Query 031432
Match_columns 159
No_of_seqs 121 out of 1027
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 14:01:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031432.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031432hhsearch_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 1.8E-50 3.9E-55 314.8 19.7 155 1-159 1-159 (159)
2 PTZ00328 eukaryotic initiation 100.0 3.6E-46 7.9E-51 290.5 17.2 159 1-159 1-166 (166)
3 TIGR00037 eIF_5A translation i 100.0 8.5E-45 1.8E-49 274.8 17.1 130 16-154 1-130 (130)
4 PRK03999 translation initiatio 100.0 7.3E-41 1.6E-45 253.0 16.6 127 19-154 3-129 (129)
5 KOG3271 Translation initiation 100.0 7.3E-40 1.6E-44 248.5 11.6 155 1-158 1-155 (156)
6 COG0231 Efp Translation elonga 100.0 1.3E-38 2.8E-43 241.3 16.8 127 20-154 2-128 (131)
7 PRK12426 elongation factor P; 100.0 1E-37 2.3E-42 248.1 15.0 124 21-154 1-124 (185)
8 PRK14578 elongation factor P; 100.0 1.5E-36 3.3E-41 241.9 15.8 125 21-154 1-126 (187)
9 PRK04542 elongation factor P; 100.0 3.6E-36 7.7E-41 240.1 16.2 125 21-154 1-127 (189)
10 PRK00529 elongation factor P; 100.0 8E-35 1.7E-39 231.8 16.6 124 21-154 1-124 (186)
11 TIGR02178 yeiP elongation fact 100.0 9.5E-35 2.1E-39 231.4 16.7 123 23-154 1-125 (186)
12 TIGR00038 efp translation elon 100.0 2.7E-34 5.8E-39 228.5 15.7 116 22-143 1-116 (184)
13 PF08207 EFP_N: Elongation fac 99.8 5.8E-21 1.3E-25 126.0 9.1 58 23-81 1-58 (58)
14 PF01287 eIF-5a: Eukaryotic el 99.6 1.7E-14 3.7E-19 98.4 10.3 68 85-154 1-69 (69)
15 cd04470 S1_EF-P_repeat_1 S1_EF 99.5 2.6E-14 5.6E-19 95.2 7.1 59 87-154 1-59 (61)
16 cd04468 S1_eIF5A S1_eIF5A: Euk 99.5 1.4E-13 2.9E-18 93.9 7.6 69 86-156 1-69 (69)
17 PF01132 EFP: Elongation facto 99.5 2.3E-14 5.1E-19 93.5 3.3 51 88-143 1-51 (55)
18 cd04469 S1_Hex1 S1_Hex1: Hex1, 99.4 2.5E-12 5.4E-17 89.0 8.0 68 88-157 2-71 (75)
19 cd04463 S1_EF_like S1_EF_like: 99.3 1.1E-11 2.4E-16 80.2 6.6 53 89-149 1-53 (55)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.8 9.2E-09 2E-13 67.7 5.9 57 86-151 1-57 (57)
21 COG1499 NMD3 NMD protein affec 97.0 0.0022 4.7E-08 56.2 6.8 110 11-142 231-344 (355)
22 PRK05338 rplS 50S ribosomal pr 77.6 10 0.00022 28.4 6.1 64 23-88 15-87 (116)
23 PF08605 Rad9_Rad53_bind: Fung 77.5 6.8 0.00015 29.7 5.3 53 7-61 42-103 (131)
24 TIGR01024 rplS_bact ribosomal 75.2 12 0.00027 27.7 6.0 64 22-87 14-86 (113)
25 CHL00084 rpl19 ribosomal prote 75.0 15 0.00033 27.5 6.4 65 22-88 18-91 (117)
26 cd06409 PB1_MUG70 The MUG70 pr 64.2 15 0.00033 25.9 4.2 50 60-110 3-63 (86)
27 PF01245 Ribosomal_L19: Riboso 63.2 23 0.00049 26.2 5.2 69 22-90 14-89 (113)
28 PF13275 S4_2: S4 domain; PDB: 60.9 11 0.00024 25.3 2.9 21 23-43 45-65 (65)
29 smart00466 SRA SET and RING fi 54.1 51 0.0011 25.7 6.0 38 26-65 115-152 (155)
30 smart00676 DM10 Domains in hyp 53.7 11 0.00023 27.3 2.1 27 20-46 67-93 (104)
31 PF05354 Phage_attach: Phage H 48.8 12 0.00027 28.0 1.8 39 16-57 64-102 (117)
32 PF13785 DUF4178: Domain of un 48.4 19 0.00042 26.4 2.8 23 27-49 1-23 (140)
33 PF13856 Gifsy-2: ATP-binding 48.3 45 0.00097 23.3 4.6 37 12-48 48-87 (95)
34 PRK11354 kil FtsZ inhibitor pr 47.8 25 0.00055 24.1 3.0 25 19-43 8-32 (73)
35 PF03829 PTSIIA_gutA: PTS syst 47.3 25 0.00053 26.1 3.2 23 23-45 48-70 (117)
36 PF02721 DUF223: Domain of unk 45.9 50 0.0011 22.9 4.5 36 102-140 2-37 (95)
37 PF11871 DUF3391: Domain of un 45.4 13 0.00028 26.8 1.4 21 20-40 3-23 (128)
38 PF11948 DUF3465: Protein of u 45.3 43 0.00093 25.6 4.2 40 23-62 82-127 (131)
39 PRK11507 ribosome-associated p 45.3 24 0.00052 24.1 2.6 21 23-43 49-69 (70)
40 PRK10377 PTS system glucitol/s 44.6 31 0.00068 25.7 3.4 22 24-45 49-70 (120)
41 TIGR00849 gutA PTS system, glu 43.0 35 0.00075 25.6 3.4 21 25-45 50-70 (121)
42 PF11302 DUF3104: Protein of u 41.7 95 0.0021 21.5 5.2 46 26-71 5-60 (75)
43 PF10665 Minor_capsid_1: Minor 41.1 38 0.00083 25.0 3.4 27 23-49 73-99 (114)
44 COG0090 RplB Ribosomal protein 39.4 89 0.0019 26.7 5.7 53 24-80 121-181 (275)
45 cd01771 Faf1_UBX Faf1 UBX doma 38.1 41 0.00089 23.0 3.0 28 57-85 4-31 (80)
46 COG2501 S4-like RNA binding pr 36.5 41 0.00089 23.1 2.7 20 25-44 51-70 (73)
47 PF05521 Phage_H_T_join: Phage 33.8 1.4E+02 0.003 19.5 5.9 33 17-49 52-85 (95)
48 PF02182 SAD_SRA: SAD/SRA doma 33.8 1.1E+02 0.0025 23.5 5.2 35 29-65 118-152 (155)
49 PF06605 Prophage_tail: Propha 33.1 1.2E+02 0.0025 25.5 5.5 38 25-64 26-63 (327)
50 COG5131 URM1 Ubiquitin-like pr 32.5 31 0.00067 24.8 1.6 32 14-45 45-76 (96)
51 PF07076 DUF1344: Protein of u 32.1 68 0.0015 21.3 3.1 26 129-154 36-61 (61)
52 PF13509 S1_2: S1 domain; PDB: 31.5 84 0.0018 20.1 3.5 45 102-153 16-60 (61)
53 PF13144 SAF_2: SAF-like 30.5 2.6E+02 0.0056 21.6 8.2 24 59-82 172-195 (196)
54 COG0335 RplS Ribosomal protein 30.2 2.4E+02 0.0051 21.1 6.9 63 24-88 18-89 (115)
55 PF07591 PT-HINT: Pretoxin HIN 29.7 63 0.0014 24.0 3.0 28 20-47 70-98 (130)
56 PF08408 DNA_pol_B_3: DNA poly 28.2 47 0.001 25.9 2.1 22 24-45 37-58 (149)
57 TIGR01397 fliM_switch flagella 28.1 1.2E+02 0.0025 25.7 4.7 40 24-64 271-317 (320)
58 COG3721 HugX Putative heme iro 26.6 1.3E+02 0.0028 23.9 4.3 46 50-95 93-138 (176)
59 PF14623 Vint: Hint-domain 26.1 1.3E+02 0.0028 23.7 4.3 43 18-60 14-56 (162)
60 PRK10883 FtsI repressor; Provi 25.7 1.8E+02 0.004 26.3 5.8 50 28-85 207-256 (471)
61 PF00467 KOW: KOW motif; Inte 25.5 1.1E+02 0.0023 17.0 2.9 21 29-49 1-26 (32)
62 COG3535 Uncharacterized conser 24.7 5E+02 0.011 23.1 10.0 91 30-142 236-326 (357)
63 PRK10965 multicopper oxidase; 24.5 2.1E+02 0.0046 26.3 6.0 47 28-82 210-256 (523)
64 COG2351 Transthyretin-like pro 24.1 3.2E+02 0.0069 20.7 6.6 85 23-111 23-119 (124)
65 PF05096 Glu_cyclase_2: Glutam 23.6 4.6E+02 0.0099 22.2 8.7 49 18-75 37-85 (264)
66 COG1326 Uncharacterized archae 23.6 95 0.002 25.4 3.1 36 17-53 62-100 (201)
67 KOG0643 Translation initiation 23.1 5.1E+02 0.011 22.6 8.0 69 27-97 43-112 (327)
68 PF00924 MS_channel: Mechanose 22.6 72 0.0016 24.6 2.3 21 25-45 59-79 (206)
69 PF01079 Hint: Hint module; I 22.2 1.6E+02 0.0034 24.0 4.3 29 20-48 99-133 (217)
70 cd04709 BAH_MTA BAH, or Bromo 21.9 1.7E+02 0.0036 22.9 4.2 21 26-46 3-29 (164)
71 PF02839 CBM_5_12: Carbohydrat 21.9 1.1E+02 0.0024 17.7 2.5 18 28-45 11-28 (41)
72 PF02559 CarD_CdnL_TRCF: CarD- 21.4 2.8E+02 0.0061 19.0 6.6 25 27-51 2-27 (98)
73 COG1030 NfeD Membrane-bound se 21.4 1.9E+02 0.0042 26.3 5.0 31 22-52 383-414 (436)
74 TIGR02480 fliN flagellar motor 21.1 1.7E+02 0.0037 19.5 3.7 14 23-36 25-38 (77)
75 smart00166 UBX Domain present 20.8 99 0.0021 20.6 2.4 27 56-85 5-31 (80)
76 cd01773 Faf1_like1_UBX Faf1 ik 20.7 1.3E+02 0.0027 21.0 2.9 21 65-85 12-32 (82)
77 PLN02792 oxidoreductase 20.6 2.5E+02 0.0054 26.0 5.7 50 29-86 178-230 (536)
78 PRK13480 3'-5' exoribonuclease 20.3 3.2E+02 0.0069 23.6 6.0 67 23-94 4-74 (314)
79 COG2828 Uncharacterized protei 20.0 4.6E+02 0.0099 23.3 6.8 82 56-144 117-200 (378)
No 1
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=1.8e-50 Score=314.80 Aligned_cols=155 Identities=83% Similarity=1.236 Sum_probs=145.5
Q ss_pred CCccccccccccCCCcceeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCc
Q 031432 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (159)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ 80 (159)
|++.+++|+ +++|++|.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+|+++
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 788668999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecceEEeeeEEEEEeeCCCc-EEEecC--CCCeeeeccCCc-hhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEecc
Q 031432 81 CDVPHVTRTDYQLIDISEDGF-VSLLTE--NGNTKDDLRLPT-DENLLSQIKDGFESGKDLVVSVQCAMGEEQINALKDI 156 (159)
Q Consensus 81 ve~~~v~~~~~qyly~d~~~~-~~fMD~--etyeq~~i~l~~-~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k~~ 156 (159)
+++|+|++++|||||+|+ +. |+|||+ ++|+|+ .||. +++|...++.+|.+|.++.|++|++||+|+|+++|+.
T Consensus 80 ve~~~ve~~~~qyly~dg-d~y~~fMD~~get~eqi--~v~~~~~el~~~i~~~f~~g~~~~v~v~~~mg~e~i~~~k~~ 156 (159)
T PLN03107 80 CDVPHVNRTDYQLIDISE-DGFVSLMDESGNTKDDL--KLPTEDDTLAEQIKDGFDEGKDLVVTVMSAMGEEQICALKEI 156 (159)
T ss_pred EEEEEEEEEEEEEEEEcC-CceEEEEcCCCCcceeE--EccCcchHHHHHHHHHHhCCCeEEEEEEecCCeEEEEEEEcc
Confidence 999999999999999985 55 599999 588885 5574 3789999999999999999999999999999999999
Q ss_pred CCC
Q 031432 157 GPK 159 (159)
Q Consensus 157 ~~~ 159 (159)
.|+
T Consensus 157 ~~~ 159 (159)
T PLN03107 157 GPK 159 (159)
T ss_pred CCC
Confidence 875
No 2
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=3.6e-46 Score=290.48 Aligned_cols=159 Identities=48% Similarity=0.855 Sum_probs=150.3
Q ss_pred CCcccccccc-ccCCCcceeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCC
Q 031432 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (159)
Q Consensus 1 ~~~~~~~~~~-~~~~~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~ 79 (159)
|||.+++|++ +++|++|.|||++++.||+|.+|+|+|+||+|++++++||||||+|++++.+++||||+++|..+|+.+
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 8887789995 599999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceecceEEeeeEEEEEeeCC------CcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEE
Q 031432 80 NCDVPHVTRTDYQLIDISED------GFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINAL 153 (159)
Q Consensus 80 ~ve~~~v~~~~~qyly~d~~------~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~ 153 (159)
++++|.|+|++||+|.++++ +++.+||+++|++++|+||.+++|+..++..|.+|.+|.|++|++||+|+|+++
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 99999999999999999854 579999999999999999964699999999999999999999999999999999
Q ss_pred eccCCC
Q 031432 154 KDIGPK 159 (159)
Q Consensus 154 k~~~~~ 159 (159)
|++..|
T Consensus 161 k~~~~~ 166 (166)
T PTZ00328 161 KNAAEK 166 (166)
T ss_pred hhhhcC
Confidence 986543
No 3
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=8.5e-45 Score=274.79 Aligned_cols=130 Identities=45% Similarity=0.758 Sum_probs=120.3
Q ss_pred cceeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEE
Q 031432 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLID 95 (159)
Q Consensus 16 ~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly 95 (159)
+|.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+|++++++|.|++++|||||
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 47799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 96 ISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 96 ~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
+| |+.|+|||++||||++|++| . ++..||++|++ |.++++||+|+|+++|
T Consensus 81 ~d-g~~~~fMd~etyeq~~i~~~---~---~~~~~Lke~~~--V~v~~~~g~~~~~~~~ 130 (130)
T TIGR00037 81 IM-GGMVQLMDLDTYETDELPIP---E---ELGDSLEPGFE--VEYIEAMGQEKIIRFK 130 (130)
T ss_pred ec-CCEEEEEcCCCcEEEEecCC---h---hHHHHhhcCCE--EEEEecCCeEEEEEeC
Confidence 98 58999999999999877444 2 34688999976 6677999999999987
No 4
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=7.3e-41 Score=252.99 Aligned_cols=127 Identities=34% Similarity=0.584 Sum_probs=117.2
Q ss_pred eeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeC
Q 031432 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISE 98 (159)
Q Consensus 19 t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~ 98 (159)
-.|+++++||+|++|+++|.||+|++++|+||||||+|++|+++|||+||+++|.+|+++++++.|.|++++|||||+|+
T Consensus 3 ~~~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg 82 (129)
T PRK03999 3 KKQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMG 82 (129)
T ss_pred cccccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecC
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999984
Q ss_pred CCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 99 DGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 99 ~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
+.|+|||++||||++| |. + + +.+.||++|+. |.++.+||+|+|+++|
T Consensus 83 -~~~~fMd~eTyeq~~i--~~-~--~-d~~~~l~eg~~--v~v~~~~g~~~~~~~~ 129 (129)
T PRK03999 83 -DVVQLMDLETYETFEI--PI-P--E-ELKDKLEPGVE--VEYWEAMGRRKIMRVK 129 (129)
T ss_pred -CEEEEecCCCceEEEe--cC-C--h-hHHhhCcCCCE--EEEEhhCCeEEEEEeC
Confidence 8999999999999765 65 3 3 34689999986 5578999999999986
No 5
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.3e-40 Score=248.53 Aligned_cols=155 Identities=67% Similarity=1.028 Sum_probs=150.7
Q ss_pred CCccccccccccCCCcceeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCc
Q 031432 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (159)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ 80 (159)
||+++|+|+ +++|++|.|||++++.|||+.+|.++|+||+|++.+++|+||||+|++++..++||||+++|..++|.++
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 899889999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecceEEeeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEeccCC
Q 031432 81 CDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALKDIGP 158 (159)
Q Consensus 81 ve~~~v~~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k~~~~ 158 (159)
+++|+++|.+||++.++ |+++.||+.+++...++++|. ++|+++|++-+.+|.++.|++.++||+|.++..|...+
T Consensus 80 ~dVp~vkr~~yqLidIs-d~~~sl~t~sG~~kdDlklp~-~el~~~i~~~~e~g~dl~v~Vlsa~gee~~~a~k~~~~ 155 (156)
T KOG3271|consen 80 MDVPVVKRVDYQLIDIS-DGYLSLMTDSGETKDDLKLPE-GELGNQIRQGFEEGKDLLVTVLSAMGEEAAVAPKSGAG 155 (156)
T ss_pred cccCccccceeEEEEec-CCeEEEEcCCCCcchhccCcc-hhHHHHHHHhhcCCCcEEEEEhhhhCchhheeecccCC
Confidence 99999999999999998 579999999999999999999 78999999999999999999999999999999998765
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=1.3e-38 Score=241.30 Aligned_cols=127 Identities=28% Similarity=0.349 Sum_probs=114.0
Q ss_pred eEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCC
Q 031432 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (159)
Q Consensus 20 ~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~ 99 (159)
.|+++++||+|++|+++|.||+|++++|+||||| +|++|+++|||+||+++|.+|+++++++.|.|+++++||||.| |
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg-~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~d-g 79 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGKG-GAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYID-G 79 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCCC-CcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcC-C
Confidence 5899999999999999999999999999999995 5699999999999999999999999999999999999999998 5
Q ss_pred CcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 100 GFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 100 ~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
+.|+|||++||||+++ |. +.+++. ..||.||++|. ++.++|+...+...
T Consensus 80 ~~~~FMD~etyeq~~v--~~-~~~~d~-~~~l~eg~~v~--v~~~~g~~i~v~lP 128 (131)
T COG0231 80 DFYVFMDLETYEQYEL--PK-DQIGDA-AKFLKEGMEVE--VLLYNGEPIAVELP 128 (131)
T ss_pred CeEEEccCCCceEEEe--cc-hhhhhH-HHhcCCCCEEE--EEEECCEEEEEECC
Confidence 8999999999999664 77 677766 59999998755 55677887777654
No 7
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=1e-37 Score=248.10 Aligned_cols=124 Identities=14% Similarity=0.073 Sum_probs=113.8
Q ss_pred EEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCCC
Q 031432 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (159)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~~ 100 (159)
|+++++||+|++|+++|.||.|++++|+|||| |+|++|+|+|||.||+++|+||+|+++++.+.|+++++||||.| ++
T Consensus 1 m~~~~dik~G~~i~~~g~~~~V~~~~h~kPGk-g~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~qylY~d-g~ 78 (185)
T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPK-GETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLE-GD 78 (185)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEecCCC-CceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEEC-CC
Confidence 57899999999999999999999999999999 89999999999999999999999999999999999999999998 48
Q ss_pred cEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 101 FVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 101 ~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
.|+|||++||||+. ||+ +.|++. ..||+||+.|.|++|+ |+ ++++.
T Consensus 79 ~~~FMd~etyeQi~--i~~-~~lgd~-~~fL~e~~~v~v~~~~--~~--~i~v~ 124 (185)
T PRK12426 79 EYLFLDLGNYDKIY--IPK-EIMKDN-FLFLKAGVTVSALVYD--GT--VFSVE 124 (185)
T ss_pred eEEEecCCCceEEE--eCH-HHhhhH-HhhccCCCEEEEEEEC--CE--EEEEE
Confidence 99999999999955 598 788887 5999999999999874 33 55553
No 8
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=1.5e-36 Score=241.90 Aligned_cols=125 Identities=11% Similarity=0.182 Sum_probs=112.6
Q ss_pred EEeccccCCceEEEEcCeEEEEEEeeeecCCCC-CceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCC
Q 031432 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (159)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKh-G~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~ 99 (159)
|+++++||+|++|+++|+||+|++++|+|||++ |+|++|+++|||.||+++|++|+|++++|.|+|+++++||||.| +
T Consensus 1 m~~~~dik~G~~i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~qylY~d-g 79 (187)
T PRK14578 1 MYTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYAD-G 79 (187)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeEEEEeC-C
Confidence 578999999999999999999999999999885 46799999999999999999999999999999999999999998 5
Q ss_pred CcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 100 GFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 100 ~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
+.|+|||++||||+. ||+ +.+++. ..||+||++|.|.+|+ |+ ++++.
T Consensus 80 ~~~~FMD~etyEQ~~--i~~-~~~g~~-~~fL~e~~~v~v~~~~--~~--~i~v~ 126 (187)
T PRK14578 80 DRGVFMDLETYEQFE--MEE-DAFSAI-APFLLDGTEVQLGLFQ--GR--MVNVD 126 (187)
T ss_pred CEEEEecCCCcEEEE--ecH-HHhhhH-HhhccCCCEEEEEEEC--CE--EEEEE
Confidence 899999999999965 588 788877 5999999999999873 33 55554
No 9
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=3.6e-36 Score=240.08 Aligned_cols=125 Identities=17% Similarity=0.167 Sum_probs=112.8
Q ss_pred EEeccccCCceEEEEcCeEEEEEEeeeecC-CCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCC
Q 031432 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (159)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kp-GKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~ 99 (159)
|+++++||+|++|+++|+||+|++++|+|| ||+|+|++|+|+|||.||+++|+||+|+++++.+++++++|||||.| +
T Consensus 1 mi~~~dik~G~~i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~qylY~d-g 79 (189)
T PRK04542 1 MPKANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYID-G 79 (189)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeC-C
Confidence 578999999999999999999999999999 79556799999999999999999999999999999999999999998 4
Q ss_pred CcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCe-EEEEEEeeCCEEEEEEEe
Q 031432 100 GFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKD-LVVSVQCAMGEEQINALK 154 (159)
Q Consensus 100 ~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~-v~V~~~~~~G~e~v~~~k 154 (159)
+.|+|||++||||+. ||+ +.|++. ..||+||+. |.|++|+ |+ ++++.
T Consensus 80 ~~~~FMd~etyEQ~~--i~~-~~lgd~-~~~L~e~~~~v~v~~~~--~~--~i~v~ 127 (189)
T PRK04542 80 DEYVFMDNEDYTPYT--FKK-DQIEDE-LLFIPEGMPGMQVLTVD--GQ--PVALE 127 (189)
T ss_pred CEEEEecCCCceEEE--ECH-HHhhhH-hhhhhcCCEEEEEEEEC--CE--EEEEE
Confidence 899999999999965 598 789887 599999998 9998874 33 55554
No 10
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=8e-35 Score=231.79 Aligned_cols=124 Identities=19% Similarity=0.253 Sum_probs=113.4
Q ss_pred EEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCCC
Q 031432 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (159)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~~ 100 (159)
|+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++++++.|.++++++||||.|+ +
T Consensus 1 ~~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dg-d 78 (186)
T PRK00529 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGK-GQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDG-D 78 (186)
T ss_pred CcchhhcCCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECC-C
Confidence 57899999999999999999999999999999 999999999999999999999999999999999999999999984 7
Q ss_pred cEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 101 FVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 101 ~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
.|+|||++||||+. ||. +.|++.+ .||++|++|.|++|+ | .++++.
T Consensus 79 ~~~fMD~etyeq~~--l~~-~~lg~~~-~~L~eg~~v~v~~~~--~--~~i~v~ 124 (186)
T PRK00529 79 GYVFMDTETYEQIE--VPA-DQVGDAA-KFLKEGMEVTVVFYN--G--EPISVE 124 (186)
T ss_pred EEEEecCCCceeeE--cCH-HHhHHHH-hhccCCCEEEEEEEC--C--EEEEEE
Confidence 89999999999955 688 7888874 899999999999884 3 355554
No 11
>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=9.5e-35 Score=231.39 Aligned_cols=123 Identities=15% Similarity=0.198 Sum_probs=110.2
Q ss_pred eccccCCceEEEEcCeEEEEEEeeeecCCCCCce-EEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCCCc
Q 031432 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGF 101 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a-~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~~~ 101 (159)
.+++||+|++|+++|.||+|++++|+|||++|+| ++|+++|||.||+++|+||+|+++++.|+++++++||||.| ++.
T Consensus 1 ~~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~d-g~~ 79 (186)
T TIGR02178 1 KASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKD-GEE 79 (186)
T ss_pred CcccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeC-CCe
Confidence 3789999999999999999999999999885655 89999999999999999999999999999999999999998 489
Q ss_pred EEEecCCCCeeeeccCCchhhHHHHHHhhccCCCe-EEEEEEeeCCEEEEEEEe
Q 031432 102 VSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKD-LVVSVQCAMGEEQINALK 154 (159)
Q Consensus 102 ~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~-v~V~~~~~~G~e~v~~~k 154 (159)
|+|||++||||+. ||+ +.|++. ..||+||+. |.|.+|+ |+ ++++.
T Consensus 80 ~~FMD~etyEQ~~--i~~-~~lgd~-~~fL~e~~~~v~v~~~~--~~--~i~v~ 125 (186)
T TIGR02178 80 YVFMDEEDYTPYT--FDK-DAIEDE-LLFISEGLSGMYVQLID--GS--PVALE 125 (186)
T ss_pred EEEccCCCcEEEE--eCH-HHhhhh-hhhhhCCCEEEEEEEEC--CE--EEEEE
Confidence 9999999999965 588 788877 599999996 9999884 33 66554
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=2.7e-34 Score=228.47 Aligned_cols=116 Identities=21% Similarity=0.263 Sum_probs=108.8
Q ss_pred EeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCCCc
Q 031432 22 QQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGF 101 (159)
Q Consensus 22 i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~~~ 101 (159)
+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++++|+++++++.|.++++++||||.|+ +.
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dg-d~ 78 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGK-GQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDG-DS 78 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECC-CE
Confidence 4689999999999999999999999999999 899999999999999999999999999999999999999999984 78
Q ss_pred EEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEe
Q 031432 102 VSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQC 143 (159)
Q Consensus 102 ~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~ 143 (159)
|+|||++||||+. ||. +.|++. ..||++|++|.|.+|+
T Consensus 79 ~~fMD~etyeq~~--i~~-~~l~~~-~~~L~eg~~v~v~~~~ 116 (184)
T TIGR00038 79 YVFMDTETYEQIE--LPK-DLLGDA-AKFLKENMEVSVTFYN 116 (184)
T ss_pred EEEeCCCCccceE--cCH-HHHHHH-HhhcCCCCEEEEEEEC
Confidence 9999999999965 587 788877 5999999999999884
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=99.85 E-value=5.8e-21 Score=126.00 Aligned_cols=58 Identities=29% Similarity=0.379 Sum_probs=53.3
Q ss_pred eccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCce
Q 031432 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~v 81 (159)
+|++||+|++|+++|+||.|++++|++||| |+|++|+++|||.||+++|.+|+++|+|
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 8999999999999999999999999986
No 14
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=99.59 E-value=1.7e-14 Score=98.39 Aligned_cols=68 Identities=49% Similarity=0.777 Sum_probs=60.3
Q ss_pred eEEeeeEEEEEeeCCCcEEEecCCCCeeee-ccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 85 HVTRTDYQLIDISEDGFVSLLTENGNTKDD-LRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 85 ~v~~~~~qyly~d~~~~~~fMD~etyeq~~-i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
+|+|++||++.+++|+++.+|| ++++..+ ++||. ++|++.++..|.+|.++.|+++++||+|+|+++|
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMd-e~get~eDl~lP~-~el~~ei~~~~~~g~~~~Vtv~~amG~e~ii~~K 69 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMD-EDGETREDLKLPD-GELGEEIKAKFEEGKEVLVTVLSAMGEEKIIAVK 69 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEE-TTS-EEEEEECCS-HHHHHHHHHHHHTTCEEEEEEEEETTEEEEEEEE
T ss_pred CeEEEEEEEEEEccCcEEEEEc-CCCCeeccEEecc-cchhHHHHhhccCCCeEEEEEEeeCCcEEEEEeC
Confidence 4789999999998667999999 6566544 99997 7999999999999999999999999999999998
No 15
>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=99.54 E-value=2.6e-14 Score=95.16 Aligned_cols=59 Identities=15% Similarity=0.196 Sum_probs=49.3
Q ss_pred EeeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 87 TRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 87 ~~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
+++++||||.| |+.|+|||++||||+. ||+ +.+++. ..||+||+.|.|++|+ |+ ++++.
T Consensus 1 e~~~~qylY~d-g~~~~FMd~etyeQ~~--i~~-~~igd~-~~~L~e~~~v~v~~~~--~~--~i~v~ 59 (61)
T cd04470 1 EEREMQYLYKD-GDNYVFMDTETYEQIE--LPK-EALGDA-AKFLKEGMEVIVLFYN--GE--PIGVE 59 (61)
T ss_pred CCceEEEEEeC-CCEEEEeCCCCceEEE--ECH-HHhhhH-HhhCcCCCEEEEEEEC--CE--EEEEE
Confidence 47899999998 4899999999999965 598 788877 5999999999999885 33 66654
No 16
>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=99.49 E-value=1.4e-13 Score=93.91 Aligned_cols=69 Identities=51% Similarity=0.896 Sum_probs=64.8
Q ss_pred EEeeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEEecc
Q 031432 86 VTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALKDI 156 (159)
Q Consensus 86 v~~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~k~~ 156 (159)
|.|++||++.+++ +++.+||.++-.+.+++||. ++|+..|+..|.+|.++.|++.++||+|+|+++|++
T Consensus 1 V~R~eYqLidI~d-GflsLm~e~G~~k~DlklP~-~elg~~I~~~f~~gk~~~vtV~samGeE~~i~~K~~ 69 (69)
T cd04468 1 VKRTEYQLIDIDD-GFLSLMDDDGETREDLKLPE-GELGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKEA 69 (69)
T ss_pred CcceeEEEEeecC-CeEEEEcCCCCcccCCcCCc-HHHHHHHHHHHhCCCcEEEEEEccCCcEeeEEeecC
Confidence 4689999999984 99999999999999999998 899999999999999999999999999999999974
No 17
>PF01132 EFP: Elongation factor P (EF-P) OB domain; InterPro: IPR001059 Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet []. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. This entry reresents the central domain of elongation factor P and its homologues. It forms an oligonucleotide-binding (OB) fold, though it is not clear if this region is involved in binding nucleic acids [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation; PDB: 1YBY_A 3A5Z_H 3TRE_A 1UEB_B 3HUW_V 3HUY_V 3OYY_B.
Probab=99.48 E-value=2.3e-14 Score=93.48 Aligned_cols=51 Identities=12% Similarity=0.132 Sum_probs=40.7
Q ss_pred eeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEe
Q 031432 88 RTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQC 143 (159)
Q Consensus 88 ~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~ 143 (159)
+|++||||.|| +.|+|||++||||+. ||+ +.+++. ..||+||+.|.|++|+
T Consensus 1 ~r~~qylY~dg-d~~~FMd~etyeQi~--v~~-~~~g~~-~~~L~eg~~v~v~~~~ 51 (55)
T PF01132_consen 1 RREMQYLYKDG-DNYVFMDTETYEQIE--VPK-DQLGDA-LKFLKEGMEVQVLFYE 51 (55)
T ss_dssp EEEEEEEEEES-SEEEEEETTT--EEE--EEH-HHHTTT-GCC--TTEEEEEEEET
T ss_pred CceEEEEEeCC-CEEEEecCCCceEEE--ecH-HHhChH-HhhCcCCCEEEEEEEC
Confidence 68999999995 789999999999955 588 788876 6999999999998875
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=99.38 E-value=2.5e-12 Score=88.99 Aligned_cols=68 Identities=32% Similarity=0.520 Sum_probs=63.7
Q ss_pred eeeEEEEEeeCCCcEEEecCCCCeeeeccCC-chhhHHHHHHhhccCCC-eEEEEEEeeCCEEEEEEEeccC
Q 031432 88 RTDYQLIDISEDGFVSLLTENGNTKDDLRLP-TDENLLSQIKDGFESGK-DLVVSVQCAMGEEQINALKDIG 157 (159)
Q Consensus 88 ~~~~qyly~d~~~~~~fMD~etyeq~~i~l~-~~~~l~~~~~~~l~eg~-~v~V~~~~~~G~e~v~~~k~~~ 157 (159)
.++||++.++ ++++.+||+++..+.+++|| . ++|+..|+..|.+|. ++.|++.++||+|+|+++|+++
T Consensus 2 ~~eYqLidI~-DG~lsLM~e~G~~kdDl~lP~~-~~l~~~I~~~f~~gk~~v~VtVlsAmGeE~iv~~K~~~ 71 (75)
T cd04469 2 FKQYRVLDIQ-DGSIVAMTETGDVKQGLPVIDQ-SNLWTRLKTAFESGRGSVRVLVVNDGGRELVVDMKVVH 71 (75)
T ss_pred ceEEEEEEec-CCeEEEEcCCCCcccCccCCCc-chHHHHHHHHHHCCCCcEEEEEEccCCeEeEEEEEEee
Confidence 3789999995 69999999999999999999 6 899999999999999 9999999999999999999976
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=99.29 E-value=1.1e-11 Score=80.23 Aligned_cols=53 Identities=17% Similarity=0.227 Sum_probs=42.1
Q ss_pred eeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEE
Q 031432 89 TDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQ 149 (159)
Q Consensus 89 ~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~ 149 (159)
|++||||.| ++.|+|||++||+|+++ |+ +. .+ ...||++|+.|.|.+| +|+..
T Consensus 1 ~~~qylY~d-g~~~~fMd~etyeq~~v--~~-~~-~~-~~~~l~eg~~v~v~~~--~g~~i 53 (55)
T cd04463 1 RELQVLDIQ-GSKPVTMDLETYEVVQV--PP-PV-DQ-SFESFEPGEVVLVDTR--TGQYV 53 (55)
T ss_pred CCEEEEEcC-CCEeEEecCCCceEEEe--CH-HH-hh-HHhhCCCCCEEEEEEE--CCEEE
Confidence 579999998 58999999999999664 76 44 44 4699999998888765 56643
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=98.84 E-value=9.2e-09 Score=67.75 Aligned_cols=57 Identities=26% Similarity=0.436 Sum_probs=46.4
Q ss_pred EEeeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEE
Q 031432 86 VTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQIN 151 (159)
Q Consensus 86 v~~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~ 151 (159)
++||..|.+++++ +...+||++||+.+++++|. +++.-+++|.+|. +|.+||+.+|.
T Consensus 1 i~k~~aqVisi~g-~~vQlMD~eTYeT~ev~~p~------~~~~~i~~G~eV~--y~~~~g~~ki~ 57 (57)
T cd04467 1 IERKTGQVLSIMG-DVVQLMDLETYETFEVPIPE------EIKDKLEPGKEVE--YWESMGKRKID 57 (57)
T ss_pred CcceEEEEEEEcC-CEEEEeccccceeEEEecch------hhcccCCCCCEEE--EEeecCeEecC
Confidence 5789999999984 78999999999999998874 2334567886654 88999998873
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=96.99 E-value=0.0022 Score=56.18 Aligned_cols=110 Identities=15% Similarity=0.188 Sum_probs=78.9
Q ss_pred ccCCCcceeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEE---
Q 031432 11 KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVT--- 87 (159)
Q Consensus 11 ~~~~~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~--- 87 (159)
+|-.-.-.|+.+..-++++|++|.+.|..+.++. +-|+ .+.++|+.||...+.++.....-+...+.
T Consensus 231 tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~----~~~~------~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~ 300 (355)
T COG1499 231 TGKRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVR----SIGK------GIVVLDLETGEPVEITWSVYKRNEGKVAVKEP 300 (355)
T ss_pred CCceEEEEEEEEECCCCCCCCEEEECCCeEEEEE----EecC------ceEEEecccCCccccChhhcccCcceeeeccc
Confidence 5555567899999999999999999996665553 3355 48899999998888887655444422222
Q ss_pred -eeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEE
Q 031432 88 -RTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQ 142 (159)
Q Consensus 88 -~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~ 142 (159)
-+.+-++..++ +...|||.+||+.+++.-| -+.+|.++.|..+
T Consensus 301 ~~~~~~vvs~~~-~~~~v~d~et~e~~~~~~~-----------~~~~g~~v~v~~~ 344 (355)
T COG1499 301 RLKKAVVVSRDP-SAIQVLDPETYEARTVKGP-----------SLEEGDEVKVFKV 344 (355)
T ss_pred cceEEEEEecCC-CceEEEecceEEEEeccCC-----------CCCCCCEEEEEEE
Confidence 24566777764 6799999999998775332 2356777766543
No 22
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=77.60 E-value=10 Score=28.36 Aligned_cols=64 Identities=19% Similarity=0.246 Sum_probs=41.0
Q ss_pred eccccCCceEEEE-----cCeEEEEEEeeeec---CCCCCceEEEEEEEECCCCcEEEEEEeCCC-ceecceEEe
Q 031432 23 QAGTIRKNGYIVI-----KGRPCKVVEVSTSK---TGKHGHAKCHFVGIDIFNGKKLEDIVPSSH-NCDVPHVTR 88 (159)
Q Consensus 23 ~~~~ikkG~~i~~-----~g~p~~Vve~~~~k---pGKhG~a~vr~k~knl~TG~~~E~t~~s~~-~ve~~~v~~ 88 (159)
...++++|+.|.+ +|...++..++-.- -++ |- --.+.+|++..|--+|.+|+... .++...|.+
T Consensus 15 ~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~-G~-~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r 87 (116)
T PRK05338 15 DIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGR-GL-NETFTVRKISYGVGVERTFPLHSPRIDSIEVVR 87 (116)
T ss_pred CCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCC-CC-CceEEEEEcccCccEEEEecCCCCcccEEEEEE
Confidence 4678899998876 45544433332221 132 22 24689999999999999999754 455555553
No 23
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=77.46 E-value=6.8 Score=29.75 Aligned_cols=53 Identities=15% Similarity=0.112 Sum_probs=36.7
Q ss_pred ccccccCCCcceeeEEeccccCCceEEEEcCe--EEEEEEeeeec--CC-----CCCceEEEEE
Q 031432 7 HFESKADAGASKTFPQQAGTIRKNGYIVIKGR--PCKVVEVSTSK--TG-----KHGHAKCHFV 61 (159)
Q Consensus 7 ~~~~~~~~~~~~t~~i~~~~ikkG~~i~~~g~--p~~Vve~~~~k--pG-----KhG~a~vr~k 61 (159)
.|+ ++. ......-+..=|||.|+.|.+++. +|.|+-+.+.- +. -+|.+.|.+|
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 577 333 334444567779999999999998 89999998872 22 1266666653
No 24
>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=75.23 E-value=12 Score=27.72 Aligned_cols=64 Identities=20% Similarity=0.255 Sum_probs=39.5
Q ss_pred EeccccCCceEEEEc-----CeEEEEEEeeee---cCCCCCceEEEEEEEECCCCcEEEEEEeCCC-ceecceEE
Q 031432 22 QQAGTIRKNGYIVIK-----GRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH-NCDVPHVT 87 (159)
Q Consensus 22 i~~~~ikkG~~i~~~-----g~p~~Vve~~~~---kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~-~ve~~~v~ 87 (159)
.+..++++|+.|.+. |...++..++-. .-++ |- --.+.+|++..|--+|.+|+... .++...|.
T Consensus 14 ~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~-G~-~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl 86 (113)
T TIGR01024 14 KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGG-GI-GETFTVRKISYGVGVERIFPLHSPNIDSIEVV 86 (113)
T ss_pred cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCC-CC-ceEEEEEEeccCccEEEEEEcCCCccceEEEE
Confidence 456788999988773 333332222211 1133 22 23689999999999999999754 45544444
No 25
>CHL00084 rpl19 ribosomal protein L19
Probab=75.05 E-value=15 Score=27.46 Aligned_cols=65 Identities=17% Similarity=0.196 Sum_probs=40.6
Q ss_pred EeccccCCceEEEE-----cCeEEEEEEeeee---cCCCCCceEEEEEEEECCCCcEEEEEEeCCC-ceecceEEe
Q 031432 22 QQAGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH-NCDVPHVTR 88 (159)
Q Consensus 22 i~~~~ikkG~~i~~-----~g~p~~Vve~~~~---kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~-~ve~~~v~~ 88 (159)
....++++|+.|.+ +|.-.++-.++-. .-|+ |-. -.+.+|++..|--+|.+|+... .++...|.+
T Consensus 18 ~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~-G~~-~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r 91 (117)
T CHL00084 18 KNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNS-GLN-TTITVRKVFQGIGVERVFLLHSPKLASIEVLR 91 (117)
T ss_pred cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCC-CCC-eeEEEEEeccCccEEEEEecCCCccceEEEEE
Confidence 35678999999875 4442222222211 1233 322 3689999999999999999754 455555543
No 26
>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=64.16 E-value=15 Score=25.94 Aligned_cols=50 Identities=18% Similarity=0.221 Sum_probs=32.5
Q ss_pred EEEEECCCCcEEEEEEeCCCcee-----------cceEEeeeEEEEEeeCCCcEEEecCCCC
Q 031432 60 FVGIDIFNGKKLEDIVPSSHNCD-----------VPHVTRTDYQLIDISEDGFVSLLTENGN 110 (159)
Q Consensus 60 ~k~knl~TG~~~E~t~~s~~~ve-----------~~~v~~~~~qyly~d~~~~~~fMD~ety 110 (159)
+|+++. .|+++-.++.+++.+. ........++..|.|+++.++.|..+.-
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 455555 7777777777555554 1221246788999997788898877643
No 27
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=63.24 E-value=23 Score=26.21 Aligned_cols=69 Identities=13% Similarity=0.152 Sum_probs=41.3
Q ss_pred EeccccCCceEEEEc-----CeEEEEEEeeeecCCCCCc-eEEEEEEEECCCCcEEEEEEeCCC-ceecceEEeee
Q 031432 22 QQAGTIRKNGYIVIK-----GRPCKVVEVSTSKTGKHGH-AKCHFVGIDIFNGKKLEDIVPSSH-NCDVPHVTRTD 90 (159)
Q Consensus 22 i~~~~ikkG~~i~~~-----g~p~~Vve~~~~kpGKhG~-a~vr~k~knl~TG~~~E~t~~s~~-~ve~~~v~~~~ 90 (159)
.+..++++|++|.+. |...++..++-.--++++. .--.+.+||+..|.-+|.+|+-.. .++...|.++.
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~~ 89 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRG 89 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEB
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEec
Confidence 456788999988653 4333333332211111110 112578899999999999999854 46666665543
No 28
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=60.94 E-value=11 Score=25.26 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=14.8
Q ss_pred eccccCCceEEEEcCeEEEEE
Q 031432 23 QAGTIRKNGYIVIKGRPCKVV 43 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vv 43 (159)
.-..|++|++|.++|..++|+
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 345799999999999999885
No 29
>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=54.06 E-value=51 Score=25.69 Aligned_cols=38 Identities=18% Similarity=0.252 Sum_probs=28.7
Q ss_pred ccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEEC
Q 031432 26 TIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (159)
Q Consensus 26 ~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl 65 (159)
.-+++....||| +|+|+++ ...+|+.|..+.|++|+-+
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 345777778876 8999987 3446777888899999865
No 30
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=53.66 E-value=11 Score=27.33 Aligned_cols=27 Identities=15% Similarity=0.173 Sum_probs=24.2
Q ss_pred eEEeccccCCceEEEEcCeEEEEEEee
Q 031432 20 FPQQAGTIRKNGYIVIKGRPCKVVEVS 46 (159)
Q Consensus 20 ~~i~~~~ikkG~~i~~~g~p~~Vve~~ 46 (159)
..+...||..|..|.+.|.++.|+++.
T Consensus 67 ~~y~~~Dl~vG~~v~i~gr~f~I~d~D 93 (104)
T smart00676 67 EYYHASDLNVGTTINVFGRQFRIYDCD 93 (104)
T ss_pred CccCHHHcCCCCEEEEeCEEEEEEECC
Confidence 457888999999999999999999874
No 31
>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=48.79 E-value=12 Score=27.98 Aligned_cols=39 Identities=10% Similarity=0.128 Sum_probs=24.6
Q ss_pred cceeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceE
Q 031432 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAK 57 (159)
Q Consensus 16 ~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~ 57 (159)
+-+.+.-.+..||+++.|.++|++|.|.+ +.|--+|...
T Consensus 64 slfv~t~dv~~L~r~DtL~I~g~~y~Vd~---v~pD~~G~t~ 102 (117)
T PF05354_consen 64 SLFVRTADVSGLKRRDTLTIGGESYWVDR---VGPDGGGSTR 102 (117)
T ss_dssp EEEESCCCCCTS-TT-EEEETTTEEEBS------SSSSS-CC
T ss_pred eEEEEehHhhhhhcCCeEEECCEEEEEEe---eccCCCccEE
Confidence 44455667889999999999999999965 4664334433
No 32
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=48.37 E-value=19 Score=26.37 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=20.0
Q ss_pred cCCceEEEEcCeEEEEEEeeeec
Q 031432 27 IRKNGYIVIKGRPCKVVEVSTSK 49 (159)
Q Consensus 27 ikkG~~i~~~g~p~~Vve~~~~k 49 (159)
|++|+.+.++|.+|.|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999998776554
No 33
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=48.34 E-value=45 Score=23.27 Aligned_cols=37 Identities=16% Similarity=0.229 Sum_probs=22.1
Q ss_pred cCCCcceeeEEeccccC---CceEEEEcCeEEEEEEeeee
Q 031432 12 ADAGASKTFPQQAGTIR---KNGYIVIKGRPCKVVEVSTS 48 (159)
Q Consensus 12 ~~~~~~~t~~i~~~~ik---kG~~i~~~g~p~~Vve~~~~ 48 (159)
+-++++.+--+..++++ +|+.|.++|+-|.|.+++.-
T Consensus 48 ~v~g~~~~L~v~~~d~~~P~~gd~v~~dG~~y~V~~~~~~ 87 (95)
T PF13856_consen 48 GVEGTQPTLYVFSSDYPKPRRGDRVVIDGESYTVTRFQEE 87 (95)
T ss_dssp ------EEEEE--SS-----TT-EEEETTEEEEEEEEEEE
T ss_pred cccCCceEEEEEcCCCCCCCCCCEEEECCeEEEEeEEecC
Confidence 34456667777776654 89999999999999988655
No 34
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=47.77 E-value=25 Score=24.10 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=22.4
Q ss_pred eeEEeccccCCceEEEEcCeEEEEE
Q 031432 19 TFPQQAGTIRKNGYIVIKGRPCKVV 43 (159)
Q Consensus 19 t~~i~~~~ikkG~~i~~~g~p~~Vv 43 (159)
|.+++=..+.+|+.|.++|+-|+.-
T Consensus 8 T~~v~Rq~V~PG~~v~~~grty~AS 32 (73)
T PRK11354 8 TDEIPRQCVTPGDYVLHEGRTYIAS 32 (73)
T ss_pred ceeecccccCCceEEEEcCcEEEEE
Confidence 7788889999999999999999754
No 35
>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=47.31 E-value=25 Score=26.13 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=16.2
Q ss_pred eccccCCceEEEEcCeEEEEEEe
Q 031432 23 QAGTIRKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~ 45 (159)
...+|++|+.+.+++..|.|..+
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 36
>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=45.86 E-value=50 Score=22.86 Aligned_cols=36 Identities=28% Similarity=0.510 Sum_probs=27.8
Q ss_pred EEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEE
Q 031432 102 VSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVS 140 (159)
Q Consensus 102 ~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~ 140 (159)
+++||+++ .+++..+|. .+.+..+..|.||.-+.+.
T Consensus 2 mvL~De~G-~~I~A~I~~--~~~~~f~~~l~Eg~~y~i~ 37 (95)
T PF02721_consen 2 MVLVDEKG-DKIQATIPK--ELVDKFKDSLKEGSWYTIS 37 (95)
T ss_pred EEEEecCC-CEEEEEECH--HHHHHHHhhcccCCEEEeE
Confidence 68999997 566777885 6777888999999766554
No 37
>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=45.38 E-value=13 Score=26.82 Aligned_cols=21 Identities=10% Similarity=0.091 Sum_probs=17.6
Q ss_pred eEEeccccCCceEEEEcCeEE
Q 031432 20 FPQQAGTIRKNGYIVIKGRPC 40 (159)
Q Consensus 20 ~~i~~~~ikkG~~i~~~g~p~ 40 (159)
..|++++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 578999999999998766666
No 38
>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=45.32 E-value=43 Score=25.58 Aligned_cols=40 Identities=15% Similarity=0.187 Sum_probs=29.5
Q ss_pred eccccCCceEEEEcCeEE-----EEEEeeeecC-CCCCceEEEEEE
Q 031432 23 QAGTIRKNGYIVIKGRPC-----KVVEVSTSKT-GKHGHAKCHFVG 62 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~-----~Vve~~~~kp-GKhG~a~vr~k~ 62 (159)
...+|++|+.|+..|+-. -|+.++|+-| |+|-.+.+...+
T Consensus 82 rip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~~h~~Gwl~~nG 127 (131)
T PF11948_consen 82 RIPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRGRHPDGWLKHNG 127 (131)
T ss_pred cCcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCCCCCCeeEEECC
Confidence 345799999999998753 4799999988 566555665543
No 39
>PRK11507 ribosome-associated protein; Provisional
Probab=45.30 E-value=24 Score=24.08 Aligned_cols=21 Identities=19% Similarity=0.267 Sum_probs=17.7
Q ss_pred eccccCCceEEEEcCeEEEEE
Q 031432 23 QAGTIRKNGYIVIKGRPCKVV 43 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vv 43 (159)
.--.|++|+.|.++|.-++|+
T Consensus 49 RgkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 49 KRCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred cCCCCCCCCEEEECCEEEEEe
Confidence 445799999999999988875
No 40
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=44.62 E-value=31 Score=25.74 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=19.9
Q ss_pred ccccCCceEEEEcCeEEEEEEe
Q 031432 24 AGTIRKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~ 45 (159)
..+|++|+.+.+++..|.|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAV 70 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEE
Confidence 4679999999999999999876
No 41
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=42.99 E-value=35 Score=25.56 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=19.3
Q ss_pred cccCCceEEEEcCeEEEEEEe
Q 031432 25 GTIRKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 25 ~~ikkG~~i~~~g~p~~Vve~ 45 (159)
.+|++|+.+.+++..|.|..+
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaV 70 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAV 70 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEE
Confidence 479999999999999999876
No 42
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=41.74 E-value=95 Score=21.49 Aligned_cols=46 Identities=11% Similarity=0.162 Sum_probs=28.7
Q ss_pred ccCCceEEEEcCeE---------EEEEEeeeecCCCC-CceEEEEEEEECCCCcEE
Q 031432 26 TIRKNGYIVIKGRP---------CKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKL 71 (159)
Q Consensus 26 ~ikkG~~i~~~g~p---------~~Vve~~~~kpGKh-G~a~vr~k~knl~TG~~~ 71 (159)
.+|.|++|++.... |-+=++-++..|.+ ..+---+..-|+.||.+.
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 223344677788888764
No 43
>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=41.11 E-value=38 Score=24.96 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=23.2
Q ss_pred eccccCCceEEEEcCeEEEEEEeeeec
Q 031432 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~k 49 (159)
++-+++.|+.|.++|..|.|..+...-
T Consensus 73 p~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 73 PFPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred cccccCCCCEEEECCceEEEEEEEecc
Confidence 345888899999999999999997775
No 44
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=39.41 E-value=89 Score=26.69 Aligned_cols=53 Identities=23% Similarity=0.307 Sum_probs=27.4
Q ss_pred ccccCCceEEEEcCeEE--EEEEeeeecCCCCCc------eEEEEEEEECCCCcEEEEEEeCCCc
Q 031432 24 AGTIRKNGYIVIKGRPC--KVVEVSTSKTGKHGH------AKCHFVGIDIFNGKKLEDIVPSSHN 80 (159)
Q Consensus 24 ~~~ikkG~~i~~~g~p~--~Vve~~~~kpGKhG~------a~vr~k~knl~TG~~~E~t~~s~~~ 80 (159)
..+|+.|+.+-|.+-|- .|-.+ -.+||++|+ +.+++..++ |...--.++|++.
T Consensus 121 ~a~ik~GN~lpL~~IP~Gt~VhNV-E~~pG~GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~ 181 (275)
T COG0090 121 DADIKPGNALPLGNIPEGTIVHNV-ELKPGDGGQLARSAGTYAQVVGKE---GNYVIVRLPSGEM 181 (275)
T ss_pred CCCcCCcceeeeccCCCCceEEee-eeccCCCceEEEeCCceEEEEEcc---CCEEEEECCCCCe
Confidence 34677777777776662 22222 236888432 334445554 4444455555543
No 45
>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=38.06 E-value=41 Score=23.02 Aligned_cols=28 Identities=14% Similarity=-0.066 Sum_probs=20.9
Q ss_pred EEEEEEEECCCCcEEEEEEeCCCceecce
Q 031432 57 KCHFVGIDIFNGKKLEDIVPSSHNCDVPH 85 (159)
Q Consensus 57 ~vr~k~knl~TG~~~E~t~~s~~~ve~~~ 85 (159)
.+++.+| +-+|+.++++|.+++++..+.
T Consensus 4 ~~~i~iR-lP~G~r~~rrF~~t~~L~~l~ 31 (80)
T cd01771 4 ISKLRVR-TPSGDFLERRFLGDTPLQVLL 31 (80)
T ss_pred eEEEEEE-CCCCCEEEEEeCCCCcHHHHH
Confidence 3344333 678999999999999998553
No 46
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=36.47 E-value=41 Score=23.14 Aligned_cols=20 Identities=25% Similarity=0.434 Sum_probs=17.7
Q ss_pred cccCCceEEEEcCeEEEEEE
Q 031432 25 GTIRKNGYIVIKGRPCKVVE 44 (159)
Q Consensus 25 ~~ikkG~~i~~~g~p~~Vve 44 (159)
-.||.|+.|++.|.++.|..
T Consensus 51 kKlr~gd~V~i~~~~~~v~~ 70 (73)
T COG2501 51 KKLRDGDVVEIPGQRYQVVA 70 (73)
T ss_pred CEeecCCEEEECCEEEEEEe
Confidence 46899999999999999875
No 47
>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=33.82 E-value=1.4e+02 Score=19.53 Aligned_cols=33 Identities=12% Similarity=0.221 Sum_probs=22.2
Q ss_pred ceeeEEecc-ccCCceEEEEcCeEEEEEEeeeec
Q 031432 17 SKTFPQQAG-TIRKNGYIVIKGRPCKVVEVSTSK 49 (159)
Q Consensus 17 ~~t~~i~~~-~ikkG~~i~~~g~p~~Vve~~~~k 49 (159)
+..+.|--. +|..++.|.++|..|.|..+....
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 445555333 699999999999999999876554
No 48
>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=33.81 E-value=1.1e+02 Score=23.51 Aligned_cols=35 Identities=31% Similarity=0.389 Sum_probs=24.9
Q ss_pred CceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEEC
Q 031432 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (159)
Q Consensus 29 kG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl 65 (159)
++..+.||| +|+|+++...+ |+.|...++++|+-+
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 344578888 99999987664 444778899999865
No 49
>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=33.08 E-value=1.2e+02 Score=25.54 Aligned_cols=38 Identities=16% Similarity=0.309 Sum_probs=22.9
Q ss_pred cccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEE
Q 031432 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (159)
Q Consensus 25 ~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~kn 64 (159)
.-|.++.+|.++|+.|+|..+....-|. + ..+.+.+++
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 5688999999999999999987776664 2 347888888
No 50
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=32.51 E-value=31 Score=24.84 Aligned_cols=32 Identities=16% Similarity=0.178 Sum_probs=26.3
Q ss_pred CCcceeeEEeccccCCceEEEEcCeEEEEEEe
Q 031432 14 AGASKTFPQQAGTIRKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 14 ~~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~ 45 (159)
|.+....-+.-++||+|.++.+|+.-|.+.+-
T Consensus 45 ~p~~~sifie~g~lrpGiI~LINd~DWeLlek 76 (96)
T COG5131 45 APTRDSIFIEHGELRPGIICLINDMDWELLEK 76 (96)
T ss_pred CCccceeeecCCCCcccEEEEEcCccHhhhhc
Confidence 33445667788999999999999999999864
No 51
>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=32.11 E-value=68 Score=21.34 Aligned_cols=26 Identities=27% Similarity=0.452 Sum_probs=21.5
Q ss_pred hhccCCCeEEEEEEeeCCEEEEEEEe
Q 031432 129 DGFESGKDLVVSVQCAMGEEQINALK 154 (159)
Q Consensus 129 ~~l~eg~~v~V~~~~~~G~e~v~~~k 154 (159)
..|+.|+.|.|.+-...|+..|.+++
T Consensus 36 ~~L~~G~kV~V~yd~~~gk~vitdi~ 61 (61)
T PF07076_consen 36 DGLKPGMKVVVFYDEVDGKRVITDIE 61 (61)
T ss_pred cccCCCCEEEEEEEccCCcEEeeecC
Confidence 55678999999988888998887753
No 52
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=31.53 E-value=84 Score=20.11 Aligned_cols=45 Identities=13% Similarity=0.202 Sum_probs=23.5
Q ss_pred EEEecCCCCeeeeccCCchhhHHHHHHhhccCCCeEEEEEEeeCCEEEEEEE
Q 031432 102 VSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINAL 153 (159)
Q Consensus 102 ~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~~~~G~e~v~~~ 153 (159)
-.|+|...-.. +-||. .++... ++.|+++.|.+|..-....+-.+
T Consensus 16 g~fL~~~~~~~--vlLp~-~e~~~~----~~~Gd~v~VFvY~D~~~rl~AT~ 60 (61)
T PF13509_consen 16 GYFLDDGEGKE--VLLPK-SEVPEP----LKVGDEVEVFVYLDKEGRLVATT 60 (61)
T ss_dssp EEEEEETT-EE--EEEEG-GG----------TTSEEEEEEEE-TTS-EEEE-
T ss_pred EEEEECCCCCE--EEech-HHcCCC----CCCCCEEEEEEEECCCCCEEEec
Confidence 35566554343 55787 555433 46799999998877655555544
No 53
>PF13144 SAF_2: SAF-like
Probab=30.45 E-value=2.6e+02 Score=21.64 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=19.5
Q ss_pred EEEEEECCCCcEEEEEEeCCCcee
Q 031432 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (159)
Q Consensus 59 r~k~knl~TG~~~E~t~~s~~~ve 82 (159)
.++.+|+.||+++.-+.-+...++
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 688899999999988877766665
No 54
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=30.20 E-value=2.4e+02 Score=21.12 Aligned_cols=63 Identities=19% Similarity=0.284 Sum_probs=39.6
Q ss_pred ccccCCceEEE-----EcCeEEEEEEeeee---cCCCCCceEEEEEEEECCCCcEEEEEEeCC-CceecceEEe
Q 031432 24 AGTIRKNGYIV-----IKGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSS-HNCDVPHVTR 88 (159)
Q Consensus 24 ~~~ikkG~~i~-----~~g~p~~Vve~~~~---kpGKhG~a~vr~k~knl~TG~~~E~t~~s~-~~ve~~~v~~ 88 (159)
..++++|+.|. .+|.-|.+--++-. .-|+ |-.. .+.++.+..|-=+|.+|+.. ..++...|.+
T Consensus 18 iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~-G~~~-tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~r 89 (115)
T COG0335 18 IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGR-GISE-TFTVRKISYGVGVERVFPLHSPLIESIEVVR 89 (115)
T ss_pred CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCC-Cccc-eEEEEEeecCceEEEEeecCCCceeEEEEEe
Confidence 55667777654 34555666555433 2343 3333 56788889999999999974 3566555553
No 55
>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=29.75 E-value=63 Score=23.96 Aligned_cols=28 Identities=11% Similarity=0.078 Sum_probs=15.8
Q ss_pred eEEeccccCCceEEEE-cCeEEEEEEeee
Q 031432 20 FPQQAGTIRKNGYIVI-KGRPCKVVEVST 47 (159)
Q Consensus 20 ~~i~~~~ikkG~~i~~-~g~p~~Vve~~~ 47 (159)
--+.|.+|++|+.|.- +|.+..|..+..
T Consensus 70 gWv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 70 GWVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp --EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 3689999999999865 677777766644
No 56
>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=28.21 E-value=47 Score=25.90 Aligned_cols=22 Identities=18% Similarity=0.410 Sum_probs=18.8
Q ss_pred ccccCCceEEEEcCeEEEEEEe
Q 031432 24 AGTIRKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~ 45 (159)
..=|+-|.+|.+++.+|+|++=
T Consensus 37 ~~VL~TgNYitI~d~v~kI~~K 58 (149)
T PF08408_consen 37 SEVLSTGNYITINDDVYKILDK 58 (149)
T ss_pred HHHHhcCCeEEECCeeeeeecc
Confidence 3447899999999999999964
No 57
>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=28.09 E-value=1.2e+02 Score=25.67 Aligned_cols=40 Identities=8% Similarity=-0.006 Sum_probs=24.6
Q ss_pred ccccCCceEEEEc---CeEEEE----EEeeeecCCCCCceEEEEEEEE
Q 031432 24 AGTIRKNGYIVIK---GRPCKV----VEVSTSKTGKHGHAKCHFVGID 64 (159)
Q Consensus 24 ~~~ikkG~~i~~~---g~p~~V----ve~~~~kpGKhG~a~vr~k~kn 64 (159)
.-+|++|++|.++ ++|..| ..+-..++|++|+.+ -+++.+
T Consensus 271 ll~L~~GDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~-Av~I~~ 317 (320)
T TIGR01397 271 LLNLQVGDVIPLNTDMPEEVSLRVGGRPKFRAQPGVRGGKL-AVQITR 317 (320)
T ss_pred HhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEECCEE-EEEEEE
Confidence 4578999999998 356665 334455677764433 344433
No 58
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=26.56 E-value=1.3e+02 Score=23.85 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=36.0
Q ss_pred CCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEE
Q 031432 50 TGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLID 95 (159)
Q Consensus 50 pGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly 95 (159)
.|.|+++.+.+.+|+-..|.+.-.+|..-.-++.|..-++.+.+.+
T Consensus 93 ~G~~~hGyfNL~gk~~l~GHiK~eNcs~Ialv~rpFmG~~s~si~F 138 (176)
T COG3721 93 SGTHRHGYFNLRGKDGLSGHIKAENCSHIALVERPFMGMESASILF 138 (176)
T ss_pred CCccccceEeecCCCCCcceeeccccceeeEeccccCCccceeeee
Confidence 3888999999999999999998888887777777776555444333
No 59
>PF14623 Vint: Hint-domain
Probab=26.08 E-value=1.3e+02 Score=23.74 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=27.1
Q ss_pred eeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEE
Q 031432 18 KTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60 (159)
Q Consensus 18 ~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~ 60 (159)
.+.++++.+||+|+.|.--..|-+|.-+-..+-...+..++++
T Consensus 14 ~~~~v~i~~lR~G~~V~tp~G~r~V~~Vlkt~v~~~~~~lc~v 56 (162)
T PF14623_consen 14 GRAPVRIDDLRAGDKVWTPRGPRKVAAVLKTPVESGSEDLCRV 56 (162)
T ss_pred CceeEEHHHccCCCEEECCCCCeEEEEEEEEeecCCceEEEEE
Confidence 3445999999999998877667666555444322212345555
No 60
>PRK10883 FtsI repressor; Provisional
Probab=25.73 E-value=1.8e+02 Score=26.28 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=36.2
Q ss_pred CCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecce
Q 031432 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPH 85 (159)
Q Consensus 28 kkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~ 85 (159)
..|+.+.+||..+-++++ +|| .+|+++.|--.-+.+...+..++.+.++-
T Consensus 207 ~~gd~~lvNG~~~p~~~v---~~~-----~~RlRliNas~~~~~~l~l~d~~~~~vIa 256 (471)
T PRK10883 207 FVGDTLLVNGVQSPYVEV---SRG-----WVRLRLLNASNARRYQLQMSDGRPLHVIA 256 (471)
T ss_pred ccCCeeEECCccCCeEEe---cCC-----EEEEEEEEccCCceEEEEEcCCCeEEEEE
Confidence 468999999997766654 343 47999999999888877775455544333
No 61
>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=25.53 E-value=1.1e+02 Score=17.02 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=14.8
Q ss_pred CceEEEE-----cCeEEEEEEeeeec
Q 031432 29 KNGYIVI-----KGRPCKVVEVSTSK 49 (159)
Q Consensus 29 kG~~i~~-----~g~p~~Vve~~~~k 49 (159)
+|+.+.+ .|..++|+++...+
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 4667776 77888888876553
No 62
>COG3535 Uncharacterized conserved protein [Function unknown]
Probab=24.68 E-value=5e+02 Score=23.07 Aligned_cols=91 Identities=22% Similarity=0.366 Sum_probs=60.3
Q ss_pred ceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEeeCCCcEEEecCCC
Q 031432 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENG 109 (159)
Q Consensus 30 G~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d~~~~~~fMD~et 109 (159)
|.+++++|..-.|. ...-|-.....+++.+.+-..|++++-.|.-.- .+-+++-|++-.-. |-.+++|.+|
T Consensus 236 ~g~~lf~Gki~dV~---R~t~gGF~~G~~~I~G~~~~~g~t~~i~FqNEf-----l~a~~~G~~l~~~P-DLI~lld~~T 306 (357)
T COG3535 236 GGKILFKGKIVDVK---RETRGGFARGRVTIDGLEEYRGSTLEIAFQNEF-----LVAEKDGKILATTP-DLIVLLDLNT 306 (357)
T ss_pred CcEEEEccEEEEEE---EeeecceeeeeEEEechhhcCCceEEEEEEeee-----eEEecCCcEEEecC-ceEEEEecCC
Confidence 46788888655544 343331123458889999999999999997533 23458888888875 8889999998
Q ss_pred CeeeeccCCchhhHHHHHHhhccCCCeEEEEEE
Q 031432 110 NTKDDLRLPTDENLLSQIKDGFESGKDLVVSVQ 142 (159)
Q Consensus 110 yeq~~i~l~~~~~l~~~~~~~l~eg~~v~V~~~ 142 (159)
.-. +.. +.++. |+.|.|.-+
T Consensus 307 g~p----iTT-----e~lky----G~rV~V~aI 326 (357)
T COG3535 307 GLP----ITT-----ESLKY----GQRVVVIAI 326 (357)
T ss_pred CCc----cch-----HHhhc----CcEEEEEEe
Confidence 753 233 23323 877666544
No 63
>PRK10965 multicopper oxidase; Provisional
Probab=24.45 E-value=2.1e+02 Score=26.33 Aligned_cols=47 Identities=6% Similarity=-0.070 Sum_probs=33.7
Q ss_pred CCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCcee
Q 031432 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (159)
Q Consensus 28 kkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve 82 (159)
..|+.+.+||.++-.+. .||+ .+|+++.|--+-+.+...+..++.+.
T Consensus 210 ~~gd~~lVNG~~~p~~~----v~~~----~~RlRliNas~~r~~~l~~~dg~~~~ 256 (523)
T PRK10965 210 WFGDTLLTNGAIYPQHA----APRG----WLRLRLLNGCNARSLNLATSDGRPLY 256 (523)
T ss_pred ccCCeEEECCcccceee----cCCC----EEEEEEEeccCCceEEEEEcCCceEE
Confidence 46899999999775543 2443 68999999988888777764444443
No 64
>COG2351 Transthyretin-like protein [General function prediction only]
Probab=24.13 E-value=3.2e+02 Score=20.66 Aligned_cols=85 Identities=16% Similarity=0.209 Sum_probs=44.0
Q ss_pred eccccCCceEEEEcCeEE-EEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCcee--------cceEEeeeEEE
Q 031432 23 QAGTIRKNGYIVIKGRPC-KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD--------VPHVTRTDYQL 93 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~-~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve--------~~~v~~~~~qy 93 (159)
++..++...+ .++|+-+ .+-+..+..-||..++. +.+.++.+| ++|-.|..+|=+. .|.++..++.|
T Consensus 23 PAagv~V~L~-rl~~~~~~~l~t~~Tn~DGR~d~pl--l~g~~~~~G-~Y~l~F~~gdYf~~~g~~~~~~~Fl~~V~vrF 98 (124)
T COG2351 23 PAAGVKVELY-RLEGNQWELLKTVVTNADGRIDAPL--LAGETLATG-IYELVFHTGDYFKSRGVQLADPPFLDVVPVRF 98 (124)
T ss_pred cCCCCEEEEE-EecCCcceeeeEEEecCCCcccccc--cCccccccc-eEEEEEEcchhhhccCcccCCCCccceEEEEE
Confidence 3444444433 2333333 33333444456533222 455666666 4578887765443 35777777777
Q ss_pred EEeeCCCcEE---EecCCCCe
Q 031432 94 IDISEDGFVS---LLTENGNT 111 (159)
Q Consensus 94 ly~d~~~~~~---fMD~etye 111 (159)
=-.|.+..|| ++-+-+|.
T Consensus 99 ~iad~~~HYHVPLLlSPygYS 119 (124)
T COG2351 99 GIADVDEHYHVPLLLSPYGYS 119 (124)
T ss_pred EEcCCCCceeeeeEecCcccc
Confidence 7666445665 34444444
No 65
>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=23.62 E-value=4.6e+02 Score=22.24 Aligned_cols=49 Identities=20% Similarity=0.367 Sum_probs=31.9
Q ss_pred eeeEEeccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEE
Q 031432 18 KTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 75 (159)
Q Consensus 18 ~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~ 75 (159)
.+||-..+.+-.|..+.-+|..|. .+|.-|++. ++-.|+.||++.....
T Consensus 37 ~~ypHd~~aFTQGL~~~~~g~LyE-------STG~yG~S~--l~~~d~~tg~~~~~~~ 85 (264)
T PF05096_consen 37 ETYPHDPTAFTQGLEFLDDGTLYE-------STGLYGQSS--LRKVDLETGKVLQSVP 85 (264)
T ss_dssp EEEE--TT-EEEEEEEEETTEEEE-------EECSTTEEE--EEEEETTTSSEEEEEE
T ss_pred EECCCCCcccCccEEecCCCEEEE-------eCCCCCcEE--EEEEECCCCcEEEEEE
Confidence 356667788888887777887762 457666555 5577999998874433
No 66
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.56 E-value=95 Score=25.37 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=26.8
Q ss_pred ceeeEE---eccccCCceEEEEcCeEEEEEEeeeecCCCC
Q 031432 17 SKTFPQ---QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKH 53 (159)
Q Consensus 17 ~~t~~i---~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKh 53 (159)
|+|..+ +--.|++|+.|+++|+-..|++++.. +||+
T Consensus 62 S~~~~vel~~gE~l~vGDei~vd~e~veITSIE~~-~gkR 100 (201)
T COG1326 62 SFTKEVELDPGETLKVGDEIEVDGEEVEITSIELG-GGKR 100 (201)
T ss_pred ccceeEecCCCCeEecCCEEEEcCCEEEEEEEeeC-CCcc
Confidence 444444 33468999999999999999998654 5663
No 67
>KOG0643 consensus Translation initiation factor 3, subunit i (eIF-3i)/TGF-beta receptor-interacting protein (TRIP-1) [Translation, ribosomal structure and biogenesis; Signal transduction mechanisms]
Probab=23.10 E-value=5.1e+02 Score=22.59 Aligned_cols=69 Identities=13% Similarity=0.042 Sum_probs=46.1
Q ss_pred cCCceEEEEcCeEEEE-EEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceEEeeeEEEEEee
Q 031432 27 IRKNGYIVIKGRPCKV-VEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDIS 97 (159)
Q Consensus 27 ikkG~~i~~~g~p~~V-ve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v~~~~~qyly~d 97 (159)
=|-|.|==..|..|-| ++.....-=- |+|-..+++=|+.||+.+ .+++....+..+++.+-.-+.++..
T Consensus 43 erlGty~GHtGavW~~Did~~s~~liT-GSAD~t~kLWDv~tGk~l-a~~k~~~~Vk~~~F~~~gn~~l~~t 112 (327)
T KOG0643|consen 43 ERLGTYDGHTGAVWCCDIDWDSKHLIT-GSADQTAKLWDVETGKQL-ATWKTNSPVKRVDFSFGGNLILAST 112 (327)
T ss_pred ceeeeecCCCceEEEEEecCCcceeee-ccccceeEEEEcCCCcEE-EEeecCCeeEEEeeccCCcEEEEEe
Confidence 3455544444555543 3332211111 778999999999999998 8999999888888776666666664
No 68
>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=22.61 E-value=72 Score=24.57 Aligned_cols=21 Identities=24% Similarity=0.284 Sum_probs=16.0
Q ss_pred cccCCceEEEEcCeEEEEEEe
Q 031432 25 GTIRKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 25 ~~ikkG~~i~~~g~p~~Vve~ 45 (159)
.-++.|+.|.++|...+|+++
T Consensus 59 ~pf~vGD~I~i~~~~G~V~~I 79 (206)
T PF00924_consen 59 RPFKVGDRIEIGGVEGRVEEI 79 (206)
T ss_dssp -SS-TT-EEESSS-EEEEEEE
T ss_pred CCccCCCEEEEEEeehHHHhc
Confidence 468999999999999999988
No 69
>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=22.22 E-value=1.6e+02 Score=24.03 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=20.1
Q ss_pred eEEeccccCCceEEEE------cCeEEEEEEeeee
Q 031432 20 FPQQAGTIRKNGYIVI------KGRPCKVVEVSTS 48 (159)
Q Consensus 20 ~~i~~~~ikkG~~i~~------~g~p~~Vve~~~~ 48 (159)
.++-|+++++|++|.. .-.|-+|+.+...
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 7899999999999999 2347777777655
No 70
>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=21.87 E-value=1.7e+02 Score=22.94 Aligned_cols=21 Identities=19% Similarity=0.485 Sum_probs=13.9
Q ss_pred ccCCceEEEEc---CeE---EEEEEee
Q 031432 26 TIRKNGYIVIK---GRP---CKVVEVS 46 (159)
Q Consensus 26 ~ikkG~~i~~~---g~p---~~Vve~~ 46 (159)
-+|.|++|.++ +.| |+|+++.
T Consensus 3 ~yrvGD~Vy~~~~~~~Py~I~rI~e~~ 29 (164)
T cd04709 3 MYRVGDYVYFESSPNNPYLIRRIEELN 29 (164)
T ss_pred EEecCCEEEEECCCCCCCEEEEEEEEE
Confidence 46889999887 445 4555553
No 71
>PF02839 CBM_5_12: Carbohydrate binding domain; InterPro: IPR003610 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM5 from CAZY and CBM12 from CAZY. These modules have a core structure consisting of a 3-stranded meander beta-sheet, which contain six aromatic groups that may be important for binding. CBM5/12 is found in proteins such as chitinase A1, chitinase B [], and endoglucanase Z []. The overall topology of the CBM is structurally similar to the C-terminal chitin-binding domains (ChBD) of chitinase A1 and chitinase B, however the binding mechanism for the ChBD may be different from that of the CBM [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1ED7_A 1W1V_A 1E15_B 1UR8_A 1E6Z_B 1E6P_A 1W1T_A 1W1P_B 1UR9_A 1E6R_A ....
Probab=21.85 E-value=1.1e+02 Score=17.68 Aligned_cols=18 Identities=6% Similarity=0.008 Sum_probs=13.5
Q ss_pred CCceEEEEcCeEEEEEEe
Q 031432 28 RKNGYIVIKGRPCKVVEV 45 (159)
Q Consensus 28 kkG~~i~~~g~p~~Vve~ 45 (159)
..|++|.++|..|+..-.
T Consensus 11 ~~Gd~V~~~g~~y~a~~~ 28 (41)
T PF02839_consen 11 NAGDRVSYNGKLYQAKWW 28 (41)
T ss_dssp -TT-EEEETTEEEEESSS
T ss_pred cCCCEEEECCCEEEEeec
Confidence 569999999999988543
No 72
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=21.37 E-value=2.8e+02 Score=18.99 Aligned_cols=25 Identities=12% Similarity=0.259 Sum_probs=20.8
Q ss_pred cCCceEEEEcC-eEEEEEEeeeecCC
Q 031432 27 IRKNGYIVIKG-RPCKVVEVSTSKTG 51 (159)
Q Consensus 27 ikkG~~i~~~g-~p~~Vve~~~~kpG 51 (159)
+++|++|.+.+ ..|+|..++....+
T Consensus 2 f~~GD~VVh~~~Gv~~i~~i~~~~~~ 27 (98)
T PF02559_consen 2 FKIGDYVVHPNHGVGRIEGIEEIEFG 27 (98)
T ss_dssp --TTSEEEETTTEEEEEEEEEEEECT
T ss_pred CCCCCEEEECCCceEEEEEEEEEeeC
Confidence 68999999988 59999999998886
No 73
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=21.35 E-value=1.9e+02 Score=26.31 Aligned_cols=31 Identities=16% Similarity=0.486 Sum_probs=24.7
Q ss_pred EeccccCCceEEEEcCeEEEEEE-eeeecCCC
Q 031432 22 QQAGTIRKNGYIVIKGRPCKVVE-VSTSKTGK 52 (159)
Q Consensus 22 i~~~~ikkG~~i~~~g~p~~Vve-~~~~kpGK 52 (159)
....++++...|.++|++|++++ -+....|+
T Consensus 383 ~~vt~~~p~G~V~v~GE~W~AvS~~~~I~kG~ 414 (436)
T COG1030 383 KTVTPLRPEGFVLVEGERWRAVSEGEPIEKGE 414 (436)
T ss_pred eecccCCCCeEEEECCEEEEEeeCCCcccCCC
Confidence 45678999999999999999998 55554454
No 74
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=21.14 E-value=1.7e+02 Score=19.54 Aligned_cols=14 Identities=7% Similarity=0.086 Sum_probs=11.4
Q ss_pred eccccCCceEEEEc
Q 031432 23 QAGTIRKNGYIVIK 36 (159)
Q Consensus 23 ~~~~ikkG~~i~~~ 36 (159)
+.-++++|++|.++
T Consensus 25 ell~L~~Gdvi~L~ 38 (77)
T TIGR02480 25 DLLKLGEGSVIELD 38 (77)
T ss_pred HHhcCCCCCEEEcC
Confidence 44578999999998
No 75
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=20.81 E-value=99 Score=20.59 Aligned_cols=27 Identities=19% Similarity=0.237 Sum_probs=20.2
Q ss_pred eEEEEEEEECCCCcEEEEEEeCCCceecce
Q 031432 56 AKCHFVGIDIFNGKKLEDIVPSSHNCDVPH 85 (159)
Q Consensus 56 a~vr~k~knl~TG~~~E~t~~s~~~ve~~~ 85 (159)
+.++++ +-+|+.+..+|++.+.+..+.
T Consensus 5 ~~I~iR---lPdG~ri~~~F~~~~tl~~v~ 31 (80)
T smart00166 5 CRLQIR---LPDGSRLVRRFPSSDTLRTVY 31 (80)
T ss_pred EEEEEE---cCCCCEEEEEeCCCCcHHHHH
Confidence 444444 378999999999999988543
No 76
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. 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=20.68 E-value=1.3e+02 Score=21.01 Aligned_cols=21 Identities=14% Similarity=0.075 Sum_probs=18.4
Q ss_pred CCCCcEEEEEEeCCCceecce
Q 031432 65 IFNGKKLEDIVPSSHNCDVPH 85 (159)
Q Consensus 65 l~TG~~~E~t~~s~~~ve~~~ 85 (159)
+-+|..++++|.+.+++..+.
T Consensus 12 lP~G~r~~rrF~~~~~L~~v~ 32 (82)
T cd01773 12 YPDGKREQIALPEQAKLLALV 32 (82)
T ss_pred CCCCCEEEEEeCCCCcHHHHH
Confidence 688999999999999998554
No 77
>PLN02792 oxidoreductase
Probab=20.56 E-value=2.5e+02 Score=26.00 Aligned_cols=50 Identities=18% Similarity=0.165 Sum_probs=33.9
Q ss_pred CceEEEEcCeE---EEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCceecceE
Q 031432 29 KNGYIVIKGRP---CKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHV 86 (159)
Q Consensus 29 kG~~i~~~g~p---~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~ve~~~v 86 (159)
.++.+.+||.+ +-++ .++||| .+|+++.|.-.-..+...+. ++++.++..
T Consensus 178 ~~d~~liNG~~~~~~~~~---~v~~Gk----~yRlRliNa~~~~~~~f~i~-gH~~tVI~~ 230 (536)
T PLN02792 178 MPDGVMINGQGVSYVYSI---TVDKGK----TYRFRISNVGLQTSLNFEIL-GHQLKLIEV 230 (536)
T ss_pred CCCEEEEeccCCCCcceE---EECCCC----EEEEEEEEcCCCceEEEEEC-CcEEEEEEe
Confidence 46889999984 4333 358888 68899988877666655554 555654443
No 78
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=20.30 E-value=3.2e+02 Score=23.57 Aligned_cols=67 Identities=7% Similarity=0.015 Sum_probs=45.5
Q ss_pred eccccCCceEEEEcCeEEEEEEeeeecCCCCCceEEEEEEEECCCCcEEEEEEeCCCc----eecceEEeeeEEEE
Q 031432 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN----CDVPHVTRTDYQLI 94 (159)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~kpGKhG~a~vr~k~knl~TG~~~E~t~~s~~~----ve~~~v~~~~~qyl 94 (159)
.+++++.|..+. .+|.|.+.+... .|.|+.+.++.+.| .||.+-=+.|...+. ++.-.+.+...+..
T Consensus 4 ~i~~l~~g~~v~---~~~lv~~~~~~~-~knG~~yl~l~l~D-~tG~I~ak~W~~~~~~~~~~~~g~vv~v~G~v~ 74 (314)
T PRK13480 4 GIEELEVGEQVD---HFLLIKSATKGV-ASNGKPFLTLILQD-KSGDIEAKLWDVSPEDEATYVPETIVHVKGDII 74 (314)
T ss_pred hHhhcCCCCEee---EEEEEEEceeee-cCCCCeEEEEEEEc-CCcEEEEEeCCCChhhHhhcCCCCEEEEEEEEE
Confidence 578899998543 367777776544 45478899999999 899988777776532 34444444444444
No 79
>COG2828 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.05 E-value=4.6e+02 Score=23.31 Aligned_cols=82 Identities=20% Similarity=0.225 Sum_probs=47.3
Q ss_pred eEEEEEEEECCCCcEEEEEEeCCCc--eecceEEeeeEEEEEeeCCCcEEEecCCCCeeeeccCCchhhHHHHHHhhccC
Q 031432 56 AKCHFVGIDIFNGKKLEDIVPSSHN--CDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFES 133 (159)
Q Consensus 56 a~vr~k~knl~TG~~~E~t~~s~~~--ve~~~v~~~~~qyly~d~~~~~~fMD~etyeq~~i~l~~~~~l~~~~~~~l~e 133 (159)
..+.+++.|..||+.++...+..+- .+.-+.+---+-+.-. .=.+.|||..+-..=.+ +|. +++.|.+ + ..
T Consensus 117 g~t~VRI~~~Nt~k~I~A~Vp~~nG~V~y~Gd~~idGVp~~aA--pv~L~F~daAg~~~G~l-fPT-Gn~vd~l-d--~p 189 (378)
T COG2828 117 GVTAVRIWNVNTGKTIEAHVPTPNGQVQYTGDAEIDGVPGPAA--PVALTFLDAAGSKTGAL-FPT-GNLVDEL-D--VP 189 (378)
T ss_pred CceEEEEEeccCcceEEEEeecCCCcEEeccceEeccCCCCCC--ceEEEEEccccCCCccc-ccC-CCchhhc-c--cC
Confidence 4678899999999999877665321 1111111111111111 13578999886544334 787 6777765 2 23
Q ss_pred CCeEEEEEEee
Q 031432 134 GKDLVVSVQCA 144 (159)
Q Consensus 134 g~~v~V~~~~~ 144 (159)
|-.+.+++++.
T Consensus 190 ~g~v~~T~Id~ 200 (378)
T COG2828 190 GGTVEVTLIDA 200 (378)
T ss_pred CceEEEEEEcC
Confidence 44678887765
Done!