Query psy15835
Match_columns 116
No_of_seqs 102 out of 1032
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 22:36:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15835hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00084 rpl19 ribosomal prote 100.0 2.5E-34 5.3E-39 208.3 12.1 89 14-108 4-93 (117)
2 PF01245 Ribosomal_L19: Riboso 100.0 4.7E-34 1E-38 205.4 12.2 88 15-108 1-89 (113)
3 PRK05338 rplS 50S ribosomal pr 100.0 3.1E-34 6.7E-39 207.5 11.3 88 15-108 1-89 (116)
4 TIGR01024 rplS_bact ribosomal 100.0 3.9E-34 8.4E-39 206.2 11.3 87 16-108 2-89 (113)
5 COG0335 RplS Ribosomal protein 100.0 6.2E-34 1.3E-38 205.4 11.2 86 16-107 4-90 (115)
6 KOG1698|consensus 100.0 6.2E-31 1.4E-35 204.5 10.8 104 2-108 63-166 (201)
7 PF05641 Agenet: Agenet domain 90.0 1.4 3E-05 28.3 5.6 38 38-80 1-38 (68)
8 smart00743 Agenet Tudor-like d 81.3 10 0.00022 23.2 6.4 47 37-91 2-48 (61)
9 PRK04183 glutamyl-tRNA(Gln) am 66.4 13 0.00028 32.2 5.1 54 38-107 3-56 (419)
10 PF02211 NHase_beta: Nitrile h 66.2 6.5 0.00014 31.3 3.0 54 15-69 113-170 (222)
11 TIGR03170 flgA_cterm flagella 63.0 37 0.00081 23.4 6.1 47 34-85 62-108 (122)
12 PRK08571 rpl14p 50S ribosomal 59.6 29 0.00064 25.7 5.3 35 35-69 44-78 (132)
13 PF02765 POT1: Telomeric singl 59.3 15 0.00032 26.6 3.6 46 34-87 69-116 (146)
14 cd04497 hPOT1_OB1_like hPOT1_O 58.7 29 0.00063 24.9 5.1 48 33-87 64-111 (138)
15 TIGR03673 rpl14p_arch 50S ribo 55.9 36 0.00079 25.2 5.2 35 35-69 43-77 (131)
16 PTZ00054 60S ribosomal protein 53.0 37 0.0008 25.5 4.9 34 35-68 51-84 (139)
17 PF12701 LSM14: Scd6-like Sm d 52.7 77 0.0017 22.1 6.9 61 39-110 6-82 (96)
18 PF12969 DUF3857: Domain of Un 51.6 13 0.00029 26.5 2.3 20 33-52 85-104 (177)
19 PF12961 DUF3850: Domain of Un 51.2 22 0.00049 23.9 3.2 16 37-52 28-43 (72)
20 cd08544 Reeler Reeler, the N-t 51.1 43 0.00092 23.6 4.8 70 37-112 29-108 (135)
21 TIGR01750 fabZ beta-hydroxyacy 48.4 34 0.00074 23.8 4.0 27 38-64 98-124 (140)
22 PF13358 DDE_3: DDE superfamil 48.2 9.3 0.0002 25.6 1.0 42 62-103 81-124 (146)
23 PF13144 SAF_2: SAF-like 48.1 74 0.0016 23.7 5.9 47 33-84 135-181 (196)
24 PRK03999 translation initiatio 47.3 57 0.0012 23.7 5.1 54 33-91 6-59 (129)
25 COG2139 RPL21A Ribosomal prote 47.3 25 0.00054 25.1 3.0 46 35-80 30-79 (98)
26 PF04319 NifZ: NifZ domain; I 44.3 23 0.00051 24.0 2.4 34 36-69 3-36 (75)
27 cd00493 FabA_FabZ FabA/Z, beta 43.5 50 0.0011 22.1 4.1 30 37-66 88-117 (131)
28 cd01288 FabZ FabZ is a 17kD be 42.4 43 0.00093 22.5 3.6 27 38-64 88-114 (131)
29 PRK05483 rplN 50S ribosomal pr 42.4 57 0.0012 23.7 4.4 34 36-69 31-67 (122)
30 PRK07018 flgA flagellar basal 42.0 1E+02 0.0022 24.1 6.1 47 34-85 173-219 (235)
31 cd05704 S1_Rrp5_repeat_hs13 S1 41.9 30 0.00066 21.9 2.6 17 36-52 47-63 (72)
32 PF10447 EXOSC1: Exosome compo 41.4 20 0.00043 24.4 1.8 13 36-48 67-79 (82)
33 PF09269 DUF1967: Domain of un 41.3 45 0.00097 21.6 3.4 31 14-47 33-63 (69)
34 PF11717 Tudor-knot: RNA bindi 40.9 85 0.0018 19.2 4.7 36 38-79 1-36 (55)
35 PRK00006 fabZ (3R)-hydroxymyri 40.7 44 0.00095 23.5 3.6 27 38-64 102-128 (147)
36 PF12945 YcgR_2: Flagellar pro 40.3 95 0.0021 19.6 5.4 32 37-71 47-78 (87)
37 PF09926 DUF2158: Uncharacteri 39.8 20 0.00043 22.6 1.5 10 38-47 1-10 (53)
38 PF00238 Ribosomal_L14: Riboso 39.6 54 0.0012 23.7 3.9 36 34-69 29-67 (122)
39 TIGR01955 RfaH transcriptional 38.6 59 0.0013 23.3 4.0 29 36-70 107-135 (159)
40 COG0250 NusG Transcription ant 38.1 36 0.00079 26.1 2.9 47 14-70 104-150 (178)
41 COG1499 NMD3 NMD protein affec 37.9 21 0.00045 30.4 1.7 15 34-48 243-257 (355)
42 PF12148 DUF3590: Protein of u 37.7 18 0.0004 25.1 1.1 22 35-56 63-84 (85)
43 TIGR01067 rplN_bact ribosomal 37.7 98 0.0021 22.5 5.0 34 36-69 31-67 (122)
44 PRK01191 rpl24p 50S ribosomal 37.6 1.6E+02 0.0035 21.5 6.7 63 31-103 40-104 (120)
45 KOG3409|consensus 35.8 64 0.0014 25.6 4.0 17 34-50 119-135 (193)
46 smart00739 KOW KOW (Kyprides, 34.9 35 0.00075 17.3 1.7 25 38-68 2-26 (28)
47 PF02014 Reeler: Reeler domain 34.5 30 0.00064 24.4 1.8 67 37-111 29-111 (132)
48 PF07238 PilZ: PilZ domain; I 33.6 1.2E+02 0.0026 18.8 5.8 32 37-70 44-75 (102)
49 TIGR00405 L26e_arch ribosomal 33.5 1.8E+02 0.0039 20.7 7.6 32 36-73 85-116 (145)
50 PF07977 FabA: FabA-like domai 33.5 38 0.00083 23.7 2.3 28 37-64 96-127 (138)
51 cd05708 S1_Rrp5_repeat_sc12 S1 33.1 74 0.0016 19.4 3.3 16 37-52 47-62 (77)
52 PTZ00194 60S ribosomal protein 32.8 1.7E+02 0.0036 22.1 5.7 63 31-103 41-105 (143)
53 PF02752 Arrestin_C: Arrestin 32.2 1E+02 0.0022 20.4 4.1 31 37-67 15-46 (136)
54 cd01289 FabA_like Domain of un 32.0 80 0.0017 22.5 3.8 30 36-65 91-121 (138)
55 PRK06005 flgA flagellar basal 31.8 2.1E+02 0.0044 21.4 6.1 48 35-87 98-145 (160)
56 TIGR01956 NusG_myco NusG famil 31.6 2.9E+02 0.0063 22.7 7.3 30 35-70 203-232 (258)
57 TIGR02754 sod_Ni_protease nick 31.5 1.4E+02 0.0029 19.3 4.6 14 35-48 9-22 (90)
58 cd00164 S1_like S1_like: Ribos 31.2 75 0.0016 18.0 3.0 15 37-51 41-55 (65)
59 cd03451 FkbR2 FkbR2 is a Strep 31.2 78 0.0017 21.8 3.5 15 38-52 92-106 (146)
60 PRK00276 infA translation init 30.9 77 0.0017 20.5 3.2 25 38-68 47-71 (72)
61 PF05697 Trigger_N: Bacterial 30.9 62 0.0013 23.1 3.0 26 17-42 23-48 (145)
62 cd05686 S1_pNO40 S1_pNO40: pNO 30.7 70 0.0015 20.1 3.0 15 38-52 49-63 (73)
63 cd05698 S1_Rrp5_repeat_hs6_sc5 30.5 99 0.0021 18.8 3.6 16 37-52 44-59 (70)
64 PF14326 DUF4384: Domain of un 30.4 60 0.0013 21.2 2.7 16 36-51 1-16 (83)
65 PRK15136 multidrug efflux syst 30.3 1.2E+02 0.0026 25.3 5.1 32 34-68 262-293 (390)
66 cd05688 S1_RPS1_repeat_ec3 S1_ 30.2 66 0.0014 19.0 2.7 16 37-52 44-59 (68)
67 cd01737 LSm16_N LSm16 belongs 30.2 1.6E+02 0.0036 19.4 4.6 28 39-71 4-31 (62)
68 TIGR03595 Obg_CgtA_exten Obg f 29.3 68 0.0015 20.8 2.8 29 16-47 35-63 (69)
69 cd05690 S1_RPS1_repeat_ec5 S1_ 28.9 74 0.0016 19.2 2.8 20 37-56 45-65 (69)
70 COG2030 MaoC Acyl dehydratase 28.8 67 0.0015 23.5 3.0 16 37-52 106-121 (159)
71 COG2100 Predicted Fe-S oxidore 28.8 2.7E+02 0.0059 24.4 6.9 38 32-69 345-385 (414)
72 PF14438 SM-ATX: Ataxin 2 SM d 28.7 1.3E+02 0.0029 19.2 4.1 36 39-80 10-45 (77)
73 cd04452 S1_IF2_alpha S1_IF2_al 28.6 96 0.0021 19.0 3.3 14 38-51 50-63 (76)
74 PRK04424 fatty acid biosynthes 28.4 1E+02 0.0022 23.3 3.9 27 38-64 139-165 (185)
75 cd05706 S1_Rrp5_repeat_sc10 S1 28.1 1.1E+02 0.0024 18.8 3.5 16 37-52 47-62 (73)
76 PF08605 Rad9_Rad53_bind: Fung 28.1 33 0.00072 25.3 1.2 13 36-48 58-70 (131)
77 CHL00057 rpl14 ribosomal prote 28.0 1.6E+02 0.0035 21.4 4.8 34 36-69 31-67 (122)
78 cd06462 Peptidase_S24_S26 The 28.0 1.5E+02 0.0032 18.1 5.2 43 35-85 11-53 (84)
79 cd04471 S1_RNase_R S1_RNase_R: 27.7 1E+02 0.0022 19.1 3.3 17 36-52 56-72 (83)
80 COG1566 EmrA Multidrug resista 27.7 1.4E+02 0.003 25.4 5.0 56 33-91 254-318 (352)
81 PF11325 DUF3127: Domain of un 27.5 64 0.0014 22.2 2.5 17 36-52 51-67 (84)
82 COG0425 SirA Predicted redox p 27.4 35 0.00076 22.7 1.1 45 36-80 27-76 (78)
83 PF00386 C1q: C1q domain; Int 27.3 1.1E+02 0.0024 20.9 3.8 29 37-65 94-127 (127)
84 PF15344 FAM217: FAM217 family 27.1 29 0.00063 28.3 0.8 10 1-10 47-56 (233)
85 smart00276 GLECT Galectin. Gal 27.1 1.2E+02 0.0027 21.1 4.0 49 34-82 4-57 (128)
86 PF08206 OB_RNB: Ribonuclease 26.8 1.6E+02 0.0034 18.1 4.3 25 39-66 33-57 (58)
87 cd05691 S1_RPS1_repeat_ec6 S1_ 26.7 1.2E+02 0.0026 18.3 3.5 16 37-52 44-59 (73)
88 cd05696 S1_Rrp5_repeat_hs4 S1_ 26.6 1E+02 0.0022 19.3 3.2 16 37-52 46-61 (71)
89 cd04491 SoSSB_OBF SoSSB_OBF: A 26.5 1.2E+02 0.0026 19.3 3.6 24 35-58 46-70 (82)
90 smart00316 S1 Ribosomal protei 25.5 1.3E+02 0.0028 17.3 3.3 16 37-52 46-61 (72)
91 cd05692 S1_RPS1_repeat_hs4 S1_ 25.3 1.1E+02 0.0024 17.8 3.1 14 38-51 45-58 (69)
92 TIGR02266 gmx_TIGR02266 Myxoco 25.2 1.9E+02 0.0042 18.5 6.5 34 37-71 36-69 (96)
93 COG5496 Predicted thioesterase 25.2 2.1E+02 0.0046 21.4 5.0 27 39-65 72-98 (130)
94 TIGR01000 bacteriocin_acc bact 25.2 1.9E+02 0.0041 24.6 5.4 69 33-105 367-439 (457)
95 cd05697 S1_Rrp5_repeat_hs5 S1_ 24.8 1.3E+02 0.0027 18.4 3.3 16 37-52 44-59 (69)
96 PF15493 YrpD: Domain of unkno 24.7 3E+02 0.0065 22.1 6.1 47 35-81 93-141 (208)
97 KOG3416|consensus 24.6 44 0.00096 25.1 1.3 20 37-62 61-80 (134)
98 PF11604 CusF_Ec: Copper bindi 24.6 1.1E+02 0.0024 19.7 3.1 23 32-54 37-59 (70)
99 cd00070 GLECT Galectin/galacto 24.5 1.5E+02 0.0032 20.6 4.0 25 34-58 5-30 (127)
100 PRK04306 50S ribosomal protein 24.3 97 0.0021 22.0 3.0 44 36-79 33-80 (98)
101 PHA02561 D tail protein; Provi 24.2 3E+02 0.0064 22.3 6.2 50 34-83 298-348 (351)
102 PRK06763 F0F1 ATP synthase sub 24.1 52 0.0011 26.5 1.7 14 37-50 164-177 (213)
103 cd05703 S1_Rrp5_repeat_hs12_sc 24.1 1.1E+02 0.0024 19.4 3.1 22 37-58 46-68 (73)
104 PF07154 DUF1392: Protein of u 24.1 69 0.0015 24.5 2.3 49 34-98 84-132 (150)
105 COG5636 Uncharacterized conser 23.8 54 0.0012 27.0 1.8 18 33-50 258-275 (284)
106 cd05791 S1_CSL4 S1_CSL4: CSL4, 23.3 67 0.0014 21.7 1.9 15 37-51 60-74 (92)
107 PF13437 HlyD_3: HlyD family s 22.8 2.3E+02 0.0049 18.4 5.5 33 33-69 45-78 (105)
108 PRK06461 single-stranded DNA-b 22.8 1.2E+02 0.0027 21.6 3.3 12 36-47 63-74 (129)
109 cd05685 S1_Tex S1_Tex: The C-t 22.6 1.2E+02 0.0026 17.7 2.8 15 38-52 45-59 (68)
110 PF07076 DUF1344: Protein of u 22.5 1.1E+02 0.0024 20.0 2.7 24 32-55 32-55 (61)
111 COG1096 Predicted RNA-binding 22.4 2E+02 0.0044 22.7 4.7 36 36-71 117-155 (188)
112 TIGR00192 urease_beta urease, 22.1 94 0.002 22.3 2.6 33 32-64 60-97 (101)
113 cd05705 S1_Rrp5_repeat_hs14 S1 21.9 1.2E+02 0.0027 19.3 2.9 21 37-57 50-71 (74)
114 PRK12786 flgA flagellar basal 21.8 3.4E+02 0.0074 22.8 6.2 48 35-87 256-303 (338)
115 cd05794 S1_EF-P_repeat_2 S1_EF 21.8 51 0.0011 21.0 1.1 18 34-51 33-51 (56)
116 cd05687 S1_RPS1_repeat_ec1_hs1 21.7 1.6E+02 0.0034 17.9 3.3 15 37-51 44-58 (70)
117 PF03061 4HBT: Thioesterase su 21.7 1.4E+02 0.003 17.8 3.1 23 38-60 44-66 (79)
118 cd05707 S1_Rrp5_repeat_sc11 S1 21.7 1.4E+02 0.003 18.1 3.1 15 38-52 45-59 (68)
119 PRK13203 ureB urease subunit b 21.6 96 0.0021 22.3 2.5 33 32-64 60-97 (102)
120 cd05684 S1_DHX8_helicase S1_DH 21.5 1.3E+02 0.0027 19.0 2.9 16 37-52 48-63 (79)
121 COG3269 Predicted RNA-binding 21.3 2.7E+02 0.0059 18.8 7.2 56 31-86 6-64 (73)
122 cd05689 S1_RPS1_repeat_ec4 S1_ 21.2 1.4E+02 0.003 18.3 3.0 16 37-52 48-63 (72)
123 PF04411 DUF524: Protein of un 21.0 1.6E+02 0.0034 21.0 3.6 40 74-114 46-87 (154)
124 PF06819 Arc_PepC: Archaeal Pe 20.9 1.4E+02 0.003 21.7 3.3 36 16-54 15-50 (110)
125 cd05702 S1_Rrp5_repeat_hs11_sc 20.9 1.1E+02 0.0024 18.8 2.5 15 37-51 46-60 (70)
126 cd04455 S1_NusA S1_NusA: N-uti 20.8 1.5E+02 0.0032 18.3 3.0 16 37-52 40-55 (67)
127 PRK08515 flgA flagellar basal 20.8 3.5E+02 0.0075 21.2 5.8 45 34-84 162-206 (222)
128 TIGR00008 infA translation ini 20.7 97 0.0021 20.5 2.2 15 38-52 45-59 (68)
129 PF01472 PUA: PUA domain; Int 20.6 69 0.0015 20.5 1.5 14 36-49 29-42 (74)
130 PF05093 CIAPIN1: Cytokine-ind 20.6 48 0.001 23.6 0.8 13 33-45 87-99 (100)
131 cd04454 S1_Rrp4_like S1_Rrp4_l 20.4 1.5E+02 0.0031 18.9 3.1 17 36-52 49-65 (82)
132 smart00110 C1Q Complement comp 20.4 1.9E+02 0.0042 20.8 4.0 32 35-66 97-133 (135)
133 cd01735 LSm12_N LSm12 belongs 20.3 1.7E+02 0.0036 19.0 3.3 26 38-69 3-28 (61)
134 cd03442 BFIT_BACH Brown fat-in 20.3 2E+02 0.0044 18.6 3.8 27 37-63 63-89 (123)
135 TIGR00038 efp translation elon 20.1 4E+02 0.0087 20.3 6.3 46 37-94 5-55 (184)
No 1
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00 E-value=2.5e-34 Score=208.32 Aligned_cols=89 Identities=20% Similarity=0.324 Sum_probs=84.4
Q ss_pred hHHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecC-CCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEc
Q psy15835 14 RNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTG 92 (116)
Q Consensus 14 ~~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~ 92 (116)
++++++.+|.+++ +.++|+|++||||+|++++.| +++|+|.|+|+||+++|+|+++||||||+++|+|||++|
T Consensus 4 ~~~~i~~~~~~~~-----~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~f- 77 (117)
T CHL00084 4 LQQLVKEIESEFL-----KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVF- 77 (117)
T ss_pred HHHHHHHHHHHHh-----hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEE-
Confidence 5779999999999 458999999999999999997 679999999999999999999999999999999999999
Q ss_pred cccCCCcceEEEeecC
Q psy15835 93 DRHGPYLSLLGALGLD 108 (116)
Q Consensus 93 pl~SP~I~~IeVl~~~ 108 (116)
|+|||.|++|+|+++.
T Consensus 78 pl~SP~I~~IeV~r~g 93 (117)
T CHL00084 78 LLHSPKLASIEVLRRS 93 (117)
T ss_pred ecCCCccceEEEEEeC
Confidence 9999999999999864
No 2
>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=100.00 E-value=4.7e-34 Score=205.39 Aligned_cols=88 Identities=27% Similarity=0.437 Sum_probs=83.5
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecC-CCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEcc
Q psy15835 15 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTGD 93 (116)
Q Consensus 15 ~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~p 93 (116)
|+||+.+|++++ +.++|+|++||+|+|++.+.| +++|+|.|+|+||+++++|++|||||||+++|+|||++| |
T Consensus 1 ~~~i~~~e~~~~-----~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f-~ 74 (113)
T PF01245_consen 1 MNLIEEVEREQI-----KKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVF-P 74 (113)
T ss_dssp -HHHHHHHHTTC-----SSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEE-E
T ss_pred ChHHHHHHHHHh-----hcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEE-E
Confidence 689999999999 569999999999999999996 789999999999999999999999999999999999999 9
Q ss_pred ccCCCcceEEEeecC
Q psy15835 94 RHGPYLSLLGALGLD 108 (116)
Q Consensus 94 l~SP~I~~IeVl~~~ 108 (116)
+|||.|++|+|+++.
T Consensus 75 l~SP~I~~IeV~~~~ 89 (113)
T PF01245_consen 75 LYSPLIKSIEVLRRG 89 (113)
T ss_dssp TTSTTEEEEEEEEEB
T ss_pred cCCCCeEEEEEEEec
Confidence 999999999999864
No 3
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00 E-value=3.1e-34 Score=207.51 Aligned_cols=88 Identities=20% Similarity=0.361 Sum_probs=83.1
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecC-CCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEcc
Q psy15835 15 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTGD 93 (116)
Q Consensus 15 ~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~p 93 (116)
+++|+.+|++++ +.++|+|++||+|+|++++.+ +++|+|.|+|+||+++|+|+++||||||+++|+|||++| |
T Consensus 1 ~~~i~~~~~~~~-----~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~f-p 74 (116)
T PRK05338 1 MNLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTF-P 74 (116)
T ss_pred CcHHHHHHHHHh-----hcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEe-c
Confidence 358999999999 458999999999999999997 789999999999999999999999999999999999999 9
Q ss_pred ccCCCcceEEEeecC
Q psy15835 94 RHGPYLSLLGALGLD 108 (116)
Q Consensus 94 l~SP~I~~IeVl~~~ 108 (116)
+|||.|++|+|+++.
T Consensus 75 l~SP~I~~IeV~r~g 89 (116)
T PRK05338 75 LHSPRIDSIEVVRRG 89 (116)
T ss_pred CCCCcccEEEEEEec
Confidence 999999999999763
No 4
>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=100.00 E-value=3.9e-34 Score=206.22 Aligned_cols=87 Identities=20% Similarity=0.376 Sum_probs=82.9
Q ss_pred HHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecC-CCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEccc
Q psy15835 16 QVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTGDR 94 (116)
Q Consensus 16 ~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~pl 94 (116)
++|+.+|++++ +.++|+|++||+|+|++++.| +++|+|.|+|+||+++|+|+++||||||+++|+|||++| |+
T Consensus 2 ~~i~~~e~~~~-----~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~f-pl 75 (113)
T TIGR01024 2 NLIKQIEQEQL-----KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIF-PL 75 (113)
T ss_pred cHHHHHHHHHh-----hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEE-Ec
Confidence 58999999999 568999999999999999998 789999999999999999999999999999999999999 99
Q ss_pred cCCCcceEEEeecC
Q psy15835 95 HGPYLSLLGALGLD 108 (116)
Q Consensus 95 ~SP~I~~IeVl~~~ 108 (116)
|||.|++|+|+.+.
T Consensus 76 ~SP~I~~IeVl~~~ 89 (113)
T TIGR01024 76 HSPNIDSIEVVRRG 89 (113)
T ss_pred CCCccceEEEEEeC
Confidence 99999999999764
No 5
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.2e-34 Score=205.39 Aligned_cols=86 Identities=23% Similarity=0.415 Sum_probs=82.5
Q ss_pred HHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecC-CCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEccc
Q psy15835 16 QVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTGDR 94 (116)
Q Consensus 16 ~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~pl 94 (116)
.+|+.||++|+.+ ++|+|+|||||+|++++.| +++|+|.|+|+||+++|+|+++||||||+++|+|||++| |+
T Consensus 4 ~~i~~le~~q~~~-----~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~F-p~ 77 (115)
T COG0335 4 PIIQQLEQEQIKK-----DIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVF-PL 77 (115)
T ss_pred HHHHHHHHHHHHh-----hCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEe-ec
Confidence 5999999999954 7999999999999999997 789999999999999999999999999999999999999 99
Q ss_pred cCCCcceEEEeec
Q psy15835 95 HGPYLSLLGALGL 107 (116)
Q Consensus 95 ~SP~I~~IeVl~~ 107 (116)
|||.|++|+|+++
T Consensus 78 ~SP~Ie~IeV~rr 90 (115)
T COG0335 78 HSPLIESIEVVRR 90 (115)
T ss_pred CCCceeEEEEEec
Confidence 9999999999976
No 6
>KOG1698|consensus
Probab=99.97 E-value=6.2e-31 Score=204.46 Aligned_cols=104 Identities=39% Similarity=0.674 Sum_probs=98.3
Q ss_pred CCCCCCCccchhhHHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeee
Q psy15835 2 YQEFLPDPELKFRNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV 81 (116)
Q Consensus 2 ~~~~~p~~~~~~~~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni 81 (116)
|++|.|.+.. ..++++.||+++|+.++..+++|+|++||+|+|++.+++++.++.+|.|+||+++|+|+++||+|||+
T Consensus 63 ~~~f~~~~~~--~~~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~atf~LRnv 140 (201)
T KOG1698|consen 63 YPEFLPLRKV--AKRIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLNATFLLRNV 140 (201)
T ss_pred CcccccchhH--HHHHHHhhCHHHHHHHHhcccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCCcceEEeeeh
Confidence 6778877766 55699999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeeeeEEEccccCCCcceEEEeecC
Q psy15835 82 VDNLGAVPCTGDRHGPYLSLLGALGLD 108 (116)
Q Consensus 82 ~~gvGVEr~f~pl~SP~I~~IeVl~~~ 108 (116)
+.|+|||.+| |||||+|++|+|+...
T Consensus 141 IagvGVEi~~-pLYsP~IkeI~Vlk~~ 166 (201)
T KOG1698|consen 141 IAGVGVEIVF-PLYSPNIKEIKVLKLE 166 (201)
T ss_pred hhCceeEEEE-eccCCCeeEEEEechh
Confidence 9999999999 9999999999999753
No 7
>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=89.96 E-value=1.4 Score=28.34 Aligned_cols=38 Identities=16% Similarity=0.248 Sum_probs=25.6
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEee
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 80 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRn 80 (116)
|++||.|+|.... +.-+..=|.|+|++..+.+ +|.|+-
T Consensus 1 F~~G~~VEV~s~e--~g~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDE--DGFRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-S--BTT--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEcC--CCCCcEEEEEEEEEeCCCc---EEEEEE
Confidence 7899999998644 3347889999999999887 777775
No 8
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=81.28 E-value=10 Score=23.24 Aligned_cols=47 Identities=11% Similarity=0.139 Sum_probs=35.2
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEE
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCT 91 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f 91 (116)
.|++||.|.+.+.. .-.=|.|+|++..+ +..|.|+=...+.|-+.++
T Consensus 2 ~~~~G~~Ve~~~~~-----~~~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v 48 (61)
T smart00743 2 DFKKGDRVEVFSKE-----EDSWWEAVVTKVLG---DGKYLVRYLTESEPLKETV 48 (61)
T ss_pred CcCCCCEEEEEECC-----CCEEEEEEEEEECC---CCEEEEEECCCCcccEEEE
Confidence 58999999999864 23577899999877 4468887765457766666
No 9
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=66.45 E-value=13 Score=32.17 Aligned_cols=54 Identities=20% Similarity=0.137 Sum_probs=33.2
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEccccCCCcceEEEeec
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTGDRHGPYLSLLGALGL 107 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~pl~SP~I~~IeVl~~ 107 (116)
+.+||.|+|.... ..|+|+++-... +-.-...|.|= +++|+.+-- |++||++.+
T Consensus 3 ~~~gd~v~~~~~~-------~~~~g~~~p~~~-~~~~~~kl~~g-yn~g~~~~~-------~~~~~~~~~ 56 (419)
T PRK04183 3 MEVGDRVRVEKDD-------VVYEGILMPSYE-DDHIVIKLDNG-YNIGIDIDK-------IAEIELLEK 56 (419)
T ss_pred CCCCCEEEEEECC-------eEEEEEEecCCC-CCEEEEEcCCC-ceeeecccc-------ccceEEccc
Confidence 6789999997543 799999997766 11222223332 336665444 566666654
No 10
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=66.19 E-value=6.5 Score=31.34 Aligned_cols=54 Identities=26% Similarity=0.324 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecCCCceeeeEE----EEEEEEec
Q psy15835 15 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFV----GICIQKRY 69 (116)
Q Consensus 15 ~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e~k~r~q~F~----Gv~Ia~r~ 69 (116)
.++...|.+-+=.+| -...-|.|.+||.|+|.-.....-.|...|. |+|.+.++
T Consensus 113 ~~v~~~l~~G~p~~r-~~~~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 113 DQVAAALARGDPADR-PVDAPPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp HHHHHHHHH----EE-TTSSS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEE
T ss_pred HHHHHHhhcCCCccC-CCCCCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEec
Confidence 345555555543333 2335789999999999988777778887764 77776654
No 11
>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=62.96 E-value=37 Score=23.38 Aligned_cols=47 Identities=9% Similarity=-0.062 Sum_probs=35.3
Q ss_pred CCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCe
Q psy15835 34 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNL 85 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gv 85 (116)
.-|-++-||.|.+.+.... -..+--..|..+..++.++.+||...|-
T Consensus 62 ~~~~V~~G~~V~i~~~~~~-----~~i~~~g~Al~~g~~G~~I~V~N~~s~k 108 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGG-----LSVTTEGKALEDGAVGDQIRVRNLSSGK 108 (122)
T ss_pred CccEEcCCCEEEEEEecCC-----EEEEEEEEEccccCCCCEEEEEECCCCC
Confidence 3467899999999987643 2233566788899999999999975543
No 12
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=59.60 E-value=29 Score=25.75 Aligned_cols=35 Identities=14% Similarity=0.296 Sum_probs=28.2
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEec
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRY 69 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~ 69 (116)
+|.-.+||++.|.++......+.+.+.++++..+.
T Consensus 44 ~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 78 (132)
T PRK08571 44 LPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQRK 78 (132)
T ss_pred CCccccCCEEEEEEEECCCcccCCEeEEEEEEecc
Confidence 46778999999999876545677999999998653
No 13
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=59.32 E-value=15 Score=26.65 Aligned_cols=46 Identities=13% Similarity=0.188 Sum_probs=30.9
Q ss_pred CCCCcCC-CCEEEEE-EEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeee
Q psy15835 34 DIPSFFV-GSILSVT-SADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGA 87 (116)
Q Consensus 34 ~iP~f~~-GD~v~V~-~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGV 87 (116)
.+|.... ||+|.++ ++ +|.|.|-..+..+.+-+++|-|= ..++.|.
T Consensus 69 ~LP~v~~~GDii~l~r~k-------v~~~~~~~~~~~~~~~~ss~~vf-~~~~~~~ 116 (146)
T PF02765_consen 69 SLPNVKSVGDIIRLRRVK-------VQSYNGKPQGLSNSTSNSSWAVF-SSGGSGA 116 (146)
T ss_dssp HSCTTCSTTHEEEEEEEE-------EEEETTEEEEEEECECTEEEEEE-CTSSTTT
T ss_pred HCCCCCCCCCEEEEEEEE-------EEEECCEEEEEecCCCcEEEEEE-ecCCCCC
Confidence 4788888 9999998 44 46666665566666667777766 3344443
No 14
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=58.69 E-value=29 Score=24.94 Aligned_cols=48 Identities=13% Similarity=0.092 Sum_probs=34.2
Q ss_pred CCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeee
Q psy15835 33 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGA 87 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGV 87 (116)
..+|...+||+|.++=.- +|.|.|-..+..+. -.++|-|=+-..+...
T Consensus 64 ~~LP~v~~GDVIll~~~k------v~~~~g~~~~~~~~-~~ss~avf~~~~~~~~ 111 (138)
T cd04497 64 ESLPIVKVGDIILLRRVK------IQSYNGKPQGISND-RGSSWAVFRGDDGVVP 111 (138)
T ss_pred hhCCCCCCCCEEEEEEEE------EEEECCceEEEECC-CceeEEEEcCCCCCCc
Confidence 468988999999998543 78888887777766 4566766554444443
No 15
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=55.85 E-value=36 Score=25.22 Aligned_cols=35 Identities=17% Similarity=0.346 Sum_probs=27.8
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEec
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRY 69 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~ 69 (116)
+|...+||++.|.++......+.+.+.|+++..+.
T Consensus 43 ~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtkk 77 (131)
T TIGR03673 43 LPCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQRK 77 (131)
T ss_pred CCccccCCEEEEEEEECCccccCCEeEEEEEEeCc
Confidence 46678999999999875545667899999998663
No 16
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=53.00 E-value=37 Score=25.50 Aligned_cols=34 Identities=18% Similarity=0.329 Sum_probs=28.0
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEe
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 68 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r 68 (116)
+|...+||++.|.++.....++.+.+.++++..+
T Consensus 51 ~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVRtK 84 (139)
T PTZ00054 51 LPSASLGDMVLATVKKGKPELRKKVLNAVIIRQR 84 (139)
T ss_pred CcccccCCEEEEEEEECCCcccCCEeeEEEEEEC
Confidence 4677899999999987655567799999999865
No 17
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=52.67 E-value=77 Score=22.13 Aligned_cols=61 Identities=20% Similarity=0.214 Sum_probs=42.7
Q ss_pred CCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeee-cCCe---------------eeeEEEccccCCCcceE
Q psy15835 39 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV-VDNL---------------GAVPCTGDRHGPYLSLL 102 (116)
Q Consensus 39 ~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni-~~gv---------------GVEr~f~pl~SP~I~~I 102 (116)
..|..|.+..+. --+|+|++..+-. -++|++|+|+ ..|. --..+| ..-.|+.+
T Consensus 6 ~IGs~ISlisk~------~iRYeG~L~~Id~--~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~F---r~sDIkdL 74 (96)
T PF12701_consen 6 YIGSKISLISKS------DIRYEGILYSIDT--EDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVF---RGSDIKDL 74 (96)
T ss_dssp CTTCEEEEEETT------TEEEEEEEEEEET--TTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEE---ETTTEEEE
T ss_pred ccCCEEEEEECC------CcEEEEEEEEEcC--CCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEE---EccccceE
Confidence 478888887543 2589999998875 5789999998 4665 112233 67789999
Q ss_pred EEeecCCc
Q psy15835 103 GALGLDPK 110 (116)
Q Consensus 103 eVl~~~p~ 110 (116)
+|+.-.+.
T Consensus 75 ~v~e~~~~ 82 (96)
T PF12701_consen 75 KVIEPPPP 82 (96)
T ss_dssp EECE-S-S
T ss_pred EEEcCCCC
Confidence 99887653
No 18
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=51.58 E-value=13 Score=26.47 Aligned_cols=20 Identities=25% Similarity=0.376 Sum_probs=13.1
Q ss_pred CCCCCcCCCCEEEEEEEecC
Q psy15835 33 IDIPSFFVGSILSVTSADKH 52 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i~e 52 (116)
..+|.+++||+|...+.+..
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~ 104 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKS 104 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE
T ss_pred EEcCCCCCCcEEEEEEEEEe
Confidence 57999999999999999864
No 19
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=51.25 E-value=22 Score=23.90 Aligned_cols=16 Identities=38% Similarity=0.515 Sum_probs=13.1
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
+|++||++...-+..+
T Consensus 28 df~VGD~L~L~E~~~~ 43 (72)
T PF12961_consen 28 DFQVGDILVLREWDNG 43 (72)
T ss_pred CCCCCCEEEEEEecCC
Confidence 4899999999887643
No 20
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=51.11 E-value=43 Score=23.55 Aligned_cols=70 Identities=19% Similarity=0.150 Sum_probs=44.0
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCC---CceeEEEeee-----cCCeeeeEEEccccC--CCcceEEEee
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCG---LRHEFVLRNV-----VDNLGAVPCTGDRHG--PYLSLLGALG 106 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~G---l~stFtlRni-----~~gvGVEr~f~pl~S--P~I~~IeVl~ 106 (116)
.+.+|+.+.|++..... ..|.|..|.-|+.+ .--+|+...- +...+. ... -.|+ -.-.++.+.+
T Consensus 29 ~y~pG~~~~Vtl~~~~~----~~F~GF~lqAr~~~~~~~vG~f~~~~~~~tk~~~c~~~-~~a-vtH~~~~~k~~v~~~W 102 (135)
T cd08544 29 SYVPGETYTVTLSGSSP----SPFRGFLLQARDASSNEPVGTFQLPPDSGTKLLTCCGS-DNA-VTHSNNSKKTSVTFTW 102 (135)
T ss_pred EECCCCEEEEEEECCCC----CceeEEEEEEEcCCCCcceEEEEeCCCcccEEecCCCC-CCc-ceeCCCCCCceeEEEE
Confidence 68999999999887554 79999999988865 3355665542 222221 111 1233 3445677888
Q ss_pred cCCccc
Q psy15835 107 LDPKIV 112 (116)
Q Consensus 107 ~~p~~~ 112 (116)
..|.-.
T Consensus 103 ~AP~~~ 108 (135)
T cd08544 103 TAPSNG 108 (135)
T ss_pred ECCCCC
Confidence 877643
No 21
>TIGR01750 fabZ beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ. This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains.
Probab=48.38 E-value=34 Score=23.83 Aligned_cols=27 Identities=22% Similarity=0.209 Sum_probs=19.8
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEE
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGIC 64 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~ 64 (116)
.+|||++.++.++.....+.-.|.|.+
T Consensus 98 v~pGd~l~i~~~i~~~~~~~~~~~~~~ 124 (140)
T TIGR01750 98 VVPGDQLILHAEFLKKRRKIGKFKGEA 124 (140)
T ss_pred cCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 578999999999876545555666654
No 22
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=48.24 E-value=9.3 Score=25.60 Aligned_cols=42 Identities=10% Similarity=0.044 Sum_probs=37.0
Q ss_pred EEEEEEecCCCceeEEEeeecCC--eeeeEEEccccCCCcceEE
Q psy15835 62 GICIQKRYCGLRHEFVLRNVVDN--LGAVPCTGDRHGPYLSLLG 103 (116)
Q Consensus 62 Gv~Ia~r~~Gl~stFtlRni~~g--vGVEr~f~pl~SP~I~~Ie 103 (116)
++++---|...+++=.++..+.. .|++..|.|-|||.+.=||
T Consensus 81 ~~~li~DNa~~H~~~~~~~~l~~~~~~~~~~~~P~~sPdLNpiE 124 (146)
T PF13358_consen 81 RIVLIMDNASIHKSKKVQEWLEEHERGIELLFLPPYSPDLNPIE 124 (146)
T ss_pred EEEEecccccccccccccceeeccccccccccccCcCCccCHHH
Confidence 78888889999999889998888 9999999999999987665
No 23
>PF13144 SAF_2: SAF-like
Probab=48.11 E-value=74 Score=23.67 Aligned_cols=47 Identities=13% Similarity=0.044 Sum_probs=34.9
Q ss_pred CCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCC
Q psy15835 33 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDN 84 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~g 84 (116)
...|..+-||.|.|.+.... -...--.+|..+..++.++.|||...|
T Consensus 135 ~~~~~V~~G~~V~v~~~~g~-----i~i~~~g~Al~~G~~G~~I~V~N~~S~ 181 (196)
T PF13144_consen 135 EPPPLVKRGDIVTVIARSGG-----ISISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred ccceecCCCCEEEEEEEeCC-----EEEEEEEEEccCCCCCCEEEEEECCCC
Confidence 34578899999998887633 223345678889999999999997544
No 24
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=47.32 E-value=57 Score=23.68 Aligned_cols=54 Identities=13% Similarity=0.139 Sum_probs=31.6
Q ss_pred CCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEE
Q psy15835 33 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCT 91 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f 91 (116)
...++|+.|++|... +..=.+..+.-.--.++ .+.--.+.+||+..|--.|.+|
T Consensus 6 ~~~~~lrkG~~i~~~----g~p~~V~~~~~~kpGkh-g~a~vr~k~knL~tG~~~e~~~ 59 (129)
T PRK03999 6 VEVGELKEGSYVVID----GEPCKIVEISKSKPGKH-GSAKARIVAIGIFDGQKRSLVQ 59 (129)
T ss_pred ccHHHccCCCEEEEC----CEEEEEEEEEeecCCCC-CcEEEEEEEEECCCCCEEEEEe
Confidence 356789999999643 11111111111111111 2235667799999999999999
No 25
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=47.29 E-value=25 Score=25.13 Aligned_cols=46 Identities=13% Similarity=0.133 Sum_probs=33.5
Q ss_pred CCCcCCCCEEEEEEEec--C--CCceeeeEEEEEEEEecCCCceeEEEee
Q psy15835 35 IPSFFVGSILSVTSADK--H--DPNKTRKFVGICIQKRYCGLRHEFVLRN 80 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~--e--~k~r~q~F~Gv~Ia~r~~Gl~stFtlRn 80 (116)
+-+|++||.|-+.+.=+ . --.|.|=..|+|+.++++...-...+.+
T Consensus 30 l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~ 79 (98)
T COG2139 30 LQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGN 79 (98)
T ss_pred HhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCC
Confidence 56899999998887533 2 2278888999999999876655544333
No 26
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=44.27 E-value=23 Score=23.96 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=22.8
Q ss_pred CCcCCCCEEEEEEEecCCCceeeeEEEEEEEEec
Q psy15835 36 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRY 69 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~ 69 (116)
|.|..||.|++.-.+..+.+=...-.|-++++++
T Consensus 3 p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~~G 36 (75)
T PF04319_consen 3 PRFEWGDKVRARKDIRNDGTFPGKEIGELLVRKG 36 (75)
T ss_pred CccCCCCEEEEEEEeEcCCCCCCCCCCCEEEcCC
Confidence 7899999999998886544322333455666554
No 27
>cd00493 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface.
Probab=43.50 E-value=50 Score=22.06 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=21.9
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEE
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQ 66 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia 66 (116)
...+||++.+++++.+.......|.+.+..
T Consensus 88 ~v~pgd~l~i~~~i~~~~~~~~~~~~~~~~ 117 (131)
T cd00493 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAYV 117 (131)
T ss_pred CcCCCCEEEEEEEEEEeeCCEEEEEEEEEE
Confidence 357999999999987655566677666543
No 28
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=42.45 E-value=43 Score=22.53 Aligned_cols=27 Identities=19% Similarity=0.091 Sum_probs=20.2
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEE
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGIC 64 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~ 64 (116)
..+||++.+..++.+...+.-.|.+.+
T Consensus 88 v~pgd~l~i~~~v~~~~~~~~~~~~~~ 114 (131)
T cd01288 88 VVPGDQLILEVELLKLRRGIGKFKGKA 114 (131)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 468999999999876555566666655
No 29
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=42.44 E-value=57 Score=23.74 Aligned_cols=34 Identities=9% Similarity=0.172 Sum_probs=26.0
Q ss_pred CCcCCCCEEEEEEEecC--C-CceeeeEEEEEEEEec
Q psy15835 36 PSFFVGSILSVTSADKH--D-PNKTRKFVGICIQKRY 69 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e--~-k~r~q~F~Gv~Ia~r~ 69 (116)
+.-.+||++.|.++-.. . -++.+.+.|+++..+.
T Consensus 31 ~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T PRK05483 31 RYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEecc
Confidence 45689999999997543 2 3567899999998663
No 30
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=41.98 E-value=1e+02 Score=24.13 Aligned_cols=47 Identities=9% Similarity=-0.007 Sum_probs=34.7
Q ss_pred CCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCe
Q psy15835 34 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNL 85 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gv 85 (116)
.-|-++-||.|.|.+.... -...--..|..+.+++.++.|||...|-
T Consensus 173 ~~~~V~~G~~V~i~~~~g~-----~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGDG-----FSVKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred CccEeCCCCEEEEEEecCC-----EEEEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 4567899999999987632 1223456778899999999999976553
No 31
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=41.92 E-value=30 Score=21.92 Aligned_cols=17 Identities=24% Similarity=0.294 Sum_probs=13.6
Q ss_pred CCcCCCCEEEEEEEecC
Q psy15835 36 PSFFVGSILSVTSADKH 52 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e 52 (116)
..|++||.|++.+.-..
T Consensus 47 ~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 47 EGFKPGKIVRCCILSKK 63 (72)
T ss_pred HhCCCCCEEEEEEEEec
Confidence 34899999999986654
No 32
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=41.40 E-value=20 Score=24.37 Aligned_cols=13 Identities=23% Similarity=0.335 Sum_probs=8.3
Q ss_pred CCcCCCCEEEEEE
Q psy15835 36 PSFFVGSILSVTS 48 (116)
Q Consensus 36 P~f~~GD~v~V~~ 48 (116)
-.|+|||+|+=.+
T Consensus 67 ~~FrpGDIVrA~V 79 (82)
T PF10447_consen 67 DCFRPGDIVRARV 79 (82)
T ss_dssp GT--SSSEEEEEE
T ss_pred hccCCCCEEEEEE
Confidence 3599999998654
No 33
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=41.29 E-value=45 Score=21.61 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEE
Q psy15835 14 RNQVREKLERSDMIKRRSVIDIPSFFVGSILSVT 47 (116)
Q Consensus 14 ~~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~ 47 (116)
...+.+.|++.-+.+...+..+ +.||+|++.
T Consensus 33 ~~rf~~~L~~~Gv~~~L~~~G~---~~GD~V~Ig 63 (69)
T PF09269_consen 33 LRRFQRKLKKMGVEKALRKAGA---KEGDTVRIG 63 (69)
T ss_dssp HHHHHHHHHHTTHHHHHHTTT-----TT-EEEET
T ss_pred HHHHHHHHHHCCHHHHHHHcCC---CCCCEEEEc
Confidence 4456666666666665556664 799999874
No 34
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=40.86 E-value=85 Score=19.17 Aligned_cols=36 Identities=14% Similarity=0.131 Sum_probs=25.1
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEe
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLR 79 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlR 79 (116)
|.+|+.|.+.. +..+.+.+-|++++..+-...|.|-
T Consensus 1 ~~vG~~v~~~~------~~~~~y~A~I~~~r~~~~~~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKY------KDGQWYEAKILDIREKNGEPEYYVH 36 (55)
T ss_dssp --TTEEEEEEE------TTTEEEEEEEEEEEECTTCEEEEEE
T ss_pred CCcCCEEEEEE------CCCcEEEEEEEEEEecCCCEEEEEE
Confidence 57899998887 2246888999999886655555543
No 35
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=40.73 E-value=44 Score=23.53 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=19.5
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEE
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGIC 64 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~ 64 (116)
.++||+|.++.++.+.+.+.-.|.+-+
T Consensus 102 v~pGd~l~i~~~i~~~~~~~v~~~~~~ 128 (147)
T PRK00006 102 VVPGDQLILEVELLKQRRGIWKFKGVA 128 (147)
T ss_pred cCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 369999999999876555555666655
No 36
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=40.27 E-value=95 Score=19.57 Aligned_cols=32 Identities=13% Similarity=0.017 Sum_probs=23.8
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCC
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCG 71 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~G 71 (116)
-|+.|+.|.|.+....+ .-.|+..|+++....
T Consensus 47 ~l~~g~~v~v~~~~~~~---~y~F~s~V~~~~~~p 78 (87)
T PF12945_consen 47 PLREGEEVIVRFISEDG---VYAFKSKVIGRISEP 78 (87)
T ss_dssp CS-TT-EEEEEEEE-SC---EEEEEEEEEEEE-SS
T ss_pred eecCCCEEEEEEEECCe---EEEEEEEEEEEEcCC
Confidence 47899999999998766 889999999987543
No 37
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=39.84 E-value=20 Score=22.58 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=8.4
Q ss_pred cCCCCEEEEE
Q psy15835 38 FFVGSILSVT 47 (116)
Q Consensus 38 f~~GD~v~V~ 47 (116)
|++||+|...
T Consensus 1 f~~GDvV~LK 10 (53)
T PF09926_consen 1 FKIGDVVQLK 10 (53)
T ss_pred CCCCCEEEEc
Confidence 7899999875
No 38
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=39.59 E-value=54 Score=23.68 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=26.8
Q ss_pred CCCCcCCCCEEEEEEEec--C-CCceeeeEEEEEEEEec
Q psy15835 34 DIPSFFVGSILSVTSADK--H-DPNKTRKFVGICIQKRY 69 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~--e-~k~r~q~F~Gv~Ia~r~ 69 (116)
..+...+||+|.|.++-. . .-++.+.+.|+++..+.
T Consensus 29 ~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~ 67 (122)
T PF00238_consen 29 RRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKK 67 (122)
T ss_dssp TTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSS
T ss_pred CccccccceEEEEEEeecccCccccccceEEEEEEEEeE
Confidence 345678999999999765 3 33566899999998765
No 39
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=38.57 E-value=59 Score=23.31 Aligned_cols=29 Identities=14% Similarity=0.140 Sum_probs=20.9
Q ss_pred CCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecC
Q psy15835 36 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 70 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~ 70 (116)
..|.+||.|+|.-=- .+-|+|++....++
T Consensus 107 ~~~~~G~~V~V~~GP------f~g~~g~v~~~~~~ 135 (159)
T TIGR01955 107 TLPYKGDKVRITDGA------FAGFEAIFLEPDGE 135 (159)
T ss_pred cCCCCCCEEEEeccC------CCCcEEEEEEECCC
Confidence 458999999886321 45688998888643
No 40
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=38.09 E-value=36 Score=26.08 Aligned_cols=47 Identities=11% Similarity=0.007 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecC
Q psy15835 14 RNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 70 (116)
Q Consensus 14 ~~~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~ 70 (116)
.++++..++..+. ......+|.+||.|+|.-=- ..-|.|.+....+.
T Consensus 104 i~~~l~~~~~~~~----~~~~~~~~e~Gd~VrI~~Gp------Fa~f~g~V~evd~e 150 (178)
T COG0250 104 IEHILGFLEEEVA----PKKPKVDFEPGDVVRIIDGP------FAGFKAKVEEVDEE 150 (178)
T ss_pred HHHHHhhcccccc----CCcccccCCCCCEEEEeccC------CCCccEEEEEEcCc
Confidence 3446666665522 13345689999999987322 23467788877665
No 41
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=37.93 E-value=21 Score=30.43 Aligned_cols=15 Identities=47% Similarity=0.716 Sum_probs=13.4
Q ss_pred CCCCcCCCCEEEEEE
Q psy15835 34 DIPSFFVGSILSVTS 48 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~ 48 (116)
.||+|++||+|.+.-
T Consensus 243 rip~~~~gDiV~~~~ 257 (355)
T COG1499 243 RIPEFRPGDIVSVRG 257 (355)
T ss_pred ECCCCCCCCEEEECC
Confidence 489999999999874
No 42
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=37.69 E-value=18 Score=25.08 Aligned_cols=22 Identities=14% Similarity=0.185 Sum_probs=13.9
Q ss_pred CCCcCCCCEEEEEEEecCCCce
Q psy15835 35 IPSFFVGSILSVTSADKHDPNK 56 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r 56 (116)
.-++.+|++|.|.|.+.+-++|
T Consensus 63 w~~L~VG~~VMvNYN~d~P~er 84 (85)
T PF12148_consen 63 WDELKVGQVVMVNYNVDEPKER 84 (85)
T ss_dssp GGG--TT-EEEEEE-TTSTTS-
T ss_pred HHhCCcccEEEEecCCCCcccC
Confidence 3478999999999998876665
No 43
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=37.68 E-value=98 Score=22.49 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=26.1
Q ss_pred CCcCCCCEEEEEEEecC--C-CceeeeEEEEEEEEec
Q psy15835 36 PSFFVGSILSVTSADKH--D-PNKTRKFVGICIQKRY 69 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e--~-k~r~q~F~Gv~Ia~r~ 69 (116)
+.-.+||++.|.++-.. . -++.+.+.|+++..+.
T Consensus 31 ~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk 67 (122)
T TIGR01067 31 RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKK 67 (122)
T ss_pred CccccCCEEEEEEEEcCCCCccccccEEEEEEEEeec
Confidence 45689999999998543 2 3567899999998663
No 44
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=37.65 E-value=1.6e+02 Score=21.53 Aligned_cols=63 Identities=11% Similarity=0.068 Sum_probs=34.2
Q ss_pred cCCCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeee--cCCeeeeEEEccccCCCcceEE
Q psy15835 31 SVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV--VDNLGAVPCTGDRHGPYLSLLG 103 (116)
Q Consensus 31 ~~~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni--~~gvGVEr~f~pl~SP~I~~Ie 103 (116)
..+.+ .++.||.|.|..=-..++ +|.|+++-...- ..+|-++ ....|.|+-. |+|..++.=+.
T Consensus 40 ~ir~~-~IkkGD~V~VisG~~KGk------~GkV~~V~~~~~--~V~VeGvn~~k~~G~~~e~-pIh~SNV~l~~ 104 (120)
T PRK01191 40 GIRSL-PVRKGDTVKVMRGDFKGE------EGKVVEVDLKRG--RIYVEGVTVKKADGTEVPR-PIHPSNVMITK 104 (120)
T ss_pred CCccc-eEeCCCEEEEeecCCCCc------eEEEEEEEcCCC--EEEEeCcEEECCCCeEEEc-ccchhHeEEEe
Confidence 34444 589999999874221111 266666533211 2222211 1124578888 99988775443
No 45
>KOG3409|consensus
Probab=35.82 E-value=64 Score=25.59 Aligned_cols=17 Identities=24% Similarity=0.192 Sum_probs=13.1
Q ss_pred CCCCcCCCCEEEEEEEe
Q psy15835 34 DIPSFFVGSILSVTSAD 50 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i 50 (116)
-+-.|+|||+|.-.+.-
T Consensus 119 v~ksFrPgDiVlAkVis 135 (193)
T KOG3409|consen 119 VYKSFRPGDIVLAKVIS 135 (193)
T ss_pred hhhccCCCcEEEEEEee
Confidence 35679999999877654
No 46
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=34.87 E-value=35 Score=17.32 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=15.7
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEEEEEe
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGICIQKR 68 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r 68 (116)
|.+||.|+|.-=. ..-+.|++++..
T Consensus 2 ~~~G~~V~I~~G~------~~g~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIAGP------FKGKVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeECC------CCCcEEEEEEEc
Confidence 6899999998522 123356666554
No 47
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=34.49 E-value=30 Score=24.40 Aligned_cols=67 Identities=18% Similarity=0.181 Sum_probs=36.4
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCc-----eeEEEee-----ecCCe------eeeEEEccccCCCcc
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLR-----HEFVLRN-----VVDNL------GAVPCTGDRHGPYLS 100 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~-----stFtlRn-----i~~gv------GVEr~f~pl~SP~I~ 100 (116)
.+.+|+.+.|++ +......|+|..|.-+..... -+|.+-. ....+ .|.. --.++. .
T Consensus 29 ~y~pg~~~~Vtl----~~~~~~~F~GFllqAr~~~~~~~~~vG~f~~~~~~~~~~~~~C~~~~~~avTH---~~~~~K-~ 100 (132)
T PF02014_consen 29 SYEPGQTYTVTL----SSSGSSSFRGFLLQARDANNSSPAPVGTFQLPPDSDTTQLLDCSGGDNNAVTH---SNNSPK-T 100 (132)
T ss_dssp SB-TTBEEEEEE----EETTTEEBSEEEEEEEETT--SSSBSSEEEES-TTTEEEETTE----EEEEEE---SS-S-B-S
T ss_pred eEcCCCEEEEEE----ECCCCCceeEEEEEEEeCCCCCcccccccCcCCcccceEeecccccccceEEe---cCCCCc-c
Confidence 579999999999 233457899988887754433 3454331 11222 2222 222333 6
Q ss_pred eEEEeecCCcc
Q psy15835 101 LLGALGLDPKI 111 (116)
Q Consensus 101 ~IeVl~~~p~~ 111 (116)
++++.+..|.-
T Consensus 101 ~v~~~W~AP~~ 111 (132)
T PF02014_consen 101 SVTFTWTAPAD 111 (132)
T ss_dssp EEEEEEE--ST
T ss_pred EEEEEEcCCCC
Confidence 78888888864
No 48
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=33.58 E-value=1.2e+02 Score=18.80 Aligned_cols=32 Identities=6% Similarity=-0.041 Sum_probs=24.1
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 70 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~ 70 (116)
.+.+||.+.+.+.......-. +.|.|+..++.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~~--~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFPI--VTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSCEE--EEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCeeE--EEEEEEEEECC
Confidence 578999999999887655533 88999988877
No 49
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=33.50 E-value=1.8e+02 Score=20.74 Aligned_cols=32 Identities=16% Similarity=0.050 Sum_probs=22.3
Q ss_pred CCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCc
Q psy15835 36 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLR 73 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~ 73 (116)
..|.+||.|+|.-=- .+-|+|.+++..+....
T Consensus 85 ~~~~~Gd~V~I~~GP------f~G~~g~v~~~d~~k~~ 116 (145)
T TIGR00405 85 ESIKKGDIVEIISGP------FKGERAKVIRVDESKEE 116 (145)
T ss_pred cccCCCCEEEEeecC------CCCCeEEEEEEcCCCCE
Confidence 459999999997311 34677888888764443
No 50
>PF07977 FabA: FabA-like domain; InterPro: IPR013114 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes []. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. This enzyme domain has a HotDog fold.; PDB: 3D6X_F 2GLV_J 2GLM_E 2GLP_E 2GLL_C 1U1Z_F 3ESI_A 3AZB_T 3AZA_M 3AZ9_U ....
Probab=33.49 E-value=38 Score=23.70 Aligned_cols=28 Identities=18% Similarity=0.262 Sum_probs=19.2
Q ss_pred CcCCCC-EEEEEEEecC---CCceeeeEEEEE
Q psy15835 37 SFFVGS-ILSVTSADKH---DPNKTRKFVGIC 64 (116)
Q Consensus 37 ~f~~GD-~v~V~~~i~e---~k~r~q~F~Gv~ 64 (116)
...||| ++++++.+.+ .......|.|.+
T Consensus 96 ~v~Pg~~~l~~~v~i~~~~~~~~~~~~~~~~~ 127 (138)
T PF07977_consen 96 PVYPGDKTLRIEVEIKKIRRREGGMAIFDGTA 127 (138)
T ss_dssp -B-TTE-EEEEEEEEEEEEEEETTEEEEEEEE
T ss_pred cEeCCCcEEEEEEEEEEeecccCCEEEEEEEE
Confidence 467999 9999988876 555566666654
No 51
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=33.10 E-value=74 Score=19.41 Aligned_cols=16 Identities=19% Similarity=0.179 Sum_probs=12.6
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.|+|.+.-..
T Consensus 47 ~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 47 LFRVGDKVRAKVLKID 62 (77)
T ss_pred eecCCCEEEEEEEEEe
Confidence 4799999999976543
No 52
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=32.85 E-value=1.7e+02 Score=22.14 Aligned_cols=63 Identities=8% Similarity=-0.017 Sum_probs=32.8
Q ss_pred cCCCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeee--cCCeeeeEEEccccCCCcceEE
Q psy15835 31 SVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV--VDNLGAVPCTGDRHGPYLSLLG 103 (116)
Q Consensus 31 ~~~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni--~~gvGVEr~f~pl~SP~I~~Ie 103 (116)
..+.+ .++.||+|.|-.=...++ +|.|+++-...- .+.|-.+ ....|-..-+ |+|..++.=+.
T Consensus 41 ~~Rs~-~IkkGD~V~Vi~Gk~KGk------~GkV~~V~~k~~--~ViVEgvn~~Kk~gk~~e~-PIh~SNV~iv~ 105 (143)
T PTZ00194 41 NVRSM-PVRKDDEVMVVRGHHKGR------EGKVTAVYRKKW--VIHIEKITREKANGEPVQI-GIHPSNVIITK 105 (143)
T ss_pred CCccc-eeecCCEEEEecCCCCCC------ceEEEEEEcCCC--EEEEeCeEEEecCCCEeec-CcCchheEEEc
Confidence 34455 489999999874222121 277777643321 2322221 1122333455 89988775443
No 53
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=32.24 E-value=1e+02 Score=20.44 Aligned_cols=31 Identities=13% Similarity=0.261 Sum_probs=20.0
Q ss_pred CcCCCCEEEEEEEecC-CCceeeeEEEEEEEE
Q psy15835 37 SFFVGSILSVTSADKH-DPNKTRKFVGICIQK 67 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~ 67 (116)
.|.+||++.|++.+.. .+.+++...--++.+
T Consensus 15 ~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~~ 46 (136)
T PF02752_consen 15 AYVPGETIPVNVEIDNQSKKKIKKIKVSLVER 46 (136)
T ss_dssp EEETT--EEEEEEEEE-SSSEEEEEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCCCEEEEEEEEEEEE
Confidence 4789999999999974 455666665444443
No 54
>cd01289 FabA_like Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ.
Probab=31.99 E-value=80 Score=22.49 Aligned_cols=30 Identities=20% Similarity=0.133 Sum_probs=20.6
Q ss_pred CCcCCCCEEEEEEEecCCCc-eeeeEEEEEE
Q psy15835 36 PSFFVGSILSVTSADKHDPN-KTRKFVGICI 65 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e~k~-r~q~F~Gv~I 65 (116)
|.+.+||++.++++...... ..-.|.|.+.
T Consensus 91 ~v~p~Gd~l~i~~~~~~~~~~~~~~~~~~~~ 121 (138)
T cd01289 91 DRFDLGSTLLIVVAELLQGDSGLGVFECTIE 121 (138)
T ss_pred ceeCCCCeeEEEeeeeeeCCCcEEEEEEEEE
Confidence 33455999999988766553 6777777643
No 55
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.81 E-value=2.1e+02 Score=21.44 Aligned_cols=48 Identities=10% Similarity=-0.044 Sum_probs=33.5
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeee
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGA 87 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGV 87 (116)
-|-++-||.|.+.+.... + .-.---.|..+.+.+..+.+||...|-=|
T Consensus 98 p~~V~rG~~V~i~~~~~g----~-~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv 145 (160)
T PRK06005 98 PSLVTRGSPVKLVFSAGG----L-TITAAGTPLQSGAAGDLIRVRNVDSGVIV 145 (160)
T ss_pred CcEEeCCCEEEEEEecCC----E-EEEEEEEEcccCCCCCEEEEEECCCCCEE
Confidence 456888999999887643 1 12234457778899999999997665433
No 56
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=31.63 E-value=2.9e+02 Score=22.75 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=23.0
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecC
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 70 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~ 70 (116)
.+.|.+||.|+|.-=- .+-|.|++......
T Consensus 203 ~~~f~vGd~VrI~dGP------F~GfeG~I~eid~~ 232 (258)
T TIGR01956 203 LSKFRVGNFVKIVDGP------FKGIVGKIKKIDQE 232 (258)
T ss_pred ccCCCCCCEEEEEecC------CCCcEEEEEEEeCC
Confidence 4569999999998433 56788898888753
No 57
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=31.49 E-value=1.4e+02 Score=19.30 Aligned_cols=14 Identities=21% Similarity=0.316 Sum_probs=11.9
Q ss_pred CCCcCCCCEEEEEE
Q psy15835 35 IPSFFVGSILSVTS 48 (116)
Q Consensus 35 iP~f~~GD~v~V~~ 48 (116)
.|.|+.||+|-|.-
T Consensus 9 ~P~l~~GD~vlv~~ 22 (90)
T TIGR02754 9 SPTLPPGDRIIVVP 22 (90)
T ss_pred cCccCCCCEEEEEE
Confidence 58899999998874
No 58
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=31.24 E-value=75 Score=18.04 Aligned_cols=15 Identities=27% Similarity=0.330 Sum_probs=12.6
Q ss_pred CcCCCCEEEEEEEec
Q psy15835 37 SFFVGSILSVTSADK 51 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~ 51 (116)
.|++||+|++.+.-.
T Consensus 41 ~~~~G~~v~~~v~~~ 55 (65)
T cd00164 41 VFKVGDEVEVKVLEV 55 (65)
T ss_pred EeCCCCEEEEEEEEE
Confidence 489999999998754
No 59
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=31.18 E-value=78 Score=21.84 Aligned_cols=15 Identities=27% Similarity=0.239 Sum_probs=12.6
Q ss_pred cCCCCEEEEEEEecC
Q psy15835 38 FFVGSILSVTSADKH 52 (116)
Q Consensus 38 f~~GD~v~V~~~i~e 52 (116)
.++||+|.++..+.+
T Consensus 92 v~~GDtl~~~~~v~~ 106 (146)
T cd03451 92 VFHGDTLYAESEVLS 106 (146)
T ss_pred CCCCCEEEEEEEEEE
Confidence 689999999888764
No 60
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.91 E-value=77 Score=20.49 Aligned_cols=25 Identities=12% Similarity=0.107 Sum_probs=16.6
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEEEEEe
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGICIQKR 68 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r 68 (116)
..+||.|.|+.+..+.. +|.+|.+.
T Consensus 47 i~vGD~V~ve~~~~~~~------~g~Iv~r~ 71 (72)
T PRK00276 47 ILPGDKVTVELSPYDLT------KGRITYRH 71 (72)
T ss_pred cCCCCEEEEEEcccCCC------eEEEEEEe
Confidence 47999999997664322 36666553
No 61
>PF05697 Trigger_N: Bacterial trigger factor protein (TF); InterPro: IPR008881 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This group of sequences contain the ribosomal subunit association domain.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 2D3O_1 1W26_A 1P9Y_A 1OMS_C 1T11_A 3GU0_A 2NSB_A 2NSC_A 3GTY_X.
Probab=30.89 E-value=62 Score=23.06 Aligned_cols=26 Identities=23% Similarity=0.272 Sum_probs=17.7
Q ss_pred HHHHHHHHHhhhhhcCCCCCCcCCCC
Q psy15835 17 VREKLERSDMIKRRSVIDIPSFFVGS 42 (116)
Q Consensus 17 li~~ler~~~~~r~~~~~iP~f~~GD 42 (116)
-++..-++.+.+.+.+..+|.||+|-
T Consensus 23 ~~~~~~~~~l~~~~k~~~ipGFRkGK 48 (145)
T PF05697_consen 23 EVEKAYEKALKELAKKVKIPGFRKGK 48 (145)
T ss_dssp HHHHHHHHHHHHHHTTTTBTTS-TTS
T ss_pred HHHHHHHHHHHHHHhhCCCCCCCCCC
Confidence 34455556666667778999999994
No 62
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=30.70 E-value=70 Score=20.08 Aligned_cols=15 Identities=20% Similarity=0.160 Sum_probs=12.4
Q ss_pred cCCCCEEEEEEEecC
Q psy15835 38 FFVGSILSVTSADKH 52 (116)
Q Consensus 38 f~~GD~v~V~~~i~e 52 (116)
|+.||.|+|.+.-..
T Consensus 49 ~~~Gd~v~vkv~~vd 63 (73)
T cd05686 49 VDVGEKVWVKVIGRE 63 (73)
T ss_pred ECCCCEEEEEEEEEC
Confidence 799999999986544
No 63
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.47 E-value=99 Score=18.75 Aligned_cols=16 Identities=25% Similarity=0.380 Sum_probs=13.1
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.++|.+.-..
T Consensus 44 ~~~~G~~i~v~v~~~d 59 (70)
T cd05698 44 HFRVGQVVKVKVLSCD 59 (70)
T ss_pred cccCCCEEEEEEEEEc
Confidence 3899999999987654
No 64
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=30.38 E-value=60 Score=21.18 Aligned_cols=16 Identities=13% Similarity=0.235 Sum_probs=13.6
Q ss_pred CCcCCCCEEEEEEEec
Q psy15835 36 PSFFVGSILSVTSADK 51 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~ 51 (116)
|.|+.||.|++.+...
T Consensus 1 ~~~~~Ge~v~~~~~~~ 16 (83)
T PF14326_consen 1 TVYRVGERVRFRVTSN 16 (83)
T ss_pred CcccCCCEEEEEEEeC
Confidence 4689999999999873
No 65
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=30.33 E-value=1.2e+02 Score=25.32 Aligned_cols=32 Identities=16% Similarity=0.217 Sum_probs=23.0
Q ss_pred CCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEe
Q psy15835 34 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 68 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r 68 (116)
++..+++|+.+.|++-.-.+. ..|.|.|..+.
T Consensus 262 ~l~~v~~Gq~V~I~~da~p~~---~~~~G~V~~I~ 293 (390)
T PRK15136 262 QLANMRIGQPATITSDIYGDD---VVYTGKVVGLD 293 (390)
T ss_pred HHhcCCCCCEEEEEEecCCCC---ceEEEEEEEEC
Confidence 456789999999987543221 36999999883
No 66
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=30.24 E-value=66 Score=19.00 Aligned_cols=16 Identities=19% Similarity=0.125 Sum_probs=12.9
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.|+|.+.-..
T Consensus 44 ~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 44 VVNVGDEVEVKVLKID 59 (68)
T ss_pred EECCCCEEEEEEEEEE
Confidence 3899999999986543
No 67
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=30.23 E-value=1.6e+02 Score=19.37 Aligned_cols=28 Identities=18% Similarity=0.311 Sum_probs=19.7
Q ss_pred CCCCEEEEEEEecCCCceeeeEEEEEEEEecCC
Q psy15835 39 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCG 71 (116)
Q Consensus 39 ~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~G 71 (116)
..|+.|+++- .+..-.|.|.+.+....-
T Consensus 4 WiGs~VSI~C-----~~~lGVyQG~i~~V~~~~ 31 (62)
T cd01737 4 WLGSIVSINC-----GETLGVYQGLVSAVDQES 31 (62)
T ss_pred ccceEEEEec-----CCceEEEEEEEEEeCccc
Confidence 3677777763 344679999998887644
No 68
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=29.33 E-value=68 Score=20.79 Aligned_cols=29 Identities=10% Similarity=0.090 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEE
Q psy15835 16 QVREKLERSDMIKRRSVIDIPSFFVGSILSVT 47 (116)
Q Consensus 16 ~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~ 47 (116)
.+...|.+.-+.++..+..+ +.||+|++.
T Consensus 35 ~f~~~L~~~Gv~~~L~~~G~---~~GD~V~Ig 63 (69)
T TIGR03595 35 RFARKLKKLGVEDALRKAGA---KDGDTVRIG 63 (69)
T ss_pred HHHHHHHHCCHHHHHHHcCC---CCCCEEEEc
Confidence 34455555555555445554 799999986
No 69
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=28.90 E-value=74 Score=19.15 Aligned_cols=20 Identities=5% Similarity=0.139 Sum_probs=14.3
Q ss_pred CcCCCCEEEEEEEecC-CCce
Q psy15835 37 SFFVGSILSVTSADKH-DPNK 56 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e-~k~r 56 (116)
.|++||.|+|.+.-.. .++|
T Consensus 45 ~~~~G~~v~v~v~~id~~~~~ 65 (69)
T cd05690 45 IYKKGQEVEAVVLNIDVERER 65 (69)
T ss_pred EECCCCEEEEEEEEEECCcCE
Confidence 4899999999976543 4444
No 70
>COG2030 MaoC Acyl dehydratase [Lipid metabolism]
Probab=28.83 E-value=67 Score=23.49 Aligned_cols=16 Identities=19% Similarity=0.216 Sum_probs=13.7
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
...+||+|++...+.+
T Consensus 106 PV~~Gdtl~~~~~v~~ 121 (159)
T COG2030 106 PVFPGDTLRARVEVLD 121 (159)
T ss_pred CCCCCCEEEEEEEEEE
Confidence 3689999999998865
No 71
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=28.77 E-value=2.7e+02 Score=24.41 Aligned_cols=38 Identities=11% Similarity=-0.006 Sum_probs=23.9
Q ss_pred CCCCC-CcCCCCEEEEEEEecC--CCceeeeEEEEEEEEec
Q psy15835 32 VIDIP-SFFVGSILSVTSADKH--DPNKTRKFVGICIQKRY 69 (116)
Q Consensus 32 ~~~iP-~f~~GD~v~V~~~i~e--~k~r~q~F~Gv~Ia~r~ 69 (116)
+..+| .|+.||+|++.+-..+ ..+-...-.+-+|+.-+
T Consensus 345 Rp~lp~PF~rGevv~aevV~~Gr~kGEmlavArdRvIav~~ 385 (414)
T COG2100 345 RPRLPKPFKRGEVVKAEVVLPGRLKGEMLAVARDRVIAVIN 385 (414)
T ss_pred CCCCCCccccCcEEEEEEEecceecceEEEEecccEEEEec
Confidence 34577 5999999999998865 22333333344555443
No 72
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=28.72 E-value=1.3e+02 Score=19.22 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=22.5
Q ss_pred CCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEee
Q psy15835 39 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 80 (116)
Q Consensus 39 ~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRn 80 (116)
-+|-.|.|+++. -..|+|+.-+-.-.+-...+.|+.
T Consensus 10 lvG~~V~V~~~~------G~~yeGif~s~s~~~~~~~vvLk~ 45 (77)
T PF14438_consen 10 LVGQTVEVTTKN------GSVYEGIFHSASPESNEFDVVLKM 45 (77)
T ss_dssp TTTSEEEEEETT------S-EEEEEEEEE-T---T--EEEEE
T ss_pred CcCCEEEEEECC------CCEEEEEEEeCCCcccceeEEEEe
Confidence 379999999776 458999998877655456666644
No 73
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=28.60 E-value=96 Score=19.02 Aligned_cols=14 Identities=21% Similarity=0.012 Sum_probs=11.8
Q ss_pred cCCCCEEEEEEEec
Q psy15835 38 FFVGSILSVTSADK 51 (116)
Q Consensus 38 f~~GD~v~V~~~i~ 51 (116)
|++||+|+|.+.-.
T Consensus 50 ~~~Gd~v~vkv~~~ 63 (76)
T cd04452 50 VKVGRKEVVKVIRV 63 (76)
T ss_pred eCCCCEEEEEEEEE
Confidence 79999999997653
No 74
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=28.39 E-value=1e+02 Score=23.34 Aligned_cols=27 Identities=4% Similarity=-0.105 Sum_probs=18.9
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEE
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGIC 64 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~ 64 (116)
..|||+|.++.++.+.+.+.-.+.+.+
T Consensus 139 V~pGD~L~~ea~v~~~~~~~~~v~~~~ 165 (185)
T PRK04424 139 VKLGERVVAKAEVVRKKGNKYIVEVKS 165 (185)
T ss_pred CCCCCEEEEEEEEEEccCCEEEEEEEE
Confidence 579999999999876555444554443
No 75
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.12 E-value=1.1e+02 Score=18.77 Aligned_cols=16 Identities=13% Similarity=0.111 Sum_probs=12.9
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||+|++.+.-..
T Consensus 47 ~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 47 KFKKNDIVRACVLSVD 62 (73)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3899999999986543
No 76
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=28.06 E-value=33 Score=25.30 Aligned_cols=13 Identities=15% Similarity=0.317 Sum_probs=10.9
Q ss_pred CCcCCCCEEEEEE
Q psy15835 36 PSFFVGSILSVTS 48 (116)
Q Consensus 36 P~f~~GD~v~V~~ 48 (116)
=++|+||+|+|..
T Consensus 58 LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 58 LDLRIGDTVKVDG 70 (131)
T ss_pred eeeecCCEEEECC
Confidence 3689999999975
No 77
>CHL00057 rpl14 ribosomal protein L14
Probab=28.01 E-value=1.6e+02 Score=21.44 Aligned_cols=34 Identities=3% Similarity=0.079 Sum_probs=26.1
Q ss_pred CCcCCCCEEEEEEEecC--C-CceeeeEEEEEEEEec
Q psy15835 36 PSFFVGSILSVTSADKH--D-PNKTRKFVGICIQKRY 69 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e--~-k~r~q~F~Gv~Ia~r~ 69 (116)
+.-.+||++.|.++-.. . -++.|.+.|+++.-+.
T Consensus 31 ~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~ 67 (122)
T CHL00057 31 KYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCK 67 (122)
T ss_pred ccccCCCEEEEEEEeccCCCceecCCEEEEEEEEecc
Confidence 45689999999997642 2 3577999999998664
No 78
>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=27.98 E-value=1.5e+02 Score=18.09 Aligned_cols=43 Identities=19% Similarity=0.206 Sum_probs=26.7
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCe
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNL 85 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gv 85 (116)
.|.|..||+|-|.-... ..-.|=+++.+..| ...++|++...-
T Consensus 11 ~P~i~~gd~v~i~~~~~------~~~~G~iv~~~~~~--~~~~ikrl~~~~ 53 (84)
T cd06462 11 EPTIPDGDLVLVDKSSY------EPKRGDIVVFRLPG--GELTVKRVIGLP 53 (84)
T ss_pred cCcccCCCEEEEEecCC------CCcCCEEEEEEcCC--CcEEEEEEEEEC
Confidence 57799999999885432 12334333434334 667888876555
No 79
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=27.74 E-value=1e+02 Score=19.15 Aligned_cols=17 Identities=18% Similarity=0.229 Sum_probs=13.5
Q ss_pred CCcCCCCEEEEEEEecC
Q psy15835 36 PSFFVGSILSVTSADKH 52 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e 52 (116)
-.|++||.|+|.+.-..
T Consensus 56 ~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 56 KVFRLGDKVKVRVVRVD 72 (83)
T ss_pred CEEcCCCEEEEEEEEec
Confidence 35899999999987654
No 80
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=27.71 E-value=1.4e+02 Score=25.40 Aligned_cols=56 Identities=11% Similarity=-0.097 Sum_probs=37.3
Q ss_pred CCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCC---------ceeEEEeeecCCeeeeEEE
Q psy15835 33 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGL---------RHEFVLRNVVDNLGAVPCT 91 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl---------~stFtlRni~~gvGVEr~f 91 (116)
.++..+++|+-++|++....+. ..|+|++-++...-. +.|+.-=|+.+++.|...+
T Consensus 254 TqL~~~r~Gq~a~I~~da~~~~---~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~l 318 (352)
T COG1566 254 TQLARVRPGQPAEITLDAYPGN---GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIEL 318 (352)
T ss_pred eecCcccCCCeEEEEEEcCCCc---eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEe
Confidence 4688899999999998776543 789999988864322 2222333455555555555
No 81
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=27.49 E-value=64 Score=22.19 Aligned_cols=17 Identities=24% Similarity=0.239 Sum_probs=14.7
Q ss_pred CCcCCCCEEEEEEEecC
Q psy15835 36 PSFFVGSILSVTSADKH 52 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e 52 (116)
-.|++||.|+|.+.+..
T Consensus 51 ~~~~~Gd~V~Vsf~i~~ 67 (84)
T PF11325_consen 51 DNFQVGDEVKVSFNIEG 67 (84)
T ss_pred ccCCCCCEEEEEEEeec
Confidence 56899999999998854
No 82
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=27.45 E-value=35 Score=22.70 Aligned_cols=45 Identities=16% Similarity=0.198 Sum_probs=30.7
Q ss_pred CCcCCCCEEEEEEEecCCCceeeeE----EE-EEEEEecCCCceeEEEee
Q psy15835 36 PSFFVGSILSVTSADKHDPNKTRKF----VG-ICIQKRYCGLRHEFVLRN 80 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e~k~r~q~F----~G-v~Ia~r~~Gl~stFtlRn 80 (116)
.++.+|++++|...++.+.+-+..| .| -+.+..-.|-...|++|+
T Consensus 27 ~~m~~Ge~LeV~~ddp~~~~dIp~~~~~~~~~~ll~~e~~~~~~~~~Ikk 76 (78)
T COG0425 27 AKLKPGEILEVIADDPAAKEDIPAWAKKEGGHELLEVEQEGGVYRILIKK 76 (78)
T ss_pred HcCCCCCEEEEEecCcchHHHHHHHHHHcCCcEEEEEEecCCcEEEEEEe
Confidence 3457999999999988766555443 23 556666555566777765
No 83
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=27.26 E-value=1.1e+02 Score=20.92 Aligned_cols=29 Identities=17% Similarity=0.220 Sum_probs=17.6
Q ss_pred CcCCCCEEEEEEEec----C-CCceeeeEEEEEE
Q psy15835 37 SFFVGSILSVTSADK----H-DPNKTRKFVGICI 65 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~----e-~k~r~q~F~Gv~I 65 (116)
+++.||.|.|..... . .......|.|..|
T Consensus 94 ~L~~GD~V~v~~~~~~~~~~~~~~~~stFsGfLl 127 (127)
T PF00386_consen 94 QLNKGDTVWVRLDSGNGIYSSGSNPYSTFSGFLL 127 (127)
T ss_dssp EE-TT-EEEEEEEEEEEEEBBTTSBTEEEEEEEE
T ss_pred EeCCCCEEEEEEecCceEEeCCCCCCEEEEEEEC
Confidence 478999999998752 1 2235567777654
No 84
>PF15344 FAM217: FAM217 family
Probab=27.14 E-value=29 Score=28.26 Aligned_cols=10 Identities=50% Similarity=1.055 Sum_probs=8.2
Q ss_pred CCCCCCCCcc
Q psy15835 1 MYQEFLPDPE 10 (116)
Q Consensus 1 ~~~~~~p~~~ 10 (116)
-||||+|+|-
T Consensus 47 ~YPDFLPPPF 56 (233)
T PF15344_consen 47 YYPDFLPPPF 56 (233)
T ss_pred cCCCCCCCCC
Confidence 3999999974
No 85
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=27.09 E-value=1.2e+02 Score=21.11 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=30.0
Q ss_pred CCC-CcCCCCEEEEEEEecCCCceee-eEE-EE-EEEEe-cCCCceeEEEeeec
Q psy15835 34 DIP-SFFVGSILSVTSADKHDPNKTR-KFV-GI-CIQKR-YCGLRHEFVLRNVV 82 (116)
Q Consensus 34 ~iP-~f~~GD~v~V~~~i~e~k~r~q-~F~-Gv-~Ia~r-~~Gl~stFtlRni~ 82 (116)
.+| .|++|+.+.++=....+.+|.+ .|. |- =|+-+ +--.+..-.+||..
T Consensus 4 ~lp~~l~~G~~i~i~G~~~~~~~~F~inl~~~~~di~lH~n~rf~~~~iV~Ns~ 57 (128)
T smart00276 4 PIPGGLKPGQTLTVRGIVLPDAKRFSINLLTGGDDIALHFNPRFNENKIVCNSK 57 (128)
T ss_pred cCCCCCCCCCEEEEEEEECCCCCEEEEEeecCCCCEEEEEeccCCCCEEEEeCc
Confidence 567 6999999999999887666654 232 31 11211 22233456778874
No 86
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=26.82 E-value=1.6e+02 Score=18.06 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=16.0
Q ss_pred CCCCEEEEEEEecCCCceeeeEEEEEEE
Q psy15835 39 FVGSILSVTSADKHDPNKTRKFVGICIQ 66 (116)
Q Consensus 39 ~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia 66 (116)
--||.|.|.+.- +++...-+|-|+.
T Consensus 33 ~~gD~V~v~i~~---~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 33 MDGDKVLVRITP---PSRGKRPEGEVVE 57 (58)
T ss_dssp -TT-EEEEEEEE---SSSEEEEEEEEEE
T ss_pred CCCCEEEEEEec---CCCCCCCCEEEEe
Confidence 479999999887 3344556676654
No 87
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.70 E-value=1.2e+02 Score=18.31 Aligned_cols=16 Identities=19% Similarity=0.277 Sum_probs=12.7
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||++++.+.-..
T Consensus 44 ~~~~Gd~v~~~v~~~d 59 (73)
T cd05691 44 RFKVGDEVEAKITNVD 59 (73)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 3799999999876543
No 88
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.60 E-value=1e+02 Score=19.32 Aligned_cols=16 Identities=13% Similarity=0.106 Sum_probs=13.1
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.+++.+....
T Consensus 46 ~~~vG~~v~~kV~~id 61 (71)
T cd05696 46 PFKAGTTHKARIIGYS 61 (71)
T ss_pred ccCCCCEEEEEEEEEe
Confidence 4999999999986544
No 89
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=26.55 E-value=1.2e+02 Score=19.34 Aligned_cols=24 Identities=4% Similarity=0.086 Sum_probs=14.9
Q ss_pred CCCcCCCCEEEEE-EEecCCCceee
Q psy15835 35 IPSFFVGSILSVT-SADKHDPNKTR 58 (116)
Q Consensus 35 iP~f~~GD~v~V~-~~i~e~k~r~q 58 (116)
.+.+.+||++++. -++.+-+.+.|
T Consensus 46 ~~~~~~G~vv~i~~~~v~~~~g~~q 70 (82)
T cd04491 46 ADDLEPGDVVRIENAYVREFNGRLE 70 (82)
T ss_pred cccCCCCCEEEEEeEEEEecCCcEE
Confidence 4567788888887 66654333333
No 90
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=25.49 E-value=1.3e+02 Score=17.34 Aligned_cols=16 Identities=19% Similarity=0.167 Sum_probs=13.0
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.+++.+.-..
T Consensus 46 ~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 46 VLKVGDEVKVKVLSVD 61 (72)
T ss_pred eecCCCEEEEEEEEEe
Confidence 4899999999987543
No 91
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=25.27 E-value=1.1e+02 Score=17.82 Aligned_cols=14 Identities=14% Similarity=0.083 Sum_probs=11.5
Q ss_pred cCCCCEEEEEEEec
Q psy15835 38 FFVGSILSVTSADK 51 (116)
Q Consensus 38 f~~GD~v~V~~~i~ 51 (116)
|++||.|+|.+.-.
T Consensus 45 ~~~Gd~v~v~v~~~ 58 (69)
T cd05692 45 LKEGDKVKVKVLSI 58 (69)
T ss_pred cCCCCEEEEEEEEE
Confidence 79999999997543
No 92
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=25.20 E-value=1.9e+02 Score=18.46 Aligned_cols=34 Identities=12% Similarity=0.122 Sum_probs=25.0
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCC
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCG 71 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~G 71 (116)
.+.+||.|.+.+..+.+.. .-...|.|...+..+
T Consensus 36 ~~~~g~~v~l~l~l~~~~~-~i~~~g~Vv~~~~~~ 69 (96)
T TIGR02266 36 PLAVGTRVELKLTLPGGER-PVELKGVVAWVRPAA 69 (96)
T ss_pred CcCCCCEEEEEEEcCCCCe-EEEEEEEEEEeCCCC
Confidence 4679999999999976533 234569888877654
No 93
>COG5496 Predicted thioesterase [General function prediction only]
Probab=25.18 E-value=2.1e+02 Score=21.37 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=18.9
Q ss_pred CCCCEEEEEEEecCCCceeeeEEEEEE
Q psy15835 39 FVGSILSVTSADKHDPNKTRKFVGICI 65 (116)
Q Consensus 39 ~~GD~v~V~~~i~e~k~r~q~F~Gv~I 65 (116)
-+|++|+|...+.+-..|.-.|.+++.
T Consensus 72 ~~G~~V~i~~~l~~v~Gr~v~f~i~a~ 98 (130)
T COG5496 72 PPGLTVTIGARLEKVEGRKVKFRIIAM 98 (130)
T ss_pred CCCCeEEEEEEEEEEeccEEEEEEEEe
Confidence 489999999888764455566765554
No 94
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=25.17 E-value=1.9e+02 Score=24.57 Aligned_cols=69 Identities=9% Similarity=-0.015 Sum_probs=38.9
Q ss_pred CCCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCC----ceeEEEeeecCCeeeeEEEccccCCCcceEEEe
Q psy15835 33 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGL----RHEFVLRNVVDNLGAVPCTGDRHGPYLSLLGAL 105 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl----~stFtlRni~~gvGVEr~f~pl~SP~I~~IeVl 105 (116)
.++..+++|+.|.|++.. ...+...|.|.|..+..... +.+|+++=-+.--. .... +|..-+-.++.+.
T Consensus 367 ~di~~v~~Gq~V~v~~~a--~~~~~~~~~G~V~~Is~~~~~~~~~~~y~v~v~l~~~~-~~~~-~L~pGM~a~v~I~ 439 (457)
T TIGR01000 367 NDISGIKVGQKVRFKLTQ--NVPKPIILDGTITSISSAPTATKKGNFYKVIATIKITK-NQAE-LIRYGLTGKISTI 439 (457)
T ss_pred HHHhhcCCCCeEEEEEec--CCCCceEEEEEEEEEcCCCccCCCCCEEEEEEEecCCc-cccc-ccCCCCEEEEEEE
Confidence 356778999988887764 22223479999998875432 24677654332000 0123 4445555555554
No 95
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.84 E-value=1.3e+02 Score=18.38 Aligned_cols=16 Identities=13% Similarity=0.067 Sum_probs=13.1
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.+++.+.-..
T Consensus 44 ~~~~Gd~i~~~V~~id 59 (69)
T cd05697 44 KFKPGLKVKCRVLSVE 59 (69)
T ss_pred cCCCCCEEEEEEEEEE
Confidence 4899999999987554
No 96
>PF15493 YrpD: Domain of unknown function, YrpD
Probab=24.70 E-value=3e+02 Score=22.13 Aligned_cols=47 Identities=15% Similarity=0.188 Sum_probs=29.8
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEE--EEEEecCCCceeEEEeee
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGI--CIQKRYCGLRHEFVLRNV 81 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv--~Ia~r~~Gl~stFtlRni 81 (116)
-|.|+||..|..+++.+.+..-.-.+.|. |-.+-..--+-+++-|=+
T Consensus 93 ~ngf~pGqdVqm~~y~n~nGn~Rltl~Gta~c~d~~ct~~~dty~~~ii 141 (208)
T PF15493_consen 93 KNGFKPGQDVQMTLYKNYNGNTRLTLWGTAICADRSCTNNGDTYTGRII 141 (208)
T ss_pred cCCCCCCCeEEEEEEEeCCCCEEEEEEeeeeccccccccCCCceEEEEE
Confidence 46799999999999998755555566776 333333333334444433
No 97
>KOG3416|consensus
Probab=24.61 E-value=44 Score=25.11 Aligned_cols=20 Identities=25% Similarity=0.351 Sum_probs=14.6
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEE
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVG 62 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~G 62 (116)
.|.|||+|+.+=-. ...|+|
T Consensus 61 ~~~PGDIirLt~Gy------~Si~qg 80 (134)
T KOG3416|consen 61 LIQPGDIIRLTGGY------ASIFQG 80 (134)
T ss_pred ccCCccEEEecccc------hhhhcC
Confidence 48999999987433 346776
No 98
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=24.59 E-value=1.1e+02 Score=19.68 Aligned_cols=23 Identities=17% Similarity=0.235 Sum_probs=16.2
Q ss_pred CCCCCCcCCCCEEEEEEEecCCC
Q psy15835 32 VIDIPSFFVGSILSVTSADKHDP 54 (116)
Q Consensus 32 ~~~iP~f~~GD~v~V~~~i~e~k 54 (116)
..++..|++||.|..++...++.
T Consensus 37 ~~~l~~l~~Gd~V~F~~~~~~~~ 59 (70)
T PF11604_consen 37 PVDLAGLKPGDKVRFTFERTDDG 59 (70)
T ss_dssp TSEESS-STT-EEEEEEEEETTC
T ss_pred hhhhhcCCCCCEEEEEEEECCCC
Confidence 34577899999999999886644
No 99
>cd00070 GLECT Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
Probab=24.55 E-value=1.5e+02 Score=20.58 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=20.2
Q ss_pred CCC-CcCCCCEEEEEEEecCCCceee
Q psy15835 34 DIP-SFFVGSILSVTSADKHDPNKTR 58 (116)
Q Consensus 34 ~iP-~f~~GD~v~V~~~i~e~k~r~q 58 (116)
.+| .|.+|+.+.|+-....+.+|.+
T Consensus 5 ~l~~~l~~G~~i~i~G~~~~~~~~f~ 30 (127)
T cd00070 5 PLPGGLKPGSTLTVKGRVLPNAKRFS 30 (127)
T ss_pred ccCCCCcCCCEEEEEEEECCCCCEEE
Confidence 456 6999999999999988666654
No 100
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=24.33 E-value=97 Score=21.95 Aligned_cols=44 Identities=14% Similarity=0.046 Sum_probs=29.6
Q ss_pred CCcCCCCEEEEEEEec--C--CCceeeeEEEEEEEEecCCCceeEEEe
Q psy15835 36 PSFFVGSILSVTSADK--H--DPNKTRKFVGICIQKRYCGLRHEFVLR 79 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~--e--~k~r~q~F~Gv~Ia~r~~Gl~stFtlR 79 (116)
-+|++||.|-+...-. . --++.+--.|.|..++++...-.+.+.
T Consensus 33 ~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~vg 80 (98)
T PRK04306 33 QEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKDG 80 (98)
T ss_pred HhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEEC
Confidence 3689999998887532 2 125566667888888887666555443
No 101
>PHA02561 D tail protein; Provisional
Probab=24.16 E-value=3e+02 Score=22.27 Aligned_cols=50 Identities=8% Similarity=-0.035 Sum_probs=29.8
Q ss_pred CCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEe-cCCCceeEEEeeecC
Q psy15835 34 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKR-YCGLRHEFVLRNVVD 83 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r-~~Gl~stFtlRni~~ 83 (116)
..|.+++|..|.+.=.-.......=....+.-... ..|..++|.++....
T Consensus 298 G~~~l~aG~~v~l~g~~~~~~~g~y~V~sv~H~~~~~~gy~t~~~~~~~~~ 348 (351)
T PHA02561 298 GRADLAPELPVEVSGFKPEIDEGEWSIDKVTHRLNRGGGYTTSLELEVKLD 348 (351)
T ss_pred CCcceecCceEEEEecCccccCCeEEEEEEEEEEeCCCCEEEEEEEEEecc
Confidence 67899999999986111110011112235555554 578888999987543
No 102
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=24.10 E-value=52 Score=26.50 Aligned_cols=14 Identities=29% Similarity=0.358 Sum_probs=12.5
Q ss_pred CcCCCCEEEEEEEe
Q psy15835 37 SFFVGSILSVTSAD 50 (116)
Q Consensus 37 ~f~~GD~v~V~~~i 50 (116)
.|.+||.|+|+...
T Consensus 164 kFnVGDkVKV~~~~ 177 (213)
T PRK06763 164 VFHVGDKVKVDMKY 177 (213)
T ss_pred EEecCCEEEEEeee
Confidence 59999999999866
No 103
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.10 E-value=1.1e+02 Score=19.37 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=15.5
Q ss_pred CcCCCCEEEEEEEecC-CCceee
Q psy15835 37 SFFVGSILSVTSADKH-DPNKTR 58 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e-~k~r~q 58 (116)
.|++||.|++.+.--. +++|+.
T Consensus 46 ~~~vG~~v~~kV~~id~~~~~i~ 68 (73)
T cd05703 46 KFPIGQALKAKVVGVDKEHKLLR 68 (73)
T ss_pred hCCCCCEEEEEEEEEeCCCCEEE
Confidence 4899999999976543 444443
No 104
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=24.09 E-value=69 Score=24.52 Aligned_cols=49 Identities=10% Similarity=0.076 Sum_probs=31.2
Q ss_pred CCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeeeeEEEccccCCC
Q psy15835 34 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGAVPCTGDRHGPY 98 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGVEr~f~pl~SP~ 98 (116)
+-|.|+-||.|.+.+.-..-+.| .-.|+..-+ + +.=.+||..- |..|..
T Consensus 84 ~kp~F~LGd~V~~~f~~~~pkqR--lIlGv~lv~------------~-~W~Y~VE~~S-Ptlse~ 132 (150)
T PF07154_consen 84 QKPAFRLGDRVEFRFYSDGPKQR--LILGVFLVN------------N-SWFYAVEWRS-PTLSET 132 (150)
T ss_pred cCCceecCCEEEEEecCCCCceE--EEEEEEEec------------C-ceEEEEEEeC-Cccccc
Confidence 56899999999999865444443 344665432 2 2335677777 766654
No 105
>COG5636 Uncharacterized conserved protein, contains Zn-ribbon-like motif [Function unknown]
Probab=23.79 E-value=54 Score=27.03 Aligned_cols=18 Identities=22% Similarity=0.479 Sum_probs=14.4
Q ss_pred CCCCCcCCCCEEEEEEEe
Q psy15835 33 IDIPSFFVGSILSVTSAD 50 (116)
Q Consensus 33 ~~iP~f~~GD~v~V~~~i 50 (116)
..+|.|.|||+|......
T Consensus 258 lGlPaf~PGd~v~~~~nl 275 (284)
T COG5636 258 LGLPAFEPGDVVSFSMNL 275 (284)
T ss_pred cCCCCCCCCceeeeeccc
Confidence 368999999999876543
No 106
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=23.28 E-value=67 Score=21.68 Aligned_cols=15 Identities=20% Similarity=0.259 Sum_probs=12.2
Q ss_pred CcCCCCEEEEEEEec
Q psy15835 37 SFFVGSILSVTSADK 51 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~ 51 (116)
.|++||+|+-++.-.
T Consensus 60 ~f~~GDiV~AkVis~ 74 (92)
T cd05791 60 CFRPGDIVRAKVISL 74 (92)
T ss_pred hcCCCCEEEEEEEEc
Confidence 489999999887654
No 107
>PF13437 HlyD_3: HlyD family secretion protein
Probab=22.79 E-value=2.3e+02 Score=18.44 Aligned_cols=33 Identities=18% Similarity=0.187 Sum_probs=24.2
Q ss_pred CCCCCcC-CCCEEEEEEEecCCCceeeeEEEEEEEEec
Q psy15835 33 IDIPSFF-VGSILSVTSADKHDPNKTRKFVGICIQKRY 69 (116)
Q Consensus 33 ~~iP~f~-~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~ 69 (116)
.++..++ +||-+++++. .+.+ +.+.|.+..+..
T Consensus 45 ~~~~~i~~~g~~v~v~~~--~~~~--~~~~g~V~~I~~ 78 (105)
T PF13437_consen 45 KDIARIKDPGQKVTVRLD--PGPE--KTIEGKVSSISP 78 (105)
T ss_pred HhhcceEeCCCEEEEEEC--CCCC--cEEEEEEEEEeC
Confidence 3566787 9999999887 2222 288899988887
No 108
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=22.78 E-value=1.2e+02 Score=21.60 Aligned_cols=12 Identities=17% Similarity=0.343 Sum_probs=7.6
Q ss_pred CCcCCCCEEEEE
Q psy15835 36 PSFFVGSILSVT 47 (116)
Q Consensus 36 P~f~~GD~v~V~ 47 (116)
+.|++||+|+|.
T Consensus 63 ~~l~~GdvV~I~ 74 (129)
T PRK06461 63 GSLKEGEVVEIE 74 (129)
T ss_pred ccCCCCCEEEEE
Confidence 345667766666
No 109
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=22.58 E-value=1.2e+02 Score=17.71 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=12.2
Q ss_pred cCCCCEEEEEEEecC
Q psy15835 38 FFVGSILSVTSADKH 52 (116)
Q Consensus 38 f~~GD~v~V~~~i~e 52 (116)
|++||.++|.+.-..
T Consensus 45 ~~~Gd~v~v~i~~vd 59 (68)
T cd05685 45 VSVGDIVEVKVISID 59 (68)
T ss_pred cCCCCEEEEEEEEEE
Confidence 799999999976543
No 110
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=22.53 E-value=1.1e+02 Score=20.05 Aligned_cols=24 Identities=13% Similarity=0.079 Sum_probs=19.5
Q ss_pred CCCCCCcCCCCEEEEEEEecCCCc
Q psy15835 32 VIDIPSFFVGSILSVTSADKHDPN 55 (116)
Q Consensus 32 ~~~iP~f~~GD~v~V~~~i~e~k~ 55 (116)
..+++.+++|..|.|.|....+++
T Consensus 32 ef~~~~L~~G~kV~V~yd~~~gk~ 55 (61)
T PF07076_consen 32 EFDFDGLKPGMKVVVFYDEVDGKR 55 (61)
T ss_pred cccccccCCCCEEEEEEEccCCcE
Confidence 456888999999999998876543
No 111
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.39 E-value=2e+02 Score=22.71 Aligned_cols=36 Identities=17% Similarity=0.245 Sum_probs=22.5
Q ss_pred CCcCCCCEEEEEEEecCCCceeee---EEEEEEEEecCC
Q psy15835 36 PSFFVGSILSVTSADKHDPNKTRK---FVGICIQKRYCG 71 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e~k~r~q~---F~Gv~Ia~r~~G 71 (116)
-.|++||+|+=.+.--...=+.+. =.||+-|+.-+.
T Consensus 117 d~f~~GDivrA~Vis~~~~~~Lst~~~dlGVI~A~CsrC 155 (188)
T COG1096 117 DAFRIGDIVRARVISTGDPIQLSTKGNDLGVIYARCSRC 155 (188)
T ss_pred cccccccEEEEEEEecCCCeEEEecCCcceEEEEEccCC
Confidence 369999999987755433322222 238888876443
No 112
>TIGR00192 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions.
Probab=22.10 E-value=94 Score=22.31 Aligned_cols=33 Identities=27% Similarity=0.333 Sum_probs=26.4
Q ss_pred CCCCC-----CcCCCCEEEEEEEecCCCceeeeEEEEE
Q psy15835 32 VIDIP-----SFFVGSILSVTSADKHDPNKTRKFVGIC 64 (116)
Q Consensus 32 ~~~iP-----~f~~GD~v~V~~~i~e~k~r~q~F~Gv~ 64 (116)
+-||| .|.|||+-+|++-.-.+.+++.=|.|.+
T Consensus 60 RLdIpaGTavRFEPG~~k~V~LV~~gG~r~v~G~~gl~ 97 (101)
T TIGR00192 60 RLDIPSGTAVRFEPGEEKSVELVAIGGNRRIYGFNGLV 97 (101)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEccCceEEEccCccc
Confidence 45777 4999999999998888888777776654
No 113
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.87 E-value=1.2e+02 Score=19.34 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=15.3
Q ss_pred CcCCCCEEEEEEEecC-CCcee
Q psy15835 37 SFFVGSILSVTSADKH-DPNKT 57 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e-~k~r~ 57 (116)
.|++||.|++.+.-.. +++|+
T Consensus 50 ~~~~G~~v~~kVl~id~~~~~i 71 (74)
T cd05705 50 YLPEGKLLTAKVLSVNSEKNLV 71 (74)
T ss_pred ccCCCCEEEEEEEEEECCCCEE
Confidence 4899999999987543 44444
No 114
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.81 E-value=3.4e+02 Score=22.79 Aligned_cols=48 Identities=4% Similarity=-0.136 Sum_probs=34.9
Q ss_pred CCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCCeee
Q psy15835 35 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGA 87 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~gvGV 87 (116)
-+-++-||.|.+.+.... -....-..|..+.+.+.++.|||...|--|
T Consensus 256 p~lV~rGd~V~i~~~~gg-----l~v~~~G~ALe~G~~Gd~IrV~N~~S~kiv 303 (338)
T PRK12786 256 PDLVQRGQLVTLIYQTPG-----IYLTARGKALEDGAEGDVVRVLNLQSKRTV 303 (338)
T ss_pred ccEEcCCCEEEEEEEcCC-----EEEEEEEEEccccCCCCEEEEEECCCCCEE
Confidence 346889999999987643 223355667788899999999998555433
No 115
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: 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=21.78 E-value=51 Score=21.02 Aligned_cols=18 Identities=22% Similarity=0.410 Sum_probs=13.9
Q ss_pred CCCCc-CCCCEEEEEEEec
Q psy15835 34 DIPSF-FVGSILSVTSADK 51 (116)
Q Consensus 34 ~iP~f-~~GD~v~V~~~i~ 51 (116)
..|.| ..||.|+|.....
T Consensus 33 ~VP~FI~~Gd~I~V~T~~g 51 (56)
T cd05794 33 QVPLFIKEGEKIKVDTRTG 51 (56)
T ss_pred EcCCeecCCCEEEEECCCC
Confidence 46776 9999999986653
No 116
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.75 E-value=1.6e+02 Score=17.89 Aligned_cols=15 Identities=20% Similarity=0.093 Sum_probs=12.3
Q ss_pred CcCCCCEEEEEEEec
Q psy15835 37 SFFVGSILSVTSADK 51 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~ 51 (116)
.|++||.+++.+.-.
T Consensus 44 ~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 44 EVKVGDEVEVYVLRV 58 (70)
T ss_pred cCCCCCEEEEEEEEE
Confidence 389999999998654
No 117
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=21.72 E-value=1.4e+02 Score=17.76 Aligned_cols=23 Identities=17% Similarity=0.041 Sum_probs=13.7
Q ss_pred cCCCCEEEEEEEecCCCceeeeE
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKF 60 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F 60 (116)
.+.||.+.++..+..-.++...+
T Consensus 44 ~~~gd~l~~~~~v~~~g~~~~~~ 66 (79)
T PF03061_consen 44 VRPGDTLRVEARVVRVGRKSFTV 66 (79)
T ss_dssp BBTTSEEEEEEEEEEEESSEEEE
T ss_pred cCCCeEEEEEEEEEEECCEEEEE
Confidence 56777777777775533333333
No 118
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.70 E-value=1.4e+02 Score=18.11 Aligned_cols=15 Identities=20% Similarity=0.279 Sum_probs=12.3
Q ss_pred cCCCCEEEEEEEecC
Q psy15835 38 FFVGSILSVTSADKH 52 (116)
Q Consensus 38 f~~GD~v~V~~~i~e 52 (116)
|++||.|++.+.-..
T Consensus 45 ~~~Gd~v~~~v~~~d 59 (68)
T cd05707 45 FKVGQLVKGKIVSID 59 (68)
T ss_pred cCCCCEEEEEEEEEe
Confidence 899999999986543
No 119
>PRK13203 ureB urease subunit beta; Reviewed
Probab=21.59 E-value=96 Score=22.28 Aligned_cols=33 Identities=21% Similarity=0.280 Sum_probs=26.3
Q ss_pred CCCCC-----CcCCCCEEEEEEEecCCCceeeeEEEEE
Q psy15835 32 VIDIP-----SFFVGSILSVTSADKHDPNKTRKFVGIC 64 (116)
Q Consensus 32 ~~~iP-----~f~~GD~v~V~~~i~e~k~r~q~F~Gv~ 64 (116)
+-||| .|.|||+-+|++-.-.+.+++.=|.|.+
T Consensus 60 RLdIpaGTavRFEPG~~k~V~LV~~gG~r~v~G~ngl~ 97 (102)
T PRK13203 60 RLNIPAGTAVRFEPGQTREVELVPLAGARRVYGFRGKV 97 (102)
T ss_pred ccccCCCCeEeECCCCeEEEEEEEccCceEEEccCccc
Confidence 45777 4999999999998878888777776654
No 120
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=21.53 E-value=1.3e+02 Score=18.97 Aligned_cols=16 Identities=13% Similarity=0.038 Sum_probs=12.4
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|+.||.|+|.+.-..
T Consensus 48 ~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 48 VVKRGQKVKVKVISIQ 63 (79)
T ss_pred eeCCCCEEEEEEEEEe
Confidence 3799999999875543
No 121
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=21.34 E-value=2.7e+02 Score=18.80 Aligned_cols=56 Identities=14% Similarity=0.136 Sum_probs=40.8
Q ss_pred cCCCCCCcCCCCEEEEEEEecC-CCceeeeEEEEEEEEecCCCceeEE--EeeecCCee
Q psy15835 31 SVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFV--LRNVVDNLG 86 (116)
Q Consensus 31 ~~~~iP~f~~GD~v~V~~~i~e-~k~r~q~F~Gv~Ia~r~~Gl~stFt--lRni~~gvG 86 (116)
....-|...-||+-.|++.... ...-+..++|.++-.-+...+-+.+ +-++....+
T Consensus 6 ~~~~~~PVeeGe~y~V~I~d~g~~GDGiarveGfvVFVp~a~~Gd~V~vkI~~v~~~~a 64 (73)
T COG3269 6 EEQRTPPVEEGETYEVEIEDVGDQGDGIARVEGFVVFVPGAEVGDEVKVKITKVKPNFA 64 (73)
T ss_pred ccCCCCCcccCCEEEEEEEEeccCCCceEEEEEEEEEeCCCCCCCeeeEEEEEeeccce
Confidence 3445677899999999999875 5577888999999998866665555 444444443
No 122
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.24 E-value=1.4e+02 Score=18.25 Aligned_cols=16 Identities=19% Similarity=0.171 Sum_probs=12.7
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|+.||.|+|.+.-..
T Consensus 48 ~~~~Gd~v~v~v~~id 63 (72)
T cd05689 48 VVSLGDEVEVMVLDID 63 (72)
T ss_pred EeCCCCEEEEEEEEee
Confidence 4899999999976543
No 123
>PF04411 DUF524: Protein of unknown function (DUF524); InterPro: IPR007505 This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches []. The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix. It has been speculated that it could function as s methylation-dependent restriction [].
Probab=20.98 E-value=1.6e+02 Score=21.01 Aligned_cols=40 Identities=23% Similarity=0.167 Sum_probs=27.6
Q ss_pred eeEEEeeecCCeeeeEEEccccCCCcc--eEEEeecCCccccc
Q psy15835 74 HEFVLRNVVDNLGAVPCTGDRHGPYLS--LLGALGLDPKIVLE 114 (116)
Q Consensus 74 stFtlRni~~gvGVEr~f~pl~SP~I~--~IeVl~~~p~~~~~ 114 (116)
+.+++.+ .++..++-.|++.+++.=. .---...-|.++|+
T Consensus 46 ~~~~~~~-~~~~~i~l~Yn~~~~~~~~~~~s~s~~~rPDi~L~ 87 (154)
T PF04411_consen 46 SKFIFFN-RDGERIELYYNPKFPRKSSKTYSYSVPQRPDIVLE 87 (154)
T ss_pred eeEEEEc-CCCcEEEEEECCccCCCCCcCccCccCCCCCEEEE
Confidence 7788888 8999999999777775322 33334556676664
No 124
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=20.95 E-value=1.4e+02 Score=21.69 Aligned_cols=36 Identities=19% Similarity=0.185 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhhhhcCCCCCCcCCCCEEEEEEEecCCC
Q psy15835 16 QVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDP 54 (116)
Q Consensus 16 ~li~~ler~~~~~r~~~~~iP~f~~GD~v~V~~~i~e~k 54 (116)
.++..|-.+.+-+ ...+.+++.||++.=......++
T Consensus 15 ~~v~al~~e~l~~---~~~VeELkEgdIL~e~I~~k~~~ 50 (110)
T PF06819_consen 15 SVVYALRGEELSD---KKPVEELKEGDILGEIIYEKDDG 50 (110)
T ss_pred HHHHHHHHHHHhh---cccHhhcCccceehheEEEeCCc
Confidence 5678888888865 56788899999999887776543
No 125
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.93 E-value=1.1e+02 Score=18.84 Aligned_cols=15 Identities=13% Similarity=0.259 Sum_probs=12.4
Q ss_pred CcCCCCEEEEEEEec
Q psy15835 37 SFFVGSILSVTSADK 51 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~ 51 (116)
.|++||+|++.+.-.
T Consensus 46 ~~~~Gd~i~~kVl~~ 60 (70)
T cd05702 46 KFKIGQKIKARVIGG 60 (70)
T ss_pred hCCCCCEEEEEEEEE
Confidence 489999999998644
No 126
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=20.80 E-value=1.5e+02 Score=18.35 Aligned_cols=16 Identities=13% Similarity=0.158 Sum_probs=13.2
Q ss_pred CcCCCCEEEEEEEecC
Q psy15835 37 SFFVGSILSVTSADKH 52 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e 52 (116)
.|++||.|+|.+.-.+
T Consensus 40 ~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 40 SYRPGDRIKAYVLEVR 55 (67)
T ss_pred cCCCCCEEEEEEEEEe
Confidence 4899999999987654
No 127
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.77 E-value=3.5e+02 Score=21.15 Aligned_cols=45 Identities=9% Similarity=-0.087 Sum_probs=31.4
Q ss_pred CCCCcCCCCEEEEEEEecCCCceeeeEEEEEEEEecCCCceeEEEeeecCC
Q psy15835 34 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDN 84 (116)
Q Consensus 34 ~iP~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~~Gl~stFtlRni~~g 84 (116)
..|-++-||.|.|.+.... .+ -.---.|..+..++.++.||| ..|
T Consensus 162 ~~~lV~rGd~V~i~~~~gg----~~-I~~~G~Al~~G~~Gd~IrVrN-~Sg 206 (222)
T PRK08515 162 ALILVRKNDIINGVLKEGG----VS-IEISLKALQDGNLGDIIQAKN-KSN 206 (222)
T ss_pred CcceEecCCEEEEEEECCC----EE-EEEEEEEcccCCCCCEEEEEe-CCC
Confidence 4567899999999877633 11 112335677888999999999 444
No 128
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=20.65 E-value=97 Score=20.50 Aligned_cols=15 Identities=13% Similarity=0.180 Sum_probs=12.4
Q ss_pred cCCCCEEEEEEEecC
Q psy15835 38 FFVGSILSVTSADKH 52 (116)
Q Consensus 38 f~~GD~v~V~~~i~e 52 (116)
+.+||.|.|..+.-.
T Consensus 45 I~~GD~V~Ve~spyd 59 (68)
T TIGR00008 45 ILPGDKVKVELSPYD 59 (68)
T ss_pred ECCCCEEEEEECccc
Confidence 579999999987643
No 129
>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=20.61 E-value=69 Score=20.48 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=9.7
Q ss_pred CCcCCCCEEEEEEE
Q psy15835 36 PSFFVGSILSVTSA 49 (116)
Q Consensus 36 P~f~~GD~v~V~~~ 49 (116)
++|+.||.|.|...
T Consensus 29 ~~f~~gd~V~i~~~ 42 (74)
T PF01472_consen 29 GDFRKGDEVAIVDE 42 (74)
T ss_dssp TT--TTSEEEEEET
T ss_pred CCcCCCCEEEEEcC
Confidence 46999999998755
No 130
>PF05093 CIAPIN1: Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis; InterPro: IPR007785 Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS) []. CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis []. In addition, it has also anti-apoptotic effects in the cell. It is involved in negative control of cell death upon cytokine withdrawal and promotes development of hematopoietic cells [].
Probab=20.56 E-value=48 Score=23.64 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=10.4
Q ss_pred CCCCCcCCCCEEE
Q psy15835 33 IDIPSFFVGSILS 45 (116)
Q Consensus 33 ~~iP~f~~GD~v~ 45 (116)
..+|.|+||+.|.
T Consensus 87 lGlPaFkpGe~V~ 99 (100)
T PF05093_consen 87 LGLPAFKPGEKVK 99 (100)
T ss_pred CCCCCCCCCCeec
Confidence 3589999998875
No 131
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=20.41 E-value=1.5e+02 Score=18.86 Aligned_cols=17 Identities=12% Similarity=0.104 Sum_probs=13.5
Q ss_pred CCcCCCCEEEEEEEecC
Q psy15835 36 PSFFVGSILSVTSADKH 52 (116)
Q Consensus 36 P~f~~GD~v~V~~~i~e 52 (116)
+.|++||.+.+.+.-..
T Consensus 49 ~~~~~GD~i~~~V~~~~ 65 (82)
T cd04454 49 KSLQPGDLILAKVISLG 65 (82)
T ss_pred hcCCCCCEEEEEEEEeC
Confidence 34899999999986544
No 132
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=20.35 E-value=1.9e+02 Score=20.78 Aligned_cols=32 Identities=13% Similarity=0.162 Sum_probs=22.9
Q ss_pred CCCcCCCCEEEEEEEec-----CCCceeeeEEEEEEE
Q psy15835 35 IPSFFVGSILSVTSADK-----HDPNKTRKFVGICIQ 66 (116)
Q Consensus 35 iP~f~~GD~v~V~~~i~-----e~k~r~q~F~Gv~Ia 66 (116)
+=.++.||.|-|..... .+.++...|.|..|.
T Consensus 97 vL~L~~GD~Vwl~l~~~~~~i~~~~~~~stFSGfLl~ 133 (135)
T smart00110 97 LLQLRQGDQVWLELPDEKNGLYAGEYVDSTFSGFLLF 133 (135)
T ss_pred EEEECCCCEEEEEEeCCCCceecCCCCcEEEEEEEEe
Confidence 33578999999998652 233677889998764
No 133
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=20.31 E-value=1.7e+02 Score=18.96 Aligned_cols=26 Identities=27% Similarity=0.420 Sum_probs=19.2
Q ss_pred cCCCCEEEEEEEecCCCceeeeEEEEEEEEec
Q psy15835 38 FFVGSILSVTSADKHDPNKTRKFVGICIQKRY 69 (116)
Q Consensus 38 f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~r~ 69 (116)
|.+|++|++++-.. +.|+|=|.+--.
T Consensus 3 f~iGs~V~~kTc~g------~~ieGEV~afD~ 28 (61)
T cd01735 3 FSVGSQVSCRTCFE------QRLQGEVVAFDY 28 (61)
T ss_pred cccccEEEEEecCC------ceEEEEEEEecC
Confidence 78999999988763 467777766443
No 134
>cd03442 BFIT_BACH Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis, and brown adipose tissues. The archeal and eukaryotic members of this family have two tandem copies of the conserved hot dog fold, while most bacterial members have only one copy.
Probab=20.27 E-value=2e+02 Score=18.60 Aligned_cols=27 Identities=7% Similarity=0.009 Sum_probs=17.2
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEE
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGI 63 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv 63 (116)
.+.+||.+.++.++.+-.++...+..-
T Consensus 63 p~~~gd~l~i~~~v~~~g~~~~~~~~~ 89 (123)
T cd03442 63 PVRVGDVVELSARVVYTGRTSMEVGVE 89 (123)
T ss_pred ccccCcEEEEEEEEEEecCCeEEEEEE
Confidence 356788888888877655545555443
No 135
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=20.07 E-value=4e+02 Score=20.25 Aligned_cols=46 Identities=9% Similarity=0.084 Sum_probs=29.4
Q ss_pred CcCCCCEEEEEEEecCCCceeeeEEEEEEEE----ecCC-CceeEEEeeecCCeeeeEEEccc
Q psy15835 37 SFFVGSILSVTSADKHDPNKTRKFVGICIQK----RYCG-LRHEFVLRNVVDNLGAVPCTGDR 94 (116)
Q Consensus 37 ~f~~GD~v~V~~~i~e~k~r~q~F~Gv~Ia~----r~~G-l~stFtlRni~~gvGVEr~f~pl 94 (116)
+++.||+|... + ..| .|+.. -++| .--...+|++..|--+|++| +-
T Consensus 5 ~ik~G~~I~~~----g-----~~~--~V~~~~~~kpGkg~A~~rvk~knL~tG~~~e~~f-~~ 55 (184)
T TIGR00038 5 DLRKGLVIELD----G-----EPY--VVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTF-RS 55 (184)
T ss_pred hccCCCEEEEC----C-----EEE--EEEEEEEeeCCCCceEEEEEEEECCCCCEEEEEe-CC
Confidence 57899999653 1 122 12222 2332 33466799999999999999 64
Done!