Query 041704
Match_columns 86
No_of_seqs 148 out of 1010
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 09:49:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00194 60S ribosomal protein 99.8 2.3E-21 4.9E-26 139.8 6.2 65 1-71 43-111 (143)
2 PRK01191 rpl24p 50S ribosomal 99.8 3.1E-20 6.6E-25 130.6 6.3 66 1-72 42-111 (120)
3 TIGR01080 rplX_A_E ribosomal p 99.8 7.5E-20 1.6E-24 127.2 5.7 67 1-73 38-108 (114)
4 COG0198 RplX Ribosomal protein 99.8 3.5E-19 7.7E-24 122.7 6.4 59 1-67 1-74 (104)
5 PRK00004 rplX 50S ribosomal pr 99.7 2E-17 4.4E-22 112.5 7.1 71 1-77 1-86 (105)
6 PRK12281 rplX 50S ribosomal pr 99.7 1.6E-17 3.5E-22 108.1 4.6 57 2-64 4-75 (76)
7 CHL00141 rpl24 ribosomal prote 99.7 2.2E-17 4.8E-22 108.8 4.9 59 1-65 5-78 (83)
8 TIGR01079 rplX_bact ribosomal 99.7 1.7E-16 3.7E-21 108.2 6.7 61 3-69 2-78 (104)
9 KOG3401 60S ribosomal protein 99.4 7.4E-14 1.6E-18 101.4 3.3 64 1-70 45-113 (145)
10 KOG1708 Mitochondrial/chloropl 98.8 1E-08 2.2E-13 79.3 4.9 59 3-67 71-145 (236)
11 PF00467 KOW: KOW motif; Inte 98.7 3.8E-08 8.1E-13 54.2 4.6 32 7-44 1-32 (32)
12 smart00739 KOW KOW (Kyprides, 97.7 8.4E-05 1.8E-09 38.1 3.7 26 4-29 1-26 (28)
13 TIGR00405 L26e_arch ribosomal 97.0 0.0021 4.5E-08 44.3 5.3 39 5-49 87-125 (145)
14 TIGR00922 nusG transcription t 96.9 0.0026 5.7E-08 44.4 5.0 35 4-44 119-153 (172)
15 PRK05609 nusG transcription an 96.8 0.0033 7.3E-08 44.0 5.1 36 3-44 125-160 (181)
16 PRK08559 nusG transcription an 96.6 0.0056 1.2E-07 43.2 5.1 40 4-49 94-133 (153)
17 COG0250 NusG Transcription ant 95.9 0.014 3E-07 43.0 4.5 35 4-44 123-157 (178)
18 TIGR01955 RfaH transcriptional 95.6 0.028 6E-07 38.6 4.7 26 4-29 108-133 (159)
19 PRK09014 rfaH transcriptional 94.6 0.058 1.3E-06 37.5 4.0 26 4-29 109-134 (162)
20 TIGR01956 NusG_myco NusG famil 94.4 0.091 2E-06 41.4 5.1 36 3-44 204-239 (258)
21 PRK04333 50S ribosomal protein 89.7 1.5 3.3E-05 29.0 5.7 56 3-65 2-57 (84)
22 KOG1999 RNA polymerase II tran 89.0 0.52 1.1E-05 43.3 4.0 26 4-29 459-484 (1024)
23 COG2163 RPL14A Ribosomal prote 76.2 7.5 0.00016 27.7 4.8 58 2-66 2-60 (125)
24 PTZ00471 60S ribosomal protein 72.5 8.7 0.00019 28.0 4.5 59 4-68 4-87 (134)
25 COG5164 SPT5 Transcription elo 70.5 5.3 0.00012 35.0 3.5 25 5-29 140-164 (607)
26 PF03144 GTP_EFTU_D2: Elongati 68.5 9.1 0.0002 22.6 3.3 25 4-29 12-39 (74)
27 COG1862 YajC Preprotein transl 68.0 11 0.00024 25.7 4.0 22 4-29 43-64 (97)
28 KOG1999 RNA polymerase II tran 67.4 4.7 0.0001 37.4 2.6 26 4-29 581-606 (1024)
29 PRK05585 yajC preprotein trans 65.7 14 0.00031 25.2 4.2 29 4-44 52-80 (106)
30 PTZ00065 60S ribosomal protein 65.1 24 0.00051 25.5 5.4 57 5-68 8-64 (130)
31 TIGR00739 yajC preprotein tran 64.6 17 0.00036 23.8 4.2 22 4-29 37-58 (84)
32 PRK06531 yajC preprotein trans 64.1 15 0.00033 25.6 4.1 31 4-44 36-66 (113)
33 PRK05886 yajC preprotein trans 62.2 18 0.00039 25.2 4.2 29 4-44 38-66 (109)
34 smart00743 Agenet Tudor-like d 60.8 23 0.0005 20.6 4.0 37 3-45 1-39 (61)
35 PTZ00223 40S ribosomal protein 57.6 27 0.00059 27.9 5.0 55 3-65 170-226 (273)
36 PRK04313 30S ribosomal protein 56.5 23 0.00049 27.7 4.3 56 3-65 170-227 (237)
37 PLN00036 40S ribosomal protein 54.9 27 0.00058 27.7 4.6 55 3-65 173-229 (261)
38 PF05641 Agenet: Agenet domain 54.6 35 0.00075 20.8 4.2 39 5-49 1-44 (68)
39 COG1471 RPS4A Ribosomal protei 51.9 36 0.00079 27.0 4.8 41 3-45 172-212 (241)
40 PTZ00118 40S ribosomal protein 50.9 36 0.00078 27.0 4.7 55 3-65 173-229 (262)
41 COG1532 Predicted RNA-binding 50.6 19 0.00041 23.0 2.5 33 7-45 23-57 (57)
42 PF08206 OB_RNB: Ribonuclease 50.3 22 0.00048 21.2 2.7 23 6-28 33-58 (58)
43 COG5164 SPT5 Transcription elo 49.0 20 0.00043 31.5 3.2 30 8-43 355-384 (607)
44 KOG3418 60S ribosomal protein 47.9 44 0.00095 24.5 4.4 46 1-48 1-48 (136)
45 PF04452 Methyltrans_RNA: RNA 47.3 42 0.00091 24.5 4.3 37 2-44 14-50 (225)
46 PRK02749 photosystem I reactio 45.9 49 0.0011 22.0 4.0 46 3-50 1-48 (71)
47 PRK10334 mechanosensitive chan 45.8 28 0.0006 27.0 3.3 28 3-35 128-155 (286)
48 PF11623 DUF3252: Protein of u 44.0 57 0.0012 20.5 3.9 40 5-50 2-43 (53)
49 PF14505 DUF4438: Domain of un 42.9 23 0.0005 28.4 2.5 23 7-29 60-82 (258)
50 COG3700 AphA Acid phosphatase 42.7 9.1 0.0002 30.1 0.3 28 2-29 124-151 (237)
51 PF11910 NdhO: Cyanobacterial 42.2 15 0.00031 24.2 1.1 16 5-20 1-16 (67)
52 cd00174 SH3 Src homology 3 dom 41.7 33 0.00072 18.0 2.4 18 3-20 16-33 (54)
53 cd03692 mtIF2_IVc mtIF2_IVc: t 40.8 53 0.0011 20.6 3.6 26 4-29 26-51 (84)
54 cd04456 S1_IF1A_like S1_IF1A_l 40.6 51 0.0011 21.3 3.5 28 2-29 36-64 (78)
55 PF11717 Tudor-knot: RNA bindi 40.1 51 0.0011 19.4 3.2 53 5-61 1-53 (55)
56 cd05793 S1_IF1A S1_IF1A: Trans 40.1 41 0.00088 21.6 3.0 28 2-29 36-63 (77)
57 PF00924 MS_channel: Mechanose 39.6 23 0.0005 24.6 1.9 23 3-30 59-81 (206)
58 PF07653 SH3_2: Variant SH3 do 38.7 24 0.00053 20.2 1.6 12 3-14 16-27 (55)
59 smart00326 SH3 Src homology 3 37.3 42 0.00091 17.7 2.4 17 3-19 19-35 (58)
60 COG1465 Predicted alternative 36.8 96 0.0021 26.1 5.3 64 4-76 280-358 (376)
61 PF02699 YajC: Preprotein tran 36.8 11 0.00025 24.2 0.0 22 4-29 36-57 (82)
62 PF01176 eIF-1a: Translation i 35.0 69 0.0015 19.5 3.3 25 2-26 39-63 (65)
63 cd05792 S1_eIF1AD_like S1_eIF1 34.9 63 0.0014 21.2 3.3 27 3-29 37-64 (78)
64 PRK00409 recombination and DNA 34.6 65 0.0014 28.5 4.2 23 4-29 636-658 (782)
65 smart00652 eIF1a eukaryotic tr 34.5 69 0.0015 20.8 3.4 28 2-29 41-68 (83)
66 PF09953 DUF2187: Uncharacteri 34.0 1E+02 0.0023 19.4 4.0 27 6-44 5-31 (57)
67 PF01079 Hint: Hint module; I 33.4 72 0.0016 24.1 3.8 43 4-46 105-153 (217)
68 TIGR01069 mutS2 MutS2 family p 33.1 75 0.0016 28.2 4.3 21 6-29 626-646 (771)
69 CHL00125 psaE photosystem I su 30.3 1.2E+02 0.0026 19.7 3.9 42 5-48 2-45 (64)
70 cd04091 mtEFG1_II_like mtEFG1_ 29.7 83 0.0018 19.2 3.1 23 4-29 25-47 (81)
71 PRK11713 16S ribosomal RNA met 28.8 1.3E+02 0.0028 22.2 4.5 28 2-29 27-54 (234)
72 PF02887 PK_C: Pyruvate kinase 28.7 72 0.0016 20.8 2.8 22 5-26 90-111 (117)
73 TIGR00523 eIF-1A eukaryotic/ar 28.7 57 0.0012 22.1 2.4 26 2-29 55-83 (99)
74 cd03688 eIF2_gamma_II eIF2_gam 28.0 1.3E+02 0.0028 21.3 4.1 23 4-26 39-61 (113)
75 TIGR00046 RNA methyltransferas 27.7 1.4E+02 0.003 22.2 4.5 26 2-29 29-56 (240)
76 COG1193 Mismatch repair ATPase 27.2 72 0.0016 28.6 3.3 22 4-29 612-633 (753)
77 PRK04012 translation initiatio 26.0 93 0.002 21.1 3.0 28 2-29 57-84 (100)
78 COG1385 Uncharacterized protei 25.4 1.3E+02 0.0028 23.1 4.0 28 2-29 31-58 (246)
79 cd04090 eEF2_II_snRNP Loc2 eEF 25.3 1.2E+02 0.0026 19.1 3.3 26 4-29 27-58 (94)
80 PF00018 SH3_1: SH3 domain; I 24.0 65 0.0014 17.9 1.7 17 3-19 14-30 (48)
81 cd03691 BipA_TypA_II BipA_TypA 23.9 1.3E+02 0.0028 18.3 3.1 26 4-29 26-51 (86)
82 cd03698 eRF3_II_like eRF3_II_l 23.8 1.3E+02 0.0029 18.4 3.3 12 5-16 27-38 (83)
83 PRK10929 putative mechanosensi 23.7 98 0.0021 29.1 3.6 28 4-36 935-962 (1109)
84 KOG0199 ACK and related non-re 23.6 59 0.0013 30.4 2.2 17 2-18 390-406 (1039)
85 PF02941 FeThRed_A: Ferredoxin 23.0 1E+02 0.0022 20.1 2.7 12 18-29 26-37 (67)
86 COG0361 InfA Translation initi 22.8 1.3E+02 0.0029 19.7 3.2 28 2-29 44-71 (75)
87 cd04467 S1_aIF5A S1_aIF5A: Arc 22.7 67 0.0014 20.0 1.7 16 3-18 37-54 (57)
88 PRK04306 50S ribosomal protein 21.8 1.9E+02 0.004 19.9 3.9 33 5-43 35-77 (98)
89 cd04088 EFG_mtEFG_II EFG_mtEFG 20.8 1.5E+02 0.0033 17.8 3.0 23 4-29 26-48 (83)
No 1
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.84 E-value=2.3e-21 Score=139.78 Aligned_cols=65 Identities=37% Similarity=0.528 Sum_probs=62.6
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc----ccCCCccEEEeeccCCc
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE----PVGHSSVMSSVGRMSPE 71 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~----pV~~snvmi~~~~~~~~ 71 (86)
|+++|++||+|+|++|+|||++|+|++|+ +++++|+|||||+.|+||+ |+++|||||+.+.++|+
T Consensus 43 Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V~------~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~l~l~~~ 111 (143)
T PTZ00194 43 RSMPVRKDDEVMVVRGHHKGREGKVTAVY------RKKWVIHIEKITREKANGEPVQIGIHPSNVIITKLKLNKD 111 (143)
T ss_pred ccceeecCCEEEEecCCCCCCceEEEEEE------cCCCEEEEeCeEEEecCCCEeecCcCchheEEEccccCch
Confidence 58999999999999999999999999999 9999999999999999999 78899999999999887
No 2
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.81 E-value=3.1e-20 Score=130.64 Aligned_cols=66 Identities=32% Similarity=0.385 Sum_probs=62.8
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc----ccCCCccEEEeeccCCce
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE----PVGHSSVMSSVGRMSPEV 72 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~----pV~~snvmi~~~~~~~~~ 72 (86)
++++|++||+|+|++|+|||++|+|++|+ +++++|+|||||+.+++|. |++.||||++++.|+|+.
T Consensus 42 r~~~IkkGD~V~VisG~~KGk~GkV~~V~------~~~~~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l~l~~~~ 111 (120)
T PRK01191 42 RSLPVRKGDTVKVMRGDFKGEEGKVVEVD------LKRGRIYVEGVTVKKADGTEVPRPIHPSNVMITKLDLSDER 111 (120)
T ss_pred ccceEeCCCEEEEeecCCCCceEEEEEEE------cCCCEEEEeCcEEECCCCeEEEcccchhHeEEEeCccCCHH
Confidence 47899999999999999999999999999 9999999999999999887 899999999999999875
No 3
>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=99.80 E-value=7.5e-20 Score=127.21 Aligned_cols=67 Identities=25% Similarity=0.410 Sum_probs=63.0
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc----ccCCCccEEEeeccCCcee
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE----PVGHSSVMSSVGRMSPEVS 73 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~----pV~~snvmi~~~~~~~~~~ 73 (86)
++|+|++||+|+|++|+|||++|+|++|+ +++++|+|||||+.|.+|. |++.||||++.+.++|++-
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~------~~~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~l~l~~~~R 108 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVD------LKRYRIYVEGVTKEKVNGTEVPVPIHPSNVMITKLNLDDEKR 108 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEE------cCCCEEEEcCeEEECCCCeEEEeeechHHeEEEeccCChHHH
Confidence 47899999999999999999999999999 9999999999999998877 8899999999999999853
No 4
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=3.5e-19 Score=122.74 Aligned_cols=59 Identities=31% Similarity=0.469 Sum_probs=55.9
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc---------------ccCCCccEEEe
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE---------------PVGHSSVMSSV 65 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~---------------pV~~snvmi~~ 65 (86)
|+++||+||+|.|++|++||++|+|++++ +++ |+|||||+.++|++ |++.|||||+.
T Consensus 1 ~~~~IrkGD~V~Vi~GkdKGk~GkVl~v~------~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~ 72 (104)
T COG0198 1 MKMKVKKGDTVKVIAGKDKGKEGKVLKVL------PKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIID 72 (104)
T ss_pred CCcceecCCEEEEEecCCCCcceEEEEEe------cCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEec
Confidence 68999999999999999999999999999 877 99999999999998 78899999999
Q ss_pred ec
Q 041704 66 GR 67 (86)
Q Consensus 66 ~~ 67 (86)
..
T Consensus 73 ~~ 74 (104)
T COG0198 73 PN 74 (104)
T ss_pred cc
Confidence 84
No 5
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=99.72 E-value=2e-17 Score=112.46 Aligned_cols=71 Identities=24% Similarity=0.322 Sum_probs=61.6
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCC---------Cc------ccCCCccEEEe
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIP---------LE------PVGHSSVMSSV 65 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~---------g~------pV~~snvmi~~ 65 (86)
|.++|++||+|+|++|++||++|+|++|+ +++++|+|||+|+.++| |. |++.||||+..
T Consensus 1 ~~~~i~kGD~V~Vi~G~dKGk~G~V~~V~------~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~ 74 (105)
T PRK00004 1 MMMKIKKGDTVIVIAGKDKGKRGKVLKVL------PKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVD 74 (105)
T ss_pred CCCcccCCCEEEEeEcCCCCcEEEEEEEE------cCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEe
Confidence 56899999999999999999999999999 99999999999999887 22 89999999999
Q ss_pred eccCCceeeeee
Q 041704 66 GRMSPEVSTSFS 77 (86)
Q Consensus 66 ~~~~~~~~~~~~ 77 (86)
..+.+.....|.
T Consensus 75 p~~~~~~rv~~~ 86 (105)
T PRK00004 75 PKTGKATRVGFK 86 (105)
T ss_pred CcCCCCeEEEEE
Confidence 877654444443
No 6
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.70 E-value=1.6e-17 Score=108.13 Aligned_cols=57 Identities=26% Similarity=0.424 Sum_probs=50.5
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc---------------ccCCCccEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE---------------PVGHSSVMSS 64 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~---------------pV~~snvmi~ 64 (86)
.|+|++||+|+|++|+|||++|+|++|+ +++++|+|||+|+.++|.+ |++.|||+..
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 KLKVKKGDMVKVIAGDDKGKTGKVLAVL------PKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKKV 75 (76)
T ss_pred cccccCCCEEEEeEcCCCCcEEEEEEEE------cCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHHHceec
Confidence 5899999999999999999999999999 9999999999999877753 6667777653
No 7
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.70 E-value=2.2e-17 Score=108.84 Aligned_cols=59 Identities=27% Similarity=0.362 Sum_probs=52.9
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc---------------ccCCCccEEEe
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE---------------PVGHSSVMSSV 65 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~---------------pV~~snvmi~~ 65 (86)
+.|+|++||+|+|++|+|||++|+|++|+ +++++|+|||+|+.++|.+ |++.|||++.+
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~------~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvd 78 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKII------KKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYN 78 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEE------cCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeC
Confidence 36899999999999999999999999999 9999999999998775432 78889999975
No 8
>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=99.67 E-value=1.7e-16 Score=108.22 Aligned_cols=61 Identities=26% Similarity=0.403 Sum_probs=56.0
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc----------------ccCCCccEEEee
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE----------------PVGHSSVMSSVG 66 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~----------------pV~~snvmi~~~ 66 (86)
|+|++||+|+|++|++||++|+|++|+ +++++|+|||+|+.++|.+ |++.||||+...
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~------~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p 75 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVL------PKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDP 75 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEE------cCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcC
Confidence 689999999999999999999999999 9999999999999998864 899999999885
Q ss_pred ccC
Q 041704 67 RMS 69 (86)
Q Consensus 67 ~~~ 69 (86)
.+.
T Consensus 76 ~~~ 78 (104)
T TIGR01079 76 KTG 78 (104)
T ss_pred cCC
Confidence 443
No 9
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=99.43 E-value=7.4e-14 Score=101.44 Aligned_cols=64 Identities=33% Similarity=0.495 Sum_probs=59.7
Q ss_pred CcccccCCCEEEEeeccCCC-eeeeEEEEEeccccCcccceEEEeceecccCCCc----ccCCCccEEEeeccCC
Q 041704 1 MSMSVRKDDEVQVVGGTYKG-REGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE----PVGHSSVMSSVGRMSP 70 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KG-k~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~----pV~~snvmi~~~~~~~ 70 (86)
++|||+++|+|+|.+|+++| ++|+|+++| ++++.+++|.|+.+|++|. ++++|.++||++.+|.
T Consensus 45 rs~pir~ddev~v~rg~~kG~q~G~v~~vy------rKk~~iyie~v~~eK~nGt~v~vgihPsK~~iTkl~lDk 113 (145)
T KOG3401|consen 45 RSMPIRKDDEVQVVRGHFKGFQIGKVSQVY------RKKYVIYIERVQREKANGTTVPVGIHPSKVVITKLKLDK 113 (145)
T ss_pred cccceeeccEEEEEeccccccccceehhhh------hhhheeeeEeEEEeeccCcccccccCccceeecccchhh
Confidence 58999999999999999999 779999999 9999999999999999999 5669999999988764
No 10
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=98.77 E-value=1e-08 Score=79.31 Aligned_cols=59 Identities=22% Similarity=0.232 Sum_probs=50.7
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc---------------ccCCCc-cEEEee
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE---------------PVGHSS-VMSSVG 66 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~---------------pV~~sn-vmi~~~ 66 (86)
+++..||.|+|+.|++||++|.|+++. +....|+|+|+|...+|-. |.+.|| ||+.+-
T Consensus 71 w~ff~GDtVeVlvGkDkGkqG~Vtqv~------r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp 144 (236)
T KOG1708|consen 71 WHFFFGDTVEVLVGKDKGKQGEVTQVI------RHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDP 144 (236)
T ss_pred eeEecCCEEEEEecccCCccceEEEEe------ecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECc
Confidence 467789999999999999999999999 9999999999997665522 777888 888765
Q ss_pred c
Q 041704 67 R 67 (86)
Q Consensus 67 ~ 67 (86)
+
T Consensus 145 ~ 145 (236)
T KOG1708|consen 145 E 145 (236)
T ss_pred c
Confidence 4
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=98.70 E-value=3.8e-08 Score=54.20 Aligned_cols=32 Identities=38% Similarity=0.646 Sum_probs=30.1
Q ss_pred CCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 7 KDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 7 KgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
+||.|+|++|+|+|++|+|++++ +.+.+|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~------~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEID------RSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEE------TTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEE------CCCCEEEEC
Confidence 69999999999999999999999 998888876
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.67 E-value=8.4e-05 Score=38.11 Aligned_cols=26 Identities=31% Similarity=0.640 Sum_probs=23.9
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
+++.||.|+|+.|.++|++|.|++++
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~ 26 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVD 26 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEc
Confidence 36789999999999999999999886
No 13
>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=96.98 E-value=0.0021 Score=44.27 Aligned_cols=39 Identities=26% Similarity=0.474 Sum_probs=34.3
Q ss_pred ccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecc
Q 041704 5 VRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49 (86)
Q Consensus 5 IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~ 49 (86)
++.||.|.|+.|.++|.+|.|.+++ ..+..+.++-.+..
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d------~~k~~v~v~l~~~~ 125 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVD------ESKEEVTLELIEAA 125 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEc------CCCCEEEEEEEEcC
Confidence 6799999999999999999999999 77778888866643
No 14
>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=96.86 E-value=0.0026 Score=44.43 Aligned_cols=35 Identities=11% Similarity=0.190 Sum_probs=30.8
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
.++.||.|.|+.|.++|.+|.|.+++ +.+.++.|+
T Consensus 119 ~~~~G~~V~I~~Gpf~G~~g~v~~~~------~~~~r~~V~ 153 (172)
T TIGR00922 119 DFEVGEQVRVNDGPFANFTGTVEEVD------YEKSKLKVS 153 (172)
T ss_pred CCCCCCEEEEeecCCCCcEEEEEEEc------CCCCEEEEE
Confidence 47899999999999999999999998 777676665
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=96.78 E-value=0.0033 Score=44.01 Aligned_cols=36 Identities=11% Similarity=0.193 Sum_probs=31.2
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
..++.||.|.|+.|.++|.+|.|.+++ +.+.++.|+
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~------~~~~r~~v~ 160 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVD------YEKSKLKVL 160 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEe------CCCCEEEEE
Confidence 457899999999999999999999998 767666665
No 16
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=96.58 E-value=0.0056 Score=43.24 Aligned_cols=40 Identities=20% Similarity=0.424 Sum_probs=35.5
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecc
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDP 49 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~ 49 (86)
.++.||.|.|+.|.++|.+|.|.+++ ..+.++.++-++..
T Consensus 94 ~~~~G~~V~I~~Gpf~g~~g~V~~vd------~~k~~v~v~ll~~~ 133 (153)
T PRK08559 94 GIKEGDIVELIAGPFKGEKARVVRVD------ESKEEVTVELLEAA 133 (153)
T ss_pred CCCCCCEEEEeccCCCCceEEEEEEc------CCCCEEEEEEECCc
Confidence 57899999999999999999999999 88888988876543
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=95.94 E-value=0.014 Score=42.96 Aligned_cols=35 Identities=17% Similarity=0.317 Sum_probs=30.9
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
-+..||.|.|+.|.|+|..|+|..++ ..+.++.|+
T Consensus 123 ~~e~Gd~VrI~~GpFa~f~g~V~evd------~ek~~~~v~ 157 (178)
T COG0250 123 DFEPGDVVRIIDGPFAGFKAKVEEVD------EEKGKLKVE 157 (178)
T ss_pred cCCCCCEEEEeccCCCCccEEEEEEc------CcCcEEEEE
Confidence 46889999999999999999999999 777766665
No 18
>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=95.61 E-value=0.028 Score=38.63 Aligned_cols=26 Identities=27% Similarity=0.415 Sum_probs=24.3
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.++.||.|.|+.|.++|.+|.|.+++
T Consensus 108 ~~~~G~~V~V~~GPf~g~~g~v~~~~ 133 (159)
T TIGR01955 108 LPYKGDKVRITDGAFAGFEAIFLEPD 133 (159)
T ss_pred CCCCCCEEEEeccCCCCcEEEEEEEC
Confidence 46899999999999999999999987
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=94.65 E-value=0.058 Score=37.52 Aligned_cols=26 Identities=15% Similarity=0.377 Sum_probs=24.0
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.++.||.|+|+.|.++|.+|.|.+++
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 36789999999999999999999987
No 20
>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=94.45 E-value=0.091 Score=41.39 Aligned_cols=36 Identities=28% Similarity=0.358 Sum_probs=30.7
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
..+..||.|.|+.|.++|.+|.|..++ ..+.++.|.
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid------~~k~Rv~Vl 239 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKID------QEKKKAIVE 239 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEe------CCCCEEEEE
Confidence 346799999999999999999999998 666666654
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=89.67 E-value=1.5 Score=29.01 Aligned_cols=56 Identities=11% Similarity=0.009 Sum_probs=39.7
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCcccCCCccEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPVGHSSVMSSV 65 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~pV~~snvmi~~ 65 (86)
+.+..|--|.+..|.|+|+..-|+.+. . +.+++|.|-......-+..+...+..|.
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~~vIv~i~------d-~~~vlVdg~~~~~~~rk~kn~khl~lt~ 57 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRKCVIVDII------D-KNFVLVTGPSLTGVKRRRCNIKHLEPTD 57 (84)
T ss_pred CcccccEEEEEeccCCCCCEEEEEEEe------c-CCEEEEECCCcCCCCCeeechHHEEEee
Confidence 467889999999999999999998885 3 5788888874322333344444555554
No 22
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=89.00 E-value=0.52 Score=43.31 Aligned_cols=26 Identities=31% Similarity=0.583 Sum_probs=24.4
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.++.||-|+|++|.|+|.+|-|++|+
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe 484 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVE 484 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEe
Confidence 46789999999999999999999998
No 23
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=76.24 E-value=7.5 Score=27.71 Aligned_cols=58 Identities=16% Similarity=0.140 Sum_probs=37.5
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccC-CCcccCCCccEEEee
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRI-PLEPVGHSSVMSSVG 66 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~-~g~pV~~snvmi~~~ 66 (86)
...+..|=-|.+++|.+.|+..-|+++. -+ +.+++-|-..++- +-+++...-++.|+.
T Consensus 2 ~~~l~~GrVvvv~~GR~aGkk~VIv~~i------Dd-~~v~i~gp~~v~gv~r~r~n~~~l~~t~~ 60 (125)
T COG2163 2 RASLEVGRVVVVTAGRFAGKKVVIVKII------DD-NFVLITGPKKVKGVPRRRINIKHLEPTDK 60 (125)
T ss_pred CccccCCeEEEEecceeCCceEEEEEEc------cC-CEEEEeCCccccCCccccccceeeeccce
Confidence 3457789899999999999998888776 44 4788777432221 223444444444444
No 24
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=72.50 E-value=8.7 Score=27.96 Aligned_cols=59 Identities=24% Similarity=0.242 Sum_probs=42.2
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCccc------ceEEEeceecc-------------------cCCCcccCC
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRD------LVVSYEPIFDP-------------------RIPLEPVGH 58 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk------~~V~VEgVn~~-------------------K~~g~pV~~ 58 (86)
-++.|-.|+|++|.|.|+..-|++.+ ... +...|-||..- |.-.+-++.
T Consensus 4 ~~kpgkVVivL~GR~AGkKaVivk~~------ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNy 77 (134)
T PTZ00471 4 FLKPGKVVIVTSGRYAGRKAVIVQNF------DTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNH 77 (134)
T ss_pred cccCCEEEEEEccccCCcEEEEEeec------CCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEee
Confidence 46789999999999999998888876 321 58889987642 222334667
Q ss_pred CccEEEeecc
Q 041704 59 SSVMSSVGRM 68 (86)
Q Consensus 59 snvmi~~~~~ 68 (86)
.-+|=|.-..
T Consensus 78 nHlmPTRY~v 87 (134)
T PTZ00471 78 KHFLPTRYNM 87 (134)
T ss_pred ceecccceee
Confidence 7777775444
No 25
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=70.50 E-value=5.3 Score=34.95 Aligned_cols=25 Identities=28% Similarity=0.205 Sum_probs=23.7
Q ss_pred ccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 5 VRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 5 IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.++||-|.||.|.+++..|.|..|.
T Consensus 140 f~~gD~vkVI~g~~~~d~g~V~rI~ 164 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDIGTVPRID 164 (607)
T ss_pred cccCCeEEEeccccccccceEEEec
Confidence 5789999999999999999999998
No 26
>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=68.45 E-value=9.1 Score=22.64 Aligned_cols=25 Identities=32% Similarity=0.550 Sum_probs=20.3
Q ss_pred cccCCCEEEEeeccCCCee---eeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGRE---GKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~---GKV~~V~ 29 (86)
.|++||+|.++. ...++. .+|..++
T Consensus 12 ~l~~gd~v~~~~-~~~~~~~~~~~I~~i~ 39 (74)
T PF03144_consen 12 TLKKGDKVRVLP-NGTGKKGQVVKIKSIF 39 (74)
T ss_dssp EEETTEEEEEES-TTTTEECEEEEEEEEE
T ss_pred EEcCCCEEEECc-cCCcceeeeeeccccc
Confidence 589999999998 666555 8888888
No 27
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=68.05 E-value=11 Score=25.74 Aligned_cols=22 Identities=36% Similarity=0.582 Sum_probs=18.7
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+++||+|.-..| -.|+|.+|.
T Consensus 43 sL~kGD~VvT~gG----i~G~V~~v~ 64 (97)
T COG1862 43 SLKKGDEVVTIGG----IVGTVTKVG 64 (97)
T ss_pred hccCCCEEEEcCC----eEEEEEEEe
Confidence 5799999988776 579999998
No 28
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=67.40 E-value=4.7 Score=37.38 Aligned_cols=26 Identities=46% Similarity=0.926 Sum_probs=24.7
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
-||.+|.|.|+.|..+|++|.|+.++
T Consensus 581 ~I~~kD~Vkvi~Gp~~g~~G~v~~i~ 606 (1024)
T KOG1999|consen 581 EIRVKDTVKVIGGPSKGREGEVLHIY 606 (1024)
T ss_pred eecccceEEEecCCCCCccCccceee
Confidence 48899999999999999999999999
No 29
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=65.72 E-value=14 Score=25.18 Aligned_cols=29 Identities=38% Similarity=0.436 Sum_probs=22.8
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
.+++||+|.-..| -.|+|+.++ +..+.+|
T Consensus 52 ~Lk~Gd~VvT~gG----i~G~Vv~i~--------~~~v~le 80 (106)
T PRK05585 52 SLAKGDEVVTNGG----IIGKVTKVS--------EDFVIIE 80 (106)
T ss_pred hcCCCCEEEECCC----eEEEEEEEe--------CCEEEEE
Confidence 5789999998876 469999998 3566665
No 30
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=65.10 E-value=24 Score=25.47 Aligned_cols=57 Identities=12% Similarity=0.073 Sum_probs=41.5
Q ss_pred ccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCcccCCCccEEEeecc
Q 041704 5 VRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPVGHSSVMSSVGRM 68 (86)
Q Consensus 5 IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~pV~~snvmi~~~~~ 68 (86)
|..|=.|.+..|.++|+...|+.|. ...++.|+|=....-.=+.++..++.+|++..
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDII-------D~nRvLVDGP~~tgV~Rq~i~~k~l~LT~~~v 64 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIV-------TPTRVLVDGAFITGVKRQSIPLKRLKLTDEKI 64 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEE-------cCCeEEEeCCCcCCcceeEEeccceEEccEEE
Confidence 4567678888999999999999887 35799999863323334456677777777654
No 31
>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=64.56 E-value=17 Score=23.76 Aligned_cols=22 Identities=36% Similarity=0.590 Sum_probs=18.6
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+++||+|.-.+| --|+|..+.
T Consensus 37 ~L~~Gd~VvT~gG----i~G~V~~i~ 58 (84)
T TIGR00739 37 SLKKGDKVLTIGG----IIGTVTKIA 58 (84)
T ss_pred hCCCCCEEEECCC----eEEEEEEEe
Confidence 5789999998776 469999998
No 32
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=64.10 E-value=15 Score=25.62 Aligned_cols=31 Identities=23% Similarity=0.407 Sum_probs=24.0
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
.+++||+|.-..| -.|+|..+. ..+..+.+|
T Consensus 36 sLk~GD~VvT~GG----i~G~V~~I~------~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIGG----LYGTVDEVD------TEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECCC----cEEEEEEEe------cCCCEEEEE
Confidence 5799999988776 579999988 544567765
No 33
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=62.17 E-value=18 Score=25.17 Aligned_cols=29 Identities=31% Similarity=0.406 Sum_probs=23.0
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
.+++||+|.-..| --|+|..+. +..+.+|
T Consensus 38 ~Lk~GD~VvT~gG----i~G~V~~I~--------d~~v~le 66 (109)
T PRK05886 38 SLQPGDRVHTTSG----LQATIVGIT--------DDTVDLE 66 (109)
T ss_pred hcCCCCEEEECCC----eEEEEEEEe--------CCEEEEE
Confidence 5799999998776 469999998 4567766
No 34
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=60.79 E-value=23 Score=20.62 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=25.6
Q ss_pred ccccCCCEEEEeeccCCC-eeeeEEEEEeccccCc-ccceEEEec
Q 041704 3 MSVRKDDEVQVVGGTYKG-REGKFVQIFAIFSGVK-RDLVVSYEP 45 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KG-k~GKV~~V~~~~~~~r-kk~~V~VEg 45 (86)
+.+++||.|.+..=...+ -+|+|+++. . .++.|.+.+
T Consensus 1 ~~~~~G~~Ve~~~~~~~~W~~a~V~~~~------~~~~~~V~~~~ 39 (61)
T smart00743 1 SDFKKGDRVEVFSKEEDSWWEAVVTKVL------GDGKYLVRYLT 39 (61)
T ss_pred CCcCCCCEEEEEECCCCEEEEEEEEEEC------CCCEEEEEECC
Confidence 357899999998643222 249999998 5 456676665
No 35
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=57.64 E-value=27 Score=27.91 Aligned_cols=55 Identities=18% Similarity=0.184 Sum_probs=37.9
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCcc--cCCCccEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEP--VGHSSVMSSV 65 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~p--V~~snvmi~~ 65 (86)
++...|..+.|+.|+.-|+.|+|..+.. .-.....|+++. ..|.. ...+||++--
T Consensus 170 ikfe~G~l~~vtgG~n~GriG~I~~i~~---~~~~~~iv~i~d-----~~g~~F~T~~~~VfvIG 226 (273)
T PTZ00223 170 IKNRNGKVVMVTGGANRGRIGEIVSIER---HPGAFDIARLKD-----ASGHEFATRAANIFVIG 226 (273)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEe---cCCCCCEEEEEe-----CCCCeEEEEeeeEEEEe
Confidence 4677899999999999999999988851 111224666663 44543 3567877765
No 36
>PRK04313 30S ribosomal protein S4e; Validated
Probab=56.51 E-value=23 Score=27.73 Aligned_cols=56 Identities=18% Similarity=0.137 Sum_probs=38.5
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCc--ccCCCccEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLE--PVGHSSVMSSV 65 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~--pV~~snvmi~~ 65 (86)
++...|-.+.|+.|+.-|+.|+|..+.... -.....|.+| -..|. ....+||++--
T Consensus 170 i~fe~G~l~~itgG~n~GriG~I~~i~~~~--~~~~~~V~i~-----d~~G~~F~T~~~~vfvIG 227 (237)
T PRK04313 170 IPFEEGNLAIITGGKHVGEIGKIKEIEVTK--SSKPNIVTLE-----DKDGEKFETILDYVFVIG 227 (237)
T ss_pred EecCCCCEEEEECCeeeeeEEEEEEEEEcc--CCCCcEEEEE-----cCCCCEEEEEeeeEEEEc
Confidence 466789999999999999999999987100 0122567776 34454 44567777654
No 37
>PLN00036 40S ribosomal protein S4; Provisional
Probab=54.87 E-value=27 Score=27.74 Aligned_cols=55 Identities=15% Similarity=0.097 Sum_probs=38.7
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCccc--CCCccEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPV--GHSSVMSSV 65 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~pV--~~snvmi~~ 65 (86)
++...|..+.|+.|+.-|+.|+|..+. .-. .....|++| ...|... ..+||++.-
T Consensus 173 ikfe~G~l~~vtgG~n~GrvG~I~~i~-~~~--~~~~iV~i~-----d~~g~~F~T~~~~vfvIG 229 (261)
T PLN00036 173 IKFDVGNLVMVTGGRNRGRVGVIKNRE-KHK--GSFEIIHVK-----DATGHEFATRLGNVFVIG 229 (261)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEE-ecC--CCCCEEEEE-----eCCCCeEEEEeeeEEEEc
Confidence 467789999999999999999998887 111 222466666 3455533 567877764
No 38
>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=54.60 E-value=35 Score=20.83 Aligned_cols=39 Identities=23% Similarity=0.440 Sum_probs=22.2
Q ss_pred ccCCCEEEEeecc--CCCe--eeeEEEEEeccccCcc-cceEEEeceecc
Q 041704 5 VRKDDEVQVVGGT--YKGR--EGKFVQIFAIFSGVKR-DLVVSYEPIFDP 49 (86)
Q Consensus 5 IrKgDeV~VI~Gk--~KGk--~GKV~~V~~~~~~~rk-k~~V~VEgVn~~ 49 (86)
+++||+|.|.+-. +.|- .++|++.. .+ ++.|.+......
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~------~~~~~~V~Y~~~~~~ 44 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKEN------GDDKYLVEYDDLPDE 44 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEE------TT-EEEEEETT-SS-
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeC------CCcEEEEEECCcccc
Confidence 5799999998743 3343 27899888 66 666666555443
No 39
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=51.95 E-value=36 Score=27.00 Aligned_cols=41 Identities=27% Similarity=0.351 Sum_probs=30.9
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEec
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEP 45 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEg 45 (86)
++...|-.|.|+.|+.-|..|+|..+.. ..-++...|.+|+
T Consensus 172 i~fe~g~~~~vtgG~h~G~~G~I~~I~~--~~~~~~~~v~~e~ 212 (241)
T COG1471 172 IKFEEGALVYVTGGRHVGRVGTIVEIEI--QESSKPNLVTVED 212 (241)
T ss_pred eccCCCcEEEEECCccccceEEEEEEEE--ecCCCccEEEEec
Confidence 4667888999999999999999999982 1112335677774
No 40
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=50.95 E-value=36 Score=27.04 Aligned_cols=55 Identities=16% Similarity=0.095 Sum_probs=37.5
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCccc--CCCccEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPV--GHSSVMSSV 65 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~pV--~~snvmi~~ 65 (86)
++...|..+.|+.|+.-|+.|+|..+.. .-.....|++|. ..|... ..+||++.-
T Consensus 173 ikfe~G~l~~vtgG~n~GriG~I~~~~~---~~~~~~~V~i~d-----~~g~~F~T~~~~vfvIG 229 (262)
T PTZ00118 173 LKFEVGNLVMITGGHNVGRVGTIVSKEK---HPGSFDLIHVKD-----SRGKTFATRLSNVFVIG 229 (262)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEe---cCCCCcEEEEEe-----CCCCeEEEEeeeEEEEc
Confidence 4677899999999999999999988551 111224566663 455533 567877764
No 41
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=50.56 E-value=19 Score=23.01 Aligned_cols=33 Identities=21% Similarity=0.220 Sum_probs=25.2
Q ss_pred CCCEEEE--eeccCCCeeeeEEEEEeccccCcccceEEEec
Q 041704 7 KDDEVQV--VGGTYKGREGKFVQIFAIFSGVKRDLVVSYEP 45 (86)
Q Consensus 7 KgDeV~V--I~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEg 45 (86)
+||.|.. +=|.+|--.|+|.+++ ..+.++++|+
T Consensus 23 ~~e~V~a~Dilgd~ke~~G~vkriD------ldehkI~lE~ 57 (57)
T COG1532 23 TEEGVVARDILGDEKEFEGQVKRID------LDEHKIELEG 57 (57)
T ss_pred ecCcEEEEeccCCceEecceEEEEE------ccccEEEecC
Confidence 4555543 4577777789999999 8889999885
No 42
>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=50.26 E-value=22 Score=21.18 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=12.1
Q ss_pred cCCCEEEE-eeccCC--CeeeeEEEE
Q 041704 6 RKDDEVQV-VGGTYK--GREGKFVQI 28 (86)
Q Consensus 6 rKgDeV~V-I~Gk~K--Gk~GKV~~V 28 (86)
--||+|+| +....+ ..+|+|++|
T Consensus 33 ~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 33 MDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp -TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 45898876 333333 334888875
No 43
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=48.99 E-value=20 Score=31.54 Aligned_cols=30 Identities=23% Similarity=0.322 Sum_probs=25.5
Q ss_pred CCEEEEeeccCCCeeeeEEEEEeccccCcccceEEE
Q 041704 8 DDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSY 43 (86)
Q Consensus 8 gDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~V 43 (86)
|-+|++-+|.|||+-|-|..+. +...+|.+
T Consensus 355 gktVrIr~g~yKG~lGVVKdv~------~~~arVeL 384 (607)
T COG5164 355 GKTVRIRCGEYKGHLGVVKDVD------RNIARVEL 384 (607)
T ss_pred CceEEEeecccccccceeeecc------CceEEEEE
Confidence 6799999999999999999998 76666554
No 44
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=47.86 E-value=44 Score=24.53 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=31.7
Q ss_pred CcccccCCCEEEEeeccCCCeeeeEEEEEeccccCccc--ceEEEeceec
Q 041704 1 MSMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRD--LVVSYEPIFD 48 (86)
Q Consensus 1 ~Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk--~~V~VEgVn~ 48 (86)
|..-++.|-.|.|.+|.|.|+..-|++-. -.++..+ ..+.++||..
T Consensus 1 m~kflkPgkvv~v~sG~yAg~KaVivk~~--Ddg~~d~p~~h~LvAgi~r 48 (136)
T KOG3418|consen 1 MAKFLKPGKVVLVLSGRYAGKKAVIVKNI--DDGTEDKPYGHALVAGVDR 48 (136)
T ss_pred CcccccCCcEEEeecccccCccEEEEeec--ccCCccCCCceeeeeehhh
Confidence 44567889999999999999876555433 1232222 3788888864
No 45
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=47.31 E-value=42 Score=24.54 Aligned_cols=37 Identities=14% Similarity=0.262 Sum_probs=24.8
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
-++++.||.|.|.-|.-.--.+++..+. ++...+.+.
T Consensus 14 VlR~k~Gd~i~v~dg~g~~~~a~i~~i~------~~~~~~~i~ 50 (225)
T PF04452_consen 14 VLRLKEGDSIEVFDGDGGEYRAEITEIS------KKSATLRIL 50 (225)
T ss_dssp TST--TT-EEEEEESSSEEEEEEEEEEE------SSEEEEEEE
T ss_pred hcCCCCCCEEEEEECCCCEEEEEEEECc------CcEEEEEEe
Confidence 4789999999999987444458898888 655544444
No 46
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=45.91 E-value=49 Score=21.97 Aligned_cols=46 Identities=17% Similarity=0.368 Sum_probs=30.6
Q ss_pred ccccCCCEEEEeecc--CCCeeeeEEEEEeccccCcccceEEEeceeccc
Q 041704 3 MSVRKDDEVQVVGGT--YKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPR 50 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk--~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K 50 (86)
|-|++||.|.+++=. .=...|+|..|+ -++|+=.-.|-.+.+|-.-
T Consensus 1 m~i~rGskVrIlR~ESYWyn~vGtV~svD--~sgi~YPV~VRF~kvNY~g 48 (71)
T PRK02749 1 MAISRGDKVRILRPESYWYNEVGTVASVD--KSGIKYPVIVRFDKVNYNG 48 (71)
T ss_pred CccccCCEEEEccccceeecCcceEEEEc--cCCCeeeEEEEeeeeeccc
Confidence 458999999999876 223459999998 2344433455566666543
No 47
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=45.83 E-value=28 Score=27.02 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=21.5
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEeccccC
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFAIFSGV 35 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~ 35 (86)
-|+|.||.|++ .|.+|+|..+..--|.+
T Consensus 128 rpf~vGD~I~i-----~~~~G~V~~I~~r~T~i 155 (286)
T PRK10334 128 RPFRAGEYVDL-----GGVAGTVLSVQIFSTTM 155 (286)
T ss_pred CCCCCCCEEEE-----CCEEEEEEEEEeEEEEE
Confidence 38899999998 37899999998433333
No 48
>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=43.97 E-value=57 Score=20.54 Aligned_cols=40 Identities=20% Similarity=0.177 Sum_probs=28.0
Q ss_pred ccCCCEEEEeecc--CCCeeeeEEEEEeccccCcccceEEEeceeccc
Q 041704 5 VRKDDEVQVVGGT--YKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPR 50 (86)
Q Consensus 5 IrKgDeV~VI~Gk--~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K 50 (86)
|..|-.|.|+.-. |.|-+|-|.+|. ..+--|..||=|+.|
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvs------dgkaaVLFEGGnWdK 43 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVS------DGKAAVLFEGGNWDK 43 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEE------TTEEEEEEEETTEEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEee------CCeEEEEecCCCceE
Confidence 5678888888765 889999999998 777788899877654
No 49
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=42.94 E-value=23 Score=28.36 Aligned_cols=23 Identities=30% Similarity=0.424 Sum_probs=16.7
Q ss_pred CCCEEEEeeccCCCeeeeEEEEE
Q 041704 7 KDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 7 KgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
-|.+..|++|..||.+|.|+-=.
T Consensus 60 iGN~A~VvSG~AKG~~G~VtGkH 82 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTGKH 82 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEEEE
T ss_pred cCceeEEeecccCCCcCeEeccc
Confidence 47899999999999999887543
No 50
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=42.72 E-value=9.1 Score=30.12 Aligned_cols=28 Identities=21% Similarity=0.411 Sum_probs=25.4
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.|+.|+||.+.-+.|.-.|++-+|.+.+
T Consensus 124 ~MHq~RGD~i~FvTGRt~gk~d~vsk~L 151 (237)
T COG3700 124 DMHQRRGDAIYFVTGRTPGKTDTVSKTL 151 (237)
T ss_pred HHHHhcCCeEEEEecCCCCcccccchhH
Confidence 3789999999999999999998888887
No 51
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=42.19 E-value=15 Score=24.19 Aligned_cols=16 Identities=25% Similarity=0.403 Sum_probs=14.3
Q ss_pred ccCCCEEEEeeccCCC
Q 041704 5 VRKDDEVQVVGGTYKG 20 (86)
Q Consensus 5 IrKgDeV~VI~Gk~KG 20 (86)
+|||+.|.|++.+|-+
T Consensus 1 lKKG~lVrv~re~~~n 16 (67)
T PF11910_consen 1 LKKGSLVRVNREKYEN 16 (67)
T ss_pred CCcceEEEeehHhhcC
Confidence 6899999999998776
No 52
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=41.69 E-value=33 Score=18.02 Aligned_cols=18 Identities=28% Similarity=0.501 Sum_probs=13.7
Q ss_pred ccccCCCEEEEeeccCCC
Q 041704 3 MSVRKDDEVQVVGGTYKG 20 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KG 20 (86)
+.+++||.|.|+.....|
T Consensus 16 l~~~~Gd~v~v~~~~~~~ 33 (54)
T cd00174 16 LSFKKGDIIEVLEKSDDG 33 (54)
T ss_pred CCCCCCCEEEEEEcCCCC
Confidence 568899999999874443
No 53
>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=40.79 E-value=53 Score=20.62 Aligned_cols=26 Identities=19% Similarity=0.290 Sum_probs=13.9
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+++|+.+.++++.---.+|+|..+.
T Consensus 26 ~l~~g~~v~vlr~~~~~~~g~i~sl~ 51 (84)
T cd03692 26 KIKRNAKVRVLRNGEVIYEGKISSLK 51 (84)
T ss_pred EEeCCCEEEEEcCCCEEEEEEEEEEE
Confidence 35677777777763100234554444
No 54
>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=40.64 E-value=51 Score=21.28 Aligned_cols=28 Identities=7% Similarity=0.147 Sum_probs=20.5
Q ss_pred cccccCCCEEEEeeccC-CCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTY-KGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~-KGk~GKV~~V~ 29 (86)
.+.|+.||.|.|-.=.| .-..|.|+.++
T Consensus 36 ~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~ 64 (78)
T cd04456 36 NIWIKRGDFLIVDPIEEGEDVKADIIFVY 64 (78)
T ss_pred CEEEcCCCEEEEEecccCCCceEEEEEEe
Confidence 35688999998877666 33458888877
No 55
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=40.12 E-value=51 Score=19.43 Aligned_cols=53 Identities=17% Similarity=0.043 Sum_probs=31.7
Q ss_pred ccCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEeceecccCCCcccCCCcc
Q 041704 5 VRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYEPIFDPRIPLEPVGHSSV 61 (86)
Q Consensus 5 IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~~K~~g~pV~~snv 61 (86)
+..|+.|.+..+.-.-.+++|+++.. .+-...+-|+++|-| ++.-+=|+.++|
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~--~~~~~~YyVHY~g~n--kR~DeWV~~~~i 53 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIRE--KNGEPEYYVHYQGWN--KRLDEWVPESRI 53 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEE--CTTCEEEEEEETTST--GCC-EEEETTTE
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEe--cCCCEEEEEEcCCCC--CCceeeecHHHc
Confidence 35788999988444445699999982 111123678888765 455555555554
No 56
>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=40.07 E-value=41 Score=21.65 Aligned_cols=28 Identities=11% Similarity=0.222 Sum_probs=18.8
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+.|+.||.|.|--=.|.-..|.|+..+
T Consensus 36 ~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~ 63 (77)
T cd05793 36 RVWINEGDIVLVAPWDFQDDKADIIYKY 63 (77)
T ss_pred cEEEcCCCEEEEEeccccCCEEEEEEEc
Confidence 3567888888885445544457777776
No 57
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=39.59 E-value=23 Score=24.57 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=15.4
Q ss_pred ccccCCCEEEEeeccCCCeeeeEEEEEe
Q 041704 3 MSVRKDDEVQVVGGTYKGREGKFVQIFA 30 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk~GKV~~V~~ 30 (86)
-|++.||.|++= |..|+|.++-.
T Consensus 59 ~pf~vGD~I~i~-----~~~G~V~~I~l 81 (206)
T PF00924_consen 59 RPFKVGDRIEIG-----GVEGRVEEIGL 81 (206)
T ss_dssp -SS-TT-EEESS-----S-EEEEEEE-S
T ss_pred CCccCCCEEEEE-----EeehHHHhcCc
Confidence 388999998875 88999999983
No 58
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 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 []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=38.66 E-value=24 Score=20.22 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=9.4
Q ss_pred ccccCCCEEEEe
Q 041704 3 MSVRKDDEVQVV 14 (86)
Q Consensus 3 m~IrKgDeV~VI 14 (86)
+.+++||.|.|+
T Consensus 16 Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 16 LSFKKGDVIEVL 27 (55)
T ss_dssp -EB-TTEEEEEE
T ss_pred eEEecCCEEEEE
Confidence 678999999999
No 59
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=37.31 E-value=42 Score=17.72 Aligned_cols=17 Identities=24% Similarity=0.368 Sum_probs=13.4
Q ss_pred ccccCCCEEEEeeccCC
Q 041704 3 MSVRKDDEVQVVGGTYK 19 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~K 19 (86)
+.+++||.+.++.....
T Consensus 19 l~~~~Gd~v~v~~~~~~ 35 (58)
T smart00326 19 LSFKKGDIITVLEKSDD 35 (58)
T ss_pred CCCCCCCEEEEEEcCCC
Confidence 56899999999977533
No 60
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=36.82 E-value=96 Score=26.07 Aligned_cols=64 Identities=22% Similarity=0.144 Sum_probs=36.7
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCcccc------------eEEE---eceecccCCCcccCCCccEEEeecc
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDL------------VVSY---EPIFDPRIPLEPVGHSSVMSSVGRM 68 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~------------~V~V---EgVn~~K~~g~pV~~snvmi~~~~~ 68 (86)
-++.||+|+|+-++=+.+.+-|=++.. . ++.. ..++ |-|..++.+|+|+. ++.+..
T Consensus 280 EL~aGDeV~iVD~dGr~R~aiVGRvKI--E--rRPl~lIeAey~g~~i~tiLQNAETIkLv~~dG~pvS-----V~eLk~ 350 (376)
T COG1465 280 ELKAGDEVLIVDFDGRTRSAIVGRVKI--E--RRPLMLIEAEYEGVEISTILQNAETIKLVNPDGEPVS-----VAELKP 350 (376)
T ss_pred hhcCCCeEEEEecCCceeEEEEEEEEe--e--cCceEEEEEEecCcEEEEEeccceeEEEEcCCCcEee-----eEecCC
Confidence 368899999998876666654433330 0 1111 1122 34556777888864 455566
Q ss_pred CCceeeee
Q 041704 69 SPEVSTSF 76 (86)
Q Consensus 69 ~~~~~~~~ 76 (86)
-|++---+
T Consensus 351 GD~vlv~~ 358 (376)
T COG1465 351 GDEVLVYL 358 (376)
T ss_pred CCEEEEEe
Confidence 66655443
No 61
>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=36.80 E-value=11 Score=24.22 Aligned_cols=22 Identities=41% Similarity=0.619 Sum_probs=0.0
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+++||+|.-.+|= .|+|.++.
T Consensus 36 ~Lk~Gd~VvT~gGi----~G~V~~i~ 57 (82)
T PF02699_consen 36 SLKPGDEVVTIGGI----YGTVVEID 57 (82)
T ss_dssp --------------------------
T ss_pred cCCCCCEEEECCcE----EEEEEEEe
Confidence 57899999988874 58888887
No 62
>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=35.00 E-value=69 Score=19.53 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=15.3
Q ss_pred cccccCCCEEEEeeccCCCeeeeEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFV 26 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~ 26 (86)
.+.|+.||.|.|---.+.-..|.|+
T Consensus 39 ~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 39 RIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp CC---TTEEEEEEESTTCTTEEEEE
T ss_pred eEecCCCCEEEEEecccCCCeEEEE
Confidence 4678889988887666655557665
No 63
>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=34.94 E-value=63 Score=21.15 Aligned_cols=27 Identities=19% Similarity=0.242 Sum_probs=20.1
Q ss_pred ccccCCCEEEEeeccCCCe-eeeEEEEE
Q 041704 3 MSVRKDDEVQVVGGTYKGR-EGKFVQIF 29 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~KGk-~GKV~~V~ 29 (86)
+=||.||-|.|-.-.+-.+ .|.|+.++
T Consensus 37 iWIkrGd~VlV~p~~~~~kvkgeIv~i~ 64 (78)
T cd05792 37 IWIKRGDFVLVEPIEEGDKVKAEIVKIL 64 (78)
T ss_pred EEEEeCCEEEEEecccCCceEEEEEEEE
Confidence 4478999999987665444 48888887
No 64
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=34.62 E-value=65 Score=28.54 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=19.2
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
+++.||.|.|.+ -|+.|+|+.+.
T Consensus 636 ~~~~Gd~V~v~~---~~~~g~v~~i~ 658 (782)
T PRK00409 636 ELKVGDEVKYLS---LGQKGEVLSIP 658 (782)
T ss_pred CCCCCCEEEEcc---CCceEEEEEEc
Confidence 488999999966 46789999996
No 65
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=34.55 E-value=69 Score=20.84 Aligned_cols=28 Identities=14% Similarity=0.240 Sum_probs=18.3
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+.|+.||.|.|---.|--..|.|+.++
T Consensus 41 ~iwI~~GD~VlVe~~~~~~~kg~Iv~r~ 68 (83)
T smart00652 41 KVWIRRGDIVLVDPWDFQDVKADIIYKY 68 (83)
T ss_pred cEEEcCCCEEEEEecCCCCCEEEEEEEe
Confidence 3567788888876555543447777776
No 66
>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=33.97 E-value=1e+02 Score=19.43 Aligned_cols=27 Identities=15% Similarity=0.298 Sum_probs=20.4
Q ss_pred cCCCEEEEeeccCCCeeeeEEEEEeccccCcccceEEEe
Q 041704 6 RKDDEVQVVGGTYKGREGKFVQIFAIFSGVKRDLVVSYE 44 (86)
Q Consensus 6 rKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~rkk~~V~VE 44 (86)
..||.+.. -+|-+|+|.+++ .+.|+|+
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 46888876 357899999998 5667665
No 67
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=33.38 E-value=72 Score=24.12 Aligned_cols=43 Identities=21% Similarity=0.268 Sum_probs=22.0
Q ss_pred cccCCCEEEE-eeccCCCeeeeEEEEEe-----ccccCcccceEEEece
Q 041704 4 SVRKDDEVQV-VGGTYKGREGKFVQIFA-----IFSGVKRDLVVSYEPI 46 (86)
Q Consensus 4 ~IrKgDeV~V-I~Gk~KGk~GKV~~V~~-----~~~~~rkk~~V~VEgV 46 (86)
.|+.||-|.+ -.+..+-+.-+|+.|.. ++.-+...+.++|+||
T Consensus 105 ~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~GtivVdgV 153 (217)
T PF01079_consen 105 DVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSHGTIVVDGV 153 (217)
T ss_dssp G--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESSSEEEETTE
T ss_pred hCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCcceEEECCE
Confidence 6899999999 33444444577877763 1222344455566655
No 68
>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=33.09 E-value=75 Score=28.18 Aligned_cols=21 Identities=43% Similarity=0.782 Sum_probs=17.7
Q ss_pred cCCCEEEEeeccCCCeeeeEEEEE
Q 041704 6 RKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 6 rKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
+.||.|.|. .-|+.|+|+.+.
T Consensus 626 ~~Gd~V~v~---~~~~~g~v~~i~ 646 (771)
T TIGR01069 626 KIGDKVRIR---YFGQKGKIVQIL 646 (771)
T ss_pred CCCCEEEEc---cCCceEEEEEEc
Confidence 789999995 457889999996
No 69
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=30.33 E-value=1.2e+02 Score=19.75 Aligned_cols=42 Identities=17% Similarity=0.381 Sum_probs=28.3
Q ss_pred ccCCCEEEEeecc--CCCeeeeEEEEEeccccCcccceEEEeceec
Q 041704 5 VRKDDEVQVVGGT--YKGREGKFVQIFAIFSGVKRDLVVSYEPIFD 48 (86)
Q Consensus 5 IrKgDeV~VI~Gk--~KGk~GKV~~V~~~~~~~rkk~~V~VEgVn~ 48 (86)
|++||.|.+++-. .=...|+|..|+. ++++=.-.|-.+.+|-
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~--~gi~YPV~VRF~kvNY 45 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQ--SGIRYPVLVRFEKVNY 45 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcC--CCCCccEEEEEeeeec
Confidence 7899999999876 2234599999993 4554334455565554
No 70
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=29.67 E-value=83 Score=19.23 Aligned_cols=23 Identities=17% Similarity=0.390 Sum_probs=15.9
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.|++||+|.... .|++.+|.+++
T Consensus 25 ~lk~gd~v~~~~---~~~~~~v~~i~ 47 (81)
T cd04091 25 KLKKGDTIYNVR---TGKKVRVPRLV 47 (81)
T ss_pred EEcCCCEEEEcC---CCCEEEEeEEE
Confidence 578999998766 34456666665
No 71
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=28.78 E-value=1.3e+02 Score=22.19 Aligned_cols=28 Identities=14% Similarity=0.243 Sum_probs=20.6
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.++++.||.+.|.-|.-.=-.+++..+.
T Consensus 27 VlR~~~Gd~i~v~~g~g~~~~~~i~~i~ 54 (234)
T PRK11713 27 VLRLKEGDELRLFDGDGGEYLAEITEIG 54 (234)
T ss_pred hccCCCCCEEEEEeCCCCEEEEEEEEec
Confidence 4689999999999886311237887776
No 72
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=28.75 E-value=72 Score=20.80 Aligned_cols=22 Identities=32% Similarity=0.391 Sum_probs=16.0
Q ss_pred ccCCCEEEEeeccCCCeeeeEE
Q 041704 5 VRKDDEVQVVGGTYKGREGKFV 26 (86)
Q Consensus 5 IrKgDeV~VI~Gk~KGk~GKV~ 26 (86)
++.||.|.++.|..-|..|.-.
T Consensus 90 ~~~gd~vVv~~g~~~~~~g~tn 111 (117)
T PF02887_consen 90 LKPGDKVVVVAGMPFGTPGGTN 111 (117)
T ss_dssp S-TTSEEEEEEESSTTTTSSEE
T ss_pred CCCCCEEEEEeCCCCCCCCCCE
Confidence 6899999999996666655443
No 73
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=28.70 E-value=57 Score=22.07 Aligned_cols=26 Identities=19% Similarity=0.257 Sum_probs=16.1
Q ss_pred cccccCCCEEEEeeccCCCe---eeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGR---EGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk---~GKV~~V~ 29 (86)
.+.|+.||.|.|- .|--+ .|.|+..+
T Consensus 55 ~iwI~~GD~VlVs--p~d~~~~~kg~Iv~r~ 83 (99)
T TIGR00523 55 RIWIREGDVVIVK--PWEFQGDDKCDIVWRY 83 (99)
T ss_pred cEEecCCCEEEEE--EccCCCCccEEEEEEc
Confidence 3567888888882 22222 37777766
No 74
>cd03688 eIF2_gamma_II eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding.
Probab=28.00 E-value=1.3e+02 Score=21.28 Aligned_cols=23 Identities=26% Similarity=0.421 Sum_probs=16.7
Q ss_pred cccCCCEEEEeeccCCCeeeeEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFV 26 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~ 26 (86)
.+|.|||+.+..|...-++|++.
T Consensus 39 ~lkvgdeIEIrpg~~~~~~~~~~ 61 (113)
T cd03688 39 VLKVGDEIEIRPGIVVKDEGKIK 61 (113)
T ss_pred EEeCCCEEEEeeceeeecCCCee
Confidence 46889999999886554455554
No 75
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=27.72 E-value=1.4e+02 Score=22.17 Aligned_cols=26 Identities=19% Similarity=0.396 Sum_probs=20.3
Q ss_pred cccccCCCEEEEeeccCCCee--eeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGRE--GKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~--GKV~~V~ 29 (86)
-|+++.||.|.|.-|. |.. +++..+.
T Consensus 29 VlR~~~Gd~v~v~~g~--g~~~~a~i~~~~ 56 (240)
T TIGR00046 29 VLRLKKGDKLKLLDGD--GFIYHCEIKKIS 56 (240)
T ss_pred cccCCCCCEEEEEeCC--CCEEEEEEEEEc
Confidence 4789999999999884 554 6777776
No 76
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=27.24 E-value=72 Score=28.63 Aligned_cols=22 Identities=36% Similarity=0.668 Sum_probs=18.0
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.++-||+|.+++ |+.|+++++.
T Consensus 612 ~l~~gDev~~~t----~e~G~~~~i~ 633 (753)
T COG1193 612 KLKLGDEVEVIT----GEPGAVVKII 633 (753)
T ss_pred CceecceeEeec----CCccceeeee
Confidence 578899999998 5677777776
No 77
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=25.98 E-value=93 Score=21.12 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=18.5
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+.|+.||.|.|--=.|--..|.|+..+
T Consensus 57 ~IwI~~GD~VlVe~~~~~~~kg~Iv~r~ 84 (100)
T PRK04012 57 RMWIREGDVVIVAPWDFQDEKADIIWRY 84 (100)
T ss_pred cEEecCCCEEEEEecccCCCEEEEEEEc
Confidence 3567788888776555544457777776
No 78
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.35 E-value=1.3e+02 Score=23.08 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=21.9
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
-|+++.||++.+.-|...=-...+.++.
T Consensus 31 VlRl~~gd~l~l~~g~g~~~~a~i~~~~ 58 (246)
T COG1385 31 VLRLKEGDELRLFDGSGGEFLAEITKIG 58 (246)
T ss_pred eeecCCCCEEEEEeCCCcEEEEEEeecC
Confidence 3688999999999998544446787776
No 79
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=25.33 E-value=1.2e+02 Score=19.12 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=16.9
Q ss_pred cccCCCEEEEeeccC------CCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTY------KGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~------KGk~GKV~~V~ 29 (86)
.|+.||+|.++.-++ +.++.+|.+++
T Consensus 27 tl~~g~~v~~~~~~~~~~~~~~~~~~~i~~l~ 58 (94)
T cd04090 27 TIKKGQKVKVLGENYSLDDEEDMTICTIGRLW 58 (94)
T ss_pred eEcCCCEEEEECCCCCCccCCcEEEEEEeEEE
Confidence 578999998876442 22345666666
No 80
>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=24.04 E-value=65 Score=17.85 Aligned_cols=17 Identities=24% Similarity=0.401 Sum_probs=12.0
Q ss_pred ccccCCCEEEEeeccCC
Q 041704 3 MSVRKDDEVQVVGGTYK 19 (86)
Q Consensus 3 m~IrKgDeV~VI~Gk~K 19 (86)
+.+++||.+.|+.=...
T Consensus 14 Ls~~~Gd~i~v~~~~~~ 30 (48)
T PF00018_consen 14 LSFKKGDIIEVLEKSDD 30 (48)
T ss_dssp SEB-TTEEEEEEEESSS
T ss_pred EeEECCCEEEEEEecCC
Confidence 67899999999874433
No 81
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=23.89 E-value=1.3e+02 Score=18.35 Aligned_cols=26 Identities=27% Similarity=0.371 Sum_probs=15.3
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.|++||+|.+..-+.+.++-+|.+++
T Consensus 26 ~l~~g~~v~~~~~~~~~~~~~v~~l~ 51 (86)
T cd03691 26 TVKVGQQVAVVKRDGKIEKAKITKLF 51 (86)
T ss_pred EEcCCCEEEEEcCCCCEEEEEEeeEe
Confidence 57889999877654323333444544
No 82
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=23.85 E-value=1.3e+02 Score=18.43 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=6.7
Q ss_pred ccCCCEEEEeec
Q 041704 5 VRKDDEVQVVGG 16 (86)
Q Consensus 5 IrKgDeV~VI~G 16 (86)
|++||+|.+...
T Consensus 27 i~~Gd~v~i~P~ 38 (83)
T cd03698 27 IQKGDTLLVMPS 38 (83)
T ss_pred EeCCCEEEEeCC
Confidence 455666655554
No 83
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=23.68 E-value=98 Score=29.08 Aligned_cols=28 Identities=18% Similarity=0.317 Sum_probs=22.0
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEEeccccCc
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIFAIFSGVK 36 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~~~~~~~r 36 (86)
|+|.||.|.+ .|.+|.|.+|..-.|.|+
T Consensus 935 PfrVGD~I~I-----~~~~GtV~~I~lRsT~Ir 962 (1109)
T PRK10929 935 PIRIGDTVTI-----RDLTGSVTKINTRATTIS 962 (1109)
T ss_pred CCCCCCEEEE-----CCEEEEEEEEeeeEEEEE
Confidence 8999999987 367899999985555554
No 84
>KOG0199 consensus ACK and related non-receptor tyrosine kinases [Signal transduction mechanisms]
Probab=23.63 E-value=59 Score=30.41 Aligned_cols=17 Identities=29% Similarity=0.556 Sum_probs=15.0
Q ss_pred cccccCCCEEEEeeccC
Q 041704 2 SMSVRKDDEVQVVGGTY 18 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~ 18 (86)
.+++.|||++.||.|.-
T Consensus 390 aLh~~kgD~IvVIegs~ 406 (1039)
T KOG0199|consen 390 ALHLTKGDEIVVIEGSG 406 (1039)
T ss_pred ceeeccCCeEEEEecCC
Confidence 36899999999999985
No 85
>PF02941 FeThRed_A: Ferredoxin thioredoxin reductase variable alpha chain; InterPro: IPR004207 Ferredoxin thioredoxin reductase is a [4FE-4S] protein which plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit a and subunit b. Subunit a is the variable subunit, and b is the catalytic chain. This family is the alpha chain.; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0015979 photosynthesis, 0009536 plastid; PDB: 2PUK_B 2PVO_B 2PVG_B 1DJ7_B 2PVD_B 2PU9_B 2PUO_B.
Probab=23.04 E-value=1e+02 Score=20.15 Aligned_cols=12 Identities=50% Similarity=0.686 Sum_probs=8.0
Q ss_pred CCCeeeeEEEEE
Q 041704 18 YKGREGKFVQIF 29 (86)
Q Consensus 18 ~KGk~GKV~~V~ 29 (86)
.+|.+|.|.++.
T Consensus 26 l~G~EGev~~~v 37 (67)
T PF02941_consen 26 LKGMEGEVKQIV 37 (67)
T ss_dssp -TT-EEEEEEE-
T ss_pred ccCCEEEEEEEE
Confidence 578999999887
No 86
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=22.83 E-value=1.3e+02 Score=19.72 Aligned_cols=28 Identities=21% Similarity=0.291 Sum_probs=19.6
Q ss_pred cccccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 2 SMSVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 2 Sm~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.+.|+.||.|.|--=.|--..|.|+.-+
T Consensus 44 ~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry 71 (75)
T COG0361 44 RIRILPGDVVLVELSPYDLTKGRIVYRY 71 (75)
T ss_pred eEEeCCCCEEEEEecccccccccEEEEe
Confidence 3567888888887777765567666555
No 87
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=22.67 E-value=67 Score=20.00 Aligned_cols=16 Identities=19% Similarity=0.177 Sum_probs=11.3
Q ss_pred ccccCCCEEEEee--ccC
Q 041704 3 MSVRKDDEVQVVG--GTY 18 (86)
Q Consensus 3 m~IrKgDeV~VI~--Gk~ 18 (86)
..++.|++|.++. |+.
T Consensus 37 ~~i~~G~eV~y~~~~g~~ 54 (57)
T cd04467 37 DKLEPGKEVEYWESMGKR 54 (57)
T ss_pred ccCCCCCEEEEEeecCeE
Confidence 4577888888877 544
No 88
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=21.79 E-value=1.9e+02 Score=19.89 Aligned_cols=33 Identities=24% Similarity=0.407 Sum_probs=23.1
Q ss_pred ccCCCEEEEee-c---------cCCCeeeeEEEEEeccccCcccceEEE
Q 041704 5 VRKDDEVQVVG-G---------TYKGREGKFVQIFAIFSGVKRDLVVSY 43 (86)
Q Consensus 5 IrKgDeV~VI~-G---------k~KGk~GKV~~V~~~~~~~rkk~~V~V 43 (86)
.+.||.|-+.. | .|.|++|.|..+. ..-..|.|
T Consensus 35 y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~------~~A~~V~v 77 (98)
T PRK04306 35 FEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKR------GRAYIVEV 77 (98)
T ss_pred ccCCCEEEEEecCceecCCccccccCCCEEEEeec------CeEEEEEE
Confidence 46799886542 3 3789999999887 55555554
No 89
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=20.79 E-value=1.5e+02 Score=17.80 Aligned_cols=23 Identities=9% Similarity=0.300 Sum_probs=14.8
Q ss_pred cccCCCEEEEeeccCCCeeeeEEEEE
Q 041704 4 SVRKDDEVQVVGGTYKGREGKFVQIF 29 (86)
Q Consensus 4 ~IrKgDeV~VI~Gk~KGk~GKV~~V~ 29 (86)
.|++||+|.+.. .++..+|.+++
T Consensus 26 ~l~~g~~v~~~~---~~~~~~v~~l~ 48 (83)
T cd04088 26 TLKAGSTLYNST---KGKKERVGRLL 48 (83)
T ss_pred EEcCCCEEEECC---CCcEEEeeEEE
Confidence 578888887776 23444555555
Done!