Query psy16233
Match_columns 464
No_of_seqs 281 out of 474
Neff 5.8
Searched_HMMs 46136
Date Sat Aug 17 00:16:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4582|consensus 99.9 3.8E-28 8.3E-33 242.3 8.6 195 4-202 61-278 (278)
2 PF06701 MIB_HERC2: Mib_herc2; 99.9 2.9E-23 6.3E-28 165.2 3.4 61 7-68 1-68 (68)
3 PF06701 MIB_HERC2: Mib_herc2; 99.8 4.5E-21 9.7E-26 152.7 4.9 68 150-218 1-68 (68)
4 cd02344 ZZ_HERC2 Zinc finger, 99.6 4.6E-17 1E-21 119.6 2.4 45 77-123 1-45 (45)
5 cd02339 ZZ_Mind_bomb Zinc fing 99.6 5.1E-16 1.1E-20 114.4 2.5 45 77-123 1-45 (45)
6 cd02340 ZZ_NBR1_like Zinc fing 99.5 1.3E-14 2.9E-19 105.9 2.2 43 77-123 1-43 (43)
7 cd02341 ZZ_ZZZ3 Zinc finger, Z 99.4 3.2E-14 6.8E-19 106.2 2.4 45 77-123 1-48 (48)
8 cd02334 ZZ_dystrophin Zinc fin 99.4 3.4E-14 7.3E-19 106.5 2.0 44 77-122 1-48 (49)
9 PF00569 ZZ: Zinc finger, ZZ t 99.4 1.3E-13 2.7E-18 102.2 0.7 46 73-120 1-46 (46)
10 cd02338 ZZ_PCMF_like Zinc fing 99.3 4.2E-13 9E-18 100.7 2.7 44 77-122 1-48 (49)
11 cd02345 ZZ_dah Zinc finger, ZZ 99.3 3.5E-13 7.6E-18 101.1 1.8 44 77-122 1-48 (49)
12 cd02342 ZZ_UBA_plant Zinc fing 99.3 4.7E-13 1E-17 96.6 1.3 33 77-111 1-33 (43)
13 cd02249 ZZ Zinc finger, ZZ typ 99.2 4.2E-12 9.1E-17 93.9 2.2 44 77-123 1-46 (46)
14 cd02335 ZZ_ADA2 Zinc finger, Z 99.2 9.8E-12 2.1E-16 93.2 2.3 43 78-122 2-48 (49)
15 cd02343 ZZ_EF Zinc finger, ZZ 99.2 6.4E-12 1.4E-16 93.5 1.0 42 77-121 1-46 (48)
16 smart00291 ZnF_ZZ Zinc-binding 99.1 2.2E-11 4.7E-16 89.3 2.0 42 74-118 2-43 (44)
17 KOG1280|consensus 99.0 2.4E-10 5.2E-15 115.2 2.5 55 72-128 4-62 (381)
18 cd02337 ZZ_CBP Zinc finger, ZZ 99.0 1.6E-10 3.6E-15 83.5 0.9 39 78-122 2-40 (41)
19 KOG4286|consensus 98.6 1.7E-08 3.6E-13 110.0 1.6 56 72-130 600-659 (966)
20 KOG0457|consensus 97.8 6.6E-06 1.4E-10 85.9 2.0 48 76-127 14-66 (438)
21 cd02336 ZZ_RSC8 Zinc finger, Z 97.6 3.1E-05 6.7E-10 57.2 1.6 38 78-118 2-39 (45)
22 KOG4301|consensus 97.5 1.4E-05 3.1E-10 81.1 -1.4 51 72-125 237-291 (434)
23 COG5114 Histone acetyltransfer 97.3 9.4E-05 2E-09 74.6 1.6 50 76-127 5-58 (432)
24 PF07649 C1_3: C1-like domain; 90.8 0.09 2E-06 35.2 0.5 27 78-108 2-29 (30)
25 KOG1778|consensus 86.9 0.35 7.6E-06 49.9 1.8 44 75-124 168-211 (319)
26 PRK06763 F0F1 ATP synthase sub 85.5 3.6 7.7E-05 39.8 7.7 48 276-324 119-175 (213)
27 smart00652 eIF1a eukaryotic tr 82.7 4.2 9.1E-05 33.9 6.1 49 277-325 7-55 (83)
28 KOG1999|consensus 82.1 3.2 6.8E-05 48.3 6.8 68 273-364 420-490 (1024)
29 PF03107 C1_2: C1 domain; Int 80.8 1.1 2.3E-05 30.1 1.6 27 78-108 2-29 (30)
30 TIGR00008 infA translation ini 80.5 4.9 0.00011 32.4 5.6 52 275-326 5-57 (68)
31 PF15057 DUF4537: Domain of un 80.1 4.8 0.0001 36.0 6.0 89 277-383 15-114 (124)
32 COG2139 RPL21A Ribosomal prote 72.2 5 0.00011 34.5 3.6 39 240-288 32-70 (98)
33 COG1585 Membrane protein impli 71.4 9.2 0.0002 34.9 5.5 49 268-323 80-128 (140)
34 cd05793 S1_IF1A S1_IF1A: Trans 70.8 11 0.00024 31.0 5.3 48 278-325 3-50 (77)
35 PRK12442 translation initiatio 70.8 13 0.00028 31.5 5.7 53 274-326 6-59 (87)
36 COG4014 Uncharacterized protei 69.4 8 0.00017 32.8 4.2 36 347-382 20-57 (97)
37 PTZ00329 eukaryotic translatio 67.9 17 0.00036 34.0 6.4 48 277-324 34-81 (155)
38 TIGR02760 TraI_TIGR conjugativ 65.6 23 0.0005 45.2 9.1 102 239-375 680-794 (1960)
39 PF01176 eIF-1a: Translation i 65.5 10 0.00022 29.9 4.0 49 277-325 5-53 (65)
40 cd04456 S1_IF1A_like S1_IF1A_l 65.5 17 0.00036 30.0 5.4 50 277-326 2-51 (78)
41 PF01957 NfeD: NfeD-like C-ter 64.9 21 0.00045 31.4 6.4 47 271-324 86-132 (144)
42 PLN00208 translation initiatio 64.6 21 0.00046 32.9 6.4 66 277-343 34-113 (145)
43 KOG4317|consensus 64.1 2.9 6.2E-05 43.0 0.8 45 75-125 6-51 (383)
44 CHL00141 rpl24 ribosomal prote 64.1 11 0.00024 31.4 4.2 39 313-371 8-46 (83)
45 PRK04012 translation initiatio 63.9 17 0.00037 31.4 5.4 48 277-324 23-70 (100)
46 PRK12281 rplX 50S ribosomal pr 61.0 14 0.0003 30.4 4.1 39 313-371 6-44 (76)
47 COG5164 SPT5 Transcription elo 60.7 20 0.00044 38.8 6.3 85 241-379 91-176 (607)
48 TIGR00523 eIF-1A eukaryotic/ar 59.8 22 0.00048 30.7 5.3 48 277-324 21-68 (99)
49 PF11515 Cul7: Mouse developme 58.8 10 0.00022 31.4 2.9 37 314-366 18-56 (78)
50 smart00743 Agenet Tudor-like d 58.6 15 0.00032 28.0 3.8 38 313-368 2-39 (61)
51 CHL00010 infA translation init 58.3 34 0.00075 28.0 6.0 49 277-326 9-59 (78)
52 PF02207 zf-UBR: Putative zinc 57.9 6.2 0.00013 31.6 1.5 33 93-126 13-48 (71)
53 PF11061 DUF2862: Protein of u 57.1 35 0.00075 27.3 5.6 53 243-304 1-59 (64)
54 smart00743 Agenet Tudor-like d 56.1 30 0.00064 26.3 5.1 51 240-309 2-54 (61)
55 PRK13709 conjugal transfer nic 55.2 37 0.0008 42.9 8.1 83 278-376 1290-1382(1747)
56 PRK00409 recombination and DNA 54.0 20 0.00044 41.5 5.5 49 312-382 635-683 (782)
57 COG0361 InfA Translation initi 51.6 41 0.00089 27.7 5.3 53 275-327 7-60 (75)
58 PF12645 HTH_16: Helix-turn-he 51.4 13 0.00027 29.6 2.3 26 432-457 2-27 (65)
59 TIGR01079 rplX_bact ribosomal 51.1 24 0.00052 30.7 4.2 38 313-370 3-40 (104)
60 PRK00004 rplX 50S ribosomal pr 50.6 25 0.00054 30.6 4.2 39 313-371 4-42 (105)
61 PRK01191 rpl24p 50S ribosomal 50.6 24 0.00052 31.6 4.2 39 314-372 46-84 (120)
62 KOG1999|consensus 49.1 25 0.00055 41.2 5.1 90 241-358 460-560 (1024)
63 TIGR00405 L26e_arch ribosomal 47.8 50 0.0011 29.7 6.0 53 313-384 86-143 (145)
64 PF10246 MRP-S35: Mitochondria 46.9 36 0.00079 29.7 4.6 46 278-329 28-77 (104)
65 PRK00276 infA translation init 46.8 68 0.0015 25.7 5.9 50 276-326 8-59 (72)
66 PF00643 zf-B_box: B-box zinc 46.7 11 0.00023 26.6 1.1 39 77-123 4-42 (42)
67 PF13857 Ank_5: Ankyrin repeat 46.2 21 0.00047 26.6 2.8 31 432-463 19-49 (56)
68 PF05641 Agenet: Agenet domain 45.4 27 0.00059 27.5 3.4 40 241-296 1-40 (68)
69 PRK04306 50S ribosomal protein 44.6 16 0.00035 31.6 2.1 41 240-293 34-76 (98)
70 PF13606 Ank_3: Ankyrin repeat 44.6 28 0.00061 23.0 2.9 24 433-457 6-29 (30)
71 PF11061 DUF2862: Protein of u 41.2 56 0.0012 26.2 4.5 49 316-374 1-59 (64)
72 PF01157 Ribosomal_L21e: Ribos 40.5 18 0.00039 31.3 1.8 37 240-286 32-68 (99)
73 COG5259 RSC8 RSC chromatin rem 40.2 12 0.00027 40.4 0.9 35 77-114 225-259 (531)
74 smart00739 KOW KOW (Kyprides, 40.1 43 0.00094 21.0 3.2 26 314-358 2-27 (28)
75 PF00467 KOW: KOW motif; Inte 39.6 58 0.0013 21.9 3.8 16 345-360 11-26 (32)
76 PF07076 DUF1344: Protein of u 38.0 85 0.0018 24.9 5.0 47 278-328 6-52 (61)
77 PRK04914 ATP-dependent helicas 37.2 54 0.0012 39.0 5.5 54 267-323 8-63 (956)
78 COG1585 Membrane protein impli 36.9 36 0.00078 31.1 3.2 37 339-375 79-115 (140)
79 PF05641 Agenet: Agenet domain 36.7 27 0.00059 27.5 2.2 38 314-366 1-38 (68)
80 cd04451 S1_IF1 S1_IF1: Transla 36.5 1.1E+02 0.0025 23.5 5.7 47 278-325 4-52 (64)
81 TIGR01069 mutS2 MutS2 family p 36.1 50 0.0011 38.3 4.9 46 315-382 626-671 (771)
82 smart00396 ZnF_UBR1 Putative z 34.6 30 0.00066 27.8 2.1 29 94-123 14-45 (71)
83 PF00366 Ribosomal_S17: Riboso 34.4 1.2E+02 0.0027 24.2 5.6 42 279-324 1-54 (69)
84 PF08605 Rad9_Rad53_bind: Fung 33.6 81 0.0018 28.6 4.9 44 278-324 26-70 (131)
85 PRK05609 nusG transcription an 33.1 83 0.0018 29.1 5.2 50 312-380 125-179 (181)
86 COG2139 RPL21A Ribosomal prote 32.6 50 0.0011 28.5 3.2 42 313-366 32-75 (98)
87 PF09871 DUF2098: Uncharacteri 32.6 73 0.0016 27.2 4.2 35 348-382 15-50 (91)
88 PTZ00194 60S ribosomal protein 32.3 68 0.0015 29.6 4.2 37 313-369 46-82 (143)
89 PRK10413 hydrogenase 2 accesso 32.3 1.3E+02 0.0027 25.2 5.5 49 274-324 2-53 (82)
90 PF12158 DUF3592: Protein of u 31.8 90 0.0019 27.3 5.0 57 276-332 38-110 (148)
91 TIGR03635 S17_bact 30S ribosom 30.6 1.4E+02 0.0031 24.1 5.4 43 278-324 5-59 (71)
92 TIGR01080 rplX_A_E ribosomal p 30.4 69 0.0015 28.4 3.8 40 313-372 41-80 (114)
93 PF00023 Ank: Ankyrin repeat H 30.0 82 0.0018 20.7 3.4 26 433-459 6-31 (33)
94 PF01957 NfeD: NfeD-like C-ter 29.3 70 0.0015 28.0 3.8 31 343-373 86-116 (144)
95 PF02211 NHase_beta: Nitrile h 29.1 49 0.0011 32.6 3.0 39 238-286 132-170 (222)
96 PRK05609 nusG transcription an 29.1 1.4E+02 0.0029 27.7 5.9 37 240-296 126-163 (181)
97 COG4014 Uncharacterized protei 28.9 89 0.0019 26.7 4.0 36 275-312 20-57 (97)
98 cd04466 S1_YloQ_GTPase S1_YloQ 28.7 1.6E+02 0.0035 22.4 5.4 45 278-324 2-48 (68)
99 PF11347 DUF3148: Protein of u 28.5 82 0.0018 25.1 3.5 49 315-371 1-56 (63)
100 PRK01191 rpl24p 50S ribosomal 28.2 95 0.0021 27.8 4.3 37 239-296 44-80 (120)
101 KOG2990|consensus 28.0 19 0.0004 36.8 -0.2 20 75-96 51-70 (317)
102 KOG4412|consensus 27.8 47 0.001 32.2 2.5 32 432-463 75-106 (226)
103 PTZ00189 60S ribosomal protein 27.6 40 0.00086 31.7 1.9 36 240-287 33-70 (160)
104 COG0250 NusG Transcription ant 27.3 95 0.0021 29.5 4.5 35 313-366 123-158 (178)
105 TIGR03689 pup_AAA proteasome A 27.0 3E+02 0.0064 30.6 8.8 84 271-366 41-125 (512)
106 PF02237 BPL_C: Biotin protein 26.7 1.2E+02 0.0026 22.2 4.0 28 278-306 16-43 (48)
107 PF12760 Zn_Tnp_IS1595: Transp 25.7 36 0.00078 24.9 1.0 25 76-100 18-44 (46)
108 PLN00208 translation initiatio 25.4 4E+02 0.0087 24.7 8.0 30 241-272 71-114 (145)
109 KOG1280|consensus 25.2 41 0.0009 35.2 1.7 58 51-110 23-84 (381)
110 PRK00409 recombination and DNA 24.9 1E+02 0.0023 35.8 5.1 23 273-295 646-668 (782)
111 PLN00190 60S ribosomal protein 24.6 50 0.0011 30.9 2.0 36 240-287 33-70 (158)
112 PRK08559 nusG transcription an 24.5 2.2E+02 0.0047 26.1 6.2 51 313-382 94-149 (153)
113 PF04717 Phage_base_V: Phage-r 24.3 1.5E+02 0.0032 23.8 4.5 46 279-324 1-54 (79)
114 PF12073 DUF3553: Protein of u 24.1 2.3E+02 0.0049 21.8 5.1 38 333-380 9-47 (52)
115 TIGR01953 NusA transcription t 24.0 1.6E+02 0.0035 30.9 5.8 79 239-322 82-178 (341)
116 TIGR02760 TraI_TIGR conjugativ 23.8 2.7E+02 0.0058 36.0 8.7 86 277-377 1342-1438(1960)
117 COG0298 HypC Hydrogenase matur 23.7 2E+02 0.0043 24.1 5.1 46 274-323 2-48 (82)
118 KOG0512|consensus 23.6 80 0.0017 30.5 3.2 31 430-460 64-94 (228)
119 PTZ00194 60S ribosomal protein 23.5 1.6E+02 0.0034 27.3 4.9 36 240-296 46-81 (143)
120 PRK13020 riboflavin synthase s 23.3 1.3E+02 0.0028 29.2 4.7 78 241-325 76-184 (206)
121 PTZ00329 eukaryotic translatio 23.1 3.5E+02 0.0076 25.4 7.2 29 241-271 71-113 (155)
122 TIGR00922 nusG transcription t 22.8 1.4E+02 0.003 27.5 4.6 35 313-366 119-154 (172)
123 PRK05610 rpsQ 30S ribosomal pr 22.5 2.3E+02 0.005 23.7 5.4 44 277-324 9-64 (84)
124 PRK09289 riboflavin synthase s 22.4 97 0.0021 29.8 3.6 79 241-326 75-184 (194)
125 PRK10862 SoxR reducing system 21.9 1.3E+02 0.0029 27.7 4.3 53 277-330 4-75 (154)
126 TIGR00405 L26e_arch ribosomal 21.0 2.4E+02 0.0053 25.2 5.7 51 241-311 87-140 (145)
127 PF02211 NHase_beta: Nitrile h 21.0 70 0.0015 31.5 2.4 38 312-358 133-170 (222)
128 PF02237 BPL_C: Biotin protein 21.0 1.6E+02 0.0034 21.6 3.7 28 350-377 16-44 (48)
129 CHL00142 rps17 ribosomal prote 20.4 2.5E+02 0.0055 23.5 5.2 44 277-324 6-61 (84)
No 1
>KOG4582|consensus
Probab=99.95 E-value=3.8e-28 Score=242.28 Aligned_cols=195 Identities=33% Similarity=0.561 Sum_probs=175.3
Q ss_pred ccccceeeeCCCCcccCC---CCCCCccceEEEE--------e--cceEEEEecCCCCCCceeec--CCCcccccccCCC
Q psy16233 4 IEIGLRVIRGPDWKWLDE---DGGEGGLGTVVAV--------K--SNVVSVIWDLGNKSSCYRVG--SENAYDLQVYDSG 68 (464)
Q Consensus 4 i~~G~rVvRG~dW~w~~q---Dgg~g~~Gtv~~~--------~--~~~v~V~Wd~g~~~~~YR~G--~~g~~DL~~~d~a 68 (464)
+.+++||+||.||+|-.+ ++..++++++..+ + ...+.+.||..... ++|.+ +.+..++.+.+++
T Consensus 61 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~s-~~k~~~~~~~~~~~~~~~~~ 139 (278)
T KOG4582|consen 61 DGVGMRVVRGNDLFDVTNQRLADEIGHVNAVRSFNSAAPSSGSSTPATVPVPWDKIPRS-IIKVLEKYQKLASLVITLNP 139 (278)
T ss_pred cccceeEEecCCceEeecccCccccccccceeeeccccccccccCccccccccchhhhh-hhhhhHHHhhhhhhhhhcCC
Confidence 458899999999999999 5566677777766 2 46788889999999 89988 5788899999999
Q ss_pred Ccceeecc-----eEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeE---eecCCCCCCCCCCccccc
Q psy16233 69 PVGIKHET-----ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYR---VDTPTSSTASLPPRRLSK 140 (464)
Q Consensus 69 ~~gv~H~~-----v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r---~~~p~~~~~~~~~r~~~~ 140 (464)
..+..|++ +.||+|...+ |+|.||||++|+|||||+.||+.+.|+..|.|+| ..+|....+.++.++..+
T Consensus 140 ~~~~~H~~~~~~~v~CD~C~~~~--IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t~~t~~~~~~~~~~p~~~~ 217 (278)
T KOG4582|consen 140 VVGEMHPNISKLSVPCDNCGKPG--IVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLHTNETPFSGYVMLSSPPNPV 217 (278)
T ss_pred CccccCCCcccccccCCCccCCc--cccceeeecCCCccchhHHhhcCCCCCcccceeecccccCCCCcceeccCCCCcc
Confidence 99999999 9999999999 9999999999999999999999997889999999 888888889999999999
Q ss_pred ceecccccccceEEeccCccccccCCCCCCcceEEEccCCccccccceeEEEEeecCCCceE
Q psy16233 141 KIYVRGFSIGAKVSRGLNWEWENQDGGPGKTGRIISIEDGKVGKSYRSVAKVLWSIGKENIY 202 (464)
Q Consensus 141 ~~~~~gl~~GarVvRg~dW~w~~QDGg~g~~GtV~~i~~w~~~~~~r~~a~V~W~~g~~~~y 202 (464)
....+++++|..++++.+|.|+.|++.++..|++.++..|. ..+.++.+.+-|..++.+.|
T Consensus 218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 278 (278)
T KOG4582|consen 218 NLNKRPIFVGHSKVRGNDWYWTSLGGGEGRIGRVNEIVLWI-NGPRRSSAVVYWVMGSENDY 278 (278)
T ss_pred cccccccccccccccccCCccccccCCCCCCcccccccccc-ccccccceeeecCCCccCCC
Confidence 99999999999999999999999999999999999999997 88888888888888776554
No 2
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=99.87 E-value=2.9e-23 Score=165.22 Aligned_cols=61 Identities=57% Similarity=1.107 Sum_probs=46.6
Q ss_pred cceeeeCCCCcccCCCCCCCccceEEEEe-------cceEEEEecCCCCCCceeecCCCcccccccCCC
Q psy16233 7 GLRVIRGPDWKWLDEDGGEGGLGTVVAVK-------SNVVSVIWDLGNKSSCYRVGSENAYDLQVYDSG 68 (464)
Q Consensus 7 G~rVvRG~dW~w~~qDgg~g~~Gtv~~~~-------~~~v~V~Wd~g~~~~~YR~G~~g~~DL~~~d~a 68 (464)
|+||||||||+|+|||||+|++|||++|. +++|.|+||+|..+ +||+|++|+|||+++++|
T Consensus 1 G~rVvRGpDW~WgdQDGG~g~~GtV~~i~~~~~~~~~~~v~V~Wd~G~~~-~YR~G~~G~~DL~~~~~a 68 (68)
T PF06701_consen 1 GARVVRGPDWKWGDQDGGEGHVGTVVSIRDWSSESPDGWVVVQWDNGTRN-NYRVGYEGKYDLKVVDNA 68 (68)
T ss_dssp TSEEEE-TT--STTTTSSTT--EEE-S--------BTTEEEEEETTTEEE-EEEBSCCC-B-EEE-T--
T ss_pred CCeeeeCcCCCccCcCCCCCcceEEEecccccccCCCCeEEEEeCCCCce-eccccCCCCEEEEEecCC
Confidence 79999999999999999999999999963 79999999999998 899999999999999886
No 3
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=99.83 E-value=4.5e-21 Score=152.71 Aligned_cols=68 Identities=44% Similarity=0.809 Sum_probs=47.9
Q ss_pred cceEEeccCccccccCCCCCCcceEEEccCCccccccceeEEEEeecCCCceEeecCCCeeEEEEecCC
Q psy16233 150 GAKVSRGLNWEWENQDGGPGKTGRIISIEDGKVGKSYRSVAKVLWSIGKENIYRIGSYGKVDLKCVGSG 218 (464)
Q Consensus 150 GarVvRg~dW~w~~QDGg~g~~GtV~~i~~w~~~~~~r~~a~V~W~~g~~~~yRvg~~G~~Dl~~~~~~ 218 (464)
|+||+|||||+|++|||++|++|||++|..|+ ...++++|.|+|++|..|+||+|++|+|||+++++|
T Consensus 1 G~rVvRGpDW~WgdQDGG~g~~GtV~~i~~~~-~~~~~~~v~V~Wd~G~~~~YR~G~~G~~DL~~~~~a 68 (68)
T PF06701_consen 1 GARVVRGPDWKWGDQDGGEGHVGTVVSIRDWS-SESPDGWVVVQWDNGTRNNYRVGYEGKYDLKVVDNA 68 (68)
T ss_dssp TSEEEE-TT--STTTTSSTT--EEE-S---------BTTEEEEEETTTEEEEEEBSCCC-B-EEE-T--
T ss_pred CCeeeeCcCCCccCcCCCCCcceEEEeccccc-ccCCCCeEEEEeCCCCceeccccCCCCEEEEEecCC
Confidence 79999999999999999999999999999887 778899999999999999999999999999998764
No 4
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.65 E-value=4.6e-17 Score=119.61 Aligned_cols=45 Identities=36% Similarity=1.009 Sum_probs=43.5
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeEe
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRV 123 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r~ 123 (464)
|.||+|+..| |.|.||||++|+|||||+.||....|++.|+|.||
T Consensus 1 V~Cd~C~~~p--I~G~RykC~~C~dyDLC~~Cf~~~~H~~~H~F~ri 45 (45)
T cd02344 1 VTCDGCQMFP--INGPRFKCRNCDDFDFCENCFKTRKHNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCC--CccCeEECCCCCCccchHHhhCCCCcCCCCceeeC
Confidence 5799999999 99999999999999999999999999999999986
No 5
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=99.59 E-value=5.1e-16 Score=114.35 Aligned_cols=45 Identities=58% Similarity=1.407 Sum_probs=43.0
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeEe
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRV 123 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r~ 123 (464)
|.||+|+..| |.|.||||++|+|||||+.||..+.|++.|+|+|+
T Consensus 1 i~Cd~C~~~~--i~G~RykC~~C~dyDLC~~C~~~~~H~~~H~f~r~ 45 (45)
T cd02339 1 IICDTCRKQG--IIGIRWKCAECPNYDLCTTCYHGDKHDLEHRFYRY 45 (45)
T ss_pred CCCCCCCCCC--cccCeEECCCCCCccchHHHhCCCCCCCCCCEEeC
Confidence 5799999989 99999999999999999999999999999999985
No 6
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=99.48 E-value=1.3e-14 Score=105.87 Aligned_cols=43 Identities=47% Similarity=1.076 Sum_probs=40.8
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeEe
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRV 123 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r~ 123 (464)
|.||+|+. + |.|.||||++|+|||||+.||..+.| +.|+|+++
T Consensus 1 v~Cd~C~~-~--i~G~ry~C~~C~d~dLC~~C~~~~~H-~~H~f~~~ 43 (43)
T cd02340 1 VICDGCQG-P--IVGVRYKCLVCPDYDLCESCEAKGVH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCC-c--CcCCeEECCCCCCccchHHhhCcCCC-CCCCEEeC
Confidence 57999999 8 99999999999999999999999999 99999875
No 7
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.45 E-value=3.2e-14 Score=106.21 Aligned_cols=45 Identities=40% Similarity=0.928 Sum_probs=42.4
Q ss_pred eEecCCCCCCCeeeccceeecccC--CCccccccccCC-CCCCcceeeEe
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECS--NYDLCASCYHGD-EHDITHAFYRV 123 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~--d~DLC~~C~~~~-~H~~~H~f~r~ 123 (464)
+.||+|...| |.|+||||++|+ |||||+.||..+ .|++.|+|.+|
T Consensus 1 y~Cd~C~~~p--I~G~R~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEP--IPGTRYHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCc--cccceEECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence 3699999999 999999999999 999999999998 89999999875
No 8
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=99.44 E-value=3.4e-14 Score=106.50 Aligned_cols=44 Identities=39% Similarity=0.987 Sum_probs=39.8
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCC----CCCCcceeeE
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD----EHDITHAFYR 122 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~----~H~~~H~f~r 122 (464)
+.||+|++.| |.|+||||++|+|||||+.||..+ .|.+.|+|..
T Consensus 1 ~~Cd~C~~~p--i~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~e 48 (49)
T cd02334 1 AKCNICKEFP--ITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMKE 48 (49)
T ss_pred CCCCCCCCCC--ceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCeec
Confidence 5799999999 999999999999999999999874 6888888864
No 9
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=99.36 E-value=1.3e-13 Score=102.16 Aligned_cols=46 Identities=37% Similarity=1.027 Sum_probs=36.4
Q ss_pred eecceEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCccee
Q psy16233 73 KHETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAF 120 (464)
Q Consensus 73 ~H~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f 120 (464)
.|.++.||+|+..| |.|.||+|++|+|||||+.||..+.+...|.|
T Consensus 1 ~h~~~~C~~C~~~~--i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~H~~ 46 (46)
T PF00569_consen 1 IHHGYTCDGCGTDP--IIGVRYHCLVCPDYDLCEDCFSKGRHSHNHKM 46 (46)
T ss_dssp -CSSCE-SSS-SSS--EESSEEEESSSSS-EEEHHHHHH--H-SSSSE
T ss_pred CCCCeECcCCCCCc--CcCCeEECCCCCCCchhhHHHhCcCCCCCcCc
Confidence 38899999999999 99999999999999999999999877777764
No 10
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=99.34 E-value=4.2e-13 Score=100.72 Aligned_cols=44 Identities=41% Similarity=1.025 Sum_probs=40.1
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCC----CCCCcceeeE
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD----EHDITHAFYR 122 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~----~H~~~H~f~r 122 (464)
|.||+|...| |.|.||||++|+|||||+.||..+ .|.++|+|..
T Consensus 1 i~C~~C~~~~--i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 1 VSCDGCGKSN--FTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCCCCCcCCC--cEEeeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEE
Confidence 5799999889 999999999999999999999986 7888998864
No 11
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=99.33 E-value=3.5e-13 Score=101.11 Aligned_cols=44 Identities=39% Similarity=1.031 Sum_probs=40.2
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCC----CCCCcceeeE
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD----EHDITHAFYR 122 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~----~H~~~H~f~r 122 (464)
+.||+|...| |.|+||+|++|+|||||..||+.+ .|.+.|+|+.
T Consensus 1 ~~C~~C~~~~--i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02345 1 LSCSACRKQD--ISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48 (49)
T ss_pred CcCCCCCCCC--ceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCccc
Confidence 4799999999 999999999999999999999975 6999999864
No 12
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=99.31 E-value=4.7e-13 Score=96.62 Aligned_cols=33 Identities=39% Similarity=0.868 Sum_probs=31.6
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccC
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHG 111 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~ 111 (464)
|.||+|...| |.|.||||.+|+|||||+.||..
T Consensus 1 I~CDgCg~~P--I~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 1 IQCDGCGVLP--ITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCCc--ccccceEeCCCCCCccHHHHhhh
Confidence 5799999999 99999999999999999999986
No 13
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=99.22 E-value=4.2e-12 Score=93.92 Aligned_cols=44 Identities=45% Similarity=1.090 Sum_probs=40.5
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCC--CCCCcceeeEe
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD--EHDITHAFYRV 123 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~--~H~~~H~f~r~ 123 (464)
+.||+|.. + |.|.||+|++|.|||||..||+.+ .|.+.|+|.++
T Consensus 1 ~~C~~C~~-~--i~g~r~~C~~C~d~dLC~~Cf~~~~~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLK-P--IVGVRYHCLVCEDFDLCSSCYAKGKKGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCC-C--CcCCEEECCCCCCCcCHHHHHCcCcCCCCCCCCEeEC
Confidence 36999999 8 999999999999999999999997 89889999764
No 14
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.17 E-value=9.8e-12 Score=93.24 Aligned_cols=43 Identities=30% Similarity=0.818 Sum_probs=39.5
Q ss_pred EecCCCCCCCeeeccceeecccCCCccccccccCC----CCCCcceeeE
Q psy16233 78 SCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD----EHDITHAFYR 122 (464)
Q Consensus 78 ~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~----~H~~~H~f~r 122 (464)
.||+|...+ +.|.||||++|+|||||..||..+ .|.++|+|+.
T Consensus 2 ~Cd~C~~~~--~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~~~~ 48 (49)
T cd02335 2 HCDYCSKDI--TGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHNYRV 48 (49)
T ss_pred CCCCcCCCC--CCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCCeEe
Confidence 599999988 889999999999999999999985 7999999864
No 15
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.17 E-value=6.4e-12 Score=93.45 Aligned_cols=42 Identities=38% Similarity=0.994 Sum_probs=35.9
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCC----CCCCcceee
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD----EHDITHAFY 121 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~----~H~~~H~f~ 121 (464)
|.||+|.. . +.|.||||++|+|||||..||..+ .|.+.|+|.
T Consensus 1 i~CdgC~~-~--~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~ 46 (48)
T cd02343 1 ISCDGCDE-I--APWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMV 46 (48)
T ss_pred CCCCCCCC-c--CCCceEECCCCCCchhHHHHHhCCccCCCCCCCCCcc
Confidence 46999998 4 789999999999999999999984 566777664
No 16
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=99.12 E-value=2.2e-11 Score=89.33 Aligned_cols=42 Identities=45% Similarity=1.069 Sum_probs=38.9
Q ss_pred ecceEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcc
Q psy16233 74 HETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITH 118 (464)
Q Consensus 74 H~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H 118 (464)
|..+.||.|.. + |.|.||+|++|+|||||..||..+.|+..|
T Consensus 2 ~~~~~C~~C~~-~--i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 2 HHSYSCDTCGK-P--IVGVRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CCCcCCCCCCC-C--CcCCEEECCCCCCccchHHHHhCcCcCCCC
Confidence 56889999999 8 999999999999999999999998887666
No 17
>KOG1280|consensus
Probab=98.96 E-value=2.4e-10 Score=115.20 Aligned_cols=55 Identities=38% Similarity=0.832 Sum_probs=49.8
Q ss_pred eeecceEecCCCCCCCeeeccceeecccCCCccccccccC----CCCCCcceeeEeecCCC
Q psy16233 72 IKHETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHG----DEHDITHAFYRVDTPTS 128 (464)
Q Consensus 72 v~H~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~----~~H~~~H~f~r~~~p~~ 128 (464)
-.|.+|.||+|.... ..|.||||+.|.|||||..||.+ ..|+.+|++.-+-.+..
T Consensus 4 ~rHe~v~CdgC~k~~--~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~d 62 (381)
T KOG1280|consen 4 SRHEGVSCDGCGKTA--FTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVD 62 (381)
T ss_pred CCcCCceeccccccc--eeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccc
Confidence 369999999999988 99999999999999999999997 57999999988877753
No 18
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=98.96 E-value=1.6e-10 Score=83.54 Aligned_cols=39 Identities=38% Similarity=1.074 Sum_probs=33.8
Q ss_pred EecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeE
Q psy16233 78 SCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYR 122 (464)
Q Consensus 78 ~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r 122 (464)
.||+|.. +.|.||+|++|+|||||..||....| .|.+.+
T Consensus 2 ~C~~C~~----~~~~r~~C~~C~dfDLC~~C~~~~~H--~H~~~~ 40 (41)
T cd02337 2 TCNECKH----HVETRWHCTVCEDYDLCITCYNTKNH--PHKMEK 40 (41)
T ss_pred cCCCCCC----cCCCceECCCCcchhhHHHHhCCCCC--Cccccc
Confidence 5999977 56899999999999999999999887 666654
No 19
>KOG4286|consensus
Probab=98.57 E-value=1.7e-08 Score=109.98 Aligned_cols=56 Identities=34% Similarity=0.738 Sum_probs=49.8
Q ss_pred eeecceEecCCCCCCCeeeccceeecccCCCccccccccC----CCCCCcceeeEeecCCCCC
Q psy16233 72 IKHETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHG----DEHDITHAFYRVDTPTSST 130 (464)
Q Consensus 72 v~H~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~----~~H~~~H~f~r~~~p~~~~ 130 (464)
++| ..+|++|++.| |+|+||+|.+|.|||||..||.. ..|.+.|||..|.+|..++
T Consensus 600 ~kH-~~kCniCk~~p--IvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~ 659 (966)
T KOG4286|consen 600 AKH-QAKCNICKECP--IIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSG 659 (966)
T ss_pred HHh-hhhcchhhhCc--cceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCCh
Confidence 344 57899999999 99999999999999999999886 5799999999999998653
No 20
>KOG0457|consensus
Probab=97.84 E-value=6.6e-06 Score=85.87 Aligned_cols=48 Identities=33% Similarity=0.875 Sum_probs=39.4
Q ss_pred ceEecCCCCCCCeeecc-ceeecccCCCccccccccC----CCCCCcceeeEeecCC
Q psy16233 76 TISCDACQDERSCIVGT-RYSCIECSNYDLCASCYHG----DEHDITHAFYRVDTPT 127 (464)
Q Consensus 76 ~v~CD~C~~~~~~I~G~-RykC~~C~d~DLC~~C~~~----~~H~~~H~f~r~~~p~ 127 (464)
..-||.|... |.|. |.||++|+|||||-.||+. +.|...|++ ||..+.
T Consensus 14 ky~C~~C~~d---it~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Y-rim~~~ 66 (438)
T KOG0457|consen 14 KYNCDYCSLD---ITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPY-RIMDTN 66 (438)
T ss_pred CCCCccHhHH---hccceEEEeecCCCcchhHHHHhcccccCCCCCCCCc-eeecCC
Confidence 4679999983 7775 5999999999999999997 679999987 444444
No 21
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=97.58 E-value=3.1e-05 Score=57.23 Aligned_cols=38 Identities=29% Similarity=0.746 Sum_probs=32.5
Q ss_pred EecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcc
Q psy16233 78 SCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITH 118 (464)
Q Consensus 78 ~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H 118 (464)
.|+.|... +..+||+|+.+.+||||..||..+.....|
T Consensus 2 ~C~~Cg~D---~t~vryh~~~~~~~dLC~~CF~~G~f~~~~ 39 (45)
T cd02336 2 HCFTCGND---CTRVRYHNLKAKKYDLCPSCYQEGRFPSNF 39 (45)
T ss_pred cccCCCCc---cCceEEEecCCCccccChHHHhCcCCCCCC
Confidence 59999995 557999999999999999999998765554
No 22
>KOG4301|consensus
Probab=97.50 E-value=1.4e-05 Score=81.09 Aligned_cols=51 Identities=29% Similarity=0.846 Sum_probs=44.1
Q ss_pred eeecceEecCCCCCCCeeeccceeecccCCCccccccccC----CCCCCcceeeEeec
Q psy16233 72 IKHETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHG----DEHDITHAFYRVDT 125 (464)
Q Consensus 72 v~H~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~----~~H~~~H~f~r~~~ 125 (464)
|.| .+.|+.|...+ |.|.||+|..|.+|.||..|+.. +.|+..|.|-.+..
T Consensus 237 v~h-pv~cs~c~srs--~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mke~Ss 291 (434)
T KOG4301|consen 237 VFH-PVECSYCRSRS--MMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMKEYSS 291 (434)
T ss_pred cCC-CccCcceeccc--ccchhhhHhhcCCccccchhhccccCCCCcchHHHHHHhhc
Confidence 444 58999999999 99999999999999999999875 57999998865543
No 23
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.30 E-value=9.4e-05 Score=74.62 Aligned_cols=50 Identities=30% Similarity=0.604 Sum_probs=42.4
Q ss_pred ceEecCCCCCCCeeeccceeecccCCCccccccccC----CCCCCcceeeEeecCC
Q psy16233 76 TISCDACQDERSCIVGTRYSCIECSNYDLCASCYHG----DEHDITHAFYRVDTPT 127 (464)
Q Consensus 76 ~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~----~~H~~~H~f~r~~~p~ 127 (464)
.+.||.|...- ..-++-+|..|++||||-.||.+ +.|++.|++--|.+-.
T Consensus 5 k~hCdvC~~d~--T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietns 58 (432)
T COG5114 5 KIHCDVCFLDM--TDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNS 58 (432)
T ss_pred eeeehHHHHhh--hcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccC
Confidence 36799999865 66789999999999999999997 6899999986666543
No 24
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=90.76 E-value=0.09 Score=35.22 Aligned_cols=27 Identities=48% Similarity=1.089 Sum_probs=12.5
Q ss_pred EecCCCCCCCeeec-cceeecccCCCcccccc
Q psy16233 78 SCDACQDERSCIVG-TRYSCIECSNYDLCASC 108 (464)
Q Consensus 78 ~CD~C~~~~~~I~G-~RykC~~C~d~DLC~~C 108 (464)
.|+.|+. + +.| .-|.|..| ||+|...|
T Consensus 2 ~C~~C~~-~--~~~~~~Y~C~~C-df~lH~~C 29 (30)
T PF07649_consen 2 RCDACGK-P--IDGGWFYRCSEC-DFDLHEEC 29 (30)
T ss_dssp --TTTS-------S--EEE-TTT------HHH
T ss_pred cCCcCCC-c--CCCCceEECccC-CCccChhc
Confidence 6999999 4 666 99999999 89888776
No 25
>KOG1778|consensus
Probab=86.90 E-value=0.35 Score=49.95 Aligned_cols=44 Identities=27% Similarity=0.678 Sum_probs=35.4
Q ss_pred cceEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeEee
Q psy16233 75 ETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRVD 124 (464)
Q Consensus 75 ~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r~~ 124 (464)
....|..|... + ..+|.|.+|++||+|..||....| .|.+....
T Consensus 168 ~~~~c~~c~~~---~-~~~~~c~~~~d~d~~~~~~~k~~h--~h~~~~~~ 211 (319)
T KOG1778|consen 168 FAYTCPICKLE---V-LTAWHCEVCPDYDRCRACEEKPLH--PHLYEAME 211 (319)
T ss_pred eeeecCccccc---c-ccccccccCCchhhhhcccCCCCC--Ccchhccc
Confidence 35789999983 3 789999999999999999999876 56665443
No 26
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=85.54 E-value=3.6 Score=39.80 Aligned_cols=48 Identities=29% Similarity=0.223 Sum_probs=29.9
Q ss_pred CceeEEEEEecC---c-----ceEEEEecCC-eeEEEccCcceecccccCCCEEEEec
Q psy16233 276 GHTGIVHRVTEQ---T-----LVRVRFENCD-NKWTFDPRALTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 276 Gk~G~V~~I~~~---g-----D~rV~~~~~~-~~wtfnP~~L~kv~~~~~GD~V~I~~ 324 (464)
--+|.|.+++.. + -+.|+||+.. ..=+.. -.|++-..|.+||.|+|.-
T Consensus 119 YvIG~Iskv~k~~~~~~~~~dyVvV~YP~~~G~~~~V~-V~LT~GQkFnVGDkVKV~~ 175 (213)
T PRK06763 119 YVIGEVSKVYTMEDDGDGATKYVVVEYPSLNGKKLIID-VFLTKGQVFHVGDKVKVDM 175 (213)
T ss_pred eEEEEEEEecccccCCCCcccEEEEEcCCCCCCeeEEE-EEeccCCEEecCCEEEEEe
Confidence 357888888652 1 2679998722 111111 2355556799999999973
No 27
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=82.72 E-value=4.2 Score=33.90 Aligned_cols=49 Identities=16% Similarity=0.104 Sum_probs=41.8
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecC
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPD 325 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d 325 (464)
.+|+|++..+.+.++|..++...+-..=|+-+.+..-+..||.|.|...
T Consensus 7 ~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~ 55 (83)
T smart00652 7 EIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPW 55 (83)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEec
Confidence 4799999999999999998767777788888888666889999999754
No 28
>KOG1999|consensus
Probab=82.12 E-value=3.2 Score=48.28 Aligned_cols=68 Identities=26% Similarity=0.369 Sum_probs=50.7
Q ss_pred hccCceeEEEEEecCcceEEEEe---cCCeeEEEccCcceecccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCC
Q psy16233 273 NFLGHTGIVHRVTEQTLVRVRFE---NCDNKWTFDPRALTKVDPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGD 349 (464)
Q Consensus 273 ~~lGk~G~V~~I~~~gD~rV~~~---~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~ 349 (464)
+..|-.|+|..|++ .+.+-.+ +.....+|+-..|.|+ |.+||.|+|+.= ..=|+
T Consensus 420 el~glkG~ve~vdg--~~vti~~~~e~l~~pl~~~~~eLrKy--F~~GDhVKVi~G-------------------~~eG~ 476 (1024)
T KOG1999|consen 420 ELKGLKGKVESVDG--TIVTIMSKHEDLKGPLEVPASELRKY--FEPGDHVKVIAG-------------------RYEGD 476 (1024)
T ss_pred eeccceeEEEeccC--ceEEEeeccccCCCccccchHhhhhh--ccCCCeEEEEec-------------------cccCC
Confidence 45667899999986 3433332 3568999999999986 999999999752 33388
Q ss_pred ccEEEEEecCCCeEE
Q psy16233 350 IGIVIKVYEDKDVRV 364 (464)
Q Consensus 350 ~G~V~~v~~dgd~rV 364 (464)
+|-|++|+. +++-+
T Consensus 477 tGlVvrVe~-~~vi~ 490 (1024)
T KOG1999|consen 477 TGLVVRVEQ-GDVIL 490 (1024)
T ss_pred cceEEEEeC-CeEEE
Confidence 999999986 44443
No 29
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=80.76 E-value=1.1 Score=30.10 Aligned_cols=27 Identities=41% Similarity=1.016 Sum_probs=22.8
Q ss_pred EecCCCCCCCeeecc-ceeecccCCCcccccc
Q psy16233 78 SCDACQDERSCIVGT-RYSCIECSNYDLCASC 108 (464)
Q Consensus 78 ~CD~C~~~~~~I~G~-RykC~~C~d~DLC~~C 108 (464)
.|+.|.. . +.|. .|+|..|. |+|...|
T Consensus 2 ~C~~C~~-~--~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRR-K--IDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCC-C--cCCCEeEEeCCCC-CeEcCcc
Confidence 5899987 4 7888 99999998 8887777
No 30
>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=80.49 E-value=4.9 Score=32.41 Aligned_cols=52 Identities=17% Similarity=0.152 Sum_probs=43.7
Q ss_pred cCceeEEEEEecCcceEEEEecCCeeEEEccCccee-cccccCCCEEEEecCh
Q psy16233 275 LGHTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTK-VDPFVAGDFVYFIPDE 326 (464)
Q Consensus 275 lGk~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~k-v~~~~~GD~V~I~~d~ 326 (464)
+--.|+|++...++.++|+.++......+=|+-+.+ -....+||.|.|...+
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~sp 57 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSP 57 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECc
Confidence 445799999999999999998867888888888885 5668899999997654
No 31
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=80.08 E-value=4.8 Score=35.96 Aligned_cols=89 Identities=19% Similarity=0.203 Sum_probs=61.6
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCccee-----cccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCcc
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTK-----VDPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIG 351 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~k-----v~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G 351 (464)
-.|+|.+..+.+.+-|.|++ +..-.-.+.-+.. -++|++||.|....+..... |. -|
T Consensus 15 Y~GtV~~~~~~~~~lV~f~~-~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~~~~~~~~--------Y~---------Pg 76 (124)
T PF15057_consen 15 YPGTVKKCVSSGQFLVEFDD-GDTQEVPISDIIALSDAMRHSLQVGDKVLAPWEPDDCR--------YG---------PG 76 (124)
T ss_pred EeEEEEEccCCCEEEEEECC-CCEEEeChHHeEEccCcccCcCCCCCEEEEecCcCCCE--------Ee---------CE
Confidence 56889998899999999965 3333333322222 35799999999885543332 44 57
Q ss_pred EEEE-----EecCCCeEEEE-eCceeeecCcceeeecc
Q psy16233 352 IVIK-----VYEDKDVRVAF-RKNTWTLSSKCLKLIKS 383 (464)
Q Consensus 352 ~V~~-----v~~dgd~rV~~-~g~~w~~np~~lt~~~~ 383 (464)
+|+. ...+..+.|.| +|+.=...+..+.++++
T Consensus 77 ~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~I~~ 114 (124)
T PF15057_consen 77 TVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIWISP 114 (124)
T ss_pred EEEECccccccCCceEEEEEECCCCCccchhhEEECCH
Confidence 8886 77889999998 88876666666666653
No 32
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=72.20 E-value=5 Score=34.49 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=29.4
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCc
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQT 288 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~g 288 (464)
.|.+||+|-|.+|++. |+| .. -..+-|++|+|+.+.++.
T Consensus 32 ey~~Gd~V~I~IdpSv----~kG----mP--h~rf~G~TG~Vvg~~g~a 70 (98)
T COG2139 32 EYKVGDKVHIDIDPSV----HKG----MP--HPRFQGKTGTVVGVRGRA 70 (98)
T ss_pred hccCCCEEEEEeCccc----ccC----CC--CccccCcceEEEeccCCE
Confidence 4899999999999995 322 11 125789999999999743
No 33
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=71.42 E-value=9.2 Score=34.94 Aligned_cols=49 Identities=22% Similarity=0.348 Sum_probs=37.2
Q ss_pred chhhhhccCceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEe
Q psy16233 268 TPQLLNFLGHTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFI 323 (464)
Q Consensus 268 ~~~M~~~lGk~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~ 323 (464)
+...+...|++|+|++-...|..+|+++ ++.|+.... +.+.+||.|.|.
T Consensus 80 ~~~~~~l~G~~g~v~e~i~~g~g~Vkv~--g~~Wra~~~-----~~l~~G~~V~Vv 128 (140)
T COG1585 80 NQRGEQLVGRRGVVVEDIVEGRGRVKVE--GESWRARSD-----EDLPAGDRVEVV 128 (140)
T ss_pred cchhhHhcCcEEEEEeeccCCeEEEEEC--CeEeEEecC-----CCCCCCCEEEEE
Confidence 3345678899999999776899999994 699998741 223379999984
No 34
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=70.81 E-value=11 Score=30.98 Aligned_cols=48 Identities=19% Similarity=0.124 Sum_probs=41.3
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecC
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPD 325 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d 325 (464)
.|+|++..+.+-++|..++...+-..=|+-+.+-.-+..||.|.|...
T Consensus 3 ~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~ 50 (77)
T cd05793 3 YGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPW 50 (77)
T ss_pred EEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEec
Confidence 689999999999999998867788888888888666889999999754
No 35
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=70.78 E-value=13 Score=31.48 Aligned_cols=53 Identities=25% Similarity=0.263 Sum_probs=42.0
Q ss_pred ccCceeEEEEEecCcceEEEEecCCeeEEEccCccee-cccccCCCEEEEecCh
Q psy16233 274 FLGHTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTK-VDPFVAGDFVYFIPDE 326 (464)
Q Consensus 274 ~lGk~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~k-v~~~~~GD~V~I~~d~ 326 (464)
.+-..|+|+++..++.++|+.++....-.+=++=+.+ ...+.+||.|.|...+
T Consensus 6 ~ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~sp 59 (87)
T PRK12442 6 LIELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSP 59 (87)
T ss_pred eEEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECc
Confidence 4556899999999999999998756666666766666 4568899999996643
No 36
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.36 E-value=8 Score=32.80 Aligned_cols=36 Identities=22% Similarity=0.430 Sum_probs=32.6
Q ss_pred cCCccEEEEEe--cCCCeEEEEeCceeeecCcceeeec
Q psy16233 347 LGDIGIVIKVY--EDKDVRVAFRKNTWTLSSKCLKLIK 382 (464)
Q Consensus 347 lG~~G~V~~v~--~dgd~rV~~~g~~w~~np~~lt~~~ 382 (464)
-|.+|+|..|. .||+++|..+.....|+|..|..+.
T Consensus 20 TgTvgrV~dIkkdEdG~~WV~LdstdLwYre~~le~vd 57 (97)
T COG4014 20 TGTVGRVVDIKKDEDGDIWVVLDSTDLWYREHYLEVVD 57 (97)
T ss_pred cCceeeEEEEEeecCCceEEEEecCCceecccceeeec
Confidence 37899999985 8999999999999999999999887
No 37
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=67.88 E-value=17 Score=33.97 Aligned_cols=48 Identities=10% Similarity=-0.034 Sum_probs=42.2
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEec
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~ 324 (464)
..|+|++..+.+-++|...+...+...=|+-+.|..-+..||.|.|..
T Consensus 34 ~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEec
Confidence 479999999999999998776788888899999877788999999954
No 38
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=65.65 E-value=23 Score=45.19 Aligned_cols=102 Identities=13% Similarity=0.202 Sum_probs=70.7
Q ss_pred cccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEec-CcceEEEEecCCeeEEEccCcc----eec--
Q psy16233 239 YIFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTE-QTLVRVRFENCDNKWTFDPRAL----TKV-- 311 (464)
Q Consensus 239 ~~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~-~gD~rV~~~~~~~~wtfnP~~L----~kv-- 311 (464)
..|++||+|.- .+.+ ..-+..++|..|+. ++-+.|++.+ |..-+|+|..+ ..+
T Consensus 680 ~~Yr~Gdvv~~---------y~~~----------~~~~~~y~V~~V~~~~n~L~l~~~d-G~~~~~~p~~l~~~~~~~sv 739 (1960)
T TIGR02760 680 AHYKQGMVIRF---------WQKG----------KIPHDDYVVTNVNKHNNTLTLKDAQ-GKTQKFKPSSLKDLERPFSV 739 (1960)
T ss_pred hhcCCCCEEEe---------eccc----------CccCCcEEEEEEeCCCCEEEEEcCC-CCEEEECHHHhcccccceee
Confidence 45888999875 1111 11223468999987 5677888865 89999999988 222
Q ss_pred -----ccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEE-eCceeeecC
Q psy16233 312 -----DPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAF-RKNTWTLSS 375 (464)
Q Consensus 312 -----~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~-~g~~w~~np 375 (464)
.+|.+||++++.-..... + -.=|+..+|.+|..++ +.|+. +|+.+++++
T Consensus 740 y~~~~l~ia~Gdrl~~trn~~~~--------g------l~ng~~~tV~~i~~~~-i~l~~~~g~~~~L~~ 794 (1960)
T TIGR02760 740 YRPEQLEVAAGERLQVTGNHFHS--------R------VRNGELLTVSSINNEG-ITLITEDGQTLHLPH 794 (1960)
T ss_pred eccccccccCCCEEEEccCCccc--------C------ccCCCEEEEEEEcCCe-EEEEeCCCceEEccC
Confidence 369999999997653211 1 1236788899999865 77777 688888754
No 39
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=65.51 E-value=10 Score=29.90 Aligned_cols=49 Identities=24% Similarity=0.291 Sum_probs=36.5
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecC
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPD 325 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d 325 (464)
.+|+|++..+.+-++|..++....-..=|+-..+..-+..||.|.|...
T Consensus 5 ~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 5 VIGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp EEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEES
T ss_pred EEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEec
Confidence 4799999999999999998855666666666666666899999999854
No 40
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=65.47 E-value=17 Score=30.00 Aligned_cols=50 Identities=22% Similarity=0.147 Sum_probs=42.0
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecCh
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPDE 326 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d~ 326 (464)
.+|+|++..+.+-++|..++...+-..=|+-+.+-.-+..||.|.|....
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~ 51 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIE 51 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEecc
Confidence 37899999999999999988677777778888877778899999996543
No 41
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=64.89 E-value=21 Score=31.38 Aligned_cols=47 Identities=21% Similarity=0.393 Sum_probs=33.4
Q ss_pred hhhccCceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEec
Q psy16233 271 LLNFLGHTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 271 M~~~lGk~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~ 324 (464)
+...+|+.|+|..+..++.-+|++. +..|+-. .. ..+..||.|+|..
T Consensus 86 ~~~liG~~g~v~~~~~~~~G~V~~~--G~~w~A~----s~-~~i~~G~~V~Vv~ 132 (144)
T PF01957_consen 86 EDDLIGKEGTVIEIPLNGSGRVKVD--GERWRAR----SE-DEIPKGDRVRVVG 132 (144)
T ss_dssp -GGGTTSEEEEEEEBSSS-EEEEET--TEEEEEE----ES-STB-TT-EEEEEE
T ss_pred HHHHcCCeEEEEEeecCCcEEEEEC--CeEEEEE----eC-CCCCCCCEEEEEE
Confidence 4678999999988888888899994 6888753 22 2288999999853
No 42
>PLN00208 translation initiation factor (eIF); Provisional
Probab=64.62 E-value=21 Score=32.93 Aligned_cols=66 Identities=14% Similarity=-0.023 Sum_probs=51.3
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecC--------------hHHHHhhhccCchhHHH
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPD--------------ELSAKEHLKGHGEWIAA 342 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d--------------~~~vk~lQ~ghGgW~~~ 342 (464)
..|+|++..+.+.++|.-.+..++-..=|+-+.|..-+..||.|.|... .+.++.|.+. |.|-+.
T Consensus 34 ~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv~ry~~dqvr~Lkk~-G~~P~~ 112 (145)
T PLN00208 34 EYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAY-GELPEN 112 (145)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEEEEcCHHHHHHHHHc-CCCCcc
Confidence 4799999999999999987767888888999998777889999999532 5566666554 556543
Q ss_pred H
Q psy16233 343 M 343 (464)
Q Consensus 343 M 343 (464)
.
T Consensus 113 f 113 (145)
T PLN00208 113 T 113 (145)
T ss_pred e
Confidence 3
No 43
>KOG4317|consensus
Probab=64.09 E-value=2.9 Score=42.98 Aligned_cols=45 Identities=29% Similarity=0.826 Sum_probs=35.1
Q ss_pred cceEecCCCCCCCeeeccceeecccCCCccccc-cccCCCCCCcceeeEeec
Q psy16233 75 ETISCDACQDERSCIVGTRYSCIECSNYDLCAS-CYHGDEHDITHAFYRVDT 125 (464)
Q Consensus 75 ~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~-C~~~~~H~~~H~f~r~~~ 125 (464)
+-..|-.|..++ .||+|-.| |+-.|+- ||.++.|.-+-.|||-..
T Consensus 6 ~~~~C~ic~vq~-----~~YtCPRC-n~~YCsl~CYr~h~~~CsE~FyrdqV 51 (383)
T KOG4317|consen 6 SFLACGICGVQK-----REYTCPRC-NLLYCSLKCYRNHKHSCSEKFYRDQV 51 (383)
T ss_pred ceeecccccccc-----ccccCCCC-CccceeeeeecCCCccchHHHHHHHH
Confidence 356788888877 57999999 5667886 999999977777887544
No 44
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=64.07 E-value=11 Score=31.38 Aligned_cols=39 Identities=26% Similarity=0.345 Sum_probs=29.5
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCcee
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTW 371 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w 371 (464)
.+..||+|.|..=.+ -|++|+|++|+.+.. +|.+.|-+-
T Consensus 8 ~I~~GD~V~Vi~G~d-------------------KGK~G~V~~V~~~~~-~V~Vegvn~ 46 (83)
T CHL00141 8 HVKIGDTVKIISGSD-------------------KGKIGEVLKIIKKSN-KVIVKGINI 46 (83)
T ss_pred cccCCCEEEEeEcCC-------------------CCcEEEEEEEEcCCC-EEEEcCcEE
Confidence 478999999976432 289999999997554 677766554
No 45
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=63.87 E-value=17 Score=31.41 Aligned_cols=48 Identities=25% Similarity=0.251 Sum_probs=42.1
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEec
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~ 324 (464)
..|+|++..+.+-++|..++...+...=|+-+.+..-+..||.|.|..
T Consensus 23 ~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~ 70 (100)
T PRK04012 23 VFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAP 70 (100)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEe
Confidence 479999999999999998876788888888888866788999999975
No 46
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=61.03 E-value=14 Score=30.35 Aligned_cols=39 Identities=28% Similarity=0.353 Sum_probs=28.7
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCcee
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTW 371 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w 371 (464)
.+..||.|.|..=.+ =|++|+|++|+.... +|-+.|-+-
T Consensus 6 ~I~kGD~V~Vi~G~d-------------------KGK~G~V~~V~~~~~-~V~Vegvn~ 44 (76)
T PRK12281 6 KVKKGDMVKVIAGDD-------------------KGKTGKVLAVLPKKN-RVIVEGVKI 44 (76)
T ss_pred cccCCCEEEEeEcCC-------------------CCcEEEEEEEEcCCC-EEEEcCcEE
Confidence 478899999976432 289999999997554 666666544
No 47
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=60.73 E-value=20 Score=38.83 Aligned_cols=85 Identities=28% Similarity=0.446 Sum_probs=56.9
Q ss_pred cccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcceE-EEEecCCeeEEEccCcceecccccCCCE
Q psy16233 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTLVR-VRFENCDNKWTFDPRALTKVDPFVAGDF 319 (464)
Q Consensus 241 f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD~r-V~~~~~~~~wtfnP~~L~kv~~~~~GD~ 319 (464)
|++||.|-|.. | +--|..|.|.+... +|. ..|. .+++.++--.-|+| .|..||+
T Consensus 91 fqpgD~~Evl~-------------G-------eqrg~~gVV~~~~~--~I~tm~~~-~~~rl~~p~~~lRk--~f~~gD~ 145 (607)
T COG5164 91 FQPGDALEVLR-------------G-------EQRGRVGVVPRQKE--MIETMTYH-FEQRLCGPWGRLRK--GFYKGDL 145 (607)
T ss_pred cCCCCeeeeec-------------c-------eecccceeeccccc--ceeeeeec-cCceeecchhhhhc--ccccCCe
Confidence 89999988741 1 33456777776654 333 3443 36777777666776 5999999
Q ss_pred EEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCceeeecCccee
Q psy16233 320 VYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTWTLSSKCLK 379 (464)
Q Consensus 320 V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~~np~~lt 379 (464)
|+|+.-.+++ .+|.|..|+. ..-||||..+.
T Consensus 146 vkVI~g~~~~-------------------d~g~V~rI~~----------~~vtF~s~~~~ 176 (607)
T COG5164 146 VKVIEGGEMV-------------------DIGTVPRIDG----------EKVTFNSENFK 176 (607)
T ss_pred EEEecccccc-------------------ccceEEEecC----------ceeEEcccccc
Confidence 9998764443 4777777764 56788886654
No 48
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=59.82 E-value=22 Score=30.67 Aligned_cols=48 Identities=23% Similarity=0.240 Sum_probs=40.8
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEec
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~ 324 (464)
..|+|++..+.+.++|..++...+-..=|+-+.+..-+..||.|.|+.
T Consensus 21 ~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp 68 (99)
T TIGR00523 21 ILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKP 68 (99)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEE
Confidence 579999999999999998876677777788888866688999999954
No 49
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=58.75 E-value=10 Score=31.40 Aligned_cols=37 Identities=30% Similarity=0.271 Sum_probs=23.7
Q ss_pred ccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCC--CeEEEE
Q psy16233 314 FVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDK--DVRVAF 366 (464)
Q Consensus 314 ~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dg--d~rV~~ 366 (464)
+++|=+|+.+.|-|.|. .|.+|+|.+++.|| +|.|++
T Consensus 18 i~~GM~VRc~~~yeeV~----------------~GD~G~V~k~~~dg~~~lnvqv 56 (78)
T PF11515_consen 18 IQPGMRVRCCRDYEEVR----------------AGDEGEVFKQDRDGLHDLNVQV 56 (78)
T ss_dssp --TT-EEEESS-BTTB-----------------TT-EEE-EEEE-TTSSE--EEE
T ss_pred CCCCcEEEEeccccccc----------------ccccceeEeeccCCCCCcceEE
Confidence 78899999999988775 48999999999988 656777
No 50
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=58.62 E-value=15 Score=28.00 Aligned_cols=38 Identities=29% Similarity=0.420 Sum_probs=31.2
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeC
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRK 368 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g 368 (464)
.|++||.|-+..+. .|.|- .|+|+++..++...|.|.+
T Consensus 2 ~~~~G~~Ve~~~~~---------~~~W~---------~a~V~~~~~~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKE---------EDSWW---------EAVVTKVLGDGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECC---------CCEEE---------EEEEEEECCCCEEEEEECC
Confidence 47899999998753 68898 7899999987778888855
No 51
>CHL00010 infA translation initiation factor 1
Probab=58.28 E-value=34 Score=28.00 Aligned_cols=49 Identities=18% Similarity=0.239 Sum_probs=34.4
Q ss_pred ceeEEEEEecCcceEEEEecCCeeE-EEccCcceec-ccccCCCEEEEecCh
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKW-TFDPRALTKV-DPFVAGDFVYFIPDE 326 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~w-tfnP~~L~kv-~~~~~GD~V~I~~d~ 326 (464)
..|+|+++.+.+-+.|+.++ +..+ +.-++-|.+- ....+||.|.+...+
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~-g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~ 59 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDN-GCQVLGYISGKIRRNSIRILPGDRVKVELSP 59 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCC-CCEEEEEeccceecCCcccCCCCEEEEEEcc
Confidence 57999999988999998654 4444 4444455542 346789999998543
No 52
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=57.93 E-value=6.2 Score=31.62 Aligned_cols=33 Identities=24% Similarity=0.656 Sum_probs=24.2
Q ss_pred ceeecccC---CCccccccccCCCCCCcceeeEeecC
Q psy16233 93 RYSCIECS---NYDLCASCYHGDEHDITHAFYRVDTP 126 (464)
Q Consensus 93 RykC~~C~---d~DLC~~C~~~~~H~~~H~f~r~~~p 126 (464)
-|+|..|. ..=+|..||....| ..|.+..+...
T Consensus 13 ~y~C~tC~~~~~~~iC~~CF~~~~H-~gH~~~~~~~~ 48 (71)
T PF02207_consen 13 FYRCLTCSLDESSGICEECFANSCH-EGHRVVYYRSS 48 (71)
T ss_dssp EEEETTTBSSTT-BBEHHHHCTSGG-GGSSEEEEE--
T ss_pred EEECccCCCCCCEEEchhhCCCCCc-CCCcEEEEEeC
Confidence 47777775 47799999999988 48988877665
No 53
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=57.12 E-value=35 Score=27.30 Aligned_cols=53 Identities=25% Similarity=0.416 Sum_probs=36.9
Q ss_pred cCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCc--eeEEEEEe---cCc-ceEEEEecCCeeEEEc
Q psy16233 243 RGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGH--TGIVHRVT---EQT-LVRVRFENCDNKWTFD 304 (464)
Q Consensus 243 vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk--~G~V~~I~---~~g-D~rV~~~~~~~~wtfn 304 (464)
+|++|+|.+..- . -.-...|.+.||+ +|+|.... +.| =+.|++++..+.|.|.
T Consensus 1 IGqkVrV~~~~i-----r----DRi~~~l~~~l~~~~~g~I~~fKmtDG~giG~vv~~~ng~~~WFFe 59 (64)
T PF11061_consen 1 IGQKVRVNLSRI-----R----DRIPKELVDKLGKNPIGTIKGFKMTDGSGIGVVVEFSNGSRTWFFE 59 (64)
T ss_pred CCCEEEEeehhh-----h----hhccHHHHHHhccCCcEEEEEEEEecCCcEEEEEEecCCceeEEch
Confidence 588999853322 1 1234567888999 99998753 344 5779998878999885
No 54
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=56.08 E-value=30 Score=26.32 Aligned_cols=51 Identities=29% Similarity=0.405 Sum_probs=37.2
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcceEEEEec--CCeeEEEccCcce
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTLVRVRFEN--CDNKWTFDPRALT 309 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD~rV~~~~--~~~~wtfnP~~L~ 309 (464)
.|.+||+|-+..+. .+.|. .|+|+++.+.+-+.|.|.+ .+..-++....|+
T Consensus 2 ~~~~G~~Ve~~~~~----------~~~W~---------~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LR 54 (61)
T smart00743 2 DFKKGDRVEVFSKE----------EDSWW---------EAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLR 54 (61)
T ss_pred CcCCCCEEEEEECC----------CCEEE---------EEEEEEECCCCEEEEEECCCCcccEEEEeHHHcc
Confidence 37899999997543 36785 6889999987789999976 5555555544444
No 55
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=55.23 E-value=37 Score=42.87 Aligned_cols=83 Identities=18% Similarity=0.204 Sum_probs=57.2
Q ss_pred eeEEEEEecCc-ceEEEEecCCeeEEEccCcce--ec-------ccccCCCEEEEecChHHHHhhhccCchhHHHHhhhc
Q psy16233 278 TGIVHRVTEQT-LVRVRFENCDNKWTFDPRALT--KV-------DPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDL 347 (464)
Q Consensus 278 ~G~V~~I~~~g-D~rV~~~~~~~~wtfnP~~L~--kv-------~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~l 347 (464)
--+|..|+.++ -+.|+-+. |...+|+|.-+. .+ ..|.+||+|++...-. .+ |+ .-
T Consensus 1290 y~~V~~vd~~~~~ltl~~~~-G~~~~~~P~~~~~~~~~vy~~~~~ela~GDrIr~TrnDk---~~-----G~------~N 1354 (1747)
T PRK13709 1290 YHRIAGIDKDDGLITLRDAE-GNTRLISPREAVAEGVTLYTPDTIRVGTGDRMRFTKSDR---ER-----GY------VA 1354 (1747)
T ss_pred eEEEEEEcCCCCEEEEEcCC-CCEEEeChhhcccccccccccccccccCCCEEEEcccCc---cc-----cc------cc
Confidence 35788887654 45565544 889999997652 11 2599999999965421 11 21 33
Q ss_pred CCccEEEEEecCCCeEEEEeCceeeecCc
Q psy16233 348 GDIGIVIKVYEDKDVRVAFRKNTWTLSSK 376 (464)
Q Consensus 348 G~~G~V~~v~~dgd~rV~~~g~~w~~np~ 376 (464)
|+.++|..|+.++ +.+.-.+...+++|.
T Consensus 1355 g~~~tV~~I~~~~-I~l~~~~~~~~l~~~ 1382 (1747)
T PRK13709 1355 NSVWTVTAVSGDS-VTLSDGQQTRVIRPG 1382 (1747)
T ss_pred CCEEEEEEEcCCe-EEEEcCCceEEeccc
Confidence 7789999999888 777766667889875
No 56
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=53.95 E-value=20 Score=41.48 Aligned_cols=49 Identities=24% Similarity=0.346 Sum_probs=42.9
Q ss_pred ccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCceeeecCcceeeec
Q psy16233 312 DPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTWTLSSKCLKLIK 382 (464)
Q Consensus 312 ~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~~np~~lt~~~ 382 (464)
..|.+||.|+|. .+|+.|.|++|..++++.|.+++-..+.+..-|.++.
T Consensus 635 ~~~~~Gd~V~v~----------------------~~~~~g~v~~i~~~~~~~V~~g~~k~~v~~~~l~~~~ 683 (782)
T PRK00409 635 EELKVGDEVKYL----------------------SLGQKGEVLSIPDDKEAIVQAGIMKMKVPLSDLEKIQ 683 (782)
T ss_pred cCCCCCCEEEEc----------------------cCCceEEEEEEcCCCeEEEEECCEEEEEeHHHceeCc
Confidence 469999999984 3789999999987789999999999999999998776
No 57
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=51.57 E-value=41 Score=27.70 Aligned_cols=53 Identities=19% Similarity=0.206 Sum_probs=42.1
Q ss_pred cCceeEEEEEecCcceEEEEecCCeeEEEccCccee-cccccCCCEEEEecChH
Q psy16233 275 LGHTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTK-VDPFVAGDFVYFIPDEL 327 (464)
Q Consensus 275 lGk~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~k-v~~~~~GD~V~I~~d~~ 327 (464)
+--.|+|.+.-..+-++|+-++...+.--=|+-+.+ ..-+..||.|.|...+-
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~ 60 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPY 60 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEeccc
Confidence 345689999999999999988755666666777777 56789999999976543
No 58
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=51.42 E-value=13 Score=29.57 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=21.8
Q ss_pred HHHHHhhcCChHHHHHHHHhCCCccc
Q psy16233 432 AVMREVVRGNPSAVKAFLENNANLID 457 (464)
Q Consensus 432 ~lv~~aa~g~~~~v~~~l~~~p~~v~ 457 (464)
+++.+|.+||.+++.++|+.|-..++
T Consensus 2 ~vI~~A~~GD~~A~~~IL~~y~~yI~ 27 (65)
T PF12645_consen 2 EVIKAAKQGDPEAMEEILKHYEPYIS 27 (65)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 47899999999999999998765443
No 59
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=51.12 E-value=24 Score=30.69 Aligned_cols=38 Identities=26% Similarity=0.315 Sum_probs=27.6
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCce
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNT 370 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~ 370 (464)
.+..||+|.|.+=.+ -|++|+|++|+.... +|-+.|-+
T Consensus 3 ~ikkGD~V~Vi~G~d-------------------KGK~G~V~~V~~~~~-~V~VegvN 40 (104)
T TIGR01079 3 KIKKGDTVKVISGKD-------------------KGKRGKVLKVLPKTN-KVIVEGVN 40 (104)
T ss_pred cccCCCEEEEeEcCC-------------------CCcEEEEEEEEcCCC-EEEECCcE
Confidence 367899999976432 289999999987554 66665543
No 60
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=50.60 E-value=25 Score=30.57 Aligned_cols=39 Identities=28% Similarity=0.329 Sum_probs=28.5
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCcee
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTW 371 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w 371 (464)
.+..||+|.|..=.+ -|++|+|++|+.+.. +|.+.|-+-
T Consensus 4 ~i~kGD~V~Vi~G~d-------------------KGk~G~V~~V~~~~~-~V~Vegvn~ 42 (105)
T PRK00004 4 KIKKGDTVIVIAGKD-------------------KGKRGKVLKVLPKKN-KVIVEGVNI 42 (105)
T ss_pred cccCCCEEEEeEcCC-------------------CCcEEEEEEEEcCCC-EEEEcCcEE
Confidence 478899999976332 399999999997554 666655443
No 61
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=50.60 E-value=24 Score=31.60 Aligned_cols=39 Identities=23% Similarity=0.321 Sum_probs=29.0
Q ss_pred ccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCceee
Q psy16233 314 FVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTWT 372 (464)
Q Consensus 314 ~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~ 372 (464)
+..||.|.|..-.+. |+.|+|++|+.... +|-+.|-+-.
T Consensus 46 IkkGD~V~VisG~~K-------------------Gk~GkV~~V~~~~~-~V~VeGvn~~ 84 (120)
T PRK01191 46 VRKGDTVKVMRGDFK-------------------GEEGKVVEVDLKRG-RIYVEGVTVK 84 (120)
T ss_pred EeCCCEEEEeecCCC-------------------CceEEEEEEEcCCC-EEEEeCcEEE
Confidence 778999999875432 89999999987544 6666665543
No 62
>KOG1999|consensus
Probab=49.09 E-value=25 Score=41.22 Aligned_cols=90 Identities=26% Similarity=0.269 Sum_probs=56.2
Q ss_pred cccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcceEEEEecCCeeEEEccCcce---ec------
Q psy16233 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTLVRVRFENCDNKWTFDPRALT---KV------ 311 (464)
Q Consensus 241 f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~---kv------ 311 (464)
|.+||.|+|+. | .+-|.+|.|++|+. +++.+--.......++-+.-|. +|
T Consensus 460 F~~GDhVKVi~----------G----------~~eG~tGlVvrVe~-~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~ 518 (1024)
T KOG1999|consen 460 FEPGDHVKVIA----------G----------RYEGDTGLVVRVEQ-GDVILLSDLTMEELKVFARDLQLCSEVTLGVEK 518 (1024)
T ss_pred ccCCCeEEEEe----------c----------cccCCcceEEEEeC-CeEEEEecCccceeeEEehhcccchheeecccc
Confidence 88999999962 2 57789999999997 5555543222233444444444 33
Q ss_pred -ccccCCCEEEEecC-hHHHHhhhccCchhHHHHhhhcCCccEEEEEec
Q psy16233 312 -DPFVAGDFVYFIPD-ELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYE 358 (464)
Q Consensus 312 -~~~~~GD~V~I~~d-~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~ 358 (464)
..|+.+|+|+.+.- .--+-+| +| ...+.|++.|+|+.|..
T Consensus 519 ~ge~e~hdlVqLd~~~vgvI~rl--e~-----e~~~vl~~~g~v~~i~~ 560 (1024)
T KOG1999|consen 519 SGEYELHDLVQLDNQNVGVIVRL--ER-----ETFQVLGMNGKVVTIRK 560 (1024)
T ss_pred cccccccceeecCCCcEEEEEEe--cc-----hheeeecCcCceEEEee
Confidence 24889999887553 2222222 11 23467888888888765
No 63
>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=47.80 E-value=50 Score=29.75 Aligned_cols=53 Identities=25% Similarity=0.339 Sum_probs=37.4
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCC-CeEEEE--eCce--eeecCcceeeeccC
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDK-DVRVAF--RKNT--WTLSSKCLKLIKSN 384 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dg-d~rV~~--~g~~--w~~np~~lt~~~~~ 384 (464)
.|.+||.|+|..- +.-|..|.|.+++... .++|.+ .+.. -+++...|.++.++
T Consensus 86 ~~~~Gd~V~I~~G-------------------Pf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~~~ 143 (145)
T TIGR00405 86 SIKKGDIVEIISG-------------------PFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQKE 143 (145)
T ss_pred ccCCCCEEEEeec-------------------CCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEeccc
Confidence 3788999999752 5668999999998533 444444 4555 67777777777643
No 64
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=46.90 E-value=36 Score=29.68 Aligned_cols=46 Identities=17% Similarity=0.204 Sum_probs=33.8
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEccCcceec---ccccCCCEEEEe-cChHHH
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKV---DPFVAGDFVYFI-PDELSA 329 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv---~~~~~GD~V~I~-~d~~~v 329 (464)
+|+|..|-+| |+.|.| .|.|+-.|-... ..|..|++|+|. .|+|.-
T Consensus 28 ~G~I~hvv~d-dLYIDf-----G~KFhcVc~rp~~~~~~y~~G~rV~lrLkdlELs 77 (104)
T PF10246_consen 28 IGKIFHVVDD-DLYIDF-----GGKFHCVCKRPAVNGEKYVRGSRVRLRLKDLELS 77 (104)
T ss_pred EEEEEEEecC-ceEEEe-----CCceeEEEecccccccccccCCEEEEEECCHhhh
Confidence 6889999986 999987 277775554432 249999999984 477654
No 65
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=46.78 E-value=68 Score=25.72 Aligned_cols=50 Identities=20% Similarity=0.197 Sum_probs=33.7
Q ss_pred CceeEEEEEecCcceEEEEecCCeeE-EEccCccee-cccccCCCEEEEecCh
Q psy16233 276 GHTGIVHRVTEQTLVRVRFENCDNKW-TFDPRALTK-VDPFVAGDFVYFIPDE 326 (464)
Q Consensus 276 Gk~G~V~~I~~~gD~rV~~~~~~~~w-tfnP~~L~k-v~~~~~GD~V~I~~d~ 326 (464)
-..|+|++..+.+-+.|+.++ +..+ +.-++.|.+ -....+||.|.+..++
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~-g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~ 59 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELEN-GHEVLAHISGKMRKNYIRILPGDKVTVELSP 59 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-CCEEEEEEccceeeCCcccCCCCEEEEEEcc
Confidence 346899999987788887644 4344 444445553 2347899999998543
No 66
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=46.67 E-value=11 Score=26.62 Aligned_cols=39 Identities=23% Similarity=0.577 Sum_probs=27.6
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCCCCCCcceeeEe
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRV 123 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H~~~H~f~r~ 123 (464)
..|+.|...+ .+|-|..|.. -+|..|.... | ..|.+..|
T Consensus 4 ~~C~~H~~~~-----~~~~C~~C~~-~~C~~C~~~~-H-~~H~~~~i 42 (42)
T PF00643_consen 4 PKCPEHPEEP-----LSLFCEDCNE-PLCSECTVSG-H-KGHKIVPI 42 (42)
T ss_dssp SB-SSTTTSB-----EEEEETTTTE-EEEHHHHHTS-T-TTSEEEEC
T ss_pred ccCccCCccc-----eEEEecCCCC-ccCccCCCCC-C-CCCEEeEC
Confidence 4576676643 5788999877 6999999887 6 45877543
No 67
>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A.
Probab=46.17 E-value=21 Score=26.65 Aligned_cols=31 Identities=16% Similarity=0.183 Sum_probs=21.4
Q ss_pred HHHHHhhcCChHHHHHHHHhCCCcccccCCCC
Q psy16233 432 AVMREVVRGNPSAVKAFLENNANLIDCPVLGG 463 (464)
Q Consensus 432 ~lv~~aa~g~~~~v~~~l~~~p~~v~~~~~~g 463 (464)
-|..||..|+.+-|+.+| +++..++.+...|
T Consensus 19 ~LH~A~~~g~~~~v~~Ll-~~g~d~~~~d~~G 49 (56)
T PF13857_consen 19 PLHWAARYGHSEVVRLLL-QNGADPNAKDKDG 49 (56)
T ss_dssp HHHHHHHHT-HHHHHHHH-HCT--TT---TTS
T ss_pred HHHHHHHcCcHHHHHHHH-HCcCCCCCCcCCC
Confidence 399999999999999999 8888888876444
No 68
>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=45.45 E-value=27 Score=27.53 Aligned_cols=40 Identities=25% Similarity=0.565 Sum_probs=26.6
Q ss_pred cccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcceEEEEec
Q psy16233 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTLVRVRFEN 296 (464)
Q Consensus 241 f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD~rV~~~~ 296 (464)
|.+||+|-|..+.+ |.+|-|. .++|++...+.-+.|+|.+
T Consensus 1 F~~G~~VEV~s~e~-------g~~gaWf---------~a~V~~~~~~~~~~V~Y~~ 40 (68)
T PF05641_consen 1 FKKGDEVEVSSDED-------GFRGAWF---------PATVLKENGDDKYLVEYDD 40 (68)
T ss_dssp --TT-EEEEEE-SB-------TT--EEE---------EEEEEEEETT-EEEEEETT
T ss_pred CCCCCEEEEEEcCC-------CCCcEEE---------EEEEEEeCCCcEEEEEECC
Confidence 67899999987766 3367796 5788899887789999954
No 69
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=44.60 E-value=16 Score=31.58 Aligned_cols=41 Identities=27% Similarity=0.460 Sum_probs=31.1
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhh--hccCceeEEEEEecCcceEEE
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLL--NFLGHTGIVHRVTEQTLVRVR 293 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~--~~lGk~G~V~~I~~~gD~rV~ 293 (464)
.|.+||.|-|..|++. |+| |- .+=|++|+|..++.+ .+-|.
T Consensus 34 ~y~~Gd~V~I~~d~sv----~kG--------mPh~~yhGkTG~V~~v~~~-A~~V~ 76 (98)
T PRK04306 34 EFEEGDKVHIVIDPSV----HKG--------MPHPRFHGKTGTVVGKRGR-AYIVE 76 (98)
T ss_pred hccCCCEEEEEecCce----ecC--------CccccccCCCEEEEeecCe-EEEEE
Confidence 4889999999999984 333 32 478999999999985 34443
No 70
>PF13606 Ank_3: Ankyrin repeat
Probab=44.57 E-value=28 Score=22.99 Aligned_cols=24 Identities=25% Similarity=0.300 Sum_probs=20.0
Q ss_pred HHHHhhcCChHHHHHHHHhCCCccc
Q psy16233 433 VMREVVRGNPSAVKAFLENNANLID 457 (464)
Q Consensus 433 lv~~aa~g~~~~v~~~l~~~p~~v~ 457 (464)
|-.|+..|+.+.|+-+|+.. ..||
T Consensus 6 Lh~A~~~g~~e~v~~Ll~~g-advn 29 (30)
T PF13606_consen 6 LHLAASNGNIEIVKYLLEHG-ADVN 29 (30)
T ss_pred HHHHHHhCCHHHHHHHHHcC-CCCC
Confidence 78899999999999999864 4555
No 71
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=41.16 E-value=56 Score=26.15 Aligned_cols=49 Identities=22% Similarity=0.270 Sum_probs=33.9
Q ss_pred CCCEEEE--ecChHHHHhhhccCchhHHHHhhhcCC--ccEEEEE---ecCC-CeEEEE--eCceeeec
Q psy16233 316 AGDFVYF--IPDELSAKEHLKGHGEWIAAMAGDLGD--IGIVIKV---YEDK-DVRVAF--RKNTWTLS 374 (464)
Q Consensus 316 ~GD~V~I--~~d~~~vk~lQ~ghGgW~~~M~~~lG~--~G~V~~v---~~dg-d~rV~~--~g~~w~~n 374 (464)
+|+.|+| +.-.+++ ...|.+.||+ +|+|... |+.| =+.|+| ...+|-|-
T Consensus 1 IGqkVrV~~~~irDRi----------~~~l~~~l~~~~~g~I~~fKmtDG~giG~vv~~~ng~~~WFFe 59 (64)
T PF11061_consen 1 IGQKVRVNLSRIRDRI----------PKELVDKLGKNPIGTIKGFKMTDGSGIGVVVEFSNGSRTWFFE 59 (64)
T ss_pred CCCEEEEeehhhhhhc----------cHHHHHHhccCCcEEEEEEEEecCCcEEEEEEecCCceeEEch
Confidence 5888888 3334443 3468899999 9999875 3444 567777 56678774
No 72
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=40.51 E-value=18 Score=31.30 Aligned_cols=37 Identities=27% Similarity=0.474 Sum_probs=21.2
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEec
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTE 286 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~ 286 (464)
.|.+||.|-|..|+.. |+| .. -.-+=|++|+|..|+.
T Consensus 32 ~yk~GD~V~I~id~sv----~kG----mP--h~~yHGkTG~V~~v~~ 68 (99)
T PF01157_consen 32 EYKVGDKVDIKIDPSV----HKG----MP--HKRYHGKTGRVFNVTK 68 (99)
T ss_dssp ---TT-EEEE---TTS----SSS----S----GGGTTEEEEEEEE-S
T ss_pred HccCCCEEEEEecCcc----ccC----CC--cceECCCceeEEEeCC
Confidence 4899999999999884 333 11 1257899999999986
No 73
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=40.16 E-value=12 Score=40.41 Aligned_cols=35 Identities=29% Similarity=0.805 Sum_probs=29.4
Q ss_pred eEecCCCCCCCeeeccceeecccCCCccccccccCCCC
Q psy16233 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEH 114 (464)
Q Consensus 77 v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~~~~H 114 (464)
..|+.|+... .-.||+-..-..|++|..||.++..
T Consensus 225 ~~C~~cG~~~---~~t~y~nlra~~~n~C~~C~~qg~f 259 (531)
T COG5259 225 SSCSCCGNKS---FNTRYHNLRAEKYNSCSECYDQGRF 259 (531)
T ss_pred ceeeccCccc---cchhhhhhhhhhcccchHHHhcCcC
Confidence 7899999865 4459999988999999999998753
No 74
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=40.11 E-value=43 Score=21.02 Aligned_cols=26 Identities=35% Similarity=0.438 Sum_probs=19.2
Q ss_pred ccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEec
Q psy16233 314 FVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYE 358 (464)
Q Consensus 314 ~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~ 358 (464)
|.+||.|+|..- +..|++|.|++++.
T Consensus 2 ~~~G~~V~I~~G-------------------~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAG-------------------PFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeEC-------------------CCCCcEEEEEEEcC
Confidence 678999998753 33477888888864
No 75
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=39.57 E-value=58 Score=21.87 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=13.3
Q ss_pred hhcCCccEEEEEecCC
Q psy16233 345 GDLGDIGIVIKVYEDK 360 (464)
Q Consensus 345 ~~lG~~G~V~~v~~dg 360 (464)
+.-|++|+|.+|+.+.
T Consensus 11 ~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 11 PFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTTTEEEEEEEEETTT
T ss_pred CCCCceEEEEEEECCC
Confidence 4568999999999866
No 76
>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=38.00 E-value=85 Score=24.90 Aligned_cols=47 Identities=13% Similarity=0.295 Sum_probs=36.8
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecChHH
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPDELS 328 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d~~~ 328 (464)
.|+|.+|+. .-..+..++ |++|++++.. ++..|++|..|.|.-|...
T Consensus 6 eG~I~~id~-~~~titLdD-Gksy~lp~ef--~~~~L~~G~kV~V~yd~~~ 52 (61)
T PF07076_consen 6 EGTIKSIDP-ETMTITLDD-GKSYKLPEEF--DFDGLKPGMKVVVFYDEVD 52 (61)
T ss_pred eEEEEEEcC-CceEEEecC-CCEEECCCcc--cccccCCCCEEEEEEEccC
Confidence 588999987 556777765 9999988765 4678999999999876543
No 77
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=37.18 E-value=54 Score=39.03 Aligned_cols=54 Identities=26% Similarity=0.341 Sum_probs=43.7
Q ss_pred cchhhhhccCceeEEEEEecCcceEEEEecCC--eeEEEccCcceecccccCCCEEEEe
Q psy16233 267 WTPQLLNFLGHTGIVHRVTEQTLVRVRFENCD--NKWTFDPRALTKVDPFVAGDFVYFI 323 (464)
Q Consensus 267 W~~~M~~~lGk~G~V~~I~~~gD~rV~~~~~~--~~wtfnP~~L~kv~~~~~GD~V~I~ 323 (464)
|....+.-|| .|+|+.++. ..+.|.|+.++ ..|.-+-+-|++| .|.+||.|+..
T Consensus 8 w~s~~e~eLG-lG~v~~~d~-r~vtv~fpas~e~R~ya~~~apl~Rv-~~~~g~~v~~~ 63 (956)
T PRK04914 8 WISDTESELG-LGTVVAVDG-RTVTLLFPATGENRLYARNDAPLTRV-MFNPGDTITSH 63 (956)
T ss_pred cccCCCCcCC-cEEEEEEeC-CEEEEEecCCCCceeeecCCCCceee-ecCCCCEEEec
Confidence 8888887787 699999986 88999999755 5566677778876 59999999863
No 78
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=36.91 E-value=36 Score=31.09 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=30.9
Q ss_pred hHHHHhhhcCCccEEEEEecCCCeEEEEeCceeeecC
Q psy16233 339 WIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTWTLSS 375 (464)
Q Consensus 339 W~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~~np 375 (464)
-+...++..|+.|+|++--.+|.-+|+++|+.|+-..
T Consensus 79 l~~~~~~l~G~~g~v~e~i~~g~g~Vkv~g~~Wra~~ 115 (140)
T COG1585 79 LNQRGEQLVGRRGVVVEDIVEGRGRVKVEGESWRARS 115 (140)
T ss_pred ccchhhHhcCcEEEEEeeccCCeEEEEECCeEeEEec
Confidence 3445677789999999977789999999999998663
No 79
>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=36.67 E-value=27 Score=27.53 Aligned_cols=38 Identities=32% Similarity=0.440 Sum_probs=26.1
Q ss_pred ccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEE
Q psy16233 314 FVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAF 366 (464)
Q Consensus 314 ~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~ 366 (464)
|++||.|-|.++.+-. +|-|. .++|++...+..+.|++
T Consensus 1 F~~G~~VEV~s~e~g~------~gaWf---------~a~V~~~~~~~~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGF------RGAWF---------PATVLKENGDDKYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-SBTT--------EEE---------EEEEEEEETT-EEEEEE
T ss_pred CCCCCEEEEEEcCCCC------CcEEE---------EEEEEEeCCCcEEEEEE
Confidence 7889999999887665 58999 78899998877777777
No 80
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=36.55 E-value=1.1e+02 Score=23.51 Aligned_cols=47 Identities=19% Similarity=0.224 Sum_probs=30.2
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEccCc-cee-cccccCCCEEEEecC
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFDPRA-LTK-VDPFVAGDFVYFIPD 325 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~-L~k-v~~~~~GD~V~I~~d 325 (464)
.|+|++..+.+-+.|+-++ +..+.-.+.- |.+ -....+||.|.+..+
T Consensus 4 ~G~Vi~~~~g~~~~V~~~~-g~~~~c~~rGklr~~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 4 EGVVTEALPNAMFRVELEN-GHEVLAHISGKMRMNYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEEEeCCCEEEEEeCC-CCEEEEEECceeecCCcccCCCCEEEEEEe
Confidence 5788888865667776543 5566555443 321 234789999999854
No 81
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=36.07 E-value=50 Score=38.33 Aligned_cols=46 Identities=17% Similarity=0.226 Sum_probs=40.7
Q ss_pred cCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCceeeecCcceeeec
Q psy16233 315 VAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTWTLSSKCLKLIK 382 (464)
Q Consensus 315 ~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~~np~~lt~~~ 382 (464)
.+||.|+| +.+|+.|+|++|..++++.|.+++-..+.+..-|.++.
T Consensus 626 ~~Gd~V~v----------------------~~~~~~g~v~~i~~~~~~~V~~g~~k~~v~~~~l~~~~ 671 (771)
T TIGR01069 626 KIGDKVRI----------------------RYFGQKGKIVQILGGNKWNVTVGGMRMKVHGSELEKIN 671 (771)
T ss_pred CCCCEEEE----------------------ccCCceEEEEEEcCCCeEEEEECCEEEEEeHHHceecc
Confidence 88999998 45789999999986789999999999999999998776
No 82
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=34.61 E-value=30 Score=27.81 Aligned_cols=29 Identities=28% Similarity=0.777 Sum_probs=21.5
Q ss_pred eeecccC---CCccccccccCCCCCCcceeeEe
Q psy16233 94 YSCIECS---NYDLCASCYHGDEHDITHAFYRV 123 (464)
Q Consensus 94 ykC~~C~---d~DLC~~C~~~~~H~~~H~f~r~ 123 (464)
|+|..|. ..=+|..|+....| ..|.+..+
T Consensus 14 y~C~tC~~~~~~~iC~~Cf~~~~H-~gH~~~~~ 45 (71)
T smart00396 14 YRCKTCGLDPTCVLCSDCFRSNCH-KGHDYSLK 45 (71)
T ss_pred EECcCCCCCCCEeEChHHCCCCCC-CCCCEEEE
Confidence 8888885 24589999998888 57875443
No 83
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=34.40 E-value=1.2e+02 Score=24.22 Aligned_cols=42 Identities=21% Similarity=0.272 Sum_probs=30.0
Q ss_pred eEEEEEecCcceEEEEecCCeeEEEccCcceecc------------cccCCCEEEEec
Q psy16233 279 GIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVD------------PFVAGDFVYFIP 324 (464)
Q Consensus 279 G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~------------~~~~GD~V~I~~ 324 (464)
|+|+.-.-+--+.|.. .++-|+|--...+. ...+||.|+|..
T Consensus 1 G~Vvs~km~KTv~V~v----~~~~~~~ky~K~~~~~kk~~aHD~~~~~~vGD~V~I~e 54 (69)
T PF00366_consen 1 GVVVSDKMDKTVVVRV----ERLVYHPKYKKYIKRTKKYMAHDENNICKVGDKVRIRE 54 (69)
T ss_dssp EEEEEEESTTEEEEEE----EEEEEETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEE
T ss_pred CEEEEcCCCCeEEEEE----EEEEEcceEeeccCccccEEEeCCccCCCCCCEEEEEe
Confidence 6788777777788875 45777887655432 256999999953
No 84
>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=33.64 E-value=81 Score=28.60 Aligned_cols=44 Identities=16% Similarity=0.151 Sum_probs=31.1
Q ss_pred eeEEEEEecCc-ceEEEEecCCeeEEEccCcceecccccCCCEEEEec
Q psy16233 278 TGIVHRVTEQT-LVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 278 ~G~V~~I~~~g-D~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~ 324 (464)
-|+++....+. -+.|.|++ +. ...+-..|..+ .|++||.|++..
T Consensus 26 Pa~~~~~~~~~~~~~V~Fed-g~-~~i~~~dv~~L-DlRIGD~Vkv~~ 70 (131)
T PF08605_consen 26 PATCVGSGVDRDRSLVRFED-GT-YEIKNEDVKYL-DLRIGDTVKVDG 70 (131)
T ss_pred eEEEEeecCCCCeEEEEEec-Cc-eEeCcccEeee-eeecCCEEEECC
Confidence 46666664322 38899987 55 77776666443 599999999987
No 85
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=33.11 E-value=83 Score=29.14 Aligned_cols=50 Identities=20% Similarity=0.112 Sum_probs=35.8
Q ss_pred ccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEe-cCCCeEEEE--eCc--eeeecCcceee
Q psy16233 312 DPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVY-EDKDVRVAF--RKN--TWTLSSKCLKL 380 (464)
Q Consensus 312 ~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~-~dgd~rV~~--~g~--~w~~np~~lt~ 380 (464)
..|.+||+|+|.+- +.-|..|.|.+++ +.+.+.|.+ .|+ ...++...|.+
T Consensus 125 ~~~~~Gd~VrI~~G-------------------Pf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~ 179 (181)
T PRK05609 125 VDFEVGEMVRVIDG-------------------PFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEK 179 (181)
T ss_pred cCCCCCCEEEEecc-------------------CCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEE
Confidence 35889999999752 5568999999998 566787776 444 46666555543
No 86
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=32.62 E-value=50 Score=28.49 Aligned_cols=42 Identities=29% Similarity=0.299 Sum_probs=31.0
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHh--hhcCCccEEEEEecCCCeEEEE
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMA--GDLGDIGIVIKVYEDKDVRVAF 366 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~--~~lG~~G~V~~v~~dgd~rV~~ 366 (464)
.|.+||.|-|..|+..-| | |- ..=|++|+|+.+..+- ..|.+
T Consensus 32 ey~~Gd~V~I~IdpSv~k----G-------mPh~rf~G~TG~Vvg~~g~a-y~V~v 75 (98)
T COG2139 32 EYKVGDKVHIDIDPSVHK----G-------MPHPRFQGKTGTVVGVRGRA-YKVEV 75 (98)
T ss_pred hccCCCEEEEEeCccccc----C-------CCCccccCcceEEEeccCCE-EEEEE
Confidence 599999999999987655 2 32 4568999999988633 34444
No 87
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=32.61 E-value=73 Score=27.17 Aligned_cols=35 Identities=23% Similarity=0.428 Sum_probs=31.8
Q ss_pred CCccEEEEEe-cCCCeEEEEeCceeeecCcceeeec
Q psy16233 348 GDIGIVIKVY-EDKDVRVAFRKNTWTLSSKCLKLIK 382 (464)
Q Consensus 348 G~~G~V~~v~-~dgd~rV~~~g~~w~~np~~lt~~~ 382 (464)
|.+|+|..|. .|+...|.++....-|+|..|..+.
T Consensus 15 GT~G~V~diK~ed~~~wv~LD~t~L~Yr~~~Lev~e 50 (91)
T PF09871_consen 15 GTVGKVVDIKEEDGETWVLLDSTDLYYRPDYLEVIE 50 (91)
T ss_pred CeEEEEEEEEEeCCCeEEEEccCCceeecceeEEec
Confidence 7899999995 6689999999999999999999987
No 88
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=32.27 E-value=68 Score=29.63 Aligned_cols=37 Identities=27% Similarity=0.280 Sum_probs=26.3
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCc
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKN 369 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~ 369 (464)
.+..||.|.|..=.+ -|+.|+|++|+.... +|-|.|-
T Consensus 46 ~IkkGD~V~Vi~Gk~-------------------KGk~GkV~~V~~k~~-~ViVEgv 82 (143)
T PTZ00194 46 PVRKDDEVMVVRGHH-------------------KGREGKVTAVYRKKW-VIHIEKI 82 (143)
T ss_pred eeecCCEEEEecCCC-------------------CCCceEEEEEEcCCC-EEEEeCe
Confidence 377899999975322 289999999986443 6655443
No 89
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=32.25 E-value=1.3e+02 Score=25.19 Aligned_cols=49 Identities=20% Similarity=0.196 Sum_probs=31.5
Q ss_pred ccCceeEEEEEecCc--ceEEEEecCCeeEEEccCcceec-ccccCCCEEEEec
Q psy16233 274 FLGHTGIVHRVTEQT--LVRVRFENCDNKWTFDPRALTKV-DPFVAGDFVYFIP 324 (464)
Q Consensus 274 ~lGk~G~V~~I~~~g--D~rV~~~~~~~~wtfnP~~L~kv-~~~~~GD~V~I~~ 324 (464)
+||--|+|++|.++. -.+|.+.+ .+=.-+-..+... +..++||+|.|..
T Consensus 2 CLaiP~kVi~i~~~~~~~A~vd~~G--v~r~V~l~Lv~~~~~~~~vGDyVLVHa 53 (82)
T PRK10413 2 CIGVPGQVLAVGEDIHQLAQVEVCG--IKRDVNIALICEGNPADLLGQWVLVHV 53 (82)
T ss_pred ccccceEEEEECCCCCcEEEEEcCC--eEEEEEeeeeccCCcccccCCEEEEec
Confidence 577889999998763 36677643 3333443333222 3478999999854
No 90
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=31.85 E-value=90 Score=27.35 Aligned_cols=57 Identities=14% Similarity=0.094 Sum_probs=36.1
Q ss_pred CceeEEEEEe-----------cCcceEEEEecC-CeeEE-EccCc---ceecccccCCCEEEEecChHHHHhh
Q psy16233 276 GHTGIVHRVT-----------EQTLVRVRFENC-DNKWT-FDPRA---LTKVDPFVAGDFVYFIPDELSAKEH 332 (464)
Q Consensus 276 Gk~G~V~~I~-----------~~gD~rV~~~~~-~~~wt-fnP~~---L~kv~~~~~GD~V~I~~d~~~vk~l 332 (464)
--.|+|+.+. ......|+|.-. +++++ |+... -.....+++||.|.|--|++..++-
T Consensus 38 ~~~g~V~~~~~~~~~~~~~~~~~y~~~v~y~~~~G~~~~~~~~~~~~~~~~~~~~~~G~~V~V~Y~P~~P~~~ 110 (148)
T PF12158_consen 38 RVEGTVVSSETERERSDGSRSSSYRPVVEYTYQDGRTYSRFYSGSDNFGSYWPKYPIGDTVTVYYNPNNPEEA 110 (148)
T ss_pred EEEEEEEEEEEEecccCCCCceEEEEEEEEEECCCcEEEEeccCCcccccCCccCCCcCEEEEEECCcCCCeE
Confidence 3467777777 122233455433 67788 77763 2333458899999999988877653
No 91
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=30.60 E-value=1.4e+02 Score=24.13 Aligned_cols=43 Identities=21% Similarity=0.190 Sum_probs=31.1
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEccCcceec------------ccccCCCEEEEec
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKV------------DPFVAGDFVYFIP 324 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv------------~~~~~GD~V~I~~ 324 (464)
+|+|+.-.-+.-+.|.. .+.-+||--..-+ ....+||.|.|..
T Consensus 5 ~G~Vvs~km~KTvvV~v----~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~e 59 (71)
T TIGR03635 5 QGVVVSDKMDKTIVVLV----ERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIE 59 (71)
T ss_pred EEEEEcccCCceEEEEE----EEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEE
Confidence 68888887777788875 4567777664432 1378999999965
No 92
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=30.43 E-value=69 Score=28.40 Aligned_cols=40 Identities=30% Similarity=0.294 Sum_probs=29.3
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecCCCeEEEEeCceee
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAFRKNTWT 372 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~ 372 (464)
.+..||.|+|..=.+ =|++|+|++|+. .+.+|-+.|-+-.
T Consensus 41 ~IkkGD~V~Vi~Gk~-------------------KGk~GkV~~V~~-~~~~V~Vegvn~~ 80 (114)
T TIGR01080 41 PVRKGDKVRIMRGDF-------------------KGHEGKVSKVDL-KRYRIYVEGVTKE 80 (114)
T ss_pred eeecCCEEEEecCCC-------------------CCCEEEEEEEEc-CCCEEEEcCeEEE
Confidence 478899999976332 289999999995 4457777665544
No 93
>PF00023 Ank: Ankyrin repeat Hereditary spherocytosis; InterPro: IPR002110 The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; GO: 0005515 protein binding; PDB: 1D9S_A 1NFI_F 1IKN_D 1WDY_A 1OT8_C 1QYM_A 1TR4_A 1UOH_A 1N11_A 1K1A_A ....
Probab=30.01 E-value=82 Score=20.65 Aligned_cols=26 Identities=27% Similarity=0.423 Sum_probs=21.0
Q ss_pred HHHHhhcCChHHHHHHHHhCCCccccc
Q psy16233 433 VMREVVRGNPSAVKAFLENNANLIDCP 459 (464)
Q Consensus 433 lv~~aa~g~~~~v~~~l~~~p~~v~~~ 459 (464)
|..||..|+.+-|+-||+ +...+|.+
T Consensus 6 Lh~A~~~~~~~~v~~Ll~-~ga~~~~~ 31 (33)
T PF00023_consen 6 LHYAAQRGHPDIVKLLLK-HGADINAR 31 (33)
T ss_dssp HHHHHHTTCHHHHHHHHH-TTSCTTCB
T ss_pred HHHHHHHHHHHHHHHHHH-CcCCCCCC
Confidence 788999999999988888 66666655
No 94
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=29.31 E-value=70 Score=27.98 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=25.7
Q ss_pred HhhhcCCccEEEEEecCCCeEEEEeCceeee
Q psy16233 343 MAGDLGDIGIVIKVYEDKDVRVAFRKNTWTL 373 (464)
Q Consensus 343 M~~~lG~~G~V~~v~~dgd~rV~~~g~~w~~ 373 (464)
++..+|++|+|..+..++.=+|+++|..|.-
T Consensus 86 ~~~liG~~g~v~~~~~~~~G~V~~~G~~w~A 116 (144)
T PF01957_consen 86 EDDLIGKEGTVIEIPLNGSGRVKVDGERWRA 116 (144)
T ss_dssp -GGGTTSEEEEEEEBSSS-EEEEETTEEEEE
T ss_pred HHHHcCCeEEEEEeecCCcEEEEECCeEEEE
Confidence 3778999999988888899999999999853
No 95
>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=29.12 E-value=49 Score=32.63 Aligned_cols=39 Identities=28% Similarity=0.284 Sum_probs=19.9
Q ss_pred CcccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEec
Q psy16233 238 GYIFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTE 286 (464)
Q Consensus 238 ~~~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~ 286 (464)
.+.|.+||+|+|...... + |=.- -.-+.||+|+|..+.+
T Consensus 132 ~~~F~vGd~Vrv~~~~~~------~-HtR~---P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 132 PPRFAVGDRVRVRNLPPP------G-HTRL---PRYVRGKTGTIERVHG 170 (222)
T ss_dssp S-SS-TT-EEEE-----S------S---SS----GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCEEEECCCCCC------C-cccc---cHhhCCCeeEEEEEec
Confidence 356999999999754442 2 3221 1247899999998774
No 96
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=29.10 E-value=1.4e+02 Score=27.69 Aligned_cols=37 Identities=32% Similarity=0.510 Sum_probs=29.0
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEe-cCcceEEEEec
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVT-EQTLVRVRFEN 296 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~-~~gD~rV~~~~ 296 (464)
.|.+||+|+|. .| ..-|..|.|.+++ +++.+.|.++-
T Consensus 126 ~~~~Gd~VrI~-------------~G-------Pf~G~~g~v~~i~~~~~r~~v~l~~ 163 (181)
T PRK05609 126 DFEVGEMVRVI-------------DG-------PFADFNGTVEEVDYEKSKLKVLVSI 163 (181)
T ss_pred CCCCCCEEEEe-------------cc-------CCCCCEEEEEEEeCCCCEEEEEEEE
Confidence 48899999996 23 4578899999998 56678887754
No 97
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.90 E-value=89 Score=26.67 Aligned_cols=36 Identities=22% Similarity=0.287 Sum_probs=29.5
Q ss_pred cCceeEEEEEe--cCcceEEEEecCCeeEEEccCcceecc
Q psy16233 275 LGHTGIVHRVT--EQTLVRVRFENCDNKWTFDPRALTKVD 312 (464)
Q Consensus 275 lGk~G~V~~I~--~~gD~rV~~~~~~~~wtfnP~~L~kv~ 312 (464)
-|.+|+|+.|. .+|++.|..+ ++-.-|+|..|..+.
T Consensus 20 TgTvgrV~dIkkdEdG~~WV~Ld--stdLwYre~~le~vd 57 (97)
T COG4014 20 TGTVGRVVDIKKDEDGDIWVVLD--STDLWYREHYLEVVD 57 (97)
T ss_pred cCceeeEEEEEeecCCceEEEEe--cCCceecccceeeec
Confidence 57899999997 5899999985 467779999888763
No 98
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=28.71 E-value=1.6e+02 Score=22.38 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=24.5
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEc-cCccee-cccccCCCEEEEec
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFD-PRALTK-VDPFVAGDFVYFIP 324 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfn-P~~L~k-v~~~~~GD~V~I~~ 324 (464)
.|+|+.+.. +.+.|..+. +..+.-. +..+.+ .....+||+|.+..
T Consensus 2 ~grVv~~~~-~~~~v~~~~-~~~~~~~~~~~~~~~~~~~~VGD~V~~~~ 48 (68)
T cd04466 2 EGLIIKAIG-GFYYVETED-GKIYECRLRGKFRKDKNPPAVGDRVEFEP 48 (68)
T ss_pred CEEEEEEEC-CEEEEEeCC-CeEEEEEEccccccCCCCCCCCcEEEEEE
Confidence 467887775 556676542 2222222 122221 23478999998853
No 99
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=28.48 E-value=82 Score=25.14 Aligned_cols=49 Identities=24% Similarity=0.350 Sum_probs=37.7
Q ss_pred cCCCEEEEecChHHHHhhhccCchhHHHHh-------hhcCCccEEEEEecCCCeEEEEeCcee
Q psy16233 315 VAGDFVYFIPDELSAKEHLKGHGEWIAAMA-------GDLGDIGIVIKVYEDKDVRVAFRKNTW 371 (464)
Q Consensus 315 ~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~-------~~lG~~G~V~~v~~dgd~rV~~~g~~w 371 (464)
++||.|++..-+..+|. +|-|- -.+|.+|+|+..-.-+-+-|+|.--++
T Consensus 1 ~iG~~V~l~~~ppylKT--------AdpMPmLRp~dlv~~ge~G~i~~rrp~~~w~VRf~~Gtf 56 (63)
T PF11347_consen 1 SIGDKVRLIEAPPYLKT--------ADPMPMLRPPDLVKIGEVGRIVDRRPGDYWAVRFRRGTF 56 (63)
T ss_pred CCCCeEEEeecCCceec--------cCCccccCCcCccccCCcEEEEEecCCCEEEEEEeceeE
Confidence 47999999988888884 44454 278999999999997888888843333
No 100
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=28.18 E-value=95 Score=27.85 Aligned_cols=37 Identities=38% Similarity=0.548 Sum_probs=26.8
Q ss_pred cccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcceEEEEec
Q psy16233 239 YIFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTLVRVRFEN 296 (464)
Q Consensus 239 ~~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD~rV~~~~ 296 (464)
.++..||.|.|.. |. .=|+.|+|++|+.... +|.+++
T Consensus 44 ~~IkkGD~V~Vis-------------G~-------~KGk~GkV~~V~~~~~-~V~VeG 80 (120)
T PRK01191 44 LPVRKGDTVKVMR-------------GD-------FKGEEGKVVEVDLKRG-RIYVEG 80 (120)
T ss_pred ceEeCCCEEEEee-------------cC-------CCCceEEEEEEEcCCC-EEEEeC
Confidence 3578999999973 22 3489999999986543 566665
No 101
>KOG2990|consensus
Probab=28.00 E-value=19 Score=36.76 Aligned_cols=20 Identities=35% Similarity=0.766 Sum_probs=14.3
Q ss_pred cceEecCCCCCCCeeeccceee
Q psy16233 75 ETISCDACQDERSCIVGTRYSC 96 (464)
Q Consensus 75 ~~v~CD~C~~~~~~I~G~RykC 96 (464)
.+|.||||...- -.|+||.-
T Consensus 51 ynIWC~gC~nhI--gmGvRyNA 70 (317)
T KOG2990|consen 51 YNIWCDGCKNHI--GMGVRYNA 70 (317)
T ss_pred cchhhccHHHhh--hccceech
Confidence 478999998754 45677653
No 102
>KOG4412|consensus
Probab=27.78 E-value=47 Score=32.22 Aligned_cols=32 Identities=22% Similarity=0.364 Sum_probs=28.4
Q ss_pred HHHHHhhcCChHHHHHHHHhCCCcccccCCCC
Q psy16233 432 AVMREVVRGNPSAVKAFLENNANLIDCPVLGG 463 (464)
Q Consensus 432 ~lv~~aa~g~~~~v~~~l~~~p~~v~~~~~~g 463 (464)
-|.+||..||.+-|+++|-++...||+.+-+|
T Consensus 75 Plhia~s~g~~evVk~Ll~r~~advna~tn~G 106 (226)
T KOG4412|consen 75 PLHIAASNGNDEVVKELLNRSGADVNATTNGG 106 (226)
T ss_pred hhhhhhhcCcHHHHHHHhcCCCCCcceecCCC
Confidence 59999999999999999999988899887344
No 103
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=27.57 E-value=40 Score=31.68 Aligned_cols=36 Identities=31% Similarity=0.571 Sum_probs=29.1
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhh--hccCceeEEEEEecC
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLL--NFLGHTGIVHRVTEQ 287 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~--~~lGk~G~V~~I~~~ 287 (464)
.|.+||.|-|..|.+. |+| |- -+=|++|+|..++.+
T Consensus 33 ~yk~GD~VdIk~d~sv----qkG--------MPhk~YHGkTG~V~nv~~~ 70 (160)
T PTZ00189 33 TFKVGDYVDIVVDSAV----HKG--------MPYKYYHGRTGRVFNVTPR 70 (160)
T ss_pred HccCCCEEEEEecCCe----ecC--------CCcccccCCCeEEEeecCe
Confidence 3889999999999984 333 33 478999999999985
No 104
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=27.30 E-value=95 Score=29.51 Aligned_cols=35 Identities=29% Similarity=0.282 Sum_probs=29.7
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecC-CCeEEEE
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYED-KDVRVAF 366 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~d-gd~rV~~ 366 (464)
.|.+||.|+|.+. +..|-.|+|.+|+.+ +.++|.+
T Consensus 123 ~~e~Gd~VrI~~G-------------------pFa~f~g~V~evd~ek~~~~v~v 158 (178)
T COG0250 123 DFEPGDVVRIIDG-------------------PFAGFKAKVEEVDEEKGKLKVEV 158 (178)
T ss_pred cCCCCCEEEEecc-------------------CCCCccEEEEEEcCcCcEEEEEE
Confidence 5899999999874 566889999999987 6888876
No 105
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=27.01 E-value=3e+02 Score=30.58 Aligned_cols=84 Identities=13% Similarity=0.073 Sum_probs=59.3
Q ss_pred hhhccCceeEEEEE-ecCcceEEEEecCCeeEEEccCcceecccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCC
Q psy16233 271 LLNFLGHTGIVHRV-TEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGD 349 (464)
Q Consensus 271 M~~~lGk~G~V~~I-~~~gD~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~ 349 (464)
+++--...|++.+. .+++..-|... +..+...-........|.+|+.|++......|..+- .+..|+
T Consensus 41 ~~~p~~~~~~~~~~~~~~~~~~v~~~--g~~~~~~~~~~~~~~~l~~g~~v~l~e~~~~v~~~~----------~~~~g~ 108 (512)
T TIGR03689 41 LAQPPSTYGTFLQTAIDDETAEVFTA--GRRMRVTVSPNVNAAELVPGQTVRLNEALQVVEARD----------FETVGE 108 (512)
T ss_pred hcCCCcceEEEEEeccCCCeEEEEeC--CceEEEEeCCCCCHHHCCCCCEEEECCcceeeccCC----------CCCCCc
Confidence 33445567888888 66666666442 555555444444455799999999998888876542 456688
Q ss_pred ccEEEEEecCCCeEEEE
Q psy16233 350 IGIVIKVYEDKDVRVAF 366 (464)
Q Consensus 350 ~G~V~~v~~dgd~rV~~ 366 (464)
+.+|.++..++.+-|+-
T Consensus 109 ~~~~~~~~~~~~~~v~~ 125 (512)
T TIGR03689 109 IATLKEVLGDGRALVVD 125 (512)
T ss_pred eEEEEEEeCCCeEEEEe
Confidence 99999999888888876
No 106
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=26.65 E-value=1.2e+02 Score=22.21 Aligned_cols=28 Identities=21% Similarity=0.316 Sum_probs=23.1
Q ss_pred eeEEEEEecCcceEEEEecCCeeEEEccC
Q psy16233 278 TGIVHRVTEQTLVRVRFENCDNKWTFDPR 306 (464)
Q Consensus 278 ~G~V~~I~~~gD~rV~~~~~~~~wtfnP~ 306 (464)
.|++..|+++|.|.|+.++ +..-+|+.+
T Consensus 16 ~G~~~gId~~G~L~v~~~~-g~~~~i~sG 43 (48)
T PF02237_consen 16 EGIAEGIDDDGALLVRTED-GSIRTISSG 43 (48)
T ss_dssp EEEEEEEETTSEEEEEETT-EEEEEESSS
T ss_pred EEEEEEECCCCEEEEEECC-CCEEEEEEE
Confidence 7999999999999999876 656666643
No 107
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.73 E-value=36 Score=24.85 Aligned_cols=25 Identities=24% Similarity=0.643 Sum_probs=17.7
Q ss_pred ceEecCCCCC-CCeeec-cceeecccC
Q psy16233 76 TISCDACQDE-RSCIVG-TRYSCIECS 100 (464)
Q Consensus 76 ~v~CD~C~~~-~~~I~G-~RykC~~C~ 100 (464)
++.|-.|+.. .+.|.+ .+|+|..|-
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCC
Confidence 5678888874 233666 899998884
No 108
>PLN00208 translation initiation factor (eIF); Provisional
Probab=25.39 E-value=4e+02 Score=24.69 Aligned_cols=30 Identities=13% Similarity=0.070 Sum_probs=22.1
Q ss_pred cccCCEEEEe--------------cCHHHHHHhhhcCCCCcchhhh
Q psy16233 241 FRRGDRVKVI--------------TDAKTLQHVQESSKGGWTPQLL 272 (464)
Q Consensus 241 f~vGD~V~V~--------------~d~~~lk~lQ~g~hGgW~~~M~ 272 (464)
+..||.|.|. +..+.++.|++. |.|.....
T Consensus 71 I~~GD~VlVel~~~d~~KgdIv~ry~~dqvr~Lkk~--G~~P~~f~ 114 (145)
T PLN00208 71 IAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAY--GELPENTR 114 (145)
T ss_pred ecCCCEEEEEccCCCCCEEEEEEEcCHHHHHHHHHc--CCCCccee
Confidence 5567777774 677889999885 78876554
No 109
>KOG1280|consensus
Probab=25.21 E-value=41 Score=35.25 Aligned_cols=58 Identities=14% Similarity=-0.005 Sum_probs=42.8
Q ss_pred ceeecCCCccccc--ccCCCCcceee--cceEecCCCCCCCeeeccceeecccCCCcccccccc
Q psy16233 51 CYRVGSENAYDLQ--VYDSGPVGIKH--ETISCDACQDERSCIVGTRYSCIECSNYDLCASCYH 110 (464)
Q Consensus 51 ~YR~G~~g~~DL~--~~d~a~~gv~H--~~v~CD~C~~~~~~I~G~RykC~~C~d~DLC~~C~~ 110 (464)
.||+=.=..|||+ |+++....-.| .+..|+.|.... ..+.+++|..|..++.|-.|--
T Consensus 23 rYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~d--feL~f~Ge~i~~y~~qSftCPy 84 (381)
T KOG1280|consen 23 RYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVD--FELYFGGEPISHYDPQSFTCPY 84 (381)
T ss_pred eeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccc--eeeEecCccccccccccccCCc
Confidence 3444333457775 36666554455 588999999888 9999999999999999888833
No 110
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=24.95 E-value=1e+02 Score=35.80 Aligned_cols=23 Identities=22% Similarity=0.218 Sum_probs=19.2
Q ss_pred hccCceeEEEEEecCcceEEEEe
Q psy16233 273 NFLGHTGIVHRVTEQTLVRVRFE 295 (464)
Q Consensus 273 ~~lGk~G~V~~I~~~gD~rV~~~ 295 (464)
..+|+.|+|+.|.+++.+.|++.
T Consensus 646 ~~~~~~g~v~~i~~~~~~~V~~g 668 (782)
T PRK00409 646 LSLGQKGEVLSIPDDKEAIVQAG 668 (782)
T ss_pred ccCCceEEEEEEcCCCeEEEEEC
Confidence 35789999999987788999973
No 111
>PLN00190 60S ribosomal protein L21; Provisional
Probab=24.63 E-value=50 Score=30.93 Aligned_cols=36 Identities=31% Similarity=0.541 Sum_probs=29.0
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhh--hccCceeEEEEEecC
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLL--NFLGHTGIVHRVTEQ 287 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~--~~lGk~G~V~~I~~~ 287 (464)
.|.+||.|-|..|.+. |+| |- -+=|++|+|..++.+
T Consensus 33 ~yk~GD~VdIk~~~sv----qKG--------MPhk~YHGkTG~V~nv~~~ 70 (158)
T PLN00190 33 TFKVGDYVDIKVNGAI----HKG--------MPHKFYHGRTGIVWNVTKR 70 (158)
T ss_pred HhcCCCEEEEEecCCe----ecC--------CCcccccCCCeEEEeecCc
Confidence 3889999999999884 333 32 478999999999985
No 112
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=24.49 E-value=2.2e+02 Score=26.14 Aligned_cols=51 Identities=24% Similarity=0.347 Sum_probs=33.9
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEecC-CCeEEEEeCce----eeecCcceeeec
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYED-KDVRVAFRKNT----WTLSSKCLKLIK 382 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~d-gd~rV~~~g~~----w~~np~~lt~~~ 382 (464)
.|.+||.|+|.. -+.-|..|+|.+++.+ +-++|.+.++. -+.+-..|.++.
T Consensus 94 ~~~~G~~V~I~~-------------------Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 94 GIKEGDIVELIA-------------------GPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVK 149 (153)
T ss_pred CCCCCCEEEEec-------------------cCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEec
Confidence 488999999974 2556889999999854 34555555544 444444454444
No 113
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=24.26 E-value=1.5e+02 Score=23.77 Aligned_cols=46 Identities=33% Similarity=0.400 Sum_probs=22.1
Q ss_pred eEEEEEecC-cceEEEEecCC---eeEEE--ccCc--ceecccccCCCEEEEec
Q psy16233 279 GIVHRVTEQ-TLVRVRFENCD---NKWTF--DPRA--LTKVDPFVAGDFVYFIP 324 (464)
Q Consensus 279 G~V~~I~~~-gD~rV~~~~~~---~~wtf--nP~~--L~kv~~~~~GD~V~I~~ 324 (464)
|+|..|+.+ +.+||+|++.+ +.|.- .|.+ ...+.+..+||.|.|..
T Consensus 1 G~V~~v~~~~grvrV~~~~~~~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~ 54 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVRFPDDGDIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLF 54 (79)
T ss_dssp EEEEEEETTTTEEEEE-B-CTTEEEEEEEE--S-BSSSB------TT-EEEEEE
T ss_pred CeEEEEECCCCEEEEEEecCCCccceEEEeeehhccCCeeEccCCCCcEEEEEc
Confidence 788888864 89999984322 34432 1222 22234567888888754
No 114
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=24.07 E-value=2.3e+02 Score=21.85 Aligned_cols=38 Identities=24% Similarity=0.317 Sum_probs=26.2
Q ss_pred hccCchhHHHHhhhcCCccEEEEEecCCCeEEEE-eCceeeecCcceee
Q psy16233 333 LKGHGEWIAAMAGDLGDIGIVIKVYEDKDVRVAF-RKNTWTLSSKCLKL 380 (464)
Q Consensus 333 Q~ghGgW~~~M~~~lG~~G~V~~v~~dgd~rV~~-~g~~w~~np~~lt~ 380 (464)
+.+|-+|- +|.|++. .++.+.|.| ..-.-++|..-+.+
T Consensus 9 HP~~pdWG---------~GqVqS~-i~~rvTVnF~~aGK~vI~~~~v~L 47 (52)
T PF12073_consen 9 HPDHPDWG---------IGQVQSN-IGGRVTVNFEHAGKKVIDGSRVAL 47 (52)
T ss_pred CCCCCCCc---------ceEEEEe-cCCeEEEeeccCCeEEEeccEEEE
Confidence 45677887 8899884 458999999 44455566554443
No 115
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=23.95 E-value=1.6e+02 Score=30.87 Aligned_cols=79 Identities=19% Similarity=0.221 Sum_probs=44.7
Q ss_pred cccccCCEEEEecCHHHHHH-------------hhhcCCCCcchhhhhc---cCc--eeEEEEEecCcceEEEEecCCee
Q psy16233 239 YIFRRGDRVKVITDAKTLQH-------------VQESSKGGWTPQLLNF---LGH--TGIVHRVTEQTLVRVRFENCDNK 300 (464)
Q Consensus 239 ~~f~vGD~V~V~~d~~~lk~-------------lQ~g~hGgW~~~M~~~---lGk--~G~V~~I~~~gD~rV~~~~~~~~ 300 (464)
+.+++||.|.+.++++.+.+ +++. ++..-+.++ .|. .|+|.++..+|.+.|... +..
T Consensus 82 ~~~~vGD~I~~~I~~~~fgR~aaq~aKqvi~Qkire~---ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG--~~e 156 (341)
T TIGR01953 82 PDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREA---ERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG--KTE 156 (341)
T ss_pred cccccCCEEEEEecccCCCHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeE
Confidence 45889999998866543222 1111 122222233 555 499999999888788762 322
Q ss_pred EEEccCcceecccccCCCEEEE
Q psy16233 301 WTFDPRALTKVDPFVAGDFVYF 322 (464)
Q Consensus 301 wtfnP~~L~kv~~~~~GD~V~I 322 (464)
-.+...-+..-..|.+||.+++
T Consensus 157 a~LP~~E~ip~E~~~~Gd~ik~ 178 (341)
T TIGR01953 157 GILPKKEQIPGEKFRIGDRIKA 178 (341)
T ss_pred EEecHHHcCCCcCCCCCCEEEE
Confidence 2222222222234888997764
No 116
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=23.78 E-value=2.7e+02 Score=36.04 Aligned_cols=86 Identities=14% Similarity=0.054 Sum_probs=57.6
Q ss_pred ceeEEEEEecCcceE-EEEecCCeeEEEccCccee--c-------ccccCCCEEEEecChHHHHhhhccCchhHHHHhhh
Q psy16233 277 HTGIVHRVTEQTLVR-VRFENCDNKWTFDPRALTK--V-------DPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGD 346 (464)
Q Consensus 277 k~G~V~~I~~~gD~r-V~~~~~~~~wtfnP~~L~k--v-------~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~ 346 (464)
.-.+|..|+.++... ++=...+..-+|.|.-+.+ + .+|.+||++++...-... | -.
T Consensus 1342 ~y~~V~~vd~~~~~v~l~~~~~G~~~~~~p~~~~~~~~~~y~~~~~~l~~GDri~~t~~d~~~--------g------~~ 1407 (1960)
T TIGR02760 1342 AYLTIADIDREHGKLTVADIKTGSERDILPRQLDHTFTSLYSDSELPLAKGDKIRLRATDKNR--------G------IK 1407 (1960)
T ss_pred cEEEEEEecCCCCEEEEEecCCCCeEeeChhhcCcccceeeccccccccCCCEEEEeecCccc--------c------cc
Confidence 344677777654443 3321247889999998763 1 259999999996632211 1 12
Q ss_pred cCCccEEEEEecCCCeEEEE-eCceeeecCcc
Q psy16233 347 LGDIGIVIKVYEDKDVRVAF-RKNTWTLSSKC 377 (464)
Q Consensus 347 lG~~G~V~~v~~dgd~rV~~-~g~~w~~np~~ 377 (464)
-|..++|..|.. +++.+.. .++..+++|-.
T Consensus 1408 n~~~~~V~~v~~-~~~~~~~~~~~~~~l~~~~ 1438 (1960)
T TIGR02760 1408 ANEVYTVTQVVN-GLSVQLSKVKNSLSLKPIQ 1438 (1960)
T ss_pred cCCeEEEEEEcC-CcEEEEcCCCceEEecCch
Confidence 578999999987 5677776 67789998843
No 117
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.67 E-value=2e+02 Score=24.14 Aligned_cols=46 Identities=17% Similarity=0.251 Sum_probs=32.6
Q ss_pred ccCceeEEEEEecCc-ceEEEEecCCeeEEEccCcceecccccCCCEEEEe
Q psy16233 274 FLGHTGIVHRVTEQT-LVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFI 323 (464)
Q Consensus 274 ~lGk~G~V~~I~~~g-D~rV~~~~~~~~wtfnP~~L~kv~~~~~GD~V~I~ 323 (464)
+|+--|+|++|++.. -..|.|. |-.=.-|-.+|.. ..++||+|.|.
T Consensus 2 ClaiPgqI~~I~~~~~~A~Vd~g--GvkreV~l~Lv~~--~v~~GdyVLVH 48 (82)
T COG0298 2 CLAIPGQIVEIDDNNHLAIVDVG--GVKREVNLDLVGE--EVKVGDYVLVH 48 (82)
T ss_pred ccccccEEEEEeCCCceEEEEec--cEeEEEEeeeecC--ccccCCEEEEE
Confidence 466779999999855 4678884 4444555455543 67899999874
No 118
>KOG0512|consensus
Probab=23.60 E-value=80 Score=30.50 Aligned_cols=31 Identities=13% Similarity=0.256 Sum_probs=24.5
Q ss_pred HHHHHHHhhcCChHHHHHHHHhCCCcccccC
Q psy16233 430 VEAVMREVVRGNPSAVKAFLENNANLIDCPV 460 (464)
Q Consensus 430 ~~~lv~~aa~g~~~~v~~~l~~~p~~v~~~~ 460 (464)
...++.||..+-+..|+++|+--|..||.+-
T Consensus 64 ~rl~lwaae~nrl~eV~~lL~e~an~vNtrD 94 (228)
T KOG0512|consen 64 IRLLLWAAEKNRLTEVQRLLSEKANHVNTRD 94 (228)
T ss_pred HHHHHHHHhhccHHHHHHHHHhccccccccc
Confidence 4456777777888889999998888888764
No 119
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=23.46 E-value=1.6e+02 Score=27.28 Aligned_cols=36 Identities=28% Similarity=0.431 Sum_probs=26.4
Q ss_pred ccccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcceEEEEec
Q psy16233 240 IFRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTLVRVRFEN 296 (464)
Q Consensus 240 ~f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD~rV~~~~ 296 (464)
++..||.|.|. .|. .-|+.|+|++|+... -+|-+++
T Consensus 46 ~IkkGD~V~Vi-------------~Gk-------~KGk~GkV~~V~~k~-~~ViVEg 81 (143)
T PTZ00194 46 PVRKDDEVMVV-------------RGH-------HKGREGKVTAVYRKK-WVIHIEK 81 (143)
T ss_pred eeecCCEEEEe-------------cCC-------CCCCceEEEEEEcCC-CEEEEeC
Confidence 57889999997 233 348999999998644 3666655
No 120
>PRK13020 riboflavin synthase subunit alpha; Provisional
Probab=23.34 E-value=1.3e+02 Score=29.24 Aligned_cols=78 Identities=23% Similarity=0.246 Sum_probs=44.6
Q ss_pred cccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcc---eEEEEec-------CCeeEEEccCccee
Q psy16233 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTL---VRVRFEN-------CDNKWTFDPRALTK 310 (464)
Q Consensus 241 f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD---~rV~~~~-------~~~~wtfnP~~L~k 310 (464)
+.+||+|.+...+..-.++ .|...-+ ..--+|+|.+|...++ ++++++. .+..-+-|..+||-
T Consensus 76 ~~~G~~VNlEral~~~~rl----gGH~v~G---hVd~~~~i~~i~~~~~~~~~~i~~~~~~~~~i~~kgSIaidGvsLTV 148 (206)
T PRK13020 76 LRVGDRVNIERSAKFGAEI----GGHILSG---HVDTTATVVEISDTEENYDIRFRVPPEWMKYIFAKGFIGVNGCSLTV 148 (206)
T ss_pred ccCCCEEeeEecccCCCcc----CCEeEEE---EccEEEEEEEEEEcCCCEEEEEEEChHHhcccccCCEEEEeeEEEEE
Confidence 6789999988666543333 2333322 2334677888887655 3444432 11233344444442
Q ss_pred c---------------------ccccCCCEEEEecC
Q psy16233 311 V---------------------DPFVAGDFVYFIPD 325 (464)
Q Consensus 311 v---------------------~~~~~GD~V~I~~d 325 (464)
. ..+++||.|+|..|
T Consensus 149 ~~v~~~~f~v~lIp~Tl~~T~l~~~k~G~~VNiE~D 184 (206)
T PRK13020 149 GEVDESEFEVHLIPETLRATNLGAKKVGDLVNIEID 184 (206)
T ss_pred EeEcCCEEEEEEeHHHHhhcccccCCCCCEEEEeEe
Confidence 1 12889999999999
No 121
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=23.12 E-value=3.5e+02 Score=25.36 Aligned_cols=29 Identities=14% Similarity=0.197 Sum_probs=20.6
Q ss_pred cccCCEEEEe--------------cCHHHHHHhhhcCCCCcchhh
Q psy16233 241 FRRGDRVKVI--------------TDAKTLQHVQESSKGGWTPQL 271 (464)
Q Consensus 241 f~vGD~V~V~--------------~d~~~lk~lQ~g~hGgW~~~M 271 (464)
+..||.|.|. +..+.++.|++. |.|....
T Consensus 71 I~~GD~VlVel~~yd~~KgdIi~Ry~~devr~Lk~~--g~~P~~~ 113 (155)
T PTZ00329 71 INIGDIILVSLRDFQDSKADVILKYTPDEARALKQH--GELPETA 113 (155)
T ss_pred ecCCCEEEEeccCCCCCEEEEEEEcCHHHHHHHHHc--CCCCcce
Confidence 5568887775 567778888875 7776544
No 122
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=22.81 E-value=1.4e+02 Score=27.48 Aligned_cols=35 Identities=23% Similarity=0.190 Sum_probs=27.9
Q ss_pred cccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEe-cCCCeEEEE
Q psy16233 313 PFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVY-EDKDVRVAF 366 (464)
Q Consensus 313 ~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~-~dgd~rV~~ 366 (464)
.|.+||.|+|.+- +.-|.+|.|.+++ .++.+.|.+
T Consensus 119 ~~~~G~~V~I~~G-------------------pf~G~~g~v~~~~~~~~r~~V~v 154 (172)
T TIGR00922 119 DFEVGEQVRVNDG-------------------PFANFTGTVEEVDYEKSKLKVSV 154 (172)
T ss_pred CCCCCCEEEEeec-------------------CCCCcEEEEEEEcCCCCEEEEEE
Confidence 4789999999752 5568899999998 566777776
No 123
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=22.54 E-value=2.3e+02 Score=23.72 Aligned_cols=44 Identities=18% Similarity=0.088 Sum_probs=31.4
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecc------------cccCCCEEEEec
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVD------------PFVAGDFVYFIP 324 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~------------~~~~GD~V~I~~ 324 (464)
.+|+|+.-.-+--+.|.. .+..|+|---.-+. ...+||.|+|..
T Consensus 9 l~G~Vvs~km~KTvvV~v----~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e 64 (84)
T PRK05610 9 LQGRVVSDKMDKTIVVLV----ERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIME 64 (84)
T ss_pred EEEEEEcccCCceEEEEE----EEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEE
Confidence 478998887777788875 45667776544221 378999999965
No 124
>PRK09289 riboflavin synthase subunit alpha; Provisional
Probab=22.36 E-value=97 Score=29.78 Aligned_cols=79 Identities=19% Similarity=0.188 Sum_probs=44.8
Q ss_pred cccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEecCcc---eEEEEec-------CCeeEEEccCccee
Q psy16233 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTEQTL---VRVRFEN-------CDNKWTFDPRALTK 310 (464)
Q Consensus 241 f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~~gD---~rV~~~~-------~~~~wtfnP~~L~k 310 (464)
+++||+|.+.-....=.++ .|...-+ ..--+|+|.++...++ ++++++. .+..-..|-.|||-
T Consensus 75 l~~G~~VNLEra~~~~~~~----gGHm~tG---hVd~~g~I~~i~~~~~~~~~~i~~~~~~~~~l~~kgSIavdGvsLTV 147 (194)
T PRK09289 75 LKVGDRVNLERALRLGDRL----GGHIVSG---HVDGTGEIVSIEKEGNSVEFRFKAPAELAKYIVEKGSIAVDGVSLTV 147 (194)
T ss_pred ccCCCEEEEeEcccCCCcc----cceeEEE---EEEEEEEEEEEEECCCcEEEEEECChHHhcccccCCEEEEccEEEEE
Confidence 6789999887665532222 1223222 3335788888876554 3333321 12334455566653
Q ss_pred cc---------------------cccCCCEEEEecCh
Q psy16233 311 VD---------------------PFVAGDFVYFIPDE 326 (464)
Q Consensus 311 v~---------------------~~~~GD~V~I~~d~ 326 (464)
.. .+++||.|+|..|+
T Consensus 148 ~~~~~~~f~v~lipeTl~~T~l~~~k~G~~VNlE~D~ 184 (194)
T PRK09289 148 NEVDGDRFSVNLIPHTLENTTLGEKKVGDRVNLEIDL 184 (194)
T ss_pred EEEcCCEEEEEEeHHHHhhCccccCCCCCEEEEeEeh
Confidence 21 27889999988883
No 125
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=21.92 E-value=1.3e+02 Score=27.74 Aligned_cols=53 Identities=23% Similarity=0.204 Sum_probs=30.8
Q ss_pred ceeEEEEEecCcceEEEEec---CC---eeEEEccCcc-------------eecccccCCCEEEEecChHHHH
Q psy16233 277 HTGIVHRVTEQTLVRVRFEN---CD---NKWTFDPRAL-------------TKVDPFVAGDFVYFIPDELSAK 330 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~---~~---~~wtfnP~~L-------------~kv~~~~~GD~V~I~~d~~~vk 330 (464)
..|+|+++++ +-+.|+... |+ .+-.-....| ..-.++++||.|.|..+...+-
T Consensus 4 e~~~Vv~v~~-~~a~Ve~~r~saCg~C~a~~gCG~~~l~~~~~~~~~~~~v~~~~~~~vGD~V~v~i~e~~ll 75 (154)
T PRK10862 4 EWATVVSWQN-GIALLRCEVKAGCSSCASRAGCGSRLLNKLGPQTTHQLVVPSSQPLVPGQKVELGIAEGSLL 75 (154)
T ss_pred eEEEEEEEEC-CEEEEEEecCCCCcCcCCCCCchhhHHHHhcCCCceEEEecCCCCCCCCCEEEEecchhhHH
Confidence 5799999965 667777643 11 1111111111 1113599999999988765543
No 126
>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=21.04 E-value=2.4e+02 Score=25.24 Aligned_cols=51 Identities=25% Similarity=0.383 Sum_probs=34.5
Q ss_pred cccCCEEEEecCHHHHHHhhhcCCCCcchhhhhccCceeEEEEEec-CcceEEEEecCCee--EEEccCcceec
Q psy16233 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLLNFLGHTGIVHRVTE-QTLVRVRFENCDNK--WTFDPRALTKV 311 (464)
Q Consensus 241 f~vGD~V~V~~d~~~lk~lQ~g~hGgW~~~M~~~lGk~G~V~~I~~-~gD~rV~~~~~~~~--wtfnP~~L~kv 311 (464)
|.+||+|+|. .| .+-|..|.|.+++. +..++|.....+.. -++....|.++
T Consensus 87 ~~~Gd~V~I~-------------~G-------Pf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~ 140 (145)
T TIGR00405 87 IKKGDIVEII-------------SG-------PFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRII 140 (145)
T ss_pred cCCCCEEEEe-------------ec-------CCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEe
Confidence 7899999996 22 56788999999984 45556665554444 56665555543
No 127
>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=21.03 E-value=70 Score=31.54 Aligned_cols=38 Identities=24% Similarity=0.180 Sum_probs=19.4
Q ss_pred ccccCCCEEEEecChHHHHhhhccCchhHHHHhhhcCCccEEEEEec
Q psy16233 312 DPFVAGDFVYFIPDELSAKEHLKGHGEWIAAMAGDLGDIGIVIKVYE 358 (464)
Q Consensus 312 ~~~~~GD~V~I~~d~~~vk~lQ~ghGgW~~~M~~~lG~~G~V~~v~~ 358 (464)
+.|.+||.|+|...... +|-. --.-+-||+|+|..+.+
T Consensus 133 ~~F~vGd~Vrv~~~~~~------~HtR---~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 133 PRFAVGDRVRVRNLPPP------GHTR---LPRYVRGKTGTIERVHG 170 (222)
T ss_dssp -SS-TT-EEEE-----S------S--S---S-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCEEEECCCCCC------Cccc---ccHhhCCCeeEEEEEec
Confidence 35999999999765433 4432 23456799999997664
No 128
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=21.01 E-value=1.6e+02 Score=21.58 Aligned_cols=28 Identities=25% Similarity=0.162 Sum_probs=23.2
Q ss_pred ccEEEEEecCCCeEEEE-eCceeeecCcc
Q psy16233 350 IGIVIKVYEDKDVRVAF-RKNTWTLSSKC 377 (464)
Q Consensus 350 ~G~V~~v~~dgd~rV~~-~g~~w~~np~~ 377 (464)
.|++..|+.+|.|.|+. +++..+|+..-
T Consensus 16 ~G~~~gId~~G~L~v~~~~g~~~~i~sGd 44 (48)
T PF02237_consen 16 EGIAEGIDDDGALLVRTEDGSIRTISSGD 44 (48)
T ss_dssp EEEEEEEETTSEEEEEETTEEEEEESSSE
T ss_pred EEEEEEECCCCEEEEEECCCCEEEEEEEE
Confidence 79999999999999999 66577777543
No 129
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=20.42 E-value=2.5e+02 Score=23.53 Aligned_cols=44 Identities=18% Similarity=0.092 Sum_probs=30.9
Q ss_pred ceeEEEEEecCcceEEEEecCCeeEEEccCcceecc------------cccCCCEEEEec
Q psy16233 277 HTGIVHRVTEQTLVRVRFENCDNKWTFDPRALTKVD------------PFVAGDFVYFIP 324 (464)
Q Consensus 277 k~G~V~~I~~~gD~rV~~~~~~~~wtfnP~~L~kv~------------~~~~GD~V~I~~ 324 (464)
..|+|+.-.-+--+.|.. .+.-++|.-..-+. ...+||.|+|..
T Consensus 6 ~~G~Vvs~km~KTivV~v----~r~~~h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e 61 (84)
T CHL00142 6 KIGIVVSNKMNKTIVVAV----ENRYKHPIYGKIITKTKKYLVHDEENECNIGDQVLIEE 61 (84)
T ss_pred EEEEEEeCCCCceEEEEE----EEEEEcCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEE
Confidence 478888866667777765 56777776544321 378999999964
Done!