Query 030538
Match_columns 175
No_of_seqs 132 out of 1156
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 15:15:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12426 elongation factor P; 100.0 4.2E-77 9E-82 481.0 24.6 173 2-174 13-185 (185)
2 PRK14578 elongation factor P; 100.0 1.2E-74 2.6E-79 467.8 25.0 173 2-174 13-187 (187)
3 PRK04542 elongation factor P; 100.0 1.1E-74 2.4E-79 468.5 24.5 174 2-175 13-189 (189)
4 TIGR02178 yeiP elongation fact 100.0 2E-74 4.3E-79 465.9 24.1 173 2-174 11-186 (186)
5 TIGR00038 efp translation elon 100.0 6.1E-72 1.3E-76 451.5 24.0 173 2-174 12-184 (184)
6 PRK00529 elongation factor P; 100.0 8.5E-72 1.9E-76 451.3 24.4 174 2-175 13-186 (186)
7 COG0231 Efp Translation elonga 100.0 3.3E-44 7.2E-49 276.0 16.5 117 2-118 15-131 (131)
8 TIGR00037 eIF_5A translation i 100.0 1.8E-35 3.9E-40 227.3 16.3 107 2-110 18-125 (130)
9 PRK03999 translation initiatio 100.0 1.4E-33 3E-38 216.6 16.0 105 2-108 17-122 (129)
10 PLN03107 eukaryotic translatio 100.0 3.7E-30 8E-35 203.7 15.8 105 2-106 32-143 (159)
11 PF09285 Elong-fact-P_C: Elong 100.0 5.3E-29 1.2E-33 165.3 7.6 56 118-173 1-56 (56)
12 cd05794 S1_EF-P_repeat_2 S1_EF 100.0 3.9E-29 8.4E-34 166.0 6.5 56 118-173 1-56 (56)
13 smart00841 Elong-fact-P_C Elon 100.0 3.7E-29 8E-34 166.1 6.4 56 118-173 1-56 (56)
14 cd04470 S1_EF-P_repeat_1 S1_EF 99.9 2.4E-25 5.1E-30 150.5 7.5 61 55-115 1-61 (61)
15 PF01132 EFP: Elongation facto 99.9 6.8E-23 1.5E-27 135.8 7.0 55 56-110 1-55 (55)
16 cd04463 S1_EF_like S1_EF_like: 99.8 8.8E-19 1.9E-23 115.4 6.3 55 57-112 1-55 (55)
17 PF08207 EFP_N: Elongation fac 99.8 3.7E-18 8.1E-23 114.2 7.7 48 2-49 11-58 (58)
18 PTZ00328 eukaryotic initiation 99.7 1.6E-16 3.4E-21 126.1 13.4 105 2-106 34-150 (166)
19 KOG3271 Translation initiation 99.5 5.3E-14 1.1E-18 108.9 9.3 101 2-102 32-136 (156)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.4 1.4E-06 3E-11 58.2 6.0 54 54-109 1-54 (57)
21 PF01287 eIF-5a: Eukaryotic el 97.3 0.0016 3.6E-08 44.9 7.2 52 53-105 1-57 (69)
22 COG1499 NMD3 NMD protein affec 95.5 0.13 2.8E-06 45.9 9.8 80 27-113 269-352 (355)
23 cd04468 S1_eIF5A S1_eIF5A: Euk 94.2 0.17 3.7E-06 34.9 5.6 52 54-105 1-55 (69)
24 cd04469 S1_Hex1 S1_Hex1: Hex1, 84.8 4.8 0.0001 28.2 6.2 48 57-104 3-55 (75)
25 PF00900 Ribosomal_S4e: Riboso 82.8 1.5 3.4E-05 30.7 3.1 33 137-169 42-75 (77)
26 PF02941 FeThRed_A: Ferredoxin 69.4 2.7 5.9E-05 28.9 1.3 19 103-121 38-56 (67)
27 PRK14560 putative RNA-binding 58.1 33 0.00071 26.8 5.7 72 95-173 39-126 (160)
28 cd02786 MopB_CT_3 The MopB_CT_ 57.5 8.5 0.00018 27.7 2.1 21 154-174 44-64 (116)
29 cd02779 MopB_CT_Arsenite-Ox Th 54.0 9.8 0.00021 27.6 2.0 23 153-175 45-67 (115)
30 PF04014 Antitoxin-MazE: Antid 53.6 25 0.00055 21.6 3.6 31 78-110 7-38 (47)
31 PF13509 S1_2: S1 domain; PDB: 53.3 18 0.00039 23.7 3.0 38 67-107 14-51 (61)
32 TIGR00451 unchar_dom_2 unchara 52.4 34 0.00074 24.7 4.7 29 145-173 45-80 (107)
33 cd02790 MopB_CT_Formate-Dh_H F 50.6 12 0.00027 26.7 2.0 21 154-174 48-68 (116)
34 cd02787 MopB_CT_ydeP The MopB_ 48.8 12 0.00026 26.9 1.7 21 154-174 44-64 (112)
35 cd02778 MopB_CT_Thiosulfate-R- 46.8 16 0.00035 26.4 2.1 21 154-174 43-63 (123)
36 COG1153 FwdD Formylmethanofura 46.7 16 0.00034 28.1 2.1 23 153-175 43-65 (128)
37 PRK04313 30S ribosomal protein 45.5 34 0.00074 29.0 4.1 34 137-170 131-166 (237)
38 cd02792 MopB_CT_Formate-Dh-Na- 45.3 18 0.00039 26.1 2.2 20 155-174 49-68 (122)
39 KOG1999 RNA polymerase II tran 44.6 2.7E+02 0.0058 28.5 10.5 131 32-166 397-544 (1024)
40 cd01771 Faf1_UBX Faf1 UBX doma 43.7 24 0.00052 24.6 2.5 29 21-52 2-30 (80)
41 PF01568 Molydop_binding: Moly 43.5 16 0.00034 25.9 1.6 20 155-174 44-63 (110)
42 KOG1708 Mitochondrial/chloropl 43.2 38 0.00083 28.3 4.0 52 105-171 122-173 (236)
43 cd02788 MopB_CT_NDH-1_NuoG2-N7 41.6 20 0.00042 25.3 1.8 20 155-174 43-62 (96)
44 cd02794 MopB_CT_DmsA-EC The Mo 41.5 22 0.00048 25.9 2.2 20 155-174 44-63 (121)
45 cd02783 MopB_CT_2 The MopB_CT_ 40.1 23 0.00049 27.5 2.1 20 155-174 46-65 (156)
46 cd02785 MopB_CT_4 The MopB_CT_ 38.5 25 0.00055 25.7 2.1 21 154-174 45-65 (124)
47 PF09465 LBR_tudor: Lamin-B re 38.2 1.2E+02 0.0026 20.1 5.1 37 34-70 7-48 (55)
48 PF07076 DUF1344: Protein of u 38.1 1.3E+02 0.0027 20.3 5.2 39 117-164 4-47 (61)
49 TIGR00523 eIF-1A eukaryotic/ar 37.6 1.6E+02 0.0035 21.5 6.7 53 107-167 6-70 (99)
50 PF08292 RNA_pol_Rbc25: RNA po 37.5 62 0.0013 24.5 4.1 53 73-126 22-75 (122)
51 smart00359 PUA Putative RNA-bi 37.1 48 0.001 21.7 3.2 26 149-174 25-50 (77)
52 cd02781 MopB_CT_Acetylene-hydr 36.4 31 0.00066 25.2 2.3 20 155-174 47-66 (130)
53 PF05836 Chorion_S16: Chorion 36.3 30 0.00066 25.5 2.1 40 111-152 67-108 (110)
54 PF06988 NifT: NifT/FixU prote 35.8 1.4E+02 0.0031 20.3 6.3 51 98-154 1-52 (64)
55 smart00166 UBX Domain present 35.7 31 0.00066 23.5 2.0 28 22-52 3-30 (80)
56 cd02793 MopB_CT_DMSOR-BSOR-TMA 35.5 29 0.00063 25.7 2.0 21 154-174 46-66 (129)
57 cd02782 MopB_CT_1 The MopB_CT_ 35.2 32 0.0007 25.2 2.2 20 155-174 47-66 (129)
58 PLN00036 40S ribosomal protein 33.9 57 0.0012 28.1 3.8 32 138-169 136-168 (261)
59 cd02776 MopB_CT_Nitrate-R-NarG 33.4 32 0.00069 26.3 2.0 21 154-174 44-64 (141)
60 PF12158 DUF3592: Protein of u 33.3 1.3E+02 0.0029 22.0 5.4 50 58-115 64-113 (148)
61 PF00207 A2M: Alpha-2-macroglo 33.1 44 0.00094 23.3 2.5 17 148-164 59-75 (92)
62 cd07387 MPP_PolD2_C PolD2 (DNA 32.3 65 0.0014 27.4 3.9 64 98-170 185-252 (257)
63 cd00508 MopB_CT_Fdh-Nap-like T 32.2 35 0.00077 24.3 2.0 21 154-174 48-68 (120)
64 cd01767 UBX UBX (ubiquitin reg 31.9 25 0.00055 23.7 1.1 25 25-52 4-28 (77)
65 cd02777 MopB_CT_DMSOR-like The 31.8 38 0.00081 24.9 2.1 20 155-174 48-67 (127)
66 TIGR03784 marine_sortase sorta 31.0 40 0.00086 27.0 2.3 17 155-171 109-125 (174)
67 cd08759 Type_III_cohesin_like 30.8 88 0.0019 24.9 4.1 69 94-162 12-87 (160)
68 COG2016 Predicted RNA-binding 30.7 86 0.0019 25.1 4.1 70 93-169 37-122 (161)
69 PF01472 PUA: PUA domain; Int 30.2 72 0.0016 21.4 3.1 29 146-174 16-50 (74)
70 PRK04012 translation initiatio 29.8 2.2E+02 0.0049 20.8 6.2 45 116-168 21-73 (100)
71 TIGR03684 arCOG00985 arCOG0415 28.7 1.7E+02 0.0037 22.4 5.4 30 144-173 83-119 (150)
72 cd02791 MopB_CT_Nitrate-R-NapA 28.5 45 0.00097 23.9 2.0 21 154-174 48-68 (122)
73 PRK04980 hypothetical protein; 28.3 93 0.002 23.0 3.6 36 135-174 16-52 (102)
74 PF04571 Lipin_N: lipin, N-ter 28.0 55 0.0012 24.6 2.4 26 136-172 17-42 (110)
75 cd02780 MopB_CT_Tetrathionate_ 27.8 47 0.001 25.0 2.1 20 155-174 44-63 (143)
76 cd02789 MopB_CT_FmdC-FwdD The 27.1 50 0.0011 23.8 2.1 21 154-174 44-64 (106)
77 cd04458 CSP_CDS Cold-Shock Pro 26.4 1.8E+02 0.0039 18.6 5.5 46 62-107 7-54 (65)
78 PTZ00118 40S ribosomal protein 25.5 1.1E+02 0.0023 26.5 4.0 30 140-169 138-168 (262)
79 cd05706 S1_Rrp5_repeat_sc10 S1 25.4 1.9E+02 0.0042 18.6 6.1 55 94-164 1-57 (73)
80 cd04330 RNAP_III_Rpc25_N RNAP_ 25.3 1.2E+02 0.0027 20.9 3.7 24 10-33 49-74 (80)
81 PF14289 DUF4369: Domain of un 24.9 2.3E+02 0.005 19.3 6.6 30 139-169 60-91 (106)
82 KOG1920 IkappaB kinase complex 24.6 2.8E+02 0.0061 29.0 7.2 57 90-146 73-129 (1265)
83 COG2996 Predicted RNA-bindinin 23.8 5E+02 0.011 22.7 8.7 87 66-164 17-124 (287)
84 PF10703 MoaF: Molybdenum cofa 23.8 4.1E+02 0.0089 22.9 7.3 79 26-111 20-103 (265)
85 PTZ00223 40S ribosomal protein 23.6 1.1E+02 0.0024 26.5 3.8 30 140-169 135-165 (273)
86 KOG3328 HGG motif-containing t 23.6 1.8E+02 0.0038 23.1 4.6 31 11-41 102-132 (148)
87 cd01773 Faf1_like1_UBX Faf1 ik 23.4 81 0.0017 22.3 2.5 20 33-52 12-31 (82)
88 cd01234 PH_CADPS CADPS (Ca2+-d 23.1 70 0.0015 24.2 2.1 38 120-168 55-96 (117)
89 KOG1641 Mitochondrial chaperon 22.5 2.7E+02 0.0059 20.7 5.1 60 110-173 31-95 (104)
90 PF02786 CPSase_L_D2: Carbamoy 22.2 60 0.0013 26.5 1.8 28 57-84 158-186 (211)
91 PF14651 Lipocalin_7: Lipocali 22.1 1.2E+02 0.0025 23.2 3.3 50 36-89 57-107 (128)
92 PF00829 Ribosomal_L21p: Ribos 21.5 1.3E+02 0.0027 21.8 3.2 28 137-164 8-36 (96)
93 TIGR02520 pilus_B_mal_scr type 21.4 3.4E+02 0.0073 25.2 6.8 73 90-163 326-405 (497)
94 PRK15463 cold shock-like prote 21.4 1.9E+02 0.0041 19.5 3.9 45 63-107 12-58 (70)
95 KOG0238 3-Methylcrotonyl-CoA c 21.3 1.9E+02 0.0041 27.8 5.0 64 58-121 269-352 (670)
96 TIGR00369 unchar_dom_1 unchara 21.3 1.6E+02 0.0034 21.0 3.8 34 5-39 58-93 (117)
97 PF04762 IKI3: IKI3 family; I 21.1 4.4E+02 0.0096 26.6 7.9 58 90-147 80-141 (928)
98 cd00655 RNAP_Rpb7_N_like RNAP_ 20.7 1.7E+02 0.0037 20.2 3.6 17 17-33 58-74 (80)
99 PHA02030 hypothetical protein 20.5 78 0.0017 28.0 2.2 78 10-96 150-230 (336)
100 TIGR01730 RND_mfp RND family e 20.4 4.9E+02 0.011 21.4 8.4 17 88-104 179-195 (322)
101 cd01770 p47_UBX p47-like ubiqu 20.4 1.1E+02 0.0023 21.1 2.6 25 24-51 5-29 (79)
102 PF12945 YcgR_2: Flagellar pro 20.4 1.8E+02 0.004 19.3 3.8 13 152-164 45-57 (87)
103 cd06530 S26_SPase_I The S26 Ty 20.2 1.7E+02 0.0036 19.6 3.5 36 138-174 10-54 (85)
104 PF03143 GTP_EFTU_D3: Elongati 20.1 1.1E+02 0.0024 21.6 2.7 12 152-163 54-65 (99)
No 1
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=4.2e-77 Score=481.01 Aligned_cols=173 Identities=22% Similarity=0.447 Sum_probs=171.6
Q ss_pred eEEcCcEEEEEEeEEecCCCCCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcceee
Q 030538 2 TLTTGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLE 81 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi~ 81 (175)
|++||+||.|++++|+|||||+|++|+|||||.||+++++||||+|++|.|+++++++||||.||+.|+|||++||||++
T Consensus 13 i~~~g~~~~V~~~~h~kPGkg~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~qylY~dg~~~~FMd~etyeQi~ 92 (185)
T PRK12426 13 ISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDEYLFLDLGNYDKIY 92 (185)
T ss_pred EEECCEEEEEEEEEEecCCCCceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEECCCeEEEecCCCceEEE
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCchhhhchhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEE
Q 030538 82 VPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEI 161 (175)
Q Consensus 82 l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I 161 (175)
|+++.+||+.+||+|||+|.++||+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|+||+||++||+|
T Consensus 93 i~~~~lgd~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kgdTat~~~KpAtLeTG~~V~VP~FI~~Gd~I 172 (185)
T PRK12426 93 IPKEIMKDNFLFLKAGVTVSALVYDGTVFSVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEVLVPPFVEIGDVI 172 (185)
T ss_pred eCHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCcccCCCcccEEEcCCCEEEeCCcccCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEECCCCceeeec
Q 030538 162 FINPQDDSYIGRA 174 (175)
Q Consensus 162 ~V~T~~g~Y~~R~ 174 (175)
+||||+|+|++||
T Consensus 173 kVdT~~geY~~R~ 185 (185)
T PRK12426 173 KVDTRTCEYIQRV 185 (185)
T ss_pred EEECCCCeEEeeC
Confidence 9999999999997
No 2
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=1.2e-74 Score=467.78 Aligned_cols=173 Identities=28% Similarity=0.487 Sum_probs=170.4
Q ss_pred eEEcCcEEEEEEeEEecCCCC--CcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcce
Q 030538 2 TLTTGKMYQVIDAEHKQRGRG--GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQ 79 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG--~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeq 79 (175)
|++||+||+|++++|+|||+| +|++|+|||||.||++++++|+++|++|.|+++++++||||.||+.|||||+|||||
T Consensus 13 i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~qylY~dg~~~~FMD~etyEQ 92 (187)
T PRK14578 13 IQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGDRGVFMDLETYEQ 92 (187)
T ss_pred EEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeEEEEeCCCEEEEecCCCcEE
Confidence 688999999999999999987 559999999999999999999999999999999999999999999999999999999
Q ss_pred eecCchhhhchhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCC
Q 030538 80 LEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGE 159 (175)
Q Consensus 80 i~l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd 159 (175)
++||++.+|++.+||+|||+|.+++|+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|+||+||++||
T Consensus 93 ~~i~~~~~g~~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~~tep~~KGdT~t~~~KpA~leTG~~v~VP~FI~~Gd 172 (187)
T PRK14578 93 FEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVNVDLPMTVELTVTDTAPVMKNATATAQTKEAVLETGLRLQVPPYLESGE 172 (187)
T ss_pred EEecHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCccccCccCCCcceEEEcCCCEEEeCCcccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEECCCCceeeec
Q 030538 160 EIFINPQDDSYIGRA 174 (175)
Q Consensus 160 ~I~V~T~~g~Y~~R~ 174 (175)
+|+||||||+|++||
T Consensus 173 ~I~VdT~~g~Y~~R~ 187 (187)
T PRK14578 173 KIKVDTRDGRFISRA 187 (187)
T ss_pred EEEEECCCCcEEeeC
Confidence 999999999999997
No 3
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=1.1e-74 Score=468.48 Aligned_cols=174 Identities=28% Similarity=0.507 Sum_probs=170.9
Q ss_pred eEEcCcEEEEEEeEEecC-CCCC-cEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcce
Q 030538 2 TLTTGKMYQVIDAEHKQR-GRGG-AMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQ 79 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kp-GkG~-A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeq 79 (175)
|+++|+||+|++++|+|| |||+ |++|+|||||.||+++++||||+|++|.|++++++|||||.||+.|+|||++||||
T Consensus 13 i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~qylY~dg~~~~FMd~etyEQ 92 (189)
T PRK04542 13 VEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGDEYVFMDNEDYTP 92 (189)
T ss_pred EEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCEEEEecCCCceE
Confidence 789999999999999999 7984 59999999999999999999999999999999999999999999999999999999
Q ss_pred eecCchhhhchhhccCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCC
Q 030538 80 LEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIG 158 (175)
Q Consensus 80 i~l~~~~lgd~~~~L~eg~~-v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~G 158 (175)
++||++.+||+.+||+|||+ |.+++|+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|+||+||++|
T Consensus 93 ~~i~~~~lgd~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kGdT~~~~~KpAtLetG~~v~VP~FI~~G 172 (189)
T PRK04542 93 YTFKKDQIEDELLFIPEGMPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLSTGLVIQVPEYISTG 172 (189)
T ss_pred EEECHHHhhhHhhhhhcCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCCccEEEcCCCEEEeCCcccCC
Confidence 99999999999999999998 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CEEEEECCCCceeeecC
Q 030538 159 EEIFINPQDDSYIGRAK 175 (175)
Q Consensus 159 d~I~V~T~~g~Y~~R~~ 175 (175)
|+|+||||+|+|++||.
T Consensus 173 d~I~VdT~tgeYv~R~~ 189 (189)
T PRK04542 173 EKIRINTEERKFMGRAD 189 (189)
T ss_pred CEEEEECCCCcEEeecC
Confidence 99999999999999984
No 4
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=100.00 E-value=2e-74 Score=465.95 Aligned_cols=173 Identities=25% Similarity=0.462 Sum_probs=169.7
Q ss_pred eEEcCcEEEEEEeEEecCCCCCc--EEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcce
Q 030538 2 TLTTGKMYQVIDAEHKQRGRGGA--MMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQ 79 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG~A--~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeq 79 (175)
|++||+||+|++++|+|||+|+| ++|+|||||.||+++++||||+|++|.|+++++++||||.||+.|+|||++||||
T Consensus 11 i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~~~~FMD~etyEQ 90 (186)
T TIGR02178 11 VEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEYVFMDEEDYTP 90 (186)
T ss_pred EEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCeEEEccCCCcEE
Confidence 78999999999999999987666 8999999999999999999999999999999999999999999999999999999
Q ss_pred eecCchhhhchhhccCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCC
Q 030538 80 LEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIG 158 (175)
Q Consensus 80 i~l~~~~lgd~~~~L~eg~~-v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~G 158 (175)
++|+++.+||+.+||+|||+ |.+++|+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|+||+||++|
T Consensus 91 ~~i~~~~lgd~~~fL~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~KGdT~~~~~KpA~LeTG~~v~VP~FI~~G 170 (186)
T TIGR02178 91 YTFDKDAIEDELLFISEGLSGMYVQLIDGSPVALELPQHVVLEIVETPPEIKGASASKRPKPAKLITGLVVQVPEYITTG 170 (186)
T ss_pred EEeCHHHhhhhhhhhhCCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCcccccCCCCcccEEEcCCCEEEeCCeecCC
Confidence 99999999999999999997 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CEEEEECCCCceeeec
Q 030538 159 EEIFINPQDDSYIGRA 174 (175)
Q Consensus 159 d~I~V~T~~g~Y~~R~ 174 (175)
|+|+||||||+|++||
T Consensus 171 d~IkVdTrtg~Y~~R~ 186 (186)
T TIGR02178 171 ERILINTTERAFMGRA 186 (186)
T ss_pred CEEEEECCCCcEEccC
Confidence 9999999999999997
No 5
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=100.00 E-value=6.1e-72 Score=451.54 Aligned_cols=173 Identities=31% Similarity=0.592 Sum_probs=171.7
Q ss_pred eEEcCcEEEEEEeEEecCCCCCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcceee
Q 030538 2 TLTTGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLE 81 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi~ 81 (175)
|+++|+||+|++++|+|||||+|++|++||||.||++++++|+++++++.+.++++++||||.||+.|+|||+|||||++
T Consensus 12 I~~~g~~~~V~~~~~~kpGkg~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dgd~~~fMD~etyeq~~ 91 (184)
T TIGR00038 12 IELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYVFMDTETYEQIE 91 (184)
T ss_pred EEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECCCEEEEeCCCCccceE
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCchhhhchhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEE
Q 030538 82 VPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEI 161 (175)
Q Consensus 82 l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I 161 (175)
|+++.+|++.+||+|||+|.+.||+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|+||+||++||+|
T Consensus 92 i~~~~l~~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fi~~Gd~I 171 (184)
T TIGR00038 92 LPKDLLGDAAKFLKENMEVSVTFYNGEPIGVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFIEEGEKI 171 (184)
T ss_pred cCHHHHHHHHhhcCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCcccEEEcCCCEEEeCCcccCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEECCCCceeeec
Q 030538 162 FINPQDDSYIGRA 174 (175)
Q Consensus 162 ~V~T~~g~Y~~R~ 174 (175)
+|||++|+|++||
T Consensus 172 ~v~T~~g~y~~R~ 184 (184)
T TIGR00038 172 KVDTRTGEYVERA 184 (184)
T ss_pred EEECCCCcEEecC
Confidence 9999999999997
No 6
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=8.5e-72 Score=451.32 Aligned_cols=174 Identities=33% Similarity=0.588 Sum_probs=172.5
Q ss_pred eEEcCcEEEEEEeEEecCCCCCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcceee
Q 030538 2 TLTTGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLE 81 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi~ 81 (175)
|+++|+||+|++++|+|||||+|++|+++|||.||++++++|+++++++.+.++++++||||.||+.|+|||+|||||++
T Consensus 13 I~~~g~~~~V~~~~~~kpGkg~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dgd~~~fMD~etyeq~~ 92 (186)
T PRK00529 13 IEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGYVFMDTETYEQIE 92 (186)
T ss_pred EEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECCCEEEEecCCCceeeE
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCchhhhchhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEE
Q 030538 82 VPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEI 161 (175)
Q Consensus 82 l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I 161 (175)
||++.+|++.+||+|||+|.+++|+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|+||+||++||+|
T Consensus 93 l~~~~lg~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I 172 (186)
T PRK00529 93 VPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGEKI 172 (186)
T ss_pred cCHHHhHHHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccCcccCCCcccEEEcCCCEEEeCCeecCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEECCCCceeeecC
Q 030538 162 FINPQDDSYIGRAK 175 (175)
Q Consensus 162 ~V~T~~g~Y~~R~~ 175 (175)
+|||++|+|++|||
T Consensus 173 ~v~T~~g~y~~R~~ 186 (186)
T PRK00529 173 KVDTRTGEYVERAK 186 (186)
T ss_pred EEECCCCcEEeecC
Confidence 99999999999996
No 7
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-44 Score=276.00 Aligned_cols=117 Identities=35% Similarity=0.642 Sum_probs=115.3
Q ss_pred eEEcCcEEEEEEeEEecCCCCCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcceee
Q 030538 2 TLTTGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLE 81 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi~ 81 (175)
|++||+||+|++++|+|||||+|++|+++|||+||++++.+|+++++++.|.++++++||||.||+.|+|||+|||||++
T Consensus 15 i~~dg~~~~V~~~~~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~~~~FMD~etyeq~~ 94 (131)
T COG0231 15 IVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGDFYVFMDLETYEQYE 94 (131)
T ss_pred EEECCeEEEEEEEEEccCCCCCcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCCeEEEccCCCceEEE
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCchhhhchhhccCCCCEEEEEEECCEEEEEeCCCeE
Q 030538 82 VPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRV 118 (175)
Q Consensus 82 l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP~~v 118 (175)
|+.+.+|++.+||+|||+|.+.+|+|++++++||++|
T Consensus 95 v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v 131 (131)
T COG0231 95 LPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV 131 (131)
T ss_pred ecchhhhhHHHhcCCCCEEEEEEECCEEEEEECCCCC
Confidence 9999999999999999999999999999999999975
No 8
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=1.8e-35 Score=227.29 Aligned_cols=107 Identities=21% Similarity=0.315 Sum_probs=102.4
Q ss_pred eEEcCcEEEEEEeEEecCCC-CCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCccee
Q 030538 2 TLTTGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQL 80 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGk-G~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi 80 (175)
++++|+||+|++++|+|||| |+|++|+++|||+||++++++|+|++++|.|.++++++||||.||+.|+|||+|||||+
T Consensus 18 i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~qylY~dg~~~~fMd~etyeq~ 97 (130)
T TIGR00037 18 VVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQVLAIMGGMVQLMDLDTYETD 97 (130)
T ss_pred EEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEEEEEecCCEEEEEcCCCcEEE
Confidence 67899999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCchhhhchhhccCCCCEEEEEEECCEEE
Q 030538 81 EVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 110 (175)
Q Consensus 81 ~l~~~~lgd~~~~L~eg~~v~v~~~~~~~i 110 (175)
.|+.+. +..+||+||++|.++-.-|+..
T Consensus 98 ~i~~~~--~~~~~Lke~~~V~v~~~~g~~~ 125 (130)
T TIGR00037 98 ELPIPE--ELGDSLEPGFEVEYIEAMGQEK 125 (130)
T ss_pred EecCCh--hHHHHhhcCCEEEEEecCCeEE
Confidence 999986 8999999999999988777643
No 9
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=1.4e-33 Score=216.58 Aligned_cols=105 Identities=24% Similarity=0.331 Sum_probs=99.7
Q ss_pred eEEcCcEEEEEEeEEecCCC-CCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCccee
Q 030538 2 TLTTGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQL 80 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGk-G~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi 80 (175)
|.++|+||+|++++|+|||| |+|++|+++|||.||++++.+|++++++|.+.++++++||||.||+.|+|||+|||||+
T Consensus 17 i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~~~~fMd~eTyeq~ 96 (129)
T PRK03999 17 VVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGDVVQLMDLETYETF 96 (129)
T ss_pred EEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCCEEEEecCCCceEE
Confidence 67899999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCchhhhchhhccCCCCEEEEEEECCE
Q 030538 81 EVPLDVFGKAGAYLQEGMKVWLQLYDGR 108 (175)
Q Consensus 81 ~l~~~~lgd~~~~L~eg~~v~v~~~~~~ 108 (175)
+|+++ ||+..||+||++|.++---|+
T Consensus 97 ~i~~~--~d~~~~l~eg~~v~v~~~~g~ 122 (129)
T PRK03999 97 EIPIP--EELKDKLEPGVEVEYWEAMGR 122 (129)
T ss_pred EecCC--hhHHhhCcCCCEEEEEhhCCe
Confidence 99998 999999999999887654443
No 10
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=99.97 E-value=3.7e-30 Score=203.75 Aligned_cols=105 Identities=16% Similarity=0.268 Sum_probs=95.3
Q ss_pred eEEcCcEEEEEEeEEecCCC-CCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEE-EEEeC--CCc
Q 030538 2 TLTTGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA-FVIES--ETF 77 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGk-G~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~-vFMD~--ety 77 (175)
|+++|+||+|++++|+|||| |+|++|+++|||+||++++.+|+|+++++.|+++++++||||.||+.| +|||+ ++|
T Consensus 32 I~~~g~pc~V~e~~~~KpGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ve~~~ve~~~~qyly~dgd~y~~fMD~~get~ 111 (159)
T PLN03107 32 IVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCDVPHVNRTDYQLIDISEDGFVSLMDESGNTK 111 (159)
T ss_pred EEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEecCCCEEEEEEEEEEEEEEEEEcCCceEEEEcCCCCcc
Confidence 68999999999999999999 999999999999999999999999999999999999999999999995 99999 699
Q ss_pred ceeecCc---hhhhchhhccCCCCEEEEEEEC
Q 030538 78 EQLEVPL---DVFGKAGAYLQEGMKVWLQLYD 106 (175)
Q Consensus 78 eqi~l~~---~~lgd~~~~L~eg~~v~v~~~~ 106 (175)
||+.||+ ++......+..+|.++.|.+|.
T Consensus 112 eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~ 143 (159)
T PLN03107 112 DDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMS 143 (159)
T ss_pred eeEEccCcchHHHHHHHHHHhCCCeEEEEEEe
Confidence 9999986 4344444566789997777775
No 11
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=99.96 E-value=5.3e-29 Score=165.34 Aligned_cols=56 Identities=32% Similarity=0.629 Sum_probs=50.3
Q ss_pred EEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEECCCCceeee
Q 030538 118 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 173 (175)
Q Consensus 118 v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~~g~Y~~R 173 (175)
|+|+|++|+|++||||+++++|+|+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 V~l~V~etep~~kg~t~~~~~K~A~letG~~i~VP~FI~~Gd~I~VdT~~g~Yv~R 56 (56)
T PF09285_consen 1 VELEVVETEPAVKGDTASSSYKPATLETGAEIQVPLFIEEGDKIKVDTRDGSYVER 56 (56)
T ss_dssp EEEEEEEE-SSSTTSSSSTTEEEEEETTS-EEEEETT--TT-EEEEETTTTEEEEE
T ss_pred CEEEEEECCCCccCcccCCCccEEEEcCCCEEEccceecCCCEEEEECCCCeEeCC
Confidence 68999999999999999999999999999999999999999999999999999998
No 12
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.96 E-value=3.9e-29 Score=166.01 Aligned_cols=56 Identities=29% Similarity=0.526 Sum_probs=55.0
Q ss_pred EEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEECCCCceeee
Q 030538 118 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 173 (175)
Q Consensus 118 v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~~g~Y~~R 173 (175)
|+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 v~l~V~etep~~kG~T~~~~~K~A~letG~~i~VP~FI~~Gd~I~V~T~~g~Y~~R 56 (56)
T cd05794 1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCeecCCCEEEEECCCCcEecC
Confidence 58999999999999999999999999999999999999999999999999999998
No 13
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=99.96 E-value=3.7e-29 Score=166.10 Aligned_cols=56 Identities=27% Similarity=0.515 Sum_probs=55.0
Q ss_pred EEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEECCCCceeee
Q 030538 118 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 173 (175)
Q Consensus 118 v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~~g~Y~~R 173 (175)
|+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 V~l~V~etep~vkG~T~~~~~K~A~letG~~i~VP~FI~~Gd~I~V~T~~g~Y~~R 56 (56)
T smart00841 1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 56 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCcccCCCEEEEECCCCcEEcC
Confidence 58999999999999999999999999999999999999999999999999999998
No 14
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.92 E-value=2.4e-25 Score=150.52 Aligned_cols=61 Identities=33% Similarity=0.758 Sum_probs=59.8
Q ss_pred EeeEEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCCEEEEEEECCEEEEEeCC
Q 030538 55 EDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 115 (175)
Q Consensus 55 e~~~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP 115 (175)
++|++||||.||+.|||||++||||++|+++.+|++.+||+|||+|.+++|+|+||+|+||
T Consensus 1 e~~~~qylY~dg~~~~FMd~etyeQ~~i~~~~igd~~~~L~e~~~v~v~~~~~~~i~v~lP 61 (61)
T cd04470 1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61 (61)
T ss_pred CCceEEEEEeCCCEEEEeCCCCceEEEECHHHhhhHHhhCcCCCEEEEEEECCEEEEEECc
Confidence 4789999999999999999999999999999999999999999999999999999999999
No 15
>PF01132 EFP: Elongation factor P (EF-P) OB domain; InterPro: IPR001059 Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet []. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. This entry reresents the central domain of elongation factor P and its homologues. It forms an oligonucleotide-binding (OB) fold, though it is not clear if this region is involved in binding nucleic acids [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation; PDB: 1YBY_A 3A5Z_H 3TRE_A 1UEB_B 3HUW_V 3HUY_V 3OYY_B.
Probab=99.88 E-value=6.8e-23 Score=135.78 Aligned_cols=55 Identities=36% Similarity=0.748 Sum_probs=50.0
Q ss_pred eeEEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCCEEEEEEECCEEE
Q 030538 56 DKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 110 (175)
Q Consensus 56 ~~~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~~~~~i 110 (175)
+|++||||.||+.|||||++||||++|+++.+|++.+||+||++|.+.+|+|+||
T Consensus 1 ~r~~qylY~dgd~~~FMd~etyeQi~v~~~~~g~~~~~L~eg~~v~v~~~~~~~I 55 (55)
T PF01132_consen 1 RREMQYLYKDGDNYVFMDTETYEQIEVPKDQLGDALKFLKEGMEVQVLFYEGKPI 55 (55)
T ss_dssp EEEEEEEEEESSEEEEEETTT--EEEEEHHHHTTTGCC--TTEEEEEEEETTEEE
T ss_pred CceEEEEEeCCCEEEEecCCCceEEEecHHHhChHHhhCcCCCEEEEEEECCEEC
Confidence 6899999999999999999999999999999999999999999999999999997
No 16
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=99.77 E-value=8.8e-19 Score=115.44 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=51.7
Q ss_pred eEEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCCEEEEEEECCEEEEE
Q 030538 57 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSG 112 (175)
Q Consensus 57 ~~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v 112 (175)
|++||||.||+.|+|||++||||++++++.+ ++.+||+||++|.+.+|+|+|+++
T Consensus 1 ~~~qylY~dg~~~~fMd~etyeq~~v~~~~~-~~~~~l~eg~~v~v~~~~g~~i~~ 55 (55)
T cd04463 1 RELQVLDIQGSKPVTMDLETYEVVQVPPPVD-QSFESFEPGEVVLVDTRTGQYVGV 55 (55)
T ss_pred CCEEEEEcCCCEeEEecCCCceEEEeCHHHh-hHHhhCCCCCEEEEEEECCEEEeC
Confidence 5799999999999999999999999999985 599999999999999999999874
No 17
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=99.75 E-value=3.7e-18 Score=114.18 Aligned_cols=48 Identities=33% Similarity=0.650 Sum_probs=45.9
Q ss_pred eEEcCcEEEEEEeEEecCCCCCcEEEEEEEECCCCCeEEEEeCCCCcE
Q 030538 2 TLTTGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAV 49 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGkG~A~vr~klknl~TG~~~e~~f~s~dkv 49 (175)
|++||+||+|++++|++||||+|+||+|||||.||+++|++|+++|+|
T Consensus 11 i~~~g~~~~V~~~~~~k~gkg~a~v~~klknl~tG~~~e~tf~s~d~v 58 (58)
T PF08207_consen 11 IEIDGEPYVVLDFQHVKPGKGGAFVRVKLKNLRTGSKVEKTFRSGDKV 58 (58)
T ss_dssp EEETTEEEEEEEEEEECCTTSSSEEEEEEEETTTTEEEEEEEETT-EE
T ss_pred EEECCEEEEEEEEEEECCCCCCeEEEEEEEECCCCCEEEEEECCCCcC
Confidence 789999999999999999999999999999999999999999999986
No 18
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=99.72 E-value=1.6e-16 Score=126.12 Aligned_cols=105 Identities=20% Similarity=0.307 Sum_probs=92.4
Q ss_pred eEEcCcEEEEEEeEEecCCC-CCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCC-------EEEEEe
Q 030538 2 TLTTGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND-------TAFVIE 73 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGk-G~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd-------~~vFMD 73 (175)
++++|+||+|++++.+|||| |+|.+++...+|+||++.+...++.++++.+.++|++||.+..++| +..+||
T Consensus 34 vvIkGrPCKIveistSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~hnv~VP~V~r~~yqli~I~~d~~~~~~g~v~LMd 113 (166)
T PTZ00328 34 VCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNEDPSLPAHLSLMD 113 (166)
T ss_pred EEECCeeeEEEEEecCCCCcCCceEEEEEEEecCCCCEEeeecCccceeEeeeEEeeEEEEEEEcCCCcccccceEEEEc
Confidence 78999999999999999999 9999999999999999999999999999999999999999999886 478999
Q ss_pred CCCcceee--cCc-hhhhc-hhhccCCCCEEEEEEEC
Q 030538 74 SETFEQLE--VPL-DVFGK-AGAYLQEGMKVWLQLYD 106 (175)
Q Consensus 74 ~etyeqi~--l~~-~~lgd-~~~~L~eg~~v~v~~~~ 106 (175)
.+.|+-.. ||. +.|+. ....+.+|.+|.|.+|.
T Consensus 114 ~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~v~vi~ 150 (166)
T PTZ00328 114 DEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVVS 150 (166)
T ss_pred CCCCeeecccCCChhHHHHHHHHHhcCCCeEEEEEEh
Confidence 98877655 553 33332 45677999999988886
No 19
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.53 E-value=5.3e-14 Score=108.87 Aligned_cols=101 Identities=17% Similarity=0.287 Sum_probs=90.5
Q ss_pred eEEcCcEEEEEEeEEecCCC-CCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeC--CCcc
Q 030538 2 TLTTGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIES--ETFE 78 (175)
Q Consensus 2 ~~~~g~~~~V~~~~h~kpGk-G~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~--etye 78 (175)
|+++|+||+|++.+.+|.|| |+|.+.+..++|+||++.|.-++|++++++++++|++||.+-.+++..-|||+ ++-+
T Consensus 32 vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn~dVp~vkr~~yqLidIsd~~~sl~t~sG~~kd 111 (156)
T KOG3271|consen 32 VVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDGYLSLMTDSGETKD 111 (156)
T ss_pred EEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCccccCccccceeEEEEecCCeEEEEcCCCCcch
Confidence 68999999999999999999 99999999999999999999999999999999999999999999998889998 5778
Q ss_pred eeecCchhhhchhh-ccCCCCEEEE
Q 030538 79 QLEVPLDVFGKAGA-YLQEGMKVWL 102 (175)
Q Consensus 79 qi~l~~~~lgd~~~-~L~eg~~v~v 102 (175)
++.+|.+.++.++. -+.+|..+.+
T Consensus 112 Dlklp~~el~~~i~~~~e~g~dl~v 136 (156)
T KOG3271|consen 112 DLKLPEGELGNQIRQGFEEGKDLLV 136 (156)
T ss_pred hccCcchhHHHHHHHhhcCCCcEEE
Confidence 99999988887764 3355554444
No 20
>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=98.35 E-value=1.4e-06 Score=58.16 Aligned_cols=54 Identities=26% Similarity=0.319 Sum_probs=44.9
Q ss_pred EEeeEEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCCEEEEEEECCEE
Q 030538 54 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRA 109 (175)
Q Consensus 54 le~~~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~~~~~ 109 (175)
++||..|.++.+|+...+||+||||.++++.. .+...-+++|.+|.++-.-|+.
T Consensus 1 i~k~~aqVisi~g~~vQlMD~eTYeT~ev~~p--~~~~~~i~~G~eV~y~~~~g~~ 54 (57)
T cd04467 1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIP--EEIKDKLEPGKEVEYWESMGKR 54 (57)
T ss_pred CcceEEEEEEEcCCEEEEeccccceeEEEecc--hhhcccCCCCCEEEEEeecCeE
Confidence 57999999999999999999999999999985 2233458999999976666653
No 21
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=97.28 E-value=0.0016 Score=44.94 Aligned_cols=52 Identities=23% Similarity=0.365 Sum_probs=38.1
Q ss_pred eEEeeEEEEEEeeCC-EEEEEeCCCcce---eecCchhhhchh-hccCCCCEEEEEEE
Q 030538 53 FVEDKSFTCLYTEND-TAFVIESETFEQ---LEVPLDVFGKAG-AYLQEGMKVWLQLY 105 (175)
Q Consensus 53 ~le~~~~qylY~Dgd-~~vFMD~etyeq---i~l~~~~lgd~~-~~L~eg~~v~v~~~ 105 (175)
.++|++||.+..++| +..+|| ++|+. +.||...++..+ .-+.+|.++.|.++
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMd-e~get~eDl~lP~~el~~ei~~~~~~g~~~~Vtv~ 57 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMD-EDGETREDLKLPDGELGEEIKAKFEEGKEVLVTVL 57 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEE-TTS-EEEEEECCSHHHHHHHHHHHHTTCEEEEEEE
T ss_pred CeEEEEEEEEEEccCcEEEEEc-CCCCeeccEEecccchhHHHHhhccCCCeEEEEEE
Confidence 478999999999988 778999 66555 558966666554 45699999655555
No 22
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=95.52 E-value=0.13 Score=45.93 Aligned_cols=80 Identities=23% Similarity=0.246 Sum_probs=61.7
Q ss_pred EEEEEECCCCCeEEEEeCCCCcEE--eeeEE--eeEEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCCEEEE
Q 030538 27 QMELRDIDTGNKVSLRFGTEEAVE--RVFVE--DKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWL 102 (175)
Q Consensus 27 r~klknl~TG~~~e~~f~s~dkve--~~~le--~~~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v 102 (175)
.+.++|+.|+...+.++.-...-+ .+.-+ -+.+.++-.+.+...|||++|||-.++... =|.+|.++.+
T Consensus 269 ~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~vvs~~~~~~~v~d~et~e~~~~~~~-------~~~~g~~v~v 341 (355)
T COG1499 269 GIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVVVSRDPSAIQVLDPETYEARTVKGP-------SLEEGDEVKV 341 (355)
T ss_pred ceEEEecccCCccccChhhcccCcceeeeccccceEEEEEecCCCceEEEecceEEEEeccCC-------CCCCCCEEEE
Confidence 378899999988777664433333 22223 367888889999999999999999999876 4589999999
Q ss_pred EEECCEEEEEe
Q 030538 103 QLYDGRALSGS 113 (175)
Q Consensus 103 ~~~~~~~i~v~ 113 (175)
..+.|....++
T Consensus 342 ~~~~~~~~~~~ 352 (355)
T COG1499 342 FKVRGRNYVVE 352 (355)
T ss_pred EEEeceEEeec
Confidence 99998876654
No 23
>cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. 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 oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=94.21 E-value=0.17 Score=34.95 Aligned_cols=52 Identities=21% Similarity=0.350 Sum_probs=40.2
Q ss_pred EEeeEEEEEEeeCCEEEEEeC--CCcceeecCchhhhchhh-ccCCCCEEEEEEE
Q 030538 54 VEDKSFTCLYTENDTAFVIES--ETFEQLEVPLDVFGKAGA-YLQEGMKVWLQLY 105 (175)
Q Consensus 54 le~~~~qylY~Dgd~~vFMD~--etyeqi~l~~~~lgd~~~-~L~eg~~v~v~~~ 105 (175)
+.|++||.+..++++..+|+. ++-|++.||.+.++..+. -..+|..+.+...
T Consensus 1 V~R~eYqLidI~dGflsLm~e~G~~k~DlklP~~elg~~I~~~f~~gk~~~vtV~ 55 (69)
T cd04468 1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTVL 55 (69)
T ss_pred CcceeEEEEeecCCeEEEEcCCCCcccCCcCCcHHHHHHHHHHHhCCCcEEEEEE
Confidence 468999999997788899976 679999999988887763 3356766665543
No 24
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=84.80 E-value=4.8 Score=28.22 Aligned_cols=48 Identities=13% Similarity=0.146 Sum_probs=35.0
Q ss_pred eEEEEEEeeCCEEEEEeC--CCcceeecC-chhhhchhh-ccCCCC-EEEEEE
Q 030538 57 KSFTCLYTENDTAFVIES--ETFEQLEVP-LDVFGKAGA-YLQEGM-KVWLQL 104 (175)
Q Consensus 57 ~~~qylY~Dgd~~vFMD~--etyeqi~l~-~~~lgd~~~-~L~eg~-~v~v~~ 104 (175)
++||.+..++++..+||. ++-+++.|| .+.++..+. -..+|. ++.+..
T Consensus 3 ~eYqLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk~~v~VtV 55 (75)
T cd04469 3 KQYRVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGRGSVRVLV 55 (75)
T ss_pred eEEEEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCCCcEEEEE
Confidence 579999997678889975 678999999 777776653 226666 555444
No 25
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=82.81 E-value=1.5 Score=30.68 Aligned_cols=33 Identities=9% Similarity=0.199 Sum_probs=26.6
Q ss_pred CceEEEeecccEEEcc-cceeCCCEEEEECCCCc
Q 030538 137 RYRRALLDNGVTVMVP-SYLEIGEEIFINPQDDS 169 (175)
Q Consensus 137 ~~K~A~letG~~v~VP-~fI~~Gd~I~V~T~~g~ 169 (175)
+-=...|..|..+..| +-|+.||.|+|+..+++
T Consensus 42 G~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~k 75 (77)
T PF00900_consen 42 GKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQK 75 (77)
T ss_dssp GEEEEEETTTEEEES-SST--TTEEEEEETTTTE
T ss_pred CcEEEEecCceEEEcCcCCccCCCEEEEECCCCc
Confidence 3447888999999999 99999999999999886
No 26
>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=69.42 E-value=2.7 Score=28.86 Aligned_cols=19 Identities=26% Similarity=0.569 Sum_probs=12.8
Q ss_pred EEECCEEEEEeCCCeEEEE
Q 030538 103 QLYDGRALSGSIPKRVACT 121 (175)
Q Consensus 103 ~~~~~~~i~v~lP~~v~l~ 121 (175)
..|+|+|||..||-.|.+.
T Consensus 38 ~~wkGr~iSanlP~~V~F~ 56 (67)
T PF02941_consen 38 TDWKGRPISANLPVKVQFD 56 (67)
T ss_dssp SEETTEE---SS-EEEEET
T ss_pred eecCCcEecCCCcEEEEEe
Confidence 4689999999999999874
No 27
>PRK14560 putative RNA-binding protein; Provisional
Probab=58.13 E-value=33 Score=26.78 Aligned_cols=72 Identities=21% Similarity=0.345 Sum_probs=41.5
Q ss_pred CCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCC-ceEEEe--------ecccEEEcccc------eeCCC
Q 030538 95 QEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPR-YRRALL--------DNGVTVMVPSY------LEIGE 159 (175)
Q Consensus 95 ~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~-~K~A~l--------etG~~v~VP~f------I~~Gd 159 (175)
+.+..+.+.+.+|+|+-++.-..+ -|.+.|.-.-+. .+.+++ ..|+.++.|-. ++.||
T Consensus 39 ~~~~~~~~~~~~~~p~~f~~d~~~-------~Ptl~~~~~~~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~Gd 111 (160)
T PRK14560 39 ETDKKEEIYLVDGEPLFFKVDDEL-------FPTLRGALKLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGD 111 (160)
T ss_pred EcCCcEEEEEECCEEEEEEeCCcc-------cccHHHHHhCCccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCCC
Confidence 344567777778888877652122 222232211111 222332 36888888855 46799
Q ss_pred EEEEECCC-Cceeee
Q 030538 160 EIFINPQD-DSYIGR 173 (175)
Q Consensus 160 ~I~V~T~~-g~Y~~R 173 (175)
.|.|-++. |..+..
T Consensus 112 ~V~I~~~~~~~~vav 126 (160)
T PRK14560 112 IVFVVEETHGKPLAV 126 (160)
T ss_pred EEEEEECCCCeEEEE
Confidence 99998877 777653
No 28
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.55 E-value=8.5 Score=27.70 Aligned_cols=21 Identities=19% Similarity=0.124 Sum_probs=18.0
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.++.|+..-||
T Consensus 44 gi~~Gd~V~v~s~~G~~~~~v 64 (116)
T cd02786 44 GIADGDLVVVFNDRGSVTLRA 64 (116)
T ss_pred CCCCCCEEEEEcCCeEEEEEE
Confidence 367899999999999988776
No 29
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=54.00 E-value=9.8 Score=27.65 Aligned_cols=23 Identities=17% Similarity=0.033 Sum_probs=19.2
Q ss_pred cceeCCCEEEEECCCCceeeecC
Q 030538 153 SYLEIGEEIFINPQDDSYIGRAK 175 (175)
Q Consensus 153 ~fI~~Gd~I~V~T~~g~Y~~R~~ 175 (175)
+=|+.||.|+|.++.|+..-||+
T Consensus 45 lgi~~Gd~V~v~s~~G~i~~~~~ 67 (115)
T cd02779 45 EGLKNGDLVEVYNDYGSTTAMAY 67 (115)
T ss_pred cCCCCCCEEEEEeCCEEEEEEEE
Confidence 34778999999999999887763
No 30
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=53.63 E-value=25 Score=21.63 Aligned_cols=31 Identities=19% Similarity=0.307 Sum_probs=23.3
Q ss_pred ceeecCchhhhchhhccCCCCEEEEEEECC-EEE
Q 030538 78 EQLEVPLDVFGKAGAYLQEGMKVWLQLYDG-RAL 110 (175)
Q Consensus 78 eqi~l~~~~lgd~~~~L~eg~~v~v~~~~~-~~i 110 (175)
-|+.||++.... .-|++|.++.+...++ +.+
T Consensus 7 ~~v~iPk~~~~~--l~l~~Gd~v~i~~~~~g~i~ 38 (47)
T PF04014_consen 7 GQVTIPKEIREK--LGLKPGDEVEIEVEGDGKIV 38 (47)
T ss_dssp SEEEE-HHHHHH--TTSSTTTEEEEEEETTSEEE
T ss_pred ceEECCHHHHHH--cCCCCCCEEEEEEeCCCEEE
Confidence 388999987643 3789999999999987 443
No 31
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=53.31 E-value=18 Score=23.73 Aligned_cols=38 Identities=13% Similarity=0.192 Sum_probs=22.7
Q ss_pred CEEEEEeCCCcceeecCchhhhchhhccCCCCEEEEEEECC
Q 030538 67 DTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDG 107 (175)
Q Consensus 67 d~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~~~ 107 (175)
+.-.|+|...-..+.||...+. .=++.|.+|.+..|.+
T Consensus 14 ~~g~fL~~~~~~~vlLp~~e~~---~~~~~Gd~v~VFvY~D 51 (61)
T PF13509_consen 14 EFGYFLDDGEGKEVLLPKSEVP---EPLKVGDEVEVFVYLD 51 (61)
T ss_dssp SSEEEEEETT-EEEEEEGGG---------TTSEEEEEEEE-
T ss_pred CCEEEEECCCCCEEEechHHcC---CCCCCCCEEEEEEEEC
Confidence 3445566666778888877553 2379999999998854
No 32
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=52.44 E-value=34 Score=24.70 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=22.9
Q ss_pred cccEEEcccc------eeCCCEEEEECCC-Cceeee
Q 030538 145 NGVTVMVPSY------LEIGEEIFINPQD-DSYIGR 173 (175)
Q Consensus 145 tG~~v~VP~f------I~~Gd~I~V~T~~-g~Y~~R 173 (175)
.|+.++-|-. ++.||.|.|-+.+ |+.+.+
T Consensus 45 ~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~iav 80 (107)
T TIGR00451 45 NGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAV 80 (107)
T ss_pred CCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEEE
Confidence 6888888844 5779999998876 888765
No 33
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=50.56 E-value=12 Score=26.66 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=16.3
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.+..|+..-+|
T Consensus 48 gi~~Gd~V~v~~~~G~~~~~v 68 (116)
T cd02790 48 GIEDGEKVRVSSRRGSVEVRA 68 (116)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 467889999999888876554
No 34
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=48.85 E-value=12 Score=26.93 Aligned_cols=21 Identities=19% Similarity=0.213 Sum_probs=17.4
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||+|+|.++.|+-.-||
T Consensus 44 gI~dGd~V~v~s~~G~i~~~a 64 (112)
T cd02787 44 GLKAGDRVDLESAFGDGQGRI 64 (112)
T ss_pred CCCCCCEEEEEecCCCCeEEE
Confidence 356999999999999876665
No 35
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=46.79 E-value=16 Score=26.45 Aligned_cols=21 Identities=14% Similarity=0.306 Sum_probs=17.7
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.++.|+..-+|
T Consensus 43 gi~~Gd~V~v~s~~G~i~~~v 63 (123)
T cd02778 43 GIKDGDRVEVSSARGKVTGKA 63 (123)
T ss_pred CCCCCCEEEEEeCCCcEEEEE
Confidence 467899999999999987665
No 36
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=46.71 E-value=16 Score=28.09 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=19.6
Q ss_pred cceeCCCEEEEECCCCceeeecC
Q 030538 153 SYLEIGEEIFINPQDDSYIGRAK 175 (175)
Q Consensus 153 ~fI~~Gd~I~V~T~~g~Y~~R~~ 175 (175)
+=+++||.++|.++-|+-+=||+
T Consensus 43 Lgv~EGD~VkVkse~GeVVV~Ak 65 (128)
T COG1153 43 LGVSEGDKVKVKSEFGEVVVKAK 65 (128)
T ss_pred hCCCcCCeEEEEecCccEEEEEe
Confidence 55789999999999999887774
No 37
>PRK04313 30S ribosomal protein S4e; Validated
Probab=45.48 E-value=34 Score=29.02 Aligned_cols=34 Identities=15% Similarity=0.298 Sum_probs=27.2
Q ss_pred CceEEEeecccEEEcc--cceeCCCEEEEECCCCce
Q 030538 137 RYRRALLDNGVTVMVP--SYLEIGEEIFINPQDDSY 170 (175)
Q Consensus 137 ~~K~A~letG~~v~VP--~fI~~Gd~I~V~T~~g~Y 170 (175)
+--...|..|..|.+| .-++.||.|+|+-.+++=
T Consensus 131 G~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI 166 (237)
T PRK04313 131 GKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEI 166 (237)
T ss_pred CEEEEEecCCceEEccCccccccCCEEEEECCCCce
Confidence 4447788888888888 688999999999888763
No 38
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=45.30 E-value=18 Score=26.07 Aligned_cols=20 Identities=10% Similarity=0.307 Sum_probs=16.4
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||.|+|.+..|+..-+|
T Consensus 49 i~~Gd~V~v~s~~G~~~~~v 68 (122)
T cd02792 49 IKNGDMVWVSSPRGKIKVKA 68 (122)
T ss_pred CCCCCEEEEEcCCceEEEEE
Confidence 57799999999999877665
No 39
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=44.55 E-value=2.7e+02 Score=28.50 Aligned_cols=131 Identities=14% Similarity=0.145 Sum_probs=81.9
Q ss_pred ECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEe--eCCEEEEEeC--CCcceeecCchhhhchhhccCCCCEEEEEE--E
Q 030538 32 DIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYT--ENDTAFVIES--ETFEQLEVPLDVFGKAGAYLQEGMKVWLQL--Y 105 (175)
Q Consensus 32 nl~TG~~~e~~f~s~dkve~~~le~~~~qylY~--Dgd~~vFMD~--etyeqi~l~~~~lgd~~~~L~eg~~v~v~~--~ 105 (175)
-+.+.++....|..+|.++++.-+-+.++=.-. ||...+.|-. .--+-++++...| .+|+++|.-|.|.- |
T Consensus 397 t~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eL---rKyF~~GDhVKVi~G~~ 473 (1024)
T KOG1999|consen 397 TLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASEL---RKYFEPGDHVKVIAGRY 473 (1024)
T ss_pred eeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhh---hhhccCCCeEEEEeccc
Confidence 677888888889999999999999998875554 8888888865 3455677777665 78999997776653 4
Q ss_pred C---CEEEEEeCCCeE--------EEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEECC
Q 030538 106 D---GRALSGSIPKRV--------ACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQ 166 (175)
Q Consensus 106 ~---~~~i~v~lP~~v--------~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~ 166 (175)
+ |-++.|+=-.-+ +|+|--.+-..--+.++...|.--.|=+--|+.+.+ +.|=+|++.-+
T Consensus 474 eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~~-~vgvI~rle~e 544 (1024)
T KOG1999|consen 474 EGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDNQ-NVGVIVRLERE 544 (1024)
T ss_pred cCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccccccceeecCCC-cEEEEEEecch
Confidence 4 344555432222 344433322211222222233333444455677777 77766666543
No 40
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=43.74 E-value=24 Score=24.61 Aligned_cols=29 Identities=10% Similarity=0.211 Sum_probs=21.7
Q ss_pred CCCcEEEEEEEECCCCCeEEEEeCCCCcEEee
Q 030538 21 RGGAMMQMELRDIDTGNKVSLRFGTEEAVERV 52 (175)
Q Consensus 21 kG~A~vr~klknl~TG~~~e~~f~s~dkve~~ 52 (175)
+|.+.++++ |-+|+.++.+|.+++++..+
T Consensus 2 ~~~~~i~iR---lP~G~r~~rrF~~t~~L~~l 30 (80)
T cd01771 2 EPISKLRVR---TPSGDFLERRFLGDTPLQVL 30 (80)
T ss_pred CCeEEEEEE---CCCCCEEEEEeCCCCcHHHH
Confidence 344444444 57899999999999999854
No 41
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=43.49 E-value=16 Score=25.89 Aligned_cols=20 Identities=15% Similarity=0.152 Sum_probs=16.1
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||.|+|.++.|+-.-||
T Consensus 44 i~~Gd~V~v~s~~G~v~~~v 63 (110)
T PF01568_consen 44 IKDGDWVRVSSPRGSVEVRV 63 (110)
T ss_dssp --TTCEEEEEETTEEEEEEE
T ss_pred CcCCCEEEEEeccceEeeee
Confidence 78899999999999887766
No 42
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=43.19 E-value=38 Score=28.34 Aligned_cols=52 Identities=13% Similarity=0.210 Sum_probs=34.2
Q ss_pred ECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEECCCCcee
Q 030538 105 YDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYI 171 (175)
Q Consensus 105 ~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~~g~Y~ 171 (175)
+.|.++..+-|-++.-.|.=.+|.-. ...+-+- -|-+.|++|+|.||+|.-+
T Consensus 122 ~pgtivk~EaPlhvsk~VmLvdp~d~----------q~te~~w-----r~~e~GekVRvstrSG~iI 173 (236)
T KOG1708|consen 122 EPGTIVKSEAPLHVSKQVMLVDPEDD----------QPTEVEW-----RFTEDGEKVRVSTRSGRII 173 (236)
T ss_pred CCceEEeecCCceecceeEEECcccc----------CCceeeE-----EEcCCCcEEEEEecccccc
Confidence 45777888888888777777777311 1111122 2667899999999998643
No 43
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=41.55 E-value=20 Score=25.34 Aligned_cols=20 Identities=15% Similarity=0.086 Sum_probs=15.5
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||.|+|.++.|+-.-+|
T Consensus 43 i~~Gd~V~v~s~~G~i~~~v 62 (96)
T cd02788 43 LADGDLVEFSLGDGTLTLPV 62 (96)
T ss_pred CCCCCEEEEEECCeEEEEEE
Confidence 57799999999988865554
No 44
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=41.54 E-value=22 Score=25.87 Aligned_cols=20 Identities=10% Similarity=0.268 Sum_probs=15.8
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||.|+|.+..|+-.-||
T Consensus 44 i~~Gd~V~v~s~~g~i~~~a 63 (121)
T cd02794 44 IKDGDRVLVFNDRGKVIRPV 63 (121)
T ss_pred CCCCCEEEEEcCCceEEEEE
Confidence 45799999999998876665
No 45
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=40.10 E-value=23 Score=27.46 Aligned_cols=20 Identities=15% Similarity=0.405 Sum_probs=17.5
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||.|+|.++.|+-..||
T Consensus 46 I~dGd~V~v~s~~G~~~~~a 65 (156)
T cd02783 46 IKDGDWVWVESVNGRVKGQA 65 (156)
T ss_pred CCCCCEEEEEcCCeeEEEEE
Confidence 67899999999999987776
No 46
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.50 E-value=25 Score=25.67 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=17.2
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||+|+|.++.|+-.-||
T Consensus 45 gi~~Gd~V~v~s~~G~i~~~a 65 (124)
T cd02785 45 GIAHGDLVEVYNDRGSVVCKA 65 (124)
T ss_pred CCCCCCEEEEEeCCCEEEEEE
Confidence 367899999999999877665
No 47
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=38.20 E-value=1.2e+02 Score=20.07 Aligned_cols=37 Identities=19% Similarity=0.201 Sum_probs=24.3
Q ss_pred CCCCeEEEEeCCCCcEEeeeEE-----eeEEEEEEeeCCEEE
Q 030538 34 DTGNKVSLRFGTEEAVERVFVE-----DKSFTCLYTENDTAF 70 (175)
Q Consensus 34 ~TG~~~e~~f~s~dkve~~~le-----~~~~qylY~Dgd~~v 70 (175)
..|..+.-+|+.+...-++.+. .+.++.+|.||+..-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~ 48 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELE 48 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEE
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEE
Confidence 4688888999888877555444 478899999998743
No 48
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=38.07 E-value=1.3e+02 Score=20.35 Aligned_cols=39 Identities=28% Similarity=0.373 Sum_probs=30.8
Q ss_pred eEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccc-----eeCCCEEEEE
Q 030538 117 RVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY-----LEIGEEIFIN 164 (175)
Q Consensus 117 ~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~f-----I~~Gd~I~V~ 164 (175)
.++=+|...+| .+...+|+.|..-+.|.= +++|.+|+|-
T Consensus 4 ~veG~I~~id~---------~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~ 47 (61)
T PF07076_consen 4 DVEGTIKSIDP---------ETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVF 47 (61)
T ss_pred cceEEEEEEcC---------CceEEEecCCCEEECCCcccccccCCCCEEEEE
Confidence 45566777776 377899999999999974 6789998873
No 49
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=37.63 E-value=1.6e+02 Score=21.47 Aligned_cols=53 Identities=13% Similarity=0.369 Sum_probs=36.3
Q ss_pred CEEEEEeCCC----eEEEEEEEeCCCCCCccCCCCceEEEeecccEEE--cc------cceeCCCEEEEECCC
Q 030538 107 GRALSGSIPK----RVACTIKEIHASTKGPTVTPRYRRALLDNGVTVM--VP------SYLEIGEEIFINPQD 167 (175)
Q Consensus 107 ~~~i~v~lP~----~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~--VP------~fI~~Gd~I~V~T~~ 167 (175)
.+...++||. .+..+|++.-+ +..=.+.+++|.++. +| ..|..||.|.|+..+
T Consensus 6 ~~~~~~~~p~~~e~e~~g~V~~~lG--------~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~d 70 (99)
T TIGR00523 6 EQQIRVRLPRKEEGEILGVIEQMLG--------AGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWE 70 (99)
T ss_pred cCcceeeCCCCCCCEEEEEEEEEcC--------CCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEcc
Confidence 3456677774 67778887765 234567778887763 33 468999999996433
No 50
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=37.53 E-value=62 Score=24.48 Aligned_cols=53 Identities=13% Similarity=0.308 Sum_probs=40.4
Q ss_pred eCCCcceeecCchhhhchhhccCCCCEEEEEEE-CCEEEEEeCCCeEEEEEEEeC
Q 030538 73 ESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLY-DGRALSGSIPKRVACTIKEIH 126 (175)
Q Consensus 73 D~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~-~~~~i~v~lP~~v~l~V~~t~ 126 (175)
...-|++|.||++.|-+-..| .+...+-+.-| ++.-+-+++-..|.++|.+..
T Consensus 22 slgFFddI~IP~~~L~~ps~f-d~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 22 SLGFFDDIFIPPSLLPEPSRF-DEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp EECCEEEEEEECCCC-TTEEE-ECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred EecccccEEECHHHCCCCCcc-CccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 346789999999999877777 44456777778 899999999999999998754
No 51
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=37.08 E-value=48 Score=21.73 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=21.3
Q ss_pred EEcccceeCCCEEEEECCCCceeeec
Q 030538 149 VMVPSYLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 149 v~VP~fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
+.++.-++.||.|.|-+++|+++.++
T Consensus 25 ~~~~~~~~~g~~V~v~~~~g~~vg~G 50 (77)
T smart00359 25 VRVDGGIKEGDVVVIVDEKGEPLGIG 50 (77)
T ss_pred EEEeCCcCCCCEEEEEcCCCCEEEEE
Confidence 45555577899999999999999875
No 52
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=36.45 E-value=31 Score=25.25 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=15.5
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||+|+|.++.|+-.-||
T Consensus 47 i~~Gd~V~v~s~~G~~~~~v 66 (130)
T cd02781 47 IADGDWVWVETPRGRARQKA 66 (130)
T ss_pred CCCCCEEEEECCCCEEEEEE
Confidence 46789999999888766554
No 53
>PF05836 Chorion_S16: Chorion protein S16; InterPro: IPR008450 Correct eggshell formation relies on a complex series of events that relies on expression, cleavage and transport of various proteins at appropriate times. In Drosophila, the eggshell framework is laid down between the developing oocyte and the overlying follicle cells during late oogenesis. Five distinct layers are observed in Drosophila eggshells: the oocyte proximal vitelline membrane, a lipid wax layer, the inner chorion layer, the endochorion and exochorion layers []. The inner chorion layer is continuous and characterised by its periodic structure. Genes encoding chorion proteins are expressed from oocyte development stage 11 onwards. Chorion synthesis occurs during the last 5-6 hours of oogenesis and demands the production of large amounts of protein. Amplification of the two chorion gene clusters meets demand for large scale protein production and expression is precisely regulated through tight transcriptional control of the chorion genes. Chorion proteins may be described according to the times at which they are expressed in the follicular cells: developmentally early (s36, s38), middle (s19, s16) or late (s18, s15). This family consists of several examples of the Drosophila melanogaster specific chorion protein S16. The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary [].; GO: 0007275 multicellular organismal development, 0042600 chorion
Probab=36.28 E-value=30 Score=25.45 Aligned_cols=40 Identities=20% Similarity=0.341 Sum_probs=29.4
Q ss_pred EEeCCCeEEEEEEEeCCCCCCccCCC--CceEEEeecccEEEcc
Q 030538 111 SGSIPKRVACTIKEIHASTKGPTVTP--RYRRALLDNGVTVMVP 152 (175)
Q Consensus 111 ~v~lP~~v~l~V~~t~p~~kg~t~~~--~~K~A~letG~~v~VP 152 (175)
...||+. --|.+.+|.+|-++-++ +-|.++|.||.++-|-
T Consensus 67 ~aalppR--sFVaeiDPvFkks~yGg~yg~k~~~l~t~sklav~ 108 (110)
T PF05836_consen 67 AAALPPR--SFVAEIDPVFKKSSYGGSYGEKKVTLNTGSKLAVA 108 (110)
T ss_pred hhcCCch--hhhhhcChhhcccccCccccceeEEEecCCeEEEE
Confidence 3445553 23678899999988655 4689999999998763
No 54
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=35.78 E-value=1.4e+02 Score=20.28 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=28.0
Q ss_pred CEEEEEEECCEEEEEeCCCe-EEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccc
Q 030538 98 MKVWLQLYDGRALSGSIPKR-VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY 154 (175)
Q Consensus 98 ~~v~v~~~~~~~i~v~lP~~-v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~f 154 (175)
|.|.+..-+.--+++.+|.. ++=.|++.| +...--..++|+||-+..+|..
T Consensus 1 MkVmiR~~~~G~ls~YVpKKDLEE~Vv~~E------~~~~wGG~v~L~NGw~l~lp~~ 52 (64)
T PF06988_consen 1 MKVMIRKNGAGGLSAYVPKKDLEEPVVSME------KPELWGGEVTLANGWELYLPPL 52 (64)
T ss_dssp --EEEEE-SS--EEEEETTTTEEEEEEEES------SSSS-SSEEEETTS-EEE----
T ss_pred CeEEEEeCCCcCEEEEEeCCccccceeeee------ccCccCCEEEECCcCEEEeCCC
Confidence 33444433333788888865 677788875 2233456899999999999875
No 55
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=35.75 E-value=31 Score=23.54 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=21.4
Q ss_pred CCcEEEEEEEECCCCCeEEEEeCCCCcEEee
Q 030538 22 GGAMMQMELRDIDTGNKVSLRFGTEEAVERV 52 (175)
Q Consensus 22 G~A~vr~klknl~TG~~~e~~f~s~dkve~~ 52 (175)
+.+.+++|+ -+|+.+..+|++++++..+
T Consensus 3 ~~~~I~iRl---PdG~ri~~~F~~~~tl~~v 30 (80)
T smart00166 3 DQCRLQIRL---PDGSRLVRRFPSSDTLRTV 30 (80)
T ss_pred CeEEEEEEc---CCCCEEEEEeCCCCcHHHH
Confidence 344555554 7899999999999998753
No 56
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=35.55 E-value=29 Score=25.69 Aligned_cols=21 Identities=10% Similarity=0.107 Sum_probs=16.5
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.++.|+-.-||
T Consensus 46 gi~~Gd~V~v~s~~G~~~~~~ 66 (129)
T cd02793 46 GIADGDIVRVFNDRGACLAGA 66 (129)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 366799999999988876665
No 57
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=35.16 E-value=32 Score=25.20 Aligned_cols=20 Identities=15% Similarity=0.229 Sum_probs=16.0
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||.|+|.+..|+-.-||
T Consensus 47 i~~Gd~V~v~s~~g~~~~~~ 66 (129)
T cd02782 47 LADGDKVRVTSAAGSVEAEV 66 (129)
T ss_pred CCCCCEEEEEcCCCeEEEEE
Confidence 57799999999988876655
No 58
>PLN00036 40S ribosomal protein S4; Provisional
Probab=33.93 E-value=57 Score=28.09 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=21.6
Q ss_pred ceEEEeecccEEEccc-ceeCCCEEEEECCCCc
Q 030538 138 YRRALLDNGVTVMVPS-YLEIGEEIFINPQDDS 169 (175)
Q Consensus 138 ~K~A~letG~~v~VP~-fI~~Gd~I~V~T~~g~ 169 (175)
--...|..|..|..|. -|++||.|+||..+++
T Consensus 136 ~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~k 168 (261)
T PLN00036 136 IPYLNTHDGRTIRYPDPLIKANDTIKIDLETNK 168 (261)
T ss_pred eEEEEecCCceeccCCCccccCCEEEEeCCCCc
Confidence 3366677777777653 5677777777777765
No 59
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=33.37 E-value=32 Score=26.32 Aligned_cols=21 Identities=10% Similarity=0.083 Sum_probs=17.4
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.++.|+-.-||
T Consensus 44 gI~dGd~V~v~~~~G~v~~~a 64 (141)
T cd02776 44 GIKDNDWVEVFNDNGVVVARA 64 (141)
T ss_pred CCCCCCEEEEEeCCeEEEEEE
Confidence 477899999999999877665
No 60
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=33.31 E-value=1.3e+02 Score=21.96 Aligned_cols=50 Identities=14% Similarity=0.064 Sum_probs=29.5
Q ss_pred EEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCCEEEEEEECCEEEEEeCC
Q 030538 58 SFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 115 (175)
Q Consensus 58 ~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~~v~v~~~~~~~i~v~lP 115 (175)
.++|-|.||..+. ++.-+.....+..+-+..|.+|+|.+.-++|=...++
T Consensus 64 ~v~y~~~~G~~~~--------~~~~~~~~~~~~~~~~~~G~~V~V~Y~P~~P~~~~l~ 113 (148)
T PF12158_consen 64 VVEYTYQDGRTYS--------RFYSGSDNFGSYWPKYPIGDTVTVYYNPNNPEEARLE 113 (148)
T ss_pred EEEEEECCCcEEE--------EeccCCcccccCCccCCCcCEEEEEECCcCCCeEEEe
Confidence 3778888775444 1111111134444447899999998887776554444
No 61
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=33.06 E-value=44 Score=23.31 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=12.9
Q ss_pred EEEcccceeCCCEEEEE
Q 030538 148 TVMVPSYLEIGEEIFIN 164 (175)
Q Consensus 148 ~v~VP~fI~~Gd~I~V~ 164 (175)
....|.|+..||.+.|.
T Consensus 59 ~~~lP~~l~~GD~~~i~ 75 (92)
T PF00207_consen 59 QLNLPRSLRRGDQIQIP 75 (92)
T ss_dssp EEE--SEEETTSEEEEE
T ss_pred EcCCCcEEecCCEEEEE
Confidence 46899999999999874
No 62
>cd07387 MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2), C-terminal domain. PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily
Probab=32.30 E-value=65 Score=27.44 Aligned_cols=64 Identities=17% Similarity=0.188 Sum_probs=40.3
Q ss_pred CEEEEE-EECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccE---EEcccceeCCCEEEEECCCCce
Q 030538 98 MKVWLQ-LYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVT---VMVPSYLEIGEEIFINPQDDSY 170 (175)
Q Consensus 98 ~~v~v~-~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~---v~VP~fI~~Gd~I~V~T~~g~Y 170 (175)
.++... |.+..|+-++=.++|-+ -|+...-++|...-++|.. |.||.|-++|..+.||.+|-+.
T Consensus 185 DTL~~yP~~~~Dpfvi~~~PhVyf---------~Gnq~~f~t~~~~~~~~~~v~lv~vP~Fs~t~~~vlvdl~tLe~ 252 (257)
T cd07387 185 DTLWCYPFTDRDPFILEECPHVYF---------AGNQPKFGTKLVEGEEGQRVLLVCVPSFSKTGTAVLVNLRTLEC 252 (257)
T ss_pred CccccccCCCCCceeecCCCCEEE---------eCCCcceeeeEEEcCCCCeEEEEEeCCcCcCCEEEEEECCcCcE
Confidence 444443 23555655543333322 3555555566665555544 7899999999999999998764
No 63
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=32.19 E-value=35 Score=24.25 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=15.5
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.+..|+-.-+|
T Consensus 48 gi~~Gd~V~v~~~~G~~~~~v 68 (120)
T cd00508 48 GIKDGDLVRVSSRRGSVVVRA 68 (120)
T ss_pred CCCCCCEEEEEeCCEEEEEEE
Confidence 357788888888888765544
No 64
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=31.94 E-value=25 Score=23.73 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=19.2
Q ss_pred EEEEEEEECCCCCeEEEEeCCCCcEEee
Q 030538 25 MMQMELRDIDTGNKVSLRFGTEEAVERV 52 (175)
Q Consensus 25 ~vr~klknl~TG~~~e~~f~s~dkve~~ 52 (175)
.+++++ -.|+.+..+|++++++..+
T Consensus 4 ~i~iRl---pdG~~~~~~F~~~~tl~~l 28 (77)
T cd01767 4 KIQIRL---PDGKRLEQRFNSTHKLSDV 28 (77)
T ss_pred EEEEEc---CCCCEEEEEeCCCCCHHHH
Confidence 445554 5599999999999998753
No 65
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=31.80 E-value=38 Score=24.86 Aligned_cols=20 Identities=10% Similarity=0.189 Sum_probs=14.9
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||+|+|.+..|+-.-||
T Consensus 48 i~~Gd~V~v~s~~g~i~~~v 67 (127)
T cd02777 48 IKDGDIVRVFNDRGAVLAGA 67 (127)
T ss_pred CCCCCEEEEEcCCeEEEEEE
Confidence 45788888888888766554
No 66
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=31.02 E-value=40 Score=26.98 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=15.1
Q ss_pred eeCCCEEEEECCCCcee
Q 030538 155 LEIGEEIFINPQDDSYI 171 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~ 171 (175)
++.||.|.|.+.+|+|.
T Consensus 109 L~~GD~I~v~~~~g~~~ 125 (174)
T TIGR03784 109 LRPGDVIRLQTPDGQWQ 125 (174)
T ss_pred CCCCCEEEEEECCCeEE
Confidence 78999999999999753
No 67
>cd08759 Type_III_cohesin_like Cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents type III cohesins and closely related domains.
Probab=30.77 E-value=88 Score=24.95 Aligned_cols=69 Identities=14% Similarity=0.223 Sum_probs=49.2
Q ss_pred cCCCCEEEEEEECC-----EEEEEeCCCe-EEEEEEEeCCCC-CCccCCCCceEEEeecccEEEcccceeCCCEEE
Q 030538 94 LQEGMKVWLQLYDG-----RALSGSIPKR-VACTIKEIHAST-KGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIF 162 (175)
Q Consensus 94 L~eg~~v~v~~~~~-----~~i~v~lP~~-v~l~V~~t~p~~-kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~ 162 (175)
.+.|.+++|.++.. .+++..||-- =.|+.+.++++. .+..-.+-+|.-.=.+|..-.-|.|.+.||+=.
T Consensus 12 ~~aGetvti~vkg~~l~~VnA~~~~l~yD~~~le~V~~e~~~~~~~~Menls~~r~h~~g~~~ly~~faN~G~~~~ 87 (160)
T cd08759 12 VKAGETITIDLYGQGLKNVNALGAHIPFDNSKLELVKDEDGATSTAGMENLSKEKTHDDGTADVYLFFANEGDKDL 87 (160)
T ss_pred cCCCCEEEEEEEecccceeeeeeeEEecChHHcEEEcccccchhhhhheecceeeecCCCcceEEEEEEeccCccc
Confidence 58899999999853 5788888876 578888888865 222233445544445666667799999998744
No 68
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=30.75 E-value=86 Score=25.10 Aligned_cols=70 Identities=19% Similarity=0.183 Sum_probs=41.8
Q ss_pred ccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCce-EEE--------eecccEEEcccce------eC
Q 030538 93 YLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYR-RAL--------LDNGVTVMVPSYL------EI 157 (175)
Q Consensus 93 ~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K-~A~--------letG~~v~VP~fI------~~ 157 (175)
..+-..+.++.+.+|+|+-++.-..+.- .+++--..+..+ .++ +.|||-|+.|-.+ +.
T Consensus 37 v~~~~~~~~ii~vdG~pl~f~~~~~~iP-------Tl~~l~~~~~~~~~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik~ 109 (161)
T COG2016 37 VAKCDDKFEIILVDGEPLLFQRDDRLIP-------TLRLLLKLPPGKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIKE 109 (161)
T ss_pred EEecCCcEEEEEECCEEEEEEeCCeech-------hhHHHHhCCCCccEEEEcCccHhhhcCCCceeccceeecCCCccC
Confidence 3344457888889999999887764432 222222222111 333 4577889999775 56
Q ss_pred CCEEEEECCC-Cc
Q 030538 158 GEEIFINPQD-DS 169 (175)
Q Consensus 158 Gd~I~V~T~~-g~ 169 (175)
||.|.|.-+. |.
T Consensus 110 Gd~VvV~~e~~~~ 122 (161)
T COG2016 110 GDIVVVVDEKKGR 122 (161)
T ss_pred CCEEEEEEcCCCC
Confidence 7777766554 44
No 69
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=30.18 E-value=72 Score=21.43 Aligned_cols=29 Identities=24% Similarity=0.468 Sum_probs=20.9
Q ss_pred ccEEEccc------ceeCCCEEEEECCCCceeeec
Q 030538 146 GVTVMVPS------YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 146 G~~v~VP~------fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.+..|- -++.||.|.|-+++|+.+.+.
T Consensus 16 Ga~L~~~GV~~~~~~f~~gd~V~i~~~~g~~ia~G 50 (74)
T PF01472_consen 16 GASLFAPGVVEVDGDFRKGDEVAIVDEDGEVIAVG 50 (74)
T ss_dssp TSEEEGGGEEEEETT--TTSEEEEEETTSSEEEEE
T ss_pred CCCcchHHhEECCCCcCCCCEEEEEcCCCeEEEEE
Confidence 55555443 358899999999999998875
No 70
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=29.79 E-value=2.2e+02 Score=20.76 Aligned_cols=45 Identities=20% Similarity=0.358 Sum_probs=30.2
Q ss_pred CeEEEEEEEeCCCCCCccCCCCceEEEeecccEEE--cc------cceeCCCEEEEECCCC
Q 030538 116 KRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVM--VP------SYLEIGEEIFINPQDD 168 (175)
Q Consensus 116 ~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~--VP------~fI~~Gd~I~V~T~~g 168 (175)
..+.-+|++.-+ +..=.+.+++|.++. +| ..|..||.|.|...+-
T Consensus 21 ~e~~g~V~~~lG--------~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~ 73 (100)
T PRK04012 21 GEVFGVVEQMLG--------ANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDF 73 (100)
T ss_pred CEEEEEEEEEcC--------CCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEeccc
Confidence 456666776655 234466777887753 33 6789999999986543
No 71
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=28.71 E-value=1.7e+02 Score=22.41 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=22.5
Q ss_pred ecccEEEcccc------eeCCCEEEEECCC-Cceeee
Q 030538 144 DNGVTVMVPSY------LEIGEEIFINPQD-DSYIGR 173 (175)
Q Consensus 144 etG~~v~VP~f------I~~Gd~I~V~T~~-g~Y~~R 173 (175)
.+|+.++.|-. ++.||.|.|-++. |..+..
T Consensus 83 ~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vav 119 (150)
T TIGR03684 83 INGADIMAPGIVSADPSIKEGDIVFVVDETHRKPLAV 119 (150)
T ss_pred hcCcccccCceecCCCCCCCCCEEEEEECCCCeEEEE
Confidence 36888887754 5679999999887 877643
No 72
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=28.53 E-value=45 Score=23.94 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=16.3
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||+|+|.+..|+..-+|
T Consensus 48 gi~~Gd~V~v~~~~G~~~~~v 68 (122)
T cd02791 48 GLKEGDLVRVTSRRGEVVLRV 68 (122)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 357899999999988876554
No 73
>PRK04980 hypothetical protein; Provisional
Probab=28.28 E-value=93 Score=22.99 Aligned_cols=36 Identities=14% Similarity=0.216 Sum_probs=28.1
Q ss_pred CCCceEEEeecccEEEcccceeCCCEEEE-ECCCCceeeec
Q 030538 135 TPRYRRALLDNGVTVMVPSYLEIGEEIFI-NPQDDSYIGRA 174 (175)
Q Consensus 135 ~~~~K~A~letG~~v~VP~fI~~Gd~I~V-~T~~g~Y~~R~ 174 (175)
-++.|.||.-+| .....++||.+.| .-++|.|+-.+
T Consensus 16 LsGkKTiTiRd~----se~~~~~G~~~~V~~~e~g~~~c~i 52 (102)
T PRK04980 16 LAGRKTITIRDE----SESHFKPGDVLRVGTFEDDRYFCTI 52 (102)
T ss_pred HcCCceEEeeCC----cccCCCCCCEEEEEECCCCcEEEEE
Confidence 356899999885 4678899999999 56778877543
No 74
>PF04571 Lipin_N: lipin, N-terminal conserved region; InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=28.04 E-value=55 Score=24.60 Aligned_cols=26 Identities=23% Similarity=0.294 Sum_probs=20.7
Q ss_pred CCceEEEeecccEEEcccceeCCCEEEEECCCCceee
Q 030538 136 PRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIG 172 (175)
Q Consensus 136 ~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~~g~Y~~ 172 (175)
+...||+| +||. |.|.|.-.||+|.+
T Consensus 17 ~~~npatl-SGAi----------DVIVV~q~DGs~~s 42 (110)
T PF04571_consen 17 NPINPATL-SGAI----------DVIVVEQPDGSLKS 42 (110)
T ss_pred ccCCcccc-cCce----------eEEEEecCCCCEec
Confidence 45678888 6776 89999999999864
No 75
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=27.83 E-value=47 Score=24.96 Aligned_cols=20 Identities=20% Similarity=0.499 Sum_probs=15.4
Q ss_pred eeCCCEEEEECCCCceeeec
Q 030538 155 LEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 155 I~~Gd~I~V~T~~g~Y~~R~ 174 (175)
|+.||+|+|.+..|+-.-+|
T Consensus 44 I~~Gd~V~v~s~~G~i~~~v 63 (143)
T cd02780 44 IKTGDRVRVVTPGGSVVGKA 63 (143)
T ss_pred CCCCCEEEEEeCCceEEEEE
Confidence 47888888888888766554
No 76
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=27.13 E-value=50 Score=23.76 Aligned_cols=21 Identities=10% Similarity=0.009 Sum_probs=15.6
Q ss_pred ceeCCCEEEEECCCCceeeec
Q 030538 154 YLEIGEEIFINPQDDSYIGRA 174 (175)
Q Consensus 154 fI~~Gd~I~V~T~~g~Y~~R~ 174 (175)
=|+.||.|+|.++.|+-.-||
T Consensus 44 gi~~Gd~V~v~~~~G~v~~~v 64 (106)
T cd02789 44 GKPEGDKVKVTSEFGEVVVFA 64 (106)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 467788888888888765554
No 77
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=26.37 E-value=1.8e+02 Score=18.59 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=34.0
Q ss_pred EEeeCCEEEEEeCCC-cceeecCchhhhch-hhccCCCCEEEEEEECC
Q 030538 62 LYTENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYDG 107 (175)
Q Consensus 62 lY~Dgd~~vFMD~et-yeqi~l~~~~lgd~-~~~L~eg~~v~v~~~~~ 107 (175)
.|.+...|=|+..+. =+++-+..+.+... ..-|++|+.|......+
T Consensus 7 ~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 7 WFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred EEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 355556677777665 67888888887766 67889999998877654
No 78
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=25.52 E-value=1.1e+02 Score=26.45 Aligned_cols=30 Identities=13% Similarity=0.285 Sum_probs=20.0
Q ss_pred EEEeecccEEEccc-ceeCCCEEEEECCCCc
Q 030538 140 RALLDNGVTVMVPS-YLEIGEEIFINPQDDS 169 (175)
Q Consensus 140 ~A~letG~~v~VP~-fI~~Gd~I~V~T~~g~ 169 (175)
...|..|..|..|- -|++||.|+||-.+++
T Consensus 138 ~l~~hDGrni~~~d~~ik~~Dtv~i~l~~~k 168 (262)
T PTZ00118 138 IAVTHDGRTIRYVHPDVKVGDSLRLDLETGK 168 (262)
T ss_pred EEEecCcceeccCCCcccCCCEEEEECCCCc
Confidence 44577777776653 5677777777776665
No 79
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.40 E-value=1.9e+02 Score=18.59 Aligned_cols=55 Identities=13% Similarity=0.033 Sum_probs=31.5
Q ss_pred cCCCCEEEE--EEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEE
Q 030538 94 LQEGMKVWL--QLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFIN 164 (175)
Q Consensus 94 L~eg~~v~v--~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~ 164 (175)
|+.|+.+.. .-..+.-+.++|+..++--|--++-.- + + .-..+.+.+.||.|++.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~--~-----~---------~~~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD--D-----Y---------SEALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC--c-----c---------ccccccccCCCCEEEEE
Confidence 456766643 334566677888877766555443211 0 0 00126778889988774
No 80
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=25.29 E-value=1.2e+02 Score=20.89 Aligned_cols=24 Identities=17% Similarity=0.407 Sum_probs=16.8
Q ss_pred EEEEeE--EecCCCCCcEEEEEEEEC
Q 030538 10 QVIDAE--HKQRGRGGAMMQMELRDI 33 (175)
Q Consensus 10 ~V~~~~--h~kpGkG~A~vr~klknl 33 (175)
.+.+++ .+-||-|+|.+++++|=|
T Consensus 49 di~~i~eG~I~~gdG~~~~~V~Fr~l 74 (80)
T cd04330 49 DILEVEDGYILPGDGASHYKVTFRMV 74 (80)
T ss_pred EeEEEcCCEEECCCCCEEEEEEEEEE
Confidence 344444 366888999999988743
No 81
>PF14289 DUF4369: Domain of unknown function (DUF4369)
Probab=24.88 E-value=2.3e+02 Score=19.30 Aligned_cols=30 Identities=33% Similarity=0.369 Sum_probs=22.7
Q ss_pred eEEEe--ecccEEEcccceeCCCEEEEECCCCc
Q 030538 139 RRALL--DNGVTVMVPSYLEIGEEIFINPQDDS 169 (175)
Q Consensus 139 K~A~l--etG~~v~VP~fI~~Gd~I~V~T~~g~ 169 (175)
..+.| ..+..-.+|.|++.|+ |.|+.....
T Consensus 60 ~~~~l~~~~~~~~~~~~~le~g~-i~i~~d~~~ 91 (106)
T PF14289_consen 60 GFYYLSIFKGGKGYVPFFLEPGD-ITINGDANN 91 (106)
T ss_pred EEEEEEEECCCCeEEEEEEeCCE-EEEEEeccc
Confidence 45666 4566778999999999 999886544
No 82
>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]
Probab=24.64 E-value=2.8e+02 Score=29.05 Aligned_cols=57 Identities=9% Similarity=0.043 Sum_probs=39.3
Q ss_pred hhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceEEEeecc
Q 030538 90 AGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNG 146 (175)
Q Consensus 90 ~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG 146 (175)
+..||.+++.+-+.+-.|.+|-+.+-....-.|-.++-|+.-.+=++--+-.-|-||
T Consensus 73 s~~fl~d~~~i~v~~~~G~iilvd~et~~~eivg~vd~GI~aaswS~Dee~l~liT~ 129 (1265)
T KOG1920|consen 73 SVQFLADTNSICVITALGDIILVDPETLELEIVGNVDNGISAASWSPDEELLALITG 129 (1265)
T ss_pred EEEEecccceEEEEecCCcEEEEcccccceeeeeeccCceEEEeecCCCcEEEEEeC
Confidence 357899999999999999999885444444444455666666555656666666666
No 83
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=23.84 E-value=5e+02 Score=22.75 Aligned_cols=87 Identities=17% Similarity=0.329 Sum_probs=55.0
Q ss_pred CCEEEEEeCCCcc-eeecCchhhhchhhccCCCCEEEEEEE---CCEEEEE------eCCCeEEEEEEEeCCCCCCccCC
Q 030538 66 NDTAFVIESETFE-QLEVPLDVFGKAGAYLQEGMKVWLQLY---DGRALSG------SIPKRVACTIKEIHASTKGPTVT 135 (175)
Q Consensus 66 gd~~vFMD~etye-qi~l~~~~lgd~~~~L~eg~~v~v~~~---~~~~i~v------~lP~~v~l~V~~t~p~~kg~t~~ 135 (175)
.++.+|++.++++ .+.+++.... -.=++.|.+|++..| +++++.= ..-..=-++|+++.+..
T Consensus 17 ~~~g~fL~~~~~~~~ilL~k~~~~--~~e~evGdev~vFiY~D~~~rl~aTt~~p~~tvg~~g~~~Vv~v~~~l------ 88 (287)
T COG2996 17 SDFGYFLDAGEDGTTILLPKSEPE--EDELEVGDEVTVFIYVDSEDRLIATTREPKATVGEYGWLKVVEVNKDL------ 88 (287)
T ss_pred eceeEEEecCCCceEEeccccCCc--CCccccCcEEEEEEEECCCCceeheeecceEeecceeEEEEEEEcCCc------
Confidence 3567788887776 6666665332 234689999999888 4566542 22233368898887631
Q ss_pred CCceEEEeecccE--EEcc---------cceeCCCEEEEE
Q 030538 136 PRYRRALLDNGVT--VMVP---------SYLEIGEEIFIN 164 (175)
Q Consensus 136 ~~~K~A~letG~~--v~VP---------~fI~~Gd~I~V~ 164 (175)
-|-|++|+. +.|| +..+.||+..|.
T Consensus 89 ----GaFlD~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~ 124 (287)
T COG2996 89 ----GAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVY 124 (287)
T ss_pred ----ceEEecCCCcceeeehhhcccccccCCCCCCEEEEE
Confidence 355666653 3333 347889987764
No 84
>PF10703 MoaF: Molybdenum cofactor biosynthesis protein F; InterPro: IPR024724 Molybdenum cofactor biosynthesis protein F (MoaF) is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella []. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha []. MoaF is conserved in proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis.
Probab=23.77 E-value=4.1e+02 Score=22.92 Aligned_cols=79 Identities=24% Similarity=0.312 Sum_probs=58.3
Q ss_pred EEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcceeecCchhhhchhhccCCCC---EEEE
Q 030538 26 MQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGM---KVWL 102 (175)
Q Consensus 26 vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi~l~~~~lgd~~~~L~eg~---~v~v 102 (175)
.++--.+-.+|+.+..+|..|..++-...+...++.-+.++. -...|+=+++-++++ -++|++++- .+++
T Consensus 20 ~~lp~~~~L~G~~~tl~~~~G~~~~~~F~d~~~l~W~~~~~~-----g~~~y~a~evrpgif--fVdf~~~~~~~~svSl 92 (265)
T PF10703_consen 20 NRLPATDDLAGRTLTLRFDNGWTIEHRFGDDDRLTWRGVEGS-----GEAPYRATEVRPGIF--FVDFIKPERPEASVSL 92 (265)
T ss_pred ccCCCCcccCCcEEEEEeCCCCEEEEEecCCceEEEeeccCC-----CccceEEEEecCCeE--EEEeEcCCCCCceEEE
Confidence 345556778999999999999999888777788888888777 557799999998886 367887763 2444
Q ss_pred EEE--CCEEEE
Q 030538 103 QLY--DGRALS 111 (175)
Q Consensus 103 ~~~--~~~~i~ 111 (175)
.+. .|+.+.
T Consensus 93 VlDl~~g~a~~ 103 (265)
T PF10703_consen 93 VLDLTTGRATA 103 (265)
T ss_pred EEECCCCeEEE
Confidence 443 355444
No 85
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=23.60 E-value=1.1e+02 Score=26.54 Aligned_cols=30 Identities=17% Similarity=0.326 Sum_probs=16.9
Q ss_pred EEEeecccEEEccc-ceeCCCEEEEECCCCc
Q 030538 140 RALLDNGVTVMVPS-YLEIGEEIFINPQDDS 169 (175)
Q Consensus 140 ~A~letG~~v~VP~-fI~~Gd~I~V~T~~g~ 169 (175)
...|..|..|..|- -|+.||.|+|+-.+++
T Consensus 135 ql~~hDGrnI~~~d~~~k~~Dtv~i~l~~~k 165 (273)
T PTZ00223 135 VAVTHDGHRIRYPDPRTSRGDTLVYNVKEKK 165 (273)
T ss_pred EEEecCCceeccCCccccCCCEEEEECCCCe
Confidence 45555666655442 3566666666666554
No 86
>KOG3328 consensus HGG motif-containing thioesterase [General function prediction only]
Probab=23.56 E-value=1.8e+02 Score=23.05 Aligned_cols=31 Identities=29% Similarity=0.355 Sum_probs=24.4
Q ss_pred EEEeEEecCCCCCcEEEEEEEECCCCCeEEE
Q 030538 11 VIDAEHKQRGRGGAMMQMELRDIDTGNKVSL 41 (175)
Q Consensus 11 V~~~~h~kpGkG~A~vr~klknl~TG~~~e~ 41 (175)
+++..-++.||.=|+..+++++=.||+++-+
T Consensus 102 ~i~a~~vr~Gk~la~t~v~l~~K~t~kiia~ 132 (148)
T KOG3328|consen 102 EIEATVVRVGKTLAFTDVELRRKSTGKIIAK 132 (148)
T ss_pred EEEEEEeecCceEEEEEEEEEEcCCCeEEEe
Confidence 4556668889999999999998888887644
No 87
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=23.43 E-value=81 Score=22.31 Aligned_cols=20 Identities=5% Similarity=0.185 Sum_probs=17.9
Q ss_pred CCCCCeEEEEeCCCCcEEee
Q 030538 33 IDTGNKVSLRFGTEEAVERV 52 (175)
Q Consensus 33 l~TG~~~e~~f~s~dkve~~ 52 (175)
+-+|+.++++|.+.+++..+
T Consensus 12 lP~G~r~~rrF~~~~~L~~v 31 (82)
T cd01773 12 YPDGKREQIALPEQAKLLAL 31 (82)
T ss_pred CCCCCEEEEEeCCCCcHHHH
Confidence 67899999999999999855
No 88
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.06 E-value=70 Score=24.16 Aligned_cols=38 Identities=13% Similarity=0.202 Sum_probs=25.8
Q ss_pred EEEEEeCCCCCCccCCCCceEEEeecccEEEcccc----eeCCCEEEEECCCC
Q 030538 120 CTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY----LEIGEEIFINPQDD 168 (175)
Q Consensus 120 l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~f----I~~Gd~I~V~T~~g 168 (175)
++|-+++|.- || +-.|+.++=|.| |++||.|++.|.+-
T Consensus 55 yTvDy~~~~~-~~----------~~~~~~~~gg~~ff~avkegd~~~fa~~de 96 (117)
T cd01234 55 YTVDYMPESD-PD----------PNSELSLQGGRHFFNAVKEGDELKFATDDE 96 (117)
T ss_pred eEEeccCCCC-CC----------cccccccccchhhhheeccCcEEEEeccch
Confidence 5777887731 11 245666666655 78999999998763
No 89
>KOG1641 consensus Mitochondrial chaperonin [Posttranslational modification, protein turnover, chaperones]
Probab=22.46 E-value=2.7e+02 Score=20.72 Aligned_cols=60 Identities=17% Similarity=0.257 Sum_probs=42.5
Q ss_pred EEEeCCCe-E----EEEEEEeCCCCCCccCCCCceEEEeecccEEEcccceeCCCEEEEECCCCceeee
Q 030538 110 LSGSIPKR-V----ACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 173 (175)
Q Consensus 110 i~v~lP~~-v----~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~V~T~~g~Y~~R 173 (175)
=+|-||.. + +-+|+..-|+.++ +.+.-=|..+..|-.|..|.| -|-+|+..|++..++=|
T Consensus 31 gGilLPEks~~K~~~g~VvavGpG~~~--~~G~~v~~~Vk~Gd~VLlpey--gGt~V~l~~~~~~~~fr 95 (104)
T KOG1641|consen 31 GGILLPEKSVGKLLQGTVVAVGPGSRD--KGGEIVPVSVKVGDRVLLPEY--GGTKVKLGDEDEYHLFR 95 (104)
T ss_pred ceeEeccccccccceEEEEEEcCcccc--CCCCCcCccccCCCEEEeecc--CCcEEeccCCceeEEec
Confidence 35777877 3 3788888888776 344455667888888888888 57778888776655544
No 90
>PF02786 CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain; InterPro: IPR005479 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the ATP-binding domain found in the large subunit of carbamoyl phosphate synthase, as well as in related proteins.; GO: 0003824 catalytic activity, 0005524 ATP binding, 0008152 metabolic process; PDB: 3U9S_A 3U9T_A 2C00_B 2VQD_A 1W96_B 1W93_A 1M6V_C 1CS0_C 1C30_E 1C3O_G ....
Probab=22.19 E-value=60 Score=26.55 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=21.4
Q ss_pred eEEEEEEee-CCEEEEEeCCCcceeecCc
Q 030538 57 KSFTCLYTE-NDTAFVIESETFEQLEVPL 84 (175)
Q Consensus 57 ~~~qylY~D-gd~~vFMD~etyeqi~l~~ 84 (175)
=++||+|.+ ++.|+||...++=|.+.|-
T Consensus 158 ~tvef~~~~~~~~~y~lEvNpR~~~~~p~ 186 (211)
T PF02786_consen 158 GTVEFAVDPDDGEFYFLEVNPRLQREHPV 186 (211)
T ss_dssp EEEEEEEETTTTEEEEEEEESS--TTHHH
T ss_pred ceEEEEEccCccceeeecccCCCCCcchH
Confidence 478999996 7789999998888877653
No 91
>PF14651 Lipocalin_7: Lipocalin / cytosolic fatty-acid binding protein family; PDB: 2F73_A 3B2L_A 3B2J_A 3STN_A 3STK_A 3STM_X 3VG6_A 3VG4_A 3VG5_A 3B2K_A ....
Probab=22.11 E-value=1.2e+02 Score=23.20 Aligned_cols=50 Identities=20% Similarity=0.327 Sum_probs=36.1
Q ss_pred CCeEEEEeCCCCcEEeeeEEeeEEEEEEe-eCCEEEEEeCCCcceeecCchhhhc
Q 030538 36 GNKVSLRFGTEEAVERVFVEDKSFTCLYT-ENDTAFVIESETFEQLEVPLDVFGK 89 (175)
Q Consensus 36 G~~~e~~f~s~dkve~~~le~~~~qylY~-Dgd~~vFMD~etyeqi~l~~~~lgd 89 (175)
|+.+.++|.-|...|...+.-+.+.-.|. ||+.++. +-.+|+ ...++.||
T Consensus 57 gk~~tNtFtiG~E~e~~~~~G~k~K~tvt~EG~KLv~-~~~~~~---~~~Ei~gd 107 (128)
T PF14651_consen 57 GKTVTNTFTIGKECEEETMGGKKFKATVTMEGGKLVV-TYPNYD---STREIVGD 107 (128)
T ss_dssp TEEEEEEEETTCEEEEEETTSCEEEEEEEEETTEEEE-EETTEE---EEEEEETT
T ss_pred CCEEEEEEEcCcceEEEcCCCcEEEEEEEEECCEEEE-EcCCcc---EEEEEECC
Confidence 67888999999999999998888888887 7886664 323343 33455544
No 92
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 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 [, ]. Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=21.47 E-value=1.3e+02 Score=21.76 Aligned_cols=28 Identities=18% Similarity=0.334 Sum_probs=23.4
Q ss_pred CceEEEeecccEEEcccc-eeCCCEEEEE
Q 030538 137 RYRRALLDNGVTVMVPSY-LEIGEEIFIN 164 (175)
Q Consensus 137 ~~K~A~letG~~v~VP~f-I~~Gd~I~V~ 164 (175)
+.|+=.++.|-.+.||.+ .++||.|.++
T Consensus 8 ggkQykV~~gd~i~v~~l~~~~G~~i~l~ 36 (96)
T PF00829_consen 8 GGKQYKVEEGDVIDVERLDAEVGDKIELD 36 (96)
T ss_dssp SSEEEEESSSEEEEEESTSSSTTSEEEET
T ss_pred CCEEEEEeCCCEEEECCcCcCCCCEEEEE
Confidence 468888999999999988 5579999775
No 93
>TIGR02520 pilus_B_mal_scr type IVB pilus formation outer membrane protein, R64 PilN family. Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. This protein family appears to encode a secretin for pilus formation, although it is quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Scoring between the trusted and noise cutoffs are examples of bundle-forming pilus B (bfpB).
Probab=21.43 E-value=3.4e+02 Score=25.17 Aligned_cols=73 Identities=8% Similarity=0.049 Sum_probs=44.9
Q ss_pred hhhccCCCCEEE------EEEECCEEEEEeCCCeEEEEEEEeCCCCCCcc-CCCCceEEEeecccEEEcccceeCCCEEE
Q 030538 90 AGAYLQEGMKVW------LQLYDGRALSGSIPKRVACTIKEIHASTKGPT-VTPRYRRALLDNGVTVMVPSYLEIGEEIF 162 (175)
Q Consensus 90 ~~~~L~eg~~v~------v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t-~~~~~K~A~letG~~v~VP~fI~~Gd~I~ 162 (175)
.+++|...-.+. ++--|+++..+.+-..+-+-. ......-.+. ++...+++++.+|..+.|=++|..++.|.
T Consensus 326 ~i~AL~~~G~v~vlssP~i~TlNnq~A~i~vg~~~~Yv~-~~~~t~t~~~g~s~~~~~~~v~~G~~L~VtP~I~ddg~I~ 404 (497)
T TIGR02520 326 LIRALSTQGKVSVVTSPSVTTLNLQPAPFQIATQTGYLA-SQSTTVTANVGSSTDLEPGTITTGFNMTLLPDIRDDGDIL 404 (497)
T ss_pred HHHHHHhcCCeEEEecCceEEECCCEEEEEecceEEEEe-ecccccccCccceeeEeeceEeeeeEEEEEEEEcCCCeEE
Confidence 456665554443 344588888888877766532 1111100010 23457899999999999977887766665
Q ss_pred E
Q 030538 163 I 163 (175)
Q Consensus 163 V 163 (175)
.
T Consensus 405 L 405 (497)
T TIGR02520 405 L 405 (497)
T ss_pred E
Confidence 4
No 94
>PRK15463 cold shock-like protein CspF; Provisional
Probab=21.37 E-value=1.9e+02 Score=19.50 Aligned_cols=45 Identities=13% Similarity=0.234 Sum_probs=33.3
Q ss_pred EeeCCEEEEEeCCC-cceeecCchhhhch-hhccCCCCEEEEEEECC
Q 030538 63 YTENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYDG 107 (175)
Q Consensus 63 Y~Dgd~~vFMD~et-yeqi~l~~~~lgd~-~~~L~eg~~v~v~~~~~ 107 (175)
|++...|=|+.++. =+++-+..+.|... ..-|.+|..|....-++
T Consensus 12 fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 12 FDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRING 58 (70)
T ss_pred EeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEEC
Confidence 44556787887754 56888888888754 67899999999877654
No 95
>KOG0238 consensus 3-Methylcrotonyl-CoA carboxylase, biotin-containing subunit/Propionyl-CoA carboxylase, alpha chain/Acetyl-CoA carboxylase, biotin carboxylase subunit [Lipid transport and metabolism; Amino acid transport and metabolism]
Probab=21.26 E-value=1.9e+02 Score=27.76 Aligned_cols=64 Identities=19% Similarity=0.249 Sum_probs=41.8
Q ss_pred EEEEEEeeCCEEEEEeCCCcceeecCc-------hhhhchh--------hccC-----CCCEEEEEEECCEEEEEeCCCe
Q 030538 58 SFTCLYTENDTAFVIESETFEQLEVPL-------DVFGKAG--------AYLQ-----EGMKVWLQLYDGRALSGSIPKR 117 (175)
Q Consensus 58 ~~qylY~Dgd~~vFMD~etyeqi~l~~-------~~lgd~~--------~~L~-----eg~~v~v~~~~~~~i~v~lP~~ 117 (175)
.+.|++...++|+||.+.|-=|++=|- |+++|++ ++-+ .|--+....|-..|.+.-+|..
T Consensus 269 TVEFi~D~~~~FyFmEmNTRLQVEHPvTEmItg~DLVewqiRvA~ge~lp~~q~ei~l~GhafE~RiyAEdp~~~f~P~~ 348 (670)
T KOG0238|consen 269 TVEFIVDSKDNFYFMEMNTRLQVEHPVTEMITGTDLVEWQIRVAAGEPLPLKQEEIPLNGHAFEARIYAEDPYKGFLPSA 348 (670)
T ss_pred eEEEEEcCCCcEEEEEeeceeeecccchhhccchHHHHHHHHHhcCCCCCCCcceeeecceEEEEEEeecCCcccCCCCC
Confidence 467999999999999999998988764 4444433 2222 2333444556566666667765
Q ss_pred EEEE
Q 030538 118 VACT 121 (175)
Q Consensus 118 v~l~ 121 (175)
=.|.
T Consensus 349 G~L~ 352 (670)
T KOG0238|consen 349 GRLV 352 (670)
T ss_pred ccce
Confidence 5443
No 96
>TIGR00369 unchar_dom_1 uncharacterized domain 1. Most proteins containing this domain consist almost entirely of a single copy of this domain. A protein from C. elegans consists of two tandem copies of the domain. The domain is also found as the N-terminal region of an apparent initiation factor eIF-2B alpha subunit of Aquifex aeolicus. The function of the domain is unknown.
Probab=21.25 E-value=1.6e+02 Score=20.98 Aligned_cols=34 Identities=18% Similarity=0.301 Sum_probs=24.2
Q ss_pred cCcEEEE--EEeEEecCCCCCcEEEEEEEECCCCCeE
Q 030538 5 TGKMYQV--IDAEHKQRGRGGAMMQMELRDIDTGNKV 39 (175)
Q Consensus 5 ~g~~~~V--~~~~h~kpGkG~A~vr~klknl~TG~~~ 39 (175)
+|.++.- +++++.+|++++ .++++.+=++.|+.+
T Consensus 58 ~~~~~vt~~l~i~f~~p~~~g-~l~a~a~v~~~gr~~ 93 (117)
T TIGR00369 58 GGQAVVGLELNANHLRPAREG-KVRAIAQVVHLGRQT 93 (117)
T ss_pred CCceEEEEEEEeeeccccCCC-EEEEEEEEEecCceE
Confidence 3444433 456789999988 888888877777754
No 97
>PF04762 IKI3: IKI3 family; InterPro: IPR006849 Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation [].
Probab=21.13 E-value=4.4e+02 Score=26.61 Aligned_cols=58 Identities=12% Similarity=0.125 Sum_probs=41.2
Q ss_pred hhhccCCCCEEEEEEECCEEEEE----eCCCeEEEEEEEeCCCCCCccCCCCceEEEeeccc
Q 030538 90 AGAYLQEGMKVWLQLYDGRALSG----SIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGV 147 (175)
Q Consensus 90 ~~~~L~eg~~v~v~~~~~~~i~v----~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~ 147 (175)
++.||-|...+-+.+-+|.++.+ .......=.|-..+.|+....=++--=-..+-||.
T Consensus 80 s~~yl~d~~~l~~~~~~Gdi~~~~~~~~~~~~~~E~VG~vd~GI~a~~WSPD~Ella~vT~~ 141 (928)
T PF04762_consen 80 SFQYLADSESLCIALASGDIILVREDPDPDEDEIEIVGSVDSGILAASWSPDEELLALVTGE 141 (928)
T ss_pred EEEeccCCCcEEEEECCceEEEEEccCCCCCceeEEEEEEcCcEEEEEECCCcCEEEEEeCC
Confidence 36799999999999999999999 44444444456667777776656555556666654
No 98
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=20.69 E-value=1.7e+02 Score=20.17 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=13.6
Q ss_pred ecCCCCCcEEEEEEEEC
Q 030538 17 KQRGRGGAMMQMELRDI 33 (175)
Q Consensus 17 ~kpGkG~A~vr~klknl 33 (175)
+.||-|++.++++++=|
T Consensus 58 I~~gdG~~~~~V~F~~i 74 (80)
T cd00655 58 IRPGDGSAYVNVSFRAV 74 (80)
T ss_pred EECCCCCEEEEEEEEEE
Confidence 56888999999988743
No 99
>PHA02030 hypothetical protein
Probab=20.47 E-value=78 Score=27.99 Aligned_cols=78 Identities=17% Similarity=0.207 Sum_probs=43.9
Q ss_pred EEEEeEEecCC-C-CCcEEEEEEEECCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEeeCCEEEEEeCCCcceeecCchh-
Q 030538 10 QVIDAEHKQRG-R-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDV- 86 (175)
Q Consensus 10 ~V~~~~h~kpG-k-G~A~vr~klknl~TG~~~e~~f~s~dkve~~~le~~~~qylY~Dgd~~vFMD~etyeqi~l~~~~- 86 (175)
-++++.|.|-| + |.-+..+++.+|..- ++ =-+++-++.+.+..-.+|+..+|- =+.|+||.+.|+...
T Consensus 150 Fi~~I~h~k~~~~~GK~~n~id~~~i~p~--~d--~~~g~P~~VPe~~~~~~klFlW~~-----ptkEtWdsl~I~Gt~D 220 (336)
T PHA02030 150 FIIPIKRTKKGNNAGKERNDIDWGGILPP--FD--PVDGSPYNVPELDDDLLQLFLWDA-----PTKETWDALHIEGTSD 220 (336)
T ss_pred eEEEEEeecccCCCCceeeecccccccCc--cc--cCCCCcccccccCccccceeeecC-----CChhhhhheeecccCC
Confidence 35566666622 2 555556667666211 11 124555666666555555444432 356788888886533
Q ss_pred hhchhhccCC
Q 030538 87 FGKAGAYLQE 96 (175)
Q Consensus 87 lgd~~~~L~e 96 (175)
=|.+.+||+|
T Consensus 221 ~GKSKN~lQE 230 (336)
T PHA02030 221 NGKSKNFLQE 230 (336)
T ss_pred CccchHHHHH
Confidence 4677888876
No 100
>TIGR01730 RND_mfp RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane.
Probab=20.44 E-value=4.9e+02 Score=21.43 Aligned_cols=17 Identities=18% Similarity=0.261 Sum_probs=11.6
Q ss_pred hchhhccCCCCEEEEEE
Q 030538 88 GKAGAYLQEGMKVWLQL 104 (175)
Q Consensus 88 gd~~~~L~eg~~v~v~~ 104 (175)
.+....|++|+.+.+.+
T Consensus 179 ~~~~~~l~~G~~v~v~~ 195 (322)
T TIGR01730 179 ERDLPQLRRGQTLTVEL 195 (322)
T ss_pred HHHHHHhhCCCeEEEEE
Confidence 34456677788777776
No 101
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=20.44 E-value=1.1e+02 Score=21.14 Aligned_cols=25 Identities=16% Similarity=0.454 Sum_probs=19.1
Q ss_pred cEEEEEEEECCCCCeEEEEeCCCCcEEe
Q 030538 24 AMMQMELRDIDTGNKVSLRFGTEEAVER 51 (175)
Q Consensus 24 A~vr~klknl~TG~~~e~~f~s~dkve~ 51 (175)
..++++ |-+|+.+..+|+.++.+..
T Consensus 5 t~iqiR---lpdG~r~~~rF~~~~tv~~ 29 (79)
T cd01770 5 TSIQIR---LADGKRLVQKFNSSHRVSD 29 (79)
T ss_pred eEEEEE---CCCCCEEEEEeCCCCcHHH
Confidence 344444 5679999999999999864
No 102
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=20.38 E-value=1.8e+02 Score=19.30 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=6.1
Q ss_pred ccceeCCCEEEEE
Q 030538 152 PSYLEIGEEIFIN 164 (175)
Q Consensus 152 P~fI~~Gd~I~V~ 164 (175)
+.++..|+.|.|.
T Consensus 45 ~~~l~~g~~v~v~ 57 (87)
T PF12945_consen 45 PIPLREGEEVIVR 57 (87)
T ss_dssp HCCS-TT-EEEEE
T ss_pred EEeecCCCEEEEE
Confidence 3455566666554
No 103
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=20.19 E-value=1.7e+02 Score=19.56 Aligned_cols=36 Identities=19% Similarity=0.239 Sum_probs=24.2
Q ss_pred ceEEEeecccEEEcc---c---ceeCCCEEEEECCC---Cceeeec
Q 030538 138 YRRALLDNGVTVMVP---S---YLEIGEEIFINPQD---DSYIGRA 174 (175)
Q Consensus 138 ~K~A~letG~~v~VP---~---fI~~Gd~I~V~T~~---g~Y~~R~ 174 (175)
..| ++..|-.|-|. . -++.||.|.+.... ..|+.|+
T Consensus 10 M~P-~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv 54 (85)
T cd06530 10 MEP-TLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRV 54 (85)
T ss_pred CcC-cccCCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEE
Confidence 444 35666665543 2 27889999999888 4577775
No 104
>PF03143 GTP_EFTU_D3: Elongation factor Tu C-terminal domain; InterPro: IPR004160 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 the C-terminal domain, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA and to EF1B (or EF-Ts, IPR001816 from INTERPRO) []. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1TUI_C 1OB5_E 1TTT_B 1B23_P 1EFT_A 3E20_E 1R5B_A 1R5O_A 1R5N_A 3AGJ_C ....
Probab=20.06 E-value=1.1e+02 Score=21.64 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=5.2
Q ss_pred ccceeCCCEEEE
Q 030538 152 PSYLEIGEEIFI 163 (175)
Q Consensus 152 P~fI~~Gd~I~V 163 (175)
|.|++.||...|
T Consensus 54 p~~l~~g~~a~v 65 (99)
T PF03143_consen 54 PKFLKPGDRAVV 65 (99)
T ss_dssp -SEB-TTEEEEE
T ss_pred cccccccccccc
Confidence 555555554443
Done!