Query 033484
Match_columns 118
No_of_seqs 112 out of 985
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 02:48:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033484.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033484hhsearch_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 3E-44 6.4E-49 266.7 12.9 112 1-113 1-114 (159)
2 TIGR00037 eIF_5A translation i 100.0 1.6E-39 3.4E-44 234.4 11.4 97 16-113 1-97 (130)
3 PTZ00328 eukaryotic initiation 100.0 6.2E-37 1.3E-41 228.2 12.1 111 1-111 1-118 (166)
4 COG0231 Efp Translation elonga 100.0 5E-36 1.1E-40 216.5 11.1 92 20-113 2-93 (131)
5 PRK03999 translation initiatio 100.0 5.9E-36 1.3E-40 215.5 11.0 94 19-113 3-96 (129)
6 PRK12426 elongation factor P; 100.0 1.1E-34 2.3E-39 220.0 11.0 91 21-113 1-91 (185)
7 PRK14578 elongation factor P; 100.0 2.6E-33 5.5E-38 212.7 11.2 92 21-113 1-93 (187)
8 PRK04542 elongation factor P; 100.0 2.7E-33 5.9E-38 212.9 11.1 92 21-113 1-93 (189)
9 KOG3271 Translation initiation 100.0 1E-32 2.2E-37 201.1 8.3 108 1-110 1-108 (156)
10 TIGR02178 yeiP elongation fact 100.0 4.6E-32 9.9E-37 205.8 11.5 89 24-113 2-91 (186)
11 PRK00529 elongation factor P; 100.0 1.1E-31 2.3E-36 203.2 11.0 91 21-113 1-91 (186)
12 TIGR00038 efp translation elon 100.0 1.9E-31 4.1E-36 201.6 11.3 90 22-113 1-90 (184)
13 PF08207 EFP_N: Elongation fac 99.9 3.5E-22 7.6E-27 126.0 8.7 58 23-81 1-58 (58)
14 PF01132 EFP: Elongation facto 98.9 7.8E-10 1.7E-14 68.9 1.9 26 88-114 1-26 (55)
15 cd04470 S1_EF-P_repeat_1 S1_EF 98.9 7.8E-10 1.7E-14 70.2 1.4 26 87-113 1-26 (61)
16 cd04463 S1_EF_like S1_EF_like: 98.6 1.9E-08 4.2E-13 61.9 1.3 24 89-113 1-24 (55)
17 PF01287 eIF-5a: Eukaryotic el 97.2 0.00038 8.3E-09 45.3 3.4 27 85-112 1-27 (69)
18 COG1499 NMD3 NMD protein affec 96.7 0.0071 1.5E-07 50.4 7.7 92 11-113 231-326 (355)
19 cd04467 S1_aIF5A S1_aIF5A: Arc 96.0 0.0048 1E-07 38.9 2.0 27 86-113 1-27 (57)
20 cd04468 S1_eIF5A S1_eIF5A: Euk 93.6 0.064 1.4E-06 35.0 2.5 22 86-108 1-22 (69)
21 cd04469 S1_Hex1 S1_Hex1: Hex1, 86.1 0.91 2E-05 30.0 2.9 20 88-108 2-21 (75)
22 PF08605 Rad9_Rad53_bind: Fung 79.8 5.9 0.00013 28.7 5.3 51 8-60 43-102 (131)
23 COG0090 RplB Ribosomal protein 74.5 16 0.00035 29.7 6.9 55 24-82 121-183 (275)
24 PF01245 Ribosomal_L19: Riboso 73.9 19 0.00041 25.4 6.4 66 22-89 14-88 (113)
25 PRK05338 rplS 50S ribosomal pr 68.8 29 0.00062 24.7 6.4 54 22-79 14-77 (116)
26 PF13275 S4_2: S4 domain; PDB: 66.2 8 0.00017 24.8 2.9 23 21-43 43-65 (65)
27 TIGR01024 rplS_bact ribosomal 66.1 33 0.00072 24.3 6.3 53 22-78 14-76 (113)
28 smart00676 DM10 Domains in hyp 64.0 6.2 0.00013 27.2 2.2 27 20-46 67-93 (104)
29 PF13144 SAF_2: SAF-like 63.0 59 0.0013 24.0 7.6 24 59-82 172-195 (196)
30 CHL00084 rpl19 ribosomal prote 62.4 42 0.00092 23.9 6.3 53 22-78 18-80 (117)
31 PF11302 DUF3104: Protein of u 62.0 29 0.00063 23.0 5.0 44 26-71 5-60 (75)
32 PF05096 Glu_cyclase_2: Glutam 61.7 42 0.00092 27.0 6.9 85 18-113 37-123 (264)
33 PF13785 DUF4178: Domain of un 61.4 9.1 0.0002 26.6 2.7 22 27-48 1-22 (140)
34 smart00466 SRA SET and RING fi 61.1 32 0.0007 25.5 5.7 37 27-65 116-152 (155)
35 PRK11354 kil FtsZ inhibitor pr 59.7 14 0.0003 24.3 3.1 27 17-43 6-32 (73)
36 PF05354 Phage_attach: Phage H 59.7 9 0.0002 27.4 2.4 42 15-59 63-104 (117)
37 PF13856 Gifsy-2: ATP-binding 59.6 46 0.001 22.0 5.9 38 12-49 48-88 (95)
38 PF03829 PTSIIA_gutA: PTS syst 59.5 12 0.00027 26.4 3.1 23 23-45 48-70 (117)
39 TIGR03170 flgA_cterm flagella 58.4 56 0.0012 22.2 7.6 24 59-82 98-121 (122)
40 PRK10377 PTS system glucitol/s 58.2 14 0.00031 26.2 3.3 22 24-45 49-70 (120)
41 TIGR00849 gutA PTS system, glu 56.9 16 0.00034 26.1 3.3 21 25-45 50-70 (121)
42 PF10665 Minor_capsid_1: Minor 56.5 15 0.00033 25.8 3.2 27 23-49 73-99 (114)
43 PF05521 Phage_H_T_join: Phage 56.5 47 0.001 20.7 6.3 33 17-49 52-85 (95)
44 PRK07018 flgA flagellar basal 50.6 1.2E+02 0.0025 23.5 7.8 25 59-83 209-233 (235)
45 PRK11507 ribosome-associated p 50.5 18 0.00039 23.6 2.5 25 19-43 45-69 (70)
46 PRK12617 flgA flagellar basal 49.5 81 0.0018 24.4 6.5 26 59-84 188-213 (214)
47 PF02182 SAD_SRA: SAD/SRA doma 48.4 47 0.001 24.4 4.8 35 29-65 118-152 (155)
48 COG2501 S4-like RNA binding pr 48.3 22 0.00048 23.4 2.7 23 23-45 49-71 (73)
49 PF11871 DUF3391: Domain of un 47.6 11 0.00025 25.7 1.3 21 20-40 3-23 (128)
50 COG1326 Uncharacterized archae 46.4 27 0.00058 27.2 3.3 29 23-52 71-99 (201)
51 PF12690 BsuPI: Intracellular 44.4 69 0.0015 20.9 4.7 42 56-98 2-44 (82)
52 PF06605 Prophage_tail: Propha 43.9 44 0.00096 26.5 4.4 38 25-64 26-63 (327)
53 PRK06804 flgA flagellar basal 43.5 1.7E+02 0.0037 23.4 7.7 25 59-83 235-259 (261)
54 COG4043 Preprotein translocase 43.4 35 0.00077 24.1 3.3 21 25-45 32-54 (111)
55 cd01771 Faf1_UBX Faf1 UBX doma 42.3 33 0.00071 22.4 2.9 28 57-85 4-31 (80)
56 PRK13480 3'-5' exoribonuclease 42.3 82 0.0018 25.8 5.8 51 23-78 4-54 (314)
57 PF08408 DNA_pol_B_3: DNA poly 42.1 81 0.0018 23.5 5.2 25 24-48 37-61 (149)
58 PRK11835 hypothetical protein; 40.5 29 0.00064 24.7 2.5 32 25-61 66-98 (114)
59 cd04709 BAH_MTA BAH, or Bromo 39.0 59 0.0013 24.2 4.1 22 25-46 2-26 (164)
60 PF01079 Hint: Hint module; I 38.8 55 0.0012 25.4 4.1 70 8-83 13-87 (217)
61 cd06409 PB1_MUG70 The MUG70 pr 37.9 51 0.0011 22.2 3.3 48 60-108 3-61 (86)
62 PF07591 PT-HINT: Pretoxin HIN 37.6 42 0.00092 23.7 3.0 28 20-47 70-98 (130)
63 COG2351 Transthyretin-like pro 37.3 1.6E+02 0.0034 21.3 6.0 76 24-103 24-108 (124)
64 PF00436 SSB: Single-strand bi 37.2 83 0.0018 20.2 4.3 17 25-41 64-80 (104)
65 PF11948 DUF3465: Protein of u 37.0 55 0.0012 23.9 3.6 37 24-60 83-125 (131)
66 PRK10965 multicopper oxidase; 36.6 1.2E+02 0.0027 26.4 6.3 48 28-83 210-257 (523)
67 TIGR01397 fliM_switch flagella 36.1 75 0.0016 25.3 4.6 31 24-54 271-308 (320)
68 cd01767 UBX UBX (ubiquitin reg 35.6 30 0.00064 21.9 1.8 25 57-84 4-28 (77)
69 COG5131 URM1 Ubiquitin-like pr 35.5 26 0.00057 24.1 1.6 41 14-55 45-85 (96)
70 PF00467 KOW: KOW motif; Inte 34.3 61 0.0013 17.3 2.7 21 29-49 1-26 (32)
71 PRK10883 FtsI repressor; Provi 33.8 1.3E+02 0.0029 25.8 6.0 52 28-87 207-258 (471)
72 PF10844 DUF2577: Protein of u 33.3 94 0.002 20.9 4.1 24 21-44 71-98 (100)
73 cd04496 SSB_OBF SSB_OBF: A sub 32.7 80 0.0017 20.0 3.6 16 25-40 60-75 (100)
74 PF01079 Hint: Hint module; I 32.6 85 0.0018 24.3 4.2 29 20-48 99-133 (217)
75 PRK12786 flgA flagellar basal 32.4 2.9E+02 0.0063 22.8 7.7 26 59-84 291-316 (338)
76 COG1030 NfeD Membrane-bound se 32.4 1.1E+02 0.0024 26.5 5.2 31 22-52 383-414 (436)
77 KOG0267 Microtubule severing p 32.2 47 0.001 30.7 3.1 100 14-115 128-233 (825)
78 cd00603 IPT_PCSR IPT domain of 31.2 1.4E+02 0.003 18.8 6.8 33 12-44 11-46 (90)
79 PRK08515 flgA flagellar basal 29.9 2.6E+02 0.0056 21.5 7.5 24 59-83 198-221 (222)
80 KOG3514 Neurexin III-alpha [Si 29.9 1.2E+02 0.0026 29.8 5.3 62 34-101 494-563 (1591)
81 PRK06005 flgA flagellar basal 29.2 2.3E+02 0.0051 20.8 6.7 24 59-82 133-156 (160)
82 KOG1698 Mitochondrial/chloropl 28.9 2.1E+02 0.0046 22.3 5.8 51 23-77 93-152 (201)
83 PF06433 Me-amine-dh_H: Methyl 28.2 3.4E+02 0.0074 22.8 7.3 83 26-111 234-323 (342)
84 PRK12618 flgA flagellar basal 27.8 2.3E+02 0.0051 20.3 7.7 25 59-83 114-138 (141)
85 PLN02792 oxidoreductase 27.7 1.9E+02 0.0041 25.4 6.0 51 29-87 178-231 (536)
86 KOG0272 U4/U6 small nuclear ri 27.6 2E+02 0.0043 25.1 5.9 59 22-81 327-389 (459)
87 COG3731 SrlB Phosphotransferas 27.5 79 0.0017 22.8 3.0 27 20-46 45-71 (123)
88 smart00166 UBX Domain present 27.3 61 0.0013 20.5 2.3 26 56-84 5-30 (80)
89 TIGR01563 gp16_SPP1 phage head 27.1 1.7E+02 0.0038 18.6 6.1 32 11-42 47-81 (101)
90 PTZ00031 ribosomal protein L2; 27.0 2E+02 0.0044 23.9 5.7 60 19-83 133-215 (317)
91 PF13403 Hint_2: Hint domain 26.9 2.4E+02 0.0052 20.2 5.8 29 21-49 15-44 (147)
92 KOG4499 Ca2+-binding protein R 26.9 2.7E+02 0.0059 22.9 6.3 66 30-108 216-281 (310)
93 COG3721 HugX Putative heme iro 26.5 1.2E+02 0.0027 23.0 4.0 55 43-97 85-140 (176)
94 PF13989 YejG: YejG-like prote 25.9 64 0.0014 22.7 2.2 27 30-61 69-95 (106)
95 PRK11832 putative DNA-binding 25.7 36 0.00078 26.5 1.1 19 24-42 181-200 (207)
96 PF02559 CarD_CdnL_TRCF: CarD- 25.5 2E+02 0.0043 18.8 5.6 41 26-68 1-42 (98)
97 PF00924 MS_channel: Mechanose 25.3 61 0.0013 23.6 2.2 23 25-47 59-81 (206)
98 PF14623 Vint: Hint-domain 25.3 1.4E+02 0.0031 22.4 4.2 42 19-60 15-56 (162)
99 cd01773 Faf1_like1_UBX Faf1 ik 25.2 92 0.002 20.7 2.8 21 65-85 12-32 (82)
100 PRK08486 single-stranded DNA-b 25.1 1.2E+02 0.0026 22.9 3.8 16 25-40 65-80 (182)
101 cd01770 p47_UBX p47-like ubiqu 25.0 97 0.0021 20.0 2.9 26 58-84 5-30 (79)
102 PF07472 PA-IIL: Fucose-bindin 24.6 1.5E+02 0.0033 20.8 4.0 45 8-52 35-80 (107)
103 PF02839 CBM_5_12: Carbohydrat 24.4 95 0.002 17.1 2.5 18 28-45 11-28 (41)
104 PRK06788 flagellar motor switc 24.1 1.3E+02 0.0027 21.5 3.6 46 24-70 52-104 (119)
105 PRK07963 fliN flagellar motor 23.1 2.1E+02 0.0045 20.8 4.6 42 25-67 79-127 (137)
106 cd01179 IPT_plexin_repeat2 Sec 23.0 2.1E+02 0.0046 18.1 5.0 32 14-45 13-46 (85)
107 TIGR00621 ssb single stranded 22.8 1.4E+02 0.003 21.8 3.8 16 25-40 67-82 (164)
108 COG0335 RplS Ribosomal protein 22.4 3E+02 0.0065 19.7 8.2 62 24-87 18-88 (115)
109 CHL00052 rpl2 ribosomal protei 22.3 3.1E+02 0.0067 22.2 5.9 51 27-82 122-181 (273)
110 PRK13918 CRP/FNR family transc 21.9 1.8E+02 0.004 20.7 4.2 20 19-38 3-22 (202)
111 PRK06863 single-stranded DNA-b 21.8 1.3E+02 0.0028 22.5 3.4 15 26-40 69-83 (168)
112 PF15436 PGBA_N: Plasminogen-b 21.7 3.4E+02 0.0074 21.3 5.8 87 18-115 16-110 (218)
113 TIGR00307 S8e ribosomal protei 21.3 1.5E+02 0.0033 21.4 3.6 30 23-56 91-120 (127)
114 PRK09374 rplB 50S ribosomal pr 21.3 3.1E+02 0.0067 22.3 5.7 60 18-82 101-183 (276)
115 PLN02835 oxidoreductase 21.2 3.5E+02 0.0076 23.7 6.4 49 29-85 190-238 (539)
116 cd07297 PX_PLD2 The phosphoino 20.8 1.8E+02 0.0038 21.2 3.8 26 39-64 5-32 (130)
117 PRK05698 fliN flagellar motor 20.8 2.5E+02 0.0054 20.9 4.7 43 25-68 98-147 (155)
118 PF08838 DUF1811: Protein of u 20.7 1E+02 0.0022 21.6 2.4 31 19-49 47-77 (102)
119 COG1062 AdhC Zn-dependent alco 20.7 1.7E+02 0.0036 24.9 4.1 34 31-65 6-39 (366)
120 PF06938 DUF1285: Protein of u 20.6 1.8E+02 0.0039 21.3 3.9 23 32-55 47-69 (148)
121 cd03445 Thioesterase_II_repeat 20.4 2.6E+02 0.0057 18.2 4.8 36 38-74 39-74 (94)
122 cd01772 SAKS1_UBX SAKS1-like U 20.4 93 0.002 19.9 2.1 21 65-85 11-31 (79)
123 PF14014 DUF4230: Protein of u 20.1 1.3E+02 0.0028 21.1 3.0 57 56-114 48-112 (157)
No 1
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=3e-44 Score=266.70 Aligned_cols=112 Identities=85% Similarity=1.255 Sum_probs=109.5
Q ss_pred CCccccccccccCCCcceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCc
Q 033484 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (118)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ 80 (118)
|+|++|+|+ +++||++.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+|+++
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 899788999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecEEEeeeeEEEeccCCCeeEeecC--CChHHH
Q 033484 81 CDVPHVTRTDYQLIDISEDGFVCSYFV--LSCSFY 113 (118)
Q Consensus 81 ve~~~ve~~~~qyly~d~d~~l~FMd~--etyeq~ 113 (118)
+++|+|++++|||||+|+++||+|||+ +|||||
T Consensus 80 ve~~~ve~~~~qyly~dgd~y~~fMD~~get~eqi 114 (159)
T PLN03107 80 CDVPHVNRTDYQLIDISEDGFVSLMDESGNTKDDL 114 (159)
T ss_pred EEEEEEEEEEEEEEEEcCCceEEEEcCCCCcceeE
Confidence 999999999999999999998899999 699998
No 2
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=1.6e-39 Score=234.37 Aligned_cols=97 Identities=44% Similarity=0.671 Sum_probs=93.8
Q ss_pred cceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEe
Q 033484 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLID 95 (118)
Q Consensus 16 ~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly 95 (118)
++.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+|++++++|.|+++++||||
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 ccCCCeeEeecCCChHHH
Q 033484 96 ISEDGFVCSYFVLSCSFY 113 (118)
Q Consensus 96 ~d~d~~l~FMd~etyeq~ 113 (118)
+||+.| +|||+|||||+
T Consensus 81 ~dg~~~-~fMd~etyeq~ 97 (130)
T TIGR00037 81 IMGGMV-QLMDLDTYETD 97 (130)
T ss_pred ecCCEE-EEEcCCCcEEE
Confidence 988766 99999999997
No 3
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=6.2e-37 Score=228.17 Aligned_cols=111 Identities=48% Similarity=0.813 Sum_probs=107.1
Q ss_pred CCcccccccc-ccCCCcceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCC
Q 033484 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (118)
Q Consensus 1 ~~~~~~~~~~-~~~~~~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~ 79 (118)
|||++|+|+. +++|+++.|+|++++.||+|.+|+|+|+||+|++++++||||||+||+++.+.+||||+++|...|+++
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 8998889995 699999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecEEEeeeeEEEeccCC------CeeEeecCCChH
Q 033484 80 NCDVPHVTRTDYQLIDISED------GFVCSYFVLSCS 111 (118)
Q Consensus 80 ~ve~~~ve~~~~qyly~d~d------~~l~FMd~etye 111 (118)
++++|+|+|++||+|.+++| +|+.+||.++|+
T Consensus 81 nv~VP~V~r~~yqli~I~~d~~~~~~g~v~LMd~~g~~ 118 (166)
T PTZ00328 81 NVEVPFVKTFTYSVLDIQPNEDPSLPAHLSLMDDEGES 118 (166)
T ss_pred eeEeeeEEeeEEEEEEEcCCCcccccceEEEEcCCCCe
Confidence 99999999999999999887 799999998875
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=5e-36 Score=216.49 Aligned_cols=92 Identities=33% Similarity=0.405 Sum_probs=88.6
Q ss_pred eEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCC
Q 033484 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (118)
Q Consensus 20 ~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d 99 (118)
.++++++||+|++|+++|+||+|++++++|||| |+|++|+++|||+||+++|.+|+++++++.|.|+++++||||+||+
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGK-g~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~ 80 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGK-GGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGD 80 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCC-CCcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCC
Confidence 578999999999999999999999999999999 5569999999999999999999999999999999999999999998
Q ss_pred CeeEeecCCChHHH
Q 033484 100 GFVCSYFVLSCSFY 113 (118)
Q Consensus 100 ~~l~FMd~etyeq~ 113 (118)
.| +|||+||||||
T Consensus 81 ~~-~FMD~etyeq~ 93 (131)
T COG0231 81 FY-VFMDLETYEQY 93 (131)
T ss_pred eE-EEccCCCceEE
Confidence 87 99999999997
No 5
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=5.9e-36 Score=215.50 Aligned_cols=94 Identities=33% Similarity=0.580 Sum_probs=90.7
Q ss_pred eeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccC
Q 033484 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISE 98 (118)
Q Consensus 19 t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~ 98 (118)
-.|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+++++++.|.|+++++||||+||
T Consensus 3 ~~~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg 82 (129)
T PRK03999 3 KKQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMG 82 (129)
T ss_pred cccccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecC
Confidence 35899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeEeecCCChHHH
Q 033484 99 DGFVCSYFVLSCSFY 113 (118)
Q Consensus 99 d~~l~FMd~etyeq~ 113 (118)
+.| +|||+|||||+
T Consensus 83 ~~~-~fMd~eTyeq~ 96 (129)
T PRK03999 83 DVV-QLMDLETYETF 96 (129)
T ss_pred CEE-EEecCCCceEE
Confidence 665 99999999997
No 6
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=1.1e-34 Score=219.99 Aligned_cols=91 Identities=12% Similarity=0.039 Sum_probs=88.5
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCCC
Q 033484 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d~ 100 (118)
++++++||+|++|+++|+||.|++++|+|||| |+|++|+|+|||.||+++|+||+++++++.+.|+++++||||.||+.
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~~ 79 (185)
T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPK-GETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDE 79 (185)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEecCCC-CceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEECCCe
Confidence 36799999999999999999999999999999 99999999999999999999999999999999999999999999988
Q ss_pred eeEeecCCChHHH
Q 033484 101 FVCSYFVLSCSFY 113 (118)
Q Consensus 101 ~l~FMd~etyeq~ 113 (118)
| +|||+||||||
T Consensus 80 ~-~FMd~etyeQi 91 (185)
T PRK12426 80 Y-LFLDLGNYDKI 91 (185)
T ss_pred E-EEecCCCceEE
Confidence 7 99999999998
No 7
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=2.6e-33 Score=212.75 Aligned_cols=92 Identities=14% Similarity=0.193 Sum_probs=87.6
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCC-cccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCC
Q 033484 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKh-G~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d 99 (118)
++++++||+|++|+++|+||+|++++|+||||+ |+|++|+|+|||.||+++|+||++++++|.|.|+++++||||.||+
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 367999999999999999999999999999985 4679999999999999999999999999999999999999999998
Q ss_pred CeeEeecCCChHHH
Q 033484 100 GFVCSYFVLSCSFY 113 (118)
Q Consensus 100 ~~l~FMd~etyeq~ 113 (118)
.| +|||+||||||
T Consensus 81 ~~-~FMD~etyEQ~ 93 (187)
T PRK14578 81 RG-VFMDLETYEQF 93 (187)
T ss_pred EE-EEecCCCcEEE
Confidence 87 99999999998
No 8
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=2.7e-33 Score=212.89 Aligned_cols=92 Identities=18% Similarity=0.200 Sum_probs=87.7
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecC-CCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCC
Q 033484 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~P~~Vve~~~~kp-GKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d 99 (118)
++++++||+|++|+++|+||+|++++|+|| ||+|+|++|+|+|||.||+++++||+|++++|.+.|++++|||||.||+
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 7944669999999999999999999999999999999999999999998
Q ss_pred CeeEeecCCChHHH
Q 033484 100 GFVCSYFVLSCSFY 113 (118)
Q Consensus 100 ~~l~FMd~etyeq~ 113 (118)
.| +|||++|||||
T Consensus 81 ~~-~FMd~etyEQ~ 93 (189)
T PRK04542 81 EY-VFMDNEDYTPY 93 (189)
T ss_pred EE-EEecCCCceEE
Confidence 87 99999999998
No 9
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=1e-32 Score=201.10 Aligned_cols=108 Identities=67% Similarity=1.022 Sum_probs=104.9
Q ss_pred CCccccccccccCCCcceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCc
Q 033484 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (118)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ 80 (118)
|||++|+|+ .++||++.|||++++.|||+.+|.++|+||+|+|.+++|+||||+|++++..++||||+++|..++|.++
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 eeecEEEeeeeEEEeccCCCeeEeecCCCh
Q 033484 81 CDVPHVTRTDYQLIDISEDGFVCSYFVLSC 110 (118)
Q Consensus 81 ve~~~ve~~~~qyly~d~d~~l~FMd~ety 110 (118)
+++|+++|++||++.++++ |+.||+.+.+
T Consensus 80 ~dVp~vkr~~yqLidIsd~-~~sl~t~sG~ 108 (156)
T KOG3271|consen 80 MDVPVVKRVDYQLIDISDG-YLSLMTDSGE 108 (156)
T ss_pred cccCccccceeEEEEecCC-eEEEEcCCCC
Confidence 9999999999999999774 9999998763
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=99.98 E-value=4.6e-32 Score=205.75 Aligned_cols=89 Identities=15% Similarity=0.216 Sum_probs=85.0
Q ss_pred cccccCceEEEECCeeEEEEEeeEecCCCCccc-EEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCCCee
Q 033484 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFV 102 (118)
Q Consensus 24 ~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A-~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d~~l 102 (118)
+++||+|++|+++|+||+|++++|+|||+.|+| ++|+|+|||.||+++++||+|+|++|.|.|+++++||||.||+.|
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 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEY- 80 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCeE-
Confidence 789999999999999999999999999884555 899999999999999999999999999999999999999999887
Q ss_pred EeecCCChHHH
Q 033484 103 CSYFVLSCSFY 113 (118)
Q Consensus 103 ~FMd~etyeq~ 113 (118)
+|||+||||||
T Consensus 81 ~FMD~etyEQ~ 91 (186)
T TIGR02178 81 VFMDEEDYTPY 91 (186)
T ss_pred EEccCCCcEEE
Confidence 99999999998
No 11
>PRK00529 elongation factor P; Validated
Probab=99.97 E-value=1.1e-31 Score=203.17 Aligned_cols=91 Identities=23% Similarity=0.282 Sum_probs=88.2
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCCC
Q 033484 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d~ 100 (118)
++++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++.+|+++++++.|.++++++||||.|++.
T Consensus 1 ~~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dgd~ 79 (186)
T PRK00529 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGK-GQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDG 79 (186)
T ss_pred CcchhhcCCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECCCE
Confidence 36899999999999999999999999999999 99999999999999999999999999999999999999999999987
Q ss_pred eeEeecCCChHHH
Q 033484 101 FVCSYFVLSCSFY 113 (118)
Q Consensus 101 ~l~FMd~etyeq~ 113 (118)
+ +|||+||||||
T Consensus 80 ~-~fMD~etyeq~ 91 (186)
T PRK00529 80 Y-VFMDTETYEQI 91 (186)
T ss_pred E-EEecCCCceee
Confidence 6 99999999997
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=99.97 E-value=1.9e-31 Score=201.59 Aligned_cols=90 Identities=23% Similarity=0.286 Sum_probs=87.4
Q ss_pred EecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCCCe
Q 033484 22 QQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGF 101 (118)
Q Consensus 22 i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d~~ 101 (118)
+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++++|+++++++.|.++++++||||.|++.+
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dgd~~ 79 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGK-GQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSY 79 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECCCEE
Confidence 4689999999999999999999999999999 999999999999999999999999999999999999999999999876
Q ss_pred eEeecCCChHHH
Q 033484 102 VCSYFVLSCSFY 113 (118)
Q Consensus 102 l~FMd~etyeq~ 113 (118)
+|||+||||||
T Consensus 80 -~fMD~etyeq~ 90 (184)
T TIGR00038 80 -VFMDTETYEQI 90 (184)
T ss_pred -EEeCCCCccce
Confidence 99999999997
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=3.5e-22 Score=126.00 Aligned_cols=58 Identities=29% Similarity=0.379 Sum_probs=53.5
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCce
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~v 81 (118)
+|++||+|++|+++|+||+|++++|++||| |+|++|+++|||.||+++|.+|+++|++
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 9999999999999999999999999986
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=98.88 E-value=7.8e-10 Score=68.85 Aligned_cols=26 Identities=12% Similarity=0.032 Sum_probs=21.8
Q ss_pred eeeeEEEeccCCCeeEeecCCChHHHh
Q 033484 88 RTDYQLIDISEDGFVCSYFVLSCSFYL 114 (118)
Q Consensus 88 ~~~~qyly~d~d~~l~FMd~etyeq~~ 114 (118)
+|++||||.||+++ +|||++|||||.
T Consensus 1 ~r~~qylY~dgd~~-~FMd~etyeQi~ 26 (55)
T PF01132_consen 1 RREMQYLYKDGDNY-VFMDTETYEQIE 26 (55)
T ss_dssp EEEEEEEEEESSEE-EEEETTT--EEE
T ss_pred CceEEEEEeCCCEE-EEecCCCceEEE
Confidence 68999999999886 999999999973
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=98.86 E-value=7.8e-10 Score=70.23 Aligned_cols=26 Identities=8% Similarity=0.011 Sum_probs=24.0
Q ss_pred EeeeeEEEeccCCCeeEeecCCChHHH
Q 033484 87 TRTDYQLIDISEDGFVCSYFVLSCSFY 113 (118)
Q Consensus 87 e~~~~qyly~d~d~~l~FMd~etyeq~ 113 (118)
+++++||||.||+.| +|||++|||||
T Consensus 1 e~~~~qylY~dg~~~-~FMd~etyeQ~ 26 (61)
T cd04470 1 EEREMQYLYKDGDNY-VFMDTETYEQI 26 (61)
T ss_pred CCceEEEEEeCCCEE-EEeCCCCceEE
Confidence 478999999999887 89999999997
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=98.58 E-value=1.9e-08 Score=61.92 Aligned_cols=24 Identities=13% Similarity=0.134 Sum_probs=21.8
Q ss_pred eeeEEEeccCCCeeEeecCCChHHH
Q 033484 89 TDYQLIDISEDGFVCSYFVLSCSFY 113 (118)
Q Consensus 89 ~~~qyly~d~d~~l~FMd~etyeq~ 113 (118)
|++||||.||+.+ +|||+|||||+
T Consensus 1 ~~~qylY~dg~~~-~fMd~etyeq~ 24 (55)
T cd04463 1 RELQVLDIQGSKP-VTMDLETYEVV 24 (55)
T ss_pred CCEEEEEcCCCEe-EEecCCCceEE
Confidence 5799999999776 99999999997
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=97.23 E-value=0.00038 Score=45.32 Aligned_cols=27 Identities=41% Similarity=0.529 Sum_probs=23.3
Q ss_pred EEEeeeeEEEeccCCCeeEeecCCChHH
Q 033484 85 HVTRTDYQLIDISEDGFVCSYFVLSCSF 112 (118)
Q Consensus 85 ~ve~~~~qyly~d~d~~l~FMd~etyeq 112 (118)
+|+|++||.+.+++|+|+.+|| ++||.
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMd-e~get 27 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMD-EDGET 27 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEE-TTS-E
T ss_pred CeEEEEEEEEEEccCcEEEEEc-CCCCe
Confidence 4799999999999999999999 88875
No 18
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=96.75 E-value=0.0071 Score=50.36 Aligned_cols=92 Identities=13% Similarity=0.101 Sum_probs=66.7
Q ss_pred ccCCCcceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCcee--ecEEE-
Q 033484 11 KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD--VPHVT- 87 (118)
Q Consensus 11 ~~~~~~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve--~~~ve- 87 (118)
+|-.-.-.|+-+..-++++|++|.++|..+.++.. -|+ .+.++++.|++..+.++.....-+ .+.-+
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 34444567899999999999999999966665533 256 388999999988887775433333 22222
Q ss_pred -eeeeEEEeccCCCeeEeecCCChHHH
Q 033484 88 -RTDYQLIDISEDGFVCSYFVLSCSFY 113 (118)
Q Consensus 88 -~~~~qyly~d~d~~l~FMd~etyeq~ 113 (118)
-+.+.++..+.+.. .+||++|||-+
T Consensus 301 ~~~~~~vvs~~~~~~-~v~d~et~e~~ 326 (355)
T COG1499 301 RLKKAVVVSRDPSAI-QVLDPETYEAR 326 (355)
T ss_pred cceEEEEEecCCCce-EEEecceEEEE
Confidence 25788888888766 89999999854
No 19
>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=96.02 E-value=0.0048 Score=38.91 Aligned_cols=27 Identities=15% Similarity=0.111 Sum_probs=23.5
Q ss_pred EEeeeeEEEeccCCCeeEeecCCChHHH
Q 033484 86 VTRTDYQLIDISEDGFVCSYFVLSCSFY 113 (118)
Q Consensus 86 ve~~~~qyly~d~d~~l~FMd~etyeq~ 113 (118)
|+||..|.++.+|+.. -+||+||||-+
T Consensus 1 i~k~~aqVisi~g~~v-QlMD~eTYeT~ 27 (57)
T cd04467 1 IERKTGQVLSIMGDVV-QLMDLETYETF 27 (57)
T ss_pred CcceEEEEEEEcCCEE-EEeccccceeE
Confidence 5899999999999765 89999999843
No 20
>cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=93.65 E-value=0.064 Score=34.97 Aligned_cols=22 Identities=50% Similarity=0.691 Sum_probs=19.0
Q ss_pred EEeeeeEEEeccCCCeeEeecCC
Q 033484 86 VTRTDYQLIDISEDGFVCSYFVL 108 (118)
Q Consensus 86 ve~~~~qyly~d~d~~l~FMd~e 108 (118)
|.|++||++.+++ +|+.+|+.+
T Consensus 1 V~R~eYqLidI~d-GflsLm~e~ 22 (69)
T cd04468 1 VKRTEYQLIDIDD-GFLSLMDDD 22 (69)
T ss_pred CcceeEEEEeecC-CeEEEEcCC
Confidence 4689999999977 999999853
No 21
>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=86.10 E-value=0.91 Score=30.03 Aligned_cols=20 Identities=25% Similarity=0.488 Sum_probs=16.8
Q ss_pred eeeeEEEeccCCCeeEeecCC
Q 033484 88 RTDYQLIDISEDGFVCSYFVL 108 (118)
Q Consensus 88 ~~~~qyly~d~d~~l~FMd~e 108 (118)
.++||++.+ +|+|+.+||.+
T Consensus 2 ~~eYqLidI-~DG~lsLM~e~ 21 (75)
T cd04469 2 FKQYRVLDI-QDGSIVAMTET 21 (75)
T ss_pred ceEEEEEEe-cCCeEEEEcCC
Confidence 368999999 67999999853
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=79.76 E-value=5.9 Score=28.67 Aligned_cols=51 Identities=16% Similarity=0.123 Sum_probs=36.5
Q ss_pred cccccCCCcceeeEEecccccCceEEEECCe--eEEEEEeeEec--CC-----CCcccEEEE
Q 033484 8 FESKADAGASKTFPQQAGTIRKNGYIVIKGR--PCKVVEVSTSK--TG-----KHGHAKCHF 60 (118)
Q Consensus 8 ~~~~~~~~~~~t~~i~~~~lkkG~~i~i~g~--P~~Vve~~~~k--pG-----KhG~A~vri 60 (118)
|+ ++. ......-+..=|||.|+.|.+++. +|.|+-+++.- +. -+|.+.|.+
T Consensus 43 Fe-dg~-~~i~~~dv~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~L 102 (131)
T PF08605_consen 43 FE-DGT-YEIKNEDVKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYL 102 (131)
T ss_pred Ee-cCc-eEeCcccEeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEE
Confidence 66 333 555555677789999999999998 89999988762 22 126666665
No 23
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=74.55 E-value=16 Score=29.70 Aligned_cols=55 Identities=22% Similarity=0.308 Sum_probs=36.2
Q ss_pred cccccCceEEEECCee--EEEEEeeEecCCCCcc------cEEEEEEEEccCCcEEEEEecCCCcee
Q 033484 24 AGTIRKNGYIVIKGRP--CKVVEVSTSKTGKHGH------AKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (118)
Q Consensus 24 ~~~lkkG~~i~i~g~P--~~Vve~~~~kpGKhG~------A~vrik~knl~TG~~~e~t~~s~~~ve 82 (118)
..+|+.|+++-+...| -.|-.++. +||++|+ +.+++..++ |...-..++|++.-.
T Consensus 121 ~a~ik~GN~lpL~~IP~Gt~VhNVE~-~pG~GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~r~ 183 (275)
T COG0090 121 DADIKPGNALPLGNIPEGTIVHNVEL-KPGDGGQLARSAGTYAQVVGKE---GNYVIVRLPSGEMRK 183 (275)
T ss_pred CCCcCCcceeeeccCCCCceEEeeee-ccCCCceEEEeCCceEEEEEcc---CCEEEEECCCCCeEe
Confidence 4467777777776665 23444443 8999542 566777777 667778888887654
No 24
>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=73.91 E-value=19 Score=25.39 Aligned_cols=66 Identities=15% Similarity=0.212 Sum_probs=40.6
Q ss_pred EecccccCceEEEE-----CCeeEEEEEeeEe---cCCCCcccEEEEEEEEccCCcEEEEEecCCC-ceeecEEEee
Q 033484 22 QQAGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH-NCDVPHVTRT 89 (118)
Q Consensus 22 i~~~~lkkG~~i~i-----~g~P~~Vve~~~~---kpGKhG~A~vrik~knl~TG~~~e~t~~s~~-~ve~~~ve~~ 89 (118)
.+..++++|++|.+ +|....+-.++-. +-++ | .-..+.++|++.|.-+|.+|+-.. .++.+.|-++
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~-g-~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~ 88 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR-G-LNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRR 88 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS-S-TSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEE
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC-C-CCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEe
Confidence 56778999998876 4544443322211 1122 2 122578999999999999998654 3444444443
No 25
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=68.75 E-value=29 Score=24.70 Aligned_cols=54 Identities=19% Similarity=0.314 Sum_probs=36.3
Q ss_pred EecccccCceEEEE-----CCeeEEE-----EEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCC
Q 033484 22 QQAGTIRKNGYIVI-----KGRPCKV-----VEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (118)
Q Consensus 22 i~~~~lkkG~~i~i-----~g~P~~V-----ve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~ 79 (118)
....++++|+.|.+ +|....+ +-+... ++ | .--.+.+|++..|.-.|.+|+-..
T Consensus 14 ~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~--~~-G-~~~tftvRki~~gvGVEr~fpl~S 77 (116)
T PRK05338 14 KDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARR--GR-G-LNETFTVRKISYGVGVERTFPLHS 77 (116)
T ss_pred cCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEe--CC-C-CCceEEEEEcccCccEEEEecCCC
Confidence 34778999998876 5654333 223332 33 3 223589999999999999998643
No 26
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=66.19 E-value=8 Score=24.77 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=15.0
Q ss_pred EEecccccCceEEEECCeeEEEE
Q 033484 21 PQQAGTIRKNGYIVIKGRPCKVV 43 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i~g~P~~Vv 43 (118)
.-....|++|++|.++|..++|+
T Consensus 43 ~rrg~Kl~~GD~V~~~~~~~~Vv 65 (65)
T PF13275_consen 43 TRRGKKLRPGDVVEIDGEEYRVV 65 (65)
T ss_dssp --SS----SSEEEEETTEEEEEE
T ss_pred cccCCcCCCCCEEEECCEEEEEC
Confidence 33456799999999999999885
No 27
>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=66.07 E-value=33 Score=24.26 Aligned_cols=53 Identities=21% Similarity=0.315 Sum_probs=35.4
Q ss_pred EecccccCceEEEE-----CCeeEEE-----EEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCC
Q 033484 22 QQAGTIRKNGYIVI-----KGRPCKV-----VEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS 78 (118)
Q Consensus 22 i~~~~lkkG~~i~i-----~g~P~~V-----ve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~ 78 (118)
.+..++++|+.|.+ +|+...+ +-+... ++ |- --.+.+||+..|.-.|.+|+-.
T Consensus 14 ~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~--~~-G~-~~tftvR~i~~gvGVEr~fpl~ 76 (113)
T TIGR01024 14 KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARR--GG-GI-GETFTVRKISYGVGVERIFPLH 76 (113)
T ss_pred cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEe--CC-CC-ceEEEEEEeccCccEEEEEEcC
Confidence 45778999998877 4433332 222222 33 32 2358999999999999999854
No 28
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=64.01 E-value=6.2 Score=27.20 Aligned_cols=27 Identities=15% Similarity=0.173 Sum_probs=24.2
Q ss_pred eEEecccccCceEEEECCeeEEEEEee
Q 033484 20 FPQQAGTIRKNGYIVIKGRPCKVVEVS 46 (118)
Q Consensus 20 ~~i~~~~lkkG~~i~i~g~P~~Vve~~ 46 (118)
...+..||..|..|.+.|.++.|+++.
T Consensus 67 ~~y~~~Dl~vG~~v~i~gr~f~I~d~D 93 (104)
T smart00676 67 EYYHASDLNVGTTINVFGRQFRIYDCD 93 (104)
T ss_pred CccCHHHcCCCCEEEEeCEEEEEEECC
Confidence 457788999999999999999999974
No 29
>PF13144 SAF_2: SAF-like
Probab=62.96 E-value=59 Score=23.95 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=19.9
Q ss_pred EEEEEEccCCcEEEEEecCCCcee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve 82 (118)
.++++|+.||+.+.-+.-+...++
T Consensus 172 ~I~V~N~~S~k~v~g~V~~~~~V~ 195 (196)
T PF13144_consen 172 TIRVKNLSSGKIVQGRVIGPGTVE 195 (196)
T ss_pred EEEEEECCCCCEEEEEEecCCEEE
Confidence 488999999999988887776665
No 30
>CHL00084 rpl19 ribosomal protein L19
Probab=62.36 E-value=42 Score=23.90 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=35.9
Q ss_pred EecccccCceEEEE-----CCe-----eEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCC
Q 033484 22 QQAGTIRKNGYIVI-----KGR-----PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS 78 (118)
Q Consensus 22 i~~~~lkkG~~i~i-----~g~-----P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~ 78 (118)
....++++|+.|.+ +|. ++.=+-+... |+ |-. -.+.+|++..|.-+|.+|+-.
T Consensus 18 ~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r--~~-G~~-~tftvRki~~gvGVEr~fpl~ 80 (117)
T CHL00084 18 KNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKK--NS-GLN-TTITVRKVFQGIGVERVFLLH 80 (117)
T ss_pred cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEe--CC-CCC-eeEEEEEeccCccEEEEEecC
Confidence 46778999998876 454 2322223322 44 332 258999999999999999854
No 31
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=62.00 E-value=29 Score=22.98 Aligned_cols=44 Identities=9% Similarity=0.212 Sum_probs=29.9
Q ss_pred cccCceEEEECCee------------EEEEEeeEecCCCCcccEEEEEEEEccCCcEE
Q 033484 26 TIRKNGYIVIKGRP------------CKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKL 71 (118)
Q Consensus 26 ~lkkG~~i~i~g~P------------~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~ 71 (118)
.+|.|++|++...+ ..|+.++-. +|...+---+..-|+-||.+.
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 57999999997766 556655432 232334445788899999865
No 32
>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=61.73 E-value=42 Score=27.04 Aligned_cols=85 Identities=20% Similarity=0.259 Sum_probs=47.4
Q ss_pred eeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEE-EecCCCcee-ecEEEeeeeEEEe
Q 033484 18 KTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLED-IVPSSHNCD-VPHVTRTDYQLID 95 (118)
Q Consensus 18 ~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~-t~~s~~~ve-~~~ve~~~~qyly 95 (118)
.++|-..+.+..|-.+.-+|..|. .+|..|++. ++-.|+.||+.... .++..--=| ...+..+=+|+.+
T Consensus 37 ~~ypHd~~aFTQGL~~~~~g~LyE-------STG~yG~S~--l~~~d~~tg~~~~~~~l~~~~FgEGit~~~d~l~qLTW 107 (264)
T PF05096_consen 37 ETYPHDPTAFTQGLEFLDDGTLYE-------STGLYGQSS--LRKVDLETGKVLQSVPLPPRYFGEGITILGDKLYQLTW 107 (264)
T ss_dssp EEEE--TT-EEEEEEEEETTEEEE-------EECSTTEEE--EEEEETTTSSEEEEEE-TTT--EEEEEEETTEEEEEES
T ss_pred EECCCCCcccCccEEecCCCEEEE-------eCCCCCcEE--EEEEECCCCcEEEEEECCccccceeEEEECCEEEEEEe
Confidence 467777888888888778887762 236667664 55678999987754 344322222 2334445555555
Q ss_pred ccCCCeeEeecCCChHHH
Q 033484 96 ISEDGFVCSYFVLSCSFY 113 (118)
Q Consensus 96 ~d~d~~l~FMd~etyeq~ 113 (118)
.++-.| .-|.+|++++
T Consensus 108 k~~~~f--~yd~~tl~~~ 123 (264)
T PF05096_consen 108 KEGTGF--VYDPNTLKKI 123 (264)
T ss_dssp SSSEEE--EEETTTTEEE
T ss_pred cCCeEE--EEccccceEE
Confidence 555332 4455555443
No 33
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=61.44 E-value=9.1 Score=26.64 Aligned_cols=22 Identities=14% Similarity=0.126 Sum_probs=18.5
Q ss_pred ccCceEEEECCeeEEEEEeeEe
Q 033484 27 IRKNGYIVIKGRPCKVVEVSTS 48 (118)
Q Consensus 27 lkkG~~i~i~g~P~~Vve~~~~ 48 (118)
|++|+.+.++|.+|.|+-...-
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~ 22 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQY 22 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEE
Confidence 6899999999999999765443
No 34
>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=61.14 E-value=32 Score=25.51 Aligned_cols=37 Identities=19% Similarity=0.259 Sum_probs=27.5
Q ss_pred ccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 033484 27 IRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (118)
Q Consensus 27 lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl 65 (118)
-+++..+.+|| +|+|+++-. .+|++|....|.+|+.+
T Consensus 116 ~~p~~gyrYDG-LY~V~~~w~-e~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 116 YAPGKGYIYDG-LYRIVDYWR-EVGKSGFLVFKFKLVRI 152 (155)
T ss_pred CCCCCeEEECc-EEEEEEEEE-ecCCCCcEEEEEEEEeC
Confidence 45666777765 899998843 45777888889998865
No 35
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=59.75 E-value=14 Score=24.35 Aligned_cols=27 Identities=15% Similarity=0.148 Sum_probs=23.5
Q ss_pred ceeeEEecccccCceEEEECCeeEEEE
Q 033484 17 SKTFPQQAGTIRKNGYIVIKGRPCKVV 43 (118)
Q Consensus 17 ~~t~~i~~~~lkkG~~i~i~g~P~~Vv 43 (118)
..|.+++-..+.+|+.|.++|+-|..-
T Consensus 6 yGT~~v~Rq~V~PG~~v~~~grty~AS 32 (73)
T PRK11354 6 FGTDEIPRQCVTPGDYVLHEGRTYIAS 32 (73)
T ss_pred cCceeecccccCCceEEEEcCcEEEEE
Confidence 358889999999999999999999654
No 36
>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=59.68 E-value=9 Score=27.44 Aligned_cols=42 Identities=10% Similarity=0.091 Sum_probs=25.7
Q ss_pred CcceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEE
Q 033484 15 GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCH 59 (118)
Q Consensus 15 ~~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vr 59 (118)
.+-..+...+..||+++.|.+.|++|.|.+ ..|--+|...+.
T Consensus 63 Pslfv~t~dv~~L~r~DtL~I~g~~y~Vd~---v~pD~~G~t~I~ 104 (117)
T PF05354_consen 63 PSLFVRTADVSGLKRRDTLTIGGESYWVDR---VGPDGGGSTRIW 104 (117)
T ss_dssp -EEEESCCCCCTS-TT-EEEETTTEEEBS------SSSSS-CCEE
T ss_pred ceEEEEehHhhhhhcCCeEEECCEEEEEEe---eccCCCccEEEE
Confidence 334455667889999999999999999964 456334655443
No 37
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=59.62 E-value=46 Score=22.03 Aligned_cols=38 Identities=18% Similarity=0.276 Sum_probs=22.3
Q ss_pred cCCCcceeeEEecccc---cCceEEEECCeeEEEEEeeEec
Q 033484 12 ADAGASKTFPQQAGTI---RKNGYIVIKGRPCKVVEVSTSK 49 (118)
Q Consensus 12 ~~~~~~~t~~i~~~~l---kkG~~i~i~g~P~~Vve~~~~k 49 (118)
+-+++..+-.+..+++ ++|+.|.++|+-|.|.++..--
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 4455566666666665 5899999999999999887653
No 38
>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=59.53 E-value=12 Score=26.42 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=16.1
Q ss_pred ecccccCceEEEECCeeEEEEEe
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEV 45 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~ 45 (118)
...+|++|+.+.++++.|.|..+
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 46789999999999999999875
No 39
>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=58.42 E-value=56 Score=22.21 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=19.1
Q ss_pred EEEEEEccCCcEEEEEecCCCcee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve 82 (118)
.++.+|+.||+++.-+..+...++
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 488999999999988877666554
No 40
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=58.17 E-value=14 Score=26.25 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=19.7
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 033484 24 AGTIRKNGYIVIKGRPCKVVEV 45 (118)
Q Consensus 24 ~~~lkkG~~i~i~g~P~~Vve~ 45 (118)
..+|++|+.+.++|+-|.|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAV 70 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEE
Confidence 5679999999999999999875
No 41
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=56.87 E-value=16 Score=26.12 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=19.0
Q ss_pred ccccCceEEEECCeeEEEEEe
Q 033484 25 GTIRKNGYIVIKGRPCKVVEV 45 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~~Vve~ 45 (118)
.+|++|+.+.++|+-|.|..+
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaV 70 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAV 70 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEE
Confidence 479999999999999999875
No 42
>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=56.53 E-value=15 Score=25.78 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=23.1
Q ss_pred ecccccCceEEEECCeeEEEEEeeEec
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~~~~k 49 (118)
++-++++|+.|.++|..|.|.++...-
T Consensus 73 p~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 73 PFPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred cccccCCCCEEEECCceEEEEEEEecc
Confidence 345888999999999999999987764
No 43
>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=56.48 E-value=47 Score=20.72 Aligned_cols=33 Identities=12% Similarity=0.221 Sum_probs=22.3
Q ss_pred ceeeEEecc-cccCceEEEECCeeEEEEEeeEec
Q 033484 17 SKTFPQQAG-TIRKNGYIVIKGRPCKVVEVSTSK 49 (118)
Q Consensus 17 ~~t~~i~~~-~lkkG~~i~i~g~P~~Vve~~~~k 49 (118)
...+.+.-. +|..++.|.++|..|.|..+....
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 444555544 599999999999999999876654
No 44
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=50.61 E-value=1.2e+02 Score=23.51 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=21.4
Q ss_pred EEEEEEccCCcEEEEEecCCCceee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve~ 83 (118)
.++.||+.||+++.-+..+...+++
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V 233 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEV 233 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEE
Confidence 4888999999999998888877765
No 45
>PRK11507 ribosome-associated protein; Provisional
Probab=50.53 E-value=18 Score=23.59 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=19.9
Q ss_pred eeEEecccccCceEEEECCeeEEEE
Q 033484 19 TFPQQAGTIRKNGYIVIKGRPCKVV 43 (118)
Q Consensus 19 t~~i~~~~lkkG~~i~i~g~P~~Vv 43 (118)
...-..-.|++|+.|.++|.-++|+
T Consensus 45 ve~rRgkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 45 VETRKRCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred EecccCCCCCCCCEEEECCEEEEEe
Confidence 3444567899999999999988875
No 46
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=49.54 E-value=81 Score=24.44 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=22.2
Q ss_pred EEEEEEccCCcEEEEEecCCCceeec
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve~~ 84 (118)
.++.||+.+|++++-+..+...+++.
T Consensus 188 ~IrVrN~~SgrvV~g~V~~~G~V~V~ 213 (214)
T PRK12617 188 RVSVENSSSRRVVQGIVEASGTVVVS 213 (214)
T ss_pred EEEEEECCCCCEEEEEEeCCcEEEEe
Confidence 58999999999999998888777653
No 47
>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=48.38 E-value=47 Score=24.38 Aligned_cols=35 Identities=31% Similarity=0.389 Sum_probs=25.1
Q ss_pred CceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 033484 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (118)
Q Consensus 29 kG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl 65 (118)
++..+.+|| +|+|+++...+ |+.|...++++|+-+
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 344568887 99999987755 555888999998865
No 48
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=48.34 E-value=22 Score=23.39 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=19.5
Q ss_pred ecccccCceEEEECCeeEEEEEe
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEV 45 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~ 45 (118)
..-.||.|+.|.+.|.++.|...
T Consensus 49 RgkKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 49 RGKKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred cCCEeecCCEEEECCEEEEEEec
Confidence 35679999999999999998753
No 49
>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=47.56 E-value=11 Score=25.66 Aligned_cols=21 Identities=10% Similarity=0.091 Sum_probs=16.3
Q ss_pred eEEecccccCceEEEECCeeE
Q 033484 20 FPQQAGTIRKNGYIVIKGRPC 40 (118)
Q Consensus 20 ~~i~~~~lkkG~~i~i~g~P~ 40 (118)
..|++++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 368999999999987754444
No 50
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=46.37 E-value=27 Score=27.21 Aligned_cols=29 Identities=17% Similarity=0.345 Sum_probs=24.4
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCC
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGK 52 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~~~~kpGK 52 (118)
+.-.|++|+.|+++|+-..|++++. ++||
T Consensus 71 ~gE~l~vGDei~vd~e~veITSIE~-~~gk 99 (201)
T COG1326 71 PGETLKVGDEIEVDGEEVEITSIEL-GGGK 99 (201)
T ss_pred CCCeEecCCEEEEcCCEEEEEEEee-CCCc
Confidence 3456899999999999999999986 4566
No 51
>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=44.37 E-value=69 Score=20.94 Aligned_cols=42 Identities=7% Similarity=-0.097 Sum_probs=24.8
Q ss_pred cEEEEEEEEccCCcEEEEEecCCCceeecEE-EeeeeEEEeccC
Q 033484 56 AKCHFVGIDIFNGKKLEDIVPSSHNCDVPHV-TRTDYQLIDISE 98 (118)
Q Consensus 56 A~vrik~knl~TG~~~e~t~~s~~~ve~~~v-e~~~~qyly~d~ 98 (118)
..+.++++|.-+.. ++.+|+|+.+.|.... ..-+-.|-|.++
T Consensus 2 v~~~l~v~N~s~~~-v~l~f~sgq~~D~~v~d~~g~~vwrwS~~ 44 (82)
T PF12690_consen 2 VEFTLTVTNNSDEP-VTLQFPSGQRYDFVVKDKEGKEVWRWSDG 44 (82)
T ss_dssp EEEEEEEEE-SSS--EEEEESSS--EEEEEE-TT--EEEETTTT
T ss_pred EEEEEEEEeCCCCe-EEEEeCCCCEEEEEEECCCCCEEEEecCC
Confidence 34677888875544 7799999999998887 344444445444
No 52
>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=43.87 E-value=44 Score=26.52 Aligned_cols=38 Identities=16% Similarity=0.297 Sum_probs=22.8
Q ss_pred ccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEE
Q 033484 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~kn 64 (118)
.-|.++..|..+|+.|+|..++...-|. +. .+.+.+++
T Consensus 26 ~~i~~~~~I~~~~q~y~I~~~~~~~~~~-~~-~~~V~a~h 63 (327)
T PF06605_consen 26 DLIKEENIITYDGQEYRIKQVEKSRDGN-TI-TITVTAEH 63 (327)
T ss_dssp --SSTT-EEEETTEEEE--EE--B------E-EEEEEEEB
T ss_pred HhcCcCCEEEECCeEEEEEEeEEecCCC-EE-EEEEEEEe
Confidence 5688999999999999999888765554 33 37899999
No 53
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=43.55 E-value=1.7e+02 Score=23.39 Aligned_cols=25 Identities=12% Similarity=0.122 Sum_probs=21.0
Q ss_pred EEEEEEccCCcEEEEEecCCCceee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve~ 83 (118)
.|+.||+.+|+++.-+..+...|++
T Consensus 235 ~IrVrN~~SgkvV~a~V~~~g~V~v 259 (261)
T PRK06804 235 LIKVKNLSSGRVVTATVDGSGRVRM 259 (261)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEE
Confidence 5888999999999988888777753
No 54
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.39 E-value=35 Score=24.08 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=15.2
Q ss_pred ccccCceEEEECCe--eEEEEEe
Q 033484 25 GTIRKNGYIVIKGR--PCKVVEV 45 (118)
Q Consensus 25 ~~lkkG~~i~i~g~--P~~Vve~ 45 (118)
-.|++|+.|+++|. |..|+++
T Consensus 32 r~ik~GD~IiF~~~~l~v~V~~v 54 (111)
T COG4043 32 RQIKPGDKIIFNGDKLKVEVIDV 54 (111)
T ss_pred cCCCCCCEEEEcCCeeEEEEEEE
Confidence 46899999999974 4444444
No 55
>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=42.30 E-value=33 Score=22.41 Aligned_cols=28 Identities=14% Similarity=-0.066 Sum_probs=20.6
Q ss_pred EEEEEEEEccCCcEEEEEecCCCceeecE
Q 033484 57 KCHFVGIDIFNGKKLEDIVPSSHNCDVPH 85 (118)
Q Consensus 57 ~vrik~knl~TG~~~e~t~~s~~~ve~~~ 85 (118)
.+++.+| +-+|+..+++|.+++++..+.
T Consensus 4 ~~~i~iR-lP~G~r~~rrF~~t~~L~~l~ 31 (80)
T cd01771 4 ISKLRVR-TPSGDFLERRFLGDTPLQVLL 31 (80)
T ss_pred eEEEEEE-CCCCCEEEEEeCCCCcHHHHH
Confidence 3444433 568999999999999998543
No 56
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=42.28 E-value=82 Score=25.80 Aligned_cols=51 Identities=8% Similarity=-0.010 Sum_probs=38.3
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCC
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS 78 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~ 78 (118)
..++++.|..|.- +|.|.+.+... .|.|+++.++.+.| .||.+.-+-+...
T Consensus 4 ~i~~l~~g~~v~~---~~lv~~~~~~~-~knG~~yl~l~l~D-~tG~I~ak~W~~~ 54 (314)
T PRK13480 4 GIEELEVGEQVDH---FLLIKSATKGV-ASNGKPFLTLILQD-KSGDIEAKLWDVS 54 (314)
T ss_pred hHhhcCCCCEeeE---EEEEEEceeee-cCCCCeEEEEEEEc-CCcEEEEEeCCCC
Confidence 5788999986543 78888776644 45488999999999 8998876666644
No 57
>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=42.08 E-value=81 Score=23.49 Aligned_cols=25 Identities=16% Similarity=0.336 Sum_probs=20.4
Q ss_pred cccccCceEEEECCeeEEEEEeeEe
Q 033484 24 AGTIRKNGYIVIKGRPCKVVEVSTS 48 (118)
Q Consensus 24 ~~~lkkG~~i~i~g~P~~Vve~~~~ 48 (118)
..=|+-|++|.++..+|+|++=+..
T Consensus 37 ~~VL~TgNYitI~d~v~kI~~K~i~ 61 (149)
T PF08408_consen 37 SEVLSTGNYITINDDVYKILDKDII 61 (149)
T ss_pred HHHHhcCCeEEECCeeeeeeccccc
Confidence 4458899999999999999976443
No 58
>PRK11835 hypothetical protein; Provisional
Probab=40.52 E-value=29 Score=24.68 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=20.2
Q ss_pred ccccCc-eEEEECCeeEEEEEeeEecCCCCcccEEEEE
Q 033484 25 GTIRKN-GYIVIKGRPCKVVEVSTSKTGKHGHAKCHFV 61 (118)
Q Consensus 25 ~~lkkG-~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik 61 (118)
++|... .+|+.+|+||.-+..+-- .+|.||+|
T Consensus 66 ~eiqv~~~ivEweGepCLFv~~~DE-----~aa~CrLK 98 (114)
T PRK11835 66 SDIQVPCSVLECEGEPCLFVNRQDE-----SAATCRLK 98 (114)
T ss_pred HhhcccceEEEecCCceEEEecccc-----hhhheeec
Confidence 445543 488999999987754321 44556554
No 59
>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=39.04 E-value=59 Score=24.24 Aligned_cols=22 Identities=14% Similarity=0.382 Sum_probs=14.6
Q ss_pred ccccCceEEEEC---CeeEEEEEee
Q 033484 25 GTIRKNGYIVIK---GRPCKVVEVS 46 (118)
Q Consensus 25 ~~lkkG~~i~i~---g~P~~Vve~~ 46 (118)
+-+|.|++|.++ +.||.|-.|+
T Consensus 2 ~~yrvGD~Vy~~~~~~~Py~I~rI~ 26 (164)
T cd04709 2 NMYRVGDYVYFESSPNNPYLIRRIE 26 (164)
T ss_pred cEEecCCEEEEECCCCCCCEEEEEE
Confidence 347899999885 5565554444
No 60
>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=38.85 E-value=55 Score=25.40 Aligned_cols=70 Identities=10% Similarity=0.065 Sum_probs=36.9
Q ss_pred cccccCCCcceeeEEecccccCceEEEE---CCe--eEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCcee
Q 033484 8 FESKADAGASKTFPQQAGTIRKNGYIVI---KGR--PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (118)
Q Consensus 8 ~~~~~~~~~~~t~~i~~~~lkkG~~i~i---~g~--P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve 82 (118)
|.+.+.........+...+|+.|+.|+- +|+ -..|+-+.+..|.+ -+.+++++ ..+| ...++...+-|-
T Consensus 13 Fpg~a~V~~~~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~flhr~~~~-~~~F~~i~---te~g--~~l~LTp~HLI~ 86 (217)
T PF01079_consen 13 FPGDATVTLEDGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMFLHRDPEQ-RAEFVVIE---TEDG--RSLTLTPNHLIF 86 (217)
T ss_dssp B-TT-EEEBTTS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEEEEEEEEE-EEEEEEEE---ETTS---EEEE-TT-EEE
T ss_pred CCCCCEEEeCCCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEEeccCccc-cEEEEEEE---cCCC--CeEEecCCcEEE
Confidence 4434444445566899999999998777 454 46788888888865 44455443 3345 334455555544
Q ss_pred e
Q 033484 83 V 83 (118)
Q Consensus 83 ~ 83 (118)
+
T Consensus 87 v 87 (217)
T PF01079_consen 87 V 87 (217)
T ss_dssp E
T ss_pred E
Confidence 3
No 61
>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=37.88 E-value=51 Score=22.19 Aligned_cols=48 Identities=15% Similarity=0.076 Sum_probs=29.2
Q ss_pred EEEEEccCCcEEEEEecCCCceee-----------cEEEeeeeEEEeccCCCeeEeecCC
Q 033484 60 FVGIDIFNGKKLEDIVPSSHNCDV-----------PHVTRTDYQLIDISEDGFVCSYFVL 108 (118)
Q Consensus 60 ik~knl~TG~~~e~t~~s~~~ve~-----------~~ve~~~~qyly~d~d~~l~FMd~e 108 (118)
+|++.. .|++.-.++.+++.+.. .......+++.|.|+++=|+.+..+
T Consensus 3 FK~~~~-~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D 61 (86)
T cd06409 3 FKFKDP-KGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSD 61 (86)
T ss_pred EEeeCC-CCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEecc
Confidence 344544 66666566654444331 1111468899999988888888754
No 62
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=37.59 E-value=42 Score=23.66 Aligned_cols=28 Identities=11% Similarity=0.078 Sum_probs=15.8
Q ss_pred eEEecccccCceEEEE-CCeeEEEEEeeE
Q 033484 20 FPQQAGTIRKNGYIVI-KGRPCKVVEVST 47 (118)
Q Consensus 20 ~~i~~~~lkkG~~i~i-~g~P~~Vve~~~ 47 (118)
--+.|.+|++|+.|.- +|.+..|..+..
T Consensus 70 gWv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 70 GWVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp --EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 3689999999998755 788777766654
No 63
>COG2351 Transthyretin-like protein [General function prediction only]
Probab=37.32 E-value=1.6e+02 Score=21.31 Aligned_cols=76 Identities=16% Similarity=0.216 Sum_probs=45.7
Q ss_pred cccccCceEEEECCeeEEEE-EeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCce--------eecEEEeeeeEEE
Q 033484 24 AGTIRKNGYIVIKGRPCKVV-EVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC--------DVPHVTRTDYQLI 94 (118)
Q Consensus 24 ~~~lkkG~~i~i~g~P~~Vv-e~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~v--------e~~~ve~~~~qyl 94 (118)
|..++...+ .++|+-++.+ +..+..-||-..+ -+...++.+|. +|.+|..+|=+ +.|.++...+.|=
T Consensus 24 Aagv~V~L~-rl~~~~~~~l~t~~Tn~DGR~d~p--ll~g~~~~~G~-Y~l~F~~gdYf~~~g~~~~~~~Fl~~V~vrF~ 99 (124)
T COG2351 24 AAGVKVELY-RLEGNQWELLKTVVTNADGRIDAP--LLAGETLATGI-YELVFHTGDYFKSRGVQLADPPFLDVVPVRFG 99 (124)
T ss_pred CCCCEEEEE-EecCCcceeeeEEEecCCCccccc--ccCccccccce-EEEEEEcchhhhccCcccCCCCccceEEEEEE
Confidence 334444333 3345444444 4444455663333 26778888886 88999876544 4468888888888
Q ss_pred eccCCCeeE
Q 033484 95 DISEDGFVC 103 (118)
Q Consensus 95 y~d~d~~l~ 103 (118)
-.|.+.++|
T Consensus 100 iad~~~HYH 108 (124)
T COG2351 100 IADVDEHYH 108 (124)
T ss_pred EcCCCCcee
Confidence 776655444
No 64
>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=37.23 E-value=83 Score=20.22 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=10.5
Q ss_pred ccccCceEEEECCeeEE
Q 033484 25 GTIRKNGYIVIKGRPCK 41 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~~ 41 (118)
..++||+.|.+.|.+..
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 34889999999987653
No 65
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=37.00 E-value=55 Score=23.85 Aligned_cols=37 Identities=14% Similarity=0.149 Sum_probs=27.0
Q ss_pred cccccCceEEEECCeeE-----EEEEeeEecC-CCCcccEEEE
Q 033484 24 AGTIRKNGYIVIKGRPC-----KVVEVSTSKT-GKHGHAKCHF 60 (118)
Q Consensus 24 ~~~lkkG~~i~i~g~P~-----~Vve~~~~kp-GKhG~A~vri 60 (118)
..+|++|+.|.+.|+=. -|+.+.|+.| |+|-...+..
T Consensus 83 ip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~~h~~Gwl~~ 125 (131)
T PF11948_consen 83 IPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRGRHPDGWLKH 125 (131)
T ss_pred CcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCCCCCCeeEEE
Confidence 56799999999988732 4788999888 6665455444
No 66
>PRK10965 multicopper oxidase; Provisional
Probab=36.60 E-value=1.2e+02 Score=26.37 Aligned_cols=48 Identities=8% Similarity=-0.042 Sum_probs=33.2
Q ss_pred cCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceee
Q 033484 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83 (118)
Q Consensus 28 kkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~ 83 (118)
..|+.+.+||.++-.++. ||+ .+|+++.|--+-+.+...+..+.++.+
T Consensus 210 ~~gd~~lVNG~~~p~~~v----~~~----~~RlRliNas~~r~~~l~~~dg~~~~v 257 (523)
T PRK10965 210 WFGDTLLTNGAIYPQHAA----PRG----WLRLRLLNGCNARSLNLATSDGRPLYV 257 (523)
T ss_pred ccCCeEEECCcccceeec----CCC----EEEEEEEeccCCceEEEEEcCCceEEE
Confidence 468899999997654432 333 689999998887777776644444433
No 67
>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=36.11 E-value=75 Score=25.35 Aligned_cols=31 Identities=10% Similarity=0.115 Sum_probs=20.5
Q ss_pred cccccCceEEEEC---CeeEEEE----EeeEecCCCCc
Q 033484 24 AGTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHG 54 (118)
Q Consensus 24 ~~~lkkG~~i~i~---g~P~~Vv----e~~~~kpGKhG 54 (118)
.-+|++|++|.++ ++|..|. .+-..++|+++
T Consensus 271 ll~L~~GDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~ 308 (320)
T TIGR01397 271 LLNLQVGDVIPLNTDMPEEVSLRVGGRPKFRAQPGVRG 308 (320)
T ss_pred HhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEEC
Confidence 4578999999997 3566652 24455666653
No 68
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=35.57 E-value=30 Score=21.85 Aligned_cols=25 Identities=28% Similarity=0.254 Sum_probs=18.8
Q ss_pred EEEEEEEEccCCcEEEEEecCCCceeec
Q 033484 57 KCHFVGIDIFNGKKLEDIVPSSHNCDVP 84 (118)
Q Consensus 57 ~vrik~knl~TG~~~e~t~~s~~~ve~~ 84 (118)
.+++++ -+|+.+..+|++++++..+
T Consensus 4 ~i~iRl---pdG~~~~~~F~~~~tl~~l 28 (77)
T cd01767 4 KIQIRL---PDGKRLEQRFNSTHKLSDV 28 (77)
T ss_pred EEEEEc---CCCCEEEEEeCCCCCHHHH
Confidence 344444 5699999999999998754
No 69
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=35.50 E-value=26 Score=24.14 Aligned_cols=41 Identities=15% Similarity=0.157 Sum_probs=30.1
Q ss_pred CCcceeeEEecccccCceEEEECCeeEEEEEeeEecCCCCcc
Q 033484 14 AGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGH 55 (118)
Q Consensus 14 ~~~~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~ 55 (118)
|.+....-+.-++||+|..+++++.-|.+++-+. .|=+||.
T Consensus 45 ~p~~~sifie~g~lrpGiI~LINd~DWeLleke~-y~ledgD 85 (96)
T COG5131 45 APTRDSIFIEHGELRPGIICLINDMDWELLEKER-YPLEDGD 85 (96)
T ss_pred CCccceeeecCCCCcccEEEEEcCccHhhhhccc-ccCCCCC
Confidence 4445566678899999999999999999987543 3434443
No 70
>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=34.27 E-value=61 Score=17.26 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=15.7
Q ss_pred CceEEEE-----CCeeEEEEEeeEec
Q 033484 29 KNGYIVI-----KGRPCKVVEVSTSK 49 (118)
Q Consensus 29 kG~~i~i-----~g~P~~Vve~~~~k 49 (118)
+|+.+.+ .|..++|+++...+
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 4777777 78888998887544
No 71
>PRK10883 FtsI repressor; Provisional
Probab=33.81 E-value=1.3e+02 Score=25.75 Aligned_cols=52 Identities=13% Similarity=0.128 Sum_probs=37.0
Q ss_pred cCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEE
Q 033484 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVT 87 (118)
Q Consensus 28 kkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve 87 (118)
..|+.+.+||...-++++ +|| .+|+++.|--.-+.+...+..++.+.++-.+
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 468899999987666654 344 4799999998888887777555555544444
No 72
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=33.26 E-value=94 Score=20.95 Aligned_cols=24 Identities=8% Similarity=0.224 Sum_probs=18.2
Q ss_pred EEecccccCceEEEE----CCeeEEEEE
Q 033484 21 PQQAGTIRKNGYIVI----KGRPCKVVE 44 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i----~g~P~~Vve 44 (118)
..-.+.|++|+.|++ +|+-|.|++
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 555778999997776 667777775
No 73
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=32.75 E-value=80 Score=20.02 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=13.1
Q ss_pred ccccCceEEEECCeeE
Q 033484 25 GTIRKNGYIVIKGRPC 40 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~ 40 (118)
..++||+.|.+.|.+-
T Consensus 60 ~~~~kG~~V~v~G~l~ 75 (100)
T cd04496 60 KYLKKGDLVYVEGRLR 75 (100)
T ss_pred HHhCCCCEEEEEEEEE
Confidence 3589999999999864
No 74
>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=32.56 E-value=85 Score=24.35 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=19.8
Q ss_pred eEEecccccCceEEEE------CCeeEEEEEeeEe
Q 033484 20 FPQQAGTIRKNGYIVI------KGRPCKVVEVSTS 48 (118)
Q Consensus 20 ~~i~~~~lkkG~~i~i------~g~P~~Vve~~~~ 48 (118)
.++-|+++++|++|.. .-.|-+|+++...
T Consensus 99 ~~vfA~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~ 133 (217)
T PF01079_consen 99 RAVFASDVRVGDCVLVSDEGGGKLRPSRVVRVSTV 133 (217)
T ss_dssp EEEEGGG--TT-EEEEE-TTT--EEEEEEEEEEEE
T ss_pred ceeehhhCCCCCEEEEEEcCCCcEEEEEEEEEEEE
Confidence 7899999999999999 2247777776654
No 75
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=32.43 E-value=2.9e+02 Score=22.84 Aligned_cols=26 Identities=8% Similarity=0.105 Sum_probs=21.7
Q ss_pred EEEEEEccCCcEEEEEecCCCceeec
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve~~ 84 (118)
.|+.+|+.+|+++.-+..+...+++-
T Consensus 291 ~IrV~N~~S~kiv~g~V~g~g~V~V~ 316 (338)
T PRK12786 291 VVRVLNLQSKRTVTGTVTGRGQVSVD 316 (338)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEEe
Confidence 47889999999999998888877653
No 76
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=32.41 E-value=1.1e+02 Score=26.49 Aligned_cols=31 Identities=16% Similarity=0.486 Sum_probs=25.4
Q ss_pred EecccccCceEEEECCeeEEEEE-eeEecCCC
Q 033484 22 QQAGTIRKNGYIVIKGRPCKVVE-VSTSKTGK 52 (118)
Q Consensus 22 i~~~~lkkG~~i~i~g~P~~Vve-~~~~kpGK 52 (118)
....++++...+.++|++|+++. -+....|+
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 56788999999999999999998 55555555
No 77
>KOG0267 consensus Microtubule severing protein katanin p80 subunit B (contains WD40 repeats) [Cell cycle control, cell division, chromosome partitioning]
Probab=32.24 E-value=47 Score=30.74 Aligned_cols=100 Identities=18% Similarity=0.061 Sum_probs=65.7
Q ss_pred CCcceeeEEeccccc-CceEEEECCeeEEEEEeeEecCCCC---cccEEEEEEEEccCCcEEEEEecCCCceeecEEEee
Q 033484 14 AGASKTFPQQAGTIR-KNGYIVIKGRPCKVVEVSTSKTGKH---GHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRT 89 (118)
Q Consensus 14 ~~~~~t~~i~~~~lk-kG~~i~i~g~P~~Vve~~~~kpGKh---G~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~ 89 (118)
|+.+.---..+.|+| +|-.-.++|.++.|--+.+.--||- |.--.-+++-|+--|+.. ..|++.+ ..+-.+|-.
T Consensus 128 a~gStdtd~~iwD~Rk~Gc~~~~~s~~~vv~~l~lsP~Gr~v~~g~ed~tvki~d~~agk~~-~ef~~~e-~~v~sle~h 205 (825)
T KOG0267|consen 128 ASGSTDTDLKIWDIRKKGCSHTYKSHTRVVDVLRLSPDGRWVASGGEDNTVKIWDLTAGKLS-KEFKSHE-GKVQSLEFH 205 (825)
T ss_pred ccccccccceehhhhccCceeeecCCcceeEEEeecCCCceeeccCCcceeeeecccccccc-ccccccc-ccccccccC
Confidence 555555567788998 7888888998876655555444542 222355788888777755 5676432 223344466
Q ss_pred eeEEEeccC--CCeeEeecCCChHHHhh
Q 033484 90 DYQLIDISE--DGFVCSYFVLSCSFYLS 115 (118)
Q Consensus 90 ~~qyly~d~--d~~l~FMd~etyeq~~~ 115 (118)
+..||-..| |.-+-|-|.||||.|-|
T Consensus 206 p~e~Lla~Gs~d~tv~f~dletfe~I~s 233 (825)
T KOG0267|consen 206 PLEVLLAPGSSDRTVRFWDLETFEVISS 233 (825)
T ss_pred chhhhhccCCCCceeeeeccceeEEeec
Confidence 777777765 56668899999987754
No 78
>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=31.24 E-value=1.4e+02 Score=18.78 Aligned_cols=33 Identities=15% Similarity=0.372 Sum_probs=25.1
Q ss_pred cCCCcceeeEEecccccCc---eEEEECCeeEEEEE
Q 033484 12 ADAGASKTFPQQAGTIRKN---GYIVIKGRPCKVVE 44 (118)
Q Consensus 12 ~~~~~~~t~~i~~~~lkkG---~~i~i~g~P~~Vve 44 (118)
+-..+-....|..+.+..+ ..|.+++.+|.++.
T Consensus 11 g~~~Ggt~vtI~G~~f~~~~~~~~V~ig~~~C~~~~ 46 (90)
T cd00603 11 GPLSGGTRLTITGSNLGSGSPRVRVTVGGVPCKVLN 46 (90)
T ss_pred CCCCCCeEEEEEEECCCCCCceEEEEECCEECcEEe
Confidence 3444456677788888887 78899999999975
No 79
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.94 E-value=2.6e+02 Score=21.52 Aligned_cols=24 Identities=17% Similarity=0.162 Sum_probs=18.5
Q ss_pred EEEEEEccCCcEEEEEecCCCceee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve~ 83 (118)
.++.|| .+|+++.-+.-+...+++
T Consensus 198 ~IrVrN-~Sgkii~g~V~~~g~V~V 221 (222)
T PRK08515 198 IIQAKN-KSNKILKAKVLSKNKAEI 221 (222)
T ss_pred EEEEEe-CCCCEEEEEEecCCEEEE
Confidence 477888 999999888877766653
No 80
>KOG3514 consensus Neurexin III-alpha [Signal transduction mechanisms]
Probab=29.89 E-value=1.2e+02 Score=29.78 Aligned_cols=62 Identities=13% Similarity=0.236 Sum_probs=42.6
Q ss_pred EECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCC--------CceeecEEEeeeeEEEeccCCCe
Q 033484 34 VIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS--------HNCDVPHVTRTDYQLIDISEDGF 101 (118)
Q Consensus 34 ~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~--------~~ve~~~ve~~~~qyly~d~d~~ 101 (118)
++||++|.+++. |- |..++|..-|.+.+|......+.-. +.+..+....-+-..|..|++.|
T Consensus 494 Lldghlyl~ldl-----GS-G~iklras~rkv~DGeWhhv~l~R~gR~gsvsVd~~~~df~tpG~s~iL~ld~~my 563 (1591)
T KOG3514|consen 494 LLDGHLYLLLDL-----GS-GVIKLRASSRKVNDGEWHHVDLQRDGRTGSVSVDAIKTDFSTPGDSEILDLDDPMY 563 (1591)
T ss_pred EeCCeEEEEEec-----CC-ceEEeeeecccccCCceEEEEeeccCccceEEEeeeecCccCCCcceeEeecCcee
Confidence 469999999976 67 8889999999999999988877532 22333333333445566665544
No 81
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.17 E-value=2.3e+02 Score=20.76 Aligned_cols=24 Identities=8% Similarity=-0.011 Sum_probs=19.6
Q ss_pred EEEEEEccCCcEEEEEecCCCcee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve 82 (118)
.++.||+.||+++.-+..+.-.+.
T Consensus 133 ~IrVrN~~Sgkiv~g~V~~~g~V~ 156 (160)
T PRK06005 133 LIRVRNVDSGVIVSGTVLADGTIQ 156 (160)
T ss_pred EEEEEECCCCCEEEEEEecCCEEE
Confidence 589999999999988887766554
No 82
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=28.94 E-value=2.1e+02 Score=22.31 Aligned_cols=51 Identities=12% Similarity=0.233 Sum_probs=36.6
Q ss_pred ecccccCceEEEECCe---------eEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecC
Q 033484 23 QAGTIRKNGYIVIKGR---------PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPS 77 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~---------P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s 77 (118)
..-+++.|+++.+.-. -+..+-+...+-|- ...+.+||++-|.-.|..|+-
T Consensus 93 ~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl----~atf~LRnvIagvGVEi~~pL 152 (201)
T KOG1698|consen 93 DIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGL----NATFLLRNVIAGVGVEIVFPL 152 (201)
T ss_pred cCCccccccEEEEEecCCccCCceeEEEEEEEEecccCC----cceEEeeehhhCceeEEEEec
Confidence 3448999999988321 24445555555554 347899999999999999974
No 83
>PF06433 Me-amine-dh_H: Methylamine dehydrogenase heavy chain (MADH); InterPro: IPR009451 Methylamine dehydrogenase (1.4.99.3 from EC) is a periplasmic quinoprotein found in several methyltrophic bacteria []. It is induced when grown on methylamine as a carbon source MADH and catalyses the oxidative deamination of amines to their corresponding aldehydes. The redox cofactor of this enzyme is tryptophan tryptophylquinone (TTQ). Electrons derived from the oxidation of methylamine are passed to an electron acceptor, which is usually the blue-copper protein amicyanin (IPR002386 from INTERPRO). RCH2NH2 + H2O + acceptor = RCHO + NH3 + reduced acceptor MADH is a hetero-tetramer, comprised of two heavy subunits and two light subunits. The heavy subunit forms a seven-bladed beta-propeller like structure [].; GO: 0030058 amine dehydrogenase activity, 0030416 methylamine metabolic process, 0055114 oxidation-reduction process, 0042597 periplasmic space; PDB: 3RN1_F 3SVW_F 3PXT_F 3L4O_F 3L4M_D 3SJL_F 3PXS_D 3ORV_F 3RMZ_F 3RLM_F ....
Probab=28.21 E-value=3.4e+02 Score=22.75 Aligned_cols=83 Identities=22% Similarity=0.290 Sum_probs=50.9
Q ss_pred cccCceE--EEE---CCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEec--cC
Q 033484 26 TIRKNGY--IVI---KGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDI--SE 98 (118)
Q Consensus 26 ~lkkG~~--i~i---~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~--d~ 98 (118)
.=|+|.. +=+ .|+.|... ...+.|.|-.+=-.|=.-|+.|++.+ .+++-...+..+.|..-+--+||. .+
T Consensus 234 ~WrPGG~Q~~A~~~~~~rlyvLM--h~g~~gsHKdpgteVWv~D~~t~krv-~Ri~l~~~~~Si~Vsqd~~P~L~~~~~~ 310 (342)
T PF06433_consen 234 GWRPGGWQLIAYHAASGRLYVLM--HQGGEGSHKDPGTEVWVYDLKTHKRV-ARIPLEHPIDSIAVSQDDKPLLYALSAG 310 (342)
T ss_dssp TEEE-SSS-EEEETTTTEEEEEE--EE--TT-TTS-EEEEEEEETTTTEEE-EEEEEEEEESEEEEESSSS-EEEEEETT
T ss_pred CcCCcceeeeeeccccCeEEEEe--cCCCCCCccCCceEEEEEECCCCeEE-EEEeCCCccceEEEccCCCcEEEEEcCC
Confidence 4456652 333 56788654 34467888555557888999999977 556655666667777767667763 35
Q ss_pred CCeeEeecCCChH
Q 033484 99 DGFVCSYFVLSCS 111 (118)
Q Consensus 99 d~~l~FMd~etye 111 (118)
++.|..+|..|=.
T Consensus 311 ~~~l~v~D~~tGk 323 (342)
T PF06433_consen 311 DGTLDVYDAATGK 323 (342)
T ss_dssp TTEEEEEETTT--
T ss_pred CCeEEEEeCcCCc
Confidence 6777899987743
No 84
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.75 E-value=2.3e+02 Score=20.33 Aligned_cols=25 Identities=4% Similarity=0.065 Sum_probs=20.6
Q ss_pred EEEEEEccCCcEEEEEecCCCceee
Q 033484 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (118)
Q Consensus 59 rik~knl~TG~~~e~t~~s~~~ve~ 83 (118)
.++.+|+.||+++.-+..+...+++
T Consensus 114 ~IrV~N~~S~riV~g~V~~~g~V~V 138 (141)
T PRK12618 114 EIRVMNLSSRTTVSGRIAADGSVIV 138 (141)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEE
Confidence 4889999999999888887776654
No 85
>PLN02792 oxidoreductase
Probab=27.73 E-value=1.9e+02 Score=25.40 Aligned_cols=51 Identities=18% Similarity=0.161 Sum_probs=33.9
Q ss_pred CceEEEECCee---EEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEE
Q 033484 29 KNGYIVIKGRP---CKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVT 87 (118)
Q Consensus 29 kG~~i~i~g~P---~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve 87 (118)
.++.+++||.+ +.++ ..+||| .+|+++.|.-.-..+...+. ++++.++..+
T Consensus 178 ~~d~~liNG~~~~~~~~~---~v~~Gk----~yRlRliNa~~~~~~~f~i~-gH~~tVI~~D 231 (536)
T PLN02792 178 MPDGVMINGQGVSYVYSI---TVDKGK----TYRFRISNVGLQTSLNFEIL-GHQLKLIEVE 231 (536)
T ss_pred CCCEEEEeccCCCCcceE---EECCCC----EEEEEEEEcCCCceEEEEEC-CcEEEEEEeC
Confidence 46789999984 4344 347898 78888888876666655554 4555554433
No 86
>KOG0272 consensus U4/U6 small nuclear ribonucleoprotein Prp4 (contains WD40 repeats) [RNA processing and modification]
Probab=27.62 E-value=2e+02 Score=25.13 Aligned_cols=59 Identities=19% Similarity=0.231 Sum_probs=45.7
Q ss_pred EecccccCceEEEE-CCeeEEEEEeeEecCCCC---cccEEEEEEEEccCCcEEEEEecCCCce
Q 033484 22 QQAGTIRKNGYIVI-KGRPCKVVEVSTSKTGKH---GHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (118)
Q Consensus 22 i~~~~lkkG~~i~i-~g~P~~Vve~~~~kpGKh---G~A~vrik~knl~TG~~~e~t~~s~~~v 81 (118)
-.+=|||.|..|++ +|..-.|+.++++.-|-| |++-..+|+=+|.--+- -.+.+++.++
T Consensus 327 ~RvWDlRtgr~im~L~gH~k~I~~V~fsPNGy~lATgs~Dnt~kVWDLR~r~~-ly~ipAH~nl 389 (459)
T KOG0272|consen 327 GRVWDLRTGRCIMFLAGHIKEILSVAFSPNGYHLATGSSDNTCKVWDLRMRSE-LYTIPAHSNL 389 (459)
T ss_pred hheeecccCcEEEEecccccceeeEeECCCceEEeecCCCCcEEEeeeccccc-ceecccccch
Confidence 34669999998776 999999999999888888 77777788888776554 3567776554
No 87
>COG3731 SrlB Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]
Probab=27.50 E-value=79 Score=22.84 Aligned_cols=27 Identities=7% Similarity=0.185 Sum_probs=21.7
Q ss_pred eEEecccccCceEEEECCeeEEEEEee
Q 033484 20 FPQQAGTIRKNGYIVIKGRPCKVVEVS 46 (118)
Q Consensus 20 ~~i~~~~lkkG~~i~i~g~P~~Vve~~ 46 (118)
+.-.-..+.+|+.+.+++.+|.|..+-
T Consensus 45 h~e~~~~l~~G~~l~lg~~~y~ItaVG 71 (123)
T COG3731 45 HGELQEALQPGDRLTLGGHCYPITAVG 71 (123)
T ss_pred cCcccccCCCCCEEEECCceEEEEEec
Confidence 334456778999999999999998763
No 88
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=27.33 E-value=61 Score=20.55 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=19.8
Q ss_pred cEEEEEEEEccCCcEEEEEecCCCceeec
Q 033484 56 AKCHFVGIDIFNGKKLEDIVPSSHNCDVP 84 (118)
Q Consensus 56 A~vrik~knl~TG~~~e~t~~s~~~ve~~ 84 (118)
+.++++ +-+|+.+..+|++++++..+
T Consensus 5 ~~I~iR---lPdG~ri~~~F~~~~tl~~v 30 (80)
T smart00166 5 CRLQIR---LPDGSRLVRRFPSSDTLRTV 30 (80)
T ss_pred EEEEEE---cCCCCEEEEEeCCCCcHHHH
Confidence 444444 37899999999999998754
No 89
>TIGR01563 gp16_SPP1 phage head-tail adaptor, putative, SPP1 family. This family describes a small protein of about 100 amino acids found in bacteriophage and in bacterial prophage regions. Examples include gp9 of phage HK022 and gp16 of phage SPP1. This minor structural protein is suggested to be a head-tail adaptor protein (although the source of this annotation was not traced during construction of this model).
Probab=27.11 E-value=1.7e+02 Score=18.59 Aligned_cols=32 Identities=13% Similarity=0.187 Sum_probs=23.5
Q ss_pred ccCCCcceeeEEe---cccccCceEEEECCeeEEE
Q 033484 11 KADAGASKTFPQQ---AGTIRKNGYIVIKGRPCKV 42 (118)
Q Consensus 11 ~~~~~~~~t~~i~---~~~lkkG~~i~i~g~P~~V 42 (118)
.+...+..+..+. ..+|...+.|.++|..|.|
T Consensus 47 a~~~~~~~t~~~~iR~~~~i~~~~ri~~~g~~Y~I 81 (101)
T TIGR01563 47 AGQEGVEITHVILIRYRKDVTNKMRVIYDGRIYTI 81 (101)
T ss_pred cccccCceEEEEEEeccCCCChhhEEEECCEEEEE
Confidence 4445555555443 5678899999999999999
No 90
>PTZ00031 ribosomal protein L2; Provisional
Probab=27.04 E-value=2e+02 Score=23.91 Aligned_cols=60 Identities=17% Similarity=0.186 Sum_probs=32.8
Q ss_pred eeEEecccccCceEEE--------------ECCee--EEEEEeeEecCCCCccc-------EEEEEEEEccCCcEEEEEe
Q 033484 19 TFPQQAGTIRKNGYIV--------------IKGRP--CKVVEVSTSKTGKHGHA-------KCHFVGIDIFNGKKLEDIV 75 (118)
Q Consensus 19 t~~i~~~~lkkG~~i~--------------i~g~P--~~Vve~~~~kpGKhG~A-------~vrik~knl~TG~~~e~t~ 75 (118)
.|.+-+..++.|+.|. +...| ..|-.++. +||+ |.. .+++..++ +...-..+
T Consensus 133 ~YIlApeGl~vGd~I~sg~~a~i~~GN~lPL~~IP~GT~IhNIE~-~pG~-Ggkl~RSAGt~A~Ii~k~---~~~~~VkL 207 (317)
T PTZ00031 133 SYILAPLLLRPGDKIIASKYANINPGNSLPLRNIPVGSIVHNVEM-RPGA-GGQIIRAGGTYATVVSKD---EQFATLKL 207 (317)
T ss_pred EEEEccCCCCCCCEEEeCCCCCCCccCccccccCCCCCEEEEEEe-cCCC-CceEEEecCCeEEEEEcc---CCEEEEEC
Confidence 3555555555555554 43333 23344443 7888 443 33444443 56666778
Q ss_pred cCCCceee
Q 033484 76 PSSHNCDV 83 (118)
Q Consensus 76 ~s~~~ve~ 83 (118)
+|++....
T Consensus 208 PSGe~r~i 215 (317)
T PTZ00031 208 KSTEIRKF 215 (317)
T ss_pred CCCCEEEE
Confidence 88877653
No 91
>PF13403 Hint_2: Hint domain
Probab=26.93 E-value=2.4e+02 Score=20.20 Aligned_cols=29 Identities=14% Similarity=0.205 Sum_probs=21.9
Q ss_pred EEecccccCceEEEE-CCeeEEEEEeeEec
Q 033484 21 PQQAGTIRKNGYIVI-KGRPCKVVEVSTSK 49 (118)
Q Consensus 21 ~i~~~~lkkG~~i~i-~g~P~~Vve~~~~k 49 (118)
...+.+|+.|+.|+= +|.+..|..+...+
T Consensus 15 ~~~Ve~L~~GD~V~T~dgg~~~V~wig~~~ 44 (147)
T PF13403_consen 15 PRPVEDLRPGDRVLTRDGGFQPVRWIGRRT 44 (147)
T ss_pred CeEeeccCCCCEEEecCCCEEEEEEEEEEE
Confidence 567899999996655 68888887765543
No 92
>KOG4499 consensus Ca2+-binding protein Regucalcin/SMP30 [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=26.87 E-value=2.7e+02 Score=22.85 Aligned_cols=66 Identities=12% Similarity=0.032 Sum_probs=47.4
Q ss_pred ceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEeccCCCeeEeecCC
Q 033484 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVCSYFVL 108 (118)
Q Consensus 30 G~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d~~l~FMd~e 108 (118)
|+.|--+|.+|.-+ -..| ++..-|+-||+...+.--...++..+-+--+++..+|..-.. -|||++
T Consensus 216 Gm~ID~eG~L~Va~----~ng~-------~V~~~dp~tGK~L~eiklPt~qitsccFgGkn~d~~yvT~aa--~~~dp~ 281 (310)
T KOG4499|consen 216 GMTIDTEGNLYVAT----FNGG-------TVQKVDPTTGKILLEIKLPTPQITSCCFGGKNLDILYVTTAA--KFDDPV 281 (310)
T ss_pred cceEccCCcEEEEE----ecCc-------EEEEECCCCCcEEEEEEcCCCceEEEEecCCCccEEEEEehh--cccCch
Confidence 88888888888433 2333 377789999998877665678888777777888888875533 367764
No 93
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=26.55 E-value=1.2e+02 Score=22.97 Aligned_cols=55 Identities=16% Similarity=0.221 Sum_probs=40.9
Q ss_pred EEeeEecC-CCCcccEEEEEEEEccCCcEEEEEecCCCceeecEEEeeeeEEEecc
Q 033484 43 VEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDIS 97 (118)
Q Consensus 43 ve~~~~kp-GKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d 97 (118)
+|+.-.-| |.|++....+.+|+=..|.+.-..+..-.-++.|..-+..+.+.+.+
T Consensus 85 lEvkg~lP~G~~~hGyfNL~gk~~l~GHiK~eNcs~Ialv~rpFmG~~s~si~Ffn 140 (176)
T COG3721 85 LEVKGPLPSGTHRHGYFNLRGKDGLSGHIKAENCSHIALVERPFMGMESASILFFN 140 (176)
T ss_pred EEecCCCCCCccccceEeecCCCCCcceeeccccceeeEeccccCCccceeeeeec
Confidence 44433334 89999999999999999998888887777777777766666655554
No 94
>PF13989 YejG: YejG-like protein
Probab=25.88 E-value=64 Score=22.71 Aligned_cols=27 Identities=22% Similarity=0.464 Sum_probs=17.8
Q ss_pred ceEEEECCeeEEEEEeeEecCCCCcccEEEEE
Q 033484 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFV 61 (118)
Q Consensus 30 G~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik 61 (118)
..+++.+|+||.-+..+-- .+|.||+|
T Consensus 69 ~~vvE~eGepCLFv~~~DE-----sa~~CrLK 95 (106)
T PF13989_consen 69 CAVVEWEGEPCLFVHREDE-----SAAMCRLK 95 (106)
T ss_pred ceEEEecCCceEEEecccc-----hhhheeec
Confidence 4588999999987754422 34555544
No 95
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=25.70 E-value=36 Score=26.47 Aligned_cols=19 Identities=37% Similarity=0.753 Sum_probs=14.3
Q ss_pred cccccCceEEEE-CCeeEEE
Q 033484 24 AGTIRKNGYIVI-KGRPCKV 42 (118)
Q Consensus 24 ~~~lkkG~~i~i-~g~P~~V 42 (118)
.++||+|.+|.+ +|.+..|
T Consensus 181 Ls~LKkGgYIei~rG~Li~I 200 (207)
T PRK11832 181 LAALRKGGYIEMNKGKLVAI 200 (207)
T ss_pred HHHHhcCCCEEEecCEEeec
Confidence 589999999999 4554443
No 96
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=25.51 E-value=2e+02 Score=18.76 Aligned_cols=41 Identities=10% Similarity=0.079 Sum_probs=26.8
Q ss_pred cccCceEEEECC-eeEEEEEeeEecCCCCcccEEEEEEEEccCC
Q 033484 26 TIRKNGYIVIKG-RPCKVVEVSTSKTGKHGHAKCHFVGIDIFNG 68 (118)
Q Consensus 26 ~lkkG~~i~i~g-~P~~Vve~~~~kpGKhG~A~vrik~knl~TG 68 (118)
.+++|++|.+.. ..|+|..++....+. ...-.+.+.=....
T Consensus 1 mf~~GD~VVh~~~Gv~~i~~i~~~~~~~--~~~~yy~L~~~~~~ 42 (98)
T PF02559_consen 1 MFKIGDYVVHPNHGVGRIEGIEEIEFGG--EKQEYYVLEYADDD 42 (98)
T ss_dssp T--TTSEEEETTTEEEEEEEEEEEECTT--EEEEEEEEEECCCE
T ss_pred CCCCCCEEEECCCceEEEEEEEEEeeCC--eeEEEEEEEECCCC
Confidence 368999999965 699999999887743 33334555544444
No 97
>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=25.32 E-value=61 Score=23.59 Aligned_cols=23 Identities=22% Similarity=0.247 Sum_probs=16.1
Q ss_pred ccccCceEEEECCeeEEEEEeeE
Q 033484 25 GTIRKNGYIVIKGRPCKVVEVST 47 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~~Vve~~~ 47 (118)
..++.|+.|.++|....|.++..
T Consensus 59 ~pf~vGD~I~i~~~~G~V~~I~l 81 (206)
T PF00924_consen 59 RPFKVGDRIEIGGVEGRVEEIGL 81 (206)
T ss_dssp -SS-TT-EEESSS-EEEEEEE-S
T ss_pred CCccCCCEEEEEEeehHHHhcCc
Confidence 46899999999999999998643
No 98
>PF14623 Vint: Hint-domain
Probab=25.26 E-value=1.4e+02 Score=22.38 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=25.9
Q ss_pred eeEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEE
Q 033484 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60 (118)
Q Consensus 19 t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A~vri 60 (118)
..++++.+||+|+.|.=-..|-+|.-+-..+-...+...|++
T Consensus 15 ~~~v~i~~lR~G~~V~tp~G~r~V~~Vlkt~v~~~~~~lc~v 56 (162)
T PF14623_consen 15 RAPVRIDDLRAGDKVWTPRGPRKVAAVLKTPVESGSEDLCRV 56 (162)
T ss_pred ceeEEHHHccCCCEEECCCCCeEEEEEEEEeecCCceEEEEE
Confidence 345899999999998876566666544333222212455555
No 99
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=25.20 E-value=92 Score=20.69 Aligned_cols=21 Identities=14% Similarity=0.075 Sum_probs=18.1
Q ss_pred ccCCcEEEEEecCCCceeecE
Q 033484 65 IFNGKKLEDIVPSSHNCDVPH 85 (118)
Q Consensus 65 l~TG~~~e~t~~s~~~ve~~~ 85 (118)
+-+|+.++++|.+.+++..+.
T Consensus 12 lP~G~r~~rrF~~~~~L~~v~ 32 (82)
T cd01773 12 YPDGKREQIALPEQAKLLALV 32 (82)
T ss_pred CCCCCEEEEEeCCCCcHHHHH
Confidence 678999999999999998553
No 100
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=25.10 E-value=1.2e+02 Score=22.92 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=11.6
Q ss_pred ccccCceEEEECCeeE
Q 033484 25 GTIRKNGYIVIKGRPC 40 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~ 40 (118)
.-|+||+.|.++|++.
T Consensus 65 ~~l~KG~~V~VeGrL~ 80 (182)
T PRK08486 65 QYLSKGSKVLIEGRLT 80 (182)
T ss_pred HHcCCCCEEEEEEEEE
Confidence 4577888888877764
No 101
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. 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=24.97 E-value=97 Score=19.99 Aligned_cols=26 Identities=23% Similarity=0.178 Sum_probs=19.1
Q ss_pred EEEEEEEccCCcEEEEEecCCCceeec
Q 033484 58 CHFVGIDIFNGKKLEDIVPSSHNCDVP 84 (118)
Q Consensus 58 vrik~knl~TG~~~e~t~~s~~~ve~~ 84 (118)
+++.+| +-+|+.+..+|+.++.|..+
T Consensus 5 t~iqiR-lpdG~r~~~rF~~~~tv~~l 30 (79)
T cd01770 5 TSIQIR-LADGKRLVQKFNSSHRVSDV 30 (79)
T ss_pred eEEEEE-CCCCCEEEEEeCCCCcHHHH
Confidence 334333 57899999999999998643
No 102
>PF07472 PA-IIL: Fucose-binding lectin II (PA-IIL); InterPro: IPR010907 This entry represents calcium-mediated lectins. Structures have been determined for both fucose-binding lectin II (PA-IIL) [] and mannose-specific lectin II (RS-IIL) []. These proteins have homologous structures, their monomers consisting of a 9-stranded beta sandwich with Greek-key topology. Each monomer contains two calcium ions that mediate an exceptionally high binding affinity to the monosaccharide ligand in a recognition mode unique among carbohydrate-protein interactions. In Pseudomonas aeruginosa, PA-IIL contributes to the pathogenic virulence of the bacterium, functioning as a tetramer when binding fucose []. In the plant pathogen Ralstonia solanacearum (Pseudomonas solanacearum), RS-IIL recognises fucose, but displays much higher affinity to mannose and fructose, which is opposite to the preference of PA-IIL. ; PDB: 2WRA_A 2WR9_C 1OUX_C 2VUC_B 1GZT_C 2BOJ_D 2JDM_D 2JDH_D 1W8F_D 1UZV_A ....
Probab=24.56 E-value=1.5e+02 Score=20.84 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=20.4
Q ss_pred cccccCCCc-ceeeEEecccccCceEEEECCeeEEEEEeeEecCCC
Q 033484 8 FESKADAGA-SKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGK 52 (118)
Q Consensus 8 ~~~~~~~~~-~~t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~kpGK 52 (118)
|++++..+. ..|....+..=|.--.|..+|+||.+...+-.-+||
T Consensus 35 ~~G~g~~~~~~~t~~l~Sg~Gkv~i~v~~ngk~s~l~~~q~~l~~~ 80 (107)
T PF07472_consen 35 FTGSGTNDNNIGTKVLNSGSGKVRIEVTANGKPSKLRSSQNTLDGK 80 (107)
T ss_dssp EEEEEEEEEEEEEEEEE-TTSEEEEEEEETTEE-EEEEEEEEETTT
T ss_pred EEecccCCCceeeEEEecCCCeEEEEEEeCCccccceeeeeeccCc
Confidence 444444443 344444444222222344477777777665555554
No 103
>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=24.39 E-value=95 Score=17.09 Aligned_cols=18 Identities=6% Similarity=0.008 Sum_probs=13.4
Q ss_pred cCceEEEECCeeEEEEEe
Q 033484 28 RKNGYIVIKGRPCKVVEV 45 (118)
Q Consensus 28 kkG~~i~i~g~P~~Vve~ 45 (118)
..|+.|.++|..|+..-.
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 579999999999988543
No 104
>PRK06788 flagellar motor switch protein; Validated
Probab=24.09 E-value=1.3e+02 Score=21.45 Aligned_cols=46 Identities=15% Similarity=0.194 Sum_probs=27.7
Q ss_pred cccccCceEEEEC---CeeEEE----EEeeEecCCCCcccEEEEEEEEccCCcE
Q 033484 24 AGTIRKNGYIVIK---GRPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNGKK 70 (118)
Q Consensus 24 ~~~lkkG~~i~i~---g~P~~V----ve~~~~kpGKhG~A~vrik~knl~TG~~ 70 (118)
.-+|++|++|.++ ++|..| ..+-..+||..+ -..-+++..+.+.+.
T Consensus 52 lL~L~vGDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~-~~~AVrItei~~~~~ 104 (119)
T PRK06788 52 VKQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMD-EKFGIIISEIEADKK 104 (119)
T ss_pred HhCCCCCCEEEeCCcCCCCEEEEECCEEEEEEEEEEEC-CEEEEEEEEecChHH
Confidence 3468999999997 456555 223344556533 334477777776543
No 105
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=23.11 E-value=2.1e+02 Score=20.82 Aligned_cols=42 Identities=12% Similarity=0.199 Sum_probs=24.3
Q ss_pred ccccCceEEEEC---CeeEEEE----EeeEecCCCCcccEEEEEEEEccC
Q 033484 25 GTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (118)
Q Consensus 25 ~~lkkG~~i~i~---g~P~~Vv----e~~~~kpGKhG~A~vrik~knl~T 67 (118)
-+|++|++|.++ ++|..|. -+-...+|.++ -+.-+++.++.+
T Consensus 79 L~L~~GDVI~Ld~~~~epv~V~Vng~~if~GevGvv~-~k~AVrIteii~ 127 (137)
T PRK07963 79 LRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVVA-DKYGVRITDIIT 127 (137)
T ss_pred hCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEEC-CEEEEEEEEecC
Confidence 468999999998 5676663 23333444422 233455555554
No 106
>cd01179 IPT_plexin_repeat2 Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=22.97 E-value=2.1e+02 Score=18.15 Aligned_cols=32 Identities=16% Similarity=0.442 Sum_probs=24.4
Q ss_pred CCcceeeEEecccccCc--eEEEECCeeEEEEEe
Q 033484 14 AGASKTFPQQAGTIRKN--GYIVIKGRPCKVVEV 45 (118)
Q Consensus 14 ~~~~~t~~i~~~~lkkG--~~i~i~g~P~~Vve~ 45 (118)
..+-..-.|..+.|..| ..|.++|.+|.+...
T Consensus 13 ~~GGT~vtI~G~~~~~~~~~~V~ig~~~C~~~~~ 46 (85)
T cd01179 13 QSGGTRLTITGKHLNAGSSVRVTVGGQPCKILSV 46 (85)
T ss_pred CCCCEEEEEEEECCCCCCeEEEEECCeEeeEEEe
Confidence 34455667778888877 679999999999763
No 107
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.83 E-value=1.4e+02 Score=21.82 Aligned_cols=16 Identities=19% Similarity=0.412 Sum_probs=10.5
Q ss_pred ccccCceEEEECCeeE
Q 033484 25 GTIRKNGYIVIKGRPC 40 (118)
Q Consensus 25 ~~lkkG~~i~i~g~P~ 40 (118)
..|+||+.|.+.|++.
T Consensus 67 ~~l~KG~~V~V~G~L~ 82 (164)
T TIGR00621 67 QYLKKGSLVYVEGRLR 82 (164)
T ss_pred HhCCCCCEEEEEEEEE
Confidence 3567777777777654
No 108
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=22.39 E-value=3e+02 Score=19.66 Aligned_cols=62 Identities=18% Similarity=0.264 Sum_probs=38.1
Q ss_pred cccccCceEEEE-----CCeeEEEEEeeEe---cCCCCcccEEEEEEEEccCCcEEEEEecCC-CceeecEEE
Q 033484 24 AGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSS-HNCDVPHVT 87 (118)
Q Consensus 24 ~~~lkkG~~i~i-----~g~P~~Vve~~~~---kpGKhG~A~vrik~knl~TG~~~e~t~~s~-~~ve~~~ve 87 (118)
..++++|+.|.+ +|.-+.+--++-. .-|+ |-.. -+.++.+..|.-.|.+|+-. -.++.+.|-
T Consensus 18 iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~-G~~~-tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~ 88 (115)
T COG0335 18 IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGR-GISE-TFTVRKISYGVGVERVFPLHSPLIESIEVV 88 (115)
T ss_pred CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCC-Cccc-eEEEEEeecCceEEEEeecCCCceeEEEEE
Confidence 566777776653 5666665443322 2344 4333 47788889999999999864 334444443
No 109
>CHL00052 rpl2 ribosomal protein L2
Probab=22.25 E-value=3.1e+02 Score=22.24 Aligned_cols=51 Identities=18% Similarity=0.272 Sum_probs=27.4
Q ss_pred ccCceEEEECCee--EEEEEeeEecCCCCcccE-------EEEEEEEccCCcEEEEEecCCCcee
Q 033484 27 IRKNGYIVIKGRP--CKVVEVSTSKTGKHGHAK-------CHFVGIDIFNGKKLEDIVPSSHNCD 82 (118)
Q Consensus 27 lkkG~~i~i~g~P--~~Vve~~~~kpGKhG~A~-------vrik~knl~TG~~~e~t~~s~~~ve 82 (118)
++.|+++-+...| ..|-.++. +||+ |..+ +++..+ .+...-..++|++...
T Consensus 122 i~~Gn~lpL~~IP~Gt~I~NIE~-~pg~-Ggk~~RsAGt~A~ii~k---~~~~~~vkLPSGe~r~ 181 (273)
T CHL00052 122 IKIGNALPLTNIPLGTAIHNIEI-TPGK-GGQLARAAGAVAKLIAK---EGKSATLKLPSGEVRL 181 (273)
T ss_pred CCcccccccccCCCCCEEEEEEe-cCCC-CceEEEecCCeEEEEEe---cCCEEEEECCCCCeEE
Confidence 4444444444433 23444443 7888 4433 333333 4666777888887554
No 110
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=21.86 E-value=1.8e+02 Score=20.70 Aligned_cols=20 Identities=25% Similarity=0.169 Sum_probs=16.8
Q ss_pred eeEEecccccCceEEEECCe
Q 033484 19 TFPQQAGTIRKNGYIVIKGR 38 (118)
Q Consensus 19 t~~i~~~~lkkG~~i~i~g~ 38 (118)
|-+...-.+++|.+|..+|+
T Consensus 3 ~~~~~~~~~~kg~~l~~~Gd 22 (202)
T PRK13918 3 TTVVDTVTYRPGAVILYPGV 22 (202)
T ss_pred ccccceeEecCCCEEEcCCC
Confidence 55667778899999999998
No 111
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=21.79 E-value=1.3e+02 Score=22.52 Aligned_cols=15 Identities=27% Similarity=0.454 Sum_probs=9.1
Q ss_pred cccCceEEEECCeeE
Q 033484 26 TIRKNGYIVIKGRPC 40 (118)
Q Consensus 26 ~lkkG~~i~i~g~P~ 40 (118)
.|+||+.|.++|++.
T Consensus 69 ~LkKGs~V~VeGrL~ 83 (168)
T PRK06863 69 YLRKGSQVYVEGRLK 83 (168)
T ss_pred HCCCCCEEEEEEEEE
Confidence 366666666666554
No 112
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=21.68 E-value=3.4e+02 Score=21.34 Aligned_cols=87 Identities=14% Similarity=0.109 Sum_probs=46.2
Q ss_pred eeeEEecccccCce--EEEE---CCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEE---EecCCCceeecEEEee
Q 033484 18 KTFPQQAGTIRKNG--YIVI---KGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLED---IVPSSHNCDVPHVTRT 89 (118)
Q Consensus 18 ~t~~i~~~~lkkG~--~i~i---~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~---t~~s~~~ve~~~ve~~ 89 (118)
.+-.+++.+|++|+ +|+. ++..-.|-.+.-..- +.|.|++++.--+...-+-... +-+.||.+
T Consensus 16 ~~i~~~~~~l~vG~SGiV~h~~~~~~~~IiA~a~V~~~-~~g~A~~kf~~fd~L~Q~aLP~p~~~pk~GD~v-------- 86 (218)
T PF15436_consen 16 KIITFDAPDLKVGESGIVVHKFDKDHSSIIARAVVISK-KNGVAKAKFSVFDSLKQDALPTPKMVPKKGDEV-------- 86 (218)
T ss_pred CEEEecCCccccCCceEEEEEecCCcceeeeEEEEEEe-cCCeeEEEEeehhhhhhhcCCCCccccCCCCEE--------
Confidence 34455899999998 4443 222222222211111 1145777765544443221111 11234433
Q ss_pred eeEEEeccCCCeeEeecCCChHHHhh
Q 033484 90 DYQLIDISEDGFVCSYFVLSCSFYLS 115 (118)
Q Consensus 90 ~~qyly~d~d~~l~FMd~etyeq~~~ 115 (118)
-+.|+|... +|+-=|.|+|+++.+
T Consensus 87 il~~~Y~ra--llIAPn~e~Y~~i~~ 110 (218)
T PF15436_consen 87 ILNYLYNRA--LLIAPNQETYEKIKS 110 (218)
T ss_pred EEeecccce--EEEcCCHHHHHHHHH
Confidence 457888644 677889999999975
No 113
>TIGR00307 S8e ribosomal protein S8.e. Archaeal and eukaryotic ribosomal protein S8. This model could easily have been split into two models, one for eukaryotic S8 and one for archaeal S8; eukaryotic forms invariably have in insert of about 80 residues that archaeal forms of S8 do not.
Probab=21.32 E-value=1.5e+02 Score=21.39 Aligned_cols=30 Identities=23% Similarity=0.316 Sum_probs=22.7
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCccc
Q 033484 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHA 56 (118)
Q Consensus 23 ~~~~lkkG~~i~i~g~P~~Vve~~~~kpGKhG~A 56 (118)
..+-|.||.+|+.|=..++| ++.||++|..
T Consensus 91 R~niitKGaIIetd~g~A~V----TsrPgQdG~v 120 (127)
T TIGR00307 91 RRNVITKGAIVETDIGYARV----TSRPGQDGVV 120 (127)
T ss_pred hcCcEecceEEEEeeeEEEE----ecCCCcCceE
Confidence 35678999999998776666 4589998743
No 114
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=21.32 E-value=3.1e+02 Score=22.30 Aligned_cols=60 Identities=22% Similarity=0.303 Sum_probs=33.1
Q ss_pred eeeEEecccccCceEEEE--------------CCee--EEEEEeeEecCCCCccc-------EEEEEEEEccCCcEEEEE
Q 033484 18 KTFPQQAGTIRKNGYIVI--------------KGRP--CKVVEVSTSKTGKHGHA-------KCHFVGIDIFNGKKLEDI 74 (118)
Q Consensus 18 ~t~~i~~~~lkkG~~i~i--------------~g~P--~~Vve~~~~kpGKhG~A-------~vrik~knl~TG~~~e~t 74 (118)
..|.+-+..++.|+.|.. ...| ..|-.++. +||+ |.. .+++..+ .+...-..
T Consensus 101 ~~YIlAp~gl~~Gd~I~~g~~~~i~~Gn~lpL~~IP~Gt~I~NIE~-~pG~-Ggkl~RsAGt~A~ii~k---~~~~~~vk 175 (276)
T PRK09374 101 KRYILAPKGLKVGDTVVSGPDADIKPGNALPLRNIPVGTTVHNIEL-KPGK-GGQLARSAGTSAQLVAK---EGKYATLR 175 (276)
T ss_pred EEEEEecCCCCCCCEEEeCCCCCCCccCccccccCCCCCEEEEEEe-cCCC-CceeEeecCCeEEEEEe---cCCEEEEE
Confidence 346666666666666664 3322 23334443 7888 443 3334433 36666677
Q ss_pred ecCCCcee
Q 033484 75 VPSSHNCD 82 (118)
Q Consensus 75 ~~s~~~ve 82 (118)
++|++...
T Consensus 176 LPSGe~r~ 183 (276)
T PRK09374 176 LPSGEVRK 183 (276)
T ss_pred CCCCCeEE
Confidence 88876654
No 115
>PLN02835 oxidoreductase
Probab=21.19 E-value=3.5e+02 Score=23.73 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=33.0
Q ss_pred CceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEecCCCceeecE
Q 033484 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPH 85 (118)
Q Consensus 29 kG~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t~~s~~~ve~~~ 85 (118)
.++.+++||...-.+ ..+||| .+|+++.|.-.-..+...+. ++++.++.
T Consensus 190 ~~d~~liNG~~~~~~---~v~~G~----~yRlRliNa~~~~~~~f~i~-gH~~~VI~ 238 (539)
T PLN02835 190 FPDGVLINGQTQSTF---SGDQGK----TYMFRISNVGLSTSLNFRIQ-GHTMKLVE 238 (539)
T ss_pred CCceEEEccccCceE---EECCCC----EEEEEEEEcCCCccEEEEEC-CCEEEEEE
Confidence 357788999865444 357888 78888888877766655554 55555443
No 116
>cd07297 PX_PLD2 The phosphoinositide binding Phox Homology domain of Phospholipase D2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine to generate membrane-bound phosphatidic acid and choline. PLD activity has been detected in viruses, bacteria, yeast, plants, and mammals, but the PX domain is not present in PLDs from viruses and bacteria. PLDs are implicated in many cellular functions like signaling, cytoskeletal reorganization, vesicular transport, stress responses, and the control of differentiation, proliferation, and survival. PLD2 contains PX and Pleckstrin Homology (PH) domains in addition to the catalytic domain. It mediates EGF-dependent insulin secretion and EGF-induced Ras activation by the guanine nucleotide-exchange factor
Probab=20.82 E-value=1.8e+02 Score=21.23 Aligned_cols=26 Identities=19% Similarity=0.106 Sum_probs=18.6
Q ss_pred eEEEEEeeEecCCCCcc--cEEEEEEEE
Q 033484 39 PCKVVEVSTSKTGKHGH--AKCHFVGID 64 (118)
Q Consensus 39 P~~Vve~~~~kpGKhG~--A~vrik~kn 64 (118)
-|+|++++..+.|.|.- +.+.|++.+
T Consensus 5 ~~~V~~~er~~s~s~~~~~~lYtIeltH 32 (130)
T cd07297 5 TAKVENTERYTTGSKVHVCTLYTVRLTH 32 (130)
T ss_pred EEEEEEEEEeecccccccceeEEEEEec
Confidence 48999999988887644 555666554
No 117
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=20.82 E-value=2.5e+02 Score=20.90 Aligned_cols=43 Identities=12% Similarity=0.124 Sum_probs=24.1
Q ss_pred ccccCceEEEECC---eeEEEE----EeeEecCCCCcccEEEEEEEEccCC
Q 033484 25 GTIRKNGYIVIKG---RPCKVV----EVSTSKTGKHGHAKCHFVGIDIFNG 68 (118)
Q Consensus 25 ~~lkkG~~i~i~g---~P~~Vv----e~~~~kpGKhG~A~vrik~knl~TG 68 (118)
-+|++|++|.++- +|..|. -+-+..+|..+ -+.-+++.++.+.
T Consensus 98 L~L~~GDVI~Ldk~~~epv~V~VnG~~~f~Ge~Gvvn-~k~AVrIteii~~ 147 (155)
T PRK05698 98 LQLNQGSVIELDRLAGEPLDVLVNGTLIAHGEVVVVN-EKFGIRLTDVISP 147 (155)
T ss_pred hCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEEC-CEEEEEEEEecCc
Confidence 4689999999975 565552 22333444422 2334555555543
No 118
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=20.71 E-value=1e+02 Score=21.61 Aligned_cols=31 Identities=16% Similarity=0.258 Sum_probs=20.7
Q ss_pred eeEEecccccCceEEEECCeeEEEEEeeEec
Q 033484 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (118)
Q Consensus 19 t~~i~~~~lkkG~~i~i~g~P~~Vve~~~~k 49 (118)
+|.+..+++++|.+-.++|.|-.-..++..+
T Consensus 47 sYl~dp~~f~~G~~Y~i~~~~~~~F~V~yln 77 (102)
T PF08838_consen 47 SYLLDPSDFRPGEIYRIEGDPEEYFKVDYLN 77 (102)
T ss_dssp HCCS-GGGS-TT-EEEETTCCCEEEEEEEEE
T ss_pred HHhCChhhccCCCEEEecCCCCceEEEEEEe
Confidence 5678899999999999997665555555544
No 119
>COG1062 AdhC Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]
Probab=20.66 E-value=1.7e+02 Score=24.89 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=27.7
Q ss_pred eEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 033484 31 GYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (118)
Q Consensus 31 ~~i~i~g~P~~Vve~~~~kpGKhG~A~vrik~knl 65 (118)
-++.-.|+|..|.+++--.|++ |...+|++.-.+
T Consensus 6 AV~~~~~~Pl~i~ei~l~~P~~-gEVlVri~AtGV 39 (366)
T COG1062 6 AVAREAGKPLEIEEVDLDPPRA-GEVLVRITATGV 39 (366)
T ss_pred eeeecCCCCeEEEEEecCCCCC-CeEEEEEEEeec
Confidence 3444478999999999999999 888888887654
No 120
>PF06938 DUF1285: Protein of unknown function (DUF1285); InterPro: IPR010707 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.; PDB: 2RA9_A 2RE3_B.
Probab=20.60 E-value=1.8e+02 Score=21.31 Aligned_cols=23 Identities=26% Similarity=0.536 Sum_probs=17.5
Q ss_pred EEEECCeeEEEEEeeEecCCCCcc
Q 033484 32 YIVIKGRPCKVVEVSTSKTGKHGH 55 (118)
Q Consensus 32 ~i~i~g~P~~Vve~~~~kpGKhG~ 55 (118)
.|.+++.|+.|++++....|. |.
T Consensus 47 ~I~VEDaPf~iv~~~~~~~~~-~~ 69 (148)
T PF06938_consen 47 RIQVEDAPFLIVDVDVEGEGE-GQ 69 (148)
T ss_dssp EEEESS-SEEEEEEEECS-GC-CT
T ss_pred EEEEecCcEEEEEEEEeccCC-Cc
Confidence 478899999999999886666 55
No 121
>cd03445 Thioesterase_II_repeat2 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
Probab=20.42 E-value=2.6e+02 Score=18.24 Aligned_cols=36 Identities=8% Similarity=0.088 Sum_probs=26.8
Q ss_pred eeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEE
Q 033484 38 RPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDI 74 (118)
Q Consensus 38 ~P~~Vve~~~~kpGKhG~A~vrik~knl~TG~~~e~t 74 (118)
.+..-+...+..|+. ....+.++.+.|.+|+.+...
T Consensus 39 ~~~~s~~~~Fl~p~~-~~~pv~~~v~~lr~GRs~~~~ 74 (94)
T cd03445 39 RVPHSLHSYFLRPGD-PDQPIEYEVERLRDGRSFATR 74 (94)
T ss_pred CCeEEEEEEecCCCC-CCCCEEEEEEEEECCCcEEEE
Confidence 444456677888888 555678999999999987643
No 122
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=20.36 E-value=93 Score=19.89 Aligned_cols=21 Identities=10% Similarity=0.286 Sum_probs=17.7
Q ss_pred ccCCcEEEEEecCCCceeecE
Q 033484 65 IFNGKKLEDIVPSSHNCDVPH 85 (118)
Q Consensus 65 l~TG~~~e~t~~s~~~ve~~~ 85 (118)
+-+|+.+..+|++++++..+.
T Consensus 11 lp~G~~~~~~F~~~~tl~~v~ 31 (79)
T cd01772 11 LLDGTTLKQTFKAREQLAAVR 31 (79)
T ss_pred CCCCCEEEEEeCCCChHHHHH
Confidence 478999999999999998653
No 123
>PF14014 DUF4230: Protein of unknown function (DUF4230)
Probab=20.08 E-value=1.3e+02 Score=21.10 Aligned_cols=57 Identities=12% Similarity=0.059 Sum_probs=34.4
Q ss_pred cEEEEEEEEcc--------CCcEEEEEecCCCceeecEEEeeeeEEEeccCCCeeEeecCCChHHHh
Q 033484 56 AKCHFVGIDIF--------NGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVCSYFVLSCSFYL 114 (118)
Q Consensus 56 A~vrik~knl~--------TG~~~e~t~~s~~~ve~~~ve~~~~qyly~d~d~~l~FMd~etyeq~~ 114 (118)
+.+-+-++.+. .++.+..++|.-+-+ .+.++.....+...++ +++..++.+.+.+++
T Consensus 48 v~~GiDLs~i~~~~i~~d~~~~~i~I~LP~~~i~-~~~id~~~~~~~~~~~-~~~~~~~~~~~~~~~ 112 (157)
T PF14014_consen 48 VKAGIDLSKIKEEDIEVDEDGKTITITLPPPEIL-SVEIDEDSIKVYDEKG-GWFNPITPEDQNEAQ 112 (157)
T ss_pred EEEEEEhHHCCcceEEEcCCCCEEEEECCCcEEe-eeecCccceEEEEccC-CccCCCCHHHHHHHH
Confidence 44455555555 777888887765555 6667777777776544 444444555554443
Done!