Query 033076
Match_columns 128
No_of_seqs 120 out of 1026
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:32:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033076.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033076hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03107 eukaryotic translatio 100.0 2.2E-44 4.7E-49 271.4 14.0 124 1-127 1-127 (159)
2 TIGR00037 eIF_5A translation i 100.0 6.5E-42 1.4E-46 250.4 13.8 109 16-127 1-109 (130)
3 PTZ00328 eukaryotic initiation 100.0 2.2E-39 4.7E-44 244.8 13.0 127 1-127 1-134 (166)
4 COG0231 Efp Translation elonga 100.0 6.8E-38 1.5E-42 229.6 13.4 106 20-127 2-107 (131)
5 PRK03999 translation initiatio 100.0 1.9E-36 4.1E-41 221.3 13.6 97 21-118 5-101 (129)
6 PRK12426 elongation factor P; 100.0 3.7E-35 7.9E-40 225.9 13.2 94 21-116 1-94 (185)
7 PRK14578 elongation factor P; 100.0 6E-34 1.3E-38 219.5 13.7 96 21-117 1-97 (187)
8 PRK04542 elongation factor P; 100.0 7.3E-34 1.6E-38 219.3 13.4 95 21-116 1-96 (189)
9 KOG3271 Translation initiation 100.0 1.4E-34 3E-39 213.7 8.6 124 1-127 1-124 (156)
10 TIGR02178 yeiP elongation fact 100.0 1.6E-32 3.5E-37 211.4 13.9 92 24-116 2-94 (186)
11 PRK00529 elongation factor P; 100.0 4.8E-32 1E-36 208.2 13.0 95 21-117 1-95 (186)
12 TIGR00038 efp translation elon 100.0 8E-32 1.7E-36 206.8 12.9 94 22-117 1-94 (184)
13 PF08207 EFP_N: Elongation fac 99.9 2.4E-22 5.3E-27 128.5 8.7 58 23-81 1-58 (58)
14 PF01132 EFP: Elongation facto 99.0 4.3E-10 9.3E-15 71.0 4.4 28 88-116 1-28 (55)
15 cd04470 S1_EF-P_repeat_1 S1_EF 99.0 3.9E-10 8.5E-15 72.7 3.8 29 87-116 1-29 (61)
16 cd04463 S1_EF_like S1_EF_like: 98.8 5.7E-09 1.2E-13 65.2 3.5 29 89-118 1-29 (55)
17 PF01287 eIF-5a: Eukaryotic el 98.4 6.4E-07 1.4E-11 59.3 4.3 40 85-126 1-41 (69)
18 cd04467 S1_aIF5A S1_aIF5A: Arc 98.3 1.1E-06 2.3E-11 56.3 4.4 33 86-119 1-33 (57)
19 cd04468 S1_eIF5A S1_eIF5A: Euk 97.7 2.3E-05 4.9E-10 52.0 2.3 40 86-127 1-40 (69)
20 cd04469 S1_Hex1 S1_Hex1: Hex1, 97.4 0.00014 3E-09 48.9 3.1 39 88-127 2-40 (75)
21 COG1499 NMD3 NMD protein affec 97.3 0.0019 4E-08 54.6 9.3 97 11-118 231-331 (355)
22 PF08605 Rad9_Rad53_bind: Fung 79.0 6.1 0.00013 29.0 5.2 53 7-61 42-103 (131)
23 PRK05338 rplS 50S ribosomal pr 71.6 19 0.00042 25.9 6.1 54 22-77 14-75 (116)
24 COG0090 RplB Ribosomal protein 69.4 16 0.00035 30.1 5.9 56 24-83 121-184 (275)
25 PF05354 Phage_attach: Phage H 67.1 4.1 8.9E-05 29.6 1.8 42 14-58 62-103 (117)
26 PF13275 S4_2: S4 domain; PDB: 66.4 7.7 0.00017 25.2 2.9 21 23-43 45-65 (65)
27 smart00466 SRA SET and RING fi 61.9 31 0.00067 26.0 5.8 39 25-65 114-152 (155)
28 PF13856 Gifsy-2: ATP-binding 60.7 22 0.00048 24.0 4.5 38 12-49 48-88 (95)
29 smart00676 DM10 Domains in hyp 58.3 8.5 0.00018 26.9 2.1 26 21-46 68-93 (104)
30 TIGR01024 rplS_bact ribosomal 58.1 39 0.00085 24.3 5.6 55 21-77 13-75 (113)
31 PF13785 DUF4178: Domain of un 58.0 11 0.00024 26.6 2.7 23 27-49 1-23 (140)
32 PF01245 Ribosomal_L19: Riboso 57.3 38 0.00082 24.2 5.4 54 22-77 14-75 (113)
33 COG5131 URM1 Ubiquitin-like pr 53.7 9.3 0.0002 26.7 1.7 34 13-46 44-77 (96)
34 PF03829 PTSIIA_gutA: PTS syst 53.2 18 0.00039 26.0 3.1 23 23-45 48-70 (117)
35 PRK10377 PTS system glucitol/s 52.4 31 0.00068 24.9 4.3 22 24-45 49-70 (120)
36 CHL00084 rpl19 ribosomal prote 52.3 77 0.0017 22.9 6.3 53 21-77 17-79 (117)
37 PRK11507 ribosome-associated p 51.1 17 0.00037 24.0 2.5 21 23-43 49-69 (70)
38 PF11871 DUF3391: Domain of un 50.6 9.2 0.0002 26.5 1.3 21 20-40 3-23 (128)
39 TIGR00849 gutA PTS system, glu 49.1 25 0.00053 25.5 3.3 22 24-45 49-70 (121)
40 PF05521 Phage_H_T_join: Phage 47.0 72 0.0016 20.1 5.9 33 17-49 52-85 (95)
41 COG2351 Transthyretin-like pro 46.7 94 0.002 22.8 6.0 78 23-104 23-109 (124)
42 PF05096 Glu_cyclase_2: Glutam 46.5 1.6E+02 0.0035 24.1 9.5 48 18-74 37-84 (264)
43 PF02182 SAD_SRA: SAD/SRA doma 45.6 56 0.0012 24.4 4.9 35 29-65 118-152 (155)
44 PF06605 Prophage_tail: Propha 45.5 59 0.0013 26.2 5.4 38 25-64 26-63 (327)
45 COG1326 Uncharacterized archae 45.2 28 0.00061 27.5 3.3 29 24-53 72-100 (201)
46 COG1471 RPS4A Ribosomal protei 44.2 1.1E+02 0.0024 24.9 6.6 93 20-120 146-240 (241)
47 PF13144 SAF_2: SAF-like 43.8 1.3E+02 0.0029 22.4 7.9 25 59-83 172-196 (196)
48 PF11302 DUF3104: Protein of u 43.5 91 0.002 20.9 5.1 44 26-71 5-60 (75)
49 PF10665 Minor_capsid_1: Minor 42.8 36 0.00078 24.3 3.4 27 23-49 73-99 (114)
50 COG2501 S4-like RNA binding pr 41.8 31 0.00068 23.0 2.7 22 24-45 50-71 (73)
51 cd06409 PB1_MUG70 The MUG70 pr 40.7 51 0.0011 22.5 3.7 26 88-113 41-66 (86)
52 PRK12617 flgA flagellar basal 37.5 2E+02 0.0044 22.6 7.5 26 59-84 188-213 (214)
53 COG4043 Preprotein translocase 36.9 51 0.0011 23.6 3.3 22 24-45 31-54 (111)
54 cd00603 IPT_PCSR IPT domain of 36.4 1.2E+02 0.0025 19.5 6.8 34 11-44 10-46 (90)
55 PRK11354 kil FtsZ inhibitor pr 36.2 50 0.0011 22.0 3.0 25 19-43 8-32 (73)
56 PTZ00223 40S ribosomal protein 35.8 1.9E+02 0.0042 23.9 7.0 94 24-124 148-243 (273)
57 cd01771 Faf1_UBX Faf1 UBX doma 35.1 44 0.00095 22.1 2.6 20 65-84 11-30 (80)
58 PF07591 PT-HINT: Pretoxin HIN 35.1 48 0.001 23.8 3.0 27 21-47 71-98 (130)
59 TIGR03170 flgA_cterm flagella 33.1 1.6E+02 0.0035 20.2 7.5 24 59-82 98-121 (122)
60 cd04709 BAH_MTA BAH, or Bromo 31.4 93 0.002 23.6 4.2 22 25-46 2-29 (164)
61 PLN00036 40S ribosomal protein 31.1 2.9E+02 0.0062 22.7 7.2 93 23-123 150-244 (261)
62 PF00467 KOW: KOW motif; Inte 30.7 74 0.0016 17.2 2.7 21 29-49 1-26 (32)
63 PRK13480 3'-5' exoribonuclease 30.4 1.6E+02 0.0035 24.5 5.8 51 23-78 4-54 (314)
64 cd01767 UBX UBX (ubiquitin reg 29.4 40 0.00088 21.5 1.7 25 57-84 4-28 (77)
65 PF08408 DNA_pol_B_3: DNA poly 29.2 1.6E+02 0.0035 22.2 5.0 23 24-46 37-59 (149)
66 COG1030 NfeD Membrane-bound se 29.1 1.2E+02 0.0026 26.7 4.9 31 22-52 383-414 (436)
67 COG3721 HugX Putative heme iro 28.6 1.2E+02 0.0027 23.3 4.4 69 42-119 84-153 (176)
68 PF00924 MS_channel: Mechanose 28.2 50 0.0011 24.5 2.3 23 24-46 58-80 (206)
69 PRK12795 fliM flagellar motor 28.1 1.7E+02 0.0037 25.0 5.7 44 24-68 320-370 (388)
70 PRK06804 flgA flagellar basal 28.1 3.3E+02 0.0071 22.1 7.4 25 59-83 235-259 (261)
71 PRK07018 flgA flagellar basal 27.5 3E+02 0.0066 21.5 7.5 26 59-84 209-234 (235)
72 TIGR01397 fliM_switch flagella 27.2 1.4E+02 0.003 24.2 4.9 30 24-53 271-307 (320)
73 PTZ00118 40S ribosomal protein 26.6 3.6E+02 0.0077 22.2 7.0 93 24-124 151-245 (262)
74 PTZ00031 ribosomal protein L2; 26.4 2.2E+02 0.0047 24.1 5.9 61 18-83 132-215 (317)
75 PF13989 YejG: YejG-like prote 26.0 63 0.0014 23.1 2.2 16 30-45 69-84 (106)
76 PRK07963 fliN flagellar motor 25.7 1.6E+02 0.0035 21.7 4.5 43 24-67 78-127 (137)
77 PF01079 Hint: Hint module; I 25.5 1.2E+02 0.0026 23.9 4.0 29 20-48 99-133 (217)
78 PRK10965 multicopper oxidase; 24.9 2.3E+02 0.0051 25.1 6.1 47 28-82 210-256 (523)
79 KOG0238 3-Methylcrotonyl-CoA c 24.9 65 0.0014 29.4 2.6 29 90-119 269-297 (670)
80 PRK11835 hypothetical protein; 23.8 73 0.0016 23.0 2.3 32 25-61 66-98 (114)
81 PF00436 SSB: Single-strand bi 23.7 1.8E+02 0.004 18.8 4.2 17 25-41 64-80 (104)
82 PRK06788 flagellar motor switc 23.0 1.8E+02 0.004 20.9 4.3 45 24-69 52-103 (119)
83 COG3731 SrlB Phosphotransferas 22.6 1E+02 0.0023 22.5 2.9 28 18-45 43-70 (123)
84 PF13403 Hint_2: Hint domain 22.2 2.8E+02 0.0061 20.2 5.3 47 22-68 16-69 (147)
85 PF02839 CBM_5_12: Carbohydrat 22.1 1.1E+02 0.0024 17.1 2.5 18 28-45 11-28 (41)
86 PF12690 BsuPI: Intracellular 21.8 2.1E+02 0.0045 18.9 4.1 40 57-97 3-43 (82)
87 PF05203 Hom_end_hint: Hom_end 21.2 1.5E+02 0.0033 23.2 3.9 56 21-83 15-71 (215)
88 PF03869 Arc: Arc-like DNA bin 20.9 49 0.0011 20.0 0.8 18 108-127 2-19 (50)
89 KOG4499 Ca2+-binding protein R 20.9 4.1E+02 0.009 22.1 6.3 88 7-108 188-281 (310)
90 smart00166 UBX Domain present 20.5 95 0.0021 19.9 2.2 27 55-84 4-30 (80)
91 PRK10883 FtsI repressor; Provi 20.4 2.6E+02 0.0057 24.3 5.5 52 28-87 207-258 (471)
92 CHL00052 rpl2 ribosomal protei 20.3 3.7E+02 0.008 22.2 6.0 19 17-35 98-116 (273)
No 1
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=2.2e-44 Score=271.40 Aligned_cols=124 Identities=85% Similarity=1.324 Sum_probs=115.0
Q ss_pred CCccccccccccCCCcceeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCe
Q 033076 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (128)
Q Consensus 1 ~~~~~~~~~~~~~a~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ 80 (128)
|++.+++|+ +++||+|.|+++++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+|+++
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 788677999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecceEEEeeeEEEEecCCceEEEecC--CCCeEEeeeCCC-Ccchhccc
Q 033076 81 CDVPHVTRTDYQLIDISEDGFVSLLTE--NGNTKDDLRLPT-DENLLSQV 127 (128)
Q Consensus 81 ve~~~ve~~~~qylY~dgd~~~~fMD~--etyeq~~i~lp~-~~~l~~k~ 127 (128)
+++|+|++++|||||+|++++|+|||+ ++||| ++||. .++|.+||
T Consensus 80 ve~~~ve~~~~qyly~dgd~y~~fMD~~get~eq--i~v~~~~~el~~~i 127 (159)
T PLN03107 80 CDVPHVNRTDYQLIDISEDGFVSLMDESGNTKDD--LKLPTEDDTLAEQI 127 (159)
T ss_pred EEEEEEEEEEEEEEEEcCCceEEEEcCCCCccee--EEccCcchHHHHHH
Confidence 999999999999999998844699999 58888 56664 45787776
No 2
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=6.5e-42 Score=250.45 Aligned_cols=109 Identities=45% Similarity=0.754 Sum_probs=104.3
Q ss_pred cceeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEE
Q 033076 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLID 95 (128)
Q Consensus 16 ~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY 95 (128)
+|.|+++++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+|++++++|.|++++|||||
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 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCceEEEecCCCCeEEeeeCCCCcchhccc
Q 033076 96 ISEDGFVSLLTENGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 96 ~dgd~~~~fMD~etyeq~~i~lp~~~~l~~k~ 127 (128)
+||+ .|+|||+|||||++|++|. +++++|
T Consensus 81 ~dg~-~~~fMd~etyeq~~i~~~~--~~~~~L 109 (130)
T TIGR00037 81 IMGG-MVQLMDLDTYETDELPIPE--ELGDSL 109 (130)
T ss_pred ecCC-EEEEEcCCCcEEEEecCCh--hHHHHh
Confidence 9987 8999999999999999995 677765
No 3
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=2.2e-39 Score=244.78 Aligned_cols=127 Identities=48% Similarity=0.902 Sum_probs=120.0
Q ss_pred CCcccccccc-ccCCCcceeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCC
Q 033076 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (128)
Q Consensus 1 ~~~~~~~~~~-~~~a~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d 79 (128)
|||.+++|++ +++|++|.||+++++.||+|.+|+|+|+||+|++++++||||||+|++++.+.+||||+++|...|+++
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 eeecceEEEeeeEEEEecCC------ceEEEecCCCCeEEeeeCCCCcchhccc
Q 033076 80 NCDVPHVTRTDYQLIDISED------GFVSLLTENGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 80 ~ve~~~ve~~~~qylY~dgd------~~~~fMD~etyeq~~i~lp~~~~l~~k~ 127 (128)
++++|+|+|++||+|.+++| |++.+||+++|++++|+||+.++|+++|
T Consensus 81 nv~VP~V~r~~yqli~I~~d~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~i 134 (166)
T PTZ00328 81 NVEVPFVKTFTYSVLDIQPNEDPSLPAHLSLMDDEGESREDLDMPPDAALATQI 134 (166)
T ss_pred eeEeeeEEeeEEEEEEEcCCCcccccceEEEEcCCCCeeecccCCChhHHHHHH
Confidence 99999999999999999876 6899999999999999999756766654
No 4
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.8e-38 Score=229.57 Aligned_cols=106 Identities=28% Similarity=0.338 Sum_probs=99.1
Q ss_pred EEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCC
Q 033076 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (128)
Q Consensus 20 ~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd 99 (128)
.++++++||+|++|++||+||+|++++|+||||| +|++|+++|||+||++++.+|+++++++.|.|+++++||||.||+
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg-~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~ 80 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGKG-GAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGD 80 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCCC-CcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCC
Confidence 4789999999999999999999999999999995 669999999999999999999999999999999999999999998
Q ss_pred ceEEEecCCCCeEEeeeCCCCcchhccc
Q 033076 100 GFVSLLTENGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 100 ~~~~fMD~etyeq~~i~lp~~~~l~~k~ 127 (128)
.|+|||+|||||++|+.|.-++....|
T Consensus 81 -~~~FMD~etyeq~~v~~~~~~d~~~~l 107 (131)
T COG0231 81 -FYVFMDLETYEQYELPKDQIGDAAKFL 107 (131)
T ss_pred -eEEEccCCCceEEEecchhhhhHHHhc
Confidence 899999999999999998766665544
No 5
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=1.9e-36 Score=221.34 Aligned_cols=97 Identities=35% Similarity=0.662 Sum_probs=94.6
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCCc
Q 033076 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd~ 100 (128)
++++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||++++.+|+++++++.|.|++++|||||.|++
T Consensus 5 ~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~- 83 (129)
T PRK03999 5 QVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGD- 83 (129)
T ss_pred cccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCC-
Confidence 6889999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred eEEEecCCCCeEEeeeCC
Q 033076 101 FVSLLTENGNTKDDLRLP 118 (128)
Q Consensus 101 ~~~fMD~etyeq~~i~lp 118 (128)
+|+|||+|||||++|+.|
T Consensus 84 ~~~fMd~eTyeq~~i~~~ 101 (129)
T PRK03999 84 VVQLMDLETYETFEIPIP 101 (129)
T ss_pred EEEEecCCCceEEEecCC
Confidence 899999999999999887
No 6
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=3.7e-35 Score=225.85 Aligned_cols=94 Identities=14% Similarity=0.052 Sum_probs=90.1
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCCc
Q 033076 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd~ 100 (128)
++++++||+|++|+++|+||.|++++|+|||| |+|++|+|+|||.||+++|+||+++++++.+.|+++++||||.||+
T Consensus 1 m~~~~dik~G~~i~~~g~~~~V~~~~h~kPGk-g~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~qylY~dg~- 78 (185)
T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPK-GETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGD- 78 (185)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEecCCC-CceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEECCC-
Confidence 36799999999999999999999999999999 8999999999999999999999999999999999999999999998
Q ss_pred eEEEecCCCCeEEeee
Q 033076 101 FVSLLTENGNTKDDLR 116 (128)
Q Consensus 101 ~~~fMD~etyeq~~i~ 116 (128)
.|+|||++||||+.|+
T Consensus 79 ~~~FMd~etyeQi~i~ 94 (185)
T PRK12426 79 EYLFLDLGNYDKIYIP 94 (185)
T ss_pred eEEEecCCCceEEEeC
Confidence 7999999999996664
No 7
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=6e-34 Score=219.45 Aligned_cols=96 Identities=14% Similarity=0.199 Sum_probs=90.3
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCC-cccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCC
Q 033076 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~-G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd 99 (128)
++++++||+|++|+++|+||+|++++|+|||++ |+|++|+|+|||+||+++|++|+++++++.|.|+++++||||.||+
T Consensus 1 m~~~~dik~G~~i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~qylY~dg~ 80 (187)
T PRK14578 1 MYTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGD 80 (187)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeEEEEeCCC
Confidence 367899999999999999999999999999885 4679999999999999999999999999999999999999999998
Q ss_pred ceEEEecCCCCeEEeeeC
Q 033076 100 GFVSLLTENGNTKDDLRL 117 (128)
Q Consensus 100 ~~~~fMD~etyeq~~i~l 117 (128)
.|+|||++||||+.|+.
T Consensus 81 -~~~FMD~etyEQ~~i~~ 97 (187)
T PRK14578 81 -RGVFMDLETYEQFEMEE 97 (187)
T ss_pred -EEEEecCCCcEEEEecH
Confidence 79999999999977754
No 8
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=7.3e-34 Score=219.29 Aligned_cols=95 Identities=18% Similarity=0.214 Sum_probs=89.7
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecC-CCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCC
Q 033076 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kp-GK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd 99 (128)
++++++||+|++|+++|+||+|++++|+|| ||+|+|++|+|+|||.||+++++||+|+++++.+.|++++|||||.||+
T Consensus 1 mi~~~dik~G~~i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~qylY~dg~ 80 (189)
T PRK04542 1 MPKANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGD 80 (189)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCC
Confidence 468999999999999999999999999999 7955679999999999999999999999999999999999999999988
Q ss_pred ceEEEecCCCCeEEeee
Q 033076 100 GFVSLLTENGNTKDDLR 116 (128)
Q Consensus 100 ~~~~fMD~etyeq~~i~ 116 (128)
.|+|||++||||+.|+
T Consensus 81 -~~~FMd~etyEQ~~i~ 96 (189)
T PRK04542 81 -EYVFMDNEDYTPYTFK 96 (189)
T ss_pred -EEEEecCCCceEEEEC
Confidence 7999999999996665
No 9
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-34 Score=213.71 Aligned_cols=124 Identities=69% Similarity=1.099 Sum_probs=119.9
Q ss_pred CCccccccccccCCCcceeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCe
Q 033076 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (128)
Q Consensus 1 ~~~~~~~~~~~~~a~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ 80 (128)
|++.+++|+ .++||++.||+.+++.||++.+|+++|+||+|||.+.+|.||||+|++++..++||||+++|..++|+++
T Consensus 1 Msd~~~~Fe-~~dagas~t~p~q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn 79 (156)
T KOG3271|consen 1 MSDEEHRFE-TGDAGASATYPMQCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHN 79 (156)
T ss_pred CCccccccc-cCCCcccccccchhhheeeCCEEEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCc
Confidence 899999999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecceEEEeeeEEEEecCCceEEEecCCCCeEEeeeCCCCcchhccc
Q 033076 81 CDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 81 ve~~~ve~~~~qylY~dgd~~~~fMD~etyeq~~i~lp~~~~l~~k~ 127 (128)
+++|+++|.+||++.++++ ++.||+++++...++.+|+++ |.++|
T Consensus 80 ~dVp~vkr~~yqLidIsd~-~~sl~t~sG~~kdDlklp~~e-l~~~i 124 (156)
T KOG3271|consen 80 MDVPVVKRVDYQLIDISDG-YLSLMTDSGETKDDLKLPEGE-LGNQI 124 (156)
T ss_pred cccCccccceeEEEEecCC-eEEEEcCCCCcchhccCcchh-HHHHH
Confidence 9999999999999999876 999999999999999999976 77665
No 10
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=100.00 E-value=1.6e-32 Score=211.38 Aligned_cols=92 Identities=15% Similarity=0.227 Sum_probs=86.9
Q ss_pred cccccCceEEEECCeeEEEEEeeEecCCCCccc-EEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCCceE
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFV 102 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A-~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd~~~ 102 (128)
+++||+|++|+++|+||+|++++|+|||++|+| ++|+|+|||.||+++++||+|+|+++.++|+++++||||.||+ .|
T Consensus 2 ~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~-~~ 80 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGE-EY 80 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCC-eE
Confidence 789999999999999999999999999885555 8999999999999999999999999999999999999999998 79
Q ss_pred EEecCCCCeEEeee
Q 033076 103 SLLTENGNTKDDLR 116 (128)
Q Consensus 103 ~fMD~etyeq~~i~ 116 (128)
+|||++||||+.|+
T Consensus 81 ~FMD~etyEQ~~i~ 94 (186)
T TIGR02178 81 VFMDEEDYTPYTFD 94 (186)
T ss_pred EEccCCCcEEEEeC
Confidence 99999999997664
No 11
>PRK00529 elongation factor P; Validated
Probab=99.98 E-value=4.8e-32 Score=208.22 Aligned_cols=95 Identities=21% Similarity=0.258 Sum_probs=90.6
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCCc
Q 033076 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd~ 100 (128)
++++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++.+|+++++++.|.++++++||||.|++
T Consensus 1 ~~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dgd- 78 (186)
T PRK00529 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGK-GQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGD- 78 (186)
T ss_pred CcchhhcCCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECCC-
Confidence 36899999999999999999999999999999 8999999999999999999999999999999999999999999988
Q ss_pred eEEEecCCCCeEEeeeC
Q 033076 101 FVSLLTENGNTKDDLRL 117 (128)
Q Consensus 101 ~~~fMD~etyeq~~i~l 117 (128)
.|+|||+|||||++|+.
T Consensus 79 ~~~fMD~etyeq~~l~~ 95 (186)
T PRK00529 79 GYVFMDTETYEQIEVPA 95 (186)
T ss_pred EEEEecCCCceeeEcCH
Confidence 69999999999976653
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=99.98 E-value=8e-32 Score=206.77 Aligned_cols=94 Identities=23% Similarity=0.296 Sum_probs=89.9
Q ss_pred EecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCCce
Q 033076 22 QQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGF 101 (128)
Q Consensus 22 i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd~~ 101 (128)
+.+++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++.+|+++++++.+.++++++||||.|++ .
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dgd-~ 78 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGK-GQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGD-S 78 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECCC-E
Confidence 4689999999999999999999999999999 8999999999999999999999999999999999999999999988 6
Q ss_pred EEEecCCCCeEEeeeC
Q 033076 102 VSLLTENGNTKDDLRL 117 (128)
Q Consensus 102 ~~fMD~etyeq~~i~l 117 (128)
|+|||++||||++|+.
T Consensus 79 ~~fMD~etyeq~~i~~ 94 (184)
T TIGR00038 79 YVFMDTETYEQIELPK 94 (184)
T ss_pred EEEeCCCCccceEcCH
Confidence 9999999999977653
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=99.88 E-value=2.4e-22 Score=128.52 Aligned_cols=58 Identities=29% Similarity=0.379 Sum_probs=53.4
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCee
Q 033076 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~v 81 (128)
+|++||+|++|+++|+||.|++++|++||| |+|+|++++|||.||+++|.+|+++|+|
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
>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=99.01 E-value=4.3e-10 Score=71.02 Aligned_cols=28 Identities=11% Similarity=0.134 Sum_probs=23.7
Q ss_pred EeeeEEEEecCCceEEEecCCCCeEEeee
Q 033076 88 RTDYQLIDISEDGFVSLLTENGNTKDDLR 116 (128)
Q Consensus 88 ~~~~qylY~dgd~~~~fMD~etyeq~~i~ 116 (128)
+|++||||.||+ .|+|||++||||+.|+
T Consensus 1 ~r~~qylY~dgd-~~~FMd~etyeQi~v~ 28 (55)
T PF01132_consen 1 RREMQYLYKDGD-NYVFMDTETYEQIEVP 28 (55)
T ss_dssp EEEEEEEEEESS-EEEEEETTT--EEEEE
T ss_pred CceEEEEEeCCC-EEEEecCCCceEEEec
Confidence 689999999998 6999999999997776
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=99.00 E-value=3.9e-10 Score=72.66 Aligned_cols=29 Identities=10% Similarity=0.105 Sum_probs=25.9
Q ss_pred EEeeeEEEEecCCceEEEecCCCCeEEeee
Q 033076 87 TRTDYQLIDISEDGFVSLLTENGNTKDDLR 116 (128)
Q Consensus 87 e~~~~qylY~dgd~~~~fMD~etyeq~~i~ 116 (128)
+++++||||.||+ .|+|||++||||+.|+
T Consensus 1 e~~~~qylY~dg~-~~~FMd~etyeQ~~i~ 29 (61)
T cd04470 1 EEREMQYLYKDGD-NYVFMDTETYEQIELP 29 (61)
T ss_pred CCceEEEEEeCCC-EEEEeCCCCceEEEEC
Confidence 4789999999998 7999999999996665
No 16
>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=98.79 E-value=5.7e-09 Score=65.25 Aligned_cols=29 Identities=14% Similarity=0.138 Sum_probs=25.8
Q ss_pred eeeEEEEecCCceEEEecCCCCeEEeeeCC
Q 033076 89 TDYQLIDISEDGFVSLLTENGNTKDDLRLP 118 (128)
Q Consensus 89 ~~~qylY~dgd~~~~fMD~etyeq~~i~lp 118 (128)
|++||||.||+ .|+|||++||||++++.+
T Consensus 1 ~~~qylY~dg~-~~~fMd~etyeq~~v~~~ 29 (55)
T cd04463 1 RELQVLDIQGS-KPVTMDLETYEVVQVPPP 29 (55)
T ss_pred CCEEEEEcCCC-EeEEecCCCceEEEeCHH
Confidence 57999999987 799999999999888764
No 17
>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=98.35 E-value=6.4e-07 Score=59.25 Aligned_cols=40 Identities=43% Similarity=0.745 Sum_probs=31.8
Q ss_pred eEEEeeeEEEEecCCceEEEecCCCCeEEe-eeCCCCcchhcc
Q 033076 85 HVTRTDYQLIDISEDGFVSLLTENGNTKDD-LRLPTDENLLSQ 126 (128)
Q Consensus 85 ~ve~~~~qylY~dgd~~~~fMD~etyeq~~-i~lp~~~~l~~k 126 (128)
+|+|++||.+.+++||++++|| ++++..+ ++||++ +|.++
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMd-e~get~eDl~lP~~-el~~e 41 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMD-EDGETREDLKLPDG-ELGEE 41 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEE-TTS-EEEEEECCSH-HHHHH
T ss_pred CeEEEEEEEEEEccCcEEEEEc-CCCCeeccEEeccc-chhHH
Confidence 4899999999999888999999 7777766 999964 45443
No 18
>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=98.30 E-value=1.1e-06 Score=56.27 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=30.7
Q ss_pred EEEeeeEEEEecCCceEEEecCCCCeEEeeeCCC
Q 033076 86 VTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPT 119 (128)
Q Consensus 86 ve~~~~qylY~dgd~~~~fMD~etyeq~~i~lp~ 119 (128)
|+||..|.++++|+ ...+||+|||+.+++++|+
T Consensus 1 i~k~~aqVisi~g~-~vQlMD~eTYeT~ev~~p~ 33 (57)
T cd04467 1 IERKTGQVLSIMGD-VVQLMDLETYETFEVPIPE 33 (57)
T ss_pred CcceEEEEEEEcCC-EEEEeccccceeEEEecch
Confidence 57999999999988 8999999999999999994
No 19
>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=97.71 E-value=2.3e-05 Score=51.95 Aligned_cols=40 Identities=50% Similarity=0.973 Sum_probs=34.6
Q ss_pred EEEeeeEEEEecCCceEEEecCCCCeEEeeeCCCCcchhccc
Q 033076 86 VTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 86 ve~~~~qylY~dgd~~~~fMD~etyeq~~i~lp~~~~l~~k~ 127 (128)
|.|++||++.+++ |++++|+.++-.+.+++||++ +|.++|
T Consensus 1 V~R~eYqLidI~d-GflsLm~e~G~~k~DlklP~~-elg~~I 40 (69)
T cd04468 1 VKRTEYQLIDIDD-GFLSLMDDDGETREDLKLPEG-ELGKEI 40 (69)
T ss_pred CcceeEEEEeecC-CeEEEEcCCCCcccCCcCCcH-HHHHHH
Confidence 4689999999976 699999999999999999974 577665
No 20
>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=97.43 E-value=0.00014 Score=48.92 Aligned_cols=39 Identities=31% Similarity=0.592 Sum_probs=33.4
Q ss_pred EeeeEEEEecCCceEEEecCCCCeEEeeeCCCCcchhccc
Q 033076 88 RTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 88 ~~~~qylY~dgd~~~~fMD~etyeq~~i~lp~~~~l~~k~ 127 (128)
.++||++.+ .||++.+||+++-.+.+++||.+++|+.+|
T Consensus 2 ~~eYqLidI-~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I 40 (75)
T cd04469 2 FKQYRVLDI-QDGSIVAMTETGDVKQGLPVIDQSNLWTRL 40 (75)
T ss_pred ceEEEEEEe-cCCeEEEEcCCCCcccCccCCCcchHHHHH
Confidence 368999999 567999999999999999999556687765
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=97.31 E-value=0.0019 Score=54.63 Aligned_cols=97 Identities=13% Similarity=0.163 Sum_probs=72.2
Q ss_pred ccCCCcceeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceE----
Q 033076 11 KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHV---- 86 (128)
Q Consensus 11 ~~~a~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~v---- 86 (128)
+|-.-...||.+-.-++++|++|.++|..+.++.. -|+ .+.++|+.|++..+.++.-...-+...+
T Consensus 231 tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~~----~~~------~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~ 300 (355)
T COG1499 231 TGKRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVRS----IGK------GIVVLDLETGEPVEITWSVYKRNEGKVAVKEP 300 (355)
T ss_pred CCceEEEEEEEEECCCCCCCCEEEECCCeEEEEEE----ecC------ceEEEecccCCccccChhhcccCcceeeeccc
Confidence 45555678999999999999999999966655532 256 3899999999888887755444332222
Q ss_pred EEeeeEEEEecCCceEEEecCCCCeEEeeeCC
Q 033076 87 TRTDYQLIDISEDGFVSLLTENGNTKDDLRLP 118 (128)
Q Consensus 87 e~~~~qylY~dgd~~~~fMD~etyeq~~i~lp 118 (128)
+-+.+.++..+.+ ...|||.+|||-+++.-|
T Consensus 301 ~~~~~~vvs~~~~-~~~v~d~et~e~~~~~~~ 331 (355)
T COG1499 301 RLKKAVVVSRDPS-AIQVLDPETYEARTVKGP 331 (355)
T ss_pred cceEEEEEecCCC-ceEEEecceEEEEeccCC
Confidence 2246777777776 699999999999888765
No 22
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=79.04 E-value=6.1 Score=29.04 Aligned_cols=53 Identities=15% Similarity=0.112 Sum_probs=35.8
Q ss_pred ccccccCCCcceeEEEecccccCceEEEECCe--eEEEEEeeEec--CC-----CCcccEEEEE
Q 033076 7 HFESKADAGASKTFPQQAGTIRKNGYIVIKGR--PCKVVEVSTSK--TG-----KHGHAKCHFV 61 (128)
Q Consensus 7 ~~~~~~~a~~~~t~~i~~~~ikkG~~i~~~g~--p~~Vve~~~~k--pG-----K~G~A~v~~k 61 (128)
.|+ .+. ...+.--+..=|||.|+.|.+++. +|+|+-+++.- +. -+|.+.|.+|
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 566 333 233333466779999999999998 89999988872 22 1166666664
No 23
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=71.56 E-value=19 Score=25.95 Aligned_cols=54 Identities=17% Similarity=0.279 Sum_probs=35.2
Q ss_pred EecccccCceEEEE-----CCeeEEEEEeeEe---cCCCCcccEEEEEEEEccCCcEEEEeeCC
Q 033076 22 QQAGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPS 77 (128)
Q Consensus 22 i~~~~ikkG~~i~~-----~g~p~~Vve~~~~---kpGK~G~A~v~~k~knl~TG~~~e~t~~s 77 (128)
....++++|++|.+ +|....+..++-. .-++ | .--.+.+||+..|-=+|.+|+.
T Consensus 14 ~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~-G-~~~tftvRki~~gvGVEr~fpl 75 (116)
T PRK05338 14 KDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGR-G-LNETFTVRKISYGVGVERTFPL 75 (116)
T ss_pred cCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCC-C-CCceEEEEEcccCccEEEEecC
Confidence 45778899998876 4554333222211 1133 2 2336899999999999999976
No 24
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=69.39 E-value=16 Score=30.11 Aligned_cols=56 Identities=23% Similarity=0.302 Sum_probs=34.6
Q ss_pred cccccCceEEEECCee--EEEEEeeEecCCCCc------ccEEEEEEEEccCCcEEEEeeCCCCeeec
Q 033076 24 AGTIRKNGYIVIKGRP--CKVVEVSTSKTGKHG------HAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p--~~Vve~~~~kpGK~G------~A~v~~k~knl~TG~~~e~t~~s~d~ve~ 83 (128)
..+|++|+.+-|.+-| -.|-.++ .+||++| ++.+++..++ |...-.+++|++.-.+
T Consensus 121 ~a~ik~GN~lpL~~IP~Gt~VhNVE-~~pG~GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~r~v 184 (275)
T COG0090 121 DADIKPGNALPLGNIPEGTIVHNVE-LKPGDGGQLARSAGTYAQVVGKE---GNYVIVRLPSGEMRKV 184 (275)
T ss_pred CCCcCCcceeeeccCCCCceEEeee-eccCCCceEEEeCCceEEEEEcc---CCEEEEECCCCCeEee
Confidence 4466666666666655 2233332 3788853 2566677776 7777778888876543
No 25
>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=67.07 E-value=4.1 Score=29.59 Aligned_cols=42 Identities=10% Similarity=0.106 Sum_probs=25.5
Q ss_pred CCcceeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEE
Q 033076 14 AGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKC 58 (128)
Q Consensus 14 a~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v 58 (128)
+++-......+..||+++.|.++|++|.|.+ +.|--+|...+
T Consensus 62 ~Pslfv~t~dv~~L~r~DtL~I~g~~y~Vd~---v~pD~~G~t~I 103 (117)
T PF05354_consen 62 SPSLFVRTADVSGLKRRDTLTIGGESYWVDR---VGPDGGGSTRI 103 (117)
T ss_dssp S-EEEESCCCCCTS-TT-EEEETTTEEEBS------SSSSS-CCE
T ss_pred CceEEEEehHhhhhhcCCeEEECCEEEEEEe---eccCCCccEEE
Confidence 3344455567899999999999999999965 46643354443
No 26
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=66.43 E-value=7.7 Score=25.22 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=14.9
Q ss_pred ecccccCceEEEECCeeEEEE
Q 033076 23 QAGTIRKNGYIVIKGRPCKVV 43 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vv 43 (128)
....|++|++|.++|..++|+
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 356799999999999999885
No 27
>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=61.86 E-value=31 Score=26.01 Aligned_cols=39 Identities=18% Similarity=0.250 Sum_probs=29.0
Q ss_pred ccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 033076 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (128)
Q Consensus 25 ~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl 65 (128)
+..+++....+|| +|+|+++-. .+|+.|....|++|+-+
T Consensus 114 ~~~~p~~gyrYDG-LY~V~~~w~-e~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 114 SKYAPGKGYIYDG-LYRIVDYWR-EVGKSGFLVFKFKLVRI 152 (155)
T ss_pred CCCCCCCeEEECc-EEEEEEEEE-ecCCCCcEEEEEEEEeC
Confidence 3456777788876 899998844 45777788999998865
No 28
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=60.73 E-value=22 Score=23.97 Aligned_cols=38 Identities=18% Similarity=0.276 Sum_probs=22.4
Q ss_pred cCCCcceeEEEecccc---cCceEEEECCeeEEEEEeeEec
Q 033076 12 ADAGASKTFPQQAGTI---RKNGYIVIKGRPCKVVEVSTSK 49 (128)
Q Consensus 12 ~~a~~~~t~~i~~~~i---kkG~~i~~~g~p~~Vve~~~~k 49 (128)
+=+++..+..+..+++ ++|+.|.++|+-|.|.+++..-
T Consensus 48 ~v~g~~~~L~v~~~d~~~P~~gd~v~~dG~~y~V~~~~~~~ 88 (95)
T PF13856_consen 48 GVEGTQPTLYVFSSDYPKPRRGDRVVIDGESYTVTRFQEED 88 (95)
T ss_dssp ------EEEEE--SS-----TT-EEEETTEEEEEEEEEEET
T ss_pred cccCCceEEEEEcCCCCCCCCCCEEEECCeEEEEeEEecCC
Confidence 3345566666766665 4899999999999999886653
No 29
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=58.31 E-value=8.5 Score=26.91 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=23.4
Q ss_pred EEecccccCceEEEECCeeEEEEEee
Q 033076 21 PQQAGTIRKNGYIVIKGRPCKVVEVS 46 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~g~p~~Vve~~ 46 (128)
.....||+.|..|.+.|.++.|+++.
T Consensus 68 ~y~~~Dl~vG~~v~i~gr~f~I~d~D 93 (104)
T smart00676 68 YYHASDLNVGTTINVFGRQFRIYDCD 93 (104)
T ss_pred ccCHHHcCCCCEEEEeCEEEEEEECC
Confidence 36788999999999999999999984
No 30
>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=58.15 E-value=39 Score=24.25 Aligned_cols=55 Identities=18% Similarity=0.257 Sum_probs=34.8
Q ss_pred EEecccccCceEEEEC-----CeeEEEEEeeEe---cCCCCcccEEEEEEEEccCCcEEEEeeCC
Q 033076 21 PQQAGTIRKNGYIVIK-----GRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPS 77 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~~-----g~p~~Vve~~~~---kpGK~G~A~v~~k~knl~TG~~~e~t~~s 77 (128)
.....++++|++|.+. |....+..++-. .-++ | .--.+.+||+..|-=+|.+|+.
T Consensus 13 ~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~-G-~~~tftvR~i~~gvGVEr~fpl 75 (113)
T TIGR01024 13 KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGG-G-IGETFTVRKISYGVGVERIFPL 75 (113)
T ss_pred hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCC-C-CceEEEEEEeccCccEEEEEEc
Confidence 3567789999988773 333222222111 1133 2 2335899999999999999976
No 31
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=57.95 E-value=11 Score=26.61 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=19.2
Q ss_pred ccCceEEEECCeeEEEEEeeEec
Q 033076 27 IRKNGYIVIKGRPCKVVEVSTSK 49 (128)
Q Consensus 27 ikkG~~i~~~g~p~~Vve~~~~k 49 (128)
|++|+.+.++|.+|.|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999998665443
No 32
>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=57.30 E-value=38 Score=24.20 Aligned_cols=54 Identities=15% Similarity=0.239 Sum_probs=33.6
Q ss_pred EecccccCceEEEEC-----CeeEEEEEeeEec---CCCCcccEEEEEEEEccCCcEEEEeeCC
Q 033076 22 QQAGTIRKNGYIVIK-----GRPCKVVEVSTSK---TGKHGHAKCHFVGIDIFNGKKLEDIVPS 77 (128)
Q Consensus 22 i~~~~ikkG~~i~~~-----g~p~~Vve~~~~k---pGK~G~A~v~~k~knl~TG~~~e~t~~s 77 (128)
.+..++++|++|.+. |....+..++-.- -++ | .--.+.+||++.|.-+|.+|+-
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~-g-~~ssftlR~~~~g~gVE~~f~l 75 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR-G-LNSSFTLRNISQGVGVERVFPL 75 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS-S-TSSEEEEEEEETTEEEEEEEET
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC-C-CCeeEEEEEEecCccEEEEEEc
Confidence 567788999987653 4333332222111 122 1 1225788999999999999976
No 33
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=53.73 E-value=9.3 Score=26.72 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=29.2
Q ss_pred CCCcceeEEEecccccCceEEEECCeeEEEEEee
Q 033076 13 DAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVS 46 (128)
Q Consensus 13 ~a~~~~t~~i~~~~ikkG~~i~~~g~p~~Vve~~ 46 (128)
.|++...+-+.-++||+|.++++|+.-|.+++-+
T Consensus 44 ~~p~~~sifie~g~lrpGiI~LINd~DWeLleke 77 (96)
T COG5131 44 YAPTRDSIFIEHGELRPGIICLINDMDWELLEKE 77 (96)
T ss_pred hCCccceeeecCCCCcccEEEEEcCccHhhhhcc
Confidence 4667777888999999999999999999998653
No 34
>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=53.21 E-value=18 Score=26.00 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=16.4
Q ss_pred ecccccCceEEEECCeeEEEEEe
Q 033076 23 QAGTIRKNGYIVIKGRPCKVVEV 45 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~ 45 (128)
...+|++|+.+.++|..|.|..+
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 46789999999999999999977
No 35
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=52.39 E-value=31 Score=24.88 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=20.3
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEV 45 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~ 45 (128)
..+|++|+.+.++|.-|.|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAV 70 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEE
Confidence 6779999999999999999877
No 36
>CHL00084 rpl19 ribosomal protein L19
Probab=52.28 E-value=77 Score=22.91 Aligned_cols=53 Identities=13% Similarity=0.205 Sum_probs=35.4
Q ss_pred EEecccccCceEEEE-----CCe-----eEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCC
Q 033076 21 PQQAGTIRKNGYIVI-----KGR-----PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPS 77 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~-----~g~-----p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s 77 (128)
.....++++|++|.+ +|. ++.=+-+... |+ |- --.+.+|++..|-=+|.+|+.
T Consensus 17 ~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r--~~-G~-~~tftvRki~~gvGVEr~fpl 79 (117)
T CHL00084 17 KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKK--NS-GL-NTTITVRKVFQGIGVERVFLL 79 (117)
T ss_pred hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEe--CC-CC-CeeEEEEEeccCccEEEEEec
Confidence 346778999998875 344 2322223322 44 32 335899999999999999976
No 37
>PRK11507 ribosome-associated protein; Provisional
Probab=51.05 E-value=17 Score=24.02 Aligned_cols=21 Identities=19% Similarity=0.267 Sum_probs=17.8
Q ss_pred ecccccCceEEEECCeeEEEE
Q 033076 23 QAGTIRKNGYIVIKGRPCKVV 43 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vv 43 (128)
....|++|++|.++|.-+.|+
T Consensus 49 RgkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 49 KRCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred cCCCCCCCCEEEECCEEEEEe
Confidence 456799999999999888775
No 38
>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=50.64 E-value=9.2 Score=26.55 Aligned_cols=21 Identities=10% Similarity=0.091 Sum_probs=16.9
Q ss_pred EEEecccccCceEEEECCeeE
Q 033076 20 FPQQAGTIRKNGYIVIKGRPC 40 (128)
Q Consensus 20 ~~i~~~~ikkG~~i~~~g~p~ 40 (128)
-+|++++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 468999999999987755555
No 39
>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=49.12 E-value=25 Score=25.49 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=20.0
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEV 45 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~ 45 (128)
..+|++|+.+.++|.-|.|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (121)
T TIGR00849 49 KGTLKPGQVFMIGGIAYPVTAV 70 (121)
T ss_pred cCCcCCCCEEEECCEEEEEEEE
Confidence 3589999999999999999877
No 40
>PF05521 Phage_H_T_join: Phage head-tail joining protein ; InterPro: IPR008767 This entry describes the head-tail adaptor protein of bacteriophage SPP1 and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2KCA_A 2KZ4_A.
Probab=46.97 E-value=72 Score=20.13 Aligned_cols=33 Identities=12% Similarity=0.221 Sum_probs=22.1
Q ss_pred ceeEEEecc-cccCceEEEECCeeEEEEEeeEec
Q 033076 17 SKTFPQQAG-TIRKNGYIVIKGRPCKVVEVSTSK 49 (128)
Q Consensus 17 ~~t~~i~~~-~ikkG~~i~~~g~p~~Vve~~~~k 49 (128)
...+.|--. +|..++.|.++|..|.|..+....
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 344445433 699999999999999999876654
No 41
>COG2351 Transthyretin-like protein [General function prediction only]
Probab=46.71 E-value=94 Score=22.79 Aligned_cols=78 Identities=15% Similarity=0.207 Sum_probs=46.5
Q ss_pred ecccccCceEEEECCeeEE-EEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCee--------ecceEEEeeeEE
Q 033076 23 QAGTIRKNGYIVIKGRPCK-VVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC--------DVPHVTRTDYQL 93 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~-Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~v--------e~~~ve~~~~qy 93 (128)
+|..++...+ .++|+-+. +-+..+..=||..++. +.+.++.+|- ++.+|..+|-+ +.|+++..++.|
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--LAGETLATGI-YELVFHTGDYFKSRGVQLADPPFLDVVPVRF 98 (124)
T ss_pred cCCCCEEEEE-EecCCcceeeeEEEecCCCcccccc--cCccccccce-EEEEEEcchhhhccCcccCCCCccceEEEEE
Confidence 3455555544 34444443 3344444556643232 5677777775 88888776544 346888888888
Q ss_pred EEecCCceEEE
Q 033076 94 IDISEDGFVSL 104 (128)
Q Consensus 94 lY~dgd~~~~f 104 (128)
=-.|.++.||.
T Consensus 99 ~iad~~~HYHV 109 (124)
T COG2351 99 GIADVDEHYHV 109 (124)
T ss_pred EEcCCCCceee
Confidence 77766556763
No 42
>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=46.50 E-value=1.6e+02 Score=24.07 Aligned_cols=48 Identities=21% Similarity=0.381 Sum_probs=32.0
Q ss_pred eeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEe
Q 033076 18 KTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDI 74 (128)
Q Consensus 18 ~t~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t 74 (128)
++|+-..+.+..|..+.-+|.+|. ..|..|++.+| -.|+.||+.....
T Consensus 37 ~~ypHd~~aFTQGL~~~~~g~LyE-------STG~yG~S~l~--~~d~~tg~~~~~~ 84 (264)
T PF05096_consen 37 ETYPHDPTAFTQGLEFLDDGTLYE-------STGLYGQSSLR--KVDLETGKVLQSV 84 (264)
T ss_dssp EEEE--TT-EEEEEEEEETTEEEE-------EECSTTEEEEE--EEETTTSSEEEEE
T ss_pred EECCCCCcccCccEEecCCCEEEE-------eCCCCCcEEEE--EEECCCCcEEEEE
Confidence 467778889999998888888772 23666766544 5688888876543
No 43
>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=45.58 E-value=56 Score=24.37 Aligned_cols=35 Identities=31% Similarity=0.389 Sum_probs=25.2
Q ss_pred CceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 033076 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (128)
Q Consensus 29 kG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl 65 (128)
++..+.+|| +|+|+++...+ |+.|...++++|+-+
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 345578887 99999997765 454778999998865
No 44
>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=45.46 E-value=59 Score=26.24 Aligned_cols=38 Identities=16% Similarity=0.309 Sum_probs=23.2
Q ss_pred ccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEE
Q 033076 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (128)
Q Consensus 25 ~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~kn 64 (128)
.-|.++.+|.++|+.|+|..+....-|. + ..+.+.+++
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 5688999999999999999988776664 2 348899998
No 45
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=45.16 E-value=28 Score=27.49 Aligned_cols=29 Identities=17% Similarity=0.354 Sum_probs=24.0
Q ss_pred cccccCceEEEECCeeEEEEEeeEecCCCC
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKH 53 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~ 53 (128)
--.|++|+.|.++|+-..|++++. ++||.
T Consensus 72 gE~l~vGDei~vd~e~veITSIE~-~~gkR 100 (201)
T COG1326 72 GETLKVGDEIEVDGEEVEITSIEL-GGGKR 100 (201)
T ss_pred CCeEecCCEEEEcCCEEEEEEEee-CCCcc
Confidence 346899999999999999999977 45663
No 46
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=44.23 E-value=1.1e+02 Score=24.89 Aligned_cols=93 Identities=17% Similarity=0.157 Sum_probs=61.7
Q ss_pred EEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc-cCCcEEEEeeCCCCeeecceEEEeee-EEEEec
Q 033076 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI-FNGKKLEDIVPSSHNCDVPHVTRTDY-QLIDIS 97 (128)
Q Consensus 20 ~~i~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl-~TG~~~e~t~~s~d~ve~~~ve~~~~-qylY~d 97 (128)
..+....++.|+.+.++-.--+|++. -+++. |+-.+-+-++|. .+|.+.+....-+-+-+.+.++..+- .|.-+.
T Consensus 146 i~~~d~~~k~~Dtv~i~lp~~~I~~~--i~fe~-g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~ 222 (241)
T COG1471 146 IRLEDDNYKTGDTVKISLPEQKIVEH--IKFEE-GALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIK 222 (241)
T ss_pred eeccCCccccccEEEEeCCChhheeE--eccCC-CcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEee
Confidence 34455788899999988777777754 44444 333334667776 56888888777677777888887663 666663
Q ss_pred CCceEEEecCCCCeEEeeeCCCC
Q 033076 98 EDGFVSLLTENGNTKDDLRLPTD 120 (128)
Q Consensus 98 gd~~~~fMD~etyeq~~i~lp~~ 120 (128)
| |+|+=-+ +...|.||.+
T Consensus 223 -~--yVfvIG~--~k~~i~l~~e 240 (241)
T COG1471 223 -D--YVFVIGE--DKPVISLPKE 240 (241)
T ss_pred -e--EEEEEcC--CCceEeCCCC
Confidence 3 5665554 5666888753
No 47
>PF13144 SAF_2: SAF-like
Probab=43.84 E-value=1.3e+02 Score=22.36 Aligned_cols=25 Identities=16% Similarity=0.163 Sum_probs=20.1
Q ss_pred EEEEEEccCCcEEEEeeCCCCeeec
Q 033076 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (128)
Q Consensus 59 ~~k~knl~TG~~~e~t~~s~d~ve~ 83 (128)
.++.+|+.||+++.-+.-+...|++
T Consensus 172 ~I~V~N~~S~k~v~g~V~~~~~V~V 196 (196)
T PF13144_consen 172 TIRVKNLSSGKIVQGRVIGPGTVEV 196 (196)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEC
Confidence 6888999999999888877766653
No 48
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=43.47 E-value=91 Score=20.93 Aligned_cols=44 Identities=9% Similarity=0.212 Sum_probs=28.2
Q ss_pred cccCceEEEECCee------------EEEEEeeEecCCCCcccEEEEEEEEccCCcEE
Q 033076 26 TIRKNGYIVIKGRP------------CKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKL 71 (128)
Q Consensus 26 ~ikkG~~i~~~g~p------------~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~ 71 (128)
.+|.|+++++.... ..|+.+.-. .|...+---+..-|+.||.+.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg--aR~P~~~tlFQVadVDtG~I~ 60 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG--ARDPKVPTLFQVADVDTGVIR 60 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEecc--ccCCCCCceEEEEEccCCeEE
Confidence 47999999998776 445544332 232233444677788888765
No 49
>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=42.82 E-value=36 Score=24.26 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=23.3
Q ss_pred ecccccCceEEEECCeeEEEEEeeEec
Q 033076 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~k 49 (128)
.+-+++.|..|.++|..|.|.++...-
T Consensus 73 p~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 73 PFPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred cccccCCCCEEEECCceEEEEEEEecc
Confidence 345888999999999999999997764
No 50
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=41.85 E-value=31 Score=23.00 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.5
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEV 45 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~ 45 (128)
.-.||.|++|.+.|.++.|+..
T Consensus 50 gkKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 50 GKKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CCEeecCCEEEECCEEEEEEec
Confidence 4568999999999999998753
No 51
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=40.72 E-value=51 Score=22.48 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=20.0
Q ss_pred EeeeEEEEecCCceEEEecCCCCeEE
Q 033076 88 RTDYQLIDISEDGFVSLLTENGNTKD 113 (128)
Q Consensus 88 ~~~~qylY~dgd~~~~fMD~etyeq~ 113 (128)
...++..|.|++|.|++|..+..-+.
T Consensus 41 ~~~~~L~YlDDEgD~VllT~D~DL~e 66 (86)
T cd06409 41 THLYALSYVDDEGDIVLITSDSDLVA 66 (86)
T ss_pred CCcccEEEEcCCCCEEEEeccchHHH
Confidence 46788999998888999987755443
No 52
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=37.53 E-value=2e+02 Score=22.57 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=22.4
Q ss_pred EEEEEEccCCcEEEEeeCCCCeeecc
Q 033076 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (128)
Q Consensus 59 ~~k~knl~TG~~~e~t~~s~d~ve~~ 84 (128)
.++.||+.+|++++-+..+...|++.
T Consensus 188 ~IrVrN~~SgrvV~g~V~~~G~V~V~ 213 (214)
T PRK12617 188 RVSVENSSSRRVVQGIVEASGTVVVS 213 (214)
T ss_pred EEEEEECCCCCEEEEEEeCCcEEEEe
Confidence 68889999999999998888877764
No 53
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.92 E-value=51 Score=23.62 Aligned_cols=22 Identities=23% Similarity=0.475 Sum_probs=15.4
Q ss_pred cccccCceEEEECCe--eEEEEEe
Q 033076 24 AGTIRKNGYIVIKGR--PCKVVEV 45 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~--p~~Vve~ 45 (128)
-..|++|+.|+.+|. |..|+++
T Consensus 31 rr~ik~GD~IiF~~~~l~v~V~~v 54 (111)
T COG4043 31 RRQIKPGDKIIFNGDKLKVEVIDV 54 (111)
T ss_pred hcCCCCCCEEEEcCCeeEEEEEEE
Confidence 346899999999975 3444444
No 54
>cd00603 IPT_PCSR IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the macrophage-stimulating receptors and of fibrocystin. Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT_PCSR domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=36.35 E-value=1.2e+02 Score=19.46 Aligned_cols=34 Identities=15% Similarity=0.362 Sum_probs=25.9
Q ss_pred ccCCCcceeEEEecccccCc---eEEEECCeeEEEEE
Q 033076 11 KADAGASKTFPQQAGTIRKN---GYIVIKGRPCKVVE 44 (128)
Q Consensus 11 ~~~a~~~~t~~i~~~~ikkG---~~i~~~g~p~~Vve 44 (128)
.|....--..+|..+.|..+ ..|.+++.+|.++.
T Consensus 10 ~g~~~Ggt~vtI~G~~f~~~~~~~~V~ig~~~C~~~~ 46 (90)
T cd00603 10 SGPLSGGTRLTITGSNLGSGSPRVRVTVGGVPCKVLN 46 (90)
T ss_pred CCCCCCCeEEEEEEECCCCCCceEEEEECCEECcEEe
Confidence 34444455777888888887 78999999999975
No 55
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=36.17 E-value=50 Score=22.04 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=21.6
Q ss_pred eEEEecccccCceEEEECCeeEEEE
Q 033076 19 TFPQQAGTIRKNGYIVIKGRPCKVV 43 (128)
Q Consensus 19 t~~i~~~~ikkG~~i~~~g~p~~Vv 43 (128)
|-.++-..+.+|+.+..+|.-|..-
T Consensus 8 T~~v~Rq~V~PG~~v~~~grty~AS 32 (73)
T PRK11354 8 TDEIPRQCVTPGDYVLHEGRTYIAS 32 (73)
T ss_pred ceeecccccCCceEEEEcCcEEEEE
Confidence 6678888899999999999999653
No 56
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=35.78 E-value=1.9e+02 Score=23.86 Aligned_cols=94 Identities=13% Similarity=0.133 Sum_probs=54.4
Q ss_pred cccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc-cCCcEEEEeeCCCCeeecceEEEeee-EEEEecCCce
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI-FNGKKLEDIVPSSHNCDVPHVTRTDY-QLIDISEDGF 101 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl-~TG~~~e~t~~s~d~ve~~~ve~~~~-qylY~dgd~~ 101 (128)
-.+++.|+.|.++-.--+|++.-.-.+|. -.+-+-++|. ..|.+.+. -.-.-+.+.+.++...- +|..+. +
T Consensus 148 d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~---l~~vtgG~n~GriG~I~~i-~~~~~~~~iv~i~d~~g~~F~T~~-~-- 220 (273)
T PTZ00223 148 DPRTSRGDTLVYNVKEKKVVDLIKNRNGK---VVMVTGGANRGRIGEIVSI-ERHPGAFDIARLKDASGHEFATRA-A-- 220 (273)
T ss_pred CccccCCCEEEEECCCCeeeEEEecCCCC---EEEEECCeeceeEEEEEEE-EecCCCCCEEEEEeCCCCeEEEEe-e--
Confidence 45788999999986556677554444444 2333566666 44666555 33335556667775443 677774 3
Q ss_pred EEEecCCCCeEEeeeCCCCcchh
Q 033076 102 VSLLTENGNTKDDLRLPTDENLL 124 (128)
Q Consensus 102 ~~fMD~etyeq~~i~lp~~~~l~ 124 (128)
|+|+=-+.-+...|+||.+..++
T Consensus 221 ~VfvIG~~~~kp~IsLp~~kgi~ 243 (273)
T PTZ00223 221 NIFVIGKDMNSVPVTLPKQQGLR 243 (273)
T ss_pred eEEEEeCCCCCcceECcCCCCcc
Confidence 45554333223347778776553
No 57
>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=35.13 E-value=44 Score=22.13 Aligned_cols=20 Identities=20% Similarity=0.056 Sum_probs=17.7
Q ss_pred ccCCcEEEEeeCCCCeeecc
Q 033076 65 IFNGKKLEDIVPSSHNCDVP 84 (128)
Q Consensus 65 l~TG~~~e~t~~s~d~ve~~ 84 (128)
+=+|+.++.+|.+++++..+
T Consensus 11 lP~G~r~~rrF~~t~~L~~l 30 (80)
T cd01771 11 TPSGDFLERRFLGDTPLQVL 30 (80)
T ss_pred CCCCCEEEEEeCCCCcHHHH
Confidence 67899999999999999855
No 58
>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=35.12 E-value=48 Score=23.77 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=15.6
Q ss_pred EEecccccCceEEEE-CCeeEEEEEeeE
Q 033076 21 PQQAGTIRKNGYIVI-KGRPCKVVEVST 47 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~-~g~p~~Vve~~~ 47 (128)
-+.|.+|++|+.|.- +|.+..|.++..
T Consensus 71 Wv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 71 WVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp -EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 478999999998754 688777776654
No 59
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=33.15 E-value=1.6e+02 Score=20.17 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=18.8
Q ss_pred EEEEEEccCCcEEEEeeCCCCeee
Q 033076 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (128)
Q Consensus 59 ~~k~knl~TG~~~e~t~~s~d~ve 82 (128)
.++.+|+.||+++.-+..+...++
T Consensus 98 ~I~V~N~~s~k~i~~~V~~~g~V~ 121 (122)
T TIGR03170 98 QIRVRNLSSGKIISGIVTGPGTVE 121 (122)
T ss_pred EEEEEECCCCCEEEEEEeCCCEEE
Confidence 578889999999888777666554
No 60
>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=31.39 E-value=93 Score=23.55 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=14.5
Q ss_pred ccccCceEEEEC---CeeE---EEEEee
Q 033076 25 GTIRKNGYIVIK---GRPC---KVVEVS 46 (128)
Q Consensus 25 ~~ikkG~~i~~~---g~p~---~Vve~~ 46 (128)
+-+|+|++|.++ |.|+ +|+++.
T Consensus 2 ~~yrvGD~Vy~~~~~~~Py~I~rI~e~~ 29 (164)
T cd04709 2 NMYRVGDYVYFESSPNNPYLIRRIEELN 29 (164)
T ss_pred cEEecCCEEEEECCCCCCCEEEEEEEEE
Confidence 347889988887 4454 455554
No 61
>PLN00036 40S ribosomal protein S4; Provisional
Probab=31.07 E-value=2.9e+02 Score=22.71 Aligned_cols=93 Identities=17% Similarity=0.133 Sum_probs=58.1
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEcc-CCcEEEEeeCCCCeeecceEEEeee-EEEEecCCc
Q 033076 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIF-NGKKLEDIVPSSHNCDVPHVTRTDY-QLIDISEDG 100 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~-TG~~~e~t~~s~d~ve~~~ve~~~~-qylY~dgd~ 100 (128)
+-.+++.|+.|.++-.--+|++.-.-.+|. -.+-+-++|+= .|.+.+.. .-.-+.+.+.|+...- +|.... +
T Consensus 150 ~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~---l~~vtgG~n~GrvG~I~~i~-~~~~~~~iV~i~d~~g~~F~T~~-~- 223 (261)
T PLN00036 150 PDPLIKANDTIKIDLETNKIVDFIKFDVGN---LVMVTGGRNRGRVGVIKNRE-KHKGSFEIIHVKDATGHEFATRL-G- 223 (261)
T ss_pred CCCccccCCEEEEeCCCCceeeEEecCCCC---EEEEECCeeceeEEEEEEEE-ecCCCCCEEEEEeCCCCeEEEEe-e-
Confidence 345789999999986556677654445554 23346777774 47766666 3334566788886555 677774 3
Q ss_pred eEEEecCCCCeEEeeeCCCCcch
Q 033076 101 FVSLLTENGNTKDDLRLPTDENL 123 (128)
Q Consensus 101 ~~~fMD~etyeq~~i~lp~~~~l 123 (128)
|+|+=-++ +...|+||.+..+
T Consensus 224 -~vfvIG~~-~kp~isLp~~~gi 244 (261)
T PLN00036 224 -NVFVIGKG-TKPWISLPKGKGI 244 (261)
T ss_pred -eEEEEccC-CCeeEeCcCCCCc
Confidence 45555443 4445777877554
No 62
>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=30.70 E-value=74 Score=17.17 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=15.0
Q ss_pred CceEEEE-----CCeeEEEEEeeEec
Q 033076 29 KNGYIVI-----KGRPCKVVEVSTSK 49 (128)
Q Consensus 29 kG~~i~~-----~g~p~~Vve~~~~k 49 (128)
+|+.+++ .|..++|+++...+
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 4667777 67888888886543
No 63
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=30.40 E-value=1.6e+02 Score=24.45 Aligned_cols=51 Identities=8% Similarity=0.008 Sum_probs=39.2
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCC
Q 033076 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS 78 (128)
Q Consensus 23 ~~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~ 78 (128)
..++++.|..+. .+|.|.+.+... .|.|..+..+.+.| .||.+.=+-|...
T Consensus 4 ~i~~l~~g~~v~---~~~lv~~~~~~~-~knG~~yl~l~l~D-~tG~I~ak~W~~~ 54 (314)
T PRK13480 4 GIEELEVGEQVD---HFLLIKSATKGV-ASNGKPFLTLILQD-KSGDIEAKLWDVS 54 (314)
T ss_pred hHhhcCCCCEee---EEEEEEEceeee-cCCCCeEEEEEEEc-CCcEEEEEeCCCC
Confidence 568899998654 378888776644 45588999999999 9999887777654
No 64
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=29.40 E-value=40 Score=21.54 Aligned_cols=25 Identities=28% Similarity=0.254 Sum_probs=19.2
Q ss_pred EEEEEEEEccCCcEEEEeeCCCCeeecc
Q 033076 57 KCHFVGIDIFNGKKLEDIVPSSHNCDVP 84 (128)
Q Consensus 57 ~v~~k~knl~TG~~~e~t~~s~d~ve~~ 84 (128)
.+++++ -+|+.+..+|++++++..+
T Consensus 4 ~i~iRl---pdG~~~~~~F~~~~tl~~l 28 (77)
T cd01767 4 KIQIRL---PDGKRLEQRFNSTHKLSDV 28 (77)
T ss_pred EEEEEc---CCCCEEEEEeCCCCCHHHH
Confidence 445554 5599999999999998854
No 65
>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=29.23 E-value=1.6e+02 Score=22.24 Aligned_cols=23 Identities=17% Similarity=0.400 Sum_probs=19.4
Q ss_pred cccccCceEEEECCeeEEEEEee
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEVS 46 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~~ 46 (128)
..=|+-|++|.+++.+|+|++=.
T Consensus 37 ~~VL~TgNYitI~d~v~kI~~K~ 59 (149)
T PF08408_consen 37 SEVLSTGNYITINDDVYKILDKD 59 (149)
T ss_pred HHHHhcCCeEEECCeeeeeeccc
Confidence 45588999999999999998653
No 66
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=29.06 E-value=1.2e+02 Score=26.72 Aligned_cols=31 Identities=16% Similarity=0.486 Sum_probs=24.6
Q ss_pred EecccccCceEEEECCeeEEEEE-eeEecCCC
Q 033076 22 QQAGTIRKNGYIVIKGRPCKVVE-VSTSKTGK 52 (128)
Q Consensus 22 i~~~~ikkG~~i~~~g~p~~Vve-~~~~kpGK 52 (128)
....++++...+.++|++|++++ -+....|+
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 56788999999999999999997 44444444
No 67
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=28.57 E-value=1.2e+02 Score=23.31 Aligned_cols=69 Identities=16% Similarity=0.221 Sum_probs=45.0
Q ss_pred EEEeeEecC-CCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEEEeeeEEEEecCCceEEEecCCCCeEEeeeCCC
Q 033076 42 VVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPT 119 (128)
Q Consensus 42 Vve~~~~kp-GK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve~~~~qylY~dgd~~~~fMD~etyeq~~i~lp~ 119 (128)
|+|+.-.-| |.|++..+.+.+|+=..|.+.-..+..-.-|+.|+--+..+ ++.||+.++-.-+-|-|-.
T Consensus 84 IlEvkg~lP~G~~~hGyfNL~gk~~l~GHiK~eNcs~Ialv~rpFmG~~s~---------si~Ffn~~G~~mfKiylgR 153 (176)
T COG3721 84 ILEVKGPLPSGTHRHGYFNLRGKDGLSGHIKAENCSHIALVERPFMGMESA---------SILFFNAQGEAMFKIYLGR 153 (176)
T ss_pred EEEecCCCCCCccccceEeecCCCCCcceeeccccceeeEeccccCCccce---------eeeeecccCceeeeeeecc
Confidence 344443334 88888899999999999998877777666666665444333 4556666555555555544
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=28.20 E-value=50 Score=24.46 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=16.5
Q ss_pred cccccCceEEEECCeeEEEEEee
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEVS 46 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~~ 46 (128)
..-++.|+.|.++|....|+++.
T Consensus 58 ~~pf~vGD~I~i~~~~G~V~~I~ 80 (206)
T PF00924_consen 58 ERPFKVGDRIEIGGVEGRVEEIG 80 (206)
T ss_dssp C-SS-TT-EEESSS-EEEEEEE-
T ss_pred cCCccCCCEEEEEEeehHHHhcC
Confidence 34789999999999999999883
No 69
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=28.12 E-value=1.7e+02 Score=25.05 Aligned_cols=44 Identities=7% Similarity=0.167 Sum_probs=28.6
Q ss_pred cccccCceEEEECC---eeEEE----EEeeEecCCCCcccEEEEEEEEccCC
Q 033076 24 AGTIRKNGYIVIKG---RPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNG 68 (128)
Q Consensus 24 ~~~ikkG~~i~~~g---~p~~V----ve~~~~kpGK~G~A~v~~k~knl~TG 68 (128)
.-+|++|++|.++- .|..| +..-..+||++|+ .+-+++......
T Consensus 320 lL~LkvGDVI~Ld~~~~~~v~v~v~g~p~F~g~~G~~~g-~~AvrI~~~l~~ 370 (388)
T PRK12795 320 VLNLKVGDTLMLDARPDALVTLRCGDVPLTEGRMGRVGD-RVAVRVEKPLRK 370 (388)
T ss_pred HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEeccCCC-EEEEEEEeecCC
Confidence 45789999999984 35544 3345668898743 444666655443
No 70
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.11 E-value=3.3e+02 Score=22.10 Aligned_cols=25 Identities=12% Similarity=0.122 Sum_probs=20.9
Q ss_pred EEEEEEccCCcEEEEeeCCCCeeec
Q 033076 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (128)
Q Consensus 59 ~~k~knl~TG~~~e~t~~s~d~ve~ 83 (128)
.++.||+.||+++.-+..+...|.+
T Consensus 235 ~IrVrN~~SgkvV~a~V~~~g~V~v 259 (261)
T PRK06804 235 LIKVKNLSSGRVVTATVDGSGRVRM 259 (261)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEE
Confidence 5788999999999998888777764
No 71
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.48 E-value=3e+02 Score=21.51 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=21.8
Q ss_pred EEEEEEccCCcEEEEeeCCCCeeecc
Q 033076 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (128)
Q Consensus 59 ~~k~knl~TG~~~e~t~~s~d~ve~~ 84 (128)
.++.||+.||+++.-+..+...|++.
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V~ 234 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEVN 234 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEEe
Confidence 57888999999999988888877753
No 72
>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=27.16 E-value=1.4e+02 Score=24.20 Aligned_cols=30 Identities=7% Similarity=0.046 Sum_probs=20.2
Q ss_pred cccccCceEEEEC---CeeEEE----EEeeEecCCCC
Q 033076 24 AGTIRKNGYIVIK---GRPCKV----VEVSTSKTGKH 53 (128)
Q Consensus 24 ~~~ikkG~~i~~~---g~p~~V----ve~~~~kpGK~ 53 (128)
.-.|++|++|.++ ++|..| ..+-..++|++
T Consensus 271 ll~L~~GDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~ 307 (320)
T TIGR01397 271 LLNLQVGDVIPLNTDMPEEVSLRVGGRPKFRAQPGVR 307 (320)
T ss_pred HhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEE
Confidence 4578999999998 456665 23345566665
No 73
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=26.59 E-value=3.6e+02 Score=22.16 Aligned_cols=93 Identities=15% Similarity=0.133 Sum_probs=56.2
Q ss_pred cccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEcc-CCcEEEEeeCCCCeeecceEEEeee-EEEEecCCce
Q 033076 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIF-NGKKLEDIVPSSHNCDVPHVTRTDY-QLIDISEDGF 101 (128)
Q Consensus 24 ~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~-TG~~~e~t~~s~d~ve~~~ve~~~~-qylY~dgd~~ 101 (128)
-.+++.|+.|.++-.--+|++.-.-.+|. -.+-+-++|+= .|.+.+.... .-+.+.+.|+...- +|.... +
T Consensus 151 d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~---l~~vtgG~n~GriG~I~~~~~~-~~~~~~V~i~d~~g~~F~T~~-~-- 223 (262)
T PTZ00118 151 HPDVKVGDSLRLDLETGKVLEFLKFEVGN---LVMITGGHNVGRVGTIVSKEKH-PGSFDLIHVKDSRGKTFATRL-S-- 223 (262)
T ss_pred CCcccCCCEEEEECCCCceeeEEecCCCC---EEEEECCeeceeEEEEEEEEec-CCCCcEEEEEeCCCCeEEEEe-e--
Confidence 45788999999986555577554444454 23346677763 4766664333 34466778876554 677774 3
Q ss_pred EEEecCCCCeEEeeeCCCCcchh
Q 033076 102 VSLLTENGNTKDDLRLPTDENLL 124 (128)
Q Consensus 102 ~~fMD~etyeq~~i~lp~~~~l~ 124 (128)
|+|+=-++ +...|+||.++.++
T Consensus 224 ~vfvIG~~-~kp~islp~~kgi~ 245 (262)
T PTZ00118 224 NVFVIGVG-TKPYVSLPRERGIK 245 (262)
T ss_pred eEEEEccC-CCeeEeCcCCCCcc
Confidence 35544332 45557788876553
No 74
>PTZ00031 ribosomal protein L2; Provisional
Probab=26.42 E-value=2.2e+02 Score=24.09 Aligned_cols=61 Identities=16% Similarity=0.152 Sum_probs=31.8
Q ss_pred eeEEEecccccCceEEEE--------------CCee--EEEEEeeEecCCCCcccE-------EEEEEEEccCCcEEEEe
Q 033076 18 KTFPQQAGTIRKNGYIVI--------------KGRP--CKVVEVSTSKTGKHGHAK-------CHFVGIDIFNGKKLEDI 74 (128)
Q Consensus 18 ~t~~i~~~~ikkG~~i~~--------------~g~p--~~Vve~~~~kpGK~G~A~-------v~~k~knl~TG~~~e~t 74 (128)
..|.+.+..++.|++|.. .+-| ..|-.++. +||+ |+.+ +++..++ +...-..
T Consensus 132 ~~YIlApeGl~vGd~I~sg~~a~i~~GN~lPL~~IP~GT~IhNIE~-~pG~-Ggkl~RSAGt~A~Ii~k~---~~~~~Vk 206 (317)
T PTZ00031 132 LSYILAPLLLRPGDKIIASKYANINPGNSLPLRNIPVGSIVHNVEM-RPGA-GGQIIRAGGTYATVVSKD---EQFATLK 206 (317)
T ss_pred EEEEEccCCCCCCCEEEeCCCCCCCccCccccccCCCCCEEEEEEe-cCCC-CceEEEecCCeEEEEEcc---CCEEEEE
Confidence 346666666666666654 3322 22333333 6777 3333 3344432 5666667
Q ss_pred eCCCCeeec
Q 033076 75 VPSSHNCDV 83 (128)
Q Consensus 75 ~~s~d~ve~ 83 (128)
++|++...+
T Consensus 207 LPSGe~r~i 215 (317)
T PTZ00031 207 LKSTEIRKF 215 (317)
T ss_pred CCCCCEEEE
Confidence 777766553
No 75
>PF13989 YejG: YejG-like protein
Probab=25.99 E-value=63 Score=23.08 Aligned_cols=16 Identities=25% Similarity=0.503 Sum_probs=13.0
Q ss_pred ceEEEECCeeEEEEEe
Q 033076 30 NGYIVIKGRPCKVVEV 45 (128)
Q Consensus 30 G~~i~~~g~p~~Vve~ 45 (128)
..+++++|+||.-+..
T Consensus 69 ~~vvE~eGepCLFv~~ 84 (106)
T PF13989_consen 69 CAVVEWEGEPCLFVHR 84 (106)
T ss_pred ceEEEecCCceEEEec
Confidence 4589999999987754
No 76
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=25.74 E-value=1.6e+02 Score=21.70 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=25.6
Q ss_pred cccccCceEEEEC---CeeEEEE----EeeEecCCCCcccEEEEEEEEccC
Q 033076 24 AGTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (128)
Q Consensus 24 ~~~ikkG~~i~~~---g~p~~Vv----e~~~~kpGK~G~A~v~~k~knl~T 67 (128)
.-+|++|++|.++ ++|..|. -+-+..+|.. .-++-+++..+.+
T Consensus 78 LL~L~~GDVI~Ld~~~~epv~V~Vng~~if~GevGvv-~~k~AVrIteii~ 127 (137)
T PRK07963 78 LLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVV-ADKYGVRITDIIT 127 (137)
T ss_pred HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEE-CCEEEEEEEEecC
Confidence 3478999999999 5776663 2233344443 2344455555554
No 77
>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=25.52 E-value=1.2e+02 Score=23.92 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=19.6
Q ss_pred EEEecccccCceEEEE------CCeeEEEEEeeEe
Q 033076 20 FPQQAGTIRKNGYIVI------KGRPCKVVEVSTS 48 (128)
Q Consensus 20 ~~i~~~~ikkG~~i~~------~g~p~~Vve~~~~ 48 (128)
-.+-|+++++|++|.. .-.|-+|+++..+
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 5789999999999999 2247777777665
No 78
>PRK10965 multicopper oxidase; Provisional
Probab=24.88 E-value=2.3e+02 Score=25.09 Aligned_cols=47 Identities=6% Similarity=-0.067 Sum_probs=32.5
Q ss_pred cCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeee
Q 033076 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (128)
Q Consensus 28 kkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve 82 (128)
..|+.+.+||.++-.+.. ||+ .+|+++.|--+-..+...+..+..+.
T Consensus 210 ~~gd~~lVNG~~~p~~~v----~~~----~~RlRliNas~~r~~~l~~~dg~~~~ 256 (523)
T PRK10965 210 WFGDTLLTNGAIYPQHAA----PRG----WLRLRLLNGCNARSLNLATSDGRPLY 256 (523)
T ss_pred ccCCeEEECCcccceeec----CCC----EEEEEEEeccCCceEEEEEcCCceEE
Confidence 468999999997655432 332 68999998887777777664444443
No 79
>KOG0238 consensus 3-Methylcrotonyl-CoA carboxylase, biotin-containing subunit/Propionyl-CoA carboxylase, alpha chain/Acetyl-CoA carboxylase, biotin carboxylase subunit [Lipid transport and metabolism; Amino acid transport and metabolism]
Probab=24.87 E-value=65 Score=29.39 Aligned_cols=29 Identities=14% Similarity=0.092 Sum_probs=23.5
Q ss_pred eeEEEEecCCceEEEecCCCCeEEeeeCCC
Q 033076 90 DYQLIDISEDGFVSLLTENGNTKDDLRLPT 119 (128)
Q Consensus 90 ~~qylY~dgd~~~~fMD~etyeq~~i~lp~ 119 (128)
.++||+-..+ +|+||.++|--|.+-|+.+
T Consensus 269 TVEFi~D~~~-~FyFmEmNTRLQVEHPvTE 297 (670)
T KOG0238|consen 269 TVEFIVDSKD-NFYFMEMNTRLQVEHPVTE 297 (670)
T ss_pred eEEEEEcCCC-cEEEEEeeceeeecccchh
Confidence 4558887755 7999999999998888764
No 80
>PRK11835 hypothetical protein; Provisional
Probab=23.78 E-value=73 Score=23.03 Aligned_cols=32 Identities=22% Similarity=0.459 Sum_probs=19.9
Q ss_pred ccccC-ceEEEECCeeEEEEEeeEecCCCCcccEEEEE
Q 033076 25 GTIRK-NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFV 61 (128)
Q Consensus 25 ~~ikk-G~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k 61 (128)
++|.. ..+++++|+||.-+..+-- .+|.+|+|
T Consensus 66 ~eiqv~~~ivEweGepCLFv~~~DE-----~aa~CrLK 98 (114)
T PRK11835 66 SDIQVPCSVLECEGEPCLFVNRQDE-----SAATCRLK 98 (114)
T ss_pred HhhcccceEEEecCCceEEEecccc-----hhhheeec
Confidence 34444 4589999999987754321 34555554
No 81
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=23.74 E-value=1.8e+02 Score=18.82 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=10.5
Q ss_pred ccccCceEEEECCeeEE
Q 033076 25 GTIRKNGYIVIKGRPCK 41 (128)
Q Consensus 25 ~~ikkG~~i~~~g~p~~ 41 (128)
..+++|+.|.+.|.+..
T Consensus 64 ~~l~kG~~V~V~G~l~~ 80 (104)
T PF00436_consen 64 EYLKKGDRVYVEGRLRT 80 (104)
T ss_dssp HH--TT-EEEEEEEEEE
T ss_pred eEEcCCCEEEEEEEEEe
Confidence 44889999999887663
No 82
>PRK06788 flagellar motor switch protein; Validated
Probab=23.03 E-value=1.8e+02 Score=20.93 Aligned_cols=45 Identities=13% Similarity=0.175 Sum_probs=27.4
Q ss_pred cccccCceEEEEC---CeeEEE----EEeeEecCCCCcccEEEEEEEEccCCc
Q 033076 24 AGTIRKNGYIVIK---GRPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNGK 69 (128)
Q Consensus 24 ~~~ikkG~~i~~~---g~p~~V----ve~~~~kpGK~G~A~v~~k~knl~TG~ 69 (128)
.-+|++|++|.++ ++|..| ..+-...+|..+ -.+-+++..+.+.+
T Consensus 52 lL~L~vGDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~-~~~AVrItei~~~~ 103 (119)
T PRK06788 52 VKQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMD-EKFGIIISEIEADK 103 (119)
T ss_pred HhCCCCCCEEEeCCcCCCCEEEEECCEEEEEEEEEEEC-CEEEEEEEEecChH
Confidence 4468999999998 556555 223344556542 34456666666644
No 83
>COG3731 SrlB Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]
Probab=22.62 E-value=1e+02 Score=22.54 Aligned_cols=28 Identities=7% Similarity=0.182 Sum_probs=22.7
Q ss_pred eeEEEecccccCceEEEECCeeEEEEEe
Q 033076 18 KTFPQQAGTIRKNGYIVIKGRPCKVVEV 45 (128)
Q Consensus 18 ~t~~i~~~~ikkG~~i~~~g~p~~Vve~ 45 (128)
.++.-.-..+.+|+.+.+++.+|.|..+
T Consensus 43 H~h~e~~~~l~~G~~l~lg~~~y~ItaV 70 (123)
T COG3731 43 HKHGELQEALQPGDRLTLGGHCYPITAV 70 (123)
T ss_pred eecCcccccCCCCCEEEECCceEEEEEe
Confidence 3344456778899999999999999977
No 84
>PF13403 Hint_2: Hint domain
Probab=22.23 E-value=2.8e+02 Score=20.15 Aligned_cols=47 Identities=13% Similarity=0.055 Sum_probs=29.5
Q ss_pred EecccccCceE-EEECCeeEEEEEeeEecC------CCCcccEEEEEEEEccCC
Q 033076 22 QQAGTIRKNGY-IVIKGRPCKVVEVSTSKT------GKHGHAKCHFVGIDIFNG 68 (128)
Q Consensus 22 i~~~~ikkG~~-i~~~g~p~~Vve~~~~kp------GK~G~A~v~~k~knl~TG 68 (128)
+.+.+|++|+. +..+|.+..|..+...+- ..+..+-|++..--|-.|
T Consensus 16 ~~Ve~L~~GD~V~T~dgg~~~V~wig~~~~~~~~~~~~~~~~pvri~a~alG~g 69 (147)
T PF13403_consen 16 RPVEDLRPGDRVLTRDGGFQPVRWIGRRTVSPADLPAPPRLAPVRIPAGALGNG 69 (147)
T ss_pred eEeeccCCCCEEEecCCCEEEEEEEEEEEecccccCcCCCcceEEEECCccCCC
Confidence 67899999995 456688888877754432 222235566664444433
No 85
>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=22.13 E-value=1.1e+02 Score=17.10 Aligned_cols=18 Identities=6% Similarity=0.008 Sum_probs=13.4
Q ss_pred cCceEEEECCeeEEEEEe
Q 033076 28 RKNGYIVIKGRPCKVVEV 45 (128)
Q Consensus 28 kkG~~i~~~g~p~~Vve~ 45 (128)
..|++|.++|..|+..--
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 569999999999988533
No 86
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=21.85 E-value=2.1e+02 Score=18.91 Aligned_cols=40 Identities=8% Similarity=-0.080 Sum_probs=23.1
Q ss_pred EEEEEEEEccCCcEEEEeeCCCCeeecceE-EEeeeEEEEec
Q 033076 57 KCHFVGIDIFNGKKLEDIVPSSHNCDVPHV-TRTDYQLIDIS 97 (128)
Q Consensus 57 ~v~~k~knl~TG~~~e~t~~s~d~ve~~~v-e~~~~qylY~d 97 (128)
.+.+.++|.-+ ..++.+|+|+.+.+.... ..-+--|-|.+
T Consensus 3 ~~~l~v~N~s~-~~v~l~f~sgq~~D~~v~d~~g~~vwrwS~ 43 (82)
T PF12690_consen 3 EFTLTVTNNSD-EPVTLQFPSGQRYDFVVKDKEGKEVWRWSD 43 (82)
T ss_dssp EEEEEEEE-SS-S-EEEEESSS--EEEEEE-TT--EEEETTT
T ss_pred EEEEEEEeCCC-CeEEEEeCCCCEEEEEEECCCCCEEEEecC
Confidence 45677777654 457899999999998887 33333444443
No 87
>PF05203 Hom_end_hint: Hom_end-associated Hint; InterPro: IPR007868 Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [] revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This domain corresponds to the protein-splicing domain.; GO: 0030908 protein splicing; PDB: 1LWT_A 1UM2_B 1JVA_B 1GPP_A 1VDE_A 1EF0_B 1DFA_A 1LWS_A.
Probab=21.16 E-value=1.5e+02 Score=23.22 Aligned_cols=56 Identities=16% Similarity=0.188 Sum_probs=31.3
Q ss_pred EEecccccCceEEEE-CCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeec
Q 033076 21 PQQAGTIRKNGYIVI-KGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83 (128)
Q Consensus 21 ~i~~~~ikkG~~i~~-~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~ 83 (128)
...+.+|+.|+.|+= ||.|-+|+.+.. |+ ...++|+-+... +....++.+++.+-.
T Consensus 15 ~k~ie~i~~Gd~vmg~dg~~r~V~~~~~---g~--~~my~i~~~~~~--~~~~~~~~~~H~L~l 71 (215)
T PF05203_consen 15 IKPIEDIKIGDQVMGPDGRPRRVTNVPR---GR--EEMYRITQKTKH--KGEDFTCNANHILVL 71 (215)
T ss_dssp EEEGGG--TT-EEEBTTSSEEEEEE--E---EE--EEEEEEEE-SSS----SEEEEETT-EEEE
T ss_pred eeEEeecccCCEEECCCCCcEEEEEecc---cc--eeEEEEEEcccC--CcceEEEcCCeEEEE
Confidence 468899999999887 789999998832 44 356666655332 344555666655543
No 88
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=20.88 E-value=49 Score=20.05 Aligned_cols=18 Identities=33% Similarity=0.573 Sum_probs=13.6
Q ss_pred CCCeEEeeeCCCCcchhccc
Q 033076 108 NGNTKDDLRLPTDENLLSQV 127 (128)
Q Consensus 108 etyeq~~i~lp~~~~l~~k~ 127 (128)
.+..||.|.+| ++|.++|
T Consensus 2 r~~~~f~lRlP--~~l~~~l 19 (50)
T PF03869_consen 2 RKDPQFNLRLP--EELKEKL 19 (50)
T ss_dssp CCSEEEEEECE--HHHHHHH
T ss_pred CCCCceeeECC--HHHHHHH
Confidence 35789999999 5676654
No 89
>KOG4499 consensus Ca2+-binding protein Regucalcin/SMP30 [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=20.86 E-value=4.1e+02 Score=22.14 Aligned_cols=88 Identities=11% Similarity=0.048 Sum_probs=58.0
Q ss_pred ccccccCCCcceeEE-Ee-----cccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCe
Q 033076 7 HFESKADAGASKTFP-QQ-----AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (128)
Q Consensus 7 ~~~~~~~a~~~~t~~-i~-----~~~ikkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ 80 (128)
|++ .|+.+.+.-.- +. -+-+--|+.|--+|.+|+-+- ..| ++...|+-||++.-..--...+
T Consensus 188 d~~-tG~~snr~~i~dlrk~~~~e~~~PDGm~ID~eG~L~Va~~----ng~-------~V~~~dp~tGK~L~eiklPt~q 255 (310)
T KOG4499|consen 188 DCP-TGDLSNRKVIFDLRKSQPFESLEPDGMTIDTEGNLYVATF----NGG-------TVQKVDPTTGKILLEIKLPTPQ 255 (310)
T ss_pred CCC-cccccCcceeEEeccCCCcCCCCCCcceEccCCcEEEEEe----cCc-------EEEEECCCCCcEEEEEEcCCCc
Confidence 455 67766653221 11 122334899988888885441 222 4778899999998776655778
Q ss_pred eecceEEEeeeEEEEecCCceEEEecCC
Q 033076 81 CDVPHVTRTDYQLIDISEDGFVSLLTEN 108 (128)
Q Consensus 81 ve~~~ve~~~~qylY~dgd~~~~fMD~e 108 (128)
+--+-+--+.+..+|..-. --|||++
T Consensus 256 itsccFgGkn~d~~yvT~a--a~~~dp~ 281 (310)
T KOG4499|consen 256 ITSCCFGGKNLDILYVTTA--AKFDDPV 281 (310)
T ss_pred eEEEEecCCCccEEEEEeh--hcccCch
Confidence 8777777777888888643 4688876
No 90
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=20.50 E-value=95 Score=19.95 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=20.9
Q ss_pred ccEEEEEEEEccCCcEEEEeeCCCCeeecc
Q 033076 55 HAKCHFVGIDIFNGKKLEDIVPSSHNCDVP 84 (128)
Q Consensus 55 ~A~v~~k~knl~TG~~~e~t~~s~d~ve~~ 84 (128)
.+.++++ +-+|+.+..+|++++++..+
T Consensus 4 ~~~I~iR---lPdG~ri~~~F~~~~tl~~v 30 (80)
T smart00166 4 QCRLQIR---LPDGSRLVRRFPSSDTLRTV 30 (80)
T ss_pred eEEEEEE---cCCCCEEEEEeCCCCcHHHH
Confidence 3555555 47899999999999999854
No 91
>PRK10883 FtsI repressor; Provisional
Probab=20.45 E-value=2.6e+02 Score=24.32 Aligned_cols=52 Identities=13% Similarity=0.128 Sum_probs=36.7
Q ss_pred cCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEeeCCCCeeecceEE
Q 033076 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVT 87 (128)
Q Consensus 28 kkG~~i~~~g~p~~Vve~~~~kpGK~G~A~v~~k~knl~TG~~~e~t~~s~d~ve~~~ve 87 (128)
..|+.+.+||..+-++++ +|| .+|+++.|--.-..+...+..++.+.++-.+
T Consensus 207 ~~gd~~lvNG~~~p~~~v---~~~-----~~RlRliNas~~~~~~l~l~d~~~~~vIa~D 258 (471)
T PRK10883 207 FVGDTLLVNGVQSPYVEV---SRG-----WVRLRLLNASNARRYQLQMSDGRPLHVIAGD 258 (471)
T ss_pred ccCCeeEECCccCCeEEe---cCC-----EEEEEEEEccCCceEEEEEcCCCeEEEEEeC
Confidence 468899999987766654 443 4699999988888887777555555544444
No 92
>CHL00052 rpl2 ribosomal protein L2
Probab=20.34 E-value=3.7e+02 Score=22.15 Aligned_cols=19 Identities=16% Similarity=0.197 Sum_probs=10.7
Q ss_pred ceeEEEecccccCceEEEE
Q 033076 17 SKTFPQQAGTIRKNGYIVI 35 (128)
Q Consensus 17 ~~t~~i~~~~ikkG~~i~~ 35 (128)
...|.+....++.|++|..
T Consensus 98 ~~~YIlAp~gl~~Gd~I~~ 116 (273)
T CHL00052 98 EKRYILHPRGLKIGDTIVS 116 (273)
T ss_pred cEEEEEccCCCCCCCEEEe
Confidence 3446666665666655554
Done!