Query psy15688
Match_columns 70
No_of_seqs 105 out of 729
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 18:57:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15688.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15688hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2016 Predicted RNA-binding 99.9 2.8E-23 6E-28 133.3 6.5 65 1-68 96-160 (161)
2 PRK14560 putative RNA-binding 99.9 1.6E-21 3.5E-26 124.5 8.2 64 1-67 96-159 (160)
3 TIGR03684 arCOG00985 arCOG0415 99.9 2.5E-21 5.4E-26 122.5 8.2 62 1-65 89-150 (150)
4 TIGR00451 unchar_dom_2 unchara 99.8 3.4E-18 7.3E-23 102.9 8.2 58 1-61 50-107 (107)
5 KOG2523|consensus 99.7 5.9E-19 1.3E-23 113.7 3.1 67 1-67 112-179 (181)
6 KOG2522|consensus 99.7 1.5E-16 3.3E-21 115.1 6.1 68 1-68 109-177 (560)
7 PF01472 PUA: PUA domain; Int 99.6 1.6E-15 3.4E-20 86.1 5.7 55 1-59 20-74 (74)
8 PRK13534 7-cyano-7-deazaguanin 99.2 2.6E-11 5.6E-16 91.1 7.4 56 1-60 583-638 (639)
9 PRK13794 hypothetical protein; 99.1 1.7E-10 3.6E-15 84.3 7.2 54 1-58 145-198 (479)
10 PRK13795 hypothetical protein; 99.1 1.4E-10 3.1E-15 86.8 6.9 56 1-60 146-201 (636)
11 smart00359 PUA Putative RNA-bi 99.0 2.4E-09 5.2E-14 59.8 6.8 56 1-60 20-77 (77)
12 TIGR00425 CBF5 rRNA pseudourid 98.9 1.1E-08 2.3E-13 71.9 7.8 57 2-62 258-314 (322)
13 COG1549 Queuine tRNA-ribosyltr 98.9 9E-09 2E-13 75.7 6.8 54 1-59 465-518 (519)
14 PRK04270 H/ACA RNA-protein com 98.8 2.1E-08 4.6E-13 69.7 7.6 55 2-60 246-300 (300)
15 TIGR00432 arcsn_tRNA_tgt tRNA- 98.8 1.4E-08 3.1E-13 75.3 6.2 52 1-56 486-537 (540)
16 COG5270 PUA domain (predicted 98.6 9.3E-08 2E-12 63.1 5.2 52 1-56 148-199 (202)
17 COG1370 Prefoldin, molecular c 98.5 5.1E-07 1.1E-11 57.8 6.3 49 5-57 104-152 (155)
18 PRK05429 gamma-glutamyl kinase 98.4 5.6E-07 1.2E-11 64.0 4.4 43 1-47 301-343 (372)
19 TIGR01027 proB glutamate 5-kin 98.0 8E-06 1.7E-10 58.0 4.6 42 1-46 293-334 (363)
20 PRK13402 gamma-glutamyl kinase 97.0 0.00097 2.1E-08 47.7 3.9 41 2-46 298-338 (368)
21 COG0263 ProB Glutamate 5-kinas 94.6 0.045 9.8E-07 39.5 3.4 41 2-47 301-341 (369)
22 KOG2529|consensus 93.2 0.04 8.7E-07 40.1 1.1 64 1-68 295-363 (395)
23 KOG3492|consensus 89.5 0.81 1.8E-05 29.9 4.1 43 14-58 124-166 (180)
24 PRK14124 tRNA pseudouridine sy 88.0 1.8 3.9E-05 30.6 5.4 45 14-59 257-305 (308)
25 PRK08557 hypothetical protein; 84.9 1 2.2E-05 33.0 2.9 36 14-52 107-142 (417)
26 PF01878 EVE: EVE domain; Int 71.9 9.6 0.00021 23.3 4.0 25 14-38 39-65 (143)
27 PRK04980 hypothetical protein; 66.2 20 0.00044 21.5 4.4 24 14-37 31-54 (102)
28 PRK15128 23S rRNA m(5)C1962 me 61.1 26 0.00057 25.4 5.0 36 14-58 33-68 (396)
29 cd04710 BAH_fungalPHD BAH, or 60.9 11 0.00024 23.5 2.7 25 14-38 11-35 (135)
30 PRK06789 flagellar motor switc 58.1 16 0.00034 20.8 2.8 33 31-63 12-44 (74)
31 PF14505 DUF4438: Domain of un 58.0 28 0.00061 24.3 4.5 45 12-58 187-238 (258)
32 COG1374 NIP7 Protein involved 57.7 15 0.00032 24.3 3.0 32 14-46 128-159 (176)
33 PF03657 UPF0113: Uncharacteri 53.7 19 0.00042 23.1 3.0 27 4-36 114-140 (162)
34 COG1886 FliN Flagellar motor s 53.6 15 0.00032 22.8 2.4 36 29-64 74-109 (136)
35 TIGR03318 YdfZ_fam putative se 52.7 30 0.00066 19.2 3.3 44 14-60 10-54 (65)
36 KOG1698|consensus 51.8 37 0.00081 22.9 4.2 27 12-38 94-124 (201)
37 PRK00809 hypothetical protein; 47.1 49 0.0011 20.8 4.1 30 14-43 34-68 (144)
38 PF10246 MRP-S35: Mitochondria 46.9 19 0.00041 21.9 2.0 16 49-64 23-40 (104)
39 KOG3342|consensus 46.8 20 0.00044 23.5 2.3 25 13-38 60-84 (180)
40 TIGR01024 rplS_bact ribosomal 44.8 24 0.00052 21.6 2.3 16 11-26 15-30 (113)
41 PF14001 YdfZ: YdfZ protein 44.4 56 0.0012 18.1 3.9 44 14-60 9-53 (64)
42 PF01245 Ribosomal_L19: Riboso 44.0 26 0.00057 21.3 2.4 16 11-26 15-30 (113)
43 PRK05338 rplS 50S ribosomal pr 42.7 28 0.00061 21.4 2.4 15 11-25 15-29 (116)
44 PF01426 BAH: BAH domain; Int 41.3 46 0.001 19.0 3.1 24 15-38 3-26 (119)
45 KOG0126|consensus 40.5 39 0.00084 22.9 2.9 21 14-35 46-66 (219)
46 PF13403 Hint_2: Hint domain 40.4 70 0.0015 19.9 4.0 43 14-56 20-62 (147)
47 PF05641 Agenet: Agenet domain 39.0 31 0.00068 18.6 2.0 16 15-30 1-16 (68)
48 cd03703 aeIF5B_II aeIF5B_II: T 38.9 61 0.0013 19.7 3.4 30 14-44 26-55 (110)
49 CHL00084 rpl19 ribosomal prote 38.5 35 0.00076 21.0 2.3 15 11-25 19-33 (117)
50 PF14085 DUF4265: Domain of un 38.5 88 0.0019 18.7 4.6 27 13-40 24-50 (117)
51 PF13101 DUF3945: Protein of u 38.2 65 0.0014 17.1 4.1 43 16-58 12-54 (59)
52 PRK12617 flgA flagellar basal 38.0 1.2E+02 0.0027 20.2 5.1 38 14-57 155-193 (214)
53 PF04014 Antitoxin-MazE: Antid 37.3 53 0.0012 16.3 2.6 16 14-29 20-35 (47)
54 PF09926 DUF2158: Uncharacteri 37.0 57 0.0012 17.2 2.7 16 15-30 1-16 (53)
55 PF01959 DHQS: 3-dehydroquinat 37.0 55 0.0012 23.9 3.5 44 13-56 257-304 (354)
56 COG1153 FwdD Formylmethanofura 36.8 50 0.0011 20.7 2.8 34 28-61 24-59 (128)
57 TIGR02480 fliN flagellar motor 36.3 40 0.00086 18.6 2.2 22 34-55 16-37 (77)
58 cd04470 S1_EF-P_repeat_1 S1_EF 35.6 64 0.0014 17.2 2.9 19 15-34 40-58 (61)
59 PRK08916 flagellar motor switc 34.5 37 0.0008 20.8 2.0 33 31-63 50-82 (116)
60 COG4127 Uncharacterized conser 34.4 57 0.0012 23.4 3.1 27 14-41 72-98 (318)
61 PRK06788 flagellar motor switc 33.8 49 0.0011 20.4 2.5 33 31-63 39-71 (119)
62 PRK02290 3-dehydroquinate synt 32.8 68 0.0015 23.3 3.4 44 13-56 247-294 (344)
63 smart00439 BAH Bromo adjacent 32.7 62 0.0013 18.4 2.7 23 15-37 2-24 (120)
64 PRK12618 flgA flagellar basal 31.8 1.3E+02 0.0029 18.7 4.9 38 14-57 81-119 (141)
65 PF09157 TruB-C_2: Pseudouridi 31.4 81 0.0017 16.1 3.4 22 14-37 25-46 (58)
66 cd04463 S1_EF_like S1_EF_like: 31.0 66 0.0014 16.3 2.4 20 14-34 36-55 (55)
67 PRK07963 fliN flagellar motor 30.4 51 0.0011 20.8 2.2 34 31-64 65-98 (137)
68 PF13216 DUF4024: Protein of u 30.2 66 0.0014 15.4 2.1 13 50-62 3-15 (35)
69 cd05829 Sortase_E Sortase E (S 28.5 91 0.002 19.2 3.1 34 10-43 68-103 (144)
70 PRK06033 hypothetical protein; 28.5 62 0.0013 18.4 2.2 24 34-57 15-38 (83)
71 COG4118 Phd Antitoxin of toxin 28.5 61 0.0013 18.6 2.1 23 14-38 20-42 (84)
72 PF11948 DUF3465: Protein of u 28.1 66 0.0014 20.3 2.4 17 10-26 81-97 (131)
73 PRK08158 type III secretion sy 28.0 1.7E+02 0.0036 20.9 4.6 37 16-61 262-298 (303)
74 COG1465 Predicted alternative 28.0 1.1E+02 0.0023 22.3 3.7 43 13-55 279-325 (376)
75 PF07653 SH3_2: Variant SH3 do 27.9 28 0.00061 17.7 0.6 11 14-24 17-27 (55)
76 PF14306 PUA_2: PUA-like domai 27.7 1.1E+02 0.0025 19.5 3.5 22 14-36 92-113 (160)
77 PRK08515 flgA flagellar basal 27.3 1.9E+02 0.0042 19.2 4.8 38 14-57 165-203 (222)
78 PF11926 DUF3444: Domain of un 26.9 70 0.0015 21.6 2.5 20 14-33 27-46 (217)
79 COG1945 Pyruvoyl-dependent arg 26.7 1.6E+02 0.0034 19.3 4.0 22 4-25 51-72 (163)
80 KOG3572|consensus 26.6 52 0.0011 28.3 2.1 22 11-33 124-145 (1701)
81 KOG2110|consensus 26.5 2E+02 0.0043 21.4 4.8 13 47-59 192-204 (391)
82 smart00588 NEUZ domain in neur 26.1 1.4E+02 0.0031 18.0 3.6 39 4-45 32-74 (123)
83 PRK06005 flgA flagellar basal 25.8 1.8E+02 0.004 18.4 4.9 38 14-57 100-138 (160)
84 PRK08432 flagellar motor switc 25.7 64 0.0014 22.4 2.2 34 31-64 211-244 (283)
85 PF07313 DUF1460: Protein of u 25.0 63 0.0014 21.8 2.0 32 13-44 152-184 (216)
86 PF04717 Phage_base_V: Phage-r 24.9 1.3E+02 0.0028 16.3 3.2 24 14-37 43-68 (79)
87 COG1935 Uncharacterized conser 24.7 1.8E+02 0.004 18.1 3.8 13 14-26 38-50 (122)
88 PRK06804 flgA flagellar basal 24.6 2.4E+02 0.0053 19.4 4.9 37 14-56 202-239 (261)
89 PRK02268 hypothetical protein; 24.6 1.6E+02 0.0035 18.6 3.7 26 13-38 34-67 (141)
90 PF14794 DUF4479: Domain of un 24.4 98 0.0021 17.3 2.4 25 16-40 11-35 (73)
91 smart00326 SH3 Src homology 3 23.8 93 0.002 14.7 2.1 14 14-27 20-33 (58)
92 PF12913 SH3_6: SH3 domain of 23.7 72 0.0016 17.0 1.7 19 48-66 24-42 (54)
93 PRK08035 type III secretion sy 23.0 2.3E+02 0.0049 20.4 4.6 36 17-61 284-319 (323)
94 cd06462 Peptidase_S24_S26 The 22.9 1.3E+02 0.0028 15.7 3.4 14 13-26 12-25 (84)
95 PRK12281 rplX 50S ribosomal pr 22.7 77 0.0017 17.8 1.8 13 14-26 6-18 (76)
96 cd00174 SH3 Src homology 3 dom 22.3 1E+02 0.0023 14.4 2.2 13 14-26 17-29 (54)
97 COG2994 HlyC ACP:hemolysin acy 22.2 1.2E+02 0.0027 19.4 2.8 32 12-44 46-77 (148)
98 PF00018 SH3_1: SH3 domain; I 22.0 47 0.001 16.3 0.8 14 14-27 15-28 (48)
99 PF08240 ADH_N: Alcohol dehydr 21.6 91 0.002 17.7 2.0 13 13-25 51-63 (109)
100 cd02790 MopB_CT_Formate-Dh_H F 21.6 1.3E+02 0.0028 17.0 2.7 24 14-40 48-71 (116)
101 TIGR01079 rplX_bact ribosomal 21.4 1.9E+02 0.0042 17.1 4.3 13 14-26 3-15 (104)
102 COG0335 RplS Ribosomal protein 21.4 1.1E+02 0.0023 19.0 2.3 15 11-25 17-31 (115)
103 COG5301 Phage-related tail fib 21.3 1.5E+02 0.0034 22.9 3.6 35 21-56 91-125 (587)
104 PF14031 D-ser_dehydrat: Putat 21.3 1.2E+02 0.0025 17.5 2.4 22 4-25 56-77 (94)
105 PRK07018 flgA flagellar basal 21.2 2.6E+02 0.0057 18.6 5.0 37 14-56 176-213 (235)
106 KOG4078|consensus 20.8 73 0.0016 20.6 1.6 16 49-64 82-99 (173)
107 cd04714 BAH_BAHCC1 BAH, or Bro 20.4 1.8E+02 0.0038 17.4 3.2 23 14-37 3-26 (121)
108 PRK05698 fliN flagellar motor 20.4 97 0.0021 20.0 2.1 32 31-62 84-115 (155)
109 TIGR03170 flgA_cterm flagella 20.4 2E+02 0.0042 16.8 5.1 39 13-57 64-103 (122)
110 PF10574 UPF0552: Uncharacteri 20.3 71 0.0015 21.9 1.5 31 14-45 151-181 (224)
111 PRK08433 flagellar motor switc 20.2 1E+02 0.0023 18.6 2.1 28 34-61 40-67 (111)
112 cd04709 BAH_MTA BAH, or Bromo 20.2 1.2E+02 0.0026 19.5 2.6 42 14-60 3-45 (164)
113 PF03454 MoeA_C: MoeA C-termin 20.1 47 0.001 17.5 0.6 12 13-24 59-70 (72)
No 1
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=2.8e-23 Score=133.25 Aligned_cols=65 Identities=32% Similarity=0.622 Sum_probs=62.3
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeecccccccc
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLWNMKN 68 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW~~~~ 68 (70)
|+|||+++++ +|++||+|.|..++++.|+|||+++||.+||...+||++++++|++||.||++..
T Consensus 96 M~PGIv~~~~---~ik~Gd~VvV~~e~~~~plAVG~alm~~~em~~~~kGkav~~iHhvGD~lw~~~~ 160 (161)
T COG2016 96 MAPGIVSADG---EIKEGDIVVVVDEKKGRPLAVGIALMSGKEMEEKKKGKAVKNIHHVGDKLWEASV 160 (161)
T ss_pred eccceeecCC---CccCCCEEEEEEcCCCCeeEEEeeccCHHHHhhhcCCeEEEEEeccChHHHhhhc
Confidence 8999999998 9999999999999889999999999999999999999999999999999999764
No 2
>PRK14560 putative RNA-binding protein; Provisional
Probab=99.86 E-value=1.6e-21 Score=124.52 Aligned_cols=64 Identities=30% Similarity=0.634 Sum_probs=60.2
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeeccccccc
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLWNMK 67 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW~~~ 67 (70)
|+|||++.++ +|++||+|+|++++++.|+|||++.||++|+....+|++|+++|++||+||++.
T Consensus 96 m~pGV~~~~~---~~~~Gd~V~I~~~~~~~~vavG~~~~s~~ei~~~~kG~~v~~~h~~~D~lw~~~ 159 (160)
T PRK14560 96 MAPGIVEADE---DIKEGDIVFVVEETHGKPLAVGRALMDGDEMVEEKKGKAVKNIHHVGDEIWEFE 159 (160)
T ss_pred ecCeeeeCCC---CCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhcCCceEEEEEEEcCchhhccc
Confidence 7999999876 999999999999866999999999999999997789999999999999999985
No 3
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=99.86 E-value=2.5e-21 Score=122.47 Aligned_cols=62 Identities=29% Similarity=0.664 Sum_probs=58.7
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeeccccc
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLWN 65 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW~ 65 (70)
|+|||++.++ +|++||+|+|++++++.|+|||++.||++||....+|++|+++|++||.||+
T Consensus 89 m~pGV~~~~~---~~~~Gd~V~I~~~~~~~~vavG~a~~ss~ei~~~~kG~av~~~h~~~D~lw~ 150 (150)
T TIGR03684 89 MAPGIVSADP---SIKEGDIVFVVDETHRKPLAVGIALMDAEEMEEEKKGKAVKNIHHVGDKIWE 150 (150)
T ss_pred ccCceecCCC---CCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhcCCCeEEEEEEEcCccccC
Confidence 8999998876 9999999999998669999999999999999988899999999999999996
No 4
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=99.77 E-value=3.4e-18 Score=102.86 Aligned_cols=58 Identities=29% Similarity=0.601 Sum_probs=54.9
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeec
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLND 61 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D 61 (70)
|+|||++.+. +|++||+|+|+..+++.++|+|++.||++||....||++++++|+++|
T Consensus 50 ~~pGV~~~~~---~~~~gd~V~I~~~~~~~~iavG~a~~~s~e~~~~~~G~~v~~~h~~~D 107 (107)
T TIGR00451 50 MRPGIVDADE---DIKEGDDVVVVDENKDRPLAVGIALMSGEEMKEMDKGKAVKNIHHIGD 107 (107)
T ss_pred cCCeeEeCCC---CcCCCCEEEEEECCCCeEEEEEEEecCHHHHHhcCCCeEEEEEEecCC
Confidence 7999999887 999999999999855899999999999999999899999999999998
No 5
>KOG2523|consensus
Probab=99.75 E-value=5.9e-19 Score=113.74 Aligned_cols=67 Identities=73% Similarity=1.223 Sum_probs=63.2
Q ss_pred CcceeecCCCCc-CCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeeccccccc
Q psy15688 1 MCPGLTSPGAII-TPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLWNMK 67 (70)
Q Consensus 1 M~PGI~~~~~~~-~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW~~~ 67 (70)
|.||++++.+.+ |.+++|++|+|+.+++..++|||.+.||++||.+.+||..++++|++||.||.+.
T Consensus 112 McPGlts~g~~l~~~~ekd~~V~i~aeGK~~alAiG~~~ms~kei~s~nKGiGIE~~H~l~DgLw~~~ 179 (181)
T KOG2523|consen 112 MCPGLTSPGAKLPPGVEKDTIVAIMAEGKEHALAIGLTKMSAKEIKSVNKGIGIENYHYLNDGLWKMK 179 (181)
T ss_pred EcccCCCCcccCCCCccCCCEEEEEecCchhhhhhhhhhhcHHHHHhhccCCceEEEEecCCchhhee
Confidence 899999997655 6899999999999999999999999999999999999999999999999999875
No 6
>KOG2522|consensus
Probab=99.66 E-value=1.5e-16 Score=115.11 Aligned_cols=68 Identities=25% Similarity=0.335 Sum_probs=62.9
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCC-cceEEEEEEEeecccccccc
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVN-KGIGVENFHYLNDGLWNMKN 68 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~-kG~av~v~h~~~D~LW~~~~ 68 (70)
|.||.+...+++|.++.|++++|...+|..|+|||++.||++|+...+ ||++++++|+|.|.||+.++
T Consensus 109 ~l~~~~m~ppg~p~~~~G~lcai~lpgn~ap~AiGc~~Msseem~v~GlkGkav~ilH~frD~Lw~sgp 177 (560)
T KOG2522|consen 109 NLMISGMIPPGDPRCKIGTLCAIALPGNEAPLAIGCVEMSSEEMKVIGLKGKAVKILHHFRDGLWKSGP 177 (560)
T ss_pred cccccccCCCCCcccccCceeeEecCCCcCceeeeeeecchHHHHHhccccceEEEEeehhhhhhhcCC
Confidence 466777777788999999999999999999999999999999999998 99999999999999999886
No 7
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=99.61 E-value=1.6e-15 Score=86.15 Aligned_cols=55 Identities=29% Similarity=0.519 Sum_probs=50.2
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEe
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYL 59 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~ 59 (70)
|+|||++.++ +|++||+|.|++. ++.++|+|++.||++||.+..+|+++++.|++
T Consensus 20 ~~~GV~~~~~---~f~~gd~V~i~~~-~g~~ia~G~a~~ss~ei~~~~~g~~~~~~~~l 74 (74)
T PF01472_consen 20 FAPGVVEVDG---DFRKGDEVAIVDE-DGEVIAVGRANMSSEEIKKMKKGKAVKIRHVL 74 (74)
T ss_dssp EGGGEEEEET---T--TTSEEEEEET-TSSEEEEEEESSTHHHHHHHSSSEEEEEEEEC
T ss_pred chHHhEECCC---CcCCCCEEEEEcC-CCeEEEEEEEecCHHHHHHHcCCcEehhhhhC
Confidence 6899999987 9999999999998 69999999999999999999999999999985
No 8
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=99.24 E-value=2.6e-11 Score=91.09 Aligned_cols=56 Identities=16% Similarity=0.172 Sum_probs=52.3
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEee
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~ 60 (70)
|+|||++.++ ++++||.|.|..+ ++.++|||+++||++||...++|+||++.|...
T Consensus 583 ~apgVv~~d~---~ir~gDeV~Vv~e-~~~~lavG~A~~~~~em~~~~~G~avkvR~~~~ 638 (639)
T PRK13534 583 FAKFVIDCDE---EIRPYDEVLVVNE-DDELLAYGKALLNGRELMEFNYGLAVKVRGGVK 638 (639)
T ss_pred cCCcceecCC---CCCCCCEEEEEec-CCcEEEEEEEecCHHHHhhcCCceEEEEeecCC
Confidence 6899999987 9999999999987 689999999999999999999999999999754
No 9
>PRK13794 hypothetical protein; Provisional
Probab=99.14 E-value=1.7e-10 Score=84.25 Aligned_cols=54 Identities=24% Similarity=0.464 Sum_probs=50.6
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEE
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHY 58 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~ 58 (70)
|+|||++.++ +|++||.|+|+++ ++.++|+|++.||++||...++|++|++.|.
T Consensus 145 ~~~GV~~~~~---~i~~gd~V~Iv~~-~g~~iavG~a~~s~~ei~~~~~G~~Vkvr~~ 198 (479)
T PRK13794 145 LRPGVAEASE---DIEEGDDVIILDE-NGDVVGVGRARMSYEEIVNMEKGMVVKVRKS 198 (479)
T ss_pred cCCceEEecC---CcCCCCEEEEEcC-CCcEEEEEEeecCHHHHHhccCceEEEEEec
Confidence 6899999887 9999999999998 6889999999999999999999999999994
No 10
>PRK13795 hypothetical protein; Provisional
Probab=99.14 E-value=1.4e-10 Score=86.82 Aligned_cols=56 Identities=20% Similarity=0.397 Sum_probs=52.1
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEee
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~ 60 (70)
|+|||++.++ +|++||.|+|+++ ++.++|||++.||++||.+.++|++|++.|...
T Consensus 146 ~~~GI~~~~~---~i~~gd~V~I~~e-~g~~vavG~a~~s~~e~~~~~kG~~Vkvr~~~~ 201 (636)
T PRK13795 146 LAPGVVEADL---DIKKGDEVVVVTE-DGEVVGVGRAKMDGDDMIKRFRGRAVKVRKSGR 201 (636)
T ss_pred cCCceEEEeC---CCCCCCEEEEEeC-CCCEEEEEEeccCHHHHhhccCCeEEEEEEccc
Confidence 7899999887 9999999999997 688999999999999999999999999999853
No 11
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=99.01 E-value=2.4e-09 Score=59.83 Aligned_cols=56 Identities=29% Similarity=0.588 Sum_probs=50.0
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcC--CcceEEEEEEEee
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRV--NKGIGVENFHYLN 60 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~--~kG~av~v~h~~~ 60 (70)
|.|||+..++ ++++||+|.|++. ++.++|+|.+.++++++.+. .+|.++++.|+++
T Consensus 20 ~~~~v~~~~~---~~~~g~~V~v~~~-~g~~vg~G~~~~~s~~~~~~~~~~g~~v~~~~~~~ 77 (77)
T smart00359 20 LAPGVVRVDG---GIKEGDVVVIVDE-KGEPLGIGLANMSSEEMARIKGEKGLAVKVRRAVM 77 (77)
T ss_pred ccceeEEEeC---CcCCCCEEEEEcC-CCCEEEEEEEeCCHHHHHHHhccCceEEEEEEecC
Confidence 5788888766 8999999999997 79999999999999999887 4999999999863
No 12
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=98.88 E-value=1.1e-08 Score=71.89 Aligned_cols=57 Identities=25% Similarity=0.444 Sum_probs=48.9
Q ss_pred cceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeecc
Q psy15688 2 CPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDG 62 (70)
Q Consensus 2 ~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~ 62 (70)
.||+...+. .+..|+.|.|+.. ++.++|||++.+|++|+...++|++|++.|+|+|.
T Consensus 258 ~pgv~~~d~---~i~~gd~V~V~~~-~G~~LAIGea~~s~~ei~~~~kG~vV~~~~~~~~~ 314 (322)
T TIGR00425 258 VRGIARLEK---GIEKGDTVAVITL-KGEAVAVGIALMSTKDIANADKGVVADVKRVIMER 314 (322)
T ss_pred ccccccccc---ccCCCCEEEEEEC-CCEEEEEEEEecCHHHHhhcCCcEEEEEEEEeeCC
Confidence 466655543 5778999999987 68999999999999999998999999999999983
No 13
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=98.85 E-value=9e-09 Score=75.67 Aligned_cols=54 Identities=19% Similarity=0.324 Sum_probs=49.7
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEe
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYL 59 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~ 59 (70)
++||+++.++ +++.||.|.|.- +++.++||+|.||..||.+.+||.||++.|+.
T Consensus 465 ~a~GV~da~e---dIrpnDeV~vv~--~~~v~gVGrA~msg~eM~~akkGiaV~VR~~~ 518 (519)
T COG1549 465 FAPGVVDADE---DIRPNDEVVVVH--GGEVRGVGRAVMSGREMVEAKKGIAVRVRRRK 518 (519)
T ss_pred cccccccCCC---CCCcCCEEEEEe--CCeEEEEeeeecChHHhcccCCceEEEEEecc
Confidence 4899999987 999999998886 48899999999999999999999999999974
No 14
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=98.82 E-value=2.1e-08 Score=69.70 Aligned_cols=55 Identities=25% Similarity=0.481 Sum_probs=47.7
Q ss_pred cceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEee
Q psy15688 2 CPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60 (70)
Q Consensus 2 ~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~ 60 (70)
.||+...+. ++++|+.|.|+.. ++.++|+|++.+|++|+.+..+|++|++.|+++
T Consensus 246 ~~gi~~~~~---~~~~gd~V~I~~~-~G~~LAIG~~~~ss~el~~~~kG~~vk~~~~~~ 300 (300)
T PRK04270 246 APGIAKLEK---GIKKGDLVAVFTL-KGELVALGKALMDSDEILKAEKGIVVDLERVFM 300 (300)
T ss_pred cCCceeccc---ccCCCCEEEEEeC-CCcEEEEEEEccCHHHHHhcCCceEEEEEEeeC
Confidence 466665554 6788999999987 688999999999999999999999999999985
No 15
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=98.79 E-value=1.4e-08 Score=75.33 Aligned_cols=52 Identities=17% Similarity=0.251 Sum_probs=48.5
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEE
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENF 56 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~ 56 (70)
++|||++.++ ++++||.|.|+.+ ++..+|||+|.||..||...++|.||++.
T Consensus 486 fak~V~~ad~---~IR~~dEV~vv~~-~~~llavGra~lsg~em~~~~~G~AVkvR 537 (540)
T TIGR00432 486 FAKFIIDCDN---NIRANDEVLIVNA-DDELLATGKALLCAEEMMDLNHGQAVKTR 537 (540)
T ss_pred cCCccccCCC---CCCCCCeEEEEcC-CCcEEEEEehhcCHHHHHhhcCceEEEEe
Confidence 5799999887 9999999999987 68899999999999999999999999986
No 16
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=98.61 E-value=9.3e-08 Score=63.11 Aligned_cols=52 Identities=19% Similarity=0.507 Sum_probs=48.0
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEE
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENF 56 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~ 56 (70)
.+|||++.++ ++++||.|.|.+. |+.+++||++.+|++++...++|++|++.
T Consensus 148 ~~~gV~e~~~---~i~~~d~viVv~~-ng~~vGVg~a~~~~~~~in~~rG~~v~~~ 199 (202)
T COG5270 148 LPPGVIEAED---SIERGDEVIVVSE-NGRVVGVGIAKKSYEELINPERGTGVKPR 199 (202)
T ss_pred cCCceeeccC---CcccCCeEEEEec-CCEEEEEEEEecCHHHhcCcccCcccCCC
Confidence 3799999887 9999999999998 89999999999999999988899999865
No 17
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=5.1e-07 Score=57.78 Aligned_cols=49 Identities=20% Similarity=0.343 Sum_probs=43.5
Q ss_pred eecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEE
Q psy15688 5 LTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 5 I~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h 57 (70)
|+..++ ++++||.|.|+.+ +++.+|+|++.+|..||...++|.||++..
T Consensus 104 Vi~~D~---~iR~~dEvlVVne-~d~LlAvGra~ls~~E~~~~~~G~AVkVr~ 152 (155)
T COG1370 104 VIDVDE---EIRAGDEVLVVNE-DDELLAVGRALLSGAEMREFERGMAVKVRE 152 (155)
T ss_pred eeccCc---ccCCCCeEEEECC-CCcEEEeeeEeecHHHHhhccccEEEEEec
Confidence 344444 9999999999998 899999999999999999999999999863
No 18
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=98.36 E-value=5.6e-07 Score=64.00 Aligned_cols=43 Identities=26% Similarity=0.496 Sum_probs=39.8
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcC
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRV 47 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~ 47 (70)
|+|||++.++ +|++||+|.|+++ +++++|+|++.+|++|+.+.
T Consensus 301 l~~Gi~~v~g---~f~~gd~V~i~~~-~g~~va~G~~~~~s~e~~~~ 343 (372)
T PRK05429 301 LPAGVTAVEG---DFSRGDVVRIVDP-DGREIARGLVNYSSDELRRI 343 (372)
T ss_pred CccchhheEC---cccCCCEEEEECC-CCCEEEEEEecCCHHHHHHH
Confidence 5899999988 9999999999997 79999999999999999764
No 19
>TIGR01027 proB glutamate 5-kinase. Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family.
Probab=98.03 E-value=8e-06 Score=58.01 Aligned_cols=42 Identities=19% Similarity=0.454 Sum_probs=39.0
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhc
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVR 46 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~ 46 (70)
|.|||++.++ +|++||+|.|+.+ ++.++|.|++.+||+|+.+
T Consensus 293 l~~Gi~~v~g---~F~~gd~v~i~~~-~~~~ia~g~~~y~s~~~~~ 334 (363)
T TIGR01027 293 LPAGIVGVEG---NFSRGEVVEILNP-EGQDIGRGLVNYSSDELEK 334 (363)
T ss_pred CCccceeeEC---cccCCCEEEEECC-CCCEEEEEEecCCHHHHHH
Confidence 6799999998 9999999999987 7899999999999999865
No 20
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=97.01 E-value=0.00097 Score=47.75 Aligned_cols=41 Identities=12% Similarity=0.061 Sum_probs=37.2
Q ss_pred cceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhc
Q psy15688 2 CPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVR 46 (70)
Q Consensus 2 ~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~ 46 (70)
..||+..++ .|.+||+|.|+.+ ++..+|.|.+..||+|+.+
T Consensus 298 ~~gi~~v~g---~F~~gd~v~i~~~-~g~~~~rg~~~y~s~~~~~ 338 (368)
T PRK13402 298 SDDVVEIKG---DFSVGDTILVRKG-DGTKLAKGKSNYSSCLLNF 338 (368)
T ss_pred ccceEEEeC---EecCCCEEEEECC-CCCEEEEEEccCCHHHHHH
Confidence 568888887 9999999999987 7899999999999999865
No 21
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=94.57 E-value=0.045 Score=39.54 Aligned_cols=41 Identities=27% Similarity=0.456 Sum_probs=35.0
Q ss_pred cceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcC
Q psy15688 2 CPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRV 47 (70)
Q Consensus 2 ~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~ 47 (70)
.-||+...+ +|++||.|.|+ + ++..+|=|.+..||+|+.+.
T Consensus 301 paGV~~V~G---~F~rGdvV~i~-~-~g~~iarG~v~Y~s~el~~i 341 (369)
T COG0263 301 PAGVTSVEG---NFSRGDVVRIR-P-QGGEIARGLVNYSSDELRKI 341 (369)
T ss_pred cccceEeee---eecCCCEEEEe-c-CCceeEeeeccCCHHHHHHH
Confidence 347888777 99999999999 4 56699999999999998763
No 22
>KOG2529|consensus
Probab=93.22 E-value=0.04 Score=40.15 Aligned_cols=64 Identities=19% Similarity=0.318 Sum_probs=54.3
Q ss_pred CcceeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeec-----ccccccc
Q psy15688 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLND-----GLWNMKN 68 (70)
Q Consensus 1 M~PGI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D-----~LW~~~~ 68 (70)
|.||+..+++ ++..+..+.+.+. +++.++.+.+.|+.+++..+++|...+....++. ..|.+++
T Consensus 295 ~v~~~~r~~~---~i~~~~e~v~~t~-k~e~~~~~i~~~~~~~~~s~dh~~~a~~k~~~me~d~~~~~~g~~~ 363 (395)
T KOG2529|consen 295 LVPGLLRYSD---DIDGPFEVVDMTT-KGEAIASKIAEMSLRQVASCDHGVVAKTKRVIMEADVYERCWGLGP 363 (395)
T ss_pred eeccccccCc---cccCceeEEEEee-cchhhhhhhhhhhhhhhceeeeeeecccccccccccccceeeccCc
Confidence 5788888776 8999999999997 8999999999999999999999999999988665 3365554
No 23
>KOG3492|consensus
Probab=89.54 E-value=0.81 Score=29.86 Aligned_cols=43 Identities=19% Similarity=0.230 Sum_probs=36.1
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHY 58 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~ 58 (70)
++..++=|.|++. +..|++.|+++-|+.+..+ -.+.++-++|.
T Consensus 124 ~~p~~~GVvVysm-~DvPLGFGv~Akst~d~r~-~dp~aiv~~hQ 166 (180)
T KOG3492|consen 124 GIPQHQGVVVYSM-NDVPLGFGVTAKSTQDCRK-ADPTAIVVLHQ 166 (180)
T ss_pred CCCCcceEEEEec-cCCccccceeecCcccccc-cCCcEEEEEEe
Confidence 7788899999998 8999999999999999754 36667777775
No 24
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=88.04 E-value=1.8 Score=30.63 Aligned_cols=45 Identities=13% Similarity=0.105 Sum_probs=35.6
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhc----CCcceEEEEEEEe
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVR----VNKGIGVENFHYL 59 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~----~~kG~av~v~h~~ 59 (70)
++..++.|.++.. ++.++|+|....+++.+.. ..+|.+++..+++
T Consensus 257 ~~~~~~~v~v~~~-~g~~lai~~~~~~~~~~~~~~~~~~~~~v~~~~~v~ 305 (308)
T PRK14124 257 NFKKDDVVRVFDE-EGRLLAIARAERNSSFLETLKKHERNERVLKLKKVF 305 (308)
T ss_pred ccCCCCEEEEEcC-CCeEEEEEEEecCCceeeeeecccccceEEeeeeee
Confidence 3557888888876 6889999999998876553 2369999999986
No 25
>PRK08557 hypothetical protein; Provisional
Probab=84.89 E-value=1 Score=33.00 Aligned_cols=36 Identities=11% Similarity=0.099 Sum_probs=28.8
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIG 52 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~a 52 (70)
++++||.|.|.. +..++||++.++..++....+|..
T Consensus 107 ~~~~~~~v~~~~---~~~~gvg~~~~~~~k~~~~~~~~~ 142 (417)
T PRK08557 107 EILENDYVGVEI---GNFLGVGVKKEDRIKIKDLSLKKE 142 (417)
T ss_pred cCCCCCEEEEec---CCEEEEEEeecceEEEEecccCCC
Confidence 789999777765 579999999998887777766653
No 26
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=71.86 E-value=9.6 Score=23.26 Aligned_cols=25 Identities=24% Similarity=0.348 Sum_probs=15.6
Q ss_pred CCCCCCEEEEEeCC--CCcEEEEEEEe
Q psy15688 14 PVDKGTIVSIMAEG--KQHALAIGLTT 38 (70)
Q Consensus 14 ~~~~G~~V~V~~~~--~~~~vAVG~~~ 38 (70)
.+++||.|.++..+ ....+|+|+..
T Consensus 39 ~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 39 RMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp C--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred cCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 68999999999986 24566666553
No 27
>PRK04980 hypothetical protein; Provisional
Probab=66.22 E-value=20 Score=21.53 Aligned_cols=24 Identities=4% Similarity=0.004 Sum_probs=19.6
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLT 37 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~ 37 (70)
.+++||.|.|.+.+.+.++++-+.
T Consensus 31 ~~~~G~~~~V~~~e~g~~~c~ieI 54 (102)
T PRK04980 31 HFKPGDVLRVGTFEDDRYFCTIEV 54 (102)
T ss_pred CCCCCCEEEEEECCCCcEEEEEEE
Confidence 689999999987778888876544
No 28
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=61.11 E-value=26 Score=25.39 Aligned_cols=36 Identities=17% Similarity=0.245 Sum_probs=26.3
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHY 58 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~ 58 (70)
+++.|++|.|+.. ++.++|.|... ...-.++++++.
T Consensus 33 ~~~~G~~v~v~~~-~g~~lg~g~~n--------~~s~i~~Rils~ 68 (396)
T PRK15128 33 KASLGETIDIVDH-QGKWLARGAYS--------PASQIRARVWTF 68 (396)
T ss_pred CCCCCCEEEEEcC-CCCEEEEEEEC--------CCCCEEEEEEEC
Confidence 6788999999997 78999988652 223456666664
No 29
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. 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=60.85 E-value=11 Score=23.49 Aligned_cols=25 Identities=12% Similarity=0.082 Sum_probs=22.4
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEe
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTT 38 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~ 38 (70)
.++.||-|.|..++.++|.-||+..
T Consensus 11 ~~~vgD~Vyv~~~~~~ePyyIgrI~ 35 (135)
T cd04710 11 LLKVNDHIYMSSEPPGEPYYIGRIM 35 (135)
T ss_pred EEeCCCEEEEecCCCCCCCEEEEEE
Confidence 5889999999998789999999885
No 30
>PRK06789 flagellar motor switch protein; Validated
Probab=58.08 E-value=16 Score=20.76 Aligned_cols=33 Identities=18% Similarity=0.229 Sum_probs=26.3
Q ss_pred EEEEEEEecCHHHHhcCCcceEEEEEEEeeccc
Q psy15688 31 ALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGL 63 (70)
Q Consensus 31 ~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~L 63 (70)
-+=+|++.++-.|+.+-..|..++.-+..++.+
T Consensus 12 ~velGr~~~~i~dll~L~~Gsvi~Ldk~~~epv 44 (74)
T PRK06789 12 YFEIGNTKKKIEDLLHITKGTLYRLENSTKNTV 44 (74)
T ss_pred EEEEeeeEeEHHHHhcCCCCCEEEeCCcCCCCE
Confidence 355899999999998888999888877777653
No 31
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=57.98 E-value=28 Score=24.27 Aligned_cols=45 Identities=31% Similarity=0.489 Sum_probs=27.8
Q ss_pred cCCCCCCCEEEEEeCCCC-------cEEEEEEEecCHHHHhcCCcceEEEEEEE
Q psy15688 12 ITPVDKGTIVSIMAEGKQ-------HALAIGLTTLSTDDIVRVNKGIGVENFHY 58 (70)
Q Consensus 12 ~~~~~~G~~V~V~~~~~~-------~~vAVG~~~~ss~e~~~~~kG~av~v~h~ 58 (70)
+.+++=||+|+|.-.+|. -.+.||+..-| +-..+++|-.|.++=+
T Consensus 187 ld~LRfGD~Vai~D~Dn~yGr~Yr~GavsIGVVVHs--Dc~~aGHGPGvt~imt 238 (258)
T PF14505_consen 187 LDKLRFGDIVAIMDHDNRYGRGYRKGAVSIGVVVHS--DCVKAGHGPGVTTIMT 238 (258)
T ss_dssp SS--BTTBEEEEEEEE-SSS-EEEEEEEEEEEEES-----SSTT--SEEEEEEE
T ss_pred ccceeeccEEEEeccccccCchhccCceEEEEEEec--CccccCCCCceEEEEe
Confidence 347899999999987663 28889988765 3344678888876644
No 32
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=57.70 E-value=15 Score=24.29 Aligned_cols=32 Identities=22% Similarity=0.256 Sum_probs=27.6
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhc
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVR 46 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~ 46 (70)
+++....|.|+.. |+.|.++|+...|++|.-+
T Consensus 128 ~~~~~~~v~V~~~-nd~~lgiGvg~~s~~ed~~ 159 (176)
T COG1374 128 EIPENGGVFVFNM-NDVPLGIGVGALSPSEDGR 159 (176)
T ss_pred ccCCcceEEEEEc-CCCceEEEecccCchhhcc
Confidence 6788889999997 8999999999999888644
No 33
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=53.71 E-value=19 Score=23.15 Aligned_cols=27 Identities=11% Similarity=0.154 Sum_probs=17.7
Q ss_pred eeecCCCCcCCCCCCCEEEEEeCCCCcEEEEEE
Q psy15688 4 GLTSPGAIITPVDKGTIVSIMAEGKQHALAIGL 36 (70)
Q Consensus 4 GI~~~~~~~~~~~~G~~V~V~~~~~~~~vAVG~ 36 (70)
||....+ +..+. |+|++. ++.|+++|.
T Consensus 114 ~i~~i~e---~~~~~--VvV~n~-~d~~LGfG~ 140 (162)
T PF03657_consen 114 SIGRITE---DTPQN--VVVYNM-NDVPLGFGC 140 (162)
T ss_dssp GEEEEET---TS-TC--EEEEET-TS-EEEEEE
T ss_pred hcEEecC---CCCce--EEEEeC-CCCeEEEEE
Confidence 4555444 45545 889987 899999993
No 34
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=53.57 E-value=15 Score=22.85 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=30.5
Q ss_pred CcEEEEEEEecCHHHHhcCCcceEEEEEEEeecccc
Q psy15688 29 QHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLW 64 (70)
Q Consensus 29 ~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW 64 (70)
..-+-+|++.|+-.++.+.++|..+..-...++.++
T Consensus 74 ~v~velGr~~~~l~ell~l~~Gsvi~Ld~~~~~~Vd 109 (136)
T COG1886 74 RLSVELGRTKMPLGELLALGKGSVIELDKLAGEPVD 109 (136)
T ss_pred EEEEEEeeeeeeHHHHHhcCCCCEEEcCCcCCCceE
Confidence 446889999999999999999999988777777665
No 35
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=52.69 E-value=30 Score=19.25 Aligned_cols=44 Identities=20% Similarity=0.165 Sum_probs=31.0
Q ss_pred CCCCCCEEEEEeCC-CCcEEEEEEEecCHHHHhcCCcceEEEEEEEee
Q psy15688 14 PVDKGTIVSIMAEG-KQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60 (70)
Q Consensus 14 ~~~~G~~V~V~~~~-~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~ 60 (70)
.+..|.-|-|...+ -+..-|+-.--++++++ +++++|++.|+-+
T Consensus 10 ait~G~rVMia~tG~tgvikaIh~dglt~~Q~---rR~k~Vel~g~e~ 54 (65)
T TIGR03318 10 AITTGSRVMIAGTGHTGVIKAIHTEGLTAEQA---RREKCVELEGCEE 54 (65)
T ss_pred ccCCCcEEEEecCCccceeehhhhCCCCHHHh---hhccEEEEecccc
Confidence 47789999998765 34455555444666663 6899999999844
No 36
>KOG1698|consensus
Probab=51.76 E-value=37 Score=22.87 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=20.2
Q ss_pred cCCCCCCCEEEEEeCCC----CcEEEEEEEe
Q psy15688 12 ITPVDKGTIVSIMAEGK----QHALAIGLTT 38 (70)
Q Consensus 12 ~~~~~~G~~V~V~~~~~----~~~vAVG~~~ 38 (70)
.|.|+.|++|.|.++++ ..-...|++.
T Consensus 94 iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I 124 (201)
T KOG1698|consen 94 IPEFKVGSIVRVTSEDPENKRKVSRFKGICI 124 (201)
T ss_pred CCccccccEEEEEecCCccCCceeEEEEEEE
Confidence 46899999999998764 3356667664
No 37
>PRK00809 hypothetical protein; Provisional
Probab=47.09 E-value=49 Score=20.75 Aligned_cols=30 Identities=13% Similarity=0.204 Sum_probs=20.0
Q ss_pred CCCCCCEEEEEeCC-----CCcEEEEEEEecCHHH
Q psy15688 14 PVDKGTIVSIMAEG-----KQHALAIGLTTLSTDD 43 (70)
Q Consensus 14 ~~~~G~~V~V~~~~-----~~~~vAVG~~~~ss~e 43 (70)
.+++||.+.++..+ ...+-.+|++.+.++.
T Consensus 34 ~Mk~GD~v~fYhs~~~~~~~~~~~ivgi~eV~~~~ 68 (144)
T PRK00809 34 KVKPGDKLIIYVSQEYGAERLPGKIVGIYEVVSEW 68 (144)
T ss_pred hCCCCCEEEEEECCccCCCCCCceEEEEEEEecCc
Confidence 68999999999984 1234445555555444
No 38
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=46.87 E-value=19 Score=21.86 Aligned_cols=16 Identities=38% Similarity=0.663 Sum_probs=13.1
Q ss_pred cceEE--EEEEEeecccc
Q psy15688 49 KGIGV--ENFHYLNDGLW 64 (70)
Q Consensus 49 kG~av--~v~h~~~D~LW 64 (70)
+|+.| +|.|+.+|+||
T Consensus 23 ~gk~V~G~I~hvv~ddLY 40 (104)
T PF10246_consen 23 EGKIVIGKIFHVVDDDLY 40 (104)
T ss_pred cCCEEEEEEEEEecCceE
Confidence 55555 99999999997
No 39
>KOG3342|consensus
Probab=46.83 E-value=20 Score=23.50 Aligned_cols=25 Identities=8% Similarity=0.332 Sum_probs=18.9
Q ss_pred CCCCCCCEEEEEeCCCCcEEEEEEEe
Q psy15688 13 TPVDKGTIVSIMAEGKQHALAIGLTT 38 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~~~~~vAVG~~~ 38 (70)
|.|++||+...-.. +..|+-||...
T Consensus 60 PaF~RGDlLfL~N~-~~~p~~vGdiv 84 (180)
T KOG3342|consen 60 PAFHRGDLLFLTNR-NEDPIRVGDIV 84 (180)
T ss_pred cccccccEEEEecC-CCCcceeccEE
Confidence 57888888888765 66788888654
No 40
>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=44.77 E-value=24 Score=21.58 Aligned_cols=16 Identities=13% Similarity=0.185 Sum_probs=13.4
Q ss_pred CcCCCCCCCEEEEEeC
Q psy15688 11 IITPVDKGTIVSIMAE 26 (70)
Q Consensus 11 ~~~~~~~G~~V~V~~~ 26 (70)
.+|+|+.||.|.|...
T Consensus 15 ~ip~f~~GD~v~V~~~ 30 (113)
T TIGR01024 15 DLPDFRVGDTVRVHVK 30 (113)
T ss_pred CCCccCCCCEEEEEEE
Confidence 4689999999999663
No 41
>PF14001 YdfZ: YdfZ protein
Probab=44.44 E-value=56 Score=18.15 Aligned_cols=44 Identities=23% Similarity=0.209 Sum_probs=32.5
Q ss_pred CCCCCCEEEEEeCC-CCcEEEEEEEecCHHHHhcCCcceEEEEEEEee
Q psy15688 14 PVDKGTIVSIMAEG-KQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60 (70)
Q Consensus 14 ~~~~G~~V~V~~~~-~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~ 60 (70)
.+..|.-|-|...+ -+..-|+-.--++++++ .++++|++.|+-+
T Consensus 9 ~i~~G~rVMiagtG~~gvikAih~~gl~~eq~---rR~kcVel~g~~g 53 (64)
T PF14001_consen 9 AITTGSRVMIAGTGATGVIKAIHADGLTAEQI---RRAKCVELEGCEG 53 (64)
T ss_pred cCCCCCEEEEcCCCcccEEeeeecCCCCHHHh---hhccEEEEeCCCc
Confidence 57889999998765 35566666666777774 6899999988743
No 42
>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=43.96 E-value=26 Score=21.30 Aligned_cols=16 Identities=19% Similarity=0.181 Sum_probs=13.6
Q ss_pred CcCCCCCCCEEEEEeC
Q psy15688 11 IITPVDKGTIVSIMAE 26 (70)
Q Consensus 11 ~~~~~~~G~~V~V~~~ 26 (70)
.+|+|+.||.|.|...
T Consensus 15 ~~p~f~~GD~v~V~~~ 30 (113)
T PF01245_consen 15 DIPEFRVGDTVRVTYK 30 (113)
T ss_dssp SSSSSSSSSEEEEEEE
T ss_pred CCCCcCCCCEEEEEEE
Confidence 5689999999999764
No 43
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=42.75 E-value=28 Score=21.37 Aligned_cols=15 Identities=20% Similarity=0.226 Sum_probs=13.0
Q ss_pred CcCCCCCCCEEEEEe
Q psy15688 11 IITPVDKGTIVSIMA 25 (70)
Q Consensus 11 ~~~~~~~G~~V~V~~ 25 (70)
.+|+|+.||.|.|..
T Consensus 15 ~~p~f~~GD~V~V~~ 29 (116)
T PRK05338 15 DIPEFRPGDTVRVHV 29 (116)
T ss_pred CCCCcCCCCEEEEEE
Confidence 468999999999965
No 44
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=41.29 E-value=46 Score=19.02 Aligned_cols=24 Identities=8% Similarity=0.109 Sum_probs=19.6
Q ss_pred CCCCCEEEEEeCCCCcEEEEEEEe
Q psy15688 15 VDKGTIVSIMAEGKQHALAIGLTT 38 (70)
Q Consensus 15 ~~~G~~V~V~~~~~~~~vAVG~~~ 38 (70)
++.||.|.|...+...+.-||+..
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~ 26 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIE 26 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEE
Confidence 578999999998657888888774
No 45
>KOG0126|consensus
Probab=40.51 E-value=39 Score=22.89 Aligned_cols=21 Identities=14% Similarity=0.396 Sum_probs=17.3
Q ss_pred CCCCCCEEEEEeCCCCcEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIG 35 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG 35 (70)
.+.+||+++|++. -|+||-|-
T Consensus 46 ~LtEgDil~VFSq-yGe~vdin 66 (219)
T KOG0126|consen 46 ELTEGDILCVFSQ-YGEIVDIN 66 (219)
T ss_pred cccCCcEEEEeec-cCceEEEE
Confidence 6889999999997 67777663
No 46
>PF13403 Hint_2: Hint domain
Probab=40.41 E-value=70 Score=19.93 Aligned_cols=43 Identities=23% Similarity=0.091 Sum_probs=30.7
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENF 56 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~ 56 (70)
+++.||.|.=...+-.....||+..+++.++....+..-|++.
T Consensus 20 ~L~~GD~V~T~dgg~~~V~wig~~~~~~~~~~~~~~~~pvri~ 62 (147)
T PF13403_consen 20 DLRPGDRVLTRDGGFQPVRWIGRRTVSPADLPAPPRLAPVRIP 62 (147)
T ss_pred ccCCCCEEEecCCCEEEEEEEEEEEecccccCcCCCcceEEEE
Confidence 8999999887765445688999999987765554555544443
No 47
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=39.05 E-value=31 Score=18.57 Aligned_cols=16 Identities=19% Similarity=0.322 Sum_probs=9.6
Q ss_pred CCCCCEEEEEeCCCCc
Q psy15688 15 VDKGTIVSIMAEGKQH 30 (70)
Q Consensus 15 ~~~G~~V~V~~~~~~~ 30 (70)
|++|+.|-|.+..++.
T Consensus 1 F~~G~~VEV~s~e~g~ 16 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGF 16 (68)
T ss_dssp --TT-EEEEEE-SBTT
T ss_pred CCCCCEEEEEEcCCCC
Confidence 6899999999965543
No 48
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). 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 joining of 60S subunits. 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 of EF1A, eEF1A and aeIF2gamma.
Probab=38.95 E-value=61 Score=19.66 Aligned_cols=30 Identities=7% Similarity=0.113 Sum_probs=23.8
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHH
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDI 44 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~ 44 (70)
.+++||.+.+.+. ++..+.==++++++..+
T Consensus 26 tL~~GD~Iv~g~~-~Gpi~tkVRaLl~~~~~ 55 (110)
T cd03703 26 TLREGDTIVVCGL-NGPIVTKVRALLKPQPL 55 (110)
T ss_pred eEecCCEEEEccC-CCCceEEEeEecCCCCc
Confidence 6999999999987 77666666777777665
No 49
>CHL00084 rpl19 ribosomal protein L19
Probab=38.53 E-value=35 Score=21.01 Aligned_cols=15 Identities=13% Similarity=0.220 Sum_probs=12.9
Q ss_pred CcCCCCCCCEEEEEe
Q psy15688 11 IITPVDKGTIVSIMA 25 (70)
Q Consensus 11 ~~~~~~~G~~V~V~~ 25 (70)
.+|+|+.||.|.|..
T Consensus 19 ~~p~f~~GDtV~V~~ 33 (117)
T CHL00084 19 NLPKIRVGDTVKVGV 33 (117)
T ss_pred CCCccCCCCEEEEEE
Confidence 467999999999966
No 50
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=38.51 E-value=88 Score=18.72 Aligned_cols=27 Identities=11% Similarity=0.046 Sum_probs=22.0
Q ss_pred CCCCCCCEEEEEeCCCCcEEEEEEEecC
Q psy15688 13 TPVDKGTIVSIMAEGKQHALAIGLTTLS 40 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~~~~~vAVG~~~~s 40 (70)
+++..||+|.+... ++.+.+..+..-|
T Consensus 24 ~glA~gDvV~~~~~-~g~~~~~~~v~~s 50 (117)
T PF14085_consen 24 YGLALGDVVRAEPD-DGELWFQKVVESS 50 (117)
T ss_pred CCCCCCCEEEEEeC-CCeEEEEEEEecC
Confidence 48999999999997 5888888875433
No 51
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=38.17 E-value=65 Score=17.07 Aligned_cols=43 Identities=14% Similarity=0.039 Sum_probs=35.0
Q ss_pred CCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEE
Q psy15688 16 DKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHY 58 (70)
Q Consensus 16 ~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~ 58 (70)
..++++++.+..-..|--++-..+|.+|...-..|+.|.+.-.
T Consensus 12 ~Tn~l~~~~~~~i~ip~~i~g~~Ls~~q~~~L~~G~~v~le~m 54 (59)
T PF13101_consen 12 ETNELVYMPVDKIRIPDKIKGVELSPEQKEDLREGKPVYLEGM 54 (59)
T ss_pred ccCceEEeccccccccceecCccCCHHHHHHHHCCCeEEEeee
Confidence 5678888888755778888889999999888889999987643
No 52
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=38.01 E-value=1.2e+02 Score=20.25 Aligned_cols=38 Identities=13% Similarity=0.092 Sum_probs=26.7
Q ss_pred CCCCCCEEEEEeCCCCc-EEEEEEEecCHHHHhcCCcceEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQH-ALAIGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~-~vAVG~~~~ss~e~~~~~kG~av~v~h 57 (70)
-+++||.|.|...+.+. .-+-|+|+-+ ...|..|++..
T Consensus 155 lV~rG~~V~I~a~~~g~~Vs~~G~AL~~------G~~Ge~IrVrN 193 (214)
T PRK12617 155 LVRRGDTVPLVSRNGGLEVRMSGRALSD------AGENERVSVEN 193 (214)
T ss_pred eEcCCCEEEEEEecCCEEEEEEEEEccC------CCCCCEEEEEE
Confidence 58999999999986554 5567877443 33677666653
No 53
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=37.27 E-value=53 Score=16.26 Aligned_cols=16 Identities=31% Similarity=0.405 Sum_probs=13.5
Q ss_pred CCCCCCEEEEEeCCCC
Q psy15688 14 PVDKGTIVSIMAEGKQ 29 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~ 29 (70)
.+++||.|.+...+++
T Consensus 20 ~l~~Gd~v~i~~~~~g 35 (47)
T PF04014_consen 20 GLKPGDEVEIEVEGDG 35 (47)
T ss_dssp TSSTTTEEEEEEETTS
T ss_pred CCCCCCEEEEEEeCCC
Confidence 6899999999987554
No 54
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=37.04 E-value=57 Score=17.22 Aligned_cols=16 Identities=19% Similarity=0.411 Sum_probs=12.5
Q ss_pred CCCCCEEEEEeCCCCc
Q psy15688 15 VDKGTIVSIMAEGKQH 30 (70)
Q Consensus 15 ~~~G~~V~V~~~~~~~ 30 (70)
|+.||+|...+-+...
T Consensus 1 f~~GDvV~LKSGGp~M 16 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPRM 16 (53)
T ss_pred CCCCCEEEEccCCCCe
Confidence 6889999999875443
No 55
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=36.99 E-value=55 Score=23.85 Aligned_cols=44 Identities=9% Similarity=0.275 Sum_probs=33.1
Q ss_pred CCCCCCCEEEEEeCC-CCcEEEEEEEecCHHHHhcC--C-cceEEEEE
Q psy15688 13 TPVDKGTIVSIMAEG-KQHALAIGLTTLSTDDIVRV--N-KGIGVENF 56 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~-~~~~vAVG~~~~ss~e~~~~--~-kG~av~v~ 56 (70)
.+++.|+.|.++..+ +...+-||++.+....|.-- + .|+.+.++
T Consensus 257 SEL~sG~~VlvVd~~G~tR~~~VGRvKIE~RPLllIeA~~~g~~~svi 304 (354)
T PF01959_consen 257 SELRSGDEVLVVDADGRTRTAIVGRVKIERRPLLLIEAEADGKRISVI 304 (354)
T ss_pred hhhcCCCEEEEEeCCCCEEEEEeeEEEEeecceEEEEEEeCCeEEEEE
Confidence 489999999998764 56799999999998887542 2 56555443
No 56
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=36.80 E-value=50 Score=20.70 Aligned_cols=34 Identities=12% Similarity=0.175 Sum_probs=28.1
Q ss_pred CCcEEEEEEEecCHHHHhcCC--cceEEEEEEEeec
Q psy15688 28 KQHALAIGLTTLSTDDIVRVN--KGIGVENFHYLND 61 (70)
Q Consensus 28 ~~~~vAVG~~~~ss~e~~~~~--kG~av~v~h~~~D 61 (70)
..++-|...|.||++++..-+ +|--|++..-+|+
T Consensus 24 ~~Y~~a~a~~~inp~D~~~Lgv~EGD~VkVkse~Ge 59 (128)
T COG1153 24 DEYFNACAVCEINPEDMKQLGVSEGDKVKVKSEFGE 59 (128)
T ss_pred hhhhhheeEEEECHHHHHHhCCCcCCeEEEEecCcc
Confidence 467888999999999998754 8888888887774
No 57
>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=36.32 E-value=40 Score=18.65 Aligned_cols=22 Identities=23% Similarity=0.504 Sum_probs=10.1
Q ss_pred EEEEecCHHHHhcCCcceEEEE
Q psy15688 34 IGLTTLSTDDIVRVNKGIGVEN 55 (70)
Q Consensus 34 VG~~~~ss~e~~~~~kG~av~v 55 (70)
+|+..++-+|+..-+.|-.+..
T Consensus 16 Lg~~~itl~ell~L~~Gdvi~L 37 (77)
T TIGR02480 16 LGRTRITLGDLLKLGEGSVIEL 37 (77)
T ss_pred EeceEeEHHHHhcCCCCCEEEc
Confidence 4444444444444444444443
No 58
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=35.57 E-value=64 Score=17.15 Aligned_cols=19 Identities=11% Similarity=0.286 Sum_probs=15.7
Q ss_pred CCCCCEEEEEeCCCCcEEEE
Q psy15688 15 VDKGTIVSIMAEGKQHALAI 34 (70)
Q Consensus 15 ~~~G~~V~V~~~~~~~~vAV 34 (70)
++.|..|.|... ++.|++|
T Consensus 40 L~e~~~v~v~~~-~~~~i~v 58 (61)
T cd04470 40 LKEGMEVIVLFY-NGEPIGV 58 (61)
T ss_pred CcCCCEEEEEEE-CCEEEEE
Confidence 778999998887 6888876
No 59
>PRK08916 flagellar motor switch protein; Reviewed
Probab=34.48 E-value=37 Score=20.83 Aligned_cols=33 Identities=9% Similarity=0.285 Sum_probs=26.5
Q ss_pred EEEEEEEecCHHHHhcCCcceEEEEEEEeeccc
Q psy15688 31 ALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGL 63 (70)
Q Consensus 31 ~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~L 63 (70)
-+-+|...|+-.|+.+...|-++..-+...|.+
T Consensus 50 tv~LG~~~ltl~ELL~L~~GDVI~Ld~~~~e~V 82 (116)
T PRK08916 50 SAVLGRSKMDVGQLLKLGPGSVLELDRKVGEAI 82 (116)
T ss_pred EEEEecccccHHHHhcCCCCCEEEcCCCCCCCE
Confidence 466899999999999888998888876666654
No 60
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=34.41 E-value=57 Score=23.36 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=22.4
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCH
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLST 41 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss 41 (70)
.+++||.|+.+.. ...-++||+..=+.
T Consensus 72 eI~KGDlvi~y~k-~~r~y~IGkVtsdY 98 (318)
T COG4127 72 EIQKGDLVITYSK-SNRTYLIGKVTSDY 98 (318)
T ss_pred HhccCcEEEeecc-cCceEEEEEecCCc
Confidence 6899999999997 66789999986543
No 61
>PRK06788 flagellar motor switch protein; Validated
Probab=33.79 E-value=49 Score=20.36 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=26.9
Q ss_pred EEEEEEEecCHHHHhcCCcceEEEEEEEeeccc
Q psy15688 31 ALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGL 63 (70)
Q Consensus 31 ~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~L 63 (70)
-+-+|.+.++..|+..-..|-++..-|.++|.+
T Consensus 39 ~aeLG~t~ltl~DlL~L~vGDVI~Ldk~~~dpv 71 (119)
T PRK06788 39 GVKLGKASITLGDVKQLKVGDVLEVEKNLGHKV 71 (119)
T ss_pred EEEEecceecHHHHhCCCCCCEEEeCCcCCCCE
Confidence 455789999999999888999998887776654
No 62
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=32.75 E-value=68 Score=23.31 Aligned_cols=44 Identities=9% Similarity=0.268 Sum_probs=32.9
Q ss_pred CCCCCCCEEEEEeCC-CCcEEEEEEEecCHHHHhcC--C-cceEEEEE
Q psy15688 13 TPVDKGTIVSIMAEG-KQHALAIGLTTLSTDDIVRV--N-KGIGVENF 56 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~-~~~~vAVG~~~~ss~e~~~~--~-kG~av~v~ 56 (70)
.+++.|+.|.|+..+ +...+-||++.+....|.-- + .|+-+.++
T Consensus 247 sEL~sG~eVlvVd~~G~tR~~~VGRvKIE~RPL~lIeAe~~g~~~~vi 294 (344)
T PRK02290 247 SELRSGDEVLVVDADGNTREAIVGRVKIEKRPLLLIEAEYGGKRIRTI 294 (344)
T ss_pred HhhcCCCEEEEEeCCCCEEEEEeeEEEEeeccEEEEEEEeCCeEEEEE
Confidence 489999999998764 67799999999998887542 1 45555443
No 63
>smart00439 BAH Bromo adjacent homology domain.
Probab=32.66 E-value=62 Score=18.44 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=14.1
Q ss_pred CCCCCEEEEEeCCCCcEEEEEEE
Q psy15688 15 VDKGTIVSIMAEGKQHALAIGLT 37 (70)
Q Consensus 15 ~~~G~~V~V~~~~~~~~vAVG~~ 37 (70)
++.||.|.|...+...+.-||+.
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I 24 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRI 24 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEE
Confidence 56677777776643445556654
No 64
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.77 E-value=1.3e+02 Score=18.71 Aligned_cols=38 Identities=13% Similarity=0.066 Sum_probs=26.4
Q ss_pred CCCCCCEEEEEeCCCC-cEEEEEEEecCHHHHhcCCcceEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQ-HALAIGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~-~~vAVG~~~~ss~e~~~~~kG~av~v~h 57 (70)
-+++||.|.|...+.+ ..-+-|+|+-| -..|..+++..
T Consensus 81 lV~rG~~V~i~~~~ggl~i~~~G~AL~~------G~~Gd~IrV~N 119 (141)
T PRK12618 81 IVDRNQLVPLAYRLGGLEIRTEGRALSR------GGVGDEIRVMN 119 (141)
T ss_pred EEeCCCEEEEEEecCCEEEEEEEEEccc------CCCCCEEEEEE
Confidence 5889999999887644 46788888554 23566666543
No 65
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=31.42 E-value=81 Score=16.14 Aligned_cols=22 Identities=27% Similarity=0.404 Sum_probs=15.7
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLT 37 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~ 37 (70)
....| .|.|+.. ++..+++|..
T Consensus 25 ~~~~~-~vrvy~~-~~~FlGig~~ 46 (58)
T PF09157_consen 25 APPDG-LVRVYDE-DGRFLGIGEI 46 (58)
T ss_dssp --SSS-EEEEETT-TTEEEEEEEE
T ss_pred CCCCc-eEEEECC-CCEEEEEEEE
Confidence 34455 9999965 7889888876
No 66
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=31.00 E-value=66 Score=16.35 Aligned_cols=20 Identities=10% Similarity=0.303 Sum_probs=15.1
Q ss_pred CCCCCCEEEEEeCCCCcEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAI 34 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAV 34 (70)
-+++|..|.|... ++.|+.|
T Consensus 36 ~l~eg~~v~v~~~-~g~~i~~ 55 (55)
T cd04463 36 SFEPGEVVLVDTR-TGQYVGV 55 (55)
T ss_pred hCCCCCEEEEEEE-CCEEEeC
Confidence 4688999998877 6777653
No 67
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=30.36 E-value=51 Score=20.78 Aligned_cols=34 Identities=18% Similarity=0.266 Sum_probs=27.4
Q ss_pred EEEEEEEecCHHHHhcCCcceEEEEEEEeecccc
Q psy15688 31 ALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLW 64 (70)
Q Consensus 31 ~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW 64 (70)
-+-+|++.++-.++..-+.|-++..-+..+|.+.
T Consensus 65 sveLG~t~itlrdLL~L~~GDVI~Ld~~~~epv~ 98 (137)
T PRK07963 65 TVELGRTRMTIKELLRLTQGSVVALDGLAGEPLD 98 (137)
T ss_pred EEEEecccccHHHHhCCCCCCEEEeCCCCCCCEE
Confidence 4567999999999999899999998876666543
No 68
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=30.25 E-value=66 Score=15.43 Aligned_cols=13 Identities=38% Similarity=0.797 Sum_probs=11.1
Q ss_pred ceEEEEEEEeecc
Q psy15688 50 GIGVENFHYLNDG 62 (70)
Q Consensus 50 G~av~v~h~~~D~ 62 (70)
|..|.++|-+.|+
T Consensus 3 glsvt~lhlfrde 15 (35)
T PF13216_consen 3 GLSVTNLHLFRDE 15 (35)
T ss_pred ceEEEEEEEeecC
Confidence 6778999999986
No 69
>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=28.52 E-value=91 Score=19.19 Aligned_cols=34 Identities=15% Similarity=0.286 Sum_probs=21.3
Q ss_pred CCcCCCCCCCEEEEEeC-CCCcEEEE-EEEecCHHH
Q psy15688 10 AIITPVDKGTIVSIMAE-GKQHALAI-GLTTLSTDD 43 (70)
Q Consensus 10 ~~~~~~~~G~~V~V~~~-~~~~~vAV-G~~~~ss~e 43 (70)
..|.++++||.|.|.+. ++..-+-| ..-.++.++
T Consensus 68 ~~L~~l~~GD~I~v~~~~g~~~~Y~V~~~~~v~~~~ 103 (144)
T cd05829 68 FRLGDLRKGDKVEVTRADGQTATFRVDRVEVYPKDA 103 (144)
T ss_pred cchhcCCCCCEEEEEECCCCEEEEEEeEEEEECccc
Confidence 34568999999999994 34344444 333355443
No 70
>PRK06033 hypothetical protein; Validated
Probab=28.47 E-value=62 Score=18.43 Aligned_cols=24 Identities=13% Similarity=0.351 Sum_probs=10.8
Q ss_pred EEEEecCHHHHhcCCcceEEEEEE
Q psy15688 34 IGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 34 VG~~~~ss~e~~~~~kG~av~v~h 57 (70)
.|.+.++.+|+..-+.|-.+..-+
T Consensus 15 Lg~~~i~l~dlL~L~~GDVI~L~~ 38 (83)
T PRK06033 15 LGRSSMPIHQVLRMGRGAVIPLDA 38 (83)
T ss_pred EecccccHHHHhCCCCCCEEEeCC
Confidence 344444444444444444444433
No 71
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=28.47 E-value=61 Score=18.63 Aligned_cols=23 Identities=22% Similarity=0.125 Sum_probs=17.4
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEe
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTT 38 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~ 38 (70)
.++.|+.|.|... |.|+|-=+..
T Consensus 20 rV~aGEev~IT~~--G~PVArivp~ 42 (84)
T COG4118 20 RVRAGEEVIITKR--GRPVARLVPL 42 (84)
T ss_pred HHhCCCEEEEeeC--CeEEEEEeec
Confidence 7899999999865 6777755443
No 72
>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=28.05 E-value=66 Score=20.25 Aligned_cols=17 Identities=29% Similarity=0.317 Sum_probs=13.7
Q ss_pred CCcCCCCCCCEEEEEeC
Q psy15688 10 AIITPVDKGTIVSIMAE 26 (70)
Q Consensus 10 ~~~~~~~~G~~V~V~~~ 26 (70)
+++|.+++||.|.++-+
T Consensus 81 prip~l~~GD~V~f~Ge 97 (131)
T PF11948_consen 81 PRIPWLQKGDQVEFYGE 97 (131)
T ss_pred ccCcCcCCCCEEEEEEE
Confidence 45678999999998754
No 73
>PRK08158 type III secretion system protein SpaO; Validated
Probab=28.04 E-value=1.7e+02 Score=20.89 Aligned_cols=37 Identities=24% Similarity=0.288 Sum_probs=27.4
Q ss_pred CCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeec
Q psy15688 16 DKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLND 61 (70)
Q Consensus 16 ~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D 61 (70)
..++.|-|+. |+.++|-|.... .+--.+|++.++++.
T Consensus 262 ~~~~~V~I~v--Ng~lva~GELV~-------v~~~lGVrIt~i~~~ 298 (303)
T PRK08158 262 NAELNVEIRA--NGALLGNGELVQ-------MDDTLGVEIHEWLSG 298 (303)
T ss_pred CCCCceEEEE--CCEEEEEEEEEE-------ECCEEEEEEEEEecC
Confidence 5788888887 688999997753 233478888887654
No 74
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=28.01 E-value=1.1e+02 Score=22.34 Aligned_cols=43 Identities=12% Similarity=0.316 Sum_probs=30.3
Q ss_pred CCCCCCCEEEEEeCC-CCcEEEEEEEecCHHHHhcC--C-cceEEEE
Q psy15688 13 TPVDKGTIVSIMAEG-KQHALAIGLTTLSTDDIVRV--N-KGIGVEN 55 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~-~~~~vAVG~~~~ss~e~~~~--~-kG~av~v 55 (70)
..++.||.|.|+..+ +...--||++.+....|+-. + +|.-+++
T Consensus 279 aEL~aGDeV~iVD~dGr~R~aiVGRvKIErRPl~lIeAey~g~~i~t 325 (376)
T COG1465 279 AELKAGDEVLIVDFDGRTRSAIVGRVKIERRPLMLIEAEYEGVEIST 325 (376)
T ss_pred hhhcCCCeEEEEecCCceeEEEEEEEEeecCceEEEEEEecCcEEEE
Confidence 489999999999864 45566689999888776432 2 4554443
No 75
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=27.91 E-value=28 Score=17.67 Aligned_cols=11 Identities=18% Similarity=0.700 Sum_probs=9.3
Q ss_pred CCCCCCEEEEE
Q psy15688 14 PVDKGTIVSIM 24 (70)
Q Consensus 14 ~~~~G~~V~V~ 24 (70)
+|++||+|.|.
T Consensus 17 s~~~Gd~i~v~ 27 (55)
T PF07653_consen 17 SFKKGDVIEVL 27 (55)
T ss_dssp EB-TTEEEEEE
T ss_pred EEecCCEEEEE
Confidence 79999999998
No 76
>PF14306 PUA_2: PUA-like domain; PDB: 1M8P_C 1I2D_B 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2OFX_B 1J70_B 1G8F_A ....
Probab=27.66 E-value=1.1e+02 Score=19.46 Aligned_cols=22 Identities=18% Similarity=0.234 Sum_probs=17.8
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGL 36 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~ 36 (70)
++++|+.|++... .+.++|+=.
T Consensus 92 ~l~~G~~v~L~~~-~G~~~a~l~ 113 (160)
T PF14306_consen 92 SLKEGDKVALRDP-EGKPVAILE 113 (160)
T ss_dssp TCTTTSEEEEEET-TTEEEEEEE
T ss_pred hccCCCEEEEECC-CCCEEEEEE
Confidence 6899999999986 588876643
No 77
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.34 E-value=1.9e+02 Score=19.22 Aligned_cols=38 Identities=13% Similarity=-0.076 Sum_probs=26.0
Q ss_pred CCCCCCEEEEEeCCCC-cEEEEEEEecCHHHHhcCCcceEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQ-HALAIGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~-~~vAVG~~~~ss~e~~~~~kG~av~v~h 57 (70)
-+++||.|.|...+.+ ..-+-|+|+-+ ...|..+++..
T Consensus 165 lV~rGd~V~i~~~~gg~~I~~~G~Al~~------G~~Gd~IrVrN 203 (222)
T PRK08515 165 LVRKNDIINGVLKEGGVSIEISLKALQD------GNLGDIIQAKN 203 (222)
T ss_pred eEecCCEEEEEEECCCEEEEEEEEEccc------CCCCCEEEEEe
Confidence 6889999999887644 35667777443 23666666653
No 78
>PF11926 DUF3444: Domain of unknown function (DUF3444); InterPro: IPR024593 This entry represents an uncharacterised domain. This domain is found in DnaJ, cytosine-specific methyltransferases, and members from the zinc finger, C3HC4 type family.
Probab=26.90 E-value=70 Score=21.58 Aligned_cols=20 Identities=10% Similarity=0.119 Sum_probs=14.7
Q ss_pred CCCCCCEEEEEeCCCCcEEE
Q psy15688 14 PVDKGTIVSIMAEGKQHALA 33 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vA 33 (70)
.|+.|+++|++....+.|=-
T Consensus 27 ~F~~gQIWAlYd~~D~mPR~ 46 (217)
T PF11926_consen 27 KFQVGQIWALYDDDDGMPRY 46 (217)
T ss_pred hCCCCCEEEEeeCCCCCeee
Confidence 69999999999854444433
No 79
>COG1945 Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) [Amino acid transport and metabolism]
Probab=26.73 E-value=1.6e+02 Score=19.29 Aligned_cols=22 Identities=14% Similarity=0.264 Sum_probs=16.8
Q ss_pred eeecCCCCcCCCCCCCEEEEEe
Q psy15688 4 GLTSPGAIITPVDKGTIVSIMA 25 (70)
Q Consensus 4 GI~~~~~~~~~~~~G~~V~V~~ 25 (70)
.++...+++|.+..|++|..+.
T Consensus 51 ~~V~~e~gl~kl~pG~iv~~V~ 72 (163)
T COG1945 51 EIVDPEDGLPKLPPGAILFCVM 72 (163)
T ss_pred cccchhhcCCcCCCCcEEeEEE
Confidence 3456667888999999998754
No 80
>KOG3572|consensus
Probab=26.55 E-value=52 Score=28.34 Aligned_cols=22 Identities=23% Similarity=0.382 Sum_probs=17.5
Q ss_pred CcCCCCCCCEEEEEeCCCCcEEE
Q psy15688 11 IITPVDKGTIVSIMAEGKQHALA 33 (70)
Q Consensus 11 ~~~~~~~G~~V~V~~~~~~~~vA 33 (70)
.+|+++.||+|-|.+. ++.+++
T Consensus 124 ~fP~IKpGDIVEI~~~-n~~~~~ 145 (1701)
T KOG3572|consen 124 KFPEIKPGDIVEILSK-NWPVLI 145 (1701)
T ss_pred hCCCCCCCceEEEecc-CCCchh
Confidence 3579999999999997 666544
No 81
>KOG2110|consensus
Probab=26.46 E-value=2e+02 Score=21.38 Aligned_cols=13 Identities=23% Similarity=0.271 Sum_probs=11.2
Q ss_pred CCcceEEEEEEEe
Q psy15688 47 VNKGIGVENFHYL 59 (70)
Q Consensus 47 ~~kG~av~v~h~~ 59 (70)
++||.+++|.|+-
T Consensus 192 SeKGTVIRVf~v~ 204 (391)
T KOG2110|consen 192 SEKGTVIRVFSVP 204 (391)
T ss_pred ccCceEEEEEEcC
Confidence 4799999999984
No 82
>smart00588 NEUZ domain in neuralized proteins.
Probab=26.14 E-value=1.4e+02 Score=18.04 Aligned_cols=39 Identities=21% Similarity=0.281 Sum_probs=29.2
Q ss_pred eeecCCCCcCCCCCCCEEEEEeCCC----CcEEEEEEEecCHHHHh
Q psy15688 4 GLTSPGAIITPVDKGTIVSIMAEGK----QHALAIGLTTLSTDDIV 45 (70)
Q Consensus 4 GI~~~~~~~~~~~~G~~V~V~~~~~----~~~vAVG~~~~ss~e~~ 45 (70)
||+-... .++.|+.+.|...+. .-.+.+|.+..+++.+.
T Consensus 32 givFS~r---Pl~~~E~~~v~i~~~~~~w~G~l~~G~Ts~dP~~l~ 74 (123)
T smart00588 32 ALVFSAR---PLRINELFEVKIEKVVRKWSGALRFGVTTCDPATLR 74 (123)
T ss_pred eEEecCC---CCcCCCEEEEEEEEecCCccCceEEEEecCCccccc
Confidence 5554444 799999999988632 23799999999988764
No 83
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.78 E-value=1.8e+02 Score=18.43 Aligned_cols=38 Identities=18% Similarity=0.086 Sum_probs=26.0
Q ss_pred CCCCCCEEEEEeCCCCc-EEEEEEEecCHHHHhcCCcceEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQH-ALAIGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~-~vAVG~~~~ss~e~~~~~kG~av~v~h 57 (70)
-+++||.|.|...+.+. .-+-|+|+-+ -..|..+++..
T Consensus 100 ~V~rG~~V~i~~~~~g~~i~~~G~Al~~------G~~Gd~IrVrN 138 (160)
T PRK06005 100 LVTRGSPVKLVFSAGGLTITAAGTPLQS------GAAGDLIRVRN 138 (160)
T ss_pred EEeCCCEEEEEEecCCEEEEEEEEEccc------CCCCCEEEEEE
Confidence 68899999998876553 5567877443 23666666553
No 84
>PRK08432 flagellar motor switch protein FliY; Validated
Probab=25.70 E-value=64 Score=22.42 Aligned_cols=34 Identities=26% Similarity=0.294 Sum_probs=29.2
Q ss_pred EEEEEEEecCHHHHhcCCcceEEEEEEEeecccc
Q psy15688 31 ALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLW 64 (70)
Q Consensus 31 ~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~LW 64 (70)
-+-+|++.++-+|+.+-+.|-++..-|..+|.+.
T Consensus 211 ~v~lG~~~~~i~dlL~L~~GdVI~Ld~~~~~pv~ 244 (283)
T PRK08432 211 RVRIGQKKMLLKDVLSMDIGSVVELNQLANDPLE 244 (283)
T ss_pred EEEEecCcccHHHHhCCCCCCEEEeCCCCCCcEE
Confidence 4557999999999999999999999888888765
No 85
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2P1G_B 2IM9_A.
Probab=25.00 E-value=63 Score=21.76 Aligned_cols=32 Identities=19% Similarity=0.430 Sum_probs=21.4
Q ss_pred CCCCCCCEEEEEeCCCCc-EEEEEEEecCHHHH
Q psy15688 13 TPVDKGTIVSIMAEGKQH-ALAIGLTTLSTDDI 44 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~~~~-~vAVG~~~~ss~e~ 44 (70)
..++.||+++|++..++- .-=+|.+....+.+
T Consensus 152 ~~i~~GDiI~i~t~~~GLDvsH~Giav~~~~~l 184 (216)
T PF07313_consen 152 SQIKNGDIIAIVTNIKGLDVSHVGIAVWKNDGL 184 (216)
T ss_dssp TTS-TT-EEEEEEECTTECEEEEEEEEEETTEE
T ss_pred hcCCCCCEEEEEeCCCCCceeeEEEEEEECCeE
Confidence 479999999999976543 45578776665553
No 86
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=24.90 E-value=1.3e+02 Score=16.33 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=16.1
Q ss_pred CCCCCCEEEEEeCCC--CcEEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGK--QHALAIGLT 37 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~--~~~vAVG~~ 37 (70)
..+.||.|.|...+. ..++.+|..
T Consensus 43 ~P~iGeqV~v~~~~Gd~~~~~vlg~l 68 (79)
T PF04717_consen 43 PPEIGEQVLVLFPGGDPERPVVLGSL 68 (79)
T ss_dssp ---TT-EEEEEEGGCTTTSEEEEEEE
T ss_pred cCCCCcEEEEEccCCcCCCCEEEEEE
Confidence 357899999988753 679999965
No 87
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=24.67 E-value=1.8e+02 Score=18.06 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=10.9
Q ss_pred CCCCCCEEEEEeC
Q psy15688 14 PVDKGTIVSIMAE 26 (70)
Q Consensus 14 ~~~~G~~V~V~~~ 26 (70)
.+++||.|.+-+.
T Consensus 38 rl~~GDlVFlT~~ 50 (122)
T COG1935 38 RLHEGDLVFLTST 50 (122)
T ss_pred cCCCCCEEEEehh
Confidence 6889999998764
No 88
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.63 E-value=2.4e+02 Score=19.45 Aligned_cols=37 Identities=22% Similarity=0.272 Sum_probs=25.5
Q ss_pred CCCCCCEEEEEeCCCC-cEEEEEEEecCHHHHhcCCcceEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQ-HALAIGLTTLSTDDIVRVNKGIGVENF 56 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~-~~vAVG~~~~ss~e~~~~~kG~av~v~ 56 (70)
-+++||.|.|...+.+ ..-+-|+|+-| ...|..|++.
T Consensus 202 lV~rG~~V~Iva~~gg~~i~~~G~AL~~------G~~Gd~IrVr 239 (261)
T PRK06804 202 LVERGQHVLMIAAQDGIEAQTLGIAQKN------GRKGELIKVK 239 (261)
T ss_pred EEecCCEEEEEEecCCEEEEEEEEEccC------CCCCCEEEEE
Confidence 5889999999887644 35667877543 2366666665
No 89
>PRK02268 hypothetical protein; Provisional
Probab=24.56 E-value=1.6e+02 Score=18.58 Aligned_cols=26 Identities=19% Similarity=0.160 Sum_probs=19.0
Q ss_pred CCCCCCCEEEEEeCC--------CCcEEEEEEEe
Q psy15688 13 TPVDKGTIVSIMAEG--------KQHALAIGLTT 38 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~--------~~~~vAVG~~~ 38 (70)
..+++||-+..++.. -....|||+..
T Consensus 34 ~RmkpGD~ivyYsp~~~~~~~~~~qaftAig~V~ 67 (141)
T PRK02268 34 RRMKPGDWIIYYSPKTTFGGKDKLQAFTAIGKVK 67 (141)
T ss_pred hcCCCCCEEEEEeceEecCCCcccceEEEEEEEc
Confidence 368999999999832 24578888753
No 90
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=24.40 E-value=98 Score=17.28 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=17.5
Q ss_pred CCCCEEEEEeCCCCcEEEEEEEecC
Q psy15688 16 DKGTIVSIMAEGKQHALAIGLTTLS 40 (70)
Q Consensus 16 ~~G~~V~V~~~~~~~~vAVG~~~~s 40 (70)
++|+++.|+...++..++.=....|
T Consensus 11 ~kgdV~rI~~~e~~~~vGyNif~~S 35 (73)
T PF14794_consen 11 RKGDVVRIFDEETGETVGYNIFNAS 35 (73)
T ss_dssp EETTEEEEEE--TTEEEEEEEETGG
T ss_pred EeCCEEEEEecCCCcEEEEEEEccc
Confidence 5799999999657888766655554
No 91
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=23.84 E-value=93 Score=14.70 Aligned_cols=14 Identities=21% Similarity=0.641 Sum_probs=12.1
Q ss_pred CCCCCCEEEEEeCC
Q psy15688 14 PVDKGTIVSIMAEG 27 (70)
Q Consensus 14 ~~~~G~~V~V~~~~ 27 (70)
+|++||.+.|....
T Consensus 20 ~~~~Gd~v~v~~~~ 33 (58)
T smart00326 20 SFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCEEEEEEcC
Confidence 68999999999873
No 92
>PF12913 SH3_6: SH3 domain of the SH3b1 type; PDB: 3M1U_B.
Probab=23.72 E-value=72 Score=16.97 Aligned_cols=19 Identities=32% Similarity=0.576 Sum_probs=12.5
Q ss_pred CcceEEEEEEEeecccccc
Q psy15688 48 NKGIGVENFHYLNDGLWNM 66 (70)
Q Consensus 48 ~kG~av~v~h~~~D~LW~~ 66 (70)
.-|.-|.|+|.-.|.-|.+
T Consensus 24 ~~gtPv~i~H~S~D~~W~f 42 (54)
T PF12913_consen 24 HPGTPVYILHTSRDGAWAF 42 (54)
T ss_dssp -TT-EEEEEEE-TTSSEEE
T ss_pred CCCCCEEEEEECCCCCEEE
Confidence 3677788888888888854
No 93
>PRK08035 type III secretion system protein SsaQ; Validated
Probab=22.96 E-value=2.3e+02 Score=20.44 Aligned_cols=36 Identities=11% Similarity=0.003 Sum_probs=24.6
Q ss_pred CCCEEEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEEEEeec
Q psy15688 17 KGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLND 61 (70)
Q Consensus 17 ~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D 61 (70)
.++.|-|+. |+.++|-|.... .+..-+|++.+.|.+
T Consensus 284 ~~~~VdI~v--NG~~ia~GElV~-------v~~~lGVRIt~~~~~ 319 (323)
T PRK08035 284 FYPEVTIRL--NGRIIGQGELLA-------CDNELMVRITRWYLQ 319 (323)
T ss_pred CCCceEEEE--CCEEEEEEEEEE-------ECCEEEEEEEEeecc
Confidence 455566665 688888886643 444578888887654
No 94
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=22.86 E-value=1.3e+02 Score=15.68 Aligned_cols=14 Identities=14% Similarity=0.328 Sum_probs=10.0
Q ss_pred CCCCCCCEEEEEeC
Q psy15688 13 TPVDKGTIVSIMAE 26 (70)
Q Consensus 13 ~~~~~G~~V~V~~~ 26 (70)
|.|+.||++.|...
T Consensus 12 P~i~~gd~v~i~~~ 25 (84)
T cd06462 12 PTIPDGDLVLVDKS 25 (84)
T ss_pred CcccCCCEEEEEec
Confidence 46778888877754
No 95
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=22.70 E-value=77 Score=17.83 Aligned_cols=13 Identities=38% Similarity=0.675 Sum_probs=11.5
Q ss_pred CCCCCCEEEEEeC
Q psy15688 14 PVDKGTIVSIMAE 26 (70)
Q Consensus 14 ~~~~G~~V~V~~~ 26 (70)
.+++||.|.|.+-
T Consensus 6 ~I~kGD~V~Vi~G 18 (76)
T PRK12281 6 KVKKGDMVKVIAG 18 (76)
T ss_pred cccCCCEEEEeEc
Confidence 6899999999884
No 96
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=22.35 E-value=1e+02 Score=14.37 Aligned_cols=13 Identities=23% Similarity=0.647 Sum_probs=11.6
Q ss_pred CCCCCCEEEEEeC
Q psy15688 14 PVDKGTIVSIMAE 26 (70)
Q Consensus 14 ~~~~G~~V~V~~~ 26 (70)
+|++||.|.|...
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 6899999999886
No 97
>COG2994 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.25 E-value=1.2e+02 Score=19.44 Aligned_cols=32 Identities=9% Similarity=0.184 Sum_probs=24.8
Q ss_pred cCCCCCCCEEEEEeCCCCcEEEEEEEecCHHHH
Q psy15688 12 ITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDI 44 (70)
Q Consensus 12 ~~~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~ 44 (70)
+|.++.|+.+.-.++ ++.|+|.-..+.=+++.
T Consensus 46 LPalk~~Qf~ly~de-~g~Piaf~~WA~vde~~ 77 (148)
T COG2994 46 LPALKLGQFALYFDE-HGRPIAFCTWAFVDEQA 77 (148)
T ss_pred hHHHhcCceEEEEcC-CCCeeEEEEEeecCHHH
Confidence 468899998877765 89999999887655554
No 98
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=22.03 E-value=47 Score=16.27 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=10.7
Q ss_pred CCCCCCEEEEEeCC
Q psy15688 14 PVDKGTIVSIMAEG 27 (70)
Q Consensus 14 ~~~~G~~V~V~~~~ 27 (70)
+|++||.+.|....
T Consensus 15 s~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 15 SFKKGDIIEVLEKS 28 (48)
T ss_dssp EB-TTEEEEEEEES
T ss_pred eEECCCEEEEEEec
Confidence 69999999998753
No 99
>PF08240 ADH_N: Alcohol dehydrogenase GroES-like domain; InterPro: IPR013154 This is the catalytic domain of alcohol dehydrogenases (1.1.1.1 from EC). Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; a name derived from the superfamily of proteins with a GroES fold. Proteins with a GroES fold structure have a highly conserved hydrophobic core and a glycyl-aspartate dipeptide which is thought to maintain the fold [, ].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1YKF_D 2NVB_A 3FSR_D 1BXZ_B 3FTN_A 3MEQ_D 3UOG_B 3HZZ_B 4DVJ_A 1P0F_A ....
Probab=21.64 E-value=91 Score=17.66 Aligned_cols=13 Identities=23% Similarity=0.240 Sum_probs=9.6
Q ss_pred CCCCCCCEEEEEe
Q psy15688 13 TPVDKGTIVSIMA 25 (70)
Q Consensus 13 ~~~~~G~~V~V~~ 25 (70)
.+|++||.|.+..
T Consensus 51 ~~~~~Gd~V~~~~ 63 (109)
T PF08240_consen 51 TDFKVGDRVVVSP 63 (109)
T ss_dssp TSSGTT-EEEEES
T ss_pred ccccccceeeeec
Confidence 4799999999944
No 100
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.62 E-value=1.3e+02 Score=17.03 Aligned_cols=24 Identities=8% Similarity=0.177 Sum_probs=17.0
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecC
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLS 40 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~s 40 (70)
+++.||.|.|.+. .+.. .+.+.++
T Consensus 48 gi~~Gd~V~v~~~-~G~~--~~~v~i~ 71 (116)
T cd02790 48 GIEDGEKVRVSSR-RGSV--EVRARVT 71 (116)
T ss_pred CCCCCCEEEEEcC-CEEE--EEEEEEC
Confidence 7899999999987 5643 3444443
No 101
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=21.44 E-value=1.9e+02 Score=17.14 Aligned_cols=13 Identities=23% Similarity=0.555 Sum_probs=11.2
Q ss_pred CCCCCCEEEEEeC
Q psy15688 14 PVDKGTIVSIMAE 26 (70)
Q Consensus 14 ~~~~G~~V~V~~~ 26 (70)
.|++||.|.|.+-
T Consensus 3 ~ikkGD~V~Vi~G 15 (104)
T TIGR01079 3 KIKKGDTVKVISG 15 (104)
T ss_pred cccCCCEEEEeEc
Confidence 5889999999884
No 102
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=21.36 E-value=1.1e+02 Score=18.96 Aligned_cols=15 Identities=20% Similarity=0.246 Sum_probs=11.9
Q ss_pred CcCCCCCCCEEEEEe
Q psy15688 11 IITPVDKGTIVSIMA 25 (70)
Q Consensus 11 ~~~~~~~G~~V~V~~ 25 (70)
++|+|.+||.|-|..
T Consensus 17 ~iP~f~~GDtvrv~v 31 (115)
T COG0335 17 DIPSFRPGDTVRVHV 31 (115)
T ss_pred hCCCCCCCCEEEEEE
Confidence 468999999987654
No 103
>COG5301 Phage-related tail fibre protein [General function prediction only]
Probab=21.29 E-value=1.5e+02 Score=22.88 Aligned_cols=35 Identities=14% Similarity=0.096 Sum_probs=25.8
Q ss_pred EEEEeCCCCcEEEEEEEecCHHHHhcCCcceEEEEE
Q psy15688 21 VSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENF 56 (70)
Q Consensus 21 V~V~~~~~~~~vAVG~~~~ss~e~~~~~kG~av~v~ 56 (70)
|.+... .+..+|||.|--|++..+..+.|+-.-|+
T Consensus 91 vGlfDa-dG~liavgncPeSYKpqm~eGsgRtqtiR 125 (587)
T COG5301 91 VGLFDA-DGKLIAVGNCPESYKPQMEEGSGRTQTIR 125 (587)
T ss_pred eeeecC-CCCEEEEccCCccccccccCCCCceEEEE
Confidence 344443 68999999999999988887766655443
No 104
>PF14031 D-ser_dehydrat: Putative serine dehydratase domain; PDB: 3LLX_A 3ANV_A 3AWO_A 3AWN_A 3ANU_A 3GWQ_A.
Probab=21.27 E-value=1.2e+02 Score=17.50 Aligned_cols=22 Identities=18% Similarity=0.199 Sum_probs=11.8
Q ss_pred eeecCCCCcCCCCCCCEEEEEe
Q psy15688 4 GLTSPGAIITPVDKGTIVSIMA 25 (70)
Q Consensus 4 GI~~~~~~~~~~~~G~~V~V~~ 25 (70)
|+++..+..+.++.||.|.+.-
T Consensus 56 g~l~~~~~~~~~~vGd~v~iiP 77 (94)
T PF14031_consen 56 GILRLPDGADRLKVGDKVEIIP 77 (94)
T ss_dssp EEEE-STTGCGT-TT-EEEEEE
T ss_pred eEEECCCCCCCCCCCCEEEEEC
Confidence 4555443334588899988864
No 105
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.20 E-value=2.6e+02 Score=18.59 Aligned_cols=37 Identities=27% Similarity=0.195 Sum_probs=25.3
Q ss_pred CCCCCCEEEEEeCCCC-cEEEEEEEecCHHHHhcCCcceEEEEE
Q psy15688 14 PVDKGTIVSIMAEGKQ-HALAIGLTTLSTDDIVRVNKGIGVENF 56 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~-~~vAVG~~~~ss~e~~~~~kG~av~v~ 56 (70)
-+++||.|.|...+.+ ..-+-|+|+-+ ...|..|++.
T Consensus 176 ~V~~G~~V~i~~~~g~~~i~~~G~Al~~------G~~Gd~IrVr 213 (235)
T PRK07018 176 VVCKGQTVSIIARGDGFSVKTEGEALND------GAVGQQIRVR 213 (235)
T ss_pred EeCCCCEEEEEEecCCEEEEEEEEEcCC------CCCCCeEEEE
Confidence 6899999999887644 35566777443 2366666655
No 106
>KOG4078|consensus
Probab=20.82 E-value=73 Score=20.65 Aligned_cols=16 Identities=38% Similarity=0.646 Sum_probs=13.9
Q ss_pred cceEE--EEEEEeecccc
Q psy15688 49 KGIGV--ENFHYLNDGLW 64 (70)
Q Consensus 49 kG~av--~v~h~~~D~LW 64 (70)
+|+.| ++.|+.+|+|+
T Consensus 82 ~gklV~GkIfhiV~~DlY 99 (173)
T KOG4078|consen 82 KGKLVIGKIFHIVEEDLY 99 (173)
T ss_pred CCcEEEeeeeeeeccceE
Confidence 77777 89999999986
No 107
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. 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=20.43 E-value=1.8e+02 Score=17.39 Aligned_cols=23 Identities=13% Similarity=0.208 Sum_probs=15.7
Q ss_pred CCCCCCEEEEEeCCC-CcEEEEEEE
Q psy15688 14 PVDKGTIVSIMAEGK-QHALAIGLT 37 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~-~~~vAVG~~ 37 (70)
-++.||-|.|.+.+. ..|. ||+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~py-IgrI 26 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPY-VARI 26 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCE-EEEE
Confidence 367899999998654 3344 6766
No 108
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=20.42 E-value=97 Score=19.95 Aligned_cols=32 Identities=16% Similarity=0.353 Sum_probs=25.0
Q ss_pred EEEEEEEecCHHHHhcCCcceEEEEEEEeecc
Q psy15688 31 ALAIGLTTLSTDDIVRVNKGIGVENFHYLNDG 62 (70)
Q Consensus 31 ~vAVG~~~~ss~e~~~~~kG~av~v~h~~~D~ 62 (70)
-+-+|++.++-.++..-+.|-++..-+..++.
T Consensus 84 sveLG~t~itlrdLL~L~~GDVI~Ldk~~~ep 115 (155)
T PRK05698 84 SMEVGSTDINIRNLLQLNQGSVIELDRLAGEP 115 (155)
T ss_pred EEEEecCcccHHHHhCCCCCCEEEeCCCCCCC
Confidence 45578999999999988899998876654443
No 109
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=20.36 E-value=2e+02 Score=16.78 Aligned_cols=39 Identities=18% Similarity=0.159 Sum_probs=25.9
Q ss_pred CCCCCCCEEEEEeCCCC-cEEEEEEEecCHHHHhcCCcceEEEEEE
Q psy15688 13 TPVDKGTIVSIMAEGKQ-HALAIGLTTLSTDDIVRVNKGIGVENFH 57 (70)
Q Consensus 13 ~~~~~G~~V~V~~~~~~-~~vAVG~~~~ss~e~~~~~kG~av~v~h 57 (70)
+-+++||.|.|.....+ ..-+-|+|+-| ...|..+++..
T Consensus 64 ~~V~~G~~V~i~~~~~~~~i~~~g~Al~~------g~~G~~I~V~N 103 (122)
T TIGR03170 64 WLVKRGDTVTVIARGGGLSVTTEGKALED------GAVGDQIRVRN 103 (122)
T ss_pred cEEcCCCEEEEEEecCCEEEEEEEEEccc------cCCCCEEEEEE
Confidence 36899999999887544 35667777544 23566666553
No 110
>PF10574 UPF0552: Uncharacterised protein family UPF0552; InterPro: IPR018889 This family of proteins has no known function.
Probab=20.29 E-value=71 Score=21.89 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=22.8
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHh
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIV 45 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~ 45 (70)
+|+.||.|-+.|.+++ ||.--.+.|++....
T Consensus 151 ele~G~~vRlKT~GDs-pFieSlaKlD~~tvt 181 (224)
T PF10574_consen 151 ELELGDEVRLKTRGDS-PFIESLAKLDSGTVT 181 (224)
T ss_pred ecccCCeEEEEecCCc-hhheeeeeeccCceE
Confidence 6899999999999755 666666666655443
No 111
>PRK08433 flagellar motor switch protein; Validated
Probab=20.21 E-value=1e+02 Score=18.64 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=14.6
Q ss_pred EEEEecCHHHHhcCCcceEEEEEEEeec
Q psy15688 34 IGLTTLSTDDIVRVNKGIGVENFHYLND 61 (70)
Q Consensus 34 VG~~~~ss~e~~~~~kG~av~v~h~~~D 61 (70)
+|.+.++-.++...+.|-.+..-+-..|
T Consensus 40 LG~t~itl~dlL~Lq~GDVI~Ld~~~~e 67 (111)
T PRK08433 40 LGTTQISLLEILKFEKGSVIDLEKPAGE 67 (111)
T ss_pred EecccccHHHHhCCCCCCEEEeCCCCCC
Confidence 4555555555555555555554443333
No 112
>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=20.20 E-value=1.2e+02 Score=19.49 Aligned_cols=42 Identities=10% Similarity=0.115 Sum_probs=27.3
Q ss_pred CCCCCCEEEEEeCCCCcEEEEEEEecCHHHHhcCC-cceEEEEEEEee
Q psy15688 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVN-KGIGVENFHYLN 60 (70)
Q Consensus 14 ~~~~G~~V~V~~~~~~~~vAVG~~~~ss~e~~~~~-kG~av~v~h~~~ 60 (70)
-++.||-|.|.+. .+.|..||+.. ++.... .-.-+++..+|.
T Consensus 3 ~yrvGD~Vy~~~~-~~~Py~I~rI~----e~~~~~~~~~~vkV~wfYR 45 (164)
T cd04709 3 MYRVGDYVYFESS-PNNPYLIRRIE----ELNKTARGHVEAKVVCYYR 45 (164)
T ss_pred EEecCCEEEEECC-CCCCCEEEEEE----EEEeCCCCCEEEEEEEEEC
Confidence 4678999999987 67788888774 233333 334456665554
No 113
>PF03454 MoeA_C: MoeA C-terminal region (domain IV); InterPro: IPR005111 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This domain is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known [] and forms an incomplete beta barrel.; GO: 0032324 molybdopterin cofactor biosynthetic process; PDB: 1T3E_A 2FU3_A 2FTS_A 1WU2_A 1XI8_A 2NRS_A 2NRP_B 2NRO_A 2NQV_A 2NQM_B ....
Probab=20.09 E-value=47 Score=17.49 Aligned_cols=12 Identities=17% Similarity=0.429 Sum_probs=8.1
Q ss_pred CCCCCCCEEEEE
Q psy15688 13 TPVDKGTIVSIM 24 (70)
Q Consensus 13 ~~~~~G~~V~V~ 24 (70)
..+++||.|-|.
T Consensus 59 ~~~~~G~~V~v~ 70 (72)
T PF03454_consen 59 EGLEAGEEVEVI 70 (72)
T ss_dssp SEE-TTEEEEEE
T ss_pred CccCCCCEEEEE
Confidence 358888888775
Done!