Query 027318
Match_columns 225
No_of_seqs 161 out of 1147
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 08:08:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027318.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027318hhsearch_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 9.6E-68 2.1E-72 448.8 22.3 167 58-224 1-167 (185)
2 PRK14578 elongation factor P; 100.0 1.7E-65 3.6E-70 436.0 22.5 167 58-224 1-169 (187)
3 PRK04542 elongation factor P; 100.0 2.8E-65 6E-70 435.1 21.9 167 58-224 1-170 (189)
4 TIGR02178 yeiP elongation fact 100.0 6.1E-64 1.3E-68 426.0 22.4 164 61-224 2-168 (186)
5 PRK00529 elongation factor P; 100.0 5.9E-63 1.3E-67 420.1 22.4 167 58-224 1-167 (186)
6 TIGR00038 efp translation elon 100.0 9E-63 1.9E-67 418.4 22.1 166 59-224 1-166 (184)
7 COG0231 Efp Translation elonga 100.0 9.8E-47 2.1E-51 305.0 16.6 130 57-186 2-131 (131)
8 TIGR00037 eIF_5A translation i 100.0 4.2E-38 9E-43 254.3 15.9 121 57-179 5-126 (130)
9 PRK03999 translation initiatio 100.0 2.6E-36 5.6E-41 243.6 16.0 117 58-176 5-122 (129)
10 PLN03107 eukaryotic translatio 100.0 5.6E-33 1.2E-37 231.3 16.5 121 57-177 19-148 (159)
11 cd04470 S1_EF-P_repeat_1 S1_EF 99.9 1.1E-23 2.3E-28 149.8 7.3 61 123-183 1-61 (61)
12 PF08207 EFP_N: Elongation fac 99.9 1.4E-21 3E-26 137.6 8.5 58 60-117 1-58 (58)
13 PF01132 EFP: Elongation facto 99.8 2.9E-21 6.4E-26 134.5 6.5 55 124-178 1-55 (55)
14 PTZ00328 eukaryotic initiation 99.8 4.1E-20 8.9E-25 154.3 13.7 118 57-174 21-150 (166)
15 cd04463 S1_EF_like S1_EF_like: 99.7 1.1E-17 2.4E-22 115.8 5.9 55 125-180 1-55 (55)
16 smart00841 Elong-fact-P_C Elon 99.7 3.3E-17 7.2E-22 114.7 4.1 39 186-224 1-39 (56)
17 cd05794 S1_EF-P_repeat_2 S1_EF 99.7 4.3E-17 9.2E-22 114.2 4.3 39 186-224 1-39 (56)
18 PF09285 Elong-fact-P_C: Elong 99.7 1.1E-16 2.5E-21 112.0 5.0 39 186-224 1-39 (56)
19 KOG3271 Translation initiation 99.6 1.5E-15 3.3E-20 123.7 9.5 111 60-170 22-136 (156)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.7 3.6E-08 7.7E-13 69.4 5.6 54 122-177 1-54 (57)
21 COG1499 NMD3 NMD protein affec 98.3 7.3E-06 1.6E-10 76.5 11.9 115 51-181 233-352 (355)
22 PF01287 eIF-5a: Eukaryotic el 97.2 0.0018 3.9E-08 47.2 6.8 56 121-177 1-63 (69)
23 cd04468 S1_eIF5A S1_eIF5A: Euk 93.6 0.27 5.9E-06 35.9 5.9 51 122-172 1-54 (69)
24 cd04469 S1_Hex1 S1_Hex1: Hex1, 85.3 4.3 9.2E-05 30.1 6.4 52 125-176 3-61 (75)
25 PF08605 Rad9_Rad53_bind: Fung 79.5 4.5 9.7E-05 33.0 5.1 40 59-98 55-104 (131)
26 PF02941 FeThRed_A: Ferredoxin 72.1 1.9 4.2E-05 31.3 1.0 26 164-189 30-56 (67)
27 PRK05338 rplS 50S ribosomal pr 66.9 32 0.0007 27.5 7.1 66 59-125 14-88 (116)
28 PF01245 Ribosomal_L19: Riboso 64.0 33 0.00071 27.2 6.6 68 58-126 13-89 (113)
29 TIGR01024 rplS_bact ribosomal 59.4 46 0.00099 26.5 6.7 66 58-124 13-87 (113)
30 CHL00084 rpl19 ribosomal prote 59.4 54 0.0012 26.3 7.1 67 58-125 17-92 (117)
31 PF13785 DUF4178: Domain of un 55.2 99 0.0022 24.1 12.0 23 64-86 1-23 (140)
32 PF13275 S4_2: S4 domain; PDB: 53.5 15 0.00033 26.4 2.8 19 62-80 47-65 (65)
33 PF13509 S1_2: S1 domain; PDB: 50.2 20 0.00044 24.8 3.0 37 136-175 15-51 (61)
34 PF06988 NifT: NifT/FixU prote 50.1 85 0.0019 22.7 6.2 51 166-222 1-52 (64)
35 PRK11507 ribosome-associated p 48.1 20 0.00044 26.3 2.8 20 61-80 50-69 (70)
36 PF05521 Phage_H_T_join: Phage 45.4 42 0.00091 23.8 4.2 24 63-86 62-85 (95)
37 PF04014 Antitoxin-MazE: Antid 44.9 35 0.00076 22.2 3.4 31 146-178 7-37 (47)
38 PF09262 PEX-1N: Peroxisome bi 43.8 20 0.00042 26.8 2.2 63 143-219 12-78 (80)
39 PRK13480 3'-5' exoribonuclease 42.8 69 0.0015 29.7 6.1 54 58-115 2-55 (314)
40 TIGR03170 flgA_cterm flagella 42.4 67 0.0015 24.7 5.2 24 95-118 98-121 (122)
41 PRK10377 PTS system glucitol/s 40.6 38 0.00083 27.1 3.6 23 61-83 49-71 (120)
42 PRK07018 flgA flagellar basal 40.0 79 0.0017 27.7 5.8 25 95-119 209-233 (235)
43 PF13856 Gifsy-2: ATP-binding 39.5 62 0.0013 24.2 4.4 31 55-85 54-87 (95)
44 PF03829 PTSIIA_gutA: PTS syst 38.6 37 0.00081 27.0 3.2 23 61-83 49-71 (117)
45 TIGR00849 gutA PTS system, glu 38.2 45 0.00097 26.8 3.6 22 62-83 50-71 (121)
46 COG0335 RplS Ribosomal protein 36.5 2.2E+02 0.0049 22.8 7.6 66 59-125 16-90 (115)
47 PF05836 Chorion_S16: Chorion 35.9 31 0.00066 27.0 2.2 39 180-220 68-108 (110)
48 COG4043 Preprotein translocase 35.8 53 0.0011 26.0 3.5 23 61-83 31-55 (111)
49 PF01079 Hint: Hint module; I 35.6 78 0.0017 27.7 5.0 45 55-99 23-72 (217)
50 PF10665 Minor_capsid_1: Minor 35.1 1E+02 0.0022 24.4 5.1 26 61-86 74-99 (114)
51 COG2501 S4-like RNA binding pr 35.0 43 0.00093 24.8 2.8 21 62-82 51-71 (73)
52 KOG1698 Mitochondrial/chloropl 34.6 1.3E+02 0.0028 26.4 6.0 76 58-142 91-179 (201)
53 PF12158 DUF3592: Protein of u 33.9 1E+02 0.0022 23.9 5.0 49 127-183 65-113 (148)
54 TIGR01646 vgr_GE Rhs element V 33.5 1.8E+02 0.004 27.8 7.7 119 59-177 276-423 (483)
55 smart00466 SRA SET and RING fi 33.4 1.6E+02 0.0034 24.7 6.3 39 61-101 113-152 (155)
56 cd04458 CSP_CDS Cold-Shock Pro 33.2 1.4E+02 0.003 20.3 5.1 45 131-175 8-54 (65)
57 PF11948 DUF3465: Protein of u 33.2 43 0.00093 27.5 2.8 32 58-89 80-116 (131)
58 PF09465 LBR_tudor: Lamin-B re 32.1 1.5E+02 0.0033 20.8 5.0 38 101-138 6-48 (55)
59 COG1326 Uncharacterized archae 31.8 2.4E+02 0.0052 24.7 7.3 22 62-83 73-94 (201)
60 PF02182 SAD_SRA: SAD/SRA doma 31.8 99 0.0022 25.6 4.8 36 65-101 117-152 (155)
61 PF13144 SAF_2: SAF-like 31.6 1.3E+02 0.0029 25.0 5.7 24 95-118 172-195 (196)
62 PF02839 CBM_5_12: Carbohydrat 31.1 55 0.0012 20.5 2.5 19 64-82 10-28 (41)
63 KOG1999 RNA polymerase II tran 30.8 1.2E+02 0.0026 32.5 6.1 70 100-172 397-470 (1024)
64 smart00676 DM10 Domains in hyp 27.3 42 0.00091 26.0 1.7 27 57-83 67-93 (104)
65 PF11694 DUF3290: Protein of u 26.6 79 0.0017 26.2 3.3 28 56-83 98-125 (149)
66 PF05354 Phage_attach: Phage H 26.3 49 0.0011 26.6 2.0 37 59-99 70-106 (117)
67 PRK15463 cold shock-like prote 26.3 1.1E+02 0.0023 22.0 3.6 44 132-175 13-58 (70)
68 PF11871 DUF3391: Domain of un 25.0 38 0.00083 26.1 1.2 21 57-77 3-23 (128)
69 COG0090 RplB Ribosomal protein 24.7 1.9E+02 0.004 26.6 5.6 12 104-115 169-180 (275)
70 PF06905 FAIM1: Fas apoptotic 24.4 3E+02 0.0064 23.6 6.5 6 138-143 112-117 (177)
71 COG3173 Predicted aminoglycosi 24.4 82 0.0018 29.3 3.4 36 53-89 195-230 (321)
72 PRK06005 flgA flagellar basal 23.9 2E+02 0.0043 23.9 5.3 24 95-118 133-156 (160)
73 KOG0267 Microtubule severing p 23.9 1.4E+02 0.003 31.1 5.1 150 58-214 135-300 (825)
74 TIGR03361 VI_Rhs_Vgr type VI s 23.7 5.3E+02 0.011 24.9 9.0 115 59-177 284-434 (513)
75 cd01771 Faf1_UBX Faf1 UBX doma 23.6 75 0.0016 23.3 2.4 47 88-142 1-49 (80)
76 PRK11835 hypothetical protein; 23.4 75 0.0016 25.4 2.5 33 61-97 65-98 (114)
77 smart00166 UBX Domain present 23.2 68 0.0015 23.0 2.1 48 90-142 3-50 (80)
78 PF13989 YejG: YejG-like prote 22.6 75 0.0016 25.1 2.3 34 62-101 63-97 (106)
79 cd01767 UBX UBX (ubiquitin reg 21.7 57 0.0012 23.2 1.5 25 93-120 4-28 (77)
80 PF02470 MCE: mce related prot 21.6 3E+02 0.0065 19.4 5.6 40 59-99 10-50 (81)
81 COG3350 Uncharacterized conser 21.5 28 0.00061 24.2 -0.2 37 117-153 7-44 (53)
82 PF14306 PUA_2: PUA-like domai 21.2 49 0.0011 27.7 1.1 43 138-180 55-111 (160)
83 PRK11354 kil FtsZ inhibitor pr 21.0 1.3E+02 0.0027 22.3 3.1 26 57-82 9-34 (73)
84 PRK10354 RNA chaperone/anti-te 20.6 2.4E+02 0.0052 20.0 4.5 43 133-175 14-58 (70)
85 PF06605 Prophage_tail: Propha 20.5 1.5E+02 0.0032 26.7 4.2 38 62-100 26-63 (327)
86 TIGR01363 strep_his_triad stre 20.5 44 0.00094 31.3 0.7 21 61-81 118-138 (348)
87 KOG0938 Adaptor complexes medi 20.5 5.4E+02 0.012 24.8 7.9 123 95-220 206-338 (446)
No 1
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=9.6e-68 Score=448.81 Aligned_cols=167 Identities=20% Similarity=0.392 Sum_probs=165.6
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCeE
Q 027318 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~~ 137 (225)
|+++||||+|++|++||+||+|++++|+|||||+|++|+|||||.||+++++||+++|++|.|+++++++||||.||+.|
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 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEE
Q 027318 138 FVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTV 217 (225)
Q Consensus 138 ~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG~~i 217 (225)
+|||+|||||++|+++.+||+.+||+|||+|+|.+|+|+||+|+||++|+|+|+||||++|||||++++|||+||||++|
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 Eccccee
Q 027318 218 MVSEICK 224 (225)
Q Consensus 218 ~VP~FI~ 224 (225)
+||+||+
T Consensus 161 ~VP~FI~ 167 (185)
T PRK12426 161 LVPPFVE 167 (185)
T ss_pred EeCCccc
Confidence 9999997
No 2
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=1.7e-65 Score=436.01 Aligned_cols=167 Identities=25% Similarity=0.415 Sum_probs=164.3
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEeeCCCC--CeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCC
Q 027318 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRG--GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG--~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd 135 (225)
|+++||||+|++|++||+||+|++++|+|||+| +|++|+|||||.||+++|++|+++|++|.|+++++++||||.||+
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 eEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCc
Q 027318 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGV 215 (225)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG~ 215 (225)
.|+|||+|||||++|+++.+|++.+||+|||+|.|.+|||+||+|+||++|+|+|++|+|++||||+++++|||+||||+
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 EEEccccee
Q 027318 216 TVMVSEICK 224 (225)
Q Consensus 216 ~i~VP~FI~ 224 (225)
+|+||+||+
T Consensus 161 ~v~VP~FI~ 169 (187)
T PRK14578 161 RLQVPPYLE 169 (187)
T ss_pred EEEeCCccc
Confidence 999999997
No 3
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=2.8e-65 Score=435.14 Aligned_cols=167 Identities=26% Similarity=0.441 Sum_probs=164.2
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEeeC-CCC-CeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCC
Q 027318 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQR-GRG-GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py~Vv~~~h~Kp-GKG-~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd 135 (225)
|+++||||+|++|++||+||+|++++|+|| ||| +|++|+|||||.||+++++||+++|++|.|++++++|||||.||+
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 789999999999999999999999999999 798 559999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCccccccCchhhhhhhhccCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecC
Q 027318 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNG 214 (225)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~-V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG 214 (225)
.|+|||+|||||++|+++.+|++.+||+|||+ |+|.+|+|+||+|+||++|+|+|++|||++||||+++++|||+||||
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 cEEEccccee
Q 027318 215 VTVMVSEICK 224 (225)
Q Consensus 215 ~~i~VP~FI~ 224 (225)
++|+||+||+
T Consensus 161 ~~v~VP~FI~ 170 (189)
T PRK04542 161 LVIQVPEYIS 170 (189)
T ss_pred CEEEeCCccc
Confidence 9999999997
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=6.1e-64 Score=425.99 Aligned_cols=164 Identities=23% Similarity=0.415 Sum_probs=160.9
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEeeCCCCCe--EeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCeEE
Q 027318 61 ASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGA--MMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A--~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~~~ 138 (225)
+||||+|++|++||+||+|++++|+|||+|+| ++|+|||||.||+++++||+++|++|.|+++++++||||.||+.|+
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 79999999999999999999999999987666 8999999999999999999999999999999999999999999999
Q ss_pred EecCCCccccccCchhhhhhhhccCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEE
Q 027318 139 VIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTV 217 (225)
Q Consensus 139 FMD~EtyEQi~v~~~~lgd~~~yL~eg~~-V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG~~i 217 (225)
|||+|||||++|+++.+|++.+||+|||+ |+|.+|||+||+|+||++|+|+|++|+|++||||+++++|||+||||++|
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 Eccccee
Q 027318 218 MVSEICK 224 (225)
Q Consensus 218 ~VP~FI~ 224 (225)
+||+||+
T Consensus 162 ~VP~FI~ 168 (186)
T TIGR02178 162 QVPEYIT 168 (186)
T ss_pred EeCCeec
Confidence 9999997
No 5
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=5.9e-63 Score=420.06 Aligned_cols=167 Identities=34% Similarity=0.565 Sum_probs=165.5
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCeE
Q 027318 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~~ 137 (225)
|+++|+||+|++|++||+||+|++++|+|||||+|++|+++|||.||++++++|+++|+++.+.++++++||||.||+.|
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 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEE
Q 027318 138 FVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTV 217 (225)
Q Consensus 138 ~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG~~i 217 (225)
+|||+|||||++|+++.+|++.+||+|||+|+|.+|||+||+|+||++|+|+|+||+|++||||+++++|||+||||++|
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 Eccccee
Q 027318 218 MVSEICK 224 (225)
Q Consensus 218 ~VP~FI~ 224 (225)
+||+||+
T Consensus 161 ~VP~fI~ 167 (186)
T PRK00529 161 QVPLFIN 167 (186)
T ss_pred EeCCeec
Confidence 9999997
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=9e-63 Score=418.43 Aligned_cols=166 Identities=31% Similarity=0.576 Sum_probs=164.2
Q ss_pred EEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCeEE
Q 027318 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (225)
Q Consensus 59 i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~~~ 138 (225)
+++|+||+|++|++||+||+|++++|+|||||+|++|+++|||.||++++++|+++|+++.+.++++++||||.||+.|+
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 EecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEE
Q 027318 139 VIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVM 218 (225)
Q Consensus 139 FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG~~i~ 218 (225)
|||+|||||++|+++.++++.+||+|||+|.|.+|+|+||+|+||++|+|+|+||+|++|||||++++|||+||||++|+
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 ccccee
Q 027318 219 VSEICK 224 (225)
Q Consensus 219 VP~FI~ 224 (225)
||+||+
T Consensus 161 VP~fi~ 166 (184)
T TIGR00038 161 VPLFIE 166 (184)
T ss_pred eCCccc
Confidence 999997
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=9.8e-47 Score=305.01 Aligned_cols=130 Identities=35% Similarity=0.619 Sum_probs=128.3
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCe
Q 027318 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~ 136 (225)
+|+++++||+|++|++||+||+|++++|+|||||+|++|+++|||+||++++.+|+++|++|.|.++++++||||.||+.
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCCCeE
Q 027318 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRV 186 (225)
Q Consensus 137 ~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP~~V 186 (225)
|+|||+|||||++++++.+||+.+||+|||+|+|++|+|++++|+||++|
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=4.2e-38 Score=254.33 Aligned_cols=121 Identities=21% Similarity=0.313 Sum_probs=115.3
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCC
Q 027318 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGK-G~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd 135 (225)
..+++++||+|++|++||+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++|++|.|.++++++||||.||+
T Consensus 5 ~~~~~~~irkG~~i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~qylY~dg~ 84 (130)
T TIGR00037 5 KQVQVSALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQVLAIMGG 84 (130)
T ss_pred eeccHHHccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEEEEEecCC
Confidence 347899999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEE
Q 027318 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALS 179 (225)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~ 179 (225)
.|+|||+|||||++|+.+. ++.+||+||++|.|+-..|+..-
T Consensus 85 ~~~fMd~etyeq~~i~~~~--~~~~~Lke~~~V~v~~~~g~~~~ 126 (130)
T TIGR00037 85 MVQLMDLDTYETDELPIPE--ELGDSLEPGFEVEYIEAMGQEKI 126 (130)
T ss_pred EEEEEcCCCcEEEEecCCh--hHHHHhhcCCEEEEEecCCeEEE
Confidence 9999999999999999985 88999999999999998887643
No 9
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=2.6e-36 Score=243.60 Aligned_cols=117 Identities=23% Similarity=0.341 Sum_probs=111.9
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCe
Q 027318 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGK-G~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~ 136 (225)
-+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||.||++++.+|+++|++|.+.++++++||||.||+.
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 46799999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCE
Q 027318 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 176 (225)
Q Consensus 137 ~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~ 176 (225)
|+|||+|||||++|+++ +++..||+||++|.|+---|+
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 899999999999998765554
No 10
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=5.6e-33 Score=231.30 Aligned_cols=121 Identities=18% Similarity=0.286 Sum_probs=107.4
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCC
Q 027318 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGK-G~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd 135 (225)
+|+++++||+|++|++||+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++++++.|+++++++||||.||+
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 499999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred eE-EEecC--CCccccccCc---hhhhhhhhccCCCCEEEEEEEC--CEE
Q 027318 136 TA-FVIES--ETFEQLEVPL---DVFGKAGAYLQEGMKVWLQLYD--GRA 177 (225)
Q Consensus 136 ~~-~FMD~--EtyEQi~v~~---~~lgd~~~yL~eg~~V~v~~~~--g~~ 177 (225)
.| +|||+ ++|||+.||+ ++.........+|.++.|.+|. |+.
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 3333344455779985555554 554
No 11
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.90 E-value=1.1e-23 Score=149.81 Aligned_cols=61 Identities=33% Similarity=0.758 Sum_probs=59.7
Q ss_pred eeeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCC
Q 027318 123 EDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 183 (225)
Q Consensus 123 e~k~~qyLY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP 183 (225)
+++++||||.||+.|+|||+|||||++|+++.+|++.+||+|||+|+|.+|+|+||+|+||
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 5789999999999999999999999999999999999999999999999999999999999
No 12
>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=99.86 E-value=1.4e-21 Score=137.60 Aligned_cols=58 Identities=40% Similarity=0.708 Sum_probs=53.6
Q ss_pred EcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCCcE
Q 027318 60 NASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAV 117 (225)
Q Consensus 60 ~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~dkv 117 (225)
+|+|||+|++|++||+||+|++++|++||||+|+||+|||||.||+++|++|+++|+|
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 4899999999999999999999999999999999999999999999999999999986
No 13
>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=99.84 E-value=2.9e-21 Score=134.54 Aligned_cols=55 Identities=36% Similarity=0.748 Sum_probs=49.9
Q ss_pred eeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEE
Q 027318 124 DKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 178 (225)
Q Consensus 124 ~k~~qyLY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i 178 (225)
+|++||||.||+.|+|||++||||++|+++.+|++.+||+||++|+|.+|+|+||
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 14
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=99.84 E-value=4.1e-20 Score=154.30 Aligned_cols=118 Identities=19% Similarity=0.297 Sum_probs=103.9
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCC
Q 027318 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGK-G~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd 135 (225)
.-++++.||+|.+|.++|+||+|++++.+|||| |+|++++...+|+||++.+...++.+++++|.++|+++|++..++|
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 557799999999999999999999999999999 9999999999999999999999999999999999999999999886
Q ss_pred -------eEEEecCCCccccccCc---hhhhh-hhhccCCCCEEEEEEEC
Q 027318 136 -------TAFVIESETFEQLEVPL---DVFGK-AGAYLQEGMKVWLQLYD 174 (225)
Q Consensus 136 -------~~~FMD~EtyEQi~v~~---~~lgd-~~~yL~eg~~V~v~~~~ 174 (225)
...+||.+.|+-..|+. +.++. ....+.+|.+|.|.+|.
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 23332 35567999999987775
No 15
>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=99.72 E-value=1.1e-17 Score=115.76 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=51.5
Q ss_pred eEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEE
Q 027318 125 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSG 180 (225)
Q Consensus 125 k~~qyLY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v 180 (225)
|++||||.||+.|+|||+|||||++++++.. +..+||+||++|.|.+|+|+||++
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 5799999999999999999999999999974 589999999999999999999874
No 16
>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=99.67 E-value=3.3e-17 Score=114.73 Aligned_cols=39 Identities=26% Similarity=0.332 Sum_probs=37.9
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEccccee
Q 027318 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVSEICK 224 (225)
Q Consensus 186 V~l~V~etep~~KGdTat~~~K~A~LeTG~~i~VP~FI~ 224 (225)
|+|+|+||||++||||+++++|||+||||++|+||+||+
T Consensus 1 V~l~V~etep~vkG~T~~~~~K~A~letG~~i~VP~FI~ 39 (56)
T smart00841 1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFIN 39 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCccc
Confidence 589999999999999999999999999999999999997
No 17
>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=99.67 E-value=4.3e-17 Score=114.17 Aligned_cols=39 Identities=28% Similarity=0.369 Sum_probs=37.9
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEccccee
Q 027318 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVSEICK 224 (225)
Q Consensus 186 V~l~V~etep~~KGdTat~~~K~A~LeTG~~i~VP~FI~ 224 (225)
|+|+|+||+|++||||+++++|||+||||++|+||+||+
T Consensus 1 v~l~V~etep~~kG~T~~~~~K~A~letG~~i~VP~FI~ 39 (56)
T cd05794 1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIK 39 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCeec
Confidence 589999999999999999999999999999999999997
No 18
>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=99.66 E-value=1.1e-16 Score=112.02 Aligned_cols=39 Identities=26% Similarity=0.429 Sum_probs=34.5
Q ss_pred EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEccccee
Q 027318 186 VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVSEICK 224 (225)
Q Consensus 186 V~l~V~etep~~KGdTat~~~K~A~LeTG~~i~VP~FI~ 224 (225)
|+|+|+||+|++||||+++++|||+||||++|+||+||+
T Consensus 1 V~l~V~etep~~kg~t~~~~~K~A~letG~~i~VP~FI~ 39 (56)
T PF09285_consen 1 VELEVVETEPAVKGDTASSSYKPATLETGAEIQVPLFIE 39 (56)
T ss_dssp EEEEEEEE-SSSTTSSSSTTEEEEEETTS-EEEEETT--
T ss_pred CEEEEEECCCCccCcccCCCccEEEEcCCCEEEccceec
Confidence 789999999999999999999999999999999999997
No 19
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.63 E-value=1.5e-15 Score=123.72 Aligned_cols=111 Identities=17% Similarity=0.277 Sum_probs=98.9
Q ss_pred EcCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCeEE
Q 027318 60 NASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (225)
Q Consensus 60 ~a~dikkG~~I~~dG~py~Vv~~~h~KpGK-G~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~~~ 138 (225)
+++.||++-.|.++|+||+|++++.+|.|| |+|++.+..++|+||++.|.-+++.++++++.++|.++|.+-++++...
T Consensus 22 q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn~dVp~vkr~~yqLidIsd~~~s 101 (156)
T KOG3271|consen 22 QCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDGYLS 101 (156)
T ss_pred hhhheeeCCEEEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCccccCccccceeEEEEecCCeEE
Confidence 478899999999999999999999999999 9999999999999999999999999999999999999999999999889
Q ss_pred EecC--CCccccccCchhhhhhhh-ccCCCCEEEE
Q 027318 139 VIES--ETFEQLEVPLDVFGKAGA-YLQEGMKVWL 170 (225)
Q Consensus 139 FMD~--EtyEQi~v~~~~lgd~~~-yL~eg~~V~v 170 (225)
|||+ ++-+++.+|...+++.+. -..+|..+.|
T Consensus 102 l~t~sG~~kdDlklp~~el~~~i~~~~e~g~dl~v 136 (156)
T KOG3271|consen 102 LMTDSGETKDDLKLPEGELGNQIRQGFEEGKDLLV 136 (156)
T ss_pred EEcCCCCcchhccCcchhHHHHHHHhhcCCCcEEE
Confidence 9998 578889999877777643 3455544333
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=98.70 E-value=3.6e-08 Score=69.44 Aligned_cols=54 Identities=26% Similarity=0.319 Sum_probs=46.6
Q ss_pred EeeeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEE
Q 027318 122 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRA 177 (225)
Q Consensus 122 ve~k~~qyLY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~ 177 (225)
++||.+|.++.+|+..++||+||||.++++.. .+...-+++|.+|.++...|+.
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 2333458999999998887874
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=98.31 E-value=7.3e-06 Score=76.52 Aligned_cols=115 Identities=21% Similarity=0.292 Sum_probs=92.6
Q ss_pred eeeec-eeeEEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCCcEE--ee--eEeee
Q 027318 51 ATQQR-AVKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVE--RV--FVEDK 125 (225)
Q Consensus 51 ~~~~R-~~~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~dkve--~~--~ve~k 125 (225)
-..|| .+.+.+.++++|++|.++|..+.++... |+ .+.++|+.||...+.+|.....-+ .+ .-+-+
T Consensus 233 k~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~~~----~~-----~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~ 303 (355)
T COG1499 233 KRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVRSI----GK-----GIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLK 303 (355)
T ss_pred ceEEEEEEEEECCCCCCCCEEEECCCeEEEEEEe----cC-----ceEEEecccCCccccChhhcccCcceeeeccccce
Confidence 34677 5789999999999999999777766655 56 589999999998888876555544 22 22336
Q ss_pred EEEEEEEeCCeEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEe
Q 027318 126 SFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 181 (225)
Q Consensus 126 ~~qyLY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~ 181 (225)
.+.++..+++..+|||++|||-+++..+ =|.+|.+|.+..++|....++
T Consensus 304 ~~~vvs~~~~~~~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~ 352 (355)
T COG1499 304 KAVVVSRDPSAIQVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE 352 (355)
T ss_pred EEEEEecCCCceEEEecceEEEEeccCC-------CCCCCCEEEEEEEeceEEeec
Confidence 8888999999999999999999999876 368999999999999876553
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=97.18 E-value=0.0018 Score=47.20 Aligned_cols=56 Identities=23% Similarity=0.298 Sum_probs=40.0
Q ss_pred eEeeeEEEEEEEeCC-eEEEecCCCccccc---cCchhhhhh-hhccCCCCE--EEEEEECCEE
Q 027318 121 FVEDKSFTCLYTEND-TAFVIESETFEQLE---VPLDVFGKA-GAYLQEGMK--VWLQLYDGRA 177 (225)
Q Consensus 121 ~ve~k~~qyLY~Dgd-~~~FMD~EtyEQi~---v~~~~lgd~-~~yL~eg~~--V~v~~~~g~~ 177 (225)
.|+|++||.+..++| ...+|| |+||..+ +|...+++. ..-+.+|.+ |+|+-.-|+-
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 7766666 886556554 345689988 5555555553
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=93.56 E-value=0.27 Score=35.90 Aligned_cols=51 Identities=22% Similarity=0.357 Sum_probs=38.7
Q ss_pred EeeeEEEEEEEeCCeEEEecC--CCccccccCchhhhhhhh-ccCCCCEEEEEE
Q 027318 122 VEDKSFTCLYTENDTAFVIES--ETFEQLEVPLDVFGKAGA-YLQEGMKVWLQL 172 (225)
Q Consensus 122 ve~k~~qyLY~Dgd~~~FMD~--EtyEQi~v~~~~lgd~~~-yL~eg~~V~v~~ 172 (225)
|.|++||.+..+++...+||. ++-|++.||.+.++..+. -..+|..+.|..
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 589999999988887643 235566555444
No 24
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=85.30 E-value=4.3 Score=30.14 Aligned_cols=52 Identities=15% Similarity=0.165 Sum_probs=35.8
Q ss_pred eEEEEEEEeCCeEEEecC--CCccccccC-chhhhhhhh-ccCCCC-E--EEEEEECCE
Q 027318 125 KSFTCLYTENDTAFVIES--ETFEQLEVP-LDVFGKAGA-YLQEGM-K--VWLQLYDGR 176 (225)
Q Consensus 125 k~~qyLY~Dgd~~~FMD~--EtyEQi~v~-~~~lgd~~~-yL~eg~-~--V~v~~~~g~ 176 (225)
++||.+.+|++...+||. ++-|++.|| ...++..+. -..+|. + |.|+-.-|+
T Consensus 3 ~eYqLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk~~v~VtVlsAmGe 61 (75)
T cd04469 3 KQYRVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGRGSVRVLVVNDGGR 61 (75)
T ss_pred eEEEEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCCCcEEEEEEccCCe
Confidence 689999997667789976 578999999 666666543 226666 4 444444444
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=79.55 E-value=4.5 Score=33.00 Aligned_cols=40 Identities=25% Similarity=0.376 Sum_probs=31.8
Q ss_pred EEcCCCCCccEEEECCe--EEEEEEeEEee--CC------CCCeEeeEEE
Q 027318 59 VNASHVRPGNVIEKSGK--MYQVIDAEHKQ--RG------RGGAMMQMEL 98 (225)
Q Consensus 59 i~a~dikkG~~I~~dG~--py~Vv~~~h~K--pG------KG~A~vrikl 98 (225)
+..=|||.|+.|..++. +|.|+.+++.- +. ||.+.|.+|=
T Consensus 55 v~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk~ 104 (131)
T PF08605_consen 55 VKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLKR 104 (131)
T ss_pred EeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEEE
Confidence 45568999999999998 99999999872 23 5777777743
No 26
>PF02941 FeThRed_A: Ferredoxin thioredoxin reductase variable alpha chain; InterPro: IPR004207 Ferredoxin thioredoxin reductase is a [4FE-4S] protein which plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit a and subunit b. Subunit a is the variable subunit, and b is the catalytic chain. This family is the alpha chain.; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0015979 photosynthesis, 0009536 plastid; PDB: 2PUK_B 2PVO_B 2PVG_B 1DJ7_B 2PVD_B 2PU9_B 2PUO_B.
Probab=72.12 E-value=1.9 Score=31.34 Aligned_cols=26 Identities=27% Similarity=0.460 Sum_probs=14.8
Q ss_pred CCCEEEEE-EECCEEEEEeCCCeEEEE
Q 027318 164 EGMKVWLQ-LYDGRALSGSIPKRVACT 189 (225)
Q Consensus 164 eg~~V~v~-~~~g~~i~v~lP~~V~l~ 189 (225)
||..+++. .|+|+|||.+||-.|.+.
T Consensus 30 EGev~~~v~~wkGr~iSanlP~~V~F~ 56 (67)
T PF02941_consen 30 EGEVKQIVTDWKGRPISANLPVKVQFD 56 (67)
T ss_dssp EEEEEEE-SEETTEE---SS-EEEEET
T ss_pred EEEEEEEEeecCCcEecCCCcEEEEEe
Confidence 33334433 599999999999988774
No 27
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=66.88 E-value=32 Score=27.53 Aligned_cols=66 Identities=23% Similarity=0.367 Sum_probs=44.4
Q ss_pred EEcCCCCCccEEEE-----CCeEEEEEEeEEe---eCCCCCeEeeEEEeeCCCCCEEEEEecCCCc-EEeeeEeee
Q 027318 59 VNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVEDK 125 (225)
Q Consensus 59 i~a~dikkG~~I~~-----dG~py~Vv~~~h~---KpGKG~A~vriklknL~TG~kie~tf~s~dk-ve~~~ve~k 125 (225)
-+..++++||+|.. +|.-.++..++-. +.++|- .-.+.+||+..|--+|.+|+-... ++.+.+.++
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 45789999999875 5654444444432 123332 336899999999999999987553 555555554
No 28
>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=63.97 E-value=33 Score=27.24 Aligned_cols=68 Identities=22% Similarity=0.276 Sum_probs=45.5
Q ss_pred eEEcCCCCCccEEEE-----CCeEEEEEEeEEee---CCCCCeEeeEEEeeCCCCCEEEEEecCCCc-EEeeeEeeeE
Q 027318 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEHKQ---RGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVEDKS 126 (225)
Q Consensus 58 ~i~a~dikkG~~I~~-----dG~py~Vv~~~h~K---pGKG~A~vriklknL~TG~kie~tf~s~dk-ve~~~ve~k~ 126 (225)
..+..++++||+|.. +|....+..++-.- -++| .--.+.+||+..|.-+|.+|+-... ++.+.+-++.
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 457889999999864 35444444444322 2332 2336788999999999999987655 6666666654
No 29
>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=59.44 E-value=46 Score=26.54 Aligned_cols=66 Identities=23% Similarity=0.272 Sum_probs=42.9
Q ss_pred eEEcCCCCCccEEEE-----CCeEEEEEEeEEe---eCCCCCeEeeEEEeeCCCCCEEEEEecCCCc-EEeeeEee
Q 027318 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVED 124 (225)
Q Consensus 58 ~i~a~dikkG~~I~~-----dG~py~Vv~~~h~---KpGKG~A~vriklknL~TG~kie~tf~s~dk-ve~~~ve~ 124 (225)
..+..++++||+|.. +|+-.++..++-+ +.++|- --.+.+||+..|--+|.+|+-... ++.+.+-+
T Consensus 13 ~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~-~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl~ 87 (113)
T TIGR01024 13 KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGI-GETFTVRKISYGVGVERIFPLHSPNIDSIEVVR 87 (113)
T ss_pred hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCC-ceEEEEEEeccCccEEEEEEcCCCccceEEEEE
Confidence 456789999999876 4444343333321 224433 336899999999999999977553 55555544
No 30
>CHL00084 rpl19 ribosomal protein L19
Probab=59.41 E-value=54 Score=26.32 Aligned_cols=67 Identities=19% Similarity=0.230 Sum_probs=43.7
Q ss_pred eEEcCCCCCccEEEE-----CCeEEEEEEeEE---eeCCCCCeEeeEEEeeCCCCCEEEEEecCCCc-EEeeeEeee
Q 027318 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEH---KQRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVEDK 125 (225)
Q Consensus 58 ~i~a~dikkG~~I~~-----dG~py~Vv~~~h---~KpGKG~A~vriklknL~TG~kie~tf~s~dk-ve~~~ve~k 125 (225)
..+..++++||+|.. +|+-.++..++- ...|+|-. -.+.+|++..|--+|.+|+-... ++.+.+-++
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 KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLN-TTITVRKVFQGIGVERVFLLHSPKLASIEVLRR 92 (117)
T ss_pred hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCC-eeEEEEEeccCccEEEEEecCCCccceEEEEEe
Confidence 456889999999874 555333333332 12244432 35899999999999999977553 555555543
No 31
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=55.24 E-value=99 Score=24.14 Aligned_cols=23 Identities=26% Similarity=0.378 Sum_probs=20.4
Q ss_pred CCCccEEEECCeEEEEEEeEEee
Q 027318 64 VRPGNVIEKSGKMYQVIDAEHKQ 86 (225)
Q Consensus 64 ikkG~~I~~dG~py~Vv~~~h~K 86 (225)
|++|+++.++|..|.|+....-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999999887654
No 32
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=53.50 E-value=15 Score=26.43 Aligned_cols=19 Identities=42% Similarity=0.941 Sum_probs=14.0
Q ss_pred CCCCCccEEEECCeEEEEE
Q 027318 62 SHVRPGNVIEKSGKMYQVI 80 (225)
Q Consensus 62 ~dikkG~~I~~dG~py~Vv 80 (225)
..|++|++|.++|..|+|+
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 4689999999999999985
No 33
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=50.16 E-value=20 Score=24.81 Aligned_cols=37 Identities=14% Similarity=0.173 Sum_probs=22.9
Q ss_pred eEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECC
Q 027318 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDG 175 (225)
Q Consensus 136 ~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g 175 (225)
.-+|+|.+..+.+.||...+. .=+++|.+|.|..|.|
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 345567777788888877553 2389999999999854
No 34
>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=50.08 E-value=85 Score=22.66 Aligned_cols=51 Identities=20% Similarity=0.274 Sum_probs=28.7
Q ss_pred CEEEEEEECCEEEEEeCCCe-EEEEEEEeCCCCCCccCCCCceeEEEecCcEEEcccc
Q 027318 166 MKVWLQLYDGRALSGSIPKR-VACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVSEI 222 (225)
Q Consensus 166 ~~V~v~~~~g~~i~v~lP~~-V~l~V~etep~~KGdTat~~~K~A~LeTG~~i~VP~F 222 (225)
|.|.+..-+.--+++-+|.. ++=.|++.| +...-.+-++|.||.+..+|..
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 34444444444788888865 678888886 2233457899999999999864
No 35
>PRK11507 ribosome-associated protein; Provisional
Probab=48.09 E-value=20 Score=26.27 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=17.4
Q ss_pred cCCCCCccEEEECCeEEEEE
Q 027318 61 ASHVRPGNVIEKSGKMYQVI 80 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv 80 (225)
.-.|++|++|.++|.-++|+
T Consensus 50 gkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 50 RCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred CCCCCCCCEEEECCEEEEEe
Confidence 35789999999999998886
No 36
>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=45.39 E-value=42 Score=23.78 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=18.6
Q ss_pred CCCCccEEEECCeEEEEEEeEEee
Q 027318 63 HVRPGNVIEKSGKMYQVIDAEHKQ 86 (225)
Q Consensus 63 dikkG~~I~~dG~py~Vv~~~h~K 86 (225)
+|..++.|.++|+.|.|..+....
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 37
>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=44.91 E-value=35 Score=22.23 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=22.8
Q ss_pred cccccCchhhhhhhhccCCCCEEEEEEECCEEE
Q 027318 146 EQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 178 (225)
Q Consensus 146 EQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i 178 (225)
-|+.||++..... -|++|++|.+...+|..|
T Consensus 7 ~~v~iPk~~~~~l--~l~~Gd~v~i~~~~~g~i 37 (47)
T PF04014_consen 7 GQVTIPKEIREKL--GLKPGDEVEIEVEGDGKI 37 (47)
T ss_dssp SEEEE-HHHHHHT--TSSTTTEEEEEEETTSEE
T ss_pred ceEECCHHHHHHc--CCCCCCEEEEEEeCCCEE
Confidence 4788898876432 589999999999988333
No 38
>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=43.82 E-value=20 Score=26.77 Aligned_cols=63 Identities=16% Similarity=0.168 Sum_probs=32.7
Q ss_pred CCccccccCchhhhhh----hhccCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCceeEEEecCcEEE
Q 027318 143 ETFEQLEVPLDVFGKA----GAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVM 218 (225)
Q Consensus 143 EtyEQi~v~~~~lgd~----~~yL~eg~~V~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTat~~~K~A~LeTG~~i~ 218 (225)
+++|-+++..+.+++. ...+.+|+.+.++..++ ..+.++|+.++|....+ -.|.|++|.+|-
T Consensus 12 dDWEIlEl~A~~lE~~lL~QiRvv~~~~~~~v~v~~~--------~~i~~~V~~i~p~~~~~------~~~~L~~~TEv~ 77 (80)
T PF09262_consen 12 DDWEILELHAEFLEDQLLSQIRVVFPGQVFPVWVSQN--------TVIKFKVVSIEPSSSAE------GCARLSPDTEVI 77 (80)
T ss_dssp HHHHHHHHS-SSHHHHHHHH--EE-TT-EEEEESSSS---------EEEEEEEEEES--S---------SEE--TT-EEE
T ss_pred cHHHHHHHhHHHHHHHHHHhheeecCCCEEEEEEcCC--------eEEEEEEEEccCCCCce------eEEEeCCCcEEE
Confidence 3467777777666543 33445555555554333 34578899999853222 379999999987
Q ss_pred c
Q 027318 219 V 219 (225)
Q Consensus 219 V 219 (225)
|
T Consensus 78 V 78 (80)
T PF09262_consen 78 V 78 (80)
T ss_dssp E
T ss_pred E
Confidence 6
No 39
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=42.84 E-value=69 Score=29.68 Aligned_cols=54 Identities=11% Similarity=0.244 Sum_probs=42.4
Q ss_pred eEEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCC
Q 027318 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEE 115 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~d 115 (225)
|..++|++.|+.+.. +|.|.+.+-...-.|..+.++.+.| .||...-+-|...+
T Consensus 2 m~~i~~l~~g~~v~~---~~lv~~~~~~~~knG~~yl~l~l~D-~tG~I~ak~W~~~~ 55 (314)
T PRK13480 2 MKGIEELEVGEQVDH---FLLIKSATKGVASNGKPFLTLILQD-KSGDIEAKLWDVSP 55 (314)
T ss_pred cchHhhcCCCCEeeE---EEEEEEceeeecCCCCeEEEEEEEc-CCcEEEEEeCCCCh
Confidence 446889999986643 7888877765544488999999999 99999888887654
No 40
>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=42.40 E-value=67 Score=24.71 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=19.1
Q ss_pred eEEEeeCCCCCEEEEEecCCCcEE
Q 027318 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (225)
Q Consensus 95 riklknL~TG~kie~tf~s~dkve 118 (225)
.++++|+.+|+.+.-+.-+...++
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 789999999999988776655543
No 41
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=40.58 E-value=38 Score=27.12 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=20.7
Q ss_pred cCCCCCccEEEECCeEEEEEEeE
Q 027318 61 ASHVRPGNVIEKSGKMYQVIDAE 83 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv~~~ 83 (225)
..+|++|+.+.++|+-|.|..+-
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaVG 71 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAVG 71 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEEh
Confidence 46799999999999999998874
No 42
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=40.03 E-value=79 Score=27.68 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=20.7
Q ss_pred eEEEeeCCCCCEEEEEecCCCcEEe
Q 027318 95 QMELRDIDTGNKVSLRFGTEEAVER 119 (225)
Q Consensus 95 riklknL~TG~kie~tf~s~dkve~ 119 (225)
.+++||+.||+.+.-+..+...++.
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V 233 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEV 233 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEE
Confidence 7888999999999888877766654
No 43
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=39.49 E-value=62 Score=24.23 Aligned_cols=31 Identities=23% Similarity=0.319 Sum_probs=20.3
Q ss_pred ceeeEEcCC---CCCccEEEECCeEEEEEEeEEe
Q 027318 55 RAVKVNASH---VRPGNVIEKSGKMYQVIDAEHK 85 (225)
Q Consensus 55 R~~~i~a~d---ikkG~~I~~dG~py~Vv~~~h~ 85 (225)
|...+..++ .|+|+.|.+||+-|.|.+++.-
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 5699999999999999998854
No 44
>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=38.64 E-value=37 Score=27.03 Aligned_cols=23 Identities=17% Similarity=0.528 Sum_probs=15.8
Q ss_pred cCCCCCccEEEECCeEEEEEEeE
Q 027318 61 ASHVRPGNVIEKSGKMYQVIDAE 83 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv~~~ 83 (225)
..+|++|+.+.++|+.|.|..+-
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 46899999999999999998874
No 45
>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=38.17 E-value=45 Score=26.82 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=20.0
Q ss_pred CCCCCccEEEECCeEEEEEEeE
Q 027318 62 SHVRPGNVIEKSGKMYQVIDAE 83 (225)
Q Consensus 62 ~dikkG~~I~~dG~py~Vv~~~ 83 (225)
.+|++|+.+.++|+-|.|..+-
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaVG 71 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAVG 71 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEEh
Confidence 4899999999999999998874
No 46
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=36.54 E-value=2.2e+02 Score=22.82 Aligned_cols=66 Identities=26% Similarity=0.346 Sum_probs=44.6
Q ss_pred EEcCCCCCccEEE-----ECCeEEEEEEeEEee---CCCCCeEeeEEEeeCCCCCEEEEEecCCCc-EEeeeEeee
Q 027318 59 VNASHVRPGNVIE-----KSGKMYQVIDAEHKQ---RGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVEDK 125 (225)
Q Consensus 59 i~a~dikkG~~I~-----~dG~py~Vv~~~h~K---pGKG~A~vriklknL~TG~kie~tf~s~dk-ve~~~ve~k 125 (225)
-++.++++||.|. .+|.-+.+.-|+-+- .|+|- .=-..++.+..|--+|.+|+-... +|.+++-++
T Consensus 16 ~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~-~~tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~rr 90 (115)
T COG0335 16 KDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGI-SETFTVRKISYGVGVERVFPLHSPLIESIEVVRR 90 (115)
T ss_pred hhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCc-cceEEEEEeecCceEEEEeecCCCceeEEEEEec
Confidence 3477888998875 367777777776432 34332 225678888999999999987544 665665543
No 47
>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=35.94 E-value=31 Score=26.96 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=29.3
Q ss_pred EeCCCeEEEEEEEeCCCCCCccCCC--CceeEEEecCcEEEcc
Q 027318 180 GSIPKRVACTIKEIHASTKGPTVTP--RYRRALLDNGVTVMVS 220 (225)
Q Consensus 180 v~lP~~V~l~V~etep~~KGdTat~--~~K~A~LeTG~~i~VP 220 (225)
..||.. --|.|.+|.+|.+.-++ +-|.++|.||..+-|-
T Consensus 68 aalppR--sFVaeiDPvFkks~yGg~yg~k~~~l~t~sklav~ 108 (110)
T PF05836_consen 68 AALPPR--SFVAEIDPVFKKSSYGGSYGEKKVTLNTGSKLAVA 108 (110)
T ss_pred hcCCch--hhhhhcChhhcccccCccccceeEEEecCCeEEEE
Confidence 445553 23789999999888665 4589999999998763
No 48
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.79 E-value=53 Score=26.01 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=16.2
Q ss_pred cCCCCCccEEEECCe--EEEEEEeE
Q 027318 61 ASHVRPGNVIEKSGK--MYQVIDAE 83 (225)
Q Consensus 61 a~dikkG~~I~~dG~--py~Vv~~~ 83 (225)
-.+||+||+|..+|+ +..|+++.
T Consensus 31 rr~ik~GD~IiF~~~~l~v~V~~vr 55 (111)
T COG4043 31 RRQIKPGDKIIFNGDKLKVEVIDVR 55 (111)
T ss_pred hcCCCCCCEEEEcCCeeEEEEEEEe
Confidence 357899999999974 34445444
No 49
>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=35.64 E-value=78 Score=27.74 Aligned_cols=45 Identities=18% Similarity=0.237 Sum_probs=32.0
Q ss_pred ceeeEEcCCCCCccEEEE---CCe--EEEEEEeEEeeCCCCCeEeeEEEe
Q 027318 55 RAVKVNASHVRPGNVIEK---SGK--MYQVIDAEHKQRGRGGAMMQMELR 99 (225)
Q Consensus 55 R~~~i~a~dikkG~~I~~---dG~--py~Vv~~~h~KpGKG~A~vriklk 99 (225)
.+-.+.+.||+.||.|.- +|+ ...|+-+.|..|..-+-|++++..
T Consensus 23 ~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~flhr~~~~~~~F~~i~te 72 (217)
T PF01079_consen 23 DGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMFLHRDPEQRAEFVVIETE 72 (217)
T ss_dssp TS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEEEEEEEEEEEEEEEEEET
T ss_pred CCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEEeccCccccEEEEEEEcC
Confidence 366788999999998865 564 558999999999887888888754
No 50
>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=35.07 E-value=1e+02 Score=24.42 Aligned_cols=26 Identities=23% Similarity=0.270 Sum_probs=23.0
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEee
Q 027318 61 ASHVRPGNVIEKSGKMYQVIDAEHKQ 86 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv~~~h~K 86 (225)
+-+++.|+.|.+||+.|.|.++...-
T Consensus 74 ~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 74 FPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred ccccCCCCEEEECCceEEEEEEEecc
Confidence 35889999999999999999998765
No 51
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=35.00 E-value=43 Score=24.77 Aligned_cols=21 Identities=38% Similarity=0.740 Sum_probs=18.1
Q ss_pred CCCCCccEEEECCeEEEEEEe
Q 027318 62 SHVRPGNVIEKSGKMYQVIDA 82 (225)
Q Consensus 62 ~dikkG~~I~~dG~py~Vv~~ 82 (225)
-.||.|++|+++|..|.|...
T Consensus 51 kKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 51 KKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CEeecCCEEEECCEEEEEEec
Confidence 357899999999999999764
No 52
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=34.61 E-value=1.3e+02 Score=26.45 Aligned_cols=76 Identities=13% Similarity=0.256 Sum_probs=49.5
Q ss_pred eEEcCCCCCccEEEE-------CCeE--EEEEEeEEeeCCCCCeEeeEEEeeCCCCCEEEEEecCCC----cEEeeeEee
Q 027318 58 KVNASHVRPGNVIEK-------SGKM--YQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEE----AVERVFVED 124 (225)
Q Consensus 58 ~i~a~dikkG~~I~~-------dG~p--y~Vv~~~h~KpGKG~A~vriklknL~TG~kie~tf~s~d----kve~~~ve~ 124 (225)
.....++|.|+++.+ .++. +..+-++..+-|- .-++.|||+.-|.-+|..|+--+ +++++..++
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 VRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGL---NATFLLRNVIAGVGVEIVFPLYSPNIKEIKVLKLEK 167 (201)
T ss_pred cccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCC---cceEEeeehhhCceeEEEEeccCCCeeEEEEechhh
Confidence 456779999999976 2233 3334444333333 23678999999999999996543 244444454
Q ss_pred eEEEEEEEeCCeEEEecC
Q 027318 125 KSFTCLYTENDTAFVIES 142 (225)
Q Consensus 125 k~~qyLY~Dgd~~~FMD~ 142 (225)
+ .|..-|++-|.
T Consensus 168 ~------rra~LyYLRd~ 179 (201)
T KOG1698|consen 168 R------RRAKLYYLRDA 179 (201)
T ss_pred c------ccchhhhhhcc
Confidence 4 56667777775
No 53
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=33.92 E-value=1e+02 Score=23.91 Aligned_cols=49 Identities=14% Similarity=0.072 Sum_probs=27.1
Q ss_pred EEEEEEeCCeEEEecCCCccccccCchhhhhhhhccCCCCEEEEEEECCEEEEEeCC
Q 027318 127 FTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 183 (225)
Q Consensus 127 ~qyLY~Dgd~~~FMD~EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~~~g~~i~v~lP 183 (225)
++|-|.||+.+. ++.-+.+...+..+..+.|.+|+|.+.-++|=...++
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 1111111123333346788999998877776554333
No 54
>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=33.46 E-value=1.8e+02 Score=27.78 Aligned_cols=119 Identities=17% Similarity=0.114 Sum_probs=62.8
Q ss_pred EEcCCCCCccEEEECCeE-------EEEEEeEEeeCC------CCCeEeeEEEeeCCCCCEEEEE---ecCCCcEEeeeE
Q 027318 59 VNASHVRPGNVIEKSGKM-------YQVIDAEHKQRG------RGGAMMQMELRDIDTGNKVSLR---FGTEEAVERVFV 122 (225)
Q Consensus 59 i~a~dikkG~~I~~dG~p-------y~Vv~~~h~KpG------KG~A~vriklknL~TG~kie~t---f~s~dkve~~~v 122 (225)
.++-.|+.|..|.+.|.| |.|+++.|.--. -..+.++..+.-+-.+...--. .+.-.-+..+.|
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 346779999999997753 999999997321 1123455555554443321110 011111344555
Q ss_pred eeeEEEEEEEeCCe-----EEEecCCCccc-----cccCchhhhhhh--h-ccCCCCEEEEEEECCEE
Q 027318 123 EDKSFTCLYTENDT-----AFVIESETFEQ-----LEVPLDVFGKAG--A-YLQEGMKVWLQLYDGRA 177 (225)
Q Consensus 123 e~k~~qyLY~Dgd~-----~~FMD~EtyEQ-----i~v~~~~lgd~~--~-yL~eg~~V~v~~~~g~~ 177 (225)
..-.-.+.|.|+.. |.++....-++ +.+....-|+.. - .+..|++|-|.|.+|.|
T Consensus 356 ~g~~~~~~~~d~~GRvkV~f~wd~~~~~~~~~S~W~Rvaqp~AG~~~G~~f~PrvG~EVlV~F~~GDp 423 (483)
T TIGR01646 356 VGAQGEEIHTDKYGRIRVHFHWDRYGQSNDYSSCWIRVAQPWAGKNWGSLAIPRVGQEVIVGFLDGDP 423 (483)
T ss_pred ECCCCCeeccCCCCcEEEEeecCCCCCCCCCCceEEEEeccccCCCccccccCCCCCEEEEEEeCCCC
Confidence 54444477777653 22332221111 233222222211 2 34889999999998765
No 55
>smart00466 SRA SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. Domain in SET domain containing proteins and in Deinococcus radiodurans DRA1533.
Probab=33.41 E-value=1.6e+02 Score=24.68 Aligned_cols=39 Identities=26% Similarity=0.439 Sum_probs=30.5
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeEeeEEEeeC
Q 027318 61 ASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDI 101 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv~~~h~KpGK-G~A~vriklknL 101 (225)
.+..+++..+.||| +|+|+++-.. +|+ |....|.+|+-+
T Consensus 113 ~~~~~p~~gyrYDG-LY~V~~~w~e-~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 113 YSKYAPGKGYIYDG-LYRIVDYWRE-VGKSGFLVFKFKLVRI 152 (155)
T ss_pred cCCCCCCCeEEECc-EEEEEEEEEe-cCCCCcEEEEEEEEeC
Confidence 45678899999999 9999998544 455 778889998865
No 56
>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=33.24 E-value=1.4e+02 Score=20.32 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=33.1
Q ss_pred EEeCCeEEEecCCC-ccccccCchhhhhh-hhccCCCCEEEEEEECC
Q 027318 131 YTENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYDG 175 (225)
Q Consensus 131 Y~Dgd~~~FMD~Et-yEQi~v~~~~lgd~-~~yL~eg~~V~v~~~~g 175 (225)
|.+...|=|+..+. -+++-+..+.+... ..-|++|+.|......+
T Consensus 8 ~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 8 FDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred EECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 44445677777765 77888888877665 56789999988887654
No 57
>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=33.15 E-value=43 Score=27.47 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=27.0
Q ss_pred eEEcCCCCCccEEEECCeEE-----EEEEeEEeeCCC
Q 027318 58 KVNASHVRPGNVIEKSGKMY-----QVIDAEHKQRGR 89 (225)
Q Consensus 58 ~i~a~dikkG~~I~~dG~py-----~Vv~~~h~KpGK 89 (225)
+-.+.++++|+.|+..|+.+ -|+.+.|..|+.
T Consensus 80 aprip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~ 116 (131)
T PF11948_consen 80 APRIPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRG 116 (131)
T ss_pred cccCcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCC
Confidence 34567899999999999977 799999998865
No 58
>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=32.08 E-value=1.5e+02 Score=20.78 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=24.0
Q ss_pred CCCCCEEEEEecCCCcEEeeeE-----eeeEEEEEEEeCCeEE
Q 027318 101 IDTGNKVSLRFGTEEAVERVFV-----EDKSFTCLYTENDTAF 138 (225)
Q Consensus 101 L~TG~kie~tf~s~dkve~~~v-----e~k~~qyLY~Dgd~~~ 138 (225)
...|..+.-+|+.+...-++.| ..+.++.+|.||+..-
T Consensus 6 ~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~ 48 (55)
T PF09465_consen 6 FAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELE 48 (55)
T ss_dssp S-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEE
T ss_pred ccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEE
Confidence 3568889999988877644333 3578899999998743
No 59
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=31.81 E-value=2.4e+02 Score=24.74 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=20.2
Q ss_pred CCCCCccEEEECCeEEEEEEeE
Q 027318 62 SHVRPGNVIEKSGKMYQVIDAE 83 (225)
Q Consensus 62 ~dikkG~~I~~dG~py~Vv~~~ 83 (225)
-.|++|+.|+.||+-++|.+++
T Consensus 73 E~l~vGDei~vd~e~veITSIE 94 (201)
T COG1326 73 ETLKVGDEIEVDGEEVEITSIE 94 (201)
T ss_pred CeEecCCEEEEcCCEEEEEEEe
Confidence 4689999999999999999998
No 60
>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=31.76 E-value=99 Score=25.62 Aligned_cols=36 Identities=17% Similarity=0.371 Sum_probs=26.8
Q ss_pred CCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeC
Q 027318 65 RPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDI 101 (225)
Q Consensus 65 kkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL 101 (225)
.++-++.||| +|+|+++...+-..|....|.+|+-+
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 4566789999 99999999877655888889998765
No 61
>PF13144 SAF_2: SAF-like
Probab=31.60 E-value=1.3e+02 Score=25.01 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=19.3
Q ss_pred eEEEeeCCCCCEEEEEecCCCcEE
Q 027318 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (225)
Q Consensus 95 riklknL~TG~kie~tf~s~dkve 118 (225)
.++++|+.||+.+.-+.-+..+++
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 788999999999888776666554
No 62
>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=31.13 E-value=55 Score=20.49 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=14.1
Q ss_pred CCCccEEEECCeEEEEEEe
Q 027318 64 VRPGNVIEKSGKMYQVIDA 82 (225)
Q Consensus 64 ikkG~~I~~dG~py~Vv~~ 82 (225)
-..|+++.++|..|+..-.
T Consensus 10 Y~~Gd~V~~~g~~y~a~~~ 28 (41)
T PF02839_consen 10 YNAGDRVSYNGKLYQAKWW 28 (41)
T ss_dssp E-TT-EEEETTEEEEESSS
T ss_pred EcCCCEEEECCCEEEEeec
Confidence 4679999999999998443
No 63
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=30.84 E-value=1.2e+02 Score=32.51 Aligned_cols=70 Identities=20% Similarity=0.253 Sum_probs=55.3
Q ss_pred eCCCCCEEEEEecCCCcEEeeeEeeeEEEEE--EEeCCeEEEecC--CCccccccCchhhhhhhhccCCCCEEEEEE
Q 027318 100 DIDTGNKVSLRFGTEEAVERVFVEDKSFTCL--YTENDTAFVIES--ETFEQLEVPLDVFGKAGAYLQEGMKVWLQL 172 (225)
Q Consensus 100 nL~TG~kie~tf~s~dkve~~~ve~k~~qyL--Y~Dgd~~~FMD~--EtyEQi~v~~~~lgd~~~yL~eg~~V~v~~ 172 (225)
-+.+.++....|..+|.+|++.-|-+.++=. -.||+..+.|-. .--+-++++...| .+|.++|.-|.|.-
T Consensus 397 t~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eL---rKyF~~GDhVKVi~ 470 (1024)
T KOG1999|consen 397 TLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASEL---RKYFEPGDHVKVIA 470 (1024)
T ss_pred eeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhh---hhhccCCCeEEEEe
Confidence 6778888888999999999999998887654 458887777765 3456777776655 78999998888875
No 64
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=27.32 E-value=42 Score=26.00 Aligned_cols=27 Identities=22% Similarity=0.422 Sum_probs=24.2
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEeE
Q 027318 57 VKVNASHVRPGNVIEKSGKMYQVIDAE 83 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py~Vv~~~ 83 (225)
..+...||..|..|.+.|..+.|++.+
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 347789999999999999999999975
No 65
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=26.62 E-value=79 Score=26.23 Aligned_cols=28 Identities=29% Similarity=0.465 Sum_probs=24.9
Q ss_pred eeeEEcCCCCCccEEEECCeEEEEEEeE
Q 027318 56 AVKVNASHVRPGNVIEKSGKMYQVIDAE 83 (225)
Q Consensus 56 ~~~i~a~dikkG~~I~~dG~py~Vv~~~ 83 (225)
-+.++...++-|++|+.+++.|+|.-..
T Consensus 98 ~v~VNst~l~dG~iVki~~~yYrV~~n~ 125 (149)
T PF11694_consen 98 EVYVNSTALTDGMIVKIGDKYYRVIFND 125 (149)
T ss_pred eEEEecccccCCeEEEECCccEEEEEcC
Confidence 5789999999999999999999997644
No 66
>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=26.32 E-value=49 Score=26.61 Aligned_cols=37 Identities=19% Similarity=0.278 Sum_probs=21.9
Q ss_pred EEcCCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEe
Q 027318 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELR 99 (225)
Q Consensus 59 i~a~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklk 99 (225)
..+..+|+++.+.+.|++|.|.+ +.|- |....++.|.
T Consensus 70 ~dv~~L~r~DtL~I~g~~y~Vd~---v~pD-~~G~t~I~L~ 106 (117)
T PF05354_consen 70 ADVSGLKRRDTLTIGGESYWVDR---VGPD-GGGSTRIWLG 106 (117)
T ss_dssp CCCCTS-TT-EEEETTTEEEBS------SS-SSS-CCEEB-
T ss_pred hHhhhhhcCCeEEECCEEEEEEe---eccC-CCccEEEEeC
Confidence 34778999999999999999954 4452 4444444443
No 67
>PRK15463 cold shock-like protein CspF; Provisional
Probab=26.31 E-value=1.1e+02 Score=21.99 Aligned_cols=44 Identities=14% Similarity=0.201 Sum_probs=33.0
Q ss_pred EeCCeEEEecCCC-ccccccCchhhhhh-hhccCCCCEEEEEEECC
Q 027318 132 TENDTAFVIESET-FEQLEVPLDVFGKA-GAYLQEGMKVWLQLYDG 175 (225)
Q Consensus 132 ~Dgd~~~FMD~Et-yEQi~v~~~~lgd~-~~yL~eg~~V~v~~~~g 175 (225)
.+...|=|+.++. -+++-+....+... ...|++|..|+....++
T Consensus 13 n~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 13 DGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRING 58 (70)
T ss_pred eCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEEC
Confidence 3445788888765 57888888888654 56799999998887654
No 68
>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=25.00 E-value=38 Score=26.05 Aligned_cols=21 Identities=14% Similarity=0.482 Sum_probs=15.9
Q ss_pred eeEEcCCCCCccEEEECCeEE
Q 027318 57 VKVNASHVRPGNVIEKSGKMY 77 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py 77 (225)
..|.+++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 468899999999997644333
No 69
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=24.71 E-value=1.9e+02 Score=26.60 Aligned_cols=12 Identities=42% Similarity=0.587 Sum_probs=5.5
Q ss_pred CCEEEEEecCCC
Q 027318 104 GNKVSLRFGTEE 115 (225)
Q Consensus 104 G~kie~tf~s~d 115 (225)
|+..-.+++||+
T Consensus 169 ~~y~~vrLpSGe 180 (275)
T COG0090 169 GNYVIVRLPSGE 180 (275)
T ss_pred CCEEEEECCCCC
Confidence 444444444444
No 70
>PF06905 FAIM1: Fas apoptotic inhibitory molecule (FAIM1); InterPro: IPR010695 This family consists of several fas apoptotic inhibitory molecule (FAIM) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology [].; GO: 0043066 negative regulation of apoptosis; PDB: 3MX7_A 2KW1_A 2KD2_A.
Probab=24.40 E-value=3e+02 Score=23.58 Aligned_cols=6 Identities=17% Similarity=0.706 Sum_probs=2.4
Q ss_pred EEecCC
Q 027318 138 FVIESE 143 (225)
Q Consensus 138 ~FMD~E 143 (225)
+++|.+
T Consensus 112 IvLdk~ 117 (177)
T PF06905_consen 112 IVLDKD 117 (177)
T ss_dssp EEEETT
T ss_pred EEEEcc
Confidence 344443
No 71
>COG3173 Predicted aminoglycoside phosphotransferase [General function prediction only]
Probab=24.39 E-value=82 Score=29.33 Aligned_cols=36 Identities=33% Similarity=0.438 Sum_probs=29.4
Q ss_pred eeceeeEEcCCCCCccEEEECCeEEEEEEeEEeeCCC
Q 027318 53 QQRAVKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR 89 (225)
Q Consensus 53 ~~R~~~i~a~dikkG~~I~~dG~py~Vv~~~h~KpGK 89 (225)
+.+.+.+. +|++.||+|..++++--|+|++-+..|-
T Consensus 195 ~~~~~lvH-GD~~~gNlii~~~~~~gVlDwe~~~lGD 230 (321)
T COG3173 195 AGPPVLVH-GDYRPGNLIIDPGRPTGVLDWELATLGD 230 (321)
T ss_pred CCCceeee-CCcccCCEEEeCCCeeEEEeccccccCC
Confidence 33445555 9999999999999999999999877663
No 72
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.91 E-value=2e+02 Score=23.91 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=19.1
Q ss_pred eEEEeeCCCCCEEEEEecCCCcEE
Q 027318 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (225)
Q Consensus 95 riklknL~TG~kie~tf~s~dkve 118 (225)
.++.||+.+|+.+.-+..+.-.+.
T Consensus 133 ~IrVrN~~Sgkiv~g~V~~~g~V~ 156 (160)
T PRK06005 133 LIRVRNVDSGVIVSGTVLADGTIQ 156 (160)
T ss_pred EEEEEECCCCCEEEEEEecCCEEE
Confidence 789999999999988776655543
No 73
>KOG0267 consensus Microtubule severing protein katanin p80 subunit B (contains WD40 repeats) [Cell cycle control, cell division, chromosome partitioning]
Probab=23.86 E-value=1.4e+02 Score=31.13 Aligned_cols=150 Identities=19% Similarity=0.217 Sum_probs=91.8
Q ss_pred eEEcCCCC-CccEEEECCeEEEEEEeEEeeCCC----CCeEeeEEEeeCCCCCEEEEEecC-CCcEEeeeEeeeEEEEEE
Q 027318 58 KVNASHVR-PGNVIEKSGKMYQVIDAEHKQRGR----GGAMMQMELRDIDTGNKVSLRFGT-EEAVERVFVEDKSFTCLY 131 (225)
Q Consensus 58 ~i~a~dik-kG~~I~~dG~py~Vv~~~h~KpGK----G~A~vriklknL~TG~kie~tf~s-~dkve~~~ve~k~~qyLY 131 (225)
-..+.|+| +|-.-.++|.++.|--..+.--|| |+--.-+++=|+.-|+.. ..|++ ..++..+ |-.+..||-
T Consensus 135 d~~iwD~Rk~Gc~~~~~s~~~vv~~l~lsP~Gr~v~~g~ed~tvki~d~~agk~~-~ef~~~e~~v~sl--e~hp~e~Ll 211 (825)
T KOG0267|consen 135 DLKIWDIRKKGCSHTYKSHTRVVDVLRLSPDGRWVASGGEDNTVKIWDLTAGKLS-KEFKSHEGKVQSL--EFHPLEVLL 211 (825)
T ss_pred cceehhhhccCceeeecCCcceeEEEeecCCCceeeccCCcceeeeecccccccc-ccccccccccccc--ccCchhhhh
Confidence 35678999 788888999666555555555576 444467888888888776 56753 2333333 355666666
Q ss_pred EeCC---eEEEecCCCccccccCchhhhhh--hhccCCCCEE----EEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccC
Q 027318 132 TEND---TAFVIESETFEQLEVPLDVFGKA--GAYLQEGMKV----WLQLYDGRALSGSIPKRVACTIKEIHASTKGPTV 202 (225)
Q Consensus 132 ~Dgd---~~~FMD~EtyEQi~v~~~~lgd~--~~yL~eg~~V----~v~~~~g~~i~v~lP~~V~l~V~etep~~KGdTa 202 (225)
.-|. ..-|-|.||||-|.=.+....+. ..|=-+|+.+ ++.+-+. ..--.+|..++..+||-.-|+++
T Consensus 212 a~Gs~d~tv~f~dletfe~I~s~~~~~~~v~~~~fn~~~~~~~~G~q~sl~~~----~~a~ah~~~~~~~~Ep~~~~~~v 287 (825)
T KOG0267|consen 212 APGSSDRTVRFWDLETFEVISSGKPETDGVRSLAFNPDGKIVLSGEQISLSES----RTASAHVRKTLARWEPEMDGAVV 287 (825)
T ss_pred ccCCCCceeeeeccceeEEeeccCCccCCceeeeecCCceeeecCchhhhhhh----hcccceeecccccccccccccee
Confidence 6542 56788999888776544322221 1233333322 1111112 22238889999999999888886
Q ss_pred C-CCceeEEEecC
Q 027318 203 T-PRYRRALLDNG 214 (225)
Q Consensus 203 t-~~~K~A~LeTG 214 (225)
. +..|+..+.-|
T Consensus 288 qs~~~~ek~v~v~ 300 (825)
T KOG0267|consen 288 QSNSHKEKVVAVG 300 (825)
T ss_pred eecCCcccccccc
Confidence 5 56666665433
No 74
>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=23.68 E-value=5.3e+02 Score=24.87 Aligned_cols=115 Identities=18% Similarity=0.248 Sum_probs=60.1
Q ss_pred EEcCCCCCccEEEECCe-------EEEEEEeEEeeCC--------CCCeEeeEEEeeCCCCCEEEEEecCC--------C
Q 027318 59 VNASHVRPGNVIEKSGK-------MYQVIDAEHKQRG--------RGGAMMQMELRDIDTGNKVSLRFGTE--------E 115 (225)
Q Consensus 59 i~a~dikkG~~I~~dG~-------py~Vv~~~h~KpG--------KG~A~vriklknL~TG~kie~tf~s~--------d 115 (225)
.++-.|+.|..|.+.|. -|.|+++.|.--. -+...++.++.=+-... .|+.. .
T Consensus 284 s~~~~l~~G~~~~l~~~~~~~~~g~ylVt~v~H~~~~~~~~~~~~~~~~~y~~~f~~ip~~~----~~rp~~~~~~P~i~ 359 (513)
T TIGR03361 284 SNCRRLAPGYLFTLSGHPRAALNREYLVVSVHHHGRQPQVLEESGGSGAGYRNSFQCIPADV----PFRPPRRTPKPRID 359 (513)
T ss_pred eCcCeEcCCCEEEeCCCCCcccCCCEEEEEEEEEEEeCcccccccCCCceEEEEEEEEECCC----cccCCCCCCCCcCC
Confidence 34568999999999775 3999999996521 12224444443333222 22221 1
Q ss_pred cEEeeeEeeeEEEEEEEeCCe---EEEe-c-CC---Cccc--cccCchhhhhh--hh-ccCCCCEEEEEEECCEE
Q 027318 116 AVERVFVEDKSFTCLYTENDT---AFVI-E-SE---TFEQ--LEVPLDVFGKA--GA-YLQEGMKVWLQLYDGRA 177 (225)
Q Consensus 116 kve~~~ve~k~~qyLY~Dgd~---~~FM-D-~E---tyEQ--i~v~~~~lgd~--~~-yL~eg~~V~v~~~~g~~ 177 (225)
-+..+.|...+-+..|.|+.. ..|. | .. ..+. +.+....-|.. .- ....|++|-|.|.+|.|
T Consensus 360 G~q~A~V~g~~~~~i~~D~~GRvkV~f~wd~~~~~~~~~S~wvRvaqp~AG~~~G~~f~PrvG~EVlV~F~~GDp 434 (513)
T TIGR03361 360 GPQTATVVGPAGEEIYTDEYGRVKVQFHWDRYGKRDEKSSCWVRVAQPWAGNGWGSVAIPRVGQEVVVDFLEGDP 434 (513)
T ss_pred CCeEEEEECCCCCEEeECCCCCEEEEecccCCCCCCCCCceEEEecccccCCCcccccCCCCCCEEEEEEcCCCC
Confidence 144555555445556666542 1222 1 11 1111 12222222221 22 33889999999998765
No 75
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=23.55 E-value=75 Score=23.34 Aligned_cols=47 Identities=17% Similarity=0.220 Sum_probs=29.5
Q ss_pred CCCCeEeeEEEeeCCCCCEEEEEecCCCcEEeee--EeeeEEEEEEEeCCeEEEecC
Q 027318 88 GRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVF--VEDKSFTCLYTENDTAFVIES 142 (225)
Q Consensus 88 GKG~A~vriklknL~TG~kie~tf~s~dkve~~~--ve~k~~qyLY~Dgd~~~FMD~ 142 (225)
|+|...++++ +-+|+.++.+|.++++++.+. ++.. -.+.+.|.+|-+
T Consensus 1 ~~~~~~i~iR---lP~G~r~~rrF~~t~~L~~l~~fv~~~-----~~~~~~f~L~t~ 49 (80)
T cd01771 1 GEPISKLRVR---TPSGDFLERRFLGDTPLQVLLNFVASK-----GYPIDEYKLLSS 49 (80)
T ss_pred CCCeEEEEEE---CCCCCEEEEEeCCCCcHHHHHHHHHhc-----CCCCCCEEEecC
Confidence 3444555554 578999999999999988542 2211 112346877754
No 76
>PRK11835 hypothetical protein; Provisional
Probab=23.39 E-value=75 Score=25.41 Aligned_cols=33 Identities=15% Similarity=0.283 Sum_probs=21.9
Q ss_pred cCCCCC-ccEEEECCeEEEEEEeEEeeCCCCCeEeeEE
Q 027318 61 ASHVRP-GNVIEKSGKMYQVIDAEHKQRGRGGAMMQME 97 (225)
Q Consensus 61 a~dikk-G~~I~~dG~py~Vv~~~h~KpGKG~A~vrik 97 (225)
.+||.. ..+++.+|+||.-+..+ --.+|.+|+|
T Consensus 65 L~eiqv~~~ivEweGepCLFv~~~----DE~aa~CrLK 98 (114)
T PRK11835 65 LSDIQVPCSVLECEGEPCLFVNRQ----DESAATCRLK 98 (114)
T ss_pred HHhhcccceEEEecCCceEEEecc----cchhhheeec
Confidence 345554 45679999999988766 3355555543
No 77
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=23.15 E-value=68 Score=23.03 Aligned_cols=48 Identities=19% Similarity=0.274 Sum_probs=29.2
Q ss_pred CCeEeeEEEeeCCCCCEEEEEecCCCcEEeeeEeeeEEEEEEEeCCeEEEecC
Q 027318 90 GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIES 142 (225)
Q Consensus 90 G~A~vriklknL~TG~kie~tf~s~dkve~~~ve~k~~qyLY~Dgd~~~FMD~ 142 (225)
+.+.+++++ -+|+.+..+|+++++++.+.---... ...+++.|.|+-+
T Consensus 3 ~~~~I~iRl---PdG~ri~~~F~~~~tl~~v~~~v~~~--~~~~~~~f~L~t~ 50 (80)
T smart00166 3 DQCRLQIRL---PDGSRLVRRFPSSDTLRTVYEFVSAA--LTDGNDPFTLNSP 50 (80)
T ss_pred CeEEEEEEc---CCCCEEEEEeCCCCcHHHHHHHHHHc--ccCCCCCEEEEeC
Confidence 345556654 78999999999999987542111111 1123346777664
No 78
>PF13989 YejG: YejG-like protein
Probab=22.63 E-value=75 Score=25.11 Aligned_cols=34 Identities=21% Similarity=0.367 Sum_probs=21.8
Q ss_pred CCCCC-ccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEeeC
Q 027318 62 SHVRP-GNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDI 101 (225)
Q Consensus 62 ~dikk-G~~I~~dG~py~Vv~~~h~KpGKG~A~vriklknL 101 (225)
.||.. ..+++.+|+||.-+..+ --.+|.+| +||+
T Consensus 63 ~eiqv~~~vvE~eGepCLFv~~~----DEsa~~Cr--LKn~ 97 (106)
T PF13989_consen 63 AEIQVDCAVVEWEGEPCLFVHRE----DESAAMCR--LKNF 97 (106)
T ss_pred HHhcccceEEEecCCceEEEecc----cchhhhee--eccC
Confidence 34443 56779999999988776 23455544 4443
No 79
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=21.72 E-value=57 Score=23.19 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=19.3
Q ss_pred EeeEEEeeCCCCCEEEEEecCCCcEEee
Q 027318 93 MMQMELRDIDTGNKVSLRFGTEEAVERV 120 (225)
Q Consensus 93 ~vriklknL~TG~kie~tf~s~dkve~~ 120 (225)
.+++++ -+|+.+..+|++++++..+
T Consensus 4 ~i~iRl---pdG~~~~~~F~~~~tl~~l 28 (77)
T cd01767 4 KIQIRL---PDGKRLEQRFNSTHKLSDV 28 (77)
T ss_pred EEEEEc---CCCCEEEEEeCCCCCHHHH
Confidence 445554 5599999999999998754
No 80
>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=21.61 E-value=3e+02 Score=19.39 Aligned_cols=40 Identities=13% Similarity=0.167 Sum_probs=26.4
Q ss_pred EEcCCCCCccEEEECCe-EEEEEEeEEeeCCCCCeEeeEEEe
Q 027318 59 VNASHVRPGNVIEKSGK-MYQVIDAEHKQRGRGGAMMQMELR 99 (225)
Q Consensus 59 i~a~dikkG~~I~~dG~-py~Vv~~~h~KpGKG~A~vriklk 99 (225)
-+++-|.+|+-|.+.|- .=+|.+++. .+..+++.+.+++.
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 35678889999999985 347777765 44445555555554
No 81
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=21.45 E-value=28 Score=24.23 Aligned_cols=37 Identities=14% Similarity=0.113 Sum_probs=27.3
Q ss_pred EEeeeEeeeEEEEEEE-eCCeEEEecCCCccccccCch
Q 027318 117 VERVFVEDKSFTCLYT-ENDTAFVIESETFEQLEVPLD 153 (225)
Q Consensus 117 ve~~~ve~k~~qyLY~-Dgd~~~FMD~EtyEQi~v~~~ 153 (225)
|..-.|+..+.+|-|. +|..|+|...+.++++.-.++
T Consensus 7 Vcgm~v~~~~a~~k~~Y~GktYYFcse~~~~~F~~~P~ 44 (53)
T COG3350 7 VCGMKVDNENAEYKSSYGGKTYYFCSEECKEKFKDNPE 44 (53)
T ss_pred CcCccccccccceeEEeCCEEEEEeCHHHHHHHHHCHH
Confidence 3344556666777776 677999999999999887654
No 82
>PF14306 PUA_2: PUA-like domain; PDB: 1M8P_C 1I2D_B 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2OFX_B 1J70_B 1G8F_A ....
Probab=21.21 E-value=49 Score=27.68 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=27.0
Q ss_pred EEecCCCccccc----cC----------chhhhhhhhccCCCCEEEEEEECCEEEEE
Q 027318 138 FVIESETFEQLE----VP----------LDVFGKAGAYLQEGMKVWLQLYDGRALSG 180 (225)
Q Consensus 138 ~FMD~EtyEQi~----v~----------~~~lgd~~~yL~eg~~V~v~~~~g~~i~v 180 (225)
-||+.++|+++. ++ .+.=.+..+=|++|..|.+..-+|+++++
T Consensus 55 GFM~~~dy~~V~~~~rL~~G~~wpiPI~L~v~~e~~~~l~~G~~v~L~~~~G~~~a~ 111 (160)
T PF14306_consen 55 GFMNEEDYESVLETMRLPDGTLWPIPIVLDVSEEEAKSLKEGDKVALRDPEGKPVAI 111 (160)
T ss_dssp EE--HHHHHHHHHHSBETTSSB--S---EEECHHHHTTCTTTSEEEEEETTTEEEEE
T ss_pred cccCHHHHHHHHhhCCcCCCCEEeEEEEEECCHHHHHhccCCCEEEEECCCCCEEEE
Confidence 489988887762 11 11112233348999999998777999885
No 83
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=21.01 E-value=1.3e+02 Score=22.29 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=20.4
Q ss_pred eeEEcCCCCCccEEEECCeEEEEEEe
Q 027318 57 VKVNASHVRPGNVIEKSGKMYQVIDA 82 (225)
Q Consensus 57 ~~i~a~dikkG~~I~~dG~py~Vv~~ 82 (225)
..+.=..+.+||.++++|..|..-..
T Consensus 9 ~~v~Rq~V~PG~~v~~~grty~ASAN 34 (73)
T PRK11354 9 DEIPRQCVTPGDYVLHEGRTYIASAN 34 (73)
T ss_pred eeecccccCCceEEEEcCcEEEEEec
Confidence 34445678999999999999987654
No 84
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=20.65 E-value=2.4e+02 Score=19.97 Aligned_cols=43 Identities=19% Similarity=0.170 Sum_probs=29.9
Q ss_pred eCCeEEEecCCCc-cccccCchhhhhh-hhccCCCCEEEEEEECC
Q 027318 133 ENDTAFVIESETF-EQLEVPLDVFGKA-GAYLQEGMKVWLQLYDG 175 (225)
Q Consensus 133 Dgd~~~FMD~Ety-EQi~v~~~~lgd~-~~yL~eg~~V~v~~~~g 175 (225)
+...|=|+.++.- +++-+..+.+... ..-|++|+.|+...-.+
T Consensus 14 ~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 14 ADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESG 58 (70)
T ss_pred CCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEEC
Confidence 3456777777654 6788877777544 25689999988877544
No 85
>PF06605 Prophage_tail: Prophage endopeptidase tail; InterPro: IPR010572 This entry is represented by the Bacteriophage 53, Orf003. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3GS9_A.
Probab=20.54 E-value=1.5e+02 Score=26.70 Aligned_cols=38 Identities=16% Similarity=0.358 Sum_probs=22.9
Q ss_pred CCCCCccEEEECCeEEEEEEeEEeeCCCCCeEeeEEEee
Q 027318 62 SHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRD 100 (225)
Q Consensus 62 ~dikkG~~I~~dG~py~Vv~~~h~KpGKG~A~vriklkn 100 (225)
.-|..+++|..+|+.|+|..++...-|.+.. +.+++++
T Consensus 26 ~~i~~~~~I~~~~q~y~I~~~~~~~~~~~~~-~~V~a~h 63 (327)
T PF06605_consen 26 DLIKEENIITYDGQEYRIKQVEKSRDGNTIT-ITVTAEH 63 (327)
T ss_dssp --SSTT-EEEETTEEEE--EE--B-----EE-EEEEEEB
T ss_pred HhcCcCCEEEECCeEEEEEEeEEecCCCEEE-EEEEEEe
Confidence 5678899999999999999998776665444 8888888
No 86
>TIGR01363 strep_his_triad streptococcal histidine triad protein. This model represents the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Three repeats are found in the seed alignment. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice.
Probab=20.51 E-value=44 Score=31.35 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=18.7
Q ss_pred cCCCCCccEEEECCeEEEEEE
Q 027318 61 ASHVRPGNVIEKSGKMYQVID 81 (225)
Q Consensus 61 a~dikkG~~I~~dG~py~Vv~ 81 (225)
+++++.|=+|+++|+.|..++
T Consensus 118 v~e~~~GYvIkv~~~Yy~ylK 138 (348)
T TIGR01363 118 VNEIKGGYVIKVNGKYYVYLK 138 (348)
T ss_pred HhhhcCceEEEECCEEEEEEc
Confidence 589999999999999998764
No 87
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.49 E-value=5.4e+02 Score=24.80 Aligned_cols=123 Identities=15% Similarity=0.169 Sum_probs=73.7
Q ss_pred eEEEeeCCCCCEEEEEecCCCcEEeeeEee-e-----EEEEEEEeCCeEEEecCCCccc-cccCchhhhhhhhccCCCCE
Q 027318 95 QMELRDIDTGNKVSLRFGTEEAVERVFVED-K-----SFTCLYTENDTAFVIESETFEQ-LEVPLDVFGKAGAYLQEGMK 167 (225)
Q Consensus 95 riklknL~TG~kie~tf~s~dkve~~~ve~-k-----~~qyLY~Dgd~~~FMD~EtyEQ-i~v~~~~lgd~~~yL~eg~~ 167 (225)
+++||-..+|-- +-.|.-.|++.--.-+. - +-.+....|...+.+|+=+|-| +.+++=.=+....|+-+.-+
T Consensus 206 ~V~mk~~LSGmP-eckfGlNDkl~~e~kq~esks~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe 284 (446)
T KOG0938|consen 206 TVDMKTHLSGMP-ECKFGLNDKLGMESKQSESKSDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGE 284 (446)
T ss_pred EEEEEEeccCCc-ccccccCcccceeeccccccccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCc
Confidence 577777777765 36677777754221111 0 1124556677788999888887 44554333445679988888
Q ss_pred EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCC---ccCCCCceeEEEecCcEEEcc
Q 027318 168 VWLQLYDGRALSGSIPKRVACTIKEIHASTKG---PTVTPRYRRALLDNGVTVMVS 220 (225)
Q Consensus 168 V~v~~~~g~~i~v~lP~~V~l~V~etep~~KG---dTat~~~K~A~LeTG~~i~VP 220 (225)
+++.-|--. =.|.||-.|.=.|+|.--. |= -+.-+..+|-.|.-++++++|
T Consensus 285 ~ELMkYr~~-enInlPFrV~PiV~el~r~-kie~ri~iks~f~~kl~a~~v~~rIP 338 (446)
T KOG0938|consen 285 FELMKYRVT-ENINLPFRVTPIVTELGRT-KIEYRITIKSLFPPKLLAKDVVVRIP 338 (446)
T ss_pred eEeEeeeec-cCcccceEeeeheecccce-eEEEEEEEeccCCchhhhcceEEEec
Confidence 888876311 1277888887766664220 00 122234566777777777665
Done!