Query 034069
Match_columns 104
No_of_seqs 116 out of 838
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:26:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034069.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034069hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03107 eukaryotic translatio 100.0 1.7E-39 3.7E-44 234.7 12.4 100 1-101 1-100 (159)
2 TIGR00037 eIF_5A translation i 100.0 2.5E-34 5.4E-39 201.8 10.9 87 16-102 1-87 (130)
3 PTZ00328 eukaryotic initiation 100.0 2.9E-34 6.4E-39 208.1 10.8 103 1-103 1-110 (166)
4 COG0231 Efp Translation elonga 100.0 1.5E-30 3.3E-35 182.9 10.9 82 20-102 2-83 (131)
5 PRK03999 translation initiatio 100.0 2.2E-30 4.8E-35 181.5 10.5 83 20-102 4-86 (129)
6 KOG3271 Translation initiation 100.0 9.1E-31 2E-35 185.9 6.9 101 1-103 1-101 (156)
7 PRK12426 elongation factor P; 100.0 1.9E-29 4.2E-34 186.1 10.5 81 21-102 1-81 (185)
8 PRK14578 elongation factor P; 100.0 5.8E-28 1.3E-32 178.5 10.8 82 21-102 1-83 (187)
9 PRK04542 elongation factor P; 100.0 6.5E-28 1.4E-32 178.5 10.7 82 21-102 1-83 (189)
10 PRK00529 elongation factor P; 99.9 1.3E-26 2.9E-31 170.6 10.3 81 21-102 1-81 (186)
11 TIGR02178 yeiP elongation fact 99.9 3.7E-26 8.1E-31 168.8 11.3 79 24-102 2-81 (186)
12 TIGR00038 efp translation elon 99.9 3.3E-26 7.2E-31 168.3 10.4 80 22-102 1-80 (184)
13 PF08207 EFP_N: Elongation fac 99.9 2.5E-23 5.4E-28 127.9 8.8 58 23-81 1-58 (58)
14 COG1499 NMD3 NMD protein affec 83.3 6.6 0.00014 32.0 7.3 58 11-78 231-288 (355)
15 PF01245 Ribosomal_L19: Riboso 81.5 8 0.00017 26.5 6.2 63 22-88 14-87 (113)
16 PF08605 Rad9_Rad53_bind: Fung 81.3 5.5 0.00012 28.1 5.4 41 21-61 54-103 (131)
17 PRK05338 rplS 50S ribosomal pr 80.0 10 0.00022 26.3 6.3 53 23-79 15-77 (116)
18 TIGR01024 rplS_bact ribosomal 74.4 18 0.00038 25.0 6.2 54 22-79 14-77 (113)
19 smart00676 DM10 Domains in hyp 71.9 3.4 7.3E-05 27.8 2.1 26 21-46 68-93 (104)
20 COG5131 URM1 Ubiquitin-like pr 70.0 3.2 7E-05 27.9 1.6 34 13-46 44-77 (96)
21 PF13275 S4_2: S4 domain; PDB: 69.3 6.6 0.00014 24.5 2.9 21 23-43 45-65 (65)
22 PF13785 DUF4178: Domain of un 69.2 5.3 0.00011 27.1 2.7 23 27-49 1-23 (140)
23 CHL00084 rpl19 ribosomal prote 68.9 36 0.00078 23.6 8.0 54 22-79 18-81 (117)
24 PF13856 Gifsy-2: ATP-binding 67.2 30 0.00066 22.3 5.9 38 12-49 48-88 (95)
25 PF03829 PTSIIA_gutA: PTS syst 64.3 9.2 0.0002 26.3 3.1 23 23-45 48-70 (117)
26 PF05354 Phage_attach: Phage H 62.2 7.6 0.00016 27.1 2.4 42 14-58 62-103 (117)
27 PRK10377 PTS system glucitol/s 61.0 12 0.00026 25.9 3.2 22 24-45 49-70 (120)
28 TIGR00849 gutA PTS system, glu 60.1 13 0.00028 25.8 3.2 22 24-45 49-70 (121)
29 COG0090 RplB Ribosomal protein 59.1 54 0.0012 26.0 6.8 54 25-82 122-183 (275)
30 PF12690 BsuPI: Intracellular 57.6 33 0.00072 21.9 4.7 44 57-101 3-47 (82)
31 smart00466 SRA SET and RING fi 57.3 43 0.00093 24.1 5.7 38 26-65 115-152 (155)
32 PF10665 Minor_capsid_1: Minor 57.1 15 0.00032 25.2 3.1 26 24-49 74-99 (114)
33 PF05521 Phage_H_T_join: Phage 57.0 42 0.00091 20.3 6.3 35 15-49 50-85 (95)
34 PRK11354 kil FtsZ inhibitor pr 56.5 17 0.00037 23.3 3.1 25 19-43 8-32 (73)
35 PF11871 DUF3391: Domain of un 54.4 7.9 0.00017 25.7 1.4 21 20-40 3-23 (128)
36 PF11302 DUF3104: Protein of u 52.4 59 0.0013 20.9 5.1 44 26-71 5-60 (75)
37 PRK11507 ribosome-associated p 52.4 16 0.00035 23.2 2.5 23 21-43 47-69 (70)
38 PF13144 SAF_2: SAF-like 51.1 89 0.0019 22.3 7.7 24 59-82 172-195 (196)
39 COG4043 Preprotein translocase 51.0 24 0.00051 24.3 3.2 21 25-45 32-54 (111)
40 COG2501 S4-like RNA binding pr 50.8 19 0.00041 23.1 2.6 22 24-45 50-71 (73)
41 PRK10883 FtsI repressor; Provi 50.3 54 0.0012 27.3 5.9 52 28-87 207-258 (471)
42 TIGR03170 flgA_cterm flagella 49.3 74 0.0016 21.0 7.6 24 59-82 98-121 (122)
43 PRK10965 multicopper oxidase; 47.8 70 0.0015 27.1 6.3 48 28-83 210-257 (523)
44 PRK12795 fliM flagellar motor 46.3 59 0.0013 26.7 5.5 44 24-68 320-370 (388)
45 COG1326 Uncharacterized archae 45.9 28 0.00062 26.3 3.3 29 23-52 71-99 (201)
46 cd01179 IPT_plexin_repeat2 Sec 45.6 73 0.0016 19.8 4.9 34 12-45 11-46 (85)
47 PF02182 SAD_SRA: SAD/SRA doma 44.9 56 0.0012 23.3 4.6 34 30-65 119-152 (155)
48 TIGR01397 fliM_switch flagella 44.6 48 0.001 25.7 4.6 31 24-54 271-308 (320)
49 PF10844 DUF2577: Protein of u 43.4 56 0.0012 21.5 4.2 24 21-44 71-98 (100)
50 PRK07018 flgA flagellar basal 42.8 1.4E+02 0.0031 22.3 7.7 26 59-84 209-234 (235)
51 PF08408 DNA_pol_B_3: DNA poly 42.1 85 0.0018 22.8 5.1 24 25-48 38-61 (149)
52 PF06605 Prophage_tail: Propha 41.8 84 0.0018 24.2 5.6 38 25-64 26-63 (327)
53 cd01771 Faf1_UBX Faf1 UBX doma 41.7 35 0.00075 21.7 2.8 26 58-84 5-30 (80)
54 PF00436 SSB: Single-strand bi 40.7 71 0.0015 20.0 4.3 16 25-40 64-79 (104)
55 PF07591 PT-HINT: Pretoxin HIN 39.7 41 0.0009 23.1 3.2 27 21-47 71-98 (130)
56 cd00603 IPT_PCSR IPT domain of 37.7 97 0.0021 19.0 6.8 33 12-44 11-46 (90)
57 PF00467 KOW: KOW motif; Inte 37.7 49 0.0011 17.1 2.6 21 29-49 1-26 (32)
58 PF00924 MS_channel: Mechanose 37.3 30 0.00064 24.6 2.2 24 24-47 58-81 (206)
59 PLN02792 oxidoreductase 37.0 1.1E+02 0.0025 26.0 6.0 54 29-87 178-231 (536)
60 PRK06804 flgA flagellar basal 35.9 2.1E+02 0.0045 22.2 7.5 25 59-83 235-259 (261)
61 PF11948 DUF3465: Protein of u 34.8 62 0.0013 22.9 3.5 38 24-61 83-126 (131)
62 cd01180 IPT_plexin_repeat1 Fir 34.7 63 0.0014 20.6 3.3 33 11-43 10-47 (94)
63 cd01767 UBX UBX (ubiquitin reg 33.6 34 0.00074 21.0 1.8 24 57-83 4-27 (77)
64 PF01079 Hint: Hint module; I 32.6 76 0.0016 23.9 3.9 44 17-61 22-70 (217)
65 PF08838 DUF1811: Protein of u 32.4 35 0.00075 23.3 1.8 33 17-49 45-77 (102)
66 COG1030 NfeD Membrane-bound se 32.3 1E+02 0.0023 26.0 4.9 31 22-52 383-414 (436)
67 cd04496 SSB_OBF SSB_OBF: A sub 31.6 88 0.0019 19.3 3.6 16 25-40 60-75 (100)
68 cd04709 BAH_MTA BAH, or Bromo 30.8 1E+02 0.0022 22.3 4.2 25 25-49 2-32 (164)
69 KOG1698 Mitochondrial/chloropl 30.6 2.4E+02 0.0053 21.4 7.0 51 23-77 93-152 (201)
70 COG4709 Predicted membrane pro 30.5 7.9 0.00017 29.2 -1.7 19 1-19 26-44 (195)
71 PF01079 Hint: Hint module; I 29.2 1E+02 0.0022 23.2 4.0 29 20-48 99-133 (217)
72 PF13989 YejG: YejG-like prote 29.1 54 0.0012 22.5 2.3 21 26-46 64-85 (106)
73 PRK09612 rpl2p 50S ribosomal p 29.0 90 0.0019 24.2 3.8 62 17-82 65-148 (238)
74 PF02839 CBM_5_12: Carbohydrat 28.7 72 0.0016 17.1 2.4 17 28-44 11-27 (41)
75 PRK13918 CRP/FNR family transc 28.7 1.2E+02 0.0026 21.1 4.2 20 19-38 3-22 (202)
76 PRK12617 flgA flagellar basal 28.5 2.6E+02 0.0056 21.0 7.8 26 59-84 188-213 (214)
77 TIGR02480 fliN flagellar motor 28.2 1.5E+02 0.0033 18.3 4.2 13 24-36 26-38 (77)
78 COG3721 HugX Putative heme iro 27.6 77 0.0017 23.4 3.0 47 51-97 94-140 (176)
79 PRK08486 single-stranded DNA-b 27.3 1.1E+02 0.0023 22.6 3.8 16 25-40 65-80 (182)
80 cd06555 ASCH_PF0470_like ASC-1 27.2 84 0.0018 21.4 3.0 22 16-37 16-42 (109)
81 TIGR01563 gp16_SPP1 phage head 27.0 1.6E+02 0.0035 18.2 6.1 19 24-42 63-81 (101)
82 COG1471 RPS4A Ribosomal protei 26.8 1.4E+02 0.003 23.3 4.4 65 21-88 147-212 (241)
83 PRK11835 hypothetical protein; 26.4 64 0.0014 22.4 2.3 22 25-46 66-88 (114)
84 PLN02835 oxidoreductase 26.3 2.6E+02 0.0056 23.8 6.4 49 29-85 190-238 (539)
85 smart00166 UBX Domain present 26.3 67 0.0015 19.8 2.3 25 56-83 5-29 (80)
86 PRK06788 flagellar motor switc 26.2 1.6E+02 0.0035 20.4 4.3 44 25-69 53-103 (119)
87 TIGR00621 ssb single stranded 25.4 1.2E+02 0.0026 21.6 3.7 16 25-40 67-82 (164)
88 COG3731 SrlB Phosphotransferas 25.4 92 0.002 21.9 3.0 26 21-46 46-71 (123)
89 PRK06666 fliM flagellar motor 25.3 1.6E+02 0.0034 23.1 4.6 43 24-67 276-325 (337)
90 cd01773 Faf1_like1_UBX Faf1 ik 24.9 97 0.0021 20.0 2.8 20 65-84 12-31 (82)
91 PF05096 Glu_cyclase_2: Glutam 24.9 3.4E+02 0.0074 21.3 7.6 76 17-101 36-113 (264)
92 PF07472 PA-IIL: Fucose-bindin 24.7 1.9E+02 0.0042 19.8 4.4 21 32-52 60-80 (107)
93 cd04477 RPA1N RPA1N: A subfami 24.6 21 0.00046 23.5 -0.3 29 15-43 54-82 (97)
94 PRK07963 fliN flagellar motor 24.1 2E+02 0.0043 20.3 4.6 42 25-67 79-127 (137)
95 PRK08119 flagellar motor switc 24.1 1.4E+02 0.0029 24.1 4.1 42 25-67 325-373 (382)
96 COG0335 RplS Ribosomal protein 23.8 2.6E+02 0.0056 19.4 7.4 62 24-87 18-88 (115)
97 PRK09812 toxin ChpB; Provision 23.1 73 0.0016 21.4 2.1 22 25-46 5-38 (116)
98 PRK06863 single-stranded DNA-b 23.0 1.2E+02 0.0026 22.1 3.3 16 25-40 68-83 (168)
99 PF00122 E1-E2_ATPase: E1-E2 A 22.6 83 0.0018 22.6 2.5 20 18-37 43-62 (230)
100 PRK05698 fliN flagellar motor 22.6 2.2E+02 0.0048 20.6 4.6 43 25-68 98-147 (155)
101 COG1047 SlpA FKBP-type peptidy 22.3 2.3E+02 0.005 20.9 4.7 21 26-46 90-114 (174)
102 PF08816 Ivy: Inhibitor of ver 22.1 2.3E+02 0.005 19.5 4.4 66 29-98 34-102 (118)
103 COG1838 FumA Tartrate dehydrat 21.8 31 0.00067 25.8 0.1 27 23-49 12-38 (184)
104 PRK13480 3'-5' exoribonuclease 21.8 3E+02 0.0065 21.9 5.6 51 23-78 4-54 (314)
105 PF14623 Vint: Hint-domain 21.6 2E+02 0.0043 21.0 4.2 41 20-60 16-56 (162)
106 PRK12786 flgA flagellar basal 21.5 4.3E+02 0.0094 21.2 7.7 26 59-84 291-316 (338)
107 PRK10334 mechanosensitive chan 21.3 1.3E+02 0.0029 23.4 3.5 24 25-48 128-151 (286)
108 PF13550 Phage-tail_3: Putativ 21.0 1.5E+02 0.0032 19.9 3.3 30 16-45 129-162 (164)
109 COG1062 AdhC Zn-dependent alco 20.8 1.8E+02 0.0039 24.1 4.2 34 31-65 6-39 (366)
110 cd01770 p47_UBX p47-like ubiqu 20.6 1.9E+02 0.0042 18.0 3.6 18 65-82 11-28 (79)
111 PRK08515 flgA flagellar basal 20.3 3.8E+02 0.0082 20.0 7.5 24 59-83 198-221 (222)
112 KOG4146 Ubiquitin-like protein 20.2 60 0.0013 22.0 1.2 37 20-57 56-92 (101)
113 PF00789 UBX: UBX domain; Int 20.2 1.1E+02 0.0023 18.7 2.3 24 58-82 7-30 (82)
114 PRK05753 nucleoside diphosphat 20.1 2E+02 0.0044 19.9 3.9 27 26-52 101-132 (137)
No 1
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=1.7e-39 Score=234.73 Aligned_cols=100 Identities=94% Similarity=1.450 Sum_probs=98.3
Q ss_pred CCccccccccccCCCceeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCc
Q 034069 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (104)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ 80 (104)
|||++|+|| +++|+++.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+++++
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 898778999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecEEEeeeEEEEEcCCCCC
Q 034069 81 CDVPHVTRTDYQLIDISEDGF 101 (104)
Q Consensus 81 ve~~~ve~~~~qylY~dgd~y 101 (104)
+++|+|++++|||||.|||+|
T Consensus 80 ve~~~ve~~~~qyly~dgd~y 100 (159)
T PLN03107 80 CDVPHVNRTDYQLIDISEDGF 100 (159)
T ss_pred EEEEEEEEEEEEEEEEcCCce
Confidence 999999999999999999997
No 2
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=2.5e-34 Score=201.76 Aligned_cols=87 Identities=49% Similarity=0.805 Sum_probs=84.0
Q ss_pred ceeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEE
Q 034069 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLID 95 (104)
Q Consensus 16 ~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY 95 (104)
++.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|++++++++|.|++++|||||
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 cCCCCCc
Q 034069 96 ISEDGFP 102 (104)
Q Consensus 96 ~dgd~y~ 102 (104)
.||+.|+
T Consensus 81 ~dg~~~~ 87 (130)
T TIGR00037 81 IMGGMVQ 87 (130)
T ss_pred ecCCEEE
Confidence 9988764
No 3
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=2.9e-34 Score=208.13 Aligned_cols=103 Identities=50% Similarity=0.907 Sum_probs=98.9
Q ss_pred CCcccccccc-ccCCCceeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCC
Q 034069 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (104)
Q Consensus 1 ~~~~~~~~~~-~~~~~~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~ 79 (104)
|||++|+|+. +++|+++.|||++++.||+|.+|+|+|+||+|++++++||||||+|++++.+.+||||+++|..+++.+
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 8998888995 699999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecEEEeeeEEEEEcCCC------CCcc
Q 034069 80 NCDVPHVTRTDYQLIDISED------GFPA 103 (104)
Q Consensus 80 ~ve~~~ve~~~~qylY~dgd------~y~~ 103 (104)
++++|.|+|++||+|.+++| +|++
T Consensus 81 nv~VP~V~r~~yqli~I~~d~~~~~~g~v~ 110 (166)
T PTZ00328 81 NVEVPFVKTFTYSVLDIQPNEDPSLPAHLS 110 (166)
T ss_pred eeEeeeEEeeEEEEEEEcCCCcccccceEE
Confidence 99999999999999999887 6764
No 4
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.5e-30 Score=182.88 Aligned_cols=82 Identities=35% Similarity=0.455 Sum_probs=78.9
Q ss_pred EEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCC
Q 034069 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (104)
Q Consensus 20 ~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd 99 (104)
.++++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++++++.|.|+++++||||.||+
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 5669999999999999999999999999999999999999999999
Q ss_pred CCc
Q 034069 100 GFP 102 (104)
Q Consensus 100 ~y~ 102 (104)
.|+
T Consensus 81 ~~~ 83 (131)
T COG0231 81 FYV 83 (131)
T ss_pred eEE
Confidence 875
No 5
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=99.97 E-value=2.2e-30 Score=181.54 Aligned_cols=83 Identities=37% Similarity=0.680 Sum_probs=80.1
Q ss_pred EEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCC
Q 034069 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (104)
Q Consensus 20 ~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd 99 (104)
.|+++++||+|++|+++|+||+|++++|+||||||+|++|+++|||+||+++|.+|+++++++.|.|+++++||||.||+
T Consensus 4 ~~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~ 83 (129)
T PRK03999 4 KQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGD 83 (129)
T ss_pred ccccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCC
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCc
Q 034069 100 GFP 102 (104)
Q Consensus 100 ~y~ 102 (104)
.|+
T Consensus 84 ~~~ 86 (129)
T PRK03999 84 VVQ 86 (129)
T ss_pred EEE
Confidence 653
No 6
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=9.1e-31 Score=185.95 Aligned_cols=101 Identities=71% Similarity=1.122 Sum_probs=98.7
Q ss_pred CCccccccccccCCCceeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCc
Q 034069 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (104)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ 80 (104)
|||++|+|+ .++|+++.|||++++.||++.+|+|+|+||+|+|.+++|.||||+|++.+..++||||+++|..++|.++
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 999999999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecEEEeeeEEEEEcCCCCCcc
Q 034069 81 CDVPHVTRTDYQLIDISEDGFPA 103 (104)
Q Consensus 81 ve~~~ve~~~~qylY~dgd~y~~ 103 (104)
+++|+++|.+||++.++++ |+|
T Consensus 80 ~dVp~vkr~~yqLidIsd~-~~s 101 (156)
T KOG3271|consen 80 MDVPVVKRVDYQLIDISDG-YLS 101 (156)
T ss_pred cccCccccceeEEEEecCC-eEE
Confidence 9999999999999999777 765
No 7
>PRK12426 elongation factor P; Provisional
Probab=99.96 E-value=1.9e-29 Score=186.12 Aligned_cols=81 Identities=14% Similarity=0.093 Sum_probs=78.7
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCCC
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd~ 100 (104)
|+++++||+|++|+++|+||.|++++|+|||| |+|++|+|+|||.||+++|+||+++++++.+.|++++|||||.||+.
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 46899999999999999999999999999999 99999999999999999999999999999999999999999999998
Q ss_pred Cc
Q 034069 101 FP 102 (104)
Q Consensus 101 y~ 102 (104)
|+
T Consensus 80 ~~ 81 (185)
T PRK12426 80 YL 81 (185)
T ss_pred EE
Confidence 75
No 8
>PRK14578 elongation factor P; Provisional
Probab=99.95 E-value=5.8e-28 Score=178.49 Aligned_cols=82 Identities=16% Similarity=0.229 Sum_probs=77.7
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCC-cccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCC
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKh-G~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd 99 (104)
++++++||+|++|+++|+||+|++++|+|||++ |+|++|+|+|||.||+++|++|++++++|.|+|+++++||||.||+
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 468899999999999999999999999999984 4679999999999999999999999999999999999999999999
Q ss_pred CCc
Q 034069 100 GFP 102 (104)
Q Consensus 100 ~y~ 102 (104)
.|+
T Consensus 81 ~~~ 83 (187)
T PRK14578 81 RGV 83 (187)
T ss_pred EEE
Confidence 875
No 9
>PRK04542 elongation factor P; Provisional
Probab=99.95 E-value=6.5e-28 Score=178.50 Aligned_cols=82 Identities=20% Similarity=0.245 Sum_probs=77.6
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecC-CCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCC
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISED 99 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~~~Kp-GKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd 99 (104)
++++++||+|++|+++|+||+|++++|+|| ||+|+|++|+|+|||.||+++|++|+|+++++.++|++++|||||.||+
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 578999999999999999999999999999 7933669999999999999999999999999999999999999999999
Q ss_pred CCc
Q 034069 100 GFP 102 (104)
Q Consensus 100 ~y~ 102 (104)
.|+
T Consensus 81 ~~~ 83 (189)
T PRK04542 81 EYV 83 (189)
T ss_pred EEE
Confidence 875
No 10
>PRK00529 elongation factor P; Validated
Probab=99.94 E-value=1.3e-26 Score=170.56 Aligned_cols=81 Identities=26% Similarity=0.360 Sum_probs=78.1
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCCC
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDG 100 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd~ 100 (104)
++++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++++++.+.++++++||||.||+.
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 46899999999999999999999999999999 99999999999999999999999999999999999999999999987
Q ss_pred Cc
Q 034069 101 FP 102 (104)
Q Consensus 101 y~ 102 (104)
|+
T Consensus 80 ~~ 81 (186)
T PRK00529 80 YV 81 (186)
T ss_pred EE
Confidence 63
No 11
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=99.94 E-value=3.7e-26 Score=168.75 Aligned_cols=79 Identities=15% Similarity=0.263 Sum_probs=74.7
Q ss_pred cccccCceEEEECCeeEEEEEeeEecCCCCccc-EEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCCCCc
Q 034069 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFP 102 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A-~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd~y~ 102 (104)
+++||+|++|+++|+||+|++++|+|||+.|+| ++|+|+|||.||+++|++|+++|+++.++|++++|||||.||+.|+
T Consensus 2 ~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~~~~ 81 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEYV 81 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCeEE
Confidence 689999999999999999999999999884544 8999999999999999999999999999999999999999999875
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=99.94 E-value=3.3e-26 Score=168.28 Aligned_cols=80 Identities=26% Similarity=0.365 Sum_probs=77.1
Q ss_pred EecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcCCCCC
Q 034069 22 QQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGF 101 (104)
Q Consensus 22 i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~dgd~y 101 (104)
+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||+++|++|+++++++.+.++++++||||.||+.|
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 c
Q 034069 102 P 102 (104)
Q Consensus 102 ~ 102 (104)
+
T Consensus 80 ~ 80 (184)
T TIGR00038 80 V 80 (184)
T ss_pred E
Confidence 4
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=99.90 E-value=2.5e-23 Score=127.89 Aligned_cols=58 Identities=29% Similarity=0.379 Sum_probs=53.5
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCce
Q 034069 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~v 81 (104)
+|+|||+|++|+++|+||.|++++|++||| |+|++|+++|||.||+++|.+|+++|+|
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
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=83.31 E-value=6.6 Score=31.95 Aligned_cols=58 Identities=19% Similarity=0.239 Sum_probs=44.1
Q ss_pred ccCCCceeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCC
Q 034069 11 KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS 78 (104)
Q Consensus 11 ~~~~~~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~ 78 (104)
++-.-...||-+..-++++|++|.++|..+.++.. -|+ .+.+++|.|++..+.++...
T Consensus 231 tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~~----~~~------~~~~~dl~t~e~~~~~~~~~ 288 (355)
T COG1499 231 TGKRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVRS----IGK------GIVVLDLETGEPVEITWSVY 288 (355)
T ss_pred CCceEEEEEEEEECCCCCCCCEEEECCCeEEEEEE----ecC------ceEEEecccCCccccChhhc
Confidence 44445667888999999999999999976655532 255 38899999998887777533
No 15
>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=81.49 E-value=8 Score=26.53 Aligned_cols=63 Identities=16% Similarity=0.248 Sum_probs=40.3
Q ss_pred EecccccCceEEEE-----CCeeEEEEE-----eeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCc-eeecEEEe
Q 034069 22 QQAGTIRKNGYIVI-----KGRPCKVVE-----VSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN-CDVPHVTR 88 (104)
Q Consensus 22 i~~~~lkkG~~I~i-----~g~p~~Vve-----~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~-ve~~~ve~ 88 (104)
.+..+|++|++|.+ +|....+.. +....-|= + --+.++|++.|.-+|.+|+-..+ ++.+.|-+
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~-~---ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~ 87 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGL-N---SSFTLRNISQGVGVERVFPLYSPLIKSIEVLR 87 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSST-S---SEEEEEEEETTEEEEEEEETTSTTEEEEEEEE
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCC-C---eeEEEEEEecCccEEEEEEcCCCCeEEEEEEE
Confidence 45678999998865 354444332 33332222 2 24789999999999999996644 55454444
No 16
>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=81.33 E-value=5.5 Score=28.06 Aligned_cols=41 Identities=12% Similarity=0.093 Sum_probs=30.9
Q ss_pred EEecccccCceEEEECCe--eEEEEEeeEec--CC-----CCcccEEEEE
Q 034069 21 PQQAGTIRKNGYIVIKGR--PCKVVEVSTSK--TG-----KHGHAKCHFV 61 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~--p~~Vve~~~~K--pG-----KhG~A~vr~k 61 (104)
-+-.=|||.|+.|.+++. +|+|+-+.+.- +. -+|.+.|.+|
T Consensus 54 dv~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk 103 (131)
T PF08605_consen 54 DVKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLK 103 (131)
T ss_pred cEeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEE
Confidence 356679999999999998 89999988872 22 1267766663
No 17
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=80.01 E-value=10 Score=26.25 Aligned_cols=53 Identities=19% Similarity=0.311 Sum_probs=36.0
Q ss_pred ecccccCceEEEE-----CCeeEEE-----EEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCC
Q 034069 23 QAGTIRKNGYIVI-----KGRPCKV-----VEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (104)
Q Consensus 23 ~~~~lkkG~~I~i-----~g~p~~V-----ve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~ 79 (104)
...++++|++|.+ +|....+ +-+... ++ | .--.+.+||++.|--.|.+|+...
T Consensus 15 ~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~--~~-G-~~~tftvRki~~gvGVEr~fpl~S 77 (116)
T PRK05338 15 DIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARR--GR-G-LNETFTVRKISYGVGVERTFPLHS 77 (116)
T ss_pred CCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEe--CC-C-CCceEEEEEcccCccEEEEecCCC
Confidence 4678999998865 5654333 333333 22 2 223589999999999999998654
No 18
>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=74.37 E-value=18 Score=24.97 Aligned_cols=54 Identities=20% Similarity=0.308 Sum_probs=35.7
Q ss_pred EecccccCceEEEE-----CCeeEEE-----EEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCC
Q 034069 22 QQAGTIRKNGYIVI-----KGRPCKV-----VEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (104)
Q Consensus 22 i~~~~lkkG~~I~i-----~g~p~~V-----ve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~ 79 (104)
.+..++++|+.|.+ +|....+ +.+... ++ |- --.+.+||++.|--.|.+|+...
T Consensus 14 ~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~--~~-G~-~~tftvR~i~~gvGVEr~fpl~S 77 (113)
T TIGR01024 14 KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARR--GG-GI-GETFTVRKISYGVGVERIFPLHS 77 (113)
T ss_pred cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEe--CC-CC-ceEEEEEEeccCccEEEEEEcCC
Confidence 45678999998876 4433332 223332 33 22 23589999999999999998654
No 19
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=71.86 E-value=3.4 Score=27.75 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=23.5
Q ss_pred EEecccccCceEEEECCeeEEEEEee
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVS 46 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~ 46 (104)
..+..||..|..|.|.|.++.|+++.
T Consensus 68 ~y~~~Dl~vG~~v~i~gr~f~I~d~D 93 (104)
T smart00676 68 YYHASDLNVGTTINVFGRQFRIYDCD 93 (104)
T ss_pred ccCHHHcCCCCEEEEeCEEEEEEECC
Confidence 46788999999999999999999874
No 20
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=69.98 E-value=3.2 Score=27.85 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=30.1
Q ss_pred CCCceeeEEEecccccCceEEEECCeeEEEEEee
Q 034069 13 DAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVS 46 (104)
Q Consensus 13 ~~~~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~ 46 (104)
.|++....-+.-++||+|..+++|+.-|.+++-+
T Consensus 44 ~~p~~~sifie~g~lrpGiI~LINd~DWeLleke 77 (96)
T COG5131 44 YAPTRDSIFIEHGELRPGIICLINDMDWELLEKE 77 (96)
T ss_pred hCCccceeeecCCCCcccEEEEEcCccHhhhhcc
Confidence 5678888889999999999999999999998754
No 21
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=69.30 E-value=6.6 Score=24.48 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=14.8
Q ss_pred ecccccCceEEEECCeeEEEE
Q 034069 23 QAGTIRKNGYIVIKGRPCKVV 43 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~p~~Vv 43 (104)
....|++|++|.++|..++|+
T Consensus 45 rg~Kl~~GD~V~~~~~~~~Vv 65 (65)
T PF13275_consen 45 RGKKLRPGDVVEIDGEEYRVV 65 (65)
T ss_dssp SS----SSEEEEETTEEEEEE
T ss_pred cCCcCCCCCEEEECCEEEEEC
Confidence 356789999999999999885
No 22
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=69.22 E-value=5.3 Score=27.07 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=19.0
Q ss_pred ccCceEEEECCeeEEEEEeeEec
Q 034069 27 IRKNGYIVIKGRPCKVVEVSTSK 49 (104)
Q Consensus 27 lkkG~~I~i~g~p~~Vve~~~~K 49 (104)
|++|+.+.++|.+|.|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999997655443
No 23
>CHL00084 rpl19 ribosomal protein L19
Probab=68.87 E-value=36 Score=23.60 Aligned_cols=54 Identities=13% Similarity=0.196 Sum_probs=36.5
Q ss_pred EecccccCceEEEE-----CCe-----eEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCC
Q 034069 22 QQAGTIRKNGYIVI-----KGR-----PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (104)
Q Consensus 22 i~~~~lkkG~~I~i-----~g~-----p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~ 79 (104)
....++++|++|.+ +|. ++.=+-+... |+ |-. -.+.+|+++.|--.|.+|+...
T Consensus 18 ~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r--~~-G~~-~tftvRki~~gvGVEr~fpl~S 81 (117)
T CHL00084 18 KNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKK--NS-GLN-TTITVRKVFQGIGVERVFLLHS 81 (117)
T ss_pred cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEe--CC-CCC-eeEEEEEeccCccEEEEEecCC
Confidence 35678999998875 454 3333333432 33 322 3489999999999999998654
No 24
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=67.17 E-value=30 Score=22.31 Aligned_cols=38 Identities=16% Similarity=0.227 Sum_probs=22.7
Q ss_pred cCCCceeeEEEeccccc---CceEEEECCeeEEEEEeeEec
Q 034069 12 ADAGASKTFPQQAGTIR---KNGYIVIKGRPCKVVEVSTSK 49 (104)
Q Consensus 12 ~~~~~~~t~~i~~~~lk---kG~~I~i~g~p~~Vve~~~~K 49 (104)
+-++++.+..+..+++. +|+.|.++|+-|.|.++..--
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 33456666667766654 899999999999999887653
No 25
>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=64.29 E-value=9.2 Score=26.32 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=15.7
Q ss_pred ecccccCceEEEECCeeEEEEEe
Q 034069 23 QAGTIRKNGYIVIKGRPCKVVEV 45 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~p~~Vve~ 45 (104)
...+|++|+.+.|++..|.|+.+
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 45789999999999999999854
No 26
>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=62.22 E-value=7.6 Score=27.07 Aligned_cols=42 Identities=10% Similarity=0.106 Sum_probs=25.7
Q ss_pred CCceeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEE
Q 034069 14 AGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKC 58 (104)
Q Consensus 14 ~~~~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~v 58 (104)
+++-......+..||+++.|.|.|++|.|-+ +-|--+|...+
T Consensus 62 ~Pslfv~t~dv~~L~r~DtL~I~g~~y~Vd~---v~pD~~G~t~I 103 (117)
T PF05354_consen 62 SPSLFVRTADVSGLKRRDTLTIGGESYWVDR---VGPDGGGSTRI 103 (117)
T ss_dssp S-EEEESCCCCCTS-TT-EEEETTTEEEBS------SSSSS-CCE
T ss_pred CceEEEEehHhhhhhcCCeEEECCEEEEEEe---eccCCCccEEE
Confidence 4555566677899999999999999999854 44532354433
No 27
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=61.01 E-value=12 Score=25.89 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=19.6
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 034069 24 AGTIRKNGYIVIKGRPCKVVEV 45 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~Vve~ 45 (104)
..+|++|+.+.+++.-|.|+.+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAV 70 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEE
Confidence 5779999999999999999764
No 28
>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=60.09 E-value=13 Score=25.82 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=19.2
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 034069 24 AGTIRKNGYIVIKGRPCKVVEV 45 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~Vve~ 45 (104)
..+|++|+.+.+++.-|.|+.+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (121)
T TIGR00849 49 KGTLKPGQVFMIGGIAYPVTAV 70 (121)
T ss_pred cCCcCCCCEEEECCEEEEEEEE
Confidence 3579999999999999999764
No 29
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=59.07 E-value=54 Score=25.98 Aligned_cols=54 Identities=20% Similarity=0.287 Sum_probs=31.6
Q ss_pred ccccCceEEEECCeeE-EEEEeeEecCCCCcc-------cEEEEEEEEccCCcEEEEEEcCCCcee
Q 034069 25 GTIRKNGYIVIKGRPC-KVVEVSTSKTGKHGH-------AKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~-~Vve~~~~KpGKhG~-------A~vr~k~knl~TG~~~E~tf~s~~~ve 82 (104)
.+|+.|..+-|.+.|- .+|..--.+||+ |. +.+++..++ |...--.++|++.-.
T Consensus 122 a~ik~GN~lpL~~IP~Gt~VhNVE~~pG~-GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~r~ 183 (275)
T COG0090 122 ADIKPGNALPLGNIPEGTIVHNVELKPGD-GGQLARSAGTYAQVVGKE---GNYVIVRLPSGEMRK 183 (275)
T ss_pred CCcCCcceeeeccCCCCceEEeeeeccCC-CceEEEeCCceEEEEEcc---CCEEEEECCCCCeEe
Confidence 3556666665655552 123333347998 54 345566666 666667788887643
No 30
>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=57.62 E-value=33 Score=21.86 Aligned_cols=44 Identities=9% Similarity=-0.063 Sum_probs=23.5
Q ss_pred EEEEEEEEccCCcEEEEEEcCCCceeecEE-EeeeEEEEEcCCCCC
Q 034069 57 KCHFVGIDIFNGKKLEDIVPSSHNCDVPHV-TRTDYQLIDISEDGF 101 (104)
Q Consensus 57 ~vr~k~knl~TG~~~E~tf~s~~~ve~~~v-e~~~~qylY~dgd~y 101 (104)
.+.++++|.-+.. ++.+|+++.++|.... ..-+--|-|.+|-.|
T Consensus 3 ~~~l~v~N~s~~~-v~l~f~sgq~~D~~v~d~~g~~vwrwS~~~~F 47 (82)
T PF12690_consen 3 EFTLTVTNNSDEP-VTLQFPSGQRYDFVVKDKEGKEVWRWSDGKMF 47 (82)
T ss_dssp EEEEEEEE-SSS--EEEEESSS--EEEEEE-TT--EEEETTTT---
T ss_pred EEEEEEEeCCCCe-EEEEeCCCCEEEEEEECCCCCEEEEecCCchh
Confidence 4667777765544 6788888888888777 344444555444433
No 31
>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=57.29 E-value=43 Score=24.15 Aligned_cols=38 Identities=18% Similarity=0.245 Sum_probs=28.3
Q ss_pred cccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 034069 26 TIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (104)
Q Consensus 26 ~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl 65 (104)
..+++..+.+|| +|+|+++-.. +|++|....|.+|+-+
T Consensus 115 ~~~p~~gyrYDG-LY~V~~~w~e-~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 115 KYAPGKGYIYDG-LYRIVDYWRE-VGKSGFLVFKFKLVRI 152 (155)
T ss_pred CCCCCCeEEECc-EEEEEEEEEe-cCCCCcEEEEEEEEeC
Confidence 456677778887 7999987544 4777888889998865
No 32
>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=57.13 E-value=15 Score=25.15 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=22.9
Q ss_pred cccccCceEEEECCeeEEEEEeeEec
Q 034069 24 AGTIRKNGYIVIKGRPCKVVEVSTSK 49 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~Vve~~~~K 49 (104)
+-+++.|+.|.++|..|.|.++...-
T Consensus 74 ~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 74 FPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred ccccCCCCEEEECCceEEEEEEEecc
Confidence 35888999999999999999988766
No 33
>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=57.00 E-value=42 Score=20.35 Aligned_cols=35 Identities=11% Similarity=0.193 Sum_probs=23.5
Q ss_pred CceeeEEEecc-cccCceEEEECCeeEEEEEeeEec
Q 034069 15 GASKTFPQQAG-TIRKNGYIVIKGRPCKVVEVSTSK 49 (104)
Q Consensus 15 ~~~~t~~i~~~-~lkkG~~I~i~g~p~~Vve~~~~K 49 (104)
.....+.+.-. +|..++.|.++|..|.|..+....
T Consensus 50 ~~t~~~~iR~~~~I~~~~ri~~~g~~y~I~~i~~~~ 85 (95)
T PF05521_consen 50 EITHRFTIRYRKDITPDMRIKYDGKVYNIKSIDPDD 85 (95)
T ss_dssp TTEEEEEECS-TTSSTTEEEEECTEEEEE-S--EE-
T ss_pred ceEEEEEEecCcCCCcceEEEECCEEEEEEEECCCC
Confidence 33455555544 599999999999999999877655
No 34
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=56.47 E-value=17 Score=23.26 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=21.7
Q ss_pred eEEEecccccCceEEEECCeeEEEE
Q 034069 19 TFPQQAGTIRKNGYIVIKGRPCKVV 43 (104)
Q Consensus 19 t~~i~~~~lkkG~~I~i~g~p~~Vv 43 (104)
|.+++-..+.+|+.|..+|+-|..-
T Consensus 8 T~~v~Rq~V~PG~~v~~~grty~AS 32 (73)
T PRK11354 8 TDEIPRQCVTPGDYVLHEGRTYIAS 32 (73)
T ss_pred ceeecccccCCceEEEEcCcEEEEE
Confidence 6778889999999999999999653
No 35
>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=54.41 E-value=7.9 Score=25.72 Aligned_cols=21 Identities=10% Similarity=0.091 Sum_probs=16.4
Q ss_pred EEEecccccCceEEEECCeeE
Q 034069 20 FPQQAGTIRKNGYIVIKGRPC 40 (104)
Q Consensus 20 ~~i~~~~lkkG~~I~i~g~p~ 40 (104)
..|++++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 358899999999997655554
No 36
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=52.39 E-value=59 Score=20.93 Aligned_cols=44 Identities=9% Similarity=0.212 Sum_probs=29.0
Q ss_pred cccCceEEEECCee------------EEEEEeeEecCCCCcccEEEEEEEEccCCcEE
Q 034069 26 TIRKNGYIVIKGRP------------CKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKL 71 (104)
Q Consensus 26 ~lkkG~~I~i~g~p------------~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~ 71 (104)
.+|.|++|++.... ..|+.+.-. .|...+---+..-|+-||.+.
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 47999999998766 455544432 232334445788899999865
No 37
>PRK11507 ribosome-associated protein; Provisional
Probab=52.37 E-value=16 Score=23.16 Aligned_cols=23 Identities=17% Similarity=0.267 Sum_probs=18.6
Q ss_pred EEecccccCceEEEECCeeEEEE
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVV 43 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vv 43 (104)
.-..-.|++|+.|.++|.-++|+
T Consensus 47 ~rRgkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 47 TRKRCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred cccCCCCCCCCEEEECCEEEEEe
Confidence 34456899999999999888775
No 38
>PF13144 SAF_2: SAF-like
Probab=51.06 E-value=89 Score=22.33 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=19.0
Q ss_pred EEEEEEccCCcEEEEEEcCCCcee
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve 82 (104)
.++++|+.||+++.-+.-+...++
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 488899999998888877766665
No 39
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.95 E-value=24 Score=24.29 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=15.3
Q ss_pred ccccCceEEEECCe--eEEEEEe
Q 034069 25 GTIRKNGYIVIKGR--PCKVVEV 45 (104)
Q Consensus 25 ~~lkkG~~I~i~g~--p~~Vve~ 45 (104)
-.||+|+.|+++|. |..|+++
T Consensus 32 r~ik~GD~IiF~~~~l~v~V~~v 54 (111)
T COG4043 32 RQIKPGDKIIFNGDKLKVEVIDV 54 (111)
T ss_pred cCCCCCCEEEEcCCeeEEEEEEE
Confidence 56899999999975 4444443
No 40
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=50.78 E-value=19 Score=23.06 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.6
Q ss_pred cccccCceEEEECCeeEEEEEe
Q 034069 24 AGTIRKNGYIVIKGRPCKVVEV 45 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~Vve~ 45 (104)
.-.|+.|+.|.+.|.++.|+..
T Consensus 50 gkKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 50 GKKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CCEeecCCEEEECCEEEEEEec
Confidence 4568999999999999998753
No 41
>PRK10883 FtsI repressor; Provisional
Probab=50.31 E-value=54 Score=27.32 Aligned_cols=52 Identities=13% Similarity=0.128 Sum_probs=37.3
Q ss_pred cCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEE
Q 034069 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVT 87 (104)
Q Consensus 28 kkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve 87 (104)
..|+.+.+||..+-++++ +||+ +|+++.|.-+-+.+...+..++.+.++-.+
T Consensus 207 ~~gd~~lvNG~~~p~~~v---~~~~-----~RlRliNas~~~~~~l~l~d~~~~~vIa~D 258 (471)
T PRK10883 207 FVGDTLLVNGVQSPYVEV---SRGW-----VRLRLLNASNARRYQLQMSDGRPLHVIAGD 258 (471)
T ss_pred ccCCeeEECCccCCeEEe---cCCE-----EEEEEEEccCCceEEEEEcCCCeEEEEEeC
Confidence 468899999987766644 3443 799999999888888887555555544433
No 42
>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=49.34 E-value=74 Score=20.96 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=18.4
Q ss_pred EEEEEEccCCcEEEEEEcCCCcee
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCD 82 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve 82 (104)
.++++|+.+|+++.-+..+...++
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 478889999999887776665554
No 43
>PRK10965 multicopper oxidase; Provisional
Probab=47.82 E-value=70 Score=27.12 Aligned_cols=48 Identities=8% Similarity=-0.042 Sum_probs=34.1
Q ss_pred cCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceee
Q 034069 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83 (104)
Q Consensus 28 kkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~ 83 (104)
..|+.+.+||.++-.+.. ||+ .+|+++.|--+-+.+...+..+.++.+
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 468899999997754432 343 689999999888887777755555443
No 44
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=46.30 E-value=59 Score=26.68 Aligned_cols=44 Identities=7% Similarity=0.142 Sum_probs=28.8
Q ss_pred cccccCceEEEECC---eeEEE----EEeeEecCCCCcccEEEEEEEEccCC
Q 034069 24 AGTIRKNGYIVIKG---RPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNG 68 (104)
Q Consensus 24 ~~~lkkG~~I~i~g---~p~~V----ve~~~~KpGKhG~A~vr~k~knl~TG 68 (104)
.-+|++|++|.++- .|..| +..-..+||++|.- +=+++......
T Consensus 320 lL~LkvGDVI~Ld~~~~~~v~v~v~g~p~F~g~~G~~~g~-~AvrI~~~l~~ 370 (388)
T PRK12795 320 VLNLKVGDTLMLDARPDALVTLRCGDVPLTEGRMGRVGDR-VAVRVEKPLRK 370 (388)
T ss_pred HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEeccCCCE-EEEEEEeecCC
Confidence 45789999999984 35555 34566789986543 33666665543
No 45
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=45.93 E-value=28 Score=26.35 Aligned_cols=29 Identities=17% Similarity=0.345 Sum_probs=24.3
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCC
Q 034069 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGK 52 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~p~~Vve~~~~KpGK 52 (104)
+--.|++|+.|.++|+-..|++++. ++||
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 3456899999999999999999997 4566
No 46
>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=45.58 E-value=73 Score=19.80 Aligned_cols=34 Identities=15% Similarity=0.414 Sum_probs=26.1
Q ss_pred cCCCceeeEEEecccccCc--eEEEECCeeEEEEEe
Q 034069 12 ADAGASKTFPQQAGTIRKN--GYIVIKGRPCKVVEV 45 (104)
Q Consensus 12 ~~~~~~~t~~i~~~~lkkG--~~I~i~g~p~~Vve~ 45 (104)
+....-...+|..+.|..| ..|.++|.+|.++..
T Consensus 11 Gp~~GGT~vtI~G~~~~~~~~~~V~ig~~~C~~~~~ 46 (85)
T cd01179 11 GPQSGGTRLTITGKHLNAGSSVRVTVGGQPCKILSV 46 (85)
T ss_pred CCCCCCEEEEEEEECCCCCCeEEEEECCeEeeEEEe
Confidence 4445555677888888887 679999999999763
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=44.92 E-value=56 Score=23.31 Aligned_cols=34 Identities=29% Similarity=0.369 Sum_probs=24.9
Q ss_pred ceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 034069 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (104)
Q Consensus 30 G~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl 65 (104)
+..+.+|| +|+|+++...+ |+.|....+++|+-+
T Consensus 119 ~g~yrYDG-LY~V~~~w~~~-g~~G~~v~kF~L~R~ 152 (155)
T PF02182_consen 119 GGIYRYDG-LYKVVKYWREK-GKSGFKVFKFKLVRL 152 (155)
T ss_dssp SS-EEEEE-EEEEEEEEEEE--TTSSEEEEEEEEE-
T ss_pred CCCEEeCc-EEEEEEEEEEe-CCCCcEEEEEEEEEC
Confidence 44568888 99999998876 444788899998765
No 48
>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=44.63 E-value=48 Score=25.73 Aligned_cols=31 Identities=10% Similarity=0.115 Sum_probs=20.7
Q ss_pred cccccCceEEEEC---CeeEEE----EEeeEecCCCCc
Q 034069 24 AGTIRKNGYIVIK---GRPCKV----VEVSTSKTGKHG 54 (104)
Q Consensus 24 ~~~lkkG~~I~i~---g~p~~V----ve~~~~KpGKhG 54 (104)
.-+|++|++|.++ ++|..| ..+-..++|+++
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 4578999999998 356665 234555666654
No 49
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=43.35 E-value=56 Score=21.46 Aligned_cols=24 Identities=8% Similarity=0.224 Sum_probs=17.6
Q ss_pred EEecccccCceEEEE----CCeeEEEEE
Q 034069 21 PQQAGTIRKNGYIVI----KGRPCKVVE 44 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i----~g~p~~Vve 44 (104)
..-.+.|++|+.|++ +|+-|.|++
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 344578999998765 677787775
No 50
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=42.82 E-value=1.4e+02 Score=22.35 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=21.5
Q ss_pred EEEEEEccCCcEEEEEEcCCCceeec
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve~~ 84 (104)
.++++|+.||+++.-+..+...+++.
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V~ 234 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEVN 234 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEEe
Confidence 48888999999999888888777653
No 51
>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=42.12 E-value=85 Score=22.75 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=19.9
Q ss_pred ccccCceEEEECCeeEEEEEeeEe
Q 034069 25 GTIRKNGYIVIKGRPCKVVEVSTS 48 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~~Vve~~~~ 48 (104)
.=|+.|.+|.|++.+|+|++-...
T Consensus 38 ~VL~TgNYitI~d~v~kI~~K~i~ 61 (149)
T PF08408_consen 38 EVLSTGNYITINDDVYKILDKDII 61 (149)
T ss_pred HHHhcCCeEEECCeeeeeeccccc
Confidence 447899999999999999976443
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=41.82 E-value=84 Score=24.21 Aligned_cols=38 Identities=16% Similarity=0.297 Sum_probs=22.6
Q ss_pred ccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEE
Q 034069 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~kn 64 (104)
.-|..+..|.++|+.|.|..+....-|. +. .+.+.+.+
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 5688999999999999999888776554 33 37888888
No 53
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=41.68 E-value=35 Score=21.66 Aligned_cols=26 Identities=15% Similarity=-0.021 Sum_probs=19.4
Q ss_pred EEEEEEEccCCcEEEEEEcCCCceeec
Q 034069 58 CHFVGIDIFNGKKLEDIVPSSHNCDVP 84 (104)
Q Consensus 58 vr~k~knl~TG~~~E~tf~s~~~ve~~ 84 (104)
+++.+| |-+|+..+++|.+.+++..+
T Consensus 5 ~~i~iR-lP~G~r~~rrF~~t~~L~~l 30 (80)
T cd01771 5 SKLRVR-TPSGDFLERRFLGDTPLQVL 30 (80)
T ss_pred EEEEEE-CCCCCEEEEEeCCCCcHHHH
Confidence 344433 67899999999999998643
No 54
>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=40.68 E-value=71 Score=19.96 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=10.3
Q ss_pred ccccCceEEEECCeeE
Q 034069 25 GTIRKNGYIVIKGRPC 40 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~ 40 (104)
..+++|+.|.+.|.+.
T Consensus 64 ~~l~kG~~V~V~G~l~ 79 (104)
T PF00436_consen 64 EYLKKGDRVYVEGRLR 79 (104)
T ss_dssp HH--TT-EEEEEEEEE
T ss_pred eEEcCCCEEEEEEEEE
Confidence 4488999999998766
No 55
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=39.71 E-value=41 Score=23.06 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=15.6
Q ss_pred EEecccccCceEEEE-CCeeEEEEEeeE
Q 034069 21 PQQAGTIRKNGYIVI-KGRPCKVVEVST 47 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i-~g~p~~Vve~~~ 47 (104)
-+.|.+|++|+.|.- +|.+..|..+..
T Consensus 71 Wv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 71 WVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp -EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 588999999998854 788777766654
No 56
>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=37.71 E-value=97 Score=18.96 Aligned_cols=33 Identities=15% Similarity=0.372 Sum_probs=25.6
Q ss_pred cCCCceeeEEEecccccCc---eEEEECCeeEEEEE
Q 034069 12 ADAGASKTFPQQAGTIRKN---GYIVIKGRPCKVVE 44 (104)
Q Consensus 12 ~~~~~~~t~~i~~~~lkkG---~~I~i~g~p~~Vve 44 (104)
+....-...+|..+.|..+ ..|.+++.+|.++.
T Consensus 11 g~~~Ggt~vtI~G~~f~~~~~~~~V~ig~~~C~~~~ 46 (90)
T cd00603 11 GPLSGGTRLTITGSNLGSGSPRVRVTVGGVPCKVLN 46 (90)
T ss_pred CCCCCCeEEEEEEECCCCCCceEEEEECCEECcEEe
Confidence 3444466777888888887 78999999999975
No 57
>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=37.68 E-value=49 Score=17.13 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=15.6
Q ss_pred CceEEEE-----CCeeEEEEEeeEec
Q 034069 29 KNGYIVI-----KGRPCKVVEVSTSK 49 (104)
Q Consensus 29 kG~~I~i-----~g~p~~Vve~~~~K 49 (104)
+|+.+++ .|..++|+++...+
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 77888888887654
No 58
>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=37.28 E-value=30 Score=24.58 Aligned_cols=24 Identities=21% Similarity=0.237 Sum_probs=16.5
Q ss_pred cccccCceEEEECCeeEEEEEeeE
Q 034069 24 AGTIRKNGYIVIKGRPCKVVEVST 47 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~Vve~~~ 47 (104)
..-++.|+.|.++|....|+++..
T Consensus 58 ~~pf~vGD~I~i~~~~G~V~~I~l 81 (206)
T PF00924_consen 58 ERPFKVGDRIEIGGVEGRVEEIGL 81 (206)
T ss_dssp C-SS-TT-EEESSS-EEEEEEE-S
T ss_pred cCCccCCCEEEEEEeehHHHhcCc
Confidence 357899999999999999988653
No 59
>PLN02792 oxidoreductase
Probab=37.03 E-value=1.1e+02 Score=25.99 Aligned_cols=54 Identities=19% Similarity=0.134 Sum_probs=34.3
Q ss_pred CceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEE
Q 034069 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVT 87 (104)
Q Consensus 29 kG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve 87 (104)
.++.+++||.+-.....-.++||| .+|+++.|.-.-..+...+. ++++.++..+
T Consensus 178 ~~d~~liNG~~~~~~~~~~v~~Gk----~yRlRliNa~~~~~~~f~i~-gH~~tVI~~D 231 (536)
T PLN02792 178 MPDGVMINGQGVSYVYSITVDKGK----TYRFRISNVGLQTSLNFEIL-GHQLKLIEVE 231 (536)
T ss_pred CCCEEEEeccCCCCcceEEECCCC----EEEEEEEEcCCCceEEEEEC-CcEEEEEEeC
Confidence 468899999841111223457898 78899988877666655554 5556555443
No 60
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=35.85 E-value=2.1e+02 Score=22.23 Aligned_cols=25 Identities=12% Similarity=0.122 Sum_probs=20.6
Q ss_pred EEEEEEccCCcEEEEEEcCCCceee
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve~ 83 (104)
.++++|+.+|+++.-+..+...|++
T Consensus 235 ~IrVrN~~SgkvV~a~V~~~g~V~v 259 (261)
T PRK06804 235 LIKVKNLSSGRVVTATVDGSGRVRM 259 (261)
T ss_pred EEEEEECCCCCEEEEEEecCCEEEE
Confidence 4788999999999988887777654
No 61
>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=34.84 E-value=62 Score=22.95 Aligned_cols=38 Identities=13% Similarity=0.126 Sum_probs=27.0
Q ss_pred cccccCceEEEECCeeE-----EEEEeeEecC-CCCcccEEEEE
Q 034069 24 AGTIRKNGYIVIKGRPC-----KVVEVSTSKT-GKHGHAKCHFV 61 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~-----~Vve~~~~Kp-GKhG~A~vr~k 61 (104)
..+|++|+.|.+.|+=. -||.++|.-| |+|-...++..
T Consensus 83 ip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~~h~~Gwl~~n 126 (131)
T PF11948_consen 83 IPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRGRHPDGWLKHN 126 (131)
T ss_pred CcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCCCCCCeeEEEC
Confidence 45699999999988732 4788999887 56644555443
No 62
>cd01180 IPT_plexin_repeat1 First 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=34.67 E-value=63 Score=20.65 Aligned_cols=33 Identities=9% Similarity=0.168 Sum_probs=26.2
Q ss_pred ccCCCceeeEEEecccccCc-----eEEEECCeeEEEE
Q 034069 11 KADAGASKTFPQQAGTIRKN-----GYIVIKGRPCKVV 43 (104)
Q Consensus 11 ~~~~~~~~t~~i~~~~lkkG-----~~I~i~g~p~~Vv 43 (104)
.|....-...+|...+|-.+ ..|.+.|.+|.++
T Consensus 10 ~Gp~~GGT~vTI~G~nl~~~~~~~~~~V~ig~~~C~i~ 47 (94)
T cd01180 10 SGPLEGGTRLTICGSNLGLRKNDVRHGVRVGGVPCNPE 47 (94)
T ss_pred CCCCCCCEEEEEEEEcCCCCcccceeEEEECCEECccc
Confidence 34455566778888999988 4699999999998
No 63
>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=33.60 E-value=34 Score=20.96 Aligned_cols=24 Identities=29% Similarity=0.289 Sum_probs=18.1
Q ss_pred EEEEEEEEccCCcEEEEEEcCCCceee
Q 034069 57 KCHFVGIDIFNGKKLEDIVPSSHNCDV 83 (104)
Q Consensus 57 ~vr~k~knl~TG~~~E~tf~s~~~ve~ 83 (104)
.+++++ -+|+.++.+|++++++..
T Consensus 4 ~i~iRl---pdG~~~~~~F~~~~tl~~ 27 (77)
T cd01767 4 KIQIRL---PDGKRLEQRFNSTHKLSD 27 (77)
T ss_pred EEEEEc---CCCCEEEEEeCCCCCHHH
Confidence 344444 569999999999999863
No 64
>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=32.61 E-value=76 Score=23.93 Aligned_cols=44 Identities=5% Similarity=0.032 Sum_probs=27.1
Q ss_pred eeeEEEecccccCceEEEE---CCe--eEEEEEeeEecCCCCcccEEEEE
Q 034069 17 SKTFPQQAGTIRKNGYIVI---KGR--PCKVVEVSTSKTGKHGHAKCHFV 61 (104)
Q Consensus 17 ~~t~~i~~~~lkkG~~I~i---~g~--p~~Vve~~~~KpGKhG~A~vr~k 61 (104)
...-.+...+|+.|+.|+- +|+ -..|+-+.|..|.. -..|+++.
T Consensus 22 ~~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~flhr~~~~-~~~F~~i~ 70 (217)
T PF01079_consen 22 EDGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMFLHRDPEQ-RAEFVVIE 70 (217)
T ss_dssp TTS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEEEEEEEEE-EEEEEEEE
T ss_pred CCCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEEeccCccc-cEEEEEEE
Confidence 3344678899999998876 454 46788888888865 44555554
No 65
>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=32.36 E-value=35 Score=23.26 Aligned_cols=33 Identities=18% Similarity=0.285 Sum_probs=21.3
Q ss_pred eeeEEEecccccCceEEEECCeeEEEEEeeEec
Q 034069 17 SKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (104)
Q Consensus 17 ~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~K 49 (104)
+..|.+..++|++|.+..++|.|-.-..++..+
T Consensus 45 AksYl~dp~~f~~G~~Y~i~~~~~~~F~V~yln 77 (102)
T PF08838_consen 45 AKSYLLDPSDFRPGEIYRIEGDPEEYFKVDYLN 77 (102)
T ss_dssp HHHCCS-GGGS-TT-EEEETTCCCEEEEEEEEE
T ss_pred HHHHhCChhhccCCCEEEecCCCCceEEEEEEe
Confidence 356889999999999999996655444444443
No 66
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=32.34 E-value=1e+02 Score=25.95 Aligned_cols=31 Identities=16% Similarity=0.486 Sum_probs=25.1
Q ss_pred EecccccCceEEEECCeeEEEEE-eeEecCCC
Q 034069 22 QQAGTIRKNGYIVIKGRPCKVVE-VSTSKTGK 52 (104)
Q Consensus 22 i~~~~lkkG~~I~i~g~p~~Vve-~~~~KpGK 52 (104)
....++++...|.++|++|++++ -+....|+
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 45688999999999999999998 55555555
No 67
>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=31.58 E-value=88 Score=19.26 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=13.0
Q ss_pred ccccCceEEEECCeeE
Q 034069 25 GTIRKNGYIVIKGRPC 40 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~ 40 (104)
..+++|+.|.+.|.+-
T Consensus 60 ~~~~kG~~V~v~G~l~ 75 (100)
T cd04496 60 KYLKKGDLVYVEGRLR 75 (100)
T ss_pred HHhCCCCEEEEEEEEE
Confidence 4589999999998864
No 68
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=30.79 E-value=1e+02 Score=22.30 Aligned_cols=25 Identities=16% Similarity=0.429 Sum_probs=16.0
Q ss_pred ccccCceEEEEC---Cee---EEEEEeeEec
Q 034069 25 GTIRKNGYIVIK---GRP---CKVVEVSTSK 49 (104)
Q Consensus 25 ~~lkkG~~I~i~---g~p---~~Vve~~~~K 49 (104)
+-+|.|++|.++ |.| |+|+++...+
T Consensus 2 ~~yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~ 32 (164)
T cd04709 2 NMYRVGDYVYFESSPNNPYLIRRIEELNKTA 32 (164)
T ss_pred cEEecCCEEEEECCCCCCCEEEEEEEEEeCC
Confidence 346899999886 445 5566665433
No 69
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=30.56 E-value=2.4e+02 Score=21.39 Aligned_cols=51 Identities=12% Similarity=0.233 Sum_probs=37.8
Q ss_pred ecccccCceEEEECCe---------eEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcC
Q 034069 23 QAGTIRKNGYIVIKGR---------PCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPS 77 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~---------p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s 77 (104)
..-+|++|+++.+.=. -+..+.+.-..-|- ...+.+||++-|.-.|..|+-
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 34556666666565 247899999999999999984
No 70
>COG4709 Predicted membrane protein [Function unknown]
Probab=30.45 E-value=7.9 Score=29.19 Aligned_cols=19 Identities=42% Similarity=0.632 Sum_probs=15.3
Q ss_pred CCccccccccccCCCceee
Q 034069 1 MSDEEHHFESKADAGASKT 19 (104)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~t 19 (104)
|+||+.||.+.++++.++.
T Consensus 26 m~dyeehF~~a~~~GksE~ 44 (195)
T COG4709 26 MYDYEEHFREAQEAGKSEE 44 (195)
T ss_pred HHHHHHHHHhhhhcCCCHH
Confidence 7899999998888886553
No 71
>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=29.19 E-value=1e+02 Score=23.25 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=19.1
Q ss_pred EEEecccccCceEEEE------CCeeEEEEEeeEe
Q 034069 20 FPQQAGTIRKNGYIVI------KGRPCKVVEVSTS 48 (104)
Q Consensus 20 ~~i~~~~lkkG~~I~i------~g~p~~Vve~~~~ 48 (104)
..+-|+++++|++|.. .-.|-+|+++...
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 6789999999999999 2246777766654
No 72
>PF13989 YejG: YejG-like protein
Probab=29.10 E-value=54 Score=22.46 Aligned_cols=21 Identities=24% Similarity=0.446 Sum_probs=14.5
Q ss_pred cccC-ceEEEECCeeEEEEEee
Q 034069 26 TIRK-NGYIVIKGRPCKVVEVS 46 (104)
Q Consensus 26 ~lkk-G~~I~i~g~p~~Vve~~ 46 (104)
+|.. ..+++++|+||.-+..+
T Consensus 64 eiqv~~~vvE~eGepCLFv~~~ 85 (106)
T PF13989_consen 64 EIQVDCAVVEWEGEPCLFVHRE 85 (106)
T ss_pred HhcccceEEEecCCceEEEecc
Confidence 4444 35789999999776443
No 73
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=29.00 E-value=90 Score=24.16 Aligned_cols=62 Identities=21% Similarity=0.163 Sum_probs=35.8
Q ss_pred eeeEEEecccccCceEEEEC--------------CeeE-EEEEeeEecCCCCcccEEE-------EEEEEccCCcEEEEE
Q 034069 17 SKTFPQQAGTIRKNGYIVIK--------------GRPC-KVVEVSTSKTGKHGHAKCH-------FVGIDIFNGKKLEDI 74 (104)
Q Consensus 17 ~~t~~i~~~~lkkG~~I~i~--------------g~p~-~Vve~~~~KpGKhG~A~vr-------~k~knl~TG~~~E~t 74 (104)
...|.+-+..++.|++|... +.|. .++..-..+||+ |..++| +-.+ ++...-..
T Consensus 65 ~~~YIiAp~gl~~Gd~I~sg~~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~-Ggkl~RSAGt~A~Ii~k---~~~~~~vk 140 (238)
T PRK09612 65 EEFLILAPEGLYVGQEIEIGPSAEIKPGNTLPLGEIPEGTPVCNIESRPGD-GGKFARSSGTYALVVGH---EGDKVIVQ 140 (238)
T ss_pred CEEEEEccCCCCCCCEEEeCCCCCCCCccccCHhhCCCCCEEEEEEecCCC-CcceEEcCCCeEEEEEe---cCCEEEEE
Confidence 45577777888888887753 3231 223333347888 655444 3333 34555577
Q ss_pred EcCCCcee
Q 034069 75 VPSSHNCD 82 (104)
Q Consensus 75 f~s~~~ve 82 (104)
++|++...
T Consensus 141 LPSGe~r~ 148 (238)
T PRK09612 141 LPSGKIKE 148 (238)
T ss_pred CCCCCeEE
Confidence 77776544
No 74
>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=28.74 E-value=72 Score=17.10 Aligned_cols=17 Identities=6% Similarity=0.059 Sum_probs=13.0
Q ss_pred cCceEEEECCeeEEEEE
Q 034069 28 RKNGYIVIKGRPCKVVE 44 (104)
Q Consensus 28 kkG~~I~i~g~p~~Vve 44 (104)
..|+.|..+|..|+..-
T Consensus 11 ~~Gd~V~~~g~~y~a~~ 27 (41)
T PF02839_consen 11 NAGDRVSYNGKLYQAKW 27 (41)
T ss_dssp -TT-EEEETTEEEEESS
T ss_pred cCCCEEEECCCEEEEee
Confidence 56999999999998853
No 75
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=28.66 E-value=1.2e+02 Score=21.10 Aligned_cols=20 Identities=25% Similarity=0.169 Sum_probs=15.7
Q ss_pred eEEEecccccCceEEEECCe
Q 034069 19 TFPQQAGTIRKNGYIVIKGR 38 (104)
Q Consensus 19 t~~i~~~~lkkG~~I~i~g~ 38 (104)
|-+...-.+++|.+|...|+
T Consensus 3 ~~~~~~~~~~kg~~l~~~Gd 22 (202)
T PRK13918 3 TTVVDTVTYRPGAVILYPGV 22 (202)
T ss_pred ccccceeEecCCCEEEcCCC
Confidence 34556678899999999998
No 76
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.48 E-value=2.6e+02 Score=21.03 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=22.0
Q ss_pred EEEEEEccCCcEEEEEEcCCCceeec
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve~~ 84 (104)
.++.||+.+|++++-+..+.-.|++.
T Consensus 188 ~IrVrN~~SgrvV~g~V~~~G~V~V~ 213 (214)
T PRK12617 188 RVSVENSSSRRVVQGIVEASGTVVVS 213 (214)
T ss_pred EEEEEECCCCCEEEEEEeCCcEEEEe
Confidence 58899999999999998888777654
No 77
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=28.24 E-value=1.5e+02 Score=18.29 Aligned_cols=13 Identities=8% Similarity=0.069 Sum_probs=10.7
Q ss_pred cccccCceEEEEC
Q 034069 24 AGTIRKNGYIVIK 36 (104)
Q Consensus 24 ~~~lkkG~~I~i~ 36 (104)
.-+|++|++|.++
T Consensus 26 ll~L~~Gdvi~L~ 38 (77)
T TIGR02480 26 LLKLGEGSVIELD 38 (77)
T ss_pred HhcCCCCCEEEcC
Confidence 4578999999987
No 78
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=27.56 E-value=77 Score=23.40 Aligned_cols=47 Identities=15% Similarity=0.215 Sum_probs=37.5
Q ss_pred CCCcccEEEEEEEEccCCcEEEEEEcCCCceeecEEEeeeEEEEEcC
Q 034069 51 GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDIS 97 (104)
Q Consensus 51 GKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ve~~~~qylY~d 97 (104)
|.|++.-..+.+|+=..|.+.-..+..---++.|+.-+..+.+.+..
T Consensus 94 G~~~hGyfNL~gk~~l~GHiK~eNcs~Ialv~rpFmG~~s~si~Ffn 140 (176)
T COG3721 94 GTHRHGYFNLRGKDGLSGHIKAENCSHIALVERPFMGMESASILFFN 140 (176)
T ss_pred CccccceEeecCCCCCcceeeccccceeeEeccccCCccceeeeeec
Confidence 88888899999999999998888877777777777777766666554
No 79
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=27.31 E-value=1.1e+02 Score=22.55 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=12.4
Q ss_pred ccccCceEEEECCeeE
Q 034069 25 GTIRKNGYIVIKGRPC 40 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~ 40 (104)
..|+||+.|.+.|++.
T Consensus 65 ~~l~KG~~V~VeGrL~ 80 (182)
T PRK08486 65 QYLSKGSKVLIEGRLT 80 (182)
T ss_pred HHcCCCCEEEEEEEEE
Confidence 5578888888888875
No 80
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=27.21 E-value=84 Score=21.36 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=14.8
Q ss_pred ceeeEEEecc-----cccCceEEEECC
Q 034069 16 ASKTFPQQAG-----TIRKNGYIVIKG 37 (104)
Q Consensus 16 ~~~t~~i~~~-----~lkkG~~I~i~g 37 (104)
+.+|+-+..+ +|++|+.|.+++
T Consensus 16 G~KtiEiRlnD~kr~~ikvGD~I~f~~ 42 (109)
T cd06555 16 GKKTIEIRLNDEKRQQIKVGDKILFND 42 (109)
T ss_pred CCCEEEEEecccchhcCCCCCEEEEEE
Confidence 3445554443 489999999865
No 81
>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=27.00 E-value=1.6e+02 Score=18.20 Aligned_cols=19 Identities=11% Similarity=0.263 Sum_probs=17.1
Q ss_pred cccccCceEEEECCeeEEE
Q 034069 24 AGTIRKNGYIVIKGRPCKV 42 (104)
Q Consensus 24 ~~~lkkG~~I~i~g~p~~V 42 (104)
..+|...+.|.++|..|.|
T Consensus 63 ~~~i~~~~ri~~~g~~Y~I 81 (101)
T TIGR01563 63 RKDVTNKMRVIYDGRIYTI 81 (101)
T ss_pred cCCCChhhEEEECCEEEEE
Confidence 6678899999999999999
No 82
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=26.82 E-value=1.4e+02 Score=23.30 Aligned_cols=65 Identities=17% Similarity=0.097 Sum_probs=45.0
Q ss_pred EEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc-cCCcEEEEEEcCCCceeecEEEe
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI-FNGKKLEDIVPSSHNCDVPHVTR 88 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl-~TG~~~E~tf~s~~~ve~~~ve~ 88 (104)
.+...+++.|+.|.++-.--+|++ |.+++. |+-.+-+-++|. .+|.+.|....-+-+...+.++.
T Consensus 147 ~~~d~~~k~~Dtv~i~lp~~~I~~--~i~fe~-g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 147 RLEDDNYKTGDTVKISLPEQKIVE--HIKFEE-GALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred eccCCccccccEEEEeCCChhhee--EeccCC-CcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 445578899999988877777774 445554 444444777887 56888888777666666677665
No 83
>PRK11835 hypothetical protein; Provisional
Probab=26.40 E-value=64 Score=22.37 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=15.2
Q ss_pred ccccCc-eEEEECCeeEEEEEee
Q 034069 25 GTIRKN-GYIVIKGRPCKVVEVS 46 (104)
Q Consensus 25 ~~lkkG-~~I~i~g~p~~Vve~~ 46 (104)
++|... .+|+++|+||.-+..+
T Consensus 66 ~eiqv~~~ivEweGepCLFv~~~ 88 (114)
T PRK11835 66 SDIQVPCSVLECEGEPCLFVNRQ 88 (114)
T ss_pred HhhcccceEEEecCCceEEEecc
Confidence 455544 4779999999776433
No 84
>PLN02835 oxidoreductase
Probab=26.31 E-value=2.6e+02 Score=23.83 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=33.3
Q ss_pred CceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCceeecE
Q 034069 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPH 85 (104)
Q Consensus 29 kG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve~~~ 85 (104)
.++.+++||...-.+ .++||| .+|+++.|.-.-..+...+. ++++.++.
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 357789999865433 357888 78899988877766665553 55555444
No 85
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=26.28 E-value=67 Score=19.79 Aligned_cols=25 Identities=20% Similarity=0.309 Sum_probs=19.0
Q ss_pred cEEEEEEEEccCCcEEEEEEcCCCceee
Q 034069 56 AKCHFVGIDIFNGKKLEDIVPSSHNCDV 83 (104)
Q Consensus 56 A~vr~k~knl~TG~~~E~tf~s~~~ve~ 83 (104)
+.++++ +-+|+.++.+|++.+++..
T Consensus 5 ~~I~iR---lPdG~ri~~~F~~~~tl~~ 29 (80)
T smart00166 5 CRLQIR---LPDGSRLVRRFPSSDTLRT 29 (80)
T ss_pred EEEEEE---cCCCCEEEEEeCCCCcHHH
Confidence 444444 3789999999999999864
No 86
>PRK06788 flagellar motor switch protein; Validated
Probab=26.17 E-value=1.6e+02 Score=20.36 Aligned_cols=44 Identities=14% Similarity=0.178 Sum_probs=26.2
Q ss_pred ccccCceEEEEC---CeeEEE----EEeeEecCCCCcccEEEEEEEEccCCc
Q 034069 25 GTIRKNGYIVIK---GRPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNGK 69 (104)
Q Consensus 25 ~~lkkG~~I~i~---g~p~~V----ve~~~~KpGKhG~A~vr~k~knl~TG~ 69 (104)
-+|++|++|.++ ++|..| ..+-...+|..+ -..=+++..+.+.+
T Consensus 53 L~L~vGDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~-~~~AVrItei~~~~ 103 (119)
T PRK06788 53 KQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMD-EKFGIIISEIEADK 103 (119)
T ss_pred hCCCCCCEEEeCCcCCCCEEEEECCEEEEEEEEEEEC-CEEEEEEEEecChH
Confidence 468899999997 456554 223444555533 23346666666643
No 87
>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=25.41 E-value=1.2e+02 Score=21.57 Aligned_cols=16 Identities=19% Similarity=0.412 Sum_probs=11.5
Q ss_pred ccccCceEEEECCeeE
Q 034069 25 GTIRKNGYIVIKGRPC 40 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~ 40 (104)
..|+||+.|.+.|++.
T Consensus 67 ~~l~KG~~V~V~G~L~ 82 (164)
T TIGR00621 67 QYLKKGSLVYVEGRLR 82 (164)
T ss_pred HhCCCCCEEEEEEEEE
Confidence 4577888888777654
No 88
>COG3731 SrlB Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]
Probab=25.39 E-value=92 Score=21.88 Aligned_cols=26 Identities=8% Similarity=0.193 Sum_probs=21.0
Q ss_pred EEecccccCceEEEECCeeEEEEEee
Q 034069 21 PQQAGTIRKNGYIVIKGRPCKVVEVS 46 (104)
Q Consensus 21 ~i~~~~lkkG~~I~i~g~p~~Vve~~ 46 (104)
.-.-..+.+|+.+.+++.+|.|+.+-
T Consensus 46 ~e~~~~l~~G~~l~lg~~~y~ItaVG 71 (123)
T COG3731 46 GELQEALQPGDRLTLGGHCYPITAVG 71 (123)
T ss_pred CcccccCCCCCEEEECCceEEEEEec
Confidence 34456788999999999999998653
No 89
>PRK06666 fliM flagellar motor switch protein FliM; Validated
Probab=25.28 E-value=1.6e+02 Score=23.07 Aligned_cols=43 Identities=14% Similarity=0.107 Sum_probs=26.7
Q ss_pred cccccCceEEEECC---eeEEE----EEeeEecCCCCcccEEEEEEEEccC
Q 034069 24 AGTIRKNGYIVIKG---RPCKV----VEVSTSKTGKHGHAKCHFVGIDIFN 67 (104)
Q Consensus 24 ~~~lkkG~~I~i~g---~p~~V----ve~~~~KpGKhG~A~vr~k~knl~T 67 (104)
.-+|++|++|.++- +|..| ...-...+|+||.-+ =+++.++..
T Consensus 276 ll~L~vGDVI~L~~~~~~~v~v~v~~~~~f~g~~G~~~~~~-Av~I~~~~~ 325 (337)
T PRK06666 276 ILNLKVGDVIPLEKPADDPLIVYVDGKPKFLCQYGKSNGRK-ALQIEELIE 325 (337)
T ss_pred HhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEECCEE-EEEEEEEcC
Confidence 45789999999875 45555 234555677764432 355555544
No 90
>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=24.88 E-value=97 Score=20.00 Aligned_cols=20 Identities=15% Similarity=0.112 Sum_probs=17.3
Q ss_pred ccCCcEEEEEEcCCCceeec
Q 034069 65 IFNGKKLEDIVPSSHNCDVP 84 (104)
Q Consensus 65 l~TG~~~E~tf~s~~~ve~~ 84 (104)
+-+|+..|++|.+.+++..+
T Consensus 12 lP~G~r~~rrF~~~~~L~~v 31 (82)
T cd01773 12 YPDGKREQIALPEQAKLLAL 31 (82)
T ss_pred CCCCCEEEEEeCCCCcHHHH
Confidence 67899999999999998644
No 91
>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=24.88 E-value=3.4e+02 Score=21.26 Aligned_cols=76 Identities=20% Similarity=0.305 Sum_probs=46.9
Q ss_pred eeeEEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCce-e-ecEEEeeeEEEE
Q 034069 17 SKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC-D-VPHVTRTDYQLI 94 (104)
Q Consensus 17 ~~t~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~v-e-~~~ve~~~~qyl 94 (104)
-.+||-+.+.+-.|..+.-+|..|. ..|.-|.. +++-.|+.||++....--...-| | ...+..+=+|+.
T Consensus 36 v~~ypHd~~aFTQGL~~~~~g~LyE-------STG~yG~S--~l~~~d~~tg~~~~~~~l~~~~FgEGit~~~d~l~qLT 106 (264)
T PF05096_consen 36 VETYPHDPTAFTQGLEFLDDGTLYE-------STGLYGQS--SLRKVDLETGKVLQSVPLPPRYFGEGITILGDKLYQLT 106 (264)
T ss_dssp EEEEE--TT-EEEEEEEEETTEEEE-------EECSTTEE--EEEEEETTTSSEEEEEE-TTT--EEEEEEETTEEEEEE
T ss_pred EEECCCCCcccCccEEecCCCEEEE-------eCCCCCcE--EEEEEECCCCcEEEEEECCccccceeEEEECCEEEEEE
Confidence 4567788999999998888888772 23655766 45577999999875554433322 3 344456667777
Q ss_pred EcCCCCC
Q 034069 95 DISEDGF 101 (104)
Q Consensus 95 Y~dgd~y 101 (104)
+.++-.|
T Consensus 107 Wk~~~~f 113 (264)
T PF05096_consen 107 WKEGTGF 113 (264)
T ss_dssp SSSSEEE
T ss_pred ecCCeEE
Confidence 6666544
No 92
>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=24.66 E-value=1.9e+02 Score=19.79 Aligned_cols=21 Identities=24% Similarity=0.469 Sum_probs=13.6
Q ss_pred EEEECCeeEEEEEeeEecCCC
Q 034069 32 YIVIKGRPCKVVEVSTSKTGK 52 (104)
Q Consensus 32 ~I~i~g~p~~Vve~~~~KpGK 52 (104)
.|..+|+||++...+-.=+||
T Consensus 60 ~v~~ngk~s~l~~~q~~l~~~ 80 (107)
T PF07472_consen 60 EVTANGKPSKLRSSQNTLDGK 80 (107)
T ss_dssp EEEETTEE-EEEEEEEEETTT
T ss_pred EEEeCCccccceeeeeeccCc
Confidence 455688888887776665655
No 93
>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.
Probab=24.60 E-value=21 Score=23.52 Aligned_cols=29 Identities=17% Similarity=0.330 Sum_probs=21.9
Q ss_pred CceeeEEEecccccCceEEEECCeeEEEE
Q 034069 15 GASKTFPQQAGTIRKNGYIVIKGRPCKVV 43 (104)
Q Consensus 15 ~~~~t~~i~~~~lkkG~~I~i~g~p~~Vv 43 (104)
.++....+..++|++|++|.+..--|..+
T Consensus 54 atqln~~v~~g~l~~~sIirl~~y~~~~i 82 (97)
T cd04477 54 ATQLNPLVESGQLQRGSIIRLKRFICNVI 82 (97)
T ss_pred hhhhhhHHhcCCccCCcEEEECeEEEEEe
Confidence 44555667788999999999987766555
No 94
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=24.13 E-value=2e+02 Score=20.34 Aligned_cols=42 Identities=12% Similarity=0.199 Sum_probs=24.6
Q ss_pred ccccCceEEEEC---CeeEEEE----EeeEecCCCCcccEEEEEEEEccC
Q 034069 25 GTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (104)
Q Consensus 25 ~~lkkG~~I~i~---g~p~~Vv----e~~~~KpGKhG~A~vr~k~knl~T 67 (104)
-+|++|++|.++ ++|..|. -+-+..+|.++ -+.=+++..+.+
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 5776663 23334444422 233355555554
No 95
>PRK08119 flagellar motor switch protein; Validated
Probab=24.06 E-value=1.4e+02 Score=24.11 Aligned_cols=42 Identities=12% Similarity=0.166 Sum_probs=25.6
Q ss_pred ccccCceEEEEC---CeeEEEE----EeeEecCCCCcccEEEEEEEEccC
Q 034069 25 GTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (104)
Q Consensus 25 ~~lkkG~~I~i~---g~p~~Vv----e~~~~KpGKhG~A~vr~k~knl~T 67 (104)
-+|++|++|.++ ++|..|. .+-..++|.++. +.-+++..+..
T Consensus 325 l~L~~Gdvi~Ld~~~~~~v~v~v~g~~~~~g~~g~~~~-~~av~I~~~~~ 373 (382)
T PRK08119 325 LELGTGSIIELDKLAGEPVDILVNGKLIAKGEVVVIDE-NFGVRITDIVS 373 (382)
T ss_pred hcCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEECC-EEEEEEEEecC
Confidence 468999999998 5776662 344455565432 23355555543
No 96
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=23.81 E-value=2.6e+02 Score=19.44 Aligned_cols=62 Identities=18% Similarity=0.268 Sum_probs=37.9
Q ss_pred cccccCceEEEE-----CCeeEEEEEeeEe---cCCCCcccEEEEEEEEccCCcEEEEEEcCCC-ceeecEEE
Q 034069 24 AGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH-NCDVPHVT 87 (104)
Q Consensus 24 ~~~lkkG~~I~i-----~g~p~~Vve~~~~---KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~-~ve~~~ve 87 (104)
.-++++|+.|.+ +|.-+.+.-++-. .-|+ |-.. -+.++.+..|-=.|++|+-.. .++.+.|-
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 567788887653 5555555444322 2233 3222 367888899999999999653 34544443
No 97
>PRK09812 toxin ChpB; Provisional
Probab=23.12 E-value=73 Score=21.45 Aligned_cols=22 Identities=23% Similarity=0.584 Sum_probs=15.3
Q ss_pred ccccCceEEEEC----------C--eeEEEEEee
Q 034069 25 GTIRKNGYIVIK----------G--RPCKVVEVS 46 (104)
Q Consensus 25 ~~lkkG~~I~i~----------g--~p~~Vve~~ 46 (104)
+-++.|+++.++ | +||.|+.-.
T Consensus 5 ~~~~rGdI~~v~l~P~~G~E~~gk~RP~vVvS~d 38 (116)
T PRK09812 5 SKFERGDIVLVGFDPASGHEQQGAGRPALVLSVA 38 (116)
T ss_pred ccCCCCcEEEEECCCCCccccCCCcCeEEEEccc
Confidence 456778877765 4 688888643
No 98
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=23.03 E-value=1.2e+02 Score=22.05 Aligned_cols=16 Identities=25% Similarity=0.409 Sum_probs=10.7
Q ss_pred ccccCceEEEECCeeE
Q 034069 25 GTIRKNGYIVIKGRPC 40 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~ 40 (104)
..|+||+.|.+.|++.
T Consensus 68 ~~LkKGs~V~VeGrL~ 83 (168)
T PRK06863 68 EYLRKGSQVYVEGRLK 83 (168)
T ss_pred HHCCCCCEEEEEEEEE
Confidence 4467777777777654
No 99
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=22.62 E-value=83 Score=22.59 Aligned_cols=20 Identities=10% Similarity=0.151 Sum_probs=15.3
Q ss_pred eeEEEecccccCceEEEECC
Q 034069 18 KTFPQQAGTIRKNGYIVIKG 37 (104)
Q Consensus 18 ~t~~i~~~~lkkG~~I~i~g 37 (104)
....++.++|++|+.|.++.
T Consensus 43 ~~~~i~~~~L~~GDiI~l~~ 62 (230)
T PF00122_consen 43 RWQKIPSSELVPGDIIILKA 62 (230)
T ss_dssp EEEEEEGGGT-TTSEEEEET
T ss_pred ccccchHhhccceeeeeccc
Confidence 44568999999999998754
No 100
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=22.55 E-value=2.2e+02 Score=20.61 Aligned_cols=43 Identities=12% Similarity=0.124 Sum_probs=24.8
Q ss_pred ccccCceEEEECC---eeEEEE----EeeEecCCCCcccEEEEEEEEccCC
Q 034069 25 GTIRKNGYIVIKG---RPCKVV----EVSTSKTGKHGHAKCHFVGIDIFNG 68 (104)
Q Consensus 25 ~~lkkG~~I~i~g---~p~~Vv----e~~~~KpGKhG~A~vr~k~knl~TG 68 (104)
-+|++|++|.++- +|..|. .+-+..+|..+ -+.=+++.++.+.
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 4689999999985 665552 23344445422 2334666665543
No 101
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=22.31 E-value=2.3e+02 Score=20.90 Aligned_cols=21 Identities=29% Similarity=0.308 Sum_probs=17.3
Q ss_pred cccCceEEEECCe----eEEEEEee
Q 034069 26 TIRKNGYIVIKGR----PCKVVEVS 46 (104)
Q Consensus 26 ~lkkG~~I~i~g~----p~~Vve~~ 46 (104)
++.+|+.+.+++. |.+|+++.
T Consensus 90 ~~~vGm~~~~~~~~~~~~~~V~~V~ 114 (174)
T COG1047 90 ELEVGMEVEAEGGDGEIPGVVTEVS 114 (174)
T ss_pred CCCCCcEEEEcCCCceeeEEEEEEc
Confidence 7899999999996 88886643
No 102
>PF08816 Ivy: Inhibitor of vertebrate lysozyme (Ivy); InterPro: IPR014453 C-type lysozyme enzymes, such as hen egg white lysozyme (HEWL), provide anti-bacterial activity by cleaving peptidoglycan in Gram-positive bacterial cell walls. In humans, C-type lysozyme is found in all secretions, including tears and saliva. Certain Gram-positive bacteria can produce proteins with anti-lysozyme activity known as Inhibitor of Vertebrate Lysozyme (IVY), which act as virulence factors [, ]. IVY proteins have a 3-layer alpha(2)/beta(5)/alpha(2) topology, and contain a protruding 5-residue loop that is essential for their inhibitory effect [].; GO: 0043086 negative regulation of catalytic activity, 0042597 periplasmic space; PDB: 1GPQ_A 1XS0_A 1UUZ_B.
Probab=22.10 E-value=2.3e+02 Score=19.50 Aligned_cols=66 Identities=14% Similarity=0.143 Sum_probs=33.8
Q ss_pred CceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCCCcee---ecEEEeeeEEEEEcCC
Q 034069 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD---VPHVTRTDYQLIDISE 98 (104)
Q Consensus 29 kG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~~~ve---~~~ve~~~~qylY~dg 98 (104)
+...|.++|.+|.|. .-.||..+++-++.+ +-+--.++.+--.+..-+++. .|. +.-.+++|...+
T Consensus 34 P~~~V~~~G~~Y~v~--~~CkpHdC~~~~l~v-lfs~d~~~a~gl~v~v~d~~~a~~~ps-~~a~~~wlG~pd 102 (118)
T PF08816_consen 34 PMEAVTIDGKPYLVG--SACKPHDCANNRLYV-LFSPDKKQAYGLLVEVPDTPSADDSPS-KYATYRWLGKPD 102 (118)
T ss_dssp EEEEEEETTEEEEEE--EEE-TT-TTTEEEEE-EEETTTTEEEEEEEE--S-TCCCCTCC-CCEEEEEESSSC
T ss_pred CCeeEEECCEEEEEe--ccccccCCCcCeEEE-EECCCCCceEEEEEecCCCcccccCcc-hhheeeecCCCC
Confidence 456799999999998 566887776655533 333333333333322222221 122 345566666544
No 103
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=21.84 E-value=31 Score=25.81 Aligned_cols=27 Identities=4% Similarity=0.218 Sum_probs=21.8
Q ss_pred ecccccCceEEEECCeeEEEEEeeEec
Q 034069 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~p~~Vve~~~~K 49 (104)
...+||.|+.|.++|..+..-|..|.+
T Consensus 12 ~i~~LkvGd~v~lsG~I~t~RD~AH~r 38 (184)
T COG1838 12 EIAKLKVGDVVYLSGKIVTGRDAAHKR 38 (184)
T ss_pred HHHhccCCCEEEEeeEEEEehhHHHHH
Confidence 357899999999999999886666543
No 104
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=21.75 E-value=3e+02 Score=21.89 Aligned_cols=51 Identities=8% Similarity=0.008 Sum_probs=35.0
Q ss_pred ecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEccCCcEEEEEEcCC
Q 034069 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSS 78 (104)
Q Consensus 23 ~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl~TG~~~E~tf~s~ 78 (104)
..++|+.|..|. .+|.|.+.+... .|.|..+..+.+.| .||.+.=+-+...
T Consensus 4 ~i~~l~~g~~v~---~~~lv~~~~~~~-~knG~~yl~l~l~D-~tG~I~ak~W~~~ 54 (314)
T PRK13480 4 GIEELEVGEQVD---HFLLIKSATKGV-ASNGKPFLTLILQD-KSGDIEAKLWDVS 54 (314)
T ss_pred hHhhcCCCCEee---EEEEEEEceeee-cCCCCeEEEEEEEc-CCcEEEEEeCCCC
Confidence 467888887543 266676666544 44477899999998 8888776666543
No 105
>PF14623 Vint: Hint-domain
Probab=21.61 E-value=2e+02 Score=21.02 Aligned_cols=41 Identities=17% Similarity=0.248 Sum_probs=26.0
Q ss_pred EEEecccccCceEEEECCeeEEEEEeeEecCCCCcccEEEE
Q 034069 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60 (104)
Q Consensus 20 ~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~ 60 (104)
.++.+.+||+|+.|.--..|-+|.-+-..+-...+..++++
T Consensus 16 ~~v~i~~lR~G~~V~tp~G~r~V~~Vlkt~v~~~~~~lc~v 56 (162)
T PF14623_consen 16 APVRIDDLRAGDKVWTPRGPRKVAAVLKTPVESGSEDLCRV 56 (162)
T ss_pred eeEEHHHccCCCEEECCCCCeEEEEEEEEeecCCceEEEEE
Confidence 34888999999999877667666655544322202345544
No 106
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.49 E-value=4.3e+02 Score=21.20 Aligned_cols=26 Identities=8% Similarity=0.105 Sum_probs=21.6
Q ss_pred EEEEEEccCCcEEEEEEcCCCceeec
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCDVP 84 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve~~ 84 (104)
.++++|+.+|+++.-+..+...+++.
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 47889999999999988888877653
No 107
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=21.35 E-value=1.3e+02 Score=23.36 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=20.3
Q ss_pred ccccCceEEEECCeeEEEEEeeEe
Q 034069 25 GTIRKNGYIVIKGRPCKVVEVSTS 48 (104)
Q Consensus 25 ~~lkkG~~I~i~g~p~~Vve~~~~ 48 (104)
.-+|.|+.|.++|.-..|.++...
T Consensus 128 rpf~vGD~I~i~~~~G~V~~I~~r 151 (286)
T PRK10334 128 RPFRAGEYVDLGGVAGTVLSVQIF 151 (286)
T ss_pred CCCCCCCEEEECCEEEEEEEEEeE
Confidence 458999999999999999886543
No 108
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=21.00 E-value=1.5e+02 Score=19.94 Aligned_cols=30 Identities=17% Similarity=0.314 Sum_probs=20.2
Q ss_pred ceeeEEEecccccCceEEEECCe----eEEEEEe
Q 034069 16 ASKTFPQQAGTIRKNGYIVIKGR----PCKVVEV 45 (104)
Q Consensus 16 ~~~t~~i~~~~lkkG~~I~i~g~----p~~Vve~ 45 (104)
.+.+.+...-.|.+|++|.+... .|.|.++
T Consensus 129 ~~f~~~~~~~~l~pGDvi~l~~~~~~~~~RI~~i 162 (164)
T PF13550_consen 129 VSFTLPPDGLALEPGDVIALSDDGRDMRFRITEI 162 (164)
T ss_pred EEEEEChhhccCCCCCEEEEEeCCCceEEEEEEE
Confidence 34445566778999999988733 5555554
No 109
>COG1062 AdhC Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]
Probab=20.83 E-value=1.8e+02 Score=24.07 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=27.9
Q ss_pred eEEEECCeeEEEEEeeEecCCCCcccEEEEEEEEc
Q 034069 31 GYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (104)
Q Consensus 31 ~~I~i~g~p~~Vve~~~~KpGKhG~A~vr~k~knl 65 (104)
-++.=.|+|+.|.+++.-.|++ |-..||++.-.+
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 3444578999999999999999 888888887665
No 110
>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=20.58 E-value=1.9e+02 Score=18.02 Aligned_cols=18 Identities=33% Similarity=0.492 Sum_probs=15.7
Q ss_pred ccCCcEEEEEEcCCCcee
Q 034069 65 IFNGKKLEDIVPSSHNCD 82 (104)
Q Consensus 65 l~TG~~~E~tf~s~~~ve 82 (104)
|-+|+.+..+|+..++|.
T Consensus 11 lpdG~r~~~rF~~~~tv~ 28 (79)
T cd01770 11 LADGKRLVQKFNSSHRVS 28 (79)
T ss_pred CCCCCEEEEEeCCCCcHH
Confidence 678999999999999874
No 111
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.31 E-value=3.8e+02 Score=20.04 Aligned_cols=24 Identities=17% Similarity=0.162 Sum_probs=17.6
Q ss_pred EEEEEEccCCcEEEEEEcCCCceee
Q 034069 59 HFVGIDIFNGKKLEDIVPSSHNCDV 83 (104)
Q Consensus 59 r~k~knl~TG~~~E~tf~s~~~ve~ 83 (104)
.+++|| .+|++++-+.-+...+++
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 377778 888888877776666653
No 112
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.20 E-value=60 Score=21.97 Aligned_cols=37 Identities=14% Similarity=0.182 Sum_probs=27.9
Q ss_pred EEEecccccCceEEEECCeeEEEEEeeEecCCCCcccE
Q 034069 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAK 57 (104)
Q Consensus 20 ~~i~~~~lkkG~~I~i~g~p~~Vve~~~~KpGKhG~A~ 57 (104)
.-+.-..+|+|..++||..-|.+++-+-. |=+||.-.
T Consensus 56 lFi~~gsvrpGii~lINd~DWEllekedy-~ledgD~i 92 (101)
T KOG4146|consen 56 LFIHHGSVRPGIIVLINDMDWELLEKEDY-PLEDGDHI 92 (101)
T ss_pred eEeeCCcCcCcEEEEEeccchhhhccccc-CcccCCEE
Confidence 66788999999999999999999875432 33445443
No 113
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=20.16 E-value=1.1e+02 Score=18.69 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=18.2
Q ss_pred EEEEEEEccCCcEEEEEEcCCCcee
Q 034069 58 CHFVGIDIFNGKKLEDIVPSSHNCD 82 (104)
Q Consensus 58 vr~k~knl~TG~~~E~tf~s~~~ve 82 (104)
+++++| +-+|+.+..+|...+++.
T Consensus 7 ~~I~vR-lpdG~~l~~~F~~~~tl~ 30 (82)
T PF00789_consen 7 VRIQVR-LPDGSRLQRRFPKSDTLQ 30 (82)
T ss_dssp EEEEEE-ETTSTEEEEEEETTSBHH
T ss_pred EEEEEE-CCCCCEEEEEECCcchHH
Confidence 444444 367999999999999885
No 114
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=20.11 E-value=2e+02 Score=19.88 Aligned_cols=27 Identities=19% Similarity=0.169 Sum_probs=20.9
Q ss_pred cccCceEEEE---CCe--eEEEEEeeEecCCC
Q 034069 26 TIRKNGYIVI---KGR--PCKVVEVSTSKTGK 52 (104)
Q Consensus 26 ~lkkG~~I~i---~g~--p~~Vve~~~~KpGK 52 (104)
-.|+|+.+.+ +|. -++|+++++..++.
T Consensus 101 G~~~Gd~v~v~~p~G~~~~~~I~~I~y~p~~~ 132 (137)
T PRK05753 101 GLSVGQSIDWPLPGGKETHLEVLEVEYQPEAA 132 (137)
T ss_pred CCCCCCEEEEECCCCCEEEEEEEEEEeCCccc
Confidence 3588999988 564 47889999877765
Done!