Query psy15370
Match_columns 393
No_of_seqs 223 out of 348
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 19:09:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15370.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15370hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2837|consensus 100.0 6E-115 1E-119 829.5 11.9 306 1-356 1-309 (309)
2 PF10357 Kin17_mid: Domain of 100.0 3.5E-64 7.5E-69 438.4 8.9 127 52-178 1-127 (127)
3 KOG4315|consensus 99.6 4E-17 8.6E-22 165.1 2.1 111 279-393 331-445 (455)
4 KOG1999|consensus 98.2 1.2E-06 2.5E-11 97.1 4.6 106 280-393 916-1021(1024)
5 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 4.1E-05 9E-10 49.9 0.7 27 25-51 1-27 (27)
6 PF00467 KOW: KOW motif; Inte 97.2 0.00056 1.2E-08 46.5 4.4 31 340-370 1-31 (32)
7 PF12874 zf-met: Zinc-finger o 97.2 8.7E-05 1.9E-09 47.0 -0.2 25 26-50 1-25 (25)
8 smart00451 ZnF_U1 U1-like zinc 96.9 0.00028 6E-09 47.7 0.3 32 25-56 3-34 (35)
9 smart00739 KOW KOW (Kyprides, 96.7 0.003 6.4E-08 40.6 4.0 26 338-363 2-27 (28)
10 PRK12281 rplX 50S ribosomal pr 96.4 0.0061 1.3E-07 49.6 5.1 33 339-371 8-40 (76)
11 CHL00141 rpl24 ribosomal prote 96.3 0.0071 1.5E-07 50.0 5.1 33 339-371 10-42 (83)
12 PRK00004 rplX 50S ribosomal pr 95.8 0.017 3.7E-07 49.6 5.2 33 339-371 6-38 (105)
13 PRK01191 rpl24p 50S ribosomal 95.6 0.023 4.9E-07 50.3 5.2 33 339-371 47-79 (120)
14 TIGR00405 L26e_arch ribosomal 95.6 0.027 5.8E-07 49.9 5.7 51 338-392 87-139 (145)
15 TIGR01080 rplX_A_E ribosomal p 95.5 0.023 5.1E-07 49.7 4.9 33 339-371 43-75 (114)
16 PTZ00194 60S ribosomal protein 95.2 0.029 6.2E-07 51.0 4.8 33 339-371 48-80 (143)
17 TIGR01079 rplX_bact ribosomal 95.0 0.041 8.9E-07 47.3 4.9 33 339-371 5-37 (104)
18 PRK05609 nusG transcription an 94.9 0.066 1.4E-06 48.6 6.2 52 338-392 127-179 (181)
19 TIGR00922 nusG transcription t 94.6 0.081 1.7E-06 47.8 6.1 51 338-391 120-171 (172)
20 PRK08559 nusG transcription an 94.2 0.12 2.7E-06 46.6 6.3 50 338-391 95-146 (153)
21 PLN00036 40S ribosomal protein 93.6 0.46 9.9E-06 47.1 9.4 70 288-363 124-200 (261)
22 PRK04313 30S ribosomal protein 93.6 0.51 1.1E-05 46.2 9.6 79 288-371 120-209 (237)
23 PTZ00118 40S ribosomal protein 93.2 0.44 9.6E-06 47.2 8.6 72 288-365 124-202 (262)
24 PTZ00223 40S ribosomal protein 92.9 0.65 1.4E-05 46.3 9.3 71 288-364 121-198 (273)
25 COG0250 NusG Transcription ant 92.6 0.23 5E-06 46.3 5.5 53 336-392 122-176 (178)
26 COG0198 RplX Ribosomal protein 92.0 0.26 5.6E-06 42.7 4.6 30 339-370 6-35 (104)
27 PRK09014 rfaH transcriptional 91.7 0.39 8.4E-06 43.1 5.7 51 338-392 110-161 (162)
28 PF11623 DUF3252: Protein of u 91.6 0.62 1.4E-05 35.8 5.7 51 282-334 2-53 (53)
29 TIGR01955 RfaH transcriptional 91.6 0.42 9.2E-06 42.4 5.7 49 338-390 109-158 (159)
30 COG1471 RPS4A Ribosomal protei 91.4 0.68 1.5E-05 45.3 7.3 44 322-365 155-201 (241)
31 TIGR01956 NusG_myco NusG famil 89.6 0.85 1.8E-05 45.2 6.3 50 338-390 206-256 (258)
32 PF06220 zf-U1: U1 zinc finger 86.6 0.27 5.9E-06 35.1 0.6 33 25-57 3-37 (38)
33 COG5164 SPT5 Transcription elo 83.3 2.4 5.1E-05 45.5 5.9 70 302-374 297-386 (607)
34 PF15057 DUF4537: Domain of un 82.1 14 0.00031 32.5 9.5 84 289-375 3-99 (124)
35 PF07535 zf-DBF: DBF zinc fing 82.0 0.71 1.5E-05 34.9 1.1 34 24-64 4-37 (49)
36 PF15591 Imm17: Immunity prote 81.1 2.9 6.2E-05 34.3 4.4 49 287-335 10-63 (74)
37 smart00743 Agenet Tudor-like d 77.9 7.9 0.00017 29.1 5.8 54 283-339 4-59 (61)
38 KOG1999|consensus 75.2 8.4 0.00018 44.5 7.4 79 282-366 408-488 (1024)
39 smart00586 ZnF_DBF Zinc finger 75.2 1.6 3.6E-05 33.0 1.3 30 26-62 6-35 (49)
40 KOG0717|consensus 72.8 1.5 3.3E-05 46.7 0.9 40 16-58 286-325 (508)
41 PF13894 zf-C2H2_4: C2H2-type 70.9 0.79 1.7E-05 27.4 -1.0 21 26-46 1-21 (24)
42 PRK04333 50S ribosomal protein 69.6 11 0.00023 31.5 5.0 28 339-366 5-32 (84)
43 PLN00045 photosystem I reactio 68.2 7.6 0.00017 33.4 3.9 48 332-379 34-86 (101)
44 PF12756 zf-C2H2_2: C2H2 type 66.0 0.55 1.2E-05 37.3 -3.2 30 25-54 50-79 (100)
45 PF00096 zf-C2H2: Zinc finger, 65.0 0.79 1.7E-05 28.0 -1.9 22 26-47 1-22 (23)
46 smart00333 TUDOR Tudor domain. 63.8 25 0.00053 25.7 5.6 51 337-392 2-52 (57)
47 smart00333 TUDOR Tudor domain. 63.2 27 0.00059 25.4 5.7 51 283-338 4-55 (57)
48 PF12872 OST-HTH: OST-HTH/LOTU 62.1 12 0.00027 28.7 3.9 68 70-139 4-74 (74)
49 PTZ00065 60S ribosomal protein 62.1 17 0.00036 32.9 5.1 37 339-379 9-46 (130)
50 PF00567 TUDOR: Tudor domain; 60.8 59 0.0013 26.0 7.8 56 278-338 50-105 (121)
51 TIGR02760 TraI_TIGR conjugativ 59.9 56 0.0012 40.9 10.6 89 280-374 680-786 (1960)
52 PF02427 PSI_PsaE: Photosystem 57.7 41 0.00089 26.7 5.9 52 338-389 1-56 (61)
53 smart00355 ZnF_C2H2 zinc finge 55.4 2 4.4E-05 25.7 -1.3 21 26-46 1-21 (26)
54 cd01734 YlxS_C YxlS is a Bacil 52.2 32 0.00069 27.9 4.8 51 338-392 22-76 (83)
55 COG1096 Predicted RNA-binding 51.8 1.2E+02 0.0026 29.1 9.2 90 281-373 7-105 (188)
56 PTZ00471 60S ribosomal protein 50.2 25 0.00054 32.0 4.2 26 339-364 6-31 (134)
57 TIGR00405 L26e_arch ribosomal 48.1 50 0.0011 29.1 5.9 55 280-338 85-142 (145)
58 CHL00010 infA translation init 47.3 1.5E+02 0.0033 24.0 8.9 62 302-364 9-73 (78)
59 PF01176 eIF-1a: Translation i 47.1 67 0.0015 25.0 5.8 58 303-360 6-64 (65)
60 PF10771 DUF2582: Protein of u 47.0 16 0.00035 29.1 2.3 25 117-141 41-65 (65)
61 PF12855 Ecl1: Life-span regul 46.8 6.8 0.00015 28.9 0.1 25 27-54 8-34 (43)
62 PRK08559 nusG transcription an 46.8 75 0.0016 28.7 6.8 53 282-338 95-150 (153)
63 PF10615 DUF2470: Protein of u 46.6 9.2 0.0002 30.9 0.9 36 106-141 16-55 (83)
64 PF01455 HupF_HypC: HupF/HypC 44.6 69 0.0015 25.5 5.5 42 304-349 7-49 (68)
65 cd08768 Cdc6_C Winged-helix do 44.1 25 0.00054 27.8 3.0 61 75-136 10-70 (87)
66 cd04508 TUDOR Tudor domains ar 43.3 46 0.00099 23.4 4.0 35 297-333 11-46 (48)
67 PRK14639 hypothetical protein; 41.9 48 0.001 29.8 4.8 71 312-392 63-133 (140)
68 PF04717 Phage_base_V: Phage-r 41.6 66 0.0014 25.4 5.1 45 304-348 1-54 (79)
69 PRK04914 ATP-dependent helicas 40.2 1.9E+02 0.0042 33.9 10.3 63 303-370 18-82 (956)
70 PF06052 3-HAO: 3-hydroxyanthr 40.1 12 0.00025 34.7 0.6 13 20-32 114-126 (151)
71 KOG1708|consensus 39.2 43 0.00092 32.7 4.2 33 339-371 74-106 (236)
72 COG2163 RPL14A Ribosomal prote 38.9 45 0.00097 29.9 4.0 29 338-366 5-33 (125)
73 PF14968 CCDC84: Coiled coil p 35.5 41 0.0009 34.7 3.7 28 27-57 1-28 (336)
74 KOG3421|consensus 34.8 39 0.00084 30.8 3.0 37 339-379 8-44 (136)
75 PRK14631 hypothetical protein; 33.7 96 0.0021 29.0 5.6 72 312-392 92-167 (174)
76 PF09538 FYDLN_acid: Protein o 33.7 21 0.00045 31.1 1.1 12 28-39 12-23 (108)
77 PF14505 DUF4438: Domain of un 32.1 43 0.00093 33.4 3.0 36 339-374 59-94 (258)
78 cd05793 S1_IF1A S1_IF1A: Trans 31.2 2.9E+02 0.0063 22.5 7.7 58 304-361 4-62 (77)
79 CHL00125 psaE photosystem I su 31.1 72 0.0016 25.6 3.6 41 339-379 3-47 (64)
80 PRK14637 hypothetical protein; 31.1 99 0.0021 28.3 5.1 46 339-392 96-142 (151)
81 PRK13264 3-hydroxyanthranilate 30.9 21 0.00045 33.8 0.7 24 19-43 114-137 (177)
82 TIGR03037 anthran_nbaC 3-hydro 30.9 22 0.00047 33.1 0.8 24 20-44 109-132 (159)
83 TIGR02300 FYDLN_acid conserved 30.8 22 0.00048 32.1 0.8 16 25-40 9-24 (129)
84 PF13912 zf-C2H2_6: C2H2-type 30.1 12 0.00027 23.5 -0.7 22 26-47 2-23 (27)
85 PRK14638 hypothetical protein; 29.6 81 0.0018 28.7 4.2 69 312-392 75-143 (150)
86 PRK04012 translation initiatio 29.3 3.6E+02 0.0078 23.2 7.9 58 304-361 25-83 (100)
87 TIGR00008 infA translation ini 28.8 3.1E+02 0.0068 22.1 7.1 23 302-325 7-29 (68)
88 PRK14635 hypothetical protein; 28.7 81 0.0018 29.0 4.1 73 313-392 75-155 (162)
89 PF07076 DUF1344: Protein of u 28.7 2.5E+02 0.0053 22.5 6.2 43 303-350 6-50 (61)
90 PTZ00448 hypothetical protein; 28.5 20 0.00043 37.5 0.2 31 25-55 314-344 (373)
91 KOG3408|consensus 28.3 22 0.00048 32.0 0.4 37 25-61 57-93 (129)
92 COG0779 Uncharacterized protei 28.3 1.3E+02 0.0028 27.8 5.3 46 339-392 97-146 (153)
93 KOG4235|consensus 28.2 88 0.0019 30.8 4.4 47 104-156 128-174 (244)
94 PRK00276 infA translation init 28.2 3E+02 0.0066 21.7 8.3 56 303-359 10-68 (72)
95 PRK14633 hypothetical protein; 27.7 1.1E+02 0.0024 27.8 4.7 70 312-392 69-142 (150)
96 PRK12442 translation initiatio 27.6 3.7E+02 0.008 22.9 7.4 63 301-364 8-73 (87)
97 PRK14630 hypothetical protein; 27.5 1.2E+02 0.0026 27.4 4.9 68 312-392 72-139 (143)
98 PF08863 YolD: YolD-like prote 27.4 1.6E+02 0.0035 23.4 5.2 41 348-393 52-92 (92)
99 cd04456 S1_IF1A_like S1_IF1A_l 27.0 3.5E+02 0.0076 22.1 7.8 48 304-351 4-52 (78)
100 PRK02749 photosystem I reactio 26.9 1E+02 0.0022 25.3 3.8 36 339-374 4-43 (71)
101 PRK13709 conjugal transfer nic 26.9 4.7E+02 0.01 33.0 11.0 87 280-373 647-749 (1747)
102 PF04494 TFIID_90kDa: WD40 ass 25.9 27 0.00059 31.0 0.5 64 61-124 61-127 (142)
103 PRK00411 cdc6 cell division co 25.9 1.2E+02 0.0025 30.4 5.1 125 23-150 247-381 (394)
104 PHA01733 hypothetical protein 25.6 48 0.001 30.8 2.0 51 62-127 80-130 (153)
105 PRK14636 hypothetical protein; 25.4 1.4E+02 0.003 28.0 5.1 70 312-392 73-146 (176)
106 PF15490 Ten1_2: Telomere-capp 25.2 2.7E+02 0.0058 24.7 6.5 28 320-347 47-74 (118)
107 PLN02748 tRNA dimethylallyltra 25.1 28 0.00061 37.3 0.5 34 24-57 417-451 (468)
108 TIGR00523 eIF-1A eukaryotic/ar 25.0 3.4E+02 0.0073 23.3 6.9 58 285-346 8-66 (99)
109 KOG4727|consensus 24.3 68 0.0015 30.6 2.8 53 22-74 72-124 (193)
110 PRK09521 exosome complex RNA-b 24.2 3.6E+02 0.0078 25.0 7.6 46 296-344 23-68 (189)
111 PF09038 53-BP1_Tudor: Tumour 24.0 5.4E+02 0.012 23.2 11.1 83 288-373 7-93 (122)
112 PLN00208 translation initiatio 23.8 5.3E+02 0.012 23.8 8.4 59 304-362 36-95 (145)
113 PRK05585 yajC preprotein trans 23.4 1.6E+02 0.0035 25.4 4.7 30 339-374 54-83 (106)
114 COG2139 RPL21A Ribosomal prote 22.8 1.6E+02 0.0034 25.6 4.4 48 339-390 34-91 (98)
115 KOG0436|consensus 22.8 95 0.0021 33.6 3.8 79 36-139 85-163 (578)
116 PRK14712 conjugal transfer nic 22.4 5.5E+02 0.012 32.2 10.4 85 283-373 518-617 (1623)
117 cd04451 S1_IF1 S1_IF1: Transla 21.7 3.7E+02 0.0079 20.4 7.9 24 335-358 38-61 (64)
118 PRK03879 ribonuclease P protei 21.3 5.2E+02 0.011 22.0 8.2 50 285-347 15-64 (96)
119 cd05696 S1_Rrp5_repeat_hs4 S1_ 21.2 3.6E+02 0.0077 20.8 6.0 57 303-370 6-69 (71)
120 PF14444 S1-like: S1-like 21.0 2.2E+02 0.0048 22.5 4.6 38 303-347 5-43 (58)
121 PTZ00329 eukaryotic translatio 21.0 6.1E+02 0.013 23.7 8.3 59 304-362 36-95 (155)
122 PRK04306 50S ribosomal protein 20.8 2E+02 0.0043 24.9 4.7 37 351-391 58-94 (98)
No 1
>KOG2837|consensus
Probab=100.00 E-value=6.4e-115 Score=829.54 Aligned_cols=306 Identities=55% Similarity=0.911 Sum_probs=267.0
Q ss_pred CCCCCCCCHHHHHHHhhhccccceeeeecchhhhccCcCccccccCCHHHHHHHHHhhcChhhHHHHHHHHHHHHHHHHH
Q psy15370 1 MGKHEVGTPKYIANKMKAKGLQKLRWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFADNADQYLDEFSREFEEGYLELL 80 (393)
Q Consensus 1 Mgkae~~t~K~ian~~KakGLqkLrwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~~n~~~~i~~~S~~F~~~Fl~lL 80 (393)
||+|||||||||||+||||||||||||||||||||||+||||||||||||||||++|+.||.+++++||.+|+.+||+||
T Consensus 1 MGkad~~tpK~ianr~ksKGLQKlRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~Np~~~~~~fs~eF~~dFl~LL 80 (309)
T KOG2837|consen 1 MGKADFGTPKAIANRIKSKGLQKLRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFALNPGRSLERFSNEFEKDFLSLL 80 (309)
T ss_pred CCccccCCHHHHHHHHHhhhHHHHHHHHHHHHHHhccccccccccCCHHHHHHHHHHHhCcchhHHHhHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCcceeeccchhhhhhcCCCceeecccccccHHHHHHHhccccceEeeccccceEEEeecCCHHHHHHHHHHHHHHh
Q psy15370 81 RRQFSTRRVFANKVYQDYIADREHVHMNATQWETLTEFVKHLGKSGKCVVDETEKGWFVTYIDRDPETIAFQQKMAKKEK 160 (393)
Q Consensus 81 r~~~g~krv~aN~vY~eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr~g~~~v~et~kg~~i~~Id~~pe~~~r~~~~~~~~~ 160 (393)
|++||+|||+||+||||||+||+|||||||+|.|||+||+||||+|+|+||+||+||||+|||++|+++.|+.+..++++
T Consensus 81 r~~~g~KrI~aN~VYnEYI~dR~HvHMNaT~w~SLtefvk~LGR~Gkc~vdetekgw~i~yIdk~petl~r~~~d~~r~r 160 (309)
T KOG2837|consen 81 RQRHGTKRIGANKVYNEYIADRNHVHMNATRWRSLTEFVKYLGRTGKCKVDETEKGWFITYIDKFPETLKRIEEDLKRER 160 (309)
T ss_pred HHHhccceechhHHHHHHHccccceeecchhhhhHHHHHHHhccCceeeeecCCCceEEEEeccChhhhcchhhHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCHHHHHHHHHHHHHHHHHHHhhhhcccCCCCccccccccCcce---EEeeccCCCCCCCcccccccCCccccccCCC
Q psy15370 161 MEQDDNERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRNEDEKL---SLKLETFKKPSSSSISLKKVNLDKDVSESGP 237 (393)
Q Consensus 161 ~~~~dee~~~~~i~~qi~r~~~~~~~~~~~~~~~~~~l~r~~~~ki---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (393)
++.+|||+.+++|+.||.||++..+. +.+++..+||.|+.+++- ..+...+.. .+|++.+ .+
T Consensus 161 qe~~dEe~~~~~id~Qi~Rake~g~~--e~e~e~~~El~~d~~~~~~~v~~~~~~sk~--~~p~~kk-----------~~ 225 (309)
T KOG2837|consen 161 QEKDDEERGADLIDGQIKRAKEQGEK--EYEPEMNTELSRDGDDERKSVVVSSALSKR--VNPKAKK-----------LP 225 (309)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhcccc--ccccccccccccCCccccccceeeeeccCc--CChhhhc-----------CC
Confidence 99999999999999999999982221 234556789999655442 222111111 1121111 00
Q ss_pred CCCCCCcCccccCCCHHHHHhhHHHHHHHhhhhhhhcCCCCCCcccCceEEEEeeccCCcccccceeEEEEecCCceEEE
Q psy15370 238 SSSSKKFSGEKRKLTALEQIKLEEEEAKKKRIDQERQNSGEESWLHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIV 317 (393)
Q Consensus 238 ~s~~~~~~~~~~k~saldeim~~~ee~kk~~~~~~~~~~r~~~WL~~~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V 317 (393)
.++.+ .++-||||+ +||.+| | +|+|++++++.+ |++||||.+|+|.|++.|
T Consensus 226 ~~~~~--------~~~rdEi~~-~ee~kk--------------w-----~vk~~sk~l~~k-~K~K~vv~~vid~y~~~~ 276 (309)
T KOG2837|consen 226 PDKDG--------GKKRDEIMK-MEERKK--------------W-----VVKVISKSLGEK-YKQKGVVKKVIDDYTGQI 276 (309)
T ss_pred CCccc--------ccchHHHHH-hhhcCc--------------e-----EEEeehhhhhHH-hccccHHHHHHHhhhhhe
Confidence 10111 112299998 666432 8 999999999998 999999999999999999
Q ss_pred EEcCCCcEEEeecCceeeecCCCCCeEEEEecCccCceE
Q psy15370 318 SLLDSKHKIKLDQEHLETVIPNLGRQVLILCGKYKGEKA 356 (393)
Q Consensus 318 ~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G 356 (393)
+ +|+|++|+|||+|||||||+ |||||+|||..|
T Consensus 277 K-ld~g~~lk~dq~~lEtvip~-----~~vng~yRg~~~ 309 (309)
T KOG2837|consen 277 K-LDSGTVLKVDQEHLETVIPQ-----MIVNGAYRGSEA 309 (309)
T ss_pred e-ccCCceecccHHHHHHHhHH-----HHhhhhhccCCC
Confidence 9 67999999999999999999 999999999754
No 2
>PF10357 Kin17_mid: Domain of Kin17 curved DNA-binding protein; InterPro: IPR019447 This entry represents the conserved central 169 residue region of the Kin17 DNA/RNA-binding proteins. The N-terminal region of Kin17 contains a zinc-finger domain, while in the human and mouse proteins there is a RecA-like domain found in the C-terminal region. In humans, Kin17 protein forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle []. ; PDB: 2V1N_A.
Probab=100.00 E-value=3.5e-64 Score=438.42 Aligned_cols=127 Identities=62% Similarity=1.091 Sum_probs=89.9
Q ss_pred HHHHHhhcChhhHHHHHHHHHHHHHHHHHHhhcCcceeeccchhhhhhcCCCceeecccccccHHHHHHHhccccceEee
Q psy15370 52 RQLLLFADNADQYLDEFSREFEEGYLELLRRQFSTRRVFANKVYQDYIADREHVHMNATQWETLTEFVKHLGKSGKCVVD 131 (393)
Q Consensus 52 rqm~~~~~n~~~~i~~~S~~F~~~Fl~lLr~~~g~krv~aN~vY~eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr~g~~~v~ 131 (393)
|||++|++||++||++||++|+++||+|||++||+|||+||+||||||+||+|||||||+|+|||+||+||||+|+|+||
T Consensus 1 Rqm~~~~~n~~k~i~~yS~eFe~~Fl~lLr~~hg~krV~AN~vYnEyI~Dk~HvHMNaT~W~sLT~FvkyLgr~G~~~Vd 80 (127)
T PF10357_consen 1 RQMLLFAENPGKFIDEYSEEFEKDFLRLLRRRHGTKRVNANKVYNEYIQDKDHVHMNATRWTSLTEFVKYLGREGKCKVD 80 (127)
T ss_dssp ---------GGG-HHHHHHHHHHHHHHHHHHHTSS-EEEHHHHHHHHTTSS----GGGSS-SSHHHHHHHHTTTTSEEEE
T ss_pred CchHHHhhChhhHHHHHHHHHHHHHHHHHHHhcCCCeechhHHHHHHhcCccceeecccccchHHHHHHHHhhCCeeEee
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceEEEeecCCHHHHHHHHHHHHHHhhhcCHHHHHHHHHHHHHH
Q psy15370 132 ETEKGWFVTYIDRDPETIAFQQKMAKKEKMEQDDNERNMEFLERQIA 178 (393)
Q Consensus 132 et~kg~~i~~Id~~pe~~~r~~~~~~~~~~~~~dee~~~~~i~~qi~ 178 (393)
+||+||||+|||+||+++.|+++..++++++++||||.+++|++||+
T Consensus 81 etekg~~I~yID~~pe~l~r~~~~~k~~~~~~~dee~~~~~i~~Qi~ 127 (127)
T PF10357_consen 81 ETEKGWFISYIDRSPETLARQEELAKKEKAEKDDEERERKLIEKQIE 127 (127)
T ss_dssp EETTEEEEEE--SSHHHHHHHHHTGGGT-------------------
T ss_pred cCCCceEEEeeCCCHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999995
No 3
>KOG4315|consensus
Probab=99.64 E-value=4e-17 Score=165.13 Aligned_cols=111 Identities=26% Similarity=0.502 Sum_probs=102.4
Q ss_pred CCcccCceEEEEeeccCCcc-cccceeEEEEecCCceEEEEEcCCCcEE-E-eecCceeeecC-CCCCeEEEEecCccCc
Q psy15370 279 ESWLHKNIIVKIVTKNLGEK-FYKKKGTVEKVIDKYAAIVSLLDSKHKI-K-LDQEHLETVIP-NLGRQVLILCGKYKGE 354 (393)
Q Consensus 279 ~~WL~~~IvVKIidK~l~dg-yYkkKGvV~dV~d~~~c~V~l~d~g~~l-~-VdQ~~LETVIP-~~G~~V~VV~G~~RG~ 354 (393)
..|++.+|.|||+|+.+..| ||.+|++|.+|....+|.|.+++++..+ . |+|++|||++| ..|.+||||.|.|.|.
T Consensus 331 k~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~ 410 (455)
T KOG4315|consen 331 KSWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQELVQGNIRQELLETALPRRGGEKVMVVSGKHKGV 410 (455)
T ss_pred chhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccccccccchHHHHHhhhcccccCceeEEEecccccc
Confidence 38999999999999999999 9999999999999999999999877777 4 99999999999 7888899999999999
Q ss_pred eEEEEEeeCCCceEEEEecCCCCCCceeeeccccccccC
Q psy15370 355 KAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICKI 393 (393)
Q Consensus 355 ~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddicKl 393 (393)
.|.|++.|.++.+++|++.. +..++ .+.||+||.|
T Consensus 411 ~g~llskd~~Ke~~~v~~~a---~ndvv-~~~~D~v~ey 445 (455)
T KOG4315|consen 411 YGSLLSKDLDKETGVVRLVA---TNDVV-TVYLDQVCEY 445 (455)
T ss_pred hhhhhhhhhhhhhcceeccc---ccchh-hhhHHHHHHh
Confidence 99999999999999999886 56655 6999999975
No 4
>KOG1999|consensus
Probab=98.20 E-value=1.2e-06 Score=97.11 Aligned_cols=106 Identities=18% Similarity=0.203 Sum_probs=89.7
Q ss_pred CcccCceEEEEeeccCCcccccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEecCccCceEEEE
Q psy15370 280 SWLHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLK 359 (393)
Q Consensus 280 ~WL~~~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~Li 359 (393)
.| ..++.+.+.+-+++-...++.++|++|.+ +.|+|.+.++|+.+.+...+|+++.|..|+.++|+.|.++|.+|+|+
T Consensus 916 ~~-~~~~~~~~~d~~~~~~~~G~~~~ir~v~~-G~~sv~~~de~~~~~~s~~~~a~~~p~~~d~~k~~~g~~~g~~~~~~ 993 (1024)
T KOG1999|consen 916 NG-GDGNSSWGPDTSLDTQLVGQTGIIRSVAD-GGCSVWLGDEGETISNSKPHLAPAPPCKGDDVKSIWGDDRGSTGKLV 993 (1024)
T ss_pred CC-CccceEecccccccceecccccceeeccC-CceeeecCCCCcccccccccCccCCCCCCCCcccccccccccccccc
Confidence 46 67888888876555558899999999986 69999999999999999999999999999999999999999999999
Q ss_pred EeeCCCceEEEEecCCCCCCceeeeccccccccC
Q psy15370 360 DINIDDCNANVELIDPHYDNKVVRNIDYSHICKI 393 (393)
Q Consensus 360 siD~~k~~a~V~l~~G~~~g~~v~~l~yddicKl 393 (393)
++|..++.+.+...+ + +..+++--+||+
T Consensus 994 ~~dg~~g~~~~d~~~----~--~k~l~~~~~~k~ 1021 (1024)
T KOG1999|consen 994 GNDGWDGIVRIDETS----D--IKILNLGLLCKM 1021 (1024)
T ss_pred CCCcccceecccccc----c--chhhhhhhhhhc
Confidence 999999955544323 2 445777778875
No 5
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.45 E-value=4.1e-05 Score=49.88 Aligned_cols=27 Identities=37% Similarity=0.780 Sum_probs=25.1
Q ss_pred eeeecchhhhccCcCccccccCCHHHH
Q psy15370 25 RWYCQMCQKQCRDENGFKCHTSSEAHQ 51 (393)
Q Consensus 25 rwyCQ~CqKQCRDeNGFKcH~~SesH~ 51 (393)
+|||.+|.+.|.+++.|.-|+.|..|+
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 589999999999999999999999985
No 6
>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=97.24 E-value=0.00056 Score=46.53 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=28.3
Q ss_pred CCCeEEEEecCccCceEEEEEeeCCCceEEE
Q psy15370 340 LGRQVLILCGKYKGEKAVLKDINIDDCNANV 370 (393)
Q Consensus 340 ~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V 370 (393)
+|+.|+|+.|.|+|..|+++++|.++..|.|
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 5899999999999999999999999986654
No 7
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.16 E-value=8.7e-05 Score=46.98 Aligned_cols=25 Identities=36% Similarity=0.866 Sum_probs=24.1
Q ss_pred eeecchhhhccCcCccccccCCHHH
Q psy15370 26 WYCQMCQKQCRDENGFKCHTSSEAH 50 (393)
Q Consensus 26 wyCQ~CqKQCRDeNGFKcH~~SesH 50 (393)
|||.+|+++|.+++.|+.|+.|..|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 8999999999999999999999887
No 8
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.88 E-value=0.00028 Score=47.74 Aligned_cols=32 Identities=22% Similarity=0.604 Sum_probs=29.9
Q ss_pred eeeecchhhhccCcCccccccCCHHHHHHHHH
Q psy15370 25 RWYCQMCQKQCRDENGFKCHTSSEAHQRQLLL 56 (393)
Q Consensus 25 rwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~ 56 (393)
+|||.+|++.|.++..++-|..|..|.+.+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 59999999999999999999999999998864
No 9
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.69 E-value=0.003 Score=40.58 Aligned_cols=26 Identities=19% Similarity=0.452 Sum_probs=24.4
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeC
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINI 363 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~ 363 (393)
|.+|+.|+|+.|.++|..|++++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57899999999999999999999985
No 10
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=96.41 E-value=0.0061 Score=49.62 Aligned_cols=33 Identities=21% Similarity=0.270 Sum_probs=30.7
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|++|.|+.|.++|..|+++.++.++..|.|+
T Consensus 8 ~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 8 KKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 789999999999999999999999999977764
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=96.33 E-value=0.0071 Score=49.97 Aligned_cols=33 Identities=24% Similarity=0.312 Sum_probs=30.7
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|++|.||.|.++|..|+++.|+.++..|.|+
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 789999999999999999999999999977764
No 12
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=95.81 E-value=0.017 Score=49.60 Aligned_cols=33 Identities=24% Similarity=0.396 Sum_probs=30.8
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|+.|+|+.|.++|..|++++++.+...|.|+
T Consensus 6 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 6 KKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 789999999999999999999999999988764
No 13
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.58 E-value=0.023 Score=50.25 Aligned_cols=33 Identities=24% Similarity=0.499 Sum_probs=30.3
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|+.|+|+.|.++|..|+++.+|.+++.|.|+
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 569999999999999999999999999977764
No 14
>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=95.57 E-value=0.027 Score=49.85 Aligned_cols=51 Identities=24% Similarity=0.350 Sum_probs=42.4
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCce--eeecccccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKV--VRNIDYSHICK 392 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~--v~~l~yddicK 392 (393)
+.+|+.|.|+.|++.|..|.+..+|..+..|.|.+.. .+.. + .+++++|-+
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~---~~~~~~v-~v~~~~l~~ 139 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE---AAVPIPV-TVKGDQVRI 139 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEE---cCccceE-EEeeeEEEE
Confidence 5899999999999999999999999999899998886 3443 4 477777643
No 15
>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=95.47 E-value=0.023 Score=49.69 Aligned_cols=33 Identities=24% Similarity=0.501 Sum_probs=30.2
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|+.|+|+.|.++|.+|+++.|+..+..|.|+
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Ve 75 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVE 75 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEc
Confidence 679999999999999999999999999977664
No 16
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=95.24 E-value=0.029 Score=50.95 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=30.3
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|+.|+|+.|.++|..|++++++..++.|.|+
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 569999999999999999999999999977764
No 17
>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=95.01 E-value=0.041 Score=47.30 Aligned_cols=33 Identities=24% Similarity=0.338 Sum_probs=30.6
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
..|++|.||.|.++|..|++++++.++..|.|+
T Consensus 5 kkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 5 KKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 689999999999999999999999999977764
No 18
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=94.87 E-value=0.066 Score=48.57 Aligned_cols=52 Identities=12% Similarity=0.263 Sum_probs=41.0
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCc-eeeecccccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNK-VVRNIDYSHICK 392 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~-~v~~l~yddicK 392 (393)
+.+|+.|.|+.|++.|..|++..+|..+..|.|.++- -|+ +...++++++-+
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~---~G~~~~v~l~~~~l~~ 179 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSI---FGRETPVELEFSQVEK 179 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEE---CCCceEEEEchHHEEE
Confidence 4789999999999999999999999888888887764 233 233577777654
No 19
>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=94.65 E-value=0.081 Score=47.79 Aligned_cols=51 Identities=12% Similarity=0.251 Sum_probs=40.2
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCc-eeeeccccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNK-VVRNIDYSHIC 391 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~-~v~~l~yddic 391 (393)
+.+|++|.|+.|++.|..|.+..+|.++..|.|.++- -|+ +...+++++|-
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~---~g~~~~v~v~~~~l~ 171 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSI---FGRETPVELEFSQVE 171 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEE---CCCceEEEEcHHHee
Confidence 3789999999999999999999999888888888774 233 22347776653
No 20
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=94.22 E-value=0.12 Score=46.60 Aligned_cols=50 Identities=24% Similarity=0.363 Sum_probs=41.0
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCce--eeeccccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKV--VRNIDYSHIC 391 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~--v~~l~yddic 391 (393)
..+|+.|.|+.|.+.|..|++.++|.++..|+|.+.. ..-. + .++.++|.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~---~~~~~pv-~v~~~~~~ 146 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLE---AAVPIPV-TVRGDQVR 146 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEEC---CcceeeE-EEeccEEE
Confidence 4899999999999999999999999999999988875 2221 3 47777663
No 21
>PLN00036 40S ribosomal protein S4; Provisional
Probab=93.61 E-value=0.46 Score=47.13 Aligned_cols=70 Identities=19% Similarity=0.318 Sum_probs=48.5
Q ss_pred EEEeeccCCcccccceeEEEEecCCceEEEEEcC----CCcEE--EeecCceeeecC-CCCCeEEEEecCccCceEEEEE
Q psy15370 288 VKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLD----SKHKI--KLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKD 360 (393)
Q Consensus 288 VKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d----~g~~l--~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~Lis 360 (393)
+||.++ +..++|++.=+...+.. +..+| .+++| +++...+.-.+| ..|..++|+.|.+.|.+|++.+
T Consensus 124 cKV~~k-----~~~~gG~~ql~~hDGrn-i~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~ 197 (261)
T PLN00036 124 CKVRKI-----QFGQKGIPYLNTHDGRT-IRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKN 197 (261)
T ss_pred EEEEEE-----EEecCCeEEEEecCCce-eccCCCccccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEE
Confidence 466655 34456666655444444 33222 56666 444555777777 9999999999999999999999
Q ss_pred eeC
Q psy15370 361 INI 363 (393)
Q Consensus 361 iD~ 363 (393)
+..
T Consensus 198 i~~ 200 (261)
T PLN00036 198 REK 200 (261)
T ss_pred EEe
Confidence 984
No 22
>PRK04313 30S ribosomal protein S4e; Validated
Probab=93.57 E-value=0.51 Score=46.18 Aligned_cols=79 Identities=24% Similarity=0.332 Sum_probs=51.8
Q ss_pred EEEeeccCCcccccceeEEEEecCCceEEEEEc--C--CCcEE--EeecCceeeecC-CCCCeEEEEecCccCceEEEEE
Q psy15370 288 VKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLL--D--SKHKI--KLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKD 360 (393)
Q Consensus 288 VKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~--d--~g~~l--~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~Lis 360 (393)
+||.++ ...++|++.=+...+...+.-. + .+++| +++...+.-.+| ..|..++|+.|.+.|.+|++.+
T Consensus 120 ~KV~~k-----~~~~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~ 194 (237)
T PRK04313 120 CKIENK-----TTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKE 194 (237)
T ss_pred EEEEeE-----EEecCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEE
Confidence 566655 3345566655544444433321 1 56666 444454666777 9999999999999999999999
Q ss_pred eeCCC----ceEEEE
Q psy15370 361 INIDD----CNANVE 371 (393)
Q Consensus 361 iD~~k----~~a~V~ 371 (393)
|.... ..|.|+
T Consensus 195 i~~~~~~~~~~V~i~ 209 (237)
T PRK04313 195 IEVTKSSKPNIVTLE 209 (237)
T ss_pred EEEccCCCCcEEEEE
Confidence 97544 345554
No 23
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=93.20 E-value=0.44 Score=47.24 Aligned_cols=72 Identities=13% Similarity=0.210 Sum_probs=48.7
Q ss_pred EEEeeccCCcccccceeEEEEecCCceEEEEEcC----CCcEE--EeecCceeeecC-CCCCeEEEEecCccCceEEEEE
Q psy15370 288 VKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLD----SKHKI--KLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKD 360 (393)
Q Consensus 288 VKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d----~g~~l--~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~Lis 360 (393)
+||..+ +..++|++.=+...+.. +..+| .+++| +++...+.-.+| ..|..++|+.|.+.|.+|++.+
T Consensus 124 cKV~~k-----~~~~gg~~~l~~hDGrn-i~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~ 197 (262)
T PTZ00118 124 CRVKKT-----FLGPKEVSIAVTHDGRT-IRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVS 197 (262)
T ss_pred EEEeEE-----EECCCCeEEEEecCcce-eccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEE
Confidence 466554 34556666654433333 33222 56766 444555777777 9999999999999999999999
Q ss_pred eeCCC
Q psy15370 361 INIDD 365 (393)
Q Consensus 361 iD~~k 365 (393)
+....
T Consensus 198 ~~~~~ 202 (262)
T PTZ00118 198 KEKHP 202 (262)
T ss_pred EEecC
Confidence 86543
No 24
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=92.89 E-value=0.65 Score=46.34 Aligned_cols=71 Identities=14% Similarity=0.237 Sum_probs=47.9
Q ss_pred EEEeeccCCcccccceeEEEEecCCceEEEEEcC----CCcEE--EeecCceeeecC-CCCCeEEEEecCccCceEEEEE
Q psy15370 288 VKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLD----SKHKI--KLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKD 360 (393)
Q Consensus 288 VKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d----~g~~l--~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~Lis 360 (393)
+||.++ +..++|++.=+...+.. +..+| .+++| +++...+.-.+| ..|..|+|+.|.+.|.+|++.+
T Consensus 121 cKV~~k-----~~~~gG~~ql~~hDGrn-I~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~ 194 (273)
T PTZ00223 121 MKVVNV-----YTATGRIPVAVTHDGHR-IRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVS 194 (273)
T ss_pred EEEEEE-----EEecCCeeEEEecCCce-eccCCccccCCCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEE
Confidence 466655 33455665555443333 33222 56766 445455666777 9999999999999999999999
Q ss_pred eeCC
Q psy15370 361 INID 364 (393)
Q Consensus 361 iD~~ 364 (393)
+...
T Consensus 195 i~~~ 198 (273)
T PTZ00223 195 IERH 198 (273)
T ss_pred EEec
Confidence 9543
No 25
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=92.61 E-value=0.23 Score=46.35 Aligned_cols=53 Identities=23% Similarity=0.323 Sum_probs=43.3
Q ss_pred ecCCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCc--eeeecccccccc
Q psy15370 336 VIPNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNK--VVRNIDYSHICK 392 (393)
Q Consensus 336 VIP~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~--~v~~l~yddicK 392 (393)
+-+.+|+.|.|+.|++.|..|++.++|.++..++|.+.. -|+ .+ .++|++|-+
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~i---fgr~tPV-el~~~qVek 176 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSI---FGRPTPV-ELEFDQVEK 176 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEE---eCCceEE-EEehhhEEE
Confidence 445899999999999999999999999999988888775 233 23 488887755
No 26
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=92.03 E-value=0.26 Score=42.70 Aligned_cols=30 Identities=23% Similarity=0.343 Sum_probs=27.5
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANV 370 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V 370 (393)
..|+.|.|+.|.++|..|.+++++... |.|
T Consensus 6 rkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~V 35 (104)
T COG0198 6 KKGDTVKVIAGKDKGKEGKVLKVLPKK--VVV 35 (104)
T ss_pred ecCCEEEEEecCCCCcceEEEEEecCe--EEE
Confidence 679999999999999999999999998 544
No 27
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=91.70 E-value=0.39 Score=43.12 Aligned_cols=51 Identities=25% Similarity=0.369 Sum_probs=38.0
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCc-eeeecccccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNK-VVRNIDYSHICK 392 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~-~v~~l~yddicK 392 (393)
+..|++|.|+.|++.|..|.+..+|. +..+.|.++- -|+ +...+++++|-+
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~v~~---~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDG-EARSILLLNL---LNKQVKHSVDNTQFRK 161 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEeehh---hCCcEEEEECHHHeec
Confidence 47899999999999999999999995 4456577664 222 223577777754
No 28
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=91.60 E-value=0.62 Score=35.77 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=32.8
Q ss_pred ccCceEEEEeeccCCcccccceeEEEEecCCceEEEEEcCCC-cEEEeecCcee
Q psy15370 282 LHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSK-HKIKLDQEHLE 334 (393)
Q Consensus 282 L~~~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d~g-~~l~VdQ~~LE 334 (393)
+.||..|+|++ ..+-||.=.|.|..|.|+..+++.=..+= +.|.+.-++||
T Consensus 2 ilPG~~V~V~n--~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKN--PNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE 53 (53)
T ss_dssp --TT-EEEE----TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred ccCCCEEEEeC--CCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence 46899999986 34559999999999998766666543222 24577777776
No 29
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=91.56 E-value=0.42 Score=42.42 Aligned_cols=49 Identities=18% Similarity=0.191 Sum_probs=36.5
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCce-eeecccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKV-VRNIDYSHI 390 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~-v~~l~yddi 390 (393)
+.+|++|.|+.|++.|..|.++.+|. +..|.|.++- -|+. ...+++++|
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~l~~---~gr~~~v~~~~~~~ 158 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLLLNM---IGKQIKVSVPNTSV 158 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECC-CceEEEEEhh---hCCceEEEecHHHc
Confidence 47899999999999999999999994 4577777764 2332 224666554
No 30
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=91.38 E-value=0.68 Score=45.29 Aligned_cols=44 Identities=18% Similarity=0.356 Sum_probs=36.4
Q ss_pred CCcEE--EeecCceeeecC-CCCCeEEEEecCccCceEEEEEeeCCC
Q psy15370 322 SKHKI--KLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKDINIDD 365 (393)
Q Consensus 322 ~g~~l--~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~LisiD~~k 365 (393)
.|++| +++...+.-.|| ..|..|+|+.|.+.|.+|++.+|....
T Consensus 155 ~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~ 201 (241)
T COG1471 155 TGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQE 201 (241)
T ss_pred cccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEec
Confidence 45554 677777777777 999999999999999999999997653
No 31
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=89.58 E-value=0.85 Score=45.19 Aligned_cols=50 Identities=28% Similarity=0.368 Sum_probs=39.8
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCc-eeeecccccc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNK-VVRNIDYSHI 390 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~-~v~~l~yddi 390 (393)
+.+|+.|.|+.|++.|..|.+.++|.++..|.|.++- -|+ +...|+|++|
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~I---fGR~TpVeL~~~qV 256 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEI---LGKSVDVDLNFKHL 256 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEe---cCCcEEEEEchHHE
Confidence 4899999999999999999999999878878777764 233 2235777766
No 32
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=86.55 E-value=0.27 Score=35.06 Aligned_cols=33 Identities=27% Similarity=0.545 Sum_probs=20.8
Q ss_pred eeeecchhhhc-cCc-CccccccCCHHHHHHHHHh
Q psy15370 25 RWYCQMCQKQC-RDE-NGFKCHTSSEAHQRQLLLF 57 (393)
Q Consensus 25 rwyCQ~CqKQC-RDe-NGFKcH~~SesH~rqm~~~ 57 (393)
|+||..|.+-. .|- ++=|-|..+-.|++.+..+
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 79999999999 666 5779999999999988754
No 33
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=83.31 E-value=2.4 Score=45.45 Aligned_cols=70 Identities=36% Similarity=0.607 Sum_probs=50.4
Q ss_pred ceeEEEEecCCceEEEEEcCCCcEEEeecC----------------ceeeec----CCCCCeEEEEecCccCceEEEEEe
Q psy15370 302 KKGTVEKVIDKYAAIVSLLDSKHKIKLDQE----------------HLETVI----PNLGRQVLILCGKYKGEKAVLKDI 361 (393)
Q Consensus 302 kKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~----------------~LETVI----P~~G~~V~VV~G~~RG~~G~Lisi 361 (393)
.-||+... .+..|.|..-|.-..+++|-+ .||--| |++|..|.|-.|+|+|..|.+.++
T Consensus 297 nnGVfv~~-~~nv~~VAtkd~~~s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv 375 (607)
T COG5164 297 NNGVFVKI-EGNVCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDV 375 (607)
T ss_pred cCceEEEe-cCceeEEEeccchhhhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeecccccccceeeec
Confidence 44555553 467888877653333334433 455555 789999999999999999999999
Q ss_pred eCCCceEEEEecC
Q psy15370 362 NIDDCNANVELID 374 (393)
Q Consensus 362 D~~k~~a~V~l~~ 374 (393)
|.+.. +|+|.+
T Consensus 376 ~~~~a--rVeLhs 386 (607)
T COG5164 376 DRNIA--RVELHS 386 (607)
T ss_pred cCceE--EEEEec
Confidence 87775 778877
No 34
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=82.07 E-value=14 Score=32.47 Aligned_cols=84 Identities=14% Similarity=0.215 Sum_probs=54.1
Q ss_pred EEeeccCCcc-cccceeEEEEecCCceEEEEEcCCCcEEEeecCceeee----c-C-CCCCeEEEEe--cCccCceEEEE
Q psy15370 289 KIVTKNLGEK-FYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETV----I-P-NLGRQVLILC--GKYKGEKAVLK 359 (393)
Q Consensus 289 KIidK~l~dg-yYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETV----I-P-~~G~~V~VV~--G~~RG~~G~Li 359 (393)
+|+.++..|| ||- |+|++..+.....|... .++...++..++=.+ - | ++|+.|+... +.++=.-|+++
T Consensus 3 ~VlAR~~~DG~YY~--GtV~~~~~~~~~lV~f~-~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~~~~~~~~Y~Pg~V~ 79 (124)
T PF15057_consen 3 KVLARREEDGFYYP--GTVKKCVSSGQFLVEFD-DGDTQEVPISDIIALSDAMRHSLQVGDKVLAPWEPDDCRYGPGTVI 79 (124)
T ss_pred eEEEeeCCCCcEEe--EEEEEccCCCEEEEEEC-CCCEEEeChHHeEEccCcccCcCCCCCEEEEecCcCCCEEeCEEEE
Confidence 4667778899 554 89999888888888884 455555544443222 2 3 7899999994 34454558888
Q ss_pred Ee----eCCCceEEEEecCC
Q psy15370 360 DI----NIDDCNANVELIDP 375 (393)
Q Consensus 360 si----D~~k~~a~V~l~~G 375 (393)
+. -.++...+|.+-+|
T Consensus 80 ~~~~~~~~~~~~~~V~f~ng 99 (124)
T PF15057_consen 80 AGPERRASEDKEYTVRFYNG 99 (124)
T ss_pred ECccccccCCceEEEEEECC
Confidence 62 22333456777763
No 35
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=81.99 E-value=0.71 Score=34.93 Aligned_cols=34 Identities=32% Similarity=0.704 Sum_probs=27.2
Q ss_pred eeeeecchhhhccCcCccccccCCHHHHHHHHHhhcChhhH
Q psy15370 24 LRWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFADNADQY 64 (393)
Q Consensus 24 LrwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~~n~~~~ 64 (393)
=.-||..|.-.+-| |.-|+.|+.|++ ||.|+.-|
T Consensus 4 k~GYCE~C~~ky~~---l~~Hi~s~~Hr~----FA~~~~Nf 37 (49)
T PF07535_consen 4 KPGYCENCRVKYDD---LEEHIQSEKHRK----FAENDSNF 37 (49)
T ss_pred CCccCccccchhhh---HHHHhCCHHHHH----HHcCcccH
Confidence 34699999999887 999999999986 55666543
No 36
>PF15591 Imm17: Immunity protein 17
Probab=81.15 E-value=2.9 Score=34.29 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=36.4
Q ss_pred EEEEeeccCCcc-cccceeEEEEecCC----ceEEEEEcCCCcEEEeecCceee
Q psy15370 287 IVKIVTKNLGEK-FYKKKGTVEKVIDK----YAAIVSLLDSKHKIKLDQEHLET 335 (393)
Q Consensus 287 vVKIidK~l~dg-yYkkKGvV~dV~d~----~~c~V~l~d~g~~l~VdQ~~LET 335 (393)
+|+|.+....+. +++++|||...... +.-+|.+-+......++.+.|++
T Consensus 10 ~V~v~~s~p~~~ei~Gk~GVVlG~SeeD~~~~gY~Vli~d~e~~~~~ee~~l~~ 63 (74)
T PF15591_consen 10 EVEVVRSCPCDAEIWGKRGVVLGISEEDGGNFGYSVLIFDMECCWYIEEDELEA 63 (74)
T ss_pred EEEEeccCcchhhhcCceeEEEEEecCCCcEEEEEEEEeeeeeEEEechHHeee
Confidence 688887555555 99999999999653 33556666667777888888875
No 37
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=77.88 E-value=7.9 Score=29.07 Aligned_cols=54 Identities=22% Similarity=0.286 Sum_probs=41.2
Q ss_pred cCceEEEEeeccCCcccccceeEEEEecCCceEEEEEcC--CCcEEEeecCceeeecCC
Q psy15370 283 HKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLD--SKHKIKLDQEHLETVIPN 339 (393)
Q Consensus 283 ~~~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d--~g~~l~VdQ~~LETVIP~ 339 (393)
..|-.|-+-.+. .+++|- |+|..|.+...+.|.+.+ .+....++.+.|-+..|-
T Consensus 4 ~~G~~Ve~~~~~-~~~W~~--a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~w 59 (61)
T smart00743 4 KKGDRVEVFSKE-EDSWWE--AVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPPW 59 (61)
T ss_pred CCCCEEEEEECC-CCEEEE--EEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCCC
Confidence 345566666543 344654 899999886789999998 888899999999887763
No 38
>KOG1999|consensus
Probab=75.24 E-value=8.4 Score=44.46 Aligned_cols=79 Identities=22% Similarity=0.347 Sum_probs=57.5
Q ss_pred ccCceEEEEeeccCCcccccceeEEEEecCCceEEEEEc--CCCcEEEeecCceeeecCCCCCeEEEEecCccCceEEEE
Q psy15370 282 LHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLL--DSKHKIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLK 359 (393)
Q Consensus 282 L~~~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~--d~g~~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~Li 359 (393)
++|+=.|.|+- ++ +-+-||+|..|. +..++|... +...-|.+....| -=.-.+|+.|+||.|.|-|.+|.++
T Consensus 408 F~~GD~VeV~~---Ge-l~glkG~ve~vd-g~~vti~~~~e~l~~pl~~~~~eL-rKyF~~GDhVKVi~G~~eG~tGlVv 481 (1024)
T KOG1999|consen 408 FSPGDAVEVIV---GE-LKGLKGKVESVD-GTIVTIMSKHEDLKGPLEVPASEL-RKYFEPGDHVKVIAGRYEGDTGLVV 481 (1024)
T ss_pred cCCCCeEEEee---ee-eccceeEEEecc-CceEEEeeccccCCCccccchHhh-hhhccCCCeEEEEeccccCCcceEE
Confidence 56776676663 22 556799999985 345555433 3456678888888 2233889999999999999999999
Q ss_pred EeeCCCc
Q psy15370 360 DINIDDC 366 (393)
Q Consensus 360 siD~~k~ 366 (393)
.|+....
T Consensus 482 rVe~~~v 488 (1024)
T KOG1999|consen 482 RVEQGDV 488 (1024)
T ss_pred EEeCCeE
Confidence 9987653
No 39
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=75.16 E-value=1.6 Score=33.04 Aligned_cols=30 Identities=43% Similarity=0.862 Sum_probs=24.6
Q ss_pred eeecchhhhccCcCccccccCCHHHHHHHHHhhcChh
Q psy15370 26 WYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFADNAD 62 (393)
Q Consensus 26 wyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~~n~~ 62 (393)
-||..|.--+-| |.-|++|+.|++ ||.|+.
T Consensus 6 GYCE~Cr~kfd~---l~~Hi~s~~Hr~----FA~~~~ 35 (49)
T smart00586 6 GYCENCREKYDD---LETHLLSEKHRR----FAENND 35 (49)
T ss_pred cccccHhHHHhh---HHHHhccHHHHH----HHcCch
Confidence 599999988765 899999999986 556653
No 40
>KOG0717|consensus
Probab=72.76 E-value=1.5 Score=46.74 Aligned_cols=40 Identities=25% Similarity=0.535 Sum_probs=34.7
Q ss_pred hhhccccceeeeecchhhhccCcCccccccCCHHHHHHHHHhh
Q psy15370 16 MKAKGLQKLRWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFA 58 (393)
Q Consensus 16 ~KakGLqkLrwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~ 58 (393)
..-.|=+ .||-+|.|-|+.+|..|.|-.|--|.++|..+.
T Consensus 286 ~d~~ge~---lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLr 325 (508)
T KOG0717|consen 286 ADNEGEV---LYCVVCNKSFKSEKQLKNHENSKKHKENVAELR 325 (508)
T ss_pred hhhcCCc---eEEeeccccccchHHHHhhHHHHHHHHHHHHHH
Confidence 3344444 899999999999999999999999999998775
No 41
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=70.92 E-value=0.79 Score=27.42 Aligned_cols=21 Identities=24% Similarity=0.679 Sum_probs=16.7
Q ss_pred eeecchhhhccCcCccccccC
Q psy15370 26 WYCQMCQKQCRDENGFKCHTS 46 (393)
Q Consensus 26 wyCQ~CqKQCRDeNGFKcH~~ 46 (393)
|-|.+|.+.+++.+.++-|..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 679999999999999988864
No 42
>PRK04333 50S ribosomal protein L14e; Validated
Probab=69.62 E-value=11 Score=31.49 Aligned_cols=28 Identities=29% Similarity=0.439 Sum_probs=25.2
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCc
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDC 366 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~ 366 (393)
.+|.-|.++.|.+.|..+.++++-.+++
T Consensus 5 ~~GrvV~~~~Grd~gk~~vIv~i~d~~~ 32 (84)
T PRK04333 5 EVGRVCVKTAGREAGRKCVIVDIIDKNF 32 (84)
T ss_pred cccEEEEEeccCCCCCEEEEEEEecCCE
Confidence 6899999999999999999999966665
No 43
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=68.21 E-value=7.6 Score=33.39 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=37.8
Q ss_pred ceeeecCCCCCeEEEEecC--ccCceEEEEEeeCC---CceEEEEecCCCCCC
Q psy15370 332 HLETVIPNLGRQVLILCGK--YKGEKAVLKDINID---DCNANVELIDPHYDN 379 (393)
Q Consensus 332 ~LETVIP~~G~~V~VV~G~--~RG~~G~LisiD~~---k~~a~V~l~~G~~~g 379 (393)
--.++-|+.|++|+|++-+ +-..+|++.++|.+ .+-|+|+++.-.+.|
T Consensus 34 kpp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~kvNY~g 86 (101)
T PLN00045 34 KPPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEKVNYAG 86 (101)
T ss_pred CCCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeeeeeccc
Confidence 3456778999999999776 46789999999987 788899988654444
No 44
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=65.96 E-value=0.55 Score=37.31 Aligned_cols=30 Identities=23% Similarity=0.571 Sum_probs=26.2
Q ss_pred eeeecchhhhccCcCccccccCCHHHHHHH
Q psy15370 25 RWYCQMCQKQCRDENGFKCHTSSEAHQRQL 54 (393)
Q Consensus 25 rwyCQ~CqKQCRDeNGFKcH~~SesH~rqm 54 (393)
.|.|..|.+.+++..+++-|+.+.+|.+..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcc
Confidence 699999999999999999999999998753
No 45
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=64.95 E-value=0.79 Score=28.04 Aligned_cols=22 Identities=23% Similarity=0.602 Sum_probs=19.3
Q ss_pred eeecchhhhccCcCccccccCC
Q psy15370 26 WYCQMCQKQCRDENGFKCHTSS 47 (393)
Q Consensus 26 wyCQ~CqKQCRDeNGFKcH~~S 47 (393)
|-|..|.+.|.+...|+-|..+
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5799999999999999988754
No 46
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=63.79 E-value=25 Score=25.66 Aligned_cols=51 Identities=14% Similarity=0.017 Sum_probs=36.3
Q ss_pred cCCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCceeeecccccccc
Q psy15370 337 IPNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICK 392 (393)
Q Consensus 337 IP~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddicK 392 (393)
.|.+|..|++....-.=..|++++++.+ ..+.|...+ .|. ...++.++|..
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~-~~~~V~f~D---~G~-~~~v~~~~l~~ 52 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGE-QLYEVFFID---YGN-EEVVPPSDLRP 52 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCC-CEEEEEEEC---CCc-cEEEeHHHeec
Confidence 4688988888873445677899999987 556777665 244 34688887754
No 47
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=63.21 E-value=27 Score=25.43 Aligned_cols=51 Identities=14% Similarity=0.079 Sum_probs=38.2
Q ss_pred cCceEEEEeeccCCcc-cccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecC
Q psy15370 283 HKNIIVKIVTKNLGEK-FYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIP 338 (393)
Q Consensus 283 ~~~IvVKIidK~l~dg-yYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP 338 (393)
.+|-.|.+.. .++ ||. |.|.++.+...+.|...|-|....|+.++|-+..|
T Consensus 4 ~~G~~~~a~~---~d~~wyr--a~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 4 KVGDKVAARW---EDGEWYR--ARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCEEEEEe---CCCCEEE--EEEEEECCCCEEEEEEECCCccEEEeHHHeecCCC
Confidence 4555554543 344 765 79999987678999999989999999888877655
No 48
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=62.11 E-value=12 Score=28.67 Aligned_cols=68 Identities=18% Similarity=0.203 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHhhcCc-ceeeccchhhhhhcCCCceeecccccccHHHHHHHhccccceEeecc--ccceEE
Q psy15370 70 REFEEGYLELLRRQFST-RRVFANKVYQDYIADREHVHMNATQWETLTEFVKHLGKSGKCVVDET--EKGWFV 139 (393)
Q Consensus 70 ~~F~~~Fl~lLr~~~g~-krv~aN~vY~eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr~g~~~v~et--~kg~~i 139 (393)
+.|.....++|...++. .+|....+.++|.+--.++.--.=-+.+|++|++- -.+.+.|.++ ...|+|
T Consensus 4 ~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~~l~~ll~~--~~~~~~i~~~~~g~~~~v 74 (74)
T PF12872_consen 4 EELKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFSSLSELLES--LPDVVEIEERQHGGQVYV 74 (74)
T ss_dssp HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSSSHHHHHHT---TTTEEEEEEECCCC---
T ss_pred HHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCCcHHHHHHh--CCCeEEEeeeCCCCcCCC
Confidence 45677778888777763 47999999999987445566656668899999975 4788888554 344654
No 49
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=62.09 E-value=17 Score=32.85 Aligned_cols=37 Identities=27% Similarity=0.331 Sum_probs=28.6
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCC-CCC
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPH-YDN 379 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~-~~g 379 (393)
.+|.-|+|..|+|.|..+++++|-..+. | |-+|| ..|
T Consensus 9 EiGRVvli~~Gp~~GKL~vIVDIID~nR-v---LVDGP~~tg 46 (130)
T PTZ00065 9 EPGRLCLIQYGPDAGKLCFIVDIVTPTR-V---LVDGAFITG 46 (130)
T ss_pred eeceEEEEecCCCCCCEEEEEEEEcCCe-E---EEeCCCcCC
Confidence 4688899999999999999999976664 2 23578 433
No 50
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=60.78 E-value=59 Score=26.00 Aligned_cols=56 Identities=20% Similarity=0.256 Sum_probs=36.0
Q ss_pred CCCcccCceEEEEeeccCCcccccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecC
Q psy15370 278 EESWLHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIP 338 (393)
Q Consensus 278 ~~~WL~~~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP 338 (393)
...++..+..+.+. .++.||- |+|....+...+.|++.|-|.+..|..+.|-..-|
T Consensus 50 ~~~~~~~~~~~~~~---~~~~w~R--a~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~ 105 (121)
T PF00567_consen 50 PESNPGEGCLCVVS---EDGRWYR--AVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPP 105 (121)
T ss_dssp ST--TTEEEEEEET---TTSEEEE--EEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--H
T ss_pred cccccCCEEEEEEe---cCCceee--EEEEEecccceeEEEEEecCceEEEcHHHhhhhCH
Confidence 34444444444332 2344655 67755566789999999999999999998876654
No 51
>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=59.87 E-value=56 Score=40.93 Aligned_cols=89 Identities=13% Similarity=0.165 Sum_probs=62.3
Q ss_pred CcccCceEEEEeeccCCcccccceeEEEEecC-CceEEEEEcCCCcEEEeecCce-----------eeecC-CCCCeEEE
Q psy15370 280 SWLHKNIIVKIVTKNLGEKFYKKKGTVEKVID-KYAAIVSLLDSKHKIKLDQEHL-----------ETVIP-NLGRQVLI 346 (393)
Q Consensus 280 ~WL~~~IvVKIidK~l~dgyYkkKGvV~dV~d-~~~c~V~l~d~g~~l~VdQ~~L-----------ETVIP-~~G~~V~V 346 (393)
....+|-+|...++ .++.+.-++|..|.. ..+.+|.. +.|+.+.++.+.| ..+|| +.|+++++
T Consensus 680 ~~Yr~Gdvv~~y~~---~~~~~~~y~V~~V~~~~n~L~l~~-~dG~~~~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~~ 755 (1960)
T TIGR02760 680 AHYKQGMVIRFWQK---GKIPHDDYVVTNVNKHNNTLTLKD-AQGKTQKFKPSSLKDLERPFSVYRPEQLEVAAGERLQV 755 (1960)
T ss_pred hhcCCCCEEEeecc---cCccCCcEEEEEEeCCCCEEEEEc-CCCCEEEECHHHhcccccceeeeccccccccCCCEEEE
Confidence 44578888887432 125555578999865 34555544 3788888888888 44578 99999999
Q ss_pred Eec-----CccCceEEEEEeeCCCceEEEEecC
Q psy15370 347 LCG-----KYKGEKAVLKDINIDDCNANVELID 374 (393)
Q Consensus 347 V~G-----~~RG~~G~LisiD~~k~~a~V~l~~ 374 (393)
... --+|..+++.+++... ++|....
T Consensus 756 trn~~~~gl~ng~~~tV~~i~~~~--i~l~~~~ 786 (1960)
T TIGR02760 756 TGNHFHSRVRNGELLTVSSINNEG--ITLITED 786 (1960)
T ss_pred ccCCcccCccCCCEEEEEEEcCCe--EEEEeCC
Confidence 843 3578999999998865 4566554
No 52
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=57.69 E-value=41 Score=26.75 Aligned_cols=52 Identities=15% Similarity=0.190 Sum_probs=34.2
Q ss_pred CCCCCeEEEEecC--ccCceEEEEEeeCC--CceEEEEecCCCCCCceeeeccccc
Q psy15370 338 PNLGRQVLILCGK--YKGEKAVLKDINID--DCNANVELIDPHYDNKVVRNIDYSH 389 (393)
Q Consensus 338 P~~G~~V~VV~G~--~RG~~G~LisiD~~--k~~a~V~l~~G~~~g~~v~~l~ydd 389 (393)
|+.|++|+|++-+ +-..+|++.++|.+ .+-|+|+++.-.+.|-.--++..+.
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i~YPV~VRF~kvNY~g~nTnnfa~~E 56 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGIRYPVVVRFDKVNYAGVNTNNFALDE 56 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSSSSSEEEE-SSS-SSSSSEEEE-GGG
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCccccEEEEEEEecccCccccccchhh
Confidence 5679999999776 47789999999976 6888999887555443223344443
No 53
>smart00355 ZnF_C2H2 zinc finger.
Probab=55.41 E-value=2 Score=25.68 Aligned_cols=21 Identities=24% Similarity=0.575 Sum_probs=17.8
Q ss_pred eeecchhhhccCcCccccccC
Q psy15370 26 WYCQMCQKQCRDENGFKCHTS 46 (393)
Q Consensus 26 wyCQ~CqKQCRDeNGFKcH~~ 46 (393)
+-|..|.+.|+..+-|.-|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 459999999999998887765
No 54
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=52.18 E-value=32 Score=27.89 Aligned_cols=51 Identities=22% Similarity=0.212 Sum_probs=32.8
Q ss_pred CCCCCeEEEEe----cCccCceEEEEEeeCCCceEEEEecCCCCCCceeeecccccccc
Q psy15370 338 PNLGRQVLILC----GKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICK 392 (393)
Q Consensus 338 P~~G~~V~VV~----G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddicK 392 (393)
...|..|.|.. |..+-..|+|.+++.+.. ++..+.. ..+..+ .+||++|.+
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v--~l~~~~~-~~~~~~-~i~~~~I~k 76 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTV--TLEVDIK-TRGKTV-EIPLDKIAK 76 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEE--EEEEecC-CCCeEE-EEEhHHeeE
Confidence 46688888853 334556899999998754 4444310 113334 699999875
No 55
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=51.75 E-value=1.2e+02 Score=29.13 Aligned_cols=90 Identities=13% Similarity=0.228 Sum_probs=59.1
Q ss_pred cccCceEEEEeeccC-CcccccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecCCCCCeEE--EEecCccCceEE
Q psy15370 281 WLHKNIIVKIVTKNL-GEKFYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVL--ILCGKYKGEKAV 357 (393)
Q Consensus 281 WL~~~IvVKIidK~l-~dgyYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~--VV~G~~RG~~G~ 357 (393)
.+.||=+|-....-+ +++-|...|.|.... +..+..++...++.|...-.++.+|+.|+.|. |+...-+.....
T Consensus 7 ~v~PGd~~a~~EE~~~G~gt~~~~g~i~Aa~---~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~ 83 (188)
T COG1096 7 FVLPGDVLAVIEEFLPGEGTYEEGGEIRAAA---TGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVR 83 (188)
T ss_pred EEcCcceeeeeeeeecCCCeEeECCEEEEee---cccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEE
Confidence 445555555543322 344677788888765 34556666777889988888999999999885 445555666666
Q ss_pred EEEeeCCC------ceEEEEec
Q psy15370 358 LKDINIDD------CNANVELI 373 (393)
Q Consensus 358 LisiD~~k------~~a~V~l~ 373 (393)
+.+++... +.+.+.+.
T Consensus 84 i~~ve~~~r~~~~~~~~~ihvs 105 (188)
T COG1096 84 IVGVEGKERELATSGAADIHVS 105 (188)
T ss_pred EEEEecccccCCCCceeeEEEE
Confidence 77777644 55555544
No 56
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=50.23 E-value=25 Score=31.97 Aligned_cols=26 Identities=31% Similarity=0.506 Sum_probs=22.3
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCC
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINID 364 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~ 364 (393)
.+|.-|+||.|.|.|..|.++....+
T Consensus 6 kpgkVVivL~GR~AGkKaVivk~~dd 31 (134)
T PTZ00471 6 KPGKVVIVTSGRYAGRKAVIVQNFDT 31 (134)
T ss_pred cCCEEEEEEccccCCcEEEEEeecCC
Confidence 57889999999999999999886444
No 57
>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=48.12 E-value=50 Score=29.09 Aligned_cols=55 Identities=16% Similarity=0.302 Sum_probs=44.9
Q ss_pred CcccCceEEEEeeccCCcccccceeEEEEecC-CceEEEEEcCCCcE--EEeecCceeeecC
Q psy15370 280 SWLHKNIIVKIVTKNLGEKFYKKKGTVEKVID-KYAAIVSLLDSKHK--IKLDQEHLETVIP 338 (393)
Q Consensus 280 ~WL~~~IvVKIidK~l~dgyYkkKGvV~dV~d-~~~c~V~l~d~g~~--l~VdQ~~LETVIP 338 (393)
..+.+|=.|+|++=. |-+-.|+|..+.. +..+.|.+.+.+.. +.|+.++|+.+-+
T Consensus 85 ~~~~~Gd~V~I~~GP----f~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~~ 142 (145)
T TIGR00405 85 ESIKKGDIVEIISGP----FKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQK 142 (145)
T ss_pred cccCCCCEEEEeecC----CCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEecc
Confidence 358899999998522 6678899999863 56889999988988 8999999988754
No 58
>CHL00010 infA translation initiation factor 1
Probab=47.26 E-value=1.5e+02 Score=23.98 Aligned_cols=62 Identities=13% Similarity=0.035 Sum_probs=35.2
Q ss_pred ceeEEEEecCCceEEEEEcCCCcEE--EeecCce-eeecCCCCCeEEEEecCccCceEEEEEeeCC
Q psy15370 302 KKGTVEKVIDKYAAIVSLLDSKHKI--KLDQEHL-ETVIPNLGRQVLILCGKYKGEKAVLKDINID 364 (393)
Q Consensus 302 kKGvV~dV~d~~~c~V~l~d~g~~l--~VdQ~~L-ETVIP~~G~~V~VV~G~~RG~~G~LisiD~~ 364 (393)
-+|+|..+.......|.+. +|..+ .+.-..= ..+-|.+|+.|.|=.=.+-...|.++-+-..
T Consensus 9 ~~G~Vik~lg~~~y~V~~~-~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLD-NGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEeC-CCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 3566666664344555543 34333 3332221 2677899999988754455566777666443
No 59
>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=47.11 E-value=67 Score=24.99 Aligned_cols=58 Identities=16% Similarity=0.186 Sum_probs=39.7
Q ss_pred eeEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEEecCccCceEEEEE
Q psy15370 303 KGTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKD 360 (393)
Q Consensus 303 KGvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~Lis 360 (393)
-|+|..+.+.+...|.+.|....+ .++...--+|-=..|+.|+|-.-+|--..|.++-
T Consensus 6 ~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 6 IGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp EEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEEE
T ss_pred EEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEEE
Confidence 378888888889999988544444 8888855555558899998877666666666653
No 60
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=47.01 E-value=16 Score=29.08 Aligned_cols=25 Identities=16% Similarity=0.254 Sum_probs=21.8
Q ss_pred HHHHHhccccceEeeccccceEEEe
Q psy15370 117 EFVKHLGKSGKCVVDETEKGWFVTY 141 (393)
Q Consensus 117 ~Fvk~Lgr~g~~~v~et~kg~~i~~ 141 (393)
--+=||.|+|++.+++.+.-|||..
T Consensus 41 ~AiGWLarE~KI~~~~~~~~~~v~L 65 (65)
T PF10771_consen 41 LAIGWLARENKIEFEEKNGELYVSL 65 (65)
T ss_dssp HHHHHHHCTTSEEEEEETTEEEEEE
T ss_pred HHHHHHhccCceeEEeeCCEEEEEC
Confidence 3478999999999999999999864
No 61
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=46.79 E-value=6.8 Score=28.93 Aligned_cols=25 Identities=36% Similarity=0.749 Sum_probs=19.0
Q ss_pred eecchhhhc--cCcCccccccCCHHHHHHH
Q psy15370 27 YCQMCQKQC--RDENGFKCHTSSEAHQRQL 54 (393)
Q Consensus 27 yCQ~CqKQC--RDeNGFKcH~~SesH~rqm 54 (393)
||-+|+||| -+.+...| ||+-+++-
T Consensus 8 yC~~Cdk~~~~~~~~~lYC---Se~Cr~~D 34 (43)
T PF12855_consen 8 YCIVCDKQIDPPDDGSLYC---SEECRLKD 34 (43)
T ss_pred HHHHhhccccCCCCCcccc---CHHHHhHh
Confidence 899999999 67777777 66655543
No 62
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=46.77 E-value=75 Score=28.67 Aligned_cols=53 Identities=21% Similarity=0.330 Sum_probs=42.7
Q ss_pred ccCceEEEEeeccCCcccccceeEEEEecC-CceEEEEEcCCCcE--EEeecCceeeecC
Q psy15370 282 LHKNIIVKIVTKNLGEKFYKKKGTVEKVID-KYAAIVSLLDSKHK--IKLDQEHLETVIP 338 (393)
Q Consensus 282 L~~~IvVKIidK~l~dgyYkkKGvV~dV~d-~~~c~V~l~d~g~~--l~VdQ~~LETVIP 338 (393)
+.+|=.|+|++-. |-+..|.|.++.. +..+.|.+++.... +.|+.+.|.+|-+
T Consensus 95 ~~~G~~V~I~~Gp----f~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~~ 150 (153)
T PRK08559 95 IKEGDIVELIAGP----FKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVKK 150 (153)
T ss_pred CCCCCEEEEeccC----CCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEecc
Confidence 6789999998532 6667899999953 66788999987877 8999999988764
No 63
>PF10615 DUF2470: Protein of unknown function (DUF2470); InterPro: IPR019595 This entry represents a putative haem-iron utilisation family of proteins, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however the function of this domain is not known. ; PDB: 3GAS_D 3SWJ_A 2ARZ_B.
Probab=46.56 E-value=9.2 Score=30.87 Aligned_cols=36 Identities=19% Similarity=0.398 Sum_probs=23.9
Q ss_pred eecccccccHHHHHHHhccc---cceEeec-cccceEEEe
Q psy15370 106 HMNATQWETLTEFVKHLGKS---GKCVVDE-TEKGWFVTY 141 (393)
Q Consensus 106 HMNaT~W~sLt~Fvk~Lgr~---g~~~v~e-t~kg~~i~~ 141 (393)
|||.-...+|..|++++|.- +.+++.. +..|..|.|
T Consensus 16 HMN~DH~d~l~~~~~~~~~~~~~~~a~m~~id~~G~~l~~ 55 (83)
T PF10615_consen 16 HMNDDHADDLLLYARHYGGVPDAASARMTDIDRDGFDLRV 55 (83)
T ss_dssp HHHHH-HHHHHHHHHHHHT-SSSSS-EEEEEETTEEEEEE
T ss_pred HHHHhHHHHHHHHHHhcCCCCCCCCEEEEEEeccccEEEE
Confidence 99999999999999998866 2333332 345555555
No 64
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=44.56 E-value=69 Score=25.55 Aligned_cols=42 Identities=24% Similarity=0.282 Sum_probs=30.2
Q ss_pred eEEEEe-cCCceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEec
Q psy15370 304 GTVEKV-IDKYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILCG 349 (393)
Q Consensus 304 GvV~dV-~d~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~G 349 (393)
+.|.+| .+...+.|... |..-.|+-..|.. +++|+.|+|=.|
T Consensus 7 ~~Vv~v~~~~~~A~v~~~--G~~~~V~~~lv~~--v~~Gd~VLVHaG 49 (68)
T PF01455_consen 7 GRVVEVDEDGGMAVVDFG--GVRREVSLALVPD--VKVGDYVLVHAG 49 (68)
T ss_dssp EEEEEEETTTTEEEEEET--TEEEEEEGTTCTS--B-TT-EEEEETT
T ss_pred EEEEEEeCCCCEEEEEcC--CcEEEEEEEEeCC--CCCCCEEEEecC
Confidence 456777 34678888764 7777888888877 789999999776
No 65
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=44.05 E-value=25 Score=27.77 Aligned_cols=61 Identities=16% Similarity=0.260 Sum_probs=46.6
Q ss_pred HHHHHHHhhcCcceeeccchhhhhhcCCCceeecccccccHHHHHHHhccccceEeeccccc
Q psy15370 75 GYLELLRRQFSTRRVFANKVYQDYIADREHVHMNATQWETLTEFVKHLGKSGKCVVDETEKG 136 (393)
Q Consensus 75 ~Fl~lLr~~~g~krv~aN~vY~eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr~g~~~v~et~kg 136 (393)
+-+.+++ +-|...+..+.||..|-.-=.+.+++.-.+....+++.-|.-.|++.++....|
T Consensus 10 Al~~~~~-~~~~~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~~~~~g 70 (87)
T cd08768 10 ALLLLFK-RGGEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVSSKG 70 (87)
T ss_pred HHHHHHh-cCCCCCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEEEecCC
Confidence 3344443 234667889999999987555668888999999999999999999999865444
No 66
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=43.31 E-value=46 Score=23.38 Aligned_cols=35 Identities=11% Similarity=0.253 Sum_probs=26.8
Q ss_pred cc-cccceeEEEEecCCceEEEEEcCCCcEEEeecCce
Q psy15370 297 EK-FYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHL 333 (393)
Q Consensus 297 dg-yYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~L 333 (393)
++ +|- |.|.++.....+.|...|-|..-.|+.++|
T Consensus 11 d~~wyr--a~V~~~~~~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 11 DGKWYR--AKITSILSDGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred CCeEEE--EEEEEECCCCcEEEEEEcCCCcEEEeHHHc
Confidence 44 665 899999866789999998888776765554
No 67
>PRK14639 hypothetical protein; Provisional
Probab=41.91 E-value=48 Score=29.84 Aligned_cols=71 Identities=17% Similarity=0.235 Sum_probs=45.8
Q ss_pred CceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccccccc
Q psy15370 312 KYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHIC 391 (393)
Q Consensus 312 ~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddic 391 (393)
.|+-.|..+.-++-|+-+ +-.....|..|.|-...-+-..|+|.++|.+.. ++.... ++..+ .+||++|.
T Consensus 63 ~Y~LEVSSPGl~RpL~~~----~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i--~l~~~~---~~~~~-~i~~~~I~ 132 (140)
T PRK14639 63 EYFLEVSSPGLERKLSKI----EHFAKSIGELVKITTNEKEKFEGKIVSVDDENI--TLENLE---NKEKT-TINFNDIK 132 (140)
T ss_pred CeEEEEeCCCCCCcCCCH----HHHHHhCCCEEEEEECCCcEEEEEEEEEeCCEE--EEEEcc---CCcEE-EEEhHHee
Confidence 455556555555555332 234467799999976556788899999998654 443322 23434 59999987
Q ss_pred c
Q psy15370 392 K 392 (393)
Q Consensus 392 K 392 (393)
+
T Consensus 133 k 133 (140)
T PRK14639 133 K 133 (140)
T ss_pred e
Confidence 5
No 68
>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=41.63 E-value=66 Score=25.42 Aligned_cols=45 Identities=31% Similarity=0.309 Sum_probs=22.1
Q ss_pred eEEEEecC-CceEEEEEcCCCcEEE----eecC---cee-eecCCCCCeEEEEe
Q psy15370 304 GTVEKVID-KYAAIVSLLDSKHKIK----LDQE---HLE-TVIPNLGRQVLILC 348 (393)
Q Consensus 304 GvV~dV~d-~~~c~V~l~d~g~~l~----VdQ~---~LE-TVIP~~G~~V~VV~ 348 (393)
|+|.+|.. ++.+.|++.+.+..+. +-+- ..- -..|.+|+.|+|+-
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 67777755 5688888755555432 2111 122 34569999999984
No 69
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=40.18 E-value=1.9e+02 Score=33.87 Aligned_cols=63 Identities=14% Similarity=0.103 Sum_probs=49.4
Q ss_pred eeEEEEecCCceEEEEEcCCCc--EEEeecCceeeecCCCCCeEEEEecCccCceEEEEEeeCCCceEEE
Q psy15370 303 KGTVEKVIDKYAAIVSLLDSKH--KIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDINIDDCNANV 370 (393)
Q Consensus 303 KGvV~dV~d~~~c~V~l~d~g~--~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V 370 (393)
-|+|++|.+ .+++|..+.+|. ++.++..-|--|++.+|+.|.+..| ...++..+.+.++.++-
T Consensus 18 lG~v~~~d~-r~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~----~~~~v~~v~~~~gl~~y 82 (956)
T PRK04914 18 LGTVVAVDG-RTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEG----WQLTVEEVEEENGLLTY 82 (956)
T ss_pred cEEEEEEeC-CEEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCC----CEEEEEEEeccCCcEEE
Confidence 399999864 699999988766 4589999999999999999986555 45666677666775544
No 70
>PF06052 3-HAO: 3-hydroxyanthranilic acid dioxygenase; InterPro: IPR010329 Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase (1.13.11.6 from EC). It is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid [].The prokaryotic homologue is involved in the 2-nitrobenzoate degradation pathway []. The enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.; GO: 0000334 3-hydroxyanthranilate 3,4-dioxygenase activity, 0005506 iron ion binding, 0008152 metabolic process, 0055114 oxidation-reduction process; PDB: 1ZVF_A 1YFX_A 1YFW_A 1YFY_A 1YFU_A 2QNK_A 3FE5_A.
Probab=40.13 E-value=12 Score=34.65 Aligned_cols=13 Identities=54% Similarity=1.408 Sum_probs=10.2
Q ss_pred cccceeeeecchh
Q psy15370 20 GLQKLRWYCQMCQ 32 (393)
Q Consensus 20 GLqkLrwyCQ~Cq 32 (393)
-+.+|||||.-|.
T Consensus 114 ~~D~l~WyC~~c~ 126 (151)
T PF06052_consen 114 ELDGLRWYCPNCN 126 (151)
T ss_dssp S-EEEEEESTTTS
T ss_pred CcccEEEecCCCC
Confidence 4689999999885
No 71
>KOG1708|consensus
Probab=39.23 E-value=43 Score=32.70 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=28.6
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEE
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVE 371 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~ 371 (393)
-.|+.|.|+.|.++|..|.+..+-..+.-|+|.
T Consensus 74 f~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~ 106 (236)
T KOG1708|consen 74 FFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK 106 (236)
T ss_pred ecCCEEEEEecccCCccceEEEEeecCceEEEc
Confidence 459999999999999999999998888866664
No 72
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=38.90 E-value=45 Score=29.92 Aligned_cols=29 Identities=31% Similarity=0.590 Sum_probs=25.9
Q ss_pred CCCCCeEEEEecCccCceEEEEEeeCCCc
Q psy15370 338 PNLGRQVLILCGKYKGEKAVLKDINIDDC 366 (393)
Q Consensus 338 P~~G~~V~VV~G~~RG~~G~LisiD~~k~ 366 (393)
+.+|.-|.|+.|.++|..+.++++-.+++
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~~ 33 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDNF 33 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCCE
Confidence 46899999999999999999999987775
No 73
>PF14968 CCDC84: Coiled coil protein 84
Probab=35.49 E-value=41 Score=34.73 Aligned_cols=28 Identities=36% Similarity=0.763 Sum_probs=22.7
Q ss_pred eecchhhhccCcCccccccCCHHHHHHHHHh
Q psy15370 27 YCQMCQKQCRDENGFKCHTSSEAHQRQLLLF 57 (393)
Q Consensus 27 yCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~ 57 (393)
||-+|..-+ |. .+=|.-|.+|+++|..|
T Consensus 1 yC~vCr~~h-~~--gr~H~Y~~~Hq~~L~~~ 28 (336)
T PF14968_consen 1 YCEVCRRNH-DQ--GRRHVYSPKHQKSLSAF 28 (336)
T ss_pred CcchhhCcc-cc--cCCCccCHHHHHHHHHH
Confidence 899996543 44 89999999999999654
No 74
>KOG3421|consensus
Probab=34.78 E-value=39 Score=30.80 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=29.1
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCC
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDN 379 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g 379 (393)
.+|.-++|..|+|.|...-+..++..+- +. .+||.++
T Consensus 8 eVGrva~v~~G~~~GkL~AIVdviDqnr---~l-vDGp~t~ 44 (136)
T KOG3421|consen 8 EVGRVALVSFGPDAGKLVAIVDVIDQNR---AL-VDGPCTG 44 (136)
T ss_pred hcceEEEEEecCCCceEEEEEEeecchh---hh-ccCcccc
Confidence 4688999999999999999999987763 32 3577654
No 75
>PRK14631 hypothetical protein; Provisional
Probab=33.66 E-value=96 Score=29.03 Aligned_cols=72 Identities=25% Similarity=0.279 Sum_probs=44.5
Q ss_pred CceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEe----cCccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccc
Q psy15370 312 KYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILC----GKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDY 387 (393)
Q Consensus 312 ~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~----G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~y 387 (393)
.|+-.|..+.-++-|.- ..-.....|..|.|-. +..+-.+|+|.+++.++..+++.+.. +..+ .+||
T Consensus 92 ~Y~LEVSSPGldRpL~~----~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~----~~~~-~i~~ 162 (174)
T PRK14631 92 EYALEVSSPGWDRPFFQ----LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEG----KHVL-DIDS 162 (174)
T ss_pred CeEEEEeCCCCCCcCCC----HHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcC----CcEE-EEEh
Confidence 45555555554454432 2234456688888863 33577889999999545555555543 3334 5899
Q ss_pred ccccc
Q psy15370 388 SHICK 392 (393)
Q Consensus 388 ddicK 392 (393)
++|.+
T Consensus 163 ~~I~k 167 (174)
T PRK14631 163 NNIDK 167 (174)
T ss_pred HHcce
Confidence 99875
No 76
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=33.65 E-value=21 Score=31.05 Aligned_cols=12 Identities=33% Similarity=0.684 Sum_probs=6.0
Q ss_pred ecchhhhccCcC
Q psy15370 28 CQMCQKQCRDEN 39 (393)
Q Consensus 28 CQ~CqKQCRDeN 39 (393)
|+-|++-|.|=|
T Consensus 12 Cp~CG~kFYDLn 23 (108)
T PF09538_consen 12 CPSCGAKFYDLN 23 (108)
T ss_pred CCCCcchhccCC
Confidence 555555554444
No 77
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=32.09 E-value=43 Score=33.40 Aligned_cols=36 Identities=22% Similarity=0.305 Sum_probs=27.1
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEEecC
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVELID 374 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~ 374 (393)
=+|...+|+.|+-+|.+|.++.....-.-|.|.++.
T Consensus 59 CiGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~F~~ 94 (258)
T PF14505_consen 59 CIGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVDFPD 94 (258)
T ss_dssp -BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE--H
T ss_pred ecCceeEEeecccCCCcCeEecccCCeeeEEEECCH
Confidence 479999999999999999999999888878777764
No 78
>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=31.16 E-value=2.9e+02 Score=22.47 Aligned_cols=58 Identities=24% Similarity=0.287 Sum_probs=32.0
Q ss_pred eEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEEecCccCceEEEEEe
Q psy15370 304 GTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDI 361 (393)
Q Consensus 304 GvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~Lisi 361 (393)
|+|..+.+.+...|.+.|....+ .++-.+=-.+-=..|+.|+|-.=+|--..|.++-+
T Consensus 4 g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d~~kg~Iv~r 62 (77)
T cd05793 4 GQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYK 62 (77)
T ss_pred EEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEEEE
Confidence 67888887778888887533333 55444443333355666655433444444444433
No 79
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=31.12 E-value=72 Score=25.60 Aligned_cols=41 Identities=17% Similarity=0.249 Sum_probs=31.1
Q ss_pred CCCCeEEEEecC--ccCceEEEEEeeCC--CceEEEEecCCCCCC
Q psy15370 339 NLGRQVLILCGK--YKGEKAVLKDINID--DCNANVELIDPHYDN 379 (393)
Q Consensus 339 ~~G~~V~VV~G~--~RG~~G~LisiD~~--k~~a~V~l~~G~~~g 379 (393)
+.|++|+|++-+ +-..+|++.++|.+ .+-|+|+++.-.+.|
T Consensus 3 ~rGskVrIlR~ESYWyn~vGtV~svd~~gi~YPV~VRF~kvNY~g 47 (64)
T CHL00125 3 KRGSKVRILRKESYWYNEIGTVATVDQSGIRYPVLVRFEKVNYSG 47 (64)
T ss_pred ccCCEEEEccccceeecCcceEEEEcCCCCCccEEEEEeeeeccc
Confidence 569999999766 46788999999876 567888887544443
No 80
>PRK14637 hypothetical protein; Provisional
Probab=31.06 E-value=99 Score=28.25 Aligned_cols=46 Identities=15% Similarity=0.053 Sum_probs=31.0
Q ss_pred CCCCeEEEEecCccCc-eEEEEEeeCCCceEEEEecCCCCCCceeeecccccccc
Q psy15370 339 NLGRQVLILCGKYKGE-KAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICK 392 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~-~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddicK 392 (393)
..|..|.|-....+.. +|+|.+++.+.. ++... +..+ .+||++|.+
T Consensus 96 ~~G~~V~V~l~~~~~~~~G~L~~~~d~~v--~l~~~-----~~~~-~i~~~~I~k 142 (151)
T PRK14637 96 FVGETVKVWFECTGQWQVGTIAEADETCL--VLTSD-----GVPV-TIPYVQITK 142 (151)
T ss_pred hCCCEEEEEECCCCcEEEEEEEEEeCCEE--EEEEC-----CEEE-EEEHHHeee
Confidence 5688899965223445 599999987754 33332 4444 599999875
No 81
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=30.94 E-value=21 Score=33.76 Aligned_cols=24 Identities=25% Similarity=0.742 Sum_probs=17.0
Q ss_pred ccccceeeeecchhhhccCcCcccc
Q psy15370 19 KGLQKLRWYCQMCQKQCRDENGFKC 43 (393)
Q Consensus 19 kGLqkLrwyCQ~CqKQCRDeNGFKc 43 (393)
..+.+|||||.-|...-- |-=|.|
T Consensus 114 ~~~d~~~wyc~~c~~~~~-e~~f~~ 137 (177)
T PRK13264 114 GELDGFQWYCDECNHKVH-EVEVQL 137 (177)
T ss_pred CCccceEEECCCCCCeEE-EEEEEe
Confidence 347899999998865443 555666
No 82
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=30.85 E-value=22 Score=33.06 Aligned_cols=24 Identities=17% Similarity=0.661 Sum_probs=17.0
Q ss_pred cccceeeeecchhhhccCcCccccc
Q psy15370 20 GLQKLRWYCQMCQKQCRDENGFKCH 44 (393)
Q Consensus 20 GLqkLrwyCQ~CqKQCRDeNGFKcH 44 (393)
.+-+|||||.-|...-- |--|.|.
T Consensus 109 ~~d~~~wyc~~c~~~~~-e~~f~~~ 132 (159)
T TIGR03037 109 ELDGFQWFCPQCGHKLH-RAEVQLE 132 (159)
T ss_pred CCcceEEECCCCCCeEE-EEEEEec
Confidence 47899999998855433 5556665
No 83
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=30.75 E-value=22 Score=32.06 Aligned_cols=16 Identities=19% Similarity=0.246 Sum_probs=11.7
Q ss_pred eeeecchhhhccCcCc
Q psy15370 25 RWYCQMCQKQCRDENG 40 (393)
Q Consensus 25 rwyCQ~CqKQCRDeNG 40 (393)
++-|+-|++.|.|=|-
T Consensus 9 Kr~Cp~cg~kFYDLnk 24 (129)
T TIGR02300 9 KRICPNTGSKFYDLNR 24 (129)
T ss_pred cccCCCcCccccccCC
Confidence 3458888888888774
No 84
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=30.13 E-value=12 Score=23.53 Aligned_cols=22 Identities=23% Similarity=0.499 Sum_probs=18.8
Q ss_pred eeecchhhhccCcCccccccCC
Q psy15370 26 WYCQMCQKQCRDENGFKCHTSS 47 (393)
Q Consensus 26 wyCQ~CqKQCRDeNGFKcH~~S 47 (393)
+.|..|.+.+.+...|--|..+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 5799999999999999888743
No 85
>PRK14638 hypothetical protein; Provisional
Probab=29.60 E-value=81 Score=28.69 Aligned_cols=69 Identities=10% Similarity=0.055 Sum_probs=45.0
Q ss_pred CceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccccccc
Q psy15370 312 KYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHIC 391 (393)
Q Consensus 312 ~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddic 391 (393)
.|.-.|..+.-++-|+-+.++ .-..|..|.|-...-+-.+|+|.+++.+. +++... +..+ .+||++|.
T Consensus 75 ~Y~LEVSSPGldRpL~~~~~f----~r~~G~~v~V~~~~~k~~~G~L~~~~~~~--i~l~~~-----~~~~-~i~~~~I~ 142 (150)
T PRK14638 75 SYTLEVSSPGLDRPLRGPKDY----VRFTGKLAKIVTKDGKTFIGRIESFVDGT--ITISDE-----KEKY-EINIDDVK 142 (150)
T ss_pred ceEEEEeCCCCCCCCCCHHHH----HHhCCCEEEEEECCCcEEEEEEEEEeCCE--EEEEEC-----CcEE-EEEhHHcc
Confidence 456666666656666544433 24679999996544577899999998654 344322 3444 58999987
Q ss_pred c
Q psy15370 392 K 392 (393)
Q Consensus 392 K 392 (393)
+
T Consensus 143 ~ 143 (150)
T PRK14638 143 R 143 (150)
T ss_pred e
Confidence 5
No 86
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=29.31 E-value=3.6e+02 Score=23.17 Aligned_cols=58 Identities=17% Similarity=0.221 Sum_probs=34.4
Q ss_pred eEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEEecCccCceEEEEEe
Q psy15370 304 GTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDI 361 (393)
Q Consensus 304 GvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~Lisi 361 (393)
|+|..+.+.+...|.+.|...++ .++..+=-+|-=..|+.|+|-.=+|--..|.++-+
T Consensus 25 g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r 83 (100)
T PRK04012 25 GVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWR 83 (100)
T ss_pred EEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEE
Confidence 67888888788888877533333 55555444444456666666544444444554444
No 87
>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=28.79 E-value=3.1e+02 Score=22.11 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=17.4
Q ss_pred ceeEEEEecCCceEEEEEcCCCcE
Q psy15370 302 KKGTVEKVIDKYAAIVSLLDSKHK 325 (393)
Q Consensus 302 kKGvV~dV~d~~~c~V~l~d~g~~ 325 (393)
--|+|.++.......|++.+ |..
T Consensus 7 ~~G~V~e~L~~~~f~V~l~n-g~~ 29 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELEN-GHE 29 (68)
T ss_pred EEEEEEEECCCCEEEEEECC-CCE
Confidence 35889999888888888874 443
No 88
>PRK14635 hypothetical protein; Provisional
Probab=28.73 E-value=81 Score=28.98 Aligned_cols=73 Identities=18% Similarity=0.199 Sum_probs=40.2
Q ss_pred ceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEE--e-c--CccCceEEEEEeeCCCceEEEEecC--C-CCCCceeee
Q psy15370 313 YAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLIL--C-G--KYKGEKAVLKDINIDDCNANVELID--P-HYDNKVVRN 384 (393)
Q Consensus 313 ~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV--~-G--~~RG~~G~LisiD~~k~~a~V~l~~--G-~~~g~~v~~ 384 (393)
|+-.|..+.-++.|+.+.++.- ..|..|.|- . | .+.|-+|+|.++|.+.- ++.+.. + +..+..+ .
T Consensus 75 Y~LEVSSPGldRpL~~~~~~~r----~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v--~l~~~~k~~~~~~~~~~-~ 147 (162)
T PRK14635 75 FTLKVSSAGAERKLRLPEDLDR----FRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQV--ELEKFQKGKKSKVKKQT-T 147 (162)
T ss_pred eEEEEcCCCCCCcCCCHHHHHH----hCCCEEEEEEecCCCcEEEecceEEEEEcCCEE--EEEEecccccccCCeEE-E
Confidence 4455555555555554444332 346666553 1 2 45677779999987654 343321 1 1124434 6
Q ss_pred cccccccc
Q psy15370 385 IDYSHICK 392 (393)
Q Consensus 385 l~yddicK 392 (393)
+||++|.+
T Consensus 148 ip~~~I~k 155 (162)
T PRK14635 148 LNLKDILK 155 (162)
T ss_pred EEhHHeee
Confidence 99999875
No 89
>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=28.68 E-value=2.5e+02 Score=22.46 Aligned_cols=43 Identities=19% Similarity=0.296 Sum_probs=32.2
Q ss_pred eeEEEEecCCceEEEEEcCCCcEEEeecCceeeecC--CCCCeEEEEecC
Q psy15370 303 KGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIP--NLGRQVLILCGK 350 (393)
Q Consensus 303 KGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP--~~G~~V~VV~G~ 350 (393)
.|+|.+|. ..+.+|.|. +|....++.+.= ++ ++|.+|+|..-.
T Consensus 6 eG~I~~id-~~~~titLd-DGksy~lp~ef~---~~~L~~G~kV~V~yd~ 50 (61)
T PF07076_consen 6 EGTIKSID-PETMTITLD-DGKSYKLPEEFD---FDGLKPGMKVVVFYDE 50 (61)
T ss_pred eEEEEEEc-CCceEEEec-CCCEEECCCccc---ccccCCCCEEEEEEEc
Confidence 68999975 568888876 699888766532 55 779999988643
No 90
>PTZ00448 hypothetical protein; Provisional
Probab=28.53 E-value=20 Score=37.47 Aligned_cols=31 Identities=35% Similarity=0.434 Sum_probs=28.2
Q ss_pred eeeecchhhhccCcCccccccCCHHHHHHHH
Q psy15370 25 RWYCQMCQKQCRDENGFKCHTSSEAHQRQLL 55 (393)
Q Consensus 25 rwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~ 55 (393)
-+-|..|+-+|+|.+.++-|+.|+-|.-.+.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLK 344 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTK 344 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHH
Confidence 4679999999999999999999999997763
No 91
>KOG3408|consensus
Probab=28.34 E-value=22 Score=31.95 Aligned_cols=37 Identities=22% Similarity=0.539 Sum_probs=34.6
Q ss_pred eeeecchhhhccCcCccccccCCHHHHHHHHHhhcCh
Q psy15370 25 RWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFADNA 61 (393)
Q Consensus 25 rwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~~n~ 61 (393)
-|||-.|.+=|-|+--.+-|..|--|.|.+.-+.+-|
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~P 93 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTKVHKRRVKELREVP 93 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccCC
Confidence 5999999999999999999999999999998887666
No 92
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.27 E-value=1.3e+02 Score=27.80 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=32.9
Q ss_pred CCCCeEEEEe----cCccCceEEEEEeeCCCceEEEEecCCCCCCceeeecccccccc
Q psy15370 339 NLGRQVLILC----GKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICK 392 (393)
Q Consensus 339 ~~G~~V~VV~----G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddicK 392 (393)
..|..|+|.. ..-+-..|+|.++|.+.. ++.++ ++.+ .+||.+|.|
T Consensus 97 ~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v--~~~~~-----~k~v-~Ip~~~i~k 146 (153)
T COG0779 97 FIGEKVKVKLRLPIEGRKKFEGKIVAVDGETV--TLEVD-----GKEV-EIPFSDIAK 146 (153)
T ss_pred hcCcEEEEEEecccCCceEEEEEEEEEcCCeE--EEEEC-----CEEE-EEEcccchh
Confidence 3577777765 445667899999999884 44444 4556 599999876
No 93
>KOG4235|consensus
Probab=28.20 E-value=88 Score=30.80 Aligned_cols=47 Identities=19% Similarity=0.249 Sum_probs=39.5
Q ss_pred ceeecccccccHHHHHHHhccccceEeeccccceEEEeecCCHHHHHHHHHHH
Q psy15370 104 HVHMNATQWETLTEFVKHLGKSGKCVVDETEKGWFVTYIDRDPETIAFQQKMA 156 (393)
Q Consensus 104 HvHMNaT~W~sLt~Fvk~Lgr~g~~~v~et~kg~~i~~Id~~pe~~~r~~~~~ 156 (393)
-=-||-+-|+.+.+.-.|+-+++-+.+| -|-|+-.||++.-..-.++
T Consensus 128 sg~m~e~e~~iy~eW~d~i~~~~~v~~d------giIYLrasPetc~~Ri~~R 174 (244)
T KOG4235|consen 128 SGSMNEVEYVIYQEWFDWILRSMDVSLD------GIIYLRASPETCYKRIYLR 174 (244)
T ss_pred cCCcccchhhhHHHHHHHHHhccccccc------eEEEeecChHHHHHHHHHH
Confidence 3469999999999999999999888888 5889999999986554433
No 94
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=28.20 E-value=3e+02 Score=21.74 Aligned_cols=56 Identities=18% Similarity=0.196 Sum_probs=28.9
Q ss_pred eeEEEEecCCceEEEEEcCCCcEE--EeecCce-eeecCCCCCeEEEEecCccCceEEEE
Q psy15370 303 KGTVEKVIDKYAAIVSLLDSKHKI--KLDQEHL-ETVIPNLGRQVLILCGKYKGEKAVLK 359 (393)
Q Consensus 303 KGvV~dV~d~~~c~V~l~d~g~~l--~VdQ~~L-ETVIP~~G~~V~VV~G~~RG~~G~Li 359 (393)
+|+|..+..+....|.+. +|..+ .+.-..= --+-|.+|+.|.|---.+-...|.++
T Consensus 10 ~G~Vi~~~~~~~y~V~~~-~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 10 EGTVVEALPNAMFRVELE-NGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred EEEEEEEcCCCEEEEEeC-CCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEE
Confidence 466666654434445443 34332 3332211 13448999999887444444445544
No 95
>PRK14633 hypothetical protein; Provisional
Probab=27.68 E-value=1.1e+02 Score=27.81 Aligned_cols=70 Identities=23% Similarity=0.228 Sum_probs=43.2
Q ss_pred CceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEe----cCccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccc
Q psy15370 312 KYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILC----GKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDY 387 (393)
Q Consensus 312 ~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~----G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~y 387 (393)
.|.-.|..+.-++.|.-+.++ .-..|..|.|.. +..+-.+|+|.+++.+.. ++.+.. +..+ .+||
T Consensus 69 ~Y~LEVSSPGldRpL~~~~~f----~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i--~l~~~~----~~~~-~i~~ 137 (150)
T PRK14633 69 KYILEVSSPGMNRQIFNIIQA----QALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNV--ILNLED----GKEI-SFDF 137 (150)
T ss_pred CeEEEEeCCCCCCCCCCHHHH----HHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEE--EEEEcC----CcEE-EEEh
Confidence 355555555555555433332 345688888853 345667899999987654 444433 3444 5999
Q ss_pred ccccc
Q psy15370 388 SHICK 392 (393)
Q Consensus 388 ddicK 392 (393)
++|.+
T Consensus 138 ~~I~k 142 (150)
T PRK14633 138 DELKK 142 (150)
T ss_pred HHeee
Confidence 99876
No 96
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=27.58 E-value=3.7e+02 Score=22.87 Aligned_cols=63 Identities=17% Similarity=0.134 Sum_probs=42.6
Q ss_pred cceeEEEEecCCceEEEEEcCCCcEE--EeecCceeeecC-CCCCeEEEEecCccCceEEEEEeeCC
Q psy15370 301 KKKGTVEKVIDKYAAIVSLLDSKHKI--KLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKDINID 364 (393)
Q Consensus 301 kkKGvV~dV~d~~~c~V~l~d~g~~l--~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~LisiD~~ 364 (393)
.-.|+|.++.......|.+. +|..+ .|.-..=---|= -+|++|.|---.|-=..|.++-+...
T Consensus 8 e~~G~V~e~Lp~~~frV~Le-nG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLE-NGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeC-CCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 34688999988888888886 45543 454444332332 56888888888887777777776653
No 97
>PRK14630 hypothetical protein; Provisional
Probab=27.52 E-value=1.2e+02 Score=27.41 Aligned_cols=68 Identities=21% Similarity=0.230 Sum_probs=41.7
Q ss_pred CceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEEecCccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccccccc
Q psy15370 312 KYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHIC 391 (393)
Q Consensus 312 ~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddic 391 (393)
.|.-.|..+.-++.|+-+.+ ..-..|..|.|-...-.+ .|+|.+++.+.. ++..+ +..+ .+||++|.
T Consensus 72 ~Y~LEVSSPGldRpL~~~~d----f~r~~G~~v~V~l~~~~~-~G~L~~~~d~~i--~l~~~-----~~~~-~i~~~~I~ 138 (143)
T PRK14630 72 NFSLEISTPGINRKIKSDRE----FKIFEGKKIKLMLDNDFE-EGFILEAKADSF--IFKTD-----SKEV-NVLYSDVK 138 (143)
T ss_pred CeEEEEeCCCCCCcCCCHHH----HHHhCCCEEEEEEcCcce-EEEEEEEeCCEE--EEEEC-----CEEE-EEEhHhcc
Confidence 45555555555555533222 234678888886543333 899999987554 44433 3444 69999997
Q ss_pred c
Q psy15370 392 K 392 (393)
Q Consensus 392 K 392 (393)
+
T Consensus 139 k 139 (143)
T PRK14630 139 K 139 (143)
T ss_pred e
Confidence 6
No 98
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=27.42 E-value=1.6e+02 Score=23.42 Aligned_cols=41 Identities=17% Similarity=0.277 Sum_probs=30.4
Q ss_pred ecCccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccccccccC
Q psy15370 348 CGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICKI 393 (393)
Q Consensus 348 ~G~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddicKl 393 (393)
+|.+.-.+|++..+|.....+.|.-.. +. ...++|+||+.+
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~~~~~----~~-~~~I~~~~I~~I 92 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKLKDED----GE-TEKIPFDDIIDI 92 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEEEeCC----CC-EEEEEhhhEEEC
Confidence 677888899999999999866554322 33 346999999753
No 99
>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=26.95 E-value=3.5e+02 Score=22.08 Aligned_cols=48 Identities=8% Similarity=0.063 Sum_probs=31.2
Q ss_pred eEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEEecCc
Q psy15370 304 GTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLILCGKY 351 (393)
Q Consensus 304 GvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV~G~~ 351 (393)
|+|..+.+.+...|.+.|....+ .++..+=-+|-=..|+.|+|-.-+|
T Consensus 4 ~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 4 VRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEE 52 (78)
T ss_pred EEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEeccc
Confidence 67788877778888887544444 6666666664446677777754444
No 100
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=26.94 E-value=1e+02 Score=25.27 Aligned_cols=36 Identities=17% Similarity=0.209 Sum_probs=28.6
Q ss_pred CCCCeEEEEecC--ccCceEEEEEeeCC--CceEEEEecC
Q psy15370 339 NLGRQVLILCGK--YKGEKAVLKDINID--DCNANVELID 374 (393)
Q Consensus 339 ~~G~~V~VV~G~--~RG~~G~LisiD~~--k~~a~V~l~~ 374 (393)
+.|++|+|++-+ +-..+|++.++|.+ ++-|+|+++.
T Consensus 4 ~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VRF~k 43 (71)
T PRK02749 4 SRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVRFDK 43 (71)
T ss_pred ccCCEEEEccccceeecCcceEEEEccCCCeeeEEEEeee
Confidence 579999999766 46789999999876 5677888764
No 101
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=26.91 E-value=4.7e+02 Score=33.00 Aligned_cols=87 Identities=10% Similarity=0.174 Sum_probs=55.6
Q ss_pred CcccCceEEEEeeccCCcc-cccceeEEEEecCCc-eEEEEEcCCCcEEEeecCce----eee----cC-CCCCeEEEEe
Q psy15370 280 SWLHKNIIVKIVTKNLGEK-FYKKKGTVEKVIDKY-AAIVSLLDSKHKIKLDQEHL----ETV----IP-NLGRQVLILC 348 (393)
Q Consensus 280 ~WL~~~IvVKIidK~l~dg-yYkkKGvV~dV~d~~-~c~V~l~d~g~~l~VdQ~~L----ETV----IP-~~G~~V~VV~ 348 (393)
.+..+|.+|+........+ .| +|..|.... +.+|. ...|..+.++...+ +.. |+ +.|+++++..
T Consensus 647 ~~Y~~G~vi~~~~~~~~~~~~y----~V~~v~~~~n~LtL~-~~~G~~~~~~p~~~~~~~~vy~~~~ieiA~GDrLr~T~ 721 (1747)
T PRK13709 647 DMYRPGMVMEQWNPETRSHDRY----VIDRVTAQSHSLTLR-DAQGETQVVKISSLDSSWSLFRPEKMPVADGERLRVLG 721 (1747)
T ss_pred hcCCCCcEEEeeccccccCccE----EEEEEcCCCCEEEEE-cCCCCEEEeChHHhcccceeccccccccCCCCEEEEcc
Confidence 4558999998854321112 33 788876543 33443 44788888875544 333 33 8999999994
Q ss_pred c-----CccCceEEEEEeeCCCceEEEEec
Q psy15370 349 G-----KYKGEKAVLKDINIDDCNANVELI 373 (393)
Q Consensus 349 G-----~~RG~~G~LisiD~~k~~a~V~l~ 373 (393)
. -..|..+++.+|+.. .++|..+
T Consensus 722 nd~~~~l~Ngd~~tV~~i~~~--~i~l~~~ 749 (1747)
T PRK13709 722 KIPGLRLKGGDRLQVTSVSED--GLTVVVP 749 (1747)
T ss_pred CCcccCccCCCEEEEEEecCC--eEEEEEC
Confidence 4 247789999999874 4466654
No 102
>PF04494 TFIID_90kDa: WD40 associated region in TFIID subunit; InterPro: IPR007582 This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2J4B_D 2J49_A 2NXP_F.
Probab=25.90 E-value=27 Score=30.99 Aligned_cols=64 Identities=17% Similarity=0.353 Sum_probs=49.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhh---cCcceeeccchhhhhhcCCCceeecccccccHHHHHHHhcc
Q psy15370 61 ADQYLDEFSREFEEGYLELLRRQ---FSTRRVFANKVYQDYIADREHVHMNATQWETLTEFVKHLGK 124 (393)
Q Consensus 61 ~~~~i~~~S~~F~~~Fl~lLr~~---~g~krv~aN~vY~eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr 124 (393)
+..|++.|+..|...+.+.|+.= .-..-|..|..=+.|-++|-+|.|.-+.|.-|..|+.-=..
T Consensus 61 A~~F~~kf~~~~~~~~~~~i~~L~~i~~~~~l~~~~~~~~~r~~Ky~I~ls~~s~~lL~~fL~~~~~ 127 (142)
T PF04494_consen 61 AKSFLEKFSPDFEDSHQEDIEKLSSITSPEHLEENELARLFRSNKYVIRLSRDSFSLLLQFLQENEN 127 (142)
T ss_dssp HHHHHHHHGGGGHGHGHHHHHHHTT--SHHHHHHSHHHHHHHCSGEEEEEEHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHhhCcHHHHhccHHHHHHHhCCeeEEECHHHHHHHHHHHHhCCc
Confidence 46789999998888776554443 33556777888888999999999999999988888764433
No 103
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=25.90 E-value=1.2e+02 Score=30.44 Aligned_cols=125 Identities=15% Similarity=0.190 Sum_probs=70.3
Q ss_pred ceeeeecchhhhccCcCccccccCCHHHHHHHHHhhcChhhH---HHHH---HHHHHHHHHHHHHhhcCcceeeccchhh
Q psy15370 23 KLRWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFADNADQY---LDEF---SREFEEGYLELLRRQFSTRRVFANKVYQ 96 (393)
Q Consensus 23 kLrwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~~n~~~~---i~~~---S~~F~~~Fl~lLr~~~g~krv~aN~vY~ 96 (393)
-+|..+++|..-+.-...=....-++.|.+.-.--. .+..+ +... ...|......+.+. +...|....+|+
T Consensus 247 d~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~-~~~~~~~~~~~L~~~~k~~L~ai~~~~~~--~~~~~~~~~i~~ 323 (394)
T PRK00411 247 DARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS-EIVHLSEVLRTLPLHEKLLLRAIVRLLKK--GGDEVTTGEVYE 323 (394)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHHHHhc--CCCcccHHHHHH
Confidence 456666777554322111112456788886433211 12222 2222 23344444444432 445688999999
Q ss_pred hhhcCCCceeecccccccHHHHHHHhccccceEeeccccc----eEEEeecCCHHHHH
Q psy15370 97 DYIADREHVHMNATQWETLTEFVKHLGKSGKCVVDETEKG----WFVTYIDRDPETIA 150 (393)
Q Consensus 97 eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr~g~~~v~et~kg----~~i~~Id~~pe~~~ 150 (393)
+|-.--.-+.+..-.+.++.+++..|...|.+......+| +-+--+..+|+.+.
T Consensus 324 ~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~~~~~g~~g~~~~~~~~~~~~~~~ 381 (394)
T PRK00411 324 EYKELCEELGYEPRTHTRFYEYINKLDMLGIINTRYSGKGGRGRTRLISLSYDPEDVL 381 (394)
T ss_pred HHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEEEecCCCCCCeEEEEecCCHHHHH
Confidence 9864222234555578899999999999999998654333 43334566777553
No 104
>PHA01733 hypothetical protein
Probab=25.58 E-value=48 Score=30.75 Aligned_cols=51 Identities=18% Similarity=0.225 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhcCcceeeccchhhhhhcCCCceeecccccccHHHHHHHhccccc
Q psy15370 62 DQYLDEFSREFEEGYLELLRRQFSTRRVFANKVYQDYIADREHVHMNATQWETLTEFVKHLGKSGK 127 (393)
Q Consensus 62 ~~~i~~~S~~F~~~Fl~lLr~~~g~krv~aN~vY~eyI~dr~HvHMNaT~W~sLt~Fvk~Lgr~g~ 127 (393)
...|+.|+..|...|..+|-. ...=++.-|- .--+||+|. -|.+|||-...
T Consensus 80 T~~v~k~~~~f~re~r~~l~e-~~~Yp~LwNy-----V~~~N~~hi---------r~Lk~lGF~f~ 130 (153)
T PHA01733 80 TPAIEKNPIALLRGAKWWLPK-SRNYDLLWNI-----VDKRNLVHR---------KLLRKLGFKGL 130 (153)
T ss_pred cHHhHhCCHHHHHHHHHHHHH-hccccHHHHh-----HhcccHHHH---------HHHHHcCceee
Confidence 467999999999999999987 3333444444 445788775 56777775443
No 105
>PRK14636 hypothetical protein; Provisional
Probab=25.42 E-value=1.4e+02 Score=27.96 Aligned_cols=70 Identities=17% Similarity=0.125 Sum_probs=42.6
Q ss_pred CceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEE-ecCc---cCceEEEEEeeCCCceEEEEecCCCCCCceeeeccc
Q psy15370 312 KYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLIL-CGKY---KGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDY 387 (393)
Q Consensus 312 ~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV-~G~~---RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~y 387 (393)
.|+-.|..+.-++.|.-+.+ ..-..|..|.|- +.+. +-.+|+|.+++.+.. ++.+.. +..+ .+||
T Consensus 73 ~Y~LEVSSPGldRpL~~~~d----f~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v--~l~~~~----~~~~-~i~~ 141 (176)
T PRK14636 73 AYRLEVSSPGIDRPLTRPKD----FADWAGHEARIALSEPLDGRKQFRGELKGIDGDTV--TIADNK----AGEV-ILPF 141 (176)
T ss_pred CeEEEEeCCCCCCCCCCHHH----HHHhCCCeEEEEEecccCCeEEEEEEEEEEeCCEE--EEEEcC----CcEE-EEEh
Confidence 45556665655555543322 234679988885 4333 445899999987653 444433 3334 5899
Q ss_pred ccccc
Q psy15370 388 SHICK 392 (393)
Q Consensus 388 ddicK 392 (393)
++|.+
T Consensus 142 ~~I~k 146 (176)
T PRK14636 142 AAIES 146 (176)
T ss_pred HHcce
Confidence 99875
No 106
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=25.16 E-value=2.7e+02 Score=24.67 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=25.8
Q ss_pred cCCCcEEEeecCceeeecCCCCCeEEEE
Q psy15370 320 LDSKHKIKLDQEHLETVIPNLGRQVLIL 347 (393)
Q Consensus 320 ~d~g~~l~VdQ~~LETVIP~~G~~V~VV 347 (393)
.+.+..+.|+-++||++.+..|..+.+|
T Consensus 47 ~~~~~~l~V~t~~l~~~~~~~gslyq~i 74 (118)
T PF15490_consen 47 ESDQHSLKVDTKLLEPFQARVGSLYQFI 74 (118)
T ss_pred cCCCcEEEEEeeEccccccCCCCEEEEE
Confidence 6788899999999999999999999887
No 107
>PLN02748 tRNA dimethylallyltransferase
Probab=25.07 E-value=28 Score=37.31 Aligned_cols=34 Identities=15% Similarity=0.500 Sum_probs=29.5
Q ss_pred eeeeecchhh-hccCcCccccccCCHHHHHHHHHh
Q psy15370 24 LRWYCQMCQK-QCRDENGFKCHTSSEAHQRQLLLF 57 (393)
Q Consensus 24 LrwyCQ~CqK-QCRDeNGFKcH~~SesH~rqm~~~ 57 (393)
=.++|.+|.+ -.+-++-..-|+.|-.|.+.+.-.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~ 451 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRL 451 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHH
Confidence 3457999998 799999999999999999998644
No 108
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=25.00 E-value=3.4e+02 Score=23.28 Aligned_cols=58 Identities=22% Similarity=0.348 Sum_probs=31.7
Q ss_pred ceEEEEeeccCCcccccceeEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEE
Q psy15370 285 NIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLI 346 (393)
Q Consensus 285 ~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~V 346 (393)
.+.+++..+.-+. .-|.|..+.+.+...|.+.|....+ .|+..+=-.|-=..|+.|+|
T Consensus 8 ~~~~~~p~~~e~e----~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlV 66 (99)
T TIGR00523 8 QIRVRLPRKEEGE----ILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIV 66 (99)
T ss_pred cceeeCCCCCCCE----EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEE
Confidence 3455565442222 2367888888788888877433333 45444433333345555555
No 109
>KOG4727|consensus
Probab=24.27 E-value=68 Score=30.57 Aligned_cols=53 Identities=30% Similarity=0.511 Sum_probs=43.2
Q ss_pred cceeeeecchhhhccCcCccccccCCHHHHHHHHHhhcChhhHHHHHHHHHHH
Q psy15370 22 QKLRWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLFADNADQYLDEFSREFEE 74 (393)
Q Consensus 22 qkLrwyCQ~CqKQCRDeNGFKcH~~SesH~rqm~~~~~n~~~~i~~~S~~F~~ 74 (393)
|+-=|||.+|.=-..|-=-|-=|+.---|||.+-..-.-|...+++--+.|+.
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm~verst~~qv~erf~~ 124 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTLDQVKERFEQ 124 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHhccHHHHHHHhhhhcchhhhHHHHHHHHHH
Confidence 56679999999999999999999999999999866555666666666666653
No 110
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=24.15 E-value=3.6e+02 Score=24.96 Aligned_cols=46 Identities=24% Similarity=0.242 Sum_probs=29.7
Q ss_pred CcccccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecCCCCCeE
Q psy15370 296 GEKFYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQV 344 (393)
Q Consensus 296 ~dgyYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V 344 (393)
+.|-|...|.|..-. .+.+.++...+.+.|+.-..-...|++|+.|
T Consensus 23 G~Gty~~~~~i~as~---~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV 68 (189)
T PRK09521 23 GEGTYEDNGEVYASV---VGKVFIDDINRKISVIPFKKTPPLLKKGDIV 68 (189)
T ss_pred CCCEEeeCCEEEEEe---eEEEEEcCCCCEEEEecCcCCCCCCCCCCEE
Confidence 555666777777754 4556666567778886533325677888876
No 111
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=23.96 E-value=5.4e+02 Score=23.20 Aligned_cols=83 Identities=18% Similarity=0.151 Sum_probs=55.8
Q ss_pred EEEeeccCCccc-ccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecC-CCCCeEEEEecCccCceEEEEEeeCCC
Q psy15370 288 VKIVTKNLGEKF-YKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIP-NLGRQVLILCGKYKGEKAVLKDINIDD 365 (393)
Q Consensus 288 VKIidK~l~dgy-YkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP-~~G~~V~VV~G~~RG~~G~LisiD~~k 365 (393)
+||..|=-.++| |- |.|..=..++.+.|... +|..-+|-+.+|=.+.| ..|..|.-+.+..-+.-|+++..-.+.
T Consensus 7 ~rV~AkWS~n~yyY~--G~I~~~~~~~kykv~Fd-DG~~~~v~~~div~~dplpl~~eV~A~~eddY~~~GvV~~h~~~~ 83 (122)
T PF09038_consen 7 LRVFAKWSDNGYYYP--GKITSDKGKNKYKVLFD-DGYECRVLGKDIVVCDPLPLGTEVTALSEDDYFSPGVVKGHKTDS 83 (122)
T ss_dssp -EEEEESSTTSEEEE--EEEEEEETTTEEEEEET-TS-EEEEECCCEEEESSS-TTEEEEECCTTCTSEEEEEEEEEEET
T ss_pred cEEEEEEccCCcccC--ceEeecCCCCeEEEEec-CCccceeccCcEEEEcceeccceeEEeecCCcccccEEEEEEccC
Confidence 455555555665 54 54444345678998876 58888888999988889 789999998888888888887764333
Q ss_pred ce--EEEEec
Q psy15370 366 CN--ANVELI 373 (393)
Q Consensus 366 ~~--a~V~l~ 373 (393)
.. -.|+.+
T Consensus 84 ~e~yY~Ve~d 93 (122)
T PF09038_consen 84 GEVYYCVETD 93 (122)
T ss_dssp TEEEEEEEET
T ss_pred CcEEEEEEEC
Confidence 32 245544
No 112
>PLN00208 translation initiation factor (eIF); Provisional
Probab=23.79 E-value=5.3e+02 Score=23.80 Aligned_cols=59 Identities=14% Similarity=0.153 Sum_probs=40.8
Q ss_pred eEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEEecCccCceEEEEEee
Q psy15370 304 GTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDIN 362 (393)
Q Consensus 304 GvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~LisiD 362 (393)
|+|..+.+.+.+.|.+.|.-..+ .|+-.+=-.|-=..|+.|+|-.-+|--..|.++-+-
T Consensus 36 g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv~ry 95 (145)
T PLN00208 36 AQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
T ss_pred EEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEEEEc
Confidence 56777777777777777533344 666655554445788888887777777888887763
No 113
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=23.39 E-value=1.6e+02 Score=25.45 Aligned_cols=30 Identities=23% Similarity=0.235 Sum_probs=23.0
Q ss_pred CCCCeEEEEecCccCceEEEEEeeCCCceEEEEecC
Q psy15370 339 NLGRQVLILCGKYKGEKAVLKDINIDDCNANVELID 374 (393)
Q Consensus 339 ~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V~l~~ 374 (393)
++|++|+-..| -.|++.++|.+ .+.|++.+
T Consensus 54 k~Gd~VvT~gG----i~G~Vv~i~~~--~v~lei~~ 83 (106)
T PRK05585 54 AKGDEVVTNGG----IIGKVTKVSED--FVIIELND 83 (106)
T ss_pred CCCCEEEECCC----eEEEEEEEeCC--EEEEEECC
Confidence 46888877766 88999999863 66777765
No 114
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=22.83 E-value=1.6e+02 Score=25.63 Aligned_cols=48 Identities=15% Similarity=0.219 Sum_probs=0.0
Q ss_pred CCCCeEEEE-ec---------CccCceEEEEEeeCCCceEEEEecCCCCCCceeeecccccc
Q psy15370 339 NLGRQVLIL-CG---------KYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHI 390 (393)
Q Consensus 339 ~~G~~V~VV-~G---------~~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddi 390 (393)
.+|+.|-|+ ++ .|-|.+|+++.+-.+.+.|.|.+.+ ..+.| .+.-+++
T Consensus 34 ~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~---k~K~l-iv~peHL 91 (98)
T COG2139 34 KVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGN---KEKTL-IVRPEHL 91 (98)
T ss_pred cCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCC---ceEEE-EeCHHHc
No 115
>KOG0436|consensus
Probab=22.78 E-value=95 Score=33.65 Aligned_cols=79 Identities=24% Similarity=0.434 Sum_probs=60.9
Q ss_pred cCcCccccccCCHHHHHHHHHhhcChhhHHHHHHHHHHHHHHHHHHhhcCcceeeccchhhhhhcCCCceeecccccccH
Q psy15370 36 RDENGFKCHTSSEAHQRQLLLFADNADQYLDEFSREFEEGYLELLRRQFSTRRVFANKVYQDYIADREHVHMNATQWETL 115 (393)
Q Consensus 36 RDeNGFKcH~~SesH~rqm~~~~~n~~~~i~~~S~~F~~~Fl~lLr~~~g~krv~aN~vY~eyI~dr~HvHMNaT~W~sL 115 (393)
-||.|.|--|.+++. |-||.++.|.-|++|..=|. .||.-|-.||+--+-=|- ..+
T Consensus 85 TDEHGlKIqtaaatn-------G~~P~e~cDr~s~~f~qL~k------------~~gi~yt~FIRTTdpkH~-----a~V 140 (578)
T KOG0436|consen 85 TDEHGLKIQTAAATN-------GRNPPELCDRISQSFRQLWK------------DAGIAYTKFIRTTDPKHE-----AIV 140 (578)
T ss_pred CCccchhhhhhHhhc-------CCChHHHHhhhhHHHHHHHH------------HhCcchhheeecCCchHH-----HHH
Confidence 588888877776553 67899999999999987664 579999999984444343 468
Q ss_pred HHHHHHhccccceEeeccccceEE
Q psy15370 116 TEFVKHLGKSGKCVVDETEKGWFV 139 (393)
Q Consensus 116 t~Fvk~Lgr~g~~~v~et~kg~~i 139 (393)
.+|-.-+-++|.+--. .-+|||-
T Consensus 141 qefw~~~~knG~iy~g-~~eGwYc 163 (578)
T KOG0436|consen 141 QEFWARVFKNGDIYRG-DYEGWYC 163 (578)
T ss_pred HHHHHHHHhCCceeee-cccceEe
Confidence 8999999999987653 4679985
No 116
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=22.35 E-value=5.5e+02 Score=32.16 Aligned_cols=85 Identities=11% Similarity=0.141 Sum_probs=56.9
Q ss_pred cCceEEEEeeccCCcc-cccceeEEEEecCCceEEEEEcCCCcEEEeecCce----eee----cC-CCCCeEEEEecC--
Q psy15370 283 HKNIIVKIVTKNLGEK-FYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHL----ETV----IP-NLGRQVLILCGK-- 350 (393)
Q Consensus 283 ~~~IvVKIidK~l~dg-yYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~L----ETV----IP-~~G~~V~VV~G~-- 350 (393)
.||.+|+--++.+..+ .| +|..|.....+.+-....|....++...+ +-. |. +.|++|.+....
T Consensus 518 ~~GmVl~~~~r~~k~~~~y----~V~~V~~~~n~LtL~~~dG~~~~~~p~~~~~~~~vy~~e~lelA~GDrlr~t~nd~~ 593 (1623)
T PRK14712 518 RPGMVMEQWNPETRSHDRY----VTERVTAQSHSLTLRNAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKIPG 593 (1623)
T ss_pred CCCCEEEecccCcCcCceE----EEEEEcCCCceEEEEcCCCcEEEechHHcccceeeecccccccCCCCEEEEccCCcc
Confidence 7899997333444333 44 78888765555444455788888888776 222 33 889999999653
Q ss_pred ---ccCceEEEEEeeCCCceEEEEec
Q psy15370 351 ---YKGEKAVLKDINIDDCNANVELI 373 (393)
Q Consensus 351 ---~RG~~G~LisiD~~k~~a~V~l~ 373 (393)
-.|..+++.+++.+.- +|...
T Consensus 594 ~~L~ngd~~tV~~i~~~~i--tl~~~ 617 (1623)
T PRK14712 594 LRVSGGDRLQVASVSEDAM--TVVVP 617 (1623)
T ss_pred cCccCCCEEEEEEecCCeE--EEEEC
Confidence 3568899988887664 44433
No 117
>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=21.67 E-value=3.7e+02 Score=20.43 Aligned_cols=24 Identities=17% Similarity=0.098 Sum_probs=14.5
Q ss_pred eecCCCCCeEEEEecCccCceEEE
Q psy15370 335 TVIPNLGRQVLILCGKYKGEKAVL 358 (393)
Q Consensus 335 TVIP~~G~~V~VV~G~~RG~~G~L 358 (393)
.+-|..|+.|.+-...+-+..|.+
T Consensus 38 ~~~~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 38 YIRILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred CcccCCCCEEEEEEeecCCCEEEE
Confidence 445899999987743333334444
No 118
>PRK03879 ribonuclease P protein component 1; Validated
Probab=21.28 E-value=5.2e+02 Score=22.00 Aligned_cols=50 Identities=16% Similarity=0.255 Sum_probs=29.3
Q ss_pred ceEEEEeeccCCcccccceeEEEEecCCceEEEEEcCCCcEEEeecCceeeecCCCCCeEEEE
Q psy15370 285 NIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVIPNLGRQVLIL 347 (393)
Q Consensus 285 ~IvVKIidK~l~dgyYkkKGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LETVIP~~G~~V~VV 347 (393)
|+.|+|+..+ +-.|-+-+|+|.+= .+.+..|. .++. +-+||+.|....+-
T Consensus 15 Gl~v~Vv~S~-npslvGi~GiVv~E-Tknt~~I~--~~~~---------~~~VPK~~~iF~f~ 64 (96)
T PRK03879 15 GLKVEVVDST-NPSLVGIKGRVVDE-TRNTLVIE--TDGK---------EWMVPKDGATFEFE 64 (96)
T ss_pred CCEEEEEEcC-CCCcccceEEEEEe-ceeEEEEE--cCCc---------EEEEeCCCeEEEEE
Confidence 7888888543 22388889998873 24455444 2222 34466666554444
No 119
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.25 E-value=3.6e+02 Score=20.79 Aligned_cols=57 Identities=23% Similarity=0.163 Sum_probs=33.3
Q ss_pred eeEEEEecCCceEEEEEcCCCcEEEeecCcee-eecC------CCCCeEEEEecCccCceEEEEEeeCCCceEEE
Q psy15370 303 KGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLE-TVIP------NLGRQVLILCGKYKGEKAVLKDINIDDCNANV 370 (393)
Q Consensus 303 KGvV~dV~d~~~c~V~l~d~g~~l~VdQ~~LE-TVIP------~~G~~V~VV~G~~RG~~G~LisiD~~k~~a~V 370 (393)
.|.|++|...+.+.|.+.+ |-.--|+.++|. +-++ +.|+.| .++++++|..+..+.+
T Consensus 6 ~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v----------~~kV~~id~~~~~i~l 69 (71)
T cd05696 6 SVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTH----------KARIIGYSPMDGLLQL 69 (71)
T ss_pred eeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEE----------EEEEEEEeCCCCEEEE
Confidence 4788888545778888874 433345444441 1111 345444 4566788887775544
No 120
>PF14444 S1-like: S1-like
Probab=21.02 E-value=2.2e+02 Score=22.50 Aligned_cols=38 Identities=26% Similarity=0.526 Sum_probs=23.7
Q ss_pred eeEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEE
Q psy15370 303 KGTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLIL 347 (393)
Q Consensus 303 KGvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV 347 (393)
.|+|..+.+.|-.. ++++. +. +-+.-.+|+.|++|++.
T Consensus 5 ~GvVTkl~~~yG~I-----De~vFF~~--~vv~G~~P~vGdrV~v~ 43 (58)
T PF14444_consen 5 TGVVTKLCDDYGFI-----DEDVFFQT--DVVKGNVPKVGDRVLVE 43 (58)
T ss_pred EEEEEEEeCCcceE-----cccEEEEc--ccEecCCCccCCEEEEE
Confidence 57788776654321 12222 33 33667799999999886
No 121
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=20.99 E-value=6.1e+02 Score=23.67 Aligned_cols=59 Identities=14% Similarity=0.157 Sum_probs=39.3
Q ss_pred eEEEEecCCceEEEEEcCCCcEE-EeecCceeeecCCCCCeEEEEecCccCceEEEEEee
Q psy15370 304 GTVEKVIDKYAAIVSLLDSKHKI-KLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKDIN 362 (393)
Q Consensus 304 GvV~dV~d~~~c~V~l~d~g~~l-~VdQ~~LETVIP~~G~~V~VV~G~~RG~~G~LisiD 362 (393)
|+|..+.+.....|.+.+.-.++ .|+-.+=--|-=..|+.|+|-.-+|--..|.++-+-
T Consensus 36 g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 36 AQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred EEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 56777777777777776533333 566555444444778888887777777777777663
No 122
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=20.78 E-value=2e+02 Score=24.88 Aligned_cols=37 Identities=11% Similarity=0.105 Sum_probs=26.3
Q ss_pred ccCceEEEEEeeCCCceEEEEecCCCCCCceeeeccccccc
Q psy15370 351 YKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHIC 391 (393)
Q Consensus 351 ~RG~~G~LisiD~~k~~a~V~l~~G~~~g~~v~~l~yddic 391 (393)
|-|.+|++.++...-+-|.|++.. ..+.| .+..|+|-
T Consensus 58 yhGkTG~V~~v~~~A~~V~v~vg~---k~Kri-~vr~eHlk 94 (98)
T PRK04306 58 FHGKTGTVVGKRGRAYIVEVKDGG---KEKTL-IVRPEHLR 94 (98)
T ss_pred ccCCCEEEEeecCeEEEEEEEECC---ceeEE-EcCHHHcC
Confidence 789999999999998877775543 23334 46666653
Done!