Query 034229
Match_columns 100
No_of_seqs 110 out of 616
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 11:11:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034229.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034229hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03107 eukaryotic translatio 100.0 2.3E-34 5E-39 209.3 11.2 91 1-92 1-91 (159)
2 PTZ00328 eukaryotic initiation 100.0 8.6E-34 1.9E-38 207.5 9.7 91 1-91 1-92 (166)
3 KOG3271 Translation initiation 100.0 2.4E-31 5.2E-36 191.2 5.5 91 1-92 1-91 (156)
4 TIGR00037 eIF_5A translation i 100.0 3.9E-29 8.4E-34 176.4 10.1 77 16-92 1-77 (130)
5 PRK03999 translation initiatio 99.9 3.4E-25 7.3E-30 156.2 9.6 74 19-92 3-76 (129)
6 COG0231 Efp Translation elonga 99.9 1E-24 2.2E-29 154.2 9.9 72 20-92 2-73 (131)
7 PRK12426 elongation factor P; 99.9 2.3E-22 5E-27 149.5 9.6 71 21-92 1-71 (185)
8 PF08207 EFP_N: Elongation fac 99.9 3.3E-22 7.2E-27 123.7 8.7 58 23-81 1-58 (58)
9 PRK14578 elongation factor P; 99.9 2E-21 4.3E-26 144.6 9.9 72 21-92 1-73 (187)
10 PRK00529 elongation factor P; 99.9 2.1E-21 4.5E-26 143.5 9.2 71 21-92 1-71 (186)
11 PRK04542 elongation factor P; 99.9 2.9E-21 6.2E-26 144.0 9.8 72 21-92 1-73 (189)
12 TIGR00038 efp translation elon 99.8 4.9E-21 1.1E-25 141.4 9.2 70 22-92 1-70 (184)
13 TIGR02178 yeiP elongation fact 99.8 6E-20 1.3E-24 136.6 10.3 69 24-92 2-71 (186)
14 COG1499 NMD3 NMD protein affec 90.1 1.3 2.9E-05 36.1 6.8 62 11-82 231-292 (355)
15 PF08605 Rad9_Rad53_bind: Fung 84.7 2.8 6.1E-05 29.8 5.1 42 22-63 55-105 (131)
16 PF13275 S4_2: S4 domain; PDB: 68.4 6.7 0.00015 24.7 2.8 21 23-43 45-65 (65)
17 smart00676 DM10 Domains in hyp 64.9 5.9 0.00013 26.8 2.2 26 21-46 68-93 (104)
18 PF13785 DUF4178: Domain of un 62.6 8.4 0.00018 26.1 2.7 23 27-49 1-23 (140)
19 PF13856 Gifsy-2: ATP-binding 61.4 22 0.00047 23.1 4.4 37 13-49 49-88 (95)
20 PF11871 DUF3391: Domain of un 61.0 4.7 0.0001 26.9 1.1 21 20-40 3-23 (128)
21 COG0090 RplB Ribosomal protein 60.8 46 0.001 26.6 6.8 53 26-82 123-183 (275)
22 PF03829 PTSIIA_gutA: PTS syst 60.4 12 0.00025 26.0 3.1 23 23-45 48-70 (117)
23 PRK10377 PTS system glucitol/s 58.8 14 0.0003 25.8 3.2 22 24-45 49-70 (120)
24 TIGR00849 gutA PTS system, glu 57.6 15 0.00032 25.7 3.2 21 25-45 50-70 (121)
25 PF11302 DUF3104: Protein of u 53.3 53 0.0011 21.4 5.1 46 26-71 5-60 (75)
26 PRK11507 ribosome-associated p 53.3 15 0.00032 23.6 2.4 21 23-43 49-69 (70)
27 PF10665 Minor_capsid_1: Minor 51.8 20 0.00044 24.7 3.1 26 24-49 74-99 (114)
28 PF08408 DNA_pol_B_3: DNA poly 51.6 12 0.00027 27.3 2.1 23 24-46 37-59 (149)
29 PRK11354 kil FtsZ inhibitor pr 50.4 22 0.00048 23.1 2.9 25 19-43 8-32 (73)
30 COG2501 S4-like RNA binding pr 49.0 21 0.00046 23.1 2.7 22 24-45 50-71 (73)
31 PF05354 Phage_attach: Phage H 47.6 12 0.00026 26.3 1.5 37 19-58 67-103 (117)
32 PF00467 KOW: KOW motif; Inte 47.5 30 0.00065 18.2 2.8 21 29-49 1-26 (32)
33 PRK05338 rplS 50S ribosomal pr 47.4 52 0.0011 22.9 4.6 55 23-79 15-77 (116)
34 smart00466 SRA SET and RING fi 46.9 76 0.0016 23.0 5.6 36 28-65 117-152 (155)
35 TIGR01397 fliM_switch flagella 44.1 47 0.001 25.8 4.5 33 23-55 270-309 (320)
36 PF06605 Prophage_tail: Propha 43.8 70 0.0015 24.7 5.4 38 25-64 26-63 (327)
37 TIGR01024 rplS_bact ribosomal 43.7 64 0.0014 22.4 4.6 56 22-79 14-77 (113)
38 PRK12795 fliM flagellar motor 43.5 66 0.0014 26.5 5.4 45 23-68 319-370 (388)
39 PF01245 Ribosomal_L19: Riboso 42.1 1.1E+02 0.0025 21.0 6.4 59 22-80 14-78 (113)
40 PF10844 DUF2577: Protein of u 41.5 60 0.0013 21.5 4.1 24 21-44 71-98 (100)
41 PF02559 CarD_CdnL_TRCF: CarD- 41.3 95 0.0021 19.9 6.3 41 26-68 1-42 (98)
42 PF05521 Phage_H_T_join: Phage 40.6 83 0.0018 19.0 5.7 25 25-49 61-85 (95)
43 COG1326 Uncharacterized archae 40.2 38 0.00083 25.9 3.3 27 25-52 73-99 (201)
44 PF00924 MS_channel: Mechanose 40.1 24 0.00053 25.0 2.1 23 24-46 58-80 (206)
45 PF11948 DUF3465: Protein of u 40.1 47 0.001 23.8 3.5 38 24-61 83-126 (131)
46 PRK10965 multicopper oxidase; 39.4 1.3E+02 0.0028 25.7 6.6 52 28-87 210-261 (523)
47 COG5131 URM1 Ubiquitin-like pr 37.1 24 0.00051 24.1 1.5 28 18-45 49-76 (96)
48 PRK11835 hypothetical protein; 35.9 40 0.00087 23.7 2.6 32 25-61 66-98 (114)
49 PF07591 PT-HINT: Pretoxin HIN 35.5 55 0.0012 22.5 3.3 27 21-47 71-98 (130)
50 COG1030 NfeD Membrane-bound se 35.2 85 0.0018 26.7 4.9 38 22-63 383-421 (436)
51 cd04709 BAH_MTA BAH, or Bromo 35.1 78 0.0017 23.1 4.2 38 25-63 2-45 (164)
52 COG4043 Preprotein translocase 34.5 58 0.0013 22.7 3.2 14 25-38 32-45 (111)
53 PF13550 Phage-tail_3: Putativ 34.4 54 0.0012 22.2 3.1 31 16-46 129-163 (164)
54 PF00436 SSB: Single-strand bi 33.5 1E+02 0.0023 19.2 4.2 16 25-40 64-79 (104)
55 PRK06788 flagellar motor switc 33.4 58 0.0013 22.8 3.1 46 24-70 52-104 (119)
56 cd03701 IF2_IF5B_II IF2_IF5B_I 33.4 85 0.0018 20.5 3.8 30 15-44 15-44 (95)
57 TIGR01563 gp16_SPP1 phage head 31.2 1.3E+02 0.0029 18.6 5.6 35 8-43 45-82 (101)
58 cd03702 IF2_mtIF2_II This fami 31.1 97 0.0021 20.4 3.8 32 15-46 15-46 (95)
59 cd04496 SSB_OBF SSB_OBF: A sub 30.3 94 0.002 19.2 3.5 16 25-40 60-75 (100)
60 PF01079 Hint: Hint module; I 30.2 89 0.0019 23.7 3.9 29 20-48 99-133 (217)
61 PF14623 Vint: Hint-domain 30.0 1.1E+02 0.0023 22.7 4.2 30 19-48 15-44 (162)
62 PF02182 SAD_SRA: SAD/SRA doma 29.8 1.5E+02 0.0032 21.3 4.8 34 30-65 119-152 (155)
63 COG1838 FumA Tartrate dehydrat 29.3 18 0.00039 27.3 -0.0 27 23-49 12-38 (184)
64 PRK10883 FtsI repressor; Provi 29.1 2.1E+02 0.0046 23.9 6.3 52 28-87 207-258 (471)
65 PLN02792 oxidoreductase 29.0 2.1E+02 0.0045 24.5 6.3 55 29-88 178-232 (536)
66 CHL00084 rpl19 ribosomal prote 29.0 2E+02 0.0044 20.0 6.9 54 22-79 18-81 (117)
67 COG4709 Predicted membrane pro 28.6 8.5 0.00019 29.3 -1.9 19 1-19 26-44 (195)
68 PRK11832 putative DNA-binding 27.8 31 0.00066 26.3 1.0 15 24-38 181-195 (207)
69 COG3731 SrlB Phosphotransferas 27.1 80 0.0017 22.5 2.9 24 23-46 48-71 (123)
70 cd05829 Sortase_E Sortase E (S 26.7 93 0.002 21.6 3.3 30 23-52 69-103 (144)
71 PF13403 Hint_2: Hint domain 26.5 2.3E+02 0.005 19.8 5.9 61 21-81 15-83 (147)
72 PRK07963 fliN flagellar motor 26.5 1.4E+02 0.0031 21.3 4.2 43 24-67 78-127 (137)
73 TIGR00723 ttdB_fumA_fumB hydro 26.1 24 0.00051 26.2 0.1 26 24-49 3-28 (168)
74 KOG2345 Serine/threonine prote 26.0 1.1E+02 0.0024 24.8 3.9 37 30-71 13-49 (302)
75 PF02839 CBM_5_12: Carbohydrat 24.9 90 0.0019 16.9 2.4 17 27-43 10-26 (41)
76 PRK08228 L(+)-tartrate dehydra 24.7 23 0.00049 27.1 -0.2 27 23-49 14-40 (204)
77 PF07472 PA-IIL: Fucose-bindin 24.3 1.9E+02 0.0041 20.1 4.3 45 8-52 35-80 (107)
78 PRK06842 fumarate hydratase; P 24.0 25 0.00055 26.4 -0.0 27 24-50 14-40 (185)
79 PF12148 DUF3590: Protein of u 23.8 46 0.00099 22.1 1.2 16 21-36 60-75 (85)
80 PRK06043 fumarate hydratase; P 23.5 25 0.00053 26.7 -0.2 27 23-49 13-39 (192)
81 TIGR02480 fliN flagellar motor 23.2 2E+02 0.0043 17.9 4.1 14 23-36 25-38 (77)
82 cd01179 IPT_plexin_repeat2 Sec 22.9 2E+02 0.0043 17.8 4.7 27 19-45 18-46 (85)
83 PRK10334 mechanosensitive chan 21.9 1.2E+02 0.0025 23.8 3.3 24 25-48 128-151 (286)
84 PF13989 YejG: YejG-like prote 21.7 88 0.0019 21.7 2.3 27 30-61 69-95 (106)
85 PF05954 Phage_GPD: Phage late 21.6 2.2E+02 0.0048 20.8 4.6 28 21-48 253-287 (292)
86 PRK05753 nucleoside diphosphat 21.4 1.9E+02 0.004 20.2 4.0 30 25-55 100-134 (137)
87 cd06166 Sortase_D_5 Sortase D 21.2 1.1E+02 0.0024 20.5 2.8 30 23-52 61-94 (126)
88 PRK08983 fliN flagellar motor 21.0 2.2E+02 0.0047 20.0 4.2 43 24-67 69-118 (127)
89 PRK08433 flagellar motor switc 21.0 2.3E+02 0.0049 19.5 4.2 43 23-66 49-98 (111)
90 TIGR03784 marine_sortase sorta 20.7 1.6E+02 0.0035 21.4 3.7 30 23-52 105-139 (174)
91 cd01771 Faf1_UBX Faf1 UBX doma 20.6 1.4E+02 0.0031 18.9 3.0 20 64-83 10-29 (80)
92 PRK06666 fliM flagellar motor 20.4 2.1E+02 0.0046 22.4 4.5 44 23-67 275-325 (337)
93 PRK08486 single-stranded DNA-b 20.3 1.7E+02 0.0036 21.6 3.7 16 25-40 65-80 (182)
94 TIGR00621 ssb single stranded 20.3 1.7E+02 0.0037 20.9 3.6 16 25-40 67-82 (164)
95 PF14685 Tricorn_PDZ: Tricorn 20.2 76 0.0016 20.8 1.7 17 24-40 37-54 (88)
96 PRK08395 fumarate hydratase; P 20.2 38 0.00082 25.0 0.2 25 24-48 12-36 (162)
No 1
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=2.3e-34 Score=209.26 Aligned_cols=91 Identities=85% Similarity=1.256 Sum_probs=87.9
Q ss_pred CCcccccccccccCCceeeeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCc
Q 034229 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (100)
Q Consensus 1 m~~~~~~~~~~~~~~~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ 80 (100)
|++++++|| ++|||||.|+|+++++||+|++|+++|+||+|++++|+||||||+|++|++++||+||+++|.+|+++++
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 788667899 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeEEEEeecc
Q 034229 81 CDVLIYASLSAF 92 (100)
Q Consensus 81 ve~~~le~~~~~ 92 (100)
+++|+|+++++-
T Consensus 80 ve~~~ve~~~~q 91 (159)
T PLN03107 80 CDVPHVNRTDYQ 91 (159)
T ss_pred EEEEEEEEEEEE
Confidence 999999999863
No 2
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=100.00 E-value=8.6e-34 Score=207.52 Aligned_cols=91 Identities=52% Similarity=0.913 Sum_probs=86.8
Q ss_pred CCcccccccc-cccCCceeeeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCC
Q 034229 1 MSDEEHHFES-KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (100)
Q Consensus 1 m~~~~~~~~~-~~~~~~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~ 79 (100)
|||++++|+. +++||+|.|||++|++||+|.||+|+|+||+|++++++||||||+||+|+.++|||||+++|+.+|+++
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 8887778994 599999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEeeEEEEeec
Q 034229 80 NCDVLIYASLSA 91 (100)
Q Consensus 80 ~ve~~~le~~~~ 91 (100)
++++|+++|+..
T Consensus 81 nv~VP~V~r~~y 92 (166)
T PTZ00328 81 NVEVPFVKTFTY 92 (166)
T ss_pred eeEeeeEEeeEE
Confidence 999999998753
No 3
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.4e-31 Score=191.16 Aligned_cols=91 Identities=67% Similarity=1.033 Sum_probs=88.6
Q ss_pred CCcccccccccccCCceeeeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCc
Q 034229 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHN 80 (100)
Q Consensus 1 m~~~~~~~~~~~~~~~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ 80 (100)
|++++++|+ ++|||+|.|||++++.|||+.+|+++|+||+|+|++++|.||||+|+|++.++|||||+++|..+||.|+
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 899998999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeEEEEeecc
Q 034229 81 CDVLIYASLSAF 92 (100)
Q Consensus 81 ve~~~le~~~~~ 92 (100)
+++|+++|.+.-
T Consensus 80 ~dVp~vkr~~yq 91 (156)
T KOG3271|consen 80 MDVPVVKRVDYQ 91 (156)
T ss_pred cccCccccceeE
Confidence 999999998753
No 4
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=99.96 E-value=3.9e-29 Score=176.41 Aligned_cols=77 Identities=49% Similarity=0.755 Sum_probs=74.6
Q ss_pred ceeeeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 16 ~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
||.|+|+++++||+|++|+++|+||+|++++|+||||||+|+||+++|||+||+++|++|+|++++|+|+|+++++-
T Consensus 1 ~~~~~~~~~~~irkG~~i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~q 77 (130)
T TIGR00037 1 MSATKQVQVSALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQ 77 (130)
T ss_pred CCcceeccHHHccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEE
Confidence 57799999999999999999999999999999999999999999999999999999999999999999999999863
No 5
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=99.92 E-value=3.4e-25 Score=156.17 Aligned_cols=74 Identities=38% Similarity=0.674 Sum_probs=71.3
Q ss_pred eeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 19 t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
-.|+++++||+|++|+++|+||+|++++|+||||||+|++|++++||+||+++|.+|++++++|.|.|+++++-
T Consensus 3 ~~~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~q 76 (129)
T PRK03999 3 KKQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQ 76 (129)
T ss_pred cccccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEE
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999863
No 6
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=1e-24 Score=154.22 Aligned_cols=72 Identities=36% Similarity=0.461 Sum_probs=68.6
Q ss_pred eEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 20 FPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 20 ~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
.++++++||+|++|++||+||+|++++|+|||||| |++|++++||+||+++|.+|++++++|+|.|+++.|-
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg~-a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q 73 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGKGG-AFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQ 73 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCCCC-cEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEE
Confidence 57899999999999999999999999999999955 5999999999999999999999999999999999874
No 7
>PRK12426 elongation factor P; Provisional
Probab=99.88 E-value=2.3e-22 Score=149.48 Aligned_cols=71 Identities=14% Similarity=0.025 Sum_probs=68.3
Q ss_pred EEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
++++++||+|+.|+++|+||.|++++|+|||| |+|++|+|+|||.||++.|++|+++|++|.++|++++|-
T Consensus 1 m~~~~dik~G~~i~~~g~~~~V~~~~h~kPGk-g~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~q 71 (185)
T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPK-GETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLE 71 (185)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEecCCC-CceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeE
Confidence 36789999999999999999999999999999 999999999999999999999999999999999999973
No 8
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=99.88 E-value=3.3e-22 Score=123.71 Aligned_cols=58 Identities=29% Similarity=0.379 Sum_probs=53.3
Q ss_pred eccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcE
Q 034229 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNC 81 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~v 81 (100)
++++||+|++|+++|+||.|++++|++||| |+|++|+++|||.||++.|.+|+++|++
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 479999999999999999999999999999 9999999999999999999999999985
No 9
>PRK14578 elongation factor P; Provisional
Probab=99.86 E-value=2e-21 Score=144.58 Aligned_cols=72 Identities=14% Similarity=0.233 Sum_probs=67.5
Q ss_pred EEeccccccceEEEEcCeeEEEEEeeeecCCCC-cccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKh-G~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
++.+++||+|++|++||+||+|++++|+|||++ |+|++|+|+|||.||++.|.+|++++++|.++|++++|-
T Consensus 1 m~~~~dik~G~~i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~q 73 (187)
T PRK14578 1 MYTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQ 73 (187)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeE
Confidence 357899999999999999999999999999985 467999999999999999999999999999999999973
No 10
>PRK00529 elongation factor P; Validated
Probab=99.86 E-value=2.1e-21 Score=143.51 Aligned_cols=71 Identities=23% Similarity=0.238 Sum_probs=68.2
Q ss_pred EEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
++++++||+|++|+++|+||+|++++|+|||| |+|++|++++||+||+++|.+|+++++++.|.++++++-
T Consensus 1 ~~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q 71 (186)
T PRK00529 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGK-GQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQ 71 (186)
T ss_pred CcchhhcCCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEE
Confidence 46899999999999999999999999999999 999999999999999999999999999999999999863
No 11
>PRK04542 elongation factor P; Provisional
Probab=99.86 E-value=2.9e-21 Score=143.98 Aligned_cols=72 Identities=17% Similarity=0.189 Sum_probs=67.6
Q ss_pred EEeccccccceEEEEcCeeEEEEEeeeecC-CCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 21 PQQAGTIRKNGYIVIKGRPCKVVEVSTSKT-GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~g~Pc~Vve~~~~Kp-GKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
++++++||+|+.|+++|+||+|++++|+|| ||+|+|++|+|+|||.||++.|++|+|+|++|.++|++++|-
T Consensus 1 mi~~~dik~G~~i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~q 73 (189)
T PRK04542 1 MPKANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVT 73 (189)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeE
Confidence 467899999999999999999999999999 794467999999999999999999999999999999999973
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=99.85 E-value=4.9e-21 Score=141.42 Aligned_cols=70 Identities=26% Similarity=0.291 Sum_probs=67.2
Q ss_pred EeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 22 QQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 22 i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
+.+++||+|++|+++|+||+|++++|+|||| |+|++|++++||+||+++|++|+++++++.+.++++++-
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGk-g~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q 70 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGK-GQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQ 70 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCC-CceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEE
Confidence 4689999999999999999999999999999 999999999999999999999999999999999999873
No 13
>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=99.82 E-value=6e-20 Score=136.63 Aligned_cols=69 Identities=17% Similarity=0.257 Sum_probs=65.0
Q ss_pred ccccccceEEEEcCeeEEEEEeeeecCCCCccc-EEEEEEeEccCCcEEEEEEcCCCcEEeeEEEEeecc
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHA-KCHFVGIDIFNGKKLEDIVPSSHNCDVLIYASLSAF 92 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A-~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~~~~~ 92 (100)
+++||+|+.|+++|+||+|++++|+|||+.|+| ++|+++|||.||++.|++|+++|++|.++|++++|-
T Consensus 2 ~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~q 71 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREAS 71 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeE
Confidence 689999999999999999999999999885555 899999999999999999999999999999999973
No 14
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=90.08 E-value=1.3 Score=36.14 Aligned_cols=62 Identities=18% Similarity=0.239 Sum_probs=47.1
Q ss_pred cccCCceeeeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEE
Q 034229 11 KADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (100)
Q Consensus 11 ~~~~~~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve 82 (100)
+|-.-.-.||.+..-++++|+.|.++|..+.++. +-|+ .+.++||.|++..+.+......-+
T Consensus 231 tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~----~~~~------~~~~~dl~t~e~~~~~~~~~~~~~ 292 (355)
T COG1499 231 TGKRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVR----SIGK------GIVVLDLETGEPVEITWSVYKRNE 292 (355)
T ss_pred CCceEEEEEEEEECCCCCCCCEEEECCCeEEEEE----EecC------ceEEEecccCCccccChhhcccCc
Confidence 3444456789999999999999999997776663 3366 488999999988877775555555
No 15
>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=84.74 E-value=2.8 Score=29.77 Aligned_cols=42 Identities=12% Similarity=0.087 Sum_probs=32.0
Q ss_pred EeccccccceEEEEcCe--eEEEEEeeee--cCC-----CCcccEEEEEEe
Q 034229 22 QQAGTIRKNGYIVIKGR--PCKVVEVSTS--KTG-----KHGHAKCHFVGI 63 (100)
Q Consensus 22 i~~~~LkkG~~I~i~g~--Pc~Vve~~~~--KpG-----KhG~A~vr~k~k 63 (100)
+-.=|||.|+.|.+++. +|.|+-.++. .+. -+|.+.|.+|=+
T Consensus 55 v~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk~~ 105 (131)
T PF08605_consen 55 VKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLKRR 105 (131)
T ss_pred EeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEEEc
Confidence 45569999999999998 8999988877 223 138888887533
No 16
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=68.39 E-value=6.7 Score=24.70 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=14.7
Q ss_pred eccccccceEEEEcCeeEEEE
Q 034229 23 QAGTIRKNGYIVIKGRPCKVV 43 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vv 43 (100)
.-..|++|+.|.++|..++|+
T Consensus 45 rg~Kl~~GD~V~~~~~~~~Vv 65 (65)
T PF13275_consen 45 RGKKLRPGDVVEIDGEEYRVV 65 (65)
T ss_dssp SS----SSEEEEETTEEEEEE
T ss_pred cCCcCCCCCEEEECCEEEEEC
Confidence 345799999999999999885
No 17
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=64.89 E-value=5.9 Score=26.75 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=23.3
Q ss_pred EEeccccccceEEEEcCeeEEEEEee
Q 034229 21 PQQAGTIRKNGYIVIKGRPCKVVEVS 46 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~g~Pc~Vve~~ 46 (100)
.....||+.|..|.|.|+++.|+++.
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 46778999999999999999999874
No 18
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=62.58 E-value=8.4 Score=26.11 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=19.2
Q ss_pred cccceEEEEcCeeEEEEEeeeec
Q 034229 27 IRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 27 LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
|++|+.+.++|.+|.|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 78999999999999998655443
No 19
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=61.39 E-value=22 Score=23.15 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=21.8
Q ss_pred cCCceeeeEEeccc---cccceEEEEcCeeEEEEEeeeec
Q 034229 13 DAGASKTFPQQAGT---IRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 13 ~~~~s~t~~i~~~~---LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
=++.+.+..+..++ .++|+.|.++|+-|.|.+++.--
T Consensus 49 v~g~~~~L~v~~~d~~~P~~gd~v~~dG~~y~V~~~~~~~ 88 (95)
T PF13856_consen 49 VEGTQPTLYVFSSDYPKPRRGDRVVIDGESYTVTRFQEED 88 (95)
T ss_dssp -----EEEEE--SS-----TT-EEEETTEEEEEEEEEEET
T ss_pred ccCCceEEEEEcCCCCCCCCCCEEEECCeEEEEeEEecCC
Confidence 34455566665555 55999999999999999887553
No 20
>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=61.02 E-value=4.7 Score=26.91 Aligned_cols=21 Identities=10% Similarity=0.091 Sum_probs=16.2
Q ss_pred eEEeccccccceEEEEcCeeE
Q 034229 20 FPQQAGTIRKNGYIVIKGRPC 40 (100)
Q Consensus 20 ~~i~~~~LkkG~~I~i~g~Pc 40 (100)
..|++++|++||||..-+.+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 458899999999988655444
No 21
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=60.80 E-value=46 Score=26.62 Aligned_cols=53 Identities=23% Similarity=0.297 Sum_probs=31.3
Q ss_pred ccccceEEEEcCeeE--EEEEeeeecCCCCcc------cEEEEEEeEccCCcEEEEEEcCCCcEE
Q 034229 26 TIRKNGYIVIKGRPC--KVVEVSTSKTGKHGH------AKCHFVGIDIFNGKKLEDIVPSSHNCD 82 (100)
Q Consensus 26 ~LkkG~~I~i~g~Pc--~Vve~~~~KpGKhG~------A~vr~k~knL~TG~~~E~t~~s~~~ve 82 (100)
+|+.|+.+-|.+-|- .|-.++ .+||++|+ +.+++.+++ |...-..++|++.-.
T Consensus 123 ~ik~GN~lpL~~IP~Gt~VhNVE-~~pG~GGq~aRSaGtyA~vv~~~---~~y~~vrLpSGe~r~ 183 (275)
T COG0090 123 DIKPGNALPLGNIPEGTIVHNVE-LKPGDGGQLARSAGTYAQVVGKE---GNYVIVRLPSGEMRK 183 (275)
T ss_pred CcCCcceeeeccCCCCceEEeee-eccCCCceEEEeCCceEEEEEcc---CCEEEEECCCCCeEe
Confidence 444444444444441 222333 58999542 566777777 667778888887644
No 22
>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=60.42 E-value=12 Score=26.04 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=15.7
Q ss_pred eccccccceEEEEcCeeEEEEEe
Q 034229 23 QAGTIRKNGYIVIKGRPCKVVEV 45 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vve~ 45 (100)
...+|++|+.+.++++.|.|..+
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 35689999999999999999854
No 23
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=58.80 E-value=14 Score=25.85 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=19.5
Q ss_pred ccccccceEEEEcCeeEEEEEe
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEV 45 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~ 45 (100)
..+|++|+.+.++|+.|+|..+
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaV 70 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAV 70 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEE
Confidence 4679999999999999999754
No 24
>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=57.63 E-value=15 Score=25.75 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=18.9
Q ss_pred cccccceEEEEcCeeEEEEEe
Q 034229 25 GTIRKNGYIVIKGRPCKVVEV 45 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc~Vve~ 45 (100)
.+|++|+.+.++|+.|+|..+
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaV 70 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAV 70 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEE
Confidence 579999999999999999754
No 25
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=53.35 E-value=53 Score=21.42 Aligned_cols=46 Identities=11% Similarity=0.162 Sum_probs=31.4
Q ss_pred ccccceEEEEcCee---------EEEEEeeeecCCCC-cccEEEEEEeEccCCcEE
Q 034229 26 TIRKNGYIVIKGRP---------CKVVEVSTSKTGKH-GHAKCHFVGIDIFNGKKL 71 (100)
Q Consensus 26 ~LkkG~~I~i~g~P---------c~Vve~~~~KpGKh-G~A~vr~k~knL~TG~~~ 71 (100)
.+|.|++|+++... |-+=++-+...|.+ ..+.--+..-|+-||.+.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~ 60 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIR 60 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEE
Confidence 57999999998776 33444455555433 334555788899999875
No 26
>PRK11507 ribosome-associated protein; Provisional
Probab=53.26 E-value=15 Score=23.59 Aligned_cols=21 Identities=19% Similarity=0.267 Sum_probs=17.7
Q ss_pred eccccccceEEEEcCeeEEEE
Q 034229 23 QAGTIRKNGYIVIKGRPCKVV 43 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vv 43 (100)
.-..|++|+.|.++|.-++|+
T Consensus 49 RgkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 49 KRCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred cCCCCCCCCEEEECCEEEEEe
Confidence 346799999999999988775
No 27
>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=51.80 E-value=20 Score=24.66 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=22.8
Q ss_pred ccccccceEEEEcCeeEEEEEeeeec
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
+-++..|..|.++|+.|.|.++...-
T Consensus 74 ~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 74 FPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred ccccCCCCEEEECCceEEEEEEEecc
Confidence 35888999999999999999988765
No 28
>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=51.57 E-value=12 Score=27.35 Aligned_cols=23 Identities=17% Similarity=0.400 Sum_probs=19.5
Q ss_pred ccccccceEEEEcCeeEEEEEee
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVS 46 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~ 46 (100)
..=|+-|+||.+++.+|+|++=.
T Consensus 37 ~~VL~TgNYitI~d~v~kI~~K~ 59 (149)
T PF08408_consen 37 SEVLSTGNYITINDDVYKILDKD 59 (149)
T ss_pred HHHHhcCCeEEECCeeeeeeccc
Confidence 45589999999999999999653
No 29
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=50.38 E-value=22 Score=23.09 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=22.0
Q ss_pred eeEEeccccccceEEEEcCeeEEEE
Q 034229 19 TFPQQAGTIRKNGYIVIKGRPCKVV 43 (100)
Q Consensus 19 t~~i~~~~LkkG~~I~i~g~Pc~Vv 43 (100)
|.+++=..+.+|++|.++|+-|..-
T Consensus 8 T~~v~Rq~V~PG~~v~~~grty~AS 32 (73)
T PRK11354 8 TDEIPRQCVTPGDYVLHEGRTYIAS 32 (73)
T ss_pred ceeecccccCCceEEEEcCcEEEEE
Confidence 7788888999999999999999653
No 30
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=49.03 E-value=21 Score=23.13 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.7
Q ss_pred ccccccceEEEEcCeeEEEEEe
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEV 45 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~ 45 (100)
-..||.|+.|.+.|..+.|...
T Consensus 50 gkKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 50 GKKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CCEeecCCEEEECCEEEEEEec
Confidence 3579999999999999998753
No 31
>PF05354 Phage_attach: Phage Head-Tail Attachment; InterPro: IPR008018 This entry is represented by Bacteriophage lambda, FII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The phage head-tail attachment protein is required for the joining of phage heads and tails at the last step of morphogenesis [].; GO: 0042963 phage assembly, 0019028 viral capsid; PDB: 2KX4_A 1K0H_A.
Probab=47.56 E-value=12 Score=26.34 Aligned_cols=37 Identities=11% Similarity=0.163 Sum_probs=22.9
Q ss_pred eeEEeccccccceEEEEcCeeEEEEEeeeecCCCCcccEE
Q 034229 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKC 58 (100)
Q Consensus 19 t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~v 58 (100)
.+...+..|++++.+.+.|++|.|.+ +.|--+|...+
T Consensus 67 v~t~dv~~L~r~DtL~I~g~~y~Vd~---v~pD~~G~t~I 103 (117)
T PF05354_consen 67 VRTADVSGLKRRDTLTIGGESYWVDR---VGPDGGGSTRI 103 (117)
T ss_dssp ESCCCCCTS-TT-EEEETTTEEEBS------SSSSS-CCE
T ss_pred EEehHhhhhhcCCeEEECCEEEEEEe---eccCCCccEEE
Confidence 34457899999999999999999965 44532354443
No 32
>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=47.54 E-value=30 Score=18.21 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=16.1
Q ss_pred cceEEEE-----cCeeEEEEEeeeec
Q 034229 29 KNGYIVI-----KGRPCKVVEVSTSK 49 (100)
Q Consensus 29 kG~~I~i-----~g~Pc~Vve~~~~K 49 (100)
+|+.|.+ .|..++|+++...+
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 78889999887554
No 33
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=47.44 E-value=52 Score=22.94 Aligned_cols=55 Identities=16% Similarity=0.263 Sum_probs=35.2
Q ss_pred eccccccceEEEE-----cCeeEEEEEeeee---cCCCCcccEEEEEEeEccCCcEEEEEEcCCC
Q 034229 23 QAGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (100)
Q Consensus 23 ~~~~LkkG~~I~i-----~g~Pc~Vve~~~~---KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~ 79 (100)
+..++++|+.|.+ +|....+.-++-. .-++ | .--.+.++++..|.-.|.+|+-..
T Consensus 15 ~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~-G-~~~tftvRki~~gvGVEr~fpl~S 77 (116)
T PRK05338 15 DIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGR-G-LNETFTVRKISYGVGVERTFPLHS 77 (116)
T ss_pred CCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCC-C-CCceEEEEEcccCccEEEEecCCC
Confidence 4678899998765 4554433222211 1132 2 233588999999999999997654
No 34
>smart00466 SRA SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. Domain in SET domain containing proteins and in Deinococcus radiodurans DRA1533.
Probab=46.91 E-value=76 Score=23.04 Aligned_cols=36 Identities=19% Similarity=0.273 Sum_probs=24.2
Q ss_pred ccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEc
Q 034229 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (100)
Q Consensus 28 kkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL 65 (100)
+++....+|| +|+|++.- ..+|++|....|.+|+-+
T Consensus 117 ~p~~gyrYDG-LY~V~~~w-~e~g~~G~~v~kfkL~R~ 152 (155)
T smart00466 117 APGKGYIYDG-LYRIVDYW-REVGKSGFLVFKFKLVRI 152 (155)
T ss_pred CCCCeEEECc-EEEEEEEE-EecCCCCcEEEEEEEEeC
Confidence 4555555655 78888773 345776778888888755
No 35
>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=44.11 E-value=47 Score=25.81 Aligned_cols=33 Identities=12% Similarity=0.121 Sum_probs=22.9
Q ss_pred eccccccceEEEEc---CeeEEEE----EeeeecCCCCcc
Q 034229 23 QAGTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGH 55 (100)
Q Consensus 23 ~~~~LkkG~~I~i~---g~Pc~Vv----e~~~~KpGKhG~ 55 (100)
+.-+|++|++|.++ ++|..|. .+-..++|++|.
T Consensus 270 dll~L~~GDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~ 309 (320)
T TIGR01397 270 QLLNLQVGDVIPLNTDMPEEVSLRVGGRPKFRAQPGVRGG 309 (320)
T ss_pred HHhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEECC
Confidence 35689999999998 4566653 455567777654
No 36
>PF06605 Prophage_tail: Prophage endopeptidase tail; InterPro: IPR010572 This entry is represented by the Bacteriophage 53, Orf003. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3GS9_A.
Probab=43.75 E-value=70 Score=24.69 Aligned_cols=38 Identities=16% Similarity=0.309 Sum_probs=22.3
Q ss_pred cccccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeE
Q 034229 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGID 64 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~kn 64 (100)
.-|.++.+|..+|+.|+|.++....-|. + ..+.+.+..
T Consensus 26 ~~i~~~~~I~~~~q~y~I~~~~~~~~~~-~-~~~~V~a~h 63 (327)
T PF06605_consen 26 DLIKEENIITYDGQEYRIKQVEKSRDGN-T-ITITVTAEH 63 (327)
T ss_dssp --SSTT-EEEETTEEEE--EE--B-------EEEEEEEEB
T ss_pred HhcCcCCEEEECCeEEEEEEeEEecCCC-E-EEEEEEEEe
Confidence 5788999999999999999888776664 3 337788888
No 37
>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=43.65 E-value=64 Score=22.39 Aligned_cols=56 Identities=18% Similarity=0.258 Sum_probs=34.8
Q ss_pred EeccccccceEEEE-----cCeeEEEEEeeee---cCCCCcccEEEEEEeEccCCcEEEEEEcCCC
Q 034229 22 QQAGTIRKNGYIVI-----KGRPCKVVEVSTS---KTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (100)
Q Consensus 22 i~~~~LkkG~~I~i-----~g~Pc~Vve~~~~---KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~ 79 (100)
.+..++++|+.|.+ +|....+.-++-. .-++ | .--.+.++++..|.-.|.+|+...
T Consensus 14 ~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~-G-~~~tftvR~i~~gvGVEr~fpl~S 77 (113)
T TIGR01024 14 KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGG-G-IGETFTVRKISYGVGVERIFPLHS 77 (113)
T ss_pred cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCC-C-CceEEEEEEeccCccEEEEEEcCC
Confidence 35678999998776 3333332211111 1133 3 223588999999999999997654
No 38
>PRK12795 fliM flagellar motor switch protein FliM; Reviewed
Probab=43.46 E-value=66 Score=26.54 Aligned_cols=45 Identities=7% Similarity=0.147 Sum_probs=29.9
Q ss_pred eccccccceEEEEcC---eeEEE----EEeeeecCCCCcccEEEEEEeEccCC
Q 034229 23 QAGTIRKNGYIVIKG---RPCKV----VEVSTSKTGKHGHAKCHFVGIDIFNG 68 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g---~Pc~V----ve~~~~KpGKhG~A~vr~k~knL~TG 68 (100)
+.-+|++|++|.++- .|..| +..-..+||++|+-++ +++.+....
T Consensus 319 dlL~LkvGDVI~Ld~~~~~~v~v~v~g~p~F~g~~G~~~g~~A-vrI~~~l~~ 370 (388)
T PRK12795 319 RVLNLKVGDTLMLDARPDALVTLRCGDVPLTEGRMGRVGDRVA-VRVEKPLRK 370 (388)
T ss_pred HHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEeccCCCEEE-EEEEeecCC
Confidence 356899999999984 35554 3456678999765443 555555543
No 39
>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=42.11 E-value=1.1e+02 Score=20.99 Aligned_cols=59 Identities=12% Similarity=0.168 Sum_probs=35.8
Q ss_pred EeccccccceEEEE-----cCeeEEEEEeeeecCCCCc-ccEEEEEEeEccCCcEEEEEEcCCCc
Q 034229 22 QQAGTIRKNGYIVI-----KGRPCKVVEVSTSKTGKHG-HAKCHFVGIDIFNGKKLEDIVPSSHN 80 (100)
Q Consensus 22 i~~~~LkkG~~I~i-----~g~Pc~Vve~~~~KpGKhG-~A~vr~k~knL~TG~~~E~t~~s~~~ 80 (100)
.+..++++|+.|.+ +|....+..++-.--++++ +.---+.++|++.|.-.|.+|+-...
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP 78 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSP 78 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTST
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCC
Confidence 45678999998765 2444444332222111111 11224778999999999999987644
No 40
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=41.54 E-value=60 Score=21.47 Aligned_cols=24 Identities=8% Similarity=0.224 Sum_probs=17.5
Q ss_pred EEeccccccceEEEE----cCeeEEEEE
Q 034229 21 PQQAGTIRKNGYIVI----KGRPCKVVE 44 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i----~g~Pc~Vve 44 (100)
..-.+.|++|+.|++ +|+-|.|++
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 444678999998775 577777765
No 41
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=41.32 E-value=95 Score=19.88 Aligned_cols=41 Identities=10% Similarity=0.092 Sum_probs=26.4
Q ss_pred ccccceEEEEcCe-eEEEEEeeeecCCCCcccEEEEEEeEccCC
Q 034229 26 TIRKNGYIVIKGR-PCKVVEVSTSKTGKHGHAKCHFVGIDIFNG 68 (100)
Q Consensus 26 ~LkkG~~I~i~g~-Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG 68 (100)
.+++|++|.+.+. .|+|.++.....+. ...-.+.+.=....
T Consensus 1 mf~~GD~VVh~~~Gv~~i~~i~~~~~~~--~~~~yy~L~~~~~~ 42 (98)
T PF02559_consen 1 MFKIGDYVVHPNHGVGRIEGIEEIEFGG--EKQEYYVLEYADDD 42 (98)
T ss_dssp T--TTSEEEETTTEEEEEEEEEEEECTT--EEEEEEEEEECCCE
T ss_pred CCCCCCEEEECCCceEEEEEEEEEeeCC--eeEEEEEEEECCCC
Confidence 3789999998755 99999999888863 23333444444443
No 42
>PF05521 Phage_H_T_join: Phage head-tail joining protein ; InterPro: IPR008767 This entry describes the head-tail adaptor protein of bacteriophage SPP1 and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2KCA_A 2KZ4_A.
Probab=40.56 E-value=83 Score=18.99 Aligned_cols=25 Identities=12% Similarity=0.204 Sum_probs=18.9
Q ss_pred cccccceEEEEcCeeEEEEEeeeec
Q 034229 25 GTIRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
.+|..++.|.++|+.|.|..+....
T Consensus 61 ~~I~~~~ri~~~g~~y~I~~i~~~~ 85 (95)
T PF05521_consen 61 KDITPDMRIKYDGKVYNIKSIDPDD 85 (95)
T ss_dssp TTSSTTEEEEECTEEEEE-S--EE-
T ss_pred cCCCcceEEEECCEEEEEEEECCCC
Confidence 4799999999999999999877554
No 43
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=40.17 E-value=38 Score=25.91 Aligned_cols=27 Identities=19% Similarity=0.367 Sum_probs=23.0
Q ss_pred cccccceEEEEcCeeEEEEEeeeecCCC
Q 034229 25 GTIRKNGYIVIKGRPCKVVEVSTSKTGK 52 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc~Vve~~~~KpGK 52 (100)
-.|++|+.++++|+-..|++++. ++||
T Consensus 73 E~l~vGDei~vd~e~veITSIE~-~~gk 99 (201)
T COG1326 73 ETLKVGDEIEVDGEEVEITSIEL-GGGK 99 (201)
T ss_pred CeEecCCEEEEcCCEEEEEEEee-CCCc
Confidence 46899999999999999999983 4566
No 44
>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=40.14 E-value=24 Score=25.03 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=16.2
Q ss_pred ccccccceEEEEcCeeEEEEEee
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVS 46 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~ 46 (100)
...++.|++|.++|....|.++.
T Consensus 58 ~~pf~vGD~I~i~~~~G~V~~I~ 80 (206)
T PF00924_consen 58 ERPFKVGDRIEIGGVEGRVEEIG 80 (206)
T ss_dssp C-SS-TT-EEESSS-EEEEEEE-
T ss_pred cCCccCCCEEEEEEeehHHHhcC
Confidence 35789999999999999999865
No 45
>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=40.13 E-value=47 Score=23.81 Aligned_cols=38 Identities=13% Similarity=0.126 Sum_probs=27.8
Q ss_pred ccccccceEEEEcCeeE-----EEEEeeeecC-CCCcccEEEEE
Q 034229 24 AGTIRKNGYIVIKGRPC-----KVVEVSTSKT-GKHGHAKCHFV 61 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc-----~Vve~~~~Kp-GKhG~A~vr~k 61 (100)
..+|++|+.|...|+-. -|+..+|..| |+|-...+...
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 46799999999988742 4788899888 66655555543
No 46
>PRK10965 multicopper oxidase; Provisional
Probab=39.40 E-value=1.3e+02 Score=25.67 Aligned_cols=52 Identities=8% Similarity=-0.040 Sum_probs=38.4
Q ss_pred ccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEE
Q 034229 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYA 87 (100)
Q Consensus 28 kkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le 87 (100)
..|+.+.+||+++-.+++ ||+ .+|+++.|--+-+.+...+..++.+.++-.+
T Consensus 210 ~~gd~~lVNG~~~p~~~v----~~~----~~RlRliNas~~r~~~l~~~dg~~~~vIa~D 261 (523)
T PRK10965 210 WFGDTLLTNGAIYPQHAA----PRG----WLRLRLLNGCNARSLNLATSDGRPLYVIASD 261 (523)
T ss_pred ccCCeEEECCcccceeec----CCC----EEEEEEEeccCCceEEEEEcCCceEEEEEeC
Confidence 468899999997765432 443 7899999998888888877666776655443
No 47
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.11 E-value=24 Score=24.07 Aligned_cols=28 Identities=14% Similarity=0.189 Sum_probs=23.5
Q ss_pred eeeEEeccccccceEEEEcCeeEEEEEe
Q 034229 18 KTFPQQAGTIRKNGYIVIKGRPCKVVEV 45 (100)
Q Consensus 18 ~t~~i~~~~LkkG~~I~i~g~Pc~Vve~ 45 (100)
...-+.-++||+|..+++++.-|.+++-
T Consensus 49 ~sifie~g~lrpGiI~LINd~DWeLlek 76 (96)
T COG5131 49 DSIFIEHGELRPGIICLINDMDWELLEK 76 (96)
T ss_pred ceeeecCCCCcccEEEEEcCccHhhhhc
Confidence 3455677899999999999999999864
No 48
>PRK11835 hypothetical protein; Provisional
Probab=35.91 E-value=40 Score=23.66 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=20.3
Q ss_pred cccccc-eEEEEcCeeEEEEEeeeecCCCCcccEEEEE
Q 034229 25 GTIRKN-GYIVIKGRPCKVVEVSTSKTGKHGHAKCHFV 61 (100)
Q Consensus 25 ~~LkkG-~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k 61 (100)
++|... .+++++|+||.-+..+-- ..|.+|+|
T Consensus 66 ~eiqv~~~ivEweGepCLFv~~~DE-----~aa~CrLK 98 (114)
T PRK11835 66 SDIQVPCSVLECEGEPCLFVNRQDE-----SAATCRLK 98 (114)
T ss_pred HhhcccceEEEecCCceEEEecccc-----hhhheeec
Confidence 344443 478899999987744322 44666665
No 49
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=35.54 E-value=55 Score=22.55 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=15.2
Q ss_pred EEeccccccceEEEE-cCeeEEEEEeee
Q 034229 21 PQQAGTIRKNGYIVI-KGRPCKVVEVST 47 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i-~g~Pc~Vve~~~ 47 (100)
-+.|.+|++|+.+.- +|.+..|.++..
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 578999999998754 677777766653
No 50
>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
Probab=35.20 E-value=85 Score=26.65 Aligned_cols=38 Identities=18% Similarity=0.441 Sum_probs=28.6
Q ss_pred EeccccccceEEEEcCeeEEEEE-eeeecCCCCcccEEEEEEe
Q 034229 22 QQAGTIRKNGYIVIKGRPCKVVE-VSTSKTGKHGHAKCHFVGI 63 (100)
Q Consensus 22 i~~~~LkkG~~I~i~g~Pc~Vve-~~~~KpGKhG~A~vr~k~k 63 (100)
....++++...|.++|++|++++ -+....|+ +|++..+
T Consensus 383 ~~vt~~~p~G~V~v~GE~W~AvS~~~~I~kG~----~VkVV~~ 421 (436)
T COG1030 383 KTVTPLRPEGFVLVEGERWRAVSEGEPIEKGE----KVKVVDR 421 (436)
T ss_pred eecccCCCCeEEEECCEEEEEeeCCCcccCCC----EEEEEee
Confidence 45678999999999999999997 55555555 5555444
No 51
>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=35.11 E-value=78 Score=23.09 Aligned_cols=38 Identities=18% Similarity=0.278 Sum_probs=21.6
Q ss_pred cccccceEEEEc---Cee---EEEEEeeeecCCCCcccEEEEEEe
Q 034229 25 GTIRKNGYIVIK---GRP---CKVVEVSTSKTGKHGHAKCHFVGI 63 (100)
Q Consensus 25 ~~LkkG~~I~i~---g~P---c~Vve~~~~KpGKhG~A~vr~k~k 63 (100)
+-+|.|++|.++ +.| |+|+++...+.|. =.++|++-.|
T Consensus 2 ~~yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~~~-~~vkV~wfYR 45 (164)
T cd04709 2 NMYRVGDYVYFESSPNNPYLIRRIEELNKTARGH-VEAKVVCYYR 45 (164)
T ss_pred cEEecCCEEEEECCCCCCCEEEEEEEEEeCCCCC-EEEEEEEEEC
Confidence 347899999886 445 5556665444332 2345554433
No 52
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.47 E-value=58 Score=22.69 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=12.3
Q ss_pred cccccceEEEEcCe
Q 034229 25 GTIRKNGYIVIKGR 38 (100)
Q Consensus 25 ~~LkkG~~I~i~g~ 38 (100)
-++++|+.|+.+|.
T Consensus 32 r~ik~GD~IiF~~~ 45 (111)
T COG4043 32 RQIKPGDKIIFNGD 45 (111)
T ss_pred cCCCCCCEEEEcCC
Confidence 57999999999975
No 53
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=34.37 E-value=54 Score=22.16 Aligned_cols=31 Identities=16% Similarity=0.306 Sum_probs=22.1
Q ss_pred ceeeeEEeccccccceEEEEcCe----eEEEEEee
Q 034229 16 ASKTFPQQAGTIRKNGYIVIKGR----PCKVVEVS 46 (100)
Q Consensus 16 ~s~t~~i~~~~LkkG~~I~i~g~----Pc~Vve~~ 46 (100)
-+.+.+...-.|++|++|.+... .|+|.+++
T Consensus 129 ~~f~~~~~~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 129 VSFTLPPDGLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred EEEEEChhhccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 45566677789999999998733 56666553
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=33.50 E-value=1e+02 Score=19.22 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=10.8
Q ss_pred cccccceEEEEcCeeE
Q 034229 25 GTIRKNGYIVIKGRPC 40 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc 40 (100)
..|++|+.|.+.|..-
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 4599999999999876
No 55
>PRK06788 flagellar motor switch protein; Validated
Probab=33.41 E-value=58 Score=22.76 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=29.2
Q ss_pred ccccccceEEEEc---CeeEEEE----EeeeecCCCCcccEEEEEEeEccCCcE
Q 034229 24 AGTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGHAKCHFVGIDIFNGKK 70 (100)
Q Consensus 24 ~~~LkkG~~I~i~---g~Pc~Vv----e~~~~KpGKhG~A~vr~k~knL~TG~~ 70 (100)
.-+|++|++|.++ ++|..|. .+-...+|..+. +.-+++..+.+.+.
T Consensus 52 lL~L~vGDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~~-~~AVrItei~~~~~ 104 (119)
T PRK06788 52 VKQLKVGDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMDE-KFGIIISEIEADKK 104 (119)
T ss_pred HhCCCCCCEEEeCCcCCCCEEEEECCEEEEEEEEEEECC-EEEEEEEEecChHH
Confidence 4578999999998 5565552 344556666443 33466777766443
No 56
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=33.36 E-value=85 Score=20.49 Aligned_cols=30 Identities=33% Similarity=0.386 Sum_probs=24.8
Q ss_pred CceeeeEEeccccccceEEEEcCeeEEEEE
Q 034229 15 GASKTFPQQAGTIRKNGYIVIKGRPCKVVE 44 (100)
Q Consensus 15 ~~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve 44 (100)
|.-.|..++-+.||+|++|.....-++|..
T Consensus 15 G~vatviV~~GtL~~Gd~iv~G~~~GkVr~ 44 (95)
T cd03701 15 GPVATVIVQNGTLKKGDVIVAGGTYGKIRT 44 (95)
T ss_pred CeeEEEEEEcCeEecCCEEEECCccceEEE
Confidence 556788889999999999999887777753
No 57
>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=31.18 E-value=1.3e+02 Score=18.64 Aligned_cols=35 Identities=11% Similarity=0.192 Sum_probs=26.2
Q ss_pred ccccccCCceeeeEEe---ccccccceEEEEcCeeEEEE
Q 034229 8 FESKADAGASKTFPQQ---AGTIRKNGYIVIKGRPCKVV 43 (100)
Q Consensus 8 ~~~~~~~~~s~t~~i~---~~~LkkG~~I~i~g~Pc~Vv 43 (100)
|+ .+...+..|+.+. ..+|...+.|.++|+.|.|.
T Consensus 45 ~~-a~~~~~~~t~~~~iR~~~~i~~~~ri~~~g~~Y~I~ 82 (101)
T TIGR01563 45 YR-AGQEGVEITHVILIRYRKDVTNKMRVIYDGRIYTIG 82 (101)
T ss_pred ee-cccccCceEEEEEEeccCCCChhhEEEECCEEEEEE
Confidence 44 5555666666553 57899999999999999993
No 58
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=31.13 E-value=97 Score=20.44 Aligned_cols=32 Identities=25% Similarity=0.213 Sum_probs=25.5
Q ss_pred CceeeeEEeccccccceEEEEcCeeEEEEEee
Q 034229 15 GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVS 46 (100)
Q Consensus 15 ~~s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~ 46 (100)
|...|..++-+.||+|+++.....-++|-.+.
T Consensus 15 G~vatviV~~GtL~~Gd~iv~G~~~gkVr~l~ 46 (95)
T cd03702 15 GPVATVLVQNGTLKVGDVLVAGTTYGKVRAMF 46 (95)
T ss_pred CccEEEEEEcCeEeCCCEEEEcccccEEEEEE
Confidence 45568888999999999999987777775444
No 59
>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=30.26 E-value=94 Score=19.18 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=13.6
Q ss_pred cccccceEEEEcCeeE
Q 034229 25 GTIRKNGYIVIKGRPC 40 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc 40 (100)
..++||+.|.+.|.+-
T Consensus 60 ~~~~kG~~V~v~G~l~ 75 (100)
T cd04496 60 KYLKKGDLVYVEGRLR 75 (100)
T ss_pred HHhCCCCEEEEEEEEE
Confidence 4599999999999873
No 60
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=30.18 E-value=89 Score=23.68 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=19.2
Q ss_pred eEEeccccccceEEEE------cCeeEEEEEeeee
Q 034229 20 FPQQAGTIRKNGYIVI------KGRPCKVVEVSTS 48 (100)
Q Consensus 20 ~~i~~~~LkkG~~I~i------~g~Pc~Vve~~~~ 48 (100)
.++-++++++|++|.. .-+|-+|+++...
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 6889999999999999 3346777766654
No 61
>PF14623 Vint: Hint-domain
Probab=30.04 E-value=1.1e+02 Score=22.66 Aligned_cols=30 Identities=20% Similarity=0.248 Sum_probs=21.4
Q ss_pred eeEEeccccccceEEEEcCeeEEEEEeeee
Q 034229 19 TFPQQAGTIRKNGYIVIKGRPCKVVEVSTS 48 (100)
Q Consensus 19 t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~ 48 (100)
..++++.+||+|+.|.=-..|-+|.-+-..
T Consensus 15 ~~~v~i~~lR~G~~V~tp~G~r~V~~Vlkt 44 (162)
T PF14623_consen 15 RAPVRIDDLRAGDKVWTPRGPRKVAAVLKT 44 (162)
T ss_pred ceeEEHHHccCCCEEECCCCCeEEEEEEEE
Confidence 445899999999998876666666544433
No 62
>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=29.76 E-value=1.5e+02 Score=21.31 Aligned_cols=34 Identities=26% Similarity=0.294 Sum_probs=23.5
Q ss_pred ceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEc
Q 034229 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDI 65 (100)
Q Consensus 30 G~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL 65 (100)
+....+|| +|+|+++...+. +.|....+.+|+-+
T Consensus 119 ~g~yrYDG-LY~V~~~w~~~g-~~G~~v~kF~L~R~ 152 (155)
T PF02182_consen 119 GGIYRYDG-LYKVVKYWREKG-KSGFKVFKFKLVRL 152 (155)
T ss_dssp SS-EEEEE-EEEEEEEEEEE--TTSSEEEEEEEEE-
T ss_pred CCCEEeCc-EEEEEEEEEEeC-CCCcEEEEEEEEEC
Confidence 34457777 999999887654 44778888888765
No 63
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=29.34 E-value=18 Score=27.32 Aligned_cols=27 Identities=4% Similarity=0.218 Sum_probs=22.8
Q ss_pred eccccccceEEEEcCeeEEEEEeeeec
Q 034229 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
.+.+||.|+.|.|+|..+.--|..|.+
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 467899999999999999887776654
No 64
>PRK10883 FtsI repressor; Provisional
Probab=29.13 E-value=2.1e+02 Score=23.89 Aligned_cols=52 Identities=13% Similarity=0.157 Sum_probs=39.8
Q ss_pred ccceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEE
Q 034229 28 RKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYA 87 (100)
Q Consensus 28 kkG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le 87 (100)
..|+.+.+||+.+-++++ +|| .+|+.+.|--.-+.+...+..++.+.++-.+
T Consensus 207 ~~gd~~lvNG~~~p~~~v---~~~-----~~RlRliNas~~~~~~l~l~d~~~~~vIa~D 258 (471)
T PRK10883 207 FVGDTLLVNGVQSPYVEV---SRG-----WVRLRLLNASNARRYQLQMSDGRPLHVIAGD 258 (471)
T ss_pred ccCCeeEECCccCCeEEe---cCC-----EEEEEEEEccCCceEEEEEcCCCeEEEEEeC
Confidence 468889999997766654 343 5799999999988888888667777766555
No 65
>PLN02792 oxidoreductase
Probab=28.97 E-value=2.1e+02 Score=24.55 Aligned_cols=55 Identities=16% Similarity=0.121 Sum_probs=36.4
Q ss_pred cceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCCcEEeeEEEE
Q 034229 29 KNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVLIYAS 88 (100)
Q Consensus 29 kG~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~~ve~~~le~ 88 (100)
.++.+.++|.+-.....-.++||| .+|+++.|.-.-..+...+. ++++.++-.+-
T Consensus 178 ~~d~~liNG~~~~~~~~~~v~~Gk----~yRlRliNa~~~~~~~f~i~-gH~~tVI~~DG 232 (536)
T PLN02792 178 MPDGVMINGQGVSYVYSITVDKGK----TYRFRISNVGLQTSLNFEIL-GHQLKLIEVEG 232 (536)
T ss_pred CCCEEEEeccCCCCcceEEECCCC----EEEEEEEEcCCCceEEEEEC-CcEEEEEEeCC
Confidence 457889999841111223467898 88999998877766666664 66676665543
No 66
>CHL00084 rpl19 ribosomal protein L19
Probab=28.96 E-value=2e+02 Score=20.02 Aligned_cols=54 Identities=15% Similarity=0.257 Sum_probs=35.1
Q ss_pred EeccccccceEEEE-----cCeeEEE-----EEeeeecCCCCcccEEEEEEeEccCCcEEEEEEcCCC
Q 034229 22 QQAGTIRKNGYIVI-----KGRPCKV-----VEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSH 79 (100)
Q Consensus 22 i~~~~LkkG~~I~i-----~g~Pc~V-----ve~~~~KpGKhG~A~vr~k~knL~TG~~~E~t~~s~~ 79 (100)
.+..++++|+.|.+ +|.-..+ +-+... |+ |- --.+.++++..|.-.|.+|+...
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-GL-NTTITVRKVFQGIGVERVFLLHS 81 (117)
T ss_pred cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEe--CC-CC-CeeEEEEEeccCccEEEEEecCC
Confidence 35678999998775 4442222 222322 33 32 22488999999999999997654
No 67
>COG4709 Predicted membrane protein [Function unknown]
Probab=28.57 E-value=8.5 Score=29.29 Aligned_cols=19 Identities=42% Similarity=0.632 Sum_probs=15.4
Q ss_pred CCcccccccccccCCceee
Q 034229 1 MSDEEHHFESKADAGASKT 19 (100)
Q Consensus 1 m~~~~~~~~~~~~~~~s~t 19 (100)
|+|+++||.+++++|.|+.
T Consensus 26 m~dyeehF~~a~~~GksE~ 44 (195)
T COG4709 26 MYDYEEHFREAQEAGKSEE 44 (195)
T ss_pred HHHHHHHHHhhhhcCCCHH
Confidence 6789999998999986643
No 68
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=27.83 E-value=31 Score=26.31 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=12.5
Q ss_pred ccccccceEEEEcCe
Q 034229 24 AGTIRKNGYIVIKGR 38 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~ 38 (100)
.++||+|+||.++..
T Consensus 181 Ls~LKkGgYIei~rG 195 (207)
T PRK11832 181 LAALRKGGYIEMNKG 195 (207)
T ss_pred HHHHhcCCCEEEecC
Confidence 589999999998644
No 69
>COG3731 SrlB Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]
Probab=27.06 E-value=80 Score=22.45 Aligned_cols=24 Identities=8% Similarity=0.207 Sum_probs=20.3
Q ss_pred eccccccceEEEEcCeeEEEEEee
Q 034229 23 QAGTIRKNGYIVIKGRPCKVVEVS 46 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vve~~ 46 (100)
.-.+|.+|+.+.+++++|.|+.+-
T Consensus 48 ~~~~l~~G~~l~lg~~~y~ItaVG 71 (123)
T COG3731 48 LQEALQPGDRLTLGGHCYPITAVG 71 (123)
T ss_pred ccccCCCCCEEEECCceEEEEEec
Confidence 446788999999999999998654
No 70
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=26.67 E-value=93 Score=21.65 Aligned_cols=30 Identities=17% Similarity=0.253 Sum_probs=23.3
Q ss_pred eccccccceEEEEcC-----eeEEEEEeeeecCCC
Q 034229 23 QAGTIRKNGYIVIKG-----RPCKVVEVSTSKTGK 52 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g-----~Pc~Vve~~~~KpGK 52 (100)
...+|++|+.|.+.. .-|+|.+.+...+..
T Consensus 69 ~L~~l~~GD~I~v~~~~g~~~~Y~V~~~~~v~~~~ 103 (144)
T cd05829 69 RLGDLRKGDKVEVTRADGQTATFRVDRVEVYPKDA 103 (144)
T ss_pred chhcCCCCCEEEEEECCCCEEEEEEeEEEEECccc
Confidence 357899999988865 469999888887654
No 71
>PF13403 Hint_2: Hint domain
Probab=26.50 E-value=2.3e+02 Score=19.85 Aligned_cols=61 Identities=15% Similarity=0.165 Sum_probs=36.5
Q ss_pred EEeccccccceEEE-EcCeeEEEEEeeeecC------CCCcccEEEEEEeEccCCc-EEEEEEcCCCcE
Q 034229 21 PQQAGTIRKNGYIV-IKGRPCKVVEVSTSKT------GKHGHAKCHFVGIDIFNGK-KLEDIVPSSHNC 81 (100)
Q Consensus 21 ~i~~~~LkkG~~I~-i~g~Pc~Vve~~~~Kp------GKhG~A~vr~k~knL~TG~-~~E~t~~s~~~v 81 (100)
+..+.+|+.|+.|+ .+|.+..|+.+....- ..+..+-+++..--|=.|. ..+-.....+.+
T Consensus 15 ~~~Ve~L~~GD~V~T~dgg~~~V~wig~~~~~~~~~~~~~~~~pvri~a~alG~g~P~~dl~vsp~hrv 83 (147)
T PF13403_consen 15 PRPVEDLRPGDRVLTRDGGFQPVRWIGRRTVSPADLPAPPRLAPVRIPAGALGNGRPSRDLLVSPQHRV 83 (147)
T ss_pred CeEeeccCCCCEEEecCCCEEEEEEEEEEEecccccCcCCCcceEEEECCccCCCCCCcCeEECcccce
Confidence 45788999999766 5688888876654432 3334466777665554444 223333444443
No 72
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=26.46 E-value=1.4e+02 Score=21.29 Aligned_cols=43 Identities=12% Similarity=0.186 Sum_probs=26.0
Q ss_pred ccccccceEEEEc---CeeEEEE----EeeeecCCCCcccEEEEEEeEccC
Q 034229 24 AGTIRKNGYIVIK---GRPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (100)
Q Consensus 24 ~~~LkkG~~I~i~---g~Pc~Vv----e~~~~KpGKhG~A~vr~k~knL~T 67 (100)
.-+|++|++|.++ ++|..|. -+-+..+|.++ -+.=+++.++.+
T Consensus 78 LL~L~~GDVI~Ld~~~~epv~V~Vng~~if~GevGvv~-~k~AVrIteii~ 127 (137)
T PRK07963 78 LLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVVA-DKYGVRITDIIT 127 (137)
T ss_pred HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEEC-CEEEEEEEEecC
Confidence 4578999999998 5776663 34444555533 233355555554
No 73
>TIGR00723 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=26.14 E-value=24 Score=26.18 Aligned_cols=26 Identities=4% Similarity=0.125 Sum_probs=22.5
Q ss_pred ccccccceEEEEcCeeEEEEEeeeec
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
+.+||.|+.|.|.|..|..-|..|.+
T Consensus 3 i~~L~vGD~V~LsG~i~taRD~ah~r 28 (168)
T TIGR00723 3 ILKLKVGDVVYLTGTIFTARDEAHAR 28 (168)
T ss_pred hHhCCCCCEEEEEEEEEEEEHHHHHH
Confidence 56899999999999999998876654
No 74
>KOG2345 consensus Serine/threonine protein kinase/TGF-beta stimulated factor [Transcription; Lipid transport and metabolism; Signal transduction mechanisms]
Probab=26.01 E-value=1.1e+02 Score=24.78 Aligned_cols=37 Identities=14% Similarity=0.275 Sum_probs=28.5
Q ss_pred ceEEEEcCeeEEEEEeeeecCCCCcccEEEEEEeEccCCcEE
Q 034229 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKL 71 (100)
Q Consensus 30 G~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k~knL~TG~~~ 71 (100)
+..|.||+.-|.|++-. |-+|-++| .-++|+.|+..|
T Consensus 13 ~~tv~In~~Ryri~~~L----geGGfsfv-~LV~~~s~~~~Y 49 (302)
T KOG2345|consen 13 RGTVIINNKRYRIQRLL----GEGGFSFV-DLVKGLSTGHLY 49 (302)
T ss_pred CCcEEEcCceEEEeeee----cCCCceee-eeecccCcccch
Confidence 77889999999998544 55466777 556799998776
No 75
>PF02839 CBM_5_12: Carbohydrate binding domain; InterPro: IPR003610 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM5 from CAZY and CBM12 from CAZY. These modules have a core structure consisting of a 3-stranded meander beta-sheet, which contain six aromatic groups that may be important for binding. CBM5/12 is found in proteins such as chitinase A1, chitinase B [], and endoglucanase Z []. The overall topology of the CBM is structurally similar to the C-terminal chitin-binding domains (ChBD) of chitinase A1 and chitinase B, however the binding mechanism for the ChBD may be different from that of the CBM [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1ED7_A 1W1V_A 1E15_B 1UR8_A 1E6Z_B 1E6P_A 1W1T_A 1W1P_B 1UR9_A 1E6R_A ....
Probab=24.94 E-value=90 Score=16.86 Aligned_cols=17 Identities=6% Similarity=0.129 Sum_probs=13.0
Q ss_pred cccceEEEEcCeeEEEE
Q 034229 27 IRKNGYIVIKGRPCKVV 43 (100)
Q Consensus 27 LkkG~~I~i~g~Pc~Vv 43 (100)
-..|+.|.++|..|+..
T Consensus 10 Y~~Gd~V~~~g~~y~a~ 26 (41)
T PF02839_consen 10 YNAGDRVSYNGKLYQAK 26 (41)
T ss_dssp E-TT-EEEETTEEEEES
T ss_pred EcCCCEEEECCCEEEEe
Confidence 35799999999999875
No 76
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=24.74 E-value=23 Score=27.10 Aligned_cols=27 Identities=15% Similarity=0.255 Sum_probs=23.2
Q ss_pred eccccccceEEEEcCeeEEEEEeeeec
Q 034229 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
.+.+||.|+.|.|.|..|..-|..|.+
T Consensus 14 ~i~~L~vGD~V~LsG~IytaRDaAHkr 40 (204)
T PRK08228 14 DLQDIKVGDVIYLTGTLVTCRDVAHRR 40 (204)
T ss_pred HHhhCCCCCEEEEEEEEEEEeHHHHHH
Confidence 367999999999999999998877654
No 77
>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=24.34 E-value=1.9e+02 Score=20.06 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=23.4
Q ss_pred ccccccCCc-eeeeEEeccccccceEEEEcCeeEEEEEeeeecCCC
Q 034229 8 FESKADAGA-SKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGK 52 (100)
Q Consensus 8 ~~~~~~~~~-s~t~~i~~~~LkkG~~I~i~g~Pc~Vve~~~~KpGK 52 (100)
|.+++..+. ..|....++.=|.---|..+|+||++...+-.=+||
T Consensus 35 ~~G~g~~~~~~~t~~l~Sg~Gkv~i~v~~ngk~s~l~~~q~~l~~~ 80 (107)
T PF07472_consen 35 FTGSGTNDNNIGTKVLNSGSGKVRIEVTANGKPSKLRSSQNTLDGK 80 (107)
T ss_dssp EEEEEEEEEEEEEEEEE-TTSEEEEEEEETTEE-EEEEEEEEETTT
T ss_pred EEecccCCCceeeEEEecCCCeEEEEEEeCCccccceeeeeeccCc
Confidence 554444433 333334444222223466788888888777666665
No 78
>PRK06842 fumarate hydratase; Provisional
Probab=24.02 E-value=25 Score=26.42 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=23.2
Q ss_pred ccccccceEEEEcCeeEEEEEeeeecC
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVSTSKT 50 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~~~Kp 50 (100)
+.+|+.|+.|.|.|..|.--|..|.+-
T Consensus 14 i~~L~vGD~V~LsG~i~taRDaAHkrl 40 (185)
T PRK06842 14 VKDLKAGDSVLISGYIYTARDAAHKRL 40 (185)
T ss_pred HhhCCCCCEEEEeEEEEEEeHHHHHHH
Confidence 679999999999999999988776543
No 79
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=23.76 E-value=46 Score=22.14 Aligned_cols=16 Identities=0% Similarity=0.094 Sum_probs=9.3
Q ss_pred EEeccccccceEEEEc
Q 034229 21 PQQAGTIRKNGYIVIK 36 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~ 36 (100)
.+.-++|++|+.||++
T Consensus 60 ~l~w~~L~VG~~VMvN 75 (85)
T PF12148_consen 60 ILKWDELKVGQVVMVN 75 (85)
T ss_dssp BE-GGG--TT-EEEEE
T ss_pred eccHHhCCcccEEEEe
Confidence 4566788889999886
No 80
>PRK06043 fumarate hydratase; Provisional
Probab=23.50 E-value=25 Score=26.66 Aligned_cols=27 Identities=7% Similarity=0.165 Sum_probs=23.0
Q ss_pred eccccccceEEEEcCeeEEEEEeeeec
Q 034229 23 QAGTIRKNGYIVIKGRPCKVVEVSTSK 49 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~Pc~Vve~~~~K 49 (100)
.+.+|+.|+.|.|.|..|.--|..|.+
T Consensus 13 ~i~~L~vGD~V~LsG~IytaRDaaH~r 39 (192)
T PRK06043 13 DIEKLNVGDIVYISGEILTARDEAHAR 39 (192)
T ss_pred HHhhCCCCCEEEEEEEEEEEeHHHHHH
Confidence 367999999999999999998876653
No 81
>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=23.19 E-value=2e+02 Score=17.88 Aligned_cols=14 Identities=7% Similarity=0.086 Sum_probs=11.9
Q ss_pred eccccccceEEEEc
Q 034229 23 QAGTIRKNGYIVIK 36 (100)
Q Consensus 23 ~~~~LkkG~~I~i~ 36 (100)
+.-+|++|++|.++
T Consensus 25 ell~L~~Gdvi~L~ 38 (77)
T TIGR02480 25 DLLKLGEGSVIELD 38 (77)
T ss_pred HHhcCCCCCEEEcC
Confidence 45789999999997
No 82
>cd01179 IPT_plexin_repeat2 Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=22.88 E-value=2e+02 Score=17.85 Aligned_cols=27 Identities=19% Similarity=0.508 Sum_probs=21.0
Q ss_pred eeEEeccccccc--eEEEEcCeeEEEEEe
Q 034229 19 TFPQQAGTIRKN--GYIVIKGRPCKVVEV 45 (100)
Q Consensus 19 t~~i~~~~LkkG--~~I~i~g~Pc~Vve~ 45 (100)
...|.-+.|..| ..|.++|.+|.++..
T Consensus 18 ~vtI~G~~~~~~~~~~V~ig~~~C~~~~~ 46 (85)
T cd01179 18 RLTITGKHLNAGSSVRVTVGGQPCKILSV 46 (85)
T ss_pred EEEEEEECCCCCCeEEEEECCeEeeEEEe
Confidence 556666777777 679999999999754
No 83
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=21.93 E-value=1.2e+02 Score=23.78 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=20.4
Q ss_pred cccccceEEEEcCeeEEEEEeeee
Q 034229 25 GTIRKNGYIVIKGRPCKVVEVSTS 48 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc~Vve~~~~ 48 (100)
.-+|.|++|.++|.-..|.++...
T Consensus 128 rpf~vGD~I~i~~~~G~V~~I~~r 151 (286)
T PRK10334 128 RPFRAGEYVDLGGVAGTVLSVQIF 151 (286)
T ss_pred CCCCCCCEEEECCEEEEEEEEEeE
Confidence 458999999999999999887643
No 84
>PF13989 YejG: YejG-like protein
Probab=21.72 E-value=88 Score=21.69 Aligned_cols=27 Identities=22% Similarity=0.464 Sum_probs=17.8
Q ss_pred ceEEEEcCeeEEEEEeeeecCCCCcccEEEEE
Q 034229 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFV 61 (100)
Q Consensus 30 G~~I~i~g~Pc~Vve~~~~KpGKhG~A~vr~k 61 (100)
..+++++|+||.-+..+-- .+|.+|+|
T Consensus 69 ~~vvE~eGepCLFv~~~DE-----sa~~CrLK 95 (106)
T PF13989_consen 69 CAVVEWEGEPCLFVHREDE-----SAAMCRLK 95 (106)
T ss_pred ceEEEecCCceEEEecccc-----hhhheeec
Confidence 3478999999987754422 34566654
No 85
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=21.58 E-value=2.2e+02 Score=20.83 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=21.7
Q ss_pred EEeccccccceEEEEcC-------eeEEEEEeeee
Q 034229 21 PQQAGTIRKNGYIVIKG-------RPCKVVEVSTS 48 (100)
Q Consensus 21 ~i~~~~LkkG~~I~i~g-------~Pc~Vve~~~~ 48 (100)
...+..|++|..|.+.| .-|.|.+++|.
T Consensus 253 ~~~~~~l~~G~~v~l~~~~~~~~~g~y~I~~V~h~ 287 (292)
T PF05954_consen 253 EGGVPGLRPGRRVTLSGHPGGEFDGEYLITEVEHS 287 (292)
T ss_dssp EEEEESB-TTEEEEEEETTTTCEEEEEEEEEEEEE
T ss_pred EcCCCeECcCCEEEEcCCcCccCCCcEEEEEEEEE
Confidence 44566799999999998 46888888876
No 86
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=21.40 E-value=1.9e+02 Score=20.21 Aligned_cols=30 Identities=20% Similarity=0.181 Sum_probs=22.6
Q ss_pred cccccceEEEE---cCe--eEEEEEeeeecCCCCcc
Q 034229 25 GTIRKNGYIVI---KGR--PCKVVEVSTSKTGKHGH 55 (100)
Q Consensus 25 ~~LkkG~~I~i---~g~--Pc~Vve~~~~KpGKhG~ 55 (100)
--.|+|+.+.+ +|. -++|+++++..++. |+
T Consensus 100 lG~~~Gd~v~v~~p~G~~~~~~I~~I~y~p~~~-~~ 134 (137)
T PRK05753 100 LGLSVGQSIDWPLPGGKETHLEVLEVEYQPEAA-GE 134 (137)
T ss_pred cCCCCCCEEEEECCCCCEEEEEEEEEEeCCccc-Cc
Confidence 35689999988 464 47889999877766 53
No 87
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=21.21 E-value=1.1e+02 Score=20.55 Aligned_cols=30 Identities=10% Similarity=0.194 Sum_probs=22.1
Q ss_pred eccccccceEEEEcCe----eEEEEEeeeecCCC
Q 034229 23 QAGTIRKNGYIVIKGR----PCKVVEVSTSKTGK 52 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~----Pc~Vve~~~~KpGK 52 (100)
...+|++|+.|.+... -|+|.+...+.|-.
T Consensus 61 ~L~~l~~Gd~v~v~~~~~~~~Y~V~~~~~v~~~~ 94 (126)
T cd06166 61 RLDEVEKGDEIKVTTKNGTYKYKITSIFVVEPTD 94 (126)
T ss_pred ChHHCCCCCEEEEEECCEEEEEEEEEEEEECCCc
Confidence 5678999998877533 57778888777754
No 88
>PRK08983 fliN flagellar motor switch protein; Validated
Probab=20.98 E-value=2.2e+02 Score=20.00 Aligned_cols=43 Identities=9% Similarity=0.122 Sum_probs=25.9
Q ss_pred ccccccceEEEEcC---eeEEEE----EeeeecCCCCcccEEEEEEeEccC
Q 034229 24 AGTIRKNGYIVIKG---RPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (100)
Q Consensus 24 ~~~LkkG~~I~i~g---~Pc~Vv----e~~~~KpGKhG~A~vr~k~knL~T 67 (100)
.-+|++|++|.++- +|-.|. ..-..++|.++. +.=+++..+.+
T Consensus 69 lL~L~~GDVI~Ld~~~ddpv~v~Vng~~~f~G~~G~~~~-k~AVrI~~ii~ 118 (127)
T PRK08983 69 LLQLNQGSVVELDRVAGEPLDVMVNGTLIAHGEVVVVND-KFGIRLTDVIS 118 (127)
T ss_pred HhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECC-EEEEEEEEcCC
Confidence 45789999999985 555542 344455666443 33355555554
No 89
>PRK08433 flagellar motor switch protein; Validated
Probab=20.97 E-value=2.3e+02 Score=19.50 Aligned_cols=43 Identities=7% Similarity=-0.010 Sum_probs=25.8
Q ss_pred eccccccceEEEEcCe---eEEEE----EeeeecCCCCcccEEEEEEeEcc
Q 034229 23 QAGTIRKNGYIVIKGR---PCKVV----EVSTSKTGKHGHAKCHFVGIDIF 66 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g~---Pc~Vv----e~~~~KpGKhG~A~vr~k~knL~ 66 (100)
+.-+|++|++|.++-. |-.|. -+-..+||.++.-+ =+++..+.
T Consensus 49 dlL~Lq~GDVI~Ld~~~~e~v~v~V~g~~~f~G~~G~~~~k~-AVrI~e~i 98 (111)
T PRK08433 49 EILKFEKGSVIDLEKPAGESVELYINGRIIGKGEVMVYEKNL-AIRINEIL 98 (111)
T ss_pred HHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEE-EEEEEEec
Confidence 3568899999999843 55542 34556677755322 24444443
No 90
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=20.67 E-value=1.6e+02 Score=21.41 Aligned_cols=30 Identities=13% Similarity=0.240 Sum_probs=24.6
Q ss_pred eccccccceEEEEc---Ce--eEEEEEeeeecCCC
Q 034229 23 QAGTIRKNGYIVIK---GR--PCKVVEVSTSKTGK 52 (100)
Q Consensus 23 ~~~~LkkG~~I~i~---g~--Pc~Vve~~~~KpGK 52 (100)
...+|++|+.|.+. |. -|+|.+++.+.|-.
T Consensus 105 ~L~~L~~GD~I~v~~~~g~~~~Y~V~~~~iV~~~d 139 (174)
T TIGR03784 105 FLQELRPGDVIRLQTPDGQWQSYQVTATRVVDESE 139 (174)
T ss_pred ChhhCCCCCEEEEEECCCeEEEEEEeEEEEECCcc
Confidence 46899999998874 54 49999999998875
No 91
>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=20.61 E-value=1.4e+02 Score=18.92 Aligned_cols=20 Identities=20% Similarity=0.089 Sum_probs=17.0
Q ss_pred EccCCcEEEEEEcCCCcEEe
Q 034229 64 DIFNGKKLEDIVPSSHNCDV 83 (100)
Q Consensus 64 nL~TG~~~E~t~~s~~~ve~ 83 (100)
.+-+|+..+.+|.++++++.
T Consensus 10 RlP~G~r~~rrF~~t~~L~~ 29 (80)
T cd01771 10 RTPSGDFLERRFLGDTPLQV 29 (80)
T ss_pred ECCCCCEEEEEeCCCCcHHH
Confidence 36789999999999998864
No 92
>PRK06666 fliM flagellar motor switch protein FliM; Validated
Probab=20.36 E-value=2.1e+02 Score=22.41 Aligned_cols=44 Identities=14% Similarity=0.132 Sum_probs=28.4
Q ss_pred eccccccceEEEEcC---eeEEEE----EeeeecCCCCcccEEEEEEeEccC
Q 034229 23 QAGTIRKNGYIVIKG---RPCKVV----EVSTSKTGKHGHAKCHFVGIDIFN 67 (100)
Q Consensus 23 ~~~~LkkG~~I~i~g---~Pc~Vv----e~~~~KpGKhG~A~vr~k~knL~T 67 (100)
+.-+|++|++|.++- +|..|. ..-...+|+||.-++ +++.++..
T Consensus 275 dll~L~vGDVI~L~~~~~~~v~v~v~~~~~f~g~~G~~~~~~A-v~I~~~~~ 325 (337)
T PRK06666 275 EILNLKVGDVIPLEKPADDPLIVYVDGKPKFLCQYGKSNGRKA-LQIEELIE 325 (337)
T ss_pred HHhCCCCCCEEEeCCCCCCcEEEEECCEEEEEEEEEEECCEEE-EEEEEEcC
Confidence 456899999999985 455552 455667788764433 55555443
No 93
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=20.34 E-value=1.7e+02 Score=21.65 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=14.0
Q ss_pred cccccceEEEEcCeeE
Q 034229 25 GTIRKNGYIVIKGRPC 40 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc 40 (100)
.-|+||+.|.+.|++.
T Consensus 65 ~~l~KG~~V~VeGrL~ 80 (182)
T PRK08486 65 QYLSKGSKVLIEGRLT 80 (182)
T ss_pred HHcCCCCEEEEEEEEE
Confidence 5689999999999975
No 94
>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=20.27 E-value=1.7e+02 Score=20.91 Aligned_cols=16 Identities=19% Similarity=0.412 Sum_probs=13.3
Q ss_pred cccccceEEEEcCeeE
Q 034229 25 GTIRKNGYIVIKGRPC 40 (100)
Q Consensus 25 ~~LkkG~~I~i~g~Pc 40 (100)
..|+||+.|.+.|++.
T Consensus 67 ~~l~KG~~V~V~G~L~ 82 (164)
T TIGR00621 67 QYLKKGSLVYVEGRLR 82 (164)
T ss_pred HhCCCCCEEEEEEEEE
Confidence 4689999999998765
No 95
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=20.24 E-value=76 Score=20.84 Aligned_cols=17 Identities=35% Similarity=0.800 Sum_probs=9.1
Q ss_pred ccccccceEEE-EcCeeE
Q 034229 24 AGTIRKNGYIV-IKGRPC 40 (100)
Q Consensus 24 ~~~LkkG~~I~-i~g~Pc 40 (100)
--+++.|++|+ +||+|.
T Consensus 37 Gv~v~~GD~I~aInG~~v 54 (88)
T PF14685_consen 37 GVDVREGDYILAINGQPV 54 (88)
T ss_dssp S----TT-EEEEETTEE-
T ss_pred CCCCCCCCEEEEECCEEC
Confidence 45899999876 899986
No 96
>PRK08395 fumarate hydratase; Provisional
Probab=20.17 E-value=38 Score=24.95 Aligned_cols=25 Identities=4% Similarity=0.130 Sum_probs=21.6
Q ss_pred ccccccceEEEEcCeeEEEEEeeee
Q 034229 24 AGTIRKNGYIVIKGRPCKVVEVSTS 48 (100)
Q Consensus 24 ~~~LkkG~~I~i~g~Pc~Vve~~~~ 48 (100)
+.+||.|+.|.|.|..|..-|..|.
T Consensus 12 i~~L~~GD~V~LsG~i~taRDaah~ 36 (162)
T PRK08395 12 VLKLKAGDVVYLSGIIYTARDLAHR 36 (162)
T ss_pred HhhCCCCCEEEEEEEEEEEEHHHHH
Confidence 5789999999999999998876654
Done!