Query 031387
Match_columns 160
No_of_seqs 158 out of 1046
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 13:23:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031387hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03107 eukaryotic translatio 100.0 2.4E-52 5.2E-57 324.9 19.0 156 1-159 1-159 (159)
2 PTZ00328 eukaryotic initiation 100.0 3.7E-50 8E-55 312.3 16.6 159 1-159 1-166 (166)
3 TIGR00037 eIF_5A translation i 100.0 2.8E-47 6.1E-52 288.0 16.2 130 16-154 1-130 (130)
4 KOG3271 Translation initiation 100.0 1.7E-44 3.7E-49 273.1 11.9 155 1-158 1-155 (156)
5 PRK03999 translation initiatio 100.0 8.9E-43 1.9E-47 263.1 15.9 126 20-154 4-129 (129)
6 COG0231 Efp Translation elonga 100.0 2.2E-41 4.7E-46 256.2 14.6 127 20-154 2-128 (131)
7 PRK12426 elongation factor P; 100.0 1.4E-39 3.1E-44 258.4 14.8 123 22-154 2-124 (185)
8 PRK14578 elongation factor P; 100.0 2.4E-38 5.2E-43 251.9 15.0 124 22-154 2-126 (187)
9 PRK04542 elongation factor P; 100.0 5.1E-38 1.1E-42 250.3 14.6 124 22-154 2-127 (189)
10 TIGR02178 yeiP elongation fact 100.0 7.5E-37 1.6E-41 243.1 14.9 122 24-154 2-125 (186)
11 PRK00529 elongation factor P; 100.0 2E-36 4.2E-41 240.8 16.2 123 22-154 2-124 (186)
12 TIGR00038 efp translation elon 100.0 2.1E-36 4.6E-41 240.3 15.1 123 22-154 1-123 (184)
13 PF08207 EFP_N: Elongation fac 99.9 1E-21 2.2E-26 129.5 8.8 58 23-81 1-58 (58)
14 cd04470 S1_EF-P_repeat_1 S1_EF 99.6 3.1E-16 6.7E-21 104.2 6.2 59 87-154 1-59 (61)
15 PF01132 EFP: Elongation facto 99.6 3.4E-16 7.4E-21 102.0 3.8 52 88-144 1-52 (55)
16 PF01287 eIF-5a: Eukaryotic el 99.6 1.4E-14 3.1E-19 98.6 8.8 69 85-154 1-69 (69)
17 cd04468 S1_eIF5A S1_eIF5A: Euk 99.5 1.5E-13 3.2E-18 93.5 7.6 68 86-155 1-68 (69)
18 cd04469 S1_Hex1 S1_Hex1: Hex1, 99.4 8.7E-13 1.9E-17 91.1 8.2 70 89-159 3-73 (75)
19 cd04463 S1_EF_like S1_EF_like: 99.4 3.5E-13 7.6E-18 87.2 5.1 49 89-143 1-49 (55)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.7 1.9E-08 4.2E-13 66.1 4.9 56 86-150 1-56 (57)
21 COG1499 NMD3 NMD protein affec 96.9 0.012 2.7E-07 51.5 10.6 110 11-142 231-344 (355)
22 PF08605 Rad9_Rad53_bind: Fung 85.1 2.2 4.8E-05 32.4 5.0 53 7-61 42-103 (131)
23 PF13509 S1_2: S1 domain; PDB: 62.4 15 0.00032 23.7 3.7 47 101-154 15-61 (61)
24 PF13275 S4_2: S4 domain; PDB: 62.0 10 0.00022 25.4 2.9 21 23-43 45-65 (65)
25 smart00676 DM10 Domains in hyp 61.2 7 0.00015 28.3 2.2 26 21-46 68-93 (104)
26 smart00466 SRA SET and RING fi 60.4 31 0.00068 26.8 5.8 38 26-65 115-152 (155)
27 PF13785 DUF4178: Domain of un 51.0 16 0.00035 26.7 2.8 23 27-49 1-23 (140)
28 PF13856 Gifsy-2: ATP-binding 49.8 41 0.00088 23.5 4.5 38 12-49 48-88 (95)
29 PF05354 Phage_attach: Phage H 49.6 16 0.00035 27.3 2.5 34 22-58 70-103 (117)
30 PRK05338 rplS 50S ribosomal pr 48.1 75 0.0016 23.6 5.9 55 23-79 15-77 (116)
31 PF06605 Prophage_tail: Propha 46.6 54 0.0012 27.5 5.6 38 25-64 26-63 (327)
32 PF03829 PTSIIA_gutA: PTS syst 45.1 27 0.00059 25.9 3.1 23 23-45 48-70 (117)
33 PF07076 DUF1344: Protein of u 44.8 47 0.001 22.0 3.9 36 114-154 26-61 (61)
34 PRK11507 ribosome-associated p 44.4 25 0.00054 23.9 2.6 22 22-43 48-69 (70)
35 PF05096 Glu_cyclase_2: Glutam 44.2 2E+02 0.0043 24.4 8.8 82 18-110 37-120 (264)
36 COG0090 RplB Ribosomal protein 43.2 1.1E+02 0.0023 26.2 6.7 55 25-82 122-183 (275)
37 PRK10377 PTS system glucitol/s 43.1 34 0.00073 25.5 3.4 22 24-45 49-70 (120)
38 TIGR00849 gutA PTS system, glu 42.2 36 0.00077 25.5 3.4 22 24-45 49-70 (121)
39 TIGR01563 gp16_SPP1 phage head 41.7 1.1E+02 0.0024 20.7 6.8 34 8-42 45-81 (101)
40 PF05521 Phage_H_T_join: Phage 40.9 1E+02 0.0022 20.2 6.5 33 17-49 52-85 (95)
41 cd06409 PB1_MUG70 The MUG70 pr 40.9 57 0.0012 22.9 4.1 50 60-110 3-63 (86)
42 COG3535 Uncharacterized conser 40.0 2.7E+02 0.0058 24.7 9.5 90 30-141 236-325 (357)
43 COG2501 S4-like RNA binding pr 39.9 34 0.00075 23.5 2.7 22 24-45 50-71 (73)
44 TIGR01024 rplS_bact ribosomal 38.3 1.4E+02 0.003 22.1 5.9 56 22-79 14-77 (113)
45 PRK11354 kil FtsZ inhibitor pr 38.2 44 0.00095 22.9 3.0 25 19-43 8-32 (73)
46 PF08408 DNA_pol_B_3: DNA poly 38.1 26 0.00055 27.3 2.1 24 24-47 37-60 (149)
47 PF10665 Minor_capsid_1: Minor 37.6 41 0.00088 24.8 3.1 27 23-49 73-99 (114)
48 PF11871 DUF3391: Domain of un 36.9 18 0.00039 26.0 1.1 20 21-40 4-23 (128)
49 PF08294 TIM21: TIM21; InterP 36.3 1.9E+02 0.0042 22.0 6.8 30 36-67 91-120 (145)
50 CHL00084 rpl19 ribosomal prote 36.2 1.8E+02 0.0039 21.6 6.3 54 22-79 18-81 (117)
51 PLN00208 translation initiatio 34.1 2.2E+02 0.0048 22.0 7.3 90 49-153 4-93 (145)
52 PF02182 SAD_SRA: SAD/SRA doma 34.1 1E+02 0.0022 23.7 4.9 35 29-65 118-152 (155)
53 cd01771 Faf1_UBX Faf1 UBX doma 31.7 74 0.0016 21.7 3.4 20 65-84 11-30 (80)
54 PF11302 DUF3104: Protein of u 31.0 1.8E+02 0.0038 20.1 5.1 46 26-71 5-60 (75)
55 cd04709 BAH_MTA BAH, or Bromo 30.3 93 0.002 24.3 4.2 22 25-46 2-26 (164)
56 PF00845 Gemini_BL1: Geminivir 30.0 1.3E+02 0.0029 25.5 5.2 83 13-103 74-163 (276)
57 COG4043 Preprotein translocase 29.6 76 0.0017 23.3 3.3 15 24-38 31-45 (111)
58 PF11948 DUF3465: Protein of u 28.8 1.1E+02 0.0023 23.4 4.1 38 24-61 83-126 (131)
59 PF00467 KOW: KOW motif; Inte 27.5 96 0.0021 17.2 2.9 21 29-49 1-26 (32)
60 cd00603 IPT_PCSR IPT domain of 27.4 1.9E+02 0.0041 19.1 6.7 42 11-52 10-59 (90)
61 PRK12795 fliM flagellar motor 27.1 1.7E+02 0.0036 26.0 5.7 44 24-68 320-370 (388)
62 PF07591 PT-HINT: Pretoxin HIN 26.5 77 0.0017 23.5 3.0 27 21-47 71-98 (130)
63 COG1030 NfeD Membrane-bound se 26.2 1.4E+02 0.003 27.2 5.0 38 22-63 383-421 (436)
64 COG3721 HugX Putative heme iro 25.3 1.5E+02 0.0033 23.5 4.4 47 50-96 93-139 (176)
65 PF13501 SoxY: Sulfur oxidatio 24.9 2.1E+02 0.0045 20.8 5.0 52 12-64 26-80 (111)
66 PF01079 Hint: Hint module; I 24.7 1.2E+02 0.0025 24.8 3.9 29 20-48 99-133 (217)
67 PF08806 Sep15_SelM: Sep15/Sel 24.6 55 0.0012 22.4 1.8 41 89-132 33-73 (78)
68 cd01767 UBX UBX (ubiquitin reg 24.2 79 0.0017 20.8 2.5 24 57-83 4-27 (77)
69 PF02721 DUF223: Domain of unk 24.1 1.4E+02 0.0031 20.5 3.9 45 102-149 2-49 (95)
70 PTZ00329 eukaryotic translatio 24.0 3.6E+02 0.0077 21.1 7.5 88 49-151 4-91 (155)
71 PF01245 Ribosomal_L19: Riboso 22.9 3.1E+02 0.0068 20.1 7.8 65 22-88 14-87 (113)
72 COG5131 URM1 Ubiquitin-like pr 22.7 60 0.0013 23.3 1.7 37 17-54 48-84 (96)
73 PF00924 MS_channel: Mechanose 22.1 73 0.0016 24.5 2.2 23 24-46 58-80 (206)
74 TIGR01397 fliM_switch flagella 21.2 1.9E+02 0.0041 24.3 4.7 41 24-65 271-318 (320)
75 PF13144 SAF_2: SAF-like 21.1 3.9E+02 0.0085 20.6 7.7 24 59-82 172-195 (196)
76 PF00436 SSB: Single-strand bi 21.0 2.1E+02 0.0047 19.2 4.3 17 25-41 64-80 (104)
77 COG1326 Uncharacterized archae 20.5 1.2E+02 0.0026 24.7 3.2 28 24-52 72-99 (201)
78 KOG1999 RNA polymerase II tran 20.4 3.2E+02 0.007 27.5 6.5 78 64-147 397-476 (1024)
79 cd01179 IPT_plexin_repeat2 Sec 20.3 2.8E+02 0.006 18.5 4.9 34 12-45 11-46 (85)
No 1
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=2.4e-52 Score=324.92 Aligned_cols=156 Identities=87% Similarity=1.333 Sum_probs=146.4
Q ss_pred CCccccccccccCCCceeeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCc
Q 031387 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (160)
Q Consensus 1 ~~~~~~~f~~~~~~~~s~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ 80 (160)
||++|++|+ ++++|||.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|||+++
T Consensus 1 ~~~~~~~~~-~~~~~~~~t~m~~~~~lKkG~~I~~~g~pc~V~e~~~~KpGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ 79 (159)
T PLN03107 1 MSDEEHHFE-SADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHN 79 (159)
T ss_pred CCccccccc-ccccCCCceeccchHhccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEecCCCE
Confidence 888778999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecceEEEeeeEEEEecCCCcEEEecCC--CCceecccCCc-chhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEeccC
Q 031387 81 CDAPHVTRTDYQLIDISEDGFVSLLTET--GNTKDDLRLPT-DENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIG 157 (160)
Q Consensus 81 ve~~~ve~~~~qyly~d~d~~~~fMd~e--ty~~Eqi~l~~-~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k~~~ 157 (160)
+++|+|++++|||||.|++++|+|||++ +| ||+.||+ +.+|..++..++.+|.++.|++|++||+|+|+++|+..
T Consensus 80 ve~~~ve~~~~qyly~dgd~y~~fMD~~get~--eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~~mg~e~i~~~k~~~ 157 (159)
T PLN03107 80 CDVPHVNRTDYQLIDISEDGFVSLMDESGNTK--DDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMSAMGEEQICALKEIG 157 (159)
T ss_pred EEEEEEEEEEEEEEEEcCCceEEEEcCCCCcc--eeEEccCcchHHHHHHHHHHhCCCeEEEEEEecCCeEEEEEEEccC
Confidence 9999999999999999987446999995 66 9999997 44578889999999999999999999999999999976
Q ss_pred CC
Q 031387 158 PK 159 (160)
Q Consensus 158 ~~ 159 (160)
|+
T Consensus 158 ~~ 159 (159)
T PLN03107 158 PK 159 (159)
T ss_pred CC
Confidence 64
No 2
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=3.7e-50 Score=312.29 Aligned_cols=159 Identities=46% Similarity=0.836 Sum_probs=150.8
Q ss_pred CCcccccccc-ccCCCceeeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCC
Q 031387 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (160)
Q Consensus 1 ~~~~~~~f~~-~~~~~~s~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~ 79 (160)
|||+|++|++ +++|++|.|||++++.||+|.||+|+|+||+|++++++||||||+|++|+.+++||||+++|..+|+++
T Consensus 1 m~d~~~~f~~~~~~~gas~t~p~q~~~LkkG~yvvIkGrPCKIveistSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~h 80 (166)
T PTZ00328 1 MSDEDHDFSHQGGGDNASKTYPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTH 80 (166)
T ss_pred CCccccccccccCCCCCCceecccccceeECCEEEECCeeeEEEEEecCCCCcCCceEEEEEEEecCCCCEEeeecCccc
Confidence 8997789995 699999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceecceEEEeeeEEEEecCC------CcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEE
Q 031387 80 NCDAPHVTRTDYQLIDISED------GFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICAL 153 (160)
Q Consensus 80 ~ve~~~ve~~~~qyly~d~d------~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~ 153 (160)
++++|.|+|++||+|.+++| +++.+||+++|+|+++.||.+.+|..+++..+.+|.+|.|++|++||+|+|+++
T Consensus 81 nv~VP~V~r~~yqli~I~~d~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~v~vi~amG~e~ii~~ 160 (166)
T PTZ00328 81 NVEVPFVKTFTYSVLDIQPNEDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVVSAMGTEQVLQT 160 (166)
T ss_pred eeEeeeEEeeEEEEEEEcCCCcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEEEEEEhhCCeeehhee
Confidence 99999999999999999876 689999999999999999974347777999999999999999999999999999
Q ss_pred eccCCC
Q 031387 154 KDIGPK 159 (160)
Q Consensus 154 k~~~~~ 159 (160)
|+.++|
T Consensus 161 k~~~~~ 166 (166)
T PTZ00328 161 KNAAEK 166 (166)
T ss_pred hhhhcC
Confidence 998875
No 3
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=2.8e-47 Score=287.98 Aligned_cols=130 Identities=41% Similarity=0.679 Sum_probs=123.8
Q ss_pred ceeeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEE
Q 031387 16 ASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLID 95 (160)
Q Consensus 16 ~s~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly 95 (160)
+|.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|++|+|++++++|+|++++|||||
T Consensus 1 ~~~~~~~~~~~irkG~~i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~qylY 80 (130)
T TIGR00037 1 MSATKQVQVSALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQVLA 80 (130)
T ss_pred CCcceeccHHHccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEEEEE
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 96 ISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 96 ~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
.||+ .|+|||++|| ||+.||.+ . ++.+||++|++ |.++++||+|+|+++|
T Consensus 81 ~dg~-~~~fMd~ety--eq~~i~~~---~-~~~~~Lke~~~--V~v~~~~g~~~~~~~~ 130 (130)
T TIGR00037 81 IMGG-MVQLMDLDTY--ETDELPIP---E-ELGDSLEPGFE--VEYIEAMGQEKIIRFK 130 (130)
T ss_pred ecCC-EEEEEcCCCc--EEEEecCC---h-hHHHHhhcCCE--EEEEecCCeEEEEEeC
Confidence 9866 8999999999 99999987 3 78999999997 5669999999999987
No 4
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-44 Score=273.14 Aligned_cols=155 Identities=66% Similarity=1.016 Sum_probs=150.0
Q ss_pred CCccccccccccCCCceeeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCc
Q 031387 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (160)
Q Consensus 1 ~~~~~~~f~~~~~~~~s~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ 80 (160)
|||+||+|+ ++++|+|.|||+|++.||++.+|+|+|+||+|||++++|+||||+|++++..++||||+++|..+||+|+
T Consensus 1 Msd~~~~Fe-~~dagas~t~p~q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn 79 (156)
T KOG3271|consen 1 MSDEEHRFE-TGDAGASATYPMQCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHN 79 (156)
T ss_pred CCccccccc-cCCCcccccccchhhheeeCCEEEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCc
Confidence 899999999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecceEEEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEeccCC
Q 031387 81 CDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIGP 158 (160)
Q Consensus 81 ve~~~ve~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k~~~~ 158 (160)
+++|+++|.+||++.++++ ++.||++++++++++.+|..+ |..++..-+.+|.++.|++.++||+|.+++.|.+++
T Consensus 80 ~dVp~vkr~~yqLidIsd~-~~sl~t~sG~~kdDlklp~~e-l~~~i~~~~e~g~dl~v~Vlsa~gee~~~a~k~~~~ 155 (156)
T KOG3271|consen 80 MDVPVVKRVDYQLIDISDG-YLSLMTDSGETKDDLKLPEGE-LGNQIRQGFEEGKDLLVTVLSAMGEEAAVAPKSGAG 155 (156)
T ss_pred cccCccccceeEEEEecCC-eEEEEcCCCCcchhccCcchh-HHHHHHHhhcCCCcEEEEEhhhhCchhheeecccCC
Confidence 9999999999999999855 999999999999999999987 777899999999999999999999999999998765
No 5
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=8.9e-43 Score=263.12 Aligned_cols=126 Identities=31% Similarity=0.595 Sum_probs=119.7
Q ss_pred EEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCC
Q 031387 20 FPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISED 99 (160)
Q Consensus 20 ~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d 99 (160)
-|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+++++++.|.|++++|||||.|++
T Consensus 4 ~~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~ 83 (129)
T PRK03999 4 KQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGD 83 (129)
T ss_pred ccccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999976
Q ss_pred CcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 100 GFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 100 ~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
.|+|||++|| ||+.|+.+ ++++.||+||++| .++.+||+|+|+++|
T Consensus 84 -~~~fMd~eTy--eq~~i~~~----~d~~~~l~eg~~v--~v~~~~g~~~~~~~~ 129 (129)
T PRK03999 84 -VVQLMDLETY--ETFEIPIP----EELKDKLEPGVEV--EYWEAMGRRKIMRVK 129 (129)
T ss_pred -EEEEecCCCc--eEEEecCC----hhHHhhCcCCCEE--EEEhhCCeEEEEEeC
Confidence 8999999999 99999986 4688999999964 579999999999987
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=2.2e-41 Score=256.17 Aligned_cols=127 Identities=28% Similarity=0.379 Sum_probs=117.0
Q ss_pred EEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCC
Q 031387 20 FPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISED 99 (160)
Q Consensus 20 ~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d 99 (160)
.++++++||+|++|+++|+||+|++++|+||||| +|++|+++|||+||+++|.+||++++++.|.|+++++||||.||+
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg-~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~ 80 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGKG-GAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGD 80 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCCC-CcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCC
Confidence 4789999999999999999999999999999995 569999999999999999999999999999999999999999977
Q ss_pred CcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 100 GFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 100 ~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
.|+|||++|| ||+.+|.+. +++++.||+||++|.|++ .+|+...+.+.
T Consensus 81 -~~~FMD~ety--eq~~v~~~~--~~d~~~~l~eg~~v~v~~--~~g~~i~v~lP 128 (131)
T COG0231 81 -FYVFMDLETY--EQYELPKDQ--IGDAAKFLKEGMEVEVLL--YNGEPIAVELP 128 (131)
T ss_pred -eEEEccCCCc--eEEEecchh--hhhHHHhcCCCCEEEEEE--ECCEEEEEECC
Confidence 8999999999 999999996 899999999999976654 56777666554
No 7
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=1.4e-39 Score=258.44 Aligned_cols=123 Identities=13% Similarity=0.117 Sum_probs=116.1
Q ss_pred EeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCc
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGF 101 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~ 101 (160)
+++|+||+|++|+++|+||.|++++|+|||| |+|++|+|+|||.||+++|+||+|+++++.|+|+++++||||.||+ .
T Consensus 2 ~~~~dik~G~~i~~~g~~~~V~~~~h~kPGk-g~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~qylY~dg~-~ 79 (185)
T PRK12426 2 VLSSQLSVGMFISTKDGLYKVVSVSKVTGPK-GETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGD-E 79 (185)
T ss_pred CchhhcCCCCEEEECCEEEEEEEEEEecCCC-CceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEECCC-e
Confidence 5789999999999999999999999999999 8999999999999999999999999999999999999999999977 8
Q ss_pred EEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 102 VSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 102 ~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
|+|||++|| ||+.|+++. +++...||+||+.|.|++|+. .++++.
T Consensus 80 ~~FMd~ety--eQi~i~~~~--lgd~~~fL~e~~~v~v~~~~~----~~i~v~ 124 (185)
T PRK12426 80 YLFLDLGNY--DKIYIPKEI--MKDNFLFLKAGVTVSALVYDG----TVFSVE 124 (185)
T ss_pred EEEecCCCc--eEEEeCHHH--hhhHHhhccCCCEEEEEEECC----EEEEEE
Confidence 999999999 999999984 999999999999999999964 366654
No 8
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=2.4e-38 Score=251.94 Aligned_cols=124 Identities=13% Similarity=0.250 Sum_probs=115.1
Q ss_pred EeccccCCceEEEEcCeeEEEEEeeeecCCCC-cccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCC
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDG 100 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKh-G~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~ 100 (160)
+++++||+|++|+++|+||+|++++|+||||+ |+|++|+|+|||+||+++|+||+|+++++.|+|+++++||||.||+
T Consensus 2 ~~~~dik~G~~i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~qylY~dg~- 80 (187)
T PRK14578 2 YTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGD- 80 (187)
T ss_pred CchhhcCCCCEEEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeEEEEeCCC-
Confidence 57899999999999999999999999999985 4679999999999999999999999999999999999999999977
Q ss_pred cEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 101 FVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 101 ~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
.|+|||++|| ||+.||++. +|+...||+||++|.|++|+. .++++.
T Consensus 81 ~~~FMD~ety--EQ~~i~~~~--~g~~~~fL~e~~~v~v~~~~~----~~i~v~ 126 (187)
T PRK14578 81 RGVFMDLETY--EQFEMEEDA--FSAIAPFLLDGTEVQLGLFQG----RMVNVD 126 (187)
T ss_pred EEEEecCCCc--EEEEecHHH--hhhHHhhccCCCEEEEEEECC----EEEEEE
Confidence 8999999999 999999984 999999999999999999954 355554
No 9
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=5.1e-38 Score=250.34 Aligned_cols=124 Identities=18% Similarity=0.196 Sum_probs=115.3
Q ss_pred EeccccCCceEEEEcCeeEEEEEeeeecC-CCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCC
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDG 100 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve~~~~kp-GKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~ 100 (160)
+++|+||+|++|+++|+||+|++++|+|| ||+|+|++|+|+|||.||+++++||+|+++++.|+|++++|||||.|++
T Consensus 2 i~~~dik~G~~i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~qylY~dg~- 80 (189)
T PRK04542 2 PKANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGD- 80 (189)
T ss_pred CchhhcCCCCEEEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCC-
Confidence 67899999999999999999999999999 7955679999999999999999999999999999999999999999977
Q ss_pred cEEEecCCCCceecccCCcchhhHHHHHhhccCCCe-EEEEEEccCCcEEEEEEe
Q 031387 101 FVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKD-LVVTVMSSMGEEQICALK 154 (160)
Q Consensus 101 ~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~-v~v~~~~~mg~e~v~~~k 154 (160)
.|+|||++|| ||+.||++. +++..+||+||++ |.|++|+. .++++.
T Consensus 81 ~~~FMd~ety--EQ~~i~~~~--lgd~~~~L~e~~~~v~v~~~~~----~~i~v~ 127 (189)
T PRK04542 81 EYVFMDNEDY--TPYTFKKDQ--IEDELLFIPEGMPGMQVLTVDG----QPVALE 127 (189)
T ss_pred EEEEecCCCc--eEEEECHHH--hhhHhhhhhcCCEEEEEEEECC----EEEEEE
Confidence 8999999999 999999974 9999999999998 99999965 366654
No 10
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=100.00 E-value=7.5e-37 Score=243.13 Aligned_cols=122 Identities=15% Similarity=0.210 Sum_probs=113.1
Q ss_pred ccccCCceEEEEcCeeEEEEEeeeecCCCCccc-EEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCcE
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFV 102 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A-~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~~ 102 (160)
+++||+|++|+++|+||+|++++|+|||++|+| ++|+++|||.||+++++||+|+++++.|+|+++++||||.|++ .|
T Consensus 2 ~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~-~~ 80 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGE-EY 80 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCC-eE
Confidence 689999999999999999999999999885655 8999999999999999999999999999999999999999977 89
Q ss_pred EEecCCCCceecccCCcchhhHHHHHhhccCCCe-EEEEEEccCCcEEEEEEe
Q 031387 103 SLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKD-LVVTVMSSMGEEQICALK 154 (160)
Q Consensus 103 ~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~-v~v~~~~~mg~e~v~~~k 154 (160)
+|||++|| ||+.|+++. +++...||+||++ |.|++|+. .++++.
T Consensus 81 ~FMD~ety--EQ~~i~~~~--lgd~~~fL~e~~~~v~v~~~~~----~~i~v~ 125 (186)
T TIGR02178 81 VFMDEEDY--TPYTFDKDA--IEDELLFISEGLSGMYVQLIDG----SPVALE 125 (186)
T ss_pred EEccCCCc--EEEEeCHHH--hhhhhhhhhCCCEEEEEEEECC----EEEEEE
Confidence 99999999 999999984 9999999999997 99999953 366655
No 11
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=2e-36 Score=240.84 Aligned_cols=123 Identities=20% Similarity=0.301 Sum_probs=116.0
Q ss_pred EeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCc
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGF 101 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~ 101 (160)
+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||+++|++|+++++++.|.++++++||||.|++ .
T Consensus 2 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dgd-~ 79 (186)
T PRK00529 2 ISANDLRKGLVIEIDGEPYVVLEFEHVKPGK-GQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGD-G 79 (186)
T ss_pred cchhhcCCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECCC-E
Confidence 5789999999999999999999999999999 8999999999999999999999999999999999999999999977 7
Q ss_pred EEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 102 VSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 102 ~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
|+|||+++| ||+.||.+. +++..+||+||++|.|++|+ +.++++.
T Consensus 80 ~~fMD~ety--eq~~l~~~~--lg~~~~~L~eg~~v~v~~~~----~~~i~v~ 124 (186)
T PRK00529 80 YVFMDTETY--EQIEVPADQ--VGDAAKFLKEGMEVTVVFYN----GEPISVE 124 (186)
T ss_pred EEEecCCCc--eeeEcCHHH--hHHHHhhccCCCEEEEEEEC----CEEEEEE
Confidence 999999999 999999984 99999999999999999995 3466654
No 12
>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=2.1e-36 Score=240.31 Aligned_cols=123 Identities=22% Similarity=0.305 Sum_probs=115.1
Q ss_pred EeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCc
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGF 101 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~ 101 (160)
+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++++|+++++++.|.++++++||||.|++ .
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dgd-~ 78 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGK-GQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGD-S 78 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECCC-E
Confidence 4689999999999999999999999999999 8999999999999999999999999999999999999999999977 7
Q ss_pred EEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 102 VSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 102 ~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
|+|||+++| ||+.||.+. +++...||+||++|.|++|+. .++++.
T Consensus 79 ~~fMD~ety--eq~~i~~~~--l~~~~~~L~eg~~v~v~~~~~----~~i~v~ 123 (184)
T TIGR00038 79 YVFMDTETY--EQIELPKDL--LGDAAKFLKENMEVSVTFYNG----EPIGVE 123 (184)
T ss_pred EEEeCCCCc--cceEcCHHH--HHHHHhhcCCCCEEEEEEECC----EEEEEE
Confidence 999999999 999999884 999999999999999999953 355554
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=99.87 E-value=1e-21 Score=129.46 Aligned_cols=58 Identities=28% Similarity=0.344 Sum_probs=53.3
Q ss_pred eccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCce
Q 031387 23 QAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (160)
Q Consensus 23 ~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~v 81 (160)
++++||+|++|+++|+||.|++++|++||| |+|++++++|||.||+++|.+|+|+|+|
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 SASDLRKGMVIEIDGEPYVVLDFQHVKPGK-GGAFVRVKLKNLRTGSKVEKTFRSGDKV 58 (58)
T ss_dssp EGGG--TTSEEEETTEEEEEEEEEEECCTT-SSSEEEEEEEETTTTEEEEEEEETT-EE
T ss_pred CHHHccCCCEEEECCEEEEEEEEEEECCCC-CCeEEEEEEEECCCCCEEEEEECCCCcC
Confidence 589999999999999999999999999999 8999999999999999999999999985
No 14
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.65 E-value=3.1e-16 Score=104.24 Aligned_cols=59 Identities=14% Similarity=0.266 Sum_probs=52.3
Q ss_pred EEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 87 TRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 87 e~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
+++++||||.||+ .|+|||++|| ||+.||++. +|+..+||+||++|.|++|+ ..++++.
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--LGDAAKFLKEGMEVIVLFYN----GEPIGVE 59 (61)
T ss_pred CCceEEEEEeCCC-EEEEeCCCCc--eEEEECHHH--hhhHHhhCcCCCEEEEEEEC----CEEEEEE
Confidence 4789999999977 8999999999 999999985 99999999999999999996 3366654
No 15
>PF01132 EFP: Elongation factor P (EF-P) OB domain; InterPro: IPR001059 Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet []. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. This entry reresents the central domain of elongation factor P and its homologues. It forms an oligonucleotide-binding (OB) fold, though it is not clear if this region is involved in binding nucleic acids [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation; PDB: 1YBY_A 3A5Z_H 3TRE_A 1UEB_B 3HUW_V 3HUY_V 3OYY_B.
Probab=99.62 E-value=3.4e-16 Score=102.01 Aligned_cols=52 Identities=17% Similarity=0.292 Sum_probs=44.8
Q ss_pred EeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEcc
Q 031387 88 RTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSS 144 (160)
Q Consensus 88 ~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~ 144 (160)
+|++||||.||+ .|+|||++|| ||+.||++. +|+..+||+||++|.|++|+.
T Consensus 1 ~r~~qylY~dgd-~~~FMd~ety--eQi~v~~~~--~g~~~~~L~eg~~v~v~~~~~ 52 (55)
T PF01132_consen 1 RREMQYLYKDGD-NYVFMDTETY--EQIEVPKDQ--LGDALKFLKEGMEVQVLFYEG 52 (55)
T ss_dssp EEEEEEEEEESS-EEEEEETTT----EEEEEHHH--HTTTGCC--TTEEEEEEEETT
T ss_pred CceEEEEEeCCC-EEEEecCCCc--eEEEecHHH--hChHHhhCcCCCEEEEEEECC
Confidence 689999999988 7999999999 999999985 999999999999999999974
No 16
>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=99.58 E-value=1.4e-14 Score=98.58 Aligned_cols=69 Identities=57% Similarity=0.916 Sum_probs=61.1
Q ss_pred eEEEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 85 HVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 85 ~ve~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
+|+|++||++.+++|+++++||.++-++|+++||... +..+++..+.+|.++.|++|++||+|+|+++|
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMde~get~eDl~lP~~e-l~~ei~~~~~~g~~~~Vtv~~amG~e~ii~~K 69 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMDEDGETREDLKLPDGE-LGEEIKAKFEEGKEVLVTVLSAMGEEKIIAVK 69 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEETTS-EEEEEECCSHH-HHHHHHHHHHTTCEEEEEEEEETTEEEEEEEE
T ss_pred CeEEEEEEEEEEccCcEEEEEcCCCCeeccEEecccc-hhHHHHhhccCCCeEEEEEEeeCCcEEEEEeC
Confidence 4899999999999888999999777777889999764 67779999999999999999999999999998
No 17
>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=99.48 E-value=1.5e-13 Score=93.51 Aligned_cols=68 Identities=56% Similarity=0.963 Sum_probs=62.6
Q ss_pred EEEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEec
Q 031387 86 VTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKD 155 (160)
Q Consensus 86 ve~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k~ 155 (160)
|.|++||++++++ |++++|++++-+|++++||.+. +..+++..+.+|.++.|++.++||+|+++++|+
T Consensus 1 V~R~eYqLidI~d-GflsLm~e~G~~k~DlklP~~e-lg~~I~~~f~~gk~~~vtV~samGeE~~i~~K~ 68 (69)
T cd04468 1 VKRTEYQLIDIDD-GFLSLMDDDGETREDLKLPEGE-LGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKE 68 (69)
T ss_pred CcceeEEEEeecC-CeEEEEcCCCCcccCCcCCcHH-HHHHHHHHHhCCCcEEEEEEccCCcEeeEEeec
Confidence 5689999999975 7999999999999999999875 677788889999999999999999999999996
No 18
>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=99.42 E-value=8.7e-13 Score=91.09 Aligned_cols=70 Identities=30% Similarity=0.553 Sum_probs=62.6
Q ss_pred eeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCC-eEEEEEEccCCcEEEEEEeccCCC
Q 031387 89 TDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGK-DLVVTVMSSMGEEQICALKDIGPK 159 (160)
Q Consensus 89 ~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~-~v~v~~~~~mg~e~v~~~k~~~~~ 159 (160)
++||++.+ +||++++|++++.+|++++||.+.++..+++.-+.+|. ++.|++.++||+|+++++|++++.
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 68999999 47799999999999999999944347777888889999 999999999999999999998863
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=99.41 E-value=3.5e-13 Score=87.22 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=43.7
Q ss_pred eeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEc
Q 031387 89 TDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMS 143 (160)
Q Consensus 89 ~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~ 143 (160)
|++||||.|++ .++|||++|| ||+.+|++. . +...||++|++|.|.+|+
T Consensus 1 ~~~qylY~dg~-~~~fMd~ety--eq~~v~~~~--~-~~~~~l~eg~~v~v~~~~ 49 (55)
T cd04463 1 RELQVLDIQGS-KPVTMDLETY--EVVQVPPPV--D-QSFESFEPGEVVLVDTRT 49 (55)
T ss_pred CCEEEEEcCCC-EeEEecCCCc--eEEEeCHHH--h-hHHhhCCCCCEEEEEEEC
Confidence 57999999876 8999999999 999999983 4 489999999999998875
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=98.74 E-value=1.9e-08 Score=66.07 Aligned_cols=56 Identities=30% Similarity=0.505 Sum_probs=45.7
Q ss_pred EEEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEE
Q 031387 86 VTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQI 150 (160)
Q Consensus 86 ve~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v 150 (160)
|+||..|.++.+++ ...+||++|| |.+.+|..+ +.+.-+++|.+|. +|.+||+.++
T Consensus 1 i~k~~aqVisi~g~-~vQlMD~eTY--eT~ev~~p~----~~~~~i~~G~eV~--y~~~~g~~ki 56 (57)
T cd04467 1 IERKTGQVLSIMGD-VVQLMDLETY--ETFEVPIPE----EIKDKLEPGKEVE--YWESMGKRKI 56 (57)
T ss_pred CcceEEEEEEEcCC-EEEEeccccc--eeEEEecch----hhcccCCCCCEEE--EEeecCeEec
Confidence 57999999999977 8999999999 777777643 2344578999765 7999999886
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=96.89 E-value=0.012 Score=51.45 Aligned_cols=110 Identities=13% Similarity=0.178 Sum_probs=78.3
Q ss_pred ccCCCceeeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEE--
Q 031387 11 KADAGASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTR-- 88 (160)
Q Consensus 11 ~~~~~~s~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~-- 88 (160)
+|-.-.-.||.+..-++++|+.|.++|.++.++.. -|+ .+.++|+.|+...+.++.-...-+...+..
T Consensus 231 tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~~----~~~------~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~ 300 (355)
T COG1499 231 TGKRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVRS----IGK------GIVVLDLETGEPVEITWSVYKRNEGKVAVKEP 300 (355)
T ss_pred CCceEEEEEEEEECCCCCCCCEEEECCCeEEEEEE----ecC------ceEEEecccCCccccChhhcccCcceeeeccc
Confidence 44444567999999999999999999976665533 466 389999999988887775544444222222
Q ss_pred --eeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEE
Q 031387 89 --TDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVM 142 (160)
Q Consensus 89 --~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~ 142 (160)
+.+-++..+++ ...|||.+|| |-+++... -+.+|.++.+..+
T Consensus 301 ~~~~~~vvs~~~~-~~~v~d~et~--e~~~~~~~---------~~~~g~~v~v~~~ 344 (355)
T COG1499 301 RLKKAVVVSRDPS-AIQVLDPETY--EARTVKGP---------SLEEGDEVKVFKV 344 (355)
T ss_pred cceEEEEEecCCC-ceEEEecceE--EEEeccCC---------CCCCCCEEEEEEE
Confidence 46677777766 7999999999 76666543 2457887777554
No 22
>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=85.10 E-value=2.2 Score=32.37 Aligned_cols=53 Identities=13% Similarity=0.073 Sum_probs=36.5
Q ss_pred ccccccCCCceeeEEEeccccCCceEEEEcCe--eEEEEEeeeec--CC-----CCcccEEEEE
Q 031387 7 HFESKADAGASKTFPQQAGTIRKNGYIVIKNR--PCKVVEVSTSK--TG-----KHGHAKCHFV 61 (160)
Q Consensus 7 ~f~~~~~~~~s~t~~i~~~~lkkG~~i~i~g~--p~~Vve~~~~k--pG-----KhG~A~v~~k 61 (160)
.|+ .+. .....--+-.=|||.|+.|.+++. +|.|+-+++.- +. -+|++.|.+|
T Consensus 42 ~Fe-dg~-~~i~~~dv~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk 103 (131)
T PF08605_consen 42 RFE-DGT-YEIKNEDVKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLK 103 (131)
T ss_pred EEe-cCc-eEeCcccEeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEE
Confidence 477 333 223333356678999999999998 89999998872 23 1277877774
No 23
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=62.42 E-value=15 Score=23.72 Aligned_cols=47 Identities=19% Similarity=0.323 Sum_probs=27.9
Q ss_pred cEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 101 FVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 101 ~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
.-+|++.... ..+-||..+ ...-++.|++|.|.+|..-..+.+.++|
T Consensus 15 ~g~fL~~~~~--~~vlLp~~e-----~~~~~~~Gd~v~VFvY~D~~~rl~AT~k 61 (61)
T PF13509_consen 15 FGYFLDDGEG--KEVLLPKSE-----VPEPLKVGDEVEVFVYLDKEGRLVATTK 61 (61)
T ss_dssp SEEEEEETT---EEEEEEGGG-----------TTSEEEEEEEE-TTS-EEEE--
T ss_pred CEEEEECCCC--CEEEechHH-----cCCCCCCCCEEEEEEEECCCCCEEEecC
Confidence 4556676666 788899874 2344789999999999777667766654
No 24
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=61.97 E-value=10 Score=25.39 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=15.0
Q ss_pred eccccCCceEEEEcCeeEEEE
Q 031387 23 QAGTIRKNGYIVIKNRPCKVV 43 (160)
Q Consensus 23 ~~~~lkkG~~i~i~g~p~~Vv 43 (160)
....|++|+.|.++|..++|+
T Consensus 45 rg~Kl~~GD~V~~~~~~~~Vv 65 (65)
T PF13275_consen 45 RGKKLRPGDVVEIDGEEYRVV 65 (65)
T ss_dssp SS----SSEEEEETTEEEEEE
T ss_pred cCCcCCCCCEEEECCEEEEEC
Confidence 456899999999999999985
No 25
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=61.18 E-value=7 Score=28.27 Aligned_cols=26 Identities=12% Similarity=0.151 Sum_probs=23.6
Q ss_pred EEeccccCCceEEEEcCeeEEEEEee
Q 031387 21 PQQAGTIRKNGYIVIKNRPCKVVEVS 46 (160)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~p~~Vve~~ 46 (160)
+.+..||+.|..|.|.|+++.|+++.
T Consensus 68 ~y~~~Dl~vG~~v~i~gr~f~I~d~D 93 (104)
T smart00676 68 YYHASDLNVGTTINVFGRQFRIYDCD 93 (104)
T ss_pred ccCHHHcCCCCEEEEeCEEEEEEECC
Confidence 46788999999999999999999984
No 26
>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=60.45 E-value=31 Score=26.83 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=29.2
Q ss_pred ccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEc
Q 031387 26 TIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (160)
Q Consensus 26 ~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl 65 (160)
..+++....+|| +|+|+++ ...+|+.|....+.+|+.+
T Consensus 115 ~~~p~~gyrYDG-LY~V~~~-w~e~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 115 KYAPGKGYIYDG-LYRIVDY-WREVGKSGFLVFKFKLVRI 152 (155)
T ss_pred CCCCCCeEEECc-EEEEEEE-EEecCCCCcEEEEEEEEeC
Confidence 456777788887 8999988 4456887888899998865
No 27
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=51.02 E-value=16 Score=26.74 Aligned_cols=23 Identities=9% Similarity=0.039 Sum_probs=19.8
Q ss_pred cCCceEEEEcCeeEEEEEeeeec
Q 031387 27 IRKNGYIVIKNRPCKVVEVSTSK 49 (160)
Q Consensus 27 lkkG~~i~i~g~p~~Vve~~~~k 49 (160)
|++|+.+.++|.+|.|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999998766554
No 28
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=49.80 E-value=41 Score=23.47 Aligned_cols=38 Identities=13% Similarity=0.173 Sum_probs=22.5
Q ss_pred cCCCceeeEEEeccccC---CceEEEEcCeeEEEEEeeeec
Q 031387 12 ADAGASKTFPQQAGTIR---KNGYIVIKNRPCKVVEVSTSK 49 (160)
Q Consensus 12 ~~~~~s~t~~i~~~~lk---kG~~i~i~g~p~~Vve~~~~k 49 (160)
+-++.+.+..+..++++ +|+.|.++|+-|.|.+++.--
T Consensus 48 ~v~g~~~~L~v~~~d~~~P~~gd~v~~dG~~y~V~~~~~~~ 88 (95)
T PF13856_consen 48 GVEGTQPTLYVFSSDYPKPRRGDRVVIDGESYTVTRFQEED 88 (95)
T ss_dssp ------EEEEE--SS-----TT-EEEETTEEEEEEEEEEET
T ss_pred cccCCceEEEEEcCCCCCCCCCCEEEECCeEEEEeEEecCC
Confidence 33445566666666654 899999999999999987663
No 29
>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=49.58 E-value=16 Score=27.32 Aligned_cols=34 Identities=9% Similarity=0.147 Sum_probs=22.1
Q ss_pred EeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEE
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKC 58 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v 58 (160)
..+..||+++.|.|.|++|.|-+ +.|--+|...+
T Consensus 70 ~dv~~L~r~DtL~I~g~~y~Vd~---v~pD~~G~t~I 103 (117)
T PF05354_consen 70 ADVSGLKRRDTLTIGGESYWVDR---VGPDGGGSTRI 103 (117)
T ss_dssp CCCCTS-TT-EEEETTTEEEBS------SSSSS-CCE
T ss_pred hHhhhhhcCCeEEECCEEEEEEe---eccCCCccEEE
Confidence 57788999999999999999954 46644465544
No 30
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=48.08 E-value=75 Score=23.63 Aligned_cols=55 Identities=15% Similarity=0.225 Sum_probs=35.6
Q ss_pred eccccCCceEEEE-----cCeeEEEEEeeee---cCCCCcccEEEEEEEEccCCcEEEEeecCCC
Q 031387 23 QAGTIRKNGYIVI-----KNRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (160)
Q Consensus 23 ~~~~lkkG~~i~i-----~g~p~~Vve~~~~---kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~ 79 (160)
...++++|+.|.+ +|...++--++-. .-++ | .--.+.+|++..|-=+|.+|+...
T Consensus 15 ~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~-G-~~~tftvRki~~gvGVEr~fpl~S 77 (116)
T PRK05338 15 DIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGR-G-LNETFTVRKISYGVGVERTFPLHS 77 (116)
T ss_pred CCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCC-C-CCceEEEEEcccCccEEEEecCCC
Confidence 3568899998776 4554433222211 1233 2 234689999999999999998743
No 31
>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=46.62 E-value=54 Score=27.52 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=23.0
Q ss_pred cccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEE
Q 031387 25 GTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (160)
Q Consensus 25 ~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~kn 64 (160)
.-|.++.+|..+|+.|+|..+....-|. + ..+.+.+.+
T Consensus 26 ~~i~~~~~I~~~~q~y~I~~~~~~~~~~-~-~~~~V~a~h 63 (327)
T PF06605_consen 26 DLIKEENIITYDGQEYRIKQVEKSRDGN-T-ITITVTAEH 63 (327)
T ss_dssp --SSTT-EEEETTEEEE--EE--B-------EEEEEEEEB
T ss_pred HhcCcCCEEEECCeEEEEEEeEEecCCC-E-EEEEEEEEe
Confidence 5688999999999999999887776665 3 348899998
No 32
>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=45.11 E-value=27 Score=25.85 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=16.3
Q ss_pred eccccCCceEEEEcCeeEEEEEe
Q 031387 23 QAGTIRKNGYIVIKNRPCKVVEV 45 (160)
Q Consensus 23 ~~~~lkkG~~i~i~g~p~~Vve~ 45 (160)
...+|++|+.+.|++..|+|..+
T Consensus 48 ~~~~i~~Gd~l~i~~~~y~ItaV 70 (117)
T PF03829_consen 48 LKGDIKPGDTLIIGGQEYTITAV 70 (117)
T ss_dssp GG----TT-EEEETTEEEEEEEE
T ss_pred ccCCcCCCCEEEECCeEEEEEEE
Confidence 45689999999999999999876
No 33
>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=44.84 E-value=47 Score=22.03 Aligned_cols=36 Identities=25% Similarity=0.398 Sum_probs=27.0
Q ss_pred cccCCcchhhHHHHHhhccCCCeEEEEEEccCCcEEEEEEe
Q 031387 114 DLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 154 (160)
Q Consensus 114 qi~l~~~~~llg~~~~~l~eg~~v~v~~~~~mg~e~v~~~k 154 (160)
.+.+|++-+ ..-|++|+.|.|.+-..-|++.|.+++
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 566787742 456789999999887888888887653
No 34
>PRK11507 ribosome-associated protein; Provisional
Probab=44.37 E-value=25 Score=23.92 Aligned_cols=22 Identities=14% Similarity=0.184 Sum_probs=18.5
Q ss_pred EeccccCCceEEEEcCeeEEEE
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVV 43 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vv 43 (160)
-..-.|++|+.|.++|.-++|+
T Consensus 48 rRgkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 48 RKRCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred ccCCCCCCCCEEEECCEEEEEe
Confidence 3456899999999999988876
No 35
>PF05096 Glu_cyclase_2: Glutamine cyclotransferase; InterPro: IPR007788 This family of enzymes 2.3.2.5 from EC catalyse the cyclization of free L-glutamine and N-terminal glutaminyl residues in proteins to pyroglutamate (5-oxoproline) and pyroglutamyl residues respectively []. This family includes plant and bacterial enzymes and seems unrelated to the mammalian enzymes.; PDB: 3NOK_B 2FAW_A 2IWA_A 3NOM_A 3NOL_A 3MBR_X.
Probab=44.21 E-value=2e+02 Score=24.38 Aligned_cols=82 Identities=15% Similarity=0.142 Sum_probs=47.2
Q ss_pred eeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCcee--cceEEEeeeEEEE
Q 031387 18 KTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD--APHVTRTDYQLID 95 (160)
Q Consensus 18 ~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve--~~~ve~~~~qyly 95 (160)
.+||-..+.+-.|..+.-+|..|. .+|..|+.. +.-.|+.||++.....-...-|= ...+..+=+|+.+
T Consensus 37 ~~ypHd~~aFTQGL~~~~~g~LyE-------STG~yG~S~--l~~~d~~tg~~~~~~~l~~~~FgEGit~~~d~l~qLTW 107 (264)
T PF05096_consen 37 ETYPHDPTAFTQGLEFLDDGTLYE-------STGLYGQSS--LRKVDLETGKVLQSVPLPPRYFGEGITILGDKLYQLTW 107 (264)
T ss_dssp EEEE--TT-EEEEEEEEETTEEEE-------EECSTTEEE--EEEEETTTSSEEEEEE-TTT--EEEEEEETTEEEEEES
T ss_pred EECCCCCcccCccEEecCCCEEEE-------eCCCCCcEE--EEEEECCCCcEEEEEECCccccceeEEEECCEEEEEEe
Confidence 478889999999998888888772 347778774 45679999988755443322221 2233345555555
Q ss_pred ecCCCcEEEecCCCC
Q 031387 96 ISEDGFVSLLTETGN 110 (160)
Q Consensus 96 ~d~d~~~~fMd~ety 110 (160)
.+ . ....-|.+++
T Consensus 108 k~-~-~~f~yd~~tl 120 (264)
T PF05096_consen 108 KE-G-TGFVYDPNTL 120 (264)
T ss_dssp SS-S-EEEEEETTTT
T ss_pred cC-C-eEEEEccccc
Confidence 53 2 3444455555
No 36
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=43.21 E-value=1.1e+02 Score=26.20 Aligned_cols=55 Identities=22% Similarity=0.309 Sum_probs=31.9
Q ss_pred cccCCceEEEEcCeeE-EEEEeeeecCCCCcc------cEEEEEEEEccCCcEEEEeecCCCcee
Q 031387 25 GTIRKNGYIVIKNRPC-KVVEVSTSKTGKHGH------AKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (160)
Q Consensus 25 ~~lkkG~~i~i~g~p~-~Vve~~~~kpGKhG~------A~v~~k~knl~TG~~~e~tf~s~~~ve 82 (160)
.+|+.|+.+-|.+-|- .+|-.--.+||++|+ +.+++..++ |...--.++|++.-.
T Consensus 122 a~ik~GN~lpL~~IP~Gt~VhNVE~~pG~GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~r~ 183 (275)
T COG0090 122 ADIKPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGTYAQVVGKE---GNYVIVRLPSGEMRK 183 (275)
T ss_pred CCcCCcceeeeccCCCCceEEeeeeccCCCceEEEeCCceEEEEEcc---CCEEEEECCCCCeEe
Confidence 3666677666666552 112222237998542 456666666 666666777776533
No 37
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=43.07 E-value=34 Score=25.52 Aligned_cols=22 Identities=14% Similarity=0.179 Sum_probs=20.1
Q ss_pred ccccCCceEEEEcCeeEEEEEe
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEV 45 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~ 45 (160)
..+|++|+.+.|+|.-|+|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAV 70 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEE
Confidence 5679999999999999999877
No 38
>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=42.22 E-value=36 Score=25.45 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=19.8
Q ss_pred ccccCCceEEEEcCeeEEEEEe
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEV 45 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~ 45 (160)
..+|++|+.+.|+|.-|+|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (121)
T TIGR00849 49 KGTLKPGQVFMIGGIAYPVTAV 70 (121)
T ss_pred cCCcCCCCEEEECCEEEEEEEE
Confidence 3589999999999999999877
No 39
>TIGR01563 gp16_SPP1 phage head-tail adaptor, putative, SPP1 family. This family describes a small protein of about 100 amino acids found in bacteriophage and in bacterial prophage regions. Examples include gp9 of phage HK022 and gp16 of phage SPP1. This minor structural protein is suggested to be a head-tail adaptor protein (although the source of this annotation was not traced during construction of this model).
Probab=41.66 E-value=1.1e+02 Score=20.67 Aligned_cols=34 Identities=9% Similarity=0.169 Sum_probs=25.5
Q ss_pred cccccCCCceeeEEE---eccccCCceEEEEcCeeEEE
Q 031387 8 FESKADAGASKTFPQ---QAGTIRKNGYIVIKNRPCKV 42 (160)
Q Consensus 8 f~~~~~~~~s~t~~i---~~~~lkkG~~i~i~g~p~~V 42 (160)
|+ .+...+..|+.+ -..+|...+.|.++|+.|.|
T Consensus 45 ~~-a~~~~~~~t~~~~iR~~~~i~~~~ri~~~g~~Y~I 81 (101)
T TIGR01563 45 YR-AGQEGVEITHVILIRYRKDVTNKMRVIYDGRIYTI 81 (101)
T ss_pred ee-cccccCceEEEEEEeccCCCChhhEEEECCEEEEE
Confidence 44 555556666654 35689999999999999999
No 40
>PF05521 Phage_H_T_join: Phage head-tail joining protein ; InterPro: IPR008767 This entry describes the head-tail adaptor protein of bacteriophage SPP1 and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2KCA_A 2KZ4_A.
Probab=40.95 E-value=1e+02 Score=20.16 Aligned_cols=33 Identities=9% Similarity=0.159 Sum_probs=22.2
Q ss_pred eeeEEEecc-ccCCceEEEEcCeeEEEEEeeeec
Q 031387 17 SKTFPQQAG-TIRKNGYIVIKNRPCKVVEVSTSK 49 (160)
Q Consensus 17 s~t~~i~~~-~lkkG~~i~i~g~p~~Vve~~~~k 49 (160)
+..+.+--. +|..++.|.++|..|.|..+....
T Consensus 52 t~~~~iR~~~~I~~~~ri~~~g~~y~I~~i~~~~ 85 (95)
T PF05521_consen 52 THRFTIRYRKDITPDMRIKYDGKVYNIKSIDPDD 85 (95)
T ss_dssp EEEEEECS-TTSSTTEEEEECTEEEEE-S--EE-
T ss_pred EEEEEEecCcCCCcceEEEECCEEEEEEEECCCC
Confidence 444455444 699999999999999999876654
No 41
>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=40.85 E-value=57 Score=22.93 Aligned_cols=50 Identities=18% Similarity=0.224 Sum_probs=31.3
Q ss_pred EEEEEccCCcEEEEeecCCCcee-----------cceEEEeeeEEEEecCCCcEEEecCCCC
Q 031387 60 FVGIDIFNGKKLEDIVPSSHNCD-----------APHVTRTDYQLIDISEDGFVSLLTETGN 110 (160)
Q Consensus 60 ~k~knl~TG~~~e~tf~s~~~ve-----------~~~ve~~~~qyly~d~d~~~~fMd~ety 110 (160)
+|+++. .|+++--++.+++.+. ........+++.|.|+++.++++-.++.
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 344544 6666666665444332 2222245789999998888999887765
No 42
>COG3535 Uncharacterized conserved protein [Function unknown]
Probab=40.00 E-value=2.7e+02 Score=24.68 Aligned_cols=90 Identities=21% Similarity=0.362 Sum_probs=61.0
Q ss_pred ceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCcEEEecCCC
Q 031387 30 NGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETG 109 (160)
Q Consensus 30 G~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~~~fMd~et 109 (160)
|.+++++|..-.|..-...--.+ | .+++.+.+-..|++++-.|..- -.+-+++-|++-.-.| -..++|.+|
T Consensus 236 ~g~~lf~Gki~dV~R~t~gGF~~-G--~~~I~G~~~~~g~t~~i~FqNE-----fl~a~~~G~~l~~~PD-LI~lld~~T 306 (357)
T COG3535 236 GGKILFKGKIVDVKRETRGGFAR-G--RVTIDGLEEYRGSTLEIAFQNE-----FLVAEKDGKILATTPD-LIVLLDLNT 306 (357)
T ss_pred CcEEEEccEEEEEEEeeecceee-e--eEEEechhhcCCceEEEEEEee-----eeEEecCCcEEEecCc-eEEEEecCC
Confidence 57788998766555332221122 3 4578888899999999999753 3445688999999877 889999998
Q ss_pred CceecccCCcchhhHHHHHhhccCCCeEEEEE
Q 031387 110 NTKDDLRLPTDENLLSQIKDGFAEGKDLVVTV 141 (160)
Q Consensus 110 y~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~ 141 (160)
. .++..+ -|+.|+.|.|.-
T Consensus 307 g----~piTTe---------~lkyG~rV~V~a 325 (357)
T COG3535 307 G----LPITTE---------SLKYGQRVVVIA 325 (357)
T ss_pred C----CccchH---------HhhcCcEEEEEE
Confidence 7 334333 234677766644
No 43
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=39.91 E-value=34 Score=23.47 Aligned_cols=22 Identities=18% Similarity=0.286 Sum_probs=18.8
Q ss_pred ccccCCceEEEEcCeeEEEEEe
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEV 45 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~ 45 (160)
.-.||.|+.|++.|.++.|+..
T Consensus 50 gkKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 50 GKKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CCEeecCCEEEECCEEEEEEec
Confidence 4579999999999999998753
No 44
>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=38.31 E-value=1.4e+02 Score=22.12 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=35.2
Q ss_pred EeccccCCceEEEEc-----CeeEEEEEeeee---cCCCCcccEEEEEEEEccCCcEEEEeecCCC
Q 031387 22 QQAGTIRKNGYIVIK-----NRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (160)
Q Consensus 22 i~~~~lkkG~~i~i~-----g~p~~Vve~~~~---kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~ 79 (160)
....++++|+.|.+. |...++--++-. +-++ | .--.+.+|++..|-=+|.+|+...
T Consensus 14 ~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~-G-~~~tftvR~i~~gvGVEr~fpl~S 77 (113)
T TIGR01024 14 KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGG-G-IGETFTVRKISYGVGVERIFPLHS 77 (113)
T ss_pred cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCC-C-CceEEEEEEeccCccEEEEEEcCC
Confidence 346688999988763 333332222111 2234 2 233689999999999999998743
No 45
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=38.15 E-value=44 Score=22.90 Aligned_cols=25 Identities=12% Similarity=0.129 Sum_probs=21.6
Q ss_pred eEEEeccccCCceEEEEcCeeEEEE
Q 031387 19 TFPQQAGTIRKNGYIVIKNRPCKVV 43 (160)
Q Consensus 19 t~~i~~~~lkkG~~i~i~g~p~~Vv 43 (160)
|-+++-..+.+|+.|..+|+-|+.-
T Consensus 8 T~~v~Rq~V~PG~~v~~~grty~AS 32 (73)
T PRK11354 8 TDEIPRQCVTPGDYVLHEGRTYIAS 32 (73)
T ss_pred ceeecccccCCceEEEEcCcEEEEE
Confidence 6678888899999999999999753
No 46
>PF08408 DNA_pol_B_3: DNA polymerase family B viral insert; InterPro: IPR013617 This viral domain is found between the exonuclease domain of the DNA polymerase family B (IPR006133 from INTERPRO) and the IPR006134 from INTERPRO domain, connecting the two. ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=38.15 E-value=26 Score=27.26 Aligned_cols=24 Identities=17% Similarity=0.404 Sum_probs=19.9
Q ss_pred ccccCCceEEEEcCeeEEEEEeee
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEVST 47 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~~~ 47 (160)
..=|+.|.||.|++.+|+|++=..
T Consensus 37 ~~VL~TgNYitI~d~v~kI~~K~i 60 (149)
T PF08408_consen 37 SEVLSTGNYITINDDVYKILDKDI 60 (149)
T ss_pred HHHHhcCCeEEECCeeeeeecccc
Confidence 445889999999999999997633
No 47
>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=37.59 E-value=41 Score=24.77 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=23.1
Q ss_pred eccccCCceEEEEcCeeEEEEEeeeec
Q 031387 23 QAGTIRKNGYIVIKNRPCKVVEVSTSK 49 (160)
Q Consensus 23 ~~~~lkkG~~i~i~g~p~~Vve~~~~k 49 (160)
.+-++..|..|.++|..|.|.++...-
T Consensus 73 p~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 73 PFPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred cccccCCCCEEEECCceEEEEEEEecc
Confidence 345888999999999999999997774
No 48
>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=36.92 E-value=18 Score=26.02 Aligned_cols=20 Identities=10% Similarity=0.185 Sum_probs=16.2
Q ss_pred EEeccccCCceEEEEcCeeE
Q 031387 21 PQQAGTIRKNGYIVIKNRPC 40 (160)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~p~ 40 (160)
.|++++|++||||..-..+|
T Consensus 4 kI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 4 KIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred EEEHHHCCCCcEEEecCCCc
Confidence 47899999999997765555
No 49
>PF08294 TIM21: TIM21; InterPro: IPR013261 TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane [].; PDB: 2CIU_A.
Probab=36.26 E-value=1.9e+02 Score=21.99 Aligned_cols=30 Identities=10% Similarity=0.046 Sum_probs=18.0
Q ss_pred cCeeEEEEEeeeecCCCCcccEEEEEEEEccC
Q 031387 36 KNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFN 67 (160)
Q Consensus 36 ~g~p~~Vve~~~~kpGKhG~A~v~~k~knl~T 67 (160)
+|..+..+.+.-.-|. |.+.|++.++.-..
T Consensus 91 ~G~eh~~m~F~V~G~~--~~G~V~~e~~k~~~ 120 (145)
T PF08294_consen 91 DGREHMRMKFYVEGPR--GKGVVHLEMVKDDG 120 (145)
T ss_dssp TS-EEEEEEEEEE-SS---EEEEEEEEE--SS
T ss_pred CCCEEEEEEEEEEeCC--CeEEEEEEEEECCC
Confidence 7888888888655443 56788888776553
No 50
>CHL00084 rpl19 ribosomal protein L19
Probab=36.25 E-value=1.8e+02 Score=21.64 Aligned_cols=54 Identities=11% Similarity=0.169 Sum_probs=35.5
Q ss_pred EeccccCCceEEEE-----cCe-----eEEEEEeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCC
Q 031387 22 QQAGTIRKNGYIVI-----KNR-----PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (160)
Q Consensus 22 i~~~~lkkG~~i~i-----~g~-----p~~Vve~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~ 79 (160)
....++++|+.|.+ +|. ++.=+-+.. -|+ | .--.+.+|++..|-=+|.+|+...
T Consensus 18 ~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~--r~~-G-~~~tftvRki~~gvGVEr~fpl~S 81 (117)
T CHL00084 18 KNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAK--KNS-G-LNTTITVRKVFQGIGVERVFLLHS 81 (117)
T ss_pred cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEE--eCC-C-CCeeEEEEEeccCccEEEEEecCC
Confidence 35668999998875 444 232222222 244 3 233589999999999999998743
No 51
>PLN00208 translation initiation factor (eIF); Provisional
Probab=34.11 E-value=2.2e+02 Score=22.01 Aligned_cols=90 Identities=19% Similarity=0.176 Sum_probs=58.4
Q ss_pred cCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHH
Q 031387 49 KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIK 128 (160)
Q Consensus 49 kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~ 128 (160)
++|||| +.+=+++|-..+.+.+-.+|....+- ++.+-.-+++.|-.+..++.++ --.+|.. +.. .
T Consensus 4 ~k~kgg--k~~~~~k~~~~~~~~el~~p~egq~~--------g~V~~~lGn~~~~V~c~dG~~r-La~IpGK---mRK-r 68 (145)
T PLN00208 4 NKGKGG--KNRKRGKNEADDEKRELIFKEDGQEY--------AQVLRMLGNGRCEALCIDGTKR-LCHIRGK---MRK-K 68 (145)
T ss_pred CCCCCc--cccccccccCccceeecccCCCCcEE--------EEEEEEcCCCEEEEEECCCCEE-EEEEecc---cee-e
Confidence 457754 55667788888889999998644432 2233333566788887776633 3446665 333 5
Q ss_pred hhccCCCeEEEEEEccCCcEEEEEE
Q 031387 129 DGFAEGKDLVVTVMSSMGEEQICAL 153 (160)
Q Consensus 129 ~~l~eg~~v~v~~~~~mg~e~v~~~ 153 (160)
-|+.+|+.|.|..|..--...-|..
T Consensus 69 IWI~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 69 VWIAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred EEecCCCEEEEEccCCCCCEEEEEE
Confidence 7999999999988877544444433
No 52
>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=34.08 E-value=1e+02 Score=23.75 Aligned_cols=35 Identities=29% Similarity=0.330 Sum_probs=25.2
Q ss_pred CceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEEc
Q 031387 29 KNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (160)
Q Consensus 29 kG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~knl 65 (160)
++..+.+|| +|+|+++...+ |+.|....+++|+-+
T Consensus 118 ~~g~yrYDG-LY~V~~~w~~~-g~~G~~v~kF~L~R~ 152 (155)
T PF02182_consen 118 KGGIYRYDG-LYKVVKYWREK-GKSGFKVFKFKLVRL 152 (155)
T ss_dssp SSS-EEEEE-EEEEEEEEEEE--TTSSEEEEEEEEE-
T ss_pred cCCCEEeCc-EEEEEEEEEEe-CCCCcEEEEEEEEEC
Confidence 345578888 99999997764 455778889998765
No 53
>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=31.71 E-value=74 Score=21.71 Aligned_cols=20 Identities=15% Similarity=0.001 Sum_probs=17.6
Q ss_pred ccCCcEEEEeecCCCceecc
Q 031387 65 IFNGKKLEDIVPSSHNCDAP 84 (160)
Q Consensus 65 l~TG~~~e~tf~s~~~ve~~ 84 (160)
+-+|+.++++|++++++...
T Consensus 11 lP~G~r~~rrF~~t~~L~~l 30 (80)
T cd01771 11 TPSGDFLERRFLGDTPLQVL 30 (80)
T ss_pred CCCCCEEEEEeCCCCcHHHH
Confidence 67899999999999998843
No 54
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=30.98 E-value=1.8e+02 Score=20.11 Aligned_cols=46 Identities=11% Similarity=0.177 Sum_probs=27.6
Q ss_pred ccCCceEEEEcCee---------EEEEEeeeecCCCC-cccEEEEEEEEccCCcEE
Q 031387 26 TIRKNGYIVIKNRP---------CKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKL 71 (160)
Q Consensus 26 ~lkkG~~i~i~g~p---------~~Vve~~~~kpGKh-G~A~v~~k~knl~TG~~~ 71 (160)
.+|.|+++++.... |-+-++-++..|.+ ..+---+..-|+-||.+.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~ 60 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIR 60 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEE
Confidence 57999999999877 33334444444332 223333566677777654
No 55
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=30.29 E-value=93 Score=24.35 Aligned_cols=22 Identities=18% Similarity=0.433 Sum_probs=14.5
Q ss_pred cccCCceEEEEc---CeeEEEEEee
Q 031387 25 GTIRKNGYIVIK---NRPCKVVEVS 46 (160)
Q Consensus 25 ~~lkkG~~i~i~---g~p~~Vve~~ 46 (160)
+-+|.|++|.++ |.||.|-.+.
T Consensus 2 ~~yrvGD~Vy~~~~~~~Py~I~rI~ 26 (164)
T cd04709 2 NMYRVGDYVYFESSPNNPYLIRRIE 26 (164)
T ss_pred cEEecCCEEEEECCCCCCCEEEEEE
Confidence 347899999887 4565554443
No 56
>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=29.99 E-value=1.3e+02 Score=25.45 Aligned_cols=83 Identities=22% Similarity=0.270 Sum_probs=43.3
Q ss_pred CCCceeeEEEeccc-c--CCceEEEEcC-eeEEEE---EeeeecCCCCcccEEEEEEEEccCCcEEEEeecCCCceecce
Q 031387 13 DAGASKTFPQQAGT-I--RKNGYIVIKN-RPCKVV---EVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPH 85 (160)
Q Consensus 13 ~~~~s~t~~i~~~~-l--kkG~~i~i~g-~p~~Vv---e~~~~kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ 85 (160)
.+-|+.||||.||= | =.-.++-+++ .||+++ +=+.+.-|- -|+++|+|==++-.+. ..+=.+..|.
T Consensus 74 s~QA~~TfPI~CNidLHYfSSSfFSlKDp~PWkl~YrV~DtNV~~~t---hFak~kgKLKLStAKH----S~DI~Fr~Pt 146 (276)
T PF00845_consen 74 SLQASFTFPIRCNIDLHYFSSSFFSLKDPIPWKLYYRVEDTNVHQGT---HFAKFKGKLKLSTAKH----SVDIPFRAPT 146 (276)
T ss_pred hheeEEEeeeeeeeeeEEeeecceecCCCCCeEEEEEeecCccccce---eeeeeeceeeeccccc----ccccccCCCc
Confidence 34589999998861 1 1223444544 688873 333444444 4777776633332222 1122244566
Q ss_pred EEEeeeEEEEecCCCcEE
Q 031387 86 VTRTDYQLIDISEDGFVS 103 (160)
Q Consensus 86 ve~~~~qyly~d~d~~~~ 103 (160)
|+----||.-.+-| +++
T Consensus 147 ikILSK~ft~~~vD-F~~ 163 (276)
T PF00845_consen 147 IKILSKQFTEKDVD-FWH 163 (276)
T ss_pred eEeeecccCcCCCc-eee
Confidence 66555566665544 444
No 57
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.57 E-value=76 Score=23.33 Aligned_cols=15 Identities=13% Similarity=0.266 Sum_probs=12.5
Q ss_pred ccccCCceEEEEcCe
Q 031387 24 AGTIRKNGYIVIKNR 38 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~ 38 (160)
-.+|++|+.|+++|.
T Consensus 31 rr~ik~GD~IiF~~~ 45 (111)
T COG4043 31 RRQIKPGDKIIFNGD 45 (111)
T ss_pred hcCCCCCCEEEEcCC
Confidence 357999999999974
No 58
>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=28.85 E-value=1.1e+02 Score=23.40 Aligned_cols=38 Identities=11% Similarity=0.072 Sum_probs=27.2
Q ss_pred ccccCCceEEEEcCeeE-----EEEEeeeecC-CCCcccEEEEE
Q 031387 24 AGTIRKNGYIVIKNRPC-----KVVEVSTSKT-GKHGHAKCHFV 61 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~-----~Vve~~~~kp-GKhG~A~v~~k 61 (160)
...|++|+.|.+.|+-+ -|+..+|..| |+|-.-.+...
T Consensus 83 ip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~~h~~Gwl~~n 126 (131)
T PF11948_consen 83 IPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRGRHPDGWLKHN 126 (131)
T ss_pred CcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCCCCCCeeEEEC
Confidence 45699999999999854 4788999888 55533444443
No 59
>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=27.51 E-value=96 Score=17.20 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=15.6
Q ss_pred CceEEEE-----cCeeEEEEEeeeec
Q 031387 29 KNGYIVI-----KNRPCKVVEVSTSK 49 (160)
Q Consensus 29 kG~~i~i-----~g~p~~Vve~~~~k 49 (160)
+|+.+++ .|..++|+++...+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 4677777 78888888886554
No 60
>cd00603 IPT_PCSR IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the macrophage-stimulating receptors and of fibrocystin. Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT_PCSR domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=27.40 E-value=1.9e+02 Score=19.12 Aligned_cols=42 Identities=10% Similarity=0.258 Sum_probs=29.2
Q ss_pred ccCCCceeeEEEeccccCCc---eEEEEcCeeEEEEE-----eeeecCCC
Q 031387 11 KADAGASKTFPQQAGTIRKN---GYIVIKNRPCKVVE-----VSTSKTGK 52 (160)
Q Consensus 11 ~~~~~~s~t~~i~~~~lkkG---~~i~i~g~p~~Vve-----~~~~kpGK 52 (160)
.|....--+..|..+.|..+ ..|.+++.+|.++. +....|..
T Consensus 10 ~g~~~Ggt~vtI~G~~f~~~~~~~~V~ig~~~C~~~~~~~~~i~C~~p~~ 59 (90)
T cd00603 10 SGPLSGGTRLTITGSNLGSGSPRVRVTVGGVPCKVLNVSSTEIVCRTPAA 59 (90)
T ss_pred CCCCCCCeEEEEEEECCCCCCceEEEEECCEECcEEecCCCEEEEECCCC
Confidence 34443444667788888887 78999999999974 44555543
No 61
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=27.07 E-value=1.7e+02 Score=26.02 Aligned_cols=44 Identities=7% Similarity=0.156 Sum_probs=29.4
Q ss_pred ccccCCceEEEEcC---eeEEE----EEeeeecCCCCcccEEEEEEEEccCC
Q 031387 24 AGTIRKNGYIVIKN---RPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNG 68 (160)
Q Consensus 24 ~~~lkkG~~i~i~g---~p~~V----ve~~~~kpGKhG~A~v~~k~knl~TG 68 (160)
.-+|++|++|.++- .|..| +..-..+||++| .++-+++......
T Consensus 320 lL~LkvGDVI~Ld~~~~~~v~v~v~g~p~F~g~~G~~~-g~~AvrI~~~l~~ 370 (388)
T PRK12795 320 VLNLKVGDTLMLDARPDALVTLRCGDVPLTEGRMGRVG-DRVAVRVEKPLRK 370 (388)
T ss_pred HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEeccCC-CEEEEEEEeecCC
Confidence 44789999999984 35544 444567899975 4445666665543
No 62
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=26.48 E-value=77 Score=23.47 Aligned_cols=27 Identities=7% Similarity=0.069 Sum_probs=15.3
Q ss_pred EEeccccCCceEEEE-cCeeEEEEEeee
Q 031387 21 PQQAGTIRKNGYIVI-KNRPCKVVEVST 47 (160)
Q Consensus 21 ~i~~~~lkkG~~i~i-~g~p~~Vve~~~ 47 (160)
=+.|.+|++|+.|.- +|.+..|..+..
T Consensus 71 Wv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 71 WVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp -EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 378999999998754 678777766643
No 63
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=26.23 E-value=1.4e+02 Score=27.17 Aligned_cols=38 Identities=16% Similarity=0.386 Sum_probs=28.6
Q ss_pred EeccccCCceEEEEcCeeEEEEE-eeeecCCCCcccEEEEEEE
Q 031387 22 QQAGTIRKNGYIVIKNRPCKVVE-VSTSKTGKHGHAKCHFVGI 63 (160)
Q Consensus 22 i~~~~lkkG~~i~i~g~p~~Vve-~~~~kpGKhG~A~v~~k~k 63 (160)
....++++...+.++|++|++++ -+....|+ +|++..+
T Consensus 383 ~~vt~~~p~G~V~v~GE~W~AvS~~~~I~kG~----~VkVV~~ 421 (436)
T COG1030 383 KTVTPLRPEGFVLVEGERWRAVSEGEPIEKGE----KVKVVDR 421 (436)
T ss_pred eecccCCCCeEEEECCEEEEEeeCCCcccCCC----EEEEEee
Confidence 56678999999999999999998 55555555 4554443
No 64
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=25.27 E-value=1.5e+02 Score=23.47 Aligned_cols=47 Identities=15% Similarity=0.229 Sum_probs=37.0
Q ss_pred CCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEe
Q 031387 50 TGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDI 96 (160)
Q Consensus 50 pGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~ 96 (160)
.|.|++..+.+.+|+=..|...-..|..-.-++.|..-++.+.+.+.
T Consensus 93 ~G~~~hGyfNL~gk~~l~GHiK~eNcs~Ialv~rpFmG~~s~si~Ff 139 (176)
T COG3721 93 SGTHRHGYFNLRGKDGLSGHIKAENCSHIALVERPFMGMESASILFF 139 (176)
T ss_pred CCccccceEeecCCCCCcceeeccccceeeEeccccCCccceeeeee
Confidence 48888999999999999999888888877777777766655544443
No 65
>PF13501 SoxY: Sulfur oxidation protein SoxY; PDB: 2OXG_B 2OX5_B 2OXH_F 2NNF_A 2NNC_B.
Probab=24.94 E-value=2.1e+02 Score=20.81 Aligned_cols=52 Identities=12% Similarity=0.024 Sum_probs=32.1
Q ss_pred cCCCceeeEEEecccc---CCceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEEE
Q 031387 12 ADAGASKTFPQQAGTI---RKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (160)
Q Consensus 12 ~~~~~s~t~~i~~~~l---kkG~~i~i~g~p~~Vve~~~~kpGKhG~A~v~~k~kn 64 (160)
++.++..-..+.+... =+..+|.++.+|.-++-.-+-.|+. |.+.+.+++|=
T Consensus 26 Aenga~VPv~v~~~~~~~~v~~I~l~vd~NP~P~~a~f~~~p~~-~~~~~stRir~ 80 (111)
T PF13501_consen 26 AENGAVVPVTVSVDLPMDYVKRIHLFVDKNPSPLAATFELTPAG-GEPYVSTRIRM 80 (111)
T ss_dssp EECTTCEEEEEEET-TT--ECEEEEEETTSSSSEEEEEEE-TTC-CEEEEEEEEE-
T ss_pred ccCCCCccEEEEeCCCCceeEEEEEEecCCCCcEEEEEEEcCCC-CCceeEEEEEe
Confidence 3455555555555433 2467899999998776554556877 77877777653
No 66
>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=24.67 E-value=1.2e+02 Score=24.80 Aligned_cols=29 Identities=34% Similarity=0.455 Sum_probs=20.4
Q ss_pred EEEeccccCCceEEEE------cCeeEEEEEeeee
Q 031387 20 FPQQAGTIRKNGYIVI------KNRPCKVVEVSTS 48 (160)
Q Consensus 20 ~~i~~~~lkkG~~i~i------~g~p~~Vve~~~~ 48 (160)
-++-|+++++|++|.. .-+|-+|+.++.+
T Consensus 99 ~~vfA~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~ 133 (217)
T PF01079_consen 99 RAVFASDVRVGDCVLVSDEGGGKLRPSRVVRVSTV 133 (217)
T ss_dssp EEEEGGG--TT-EEEEE-TTT--EEEEEEEEEEEE
T ss_pred ceeehhhCCCCCEEEEEEcCCCcEEEEEEEEEEEE
Confidence 6899999999999999 3357788777665
No 67
>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=24.61 E-value=55 Score=22.41 Aligned_cols=41 Identities=15% Similarity=0.198 Sum_probs=22.8
Q ss_pred eeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHHhhcc
Q 031387 89 TDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFA 132 (160)
Q Consensus 89 ~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~ 132 (160)
-+++|+.-. +..++|+|.++-+.|.+.|..=. ...+..||.
T Consensus 33 v~vk~i~G~-~P~L~l~d~~g~~~E~i~i~~w~--~d~i~efL~ 73 (78)
T PF08806_consen 33 VEVKYIPGA-PPELVLLDEDGEEVERINIEKWK--TDEIEEFLN 73 (78)
T ss_dssp EEEEEESS----EEEEE-SSS--SEEEE-SSSS--HCHHHHHHH
T ss_pred eEEEEeCCC-CCEEEEEcCCCCEEEEEEcccCC--HHHHHHHHH
Confidence 345666654 45899999988878888886633 334555554
No 68
>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=24.24 E-value=79 Score=20.84 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=18.6
Q ss_pred EEEEEEEEccCCcEEEEeecCCCceec
Q 031387 57 KCHFVGIDIFNGKKLEDIVPSSHNCDA 83 (160)
Q Consensus 57 ~v~~k~knl~TG~~~e~tf~s~~~ve~ 83 (160)
.++++ +-+|+.+..+|++++++..
T Consensus 4 ~i~iR---lpdG~~~~~~F~~~~tl~~ 27 (77)
T cd01767 4 KIQIR---LPDGKRLEQRFNSTHKLSD 27 (77)
T ss_pred EEEEE---cCCCCEEEEEeCCCCCHHH
Confidence 44444 4569999999999999874
No 69
>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=24.06 E-value=1.4e+02 Score=20.46 Aligned_cols=45 Identities=27% Similarity=0.497 Sum_probs=32.2
Q ss_pred EEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEE---EEccCCcEE
Q 031387 102 VSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVT---VMSSMGEEQ 149 (160)
Q Consensus 102 ~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~---~~~~mg~e~ 149 (160)
++|||.++- +-|-.++.. ++......|+||.-+.+. +....|...
T Consensus 2 mvL~De~G~-~I~A~I~~~--~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr 49 (95)
T PF02721_consen 2 MVLVDEKGD-KIQATIPKE--LVDKFKDSLKEGSWYTISNFTVSPNSGSYR 49 (95)
T ss_pred EEEEecCCC-EEEEEECHH--HHHHHHhhcccCCEEEeEeEEEEeCCCcee
Confidence 689999875 457778776 588889999999887663 334445444
No 70
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=23.96 E-value=3.6e+02 Score=21.11 Aligned_cols=88 Identities=15% Similarity=0.128 Sum_probs=57.1
Q ss_pred cCCCCcccEEEEEEEEccCCcEEEEeecCCCceecceEEEeeeEEEEecCCCcEEEecCCCCceecccCCcchhhHHHHH
Q 031387 49 KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIK 128 (160)
Q Consensus 49 kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~ve~~~ve~~~~qyly~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~ 128 (160)
+.|||| +-+=++||--.+.+.+-+++....+. ++.+-.-+++.|-.+..++.++ --.+|.. +.. .
T Consensus 4 ~kgkgg--k~~~rgk~~~~~~~rel~~~eegq~~--------g~V~~~LGn~~f~V~c~dG~~r-La~I~GK---mRK-~ 68 (155)
T PTZ00329 4 NKGKGG--KNRRRGKNDNEGEKRELVFKEEGQEY--------AQVLRMLGNGRLEAYCFDGVKR-LCHIRGK---MRK-R 68 (155)
T ss_pred CCCCCC--cccccccccCccceeeeccCCCCcEE--------EEEEEEcCCCEEEEEECCCCEE-EEEeecc---cee-e
Confidence 357754 55778899988999999998643322 2333333566777787776633 3446654 333 4
Q ss_pred hhccCCCeEEEEEEccCCcEEEE
Q 031387 129 DGFAEGKDLVVTVMSSMGEEQIC 151 (160)
Q Consensus 129 ~~l~eg~~v~v~~~~~mg~e~v~ 151 (160)
-|+.+|+.|.|..|..--...-|
T Consensus 69 IWI~~GD~VlVel~~yd~~KgdI 91 (155)
T PTZ00329 69 VWINIGDIILVSLRDFQDSKADV 91 (155)
T ss_pred EEecCCCEEEEeccCCCCCEEEE
Confidence 79999999999887665444333
No 71
>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=22.90 E-value=3.1e+02 Score=20.08 Aligned_cols=65 Identities=12% Similarity=0.151 Sum_probs=38.5
Q ss_pred EeccccCCceEEEEc-----CeeEEEEEeeee---cCCCCcccEEEEEEEEccCCcEEEEeecCCCc-eecceEEE
Q 031387 22 QQAGTIRKNGYIVIK-----NRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN-CDAPHVTR 88 (160)
Q Consensus 22 i~~~~lkkG~~i~i~-----g~p~~Vve~~~~---kpGKhG~A~v~~k~knl~TG~~~e~tf~s~~~-ve~~~ve~ 88 (160)
.+..+|++|++|.+. |...++-.++-. .-+++-++ .+.++|++.|--+|.+|+-... ++...|-+
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~s--sftlR~~~~g~gVE~~f~l~SP~I~~IeV~~ 87 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNS--SFTLRNISQGVGVERVFPLYSPLIKSIEVLR 87 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSS--EEEEEEEETTEEEEEEEETTSTTEEEEEEEE
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCe--eEEEEEEecCccEEEEEEcCCCCeEEEEEEE
Confidence 456688999987653 443443322211 11221122 5788999999999999987533 44444433
No 72
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=22.72 E-value=60 Score=23.31 Aligned_cols=37 Identities=14% Similarity=0.179 Sum_probs=27.8
Q ss_pred eeeEEEeccccCCceEEEEcCeeEEEEEeeeecCCCCc
Q 031387 17 SKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHG 54 (160)
Q Consensus 17 s~t~~i~~~~lkkG~~i~i~g~p~~Vve~~~~kpGKhG 54 (160)
...+-+.-++||+|..++|++.-|.+.+-+.. |=++|
T Consensus 48 ~~sifie~g~lrpGiI~LINd~DWeLleke~y-~ledg 84 (96)
T COG5131 48 RDSIFIEHGELRPGIICLINDMDWELLEKERY-PLEDG 84 (96)
T ss_pred cceeeecCCCCcccEEEEEcCccHhhhhcccc-cCCCC
Confidence 34566788999999999999999999876433 33434
No 73
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=22.15 E-value=73 Score=24.54 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=16.5
Q ss_pred ccccCCceEEEEcCeeEEEEEee
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEVS 46 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~~ 46 (160)
...++.|++|.++|...+|.++.
T Consensus 58 ~~pf~vGD~I~i~~~~G~V~~I~ 80 (206)
T PF00924_consen 58 ERPFKVGDRIEIGGVEGRVEEIG 80 (206)
T ss_dssp C-SS-TT-EEESSS-EEEEEEE-
T ss_pred cCCccCCCEEEEEEeehHHHhcC
Confidence 34789999999999999999983
No 74
>TIGR01397 fliM_switch flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself.
Probab=21.15 E-value=1.9e+02 Score=24.34 Aligned_cols=41 Identities=10% Similarity=0.075 Sum_probs=24.5
Q ss_pred ccccCCceEEEEc---CeeEEE----EEeeeecCCCCcccEEEEEEEEc
Q 031387 24 AGTIRKNGYIVIK---NRPCKV----VEVSTSKTGKHGHAKCHFVGIDI 65 (160)
Q Consensus 24 ~~~lkkG~~i~i~---g~p~~V----ve~~~~kpGKhG~A~v~~k~knl 65 (160)
.-+|++|++|.++ ++|..| ..+-..++|++| -+.-+++.++
T Consensus 271 ll~L~~GDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~-~~~Av~I~~~ 318 (320)
T TIGR01397 271 LLNLQVGDVIPLNTDMPEEVSLRVGGRPKFRAQPGVRG-GKLAVQITRV 318 (320)
T ss_pred HhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEEC-CEEEEEEEEe
Confidence 4478999999998 456665 233455667654 2333444443
No 75
>PF13144 SAF_2: SAF-like
Probab=21.10 E-value=3.9e+02 Score=20.56 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=19.5
Q ss_pred EEEEEEccCCcEEEEeecCCCcee
Q 031387 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (160)
Q Consensus 59 ~~k~knl~TG~~~e~tf~s~~~ve 82 (160)
.++.+|+.||+++.-+.-+...++
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 488899999999988887766654
No 76
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=21.04 E-value=2.1e+02 Score=19.21 Aligned_cols=17 Identities=12% Similarity=0.231 Sum_probs=10.6
Q ss_pred cccCCceEEEEcCeeEE
Q 031387 25 GTIRKNGYIVIKNRPCK 41 (160)
Q Consensus 25 ~~lkkG~~i~i~g~p~~ 41 (160)
..+++|+.|.+.|++..
T Consensus 64 ~~l~kG~~V~V~G~l~~ 80 (104)
T PF00436_consen 64 EYLKKGDRVYVEGRLRT 80 (104)
T ss_dssp HH--TT-EEEEEEEEEE
T ss_pred eEEcCCCEEEEEEEEEe
Confidence 34899999999997663
No 77
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.52 E-value=1.2e+02 Score=24.71 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=23.5
Q ss_pred ccccCCceEEEEcCeeEEEEEeeeecCCC
Q 031387 24 AGTIRKNGYIVIKNRPCKVVEVSTSKTGK 52 (160)
Q Consensus 24 ~~~lkkG~~i~i~g~p~~Vve~~~~kpGK 52 (160)
.-.|++|+.|.++|+-..|.+++.. +||
T Consensus 72 gE~l~vGDei~vd~e~veITSIE~~-~gk 99 (201)
T COG1326 72 GETLKVGDEIEVDGEEVEITSIELG-GGK 99 (201)
T ss_pred CCeEecCCEEEEcCCEEEEEEEeeC-CCc
Confidence 3468999999999999999988764 666
No 78
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.43 E-value=3.2e+02 Score=27.51 Aligned_cols=78 Identities=12% Similarity=0.239 Sum_probs=53.9
Q ss_pred EccCCcEEEEeecCCCceecceEEEeeeEEE--EecCCCcEEEecCCCCceecccCCcchhhHHHHHhhccCCCeEEEEE
Q 031387 64 DIFNGKKLEDIVPSSHNCDAPHVTRTDYQLI--DISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTV 141 (160)
Q Consensus 64 nl~TG~~~e~tf~s~~~ve~~~ve~~~~qyl--y~d~d~~~~fMd~ety~~Eqi~l~~~~~llg~~~~~l~eg~~v~v~~ 141 (160)
-+++.++.+..|..+|.+++..-+-+.++=+ -+|++ ..+.|-.---.++-+.+|.. .+.+||+.|+-|.|.-
T Consensus 397 t~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~-~vti~~~~e~l~~pl~~~~~-----eLrKyF~~GDhVKVi~ 470 (1024)
T KOG1999|consen 397 TLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGT-IVTIMSKHEDLKGPLEVPAS-----ELRKYFEPGDHVKVIA 470 (1024)
T ss_pred eeccccccccccCCCCeEEEeeeeeccceeEEEeccCc-eEEEeeccccCCCccccchH-----hhhhhccCCCeEEEEe
Confidence 6788888999999999999999999988754 45444 44444432111234555554 4689999999888765
Q ss_pred EccCCc
Q 031387 142 MSSMGE 147 (160)
Q Consensus 142 ~~~mg~ 147 (160)
=..-|.
T Consensus 471 G~~eG~ 476 (1024)
T KOG1999|consen 471 GRYEGD 476 (1024)
T ss_pred ccccCC
Confidence 444443
No 79
>cd01179 IPT_plexin_repeat2 Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=20.32 E-value=2.8e+02 Score=18.50 Aligned_cols=34 Identities=12% Similarity=0.353 Sum_probs=24.7
Q ss_pred cCCCceeeEEEeccccCCc--eEEEEcCeeEEEEEe
Q 031387 12 ADAGASKTFPQQAGTIRKN--GYIVIKNRPCKVVEV 45 (160)
Q Consensus 12 ~~~~~s~t~~i~~~~lkkG--~~i~i~g~p~~Vve~ 45 (160)
|....--...|..+.|..| ..|.++|.+|.+...
T Consensus 11 Gp~~GGT~vtI~G~~~~~~~~~~V~ig~~~C~~~~~ 46 (85)
T cd01179 11 GPQSGGTRLTITGKHLNAGSSVRVTVGGQPCKILSV 46 (85)
T ss_pred CCCCCCEEEEEEEECCCCCCeEEEEECCeEeeEEEe
Confidence 3333333566788888877 679999999999664
Done!