Query 032740
Match_columns 135
No_of_seqs 111 out of 985
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 05:21:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032740.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032740hhsearch_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 1.3E-60 2.8E-65 374.1 17.5 132 3-134 54-185 (185)
2 TIGR02178 yeiP elongation fact 100.0 7.4E-60 1.6E-64 370.1 17.0 132 3-134 54-186 (186)
3 PRK14578 elongation factor P; 100.0 9.6E-60 2.1E-64 369.7 17.6 132 3-134 56-187 (187)
4 PRK04542 elongation factor P; 100.0 2.2E-59 4.7E-64 368.2 17.4 133 3-135 56-189 (189)
5 PRK00529 elongation factor P; 100.0 1.2E-56 2.7E-61 350.5 16.9 134 2-135 53-186 (186)
6 TIGR00038 efp translation elon 100.0 1.2E-56 2.5E-61 350.4 16.1 132 3-134 53-184 (184)
7 PF09285 Elong-fact-P_C: Elong 100.0 1.1E-29 2.4E-34 165.5 7.8 56 78-133 1-56 (56)
8 smart00841 Elong-fact-P_C Elon 100.0 1.1E-29 2.3E-34 165.5 6.5 56 78-133 1-56 (56)
9 cd05794 S1_EF-P_repeat_2 S1_EF 100.0 1.2E-29 2.5E-34 165.4 6.6 56 78-133 1-56 (56)
10 COG0231 Efp Translation elonga 99.9 7.1E-27 1.5E-31 174.6 9.5 76 3-78 56-131 (131)
11 cd04470 S1_EF-P_repeat_1 S1_EF 99.9 7.5E-27 1.6E-31 153.8 7.7 61 15-75 1-61 (61)
12 PF01132 EFP: Elongation facto 99.9 3.4E-24 7.3E-29 138.4 7.5 55 16-70 1-55 (55)
13 cd04463 S1_EF_like S1_EF_like: 99.8 6.9E-20 1.5E-24 117.2 6.8 55 17-72 1-55 (55)
14 TIGR00037 eIF_5A translation i 99.7 9.9E-18 2.1E-22 125.1 9.1 66 3-70 60-125 (130)
15 PRK03999 translation initiatio 99.7 2.6E-17 5.7E-22 122.6 7.5 64 3-68 59-122 (129)
16 PLN03107 eukaryotic translatio 99.3 7.3E-12 1.6E-16 96.5 8.1 64 3-66 74-143 (159)
17 cd04467 S1_aIF5A S1_aIF5A: Arc 97.9 5.3E-05 1.1E-09 49.6 6.4 53 14-68 1-53 (57)
18 PF01287 eIF-5a: Eukaryotic el 95.4 0.09 1.9E-06 35.4 6.6 52 13-65 1-57 (69)
19 PTZ00328 eukaryotic initiation 89.7 1.4 3.1E-05 34.5 6.4 63 4-66 77-150 (166)
20 PF00900 Ribosomal_S4e: Riboso 84.2 1.2 2.7E-05 30.4 3.0 34 96-129 41-75 (77)
21 PF02941 FeThRed_A: Ferredoxin 77.8 1.2 2.6E-05 30.1 1.1 29 53-81 24-56 (67)
22 COG1499 NMD3 NMD protein affec 74.7 15 0.00033 31.9 7.3 50 17-73 303-352 (355)
23 PRK14560 putative RNA-binding 69.4 16 0.00035 27.6 5.6 73 54-133 38-126 (160)
24 cd02786 MopB_CT_3 The MopB_CT_ 65.2 5.7 0.00012 27.5 2.3 21 114-134 44-64 (116)
25 TIGR00451 unchar_dom_2 unchara 62.6 21 0.00046 25.0 4.8 29 105-133 45-80 (107)
26 PF13509 S1_2: S1 domain; PDB: 62.4 13 0.00028 23.7 3.4 38 27-67 14-51 (61)
27 cd02779 MopB_CT_Arsenite-Ox Th 61.7 6.7 0.00014 27.5 2.1 23 113-135 45-67 (115)
28 TIGR00523 eIF-1A eukaryotic/ar 59.3 62 0.0013 23.1 6.8 52 67-126 6-69 (99)
29 PF04014 Antitoxin-MazE: Antid 57.6 26 0.00056 21.0 4.0 31 38-70 7-38 (47)
30 cd02790 MopB_CT_Formate-Dh_H F 57.2 9.2 0.0002 26.3 2.2 21 114-134 48-68 (116)
31 cd02787 MopB_CT_ydeP The MopB_ 56.5 7.8 0.00017 26.9 1.7 20 115-134 45-64 (112)
32 COG1153 FwdD Formylmethanofura 56.0 9.5 0.0002 28.7 2.1 23 113-135 43-65 (128)
33 PF01472 PUA: PUA domain; Int 54.2 15 0.00033 24.1 2.7 30 105-134 15-50 (74)
34 PF01568 Molydop_binding: Moly 53.2 9.9 0.00021 25.9 1.8 20 115-134 44-63 (110)
35 cd02792 MopB_CT_Formate-Dh-Na- 53.1 13 0.00028 25.9 2.4 20 115-134 49-68 (122)
36 cd02778 MopB_CT_Thiosulfate-R- 52.2 12 0.00027 26.0 2.2 21 114-134 43-63 (123)
37 PRK04313 30S ribosomal protein 49.3 30 0.00064 28.6 4.2 38 94-131 128-167 (237)
38 cd02794 MopB_CT_DmsA-EC The Mo 48.7 16 0.00035 25.7 2.3 20 115-134 44-63 (121)
39 cd02788 MopB_CT_NDH-1_NuoG2-N7 48.5 15 0.00031 25.2 2.0 20 115-134 43-62 (96)
40 cd02783 MopB_CT_2 The MopB_CT_ 47.3 16 0.00035 27.3 2.3 20 115-134 46-65 (156)
41 cd02785 MopB_CT_4 The MopB_CT_ 46.4 18 0.00039 25.5 2.3 21 114-134 45-65 (124)
42 TIGR03684 arCOG00985 arCOG0415 45.3 74 0.0016 23.6 5.6 30 104-133 83-119 (150)
43 PLN00036 40S ribosomal protein 44.9 42 0.0009 28.1 4.5 35 96-130 134-169 (261)
44 COG2016 Predicted RNA-binding 44.8 41 0.00089 26.3 4.2 72 52-130 36-123 (161)
45 cd07387 MPP_PolD2_C PolD2 (DNA 43.9 35 0.00075 28.2 3.9 41 90-130 209-252 (257)
46 PRK12442 translation initiatio 43.8 1E+02 0.0022 21.8 5.6 41 78-126 9-58 (87)
47 cd02793 MopB_CT_DMSOR-BSOR-TMA 43.5 20 0.00044 25.6 2.2 21 114-134 46-66 (129)
48 cd02781 MopB_CT_Acetylene-hydr 43.1 23 0.0005 24.9 2.4 20 115-134 47-66 (130)
49 KOG1708 Mitochondrial/chloropl 41.7 42 0.0009 27.6 3.9 50 66-130 123-172 (236)
50 cd02782 MopB_CT_1 The MopB_CT_ 41.2 25 0.00054 24.8 2.4 20 115-134 47-66 (129)
51 PF00207 A2M: Alpha-2-macroglo 40.8 25 0.00054 23.8 2.2 53 68-124 16-75 (92)
52 PF08292 RNA_pol_Rbc25: RNA po 40.8 77 0.0017 23.3 4.9 53 33-86 22-75 (122)
53 PRK14578 elongation factor P; 40.6 1.5E+02 0.0032 23.5 6.8 67 54-132 7-76 (187)
54 cd02777 MopB_CT_DMSOR-like The 39.9 26 0.00056 24.8 2.3 20 115-134 48-67 (127)
55 cd02776 MopB_CT_Nitrate-R-NarG 39.8 24 0.00052 26.1 2.1 21 114-134 44-64 (141)
56 smart00359 PUA Putative RNA-bi 39.5 44 0.00096 21.1 3.2 26 109-134 25-50 (77)
57 cd00508 MopB_CT_Fdh-Nap-like T 39.1 26 0.00056 24.0 2.1 20 115-134 49-68 (120)
58 COG0361 InfA Translation initi 38.7 1.3E+02 0.0028 20.6 5.8 42 79-128 10-60 (75)
59 PF01176 eIF-1a: Translation i 38.2 1.1E+02 0.0024 19.7 5.3 32 97-128 16-55 (65)
60 cd04458 CSP_CDS Cold-Shock Pro 38.0 1E+02 0.0022 19.2 6.0 45 22-66 7-53 (65)
61 KOG0022 Alcohol dehydrogenase, 37.5 33 0.00071 30.1 2.9 30 16-45 126-155 (375)
62 PF05836 Chorion_S16: Chorion 36.7 31 0.00067 25.0 2.2 40 71-112 67-108 (110)
63 TIGR03784 marine_sortase sorta 36.4 31 0.00067 26.7 2.4 17 115-131 109-125 (174)
64 PRK15463 cold shock-like prote 35.8 95 0.0021 20.5 4.4 45 22-66 11-57 (70)
65 cd08759 Type_III_cohesin_like 35.8 72 0.0016 24.8 4.3 69 54-122 12-87 (160)
66 PTZ00118 40S ribosomal protein 34.6 1E+02 0.0022 25.9 5.2 34 97-130 135-169 (262)
67 cd05706 S1_Rrp5_repeat_sc10 S1 34.5 1.2E+02 0.0026 19.0 6.0 55 54-124 1-57 (73)
68 cd02789 MopB_CT_FmdC-FwdD The 34.5 35 0.00075 23.8 2.2 21 114-134 44-64 (106)
69 smart00652 eIF1a eukaryotic tr 34.4 1.5E+02 0.0033 20.2 6.1 43 77-127 6-56 (83)
70 cd02791 MopB_CT_Nitrate-R-NapA 34.2 35 0.00076 23.6 2.2 20 115-134 49-68 (122)
71 cd02780 MopB_CT_Tetrathionate_ 34.0 35 0.00076 24.7 2.2 20 115-134 44-63 (143)
72 PF12158 DUF3592: Protein of u 33.9 1.1E+02 0.0024 21.5 4.8 51 17-75 63-113 (148)
73 cd06530 S26_SPase_I The S26 Ty 33.3 76 0.0017 20.6 3.6 37 97-134 9-54 (85)
74 PRK04980 hypothetical protein; 32.6 75 0.0016 23.0 3.7 35 96-134 17-52 (102)
75 PF07076 DUF1344: Protein of u 31.9 1.5E+02 0.0033 19.5 5.1 38 78-124 5-47 (61)
76 TIGR01730 RND_mfp RND family e 31.6 1.9E+02 0.0041 22.9 6.3 34 28-64 162-195 (322)
77 TIGR02520 pilus_B_mal_scr type 30.2 2E+02 0.0042 25.8 6.7 73 50-123 326-405 (497)
78 cd00604 IPT_CGTD IPT domain (d 29.9 81 0.0018 21.3 3.3 40 38-77 15-55 (81)
79 PRK04163 exosome complex RNA-b 29.9 2.2E+02 0.0048 22.8 6.4 68 29-114 78-154 (235)
80 KOG1641 Mitochondrial chaperon 29.6 1.9E+02 0.0042 21.1 5.3 59 71-133 32-95 (104)
81 TIGR00008 infA translation ini 29.0 1.8E+02 0.0039 19.4 5.9 41 78-126 7-56 (68)
82 PF03143 GTP_EFTU_D3: Elongati 28.9 55 0.0012 22.5 2.4 12 112-123 54-65 (99)
83 PRK04517 hypothetical protein; 28.5 2.1E+02 0.0046 22.8 6.0 53 70-123 23-80 (216)
84 PRK04012 translation initiatio 28.4 2.2E+02 0.0048 20.3 7.2 45 76-128 21-73 (100)
85 PTZ00223 40S ribosomal protein 28.1 88 0.0019 26.4 3.9 35 96-130 131-166 (273)
86 COG2996 Predicted RNA-bindinin 28.1 3.8E+02 0.0083 22.9 8.3 86 27-124 18-124 (287)
87 PF12385 Peptidase_C70: Papain 26.6 50 0.0011 26.0 2.0 35 19-53 129-163 (166)
88 PF06988 NifT: NifT/FixU prote 26.3 2E+02 0.0044 19.1 6.2 51 58-114 1-52 (64)
89 PF07202 Tcp10_C: T-complex pr 25.3 3.4E+02 0.0073 21.3 9.8 93 14-113 43-136 (179)
90 PRK09890 cold shock protein Cs 25.0 1.6E+02 0.0035 19.2 4.0 44 23-66 12-57 (70)
91 KOG3048 Molecular chaperone Pr 24.8 1.3E+02 0.0029 23.3 4.0 39 95-133 59-97 (153)
92 cd02849 CGTase_C_term Cgtase ( 24.8 1.1E+02 0.0025 20.6 3.3 40 38-77 17-57 (81)
93 cd02784 MopB_CT_PHLH The MopB_ 24.8 59 0.0013 24.1 2.1 20 115-134 52-71 (137)
94 PF00829 Ribosomal_L21p: Ribos 24.6 1.1E+02 0.0024 21.5 3.3 29 97-125 8-37 (96)
95 PRK12473 hypothetical protein; 24.5 44 0.00095 27.0 1.4 39 7-47 118-166 (198)
96 KOG0238 3-Methylcrotonyl-CoA c 24.1 77 0.0017 29.6 3.0 64 17-80 268-351 (670)
97 TIGR02609 doc_partner putative 23.7 1.7E+02 0.0037 19.3 4.0 32 38-71 10-41 (74)
98 PRK10354 RNA chaperone/anti-te 23.6 2.2E+02 0.0047 18.5 5.5 45 22-66 11-57 (70)
99 TIGR00999 8a0102 Membrane Fusi 23.5 3.4E+02 0.0074 21.0 6.3 36 28-67 116-152 (265)
100 PF10055 DUF2292: Uncharacteri 23.1 1.5E+02 0.0032 17.8 3.2 17 59-75 17-33 (38)
101 cd04468 S1_eIF5A S1_eIF5A: Euk 22.7 81 0.0018 21.2 2.2 47 14-61 1-51 (69)
102 PF02786 CPSase_L_D2: Carbamoy 22.1 42 0.0009 26.6 0.8 27 17-43 158-185 (211)
103 PF09262 PEX-1N: Peroxisome bi 22.0 2.7E+02 0.0058 19.0 5.2 40 66-111 37-78 (80)
104 COG3269 Predicted RNA-binding 21.5 2.7E+02 0.0059 19.0 4.6 39 76-124 17-55 (73)
105 PF00717 Peptidase_S24: Peptid 21.4 89 0.0019 19.3 2.2 21 114-134 24-46 (70)
106 PRK01203 prefoldin subunit alp 21.4 1.8E+02 0.0038 21.9 4.0 38 97-134 47-84 (130)
107 TIGR02166 dmsA_ynfE anaerobic 21.1 67 0.0015 29.8 2.1 21 115-135 719-739 (797)
108 PF14801 GCD14_N: tRNA methylt 20.7 1.1E+02 0.0024 19.8 2.5 29 3-31 6-34 (54)
109 cd02775 MopB_CT Molybdopterin- 20.7 97 0.0021 20.3 2.3 17 115-131 37-53 (101)
110 cd04455 S1_NusA S1_NusA: N-uti 20.5 2.3E+02 0.0051 17.7 4.1 35 28-64 17-51 (67)
111 PF00166 Cpn10: Chaperonin 10 20.3 1.4E+02 0.0029 20.6 3.1 20 110-129 53-72 (93)
112 PRK14990 anaerobic dimethyl su 20.2 77 0.0017 29.7 2.3 22 114-135 735-756 (814)
No 1
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=1.3e-60 Score=374.14 Aligned_cols=132 Identities=23% Similarity=0.437 Sum_probs=131.1
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCCCeEEEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTI 82 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~V 82 (135)
|||||+++.|++++++|||||.||+.|||||++||||++|+++.+|++.+||+|||.|.++||+|+||+|+||.+|+|+|
T Consensus 54 f~s~ek~e~a~ve~~~~qylY~dg~~~~FMd~etyeQi~i~~~~lgd~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V 133 (185)
T PRK12426 54 FKAGQEVKEAQFEPRNLEYLYLEGDEYLFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVFSVELPHFLELMV 133 (185)
T ss_pred ECCCCeEEEeEEEeeEeEEEEECCCeEEEecCCCceEEEeCHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeec
Q 032740 83 KEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 83 ~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
++|+|++||||||+++|||+||||++|+||+||++||+|+||||+|+|++||
T Consensus 134 ~etep~~kgdTat~~~KpAtLeTG~~V~VP~FI~~Gd~IkVdT~~geY~~R~ 185 (185)
T PRK12426 134 SKTDFPGDSLSLSGGAKKALLETGVEVLVPPFVEIGDVIKVDTRTCEYIQRV 185 (185)
T ss_pred EECCCCCCCcccCCCcccEEEcCCCEEEeCCcccCCCEEEEECCCCeEEeeC
Confidence 9999999999999999999999999999999999999999999999999997
No 2
>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=7.4e-60 Score=370.07 Aligned_cols=132 Identities=25% Similarity=0.451 Sum_probs=130.9
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCE-EEEEEECCEEEEEeCCCeEEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACT 81 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~-v~v~~~~~~~i~v~lP~~V~l~ 81 (135)
|||||+++.|++++++|||||.||+.|||||++||||++|+++.+|++.+||+|||+ |.+.+|+|+||+|+||.+|+|+
T Consensus 54 f~s~e~ve~a~le~~~~qylY~dg~~~~FMD~etyEQ~~i~~~~lgd~~~fL~e~~~~v~v~~~~~~~i~v~lP~~V~l~ 133 (186)
T TIGR02178 54 FKADDMLDTVELLRREASFSYKDGEEYVFMDEEDYTPYTFDKDAIEDELLFISEGLSGMYVQLIDGSPVALELPQHVVLE 133 (186)
T ss_pred ECCCCeEEEEEEEEeEeEEEEeCCCeEEEccCCCcEEEEeCHHHhhhhhhhhhCCCEEEEEEEECCEEEEEECCCEEEEE
Confidence 899999999999999999999999999999999999999999999999999999997 9999999999999999999999
Q ss_pred EEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeec
Q 032740 82 IKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 82 V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|++|+|++||||+++++|||+||||++|+||+||++||+|+||||||+|++||
T Consensus 134 V~etep~~KGdT~~~~~KpA~LeTG~~v~VP~FI~~Gd~IkVdTrtg~Y~~R~ 186 (186)
T TIGR02178 134 IVETPPEIKGASASKRPKPAKLITGLVVQVPEYITTGERILINTTERAFMGRA 186 (186)
T ss_pred EEECCCCcccccCCCCcccEEEcCCCEEEeCCeecCCCEEEEECCCCcEEccC
Confidence 99999999999999999999999999999999999999999999999999997
No 3
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=9.6e-60 Score=369.69 Aligned_cols=132 Identities=30% Similarity=0.499 Sum_probs=131.2
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCCCeEEEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTI 82 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~V 82 (135)
|||||++|.|++++++|||||.||+.|||||++||||++||++.+|++.+||+|||+|.+.||+|+||+|+||.+|+|+|
T Consensus 56 f~s~d~ve~a~ve~~~~qylY~dg~~~~FMD~etyEQ~~i~~~~~g~~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V 135 (187)
T PRK14578 56 FRSGDKVEEADFERHKGQFLYADGDRGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVNVDLPMTVELTV 135 (187)
T ss_pred ECCCCEEEEeEEEEeEeEEEEeCCCEEEEecCCCcEEEEecHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeec
Q 032740 83 KEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 83 ~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
++|+|++||||+++++|||+||||++|+||+||++||+|+||||||+|++||
T Consensus 136 ~~tep~~KGdT~t~~~KpA~leTG~~v~VP~FI~~Gd~I~VdT~~g~Y~~R~ 187 (187)
T PRK14578 136 TDTAPVMKNATATAQTKEAVLETGLRLQVPPYLESGEKIKVDTRDGRFISRA 187 (187)
T ss_pred EECCCccccCccCCCcceEEEcCCCEEEeCCcccCCCEEEEECCCCcEEeeC
Confidence 9999999999999999999999999999999999999999999999999997
No 4
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=2.2e-59 Score=368.21 Aligned_cols=133 Identities=25% Similarity=0.432 Sum_probs=131.7
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCE-EEEEEECCEEEEEeCCCeEEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACT 81 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~-v~v~~~~~~~i~v~lP~~V~l~ 81 (135)
|||||++|.|++++++|||||.||+.|||||++||||++||++++|++.+||+|||+ |.+++|+|+||+|+||.+|+|+
T Consensus 56 frs~ekve~a~~~~~~~qylY~dg~~~~FMd~etyEQ~~i~~~~lgd~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~ 135 (189)
T PRK04542 56 FKGDDILDTVDLTRRPVTFSYIDGDEYVFMDNEDYTPYTFKKDQIEDELLFIPEGMPGMQVLTVDGQPVALELPQTVDLE 135 (189)
T ss_pred ECCCCeEEEEEEEEeEeEEEEeCCCEEEEecCCCceEEEECHHHhhhHhhhhhcCCEEEEEEEECCEEEEEECCCEEEEE
Confidence 899999999999999999999999999999999999999999999999999999998 9999999999999999999999
Q ss_pred EEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeecC
Q 032740 82 IKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 135 (135)
Q Consensus 82 V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~k 135 (135)
|++|+|++||||+++++|||+||||++|+||+||++||+|+||||+|+|++||.
T Consensus 136 V~etep~~kGdT~~~~~KpAtLetG~~v~VP~FI~~Gd~I~VdT~tgeYv~R~~ 189 (189)
T PRK04542 136 IVETAPSIKGASASARTKPATLSTGLVIQVPEYISTGEKIRINTEERKFMGRAD 189 (189)
T ss_pred EEECCCCccccccCCCCccEEEcCCCEEEeCCcccCCCEEEEECCCCcEEeecC
Confidence 999999999999999999999999999999999999999999999999999984
No 5
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=1.2e-56 Score=350.53 Aligned_cols=134 Identities=32% Similarity=0.534 Sum_probs=132.3
Q ss_pred ccccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCCCeEEEE
Q 032740 2 FINAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACT 81 (135)
Q Consensus 2 ~~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~ 81 (135)
-|+++++++.+.++++++||||.||+.|+|||+|||||++||++.++++.+||+|||+|++.+|+|+||+|+||++|+|+
T Consensus 53 ~f~~~e~ve~~~ve~~~~q~ly~dgd~~~fMD~etyeq~~l~~~~lg~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~ 132 (186)
T PRK00529 53 TFKAGDKVERADVERREMQYLYNDGDGYVFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELE 132 (186)
T ss_pred EeCCCCEEEeccEEeEEEEEEEECCCEEEEecCCCceeeEcCHHHhHHHHhhccCCCEEEEEEECCEEEEEECCCEEEEE
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeecC
Q 032740 82 IKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 135 (135)
Q Consensus 82 V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~k 135 (135)
|++|+|++||||+++++|||+||||++|+||+||++||+|+||||+|+|++|||
T Consensus 133 V~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fI~~Gd~I~v~T~~g~y~~R~~ 186 (186)
T PRK00529 133 VTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGEKIKVDTRTGEYVERAK 186 (186)
T ss_pred EEECCCCccCcccCCCcccEEEcCCCEEEeCCeecCCCEEEEECCCCcEEeecC
Confidence 999999999999999999999999999999999999999999999999999996
No 6
>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=1.2e-56 Score=350.37 Aligned_cols=132 Identities=30% Similarity=0.546 Sum_probs=131.1
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCCCeEEEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTI 82 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~V 82 (135)
|+++++++.+.++++++||||.||+.|+|||++||||++|+++.++++.+||+|||+|.+.||+|+||+|+||++|+|+|
T Consensus 53 f~~~~kve~~~~e~~~~q~ly~dgd~~~fMD~etyeq~~i~~~~l~~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V 132 (184)
T TIGR00038 53 FRSGEKVEKADVEEREMQYLYKDGDSYVFMDTETYEQIELPKDLLGDAAKFLKENMEVSVTFYNGEPIGVELPNFVELEV 132 (184)
T ss_pred eCCCCEEEcccEEeEEEEEEEECCCEEEEeCCCCccceEcCHHHHHHHHhhcCCCCEEEEEEECCEEEEEECCCEEEEEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeec
Q 032740 83 KEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 83 ~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
++|+|++|||||++++|||+||||++|+||+||++||+|+||||+|+|++||
T Consensus 133 ~~t~p~~kg~t~~~~~K~A~letG~~v~VP~fi~~Gd~I~v~T~~g~y~~R~ 184 (184)
T TIGR00038 133 TETEPGVKGDTASGGTKPATLETGAVVQVPLFIEEGEKIKVDTRTGEYVERA 184 (184)
T ss_pred EECCCCccccccCCCcccEEEcCCCEEEeCCcccCCCEEEEECCCCcEEecC
Confidence 9999999999999999999999999999999999999999999999999997
No 7
>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=1.1e-29 Score=165.46 Aligned_cols=56 Identities=32% Similarity=0.629 Sum_probs=50.3
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEee
Q 032740 78 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 133 (135)
Q Consensus 78 V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 133 (135)
|+|+|++|+|++||||+++++|+|+|+||++||||+||++||+|+|||++|+|++|
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 8
>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=1.1e-29 Score=165.54 Aligned_cols=56 Identities=27% Similarity=0.515 Sum_probs=55.0
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEee
Q 032740 78 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 133 (135)
Q Consensus 78 V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 133 (135)
|+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
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 9
>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=1.2e-29 Score=165.38 Aligned_cols=56 Identities=29% Similarity=0.526 Sum_probs=55.0
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEee
Q 032740 78 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 133 (135)
Q Consensus 78 V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 133 (135)
|+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+||||+|+|++|
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 10
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=7.1e-27 Score=174.58 Aligned_cols=76 Identities=34% Similarity=0.527 Sum_probs=74.8
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCCCeE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRV 78 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP~~V 78 (135)
|+|+++++.|.|+++++||||.||+.|+|||+|||||++++++.++++.+||+|||+|++++|+|+|++++||.+|
T Consensus 56 f~~~~kve~a~ie~~~~q~lY~dg~~~~FMD~etyeq~~v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v 131 (131)
T COG0231 56 FKADDKVEVAIVERKTAQYLYIDGDFYVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV 131 (131)
T ss_pred EcCCCEEEEeEEeeeeEEEEEcCCCeEEEccCCCceEEEecchhhhhHHHhcCCCCEEEEEEECCEEEEEECCCCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999975
No 11
>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=99.94 E-value=7.5e-27 Score=153.80 Aligned_cols=61 Identities=33% Similarity=0.758 Sum_probs=59.7
Q ss_pred EEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCC
Q 032740 15 EDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 75 (135)
Q Consensus 15 ~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP 75 (135)
+++++||||.||+.|||||++||||++|+++.+|++.+||+|||+|.|++|+|+||+|+||
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 12
>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=99.91 E-value=3.4e-24 Score=138.44 Aligned_cols=55 Identities=36% Similarity=0.748 Sum_probs=50.0
Q ss_pred EeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEE
Q 032740 16 DKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 70 (135)
Q Consensus 16 ~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i 70 (135)
+|++||||.||+.|||||++||||++|+++.+|++.+||+|||+|+|++|+|+||
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 13
>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=99.81 E-value=6.9e-20 Score=117.16 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=51.8
Q ss_pred eeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEE
Q 032740 17 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSG 72 (135)
Q Consensus 17 ~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v 72 (135)
+++||||.||+.|+|||++||||++++++.. ++.+||+||++|.|.+|+|+|+++
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 14
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=99.74 E-value=9.9e-18 Score=125.06 Aligned_cols=66 Identities=17% Similarity=0.210 Sum_probs=61.8
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 70 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i 70 (135)
|+|+++++.+.++++++||||.||+.|+|||++||||+.|+.+. +..+||+||++|.++-.-|+..
T Consensus 60 f~s~~~ve~~~ve~~~~qylY~dg~~~~fMd~etyeq~~i~~~~--~~~~~Lke~~~V~v~~~~g~~~ 125 (130)
T TIGR00037 60 SPSTSKVEVPIVDRREYQVLAIMGGMVQLMDLDTYETDELPIPE--ELGDSLEPGFEVEYIEAMGQEK 125 (130)
T ss_pred ECCCCEEEEeEEEEEEEEEEEecCCEEEEEcCCCcEEEEecCCh--hHHHHhhcCCEEEEEecCCeEE
Confidence 79999999999999999999999999999999999999999986 8899999999999888777644
No 15
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=99.71 E-value=2.6e-17 Score=122.62 Aligned_cols=64 Identities=22% Similarity=0.215 Sum_probs=59.3
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 68 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~ 68 (135)
|+++++++.+.++++++||||.||+.|+|||+|||||++|+++ +|+..||+|||+|.++---|+
T Consensus 59 ~~s~d~~e~~~ve~~~~qylY~dg~~~~fMd~eTyeq~~i~~~--~d~~~~l~eg~~v~v~~~~g~ 122 (129)
T PRK03999 59 QPVDAKVEVPIIEKKTGQVLSIMGDVVQLMDLETYETFEIPIP--EELKDKLEPGVEVEYWEAMGR 122 (129)
T ss_pred ecCCCceeeeeEEeEEEEEEEecCCEEEEecCCCceEEEecCC--hhHHhhCcCCCEEEEEhhCCe
Confidence 7899999999999999999999999999999999999999998 999999999999987654443
No 16
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=99.31 E-value=7.3e-12 Score=96.52 Aligned_cols=64 Identities=11% Similarity=0.168 Sum_probs=52.6
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeE-EEEeC--CCceeEEeCh---hhhccccccccCCCEEEEEEEC
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTA-FVIES--ETFEQLEVPL---DVFGKAGAYLQEGMKVWLQLYD 66 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~-~FMd~--etyeQ~~i~~---~~~g~~~~fL~eg~~v~v~~~~ 66 (135)
|+|+++++.+.|+++++||||.||+.| +|||+ ++|||+.||+ ++...-..+..+|.++.|..|.
T Consensus 74 f~s~~~ve~~~ve~~~~qyly~dgd~y~~fMD~~get~eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~ 143 (159)
T PLN03107 74 VPSSHNCDVPHVNRTDYQLIDISEDGFVSLMDESGNTKDDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMS 143 (159)
T ss_pred ecCCCEEEEEEEEEEEEEEEEEcCCceEEEEcCCCCcceeEEccCcchHHHHHHHHHHhCCCeEEEEEEe
Confidence 799999999999999999999999995 99999 6999999986 3333333455779886666664
No 17
>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=97.91 E-value=5.3e-05 Score=49.61 Aligned_cols=53 Identities=26% Similarity=0.329 Sum_probs=43.8
Q ss_pred EEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCE
Q 032740 14 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 68 (135)
Q Consensus 14 i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~ 68 (135)
|+++..|-++.+|+..-+||+||||-++++.. .+...-+++|.+|..+-.-|+
T Consensus 1 i~k~~aqVisi~g~~vQlMD~eTYeT~ev~~p--~~~~~~i~~G~eV~y~~~~g~ 53 (57)
T cd04467 1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIP--EEIKDKLEPGKEVEYWESMGK 53 (57)
T ss_pred CcceEEEEEEEcCCEEEEeccccceeEEEecc--hhhcccCCCCCEEEEEeecCe
Confidence 57999999999999999999999999999985 232345899999886655565
No 18
>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=95.43 E-value=0.09 Score=35.42 Aligned_cols=52 Identities=23% Similarity=0.340 Sum_probs=37.7
Q ss_pred EEEEeeEEEEEccCC-eEEEEeCCCceeEE---eChhhhcccc-ccccCCCEEEEEEE
Q 032740 13 FVEDKSFTCLYTEND-TAFVIESETFEQLE---VPLDVFGKAG-AYLQEGMKVWLQLY 65 (135)
Q Consensus 13 ~i~~~~~~ylY~dgd-~~~FMd~etyeQ~~---i~~~~~g~~~-~fL~eg~~v~v~~~ 65 (135)
.|+++++|.+--++| ...+|| ++|+..+ +|...++..+ .-+.+|..+.|..+
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 667999 8888877 7855565443 45588888544444
No 19
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=89.70 E-value=1.4 Score=34.54 Aligned_cols=63 Identities=10% Similarity=0.157 Sum_probs=48.6
Q ss_pred ccccceEeeEEEEeeEEEEEccCCe-------EEEEeCCCceeEEeCh---hhhcc-ccccccCCCEEEEEEEC
Q 032740 4 NAIYFAAGVFVEDKSFTCLYTENDT-------AFVIESETFEQLEVPL---DVFGK-AGAYLQEGMKVWLQLYD 66 (135)
Q Consensus 4 ~~~~~~e~~~i~~~~~~ylY~dgd~-------~~FMd~etyeQ~~i~~---~~~g~-~~~fL~eg~~v~v~~~~ 66 (135)
.+...++...++++++|.+-.++|. ..+||.+.|+-..|+. +.++. -...+.+|.++.|..|.
T Consensus 77 Ps~hnv~VP~V~r~~yqli~I~~d~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~v~vi~ 150 (166)
T PTZ00328 77 PSTHNVEVPFVKTFTYSVLDIQPNEDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVVS 150 (166)
T ss_pred CccceeEeeeEEeeEEEEEEEcCCCcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEEEEEEh
Confidence 4556789999999999999998873 6799999998777543 33332 34566899999888875
No 20
>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=84.15 E-value=1.2 Score=30.40 Aligned_cols=34 Identities=9% Similarity=0.178 Sum_probs=27.1
Q ss_pred CCceeEEEecCcEEEcc-cceecCCEEEEeCCCCe
Q 032740 96 PRYRRALLDNGVTVMVP-SYLEIGEEIFINPQDDS 129 (135)
Q Consensus 96 ~~~K~A~LetG~~i~VP-~FI~~Gd~I~VdT~~g~ 129 (135)
++-=...|..|..|..| +-++.||.|+|+..+++
T Consensus 41 gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~k 75 (77)
T PF00900_consen 41 GGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQK 75 (77)
T ss_dssp GGEEEEEETTTEEEES-SST--TTEEEEEETTTTE
T ss_pred CCcEEEEecCceEEEcCcCCccCCCEEEEECCCCc
Confidence 34457889999999999 99999999999999886
No 21
>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=77.78 E-value=1.2 Score=30.14 Aligned_cols=29 Identities=24% Similarity=0.454 Sum_probs=15.7
Q ss_pred cccCCCEEE----EEEECCEEEEEeCCCeEEEE
Q 032740 53 YLQEGMKVW----LQLYDGRALSGSIPKRVACT 81 (135)
Q Consensus 53 fL~eg~~v~----v~~~~~~~i~v~lP~~V~l~ 81 (135)
|=..||+=. +.-|+|+|||.+||-.|.+.
T Consensus 24 fDl~G~EGev~~~v~~wkGr~iSanlP~~V~F~ 56 (67)
T PF02941_consen 24 FDLKGMEGEVKQIVTDWKGRPISANLPVKVQFD 56 (67)
T ss_dssp EE-TT-EEEEEEE-SEETTEE---SS-EEEEET
T ss_pred ccccCCEEEEEEEEeecCCcEecCCCcEEEEEe
Confidence 334466532 44689999999999998873
No 22
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=74.67 E-value=15 Score=31.85 Aligned_cols=50 Identities=24% Similarity=0.230 Sum_probs=42.8
Q ss_pred eeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEe
Q 032740 17 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 73 (135)
Q Consensus 17 ~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~ 73 (135)
+.+..+=.+.+...|||++|||-+++... =|.+|.++.+..++|....++
T Consensus 303 ~~~~vvs~~~~~~~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~ 352 (355)
T COG1499 303 KKAVVVSRDPSAIQVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE 352 (355)
T ss_pred eEEEEEecCCCceEEEecceEEEEeccCC-------CCCCCCEEEEEEEeceEEeec
Confidence 67888888999999999999999999876 467899999999988876553
No 23
>PRK14560 putative RNA-binding protein; Provisional
Probab=69.37 E-value=16 Score=27.60 Aligned_cols=73 Identities=21% Similarity=0.344 Sum_probs=41.9
Q ss_pred ccCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCC-ceeEEE--------ecCcEEEcccce------ecC
Q 032740 54 LQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPR-YRRALL--------DNGVTVMVPSYL------EIG 118 (135)
Q Consensus 54 L~eg~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kGdTat~~-~K~A~L--------etG~~i~VP~FI------~~G 118 (135)
.+.+..+.+.+.+|+|+.+..=..+ -|.+.|.-.-+. .+.+++ .+|+.++.|-.+ +.|
T Consensus 38 ~~~~~~~~~~~~~~~p~~f~~d~~~-------~Ptl~~~~~~~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~G 110 (160)
T PRK14560 38 VETDKKEEIYLVDGEPLFFKVDDEL-------FPTLRGALKLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEG 110 (160)
T ss_pred EEcCCcEEEEEECCEEEEEEeCCcc-------cccHHHHHhCCccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCC
Confidence 3345567777778888887651112 222322211111 122222 378888888554 678
Q ss_pred CEEEEeCCC-CeeEee
Q 032740 119 EEIFINPQD-DSYIGR 133 (135)
Q Consensus 119 d~I~VdT~~-g~Y~~R 133 (135)
|.|.|-++. |..+..
T Consensus 111 d~V~I~~~~~~~~vav 126 (160)
T PRK14560 111 DIVFVVEETHGKPLAV 126 (160)
T ss_pred CEEEEEECCCCeEEEE
Confidence 999888766 777653
No 24
>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=65.15 E-value=5.7 Score=27.53 Aligned_cols=21 Identities=19% Similarity=0.124 Sum_probs=17.8
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||.|+|.++.|+..-||
T Consensus 44 gi~~Gd~V~v~s~~G~~~~~v 64 (116)
T cd02786 44 GIADGDLVVVFNDRGSVTLRA 64 (116)
T ss_pred CCCCCCEEEEEcCCeEEEEEE
Confidence 367899999999999987766
No 25
>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=62.55 E-value=21 Score=24.97 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=22.9
Q ss_pred cCcEEEcccc------eecCCEEEEeCCC-CeeEee
Q 032740 105 NGVTVMVPSY------LEIGEEIFINPQD-DSYIGR 133 (135)
Q Consensus 105 tG~~i~VP~F------I~~Gd~I~VdT~~-g~Y~~R 133 (135)
+|+.++-|-. ++.||.|.|-+.+ |+.+.+
T Consensus 45 ~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~iav 80 (107)
T TIGR00451 45 NGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAV 80 (107)
T ss_pred CCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEEE
Confidence 6899888844 5779999998776 888765
No 26
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=62.35 E-value=13 Score=23.74 Aligned_cols=38 Identities=13% Similarity=0.203 Sum_probs=24.9
Q ss_pred CeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECC
Q 032740 27 DTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDG 67 (135)
Q Consensus 27 d~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~ 67 (135)
+.-+|+|...-..+.+|+..+.. =++.|.++.+..|.|
T Consensus 14 ~~g~fL~~~~~~~vlLp~~e~~~---~~~~Gd~v~VFvY~D 51 (61)
T PF13509_consen 14 EFGYFLDDGEGKEVLLPKSEVPE---PLKVGDEVEVFVYLD 51 (61)
T ss_dssp SSEEEEEETT-EEEEEEGGG---------TTSEEEEEEEE-
T ss_pred CCEEEEECCCCCEEEechHHcCC---CCCCCCEEEEEEEEC
Confidence 45566787878999999987752 289999999999843
No 27
>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=61.74 E-value=6.7 Score=27.53 Aligned_cols=23 Identities=17% Similarity=0.033 Sum_probs=19.0
Q ss_pred cceecCCEEEEeCCCCeeEeecC
Q 032740 113 SYLEIGEEIFINPQDDSYIGRAK 135 (135)
Q Consensus 113 ~FI~~Gd~I~VdT~~g~Y~~R~k 135 (135)
+=|+.||.|+|.++.|+..-||+
T Consensus 45 lgi~~Gd~V~v~s~~G~i~~~~~ 67 (115)
T cd02779 45 EGLKNGDLVEVYNDYGSTTAMAY 67 (115)
T ss_pred cCCCCCCEEEEEeCCEEEEEEEE
Confidence 34678999999999999887763
No 28
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=59.34 E-value=62 Score=23.06 Aligned_cols=52 Identities=13% Similarity=0.318 Sum_probs=35.8
Q ss_pred CEEEEEeCCC----eEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEc--c------cceecCCEEEEeCC
Q 032740 67 GRALSGSIPK----RVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P------SYLEIGEEIFINPQ 126 (135)
Q Consensus 67 ~~~i~v~lP~----~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~V--P------~FI~~Gd~I~VdT~ 126 (135)
.+....+||. .+..+|++.-+ +..=.+.+++|.++.+ | ..|..||.|.|+..
T Consensus 6 ~~~~~~~~p~~~e~e~~g~V~~~lG--------~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~ 69 (99)
T TIGR00523 6 EQQIRVRLPRKEEGEILGVIEQMLG--------AGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPW 69 (99)
T ss_pred cCcceeeCCCCCCCEEEEEEEEEcC--------CCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEc
Confidence 3455677774 57778887765 3355677888877543 3 46999999999643
No 29
>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=57.58 E-value=26 Score=21.04 Aligned_cols=31 Identities=19% Similarity=0.307 Sum_probs=23.6
Q ss_pred eeEEeChhhhccccccccCCCEEEEEEECC-EEE
Q 032740 38 EQLEVPLDVFGKAGAYLQEGMKVWLQLYDG-RAL 70 (135)
Q Consensus 38 eQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~-~~i 70 (135)
-|+.||++..... -|++|.++.+...++ +.+
T Consensus 7 ~~v~iPk~~~~~l--~l~~Gd~v~i~~~~~g~i~ 38 (47)
T PF04014_consen 7 GQVTIPKEIREKL--GLKPGDEVEIEVEGDGKIV 38 (47)
T ss_dssp SEEEE-HHHHHHT--TSSTTTEEEEEEETTSEEE
T ss_pred ceEECCHHHHHHc--CCCCCCEEEEEEeCCCEEE
Confidence 4889999887533 789999999999987 443
No 30
>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=57.19 E-value=9.2 Score=26.27 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=15.8
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||.|+|.+..|+..-+|
T Consensus 48 gi~~Gd~V~v~~~~G~~~~~v 68 (116)
T cd02790 48 GIEDGEKVRVSSRRGSVEVRA 68 (116)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 357788888888888766554
No 31
>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=56.52 E-value=7.8 Score=26.93 Aligned_cols=20 Identities=20% Similarity=0.290 Sum_probs=16.9
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.++.|+-.-||
T Consensus 45 I~dGd~V~v~s~~G~i~~~a 64 (112)
T cd02787 45 LKAGDRVDLESAFGDGQGRI 64 (112)
T ss_pred CCCCCEEEEEecCCCCeEEE
Confidence 56999999999999876665
No 32
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=55.96 E-value=9.5 Score=28.74 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=19.7
Q ss_pred cceecCCEEEEeCCCCeeEeecC
Q 032740 113 SYLEIGEEIFINPQDDSYIGRAK 135 (135)
Q Consensus 113 ~FI~~Gd~I~VdT~~g~Y~~R~k 135 (135)
+=+++||+++|.++.|+=+=||+
T Consensus 43 Lgv~EGD~VkVkse~GeVVV~Ak 65 (128)
T COG1153 43 LGVSEGDKVKVKSEFGEVVVKAK 65 (128)
T ss_pred hCCCcCCeEEEEecCccEEEEEe
Confidence 45789999999999999887774
No 33
>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=54.22 E-value=15 Score=24.10 Aligned_cols=30 Identities=27% Similarity=0.513 Sum_probs=21.9
Q ss_pred cCcEEEcccc------eecCCEEEEeCCCCeeEeec
Q 032740 105 NGVTVMVPSY------LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 105 tG~~i~VP~F------I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
+|+.+..|-. ++.||.|.|-+.+|+.+.|.
T Consensus 15 ~Ga~L~~~GV~~~~~~f~~gd~V~i~~~~g~~ia~G 50 (74)
T PF01472_consen 15 NGASLFAPGVVEVDGDFRKGDEVAIVDEDGEVIAVG 50 (74)
T ss_dssp TTSEEEGGGEEEEETT--TTSEEEEEETTSSEEEEE
T ss_pred cCCCcchHHhEECCCCcCCCCEEEEEcCCCeEEEEE
Confidence 3666665543 58999999999999998875
No 34
>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=53.24 E-value=9.9 Score=25.92 Aligned_cols=20 Identities=15% Similarity=0.152 Sum_probs=16.1
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||.|+|.++.|+-.-||
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 78999999999999887765
No 35
>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=53.07 E-value=13 Score=25.85 Aligned_cols=20 Identities=10% Similarity=0.307 Sum_probs=16.0
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.+..|+..-++
T Consensus 49 i~~Gd~V~v~s~~G~~~~~v 68 (122)
T cd02792 49 IKNGDMVWVSSPRGKIKVKA 68 (122)
T ss_pred CCCCCEEEEEcCCceEEEEE
Confidence 57799999999988876655
No 36
>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=52.15 E-value=12 Score=26.03 Aligned_cols=21 Identities=14% Similarity=0.306 Sum_probs=17.3
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||.|+|.++.|+..-+|
T Consensus 43 gi~~Gd~V~v~s~~G~i~~~v 63 (123)
T cd02778 43 GIKDGDRVEVSSARGKVTGKA 63 (123)
T ss_pred CCCCCCEEEEEeCCCcEEEEE
Confidence 367899999999999877665
No 37
>PRK04313 30S ribosomal protein S4e; Validated
Probab=49.30 E-value=30 Score=28.58 Aligned_cols=38 Identities=16% Similarity=0.310 Sum_probs=30.8
Q ss_pred CCCCceeEEEecCcEEEcc--cceecCCEEEEeCCCCeeE
Q 032740 94 VTPRYRRALLDNGVTVMVP--SYLEIGEEIFINPQDDSYI 131 (135)
Q Consensus 94 at~~~K~A~LetG~~i~VP--~FI~~Gd~I~VdT~~g~Y~ 131 (135)
..++--...|..|..|.+| .-++.||.|+|+-.+++=+
T Consensus 128 ~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~ 167 (237)
T PRK04313 128 VKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIV 167 (237)
T ss_pred ecCCEEEEEecCCceEEccCccccccCCEEEEECCCCcee
Confidence 3445557889999999999 6899999999998888643
No 38
>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=48.74 E-value=16 Score=25.66 Aligned_cols=20 Identities=10% Similarity=0.268 Sum_probs=15.3
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||.|+|.+..|+-.-||
T Consensus 44 i~~Gd~V~v~s~~g~i~~~a 63 (121)
T cd02794 44 IKDGDRVLVFNDRGKVIRPV 63 (121)
T ss_pred CCCCCEEEEEcCCceEEEEE
Confidence 45688999988888776555
No 39
>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=48.49 E-value=15 Score=25.15 Aligned_cols=20 Identities=15% Similarity=0.086 Sum_probs=15.1
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.++.|+-.-++
T Consensus 43 i~~Gd~V~v~s~~G~i~~~v 62 (96)
T cd02788 43 LADGDLVEFSLGDGTLTLPV 62 (96)
T ss_pred CCCCCEEEEEECCeEEEEEE
Confidence 46788998888888865444
No 40
>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=47.32 E-value=16 Score=27.29 Aligned_cols=20 Identities=15% Similarity=0.405 Sum_probs=17.4
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||.|+|.++.|+-.-||
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 41
>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=46.36 E-value=18 Score=25.53 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=17.0
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||+|+|.++.|+-.-||
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 42
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=45.31 E-value=74 Score=23.64 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=22.7
Q ss_pred ecCcEEEcccc------eecCCEEEEeCCC-CeeEee
Q 032740 104 DNGVTVMVPSY------LEIGEEIFINPQD-DSYIGR 133 (135)
Q Consensus 104 etG~~i~VP~F------I~~Gd~I~VdT~~-g~Y~~R 133 (135)
.+|+.++.|-. ++.||.|.|-++. |..+..
T Consensus 83 ~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vav 119 (150)
T TIGR03684 83 INGADIMAPGIVSADPSIKEGDIVFVVDETHRKPLAV 119 (150)
T ss_pred hcCcccccCceecCCCCCCCCCEEEEEECCCCeEEEE
Confidence 37888888855 4679999888876 877643
No 43
>PLN00036 40S ribosomal protein S4; Provisional
Probab=44.86 E-value=42 Score=28.13 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=25.5
Q ss_pred CCceeEEEecCcEEEccc-ceecCCEEEEeCCCCee
Q 032740 96 PRYRRALLDNGVTVMVPS-YLEIGEEIFINPQDDSY 130 (135)
Q Consensus 96 ~~~K~A~LetG~~i~VP~-FI~~Gd~I~VdT~~g~Y 130 (135)
++--...|..|..|..|. -|+.||.|+||..+++=
T Consensus 134 gG~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~kI 169 (261)
T PLN00036 134 KGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKI 169 (261)
T ss_pred CCeEEEEecCCceeccCCCccccCCEEEEeCCCCce
Confidence 344477788888887764 57888888888877753
No 44
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=44.77 E-value=41 Score=26.28 Aligned_cols=72 Identities=18% Similarity=0.173 Sum_probs=41.4
Q ss_pred ccccCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCce-eEE--------EecCcEEEcccce------e
Q 032740 52 AYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYR-RAL--------LDNGVTVMVPSYL------E 116 (135)
Q Consensus 52 ~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kGdTat~~~K-~A~--------LetG~~i~VP~FI------~ 116 (135)
...+-..+.++.+.+|+|+.++.=..+ =|.+++--..+..+ .++ +.|||-||.|-.+ +
T Consensus 36 ~v~~~~~~~~ii~vdG~pl~f~~~~~~-------iPTl~~l~~~~~~~~~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik 108 (161)
T COG2016 36 EVAKCDDKFEIILVDGEPLLFQRDDRL-------IPTLRLLLKLPPGKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIK 108 (161)
T ss_pred EEEecCCcEEEEEECCEEEEEEeCCee-------chhhHHHHhCCCCccEEEEcCccHhhhcCCCceeccceeecCCCcc
Confidence 344444567788888999888766533 23233222222121 222 4588889999875 4
Q ss_pred cCCEEEEeCCC-Cee
Q 032740 117 IGEEIFINPQD-DSY 130 (135)
Q Consensus 117 ~Gd~I~VdT~~-g~Y 130 (135)
.||.|.|.-+. +..
T Consensus 109 ~Gd~VvV~~e~~~~p 123 (161)
T COG2016 109 EGDIVVVVDEKKGRP 123 (161)
T ss_pred CCCEEEEEEcCCCCe
Confidence 67777655433 543
No 45
>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=43.94 E-value=35 Score=28.18 Aligned_cols=41 Identities=20% Similarity=0.258 Sum_probs=30.0
Q ss_pred CCccCCCCceeEEEecCcE---EEcccceecCCEEEEeCCCCee
Q 032740 90 KGPTVTPRYRRALLDNGVT---VMVPSYLEIGEEIFINPQDDSY 130 (135)
Q Consensus 90 kGdTat~~~K~A~LetG~~---i~VP~FI~~Gd~I~VdT~~g~Y 130 (135)
-|+...-++|..+-++|.. |.||.|-+.|..+.||.+|-+.
T Consensus 209 ~Gnq~~f~t~~~~~~~~~~v~lv~vP~Fs~t~~~vlvdl~tLe~ 252 (257)
T cd07387 209 AGNQPKFGTKLVEGEEGQRVLLVCVPSFSKTGTAVLVNLRTLEC 252 (257)
T ss_pred eCCCcceeeeEEEcCCCCeEEEEEeCCcCcCCEEEEEECCcCcE
Confidence 3555444555555554544 8899999999999999998764
No 46
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=43.77 E-value=1e+02 Score=21.82 Aligned_cols=41 Identities=20% Similarity=0.266 Sum_probs=27.4
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEc---------ccceecCCEEEEeCC
Q 032740 78 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV---------PSYLEIGEEIFINPQ 126 (135)
Q Consensus 78 V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~V---------P~FI~~Gd~I~VdT~ 126 (135)
++-+|+++=| +..-.+.|+||.+|.. =.=|.+||+|+|.-.
T Consensus 9 ~~G~V~e~Lp--------~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~s 58 (87)
T PRK12442 9 LDGIVDEVLP--------DSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELS 58 (87)
T ss_pred EEEEEEEECC--------CCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEEC
Confidence 4456666655 4466788888888653 234678999988643
No 47
>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=43.48 E-value=20 Score=25.61 Aligned_cols=21 Identities=10% Similarity=0.107 Sum_probs=16.1
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||.|+|.++.|+-.-||
T Consensus 46 gi~~Gd~V~v~s~~G~~~~~~ 66 (129)
T cd02793 46 GIADGDIVRVFNDRGACLAGA 66 (129)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 356788999988888876665
No 48
>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=43.08 E-value=23 Score=24.93 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=14.9
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.++.|+-.-|+
T Consensus 47 i~~Gd~V~v~s~~G~~~~~v 66 (130)
T cd02781 47 IADGDWVWVETPRGRARQKA 66 (130)
T ss_pred CCCCCEEEEECCCCEEEEEE
Confidence 45788888888888766554
No 49
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=41.70 E-value=42 Score=27.58 Aligned_cols=50 Identities=12% Similarity=0.242 Sum_probs=29.3
Q ss_pred CCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCee
Q 032740 66 DGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSY 130 (135)
Q Consensus 66 ~~~~i~v~lP~~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y 130 (135)
.|..+..+-|-++.-.|.=.+|.-. +|. +-|- -|-+.|++|+|+||+|.-
T Consensus 123 pgtivk~EaPlhvsk~VmLvdp~d~--------q~t--e~~w-----r~~e~GekVRvstrSG~i 172 (236)
T KOG1708|consen 123 PGTIVKSEAPLHVSKQVMLVDPEDD--------QPT--EVEW-----RFTEDGEKVRVSTRSGRI 172 (236)
T ss_pred CceEEeecCCceecceeEEECcccc--------CCc--eeeE-----EEcCCCcEEEEEeccccc
Confidence 3566666666666655555555211 011 1111 267889999999999864
No 50
>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=41.23 E-value=25 Score=24.84 Aligned_cols=20 Identities=15% Similarity=0.229 Sum_probs=15.6
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||.|+|.+..|+-.-|+
T Consensus 47 i~~Gd~V~v~s~~g~~~~~~ 66 (129)
T cd02782 47 LADGDKVRVTSAAGSVEAEV 66 (129)
T ss_pred CCCCCEEEEEcCCCeEEEEE
Confidence 56789999988888776554
No 51
>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=40.80 E-value=25 Score=23.76 Aligned_cols=53 Identities=17% Similarity=0.298 Sum_probs=27.7
Q ss_pred EEEEEeCCCeE---EEEEEEeCCCC-CCccCC---CCceeEEEecCcEEEcccceecCCEEEEe
Q 032740 68 RALSGSIPKRV---ACTIKEIHAST-KGPTVT---PRYRRALLDNGVTVMVPSYLEIGEEIFIN 124 (135)
Q Consensus 68 ~~i~v~lP~~V---~l~V~et~p~~-kGdTat---~~~K~A~LetG~~i~VP~FI~~Gd~I~Vd 124 (135)
.-+++.+|+++ .+...-..+.. =|-+.+ .+.||.-+ ...+|.|+..||++.|.
T Consensus 16 ~~~~~~lPd~it~w~v~a~a~s~~~~~g~~~~~~~~v~~p~~i----~~~lP~~l~~GD~~~i~ 75 (92)
T PF00207_consen 16 ATFSFTLPDSITSWRVTAFAVSPTGGFGIAEPPEITVFKPFFI----QLNLPRSLRRGDQIQIP 75 (92)
T ss_dssp EEEEEE-SSSSSEEEEEEEEEETTTEEEEECCEEEEEB-SEEE----EEE--SEEETTSEEEEE
T ss_pred EEEEEECCCCccEEEEEEEEECCCCcceEecceEEEEEeeEEE----EcCCCcEEecCCEEEEE
Confidence 45678899887 33333333321 111111 23455543 68899999999999774
No 52
>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=40.79 E-value=77 Score=23.29 Aligned_cols=53 Identities=13% Similarity=0.277 Sum_probs=40.5
Q ss_pred eCCCceeEEeChhhhccccccccCCCEEEEEEE-CCEEEEEeCCCeEEEEEEEeC
Q 032740 33 ESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLY-DGRALSGSIPKRVACTIKEIH 86 (135)
Q Consensus 33 d~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~-~~~~i~v~lP~~V~l~V~et~ 86 (135)
...=|+.|.||++.|-+-..|= ++..+-+.-| ++.-+-+++-..|.++|.+..
T Consensus 22 slgFFddI~IP~~~L~~ps~fd-~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 22 SLGFFDDIFIPPSLLPEPSRFD-EEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp EECCEEEEEEECCCC-TTEEEE-CCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred EecccccEEECHHHCCCCCccC-ccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 4467899999999998888884 4455777788 899999999999999987653
No 53
>PRK14578 elongation factor P; Provisional
Probab=40.59 E-value=1.5e+02 Score=23.49 Aligned_cols=67 Identities=12% Similarity=0.204 Sum_probs=42.3
Q ss_pred ccCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEE---EEeCCCCee
Q 032740 54 LQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEI---FINPQDDSY 130 (135)
Q Consensus 54 L~eg~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I---~VdT~~g~Y 130 (135)
|+.|+.+. |+|+|..| ++....-||-+|..|--+.|---|.||..+. .=.+.||++ .|+.++..|
T Consensus 7 ik~G~~i~---~dg~~~~V-------~~~~~~kpg~~g~~a~vr~klknl~tG~~~e--~tf~s~d~ve~a~ve~~~~qy 74 (187)
T PRK14578 7 FKKGLVIQ---LDGAPCLL-------LDVTFQSPSARGANTMVKTKYRNLLTGQVLE--KTFRSGDKVEEADFERHKGQF 74 (187)
T ss_pred cCCCCEEE---ECCEEEEE-------EEEEEEcCCCCCCceEEEEEEEECCCCCEEE--EEECCCCEEEEeEEEEeEeEE
Confidence 56677555 68888653 4555666876655544567777788887743 334667665 466666666
Q ss_pred Ee
Q 032740 131 IG 132 (135)
Q Consensus 131 ~~ 132 (135)
+-
T Consensus 75 lY 76 (187)
T PRK14578 75 LY 76 (187)
T ss_pred EE
Confidence 54
No 54
>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=39.90 E-value=26 Score=24.82 Aligned_cols=20 Identities=10% Similarity=0.189 Sum_probs=14.4
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.+..|+-.-||
T Consensus 48 i~~Gd~V~v~s~~g~i~~~v 67 (127)
T cd02777 48 IKDGDIVRVFNDRGAVLAGA 67 (127)
T ss_pred CCCCCEEEEEcCCeEEEEEE
Confidence 45688888888888765554
No 55
>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=39.79 E-value=24 Score=26.13 Aligned_cols=21 Identities=10% Similarity=0.083 Sum_probs=17.1
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||.|+|.++.|+-.-||
T Consensus 44 gI~dGd~V~v~~~~G~v~~~a 64 (141)
T cd02776 44 GIKDNDWVEVFNDNGVVVARA 64 (141)
T ss_pred CCCCCCEEEEEeCCeEEEEEE
Confidence 467899999999988877665
No 56
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=39.47 E-value=44 Score=21.12 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=21.1
Q ss_pred EEcccceecCCEEEEeCCCCeeEeec
Q 032740 109 VMVPSYLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 109 i~VP~FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
+.++.-++.||.|.|-+++|+++.|.
T Consensus 25 ~~~~~~~~~g~~V~v~~~~g~~vg~G 50 (77)
T smart00359 25 VRVDGGIKEGDVVVIVDEKGEPLGIG 50 (77)
T ss_pred EEEeCCcCCCCEEEEEcCCCCEEEEE
Confidence 45555577899999999999999875
No 57
>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=39.12 E-value=26 Score=23.99 Aligned_cols=20 Identities=20% Similarity=0.340 Sum_probs=14.6
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.+..|+-.-+|
T Consensus 49 i~~Gd~V~v~~~~G~~~~~v 68 (120)
T cd00508 49 IKDGDLVRVSSRRGSVVVRA 68 (120)
T ss_pred CCCCCEEEEEeCCEEEEEEE
Confidence 57788888888888765444
No 58
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=38.67 E-value=1.3e+02 Score=20.63 Aligned_cols=42 Identities=17% Similarity=0.167 Sum_probs=26.0
Q ss_pred EEEEEEeCCCCCCccCCCCceeEEEecCcEEEc---------ccceecCCEEEEeCCCC
Q 032740 79 ACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV---------PSYLEIGEEIFINPQDD 128 (135)
Q Consensus 79 ~l~V~et~p~~kGdTat~~~K~A~LetG~~i~V---------P~FI~~Gd~I~VdT~~g 128 (135)
.-+|.++-| +..=.+.|+||.+++- =.=|.+||+|.|....-
T Consensus 10 ~g~V~e~L~--------~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~ 60 (75)
T COG0361 10 EGTVIEMLP--------NGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPY 60 (75)
T ss_pred EEEEEEecC--------CCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEeccc
Confidence 345555555 3355667777776542 23467899998877543
No 59
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=38.23 E-value=1.1e+02 Score=19.68 Aligned_cols=32 Identities=13% Similarity=0.355 Sum_probs=20.1
Q ss_pred CceeEEEecCcEEEc--c------cceecCCEEEEeCCCC
Q 032740 97 RYRRALLDNGVTVMV--P------SYLEIGEEIFINPQDD 128 (135)
Q Consensus 97 ~~K~A~LetG~~i~V--P------~FI~~Gd~I~VdT~~g 128 (135)
..=.+.+++|.++.+ | ..|+.||.|.|+....
T Consensus 16 ~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~ 55 (65)
T PF01176_consen 16 NLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPY 55 (65)
T ss_dssp SEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTT
T ss_pred CEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEeccc
Confidence 355677777766544 3 5899999999997654
No 60
>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=37.96 E-value=1e+02 Score=19.23 Aligned_cols=45 Identities=18% Similarity=0.183 Sum_probs=36.5
Q ss_pred EEccCCeEEEEeCCC-ceeEEeChhhhccc-cccccCCCEEEEEEEC
Q 032740 22 LYTENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYD 66 (135)
Q Consensus 22 lY~dgd~~~FMd~et-yeQ~~i~~~~~g~~-~~fL~eg~~v~v~~~~ 66 (135)
.|.+...|=|+..+. -+.+.+..+.+... ..-|++|+.|......
T Consensus 7 ~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~ 53 (65)
T cd04458 7 WFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEE 53 (65)
T ss_pred EEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEE
Confidence 566767888888877 78999999999876 6889999988866654
No 61
>KOG0022 consensus Alcohol dehydrogenase, class III [Secondary metabolites biosynthesis, transport and catabolism]
Probab=37.47 E-value=33 Score=30.09 Aligned_cols=30 Identities=17% Similarity=0.148 Sum_probs=23.7
Q ss_pred EeeEEEEEccCCeEEEEeCCCceeEEeChh
Q 032740 16 DKSFTCLYTENDTAFVIESETFEQLEVPLD 45 (135)
Q Consensus 16 ~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~ 45 (135)
..+-.|.-++.+-||||+.-||.||.+=.+
T Consensus 126 DgtSRF~~~gk~iyHfmg~StFsEYTVv~~ 155 (375)
T KOG0022|consen 126 DGTSRFTCKGKPIYHFMGTSTFSEYTVVDD 155 (375)
T ss_pred CCceeeeeCCCceEEecccccceeEEEeec
Confidence 344567777778999999999999998543
No 62
>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=36.69 E-value=31 Score=25.04 Aligned_cols=40 Identities=20% Similarity=0.332 Sum_probs=28.7
Q ss_pred EEeCCCeEEEEEEEeCCCCCCccCCC--CceeEEEecCcEEEcc
Q 032740 71 SGSIPKRVACTIKEIHASTKGPTVTP--RYRRALLDNGVTVMVP 112 (135)
Q Consensus 71 ~v~lP~~V~l~V~et~p~~kGdTat~--~~K~A~LetG~~i~VP 112 (135)
...||+.- -|.+.+|..|-+.-++ +-|.++|.||.++-|-
T Consensus 67 ~aalppRs--FVaeiDPvFkks~yGg~yg~k~~~l~t~sklav~ 108 (110)
T PF05836_consen 67 AAALPPRS--FVAEIDPVFKKSSYGGSYGEKKVTLNTGSKLAVA 108 (110)
T ss_pred hhcCCchh--hhhhcChhhcccccCccccceeEEEecCCeEEEE
Confidence 34455432 3677899998877654 4689999999998763
No 63
>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=36.37 E-value=31 Score=26.74 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=15.1
Q ss_pred eecCCEEEEeCCCCeeE
Q 032740 115 LEIGEEIFINPQDDSYI 131 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~ 131 (135)
++.||+|.|.+.+|.|.
T Consensus 109 L~~GD~I~v~~~~g~~~ 125 (174)
T TIGR03784 109 LRPGDVIRLQTPDGQWQ 125 (174)
T ss_pred CCCCCEEEEEECCCeEE
Confidence 78999999999999753
No 64
>PRK15463 cold shock-like protein CspF; Provisional
Probab=35.83 E-value=95 Score=20.47 Aligned_cols=45 Identities=11% Similarity=0.176 Sum_probs=35.3
Q ss_pred EEccCCeEEEEeCCC-ceeEEeChhhhccc-cccccCCCEEEEEEEC
Q 032740 22 LYTENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYD 66 (135)
Q Consensus 22 lY~dgd~~~FMd~et-yeQ~~i~~~~~g~~-~~fL~eg~~v~v~~~~ 66 (135)
-|++...|=|+.+++ =+++.+..+.|... ..-|++|..|+...-+
T Consensus 11 ~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 11 TFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRIN 57 (70)
T ss_pred EEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEE
Confidence 366667888998766 47899999999765 6789999988866654
No 65
>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=35.80 E-value=72 Score=24.79 Aligned_cols=69 Identities=14% Similarity=0.223 Sum_probs=49.9
Q ss_pred ccCCCEEEEEEECC-----EEEEEeCCCe-EEEEEEEeCCCC-CCccCCCCceeEEEecCcEEEcccceecCCEEE
Q 032740 54 LQEGMKVWLQLYDG-----RALSGSIPKR-VACTIKEIHAST-KGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIF 122 (135)
Q Consensus 54 L~eg~~v~v~~~~~-----~~i~v~lP~~-V~l~V~et~p~~-kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~ 122 (135)
.+.|.+++|.++.. .+++..||-- =.++.+.++++. .+..-.+-+|.-.=.+|..-.-|.|.+.||+=.
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 67899999999843 5788888876 578888888866 232333455655555666677799999999744
No 66
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=34.63 E-value=1e+02 Score=25.90 Aligned_cols=34 Identities=12% Similarity=0.232 Sum_probs=24.9
Q ss_pred CceeEEEecCcEEEccc-ceecCCEEEEeCCCCee
Q 032740 97 RYRRALLDNGVTVMVPS-YLEIGEEIFINPQDDSY 130 (135)
Q Consensus 97 ~~K~A~LetG~~i~VP~-FI~~Gd~I~VdT~~g~Y 130 (135)
+.-...|..|..|..|. -|+.||.|+||-.+++=
T Consensus 135 g~~~l~~hDGrni~~~d~~ik~~Dtv~i~l~~~kI 169 (262)
T PTZ00118 135 EVSIAVTHDGRTIRYVHPDVKVGDSLRLDLETGKV 169 (262)
T ss_pred CeEEEEecCcceeccCCCcccCCCEEEEECCCCce
Confidence 34455688888888764 67888888888877753
No 67
>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=34.52 E-value=1.2e+02 Score=19.01 Aligned_cols=55 Identities=11% Similarity=0.013 Sum_probs=32.4
Q ss_pred ccCCCEEE--EEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEe
Q 032740 54 LQEGMKVW--LQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFIN 124 (135)
Q Consensus 54 L~eg~~v~--v~~~~~~~i~v~lP~~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~Vd 124 (135)
|+.|+.+. |.-..+.-+.++|+..++-.|--++-.-. ..+ ..+.+++.||.|++.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~------~~~----------~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD------YSE----------ALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc------ccc----------ccccccCCCCEEEEE
Confidence 45677653 44556677788888777666654432110 000 126778899988763
No 68
>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=34.51 E-value=35 Score=23.81 Aligned_cols=21 Identities=10% Similarity=0.009 Sum_probs=15.6
Q ss_pred ceecCCEEEEeCCCCeeEeec
Q 032740 114 YLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
=|+.||+|+|.++.|+-.-|+
T Consensus 44 gi~~Gd~V~v~~~~G~v~~~v 64 (106)
T cd02789 44 GKPEGDKVKVTSEFGEVVVFA 64 (106)
T ss_pred CCCCCCEEEEEcCCEEEEEEE
Confidence 467888888888888765554
No 69
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=34.37 E-value=1.5e+02 Score=20.23 Aligned_cols=43 Identities=12% Similarity=0.347 Sum_probs=27.4
Q ss_pred eEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEc--c------cceecCCEEEEeCCC
Q 032740 77 RVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P------SYLEIGEEIFINPQD 127 (135)
Q Consensus 77 ~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~V--P------~FI~~Gd~I~VdT~~ 127 (135)
.+..+|++.-+ +..=.+.+++|.++.+ | ..|+.||.|.|+..+
T Consensus 6 q~~g~V~~~lG--------~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~ 56 (83)
T smart00652 6 QEIAQVVKMLG--------NGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWD 56 (83)
T ss_pred cEEEEEEEEcC--------CCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecC
Confidence 34455555544 3345667777766443 2 468999999998754
No 70
>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=34.18 E-value=35 Score=23.59 Aligned_cols=20 Identities=15% Similarity=0.282 Sum_probs=15.4
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.+..|+..-++
T Consensus 49 i~~Gd~V~v~~~~G~~~~~v 68 (122)
T cd02791 49 LKEGDLVRVTSRRGEVVLRV 68 (122)
T ss_pred CCCCCEEEEEcCCEEEEEEE
Confidence 57889998888888866544
No 71
>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=33.96 E-value=35 Score=24.74 Aligned_cols=20 Identities=20% Similarity=0.499 Sum_probs=14.6
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||+|+|.+..|+-.-|+
T Consensus 44 I~~Gd~V~v~s~~G~i~~~v 63 (143)
T cd02780 44 IKTGDRVRVVTPGGSVVGKA 63 (143)
T ss_pred CCCCCEEEEEeCCceEEEEE
Confidence 46788888888888765554
No 72
>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=33.87 E-value=1.1e+02 Score=21.55 Aligned_cols=51 Identities=14% Similarity=0.059 Sum_probs=30.7
Q ss_pred eeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCC
Q 032740 17 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 75 (135)
Q Consensus 17 ~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP 75 (135)
..++|.|.||..+. ++.-+.....+..+-.+.|.+|+|.+.-++|=...++
T Consensus 63 ~~v~y~~~~G~~~~--------~~~~~~~~~~~~~~~~~~G~~V~V~Y~P~~P~~~~l~ 113 (148)
T PF12158_consen 63 PVVEYTYQDGRTYS--------RFYSGSDNFGSYWPKYPIGDTVTVYYNPNNPEEARLE 113 (148)
T ss_pred EEEEEEECCCcEEE--------EeccCCcccccCCccCCCcCEEEEEECCcCCCeEEEe
Confidence 34788888774444 1222222244444458899999998887776654444
No 73
>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=33.29 E-value=76 Score=20.56 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=25.5
Q ss_pred CceeEEEecCcEEEccc------ceecCCEEEEeCCC---CeeEeec
Q 032740 97 RYRRALLDNGVTVMVPS------YLEIGEEIFINPQD---DSYIGRA 134 (135)
Q Consensus 97 ~~K~A~LetG~~i~VP~------FI~~Gd~I~VdT~~---g~Y~~R~ 134 (135)
++.| ++..|-.|.|.. -++.||.|.+.... ..|+.|+
T Consensus 9 SM~P-~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv 54 (85)
T cd06530 9 SMEP-TLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRV 54 (85)
T ss_pred CCcC-cccCCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEE
Confidence 4555 356676665542 27899999999877 5677875
No 74
>PRK04980 hypothetical protein; Provisional
Probab=32.63 E-value=75 Score=22.95 Aligned_cols=35 Identities=14% Similarity=0.270 Sum_probs=27.5
Q ss_pred CCceeEEEecCcEEEcccceecCCEEEEeC-CCCeeEeec
Q 032740 96 PRYRRALLDNGVTVMVPSYLEIGEEIFINP-QDDSYIGRA 134 (135)
Q Consensus 96 ~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT-~~g~Y~~R~ 134 (135)
++-|.||+-+| .....++||.+.|.| ++|.++-.+
T Consensus 17 sGkKTiTiRd~----se~~~~~G~~~~V~~~e~g~~~c~i 52 (102)
T PRK04980 17 AGRKTITIRDE----SESHFKPGDVLRVGTFEDDRYFCTI 52 (102)
T ss_pred cCCceEEeeCC----cccCCCCCCEEEEEECCCCcEEEEE
Confidence 56899999885 477889999999965 778777543
No 75
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=31.92 E-value=1.5e+02 Score=19.55 Aligned_cols=38 Identities=29% Similarity=0.386 Sum_probs=28.9
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccc-----eecCCEEEEe
Q 032740 78 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY-----LEIGEEIFIN 124 (135)
Q Consensus 78 V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~F-----I~~Gd~I~Vd 124 (135)
++=+|...+| .+...+|+.|..-++|.= +++|.+|+|-
T Consensus 5 veG~I~~id~---------~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~ 47 (61)
T PF07076_consen 5 VEGTIKSIDP---------ETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVF 47 (61)
T ss_pred ceEEEEEEcC---------CceEEEecCCCEEECCCcccccccCCCCEEEEE
Confidence 4455666655 456899999999999963 7899998773
No 76
>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=31.57 E-value=1.9e+02 Score=22.94 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=20.0
Q ss_pred eEEEEeCCCceeEEeChhhhccccccccCCCEEEEEE
Q 032740 28 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQL 64 (135)
Q Consensus 28 ~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~ 64 (135)
-+.+.|.++ +.+....-.+....|+.|+.+++.+
T Consensus 162 l~~i~~~~~---~~v~~~v~~~~~~~l~~G~~v~v~~ 195 (322)
T TIGR01730 162 LATIVDLDP---LEADFSVPERDLPQLRRGQTLTVEL 195 (322)
T ss_pred EEEEEcCCc---EEEEEEeCHHHHHHhhCCCeEEEEE
Confidence 344555443 3333333334456889999999887
No 77
>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=30.23 E-value=2e+02 Score=25.78 Aligned_cols=73 Identities=8% Similarity=0.049 Sum_probs=44.9
Q ss_pred ccccccCCCEEEE------EEECCEEEEEeCCCeEEEEEEEeCCCCCCcc-CCCCceeEEEecCcEEEcccceecCCEEE
Q 032740 50 AGAYLQEGMKVWL------QLYDGRALSGSIPKRVACTIKEIHASTKGPT-VTPRYRRALLDNGVTVMVPSYLEIGEEIF 122 (135)
Q Consensus 50 ~~~fL~eg~~v~v------~~~~~~~i~v~lP~~V~l~V~et~p~~kGdT-at~~~K~A~LetG~~i~VP~FI~~Gd~I~ 122 (135)
.+++|...-.+.+ .--|+++..+..-..+-+-. ......-.+. ++...+++++.+|..+.|=++|..+++|.
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 3456666544443 34588888888877766532 1111100010 23457899999999999977887766664
Q ss_pred E
Q 032740 123 I 123 (135)
Q Consensus 123 V 123 (135)
.
T Consensus 405 L 405 (497)
T TIGR02520 405 L 405 (497)
T ss_pred E
Confidence 4
No 78
>cd00604 IPT_CGTD IPT domain (domain D) of cyclodextrin glycosyltransferase (CGTase) and similar enzymes. These enzymes are involved in the enzymatic hydrolysis of alpha-1,4 linkages of starch polymers and belong to the glycosyl hydrolase family 13. Most consist of three domains (A,B,C) but CGTase is more complex and has two additional domains (D,E). The function of the IPT/D domain is unknown.
Probab=29.87 E-value=81 Score=21.32 Aligned_cols=40 Identities=13% Similarity=0.279 Sum_probs=27.4
Q ss_pred eeEEeChhhhccc-cccccCCCEEEEEEECCEEEEEeCCCe
Q 032740 38 EQLEVPLDVFGKA-GAYLQEGMKVWLQLYDGRALSGSIPKR 77 (135)
Q Consensus 38 eQ~~i~~~~~g~~-~~fL~eg~~v~v~~~~~~~i~v~lP~~ 77 (135)
.++.|.-.-|+.. ..-.-.+..+.+..|.+.-|.+.+|..
T Consensus 15 ~~VtI~G~gFg~~~~~V~~g~~~a~v~s~sdt~I~~~VP~~ 55 (81)
T cd00604 15 NTVTISGEGFGSTGGTVYFGGTAAEVLSWSDTSIVVEVPRV 55 (81)
T ss_pred CEEEEEEECCCCCccEEEECCEEEEEEEECCCEEEEEeCCC
Confidence 3555655566652 222225578999999999999999975
No 79
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=29.85 E-value=2.2e+02 Score=22.83 Aligned_cols=68 Identities=13% Similarity=0.150 Sum_probs=37.9
Q ss_pred EEEEeCCCceeEEeChhhhccc---------cccccCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCce
Q 032740 29 AFVIESETFEQLEVPLDVFGKA---------GAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYR 99 (135)
Q Consensus 29 ~~FMd~etyeQ~~i~~~~~g~~---------~~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kGdTat~~~K 99 (135)
.+|+|-...-+=.|+...+.+. .++|++|..|.+ +++++..=..+.|+..+. +
T Consensus 78 ~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~a-----kV~~i~~~~~~~LS~k~~-------------~ 139 (235)
T PRK04163 78 GWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIA-----KVKDVDRTRDVVLTLKGK-------------G 139 (235)
T ss_pred eEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEE-----EEEEECCCCcEEEEEcCC-------------C
Confidence 4577766444456666666443 467888987653 233333211244444221 2
Q ss_pred eEEEecCcEEEcccc
Q 032740 100 RALLDNGVTVMVPSY 114 (135)
Q Consensus 100 ~A~LetG~~i~VP~F 114 (135)
-=.|++|..++||+-
T Consensus 140 lG~L~~G~~~~V~~~ 154 (235)
T PRK04163 140 LGKIEGGTIVEIKPV 154 (235)
T ss_pred CCccCCCEEEEECHH
Confidence 345778888888763
No 80
>KOG1641 consensus Mitochondrial chaperonin [Posttranslational modification, protein turnover, chaperones]
Probab=29.58 E-value=1.9e+02 Score=21.10 Aligned_cols=59 Identities=17% Similarity=0.290 Sum_probs=42.1
Q ss_pred EEeCCCe-EE----EEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEee
Q 032740 71 SGSIPKR-VA----CTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 133 (135)
Q Consensus 71 ~v~lP~~-V~----l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 133 (135)
+|-||.. +. -+|+..-||.++ +.+.-=|.....|-+|..|.| -|-+|+..|++..++=|
T Consensus 32 GilLPEks~~K~~~g~VvavGpG~~~--~~G~~v~~~Vk~Gd~VLlpey--gGt~V~l~~~~~~~~fr 95 (104)
T KOG1641|consen 32 GILLPEKSVGKLLQGTVVAVGPGSRD--KGGEIVPVSVKVGDRVLLPEY--GGTKVKLGDEDEYHLFR 95 (104)
T ss_pred eeEeccccccccceEEEEEEcCcccc--CCCCCcCccccCCCEEEeecc--CCcEEeccCCceeEEec
Confidence 4667877 33 788888888876 334445667888888888888 57778888776665544
No 81
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=29.05 E-value=1.8e+02 Score=19.44 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=27.2
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEc--c-------cceecCCEEEEeCC
Q 032740 78 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P-------SYLEIGEEIFINPQ 126 (135)
Q Consensus 78 V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~V--P-------~FI~~Gd~I~VdT~ 126 (135)
++-.|+++=| +..-.+.|+||.++.- | .-|.+||+|+|.-.
T Consensus 7 ~~G~V~e~L~--------~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~s 56 (68)
T TIGR00008 7 MEGKVTESLP--------NAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELS 56 (68)
T ss_pred EEEEEEEECC--------CCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEEC
Confidence 3445666655 4466788888887652 2 23778999988644
No 82
>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=28.92 E-value=55 Score=22.49 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=5.9
Q ss_pred ccceecCCEEEE
Q 032740 112 PSYLEIGEEIFI 123 (135)
Q Consensus 112 P~FI~~Gd~I~V 123 (135)
|.|++.||...|
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 666666665544
No 83
>PRK04517 hypothetical protein; Provisional
Probab=28.50 E-value=2.1e+02 Score=22.75 Aligned_cols=53 Identities=15% Similarity=0.273 Sum_probs=29.3
Q ss_pred EEEeCCCeEEEEEEEeCCC-CCCccCCCCceeEEEecCc---EEEcccceecC-CEEEE
Q 032740 70 LSGSIPKRVACTIKEIHAS-TKGPTVTPRYRRALLDNGV---TVMVPSYLEIG-EEIFI 123 (135)
Q Consensus 70 i~v~lP~~V~l~V~et~p~-~kGdTat~~~K~A~LetG~---~i~VP~FI~~G-d~I~V 123 (135)
+.+++|..|++.++.=... .-| .--++.+..+|++|. .+++=..++.| |+.++
T Consensus 23 vtL~~p~~i~lL~vnG~k~~~s~-~l~~~~~~l~L~~G~nQIvfry~~~~~~~~~~~~~ 80 (216)
T PRK04517 23 VTMEVPDDVDLLVANGSKPKLSG-GFFASTKTLELPDGENQIVFRYSPYFSQGNDRIIV 80 (216)
T ss_pred EEEeCCCceEEEEECCEeccccc-ccccCCceeEeCCCceEEEEEEeEeeccCCCceEE
Confidence 5678888888887754431 111 001234788898884 34444444433 44333
No 84
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=28.41 E-value=2.2e+02 Score=20.26 Aligned_cols=45 Identities=20% Similarity=0.358 Sum_probs=30.4
Q ss_pred CeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEE--cc------cceecCCEEEEeCCCC
Q 032740 76 KRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVM--VP------SYLEIGEEIFINPQDD 128 (135)
Q Consensus 76 ~~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~--VP------~FI~~Gd~I~VdT~~g 128 (135)
..+..+|++.-+ +..=.+.+++|.++. +| ..|..||.|.|....-
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 456667777655 335567777777654 33 6799999999986543
No 85
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=28.13 E-value=88 Score=26.40 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=23.9
Q ss_pred CCceeEEEecCcEEEccc-ceecCCEEEEeCCCCee
Q 032740 96 PRYRRALLDNGVTVMVPS-YLEIGEEIFINPQDDSY 130 (135)
Q Consensus 96 ~~~K~A~LetG~~i~VP~-FI~~Gd~I~VdT~~g~Y 130 (135)
++--...|..|..|..|. -|+.||.|+||-.+++=
T Consensus 131 gG~~ql~~hDGrnI~~~d~~~k~~Dtv~i~l~~~kI 166 (273)
T PTZ00223 131 GRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVKEKKV 166 (273)
T ss_pred CCeeEEEecCCceeccCCccccCCCEEEEECCCCee
Confidence 334467777777777653 46788888888777753
No 86
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=28.11 E-value=3.8e+02 Score=22.87 Aligned_cols=86 Identities=19% Similarity=0.342 Sum_probs=56.8
Q ss_pred CeEEEEeCCCce-eEEeChhhhccccccccCCCEEEEEEE---CCEEEEEe-CC-----CeEEEEEEEeCCCCCCccCCC
Q 032740 27 DTAFVIESETFE-QLEVPLDVFGKAGAYLQEGMKVWLQLY---DGRALSGS-IP-----KRVACTIKEIHASTKGPTVTP 96 (135)
Q Consensus 27 d~~~FMd~etye-Q~~i~~~~~g~~~~fL~eg~~v~v~~~---~~~~i~v~-lP-----~~V~l~V~et~p~~kGdTat~ 96 (135)
+.-+|++.++++ .+.+++.... -.=++.|.+|++..| +++++.=. -| ..=-++|++..+..
T Consensus 18 ~~g~fL~~~~~~~~ilL~k~~~~--~~e~evGdev~vFiY~D~~~rl~aTt~~p~~tvg~~g~~~Vv~v~~~l------- 88 (287)
T COG2996 18 DFGYFLDAGEDGTTILLPKSEPE--EDELEVGDEVTVFIYVDSEDRLIATTREPKATVGEYGWLKVVEVNKDL------- 88 (287)
T ss_pred ceeEEEecCCCceEEeccccCCc--CCccccCcEEEEEEEECCCCceeheeecceEeecceeEEEEEEEcCCc-------
Confidence 566777877776 5666665332 244789999999998 56665533 23 33368899887644
Q ss_pred CceeEEEecCcE--EEcc---------cceecCCEEEEe
Q 032740 97 RYRRALLDNGVT--VMVP---------SYLEIGEEIFIN 124 (135)
Q Consensus 97 ~~K~A~LetG~~--i~VP---------~FI~~Gd~I~Vd 124 (135)
-|-|++|+. +.|| +-.+.||+..|.
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 467777764 4444 237889988664
No 87
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=26.56 E-value=50 Score=25.96 Aligned_cols=35 Identities=29% Similarity=0.399 Sum_probs=29.9
Q ss_pred EEEEEccCCeEEEEeCCCceeEEeChhhhcccccc
Q 032740 19 FTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAY 53 (135)
Q Consensus 19 ~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~f 53 (135)
++=+|.||+..+|+|++.--...++.+.|..+..|
T Consensus 129 iTGI~~dg~~i~~~DP~~gP~~~m~l~~fn~~~~w 163 (166)
T PF12385_consen 129 ITGIDGDGDSIHVHDPEQGPNLRMSLDMFNQALAW 163 (166)
T ss_pred EEeecCCCCeEEecCcccCCCceecHHHHhhhhcc
Confidence 45679999999999999988889999888777665
No 88
>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=26.35 E-value=2e+02 Score=19.15 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=26.7
Q ss_pred CEEEEEEECCEEEEEeCCCe-EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccc
Q 032740 58 MKVWLQLYDGRALSGSIPKR-VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY 114 (135)
Q Consensus 58 ~~v~v~~~~~~~i~v~lP~~-V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~F 114 (135)
|+|.+..-+.--+++=+|.. ++=.|++.+ +...--+.++|.||-+..+|..
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 34444444433677777754 677788885 2222345799999999999875
No 89
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=25.33 E-value=3.4e+02 Score=21.31 Aligned_cols=93 Identities=15% Similarity=0.137 Sum_probs=56.2
Q ss_pred EEEeeEEEEEccCCeEEEEeCCCceeEEeChhhhccccccccCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCcc
Q 032740 14 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPT 93 (135)
Q Consensus 14 i~~~~~~ylY~dgd~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kGdT 93 (135)
+....+.|-|.+...++...++.-+=+++|..+++ ....+|.. +|.|=+|.. ....|+-.+- ...+.|.-=-+
T Consensus 43 ~pDg~v~Y~ya~~~T~~tt~pdG~ev~~FpngQ~E---~h~pDG~k-eI~fPDGt~-k~~~~dG~e~--~~fpDGT~~~~ 115 (179)
T PF07202_consen 43 LPDGRVIYYYADAQTTHTTYPDGLEVYEFPNGQIE---KHYPDGSK-EIVFPDGTI-KYIHPDGREE--TVFPDGTIVTI 115 (179)
T ss_pred ecCCcEEEEEeCCCEEEEEcCCCcEEEEeCCCceE---EEcCCCCE-EEEeCCCcE-EEEeCCCcEE--EECCCceEEEE
Confidence 44456889999989999999998899999998877 46667754 566656544 3333333321 11111111111
Q ss_pred CCCCceeEEEecCcE-EEccc
Q 032740 94 VTPRYRRALLDNGVT-VMVPS 113 (135)
Q Consensus 94 at~~~K~A~LetG~~-i~VP~ 113 (135)
-.++.|...+.||.. |.-+.
T Consensus 116 ~~nG~k~i~~pnGq~ei~t~~ 136 (179)
T PF07202_consen 116 DPNGDKTITFPNGQKEIHTAD 136 (179)
T ss_pred eCCCcEEEEeCCCcEEEEccc
Confidence 125677888888854 44433
No 90
>PRK09890 cold shock protein CspG; Provisional
Probab=24.98 E-value=1.6e+02 Score=19.22 Aligned_cols=44 Identities=14% Similarity=0.088 Sum_probs=32.5
Q ss_pred EccCCeEEEEeCCCc-eeEEeChhhhccc-cccccCCCEEEEEEEC
Q 032740 23 YTENDTAFVIESETF-EQLEVPLDVFGKA-GAYLQEGMKVWLQLYD 66 (135)
Q Consensus 23 Y~dgd~~~FMd~ety-eQ~~i~~~~~g~~-~~fL~eg~~v~v~~~~ 66 (135)
|.+...|=|+.+++- +++.+..+.+... ..-|++|..|....-+
T Consensus 12 f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 12 FNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQ 57 (70)
T ss_pred EECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEE
Confidence 555678888888766 6888888888755 4678999987765543
No 91
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=24.82 E-value=1.3e+02 Score=23.29 Aligned_cols=39 Identities=13% Similarity=0.263 Sum_probs=32.1
Q ss_pred CCCceeEEEecCcEEEcccceecCCEEEEeCCCCeeEee
Q 032740 95 TPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 133 (135)
Q Consensus 95 t~~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 133 (135)
++..|.+.+.=-.++=||-=++--++..||--||=|+|.
T Consensus 59 ~~eGk~~LVPLTsSlYVPGkl~d~~k~lVDIGTGYyVEK 97 (153)
T KOG3048|consen 59 ANEGKKLLVPLTSSLYVPGKLSDNSKFLVDIGTGYYVEK 97 (153)
T ss_pred CCCCCeEEEecccceeccceeccccceeEeccCceEEee
Confidence 345566666666778888889999999999999999986
No 92
>cd02849 CGTase_C_term Cgtase (cyclodextrin glycosyltransferase) C-terminus domain. Enzymes such as amylases, cyclomaltodextrinase (CDase), and CGTase degrade starch to smaller oligosaccharides by hydrolyzing the alpha-D-(1,4) linkages between glucose residues present in starch. In the case of CGTases, an additional cyclization reaction is catalyzed yielding mixtures of cyclic oligosaccharides which are referred to as alpha-, beta-, or gamma-cyclodextrins (CDs) (consisting of six, seven, or eight glucoses, respectively). CGTases are characterized as depending on the major product of the cyclization reaction. Besides having similar catalytic site residues, amylases and CGTases contain carbohydrate binding domains that are distant from the active site and which are implicated in attaching the enzyme to raw starch granules and in guiding the amylose chain into the active site. The C-terminus of CGTase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These d
Probab=24.79 E-value=1.1e+02 Score=20.60 Aligned_cols=40 Identities=13% Similarity=0.215 Sum_probs=28.2
Q ss_pred eeEEeChhhhccc-cccccCCCEEEEEEECCEEEEEeCCCe
Q 032740 38 EQLEVPLDVFGKA-GAYLQEGMKVWLQLYDGRALSGSIPKR 77 (135)
Q Consensus 38 eQ~~i~~~~~g~~-~~fL~eg~~v~v~~~~~~~i~v~lP~~ 77 (135)
+++.|.-.-|+.+ ..=.-.+..+.+..|.+.-|.+.+|..
T Consensus 17 ~~VtI~G~gFg~~~~~V~~g~~~a~v~s~sdt~I~~~vP~~ 57 (81)
T cd02849 17 NTVTISGEGFGSAPGTVYFGTTAATVISWSDTRIVVTVPNV 57 (81)
T ss_pred CEEEEEEECCCCCCcEEEECCEEeEEEEECCCEEEEEeCCC
Confidence 4566666666632 111223578999999999999999976
No 93
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.75 E-value=59 Score=24.12 Aligned_cols=20 Identities=15% Similarity=0.031 Sum_probs=15.1
Q ss_pred eecCCEEEEeCCCCeeEeec
Q 032740 115 LEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~ 134 (135)
|+.||.|+|.+..|+-.-+|
T Consensus 52 I~dGD~V~V~s~~G~i~~~a 71 (137)
T cd02784 52 LLQGDVVRIRRGGRTIELPV 71 (137)
T ss_pred CCCCCEEEEEeCCeEEEEEE
Confidence 46789999988888765544
No 94
>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=24.64 E-value=1.1e+02 Score=21.47 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=24.2
Q ss_pred CceeEEEecCcEEEcccc-eecCCEEEEeC
Q 032740 97 RYRRALLDNGVTVMVPSY-LEIGEEIFINP 125 (135)
Q Consensus 97 ~~K~A~LetG~~i~VP~F-I~~Gd~I~VdT 125 (135)
+.|+=.++.|-.+.||.+ .++||.|.++.
T Consensus 8 ggkQykV~~gd~i~v~~l~~~~G~~i~l~~ 37 (96)
T PF00829_consen 8 GGKQYKVEEGDVIDVERLDAEVGDKIELDK 37 (96)
T ss_dssp SSEEEEESSSEEEEEESTSSSTTSEEEETT
T ss_pred CCEEEEEeCCCEEEECCcCcCCCCEEEEEE
Confidence 568888999999999988 66899997753
No 95
>PRK12473 hypothetical protein; Provisional
Probab=24.52 E-value=44 Score=26.98 Aligned_cols=39 Identities=10% Similarity=0.189 Sum_probs=29.5
Q ss_pred cceEeeEEEEeeEEEE----------EccCCeEEEEeCCCceeEEeChhhh
Q 032740 7 YFAAGVFVEDKSFTCL----------YTENDTAFVIESETFEQLEVPLDVF 47 (135)
Q Consensus 7 ~~~e~~~i~~~~~~yl----------Y~dgd~~~FMd~etyeQ~~i~~~~~ 47 (135)
+.++.+.++.+.++|= |.+ .|+..|..+|.||.-+...+
T Consensus 118 ee~K~i~l~gKki~Ye~n~WiG~~R~y~~--~~vIV~d~~YkeI~~~E~tm 166 (198)
T PRK12473 118 EEVKNATLDGKKMKYEGNVIIGSGRKYTD--MYAIVDDATYAKIKGDEKTV 166 (198)
T ss_pred cchhceeECCeEEEEeccEEEecCCCCCc--EEEEEehhhhhhcccceEEE
Confidence 5589999999999763 332 67788999999987765544
No 96
>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=24.09 E-value=77 Score=29.62 Aligned_cols=64 Identities=19% Similarity=0.219 Sum_probs=40.8
Q ss_pred eeEEEEEccCCeEEEEeCCCceeEEeCh-------hhhccc--------cccccCC-----CEEEEEEECCEEEEEeCCC
Q 032740 17 KSFTCLYTENDTAFVIESETFEQLEVPL-------DVFGKA--------GAYLQEG-----MKVWLQLYDGRALSGSIPK 76 (135)
Q Consensus 17 ~~~~ylY~dgd~~~FMd~etyeQ~~i~~-------~~~g~~--------~~fL~eg-----~~v~v~~~~~~~i~v~lP~ 76 (135)
-+++|++...++||||.+.|==|++=|- |+++|. +++=++. .-.+...|-..|.+--||.
T Consensus 268 GTVEFi~D~~~~FyFmEmNTRLQVEHPvTEmItg~DLVewqiRvA~ge~lp~~q~ei~l~GhafE~RiyAEdp~~~f~P~ 347 (670)
T KOG0238|consen 268 GTVEFIVDSKDNFYFMEMNTRLQVEHPVTEMITGTDLVEWQIRVAAGEPLPLKQEEIPLNGHAFEARIYAEDPYKGFLPS 347 (670)
T ss_pred ceEEEEEcCCCcEEEEEeeceeeecccchhhccchHHHHHHHHHhcCCCCCCCcceeeecceEEEEEEeecCCcccCCCC
Confidence 3689999999999999999999998764 344433 3343432 2234444545555555665
Q ss_pred eEEE
Q 032740 77 RVAC 80 (135)
Q Consensus 77 ~V~l 80 (135)
.=.|
T Consensus 348 ~G~L 351 (670)
T KOG0238|consen 348 AGRL 351 (670)
T ss_pred Cccc
Confidence 4444
No 97
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=23.68 E-value=1.7e+02 Score=19.31 Aligned_cols=32 Identities=19% Similarity=0.247 Sum_probs=23.5
Q ss_pred eeEEeChhhhccccccccCCCEEEEEEECCEEEE
Q 032740 38 EQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALS 71 (135)
Q Consensus 38 eQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~~~i~ 71 (135)
-.+.||++.+. .+ =|.+|.++.+...+|..+-
T Consensus 10 ~~vtIPk~i~~-~l-gl~~Gd~v~v~~~~~~iii 41 (74)
T TIGR02609 10 LVVTLPKEVLE-SL-GLKEGDTLYVDEEEGGLKL 41 (74)
T ss_pred eEEEECHHHHH-Hc-CcCCCCEEEEEEECCEEEE
Confidence 36789998875 33 3689999998888876543
No 98
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=23.64 E-value=2.2e+02 Score=18.52 Aligned_cols=45 Identities=16% Similarity=0.150 Sum_probs=33.0
Q ss_pred EEccCCeEEEEeCCCc-eeEEeChhhhccc-cccccCCCEEEEEEEC
Q 032740 22 LYTENDTAFVIESETF-EQLEVPLDVFGKA-GAYLQEGMKVWLQLYD 66 (135)
Q Consensus 22 lY~dgd~~~FMd~ety-eQ~~i~~~~~g~~-~~fL~eg~~v~v~~~~ 66 (135)
-|.+...|=|+.+++- +++.+..+.+... ..-|++|+.|+...-.
T Consensus 11 ~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 11 WFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIES 57 (70)
T ss_pred EEeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEE
Confidence 3556678888887765 6899888888754 3668999988765543
No 99
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=23.48 E-value=3.4e+02 Score=20.96 Aligned_cols=36 Identities=22% Similarity=0.236 Sum_probs=21.5
Q ss_pred eEEEEeCCCc-eeEEeChhhhccccccccCCCEEEEEEECC
Q 032740 28 TAFVIESETF-EQLEVPLDVFGKAGAYLQEGMKVWLQLYDG 67 (135)
Q Consensus 28 ~~~FMd~ety-eQ~~i~~~~~g~~~~fL~eg~~v~v~~~~~ 67 (135)
-+.++|...+ =++.||.+ ...+|+.|+.+.+.+..|
T Consensus 116 l~~i~~~~~~~i~~~v~~~----~~~~i~~g~~v~i~~~~~ 152 (265)
T TIGR00999 116 LFRVADLGAVWVEAEVPAK----DVSRIRKGSKATVLLENG 152 (265)
T ss_pred eEEEEcCCcEEEEEEECHH----HHhhCCCCCEEEEEECCC
Confidence 3346665433 22344544 446899999998887543
No 100
>PF10055 DUF2292: Uncharacterized small protein (DUF2292); InterPro: IPR018743 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.10 E-value=1.5e+02 Score=17.76 Aligned_cols=17 Identities=24% Similarity=0.272 Sum_probs=14.1
Q ss_pred EEEEEEECCEEEEEeCC
Q 032740 59 KVWLQLYDGRALSGSIP 75 (135)
Q Consensus 59 ~v~v~~~~~~~i~v~lP 75 (135)
.+++..+||+++.++--
T Consensus 17 sV~iiiqdG~vvQIe~~ 33 (38)
T PF10055_consen 17 SVTIIIQDGRVVQIEKT 33 (38)
T ss_pred eEEEEEECCEEEEEEhh
Confidence 58899999999988743
No 101
>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=22.69 E-value=81 Score=21.17 Aligned_cols=47 Identities=23% Similarity=0.398 Sum_probs=33.9
Q ss_pred EEEeeEEEEEccCCeEEEEe--CCCceeEEeChhhhccccc--cccCCCEEE
Q 032740 14 VEDKSFTCLYTENDTAFVIE--SETFEQLEVPLDVFGKAGA--YLQEGMKVW 61 (135)
Q Consensus 14 i~~~~~~ylY~dgd~~~FMd--~etyeQ~~i~~~~~g~~~~--fL~eg~~v~ 61 (135)
+.|+++|.+--++....+|+ -++-+.+.+|.+.++..+. | .+|-.+.
T Consensus 1 V~R~eYqLidI~dGflsLm~e~G~~k~DlklP~~elg~~I~~~f-~~gk~~~ 51 (69)
T cd04468 1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKF-DEGKDVL 51 (69)
T ss_pred CcceeEEEEeecCCeEEEEcCCCCcccCCcCCcHHHHHHHHHHH-hCCCcEE
Confidence 45789999999877778995 3456789999988886653 4 3454433
No 102
>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=22.10 E-value=42 Score=26.56 Aligned_cols=27 Identities=15% Similarity=0.150 Sum_probs=20.5
Q ss_pred eeEEEEEcc-CCeEEEEeCCCceeEEeC
Q 032740 17 KSFTCLYTE-NDTAFVIESETFEQLEVP 43 (135)
Q Consensus 17 ~~~~ylY~d-gd~~~FMd~etyeQ~~i~ 43 (135)
-++||+|.+ ++.|+||...++=|.+.|
T Consensus 158 ~tvef~~~~~~~~~y~lEvNpR~~~~~p 185 (211)
T PF02786_consen 158 GTVEFAVDPDDGEFYFLEVNPRLQREHP 185 (211)
T ss_dssp EEEEEEEETTTTEEEEEEEESS--TTHH
T ss_pred ceEEEEEccCccceeeecccCCCCCcch
Confidence 478999997 779999998888776654
No 103
>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.
Probab=22.03 E-value=2.7e+02 Score=18.97 Aligned_cols=40 Identities=18% Similarity=0.226 Sum_probs=20.7
Q ss_pred CCEEEEEeCC--CeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEc
Q 032740 66 DGRALSGSIP--KRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV 111 (135)
Q Consensus 66 ~~~~i~v~lP--~~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~V 111 (135)
.|+++-+-+. ..+.++|..+.|....+ -.|+|++|.+|-|
T Consensus 37 ~~~~~~v~v~~~~~i~~~V~~i~p~~~~~------~~~~L~~~TEv~V 78 (80)
T PF09262_consen 37 PGQVFPVWVSQNTVIKFKVVSIEPSSSAE------GCARLSPDTEVIV 78 (80)
T ss_dssp TT-EEEEESSSS-EEEEEEEEEES--S---------SEE--TT-EEEE
T ss_pred CCCEEEEEEcCCeEEEEEEEEccCCCCce------eEEEeCCCcEEEE
Confidence 3444444442 34578899998844211 3799999999876
No 104
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=21.47 E-value=2.7e+02 Score=19.03 Aligned_cols=39 Identities=26% Similarity=0.556 Sum_probs=27.5
Q ss_pred CeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccceecCCEEEEe
Q 032740 76 KRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFIN 124 (135)
Q Consensus 76 ~~V~l~V~et~p~~kGdTat~~~K~A~LetG~~i~VP~FI~~Gd~I~Vd 124 (135)
...+.+|.++ +.+||- -|..+ |.+|=||- .+.||.++|.
T Consensus 17 e~y~V~I~d~--g~~GDG------iarve-GfvVFVp~-a~~Gd~V~vk 55 (73)
T COG3269 17 ETYEVEIEDV--GDQGDG------IARVE-GFVVFVPG-AEVGDEVKVK 55 (73)
T ss_pred CEEEEEEEEe--ccCCCc------eEEEE-EEEEEeCC-CCCCCeeeEE
Confidence 4445566555 555655 56777 99999997 5889988775
No 105
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=21.41 E-value=89 Score=19.26 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=14.6
Q ss_pred ceecCCEEEEeCCCC--eeEeec
Q 032740 114 YLEIGEEIFINPQDD--SYIGRA 134 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g--~Y~~R~ 134 (135)
-++.||.|.+....+ .|+.|.
T Consensus 24 ~~~~gdivv~~~~~~~~~~iKrv 46 (70)
T PF00717_consen 24 EPKDGDIVVVKIDGDEELYIKRV 46 (70)
T ss_dssp ---TTSEEEEEETTEESEEEEEE
T ss_pred CCccCeEEEEEECCceeeEEEEE
Confidence 566888888888877 688775
No 106
>PRK01203 prefoldin subunit alpha; Provisional
Probab=21.38 E-value=1.8e+02 Score=21.90 Aligned_cols=38 Identities=11% Similarity=0.291 Sum_probs=33.2
Q ss_pred CceeEEEecCcEEEcccceecCCEEEEeCCCCeeEeec
Q 032740 97 RYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRA 134 (135)
Q Consensus 97 ~~K~A~LetG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R~ 134 (135)
..|.+.+.=|..+-||-=|..-|+|.||-=+|=|+++-
T Consensus 47 ~~~eiLVPLg~slYV~gki~d~~kVlVdIGTGy~VEK~ 84 (130)
T PRK01203 47 NSKELLISIGSGIFADGNIKKDKDLIVPIGSGVYIAEE 84 (130)
T ss_pred CCCeEEEEccCCceEeEEecCCCeEEEEcCCCeEEEec
Confidence 34788888888888888999999999999999999873
No 107
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.
Probab=21.11 E-value=67 Score=29.81 Aligned_cols=21 Identities=19% Similarity=0.061 Sum_probs=18.1
Q ss_pred eecCCEEEEeCCCCeeEeecC
Q 032740 115 LEIGEEIFINPQDDSYIGRAK 135 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~~R~k 135 (135)
|+.||.|+|.++.|+..-||+
T Consensus 719 I~dGD~V~V~s~~G~~~~~a~ 739 (797)
T TIGR02166 719 ITNGDMVRIFNSRGEVEIPAK 739 (797)
T ss_pred CCcCCEEEEEeCCeEEEEEEE
Confidence 568999999999999887763
No 108
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=20.73 E-value=1.1e+02 Score=19.79 Aligned_cols=29 Identities=7% Similarity=-0.182 Sum_probs=17.9
Q ss_pred cccccceEeeEEEEeeEEEEEccCCeEEE
Q 032740 3 INAIYFAAGVFVEDKSFTCLYTENDTAFV 31 (135)
Q Consensus 3 ~~~~~~~e~~~i~~~~~~ylY~dgd~~~F 31 (135)
|++||++.-.+--.+..+..-..|..|+.
T Consensus 6 f~~GdrVQlTD~Kgr~~Ti~L~~G~~fhT 34 (54)
T PF14801_consen 6 FRAGDRVQLTDPKGRKHTITLEPGGEFHT 34 (54)
T ss_dssp --TT-EEEEEETT--EEEEE--TT-EEEE
T ss_pred CCCCCEEEEccCCCCeeeEEECCCCeEEc
Confidence 78999999988888888888888887764
No 109
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=20.70 E-value=97 Score=20.28 Aligned_cols=17 Identities=12% Similarity=0.325 Sum_probs=11.4
Q ss_pred eecCCEEEEeCCCCeeE
Q 032740 115 LEIGEEIFINPQDDSYI 131 (135)
Q Consensus 115 I~~Gd~I~VdT~~g~Y~ 131 (135)
|+.||+|.|.+..|+-.
T Consensus 37 l~~Gd~v~v~~~~g~~~ 53 (101)
T cd02775 37 IKDGDLVRVESRRGSVV 53 (101)
T ss_pred CCCCCEEEEEcCCcEEE
Confidence 45677777777776644
No 110
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=20.49 E-value=2.3e+02 Score=17.71 Aligned_cols=35 Identities=6% Similarity=0.026 Sum_probs=23.5
Q ss_pred eEEEEeCCCceeEEeChhhhccccccccCCCEEEEEE
Q 032740 28 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQL 64 (135)
Q Consensus 28 ~~~FMd~etyeQ~~i~~~~~g~~~~fL~eg~~v~v~~ 64 (135)
.++|+|-.. -+-.||++.+.... .++.|..+.+..
T Consensus 17 ~~~~vdig~-~eg~lp~~e~~~~~-~~~~Gd~v~v~v 51 (67)
T cd04455 17 GNVIVDLGK-VEAILPKKEQIPGE-SYRPGDRIKAYV 51 (67)
T ss_pred CCEEEEcCC-eEEEeeHHHCCCCC-cCCCCCEEEEEE
Confidence 456677754 56688888886543 348887777654
No 111
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=20.27 E-value=1.4e+02 Score=20.55 Aligned_cols=20 Identities=15% Similarity=0.428 Sum_probs=14.3
Q ss_pred EcccceecCCEEEEeCCCCe
Q 032740 110 MVPSYLEIGEEIFINPQDDS 129 (135)
Q Consensus 110 ~VP~FI~~Gd~I~VdT~~g~ 129 (135)
.+|.-+++||+|..+--.|.
T Consensus 53 ~~~~~vk~GD~Vl~~~~~g~ 72 (93)
T PF00166_consen 53 EVPMDVKVGDKVLFPKYAGT 72 (93)
T ss_dssp EEETSS-TTSEEEEETTTSE
T ss_pred EeeeeeeeccEEeccccCce
Confidence 55778999999988866553
No 112
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=20.16 E-value=77 Score=29.66 Aligned_cols=22 Identities=18% Similarity=0.099 Sum_probs=19.1
Q ss_pred ceecCCEEEEeCCCCeeEeecC
Q 032740 114 YLEIGEEIFINPQDDSYIGRAK 135 (135)
Q Consensus 114 FI~~Gd~I~VdT~~g~Y~~R~k 135 (135)
=|+.||+|+|.++.|+..-||+
T Consensus 735 GI~dGD~V~V~n~~G~v~~~a~ 756 (814)
T PRK14990 735 GINNGDKVRIFNDRGEVHIEAK 756 (814)
T ss_pred CCCCCCEEEEEcCCceEEEEEE
Confidence 4788999999999999988773
Done!