Query 026237
Match_columns 241
No_of_seqs 155 out of 1155
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:24:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026237.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026237hhsearch_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 1.7E-75 3.8E-80 501.0 24.7 184 58-241 1-184 (185)
2 PRK14578 elongation factor P; 100.0 3.5E-73 7.5E-78 487.8 25.0 184 58-241 1-186 (187)
3 PRK04542 elongation factor P; 100.0 4.5E-73 9.7E-78 487.7 24.3 184 58-241 1-187 (189)
4 TIGR02178 yeiP elongation fact 100.0 5.6E-72 1.2E-76 479.8 24.6 181 61-241 2-185 (186)
5 PRK00529 elongation factor P; 100.0 1.3E-70 2.9E-75 471.9 24.6 184 58-241 1-184 (186)
6 TIGR00038 efp translation elon 100.0 1.5E-70 3.4E-75 470.8 24.5 183 59-241 1-183 (184)
7 COG0231 Efp Translation elonga 100.0 1.2E-45 2.7E-50 301.5 16.7 130 57-186 2-131 (131)
8 TIGR00037 eIF_5A translation i 100.0 2.5E-37 5.3E-42 252.3 16.1 120 58-179 6-126 (130)
9 PRK03999 translation initiatio 100.0 1.7E-35 3.7E-40 241.2 16.2 117 58-176 5-122 (129)
10 PLN03107 eukaryotic translatio 100.0 4.3E-32 9.2E-37 228.2 16.3 121 57-177 19-148 (159)
11 smart00841 Elong-fact-P_C Elon 99.9 3.2E-27 6.9E-32 166.6 6.5 56 186-241 1-56 (56)
12 cd05794 S1_EF-P_repeat_2 S1_EF 99.9 3.5E-27 7.5E-32 166.4 6.6 56 186-241 1-56 (56)
13 PF09285 Elong-fact-P_C: Elong 99.9 4.3E-27 9.2E-32 166.0 6.9 56 186-241 1-56 (56)
14 cd04470 S1_EF-P_repeat_1 S1_EF 99.9 3.7E-23 8E-28 148.4 7.3 61 123-183 1-61 (61)
15 PF08207 EFP_N: Elongation fac 99.8 4.2E-21 9E-26 136.4 8.4 58 60-117 1-58 (58)
16 PTZ00328 eukaryotic initiation 99.8 5.5E-20 1.2E-24 154.9 13.9 118 57-174 21-150 (166)
17 PF01132 EFP: Elongation facto 99.8 8.2E-21 1.8E-25 133.5 6.6 55 124-178 1-55 (55)
18 cd04463 S1_EF_like S1_EF_like: 99.7 2.6E-17 5.6E-22 115.0 6.0 55 125-180 1-55 (55)
19 KOG3271 Translation initiation 99.6 2.8E-15 6.2E-20 123.2 9.6 112 59-170 21-136 (156)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.7 2.9E-08 6.3E-13 70.5 5.6 54 122-177 1-54 (57)
21 COG1499 NMD3 NMD protein affec 98.1 4.1E-05 8.9E-10 72.3 11.8 111 55-181 237-352 (355)
22 PF01287 eIF-5a: Eukaryotic el 97.1 0.004 8.8E-08 45.8 7.8 56 121-177 1-63 (69)
23 cd04468 S1_eIF5A S1_eIF5A: Euk 92.7 0.43 9.3E-06 35.2 5.9 51 122-172 1-54 (69)
24 PF00900 Ribosomal_S4e: Riboso 78.5 3 6.5E-05 31.2 3.6 67 165-237 3-75 (77)
25 PF08605 Rad9_Rad53_bind: Fung 77.6 5.6 0.00012 32.8 5.2 39 59-97 55-103 (131)
26 cd04469 S1_Hex1 S1_Hex1: Hex1, 75.0 16 0.00034 27.4 6.6 53 125-177 3-62 (75)
27 PF02941 FeThRed_A: Ferredoxin 63.8 3.6 7.8E-05 30.2 1.0 18 172-189 39-56 (67)
28 PRK05338 rplS 50S ribosomal pr 59.9 47 0.001 26.9 6.9 66 59-125 14-88 (116)
29 KOG1999 RNA polymerase II tran 57.8 1.1E+02 0.0024 33.1 10.8 131 100-234 397-544 (1024)
30 PRK14560 putative RNA-binding 55.0 30 0.00064 28.9 5.3 71 162-239 38-124 (160)
31 TIGR00523 eIF-1A eukaryotic/ar 53.5 67 0.0015 25.1 6.7 51 176-234 7-69 (99)
32 CHL00084 rpl19 ribosomal prote 51.6 78 0.0017 25.7 6.9 67 58-125 17-92 (117)
33 PF01245 Ribosomal_L19: Riboso 51.5 52 0.0011 26.4 5.9 68 58-126 13-89 (113)
34 TIGR01024 rplS_bact ribosomal 50.8 70 0.0015 25.8 6.5 67 57-124 12-87 (113)
35 PF13275 S4_2: S4 domain; PDB: 48.9 19 0.00042 26.1 2.8 19 62-80 47-65 (65)
36 PRK12366 replication factor A; 47.1 3.4E+02 0.0073 27.9 12.7 54 58-112 63-119 (637)
37 PF06988 NifT: NifT/FixU prote 45.7 1.1E+02 0.0024 22.3 6.2 51 166-222 1-52 (64)
38 PF13509 S1_2: S1 domain; PDB: 45.4 27 0.00059 24.4 3.1 37 136-175 15-51 (61)
39 PRK11507 ribosome-associated p 44.4 25 0.00054 26.0 2.8 20 61-80 50-69 (70)
40 TIGR01646 vgr_GE Rhs element V 43.7 1.2E+02 0.0026 29.4 8.3 118 59-176 276-422 (483)
41 PRK04313 30S ribosomal protein 43.6 52 0.0011 29.8 5.2 32 206-237 132-165 (237)
42 PRK04012 translation initiatio 41.6 1.5E+02 0.0032 23.2 7.0 44 184-235 21-72 (100)
43 PRK10377 PTS system glucitol/s 40.8 38 0.00082 27.4 3.6 23 61-83 49-71 (120)
44 PF05521 Phage_H_T_join: Phage 40.3 58 0.0013 23.3 4.3 24 63-86 62-85 (95)
45 PF13785 DUF4178: Domain of un 39.8 1.9E+02 0.004 22.8 12.1 23 64-86 1-23 (140)
46 PF03829 PTSIIA_gutA: PTS syst 39.4 36 0.00077 27.4 3.2 23 61-83 49-71 (117)
47 TIGR00849 gutA PTS system, glu 38.6 44 0.00094 27.1 3.6 22 62-83 50-71 (121)
48 TIGR00451 unchar_dom_2 unchara 38.3 57 0.0012 25.1 4.2 28 213-240 45-79 (107)
49 PF04014 Antitoxin-MazE: Antid 38.1 51 0.0011 21.7 3.3 29 146-176 7-35 (47)
50 PRK08572 rps17p 30S ribosomal 37.9 2E+02 0.0043 23.0 7.2 78 148-232 7-87 (108)
51 PF08292 RNA_pol_Rbc25: RNA po 37.8 2.2E+02 0.0047 23.0 7.6 65 128-194 10-75 (122)
52 COG2501 S4-like RNA binding pr 36.5 39 0.00085 25.2 2.8 21 62-82 51-71 (73)
53 smart00652 eIF1a eukaryotic tr 36.4 1.5E+02 0.0032 22.3 6.0 44 184-235 5-56 (83)
54 PLN00036 40S ribosomal protein 35.5 73 0.0016 29.3 4.9 31 110-141 81-113 (261)
55 KOG3297 DNA-directed RNA polym 34.5 3.3E+02 0.0071 24.1 10.9 101 77-193 49-156 (202)
56 PF15415 DUF4622: Protein of u 34.3 3.3E+02 0.0072 25.2 8.8 73 160-239 38-128 (310)
57 COG0335 RplS Ribosomal protein 34.3 1.3E+02 0.0028 24.4 5.6 70 55-125 12-90 (115)
58 TIGR03170 flgA_cterm flagella 33.5 2.3E+02 0.0049 21.9 7.7 24 95-118 98-121 (122)
59 TIGR03361 VI_Rhs_Vgr type VI s 33.5 2.8E+02 0.006 27.1 9.0 114 60-177 285-434 (513)
60 PF11948 DUF3465: Protein of u 33.4 42 0.00091 27.8 2.8 31 59-89 81-116 (131)
61 COG2996 Predicted RNA-bindinin 32.5 4.2E+02 0.0091 24.7 10.5 87 134-232 17-124 (287)
62 PF13856 Gifsy-2: ATP-binding 32.5 62 0.0013 24.5 3.5 31 55-85 54-87 (95)
63 PF13144 SAF_2: SAF-like 32.2 2.8E+02 0.0061 23.3 7.9 24 95-118 172-195 (196)
64 PF02839 CBM_5_12: Carbohydrat 31.6 53 0.0012 20.8 2.6 20 63-82 9-28 (41)
65 PF05610 DUF779: Protein of un 31.3 74 0.0016 24.9 3.7 47 36-93 19-79 (95)
66 PF07076 DUF1344: Protein of u 31.1 1.7E+02 0.0036 21.1 5.2 39 185-232 4-47 (61)
67 cd05706 S1_Rrp5_repeat_sc10 S1 31.1 1.8E+02 0.0039 20.1 6.1 55 162-232 1-57 (73)
68 COG4043 Preprotein translocase 30.9 70 0.0015 25.5 3.5 23 61-83 31-55 (111)
69 PF10665 Minor_capsid_1: Minor 30.8 67 0.0014 25.7 3.5 26 61-86 74-99 (114)
70 PF01176 eIF-1a: Translation i 30.5 1.7E+02 0.0038 20.6 5.3 43 186-236 5-55 (65)
71 PRK13480 3'-5' exoribonuclease 30.4 2.9E+02 0.0062 25.9 8.1 54 58-115 2-55 (314)
72 PF01079 Hint: Hint module; I 29.3 93 0.002 27.5 4.5 46 54-99 22-72 (217)
73 PF09465 LBR_tudor: Lamin-B re 29.0 2.1E+02 0.0046 20.2 5.5 39 101-139 6-49 (55)
74 PRK12442 translation initiatio 28.8 1.9E+02 0.0042 22.3 5.5 41 186-234 9-58 (87)
75 PTZ00118 40S ribosomal protein 28.8 1.2E+02 0.0026 27.9 5.2 30 110-140 81-112 (262)
76 PF09262 PEX-1N: Peroxisome bi 28.3 52 0.0011 24.7 2.4 62 144-219 13-78 (80)
77 PRK07018 flgA flagellar basal 28.3 1.4E+02 0.0031 26.3 5.6 25 95-119 209-233 (235)
78 KOG1698 Mitochondrial/chloropl 28.1 1.6E+02 0.0035 26.0 5.7 76 58-142 91-179 (201)
79 PTZ00241 40S ribosomal protein 27.6 2.6E+02 0.0057 23.9 6.7 61 166-232 64-126 (158)
80 smart00676 DM10 Domains in hyp 26.9 55 0.0012 25.6 2.3 27 57-83 67-93 (104)
81 cd02790 MopB_CT_Formate-Dh_H F 26.2 50 0.0011 25.0 2.0 18 222-239 48-65 (116)
82 PF12158 DUF3592: Protein of u 26.0 1.6E+02 0.0034 23.0 5.0 49 127-183 65-113 (148)
83 cd02787 MopB_CT_ydeP The MopB_ 26.0 45 0.00098 25.5 1.7 17 222-238 44-60 (112)
84 KOG0267 Microtubule severing p 25.5 1.2E+02 0.0026 31.9 5.0 151 59-216 136-302 (825)
85 cd02786 MopB_CT_3 The MopB_CT_ 25.3 50 0.0011 25.2 1.9 18 222-239 44-61 (116)
86 KOG1708 Mitochondrial/chloropl 25.3 1E+02 0.0023 27.5 4.0 52 173-239 122-173 (236)
87 PTZ00223 40S ribosomal protein 25.1 1.4E+02 0.003 27.7 4.9 31 110-141 78-110 (273)
88 cd01763 Sumo Small ubiquitin-r 25.0 94 0.002 23.0 3.3 67 90-172 8-82 (87)
89 COG2016 Predicted RNA-binding 24.5 1.1E+02 0.0024 26.2 3.9 69 160-235 36-119 (161)
90 COG0361 InfA Translation initi 24.4 2.9E+02 0.0062 20.7 5.6 31 205-235 20-59 (75)
91 cd04458 CSP_CDS Cold-Shock Pro 24.1 2.4E+02 0.0053 19.3 5.2 45 131-175 8-54 (65)
92 TIGR03684 arCOG00985 arCOG0415 23.8 1.9E+02 0.0041 23.6 5.2 28 212-239 83-117 (150)
93 smart00359 PUA Putative RNA-bi 23.6 88 0.0019 21.8 2.8 25 217-241 25-49 (77)
94 cd02788 MopB_CT_NDH-1_NuoG2-N7 23.1 52 0.0011 24.7 1.5 17 222-238 42-58 (96)
95 KOG0272 U4/U6 small nuclear ri 23.0 1.9E+02 0.0042 28.5 5.6 65 33-107 311-380 (459)
96 TIGR03784 marine_sortase sorta 23.0 61 0.0013 27.7 2.1 16 223-238 109-124 (174)
97 PF11871 DUF3391: Domain of un 22.7 41 0.00089 26.2 0.9 21 57-77 3-23 (128)
98 PF05836 Chorion_S16: Chorion 22.6 69 0.0015 25.2 2.1 38 180-219 68-107 (110)
99 PF07591 PT-HINT: Pretoxin HIN 22.6 76 0.0016 25.6 2.5 27 58-84 71-98 (130)
100 cd07387 MPP_PolD2_C PolD2 (DNA 22.2 1.2E+02 0.0026 27.6 3.9 40 199-238 210-252 (257)
101 PF00207 A2M: Alpha-2-macroglo 22.2 74 0.0016 23.6 2.2 17 216-232 59-75 (92)
102 KOG1920 IkappaB kinase complex 21.8 2.8E+02 0.006 30.9 7.0 56 159-214 74-129 (1265)
103 PF02182 SAD_SRA: SAD/SRA doma 21.6 1.9E+02 0.0041 24.2 4.8 36 65-101 117-152 (155)
104 PF02470 MCE: mce related prot 21.5 3.1E+02 0.0067 19.5 5.7 40 59-99 10-50 (81)
105 cd02792 MopB_CT_Formate-Dh-Na- 21.3 69 0.0015 24.5 1.9 18 222-239 48-65 (122)
106 COG3535 Uncharacterized conser 21.2 7.4E+02 0.016 23.8 9.9 89 67-171 236-324 (357)
107 cd02779 MopB_CT_Arsenite-Ox Th 21.1 63 0.0014 24.9 1.7 19 221-239 45-63 (115)
108 cd02794 MopB_CT_DmsA-EC The Mo 20.9 70 0.0015 24.7 1.9 16 223-238 44-59 (121)
109 PF11694 DUF3290: Protein of u 20.9 1.2E+02 0.0025 25.5 3.3 28 55-82 97-124 (149)
110 PRK06804 flgA flagellar basal 20.8 5.4E+02 0.012 23.4 7.9 25 95-119 235-259 (261)
111 PRK11354 kil FtsZ inhibitor pr 20.8 1E+02 0.0023 22.9 2.6 25 59-83 11-35 (73)
112 COG1153 FwdD Formylmethanofura 20.5 73 0.0016 26.2 1.9 19 221-239 43-61 (128)
113 cd05793 S1_IF1A S1_IF1A: Trans 20.4 3.3E+02 0.0072 20.1 5.4 30 205-234 13-50 (77)
114 COG3173 Predicted aminoglycosi 20.2 1.3E+02 0.0028 28.3 3.8 34 55-89 197-230 (321)
115 PF05354 Phage_attach: Phage H 20.1 73 0.0016 25.9 1.9 35 60-98 71-105 (117)
No 1
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=1.7e-75 Score=500.96 Aligned_cols=184 Identities=22% Similarity=0.443 Sum_probs=182.6
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEE
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~ 137 (241)
|+++||||+|++|++||+||+|++++|+|||||+|++|+|||||.||++++++|+++|++|.|+++++++||||.|||.|
T Consensus 1 m~~~~dik~G~~i~~~g~~~~V~~~~h~kPGkg~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~qylY~dg~~~ 80 (185)
T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDEY 80 (185)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEecCCCCceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEECCCeE
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEE
Q 026237 138 FVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTV 217 (241)
Q Consensus 138 ~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v 217 (241)
+|||+|||||++|+++.+||+.+||+|||+|++++|||+||+|+||++|+|+|+||+|++||||+++++|||+||||++|
T Consensus 81 ~FMd~etyeQi~i~~~~lgd~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kgdTat~~~KpAtLeTG~~V 160 (185)
T PRK12426 81 LFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVFSVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEV 160 (185)
T ss_pred EEecCCCceEEEeCHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCcccCCCcccEEEcCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EccccccCCCEEEEECCCCceecC
Q 026237 218 MVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 218 ~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
+||+||++||+|+||||+|+|++|
T Consensus 161 ~VP~FI~~Gd~IkVdT~~geY~~R 184 (185)
T PRK12426 161 LVPPFVEIGDVIKVDTRTCEYIQR 184 (185)
T ss_pred EeCCcccCCCEEEEECCCCeEEee
Confidence 999999999999999999999998
No 2
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=3.5e-73 Score=487.84 Aligned_cols=184 Identities=28% Similarity=0.486 Sum_probs=181.2
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecCCCC--CeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCC
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRG--GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG--~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd 135 (241)
|++++|||+|++|++||+||+|++++|+|||+| +|++|+|||||.||++++++|+++|++|.|+++++++||||.||+
T Consensus 1 m~~~~dik~G~~i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~qylY~dg~ 80 (187)
T PRK14578 1 MYTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGD 80 (187)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeEEEEeCCC
Confidence 678999999999999999999999999999987 569999999999999999999999999999999999999999999
Q ss_pred EEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCc
Q 026237 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGV 215 (241)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~ 215 (241)
.|+|||+|||||++|+++.+|++.+||+|||+|.+++|||+||+|+||++|+|+|++|+|++||||+++++|||+||||+
T Consensus 81 ~~~FMD~etyEQ~~i~~~~~g~~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~~tep~~KGdT~t~~~KpA~leTG~ 160 (187)
T PRK14578 81 RGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVNVDLPMTVELTVTDTAPVMKNATATAQTKEAVLETGL 160 (187)
T ss_pred EEEEecCCCcEEEEecHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCccccCccCCCcceEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccccccCCCEEEEECCCCceecC
Q 026237 216 TVMVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 216 ~v~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
+|+||+||++||+|+|||+||+|++|
T Consensus 161 ~v~VP~FI~~Gd~I~VdT~~g~Y~~R 186 (187)
T PRK14578 161 RLQVPPYLESGEKIKVDTRDGRFISR 186 (187)
T ss_pred EEEeCCcccCCCEEEEECCCCcEEee
Confidence 99999999999999999999999998
No 3
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=4.5e-73 Score=487.67 Aligned_cols=184 Identities=28% Similarity=0.507 Sum_probs=181.2
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecC-CCC-CeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCC
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQR-GRG-GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~Kp-GKG-~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd 135 (241)
|+++||||+|++|++||+||+|++++|+|| ||| +|++|+|||||.||++++++|+++|++|.|++++++|||||.||+
T Consensus 1 mi~~~dik~G~~i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~qylY~dg~ 80 (189)
T PRK04542 1 MPKANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGD 80 (189)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCC
Confidence 688999999999999999999999999999 798 559999999999999999999999999999999999999999999
Q ss_pred EEEEEeCCCccccccCchhhhhhhhccCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecC
Q 026237 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNG 214 (241)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~-v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG 214 (241)
.|+|||+|||||++|+++.+|++.+||+|||+ |++++|||+||+|+||++|+|+|++|+|++||||+++++|||+||||
T Consensus 81 ~~~FMd~etyEQ~~i~~~~lgd~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kGdT~~~~~KpAtLetG 160 (189)
T PRK04542 81 EYVFMDNEDYTPYTFKKDQIEDELLFIPEGMPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLSTG 160 (189)
T ss_pred EEEEecCCCceEEEECHHHhhhHhhhhhcCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCCccEEEcCC
Confidence 99999999999999999999999999999998 99999999999999999999999999999999999999999999999
Q ss_pred cEEEccccccCCCEEEEECCCCceecC
Q 026237 215 VTVMVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 215 ~~v~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
++|+||+||++||+|+||||+|+|++|
T Consensus 161 ~~v~VP~FI~~Gd~I~VdT~tgeYv~R 187 (189)
T PRK04542 161 LVIQVPEYISTGEKIRINTEERKFMGR 187 (189)
T ss_pred CEEEeCCcccCCCEEEEECCCCcEEee
Confidence 999999999999999999999999998
No 4
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=100.00 E-value=5.6e-72 Score=479.83 Aligned_cols=181 Identities=25% Similarity=0.491 Sum_probs=177.9
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEecCCCCCe--EEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEEE
Q 026237 61 ASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGA--MMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (241)
Q Consensus 61 a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A--~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~~ 138 (241)
++|||+|++|++||+||+|++++|+|||+|+| ++|+|||||.||++++++|+++|++|.|+++++++||||.||+.|+
T Consensus 2 ~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~~~~ 81 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEYV 81 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCeEE
Confidence 78999999999999999999999999987666 8999999999999999999999999999999999999999999999
Q ss_pred EEeCCCccccccCchhhhhhhhccCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEE
Q 026237 139 VIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTV 217 (241)
Q Consensus 139 FMD~EtyEQi~v~~~~lgd~~~~L~eg~~-v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v 217 (241)
|||+|||||++|+++.+|++.+||+|||+ |++++|||+||+|+||++|+|+|++|+|++||||+++++|||+||||++|
T Consensus 82 FMD~etyEQ~~i~~~~lgd~~~fL~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~KGdT~~~~~KpA~LeTG~~v 161 (186)
T TIGR02178 82 FMDEEDYTPYTFDKDAIEDELLFISEGLSGMYVQLIDGSPVALELPQHVVLEIVETPPEIKGASASKRPKPAKLITGLVV 161 (186)
T ss_pred EccCCCcEEEEeCHHHhhhhhhhhhCCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCcccccCCCCcccEEEcCCCEE
Confidence 99999999999999999999999999997 99999999999999999999999999999999999999999999999999
Q ss_pred EccccccCCCEEEEECCCCceecC
Q 026237 218 MVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 218 ~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
+||+||++||+|+||||||+|++|
T Consensus 162 ~VP~FI~~Gd~IkVdTrtg~Y~~R 185 (186)
T TIGR02178 162 QVPEYITTGERILINTTERAFMGR 185 (186)
T ss_pred EeCCeecCCCEEEEECCCCcEEcc
Confidence 999999999999999999999998
No 5
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=1.3e-70 Score=471.85 Aligned_cols=184 Identities=34% Similarity=0.598 Sum_probs=182.5
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEE
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~ 137 (241)
|+++|+||+|++|+++|+||+|++++|+|||||+|++|+++|||.||++++.+|+++|+++.+.++++++||||.|||.|
T Consensus 1 ~~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGkg~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dgd~~ 80 (186)
T PRK00529 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGY 80 (186)
T ss_pred CcchhhcCCCCEEEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECCCEE
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEE
Q 026237 138 FVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTV 217 (241)
Q Consensus 138 ~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v 217 (241)
+|||+|||||++||.+.+|++.+||+|||+|++++|||+||+|+||++|+|+|+||+|++||||+++++|||+||||++|
T Consensus 81 ~fMD~etyeq~~l~~~~lg~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v 160 (186)
T PRK00529 81 VFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVV 160 (186)
T ss_pred EEecCCCceeeEcCHHHhHHHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccCcccCCCcccEEEcCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EccccccCCCEEEEECCCCceecC
Q 026237 218 MVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 218 ~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
+||+||++||+|+|||++|+|++|
T Consensus 161 ~VP~fI~~Gd~I~v~T~~g~y~~R 184 (186)
T PRK00529 161 QVPLFINEGEKIKVDTRTGEYVER 184 (186)
T ss_pred EeCCeecCCCEEEEECCCCcEEee
Confidence 999999999999999999999998
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=1.5e-70 Score=470.80 Aligned_cols=183 Identities=32% Similarity=0.613 Sum_probs=181.2
Q ss_pred EEcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEEE
Q 026237 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~~ 138 (241)
+++|+||+|++|+++|+||+|++++|+|||||+|++|+++|||.||++++++|+++|+++.+.++++++||||.|||.|+
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGkg~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dgd~~~ 80 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYV 80 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECCCEEE
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEE
Q 026237 139 VIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVM 218 (241)
Q Consensus 139 FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~ 218 (241)
|||+|||||++|+.+.+++..+||+|||+|.+.+|||+||+|+||++|+|+|+||+|++||||+++++|||+||||++|+
T Consensus 81 fMD~etyeq~~i~~~~l~~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~ 160 (184)
T TIGR00038 81 FMDTETYEQIELPKDLLGDAAKFLKENMEVSVTFYNGEPIGVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQ 160 (184)
T ss_pred EeCCCCccceEcCHHHHHHHHhhcCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCcccEEEcCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCCEEEEECCCCceecC
Q 026237 219 VPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 219 VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
||+||++||+|+|||++|+|++|
T Consensus 161 VP~fi~~Gd~I~v~T~~g~y~~R 183 (184)
T TIGR00038 161 VPLFIEEGEKIKVDTRTGEYVER 183 (184)
T ss_pred eCCcccCCCEEEEECCCCcEEec
Confidence 99999999999999999999998
No 7
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-45 Score=301.47 Aligned_cols=130 Identities=35% Similarity=0.619 Sum_probs=128.2
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCE
Q 026237 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (241)
Q Consensus 57 ~~i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~ 136 (241)
+|+++++||+|++|++||+||+|++++|+|||||+|++|+++|||+||++++.+|+++|++|.|.++++++||||.||+.
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~~ 81 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGDF 81 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCCCCcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCCe
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeE
Q 026237 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRV 186 (241)
Q Consensus 137 ~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP~~V 186 (241)
|+|||+|||||++++.+.++|..+||+|||+|++++|+|++++++||++|
T Consensus 82 ~~FMD~etyeq~~v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v 131 (131)
T COG0231 82 YVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV 131 (131)
T ss_pred EEEccCCCceEEEecchhhhhHHHhcCCCCEEEEEEECCEEEEEECCCCC
Confidence 99999999999999999999999999999999999999999999999975
No 8
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=2.5e-37 Score=252.31 Aligned_cols=120 Identities=22% Similarity=0.320 Sum_probs=114.8
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecCCC-CCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCE
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~KpGK-G~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~ 136 (241)
.+++++||+|++|++||+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++|++|.|.++++++||||.|||.
T Consensus 6 ~~~~~~irkG~~i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~qylY~dg~~ 85 (130)
T TIGR00037 6 QVQVSALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQVLAIMGGM 85 (130)
T ss_pred eccHHHccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEEEEEecCCE
Confidence 46799999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred EEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEE
Q 026237 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALS 179 (241)
Q Consensus 137 ~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~ 179 (241)
|+|||+|||||++|+.+. +..+||+||++|.++-..|+..-
T Consensus 86 ~~fMd~etyeq~~i~~~~--~~~~~Lke~~~V~v~~~~g~~~~ 126 (130)
T TIGR00037 86 VQLMDLDTYETDELPIPE--ELGDSLEPGFEVEYIEAMGQEKI 126 (130)
T ss_pred EEEEcCCCcEEEEecCCh--hHHHHhhcCCEEEEEecCCeEEE
Confidence 999999999999999985 88999999999999988887543
No 9
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=1.7e-35 Score=241.18 Aligned_cols=117 Identities=23% Similarity=0.341 Sum_probs=112.0
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecCCC-CCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCE
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~KpGK-G~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~ 136 (241)
.+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||.||++++.+|+++|++|.+.++++++||||.||+.
T Consensus 5 ~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~~ 84 (129)
T PRK03999 5 QVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGDV 84 (129)
T ss_pred cccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCCE
Confidence 36789999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred EEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCE
Q 026237 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 176 (241)
Q Consensus 137 ~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~ 176 (241)
|+|||+|||||++|+.+ +++..||+||++|.|+---|+
T Consensus 85 ~~fMd~eTyeq~~i~~~--~d~~~~l~eg~~v~v~~~~g~ 122 (129)
T PRK03999 85 VQLMDLETYETFEIPIP--EELKDKLEPGVEVEYWEAMGR 122 (129)
T ss_pred EEEecCCCceEEEecCC--hhHHhhCcCCCEEEEEhhCCe
Confidence 99999999999999998 889999999999998765555
No 10
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=4.3e-32 Score=228.21 Aligned_cols=121 Identities=18% Similarity=0.286 Sum_probs=107.0
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEecCCC-CCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCC
Q 026237 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (241)
Q Consensus 57 ~~i~a~dirkG~~I~~dG~py~V~~~~h~KpGK-G~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd 135 (241)
+|+++++||+|++|++||+||+|++++|+|||| |+|++|+++|||+||++++.+|+++++++.|+++++++||||.|||
T Consensus 19 ~m~~~~~lKkG~~I~~~g~pc~V~e~~~~KpGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ve~~~ve~~~~qyly~dgd 98 (159)
T PLN03107 19 YPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCDVPHVNRTDYQLIDISED 98 (159)
T ss_pred eccchHhccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEecCCCEEEEEEEEEEEEEEEEEcCC
Confidence 589999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred EE-EEEeC--CCccccccCc---hhhhhhhhccCCCCEEEEEEEC--CEE
Q 026237 136 TA-FVIES--ETFEQLEVPL---DVFGKAGAYLQEGMKVWLQLYD--GRA 177 (241)
Q Consensus 136 ~~-~FMD~--EtyEQi~v~~---~~lgd~~~~L~eg~~v~v~~~d--g~~ 177 (241)
.| +|||+ ++|||+.||. ++......+..+|.++.|.+|. |+.
T Consensus 99 ~y~~fMD~~get~eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~~mg~e 148 (159)
T PLN03107 99 GFVSLMDESGNTKDDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMSAMGEE 148 (159)
T ss_pred ceEEEEcCCCCcceeEEccCcchHHHHHHHHHHhCCCeEEEEEEecCCeE
Confidence 95 99999 6999999986 3333334455679985555544 654
No 11
>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=99.94 E-value=3.2e-27 Score=166.60 Aligned_cols=56 Identities=27% Similarity=0.515 Sum_probs=55.1
Q ss_pred EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEccccccCCCEEEEECCCCceecC
Q 026237 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 186 V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
|+|+|+||+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
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 68999999999999999999999999999999999999999999999999999998
No 12
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.94 E-value=3.5e-27 Score=166.41 Aligned_cols=56 Identities=29% Similarity=0.526 Sum_probs=55.0
Q ss_pred EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEccccccCCCEEEEECCCCceecC
Q 026237 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 186 V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
|+|+|+||+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 v~l~V~etep~~kG~T~~~~~K~A~letG~~i~VP~FI~~Gd~I~V~T~~g~Y~~R 56 (56)
T cd05794 1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCeecCCCEEEEECCCCcEecC
Confidence 58999999999999999999999999999999999999999999999999999998
No 13
>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=99.94 E-value=4.3e-27 Score=165.95 Aligned_cols=56 Identities=32% Similarity=0.629 Sum_probs=50.2
Q ss_pred EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEccccccCCCEEEEECCCCceecC
Q 026237 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 186 V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
|+|+|+||+|++||||+++++|+|+||||++|+||+||++||+|+|||++|+|++|
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 78999999999999999999999999999999999999999999999999999998
No 14
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.89 E-value=3.7e-23 Score=148.36 Aligned_cols=61 Identities=33% Similarity=0.758 Sum_probs=59.7
Q ss_pred EeeEEEEEEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCC
Q 026237 123 EDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 183 (241)
Q Consensus 123 e~k~~qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP 183 (241)
+++++||||.||+.|+|||+|||||++|+++.+|++.+||+||++|++++|+|+||+|+||
T Consensus 1 e~~~~qylY~dg~~~~FMd~etyeQ~~i~~~~igd~~~~L~e~~~v~v~~~~~~~i~v~lP 61 (61)
T cd04470 1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61 (61)
T ss_pred CCceEEEEEeCCCEEEEeCCCCceEEEECHHHhhhHHhhCcCCCEEEEEEECCEEEEEECc
Confidence 4789999999999999999999999999999999999999999999999999999999999
No 15
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=99.85 E-value=4.2e-21 Score=136.39 Aligned_cols=58 Identities=40% Similarity=0.708 Sum_probs=53.6
Q ss_pred EcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcE
Q 026237 60 NASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAV 117 (241)
Q Consensus 60 ~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkv 117 (241)
+|+|||+|++|++||+||+|++++|++||||+|+||+|||||.||+++|.+|+++|+|
T Consensus 1 sa~dlr~G~~i~~~g~~~~V~~~~~~k~gkg~a~v~~klknl~tG~~~e~tf~s~d~v 58 (58)
T PF08207_consen 1 SASDLRKGMVIEIDGEPYVVLDFQHVKPGKGGAFVRVKLKNLRTGSKVEKTFRSGDKV 58 (58)
T ss_dssp EGGG--TTSEEEETTEEEEEEEEEEECCTTSSSEEEEEEEETTTTEEEEEEEETT-EE
T ss_pred CHHHccCCCEEEECCEEEEEEEEEEECCCCCCeEEEEEEEECCCCCEEEEEECCCCcC
Confidence 5899999999999999999999999999999999999999999999999999999986
No 16
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=99.84 E-value=5.5e-20 Score=154.92 Aligned_cols=118 Identities=19% Similarity=0.297 Sum_probs=103.3
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEecCCC-CCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCC
Q 026237 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (241)
Q Consensus 57 ~~i~a~dirkG~~I~~dG~py~V~~~~h~KpGK-G~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd 135 (241)
.-++++.||+|.+|+++|+||+|++++.+|||| |+|++++...+|+||++.+...++++++++|.++|+++|+|..++|
T Consensus 21 ~p~q~~~LkkG~yvvIkGrPCKIveistSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~hnv~VP~V~r~~yqli~I~~d 100 (166)
T PTZ00328 21 YPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPN 100 (166)
T ss_pred ecccccceeECCEEEECCeeeEEEEEecCCCCcCCceEEEEEEEecCCCCEEeeecCccceeEeeeEEeeEEEEEEEcCC
Confidence 346789999999999999999999999999999 9999999999999999999999999999999999999999999886
Q ss_pred -------EEEEEeCCCccccccCc---hhhhh-hhhccCCCCEEEEEEEC
Q 026237 136 -------TAFVIESETFEQLEVPL---DVFGK-AGAYLQEGMKVWLQLYD 174 (241)
Q Consensus 136 -------~~~FMD~EtyEQi~v~~---~~lgd-~~~~L~eg~~v~v~~~d 174 (241)
...+||.+.|+...|+. +.++. ....+.+|.+|.|.+|.
T Consensus 101 ~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~v~vi~ 150 (166)
T PTZ00328 101 EDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVVS 150 (166)
T ss_pred CcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEEEEEEh
Confidence 37899999887766543 23322 35677999999977775
No 17
>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=99.83 E-value=8.2e-21 Score=133.52 Aligned_cols=55 Identities=36% Similarity=0.748 Sum_probs=49.9
Q ss_pred eeEEEEEEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEE
Q 026237 124 DKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 178 (241)
Q Consensus 124 ~k~~qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i 178 (241)
+|++||||.||+.|+|||++||||++|+++.+|++.+||+||++|+|.+|+|+||
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 18
>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=99.70 E-value=2.6e-17 Score=114.99 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=51.4
Q ss_pred eEEEEEEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEE
Q 026237 125 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSG 180 (241)
Q Consensus 125 k~~qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v 180 (241)
+++||||.||+.|+|||+|||||++++++.. +..+||+||++|.|++|+|+|+++
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 5799999999999999999999999999874 589999999999999999999874
No 19
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.61 E-value=2.8e-15 Score=123.17 Aligned_cols=112 Identities=17% Similarity=0.279 Sum_probs=99.1
Q ss_pred EEcCCCCCccEEEECCeEEEEEEeEEecCCC-CCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEE
Q 026237 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~py~V~~~~h~KpGK-G~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~ 137 (241)
.+.+.||++-+|.++|+||+|+++..+|.|| |+|++.+..++|+||++.|.-++++++++++.++|.++|.+-++++..
T Consensus 21 ~q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn~dVp~vkr~~yqLidIsd~~~ 100 (156)
T KOG3271|consen 21 MQCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDGYL 100 (156)
T ss_pred chhhheeeCCEEEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCccccCccccceeEEEEecCCeE
Confidence 3568899999999999999999999999999 999999999999999999999999999999999999999999999988
Q ss_pred EEEeC--CCccccccCchhhhhhhh-ccCCCCEEEE
Q 026237 138 FVIES--ETFEQLEVPLDVFGKAGA-YLQEGMKVWL 170 (241)
Q Consensus 138 ~FMD~--EtyEQi~v~~~~lgd~~~-~L~eg~~v~v 170 (241)
.|||+ ++-+++.+|...+++... -..+|..+.|
T Consensus 101 sl~t~sG~~kdDlklp~~el~~~i~~~~e~g~dl~v 136 (156)
T KOG3271|consen 101 SLMTDSGETKDDLKLPEGELGNQIRQGFEEGKDLLV 136 (156)
T ss_pred EEEcCCCCcchhccCcchhHHHHHHHhhcCCCcEEE
Confidence 99998 578889999877877643 3345544433
No 20
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=98.71 E-value=2.9e-08 Score=70.49 Aligned_cols=54 Identities=26% Similarity=0.319 Sum_probs=46.5
Q ss_pred EEeeEEEEEEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEE
Q 026237 122 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRA 177 (241)
Q Consensus 122 ve~k~~qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~ 177 (241)
++||.+|.++.+|+..++||+||||.++++.. .+...-+++|.+|.++-..|+.
T Consensus 1 i~k~~aqVisi~g~~vQlMD~eTYeT~ev~~p--~~~~~~i~~G~eV~y~~~~g~~ 54 (57)
T cd04467 1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIP--EEIKDKLEPGKEVEYWESMGKR 54 (57)
T ss_pred CcceEEEEEEEcCCEEEEeccccceeEEEecc--hhhcccCCCCCEEEEEeecCeE
Confidence 58999999999999999999999999999986 2233458999999998887864
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=98.08 E-value=4.1e-05 Score=72.31 Aligned_cols=111 Identities=22% Similarity=0.300 Sum_probs=88.2
Q ss_pred ce-eeEEcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEE----eeeEEeeEEEE
Q 026237 55 RA-VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVE----RVFVEDKSFTC 129 (241)
Q Consensus 55 R~-~~i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve----~v~ve~k~~qy 129 (241)
|+ +.+...++++|++|.++|..+.++... |+ .+.++|+.||+..+.++.....-+ ...-+-+.+.+
T Consensus 237 R~t~Svrip~~~~gDiV~~~~~~~~~v~~~----~~-----~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~v 307 (355)
T COG1499 237 RFTYSVRIPEFRPGDIVSVRGRQLVLVRSI----GK-----GIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVV 307 (355)
T ss_pred EEEEEEECCCCCCCCEEEECCCeEEEEEEe----cC-----ceEEEecccCCccccChhhcccCcceeeeccccceEEEE
Confidence 44 678899999999999999666665554 44 589999999988888775544333 33334478899
Q ss_pred EEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEe
Q 026237 130 LYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 181 (241)
Q Consensus 130 lY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~ 181 (241)
+..+++..+|||++|||-+++..+ =|.+|.+|.+..++|....++
T Consensus 308 vs~~~~~~~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~ 352 (355)
T COG1499 308 VSRDPSAIQVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE 352 (355)
T ss_pred EecCCCceEEEecceEEEEeccCC-------CCCCCCEEEEEEEeceEEeec
Confidence 999999999999999999999876 368999999999999876543
No 22
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=97.06 E-value=0.004 Score=45.80 Aligned_cols=56 Identities=23% Similarity=0.298 Sum_probs=40.1
Q ss_pred eEEeeEEEEEEEeCC-EEEEEeCCCccccc---cCchhhhhh-hhccCCCCE--EEEEEECCEE
Q 026237 121 FVEDKSFTCLYTEND-TAFVIESETFEQLE---VPLDVFGKA-GAYLQEGMK--VWLQLYDGRA 177 (241)
Q Consensus 121 ~ve~k~~qylY~Dgd-~~~FMD~EtyEQi~---v~~~~lgd~-~~~L~eg~~--v~v~~~dg~~ 177 (241)
.|+|+++|.+..++| ...+|| |+||+.+ +|...+++. ...+.+|.+ |+|+-.-|+-
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMd-e~get~eDl~lP~~el~~ei~~~~~~g~~~~Vtv~~amG~e 63 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMD-EDGETREDLKLPDGELGEEIKAKFEEGKEVLVTVLSAMGEE 63 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEE-TTS-EEEEEECCSHHHHHHHHHHHHTTCEEEEEEEEETTEE
T ss_pred CeEEEEEEEEEEccCcEEEEEc-CCCCeeccEEecccchhHHHHhhccCCCeEEEEEEeeCCcE
Confidence 478999999999988 678999 6666555 886555544 355689988 6666666653
No 23
>cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=92.70 E-value=0.43 Score=35.18 Aligned_cols=51 Identities=22% Similarity=0.357 Sum_probs=38.3
Q ss_pred EEeeEEEEEEEeCCEEEEEeC--CCccccccCchhhhhhhh-ccCCCCEEEEEE
Q 026237 122 VEDKSFTCLYTENDTAFVIES--ETFEQLEVPLDVFGKAGA-YLQEGMKVWLQL 172 (241)
Q Consensus 122 ve~k~~qylY~Dgd~~~FMD~--EtyEQi~v~~~~lgd~~~-~L~eg~~v~v~~ 172 (241)
|.|++||.+..+++...+|+. ++-|++.+|.+.++.... ...+|..+.+..
T Consensus 1 V~R~eYqLidI~dGflsLm~e~G~~k~DlklP~~elg~~I~~~f~~gk~~~vtV 54 (69)
T cd04468 1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTV 54 (69)
T ss_pred CcceeEEEEeecCCeEEEEcCCCCcccCCcCCcHHHHHHHHHHHhCCCcEEEEE
Confidence 468999999998777899976 679999999988886642 235565555443
No 24
>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=78.46 E-value=3 Score=31.18 Aligned_cols=67 Identities=13% Similarity=0.220 Sum_probs=40.1
Q ss_pred CCEEEEEEEC-CEEEEEeCCCe----EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEcc-ccccCCCEEEEECCCCc
Q 026237 165 GMKVWLQLYD-GRALSGSIPKR----VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVP-SYLEIGEEIFINPQDDS 237 (241)
Q Consensus 165 g~~v~v~~~d-g~~i~v~lP~~----V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP-~FI~~Gd~I~V~T~~g~ 237 (241)
|..+-|++.. |+..-++++.. =-++|..-. +..++-=...|..|..|..| +-|++||.|+|+..+++
T Consensus 3 ~e~yRvl~d~kgr~~l~~I~~eea~~KLckV~~k~------~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~k 75 (77)
T PF00900_consen 3 GEHYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKT------TGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQK 75 (77)
T ss_dssp TEEEEEEE-TTS-EEEEEE-TTGGGEEEEEEEEEE------EEGGGEEEEEETTTEEEES-SST--TTEEEEEETTTTE
T ss_pred CcEEEEEECCCCcEEEEECCHHHccCeEEEEeEEE------EecCCcEEEEecCceEEEcCcCCccCCCEEEEECCCCc
Confidence 3444454433 55555554443 245555542 22334446788999999999 99999999999999886
No 25
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=77.57 E-value=5.6 Score=32.76 Aligned_cols=39 Identities=26% Similarity=0.422 Sum_probs=31.5
Q ss_pred EEcCCCCCccEEEECCe--EEEEEEeEEe--cCC------CCCeEEEEE
Q 026237 59 VNASHVRPGNVIEKSGK--MYQVIDAEHK--QRG------RGGAMMQME 97 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~--py~V~~~~h~--KpG------KG~A~vrik 97 (241)
+..=|||.|+.|..++. +|.|+.+++. .+. ||.+.|.+|
T Consensus 55 v~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk 103 (131)
T PF08605_consen 55 VKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLK 103 (131)
T ss_pred EeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEE
Confidence 45578999999999998 9999999987 233 577877774
No 26
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=75.02 E-value=16 Score=27.36 Aligned_cols=53 Identities=15% Similarity=0.162 Sum_probs=36.1
Q ss_pred eEEEEEEEeCCEEEEEeC--CCccccccC-chhhhhhhh-ccCCCC-E--EEEEEECCEE
Q 026237 125 KSFTCLYTENDTAFVIES--ETFEQLEVP-LDVFGKAGA-YLQEGM-K--VWLQLYDGRA 177 (241)
Q Consensus 125 k~~qylY~Dgd~~~FMD~--EtyEQi~v~-~~~lgd~~~-~L~eg~-~--v~v~~~dg~~ 177 (241)
++||.+..+++...+||. ++-|++.|| .+.++.... -..+|. + |.|+-.-|+-
T Consensus 3 ~eYqLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk~~v~VtVlsAmGeE 62 (75)
T cd04469 3 KQYRVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGRGSVRVLVVNDGGRE 62 (75)
T ss_pred eEEEEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCCCcEEEEEEccCCeE
Confidence 689999996667789976 578999999 666665542 226666 4 4444444543
No 27
>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=63.76 E-value=3.6 Score=30.23 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=12.2
Q ss_pred EECCEEEEEeCCCeEEEE
Q 026237 172 LYDGRALSGSIPKRVACT 189 (241)
Q Consensus 172 ~~dg~~i~v~lP~~V~l~ 189 (241)
.|+|+|||.+||-.|.+.
T Consensus 39 ~wkGr~iSanlP~~V~F~ 56 (67)
T PF02941_consen 39 DWKGRPISANLPVKVQFD 56 (67)
T ss_dssp EETTEE---SS-EEEEET
T ss_pred ecCCcEecCCCcEEEEEe
Confidence 599999999999998874
No 28
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=59.92 E-value=47 Score=26.88 Aligned_cols=66 Identities=23% Similarity=0.362 Sum_probs=44.8
Q ss_pred EEcCCCCCccEEEE-----CCeEEEEEEeEEe---cCCCCCeEEEEEEeeCCCCCeEEEEeCCCC-cEEeeeEEee
Q 026237 59 VNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEE-AVERVFVEDK 125 (241)
Q Consensus 59 i~a~dirkG~~I~~-----dG~py~V~~~~h~---KpGKG~A~vriklknL~TG~k~e~tf~s~d-kve~v~ve~k 125 (241)
.+..++++||+|.. +|.-..+..++-+ +-++|- .-.+.++|+..|--+|..|+-.. .++.+.+.++
T Consensus 14 ~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~-~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~ 88 (116)
T PRK05338 14 KDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGL-NETFTVRKISYGVGVERTFPLHSPRIDSIEVVRR 88 (116)
T ss_pred cCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCC-CceEEEEEcccCccEEEEecCCCCcccEEEEEEe
Confidence 56789999999875 5655555444432 123332 33689999999999999998755 5555555544
No 29
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=57.82 E-value=1.1e+02 Score=33.11 Aligned_cols=131 Identities=14% Similarity=0.143 Sum_probs=82.6
Q ss_pred eCCCCCeEEEEeCCCCcEEeeeEEeeEEEEE--EEeCCEEEEEeC--CCccccccCchhhhhhhhccCCCCEEEEEE--E
Q 026237 100 DIDTGNKVSLRFGTEEAVERVFVEDKSFTCL--YTENDTAFVIES--ETFEQLEVPLDVFGKAGAYLQEGMKVWLQL--Y 173 (241)
Q Consensus 100 nL~TG~k~e~tf~s~dkve~v~ve~k~~qyl--Y~Dgd~~~FMD~--EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~--~ 173 (241)
-+++.++....|..+|.+|+..-|-+.++-. -.||+..+.|-. .--+-++++...| .+|.++|.-|+|.- |
T Consensus 397 t~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eL---rKyF~~GDhVKVi~G~~ 473 (1024)
T KOG1999|consen 397 TLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASEL---RKYFEPGDHVKVIAGRY 473 (1024)
T ss_pred eeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhh---hhhccCCCeEEEEeccc
Confidence 5678888888999999999999998887654 458888877765 3356677776544 78999999999874 4
Q ss_pred C---CEEEEEeCCCeE--------EEEEEEecCCCCCcCCCCCceeEEeecCcEEEccccccCCCEEEEECC
Q 026237 174 D---GRALSGSIPKRV--------ACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQ 234 (241)
Q Consensus 174 d---g~~i~v~lP~~V--------~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~ 234 (241)
+ |-+|-|+==.-+ +|+|.-.+-..--+.++...|---.|=+-.|+.+.+ +.|-+|++.-+
T Consensus 474 eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~~-~vgvI~rle~e 544 (1024)
T KOG1999|consen 474 EGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDNQ-NVGVIVRLERE 544 (1024)
T ss_pred cCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccccccceeecCCC-cEEEEEEecch
Confidence 4 334444432211 333333222211122222333334445556777777 88877776544
No 30
>PRK14560 putative RNA-binding protein; Provisional
Probab=55.00 E-value=30 Score=28.87 Aligned_cols=71 Identities=21% Similarity=0.355 Sum_probs=40.3
Q ss_pred cCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCC-ceeEEe--------ecCcEEEcccc------ccCC
Q 026237 162 LQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPR-YRRALL--------DNGVTVMVPSY------LEIG 226 (241)
Q Consensus 162 L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~-~K~A~L--------etG~~v~VP~F------I~~G 226 (241)
...+..+.+.+.||+|+-++.=..+. |.+.|.-.-+. .+.+++ .+|+.++.|-. ++.|
T Consensus 38 ~~~~~~~~~~~~~~~p~~f~~d~~~~-------Ptl~~~~~~~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~G 110 (160)
T PRK14560 38 VETDKKEEIYLVDGEPLFFKVDDELF-------PTLRGALKLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEG 110 (160)
T ss_pred EEcCCcEEEEEECCEEEEEEeCCccc-------ccHHHHHhCCccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCC
Confidence 34456777778888888775421222 22222111111 122333 36888877744 4679
Q ss_pred CEEEEECCC-Ccee
Q 026237 227 EEIFINPQD-DSYI 239 (241)
Q Consensus 227 d~I~V~T~~-g~Yv 239 (241)
|.|.|-++. |+.+
T Consensus 111 d~V~I~~~~~~~~v 124 (160)
T PRK14560 111 DIVFVVEETHGKPL 124 (160)
T ss_pred CEEEEEECCCCeEE
Confidence 999998876 7665
No 31
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=53.46 E-value=67 Score=25.12 Aligned_cols=51 Identities=14% Similarity=0.330 Sum_probs=35.8
Q ss_pred EEEEEeCCC----eEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEc--c------ccccCCCEEEEECC
Q 026237 176 RALSGSIPK----RVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P------SYLEIGEEIFINPQ 234 (241)
Q Consensus 176 ~~i~v~lP~----~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~ 234 (241)
....++||. .+..+|++.-+ +..=.+.+++|.++.+ | ..|+.||.|.|+..
T Consensus 7 ~~~~~~~p~~~e~e~~g~V~~~lG--------~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~ 69 (99)
T TIGR00523 7 QQIRVRLPRKEEGEILGVIEQMLG--------AGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPW 69 (99)
T ss_pred CcceeeCCCCCCCEEEEEEEEEcC--------CCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEc
Confidence 445677774 67888888753 3455678889987644 4 46899999999543
No 32
>CHL00084 rpl19 ribosomal protein L19
Probab=51.58 E-value=78 Score=25.65 Aligned_cols=67 Identities=19% Similarity=0.217 Sum_probs=44.3
Q ss_pred eEEcCCCCCccEEEE-----CCeEEEEEEeEE---ecCCCCCeEEEEEEeeCCCCCeEEEEeCCCC-cEEeeeEEee
Q 026237 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEH---KQRGRGGAMMQMELRDIDTGNKVSLRFGTEE-AVERVFVEDK 125 (241)
Q Consensus 58 ~i~a~dirkG~~I~~-----dG~py~V~~~~h---~KpGKG~A~vriklknL~TG~k~e~tf~s~d-kve~v~ve~k 125 (241)
..+..++++||+|.. +|.-..+..++- ..-|+|- .-.+.+|++..|--+|.+|+-.. .++.+.+-++
T Consensus 17 ~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~-~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~ 92 (117)
T CHL00084 17 KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGL-NTTITVRKVFQGIGVERVFLLHSPKLASIEVLRR 92 (117)
T ss_pred hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCC-CeeEEEEEeccCccEEEEEecCCCccceEEEEEe
Confidence 457889999999874 555444443432 1224443 23588999999999999998654 5555555543
No 33
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=51.47 E-value=52 Score=26.37 Aligned_cols=68 Identities=22% Similarity=0.283 Sum_probs=45.1
Q ss_pred eEEcCCCCCccEEEE-----CCeEEEEEEeEEe---cCCCCCeEEEEEEeeCCCCCeEEEEeCCCC-cEEeeeEEeeE
Q 026237 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEE-AVERVFVEDKS 126 (241)
Q Consensus 58 ~i~a~dirkG~~I~~-----dG~py~V~~~~h~---KpGKG~A~vriklknL~TG~k~e~tf~s~d-kve~v~ve~k~ 126 (241)
..+..++++||+|.. +|....+..++-. +-++| ..-.+.++|+..|.-+|..|+-.. .++.+.+-++.
T Consensus 13 ~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g-~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~~ 89 (113)
T PF01245_consen 13 KKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRG-LNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRG 89 (113)
T ss_dssp SSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSS-TSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEB
T ss_pred hcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCC-CCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEec
Confidence 467889999999864 3544444444421 12332 223678899999999999998755 56666666654
No 34
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=50.76 E-value=70 Score=25.76 Aligned_cols=67 Identities=22% Similarity=0.274 Sum_probs=43.7
Q ss_pred eeEEcCCCCCccEEEE-----CCeEEEEEEeEEe---cCCCCCeEEEEEEeeCCCCCeEEEEeCCCC-cEEeeeEEe
Q 026237 57 VKVNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEE-AVERVFVED 124 (241)
Q Consensus 57 ~~i~a~dirkG~~I~~-----dG~py~V~~~~h~---KpGKG~A~vriklknL~TG~k~e~tf~s~d-kve~v~ve~ 124 (241)
+..+..++++||+|.. +|+.-.+..++-+ +.++|- .-.+.+||+..|-=+|.+|+-.. .++.+.+-+
T Consensus 12 ~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~-~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl~ 87 (113)
T TIGR01024 12 LKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGI-GETFTVRKISYGVGVERIFPLHSPNIDSIEVVR 87 (113)
T ss_pred hhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCC-ceEEEEEEeccCccEEEEEEcCCCccceEEEEE
Confidence 3456889999999876 4444444434421 224433 33689999999999999998655 455555444
No 35
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=48.94 E-value=19 Score=26.13 Aligned_cols=19 Identities=42% Similarity=0.941 Sum_probs=14.0
Q ss_pred CCCCCccEEEECCeEEEEE
Q 026237 62 SHVRPGNVIEKSGKMYQVI 80 (241)
Q Consensus 62 ~dirkG~~I~~dG~py~V~ 80 (241)
..|++|++|.++|..|+|+
T Consensus 47 ~Kl~~GD~V~~~~~~~~Vv 65 (65)
T PF13275_consen 47 KKLRPGDVVEIDGEEYRVV 65 (65)
T ss_dssp ----SSEEEEETTEEEEEE
T ss_pred CcCCCCCEEEECCEEEEEC
Confidence 5689999999999999885
No 36
>PRK12366 replication factor A; Reviewed
Probab=47.15 E-value=3.4e+02 Score=27.88 Aligned_cols=54 Identities=19% Similarity=0.434 Sum_probs=35.9
Q ss_pred eEEcCCCCCccE-EEECCeEEEEEEeEEecCCCC--CeEEEEEEeeCCCCCeEEEEeC
Q 026237 58 KVNASHVRPGNV-IEKSGKMYQVIDAEHKQRGRG--GAMMQMELRDIDTGNKVSLRFG 112 (241)
Q Consensus 58 ~i~a~dirkG~~-I~~dG~py~V~~~~h~KpGKG--~A~vriklknL~TG~k~e~tf~ 112 (241)
.+.+++|.+|+. +.+.++...+-+...-.-.+| +-...+.+-| .||...---|.
T Consensus 63 ~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~D-etG~Ir~t~W~ 119 (637)
T PRK12366 63 DFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD-NTGTIRLTLWN 119 (637)
T ss_pred eeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEc-CCCEEEEEEEc
Confidence 446889999985 888888777766554433334 3345677777 88876555554
No 37
>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=45.70 E-value=1.1e+02 Score=22.31 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=28.8
Q ss_pred CEEEEEEECCEEEEEeCCCe-EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEcccc
Q 026237 166 MKVWLQLYDGRALSGSIPKR-VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY 222 (241)
Q Consensus 166 ~~v~v~~~dg~~i~v~lP~~-V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~F 222 (241)
|+|.+..-+.--+++-+|.. ++=.|++.| +...--..++|.||.+..+|..
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 34444433333788888865 677888886 3334567899999999999875
No 38
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=45.39 E-value=27 Score=24.41 Aligned_cols=37 Identities=14% Similarity=0.173 Sum_probs=22.4
Q ss_pred EEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECC
Q 026237 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDG 175 (241)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg 175 (241)
.-+|+|.+.-+.+.||..... .=+++|++|.+..|.|
T Consensus 15 ~g~fL~~~~~~~vlLp~~e~~---~~~~~Gd~v~VFvY~D 51 (61)
T PF13509_consen 15 FGYFLDDGEGKEVLLPKSEVP---EPLKVGDEVEVFVYLD 51 (61)
T ss_dssp SEEEEEETT-EEEEEEGGG---------TTSEEEEEEEE-
T ss_pred CEEEEECCCCCEEEechHHcC---CCCCCCCEEEEEEEEC
Confidence 345566666788888876543 2389999999998853
No 39
>PRK11507 ribosome-associated protein; Provisional
Probab=44.42 E-value=25 Score=26.01 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=17.5
Q ss_pred cCCCCCccEEEECCeEEEEE
Q 026237 61 ASHVRPGNVIEKSGKMYQVI 80 (241)
Q Consensus 61 a~dirkG~~I~~dG~py~V~ 80 (241)
...|++|++|.++|+-++|.
T Consensus 50 gkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 50 RCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred CCCCCCCCEEEECCEEEEEe
Confidence 35799999999999998885
No 40
>TIGR01646 vgr_GE Rhs element Vgr protein. This model represents the Vgr family of proteins, associated with some classes of Rhs elements. This model does not include a large octapeptide repeat region, VGXXXXXX, found in the Vgr of Rhs classes G and E.
Probab=43.67 E-value=1.2e+02 Score=29.38 Aligned_cols=118 Identities=17% Similarity=0.111 Sum_probs=62.4
Q ss_pred EEcCCCCCccEEEECCeE-------EEEEEeEEecCC------CCCeEEEEEEeeCCCCCeEEE---EeCCCCcEEeeeE
Q 026237 59 VNASHVRPGNVIEKSGKM-------YQVIDAEHKQRG------RGGAMMQMELRDIDTGNKVSL---RFGTEEAVERVFV 122 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~p-------y~V~~~~h~KpG------KG~A~vriklknL~TG~k~e~---tf~s~dkve~v~v 122 (241)
.++..|+.|..|.+.|.| |.|+++.|.--. -..+.++..+.-+-.+...-- ..+.-.-+..+.|
T Consensus 276 ~~~~~L~~G~~~~l~~~~~~~~~~~~~v~~v~h~~~~~~~~~~~~~~~y~~~f~~~p~~~~~rp~~~~~p~i~G~~~a~V 355 (483)
T TIGR01646 276 GNAAGLAPGQLFVLSGHPRNDQNNGYLIVSAIHSIVQLGWDTGIQGYELPNQFIAIEVDVIWRPAATPLPKVNGPQIAVV 355 (483)
T ss_pred eCCCeecCCCEEEecCCCCcccCCCEEEEEEEEEEEcCccccCCCCceEEEEEEEEECCCccCCCCCCCCCCCCcceEEE
Confidence 346779999999998764 999999986211 112345555555444332111 0111112334455
Q ss_pred EeeEEEEEEEeCCE-----EEEEeCCCcc---c--cccCchhhhhhh--h-ccCCCCEEEEEEECCE
Q 026237 123 EDKSFTCLYTENDT-----AFVIESETFE---Q--LEVPLDVFGKAG--A-YLQEGMKVWLQLYDGR 176 (241)
Q Consensus 123 e~k~~qylY~Dgd~-----~~FMD~EtyE---Q--i~v~~~~lgd~~--~-~L~eg~~v~v~~~dg~ 176 (241)
..-.-+++|.|+.. +.++....-+ . +.+-...-|+.. - .+..|++|-|-|.+|.
T Consensus 356 ~g~~~~~~~~d~~GRvkV~f~wd~~~~~~~~~S~W~Rvaqp~AG~~~G~~f~PrvG~EVlV~F~~GD 422 (483)
T TIGR01646 356 VGAQGEEIHTDKYGRIRVHFHWDRYGQSNDYSSCWIRVAQPWAGKNWGSLAIPRVGQEVIVGFLDGD 422 (483)
T ss_pred ECCCCCeeccCCCCcEEEEeecCCCCCCCCCCceEEEEeccccCCCccccccCCCCCEEEEEEeCCC
Confidence 54334577777654 2233222111 1 333333222221 2 2489999999999865
No 41
>PRK04313 30S ribosomal protein S4e; Validated
Probab=43.64 E-value=52 Score=29.82 Aligned_cols=32 Identities=16% Similarity=0.334 Sum_probs=22.0
Q ss_pred ceeEEeecCcEEEcc--ccccCCCEEEEECCCCc
Q 026237 206 YRRALLDNGVTVMVP--SYLEIGEEIFINPQDDS 237 (241)
Q Consensus 206 ~K~A~LetG~~v~VP--~FI~~Gd~I~V~T~~g~ 237 (241)
--...|..|..|.+| .-+++||.|+|+-.+++
T Consensus 132 ~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~k 165 (237)
T PRK04313 132 KIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQE 165 (237)
T ss_pred EEEEEecCCceEEccCccccccCCEEEEECCCCc
Confidence 345666777777777 57777777777776664
No 42
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=41.60 E-value=1.5e+02 Score=23.23 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=31.0
Q ss_pred CeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEc--c------ccccCCCEEEEECCC
Q 026237 184 KRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P------SYLEIGEEIFINPQD 235 (241)
Q Consensus 184 ~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~~ 235 (241)
..+...|++.-+ +..=.+.++||.++.+ | ..|+.||.|.|....
T Consensus 21 ~e~~g~V~~~lG--------~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~ 72 (100)
T PRK04012 21 GEVFGVVEQMLG--------ANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWD 72 (100)
T ss_pred CEEEEEEEEEcC--------CCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecc
Confidence 556777777743 3455677788877643 4 678999999998644
No 43
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=40.83 E-value=38 Score=27.43 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=20.7
Q ss_pred cCCCCCccEEEECCeEEEEEEeE
Q 026237 61 ASHVRPGNVIEKSGKMYQVIDAE 83 (241)
Q Consensus 61 a~dirkG~~I~~dG~py~V~~~~ 83 (241)
..+|++|+.+.++|+-|.|..+-
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaVG 71 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAVG 71 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEEh
Confidence 46799999999999999999983
No 44
>PF05521 Phage_H_T_join: Phage head-tail joining protein ; InterPro: IPR008767 This entry describes the head-tail adaptor protein of bacteriophage SPP1 and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2KCA_A 2KZ4_A.
Probab=40.26 E-value=58 Score=23.29 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=18.6
Q ss_pred CCCCccEEEECCeEEEEEEeEEec
Q 026237 63 HVRPGNVIEKSGKMYQVIDAEHKQ 86 (241)
Q Consensus 63 dirkG~~I~~dG~py~V~~~~h~K 86 (241)
+|..++.|.++|+.|.|..+....
T Consensus 62 ~I~~~~ri~~~g~~y~I~~i~~~~ 85 (95)
T PF05521_consen 62 DITPDMRIKYDGKVYNIKSIDPDD 85 (95)
T ss_dssp TSSTTEEEEECTEEEEE-S--EE-
T ss_pred CCCcceEEEECCEEEEEEEECCCC
Confidence 799999999999999999977654
No 45
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=39.78 E-value=1.9e+02 Score=22.82 Aligned_cols=23 Identities=26% Similarity=0.378 Sum_probs=20.2
Q ss_pred CCCccEEEECCeEEEEEEeEEec
Q 026237 64 VRPGNVIEKSGKMYQVIDAEHKQ 86 (241)
Q Consensus 64 irkG~~I~~dG~py~V~~~~h~K 86 (241)
|++|+.+.++|++|+|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999998887654
No 46
>PF03829 PTSIIA_gutA: PTS system glucitol/sorbitol-specific IIA component; InterPro: IPR004716 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2F9H_A.
Probab=39.40 E-value=36 Score=27.42 Aligned_cols=23 Identities=17% Similarity=0.528 Sum_probs=16.1
Q ss_pred cCCCCCccEEEECCeEEEEEEeE
Q 026237 61 ASHVRPGNVIEKSGKMYQVIDAE 83 (241)
Q Consensus 61 a~dirkG~~I~~dG~py~V~~~~ 83 (241)
..+|++|+.+.++|+.|.|..+-
T Consensus 49 ~~~i~~Gd~l~i~~~~y~ItaVG 71 (117)
T PF03829_consen 49 KGDIKPGDTLIIGGQEYTITAVG 71 (117)
T ss_dssp G----TT-EEEETTEEEEEEEE-
T ss_pred cCCcCCCCEEEECCeEEEEEEEh
Confidence 46899999999999999999883
No 47
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=38.57 E-value=44 Score=27.14 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=20.1
Q ss_pred CCCCCccEEEECCeEEEEEEeE
Q 026237 62 SHVRPGNVIEKSGKMYQVIDAE 83 (241)
Q Consensus 62 ~dirkG~~I~~dG~py~V~~~~ 83 (241)
.+|++|+.+.++|+-|.|..+-
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaVG 71 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAVG 71 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEEh
Confidence 4799999999999999999983
No 48
>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=38.29 E-value=57 Score=25.14 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=21.6
Q ss_pred cCcEEEccc------cccCCCEEEEECCC-Cceec
Q 026237 213 NGVTVMVPS------YLEIGEEIFINPQD-DSYIG 240 (241)
Q Consensus 213 tG~~v~VP~------FI~~Gd~I~V~T~~-g~Yv~ 240 (241)
+|+.++.|- -++.||.|.|-+.+ |+.+.
T Consensus 45 ~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~ia 79 (107)
T TIGR00451 45 NGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLA 79 (107)
T ss_pred CCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEE
Confidence 688888884 45789999998776 87764
No 49
>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=38.09 E-value=51 Score=21.67 Aligned_cols=29 Identities=21% Similarity=0.274 Sum_probs=21.9
Q ss_pred cccccCchhhhhhhhccCCCCEEEEEEECCE
Q 026237 146 EQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 176 (241)
Q Consensus 146 EQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~ 176 (241)
-|+.||++.... .-|++|+++.+...+|.
T Consensus 7 ~~v~iPk~~~~~--l~l~~Gd~v~i~~~~~g 35 (47)
T PF04014_consen 7 GQVTIPKEIREK--LGLKPGDEVEIEVEGDG 35 (47)
T ss_dssp SEEEE-HHHHHH--TTSSTTTEEEEEEETTS
T ss_pred ceEECCHHHHHH--cCCCCCCEEEEEEeCCC
Confidence 478899887643 35899999999998873
No 50
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=37.90 E-value=2e+02 Score=23.01 Aligned_cols=78 Identities=15% Similarity=0.218 Sum_probs=50.9
Q ss_pred cccCchhhhhh-hhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEccc-c-cc
Q 026237 148 LEVPLDVFGKA-GAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPS-Y-LE 224 (241)
Q Consensus 148 i~v~~~~lgd~-~~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~-F-I~ 224 (241)
|..|++...|. .+|= -+..+.-....|.+++-.+..+|..+|...-.- .--.|-+.-.+-..+--|. + ++
T Consensus 7 ~~~p~~~~~d~~cP~~-g~l~irgk~l~G~VvS~Km~KTvvV~v~r~~~h------pkY~K~i~r~kky~aHDe~cn~~k 79 (108)
T PRK08572 7 VKPPEEECDDPNCPFH-GTLPVRGQVLEGTVVSDKMHKTVVVEREYLHYV------PKYERYEKRRSRIHAHNPPCIDAK 79 (108)
T ss_pred CCCCcccccCCCCCCc-ceeeeeeEEEEEEEEecCCCceEEEEEEEEEec------CCccEEEEEeeeEEEECCCCCCCC
Confidence 44455444332 2332 236677778899999999999999999887421 1123444445556666676 4 89
Q ss_pred CCCEEEEE
Q 026237 225 IGEEIFIN 232 (241)
Q Consensus 225 ~Gd~I~V~ 232 (241)
+||.|.|.
T Consensus 80 vGD~V~I~ 87 (108)
T PRK08572 80 VGDKVKIA 87 (108)
T ss_pred CCCEEEEE
Confidence 99999985
No 51
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=37.79 E-value=2.2e+02 Score=23.00 Aligned_cols=65 Identities=12% Similarity=0.237 Sum_probs=46.7
Q ss_pred EEEEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEE-CCEEEEEeCCCeEEEEEEEec
Q 026237 128 TCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLY-DGRALSGSIPKRVACTIKEIH 194 (241)
Q Consensus 128 qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~-dg~~i~v~lP~~V~l~V~et~ 194 (241)
.....+.+..++ ..+=|++|.||.+.|-+...| .++..+-++-| ++.-+-+++-..|-++|.+..
T Consensus 10 ~I~~~~~~Gi~v-slgFFddI~IP~~~L~~ps~f-d~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 10 KIKSSTAEGIRV-SLGFFDDIFIPPSLLPEPSRF-DEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp EEEEEETTEEEE-EECCEEEEEEECCCC-TTEEE-ECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred EEEecCCCcEEE-EecccccEEECHHHCCCCCcc-CccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 445555555432 336799999999999887777 45567888888 899999999999999998764
No 52
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=36.50 E-value=39 Score=25.21 Aligned_cols=21 Identities=38% Similarity=0.740 Sum_probs=18.3
Q ss_pred CCCCCccEEEECCeEEEEEEe
Q 026237 62 SHVRPGNVIEKSGKMYQVIDA 82 (241)
Q Consensus 62 ~dirkG~~I~~dG~py~V~~~ 82 (241)
..||.|+.|++.|..|.|...
T Consensus 51 kKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 51 KKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CEeecCCEEEECCEEEEEEec
Confidence 458999999999999999764
No 53
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=36.44 E-value=1.5e+02 Score=22.32 Aligned_cols=44 Identities=11% Similarity=0.331 Sum_probs=29.1
Q ss_pred CeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEc--c------ccccCCCEEEEECCC
Q 026237 184 KRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P------SYLEIGEEIFINPQD 235 (241)
Q Consensus 184 ~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~~ 235 (241)
..+..+|+++-+ +..-.+.+++|.++.+ | ..|+.||.|.|+..+
T Consensus 5 ~q~~g~V~~~lG--------~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~ 56 (83)
T smart00652 5 GQEIAQVVKMLG--------NGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWD 56 (83)
T ss_pred CcEEEEEEEEcC--------CCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecC
Confidence 345566666643 3455677778877643 3 468899999998654
No 54
>PLN00036 40S ribosomal protein S4; Provisional
Probab=35.52 E-value=73 Score=29.30 Aligned_cols=31 Identities=10% Similarity=0.225 Sum_probs=16.3
Q ss_pred EeCCCCcEEeeeEEe--eEEEEEEEeCCEEEEEe
Q 026237 110 RFGTEEAVERVFVED--KSFTCLYTENDTAFVIE 141 (241)
Q Consensus 110 tf~s~dkve~v~ve~--k~~qylY~Dgd~~~FMD 141 (241)
+|+.| -++++.+++ ..|..+|.....|.+.-
T Consensus 81 ~fPvG-~mDVIsI~kt~e~yRvl~D~kGrf~l~~ 113 (261)
T PLN00036 81 TYPAG-FMDVISIPKTNENFRLLYDTKGRFRLHR 113 (261)
T ss_pred CCCCc-eeEEEEEcCCCCeEEEEECCCceEEEEE
Confidence 44433 355555543 45666666555555543
No 55
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=34.52 E-value=3.3e+02 Score=24.09 Aligned_cols=101 Identities=15% Similarity=0.266 Sum_probs=62.5
Q ss_pred EEEEEeE--EecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEEEEEeCCCccccccCchh
Q 026237 77 YQVIDAE--HKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDV 154 (241)
Q Consensus 77 y~V~~~~--h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~~FMD~EtyEQi~v~~~~ 154 (241)
|-|+++. .++||-|++..++.+|=+. .+.=-|+-+. ..+.-.+.++..+-=. -||+|-||++.
T Consensus 49 yDi~~v~e~~v~pGDGas~~~V~FR~vV------FrPF~gEVi~--------gki~~cs~eG~rvtl~-FFdDI~IP~~~ 113 (202)
T KOG3297|consen 49 YDILEVEEGIVLPGDGASYARVWFRVVV------FRPFVGEVIT--------GKIKECSEEGLRVTLG-FFDDIFIPKEM 113 (202)
T ss_pred eEeeeecceEEecCCCceEEEEEEEEEE------EecccceEEE--------EEeecCCccceEEEEE-eeeceeechhh
Confidence 5666665 5889999999999887542 1111232222 1112222222222211 47889999999
Q ss_pred hhhhhhccCCCCEEEEEEEC-----CEEEEEeCCCeEEEEEEEe
Q 026237 155 FGKAGAYLQEGMKVWLQLYD-----GRALSGSIPKRVACTIKEI 193 (241)
Q Consensus 155 lgd~~~~L~eg~~v~v~~~d-----g~~i~v~lP~~V~l~V~et 193 (241)
|.+...|- +...+-|+-|+ +.-+-+..-..|-+.|.+-
T Consensus 114 L~~p~~f~-~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 114 LPEPCVFE-PDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred CCCCcccc-cccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 88776654 44778888776 4557777778888888764
No 56
>PF15415 DUF4622: Protein of unknown function (DUF4622)
Probab=34.32 E-value=3.3e+02 Score=25.18 Aligned_cols=73 Identities=21% Similarity=0.281 Sum_probs=45.1
Q ss_pred hccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEe-ecCcEEEc---cccccCCCE-------
Q 026237 160 AYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALL-DNGVTVMV---PSYLEIGEE------- 228 (241)
Q Consensus 160 ~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~L-etG~~v~V---P~FI~~Gd~------- 228 (241)
..|.+|..+-+.++++.-=..+--. .--|+.| |+...+..-|.+. |||..|.+ |+|.++|-.
T Consensus 38 ~lL~~GSTlwL~~~~~ak~gtt~~t--qgYvVrt-----gtgG~~~LYPC~~deNG~~i~~s~tPLyl~aGtY~F~~iSP 110 (310)
T PF15415_consen 38 FLLPIGSTLWLFYYDQAKNGTTYYT--QGYVVRT-----GTGGYNSLYPCQFDENGKYINSSSTPLYLNAGTYYFRMISP 110 (310)
T ss_pred EEccCCCEEEEEEeccccccceeee--eEEEEEe-----cCCCcceeeeeEEcCCCcEEeccCCceEEecceEEEEEecc
Confidence 3568889999988875432211111 1112223 3444566788888 89988755 999999953
Q ss_pred -------EEEECCCCcee
Q 026237 229 -------IFINPQDDSYI 239 (241)
Q Consensus 229 -------I~V~T~~g~Yv 239 (241)
-+++..+|+|+
T Consensus 111 Aka~~~dgk~~I~NGeYl 128 (310)
T PF15415_consen 111 AKASNSDGKMNIDNGEYL 128 (310)
T ss_pred ccccccCceEEeCCceEE
Confidence 34555667765
No 57
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=34.26 E-value=1.3e+02 Score=24.38 Aligned_cols=70 Identities=26% Similarity=0.364 Sum_probs=47.1
Q ss_pred ceeeEEcCCCCCccEEE-----ECCeEEEEEEeEEe---cCCCCCeEEEEEEeeCCCCCeEEEEeCCCC-cEEeeeEEee
Q 026237 55 RAVKVNASHVRPGNVIE-----KSGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEE-AVERVFVEDK 125 (241)
Q Consensus 55 R~~~i~a~dirkG~~I~-----~dG~py~V~~~~h~---KpGKG~A~vriklknL~TG~k~e~tf~s~d-kve~v~ve~k 125 (241)
..++-++.++++||.|. .+|.-+.+..|+-+ ..|+|- .=-..++.+..|-=+|.+|+-.. .+|.+++-++
T Consensus 12 ~q~~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~-~~tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~rr 90 (115)
T COG0335 12 EQIKKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGI-SETFTVRKISYGVGVERVFPLHSPLIESIEVVRR 90 (115)
T ss_pred HHHHhhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCc-cceEEEEEeecCceEEEEeecCCCceeEEEEEec
Confidence 33444578899999875 36777777777742 234333 22566788899999999998754 5666665553
No 58
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=33.55 E-value=2.3e+02 Score=21.95 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=19.4
Q ss_pred EEEEeeCCCCCeEEEEeCCCCcEE
Q 026237 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (241)
Q Consensus 95 riklknL~TG~k~e~tf~s~dkve 118 (241)
.++++|+.+|+.+.-+.-+...++
T Consensus 98 ~I~V~N~~s~k~i~~~V~~~g~V~ 121 (122)
T TIGR03170 98 QIRVRNLSSGKIISGIVTGPGTVE 121 (122)
T ss_pred EEEEEECCCCCEEEEEEeCCCEEE
Confidence 789999999999988876665554
No 59
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=33.47 E-value=2.8e+02 Score=27.14 Aligned_cols=114 Identities=18% Similarity=0.249 Sum_probs=60.1
Q ss_pred EcCCCCCccEEEECCeE-------EEEEEeEEecCC--------CCCeEEEEEEeeCCCCCeEEEEeCCC--------Cc
Q 026237 60 NASHVRPGNVIEKSGKM-------YQVIDAEHKQRG--------RGGAMMQMELRDIDTGNKVSLRFGTE--------EA 116 (241)
Q Consensus 60 ~a~dirkG~~I~~dG~p-------y~V~~~~h~KpG--------KG~A~vriklknL~TG~k~e~tf~s~--------dk 116 (241)
++-.|+.|..|.+.|.| |.|++++|.--. -+...++..+.=+-... .|++. .-
T Consensus 285 ~~~~l~~G~~~~l~~~~~~~~~g~ylVt~v~H~~~~~~~~~~~~~~~~~y~~~f~~ip~~~----~~rp~~~~~~P~i~G 360 (513)
T TIGR03361 285 NCRRLAPGYLFTLSGHPRAALNREYLVVSVHHHGRQPQVLEESGGSGAGYRNSFQCIPADV----PFRPPRRTPKPRIDG 360 (513)
T ss_pred CcCeEcCCCEEEeCCCCCcccCCCEEEEEEEEEEEeCcccccccCCCceEEEEEEEEECCC----cccCCCCCCCCcCCC
Confidence 45689999999997753 999999995410 11223444443333221 22221 11
Q ss_pred EEeeeEEeeEEEEEEEeCCE---EEEE-e-C---CCccc--cccCchhhhhhh--h-ccCCCCEEEEEEECCEE
Q 026237 117 VERVFVEDKSFTCLYTENDT---AFVI-E-S---ETFEQ--LEVPLDVFGKAG--A-YLQEGMKVWLQLYDGRA 177 (241)
Q Consensus 117 ve~v~ve~k~~qylY~Dgd~---~~FM-D-~---EtyEQ--i~v~~~~lgd~~--~-~L~eg~~v~v~~~dg~~ 177 (241)
+..+.|...+-+.+|.|+.. ..|. | . +..+. +.+-...-|... - ....|++|-|.|.+|.|
T Consensus 361 ~q~A~V~g~~~~~i~~D~~GRvkV~f~wd~~~~~~~~~S~wvRvaqp~AG~~~G~~f~PrvG~EVlV~F~~GDp 434 (513)
T TIGR03361 361 PQTATVVGPAGEEIYTDEYGRVKVQFHWDRYGKRDEKSSCWVRVAQPWAGNGWGSVAIPRVGQEVVVDFLEGDP 434 (513)
T ss_pred CeEEEEECCCCCEEeECCCCCEEEEecccCCCCCCCCCceEEEecccccCCCcccccCCCCCCEEEEEEcCCCC
Confidence 44555555555566776643 2232 1 1 11111 222222222222 2 23889999999998653
No 60
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=33.36 E-value=42 Score=27.79 Aligned_cols=31 Identities=19% Similarity=0.232 Sum_probs=26.4
Q ss_pred EEcCCCCCccEEEECCeEE-----EEEEeEEecCCC
Q 026237 59 VNASHVRPGNVIEKSGKMY-----QVIDAEHKQRGR 89 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~py-----~V~~~~h~KpGK 89 (241)
-...+|++|+.|+..|+.+ -|+.+.|.-|+.
T Consensus 81 prip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~ 116 (131)
T PF11948_consen 81 PRIPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRG 116 (131)
T ss_pred ccCcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCC
Confidence 4467899999999999987 799999988865
No 61
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=32.53 E-value=4.2e+02 Score=24.75 Aligned_cols=87 Identities=18% Similarity=0.343 Sum_probs=55.1
Q ss_pred CCEEEEEeCCCcc-ccccCchhhhhhhhccCCCCEEEEEEE---CCEEEE-EeCC-----CeEEEEEEEecCCCCCcCCC
Q 026237 134 NDTAFVIESETFE-QLEVPLDVFGKAGAYLQEGMKVWLQLY---DGRALS-GSIP-----KRVACTIKEIHASTKGPTVT 203 (241)
Q Consensus 134 gd~~~FMD~EtyE-Qi~v~~~~lgd~~~~L~eg~~v~v~~~---dg~~i~-v~lP-----~~V~l~V~et~p~~kGdT~~ 203 (241)
.+.-+|.+.++++ .+-+++....+ +=+++|++|++..| +++++. -+.| ..=-++|+++.+..
T Consensus 17 ~~~g~fL~~~~~~~~ilL~k~~~~~--~e~evGdev~vFiY~D~~~rl~aTt~~p~~tvg~~g~~~Vv~v~~~l------ 88 (287)
T COG2996 17 SDFGYFLDAGEDGTTILLPKSEPEE--DELEVGDEVTVFIYVDSEDRLIATTREPKATVGEYGWLKVVEVNKDL------ 88 (287)
T ss_pred eceeEEEecCCCceEEeccccCCcC--CccccCcEEEEEEEECCCCceeheeecceEeecceeEEEEEEEcCCc------
Confidence 3566788888776 66666653322 23789999999887 566653 2333 33468898886521
Q ss_pred CCceeEEeecCcE--EEcc---------ccccCCCEEEEE
Q 026237 204 PRYRRALLDNGVT--VMVP---------SYLEIGEEIFIN 232 (241)
Q Consensus 204 ~~~K~A~LetG~~--v~VP---------~FI~~Gd~I~V~ 232 (241)
-|-|++|+. +.|| +-.++||+.-|.
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 255666654 3333 337889987764
No 62
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=32.46 E-value=62 Score=24.51 Aligned_cols=31 Identities=23% Similarity=0.319 Sum_probs=20.3
Q ss_pred ceeeEEcCC---CCCccEEEECCeEEEEEEeEEe
Q 026237 55 RAVKVNASH---VRPGNVIEKSGKMYQVIDAEHK 85 (241)
Q Consensus 55 R~~~i~a~d---irkG~~I~~dG~py~V~~~~h~ 85 (241)
+.+.+..++ .++|+.|.+||+-|.|.+++.-
T Consensus 54 ~~L~v~~~d~~~P~~gd~v~~dG~~y~V~~~~~~ 87 (95)
T PF13856_consen 54 PTLYVFSSDYPKPRRGDRVVIDGESYTVTRFQEE 87 (95)
T ss_dssp EEEEE--SS-----TT-EEEETTEEEEEEEEEEE
T ss_pred eEEEEEcCCCCCCCCCCEEEECCeEEEEeEEecC
Confidence 334444444 5699999999999999999754
No 63
>PF13144 SAF_2: SAF-like
Probab=32.23 E-value=2.8e+02 Score=23.26 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=19.7
Q ss_pred EEEEeeCCCCCeEEEEeCCCCcEE
Q 026237 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (241)
Q Consensus 95 riklknL~TG~k~e~tf~s~dkve 118 (241)
.++++|+.||+.+.-+.-+..+++
T Consensus 172 ~I~V~N~~S~k~v~g~V~~~~~V~ 195 (196)
T PF13144_consen 172 TIRVKNLSSGKIVQGRVIGPGTVE 195 (196)
T ss_pred EEEEEECCCCCEEEEEEecCCEEE
Confidence 788999999999988877666655
No 64
>PF02839 CBM_5_12: Carbohydrate binding domain; InterPro: IPR003610 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM5 from CAZY and CBM12 from CAZY. These modules have a core structure consisting of a 3-stranded meander beta-sheet, which contain six aromatic groups that may be important for binding. CBM5/12 is found in proteins such as chitinase A1, chitinase B [], and endoglucanase Z []. The overall topology of the CBM is structurally similar to the C-terminal chitin-binding domains (ChBD) of chitinase A1 and chitinase B, however the binding mechanism for the ChBD may be different from that of the CBM [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1ED7_A 1W1V_A 1E15_B 1UR8_A 1E6Z_B 1E6P_A 1W1T_A 1W1P_B 1UR9_A 1E6R_A ....
Probab=31.64 E-value=53 Score=20.77 Aligned_cols=20 Identities=25% Similarity=0.341 Sum_probs=14.6
Q ss_pred CCCCccEEEECCeEEEEEEe
Q 026237 63 HVRPGNVIEKSGKMYQVIDA 82 (241)
Q Consensus 63 dirkG~~I~~dG~py~V~~~ 82 (241)
....|++|.++|..|+..-.
T Consensus 9 ~Y~~Gd~V~~~g~~y~a~~~ 28 (41)
T PF02839_consen 9 TYNAGDRVSYNGKLYQAKWW 28 (41)
T ss_dssp EE-TT-EEEETTEEEEESSS
T ss_pred EEcCCCEEEECCCEEEEeec
Confidence 34679999999999998544
No 65
>PF05610 DUF779: Protein of unknown function (DUF779); InterPro: IPR008497 This family consists of several bacterial proteins of unknown function.
Probab=31.30 E-value=74 Score=24.95 Aligned_cols=47 Identities=26% Similarity=0.462 Sum_probs=27.7
Q ss_pred CCCCCcCccccCcccceecceeeEEcCCCCCccEEEECCeEE--------------EEEEeEEecCCCCCeE
Q 026237 36 SSGDRDTCLLRFPWSATQQRAVKVNASHVRPGNVIEKSGKMY--------------QVIDAEHKQRGRGGAM 93 (241)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~R~~~i~a~dirkG~~I~~dG~py--------------~V~~~~h~KpGKG~A~ 93 (241)
||||-++...--| ..-..+..+|+.-|.+ .|-|+ .++++ .||+|+.|
T Consensus 19 GGCCDGSaPmC~p-----~gef~~g~~DV~LG~i---~g~~fym~~~qfeywkht~L~iDV---v~GrG~~F 79 (95)
T PF05610_consen 19 GGCCDGSAPMCYP-----AGEFRVGDSDVLLGEI---GGVPFYMSKDQFEYWKHTQLTIDV---VPGRGGGF 79 (95)
T ss_pred CCCCCCCcceeEe-----CCceecCCCcEEEEEe---cCeEEEEchHHHHHhhCcEEEEEE---EecCCCee
Confidence 7888776543222 3334555666666655 66665 34444 58998766
No 66
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=31.14 E-value=1.7e+02 Score=21.15 Aligned_cols=39 Identities=28% Similarity=0.373 Sum_probs=30.3
Q ss_pred eEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEcccc-----ccCCCEEEEE
Q 026237 185 RVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY-----LEIGEEIFIN 232 (241)
Q Consensus 185 ~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~F-----I~~Gd~I~V~ 232 (241)
.++=+|.+.+| .+...+|+.|..-++|.= +++|.+|+|-
T Consensus 4 ~veG~I~~id~---------~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~ 47 (61)
T PF07076_consen 4 DVEGTIKSIDP---------ETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVF 47 (61)
T ss_pred cceEEEEEEcC---------CceEEEecCCCEEECCCcccccccCCCCEEEEE
Confidence 45556777755 367899999999999863 7889999884
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=31.08 E-value=1.8e+02 Score=20.08 Aligned_cols=55 Identities=11% Similarity=-0.032 Sum_probs=32.8
Q ss_pred cCCCCEEEE--EEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEccccccCCCEEEEE
Q 026237 162 LQEGMKVWL--QLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFIN 232 (241)
Q Consensus 162 L~eg~~v~v--~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~ 232 (241)
|+.|+.+.. .-..+.-+-++|+..++-.|--++-.- + ..+ ..+.+++.||.|++.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~--~----~~~----------~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD--D----YSE----------ALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC--c----ccc----------ccccccCCCCEEEEE
Confidence 456766643 445666677888887776666553210 0 000 126778889988774
No 68
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.88 E-value=70 Score=25.54 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=16.3
Q ss_pred cCCCCCccEEEECCe--EEEEEEeE
Q 026237 61 ASHVRPGNVIEKSGK--MYQVIDAE 83 (241)
Q Consensus 61 a~dirkG~~I~~dG~--py~V~~~~ 83 (241)
-.+|++|++|+.+|. +..|+++.
T Consensus 31 rr~ik~GD~IiF~~~~l~v~V~~vr 55 (111)
T COG4043 31 RRQIKPGDKIIFNGDKLKVEVIDVR 55 (111)
T ss_pred hcCCCCCCEEEEcCCeeEEEEEEEe
Confidence 457899999999974 44445544
No 69
>PF10665 Minor_capsid_1: Minor capsid protein; InterPro: IPR019612 This entry is represented by Bacteriophage A118, Gp9. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a putative tail-knob protein from Listeria phage A118.
Probab=30.78 E-value=67 Score=25.69 Aligned_cols=26 Identities=23% Similarity=0.270 Sum_probs=22.8
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEec
Q 026237 61 ASHVRPGNVIEKSGKMYQVIDAEHKQ 86 (241)
Q Consensus 61 a~dirkG~~I~~dG~py~V~~~~h~K 86 (241)
+-+++.|+.|.+||+.|.|.++...-
T Consensus 74 ~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 74 FPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred ccccCCCCEEEECCceEEEEEEEecc
Confidence 35889999999999999999998754
No 70
>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=30.52 E-value=1.7e+02 Score=20.60 Aligned_cols=43 Identities=14% Similarity=0.322 Sum_probs=26.4
Q ss_pred EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEc--c------ccccCCCEEEEECCCC
Q 026237 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV--P------SYLEIGEEIFINPQDD 236 (241)
Q Consensus 186 V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~~g 236 (241)
+...|++.-+ +..=.+.+++|.++.+ | ..|+.||.|.|+....
T Consensus 5 ~~~~V~~~lG--------~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~ 55 (65)
T PF01176_consen 5 VIGRVTEMLG--------NNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPY 55 (65)
T ss_dssp EEEEEEEEES--------SSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTT
T ss_pred EEEEEEEECC--------CCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEeccc
Confidence 4455666543 3456777888877654 3 5899999999997643
No 71
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=30.39 E-value=2.9e+02 Score=25.89 Aligned_cols=54 Identities=11% Similarity=0.244 Sum_probs=41.4
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCC
Q 026237 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEE 115 (241)
Q Consensus 58 ~i~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~d 115 (241)
|..+++++.|+.|. .+|.|.+.+-...-.|..+..+.+.| .||...-+-|..++
T Consensus 2 m~~i~~l~~g~~v~---~~~lv~~~~~~~~knG~~yl~l~l~D-~tG~I~ak~W~~~~ 55 (314)
T PRK13480 2 MKGIEELEVGEQVD---HFLLIKSATKGVASNGKPFLTLILQD-KSGDIEAKLWDVSP 55 (314)
T ss_pred cchHhhcCCCCEee---EEEEEEEceeeecCCCCeEEEEEEEc-CCcEEEEEeCCCCh
Confidence 44688999998664 36777777654434488999999999 99999888887654
No 72
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=29.34 E-value=93 Score=27.55 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=31.9
Q ss_pred cceeeEEcCCCCCccEEEE---CCe--EEEEEEeEEecCCCCCeEEEEEEe
Q 026237 54 QRAVKVNASHVRPGNVIEK---SGK--MYQVIDAEHKQRGRGGAMMQMELR 99 (241)
Q Consensus 54 ~R~~~i~a~dirkG~~I~~---dG~--py~V~~~~h~KpGKG~A~vriklk 99 (241)
..+-.+.+.||+.||.|.- +|+ ...|+-+.|..|..-+-|++++..
T Consensus 22 ~~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~flhr~~~~~~~F~~i~te 72 (217)
T PF01079_consen 22 EDGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMFLHRDPEQRAEFVVIETE 72 (217)
T ss_dssp TTS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEEEEEEEEEEEEEEEEEET
T ss_pred CCCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEEeccCccccEEEEEEEcC
Confidence 3455678899999999875 564 558999999999887778888654
No 73
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=29.02 E-value=2.1e+02 Score=20.22 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=24.6
Q ss_pred CCCCCeEEEEeCCCCcEEeeeE-----EeeEEEEEEEeCCEEEE
Q 026237 101 IDTGNKVSLRFGTEEAVERVFV-----EDKSFTCLYTENDTAFV 139 (241)
Q Consensus 101 L~TG~k~e~tf~s~dkve~v~v-----e~k~~qylY~Dgd~~~F 139 (241)
...|.++.-+|+.+...-++.| ..+.++.+|.||+..-+
T Consensus 6 ~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~l 49 (55)
T PF09465_consen 6 FAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELEL 49 (55)
T ss_dssp S-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEE
T ss_pred ccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEe
Confidence 3468889999998886544443 35788999999987443
No 74
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=28.80 E-value=1.9e+02 Score=22.27 Aligned_cols=41 Identities=20% Similarity=0.266 Sum_probs=27.4
Q ss_pred EEEEEEEecCCCCCcCCCCCceeEEeecCcEEEc---------cccccCCCEEEEECC
Q 026237 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV---------PSYLEIGEEIFINPQ 234 (241)
Q Consensus 186 V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~V---------P~FI~~Gd~I~V~T~ 234 (241)
++-+|+|+=| +..-.+.||||.+|.. =.-|.+||+|+|.-.
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 4456666644 3466788899988743 234667999998654
No 75
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=28.79 E-value=1.2e+02 Score=27.91 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=14.9
Q ss_pred EeCCCCcEEeeeEEe--eEEEEEEEeCCEEEEE
Q 026237 110 RFGTEEAVERVFVED--KSFTCLYTENDTAFVI 140 (241)
Q Consensus 110 tf~s~dkve~v~ve~--k~~qylY~Dgd~~~FM 140 (241)
+|+.| -++++.+++ ..|..+|.....|.+.
T Consensus 81 ~fPvG-~mDVIsI~kt~e~yRvl~D~kGr~~l~ 112 (262)
T PTZ00118 81 TYPVG-FMDVVSLTKTNEYFRLLYDTKGRFVPH 112 (262)
T ss_pred CCCCc-eeEEEEEcCCCCeEEEEECCCccEEEE
Confidence 44433 355555543 4555666555544443
No 76
>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=28.32 E-value=52 Score=24.70 Aligned_cols=62 Identities=16% Similarity=0.155 Sum_probs=32.1
Q ss_pred CccccccCchhhhhhh----hccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEc
Q 026237 144 TFEQLEVPLDVFGKAG----AYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMV 219 (241)
Q Consensus 144 tyEQi~v~~~~lgd~~----~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~V 219 (241)
++|-+++..+.+++.. .-+.+|+.+.++..++. .+.++|+.++|....+ -.|.|++|.+|-|
T Consensus 13 DWEIlEl~A~~lE~~lL~QiRvv~~~~~~~v~v~~~~--------~i~~~V~~i~p~~~~~------~~~~L~~~TEv~V 78 (80)
T PF09262_consen 13 DWEILELHAEFLEDQLLSQIRVVFPGQVFPVWVSQNT--------VIKFKVVSIEPSSSAE------GCARLSPDTEVIV 78 (80)
T ss_dssp HHHHHHHS-SSHHHHHHHH--EE-TT-EEEEESSSS---------EEEEEEEEEES--S---------SEE--TT-EEEE
T ss_pred HHHHHHHhHHHHHHHHHHhheeecCCCEEEEEEcCCe--------EEEEEEEEccCCCCce------eEEEeCCCcEEEE
Confidence 4677777776666532 33455555555443333 4578899998843211 3799999999876
No 77
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.26 E-value=1.4e+02 Score=26.33 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=21.2
Q ss_pred EEEEeeCCCCCeEEEEeCCCCcEEe
Q 026237 95 QMELRDIDTGNKVSLRFGTEEAVER 119 (241)
Q Consensus 95 riklknL~TG~k~e~tf~s~dkve~ 119 (241)
.+++||+.||+.+.-+..+...++.
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V 233 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEV 233 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEE
Confidence 7889999999999988877777764
No 78
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=28.11 E-value=1.6e+02 Score=26.04 Aligned_cols=76 Identities=13% Similarity=0.267 Sum_probs=49.7
Q ss_pred eEEcCCCCCccEEEE-------CCeE--EEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCC----cEEeeeEEe
Q 026237 58 KVNASHVRPGNVIEK-------SGKM--YQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEE----AVERVFVED 124 (241)
Q Consensus 58 ~i~a~dirkG~~I~~-------dG~p--y~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~d----kve~v~ve~ 124 (241)
.....++++|+++.+ .++. +..+-++..+-|-+ -.+.++|+.-|.=+|..|+--+ .++++.+++
T Consensus 91 ~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~---atf~LRnvIagvGVEi~~pLYsP~IkeI~Vlk~~k 167 (201)
T KOG1698|consen 91 VRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLN---ATFLLRNVIAGVGVEIVFPLYSPNIKEIKVLKLEK 167 (201)
T ss_pred cccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCCc---ceEEeeehhhCceeEEEEeccCCCeeEEEEechhh
Confidence 355679999999876 2232 33344443333433 3688999999999999997644 444444444
Q ss_pred eEEEEEEEeCCEEEEEeC
Q 026237 125 KSFTCLYTENDTAFVIES 142 (241)
Q Consensus 125 k~~qylY~Dgd~~~FMD~ 142 (241)
+ .|..-||+-|.
T Consensus 168 ~------rra~LyYLRd~ 179 (201)
T KOG1698|consen 168 R------RRAKLYYLRDA 179 (201)
T ss_pred c------ccchhhhhhcc
Confidence 4 56667788775
No 79
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=27.57 E-value=2.6e+02 Score=23.86 Aligned_cols=61 Identities=10% Similarity=0.186 Sum_probs=44.6
Q ss_pred CEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEcccc--ccCCCEEEEE
Q 026237 166 MKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSY--LEIGEEIFIN 232 (241)
Q Consensus 166 ~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~F--I~~Gd~I~V~ 232 (241)
..|.-....|.+++-.+..+|+.+|...-.- .--.|-..--+-..+-.|+- +++||.|.|-
T Consensus 64 ~~iRgril~G~VvS~KM~KTIVV~ve~~~~h------~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~ 126 (158)
T PTZ00241 64 VSIRGRILRGVVISTKMKRTIIIRRDYLHYV------KKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVG 126 (158)
T ss_pred eeEcceEEEEEEEEccCCccEEEEEEEEEec------CccceEEEeeecEEEeCCccCCCCCCCEEEEE
Confidence 5556667889999999999999999988542 22344555566666676532 7899999884
No 80
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=26.88 E-value=55 Score=25.61 Aligned_cols=27 Identities=22% Similarity=0.422 Sum_probs=24.2
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeE
Q 026237 57 VKVNASHVRPGNVIEKSGKMYQVIDAE 83 (241)
Q Consensus 57 ~~i~a~dirkG~~I~~dG~py~V~~~~ 83 (241)
..+...||..|..|.+.|..+.|++.+
T Consensus 67 ~~y~~~Dl~vG~~v~i~gr~f~I~d~D 93 (104)
T smart00676 67 EYYHASDLNVGTTINVFGRQFRIYDCD 93 (104)
T ss_pred CccCHHHcCCCCEEEEeCEEEEEEECC
Confidence 457789999999999999999999875
No 81
>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=26.18 E-value=50 Score=24.99 Aligned_cols=18 Identities=22% Similarity=0.261 Sum_probs=14.7
Q ss_pred cccCCCEEEEECCCCcee
Q 026237 222 YLEIGEEIFINPQDDSYI 239 (241)
Q Consensus 222 FI~~Gd~I~V~T~~g~Yv 239 (241)
=|+.||.|+|.+..|+..
T Consensus 48 gi~~Gd~V~v~~~~G~~~ 65 (116)
T cd02790 48 GIEDGEKVRVSSRRGSVE 65 (116)
T ss_pred CCCCCCEEEEEcCCEEEE
Confidence 468899999999988753
No 82
>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=26.00 E-value=1.6e+02 Score=23.04 Aligned_cols=49 Identities=14% Similarity=0.072 Sum_probs=26.9
Q ss_pred EEEEEEeCCEEEEEeCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCC
Q 026237 127 FTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 183 (241)
Q Consensus 127 ~qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~L~eg~~v~v~~~dg~~i~v~lP 183 (241)
++|-|.||..+. ++.-+.+...+.....+.|.+|+|.+.-++|=...++
T Consensus 65 v~y~~~~G~~~~--------~~~~~~~~~~~~~~~~~~G~~V~V~Y~P~~P~~~~l~ 113 (148)
T PF12158_consen 65 VEYTYQDGRTYS--------RFYSGSDNFGSYWPKYPIGDTVTVYYNPNNPEEARLE 113 (148)
T ss_pred EEEEECCCcEEE--------EeccCCcccccCCccCCCcCEEEEEECCcCCCeEEEe
Confidence 677777664444 1111111133333346789999998877776554433
No 83
>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=25.96 E-value=45 Score=25.47 Aligned_cols=17 Identities=12% Similarity=0.094 Sum_probs=14.2
Q ss_pred cccCCCEEEEECCCCce
Q 026237 222 YLEIGEEIFINPQDDSY 238 (241)
Q Consensus 222 FI~~Gd~I~V~T~~g~Y 238 (241)
=|+.||+|+|.++.|+-
T Consensus 44 gI~dGd~V~v~s~~G~i 60 (112)
T cd02787 44 GLKAGDRVDLESAFGDG 60 (112)
T ss_pred CCCCCCEEEEEecCCCC
Confidence 46689999999999873
No 84
>KOG0267 consensus Microtubule severing protein katanin p80 subunit B (contains WD40 repeats) [Cell cycle control, cell division, chromosome partitioning]
Probab=25.50 E-value=1.2e+02 Score=31.87 Aligned_cols=151 Identities=19% Similarity=0.217 Sum_probs=94.7
Q ss_pred EEcCCCC-CccEEEECCeEEEEEEeEEecCCC----CCeEEEEEEeeCCCCCeEEEEeCCC-CcEEeeeEEeeEEEEEEE
Q 026237 59 VNASHVR-PGNVIEKSGKMYQVIDAEHKQRGR----GGAMMQMELRDIDTGNKVSLRFGTE-EAVERVFVEDKSFTCLYT 132 (241)
Q Consensus 59 i~a~dir-kG~~I~~dG~py~V~~~~h~KpGK----G~A~vriklknL~TG~k~e~tf~s~-dkve~v~ve~k~~qylY~ 132 (241)
..+.|+| +|-.-.++|.++.|--..+..-|| |+--.-+++=|+.-|+.. ..|++. .++..+ |-.+..||-.
T Consensus 136 ~~iwD~Rk~Gc~~~~~s~~~vv~~l~lsP~Gr~v~~g~ed~tvki~d~~agk~~-~ef~~~e~~v~sl--e~hp~e~Lla 212 (825)
T KOG0267|consen 136 LKIWDIRKKGCSHTYKSHTRVVDVLRLSPDGRWVASGGEDNTVKIWDLTAGKLS-KEFKSHEGKVQSL--EFHPLEVLLA 212 (825)
T ss_pred ceehhhhccCceeeecCCcceeEEEeecCCCceeeccCCcceeeeecccccccc-ccccccccccccc--ccCchhhhhc
Confidence 4578888 888889999777666666666676 444467888888888776 566632 244433 3556667766
Q ss_pred eC---CEEEEEeCCCccccccCchhhhhh--hhccCCCCEEE----EEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCC
Q 026237 133 EN---DTAFVIESETFEQLEVPLDVFGKA--GAYLQEGMKVW----LQLYDGRALSGSIPKRVACTIKEIHASTKGPTVT 203 (241)
Q Consensus 133 Dg---d~~~FMD~EtyEQi~v~~~~lgd~--~~~L~eg~~v~----v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~ 203 (241)
-| ...-|-|.||||-|.=.+....+. ..|=.+|+.+. +.+-+.+. --.+|..++..+||-..|+++.
T Consensus 213 ~Gs~d~tv~f~dletfe~I~s~~~~~~~v~~~~fn~~~~~~~~G~q~sl~~~~~----a~ah~~~~~~~~Ep~~~~~~vq 288 (825)
T KOG0267|consen 213 PGSSDRTVRFWDLETFEVISSGKPETDGVRSLAFNPDGKIVLSGEQISLSESRT----ASAHVRKTLARWEPEMDGAVVQ 288 (825)
T ss_pred cCCCCceeeeeccceeEEeeccCCccCCceeeeecCCceeeecCchhhhhhhhc----ccceeeccccccccccccceee
Confidence 55 246799999998876544332222 12333333221 11111222 2388999999999999998864
Q ss_pred -CCceeEEeecCcE
Q 026237 204 -PRYRRALLDNGVT 216 (241)
Q Consensus 204 -~~~K~A~LetG~~ 216 (241)
+..|+..+.-|..
T Consensus 289 s~~~~ek~v~v~~d 302 (825)
T KOG0267|consen 289 SNSHKEKVVAVGRD 302 (825)
T ss_pred ecCCcccccccccC
Confidence 5677776655543
No 85
>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=25.34 E-value=50 Score=25.15 Aligned_cols=18 Identities=11% Similarity=0.095 Sum_probs=15.0
Q ss_pred cccCCCEEEEECCCCcee
Q 026237 222 YLEIGEEIFINPQDDSYI 239 (241)
Q Consensus 222 FI~~Gd~I~V~T~~g~Yv 239 (241)
=|+.||.|+|.++.|+..
T Consensus 44 gi~~Gd~V~v~s~~G~~~ 61 (116)
T cd02786 44 GIADGDLVVVFNDRGSVT 61 (116)
T ss_pred CCCCCCEEEEEcCCeEEE
Confidence 467899999999999764
No 86
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=25.28 E-value=1e+02 Score=27.54 Aligned_cols=52 Identities=13% Similarity=0.204 Sum_probs=32.2
Q ss_pred ECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecCcEEEccccccCCCEEEEECCCCcee
Q 026237 173 YDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYI 239 (241)
Q Consensus 173 ~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Yv 239 (241)
+.|..+..+-|-+|.=.|.=.+|.- ..--|-+. -|-+.|++|+|.||+|.-|
T Consensus 122 ~pgtivk~EaPlhvsk~VmLvdp~d----------~q~te~~w-----r~~e~GekVRvstrSG~iI 173 (236)
T KOG1708|consen 122 EPGTIVKSEAPLHVSKQVMLVDPED----------DQPTEVEW-----RFTEDGEKVRVSTRSGRII 173 (236)
T ss_pred CCceEEeecCCceecceeEEECccc----------cCCceeeE-----EEcCCCcEEEEEecccccc
Confidence 4677777888887766666666531 11111122 2567788999999888643
No 87
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=25.07 E-value=1.4e+02 Score=27.70 Aligned_cols=31 Identities=13% Similarity=0.289 Sum_probs=16.4
Q ss_pred EeCCCCcEEeeeEEe--eEEEEEEEeCCEEEEEe
Q 026237 110 RFGTEEAVERVFVED--KSFTCLYTENDTAFVIE 141 (241)
Q Consensus 110 tf~s~dkve~v~ve~--k~~qylY~Dgd~~~FMD 141 (241)
+|+.| -++++.+++ ..|..+|.....|.+.-
T Consensus 78 ~~PvG-lMDVIsI~kt~e~yRvl~D~kGrf~l~~ 110 (273)
T PTZ00223 78 KYPAG-FMDVVEIPKTGDRFRILYDVKGRFALVK 110 (273)
T ss_pred CCCCc-eeEEEEEcCCCCeEEEEECCCCcEEEEE
Confidence 44433 345555533 55666676655555543
No 88
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=25.03 E-value=94 Score=23.03 Aligned_cols=67 Identities=13% Similarity=0.309 Sum_probs=43.5
Q ss_pred CCeEEEEEEeeCCCCCeEEEEeCCCCcEEee--------eEEeeEEEEEEEeCCEEEEEeCCCccccccCchhhhhhhhc
Q 026237 90 GGAMMQMELRDIDTGNKVSLRFGTEEAVERV--------FVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAY 161 (241)
Q Consensus 90 G~A~vriklknL~TG~k~e~tf~s~dkve~v--------~ve~k~~qylY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~~ 161 (241)
-..++.+++++. +|+.+....+.+++++.+ .+......|+| +|. .+.|.+|-+++.
T Consensus 8 ~~~~i~I~v~~~-~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f-~G~--~L~~~~T~~~l~------------ 71 (87)
T cd01763 8 ISEHINLKVKGQ-DGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLF-DGQ--RIRDNQTPDDLG------------ 71 (87)
T ss_pred CCCeEEEEEECC-CCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEE-CCe--ECCCCCCHHHcC------------
Confidence 467899999999 899999999999977643 34445566666 343 334444444433
Q ss_pred cCCCCEEEEEE
Q 026237 162 LQEGMKVWLQL 172 (241)
Q Consensus 162 L~eg~~v~v~~ 172 (241)
|++|..+.+.+
T Consensus 72 m~d~d~I~v~l 82 (87)
T cd01763 72 MEDGDEIEVML 82 (87)
T ss_pred CCCCCEEEEEE
Confidence 45566665543
No 89
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=24.49 E-value=1.1e+02 Score=26.21 Aligned_cols=69 Identities=20% Similarity=0.211 Sum_probs=41.3
Q ss_pred hccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCce-eEE--------eecCcEEEccccc------c
Q 026237 160 AYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYR-RAL--------LDNGVTVMVPSYL------E 224 (241)
Q Consensus 160 ~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K-~A~--------LetG~~v~VP~FI------~ 224 (241)
...+...+..+.+.||+|+-++.-..+.-+| ++--..+..+ .++ +-||+-|+.|-.+ +
T Consensus 36 ~v~~~~~~~~ii~vdG~pl~f~~~~~~iPTl-------~~l~~~~~~~~~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik 108 (161)
T COG2016 36 EVAKCDDKFEIILVDGEPLLFQRDDRLIPTL-------RLLLKLPPGKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIK 108 (161)
T ss_pred EEEecCCcEEEEEECCEEEEEEeCCeechhh-------HHHHhCCCCccEEEEcCccHhhhcCCCceeccceeecCCCcc
Confidence 3445666888889999999887665443222 2211111111 333 3477789999764 5
Q ss_pred CCCEEEEECCC
Q 026237 225 IGEEIFINPQD 235 (241)
Q Consensus 225 ~Gd~I~V~T~~ 235 (241)
.||.|.|.-+.
T Consensus 109 ~Gd~VvV~~e~ 119 (161)
T COG2016 109 EGDIVVVVDEK 119 (161)
T ss_pred CCCEEEEEEcC
Confidence 68887776544
No 90
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=24.43 E-value=2.9e+02 Score=20.72 Aligned_cols=31 Identities=16% Similarity=0.201 Sum_probs=19.3
Q ss_pred CceeEEeecCcEEEc---------cccccCCCEEEEECCC
Q 026237 205 RYRRALLDNGVTVMV---------PSYLEIGEEIFINPQD 235 (241)
Q Consensus 205 ~~K~A~LetG~~v~V---------P~FI~~Gd~I~V~T~~ 235 (241)
..=.+.||||.++.. =.-|.+||+|.|.+..
T Consensus 20 ~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~ 59 (75)
T COG0361 20 GRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSP 59 (75)
T ss_pred CEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecc
Confidence 344566777766532 2345678888887654
No 91
>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=24.11 E-value=2.4e+02 Score=19.27 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=32.0
Q ss_pred EEeCCEEEEEeCCC-ccccccCchhhhhh-hhccCCCCEEEEEEECC
Q 026237 131 YTENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYDG 175 (241)
Q Consensus 131 Y~Dgd~~~FMD~Et-yEQi~v~~~~lgd~-~~~L~eg~~v~v~~~dg 175 (241)
|.+...|=|+..+. -+++-+....+... ..-|++|+.|......+
T Consensus 8 ~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 8 FDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred EECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 44445676777665 67888887777655 56789999999877654
No 92
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=23.78 E-value=1.9e+02 Score=23.65 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=21.0
Q ss_pred ecCcEEEcccc------ccCCCEEEEECCC-Ccee
Q 026237 212 DNGVTVMVPSY------LEIGEEIFINPQD-DSYI 239 (241)
Q Consensus 212 etG~~v~VP~F------I~~Gd~I~V~T~~-g~Yv 239 (241)
.+|+.++.|-. ++.||.|.|-++. |+.+
T Consensus 83 ~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~v 117 (150)
T TIGR03684 83 INGADIMAPGIVSADPSIKEGDIVFVVDETHRKPL 117 (150)
T ss_pred hcCcccccCceecCCCCCCCCCEEEEEECCCCeEE
Confidence 36888877744 5679999998876 7765
No 93
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=23.62 E-value=88 Score=21.81 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=19.7
Q ss_pred EEccccccCCCEEEEECCCCceecC
Q 026237 217 VMVPSYLEIGEEIFINPQDDSYIGR 241 (241)
Q Consensus 217 v~VP~FI~~Gd~I~V~T~~g~Yv~R 241 (241)
+.++.-++.||.|.|-+++|+++.+
T Consensus 25 ~~~~~~~~~g~~V~v~~~~g~~vg~ 49 (77)
T smart00359 25 VRVDGGIKEGDVVVIVDEKGEPLGI 49 (77)
T ss_pred EEEeCCcCCCCEEEEEcCCCCEEEE
Confidence 4555557789999999999998764
No 94
>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=23.13 E-value=52 Score=24.71 Aligned_cols=17 Identities=18% Similarity=0.135 Sum_probs=13.9
Q ss_pred cccCCCEEEEECCCCce
Q 026237 222 YLEIGEEIFINPQDDSY 238 (241)
Q Consensus 222 FI~~Gd~I~V~T~~g~Y 238 (241)
=|+.||+|+|.++.|+-
T Consensus 42 Gi~~Gd~V~v~s~~G~i 58 (96)
T cd02788 42 GLADGDLVEFSLGDGTL 58 (96)
T ss_pred CCCCCCEEEEEECCeEE
Confidence 35789999999998874
No 95
>KOG0272 consensus U4/U6 small nuclear ribonucleoprotein Prp4 (contains WD40 repeats) [RNA processing and modification]
Probab=22.97 E-value=1.9e+02 Score=28.51 Aligned_cols=65 Identities=14% Similarity=0.164 Sum_probs=43.7
Q ss_pred CCCCCCCCcCccccCcccceecceeeEEcCCCCCccEEE-ECCeEEEEEEeEEecCCC----CCeEEEEEEeeCCCCCeE
Q 026237 33 CHRSSGDRDTCLLRFPWSATQQRAVKVNASHVRPGNVIE-KSGKMYQVIDAEHKQRGR----GGAMMQMELRDIDTGNKV 107 (241)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~R~~~i~a~dirkG~~I~-~dG~py~V~~~~h~KpGK----G~A~vriklknL~TG~k~ 107 (241)
|+-.||++++.=+++--..| |+|.|..|+ .+|..-.|..+.++.-|- |++-..+|+=+|.-.+-+
T Consensus 311 f~~DGSL~~tGGlD~~~RvW----------DlRtgr~im~L~gH~k~I~~V~fsPNGy~lATgs~Dnt~kVWDLR~r~~l 380 (459)
T KOG0272|consen 311 FQPDGSLAATGGLDSLGRVW----------DLRTGRCIMFLAGHIKEILSVAFSPNGYHLATGSSDNTCKVWDLRMRSEL 380 (459)
T ss_pred ecCCCceeeccCccchhhee----------ecccCcEEEEecccccceeeEeECCCceEEeecCCCCcEEEeeecccccc
Confidence 44578888888777644332 667777775 477777888888887664 566666666666655543
No 96
>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=22.96 E-value=61 Score=27.67 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=14.4
Q ss_pred ccCCCEEEEECCCCce
Q 026237 223 LEIGEEIFINPQDDSY 238 (241)
Q Consensus 223 I~~Gd~I~V~T~~g~Y 238 (241)
+++||.|.|.+.+|+|
T Consensus 109 L~~GD~I~v~~~~g~~ 124 (174)
T TIGR03784 109 LRPGDVIRLQTPDGQW 124 (174)
T ss_pred CCCCCEEEEEECCCeE
Confidence 7889999999999975
No 97
>PF11871 DUF3391: Domain of unknown function (DUF3391); InterPro: IPR021812 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 122 to 139 amino acids in length. This domain is found associated with PF01966 from PFAM.
Probab=22.66 E-value=41 Score=26.19 Aligned_cols=21 Identities=14% Similarity=0.482 Sum_probs=15.8
Q ss_pred eeEEcCCCCCccEEEECCeEE
Q 026237 57 VKVNASHVRPGNVIEKSGKMY 77 (241)
Q Consensus 57 ~~i~a~dirkG~~I~~dG~py 77 (241)
.+|.+++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 368899999999997644333
No 98
>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=22.63 E-value=69 Score=25.24 Aligned_cols=38 Identities=21% Similarity=0.347 Sum_probs=28.0
Q ss_pred EeCCCeEEEEEEEecCCCCCcCCCC--CceeEEeecCcEEEc
Q 026237 180 GSIPKRVACTIKEIHASTKGPTVTP--RYRRALLDNGVTVMV 219 (241)
Q Consensus 180 v~lP~~V~l~V~et~p~~kGdT~~~--~~K~A~LetG~~v~V 219 (241)
..||.. --|.|.+|.+|-+.-++ +-|.++|.||.++-|
T Consensus 68 aalppR--sFVaeiDPvFkks~yGg~yg~k~~~l~t~sklav 107 (110)
T PF05836_consen 68 AALPPR--SFVAEIDPVFKKSSYGGSYGEKKVTLNTGSKLAV 107 (110)
T ss_pred hcCCch--hhhhhcChhhcccccCccccceeEEEecCCeEEE
Confidence 445553 23678899999887654 448999999998876
No 99
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=22.57 E-value=76 Score=25.56 Aligned_cols=27 Identities=19% Similarity=0.267 Sum_probs=16.0
Q ss_pred eEEcCCCCCccEEE-ECCeEEEEEEeEE
Q 026237 58 KVNASHVRPGNVIE-KSGKMYQVIDAEH 84 (241)
Q Consensus 58 ~i~a~dirkG~~I~-~dG~py~V~~~~h 84 (241)
-+.|.+|++|+.|. .+|++..|.++..
T Consensus 71 Wv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 71 WVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp -EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 56799999999985 5888877777654
No 100
>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=22.24 E-value=1.2e+02 Score=27.59 Aligned_cols=40 Identities=20% Similarity=0.267 Sum_probs=28.6
Q ss_pred CcCCCCCceeEEeecCcE---EEccccccCCCEEEEECCCCce
Q 026237 199 GPTVTPRYRRALLDNGVT---VMVPSYLEIGEEIFINPQDDSY 238 (241)
Q Consensus 199 GdT~~~~~K~A~LetG~~---v~VP~FI~~Gd~I~V~T~~g~Y 238 (241)
|+...-.+|...-++|.. |.||.|-++|..|.||.+|-+.
T Consensus 210 Gnq~~f~t~~~~~~~~~~v~lv~vP~Fs~t~~~vlvdl~tLe~ 252 (257)
T cd07387 210 GNQPKFGTKLVEGEEGQRVLLVCVPSFSKTGTAVLVNLRTLEC 252 (257)
T ss_pred CCCcceeeeEEEcCCCCeEEEEEeCCcCcCCEEEEEECCcCcE
Confidence 444444455555554544 6889999999999999998654
No 101
>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=22.22 E-value=74 Score=23.65 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=12.7
Q ss_pred EEEccccccCCCEEEEE
Q 026237 216 TVMVPSYLEIGEEIFIN 232 (241)
Q Consensus 216 ~v~VP~FI~~Gd~I~V~ 232 (241)
...+|.|+..||.+.|.
T Consensus 59 ~~~lP~~l~~GD~~~i~ 75 (92)
T PF00207_consen 59 QLNLPRSLRRGDQIQIP 75 (92)
T ss_dssp EEE--SEEETTSEEEEE
T ss_pred EcCCCcEEecCCEEEEE
Confidence 45779999999999875
No 102
>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]
Probab=21.80 E-value=2.8e+02 Score=30.93 Aligned_cols=56 Identities=9% Similarity=0.037 Sum_probs=37.7
Q ss_pred hhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEecCCCCCcCCCCCceeEEeecC
Q 026237 159 GAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNG 214 (241)
Q Consensus 159 ~~~L~eg~~v~v~~~dg~~i~v~lP~~V~l~V~et~p~~kGdT~~~~~K~A~LetG 214 (241)
..||.+++.+-+.+-.|.+|-+.+-....-.|..++.|+.-..=++.-+-.-|-||
T Consensus 74 ~~fl~d~~~i~v~~~~G~iilvd~et~~~eivg~vd~GI~aaswS~Dee~l~liT~ 129 (1265)
T KOG1920|consen 74 VQFLADTNSICVITALGDIILVDPETLELEIVGNVDNGISAASWSPDEELLALITG 129 (1265)
T ss_pred EEEecccceEEEEecCCcEEEEcccccceeeeeeccCceEEEeecCCCcEEEEEeC
Confidence 47889999988888899999885544444445556666655554555555556555
No 103
>PF02182 SAD_SRA: SAD/SRA domain; InterPro: IPR003105 This domain has been termed SRA-YDG, for SET and Ring finger Associated, and because of the conserved YDG motif within the domain. Further characteristics of the domain are the conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The domain is mainly found in plants and animals and in bacteria. In animals, this domain is associated with the Np95-like ring finger protein and the related gene product Np97, which contains PHD and RING FINGER domains and which is an important determinant in cell cycle progression. Np95 is a chromatin-associated ubiquitin ligase, binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. The SRA-YDG domain contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo [, ]. In plants the SRA-YDG domain is associated with the SET domain, found in a family of histone methyl transferases, and in bacteria it is found in association with HNH, a non-specific nuclease motif [, ].; GO: 0042393 histone binding; PDB: 2ZO1_B 2ZKD_A 2ZO0_B 2ZKF_A 2ZKG_B 3FDE_A 3F8I_A 2ZO2_B 3F8J_B 2ZKE_A ....
Probab=21.62 E-value=1.9e+02 Score=24.20 Aligned_cols=36 Identities=17% Similarity=0.371 Sum_probs=25.8
Q ss_pred CCccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeC
Q 026237 65 RPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDI 101 (241)
Q Consensus 65 rkG~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL 101 (241)
.++-.+.||| +|+|+++...+-..|....|.+|+-+
T Consensus 117 p~~g~yrYDG-LY~V~~~w~~~g~~G~~v~kF~L~R~ 152 (155)
T PF02182_consen 117 PKGGIYRYDG-LYKVVKYWREKGKSGFKVFKFKLVRL 152 (155)
T ss_dssp -SSS-EEEEE-EEEEEEEEEEE-TTSSEEEEEEEEE-
T ss_pred CcCCCEEeCc-EEEEEEEEEEeCCCCcEEEEEEEEEC
Confidence 3455688888 99999998876545788889988755
No 104
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=21.49 E-value=3.1e+02 Score=19.52 Aligned_cols=40 Identities=13% Similarity=0.137 Sum_probs=26.9
Q ss_pred EEcCCCCCccEEEECCeE-EEEEEeEEecCCCCCeEEEEEEe
Q 026237 59 VNASHVRPGNVIEKSGKM-YQVIDAEHKQRGRGGAMMQMELR 99 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~p-y~V~~~~h~KpGKG~A~vriklk 99 (241)
-++.-|.+|+-|.+.|-. =+|.+++. .+..+++.+.+++.
T Consensus 10 ~~~~GL~~gs~V~~~Gv~VG~V~~i~l-~~~~~~v~v~~~i~ 50 (81)
T PF02470_consen 10 DDAGGLSVGSPVRYRGVEVGKVTSIEL-DPDGNRVRVTLRID 50 (81)
T ss_pred CCcCCCCCcCEEEECCEEEEEEEEEEE-cCCCCEEEEEEEEc
Confidence 356888999999999954 47777765 44444555555554
No 105
>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=21.27 E-value=69 Score=24.50 Aligned_cols=18 Identities=6% Similarity=0.233 Sum_probs=14.5
Q ss_pred cccCCCEEEEECCCCcee
Q 026237 222 YLEIGEEIFINPQDDSYI 239 (241)
Q Consensus 222 FI~~Gd~I~V~T~~g~Yv 239 (241)
=|+.||.|+|.+..|+..
T Consensus 48 gi~~Gd~V~v~s~~G~~~ 65 (122)
T cd02792 48 GIKNGDMVWVSSPRGKIK 65 (122)
T ss_pred CCCCCCEEEEEcCCceEE
Confidence 357899999999988753
No 106
>COG3535 Uncharacterized conserved protein [Function unknown]
Probab=21.24 E-value=7.4e+02 Score=23.83 Aligned_cols=89 Identities=19% Similarity=0.234 Sum_probs=61.2
Q ss_pred ccEEEECCeEEEEEEeEEecCCCCCeEEEEEEeeCCCCCeEEEEeCCCCcEEeeeEEeeEEEEEEEeCCEEEEEeCCCcc
Q 026237 67 GNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFE 146 (241)
Q Consensus 67 G~~I~~dG~py~V~~~~h~KpGKG~A~vriklknL~TG~k~e~tf~s~dkve~v~ve~k~~qylY~Dgd~~~FMD~EtyE 146 (241)
|-.+.++|+.--|... ...|--.+.++++-.+-..|+..+..|.- +--+-+++-|++-.-.|-.++.|.+|.-
T Consensus 236 ~g~~lf~Gki~dV~R~--t~gGF~~G~~~I~G~~~~~g~t~~i~FqN-----Efl~a~~~G~~l~~~PDLI~lld~~Tg~ 308 (357)
T COG3535 236 GGKILFKGKIVDVKRE--TRGGFARGRVTIDGLEEYRGSTLEIAFQN-----EFLVAEKDGKILATTPDLIVLLDLNTGL 308 (357)
T ss_pred CcEEEEccEEEEEEEe--eecceeeeeEEEechhhcCCceEEEEEEe-----eeeEEecCCcEEEecCceEEEEecCCCC
Confidence 4677788876555433 23343344556666777789999999962 2234458999999999999999999876
Q ss_pred ccccCchhhhhhhhccCCCCEEEEE
Q 026237 147 QLEVPLDVFGKAGAYLQEGMKVWLQ 171 (241)
Q Consensus 147 Qi~v~~~~lgd~~~~L~eg~~v~v~ 171 (241)
-+.= + =|+.|+.|.|.
T Consensus 309 piTT--e-------~lkyG~rV~V~ 324 (357)
T COG3535 309 PITT--E-------SLKYGQRVVVI 324 (357)
T ss_pred ccch--H-------HhhcCcEEEEE
Confidence 5542 2 25778877764
No 107
>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=21.06 E-value=63 Score=24.87 Aligned_cols=19 Identities=16% Similarity=0.055 Sum_probs=15.3
Q ss_pred ccccCCCEEEEECCCCcee
Q 026237 221 SYLEIGEEIFINPQDDSYI 239 (241)
Q Consensus 221 ~FI~~Gd~I~V~T~~g~Yv 239 (241)
+=|+.||.|+|.+..|+..
T Consensus 45 lgi~~Gd~V~v~s~~G~i~ 63 (115)
T cd02779 45 EGLKNGDLVEVYNDYGSTT 63 (115)
T ss_pred cCCCCCCEEEEEeCCEEEE
Confidence 4577899999999988764
No 108
>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=20.94 E-value=70 Score=24.75 Aligned_cols=16 Identities=6% Similarity=0.289 Sum_probs=13.2
Q ss_pred ccCCCEEEEECCCCce
Q 026237 223 LEIGEEIFINPQDDSY 238 (241)
Q Consensus 223 I~~Gd~I~V~T~~g~Y 238 (241)
|+.||.|+|.+..|+-
T Consensus 44 i~~Gd~V~v~s~~g~i 59 (121)
T cd02794 44 IKDGDRVLVFNDRGKV 59 (121)
T ss_pred CCCCCEEEEEcCCceE
Confidence 5679999999998864
No 109
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.90 E-value=1.2e+02 Score=25.47 Aligned_cols=28 Identities=29% Similarity=0.438 Sum_probs=24.8
Q ss_pred ceeeEEcCCCCCccEEEECCeEEEEEEe
Q 026237 55 RAVKVNASHVRPGNVIEKSGKMYQVIDA 82 (241)
Q Consensus 55 R~~~i~a~dirkG~~I~~dG~py~V~~~ 82 (241)
.-+.++...++-|++|..+++.|+|.-.
T Consensus 97 ~~v~VNst~l~dG~iVki~~~yYrV~~n 124 (149)
T PF11694_consen 97 EEVYVNSTALTDGMIVKIGDKYYRVIFN 124 (149)
T ss_pred heEEEecccccCCeEEEECCccEEEEEc
Confidence 3478999999999999999999999765
No 110
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.81 E-value=5.4e+02 Score=23.42 Aligned_cols=25 Identities=12% Similarity=0.299 Sum_probs=20.6
Q ss_pred EEEEeeCCCCCeEEEEeCCCCcEEe
Q 026237 95 QMELRDIDTGNKVSLRFGTEEAVER 119 (241)
Q Consensus 95 riklknL~TG~k~e~tf~s~dkve~ 119 (241)
.++++|+.+|+.+.-+..+...|+.
T Consensus 235 ~IrVrN~~SgkvV~a~V~~~g~V~v 259 (261)
T PRK06804 235 LIKVKNLSSGRVVTATVDGSGRVRM 259 (261)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEE
Confidence 7888999999999888877776653
No 111
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=20.75 E-value=1e+02 Score=22.93 Aligned_cols=25 Identities=20% Similarity=0.445 Sum_probs=20.2
Q ss_pred EEcCCCCCccEEEECCeEEEEEEeE
Q 026237 59 VNASHVRPGNVIEKSGKMYQVIDAE 83 (241)
Q Consensus 59 i~a~dirkG~~I~~dG~py~V~~~~ 83 (241)
+.=..+.+||.|+++|..|......
T Consensus 11 v~Rq~V~PG~~v~~~grty~ASAN~ 35 (73)
T PRK11354 11 IPRQCVTPGDYVLHEGRTYIASANN 35 (73)
T ss_pred ecccccCCceEEEEcCcEEEEEech
Confidence 4445789999999999999987653
No 112
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=20.51 E-value=73 Score=26.19 Aligned_cols=19 Identities=5% Similarity=0.130 Sum_probs=15.3
Q ss_pred ccccCCCEEEEECCCCcee
Q 026237 221 SYLEIGEEIFINPQDDSYI 239 (241)
Q Consensus 221 ~FI~~Gd~I~V~T~~g~Yv 239 (241)
+=+++||.|+|.++-|+-+
T Consensus 43 Lgv~EGD~VkVkse~GeVV 61 (128)
T COG1153 43 LGVSEGDKVKVKSEFGEVV 61 (128)
T ss_pred hCCCcCCeEEEEecCccEE
Confidence 4578899999999988743
No 113
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=20.36 E-value=3.3e+02 Score=20.08 Aligned_cols=30 Identities=10% Similarity=0.201 Sum_probs=20.2
Q ss_pred CceeEEeecCcEEEc--c------ccccCCCEEEEECC
Q 026237 205 RYRRALLDNGVTVMV--P------SYLEIGEEIFINPQ 234 (241)
Q Consensus 205 ~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~ 234 (241)
..=.+.++||.++.+ | ..|+.||.|.|...
T Consensus 13 ~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~ 50 (77)
T cd05793 13 GRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPW 50 (77)
T ss_pred CEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEec
Confidence 445666777766543 3 56888999998754
No 114
>COG3173 Predicted aminoglycoside phosphotransferase [General function prediction only]
Probab=20.17 E-value=1.3e+02 Score=28.32 Aligned_cols=34 Identities=35% Similarity=0.456 Sum_probs=28.1
Q ss_pred ceeeEEcCCCCCccEEEECCeEEEEEEeEEecCCC
Q 026237 55 RAVKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR 89 (241)
Q Consensus 55 R~~~i~a~dirkG~~I~~dG~py~V~~~~h~KpGK 89 (241)
+.+.+ =+|++.||+|..++++-=|++++-+..|-
T Consensus 197 ~~~lv-HGD~~~gNlii~~~~~~gVlDwe~~~lGD 230 (321)
T COG3173 197 PPVLV-HGDYRPGNLIIDPGRPTGVLDWELATLGD 230 (321)
T ss_pred Cceee-eCCcccCCEEEeCCCeeEEEeccccccCC
Confidence 33444 49999999999999999999999877664
No 115
>PF05354 Phage_attach: Phage Head-Tail Attachment; InterPro: IPR008018 This entry is represented by Bacteriophage lambda, FII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The phage head-tail attachment protein is required for the joining of phage heads and tails at the last step of morphogenesis [].; GO: 0042963 phage assembly, 0019028 viral capsid; PDB: 2KX4_A 1K0H_A.
Probab=20.10 E-value=73 Score=25.89 Aligned_cols=35 Identities=20% Similarity=0.303 Sum_probs=21.4
Q ss_pred EcCCCCCccEEEECCeEEEEEEeEEecCCCCCeEEEEEE
Q 026237 60 NASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMEL 98 (241)
Q Consensus 60 ~a~dirkG~~I~~dG~py~V~~~~h~KpGKG~A~vrikl 98 (241)
.+..|++++.+.+.|++|.|.+ +.|- |....++.|
T Consensus 71 dv~~L~r~DtL~I~g~~y~Vd~---v~pD-~~G~t~I~L 105 (117)
T PF05354_consen 71 DVSGLKRRDTLTIGGESYWVDR---VGPD-GGGSTRIWL 105 (117)
T ss_dssp CCCTS-TT-EEEETTTEEEBS------SS-SSS-CCEEB
T ss_pred HhhhhhcCCeEEECCEEEEEEe---eccC-CCccEEEEe
Confidence 4789999999999999999955 4443 333444444
Done!