Query 030552
Match_columns 175
No_of_seqs 132 out of 809
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 15:28:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030552hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00328 eukaryotic initiation 100.0 1.1E-52 2.4E-57 340.5 16.1 159 1-174 1-166 (166)
2 PLN03107 eukaryotic translatio 100.0 7E-50 1.5E-54 322.5 19.1 158 1-174 1-159 (159)
3 KOG3271 Translation initiation 100.0 9.7E-51 2.1E-55 322.5 11.4 155 1-173 1-155 (156)
4 TIGR00037 eIF_5A translation i 100.0 2.3E-42 4.9E-47 270.4 15.8 130 16-169 1-130 (130)
5 PRK03999 translation initiatio 100.0 4.1E-38 8.8E-43 246.1 15.3 126 20-169 4-129 (129)
6 COG0231 Efp Translation elonga 100.0 8.4E-37 1.8E-41 239.4 15.4 125 20-167 2-126 (131)
7 PRK12426 elongation factor P; 100.0 4.2E-33 9.1E-38 229.8 15.5 123 22-169 2-124 (185)
8 PRK14578 elongation factor P; 100.0 1.7E-32 3.7E-37 226.4 15.7 124 22-169 2-126 (187)
9 PRK00529 elongation factor P; 100.0 2.6E-32 5.6E-37 224.0 15.8 123 22-169 2-124 (186)
10 TIGR00038 efp translation elon 100.0 5.1E-32 1.1E-36 222.1 15.8 123 22-169 1-123 (184)
11 PRK04542 elongation factor P; 100.0 8.4E-32 1.8E-36 222.6 15.3 124 22-169 2-127 (189)
12 TIGR02178 yeiP elongation fact 100.0 1.2E-30 2.5E-35 215.4 15.7 122 24-169 2-125 (186)
13 PF08207 EFP_N: Elongation fac 99.7 1.3E-17 2.8E-22 114.1 8.3 58 23-96 1-58 (58)
14 PF01287 eIF-5a: Eukaryotic el 99.7 1.6E-16 3.4E-21 112.9 9.5 69 100-169 1-69 (69)
15 cd04468 S1_eIF5A S1_eIF5A: Euk 99.7 1.9E-16 4E-21 112.7 7.5 69 101-171 1-69 (69)
16 cd04469 S1_Hex1 S1_Hex1: Hex1, 99.6 7.2E-16 1.6E-20 111.4 8.4 70 104-174 3-73 (75)
17 cd04470 S1_EF-P_repeat_1 S1_EF 99.5 1.6E-13 3.5E-18 94.8 6.3 59 102-169 1-59 (61)
18 PF01132 EFP: Elongation facto 99.4 3.2E-13 7E-18 91.5 3.4 50 103-157 1-50 (55)
19 cd04463 S1_EF_like S1_EF_like: 99.1 1E-10 2.2E-15 78.2 5.4 48 104-157 1-48 (55)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.4 5.7E-07 1.2E-11 62.0 4.9 56 101-165 1-56 (57)
21 COG1499 NMD3 NMD protein affec 96.2 0.064 1.4E-06 48.8 11.0 110 11-157 231-344 (355)
22 PF13509 S1_2: S1 domain; PDB: 68.2 14 0.00031 24.9 4.7 52 107-167 8-59 (61)
23 PF08605 Rad9_Rad53_bind: Fung 54.4 27 0.00058 27.7 4.6 41 22-77 55-104 (131)
24 cd06409 PB1_MUG70 The MUG70 pr 41.1 44 0.00094 24.7 3.7 50 75-125 3-63 (86)
25 TIGR00999 8a0102 Membrane Fusi 41.0 1.1E+02 0.0025 24.9 6.6 72 80-154 186-258 (265)
26 PF07076 DUF1344: Protein of u 39.5 1.3E+02 0.0029 21.1 5.9 36 129-169 26-61 (61)
27 COG0090 RplB Ribosomal protein 38.6 1.4E+02 0.0031 26.6 7.1 55 26-97 123-183 (275)
28 KOG1999 RNA polymerase II tran 36.8 1.3E+02 0.0027 31.5 7.2 87 79-170 397-485 (1024)
29 COG3535 Uncharacterized conser 36.2 3.6E+02 0.0078 25.1 10.2 68 71-157 259-326 (357)
30 COG3721 HugX Putative heme iro 35.1 49 0.0011 27.6 3.4 56 57-112 84-140 (176)
31 smart00676 DM10 Domains in hyp 32.1 28 0.00062 26.1 1.5 21 21-41 68-88 (104)
32 PF00845 Gemini_BL1: Geminivir 28.1 1.4E+02 0.0031 26.5 5.3 83 13-114 74-160 (276)
33 PF08806 Sep15_SelM: Sep15/Sel 27.4 42 0.00091 24.1 1.6 40 105-147 34-73 (78)
34 PF02721 DUF223: Domain of unk 26.8 86 0.0019 22.5 3.2 36 117-155 2-37 (95)
35 PF13856 Gifsy-2: ATP-binding 26.5 1.5E+02 0.0033 21.4 4.5 38 12-64 48-88 (95)
36 PF03829 PTSIIA_gutA: PTS syst 25.5 76 0.0016 24.6 2.8 19 23-41 48-66 (117)
37 PRK10377 PTS system glucitol/s 25.3 84 0.0018 24.5 3.1 19 23-41 48-66 (120)
38 PRK05338 rplS 50S ribosomal pr 25.2 2E+02 0.0044 22.4 5.2 31 73-103 56-87 (116)
39 PF13275 S4_2: S4 domain; PDB: 25.2 76 0.0017 22.2 2.6 19 23-41 45-63 (65)
40 TIGR01730 RND_mfp RND family e 24.7 2.3E+02 0.005 23.6 5.9 102 57-162 207-315 (322)
41 TIGR00849 gutA PTS system, glu 24.3 90 0.002 24.4 3.1 18 24-41 49-66 (121)
42 COG1098 VacB Predicted RNA bin 24.2 89 0.0019 25.0 3.0 27 137-163 41-67 (129)
43 PF11948 DUF3465: Protein of u 23.2 1.6E+02 0.0035 23.6 4.3 42 23-74 82-124 (131)
44 PF11268 DUF3071: Protein of u 22.1 1.3E+02 0.0028 24.9 3.7 37 104-143 2-39 (170)
45 PF08206 OB_RNB: Ribonuclease 20.7 2.6E+02 0.0057 18.4 4.6 25 128-158 20-44 (58)
46 PF11871 DUF3391: Domain of un 20.3 52 0.0011 24.3 1.0 21 21-41 4-24 (128)
47 PF00467 KOW: KOW motif; Inte 20.1 1.3E+02 0.0028 17.6 2.6 13 29-41 1-18 (32)
No 1
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=1.1e-52 Score=340.49 Aligned_cols=159 Identities=46% Similarity=0.836 Sum_probs=153.0
Q ss_pred CCcccccccc-ccCCCcceeeEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEe
Q 030552 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGID 79 (175)
Q Consensus 1 m~~~~~~f~~-~~~~~~s~t~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~n 79 (175)
|||+||+|++ +++||+|.|||++|++||+|+||+|+|+||+ |++++++|||||||||||++++|
T Consensus 1 m~d~~~~f~~~~~~~gas~t~p~q~~~LkkG~yvvIkGrPCK---------------IveistSKtGKHGhAK~~ivaid 65 (166)
T PTZ00328 1 MSDEDHDFSHQGGGDNASKTYPLPAGALKKGGYVCINGRPCK---------------VIDLSVSKTGKHGHAKVSIVATD 65 (166)
T ss_pred CCccccccccccCCCCCCceecccccceeECCEEEECCeeeE---------------EEEEecCCCCcCCceEEEEEEEe
Confidence 8997889996 7999999999999999999999999999999 99999999999999999999999
Q ss_pred ccCCcEEEEeecCCCceecceEEeeeeEEEEecCC------ccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEE
Q 030552 80 IFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISED------GFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLV 153 (175)
Q Consensus 80 i~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d~d------~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~ 153 (175)
||||+++|+++|++||+++|.|+|++||+|++++| ||++|||++|++|++++||.+.+|..+++..|.+|++|.
T Consensus 66 IFTgkK~edi~Ps~hnv~VP~V~r~~yqli~I~~d~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~ 145 (166)
T PTZ00328 66 IFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNEDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVL 145 (166)
T ss_pred cCCCCEEeeecCccceeEeeeEEeeEEEEEEEcCCCcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEE
Confidence 99999999999999999999999999999999887 799999999999999999985568889999999999999
Q ss_pred EEEEeeCCeeeEEEEeecCCC
Q 030552 154 VTVMSSMGEEQICALKDIGPK 174 (175)
Q Consensus 154 V~~~~~mGeE~v~~~k~~~~~ 174 (175)
|++|++||+|+|+++|++++|
T Consensus 146 v~vi~amG~e~ii~~k~~~~~ 166 (166)
T PTZ00328 146 VVVVSAMGTEQVLQTKNAAEK 166 (166)
T ss_pred EEEEhhCCeeehheehhhhcC
Confidence 999999999999999998765
No 2
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=7e-50 Score=322.47 Aligned_cols=158 Identities=88% Similarity=1.351 Sum_probs=149.6
Q ss_pred CCccccccccccCCCcceeeEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEec
Q 030552 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDI 80 (175)
Q Consensus 1 m~~~~~~f~~~~~~~~s~t~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni 80 (175)
||++||+|+ ++++|+|.|+|++|++||+|++|+++|+||+ |++++|+||||||+|+||++++||
T Consensus 1 ~~~~~~~~~-~~~~~~~~t~m~~~~~lKkG~~I~~~g~pc~---------------V~e~~~~KpGKHG~A~vr~k~knl 64 (159)
T PLN03107 1 MSDEEHHFE-SADAGASKTYPQQAGTIRKGGYIVIKGRPCK---------------VVEVSTSKTGKHGHAKCHFVAIDI 64 (159)
T ss_pred CCccccccc-ccccCCCceeccchHhccCCCEEEECCEEEE---------------EEEEEecCCCCCCcEEEEEEEEEC
Confidence 888778999 9999999999999999999999999999999 999999999999999999999999
Q ss_pred cCCcEEEEeecCCCceecceEEeeeeEEEEecCCccEEEecCCCCceecccCCc-chhhHHHHHhhccCCCeEEEEEEee
Q 030552 81 FNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPT-DENLLSQIKDGFAEGKDLVVTVMSS 159 (175)
Q Consensus 81 ~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~-~~~l~~~~~~~l~eg~~v~V~~~~~ 159 (175)
+||+++|.+|||++++++|.|++++|||||+++|++++|||++|++.||+.||. +.+|..+++.+|.+|+++.|++|++
T Consensus 65 ~TG~k~e~~f~s~~~ve~~~ve~~~~qyly~dgd~y~~fMD~~get~eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~~ 144 (159)
T PLN03107 65 FTGKKLEDIVPSSHNCDVPHVNRTDYQLIDISEDGFVSLMDESGNTKDDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMSA 144 (159)
T ss_pred CCCCEEEEEecCCCEEEEEEEEEEEEEEEEEcCCceEEEEcCCCCcceeEEccCcchHHHHHHHHHHhCCCeEEEEEEec
Confidence 999999999999999999999999999999999865799999655559999997 6678999999999999999999999
Q ss_pred CCeeeEEEEeecCCC
Q 030552 160 MGEEQICALKDIGPK 174 (175)
Q Consensus 160 mGeE~v~~~k~~~~~ 174 (175)
||+++|+++|+..|+
T Consensus 145 mg~e~i~~~k~~~~~ 159 (159)
T PLN03107 145 MGEEQICALKEIGPK 159 (159)
T ss_pred CCeEEEEEEEccCCC
Confidence 999999999997764
No 3
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-51 Score=322.46 Aligned_cols=155 Identities=66% Similarity=1.016 Sum_probs=151.1
Q ss_pred CCccccccccccCCCcceeeEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEec
Q 030552 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDI 80 (175)
Q Consensus 1 m~~~~~~f~~~~~~~~s~t~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni 80 (175)
|||+||+|+ .++||+|.|||+||+.||||++|+|+||||+ |||++++|+||||||||+++.+||
T Consensus 1 Msd~~~~Fe-~~dagas~t~p~q~salrkNG~vviK~rpck---------------ivEmSTsKtGKHGhAKvh~vaidi 64 (156)
T KOG3271|consen 1 MSDEEHRFE-TGDAGASATYPMQCSALRKNGHVVIKGRPCK---------------IVEMSTSKTGKHGHAKVHIVAIDI 64 (156)
T ss_pred CCccccccc-cCCCcccccccchhhheeeCCEEEEcCCCce---------------EEEeecccCCcCCceEEEEEEEEe
Confidence 899999999 9999999999999999999999999999999 999999999999999999999999
Q ss_pred cCCcEEEEeecCCCceecceEEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeC
Q 030552 81 FNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSM 160 (175)
Q Consensus 81 ~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~m 160 (175)
|||+++|+++||+|||++|+++|.+||+|+|+++ |++|||.+|+.++++++|..+ |+.+|++.|.+|+++.|+|+++|
T Consensus 65 fTgkk~edI~psthn~dVp~vkr~~yqLidIsd~-~~sl~t~sG~~kdDlklp~~e-l~~~i~~~~e~g~dl~v~Vlsa~ 142 (156)
T KOG3271|consen 65 FTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDG-YLSLMTDSGETKDDLKLPEGE-LGNQIRQGFEEGKDLLVTVLSAM 142 (156)
T ss_pred ecCcccccccCCCCccccCccccceeEEEEecCC-eEEEEcCCCCcchhccCcchh-HHHHHHHhhcCCCcEEEEEhhhh
Confidence 9999999999999999999999999999999876 999999999999999999987 89999999999999999999999
Q ss_pred CeeeEEEEeecCC
Q 030552 161 GEEQICALKDIGP 173 (175)
Q Consensus 161 GeE~v~~~k~~~~ 173 (175)
|+|.++++|...+
T Consensus 143 gee~~~a~k~~~~ 155 (156)
T KOG3271|consen 143 GEEAAVAPKSGAG 155 (156)
T ss_pred CchhheeecccCC
Confidence 9999999998765
No 4
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=2.3e-42 Score=270.36 Aligned_cols=130 Identities=42% Similarity=0.695 Sum_probs=123.3
Q ss_pred cceeeEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCc
Q 030552 16 ASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 95 (175)
Q Consensus 16 ~s~t~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~ 95 (175)
+|.|+|++|++||+|++|+++|+||+ |++++|+||||||+|+||+++|||+||+++|.+|||+++
T Consensus 1 ~~~~~~~~~~~irkG~~i~~~g~p~~---------------V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ 65 (130)
T TIGR00037 1 MSATKQVQVSALRVGGYVVIDGRPCK---------------IVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSK 65 (130)
T ss_pred CCcceeccHHHccCCCEEEECCEEEE---------------EEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCE
Confidence 57899999999999999999999999 999999999999999999999999999999999999999
Q ss_pred eecceEEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 96 CDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 96 ~e~p~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
++.|+|++++|||||+|+| +|+|||++|| ||+.||.+. ++++||+||++ |.++++||+|+|+++|
T Consensus 66 ve~~~ve~~~~qylY~dg~-~~~fMd~ety--eq~~i~~~~----~~~~~Lke~~~--V~v~~~~g~~~~~~~~ 130 (130)
T TIGR00037 66 VEVPIVDRREYQVLAIMGG-MVQLMDLDTY--ETDELPIPE----ELGDSLEPGFE--VEYIEAMGQEKIIRFK 130 (130)
T ss_pred EEEeEEEEEEEEEEEecCC-EEEEEcCCCc--EEEEecCCh----hHHHHhhcCCE--EEEEecCCeEEEEEeC
Confidence 9999999999999999877 8999999999 888888762 78899999997 7779999999999986
No 5
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=4.1e-38 Score=246.08 Aligned_cols=126 Identities=32% Similarity=0.599 Sum_probs=119.9
Q ss_pred eEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCceecc
Q 030552 20 FPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAP 99 (175)
Q Consensus 20 ~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p 99 (175)
-|+++++||+|++|.++|+||+ |++++|+||||||+|++|++++||+||+++|.+|+++++++.|
T Consensus 4 ~~~~~~~lrkG~~i~~~g~p~~---------------V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~ 68 (129)
T PRK03999 4 KQVEVGELKEGSYVVIDGEPCK---------------IVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVP 68 (129)
T ss_pred ccccHHHccCCCEEEECCEEEE---------------EEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeee
Confidence 4899999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred eEEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 100 HVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 100 ~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
.|++++|||||+|++ +++|||++|| ||+.||.+ ++++.||.||+. |.++.+||+|+|+++|
T Consensus 69 ~ve~~~~qylY~dg~-~~~fMd~eTy--eq~~i~~~----~d~~~~l~eg~~--v~v~~~~g~~~~~~~~ 129 (129)
T PRK03999 69 IIEKKTGQVLSIMGD-VVQLMDLETY--ETFEIPIP----EELKDKLEPGVE--VEYWEAMGRRKIMRVK 129 (129)
T ss_pred eEEeEEEEEEEecCC-EEEEecCCCc--eEEEecCC----hhHHhhCcCCCE--EEEEhhCCeEEEEEeC
Confidence 999999999999987 8999999999 99999976 568899999996 6689999999999986
No 6
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-37 Score=239.45 Aligned_cols=125 Identities=28% Similarity=0.393 Sum_probs=114.6
Q ss_pred eEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCceecc
Q 030552 20 FPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAP 99 (175)
Q Consensus 20 ~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p 99 (175)
.++++++||+|++|++||.||+ |++++|+||||||+ ++|++++|++||+++|.+||+++++++|
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~---------------V~~~~~~KpGKg~a-~vrvk~k~l~tG~~~e~~f~~~~kve~a 65 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYV---------------VVEISHVKPGKGGA-FVRVKLKNLFTGKKVEKTFKADDKVEVA 65 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEE---------------EEEEEEccCCCCCc-EEEEEEEEccCCCEEEEEEcCCCEEEEe
Confidence 5789999999999999999999 99999999999765 9999999999999999999999999999
Q ss_pred eEEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEE
Q 030552 100 HVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICA 167 (175)
Q Consensus 100 ~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~ 167 (175)
.|+|+++||||+||| .++|||++|| ||+.||.+. +++...||.||++|.|..| +|+-..+.
T Consensus 66 ~ie~~~~q~lY~dg~-~~~FMD~ety--eq~~v~~~~--~~d~~~~l~eg~~v~v~~~--~g~~i~v~ 126 (131)
T COG0231 66 IVERKTAQYLYIDGD-FYVFMDLETY--EQYELPKDQ--IGDAAKFLKEGMEVEVLLY--NGEPIAVE 126 (131)
T ss_pred EEeeeeEEEEEcCCC-eEEEccCCCc--eEEEecchh--hhhHHHhcCCCCEEEEEEE--CCEEEEEE
Confidence 999999999999998 7999999999 999999987 8999999999999666555 55544443
No 7
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=4.2e-33 Score=229.77 Aligned_cols=123 Identities=13% Similarity=0.119 Sum_probs=117.5
Q ss_pred EeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCceecceE
Q 030552 22 QQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHV 101 (175)
Q Consensus 22 i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~v 101 (175)
+++++||+|++|.++|.||. |++++|+|||| |+|++|+++|||.||+++|.+|+|+++++.+.|
T Consensus 2 ~~~~dik~G~~i~~~g~~~~---------------V~~~~h~kPGk-g~A~vr~klknl~tG~~~e~tf~s~ek~e~a~v 65 (185)
T PRK12426 2 VLSSQLSVGMFISTKDGLYK---------------VVSVSKVTGPK-GETFIKVSLQAADSDVVVERNFKAGQEVKEAQF 65 (185)
T ss_pred CchhhcCCCCEEEECCEEEE---------------EEEEEEecCCC-CceEEEEEEEEcCCCCeEEEEECCCCeEEEeEE
Confidence 57899999999999999999 99999999999 889999999999999999999999999999999
Q ss_pred EeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 102 TRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 102 ~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
++++|||||.||| .|+|||.++| ||+.||.+. +++...||+||+.|.|++| ++.+++++
T Consensus 66 e~~~~qylY~dg~-~~~FMd~ety--eQi~i~~~~--lgd~~~fL~e~~~v~v~~~----~~~~i~v~ 124 (185)
T PRK12426 66 EPRNLEYLYLEGD-EYLFLDLGNY--DKIYIPKEI--MKDNFLFLKAGVTVSALVY----DGTVFSVE 124 (185)
T ss_pred EeeEeEEEEECCC-eEEEecCCCc--eEEEeCHHH--hhhHHhhccCCCEEEEEEE----CCEEEEEE
Confidence 9999999999998 7999999999 999999875 9999999999999999998 77788876
No 8
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=1.7e-32 Score=226.43 Aligned_cols=124 Identities=13% Similarity=0.251 Sum_probs=116.9
Q ss_pred EeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCC-cccEEEEEEEeccCCcEEEEeecCCCceecce
Q 030552 22 QQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPH 100 (175)
Q Consensus 22 i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKh-G~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~ 100 (175)
+.+++||+|++|.++|.||+ |++++|+||||+ |+|++|+++|||.||+++|.+|+|+++++.+.
T Consensus 2 ~~~~dik~G~~i~~dg~~~~---------------V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ 66 (187)
T PRK14578 2 YTTSDFKKGLVIQLDGAPCL---------------LLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEAD 66 (187)
T ss_pred CchhhcCCCCEEEECCEEEE---------------EEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeE
Confidence 57899999999999999999 999999999986 46799999999999999999999999999999
Q ss_pred EEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 101 VTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 101 v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
|++++|||||.||+ .|+|||++|| ||+.||.+. +++...||+||+.|.|.+| ++.+++++
T Consensus 67 ve~~~~qylY~dg~-~~~FMD~ety--EQ~~i~~~~--~g~~~~fL~e~~~v~v~~~----~~~~i~v~ 126 (187)
T PRK14578 67 FERHKGQFLYADGD-RGVFMDLETY--EQFEMEEDA--FSAIAPFLLDGTEVQLGLF----QGRMVNVD 126 (187)
T ss_pred EEEeEeEEEEeCCC-EEEEecCCCc--EEEEecHHH--hhhHHhhccCCCEEEEEEE----CCEEEEEE
Confidence 99999999999998 7899999999 999999875 9999999999999999998 77788886
No 9
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=2.6e-32 Score=224.00 Aligned_cols=123 Identities=20% Similarity=0.301 Sum_probs=117.1
Q ss_pred EeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCceecceE
Q 030552 22 QQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHV 101 (175)
Q Consensus 22 i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~v 101 (175)
+++++||+|++|+++|+||+ |++++|+|||| |+|++|++++||+||+++|.+|+++++++.|.+
T Consensus 2 ~~a~~ik~G~~I~~~g~~~~---------------V~~~~~~kpGk-g~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~v 65 (186)
T PRK00529 2 ISANDLRKGLVIEIDGEPYV---------------VLEFEHVKPGK-GQAFVRTKLKNLLTGSVVEKTFKAGDKVERADV 65 (186)
T ss_pred cchhhcCCCCEEEECCEEEE---------------EEEEEEeeCCC-CceEEEEEEEECCCCCeEEEEeCCCCEEEeccE
Confidence 57899999999999999999 99999999999 999999999999999999999999999999999
Q ss_pred EeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 102 TRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 102 ~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
++++|||||.|+| .++|||+++| ||+.||.+. +++...||+||+.|.|++| ++.+++++
T Consensus 66 e~~~~q~ly~dgd-~~~fMD~ety--eq~~l~~~~--lg~~~~~L~eg~~v~v~~~----~~~~i~v~ 124 (186)
T PRK00529 66 ERREMQYLYNDGD-GYVFMDTETY--EQIEVPADQ--VGDAAKFLKEGMEVTVVFY----NGEPISVE 124 (186)
T ss_pred EeEEEEEEEECCC-EEEEecCCCc--eeeEcCHHH--hHHHHhhccCCCEEEEEEE----CCEEEEEE
Confidence 9999999999988 6999999999 999999875 8888999999999999999 77888876
No 10
>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=5.1e-32 Score=222.08 Aligned_cols=123 Identities=22% Similarity=0.302 Sum_probs=116.9
Q ss_pred EeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCceecceE
Q 030552 22 QQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHV 101 (175)
Q Consensus 22 i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~v 101 (175)
+++++||+|++|+++|+||+ |++++|+|||| |+|++|++++||+||++++.+|+++++++.|.+
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~---------------V~~~~~~kpGk-g~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~ 64 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYV---------------VLEFEHVKPGK-GQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADV 64 (184)
T ss_pred CchhhccCCCEEEECCEEEE---------------EEEEEEeeCCC-CceEEEEEEEECCCCCEEEEEeCCCCEEEcccE
Confidence 46899999999999999999 99999999999 889999999999999999999999999999999
Q ss_pred EeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 102 TRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 102 ~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
+++++||||.++| .++|||.++| ||+.||.+. +++...||+||+.|.|.+| ++.++++.
T Consensus 65 e~~~~q~ly~dgd-~~~fMD~ety--eq~~i~~~~--l~~~~~~L~eg~~v~v~~~----~~~~i~v~ 123 (184)
T TIGR00038 65 EEREMQYLYKDGD-SYVFMDTETY--EQIELPKDL--LGDAAKFLKENMEVSVTFY----NGEPIGVE 123 (184)
T ss_pred EeEEEEEEEECCC-EEEEeCCCCc--cceEcCHHH--HHHHHhhcCCCCEEEEEEE----CCEEEEEE
Confidence 9999999999998 6899999999 999999774 8899999999999999999 77888876
No 11
>PRK04542 elongation factor P; Provisional
Probab=99.98 E-value=8.4e-32 Score=222.64 Aligned_cols=124 Identities=18% Similarity=0.199 Sum_probs=116.4
Q ss_pred EeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecC-CCCcccEEEEEEEeccCCcEEEEeecCCCceecce
Q 030552 22 QQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPH 100 (175)
Q Consensus 22 i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~Kp-GKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~ 100 (175)
+++++||+|+.|+++|.||+ |++++|+|| ||+|+|++|+++|||.||+++|.+|+|+++++.++
T Consensus 2 i~~~dik~G~~i~~~g~~~~---------------V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~ 66 (189)
T PRK04542 2 PKANEIKKGMVVEYNGKLLL---------------VKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVD 66 (189)
T ss_pred CchhhcCCCCEEEECCEEEE---------------EEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEE
Confidence 57899999999999999999 999999999 79557799999999999999999999999999999
Q ss_pred EEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCe-EEEEEEeeCCeeeEEEEe
Q 030552 101 VTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKD-LVVTVMSSMGEEQICALK 169 (175)
Q Consensus 101 v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~-v~V~~~~~mGeE~v~~~k 169 (175)
+++++|||||.|++ .|+|||.++| ||+.||.+. +++...||+||+. |.|++| ++.+++++
T Consensus 67 ~~~~~~qylY~dg~-~~~FMd~ety--EQ~~i~~~~--lgd~~~~L~e~~~~v~v~~~----~~~~i~v~ 127 (189)
T PRK04542 67 LTRRPVTFSYIDGD-EYVFMDNEDY--TPYTFKKDQ--IEDELLFIPEGMPGMQVLTV----DGQPVALE 127 (189)
T ss_pred EEEeEeEEEEeCCC-EEEEecCCCc--eEEEECHHH--hhhHhhhhhcCCEEEEEEEE----CCEEEEEE
Confidence 99999999999988 7899999999 999999864 8999999999998 999988 66788876
No 12
>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=99.97 E-value=1.2e-30 Score=215.42 Aligned_cols=122 Identities=15% Similarity=0.213 Sum_probs=114.6
Q ss_pred ccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCccc-EEEEEEEeccCCcEEEEeecCCCceecceEE
Q 030552 24 AGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDAPHVT 102 (175)
Q Consensus 24 as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~A-kv~~k~~ni~TGk~~e~~~~s~~~~e~p~v~ 102 (175)
+++||+|+.|.++|.||+ |++++|+|||+.|+| ++++++|||.||++++.+|+|+++++.+.++
T Consensus 2 ~~~lk~G~~i~~dg~~~~---------------V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le 66 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLL---------------IKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELL 66 (186)
T ss_pred cccccCCCEEEECCEEEE---------------EEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEE
Confidence 689999999999999999 999999999885655 8999999999999999999999999999999
Q ss_pred eeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCe-EEEEEEeeCCeeeEEEEe
Q 030552 103 RTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKD-LVVTVMSSMGEEQICALK 169 (175)
Q Consensus 103 r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~-v~V~~~~~mGeE~v~~~k 169 (175)
+++|||||.|++ .|+|||.++| ||+.||.+. +++...||+||+. |.|++| ++.+++++
T Consensus 67 ~~~~qylY~dg~-~~~FMD~ety--EQ~~i~~~~--lgd~~~fL~e~~~~v~v~~~----~~~~i~v~ 125 (186)
T TIGR02178 67 RREASFSYKDGE-EYVFMDEEDY--TPYTFDKDA--IEDELLFISEGLSGMYVQLI----DGSPVALE 125 (186)
T ss_pred EeEeEEEEeCCC-eEEEccCCCc--EEEEeCHHH--hhhhhhhhhCCCEEEEEEEE----CCEEEEEE
Confidence 999999999998 7899999999 999999874 8999999999996 999999 77788886
No 13
>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=99.73 E-value=1.3e-17 Score=114.07 Aligned_cols=58 Identities=28% Similarity=0.344 Sum_probs=53.1
Q ss_pred eccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEeecCCCce
Q 030552 23 QAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 96 (175)
Q Consensus 23 ~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~ 96 (175)
+|++||+|++|+++|+||. |++++|++||| |+|+|+++++||.||+++|.+|+|++++
T Consensus 1 sa~dlr~G~~i~~~g~~~~---------------V~~~~~~k~gk-g~a~v~~klknl~tG~~~e~tf~s~d~v 58 (58)
T PF08207_consen 1 SASDLRKGMVIEIDGEPYV---------------VLDFQHVKPGK-GGAFVRVKLKNLRTGSKVEKTFRSGDKV 58 (58)
T ss_dssp EGGG--TTSEEEETTEEEE---------------EEEEEEECCTT-SSSEEEEEEEETTTTEEEEEEEETT-EE
T ss_pred CHHHccCCCEEEECCEEEE---------------EEEEEEECCCC-CCeEEEEEEEECCCCCEEEEEECCCCcC
Confidence 4899999999999999999 99999999999 8999999999999999999999999875
No 14
>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=99.69 E-value=1.6e-16 Score=112.94 Aligned_cols=69 Identities=55% Similarity=0.903 Sum_probs=63.4
Q ss_pred eEEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 100 HVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 100 ~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
+|+|++||+|++++||+++|||+++.++|+++||.. +|..+++..|.+|+++.|+++++||+|+|+++|
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMde~get~eDl~lP~~-el~~ei~~~~~~g~~~~Vtv~~amG~e~ii~~K 69 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMDEDGETREDLKLPDG-ELGEEIKAKFEEGKEVLVTVLSAMGEEKIIAVK 69 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEETTS-EEEEEECCSH-HHHHHHHHHHHTTCEEEEEEEEETTEEEEEEEE
T ss_pred CeEEEEEEEEEEccCcEEEEEcCCCCeeccEEeccc-chhHHHHhhccCCCeEEEEEEeeCCcEEEEEeC
Confidence 489999999999999999999999999999999955 588889999999999999999999999999987
No 15
>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=99.67 E-value=1.9e-16 Score=112.75 Aligned_cols=69 Identities=54% Similarity=0.932 Sum_probs=64.3
Q ss_pred EEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEeec
Q 030552 101 VTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDI 171 (175)
Q Consensus 101 v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k~~ 171 (175)
|.|++||+|++++ ||+++|+++|.+||+++||.+ +|..+|+..|.+|+++.|+++++||+|.++++|+.
T Consensus 1 V~R~eYqLidI~d-GflsLm~e~G~~k~DlklP~~-elg~~I~~~f~~gk~~~vtV~samGeE~~i~~K~~ 69 (69)
T cd04468 1 VKRTEYQLIDIDD-GFLSLMDDDGETREDLKLPEG-ELGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKEA 69 (69)
T ss_pred CcceeEEEEeecC-CeEEEEcCCCCcccCCcCCcH-HHHHHHHHHHhCCCcEEEEEEccCCcEeeEEeecC
Confidence 5799999999977 899999999999999999976 48888999999999999999999999999999963
No 16
>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=99.65 E-value=7.2e-16 Score=111.35 Aligned_cols=70 Identities=30% Similarity=0.553 Sum_probs=65.4
Q ss_pred eeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCC-eEEEEEEeeCCeeeEEEEeecCCC
Q 030552 104 TDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGK-DLVVTVMSSMGEEQICALKDIGPK 174 (175)
Q Consensus 104 ~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~-~v~V~~~~~mGeE~v~~~k~~~~~ 174 (175)
++||+|+| +|||+++||++|.+|++++||.+.+|..+|+..|.+|+ ++.|+++++||+|.++++|++++.
T Consensus 3 ~eYqLidI-~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk~~v~VtVlsAmGeE~iv~~K~~~~~ 73 (75)
T cd04469 3 KQYRVLDI-QDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGRGSVRVLVVNDGGRELVVDMKVVHGS 73 (75)
T ss_pred eEEEEEEe-cCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCCCcEEEEEEccCCeEeEEEEEEeecc
Confidence 79999999 77899999999999999999966668999999999999 999999999999999999998863
No 17
>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=99.46 E-value=1.6e-13 Score=94.78 Aligned_cols=59 Identities=14% Similarity=0.266 Sum_probs=53.9
Q ss_pred EeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 102 TRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 102 ~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
+++++||||.||+ .++|||.+|| ||+.||.+. +++...||+||+.|.|++| ++.++++.
T Consensus 1 e~~~~qylY~dg~-~~~FMd~ety--eQ~~i~~~~--igd~~~~L~e~~~v~v~~~----~~~~i~v~ 59 (61)
T cd04470 1 EEREMQYLYKDGD-NYVFMDTETY--EQIELPKEA--LGDAAKFLKEGMEVIVLFY----NGEPIGVE 59 (61)
T ss_pred CCceEEEEEeCCC-EEEEeCCCCc--eEEEECHHH--hhhHHhhCcCCCEEEEEEE----CCEEEEEE
Confidence 4789999999998 6899999999 999999875 9999999999999999999 67888875
No 18
>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=99.37 E-value=3.2e-13 Score=91.46 Aligned_cols=50 Identities=18% Similarity=0.300 Sum_probs=43.1
Q ss_pred eeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEE
Q 030552 103 RTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVM 157 (175)
Q Consensus 103 r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~ 157 (175)
||++||||.||| .++|||.+|| ||+.||.+. +++...||+||+.|.|++|
T Consensus 1 ~r~~qylY~dgd-~~~FMd~ety--eQi~v~~~~--~g~~~~~L~eg~~v~v~~~ 50 (55)
T PF01132_consen 1 RREMQYLYKDGD-NYVFMDTETY--EQIEVPKDQ--LGDALKFLKEGMEVQVLFY 50 (55)
T ss_dssp EEEEEEEEEESS-EEEEEETTT----EEEEEHHH--HTTTGCC--TTEEEEEEEE
T ss_pred CceEEEEEeCCC-EEEEecCCCc--eEEEecHHH--hChHHhhCcCCCEEEEEEE
Confidence 689999999999 6999999999 999999875 9999999999999999998
No 19
>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=99.13 E-value=1e-10 Score=78.22 Aligned_cols=48 Identities=17% Similarity=0.223 Sum_probs=42.0
Q ss_pred eeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEE
Q 030552 104 TDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVM 157 (175)
Q Consensus 104 ~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~ 157 (175)
++|||||.+++ .++|||.+|| ||+.+|.+. . +...||++|+.|.|.++
T Consensus 1 ~~~qylY~dg~-~~~fMd~ety--eq~~v~~~~--~-~~~~~l~eg~~v~v~~~ 48 (55)
T cd04463 1 RELQVLDIQGS-KPVTMDLETY--EVVQVPPPV--D-QSFESFEPGEVVLVDTR 48 (55)
T ss_pred CCEEEEEcCCC-EeEEecCCCc--eEEEeCHHH--h-hHHhhCCCCCEEEEEEE
Confidence 57999999987 7999999999 999999874 4 48899999999887766
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=98.39 E-value=5.7e-07 Score=62.02 Aligned_cols=56 Identities=32% Similarity=0.525 Sum_probs=45.0
Q ss_pred EEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeE
Q 030552 101 VTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQI 165 (175)
Q Consensus 101 v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v 165 (175)
|+|+..|.+++++| .+.|||++|| +.+.+|..+ +++.-+++|.+ |.+|.+||+.+|
T Consensus 1 i~k~~aqVisi~g~-~vQlMD~eTY--eT~ev~~p~----~~~~~i~~G~e--V~y~~~~g~~ki 56 (57)
T cd04467 1 IERKTGQVLSIMGD-VVQLMDLETY--ETFEVPIPE----EIKDKLEPGKE--VEYWESMGKRKI 56 (57)
T ss_pred CcceEEEEEEEcCC-EEEEeccccc--eeEEEecch----hhcccCCCCCE--EEEEeecCeEec
Confidence 57999999999998 8999999999 666666543 24556789998 557999999876
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=96.21 E-value=0.064 Score=48.83 Aligned_cols=110 Identities=13% Similarity=0.166 Sum_probs=76.6
Q ss_pred ccCCCcceeeEEeccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEEee
Q 030552 11 KADAGASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 90 (175)
Q Consensus 11 ~~~~~~s~t~~i~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~~~ 90 (175)
.|-.-.-.||.+..-++++|+.|.++|+++. ++. +-|+ .++++|+.|++..+.++
T Consensus 231 tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~---------------~v~----~~~~------~~~~~dl~t~e~~~~~~ 285 (355)
T COG1499 231 TGKRVYRFTYSVRIPEFRPGDIVSVRGRQLV---------------LVR----SIGK------GIVVLDLETGEPVEITW 285 (355)
T ss_pred CCceEEEEEEEEECCCCCCCCEEEECCCeEE---------------EEE----EecC------ceEEEecccCCccccCh
Confidence 4444566799999999999999999997765 332 3466 38999999998887776
Q ss_pred cCCCceecceEE----eeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEE
Q 030552 91 PSSHNCDAPHVT----RTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVM 157 (175)
Q Consensus 91 ~s~~~~e~p~v~----r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~ 157 (175)
.-...-+...+. -+.+-++..+.+ .+.|||.+|| |-..+... -+.+|..+.|..+
T Consensus 286 ~~~~~~~~~~~~~~~~~~~~~vvs~~~~-~~~v~d~et~--e~~~~~~~---------~~~~g~~v~v~~~ 344 (355)
T COG1499 286 SVYKRNEGKVAVKEPRLKKAVVVSRDPS-AIQVLDPETY--EARTVKGP---------SLEEGDEVKVFKV 344 (355)
T ss_pred hhcccCcceeeeccccceEEEEEecCCC-ceEEEecceE--EEEeccCC---------CCCCCCEEEEEEE
Confidence 554444422222 245667777776 6899999999 55544332 3458887666444
No 22
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=68.15 E-value=14 Score=24.85 Aligned_cols=52 Identities=17% Similarity=0.293 Sum_probs=28.2
Q ss_pred EEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEE
Q 030552 107 QLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICA 167 (175)
Q Consensus 107 q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~ 167 (175)
+.....+. -+|++.... .++.||..+ +..-++.|+.|.|.+|..-....+..
T Consensus 8 ~V~~~~~~--g~fL~~~~~--~~vlLp~~e-----~~~~~~~Gd~v~VFvY~D~~~rl~AT 59 (61)
T PF13509_consen 8 KVVDKNEF--GYFLDDGEG--KEVLLPKSE-----VPEPLKVGDEVEVFVYLDKEGRLVAT 59 (61)
T ss_dssp -EEEE-SS--EEEEEETT---EEEEEEGGG-----------TTSEEEEEEEE-TTS-EEEE
T ss_pred EEEEEeCC--EEEEECCCC--CEEEechHH-----cCCCCCCCCEEEEEEEECCCCCEEEe
Confidence 34455444 356776666 689999764 34557899999998886654444443
No 23
>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=54.40 E-value=27 Score=27.69 Aligned_cols=41 Identities=10% Similarity=0.041 Sum_probs=30.6
Q ss_pred EeccccCCceEEEEcCe--EeccccccCCccccCcccEEEEEeec--CC-----CCcccEEEEEE
Q 030552 22 QQAGTIRKNGYIVIKNR--PCKPQVFKFPSFSLHSKQVVEVSTSK--TG-----KHGHAKCHFVG 77 (175)
Q Consensus 22 i~as~lrkG~~i~i~g~--pck~~~~~~~~~~~~~~~Vve~~~~K--pG-----KhG~Akv~~k~ 77 (175)
+..=+||.|+.|.+++. +|. |+-+.+.- +. -+|++-|+++=
T Consensus 55 v~~LDlRIGD~Vkv~~~k~~yi---------------V~Gl~~~~~~~~~~i~cirGy~tV~Lk~ 104 (131)
T PF08605_consen 55 VKYLDLRIGDTVKVDGPKVTYI---------------VVGLECKISSEDNIITCIRGYNTVYLKR 104 (131)
T ss_pred EeeeeeecCCEEEECCCCccEE---------------EEEeeecCCCCCCceEEcCCCcEEEEEE
Confidence 56678999999999997 788 88888762 22 23777777743
No 24
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=41.13 E-value=44 Score=24.73 Aligned_cols=50 Identities=18% Similarity=0.224 Sum_probs=30.8
Q ss_pred EEEEeccCCcEEEEeecCCCcee-----------cceEEeeeeEEEEecCCccEEEecCCCC
Q 030552 75 FVGIDIFNGKKLEDIVPSSHNCD-----------APHVTRTDYQLIDISEDGFVSLLTETGN 125 (175)
Q Consensus 75 ~k~~ni~TGk~~e~~~~s~~~~e-----------~p~v~r~~~q~ly~d~d~~~~fMd~~t~ 125 (175)
+|+++. .|++.--++.+++.+. .....+..+++.|.|+||..++|+.+..
T Consensus 3 FK~~~~-~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D~D 63 (86)
T cd06409 3 FKFKDP-KGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSDSD 63 (86)
T ss_pred EEeeCC-CCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEeccch
Confidence 344444 5666555555433332 2222256889999998888888887765
No 25
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=40.98 E-value=1.1e+02 Score=24.93 Aligned_cols=72 Identities=14% Similarity=0.105 Sum_probs=35.9
Q ss_pred ccCCcEEEEeecCCCceecceEEeeeeEEEEec-CCccEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEE
Q 030552 80 IFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDIS-EDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVV 154 (175)
Q Consensus 80 i~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d-~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V 154 (175)
+..|...+-.+.....=+...|-+. .++.+ +.-+++.++.++..+..+++-...+-.-.+...|.+|+.|.+
T Consensus 186 l~~G~~v~v~i~~~~~~~~~~vP~~---Ai~~~~~~~~V~v~~~~~~~~~~V~ig~~~~~~~~I~~gL~~gd~vv~ 258 (265)
T TIGR00999 186 LKPGLFVQVRVETKIGEPAIAVPED---AVQDLGGRKVVFVRTQEGFRPRPVKVGRRLGGYYEVLEGLKPGERVAV 258 (265)
T ss_pred cCCCCEEEEEEecCCCCceEEeehH---HhEeeCCcEEEEEEeCCceEEEEEEEccccCCEEEEecCCCCCCEEEE
Confidence 5677777777766543333333222 23332 332556666666654555543321001124567777776543
No 26
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=39.50 E-value=1.3e+02 Score=21.06 Aligned_cols=36 Identities=25% Similarity=0.398 Sum_probs=27.3
Q ss_pred cccCCcchhhHHHHHhhccCCCeEEEEEEeeCCeeeEEEEe
Q 030552 129 DLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169 (175)
Q Consensus 129 qi~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGeE~v~~~k 169 (175)
.+.||.+-+ .+.|++|+.|.|.+-...|+..|.+++
T Consensus 26 sy~lp~ef~-----~~~L~~G~kV~V~yd~~~gk~vitdi~ 61 (61)
T PF07076_consen 26 SYKLPEEFD-----FDGLKPGMKVVVFYDEVDGKRVITDIE 61 (61)
T ss_pred EEECCCccc-----ccccCCCCEEEEEEEccCCcEEeeecC
Confidence 567887642 457889999999888778888777653
No 27
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=38.63 E-value=1.4e+02 Score=26.64 Aligned_cols=55 Identities=22% Similarity=0.300 Sum_probs=31.8
Q ss_pred ccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecCCCCcc------cEEEEEEEeccCCcEEEEeecCCCcee
Q 030552 26 TIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGH------AKCHFVGIDIFNGKKLEDIVPSSHNCD 97 (175)
Q Consensus 26 ~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~------Akv~~k~~ni~TGk~~e~~~~s~~~~e 97 (175)
+|+.|..+-|..-|--. ++----.+||++|. +.+++.+++ |+..--.+||++.-.
T Consensus 123 ~ik~GN~lpL~~IP~Gt--------------~VhNVE~~pG~GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~r~ 183 (275)
T COG0090 123 DIKPGNALPLGNIPEGT--------------IVHNVELKPGDGGQLARSAGTYAQVVGKE---GNYVIVRLPSGEMRK 183 (275)
T ss_pred CcCCcceeeeccCCCCc--------------eEEeeeeccCCCceEEEeCCceEEEEEcc---CCEEEEECCCCCeEe
Confidence 56666666666655431 22222248999542 455566666 666667777776543
No 28
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=36.81 E-value=1.3e+02 Score=31.55 Aligned_cols=87 Identities=13% Similarity=0.191 Sum_probs=60.7
Q ss_pred eccCCcEEEEeecCCCceecceEEeeeeEEEEecCCccEEEecCC-CCceecccCCcchhhHHHHHhhccCCCeEEEEEE
Q 030552 79 DIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTET-GNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVM 157 (175)
Q Consensus 79 ni~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d~d~~~~fMd~~-t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~ 157 (175)
-+++.++-+..|..++++++...+-+.++-+-..=||..++|-.+ -..++-|.+|.. ++++||+.|+-|.|.-=
T Consensus 397 t~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~-----eLrKyF~~GDhVKVi~G 471 (1024)
T KOG1999|consen 397 TLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPAS-----ELRKYFEPGDHVKVIAG 471 (1024)
T ss_pred eeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchH-----hhhhhccCCCeEEEEec
Confidence 677888888889999999999999999886554433334444333 122244666644 46999999999888776
Q ss_pred eeCCe-eeEEEEee
Q 030552 158 SSMGE-EQICALKD 170 (175)
Q Consensus 158 ~~mGe-E~v~~~k~ 170 (175)
.+.|. ..|+.|+.
T Consensus 472 ~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 472 RYEGDTGLVVRVEQ 485 (1024)
T ss_pred cccCCcceEEEEeC
Confidence 66655 56666653
No 29
>COG3535 Uncharacterized conserved protein [Function unknown]
Probab=36.24 E-value=3.6e+02 Score=25.06 Aligned_cols=68 Identities=21% Similarity=0.373 Sum_probs=49.4
Q ss_pred cEEEEEEEeccCCcEEEEeecCCCceecceEEeeeeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhccCCC
Q 030552 71 AKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGK 150 (175)
Q Consensus 71 Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~ 150 (175)
..+++.+.+-..|+.++..|.-- -.+-+++-|++-...| -+.++|.+|. .++.++. ++.|+
T Consensus 259 G~~~I~G~~~~~g~t~~i~FqNE-----fl~a~~~G~~l~~~PD-LI~lld~~Tg----~piTTe~---------lkyG~ 319 (357)
T COG3535 259 GRVTIDGLEEYRGSTLEIAFQNE-----FLVAEKDGKILATTPD-LIVLLDLNTG----LPITTES---------LKYGQ 319 (357)
T ss_pred eeEEEechhhcCCceEEEEEEee-----eeEEecCCcEEEecCc-eEEEEecCCC----CccchHH---------hhcCc
Confidence 35778899999999999988642 2345588999999888 7899998876 4454442 34777
Q ss_pred eEEEEEE
Q 030552 151 DLVVTVM 157 (175)
Q Consensus 151 ~v~V~~~ 157 (175)
.|.|.-+
T Consensus 320 rV~V~aI 326 (357)
T COG3535 320 RVVVIAI 326 (357)
T ss_pred EEEEEEe
Confidence 7666543
No 30
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=35.09 E-value=49 Score=27.59 Aligned_cols=56 Identities=16% Similarity=0.244 Sum_probs=39.7
Q ss_pred EEEEEeecC-CCCcccEEEEEEEeccCCcEEEEeecCCCceecceEEeeeeEEEEec
Q 030552 57 VVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDIS 112 (175)
Q Consensus 57 Vve~~~~Kp-GKhG~Akv~~k~~ni~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d 112 (175)
|.|+.-.-| |.|+|..+.+.++|-..|-..-+.|..-.=++.|..-+..+.+....
T Consensus 84 IlEvkg~lP~G~~~hGyfNL~gk~~l~GHiK~eNcs~Ialv~rpFmG~~s~si~Ffn 140 (176)
T COG3721 84 ILEVKGPLPSGTHRHGYFNLRGKDGLSGHIKAENCSHIALVERPFMGMESASILFFN 140 (176)
T ss_pred EEEecCCCCCCccccceEeecCCCCCcceeeccccceeeEeccccCCccceeeeeec
Confidence 445544434 99999999999999999998877777766677776655555444433
No 31
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=32.09 E-value=28 Score=26.15 Aligned_cols=21 Identities=14% Similarity=0.104 Sum_probs=19.4
Q ss_pred EEeccccCCceEEEEcCeEec
Q 030552 21 PQQAGTIRKNGYIVIKNRPCK 41 (175)
Q Consensus 21 ~i~as~lrkG~~i~i~g~pck 41 (175)
+....||+.|..|.|.|+++.
T Consensus 68 ~y~~~Dl~vG~~v~i~gr~f~ 88 (104)
T smart00676 68 YYHASDLNVGTTINVFGRQFR 88 (104)
T ss_pred ccCHHHcCCCCEEEEeCEEEE
Confidence 467889999999999999999
No 32
>PF00845 Gemini_BL1: Geminivirus BL1 movement protein; InterPro: IPR000211 The movement of bipartite Geminiviruses such as squash leaf curl virus (SqLCV) requires the cooperative interaction of two essential virus-encoded movement proteins, BR1 and BL1. Recent studies of SqLCV and bean dwarf mosaic virus have shown that BR1 and BL1 act in a cooperative manner to move the viral genome intracellularly from the nucleus to the cytoplasm and across the wall cell to cell. BR1 is a nuclear shuttle protein, and it has been proposed to bind newly replicated viral ssDNA genomes and move these between the nucleus and cytoplasm. These BR1-genome complexes are then directed to the cell periphery through interactions between BR1 and BL1, where, as the result of BL1 action, the complexes are moved to adjacent uninfected cells. The precise mechanism by which BL1 acts to transport these genome complexes across the cell wall, and whether this may differ in different cell types, remains at issue [].; GO: 0003677 DNA binding, 0046740 spread of virus in host, cell to cell, 0033644 host cell membrane
Probab=28.08 E-value=1.4e+02 Score=26.54 Aligned_cols=83 Identities=20% Similarity=0.261 Sum_probs=40.0
Q ss_pred CCCcceeeEEecc-ccC--CceEEEEcC-eEeccccccCCccccCcccEEEEEeecCCCCcccEEEEEEEeccCCcEEEE
Q 030552 13 DAGASKTFPQQAG-TIR--KNGYIVIKN-RPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLED 88 (175)
Q Consensus 13 ~~~~s~t~~i~as-~lr--kG~~i~i~g-~pck~~~~~~~~~~~~~~~Vve~~~~KpGKhG~Akv~~k~~ni~TGk~~e~ 88 (175)
.+-|+.||||.|+ +|+ --+++-+++ .||++ | -.++-+.-=. |--|+++++|==.+-.|.
T Consensus 74 s~QA~~TfPI~CNidLHYfSSSfFSlKDp~PWkl----------~----YrV~DtNV~~-~thFak~kgKLKLStAKH-- 136 (276)
T PF00845_consen 74 SLQASFTFPIRCNIDLHYFSSSFFSLKDPIPWKL----------Y----YRVEDTNVHQ-GTHFAKFKGKLKLSTAKH-- 136 (276)
T ss_pred hheeEEEeeeeeeeeeEEeeecceecCCCCCeEE----------E----EEeecCcccc-ceeeeeeeceeeeccccc--
Confidence 3458999999996 222 133444554 46663 2 2222222212 334777766532222221
Q ss_pred eecCCCceecceEEeeeeEEEEecCC
Q 030552 89 IVPSSHNCDAPHVTRTDYQLIDISED 114 (175)
Q Consensus 89 ~~~s~~~~e~p~v~r~~~q~ly~d~d 114 (175)
..+=.+..|.|+--.-||...+-|
T Consensus 137 --S~DI~Fr~PtikILSK~ft~~~vD 160 (276)
T PF00845_consen 137 --SVDIPFRAPTIKILSKQFTEKDVD 160 (276)
T ss_pred --ccccccCCCceEeeecccCcCCCc
Confidence 111224455665555566555544
No 33
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=27.41 E-value=42 Score=24.14 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=21.9
Q ss_pred eeEEEEecCCccEEEecCCCCceecccCCcchhhHHHHHhhcc
Q 030552 105 DYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFA 147 (175)
Q Consensus 105 ~~q~ly~d~d~~~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~ 147 (175)
.++|+.-.. -.++|+|.+|..+|.+.|..=. .+.+.+||.
T Consensus 34 ~vk~i~G~~-P~L~l~d~~g~~~E~i~i~~w~--~d~i~efL~ 73 (78)
T PF08806_consen 34 EVKYIPGAP-PELVLLDEDGEEVERINIEKWK--TDEIEEFLN 73 (78)
T ss_dssp EEEEESS----EEEEE-SSS--SEEEE-SSSS--HCHHHHHHH
T ss_pred EEEEeCCCC-CEEEEEcCCCCEEEEEEcccCC--HHHHHHHHH
Confidence 344554332 3789999999988999886633 344666654
No 34
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=26.78 E-value=86 Score=22.48 Aligned_cols=36 Identities=28% Similarity=0.551 Sum_probs=28.2
Q ss_pred EEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEE
Q 030552 117 VSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVT 155 (175)
Q Consensus 117 ~~fMd~~t~~~eqi~lp~~~~l~~~~~~~l~eg~~v~V~ 155 (175)
++|+|+.|. +-|..+|.. ++......|.||.-+.+.
T Consensus 2 mvL~De~G~-~I~A~I~~~--~~~~f~~~l~Eg~~y~i~ 37 (95)
T PF02721_consen 2 MVLVDEKGD-KIQATIPKE--LVDKFKDSLKEGSWYTIS 37 (95)
T ss_pred EEEEecCCC-EEEEEECHH--HHHHHHhhcccCCEEEeE
Confidence 689999986 556777754 688899999999876553
No 35
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=26.52 E-value=1.5e+02 Score=21.40 Aligned_cols=38 Identities=13% Similarity=0.173 Sum_probs=22.0
Q ss_pred cCCCcceeeEEeccccC---CceEEEEcCeEeccccccCCccccCcccEEEEEeec
Q 030552 12 ADAGASKTFPQQAGTIR---KNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSK 64 (175)
Q Consensus 12 ~~~~~s~t~~i~as~lr---kG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~K 64 (175)
+-++...+..+..++++ +|+.|.++|+-|. |.++..--
T Consensus 48 ~v~g~~~~L~v~~~d~~~P~~gd~v~~dG~~y~---------------V~~~~~~~ 88 (95)
T PF13856_consen 48 GVEGTQPTLYVFSSDYPKPRRGDRVVIDGESYT---------------VTRFQEED 88 (95)
T ss_dssp ------EEEEE--SS-----TT-EEEETTEEEE---------------EEEEEEET
T ss_pred cccCCceEEEEEcCCCCCCCCCCEEEECCeEEE---------------EeEEecCC
Confidence 44455666667766654 8999999999999 88876543
No 36
>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=25.47 E-value=76 Score=24.56 Aligned_cols=19 Identities=16% Similarity=0.337 Sum_probs=13.0
Q ss_pred eccccCCceEEEEcCeEec
Q 030552 23 QAGTIRKNGYIVIKNRPCK 41 (175)
Q Consensus 23 ~as~lrkG~~i~i~g~pck 41 (175)
...+|++|+.+.|+|+.|.
T Consensus 48 ~~~~i~~Gd~l~i~~~~y~ 66 (117)
T PF03829_consen 48 LKGDIKPGDTLIIGGQEYT 66 (117)
T ss_dssp GG----TT-EEEETTEEEE
T ss_pred ccCCcCCCCEEEECCeEEE
Confidence 5678999999999999999
No 37
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=25.26 E-value=84 Score=24.48 Aligned_cols=19 Identities=5% Similarity=0.060 Sum_probs=17.3
Q ss_pred eccccCCceEEEEcCeEec
Q 030552 23 QAGTIRKNGYIVIKNRPCK 41 (175)
Q Consensus 23 ~as~lrkG~~i~i~g~pck 41 (175)
...+|++|+.+.|+|.-|+
T Consensus 48 ~~~~i~~Gd~l~i~~~~Y~ 66 (120)
T PRK10377 48 LKGALQPGLQFELGQHRYP 66 (120)
T ss_pred ccCccCCCCEEEECCEEEE
Confidence 3577999999999999999
No 38
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=25.21 E-value=2e+02 Score=22.37 Aligned_cols=31 Identities=26% Similarity=0.246 Sum_probs=22.9
Q ss_pred EEEEEEeccCCcEEEEeecCCC-ceecceEEe
Q 030552 73 CHFVGIDIFNGKKLEDIVPSSH-NCDAPHVTR 103 (175)
Q Consensus 73 v~~k~~ni~TGk~~e~~~~s~~-~~e~p~v~r 103 (175)
-.+.+++++.|--+|.+||... .++...|.+
T Consensus 56 ~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r 87 (116)
T PRK05338 56 ETFTVRKISYGVGVERTFPLHSPRIDSIEVVR 87 (116)
T ss_pred ceEEEEEcccCccEEEEecCCCCcccEEEEEE
Confidence 3699999999999999999753 344444433
No 39
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=25.17 E-value=76 Score=22.25 Aligned_cols=19 Identities=11% Similarity=0.274 Sum_probs=12.8
Q ss_pred eccccCCceEEEEcCeEec
Q 030552 23 QAGTIRKNGYIVIKNRPCK 41 (175)
Q Consensus 23 ~as~lrkG~~i~i~g~pck 41 (175)
.-..|++|+.|.++|..++
T Consensus 45 rg~Kl~~GD~V~~~~~~~~ 63 (65)
T PF13275_consen 45 RGKKLRPGDVVEIDGEEYR 63 (65)
T ss_dssp SS----SSEEEEETTEEEE
T ss_pred cCCcCCCCCEEEECCEEEE
Confidence 4457899999999999887
No 40
>TIGR01730 RND_mfp RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane.
Probab=24.73 E-value=2.3e+02 Score=23.60 Aligned_cols=102 Identities=12% Similarity=0.169 Sum_probs=47.0
Q ss_pred EEEEEee-cCCCCcccEEEEEEEe----ccCCcEEEEeecCCCceecceEEeeeeEEEEecCCc-cEEEecC-CCCceec
Q 030552 57 VVEVSTS-KTGKHGHAKCHFVGID----IFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDG-FVSLLTE-TGNTKDD 129 (175)
Q Consensus 57 Vve~~~~-KpGKhG~Akv~~k~~n----i~TGk~~e~~~~s~~~~e~p~v~r~~~q~ly~d~d~-~~~fMd~-~t~~~eq 129 (175)
|..+... .++. +...+++.+-+ +.-|...+-++.....-+...|-+. .+..++.+ +++..+. ..+.+..
T Consensus 207 I~~I~~~~~~~~-~~~~v~~~~~~~~~~l~~G~~v~v~i~~~~~~~~~~iP~~---av~~~~~~~~V~v~~~~~~~~~~~ 282 (322)
T TIGR01730 207 LRFIDPRVDSGT-GTVRVRATFPNPDGRLLPGMFGRVTISLKVRSSAIVVPTQ---AVIEDLNGKYVYVVKNDGKVSKRP 282 (322)
T ss_pred EEEEeccccCCC-CeEEEEEEEcCCCCcCCCCCEEEEEEecCccCCcEEEcHH---HheeCCCccEEEEEeCCCeEEEEE
Confidence 5555432 2233 34556666554 5667777666655443222221111 12222222 4444555 4454455
Q ss_pred ccCCcchhhHHHHHhhccCCCeEEEEEEeeCCe
Q 030552 130 LRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGE 162 (175)
Q Consensus 130 i~lp~~~~l~~~~~~~l~eg~~v~V~~~~~mGe 162 (175)
+.+-...+-.-.+...|.+|+.|.+.=.....+
T Consensus 283 V~v~~~~~~~~~v~~gL~~Gd~Vv~~~~~~l~~ 315 (322)
T TIGR01730 283 VEVGLRNGGYVEIESGLKAGDQIVTAGVVKLRD 315 (322)
T ss_pred EEEccccCCEEEEccCCCCCCEEEEeChhhCCC
Confidence 555432210112556788888766644444433
No 41
>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=24.30 E-value=90 Score=24.37 Aligned_cols=18 Identities=17% Similarity=0.272 Sum_probs=16.6
Q ss_pred ccccCCceEEEEcCeEec
Q 030552 24 AGTIRKNGYIVIKNRPCK 41 (175)
Q Consensus 24 as~lrkG~~i~i~g~pck 41 (175)
.++|++|+.+.|+|+-|+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ 66 (121)
T TIGR00849 49 KGTLKPGQVFMIGGIAYP 66 (121)
T ss_pred cCCcCCCCEEEECCEEEE
Confidence 358999999999999999
No 42
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=24.17 E-value=89 Score=25.03 Aligned_cols=27 Identities=19% Similarity=0.352 Sum_probs=22.4
Q ss_pred hhHHHHHhhccCCCeEEEEEEeeCCee
Q 030552 137 NLLSQIKDGFAEGKDLVVTVMSSMGEE 163 (175)
Q Consensus 137 ~l~~~~~~~l~eg~~v~V~~~~~mGeE 163 (175)
+.+.+|.++|.+|++|.|.|++.....
T Consensus 41 ~fVkdI~d~L~vG~eV~vKVl~ide~G 67 (129)
T COG1098 41 GFVKDIHDHLKVGQEVKVKVLDIDENG 67 (129)
T ss_pred hhHHhHHHHhcCCCEEEEEEEeeccCC
Confidence 368899999999999999998765543
No 43
>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=23.17 E-value=1.6e+02 Score=23.57 Aligned_cols=42 Identities=10% Similarity=0.105 Sum_probs=29.5
Q ss_pred eccccCCceEEEEcCeEeccccccCCccccCcccEEEEEeecC-CCCcccEEE
Q 030552 23 QAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKT-GKHGHAKCH 74 (175)
Q Consensus 23 ~as~lrkG~~i~i~g~pck~~~~~~~~~~~~~~~Vve~~~~Kp-GKhG~Akv~ 74 (175)
+...|++|+.|...|+=. |+. ...|+..+|..| |+|-...+.
T Consensus 82 rip~l~~GD~V~f~GeYe---------~n~-kggvIHWTH~dp~~~h~~Gwl~ 124 (131)
T PF11948_consen 82 RIPWLQKGDQVEFYGEYE---------WNP-KGGVIHWTHHDPRGRHPDGWLK 124 (131)
T ss_pred cCcCcCCCCEEEEEEEEE---------ECC-CCCEEEeeccCCCCCCCCeeEE
Confidence 345799999999999853 222 345999999988 566444444
No 44
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=22.07 E-value=1.3e+02 Score=24.86 Aligned_cols=37 Identities=30% Similarity=0.667 Sum_probs=25.6
Q ss_pred eeeEEEEecCCc-cEEEecCCCCceecccCCcchhhHHHHH
Q 030552 104 TDYQLIDISEDG-FVSLLTETGNTKDDLRLPTDENLLSQIK 143 (175)
Q Consensus 104 ~~~q~ly~d~d~-~~~fMd~~t~~~eqi~lp~~~~l~~~~~ 143 (175)
++..++..++|| .++|.+.+| +.+.||.++.|-..+.
T Consensus 2 ~eLrlvgv~~dg~~Lvl~~~~G---e~f~l~idd~LRaair 39 (170)
T PF11268_consen 2 RELRLVGVDDDGEHLVLEDPDG---ERFRLPIDDRLRAAIR 39 (170)
T ss_pred ceeEEEeEcCCCCEEEEEcCCC---CEEEEecCHHHHHHHh
Confidence 356677777776 677777766 4899999875544443
No 45
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=20.73 E-value=2.6e+02 Score=18.38 Aligned_cols=25 Identities=20% Similarity=0.541 Sum_probs=16.3
Q ss_pred ecccCCcchhhHHHHHhhccCCCeEEEEEEe
Q 030552 128 DDLRLPTDENLLSQIKDGFAEGKDLVVTVMS 158 (175)
Q Consensus 128 eqi~lp~~~~l~~~~~~~l~eg~~v~V~~~~ 158 (175)
+++-||... +..+ ..|+.|.|.++.
T Consensus 20 ~DifIp~~~--l~~A----~~gD~V~v~i~~ 44 (58)
T PF08206_consen 20 EDIFIPPRN--LNGA----MDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-HHH--HTTS-----TT-EEEEEEEE
T ss_pred CCEEECHHH--HCCC----CCCCEEEEEEec
Confidence 789999865 3333 388999998886
No 46
>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=20.25 E-value=52 Score=24.33 Aligned_cols=21 Identities=10% Similarity=0.143 Sum_probs=16.9
Q ss_pred EEeccccCCceEEEEcCeEec
Q 030552 21 PQQAGTIRKNGYIVIKNRPCK 41 (175)
Q Consensus 21 ~i~as~lrkG~~i~i~g~pck 41 (175)
.|++++|+.||||..-.++|.
T Consensus 4 kI~v~~L~~GM~V~~~~~~w~ 24 (128)
T PF11871_consen 4 KIPVDQLKPGMYVSRLDRSWL 24 (128)
T ss_pred EEEHHHCCCCcEEEecCCCcc
Confidence 478899999999987666655
No 47
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=20.13 E-value=1.3e+02 Score=17.59 Aligned_cols=13 Identities=15% Similarity=0.164 Sum_probs=9.4
Q ss_pred CceEEEE-----cCeEec
Q 030552 29 KNGYIVI-----KNRPCK 41 (175)
Q Consensus 29 kG~~i~i-----~g~pck 41 (175)
+|+.|++ +|+.++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~ 18 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGK 18 (32)
T ss_dssp TTSEEEESSSTTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEE
Confidence 4777777 677777
Done!