0.0085 1.8E-07 51.9 2.6 52 4-58 48-108 (143)
26 PF00467 KOW: KOW motif; Inte 94.7 0.018 3.9E-07 37.3 1.6 24 5-28 1-25 (32)
27 TIGR01955 RfaH transcriptional 94.6 0.047 1E-06 45.8 4.3 35 153-188 107-141 (159)
28 TIGR01080 rplX_A_E ribosomal p 94.4 0.03 6.5E-07 46.7 2.6 53 3-58 42-103 (114)
29 PRK09014 rfaH transcriptional 94.0 0.076 1.6E-06 45.0 4.2 33 155-188 110-142 (162)
30 TIGR01956 NusG_myco NusG famil 93.8 0.096 2.1E-06 49.3 5.0 37 152-188 203-239 (258)
31 PRK04333 50S ribosomal protein 91.8 0.33 7.1E-06 38.5 4.7 37 154-191 3-39 (84)
32 smart00739 KOW KOW (Kyprides, 86.6 0.85 1.8E-05 27.5 2.8 25 3-27 2-27 (28)
33 PTZ00065 60S ribosomal protein 84.6 1.9 4.2E-05 37.0 4.9 34 156-190 9-42 (130)
34 KOG1999|consensus 84.5 1 2.2E-05 49.2 3.9 30 152-181 457-486 (1024)
35 PTZ00471 60S ribosomal protein 78.5 3.1 6.8E-05 35.9 4.1 41 155-195 5-51 (134)
36 COG2163 RPL14A Ribosomal prote 75.7 4.3 9.3E-05 34.6 4.1 36 155-191 5-40 (125)
37 COG5164 SPT5 Transcription elo 65.5 4.8 0.0001 41.4 2.6 29 154-182 139-167 (607)
38 PRK04313 30S ribosomal protein 63.8 8.5 0.00018 36.0 3.7 39 151-189 168-210 (237)
39 PRK06531 yajC preprotein trans 60.0 14 0.00031 30.9 4.0 31 154-188 36-66 (113)
40 KOG1999|consensus 58.0 7.3 0.00016 42.9 2.5 29 153-181 406-434 (1024)
41 PF09953 DUF2187: Uncharacteri 57.8 20 0.00042 27.0 4.0 27 156-188 5-31 (57)
42 PF05641 Agenet: Agenet domain 52.7 31 0.00068 25.5 4.5 33 155-188 1-37 (68)
43 COG1862 YajC Preprotein transl 49.3 24 0.00052 28.8 3.7 26 153-182 42-67 (97)
44 PRK05585 yajC preprotein trans 49.0 26 0.00057 28.7 3.9 30 153-188 51-80 (106)
45 PLN00036 40S ribosomal protein 45.1 31 0.00067 32.8 4.2 38 151-188 171-211 (261)
46 PF11623 DUF3252: Protein of u 44.4 39 0.00085 25.1 3.7 40 155-194 2-43 (53)
47 PF10030 DUF2272: Uncharacteri 44.0 1.2E+02 0.0025 27.4 7.5 94 98-192 12-146 (183)
48 PF03144 GTP_EFTU_D2: Elongati 43.5 38 0.00083 24.3 3.7 40 152-192 10-54 (74)
49 COG1471 RPS4A Ribosomal protei 42.6 37 0.00081 32.0 4.3 39 151-189 170-212 (241)
50 PRK05886 yajC preprotein trans 42.2 38 0.00083 28.2 3.9 30 153-188 37-66 (109)
51 PTZ00223 40S ribosomal protein 41.6 31 0.00068 33.0 3.7 38 151-188 168-208 (273)
52 PF08206 OB_RNB: Ribonuclease 38.6 22 0.00047 25.7 1.7 35 144-178 21-58 (58)
53 TIGR00739 yajC preprotein tran 38.4 50 0.0011 25.9 3.8 30 153-188 36-65 (84)
54 PTZ00118 40S ribosomal protein 38.2 43 0.00094 31.9 4.0 38 151-188 171-211 (262)
55 PF02699 YajC: Preprotein tran 37.5 11 0.00024 29.3 0.0 30 153-188 35-64 (82)
56 PRK00409 recombination and DNA 37.0 52 0.0011 35.4 4.9 38 153-193 635-673 (782)
57 PF01176 eIF-1a: Translation i 32.4 40 0.00087 24.9 2.3 34 135-177 31-64 (65)
58 cd05793 S1_IF1A S1_IF1A: Trans 31.7 45 0.00097 25.8 2.6 39 134-182 27-66 (77)
59 KOG3344|consensus 31.4 14 0.0003 32.5 -0.4 59 74-134 37-104 (150)
60 COG1532 Predicted RNA-binding 31.2 94 0.002 23.4 4.0 34 156-189 22-57 (57)
61 KOG3418|consensus 31.0 69 0.0015 27.9 3.8 39 155-193 5-49 (136)
62 COG0361 InfA Translation initi 29.9 73 0.0016 25.1 3.4 37 134-178 34-70 (75)
63 PF12353 eIF3g: Eukaryotic tra 29.8 75 0.0016 26.8 3.8 28 219-246 7-34 (128)
64 cd04456 S1_IF1A_like S1_IF1A_l 29.5 62 0.0013 25.2 3.0 40 134-182 27-67 (78)
65 smart00652 eIF1a eukaryotic tr 28.9 61 0.0013 25.4 2.9 40 134-182 32-71 (83)
66 COG3700 AphA Acid phosphatase 28.6 18 0.00039 33.5 -0.1 34 152-185 124-157 (237)
67 PF15269 zf-C2H2_7: Zinc-finge 27.8 39 0.00083 24.8 1.5 20 101-120 3-22 (54)
68 PRK02749 photosystem I reactio 27.6 1E+02 0.0022 24.1 3.8 29 154-182 2-32 (71)
69 PF00018 SH3_1: SH3 domain; I 27.1 69 0.0015 21.6 2.6 17 151-167 12-28 (48)
70 PF01157 Ribosomal_L21e: Ribos 27.0 93 0.002 25.5 3.7 34 149-182 25-70 (99)
71 cd04466 S1_YloQ_GTPase S1_YloQ 27.0 1.1E+02 0.0024 21.6 3.8 30 154-185 37-66 (68)
72 COG0361 InfA Translation initi 26.5 3.2E+02 0.007 21.5 6.6 61 172-235 10-73 (75)
73 PF12701 LSM14: Scd6-like Sm d 26.4 1.2E+02 0.0025 24.7 4.2 36 157-192 7-42 (96)
74 TIGR03170 flgA_cterm flagella 26.3 94 0.002 24.8 3.7 34 152-185 63-109 (122)
75 smart00743 Agenet Tudor-like d 24.8 1.7E+02 0.0037 20.6 4.4 33 154-187 2-35 (61)
76 PRK07018 flgA flagellar basal 24.7 96 0.0021 28.2 3.8 34 152-185 174-220 (235)
77 TIGR01069 mutS2 MutS2 family p 24.0 1.1E+02 0.0023 33.0 4.6 34 156-193 626-661 (771)
78 PRK04306 50S ribosomal protein 23.7 1.1E+02 0.0025 25.1 3.7 39 149-187 27-77 (98)
79 CHL00125 psaE photosystem I su 23.5 1.1E+02 0.0025 23.4 3.4 28 155-182 2-31 (64)
80 cd03692 mtIF2_IVc mtIF2_IVc: t 23.4 1.3E+02 0.0028 22.9 3.8 35 151-185 23-57 (84)
81 PRK02935 hypothetical protein; 23.4 41 0.00088 28.3 1.0 35 213-254 66-100 (110)
82 KOG4315|consensus 22.9 36 0.00079 34.6 0.8 37 154-190 393-429 (455)
83 cd05695 S1_Rrp5_repeat_hs3 S1_ 22.8 1.3E+02 0.0027 21.8 3.5 24 154-187 42-65 (66)
84 PF11904 GPCR_chapero_1: GPCR- 22.6 51 0.0011 31.6 1.7 88 1-100 12-103 (307)
85 PRK12618 flgA flagellar basal 22.5 1.1E+02 0.0024 26.1 3.5 33 152-184 79-124 (141)
86 COG1193 Mismatch repair ATPase 22.0 84 0.0018 34.0 3.3 34 152-189 610-643 (753)
87 PLN00045 photosystem I reactio 21.7 1.2E+02 0.0025 25.3 3.3 29 153-181 38-68 (101)
88 cd05698 S1_Rrp5_repeat_hs6_sc5 21.4 1.5E+02 0.0032 21.0 3.5 24 154-187 44-67 (70)
89 cd05707 S1_Rrp5_repeat_sc11 S1 21.1 1.4E+02 0.003 21.1 3.4 24 154-187 44-67 (68)
90 COG2139 RPL21A Ribosomal prote 21.0 1.6E+02 0.0035 24.4 4.0 44 149-192 25-80 (98)
91 cd06529 S24_LexA-like Peptidas 20.5 2.4E+02 0.0052 20.2 4.6 44 143-192 18-62 (81)
92 cd05688 S1_RPS1_repeat_ec3 S1_ 20.3 1.8E+02 0.0038 20.0 3.7 24 154-187 44-67 (68)
93 cd05792 S1_eIF1AD_like S1_eIF1 20.2 1.9E+02 0.0041 22.7 4.1 40 134-182 27-67 (78)
No 1
>KOG1708|consensus
Probab=100.00 E-value=1.2e-43 Score=315.76 Aligned_cols=163 Identities=48% Similarity=0.809 Sum_probs=145.5
Q ss_pred hcceeecCCCCCC-cceeecCCCCCcccCCCCCCChhhhhcCCCccccCCCCCcccC--cccceecCCeEEEeecCCCCc
Q psy5495 95 LGQVYHVYPKGPQ-YTVVDQGKDSDFDFSTDRPWEVPFLARNRPWEKNKKKIPIEPI--KDWSIFKGDRVEILVGKDKGK 171 (273)
Q Consensus 95 ~~~v~~~~p~~~~-y~~~~~~~~~~y~~~~~rPwt~~~~~~n~p~~~r~~kv~vePi--~~w~I~kGD~V~VI~GkDKGK 171 (273)
.+.+||.+|..-+ |.|+++ +.+. -.+..+|+|+.+|+ .+.+||| .+|++|.||+|+||+||||||
T Consensus 22 ~er~y~isP~~~~~~~pr~~-adk~----------~~~~qk~~~w~rrr-~~~~e~i~d~dw~ff~GDtVeVlvGkDkGk 89 (236)
T KOG1708|consen 22 FERQYLISPISLSVTSPRKV-ADKR----------CLVLQKNKPWERRR-CVPVEPIIDEDWHFFFGDTVEVLVGKDKGK 89 (236)
T ss_pred hhceeeeccccccccCCCCh-hhhh----------hhHHhhcCcccccc-CCCCCCccccceeEecCCEEEEEecccCCc
Confidence 3447887776333 666666 3333 23466899999999 9999999 699999999999999999999
Q ss_pred eeEEEEEEccCCEEEEcCeeeEEeecCCC-----CceEEEeeecccCCC-eeeeCCCCCCceeEEEEEecCCcEEEEEcc
Q psy5495 172 QGYVIQIFQEINSVIVEGLNTYLKKMGDS-----QFIIKQEAPLLVTNE-VALVDPSDRMGCQVEWRYTEAGDRVRVSKR 245 (273)
Q Consensus 172 ~GkV~~V~r~~n~ViVEGvN~~~k~v~~~-----Ggii~~EaPIhvtSN-V~LVdP~~~KptrV~~r~~edGkKVRvskk 245 (273)
||+|++|++++|||+|+|+|++++|++.. |.|+.+|||||+ || ||||||++.++|+++|+++++|+|||||.+
T Consensus 90 qG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhv-sk~VmLvdp~d~q~te~~wr~~e~GekVRvstr 168 (236)
T KOG1708|consen 90 QGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHV-SKQVMLVDPEDDQPTEVEWRFTEDGEKVRVSTR 168 (236)
T ss_pred cceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCcee-cceeEEECccccCCceeeEEEcCCCcEEEEEec
Confidence 99999999999999999999999999743 999999999999 77 999999999999999999999999999999
Q ss_pred CCcccCCCCCccccccCCCCCcceecc
Q psy5495 246 SGRIIPIPMAAYETHDYKTPGTYKVTE 272 (273)
Q Consensus 246 sG~iIP~P~~a~~~~D~~~pe~y~e~~ 272 (273)
||++||+|+.+ |+||++||+|+|.|
T Consensus 169 SG~iIpipe~~--t~dy~~pe~yiE~e 193 (236)
T KOG1708|consen 169 SGRIIPIPEKW--TADYIKPELYIEAE 193 (236)
T ss_pred ccccccCcccc--cccccCchheeecc
Confidence 99999999996 99999999999986
No 2
>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=100.00 E-value=4.3e-33 Score=225.45 Aligned_cols=97 Identities=42% Similarity=0.680 Sum_probs=92.9
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCC------CCceEEEeeecccCCCeeeeCCCCCCc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGD------SQFIIKQEAPLLVTNEVALVDPSDRMG 226 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~------~Ggii~~EaPIhvtSNV~LVdP~~~Kp 226 (273)
++|++||+|+||+|+||||+|+|++|++++|+|+|||+|++++|+++ .|+++++|+|||+ |||+|+||++++|
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~-SnV~lv~p~~~k~ 80 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHI-SNVMLFDPKTGKA 80 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCH-HHeEEEcCcCCCC
Confidence 48999999999999999999999999999999999999999999863 3999999999999 9999999999999
Q ss_pred eeEEEEEecCCcEEEEEccCCccc
Q psy5495 227 CQVEWRYTEAGDRVRVSKRSGRII 250 (273)
Q Consensus 227 trV~~r~~edGkKVRvskksG~iI 250 (273)
|||+|++++||+++|+|++||++|
T Consensus 81 ~rv~~~~~~~g~kvRv~k~~g~~i 104 (104)
T TIGR01079 81 TRVGIRFEEDGKKVRVFKKTGEII 104 (104)
T ss_pred eEEEEEEccCCcEEEEEeccCCcC
Confidence 999999999999999999999876
No 3
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=100.00 E-value=7.3e-33 Score=224.09 Aligned_cols=99 Identities=42% Similarity=0.674 Sum_probs=94.5
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCCC-----CceEEEeeecccCCCeeeeCCCCCCc
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDS-----QFIIKQEAPLLVTNEVALVDPSDRMG 226 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~~-----Ggii~~EaPIhvtSNV~LVdP~~~Kp 226 (273)
.|+|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|++++ |++++.|+|||+ |||+|+||.+++|
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~-SnV~lv~p~~~~~ 80 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHI-SNVALVDPKTGKA 80 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCH-HHEEEEeCcCCCC
Confidence 5899999999999999999999999999999999999999999998642 999999999999 9999999999999
Q ss_pred eeEEEEEecCCcEEEEEccCCcccC
Q psy5495 227 CQVEWRYTEAGDRVRVSKRSGRIIP 251 (273)
Q Consensus 227 trV~~r~~edGkKVRvskksG~iIP 251 (273)
+||+|+++++|+++|+|++||+.|.
T Consensus 81 ~rv~~~~~~~g~kvRv~k~~g~~i~ 105 (105)
T PRK00004 81 TRVGFKFLEDGKKVRVAKKSGEVID 105 (105)
T ss_pred eEEEEEEccCCcEEEEEecCCCCcC
Confidence 9999999999999999999999873
No 4
>KOG1708|consensus
Probab=100.00 E-value=4.6e-34 Score=254.59 Aligned_cols=100 Identities=38% Similarity=0.515 Sum_probs=93.8
Q ss_pred CCceecce-EEEeecCCCccceEEEE------------eceee-cccccc-ccceeeecccchhcc---cccc-------
Q psy5495 1 MSWYCGGG-FLLIGNNKGRTGVFGIF------------NNTYN-MYLEFE-YPKIVNEYERKYATG---CFSD------- 55 (273)
Q Consensus 1 ~~~~~gd~-~~l~g~d~gkqg~v~~~------------n~~~~-~~~~~~-~~~~~~~~e~pl~~~---~l~d------- 55 (273)
|++|+||+ |||+||||||||.|+|| |+||| +|.+++ |+||++.|||||-+. -|+|
T Consensus 71 w~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~d~q~t 150 (236)
T KOG1708|consen 71 WHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPEDDQPT 150 (236)
T ss_pred eeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECccccCCc
Confidence 57899999 99999999999999999 99999 999999 999999999999664 7888
Q ss_pred ---------------------------------------cccCCCCChhhhhhhhcccccccchHHHHHHhcChhhh-hh
Q psy5495 56 ---------------------------------------IENEDKDTKEQDVLAVTYQPKLSTFEMDIMEEHKIEVL-FL 95 (273)
Q Consensus 56 ---------------------------------------~e~~~kdt~~~~~~~~t~~p~l~tfe~~ime~mgI~~~-~~ 95 (273)
+|.++|||++++|+|+||+|+|+||||||||+|||+|. --
T Consensus 151 e~~wr~~e~GekVRvstrSG~iIpipe~~t~dy~~pe~yiE~e~KdTp~~av~erTy~pkl~tfe~eimeemgikeertp 230 (236)
T KOG1708|consen 151 EVEWRFTEDGEKVRVSTRSGRIIPIPEKWTADYIKPELYIEAEDKDTPQVAVLERTYVPKLKTFEEEIMEEMGIKEERTP 230 (236)
T ss_pred eeeEEEcCCCcEEEEEecccccccCcccccccccCchheeecccCCCcHhhhhhhhcchhHHHHHHHHHHHhCccccccc
Confidence 78877999999999999999999999999999999998 66
Q ss_pred cceee
Q psy5495 96 GQVYH 100 (273)
Q Consensus 96 ~~v~~ 100 (273)
..+||
T Consensus 231 kk~yw 235 (236)
T KOG1708|consen 231 KKVYW 235 (236)
T ss_pred ccccc
Confidence 77887
No 5
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.7e-29 Score=204.92 Aligned_cols=97 Identities=38% Similarity=0.679 Sum_probs=91.8
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCC---C--CceEEEeeecccCCCeeeeCC-CCCC
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGD---S--QFIIKQEAPLLVTNEVALVDP-SDRM 225 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~---~--Ggii~~EaPIhvtSNV~LVdP-~~~K 225 (273)
.|+|++||+|.||+|+|||++|+|++|++++ |+|||+|+.++|.++ + ||++++|+|||+ |||||+|| .+++
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~-SnV~i~~~~~~~~ 78 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHI-SNVAIIDPNKTGK 78 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccH-HHeEEeccccCCC
Confidence 5899999999999999999999999999998 999999999999982 2 999999999999 99999999 7999
Q ss_pred ceeEEEEEecCCcEEEEEccCCcccC
Q psy5495 226 GCQVEWRYTEAGDRVRVSKRSGRIIP 251 (273)
Q Consensus 226 ptrV~~r~~edGkKVRvskksG~iIP 251 (273)
++|++|++.++|+++|++++||+.|.
T Consensus 79 ~~Rv~~~~~~~~kkvr~~Kk~g~~i~ 104 (104)
T COG0198 79 PTRVGYKVEEDGKKVRVAKKSGEVID 104 (104)
T ss_pred cceEEEEEecCCcEEEEEeccCcccC
Confidence 99999999889999999999999873
No 6
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.90 E-value=3.2e-24 Score=167.62 Aligned_cols=72 Identities=35% Similarity=0.518 Sum_probs=68.2
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCCC-----CceEEEeeecccCCCeeeeCCCCC
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDS-----QFIIKQEAPLLVTNEVALVDPSDR 224 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~~-----Ggii~~EaPIhvtSNV~LVdP~~~ 224 (273)
.++|++||+|+||+|+||||+|+|++|++++++|+|||+|++++|++++ |+++++|+|||+ |||+|+||+|+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~-SnV~lvdp~~~ 82 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHS-SNVMLYNEESN 82 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCH-HHEEEeCcccC
Confidence 5799999999999999999999999999999999999999999999742 999999999999 99999999875
No 7
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.88 E-value=9.9e-23 Score=156.98 Aligned_cols=67 Identities=36% Similarity=0.560 Sum_probs=63.6
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCCC-----CceEEEeeecccCCCeeee
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDS-----QFIIKQEAPLLVTNEVALV 219 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~~-----Ggii~~EaPIhvtSNV~LV 219 (273)
.++|++||+|+||+|+||||+|+|++|++++++|+|||+|++++|++++ |+++++|+|||+ |||+|+
T Consensus 4 ~~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~-SnV~l~ 75 (76)
T PRK12281 4 KLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHI-SNVKKV 75 (76)
T ss_pred cccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCH-HHceec
Confidence 5799999999999999999999999999999999999999999999642 999999999999 999996
No 8
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.79 E-value=2.1e-19 Score=149.34 Aligned_cols=72 Identities=21% Similarity=0.320 Sum_probs=64.8
Q ss_pred CcccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCCCCceEEEeeecccCCCeeeeCCCCCCcee
Q psy5495 150 IKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQFIIKQEAPLLVTNEVALVDPSDRMGCQ 228 (273)
Q Consensus 150 i~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~~Ggii~~EaPIhvtSNV~LVdP~~~Kptr 228 (273)
|+.|+|++||.|+|++|+|||++|+|++|++++++|+|||||+.+. .| .++|+|||+ |||+|+|+..+...|
T Consensus 41 ir~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~----~G--~~~e~pIh~-SNV~l~~l~l~~~~R 112 (120)
T PRK01191 41 IRSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA----DG--TEVPRPIHP-SNVMITKLDLSDERR 112 (120)
T ss_pred CccceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC----CC--eEEEcccch-hHeEEEeCccCCHHH
Confidence 4689999999999999999999999999999999999999999873 46 699999999 999999997654433
No 9
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.77 E-value=6.6e-19 Score=150.15 Aligned_cols=70 Identities=14% Similarity=0.236 Sum_probs=64.6
Q ss_pred CcccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCCCCceEEEeeecccCCCeeeeCCCCCCc
Q psy5495 150 IKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQFIIKQEAPLLVTNEVALVDPSDRMG 226 (273)
Q Consensus 150 i~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~~Ggii~~EaPIhvtSNV~LVdP~~~Kp 226 (273)
++.|+|++||.|+||+|+|||++|+|++|++++++|+|||||+.++|.+ ..|+|||+ |||+|+|+..+..
T Consensus 42 ~Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk------~~e~PIh~-SNV~iv~l~l~~~ 111 (143)
T PTZ00194 42 VRSMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGE------PVQIGIHP-SNVIITKLKLNKD 111 (143)
T ss_pred CccceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCC------EeecCcCc-hheEEEccccCch
Confidence 4689999999999999999999999999999999999999999988643 47999999 9999999987766
No 10
>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=99.73 E-value=7.4e-18 Score=138.98 Aligned_cols=70 Identities=21% Similarity=0.271 Sum_probs=63.9
Q ss_pred CcccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeEEeecCCCCceEEEeeecccCCCeeeeCCCCCCc
Q psy5495 150 IKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTYLKKMGDSQFIIKQEAPLLVTNEVALVDPSDRMG 226 (273)
Q Consensus 150 i~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~~k~v~~~Ggii~~EaPIhvtSNV~LVdP~~~Kp 226 (273)
++.++|++||+|+||+|+|||++|+|++|++++++|+|||||+.+ ++| .+.|+|||+ |||+|+|...+..
T Consensus 37 ~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~~G--~~~e~pIh~-SnV~l~~l~l~~~ 106 (114)
T TIGR01080 37 KRALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----VNG--TEVPVPIHP-SNVMITKLNLDDE 106 (114)
T ss_pred cccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----CCC--eEEEeeech-HHeEEEeccCChH
Confidence 468899999999999999999999999999999999999999987 346 789999999 9999999876654
No 11
>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=98.56 E-value=1.2e-07 Score=61.70 Aligned_cols=32 Identities=38% Similarity=0.526 Sum_probs=30.8
Q ss_pred cCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 157 KGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 157 kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
+||.|.|++|+++|+.|+|++|++++++|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999999999986
No 12
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=98.55 E-value=8e-08 Score=74.38 Aligned_cols=51 Identities=16% Similarity=0.066 Sum_probs=43.4
Q ss_pred CCceecce-EEEeecCCCccceEEEE------------eceee-ccccccc-cceeeecccchhcc
Q psy5495 1 MSWYCGGG-FLLIGNNKGRTGVFGIF------------NNTYN-MYLEFEY-PKIVNEYERKYATG 51 (273)
Q Consensus 1 ~~~~~gd~-~~l~g~d~gkqg~v~~~------------n~~~~-~~~~~~~-~~~~~~~e~pl~~~ 51 (273)
|.+.+||+ +||.|+|+||+|+|.+| |.+.+ +..+.+. .|.++..|+||-+.
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~S 70 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHIS 70 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHH
Confidence 56789999 99999999999999999 77666 6556556 58999999999764
No 13
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=98.53 E-value=9.2e-08 Score=75.10 Aligned_cols=58 Identities=16% Similarity=0.214 Sum_probs=46.8
Q ss_pred CCceecce-EEEeecCCCccceEEEE------------eceee-ccc-cccccceeeecccchhcc--ccccccc
Q psy5495 1 MSWYCGGG-FLLIGNNKGRTGVFGIF------------NNTYN-MYL-EFEYPKIVNEYERKYATG--CFSDIEN 58 (273)
Q Consensus 1 ~~~~~gd~-~~l~g~d~gkqg~v~~~------------n~~~~-~~~-~~~~~~~~~~~e~pl~~~--~l~d~e~ 58 (273)
|.+++||+ +||.|+|+||+|+|.+| |++.+ +.. .....|.++..|+||-+. +|+|...
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvdp~~ 81 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEES 81 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCccc
Confidence 56899999 99999999999999999 55444 432 246678999999999885 8888543
No 14
>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=98.38 E-value=3.8e-07 Score=74.34 Aligned_cols=58 Identities=17% Similarity=0.068 Sum_probs=46.2
Q ss_pred CCceecce-EEEeecCCCccceEEEE------------eceee---ccccccccceeeecccchhcc--ccccccc
Q psy5495 1 MSWYCGGG-FLLIGNNKGRTGVFGIF------------NNTYN---MYLEFEYPKIVNEYERKYATG--CFSDIEN 58 (273)
Q Consensus 1 ~~~~~gd~-~~l~g~d~gkqg~v~~~------------n~~~~---~~~~~~~~~~~~~~e~pl~~~--~l~d~e~ 58 (273)
|.-++||+ +||.|+|+||+|+|.+| |..-+ -.......|.++..|+||-+. +|+|...
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~ 77 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKT 77 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcC
Confidence 45689999 99999999999999999 54333 233344479999999999986 9999655
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=98.19 E-value=2.2e-06 Score=69.86 Aligned_cols=58 Identities=17% Similarity=0.120 Sum_probs=44.9
Q ss_pred CCceecce-EEEeecCCCccceEEEE------------eceee-ccc-cccccceeeecccchhcc--ccccccc
Q psy5495 1 MSWYCGGG-FLLIGNNKGRTGVFGIF------------NNTYN-MYL-EFEYPKIVNEYERKYATG--CFSDIEN 58 (273)
Q Consensus 1 ~~~~~gd~-~~l~g~d~gkqg~v~~~------------n~~~~-~~~-~~~~~~~~~~~e~pl~~~--~l~d~e~ 58 (273)
|..++||+ +||.|+|+||+|+|.+| |..-+ +.. ..+..|.++..|+|+-+. .|+|...
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~ 77 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKT 77 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcC
Confidence 34579999 99999999999999999 43322 211 125679999999999885 8888655
No 16
>KOG3401|consensus
Probab=97.82 E-value=1.7e-05 Score=68.38 Aligned_cols=66 Identities=18% Similarity=0.290 Sum_probs=57.0
Q ss_pred CcccceecCCeEEEeecCCCC-ceeEEEEEEccCCEEEEcCeeeEEeecCCCCceEEEeeecccCCCeeeeCCC
Q psy5495 150 IKDWSIFKGDRVEILVGKDKG-KQGYVIQIFQEINSVIVEGLNTYLKKMGDSQFIIKQEAPLLVTNEVALVDPS 222 (273)
Q Consensus 150 i~~w~I~kGD~V~VI~GkDKG-K~GkV~~V~r~~n~ViVEGvN~~~k~v~~~Ggii~~EaPIhvtSNV~LVdP~ 222 (273)
++.++|+++|.|.|..|.++| ++|+|++|++++.-+.+|.|-..+ .+| ....+|||+ |.|.+..|.
T Consensus 44 vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK----~nG--t~v~vgihP-sK~~iTkl~ 110 (145)
T KOG3401|consen 44 VRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREK----ANG--TTVPVGIHP-SKVVITKLK 110 (145)
T ss_pred ccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEee----ccC--cccccccCc-cceeecccc
Confidence 358999999999999999999 999999999999999999865543 246 367899999 999998764
No 17
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.45 E-value=0.0002 Score=43.89 Aligned_cols=26 Identities=35% Similarity=0.505 Sum_probs=24.3
Q ss_pred eecCCeEEEeecCCCCceeEEEEEEc
Q psy5495 155 IFKGDRVEILVGKDKGKQGYVIQIFQ 180 (273)
Q Consensus 155 I~kGD~V~VI~GkDKGK~GkV~~V~r 180 (273)
+..||.|.|+.|+++|+.|.|++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57899999999999999999999975
No 18
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=97.27 E-value=0.00034 Score=57.51 Aligned_cols=56 Identities=13% Similarity=0.029 Sum_probs=43.0
Q ss_pred Cceecce-EEEeecCCCccceEEEEece----------ee-cc-ccccccceeeecccchhcc--cccccc
Q psy5495 2 SWYCGGG-FLLIGNNKGRTGVFGIFNNT----------YN-MY-LEFEYPKIVNEYERKYATG--CFSDIE 57 (273)
Q Consensus 2 ~~~~gd~-~~l~g~d~gkqg~v~~~n~~----------~~-~~-~~~~~~~~~~~~e~pl~~~--~l~d~e 57 (273)
.-.+||+ .||+|+|+||+|+|++||.+ =+ .- ......|-.|.-||||-+. +|+|.+
T Consensus 4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~~ 74 (104)
T COG0198 4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKKVVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDPN 74 (104)
T ss_pred ceecCCEEEEEecCCCCcceEEEEEecCeEEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEeccc
Confidence 3468999 99999999999999999544 11 11 1344558899999999885 888864
No 19
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=96.52 E-value=0.0024 Score=53.78 Aligned_cols=52 Identities=13% Similarity=0.119 Sum_probs=36.8
Q ss_pred eecce-EEEeecCCCccceEEEEece-ee-----ccccccccceeeecccchhcc--ccccccc
Q psy5495 4 YCGGG-FLLIGNNKGRTGVFGIFNNT-YN-----MYLEFEYPKIVNEYERKYATG--CFSDIEN 58 (273)
Q Consensus 4 ~~gd~-~~l~g~d~gkqg~v~~~n~~-~~-----~~~~~~~~~~~~~~e~pl~~~--~l~d~e~ 58 (273)
-+||. +|++|+|+|++|+|++|+.. .+ ++..+. .| +.-|+|+-.. +|+|..-
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~-~G--~~~e~pIh~SNV~l~~l~l 107 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA-DG--TEVPRPIHPSNVMITKLDL 107 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC-CC--eEEEcccchhHeEEEeCcc
Confidence 47999 99999999999999999322 11 222221 46 6899999774 7766443
No 20
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=96.46 E-value=0.0077 Score=51.48 Aligned_cols=41 Identities=32% Similarity=0.396 Sum_probs=36.6
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeeeE
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNTY 193 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~~ 193 (273)
..+..||.|.|+.|+++|-.|.|.+++.+++.+.|+-++..
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~ 133 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAA 133 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCc
Confidence 35889999999999999999999999999999998866653
No 21
>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=96.37 E-value=0.0058 Score=51.11 Aligned_cols=38 Identities=37% Similarity=0.479 Sum_probs=34.5
Q ss_pred eecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeee
Q psy5495 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNT 192 (273)
Q Consensus 155 I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~ 192 (273)
+..||.|.|+.|+.+|-.|.|.+++..++.|.|+-++.
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~ 124 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEA 124 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEc
Confidence 78999999999999999999999998888898886654
No 22
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=96.08 E-value=0.0094 Score=51.03 Aligned_cols=36 Identities=19% Similarity=0.123 Sum_probs=32.6
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-.+.+||+|.|++|+.+|-.|.|.++++.++++.|.
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~ 160 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL 160 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE
Confidence 457899999999999999999999999888888776
No 23
>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=95.96 E-value=0.011 Score=50.35 Aligned_cols=36 Identities=19% Similarity=0.131 Sum_probs=32.3
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-.+..||+|.|+.|+.+|-.|.|.++++.++++.|.
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 447899999999999999999999999877788776
No 24
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=95.76 E-value=0.015 Score=51.53 Aligned_cols=40 Identities=25% Similarity=0.204 Sum_probs=36.1
Q ss_pred cCcccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 149 PIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 149 Pi~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
|-..-.|..||.|.|++|+++|-.|+|.+|+.+++++.|+
T Consensus 118 ~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~ 157 (178)
T COG0250 118 KKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVE 157 (178)
T ss_pred CcccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEE
Confidence 3346788999999999999999999999999999998887
No 25
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=95.61 E-value=0.0085 Score=51.87 Aligned_cols=52 Identities=12% Similarity=0.132 Sum_probs=34.1
Q ss_pred eecce-EEEeecCCCccceEEEEece-ee-----ccccccccceeeecccchhcc--ccccccc
Q psy5495 4 YCGGG-FLLIGNNKGRTGVFGIFNNT-YN-----MYLEFEYPKIVNEYERKYATG--CFSDIEN 58 (273)
Q Consensus 4 ~~gd~-~~l~g~d~gkqg~v~~~n~~-~~-----~~~~~~~~~~~~~~e~pl~~~--~l~d~e~ 58 (273)
-+||. +|+.|+|+|++|+|++|+.. ++ ++..+..- -+-|+|+-.. .|++.+.
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~g---k~~e~PIh~SNV~iv~l~l 108 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANG---EPVQIGIHPSNVIITKLKL 108 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCC---CEeecCcCchheEEEcccc
Confidence 57999 99999999999999999322 11 22222111 1258898664 6665444
No 26
>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=94.73 E-value=0.018 Score=37.30 Aligned_cols=24 Identities=21% Similarity=0.342 Sum_probs=22.4
Q ss_pred ecce-EEEeecCCCccceEEEEece
Q psy5495 5 CGGG-FLLIGNNKGRTGVFGIFNNT 28 (273)
Q Consensus 5 ~gd~-~~l~g~d~gkqg~v~~~n~~ 28 (273)
.||. .|+.|+++|+.|+|.++|.|
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~ 25 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRS 25 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECC
Confidence 4899 99999999999999999877
No 27
>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=94.65 E-value=0.047 Score=45.81 Aligned_cols=35 Identities=20% Similarity=0.180 Sum_probs=29.4
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-.+..||+|.|+.|+.+|-.|.|.+++. .+++.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~ 141 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLL 141 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECC-CceEEEE
Confidence 3477999999999999999999999974 4566654
No 28
>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=94.42 E-value=0.03 Score=46.72 Aligned_cols=53 Identities=15% Similarity=0.160 Sum_probs=36.0
Q ss_pred ceecce-EEEeecCCCccceEEEEe-ceee-----ccccccccceeeecccchhcc--ccccccc
Q psy5495 3 WYCGGG-FLLIGNNKGRTGVFGIFN-NTYN-----MYLEFEYPKIVNEYERKYATG--CFSDIEN 58 (273)
Q Consensus 3 ~~~gd~-~~l~g~d~gkqg~v~~~n-~~~~-----~~~~~~~~~~~~~~e~pl~~~--~l~d~e~ 58 (273)
--+||. .|+.|+|+|++|+|..|+ ...+ +...+ -.| ++-|+|+-.. +|+|..-
T Consensus 42 IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k-~~G--~~~e~pIh~SnV~l~~l~l 103 (114)
T TIGR01080 42 VRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK-VNG--TEVPVPIHPSNVMITKLNL 103 (114)
T ss_pred eecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC-CCC--eEEEeeechHHeEEEeccC
Confidence 458999 999999999999999993 2222 12111 125 6889997554 6666433
No 29
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=93.98 E-value=0.076 Score=45.04 Aligned_cols=33 Identities=24% Similarity=0.101 Sum_probs=28.2
Q ss_pred eecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 155 I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
+.+||+|.|+.|+.+|-.|.|.+++ ..+++.|.
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 6799999999999999999999998 45565543
No 30
>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=93.84 E-value=0.096 Score=49.28 Aligned_cols=37 Identities=35% Similarity=0.293 Sum_probs=33.2
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
...+..||.|.|+.|+++|-.|.|.+++.+++++.|.
T Consensus 203 ~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 203 LSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred ccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 3457899999999999999999999999888888876
No 31
>PRK04333 50S ribosomal protein L14e; Validated
Probab=91.83 E-value=0.33 Score=38.49 Aligned_cols=37 Identities=24% Similarity=0.402 Sum_probs=32.1
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCee
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLN 191 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN 191 (273)
.+..|-.|.+++|+|+|+...|+.+.. .|+|.|.|-.
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~~ 39 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGPS 39 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECCC
Confidence 467899999999999999999999975 4889998763
No 32
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=86.58 E-value=0.85 Score=27.50 Aligned_cols=25 Identities=20% Similarity=0.306 Sum_probs=21.8
Q ss_pred ceecce-EEEeecCCCccceEEEEec
Q psy5495 3 WYCGGG-FLLIGNNKGRTGVFGIFNN 27 (273)
Q Consensus 3 ~~~gd~-~~l~g~d~gkqg~v~~~n~ 27 (273)
+-.||. .|+.|..+|++|.|..+|-
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 346999 9999999999999998863
No 33
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=84.55 E-value=1.9 Score=36.98 Aligned_cols=34 Identities=29% Similarity=0.455 Sum_probs=29.6
Q ss_pred ecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCe
Q psy5495 156 FKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGL 190 (273)
Q Consensus 156 ~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGv 190 (273)
-.|=.|.|..|+++||...|..|+- .|+|+|+|=
T Consensus 9 EiGRVvli~~Gp~~GKL~vIVDIID-~nRvLVDGP 42 (130)
T PTZ00065 9 EPGRLCLIQYGPDAGKLCFIVDIVT-PTRVLVDGA 42 (130)
T ss_pred eeceEEEEecCCCCCCEEEEEEEEc-CCeEEEeCC
Confidence 3577788889999999999999985 589999986
No 34
>KOG1999|consensus
Probab=84.47 E-value=1 Score=49.19 Aligned_cols=30 Identities=27% Similarity=0.488 Sum_probs=27.0
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEcc
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQE 181 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~ 181 (273)
.-.|..||-|.||+|+++|.+|.|++|.+.
T Consensus 457 rKyF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 457 RKYFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hhhccCCCeEEEEeccccCCcceEEEEeCC
Confidence 346889999999999999999999999874
No 35
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=78.54 E-value=3.1 Score=35.91 Aligned_cols=41 Identities=24% Similarity=0.492 Sum_probs=35.0
Q ss_pred eecCCeEEEeecCCCCceeEEEEEEccC------CEEEEcCeeeEEe
Q psy5495 155 IFKGDRVEILVGKDKGKQGYVIQIFQEI------NSVIVEGLNTYLK 195 (273)
Q Consensus 155 I~kGD~V~VI~GkDKGK~GkV~~V~r~~------n~ViVEGvN~~~k 195 (273)
+++|-.|.||+|+..|+...|++.+.+. +.++|-|+...-+
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~ 51 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPK 51 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccch
Confidence 5688899999999999999999988765 5799999887533
No 36
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=75.70 E-value=4.3 Score=34.59 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=31.3
Q ss_pred eecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCee
Q psy5495 155 IFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLN 191 (273)
Q Consensus 155 I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN 191 (273)
+..|=.|.|++|++.||...|++++-++ .|++-|--
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~ 40 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPK 40 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCc
Confidence 5688899999999999999999998775 89888743
No 37
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=65.55 E-value=4.8 Score=41.42 Aligned_cols=29 Identities=31% Similarity=0.421 Sum_probs=26.1
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccC
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEI 182 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~ 182 (273)
.+.+||.|.||.|+.++.+|.|..|+.+.
T Consensus 139 ~f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 139 GFYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred ccccCCeEEEeccccccccceEEEecCce
Confidence 45699999999999999999999998764
No 38
>PRK04313 30S ribosomal protein S4e; Validated
Probab=63.81 E-value=8.5 Score=36.03 Aligned_cols=39 Identities=26% Similarity=0.254 Sum_probs=33.2
Q ss_pred cccceecCCeEEEeecCCCCceeEEEEEEccC----CEEEEcC
Q psy5495 151 KDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI----NSVIVEG 189 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~----n~ViVEG 189 (273)
...++..|-.|.|+.|+.-|.+|+|.++.+.. |.|.|++
T Consensus 168 ~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d 210 (237)
T PRK04313 168 DHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED 210 (237)
T ss_pred EEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc
Confidence 47889999999999999999999999997444 6677774
No 39
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=60.04 E-value=14 Score=30.89 Aligned_cols=31 Identities=29% Similarity=0.442 Sum_probs=26.1
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
.+++||+|.-+.| -.|+|.+|..+.+.|.++
T Consensus 36 sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECCC----cEEEEEEEecCCCEEEEE
Confidence 6789999987665 699999998877888886
No 40
>KOG1999|consensus
Probab=57.96 E-value=7.3 Score=42.92 Aligned_cols=29 Identities=34% Similarity=0.433 Sum_probs=26.1
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEcc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQE 181 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~ 181 (273)
-.|-+||.|+|+.|..+|-+|+|..|+-.
T Consensus 406 ~~F~~GD~VeV~~Gel~glkG~ve~vdg~ 434 (1024)
T KOG1999|consen 406 HLFSPGDAVEVIVGELKGLKGKVESVDGT 434 (1024)
T ss_pred cccCCCCeEEEeeeeeccceeEEEeccCc
Confidence 34889999999999999999999999754
No 41
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=57.82 E-value=20 Score=26.96 Aligned_cols=27 Identities=41% Similarity=0.605 Sum_probs=22.2
Q ss_pred ecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 156 FKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 156 ~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
..||.++. -+|-+|+|.+|. .|.|+|+
T Consensus 5 ~vGdiIef----k~g~~G~V~kv~--eNSVIVd 31 (57)
T PF09953_consen 5 KVGDIIEF----KDGFTGIVEKVY--ENSVIVD 31 (57)
T ss_pred ccCcEEEE----cCCcEEEEEEEe--cCcEEEE
Confidence 46999986 358999999998 5789998
No 42
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=52.67 E-value=31 Score=25.47 Aligned_cols=33 Identities=27% Similarity=0.299 Sum_probs=20.1
Q ss_pred eecCCeEEEeecC--CCC--ceeEEEEEEccCCEEEEc
Q psy5495 155 IFKGDRVEILVGK--DKG--KQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 155 I~kGD~V~VI~Gk--DKG--K~GkV~~V~r~~n~ViVE 188 (273)
|++||.|+|.+-. ..| -.|+|++...+. ++.|+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~ 37 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVE 37 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEE
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEE
Confidence 6899999999833 123 468999998774 66665
No 43
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=49.28 E-value=24 Score=28.81 Aligned_cols=26 Identities=31% Similarity=0.339 Sum_probs=21.4
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccC
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEI 182 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~ 182 (273)
-.+++||+|.-+.| -.|+|.+|..+.
T Consensus 42 ~sL~kGD~VvT~gG----i~G~V~~v~d~~ 67 (97)
T COG1862 42 NSLKKGDEVVTIGG----IVGTVTKVGDDT 67 (97)
T ss_pred HhccCCCEEEEcCC----eEEEEEEEecCc
Confidence 36789999988775 699999998765
No 44
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=49.02 E-value=26 Score=28.73 Aligned_cols=30 Identities=37% Similarity=0.399 Sum_probs=24.6
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-.+++||+|.-.+| -.|+|.+|+. +.|.||
T Consensus 51 ~~Lk~Gd~VvT~gG----i~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 51 SSLAKGDEVVTNGG----IIGKVTKVSE--DFVIIE 80 (106)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 47889999988876 6999999965 677775
No 45
>PLN00036 40S ribosomal protein S4; Provisional
Probab=45.06 E-value=31 Score=32.83 Aligned_cols=38 Identities=16% Similarity=0.203 Sum_probs=31.3
Q ss_pred cccceecCCeEEEeecCCCCceeEEEEEEccC---CEEEEc
Q psy5495 151 KDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI---NSVIVE 188 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~---n~ViVE 188 (273)
...++..|-.|.|..|+.-|.+|+|.++.... |.|.|+
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~ 211 (261)
T PLN00036 171 DFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVK 211 (261)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 47899999999999999999999999998433 345555
No 46
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=44.41 E-value=39 Score=25.08 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=30.1
Q ss_pred eecCCeEEEeecC--CCCceeEEEEEEccCCEEEEcCeeeEE
Q psy5495 155 IFKGDRVEILVGK--DKGKQGYVIQIFQEINSVIVEGLNTYL 194 (273)
Q Consensus 155 I~kGD~V~VI~Gk--DKGK~GkV~~V~r~~n~ViVEGvN~~~ 194 (273)
|.+|-.|.|+.-. .-|-+|.|.+|...+--|+.||-|.-+
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdK 43 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDK 43 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceE
Confidence 6789999999875 679999999999999899999988854
No 47
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=44.02 E-value=1.2e+02 Score=27.39 Aligned_cols=94 Identities=17% Similarity=0.209 Sum_probs=54.1
Q ss_pred eeecCCC--CCCcceeecCCCCCcccCCCCCCChhhh-----hcCCCc-----cc--------------cCCCCCcccCc
Q psy5495 98 VYHVYPK--GPQYTVVDQGKDSDFDFSTDRPWEVPFL-----ARNRPW-----EK--------------NKKKIPIEPIK 151 (273)
Q Consensus 98 v~~~~p~--~~~y~~~~~~~~~~y~~~~~rPwt~~~~-----~~n~p~-----~~--------------r~~kv~vePi~ 151 (273)
-||+.+. .+.........-..|-.+...||+.+|- +...|. .. .......+| .
T Consensus 12 ~YW~~~~~~~~~~~g~~~~~g~~~~~~~~~pWSAaFISwVMr~AG~~~~f~~s~~H~~yi~~a~~~~~~~~~~~~~~~-~ 90 (183)
T PF10030_consen 12 EYWQDAGTLEQRWTGKDCSSGTFYSEGVDEPWSAAFISWVMRKAGVPERFPYSASHSTYINAAIRDGYSPAPFRARDP-A 90 (183)
T ss_pred HHhccCCCcccCccCcccccccccCCCCCCchhHHHHHHHHHHcCCCCCCCCCchHHHHHHHHHhcccccccccccCc-C
Confidence 3885544 4444444332334466777799999993 233332 00 111223333 3
Q ss_pred ccceecCCeEEEeecC--------------CCCceeEEEEEEc-cCCEEEEcCeee
Q psy5495 152 DWSIFKGDRVEILVGK--------------DKGKQGYVIQIFQ-EINSVIVEGLNT 192 (273)
Q Consensus 152 ~w~I~kGD~V~VI~Gk--------------DKGK~GkV~~V~r-~~n~ViVEGvN~ 192 (273)
...=+.||.|..-.|. ..-..+.|.+++. +.+.|.+=|=|+
T Consensus 91 ~y~P~~GDlIc~~R~~~~~~~~~~~~~~~~~~~HcdIVVa~~~~d~~~v~~IGGNv 146 (183)
T PF10030_consen 91 EYKPRPGDLICYDRGRSKTYDFASLPTSGGFPSHCDIVVAVNVVDGRTVTTIGGNV 146 (183)
T ss_pred CCCCCCCCEEEecCCCCcccchhhhccCCCCCCceeEEEeeccCCCCEEEEEcCcc
Confidence 5555899999999887 4456677777544 335666666565
No 48
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=43.48 E-value=38 Score=24.34 Aligned_cols=40 Identities=30% Similarity=0.389 Sum_probs=28.7
Q ss_pred ccceecCCeEEEeecCCCCce---eEEEEEEccCCE--EEEcCeee
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQ---GYVIQIFQEINS--VIVEGLNT 192 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~---GkV~~V~r~~n~--ViVEGvN~ 192 (273)
+=.|++||.|.++. .+.++. ++|.++....+. .-+.+.+.
T Consensus 10 sG~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~~~~~~~~~~~ 54 (74)
T PF03144_consen 10 SGTLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGDVQEAVAGANA 54 (74)
T ss_dssp ESEEETTEEEEEES-TTTTEECEEEEEEEEEETTEEESEEETTEEE
T ss_pred EeEEcCCCEEEECc-cCCcceeeeeecccccccccCccEeCCceee
Confidence 44689999999998 666666 999998877653 34444443
No 49
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=42.58 E-value=37 Score=32.04 Aligned_cols=39 Identities=26% Similarity=0.332 Sum_probs=32.9
Q ss_pred cccceecCCeEEEeecCCCCceeEEEEEEccC----CEEEEcC
Q psy5495 151 KDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI----NSVIVEG 189 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~----n~ViVEG 189 (273)
...++-.|-.|.|..|+.-|..|+|.+|.... |-|.+|+
T Consensus 170 ~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 170 EHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred eEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 47788899999999999999999999998653 5677765
No 50
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=42.23 E-value=38 Score=28.18 Aligned_cols=30 Identities=33% Similarity=0.410 Sum_probs=24.3
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-.+++||+|.-+.| -.|+|.+|.. +.|.||
T Consensus 37 ~~Lk~GD~VvT~gG----i~G~V~~I~d--~~v~le 66 (109)
T PRK05886 37 ESLQPGDRVHTTSG----LQATIVGITD--DTVDLE 66 (109)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 46889999987765 6899999974 678877
No 51
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=41.64 E-value=31 Score=33.02 Aligned_cols=38 Identities=16% Similarity=0.212 Sum_probs=31.1
Q ss_pred cccceecCCeEEEeecCCCCceeEEEEEEccC---CEEEEc
Q psy5495 151 KDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI---NSVIVE 188 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~---n~ViVE 188 (273)
...++..|-.|.|+.|+.-|.+|+|.++.... +.|.++
T Consensus 168 ~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~ 208 (273)
T PTZ00223 168 DLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLK 208 (273)
T ss_pred EEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 47889999999999999999999999995432 345555
No 52
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=38.57 E-value=22 Score=25.65 Aligned_cols=35 Identities=26% Similarity=0.425 Sum_probs=20.7
Q ss_pred CCCcccCcccceecCCeEEE-eec--CCCCceeEEEEE
Q psy5495 144 KIPIEPIKDWSIFKGDRVEI-LVG--KDKGKQGYVIQI 178 (273)
Q Consensus 144 kv~vePi~~w~I~kGD~V~V-I~G--kDKGK~GkV~~V 178 (273)
.+||.|-.--.-.-||+|.| +.. +.+...|+|.+|
T Consensus 21 DifIp~~~l~~A~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 21 DIFIPPRNLNGAMDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp EEEE-HHHHTTS-TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CEEECHHHHCCCCCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 45664433446678999998 454 456678888876
No 53
>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=38.36 E-value=50 Score=25.92 Aligned_cols=30 Identities=37% Similarity=0.526 Sum_probs=23.8
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-.+++||+|.-.+| -.|+|.+|+. +.+.||
T Consensus 36 ~~L~~Gd~VvT~gG----i~G~V~~i~d--~~v~ve 65 (84)
T TIGR00739 36 ESLKKGDKVLTIGG----IIGTVTKIAE--NTIVIE 65 (84)
T ss_pred HhCCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 46889999988776 6899999975 466665
No 54
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=38.18 E-value=43 Score=31.89 Aligned_cols=38 Identities=18% Similarity=0.216 Sum_probs=30.5
Q ss_pred cccceecCCeEEEeecCCCCceeEEEEEEccC---CEEEEc
Q psy5495 151 KDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI---NSVIVE 188 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~---n~ViVE 188 (273)
...++..|-.|.|+.|+.-|.+|+|.++.... |.|.|+
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~ 211 (262)
T PTZ00118 171 EFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVK 211 (262)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEE
Confidence 47899999999999999999999998865443 344554
No 55
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=37.46 E-value=11 Score=29.30 Aligned_cols=30 Identities=33% Similarity=0.488 Sum_probs=0.5
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCCEEEEc
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVE 188 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVE 188 (273)
-++++||+|.-.+| -.|+|.++ +.+.|.||
T Consensus 35 ~~Lk~Gd~VvT~gG----i~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 35 ASLKPGDEVVTIGG----IYGTVVEI--DDDTVVLE 64 (82)
T ss_dssp G-----------------------------------
T ss_pred HcCCCCCEEEECCc----EEEEEEEE--eCCEEEEE
Confidence 47889999988876 58999999 55667776
No 56
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=36.97 E-value=52 Score=35.38 Aligned_cols=38 Identities=24% Similarity=0.248 Sum_probs=28.3
Q ss_pred cceecCCeEEEeecCCCCceeEEEEEEccCC-EEEEcCeeeE
Q psy5495 153 WSIFKGDRVEILVGKDKGKQGYVIQIFQEIN-SVIVEGLNTY 193 (273)
Q Consensus 153 w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n-~ViVEGvN~~ 193 (273)
..|+.||.|.|.+ -|+.|+|++|..+++ .|-+.|+.+.
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~~ 673 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGIMKMK 673 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEEE
Confidence 6689999999966 578999999975333 3555566664
No 57
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=32.43 E-value=40 Score=24.88 Aligned_cols=34 Identities=24% Similarity=0.144 Sum_probs=19.9
Q ss_pred CCCccccCCCCCcccCcccceecCCeEEEeecCCCCceeEEEE
Q psy5495 135 NRPWEKNKKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQ 177 (273)
Q Consensus 135 n~p~~~r~~kv~vePi~~w~I~kGD~V~VI~GkDKGK~GkV~~ 177 (273)
.+|+++|+ ...|++||.|.|---..--..|.|..
T Consensus 31 ~i~gK~r~---------~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 31 RIPGKFRK---------RIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp EE-HHHHT---------CC---TTEEEEEEESTTCTTEEEEEE
T ss_pred Eeccceee---------eEecCCCCEEEEEecccCCCeEEEEE
Confidence 45676444 45689999999985544466777754
No 58
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=31.73 E-value=45 Score=25.82 Aligned_cols=39 Identities=15% Similarity=-0.003 Sum_probs=27.6
Q ss_pred cCCCccccCCCCCcccCcccceecCCeEEE-eecCCCCceeEEEEEEccC
Q psy5495 134 RNRPWEKNKKKIPIEPIKDWSIFKGDRVEI-LVGKDKGKQGYVIQIFQEI 182 (273)
Q Consensus 134 ~n~p~~~r~~kv~vePi~~w~I~kGD~V~V-I~GkDKGK~GkV~~V~r~~ 182 (273)
-.+|++-|+ ...|++||.|.| ++.-| -..|.|+......
T Consensus 27 a~i~gK~rk---------~iwI~~GD~V~Ve~~~~d-~~kg~Iv~r~~~~ 66 (77)
T cd05793 27 CRIRGKMRK---------RVWINEGDIVLVAPWDFQ-DDKADIIYKYTPD 66 (77)
T ss_pred EEEchhhcc---------cEEEcCCCEEEEEecccc-CCEEEEEEEcCHH
Confidence 356776666 467889999999 56555 4578888776543
No 59
>KOG3344|consensus
Probab=31.43 E-value=14 Score=32.48 Aligned_cols=59 Identities=17% Similarity=0.044 Sum_probs=47.6
Q ss_pred cccccchHHHHHHhcChhhhhhcceeec------CCCCCCcceeecCCCCCcccCC---CCCCChhhhhc
Q psy5495 74 QPKLSTFEMDIMEEHKIEVLFLGQVYHV------YPKGPQYTVVDQGKDSDFDFST---DRPWEVPFLAR 134 (273)
Q Consensus 74 ~p~l~tfe~~ime~mgI~~~~~~~v~~~------~p~~~~y~~~~~~~~~~y~~~~---~rPwt~~~~~~ 134 (273)
+|-|.- +-.|..|.=..-+.+|+-|+ |+-+.+||...+..|..-+.++ +||++..++..
T Consensus 37 vpNL~v--ikaMQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~YLhLP~EiVpaTl~~~rP~~~rpr~~ 104 (150)
T KOG3344|consen 37 VPNLHV--IKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLREYLHLPPEIVPATLKRSRPETGRPRPP 104 (150)
T ss_pred CccHHH--HHHHHHHhhhhhHHhhhhhheeeeeechhHHHHHHHHhcCCcccccchhhccCCCCCCCCCC
Confidence 666653 45688888888888888776 6779999999999999999998 88988776543
No 60
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=31.22 E-value=94 Score=23.37 Aligned_cols=34 Identities=24% Similarity=0.308 Sum_probs=28.7
Q ss_pred ecCCeEEEe--ecCCCCceeEEEEEEccCCEEEEcC
Q psy5495 156 FKGDRVEIL--VGKDKGKQGYVIQIFQEINSVIVEG 189 (273)
Q Consensus 156 ~kGD~V~VI--~GkDKGK~GkV~~V~r~~n~ViVEG 189 (273)
..||.|... -|..|--.|+|.+|+-..+++++||
T Consensus 22 v~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 22 VTEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred EecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 467777664 5888888999999999999999986
No 61
>KOG3418|consensus
Probab=31.01 E-value=69 Score=27.91 Aligned_cols=39 Identities=23% Similarity=0.490 Sum_probs=32.2
Q ss_pred eecCCeEEEeecCCCCceeEEEEEEccC------CEEEEcCeeeE
Q psy5495 155 IFKGDRVEILVGKDKGKQGYVIQIFQEI------NSVIVEGLNTY 193 (273)
Q Consensus 155 I~kGD~V~VI~GkDKGK~GkV~~V~r~~------n~ViVEGvN~~ 193 (273)
+++|--|.|++|+..|+...|++-+-+. ..++|+|+-..
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ry 49 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRY 49 (136)
T ss_pred ccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhc
Confidence 5789999999999999999988877654 26888888763
No 62
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=29.85 E-value=73 Score=25.05 Aligned_cols=37 Identities=16% Similarity=0.141 Sum_probs=25.7
Q ss_pred cCCCccccCCCCCcccCcccceecCCeEEEeecCCCCceeEEEEE
Q psy5495 134 RNRPWEKNKKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQI 178 (273)
Q Consensus 134 ~n~p~~~r~~kv~vePi~~w~I~kGD~V~VI~GkDKGK~GkV~~V 178 (273)
.+.||+.|+ .+..|..||.|.|--=+.-=..|.|..=
T Consensus 34 ahI~GKmr~--------~~i~I~~GD~V~Ve~~~~d~~kg~I~~R 70 (75)
T COG0361 34 AHISGKMRK--------NRIRILPGDVVLVELSPYDLTKGRIVYR 70 (75)
T ss_pred EEccCcchh--------eeEEeCCCCEEEEEecccccccccEEEE
Confidence 456777777 5678889999999766555555555543
No 63
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=29.76 E-value=75 Score=26.85 Aligned_cols=28 Identities=21% Similarity=0.612 Sum_probs=21.4
Q ss_pred eCCCCCCceeEEEEEecCCcEEEEEccC
Q psy5495 219 VDPSDRMGCQVEWRYTEAGDRVRVSKRS 246 (273)
Q Consensus 219 VdP~~~KptrV~~r~~edGkKVRvskks 246 (273)
.+.++|-.+=+.|+++++|+++.+.++-
T Consensus 7 ~~~~~G~KtViey~~n~dGkkvKvtk~~ 34 (128)
T PF12353_consen 7 IPDEDGIKTVIEYKFNDDGKKVKVTKKI 34 (128)
T ss_pred ccCCCCcEEEEEEEECCCCCEEEEEEEE
Confidence 4446788899999999999887666543
No 64
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=29.46 E-value=62 Score=25.16 Aligned_cols=40 Identities=15% Similarity=0.115 Sum_probs=27.7
Q ss_pred cCCCccccCCCCCcccCcccceecCCeEEEeecCC-CCceeEEEEEEccC
Q psy5495 134 RNRPWEKNKKKIPIEPIKDWSIFKGDRVEILVGKD-KGKQGYVIQIFQEI 182 (273)
Q Consensus 134 ~n~p~~~r~~kv~vePi~~w~I~kGD~V~VI~GkD-KGK~GkV~~V~r~~ 182 (273)
-.+|++.|+ ..-|++||.|.|-.=.. .-..|.|+.+....
T Consensus 27 ~~i~gK~Rk---------~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 27 VSIPGKLRK---------NIWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred EEEchhhcc---------CEEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 456777777 36789999999965443 33577787776553
No 65
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=28.92 E-value=61 Score=25.42 Aligned_cols=40 Identities=18% Similarity=0.052 Sum_probs=26.1
Q ss_pred cCCCccccCCCCCcccCcccceecCCeEEEeecCCCCceeEEEEEEccC
Q psy5495 134 RNRPWEKNKKKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI 182 (273)
Q Consensus 134 ~n~p~~~r~~kv~vePi~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~ 182 (273)
-.+|++.|+ ...|++||.|.|=--..-=..|.|+.+..+.
T Consensus 32 a~ipgK~Rk---------~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 32 ARIPGKMRK---------KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred EEEchhhcc---------cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 456776666 4678899999996433223567777776543
No 66
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=28.61 E-value=18 Score=33.46 Aligned_cols=34 Identities=21% Similarity=0.337 Sum_probs=30.5
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEE
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSV 185 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~V 185 (273)
.+|.++||.|.-++|+-.||.-+|.....+.-.+
T Consensus 124 ~MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i 157 (237)
T COG3700 124 DMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI 157 (237)
T ss_pred HHHHhcCCeEEEEecCCCCcccccchhHHhhccc
Confidence 7999999999999999999999999998776443
No 67
>PF15269 zf-C2H2_7: Zinc-finger
Probab=27.79 E-value=39 Score=24.76 Aligned_cols=20 Identities=30% Similarity=0.489 Sum_probs=16.0
Q ss_pred cCCCCCCcceeecCCCCCcc
Q psy5495 101 VYPKGPQYTVVDQGKDSDFD 120 (273)
Q Consensus 101 ~~p~~~~y~~~~~~~~~~y~ 120 (273)
+.|++|.|+||--+.|-.|.
T Consensus 3 rkpkkphyiprp~gkp~~yk 22 (54)
T PF15269_consen 3 RKPKKPHYIPRPPGKPFKYK 22 (54)
T ss_pred CCCCCCCcCCCCCCCCccce
Confidence 56999999999887776664
No 68
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=27.59 E-value=1e+02 Score=24.15 Aligned_cols=29 Identities=28% Similarity=0.283 Sum_probs=24.2
Q ss_pred ceecCCeEEEeecC--CCCceeEEEEEEccC
Q psy5495 154 SIFKGDRVEILVGK--DKGKQGYVIQIFQEI 182 (273)
Q Consensus 154 ~I~kGD~V~VI~Gk--DKGK~GkV~~V~r~~ 182 (273)
.|.+||.|.|+.=. .-...|+|.+|+...
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC
Confidence 57899999999864 556789999999874
No 69
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=27.15 E-value=69 Score=21.59 Aligned_cols=17 Identities=35% Similarity=0.499 Sum_probs=13.1
Q ss_pred cccceecCCeEEEeecC
Q psy5495 151 KDWSIFKGDRVEILVGK 167 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~Gk 167 (273)
.+..|.+||.+.|+.=.
T Consensus 12 ~eLs~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 12 DELSFKKGDIIEVLEKS 28 (48)
T ss_dssp TBSEB-TTEEEEEEEES
T ss_pred CEEeEECCCEEEEEEec
Confidence 47899999999999643
No 70
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=27.04 E-value=93 Score=25.55 Aligned_cols=34 Identities=26% Similarity=0.434 Sum_probs=19.7
Q ss_pred cCcc--cceecCCeEEEee-cC---------CCCceeEEEEEEccC
Q psy5495 149 PIKD--WSIFKGDRVEILV-GK---------DKGKQGYVIQIFQEI 182 (273)
Q Consensus 149 Pi~~--w~I~kGD~V~VI~-Gk---------DKGK~GkV~~V~r~~ 182 (273)
|++. -.++.||.|-|.. |. +-||.|.|..|.+..
T Consensus 25 ~ls~~l~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~ 70 (99)
T PF01157_consen 25 PLSTYLQEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGA 70 (99)
T ss_dssp -CHHHH----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSC
T ss_pred cHHHHHHHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCc
Confidence 5542 2568999999874 22 779999999998765
No 71
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=26.96 E-value=1.1e+02 Score=21.58 Aligned_cols=30 Identities=30% Similarity=0.392 Sum_probs=20.5
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEE
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSV 185 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~V 185 (273)
.+..||.|.+- ..+ +-.|.|.+|.+.+|.+
T Consensus 37 ~~~VGD~V~~~-~~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 37 PPAVGDRVEFE-PED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCCCcEEEEE-ECC-CCcEEEEEEeccceEE
Confidence 35789999873 222 2357888999877743
No 72
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=26.50 E-value=3.2e+02 Score=21.48 Aligned_cols=61 Identities=23% Similarity=0.323 Sum_probs=40.2
Q ss_pred eeEEEEEEccCC-EEEEcCeeeEEeecCCCCceEEEeeecccCCCeeeeCCCC--CCceeEEEEEec
Q psy5495 172 QGYVIQIFQEIN-SVIVEGLNTYLKKMGDSQFIIKQEAPLLVTNEVALVDPSD--RMGCQVEWRYTE 235 (273)
Q Consensus 172 ~GkV~~V~r~~n-~ViVEGvN~~~k~v~~~Ggii~~EaPIhvtSNV~LVdP~~--~KptrV~~r~~e 235 (273)
.|+|+++++... +|..++=..+.-|++ |.+...-.=|.. .++-+|.+.. -+-.+|.||+..
T Consensus 10 ~g~V~e~L~~~~f~v~~edg~~~~ahI~--GKmr~~~i~I~~-GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 10 EGTVIEMLPNGRFRVELENGHERLAHIS--GKMRKNRIRILP-GDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred EEEEEEecCCCEEEEEecCCcEEEEEcc--CcchheeEEeCC-CCEEEEEecccccccccEEEEecC
Confidence 689999998652 566666555566665 444443566777 7888876654 345788899854
No 73
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=26.36 E-value=1.2e+02 Score=24.70 Aligned_cols=36 Identities=14% Similarity=0.318 Sum_probs=32.6
Q ss_pred cCCeEEEeecCCCCceeEEEEEEccCCEEEEcCeee
Q psy5495 157 KGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGLNT 192 (273)
Q Consensus 157 kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGvN~ 192 (273)
-|-+|-+++..+..-+|.+..|+.+.++|.+..+-.
T Consensus 7 IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~ 42 (96)
T PF12701_consen 7 IGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRS 42 (96)
T ss_dssp TTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEE
T ss_pred cCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeee
Confidence 588999999999999999999999999999986544
No 74
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=26.27 E-value=94 Score=24.83 Aligned_cols=34 Identities=21% Similarity=0.474 Sum_probs=25.4
Q ss_pred ccceecCCeEEEeecC------------CCCceeEEEEEE-ccCCEE
Q psy5495 152 DWSIFKGDRVEILVGK------------DKGKQGYVIQIF-QEINSV 185 (273)
Q Consensus 152 ~w~I~kGD~V~VI~Gk------------DKGK~GkV~~V~-r~~n~V 185 (273)
.+-+++||.|.|+.-. .-|..|.+.+|. ..++++
T Consensus 63 ~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~N~~s~k~ 109 (122)
T TIGR03170 63 PWLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVRNLSSGKI 109 (122)
T ss_pred ccEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEEECCCCCE
Confidence 5789999999998533 567888888887 355544
No 75
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=24.83 E-value=1.7e+02 Score=20.56 Aligned_cols=33 Identities=27% Similarity=0.377 Sum_probs=23.0
Q ss_pred ceecCCeEEEeecC-CCCceeEEEEEEccCCEEEE
Q psy5495 154 SIFKGDRVEILVGK-DKGKQGYVIQIFQEINSVIV 187 (273)
Q Consensus 154 ~I~kGD~V~VI~Gk-DKGK~GkV~~V~r~~n~ViV 187 (273)
.+++||.|.+..=. +.=-.|+|+++.. .++..|
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V 35 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLV 35 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEE
Confidence 57899999999632 2225699999987 344444
No 76
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.67 E-value=96 Score=28.22 Aligned_cols=34 Identities=26% Similarity=0.506 Sum_probs=26.0
Q ss_pred ccceecCCeEEEeecC------------CCCceeEEEEEE-ccCCEE
Q psy5495 152 DWSIFKGDRVEILVGK------------DKGKQGYVIQIF-QEINSV 185 (273)
Q Consensus 152 ~w~I~kGD~V~VI~Gk------------DKGK~GkV~~V~-r~~n~V 185 (273)
-|-|++||.|.|+... .-|..|...+|. ..++++
T Consensus 174 ~~~V~~G~~V~i~~~~g~~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~ 220 (235)
T PRK07018 174 AWVVCKGQTVSIIARGDGFSVKTEGEALNDGAVGQQIRVRNMASGQV 220 (235)
T ss_pred ccEeCCCCEEEEEEecCCEEEEEEEEEcCCCCCCCeEEEEECCCCCE
Confidence 6889999999998643 567788888887 555544
No 77
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=24.03 E-value=1.1e+02 Score=33.03 Aligned_cols=34 Identities=35% Similarity=0.487 Sum_probs=25.0
Q ss_pred ecCCeEEEeecCCCCceeEEEEEEccCCE--EEEcCeeeE
Q psy5495 156 FKGDRVEILVGKDKGKQGYVIQIFQEINS--VIVEGLNTY 193 (273)
Q Consensus 156 ~kGD~V~VI~GkDKGK~GkV~~V~r~~n~--ViVEGvN~~ 193 (273)
+.||.|.|.+ -|+.|+|++|.. ++. |-+.++.+.
T Consensus 626 ~~Gd~V~v~~---~~~~g~v~~i~~-~~~~~V~~g~~k~~ 661 (771)
T TIGR01069 626 KIGDKVRIRY---FGQKGKIVQILG-GNKWNVTVGGMRMK 661 (771)
T ss_pred CCCCEEEEcc---CCceEEEEEEcC-CCeEEEEECCEEEE
Confidence 7899999954 678999999975 343 455566663
No 78
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=23.71 E-value=1.1e+02 Score=25.07 Aligned_cols=39 Identities=28% Similarity=0.373 Sum_probs=27.7
Q ss_pred cCc-cc-ceecCCeEEEee-cC---------CCCceeEEEEEEccCCEEEE
Q psy5495 149 PIK-DW-SIFKGDRVEILV-GK---------DKGKQGYVIQIFQEINSVIV 187 (273)
Q Consensus 149 Pi~-~w-~I~kGD~V~VI~-Gk---------DKGK~GkV~~V~r~~n~ViV 187 (273)
|++ .+ .++.||.|-|.. |. +.|+.|+|..+....--|+|
T Consensus 27 ~ls~~l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v 77 (98)
T PRK04306 27 PLSRALQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEV 77 (98)
T ss_pred cHHHHHHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEE
Confidence 554 33 456799998874 32 67999999999877655555
No 79
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=23.47 E-value=1.1e+02 Score=23.44 Aligned_cols=28 Identities=25% Similarity=0.227 Sum_probs=23.0
Q ss_pred eecCCeEEEeecC--CCCceeEEEEEEccC
Q psy5495 155 IFKGDRVEILVGK--DKGKQGYVIQIFQEI 182 (273)
Q Consensus 155 I~kGD~V~VI~Gk--DKGK~GkV~~V~r~~ 182 (273)
|.+||.|.|+.=. .-...|+|.+|+...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 7899999999764 456789999999863
No 80
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=23.44 E-value=1.3e+02 Score=22.92 Aligned_cols=35 Identities=17% Similarity=0.178 Sum_probs=24.0
Q ss_pred cccceecCCeEEEeecCCCCceeEEEEEEccCCEE
Q psy5495 151 KDWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSV 185 (273)
Q Consensus 151 ~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~V 185 (273)
..=.|.+|+.|.|+.+..-=..|+|.++.+.++.|
T Consensus 23 ~~G~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~v 57 (84)
T cd03692 23 TDGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDV 57 (84)
T ss_pred EECEEeCCCEEEEEcCCCEEEEEEEEEEEEcCccc
Confidence 46678899999999874211467777777665543
No 81
>PRK02935 hypothetical protein; Provisional
Probab=23.42 E-value=41 Score=28.32 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=25.8
Q ss_pred CCCeeeeCCCCCCceeEEEEEecCCcEEEEEccCCcccCCCC
Q psy5495 213 TNEVALVDPSDRMGCQVEWRYTEAGDRVRVSKRSGRIIPIPM 254 (273)
Q Consensus 213 tSNV~LVdP~~~KptrV~~r~~edGkKVRvskksG~iIP~P~ 254 (273)
|+-|++.||+|+|+|++-=| +=.|--|++.+-.+.
T Consensus 66 tkavqV~CP~C~K~TKmLGr-------vD~CM~C~~PLTLd~ 100 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLGR-------VDACMHCNQPLTLDR 100 (110)
T ss_pred ccceeeECCCCCchhhhccc-------eeecCcCCCcCCcCc
Confidence 37899999999999987443 346777887765443
No 82
>KOG4315|consensus
Probab=22.95 E-value=36 Score=34.62 Aligned_cols=37 Identities=22% Similarity=0.298 Sum_probs=30.7
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcCe
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEGL 190 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEGv 190 (273)
.=.-|++|.|++|+.||+-|--++=++.+.+.+|.-+
T Consensus 393 pr~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~~ 429 (455)
T KOG4315|consen 393 PRRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRLV 429 (455)
T ss_pred ccccCceeEEEecccccchhhhhhhhhhhhhcceecc
Confidence 3357999999999999999999988888877776644
No 83
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.77 E-value=1.3e+02 Score=21.81 Aligned_cols=24 Identities=13% Similarity=0.180 Sum_probs=19.3
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEE
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIV 187 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViV 187 (273)
.++.||.|.+ +|+.+++++.+|.+
T Consensus 42 ~~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 42 TYKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred CcCCCCEEEE----------EEEEEeCCCCEEec
Confidence 4788998876 88999998877664
No 84
>PF11904 GPCR_chapero_1: GPCR-chaperone; InterPro: IPR021832 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 409 to 630 amino acids in length. This protein is found associated with PF00023 from PFAM. This protein has a conserved FPVK sequence motif.
Probab=22.64 E-value=51 Score=31.62 Aligned_cols=88 Identities=16% Similarity=0.284 Sum_probs=51.6
Q ss_pred CCceecce-EEEeecCCCccceEEEEeceee-ccccccccceeeecccchhc--ccccccccCCCCChhhhhhhhccccc
Q psy5495 1 MSWYCGGG-FLLIGNNKGRTGVFGIFNNTYN-MYLEFEYPKIVNEYERKYAT--GCFSDIENEDKDTKEQDVLAVTYQPK 76 (273)
Q Consensus 1 ~~~~~gd~-~~l~g~d~gkqg~v~~~n~~~~-~~~~~~~~~~~~~~e~pl~~--~~l~d~e~~~kdt~~~~~~~~t~~p~ 76 (273)
|+|-|||. .|..|.+.+-. .+..+|.-=+ +..... -+++++..- ..| ... +=-++.=|+..++|+|.
T Consensus 12 ~kwqRGd~S~iF~g~~~~~~-~l~~ldh~~k~~~~~~~-----~~~~~~~~~eV~~~--l~s-~i~~~~id~~~i~f~r~ 82 (307)
T PF11904_consen 12 MKWQRGDQSFIFKGDGSSAG-SLIELDHDKKEVYNELE-----EASEEEIDEEVDAL--LTS-PIVRTGIDTDKIEFERA 82 (307)
T ss_pred CceEeCceeEEEEcCCCCce-EEEEEECCCeEEEEEec-----ccccchhHHHHHHH--hcC-CcccccceeeEEEEEEe
Confidence 78999999 88888876654 7777754433 222111 113333211 122 122 23345567788999999
Q ss_pred ccchHHHHHHhcChhhhhhcceee
Q psy5495 77 LSTFEMDIMEEHKIEVLFLGQVYH 100 (273)
Q Consensus 77 l~tfe~~ime~mgI~~~~~~~v~~ 100 (273)
+-=|-.|-.|..| .+.++||=
T Consensus 83 ~gW~r~ek~E~Vg---~~~akvY~ 103 (307)
T PF11904_consen 83 WGWFRSEKTETVG---GWKAKVYE 103 (307)
T ss_pred ecccccccceeeC---CeeEEEEE
Confidence 4444777777776 55666653
No 85
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.46 E-value=1.1e+02 Score=26.11 Aligned_cols=33 Identities=12% Similarity=0.128 Sum_probs=25.4
Q ss_pred ccceecCCeEEEeecC------------CCCceeEEEEEE-ccCCE
Q psy5495 152 DWSIFKGDRVEILVGK------------DKGKQGYVIQIF-QEINS 184 (273)
Q Consensus 152 ~w~I~kGD~V~VI~Gk------------DKGK~GkV~~V~-r~~n~ 184 (273)
-|-|.+||.|.|++.. .-|..|...+|. ..+++
T Consensus 79 p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~G~~Gd~IrV~N~~S~r 124 (141)
T PRK12618 79 PAIVDRNQLVPLAYRLGGLEIRTEGRALSRGGVGDEIRVMNLSSRT 124 (141)
T ss_pred ccEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCC
Confidence 5889999999998643 678888888884 44444
No 86
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=22.00 E-value=84 Score=34.01 Aligned_cols=34 Identities=29% Similarity=0.536 Sum_probs=28.2
Q ss_pred ccceecCCeEEEeecCCCCceeEEEEEEccCCEEEEcC
Q psy5495 152 DWSIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIVEG 189 (273)
Q Consensus 152 ~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViVEG 189 (273)
.-.++.||.|.+++ |..|.|++|......+.|+-
T Consensus 610 ~~~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~~ 643 (753)
T COG1193 610 KRKLKLGDEVEVIT----GEPGAVVKIIAGILEALVQS 643 (753)
T ss_pred ccCceecceeEeec----CCccceeeeeccCceeEEec
Confidence 67889999999999 67889999997777766663
No 87
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=21.73 E-value=1.2e+02 Score=25.26 Aligned_cols=29 Identities=24% Similarity=0.244 Sum_probs=24.2
Q ss_pred cceecCCeEEEeecC--CCCceeEEEEEEcc
Q psy5495 153 WSIFKGDRVEILVGK--DKGKQGYVIQIFQE 181 (273)
Q Consensus 153 w~I~kGD~V~VI~Gk--DKGK~GkV~~V~r~ 181 (273)
.-+.+||.|.|+.=. .-...|+|.+|+..
T Consensus 38 ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 38 IGPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred cccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 468899999999864 45668999999987
No 88
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.38 E-value=1.5e+02 Score=21.00 Aligned_cols=24 Identities=17% Similarity=0.227 Sum_probs=17.8
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEE
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIV 187 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViV 187 (273)
.++.||.|.+ +|++++++++++.+
T Consensus 44 ~~~~G~~i~v----------~v~~~d~~~~~i~l 67 (70)
T cd05698 44 HFRVGQVVKV----------KVLSCDPEQQRLLL 67 (70)
T ss_pred cccCCCEEEE----------EEEEEcCCCCEEEE
Confidence 4778999988 56777777666654
No 89
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.10 E-value=1.4e+02 Score=21.15 Aligned_cols=24 Identities=13% Similarity=0.098 Sum_probs=18.1
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEE
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIV 187 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViV 187 (273)
.++.||.|.+ +|++++++++++.+
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 44 RFKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEec
Confidence 4788999988 67777777776654
No 90
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=20.98 E-value=1.6e+02 Score=24.35 Aligned_cols=44 Identities=27% Similarity=0.311 Sum_probs=30.6
Q ss_pred cCcc--cceecCCeEEEeec----------CCCCceeEEEEEEccCCEEEEcCeee
Q psy5495 149 PIKD--WSIFKGDRVEILVG----------KDKGKQGYVIQIFQEINSVIVEGLNT 192 (273)
Q Consensus 149 Pi~~--w~I~kGD~V~VI~G----------kDKGK~GkV~~V~r~~n~ViVEGvN~ 192 (273)
|++. -.+..||.|-|..- .+.|+.|+|.-+-...-.|.|..=|.
T Consensus 25 plsr~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k 80 (98)
T COG2139 25 PLSRYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNK 80 (98)
T ss_pred chhhHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCc
Confidence 5542 35778999998753 37899999998876665555554444
No 91
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=20.53 E-value=2.4e+02 Score=20.15 Aligned_cols=44 Identities=14% Similarity=0.071 Sum_probs=28.7
Q ss_pred CCCCcccCcccceecCCeEEEeecCCCCceeEEEEEEccC-CEEEEcCeee
Q psy5495 143 KKIPIEPIKDWSIFKGDRVEILVGKDKGKQGYVIQIFQEI-NSVIVEGLNT 192 (273)
Q Consensus 143 ~kv~vePi~~w~I~kGD~V~VI~GkDKGK~GkV~~V~r~~-n~ViVEGvN~ 192 (273)
+-+.++|... +..||.|.+.... ...|.++.... +.+.+...|-
T Consensus 18 d~lii~~~~~--~~~g~i~~~~~~~----~~~ikr~~~~~~~~~~L~s~N~ 62 (81)
T cd06529 18 DLVLVDPSDT--PRDGDIVVARLDG----ELTVKRLQRRGGGRLRLISDNP 62 (81)
T ss_pred CEEEEcCCCC--CCCCCEEEEEECC----EEEEEEEEECCCCcEEEEeCCC
Confidence 3455655443 7788888888643 45677777766 6677776664
No 92
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.29 E-value=1.8e+02 Score=19.96 Aligned_cols=24 Identities=29% Similarity=0.426 Sum_probs=17.4
Q ss_pred ceecCCeEEEeecCCCCceeEEEEEEccCCEEEE
Q psy5495 154 SIFKGDRVEILVGKDKGKQGYVIQIFQEINSVIV 187 (273)
Q Consensus 154 ~I~kGD~V~VI~GkDKGK~GkV~~V~r~~n~ViV 187 (273)
.++.||+|.| +|.+++++++++.+
T Consensus 44 ~~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 44 VVNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred EECCCCEEEE----------EEEEEECCCCEEec
Confidence 4789999998 46777776666543
No 93
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=20.23 E-value=1.9e+02 Score=22.73 Aligned_cols=40 Identities=20% Similarity=0.182 Sum_probs=26.6
Q ss_pred cCCCccccCCCCCcccCcccceecCCeEEEeecCCCCc-eeEEEEEEccC
Q psy5495 134 RNRPWEKNKKKIPIEPIKDWSIFKGDRVEILVGKDKGK-QGYVIQIFQEI 182 (273)
Q Consensus 134 ~n~p~~~r~~kv~vePi~~w~I~kGD~V~VI~GkDKGK-~GkV~~V~r~~ 182 (273)
-.+|++-|+ ..=|++||-|.|-.-..-.| .|.|..++.+.
T Consensus 27 ~~iP~KfRk---------~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 27 VSMPTKFRK---------NIWIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred EEechhhcc---------cEEEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 346666666 45579999999976443223 77888777654
Done!