Query 020729
Match_columns 322
No_of_seqs 211 out of 1547
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 04:40:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020729hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00051 RNA-binding S4 domain 100.0 1.6E-72 3.4E-77 529.8 27.6 257 65-322 11-267 (267)
2 TIGR03069 PS_II_S4 photosystem 100.0 1.1E-69 2.5E-74 508.5 26.5 254 64-320 2-257 (257)
3 COG2302 Uncharacterized conser 100.0 2.2E-68 4.8E-73 490.3 23.8 252 67-322 3-257 (257)
4 KOG4837 Uncharacterized conser 99.9 3.2E-27 6.9E-32 211.9 1.3 243 58-320 6-248 (248)
5 TIGR01017 rpsD_bact ribosomal 99.2 1.3E-11 2.9E-16 112.3 5.0 87 194-299 56-143 (200)
6 PRK05327 rpsD 30S ribosomal pr 99.1 2.5E-11 5.4E-16 110.8 3.7 87 194-299 59-146 (203)
7 PF01479 S4: S4 domain; Inter 99.1 1.4E-10 3E-15 81.7 6.0 47 247-293 1-48 (48)
8 TIGR02988 YaaA_near_RecF S4 do 99.1 5.3E-10 1.1E-14 82.5 6.9 53 242-295 4-58 (59)
9 COG1188 Ribosome-associated he 98.9 2.5E-09 5.4E-14 87.2 7.3 62 244-306 6-68 (100)
10 PRK10348 ribosome-associated h 98.8 3.8E-08 8.3E-13 84.4 8.8 67 245-312 7-76 (133)
11 smart00363 S4 S4 RNA-binding d 98.5 2.6E-07 5.7E-12 65.1 6.3 51 247-297 1-52 (60)
12 cd00165 S4 S4/Hsp/ tRNA synthe 98.5 3.3E-07 7.1E-12 66.5 6.2 52 247-298 1-53 (70)
13 CHL00113 rps4 ribosomal protei 98.5 3.2E-07 7E-12 83.8 6.8 55 246-300 88-143 (201)
14 COG0522 RpsD Ribosomal protein 98.2 2.2E-06 4.7E-11 78.7 6.2 58 246-303 93-151 (205)
15 PRK10475 23S rRNA pseudouridin 98.2 2.9E-06 6.3E-11 81.5 6.5 54 243-297 3-56 (290)
16 TIGR00478 tly hemolysin TlyA f 98.2 2.9E-06 6.3E-11 78.9 5.9 51 248-298 1-52 (228)
17 PRK10839 16S rRNA pseudouridyl 98.1 4E-06 8.6E-11 77.4 6.4 51 247-297 1-51 (232)
18 TIGR00005 rluA_subfam pseudour 98.1 8.1E-06 1.8E-10 77.8 6.7 55 244-298 3-58 (299)
19 PRK11180 rluD 23S rRNA pseudou 98.0 1.2E-05 2.6E-10 78.0 7.0 55 244-298 15-70 (325)
20 COG1187 RsuA 16S rRNA uridine- 98.0 1.4E-05 3.1E-10 75.2 6.2 53 246-298 2-55 (248)
21 COG1189 Predicted rRNA methyla 97.9 2.1E-05 4.6E-10 73.6 5.9 52 246-297 2-54 (245)
22 PRK11025 23S rRNA pseudouridyl 97.9 3E-05 6.4E-10 75.1 7.2 61 236-297 7-70 (317)
23 COG0564 RluA Pseudouridylate s 97.8 3.1E-05 6.8E-10 74.4 6.4 56 243-299 9-64 (289)
24 PRK10700 23S rRNA pseudouridyl 97.7 6.4E-05 1.4E-09 72.2 6.3 51 246-297 2-54 (289)
25 PRK11507 ribosome-associated p 97.6 0.00021 4.6E-09 55.0 6.3 53 246-298 11-64 (70)
26 PRK04051 rps4p 30S ribosomal p 97.5 0.00024 5.2E-09 63.9 6.6 53 246-298 102-157 (177)
27 PF03880 DbpA: DbpA RNA bindin 97.4 0.00022 4.9E-09 54.8 4.5 60 164-224 11-73 (74)
28 PF13275 S4_2: S4 domain; PDB: 97.3 3.7E-05 8.1E-10 58.4 -0.4 59 244-303 5-64 (65)
29 TIGR01018 rpsD_arch ribosomal 97.1 0.00093 2E-08 59.3 5.5 51 246-296 103-156 (162)
30 PLN00189 40S ribosomal protein 96.8 0.00087 1.9E-08 61.1 3.3 53 247-299 109-162 (194)
31 PTZ00155 40S ribosomal protein 96.5 0.0025 5.5E-08 57.5 3.6 50 246-295 106-156 (181)
32 COG2501 S4-like RNA binding pr 96.0 0.02 4.4E-07 44.4 5.9 54 247-300 12-66 (73)
33 KOG4837 Uncharacterized conser 95.3 0.023 5E-07 52.3 4.5 86 236-321 129-226 (248)
34 COG4332 Uncharacterized protei 95.3 0.026 5.6E-07 51.0 4.6 97 202-298 85-190 (203)
35 PF06353 DUF1062: Protein of u 94.1 0.065 1.4E-06 46.7 4.2 33 245-277 101-133 (142)
36 PRK04313 30S ribosomal protein 92.7 0.41 8.8E-06 45.1 7.3 63 244-306 35-110 (237)
37 PTZ00118 40S ribosomal protein 92.2 0.35 7.5E-06 46.2 6.2 63 244-306 39-114 (262)
38 PTZ00223 40S ribosomal protein 92.2 0.34 7.5E-06 46.5 6.2 63 244-306 36-111 (273)
39 PLN00036 40S ribosomal protein 92.1 0.37 7.9E-06 46.0 6.2 62 245-306 40-114 (261)
40 PRK13354 tyrosyl-tRNA syntheta 90.6 0.85 1.8E-05 46.1 7.5 48 246-293 342-390 (410)
41 PRK05912 tyrosyl-tRNA syntheta 90.3 1 2.2E-05 45.6 7.7 42 249-290 346-387 (408)
42 PF14451 Ub-Mut7C: Mut7-C ubiq 88.4 0.49 1.1E-05 37.4 3.1 43 247-297 33-75 (81)
43 COG1471 RPS4A Ribosomal protei 87.8 1.4 3E-05 41.5 6.1 52 246-297 40-93 (241)
44 PRK01777 hypothetical protein; 83.4 1.9 4.2E-05 35.0 4.3 57 236-296 15-74 (95)
45 cd02644 R3H_jag R3H domain fou 79.2 15 0.00033 27.8 7.7 51 78-128 6-56 (67)
46 KOG3301 Ribosomal protein S4 [ 73.3 3.6 7.9E-05 36.8 3.2 44 246-289 96-140 (183)
47 COG0162 TyrS Tyrosyl-tRNA synt 72.6 7.5 0.00016 39.4 5.7 40 248-287 338-377 (401)
48 COG0776 HimA Bacterial nucleoi 72.4 2.6 5.6E-05 34.3 1.9 49 249-305 7-55 (94)
49 PRK06437 hypothetical protein; 69.9 5.6 0.00012 29.9 3.2 43 245-296 19-61 (67)
50 PRK11634 ATP-dependent RNA hel 69.7 7.9 0.00017 41.3 5.4 61 164-225 497-560 (629)
51 COG1847 Jag Predicted RNA-bind 67.5 21 0.00046 33.1 7.0 54 80-134 149-202 (208)
52 cd00754 MoaD Ubiquitin domain 66.2 7.1 0.00015 29.4 3.1 28 267-295 46-73 (80)
53 COG4043 Preprotein translocase 65.4 12 0.00026 31.1 4.4 42 262-304 9-50 (111)
54 PRK08364 sulfur carrier protei 65.1 8.2 0.00018 29.1 3.3 42 245-295 22-63 (70)
55 cd00565 ThiS ThiaminS ubiquiti 64.1 6.9 0.00015 28.9 2.7 41 246-295 14-58 (65)
56 PLN02799 Molybdopterin synthas 61.3 24 0.00051 27.0 5.3 25 270-295 51-75 (82)
57 TIGR01683 thiS thiamine biosyn 58.0 13 0.00029 27.3 3.3 42 246-295 13-57 (64)
58 KOG1919 RNA pseudouridylate sy 56.6 17 0.00037 36.6 4.7 48 249-297 47-94 (371)
59 PF02824 TGS: TGS domain; Int 56.2 12 0.00025 27.5 2.7 24 271-295 35-58 (60)
60 PRK06488 sulfur carrier protei 56.2 13 0.00029 27.3 3.0 41 247-295 15-58 (65)
61 PRK11130 moaD molybdopterin sy 55.9 22 0.00047 27.4 4.3 23 272-295 52-74 (81)
62 PF02597 ThiS: ThiS family; I 55.9 9.9 0.00022 28.3 2.3 49 244-295 19-70 (77)
63 TIGR01682 moaD molybdopterin c 55.1 15 0.00032 28.1 3.2 23 272-295 51-73 (80)
64 TIGR01687 moaD_arch MoaD famil 53.4 21 0.00046 27.5 3.9 24 271-295 56-81 (88)
65 PRK06944 sulfur carrier protei 53.2 17 0.00036 26.5 3.1 41 246-295 15-58 (65)
66 COG2104 ThiS Sulfur transfer p 52.4 16 0.00034 27.9 2.9 41 247-295 18-61 (68)
67 PRK05659 sulfur carrier protei 51.9 19 0.00042 26.3 3.3 42 246-295 15-59 (66)
68 COG0529 CysC Adenylylsulfate k 51.7 38 0.00081 31.2 5.6 86 49-134 31-136 (197)
69 PRK07440 hypothetical protein; 49.3 22 0.00048 26.9 3.3 42 246-295 19-63 (70)
70 PRK08053 sulfur carrier protei 48.8 24 0.00051 26.2 3.4 24 272-295 33-59 (66)
71 PRK10664 transcriptional regul 47.7 14 0.0003 29.5 2.0 47 251-305 8-54 (90)
72 PF06115 DUF956: Domain of unk 46.1 11 0.00024 32.0 1.3 39 184-223 23-61 (118)
73 PRK10753 transcriptional regul 44.3 15 0.00033 29.1 1.8 46 252-305 9-54 (90)
74 PRK00199 ihfB integration host 43.3 20 0.00044 28.4 2.4 48 250-305 8-55 (94)
75 PF14453 ThiS-like: ThiS-like 42.5 34 0.00073 25.4 3.2 28 271-299 30-57 (57)
76 cd02638 R3H_unknown_1 R3H doma 42.3 79 0.0017 23.9 5.2 41 87-127 10-50 (62)
77 PF00498 FHA: FHA domain; Int 42.2 24 0.00051 25.5 2.5 26 270-295 41-67 (68)
78 PRK07696 sulfur carrier protei 41.0 29 0.00062 26.0 2.8 24 272-295 34-60 (67)
79 cd01764 Urm1 Urm1-like ubuitin 40.6 28 0.0006 28.0 2.8 24 272-295 61-87 (94)
80 PF01424 R3H: R3H domain; Int 40.3 1.4E+02 0.003 21.5 7.5 39 96-138 22-60 (63)
81 COG0481 LepA Membrane GTPase L 36.6 39 0.00084 35.5 3.7 149 99-252 344-501 (603)
82 cd01668 TGS_RelA_SpoT TGS_RelA 34.5 56 0.0012 22.7 3.3 23 272-295 36-58 (60)
83 PF07550 DUF1533: Protein of u 34.3 85 0.0018 23.3 4.4 46 271-319 9-54 (65)
84 TIGR00988 hip integration host 34.3 34 0.00073 26.9 2.4 46 252-305 10-55 (94)
85 TIGR00234 tyrS tyrosyl-tRNA sy 33.0 64 0.0014 32.3 4.6 41 247-287 330-371 (377)
86 TIGR01764 excise DNA binding d 29.7 37 0.0008 22.4 1.6 21 253-273 7-27 (49)
87 KOG4655 U3 small nucleolar rib 29.6 45 0.00097 30.1 2.5 38 258-295 119-158 (181)
88 TIGR00987 himA integration hos 27.8 41 0.00088 26.8 1.8 46 252-305 10-55 (96)
89 cd00591 HU_IHF Integration hos 27.7 42 0.0009 25.7 1.8 47 251-305 7-53 (87)
90 PRK06083 sulfur carrier protei 27.6 71 0.0015 25.3 3.1 42 246-295 33-77 (84)
91 cd01616 TGS The TGS domain, na 27.5 87 0.0019 20.8 3.3 22 273-295 37-58 (60)
92 PF01050 MannoseP_isomer: Mann 27.3 43 0.00093 29.3 2.0 109 187-304 5-123 (151)
93 smart00393 R3H Putative single 26.9 2.8E+02 0.0062 21.0 7.4 48 88-139 29-77 (79)
94 smart00252 SH2 Src homology 2 26.2 2.8E+02 0.006 20.7 7.0 57 258-317 7-63 (84)
95 KOG2623 Tyrosyl-tRNA synthetas 26.2 77 0.0017 32.5 3.7 41 246-286 398-439 (467)
96 cd01666 TGS_DRG_C TGS_DRG_C: 26.1 52 0.0011 25.5 2.0 23 272-295 51-73 (75)
97 PRK05863 sulfur carrier protei 25.3 49 0.0011 24.5 1.7 42 246-295 15-58 (65)
98 cd02640 R3H_NRF R3H domain of 25.0 2E+02 0.0042 21.4 4.9 41 93-136 16-56 (60)
99 PF01052 SpoA: Surface present 25.0 1.6E+02 0.0035 22.0 4.6 35 287-321 29-73 (77)
100 KOG1151 Tousled-like protein k 24.7 46 0.001 34.9 1.9 67 244-310 550-621 (775)
101 smart00411 BHL bacterial (prok 24.6 59 0.0013 25.0 2.2 48 251-306 8-55 (90)
102 cd02639 R3H_RRM R3H domain of 24.2 1.5E+02 0.0033 22.0 4.2 36 94-130 17-52 (60)
103 KOG4469 Uncharacterized conser 24.0 14 0.0003 35.0 -1.8 44 19-63 279-322 (391)
104 cd02645 R3H_AAA R3H domain of 23.1 3.2E+02 0.0069 20.2 5.8 50 83-135 5-55 (60)
105 PRK08433 flagellar motor switc 22.6 2E+02 0.0043 24.1 5.0 32 290-321 66-97 (111)
106 cd06007 R3H_DEXH_helicase R3H 22.6 2.6E+02 0.0056 20.6 5.1 41 94-137 16-56 (59)
107 smart00276 GLECT Galectin. Gal 22.4 1.6E+02 0.0034 24.4 4.5 36 272-307 91-126 (128)
108 PRK00285 ihfA integration host 20.7 74 0.0016 25.3 2.1 46 253-306 12-57 (99)
No 1
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=100.00 E-value=1.6e-72 Score=529.80 Aligned_cols=257 Identities=72% Similarity=1.099 Sum_probs=240.7
Q ss_pred hHHhhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEEecCCCC
Q 020729 65 FDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEA 144 (322)
Q Consensus 65 ~~~ll~~~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~i~~~~~ 144 (322)
-..+++|+.+ +++.++++++||+++|.++|.+++|+||||+|+.++.+++++..++++.++|||++|||+|++|+|+++
T Consensus 11 ~~~i~~h~~~-ee~~~~~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~~p~~~ 89 (267)
T PLN00051 11 DSALLGVVDP-AHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEV 89 (267)
T ss_pred hhHHHhhcCh-hhHHHHHHHHHHHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEEechHh
Confidence 3478999885 559999999999999999999999999999999999999988889999999999999999999975554
Q ss_pred CCCCcCceEEEEEecCCCCcCCCchhhHHHHHcCCCCCCCcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEEEE
Q 020729 145 LTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTR 224 (322)
Q Consensus 145 ~~~~~~~i~~l~i~~~~kF~~lsHrD~LGaLm~LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~ 224 (322)
++.+++|+++++|++++||.+|+|||||||||||||+||+||||++.++++||++|+++|++||++||+|||+++|++++
T Consensus 90 ~~~~~f~i~~l~i~~~~kF~~l~HrD~LGaLm~LGIkRe~iGDIlv~~~~~~~v~v~~~i~~fi~~nl~kIg~~~V~~~~ 169 (267)
T PLN00051 90 LTSQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVPVECRA 169 (267)
T ss_pred ccccCCcEEEEEEEcccCCCCCCHHHHHHHHHHcCCcHhhcCCEEEcCCCcEEEEEcHHHHHHHHHHhhhccceeEEEEE
Confidence 42223599999999999999999999999999999999999999996555799999999999999999999999999999
Q ss_pred ecCccccCCCCCceeEeecccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEE
Q 020729 225 IPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG 304 (322)
Q Consensus 225 i~~~~l~~~~~~~k~~~~~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ 304 (322)
++++++..|+++|++++.+++|+|||++++..+++||++++++|++|+|+|||++++++++.|++||+|||||+|||++.
T Consensus 170 ~~~~~~~~~~~~~~e~~~~vas~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~GR~~i~ 249 (267)
T PLN00051 170 IPLSALEVEPPRVESFKSVEASLRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGRLEVG 249 (267)
T ss_pred ecHHHcCCCccceEEccCCcCcccHHHHHHHHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeCCEEEEE
Confidence 99999888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeecccccceEEEEEEeC
Q 020729 305 EINSTRKGKFAVELIQYL 322 (322)
Q Consensus 305 ei~~TKKgR~~i~l~ry~ 322 (322)
+++.|||||++|++++|+
T Consensus 250 ~~~~TKKgr~~i~i~ky~ 267 (267)
T PLN00051 250 EINTTKKGKFAVELIRYL 267 (267)
T ss_pred EEecccCCcEEEEEEecC
Confidence 988999999999999985
No 2
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=100.00 E-value=1.1e-69 Score=508.47 Aligned_cols=254 Identities=45% Similarity=0.741 Sum_probs=234.6
Q ss_pred chHHhhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEEecCCC
Q 020729 64 NFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE 143 (322)
Q Consensus 64 ~~~~ll~~~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~i~~~~ 143 (322)
+++.+++++.++|+ +++++||+++|.++|.+.+|+||||+|+.++.+++++..++++.++|||++|||+|++|+|++
T Consensus 2 ~~~~~~~~~~~~ee---~~~~~d~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~ 78 (257)
T TIGR03069 2 PREELLKGANYPEE---LERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSD 78 (257)
T ss_pred ChHHHHHhCCCHHH---HHHHHHHHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEeccc
Confidence 46788999886343 999999999999999999999999999999999998888999999999999999999996444
Q ss_pred CCCCCc-CceEEEEEecCCCCcCCCchhhHHHHHcCCCCCCCcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEE
Q 020729 144 ALTSDP-DIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSC 222 (322)
Q Consensus 144 ~~~~~~-~~i~~l~i~~~~kF~~lsHrD~LGaLm~LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~ 222 (322)
++++.. .|+++++|++++||.+|+|||||||||||||+|+++|||++.++++||++|+++|++||.+||+|||+++|++
T Consensus 79 ~~~~~~df~i~~l~i~~~~kF~~l~Hrd~LGalm~lGi~R~~iGDI~v~~~~~~~v~v~~~i~~~i~~~l~kIg~~~V~~ 158 (257)
T TIGR03069 79 NPLDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREKIGDIWVLGDRGAQALCTPELAEFLQEKLGQVRDVEVKC 158 (257)
T ss_pred ccCCcccCceEEEEEEcccccCCCCHHHHHHHHHHcCCcHhhcCCEEEecCCcEEEEECHHHHHHHHHHhhhccceeEEE
Confidence 433333 4999999999999999999999999999999999999998877657999999999999999999999999999
Q ss_pred EEecCccccCCCCCc-eeEeecccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeE
Q 020729 223 TRIPLLALEYEPPRT-KSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRI 301 (322)
Q Consensus 223 ~~i~~~~l~~~~~~~-k~~~~~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~ 301 (322)
++++++++..+++++ +++..+++|+|||.+++..+++||++++++|++|+|+|||++++++++.|++||+|+|+|+|||
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~Gr~ 238 (257)
T TIGR03069 159 KAIPLEELQIPAPRTPKELTTVEASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGRL 238 (257)
T ss_pred EEeCHHHcCCCCcccceEecCCCccccHHHHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCCceE
Confidence 999999886666655 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeecccccceEEEEEE
Q 020729 302 KIGEINSTRKGKFAVELIQ 320 (322)
Q Consensus 302 ~i~ei~~TKKgR~~i~l~r 320 (322)
++.+++.|||||++|++.|
T Consensus 239 ~i~~~~~TKKgr~~i~i~~ 257 (257)
T TIGR03069 239 EILELEITKKERWRVELLR 257 (257)
T ss_pred EEEEeecCcCCcEEEEEeC
Confidence 9999999999999999875
No 3
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=100.00 E-value=2.2e-68 Score=490.29 Aligned_cols=252 Identities=37% Similarity=0.573 Sum_probs=238.1
Q ss_pred HhhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEEecCCCCCC
Q 020729 67 DLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 146 (322)
Q Consensus 67 ~ll~~~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~i~~~~~~~ 146 (322)
.+++|+. .|+++++++++||+++|+++|.+..||||||+|+.+...+++ ..|+++.++||||+|||+|++++ |+|++
T Consensus 3 ~iyqhf~-~eer~fidr~l~~~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l~-P~y~~ 79 (257)
T COG2302 3 GIYQHFR-AEERPFIDRVLEWIKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLILY-PAYYP 79 (257)
T ss_pred cHhhhcC-chhHHHHHHHHHHHHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEEc-ccccC
Confidence 4567776 567999999999999999999999999999999998887777 88999999999999999999995 66665
Q ss_pred -CCcC-ceEEEEEecCCCCcCCCchhhHHHHHcCCCCCCCcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEEEE
Q 020729 147 -SDPD-IVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTR 224 (322)
Q Consensus 147 -~~~~-~i~~l~i~~~~kF~~lsHrD~LGaLm~LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~ 224 (322)
++.| ++++++|.|++||.+++|+||||+||||||+|+++|||++.+ ++||++|.+++++|+..+|+|||+++|++++
T Consensus 80 ~~~~df~l~l~eI~y~~kF~~l~H~~~LGtll~lGikRe~~GDIiv~~-~~aQliv~~~~~~f~~~~Ltkig~~~V~l~e 158 (257)
T COG2302 80 LEESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEG-EGAQLIVATELADFFLLHLTKIGKAPVKLEE 158 (257)
T ss_pred hhhcccceEEEEEEcccccccccHHHHHHHHHhccCcHHhhccEEEeC-CeeEEEEehhHHHHHHHHHHhhcCcceEEEE
Confidence 4445 999999999999999999999999999999999999999976 5999999999999999999999999999999
Q ss_pred ecCccccCCCCCceeEeecccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEE
Q 020729 225 IPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG 304 (322)
Q Consensus 225 i~~~~l~~~~~~~k~~~~~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ 304 (322)
++++++..+.++|++.+++++|||||++++.++++||++++++|.+|+|+|||++++++|+.|+.||.||+||+||+++.
T Consensus 159 i~~~~l~~~~~~~~e~~~~vsSlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR~~i~ 238 (257)
T COG2302 159 IDLEELKESTEKWKELDVTVSSLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGRLKIL 238 (257)
T ss_pred cCHHHcccCccceeEEeeeeehhhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEeccccEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ee-ecccccceEEEEEEeC
Q 020729 305 EI-NSTRKGKFAVELIQYL 322 (322)
Q Consensus 305 ei-~~TKKgR~~i~l~ry~ 322 (322)
++ +.|||||++|++.+|+
T Consensus 239 ~i~g~TKKdK~ri~l~~~~ 257 (257)
T COG2302 239 EINGVTKKDKFRITLRRYK 257 (257)
T ss_pred eecCccccccEEEEEEEcC
Confidence 99 5999999999999985
No 4
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.93 E-value=3.2e-27 Score=211.92 Aligned_cols=243 Identities=60% Similarity=0.940 Sum_probs=220.3
Q ss_pred HHHhhCchHHhhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEE
Q 020729 58 IQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (322)
Q Consensus 58 ~~~~~~~~~~ll~~~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~ 137 (322)
..|+||..+.+++++++......+.+++++|.++.....+.+|+||.|. ....++|+.....+||+.||+|++
T Consensus 6 ~~~i~g~~~~~~~~vg~~~v~k~~~~~~~m~~~~~~~r~f~~t~~l~ps-------l~t~F~~v~s~~lpgl~~a~ec~~ 78 (248)
T KOG4837|consen 6 SEAIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREFLHTDFLTPS-------LLTKFADVKSVALPGLPEAEECRI 78 (248)
T ss_pred hhHhhhhhhhhhhcccHHHHHhhcHHHHHHHHHHHhhHHHHhhhhhCch-------hhhccccchhhhcCCCCCChheEe
Confidence 3789999999999999988888999999999999999999999999994 345678898999999999999999
Q ss_pred EecCCCCCCCCcCceEEEEEecCCCCcCCCchhhHHHHHcCCCCCCCcccEEEecCCeEEEEechhHHHHHHhccceeec
Q 020729 138 SVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGN 217 (322)
Q Consensus 138 ~i~~~~~~~~~~~~i~~l~i~~~~kF~~lsHrD~LGaLm~LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~ 217 (322)
.|+.|+....+.+..+.+++..++.|++.+|.||||+++ ||+.|||.|+.+ ++.+.+++.+|-.+-|.|+|
T Consensus 79 pi~~~~~~ts~k~~kksl~~td~~dsd~esh~Df~~e~~-----~e~~~D~~Vvk~---~~~i~~~v~sfr~d~llK~G- 149 (248)
T KOG4837|consen 79 PIGHPDVLTSDKDIKKSLSITDNFDSDPESHGDFLGEIL-----REKLGDILVVKE---KVLIVPEVVSFRVDALLKVG- 149 (248)
T ss_pred eccCccccccchhHHHHhhhccccCCCcccchhHHHHHH-----HHhcCCceeeeh---hhhhhhHHHHHHHHHHHHhc-
Confidence 999998877666777888999999999999999999998 999999999754 48888999999999999999
Q ss_pred eEEEEEEecCccccCCCCCceeEeecccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 218 VSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 218 ~~V~~~~i~~~~l~~~~~~~k~~~~~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
..|.+..+++.-.++. ++.-++.....|.|+|.--+..+.++|+ .+++.+..|+|||..+.+.+..++.||++..||
T Consensus 150 lgv~rnKVel~fye~e-~R~N~~Kl~kkS~~i~vgds~d~~ig~~--~~~~s~~~~rV~~~tV~~~~t~~e~~~Vvlrr~ 226 (248)
T KOG4837|consen 150 LGVTRNKVELLFYEYE-PRTNSFKLVKKSLRIDVGDSADFKIGRS--VDLISSKDVRVNWATVTKNGTIVETGDVVLRRG 226 (248)
T ss_pred cccccchhhHhhhhcc-cccCcccccccceeeecccccceeeecc--cccCCcceEEEeeeeecccceEeecceEEEEec
Confidence 9999999988666664 6777888889999999988888888888 889999999999999999999999999999999
Q ss_pred cCeEEEEEeecccccceEEEEEE
Q 020729 298 KGRIKIGEINSTRKGKFAVELIQ 320 (322)
Q Consensus 298 ~GR~~i~ei~~TKKgR~~i~l~r 320 (322)
++ +++.++.+|||||+.+++.|
T Consensus 227 Ks-Lki~~~r~tk~~k~a~~i~~ 248 (248)
T KOG4837|consen 227 KS-LKIGEIRETKKGKFAVEIIR 248 (248)
T ss_pred cc-cccccccccccccchhhhcC
Confidence 99 99999999999999988754
No 5
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=99.20 E-value=1.3e-11 Score=112.32 Aligned_cols=87 Identities=26% Similarity=0.350 Sum_probs=76.6
Q ss_pred CeEEEEechhHHHHHHhccceeeceEEEEEEecCccccCCCCCceeEeecccccHHHHHH-HhCCCcCHHHHHHHHHCCc
Q 020729 194 KGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLISNGD 272 (322)
Q Consensus 194 ~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~i~~~~l~~~~~~~k~~~~~vaS~RLD~~L-s~~~~~SRs~a~~lI~~G~ 272 (322)
+.+|+++.+++.+|+..++.++|++++.+ +.+.+ +|||.+| ...+..||+.|+++|.+|+
T Consensus 56 ~~~Yg~~e~q~~~~~~~a~~~~g~t~~~l--l~~le-----------------~RLD~~L~~~g~~~SR~~ArqlI~~G~ 116 (200)
T TIGR01017 56 KFMYGITEKQFRKYFKEAKKLKGNTGENL--LRLLE-----------------SRLDNVVYRLGFAPTRFAARQLVSHGH 116 (200)
T ss_pred HHHHhchHHHHHHHHHHHhccCCCchhHH--HHHHH-----------------HHHHHHHHHcCCCCCHHHHHHHHHCCC
Confidence 36899999999999999999999998877 22211 7999998 5556889999999999999
Q ss_pred EEECCEEecCCCcccCCCCEEEEeecC
Q 020729 273 VRVNWTTVTKNGTTLRTGDIVSVSGKG 299 (322)
Q Consensus 273 V~VNg~~v~~~s~~Vk~GD~IsVrg~G 299 (322)
|.|||+.++++++.|++||+|+|+|.-
T Consensus 117 V~VNgk~v~~ps~~V~~GD~I~V~~~~ 143 (200)
T TIGR01017 117 ILVNGKKVDIPSYQVRPGDIISIKEKS 143 (200)
T ss_pred EEECCEEeCCCCCCCCCCCEEEEeeCc
Confidence 999999999999999999999999864
No 6
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=99.14 E-value=2.5e-11 Score=110.80 Aligned_cols=87 Identities=23% Similarity=0.385 Sum_probs=76.7
Q ss_pred CeEEEEechhHHHHHHhccceeeceEEEEEEecCccccCCCCCceeEeecccccHHHHHH-HhCCCcCHHHHHHHHHCCc
Q 020729 194 KGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLISNGD 272 (322)
Q Consensus 194 ~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~i~~~~l~~~~~~~k~~~~~vaS~RLD~~L-s~~~~~SRs~a~~lI~~G~ 272 (322)
+.+|+++.+++.+|+..++.++|++++.+ +.+.| +|||.++ +..+..||+.++++|.+|+
T Consensus 59 ~~~Y~~~e~q~~~~~~~a~~~~g~t~~~l--l~~lE-----------------~RLD~iL~~~g~~~SR~~arqlI~~G~ 119 (203)
T PRK05327 59 RRIYGVLEKQFRRYFKEAARRKGNTGENL--LQLLE-----------------SRLDNVVYRLGFAPTRRQARQLVSHGH 119 (203)
T ss_pred HHHhcCcHHHHHHHHHHHHhccCCcHhHH--HHHHH-----------------HHHHHHHHHcCccCCHHHHHHHHHCCc
Confidence 47899999999999999999999998876 32211 7999998 5566899999999999999
Q ss_pred EEECCEEecCCCcccCCCCEEEEeecC
Q 020729 273 VRVNWTTVTKNGTTLRTGDIVSVSGKG 299 (322)
Q Consensus 273 V~VNg~~v~~~s~~Vk~GD~IsVrg~G 299 (322)
|.|||+.++.+++.|++||+|+|++.-
T Consensus 120 V~VNgk~v~~ps~~v~~GD~I~v~~~s 146 (203)
T PRK05327 120 ILVNGKKVNIPSYRVKPGDVIEVREKS 146 (203)
T ss_pred EEECCEEECCCCcCCCCCCEEEECCcC
Confidence 999999998899999999999999863
No 7
>PF01479 S4: S4 domain; InterPro: IPR002942 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 S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=99.12 E-value=1.4e-10 Score=81.74 Aligned_cols=47 Identities=34% Similarity=0.543 Sum_probs=44.0
Q ss_pred cHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 020729 247 LRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV 293 (322)
Q Consensus 247 ~RLD~~Ls-~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~I 293 (322)
||||.+|+ ..+..||++++++|++|.|+|||+.++++++.|++||+|
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 79999998 556889999999999999999999999999999999986
No 8
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=99.05 E-value=5.3e-10 Score=82.45 Aligned_cols=53 Identities=17% Similarity=0.272 Sum_probs=48.4
Q ss_pred ecccccHHHHHHHhCCCc--CHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 020729 242 TIEASLRVDALASAGFKL--SRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 242 ~~vaS~RLD~~Ls~~~~~--SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
...+++|||.+|+.. ++ ||+.++.+|++|.|+|||++++++++.|++||.|+|
T Consensus 4 ~~~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 4 IFTEYITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred ecchHHHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 344679999999987 67 999999999999999999999889999999999987
No 9
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.94 E-value=2.5e-09 Score=87.15 Aligned_cols=62 Identities=24% Similarity=0.311 Sum_probs=55.9
Q ss_pred ccccHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEEe
Q 020729 244 EASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 306 (322)
Q Consensus 244 vaS~RLD~~Ls-~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei 306 (322)
...||||+||. +.+-.+|+.|++++++|+|.|||+.+ +||+.|++||+|+|+...+....+|
T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~~~v~V 68 (100)
T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKEFTVKV 68 (100)
T ss_pred ccceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcEEEEEE
Confidence 45799999996 44899999999999999999999998 9999999999999999888776665
No 10
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.76 E-value=3.8e-08 Score=84.40 Aligned_cols=67 Identities=15% Similarity=0.221 Sum_probs=57.8
Q ss_pred cccHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEEe-e-ccccc
Q 020729 245 ASLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI-N-STRKG 312 (322)
Q Consensus 245 aS~RLD~~L-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei-~-~TKKg 312 (322)
.++|||.+| .+.|..||+.|+++|.+|+|.|||+. .+|+..|++||.|.|+..++....+| . ..+.|
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~v~Vl~l~~~R~ 76 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTVIVKAITEQRR 76 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEEEEEeECccccC
Confidence 468999997 56679999999999999999999999 69999999999999988888777776 3 44444
No 11
>smart00363 S4 S4 RNA-binding domain.
Probab=98.53 E-value=2.6e-07 Score=65.15 Aligned_cols=51 Identities=37% Similarity=0.510 Sum_probs=47.0
Q ss_pred cHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 247 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 247 ~RLD~~Ls~~-~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
+|||.++... +..||+.++.++++|.|.|||+.+++++..+++||.|++.+
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 5899999876 47999999999999999999999978999999999999876
No 12
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=98.50 E-value=3.3e-07 Score=66.51 Aligned_cols=52 Identities=37% Similarity=0.526 Sum_probs=47.5
Q ss_pred cHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeec
Q 020729 247 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 298 (322)
Q Consensus 247 ~RLD~~Ls~~-~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~ 298 (322)
+|||.+|+.. +..||+.+++++++|.|+|||+.++++++.+.+||.|++.+.
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~ 53 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGK 53 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCC
Confidence 5899999877 578999999999999999999999889999999999998764
No 13
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.46 E-value=3.2e-07 Score=83.83 Aligned_cols=55 Identities=20% Similarity=0.265 Sum_probs=49.9
Q ss_pred ccHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCe
Q 020729 246 SLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR 300 (322)
Q Consensus 246 S~RLD~~Ls~~-~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR 300 (322)
.+|||.+|... +..||+.|+++|.+|+|.|||+.++.+++.|++||+|+|++..+
T Consensus 88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~~~ 143 (201)
T CHL00113 88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQK 143 (201)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccccc
Confidence 48999999655 48899999999999999999999999999999999999998653
No 14
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.22 E-value=2.2e-06 Score=78.67 Aligned_cols=58 Identities=29% Similarity=0.409 Sum_probs=51.8
Q ss_pred ccHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEE
Q 020729 246 SLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI 303 (322)
Q Consensus 246 S~RLD~~L-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i 303 (322)
-.|||.++ ..+|..||..|+++|.+|+|.|||+.|+.||+.|++||+++|+.+-+-.+
T Consensus 93 ErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~ 151 (205)
T COG0522 93 ERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPI 151 (205)
T ss_pred HHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchh
Confidence 46999997 56679999999999999999999999999999999999999998765443
No 15
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=98.18 E-value=2.9e-06 Score=81.53 Aligned_cols=54 Identities=28% Similarity=0.397 Sum_probs=50.0
Q ss_pred cccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 243 IEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 243 ~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
+.+++|||.||+.....||+++.++|++|+|+|||+++ .+++.|.+||.|.|.+
T Consensus 3 ~~~~~RL~k~La~~g~~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g 56 (290)
T PRK10475 3 TDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNG 56 (290)
T ss_pred cchHHHHHHHHHhCCCCCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECC
Confidence 56789999999987788999999999999999999988 6899999999999986
No 16
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=98.16 E-value=2.9e-06 Score=78.92 Aligned_cols=51 Identities=27% Similarity=0.169 Sum_probs=47.1
Q ss_pred HHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeec
Q 020729 248 RVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 298 (322)
Q Consensus 248 RLD~~Ls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~ 298 (322)
|||.+|.... ..||++++.+|++|+|+|||++++++++.|.+||.|++.+.
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~~ 52 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQN 52 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccCc
Confidence 8999987665 77999999999999999999999999999999999999865
No 17
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=98.15 E-value=4e-06 Score=77.39 Aligned_cols=51 Identities=22% Similarity=0.232 Sum_probs=47.7
Q ss_pred cHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 247 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 247 ~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
+|||.+|+..+.+||+.++++|++|+|+|||+++.++++.|++||.|++.+
T Consensus 1 ~rld~~L~~~~~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~ 51 (232)
T PRK10839 1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDG 51 (232)
T ss_pred CcHHHHHHHcCCCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECC
Confidence 589999998889999999999999999999999867999999999999975
No 18
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=98.05 E-value=8.1e-06 Score=77.83 Aligned_cols=55 Identities=31% Similarity=0.462 Sum_probs=49.6
Q ss_pred ccccHHHHHHHhCCC-cCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeec
Q 020729 244 EASLRVDALASAGFK-LSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 298 (322)
Q Consensus 244 vaS~RLD~~Ls~~~~-~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~ 298 (322)
.+++|||.+|+..+. +||+.++++|++|.|+|||+.+.++++.|++||.|++.+.
T Consensus 3 ~~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~ 58 (299)
T TIGR00005 3 QAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVP 58 (299)
T ss_pred ccchhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecC
Confidence 468999999999885 9999999999999999999766689999999999999654
No 19
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=98.01 E-value=1.2e-05 Score=78.04 Aligned_cols=55 Identities=24% Similarity=0.323 Sum_probs=50.4
Q ss_pred ccccHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeec
Q 020729 244 EASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 298 (322)
Q Consensus 244 vaS~RLD~~Ls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~ 298 (322)
.+++|||.+|+..+ ..||+.++++|++|+|+|||+.+.++++.|++||.|++.+.
T Consensus 15 ~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~ 70 (325)
T PRK11180 15 QLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE 70 (325)
T ss_pred cCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeec
Confidence 46799999999987 68999999999999999999998789999999999999863
No 20
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=97.95 E-value=1.4e-05 Score=75.21 Aligned_cols=53 Identities=32% Similarity=0.417 Sum_probs=48.9
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC-CEEEEeec
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG-DIVSVSGK 298 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~G-D~IsVrg~ 298 (322)
+|||+++|+.....||+++.++|.+|+|+|||++++.+...+.++ |+|.+.|.
T Consensus 2 ~~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~ 55 (248)
T COG1187 2 SMRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGK 55 (248)
T ss_pred ccchHHHHHHcCCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCE
Confidence 689999999999999999999999999999999999999999998 57777665
No 21
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.88 E-value=2.1e-05 Score=73.55 Aligned_cols=52 Identities=37% Similarity=0.411 Sum_probs=48.2
Q ss_pred ccHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 246 SLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 246 S~RLD~~Ls~~-~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
-||||.+|.+. +.-||++|+.+|.+|.|.|||..+++|++.|+.++.|.|.+
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~ 54 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG 54 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcc
Confidence 48999997655 69999999999999999999999999999999999999984
No 22
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=97.88 E-value=3e-05 Score=75.09 Aligned_cols=61 Identities=26% Similarity=0.392 Sum_probs=52.0
Q ss_pred CceeEee--cccccHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 236 RTKSFKT--IEASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 236 ~~k~~~~--~vaS~RLD~~Ls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
..+.+.+ ..+++|||.+|+..+ ++||+.++.+|++|.|+|||+.+ ++++.|++||.|++..
T Consensus 7 ~~~~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~ 70 (317)
T PRK11025 7 SVKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPP 70 (317)
T ss_pred ccEEEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCC
Confidence 3344444 356899999999777 78999999999999999999998 7999999999999854
No 23
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=97.83 E-value=3.1e-05 Score=74.37 Aligned_cols=56 Identities=34% Similarity=0.464 Sum_probs=49.8
Q ss_pred cccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecC
Q 020729 243 IEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG 299 (322)
Q Consensus 243 ~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~G 299 (322)
..+++|||.+|+..+.+||+.+++++++|+|.|||+.++ +++.|++||+|++...-
T Consensus 9 ~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~ 64 (289)
T COG0564 9 EEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPE 64 (289)
T ss_pred hhcCCCHHHHHHHccCcCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEeccc
Confidence 467899999999933499999999999999999999995 99999999999997643
No 24
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=97.71 E-value=6.4e-05 Score=72.20 Aligned_cols=51 Identities=18% Similarity=0.235 Sum_probs=44.6
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEee
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSG 297 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~G--D~IsVrg 297 (322)
++|||+||+.....||+.+.++|++|+|+|||+.+ +++..|.++ |.|.+.|
T Consensus 2 ~~RL~k~La~~g~~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g 54 (289)
T PRK10700 2 SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDG 54 (289)
T ss_pred chhHHHHHHHCCCCCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECC
Confidence 48999999986669999999999999999999988 799999887 5566653
No 25
>PRK11507 ribosome-associated protein; Provisional
Probab=97.59 E-value=0.00021 Score=55.00 Aligned_cols=53 Identities=21% Similarity=0.290 Sum_probs=47.1
Q ss_pred ccHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeec
Q 020729 246 SLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 298 (322)
Q Consensus 246 S~RLD~~Ls~~-~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~ 298 (322)
-.+||.+|... .--|=..|+.+|.+|.|+|||++.+.-..++.+||+|++.|.
T Consensus 11 ~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g~ 64 (70)
T PRK11507 11 HVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH 64 (70)
T ss_pred eEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECCE
Confidence 35699999754 477888999999999999999999999999999999999884
No 26
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.51 E-value=0.00024 Score=63.90 Aligned_cols=53 Identities=17% Similarity=0.267 Sum_probs=45.8
Q ss_pred ccHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEeec
Q 020729 246 SLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSGK 298 (322)
Q Consensus 246 S~RLD~~L-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~G--D~IsVrg~ 298 (322)
..|||.+| ..++--||+.|+++|.+|+|.|||+++++|++.|.++ |.|+.-..
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~ 157 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPT 157 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCC
Confidence 36999986 5667999999999999999999999999999999998 56665443
No 27
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=97.40 E-value=0.00022 Score=54.83 Aligned_cols=60 Identities=25% Similarity=0.339 Sum_probs=42.8
Q ss_pred cCCCchhhHHHHHc-CCCCCCCcccEEEecCCeEEEEechhHHHHHHhccc--eeeceEEEEEE
Q 020729 164 QPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLE--KVGNVSVSCTR 224 (322)
Q Consensus 164 ~~lsHrD~LGaLm~-LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~--kVg~~~V~~~~ 224 (322)
+.++++|++|+|.+ .||.++.||+|-+.+ +.++|-|.++.++-+.+.|. +++.-+|+++.
T Consensus 11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-~~S~vev~~~~a~~v~~~l~~~~~~gk~v~ve~ 73 (74)
T PF03880_consen 11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD-NFSFVEVPEEVAEKVLEALNGKKIKGKKVRVER 73 (74)
T ss_dssp GT--HHHHHHHHHTCTTB-GGGEEEEEE-S-S-EEEEE-TT-HHHHHHHHTT--SSS----EEE
T ss_pred cCCCHHHHHHHHHhccCCCHHhEEEEEEee-eEEEEEECHHHHHHHHHHhcCCCCCCeeEEEEE
Confidence 57899999999999 599999999998865 58999999999999999998 67777776653
No 28
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.35 E-value=3.7e-05 Score=58.36 Aligned_cols=59 Identities=25% Similarity=0.419 Sum_probs=38.7
Q ss_pred ccccHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEE
Q 020729 244 EASLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI 303 (322)
Q Consensus 244 vaS~RLD~~Ls~~-~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i 303 (322)
....+|+.+|... +--|=..|+.+|.+|.|+|||+..+..+.++.+||+|++ ..+.+++
T Consensus 5 ~e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~-~~~~~~V 64 (65)
T PF13275_consen 5 TEYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI-DGEEYRV 64 (65)
T ss_dssp -S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE-TTEEEEE
T ss_pred CCcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE-CCEEEEE
Confidence 3456799999754 455778999999999999999999999999999999999 5555554
No 29
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=97.08 E-value=0.00093 Score=59.32 Aligned_cols=51 Identities=18% Similarity=0.255 Sum_probs=45.1
Q ss_pred ccHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEe
Q 020729 246 SLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVS 296 (322)
Q Consensus 246 S~RLD~~L-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~G--D~IsVr 296 (322)
..|||.++ ..+|--|...|.++|.+|+|.||++.++.|++.|..| |.|+.-
T Consensus 103 eRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 156 (162)
T TIGR01018 103 ERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA 156 (162)
T ss_pred HHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence 47999997 4667999999999999999999999999999999998 776654
No 30
>PLN00189 40S ribosomal protein S9; Provisional
Probab=96.84 E-value=0.00087 Score=61.06 Aligned_cols=53 Identities=19% Similarity=0.149 Sum_probs=47.3
Q ss_pred cHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecC
Q 020729 247 LRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG 299 (322)
Q Consensus 247 ~RLD~~L-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~G 299 (322)
.|||.++ ..+|--|...|.++|.+|+|.|||+.|+.|++.|..||.+.|....
T Consensus 109 RRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 109 RRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred hhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 7899886 4567999999999999999999999999999999999888886654
No 31
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=96.47 E-value=0.0025 Score=57.52 Aligned_cols=50 Identities=18% Similarity=0.130 Sum_probs=43.1
Q ss_pred ccHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 020729 246 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls-~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
..|||.++- .++--|...|.++|.+|+|.|||+.|+.|++.|..||.=-|
T Consensus 106 eRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I 156 (181)
T PTZ00155 106 ERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHI 156 (181)
T ss_pred HHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCce
Confidence 468999975 55688999999999999999999999999999999854333
No 32
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.00 E-value=0.02 Score=44.43 Aligned_cols=54 Identities=28% Similarity=0.425 Sum_probs=46.6
Q ss_pred cHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCe
Q 020729 247 LRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR 300 (322)
Q Consensus 247 ~RLD~~Ls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR 300 (322)
..|+.+|.... --|=..|+.++.+|.|+|||++.+.-..++..||+|.+.+..-
T Consensus 12 I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~~ 66 (73)
T COG2501 12 ITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQRY 66 (73)
T ss_pred EEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECCEEE
Confidence 34899987654 6677899999999999999999988999999999999987643
No 33
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.31 E-value=0.023 Score=52.33 Aligned_cols=86 Identities=23% Similarity=0.193 Sum_probs=67.4
Q ss_pred CceeEeecccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeec-----C-----eEEEEE
Q 020729 236 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK-----G-----RIKIGE 305 (322)
Q Consensus 236 ~~k~~~~~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~-----G-----R~~i~e 305 (322)
+++.+...+.|.|.|.++..+.++.|+++..+.-++..++|+...-+.|..++.||.+-+... | |+-...
T Consensus 129 ~~~~i~~~v~sfr~d~llK~Glgv~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~~ig~~~~~~s~~~~rV~~~t 208 (248)
T KOG4837|consen 129 EKVLIVPEVVSFRVDALLKVGLGVTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADFKIGRSVDLISSKDVRVNWAT 208 (248)
T ss_pred hhhhhhhHHHHHHHHHHHHhccccccchhhHhhhhcccccCcccccccceeeecccccceeeecccccCCcceEEEeeee
Confidence 445566678899999999999999999999999999999999887799999999999877432 1 333344
Q ss_pred e--ecccccceEEEEEEe
Q 020729 306 I--NSTRKGKFAVELIQY 321 (322)
Q Consensus 306 i--~~TKKgR~~i~l~ry 321 (322)
| +.|.-..+.|.+.||
T Consensus 209 V~~~~t~~e~~~Vvlrr~ 226 (248)
T KOG4837|consen 209 VTKNGTIVETGDVVLRRG 226 (248)
T ss_pred ecccceEeecceEEEEec
Confidence 4 246566666766665
No 34
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.26 E-value=0.026 Score=50.95 Aligned_cols=97 Identities=22% Similarity=0.258 Sum_probs=67.8
Q ss_pred hhHHHHHHhccceeeceEEEEEEecCccccC----CCCCcee--Eeec---ccccHHHHHHHhCCCcCHHHHHHHHHCCc
Q 020729 202 PELADYLITSLEKVGNVSVSCTRIPLLALEY----EPPRTKS--FKTI---EASLRVDALASAGFKLSRSKLVNLISNGD 272 (322)
Q Consensus 202 ~ei~~fi~~nl~kVg~~~V~~~~i~~~~l~~----~~~~~k~--~~~~---vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~ 272 (322)
++.+.+...|+.-+++..-.+++.|.-.++. ....++. +.+. -.++|||.+|++.+++||+..+.+|+.|.
T Consensus 85 a~larr~afdla~lRr~~~r~~g~pd~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~LSrS~lq~lie~g~ 164 (203)
T COG4332 85 AALARRFAFDLAILRRNNARLSGFPDFHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGLSRSELQRLIETGQ 164 (203)
T ss_pred HHHHHHHHhhHHHHHhccccccCCCchhhhhheecCcccceeEEEEEcccCcchhHHHHHHHHHhCcCHHHHHHHHHcCc
Confidence 5678888888888888777777665533222 1223332 2222 24799999999999999999999999999
Q ss_pred EEECCEEecCCCcccCCCCEEEEeec
Q 020729 273 VRVNWTTVTKNGTTLRTGDIVSVSGK 298 (322)
Q Consensus 273 V~VNg~~v~~~s~~Vk~GD~IsVrg~ 298 (322)
+..+-.........+..|-.|.|.-.
T Consensus 165 Irgdtd~~~l~rkrlr~~~~i~Id~~ 190 (203)
T COG4332 165 IRGDTDKMLLLRKRLRAGYDIQIDVE 190 (203)
T ss_pred eeecchHHHHhhhhhhcCcEEEEEcC
Confidence 99886544345567777776666543
No 35
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=94.14 E-value=0.065 Score=46.71 Aligned_cols=33 Identities=39% Similarity=0.504 Sum_probs=30.8
Q ss_pred cccHHHHHHHhCCCcCHHHHHHHHHCCcEEECC
Q 020729 245 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNW 277 (322)
Q Consensus 245 aS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg 277 (322)
.+.|||.+|+..+++||+++++++++|.|..+-
T Consensus 101 ~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 101 FPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred CCccHHHHHHHHhCcCHHHHHHHHHCCCEEecC
Confidence 379999999999999999999999999999874
No 36
>PRK04313 30S ribosomal protein S4e; Validated
Probab=92.74 E-value=0.41 Score=45.12 Aligned_cols=63 Identities=19% Similarity=0.220 Sum_probs=51.7
Q ss_pred ccccHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------cCeEEEEEe
Q 020729 244 EASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 306 (322)
Q Consensus 244 vaS~RLD~~Ls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg-----------~GR~~i~ei 306 (322)
..|+-|--+|...+ -.++++|+..+.+|.|+|||++.++..+.+---|+|+|.. +|||.+.+|
T Consensus 35 ~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I 110 (237)
T PRK04313 35 EESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPI 110 (237)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCCCeEEEEECCCCcEEEEEC
Confidence 34566777787765 6688999999999999999999999999988889999943 577776665
No 37
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=92.22 E-value=0.35 Score=46.20 Aligned_cols=63 Identities=21% Similarity=0.197 Sum_probs=51.1
Q ss_pred ccccHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------cCeEEEEEe
Q 020729 244 EASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 306 (322)
Q Consensus 244 vaS~RLD~~Ls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg-----------~GR~~i~ei 306 (322)
..|+-|--+|...+ -.+.++++..+.+|.|+|||++.++..+.+---|+|+|.. +|||.+.+|
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I 114 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKI 114 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEc
Confidence 34566777887766 5577799999999999999999998888888889999954 577776665
No 38
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=92.18 E-value=0.34 Score=46.46 Aligned_cols=63 Identities=16% Similarity=0.191 Sum_probs=51.5
Q ss_pred ccccHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------cCeEEEEEe
Q 020729 244 EASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 306 (322)
Q Consensus 244 vaS~RLD~~Ls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg-----------~GR~~i~ei 306 (322)
..|+-|--+|...+ -.+.++++..+.+|.|+|||++.++..+.+---|+|+|.. +|||.+.+|
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I 111 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKV 111 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEc
Confidence 34566777887766 5577799999999999999999999888888789999954 678777766
No 39
>PLN00036 40S ribosomal protein S4; Provisional
Probab=92.10 E-value=0.37 Score=46.02 Aligned_cols=62 Identities=18% Similarity=0.264 Sum_probs=50.7
Q ss_pred cccHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------cCeEEEEEe
Q 020729 245 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 306 (322)
Q Consensus 245 aS~RLD~~Ls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg-----------~GR~~i~ei 306 (322)
.|+-|--+|...+ -.+.++++..+.+|.|+|||++.++..+.+---|+|+|.. +|||.+.+|
T Consensus 40 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I 114 (261)
T PLN00036 40 ECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRI 114 (261)
T ss_pred cccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCCCCeEEEEECCCceEEEEEc
Confidence 4566777887765 5577799999999999999999998888887779999954 577777666
No 40
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=90.62 E-value=0.85 Score=46.14 Aligned_cols=48 Identities=25% Similarity=0.394 Sum_probs=40.0
Q ss_pred ccHH-HHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 020729 246 SLRV-DALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV 293 (322)
Q Consensus 246 S~RL-D~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~I 293 (322)
++.| |.++..++--|++.|+++|++|-|+|||+.++++.+.+.++|.+
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~l 390 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDAF 390 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhhc
Confidence 3444 44566778999999999999999999999998998888887753
No 41
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=90.29 E-value=1 Score=45.56 Aligned_cols=42 Identities=29% Similarity=0.404 Sum_probs=36.0
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC
Q 020729 249 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG 290 (322)
Q Consensus 249 LD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~G 290 (322)
+|.++..++--|++.|+++|++|-|+|||+.+++.+..+.+.
T Consensus 346 ~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~~ 387 (408)
T PRK05912 346 LALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTAD 387 (408)
T ss_pred HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCcccccccc
Confidence 455566778999999999999999999999998888877763
No 42
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=88.36 E-value=0.49 Score=37.38 Aligned_cols=43 Identities=23% Similarity=0.297 Sum_probs=34.3
Q ss_pred cHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 247 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 247 ~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
-.+-.++.+ +|+...++ |.|.|||+.+ ..++.+++||.|.|.-
T Consensus 33 ~tvkd~IEs-LGVP~tEV------~~i~vNG~~v-~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 33 ATVKDVIES-LGVPHTEV------GLILVNGRPV-DFDYRLKDGDRVAVYP 75 (81)
T ss_pred CcHHHHHHH-cCCChHHe------EEEEECCEEC-CCcccCCCCCEEEEEe
Confidence 346666655 67777665 7899999998 8999999999999853
No 43
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=87.79 E-value=1.4 Score=41.49 Aligned_cols=52 Identities=17% Similarity=0.162 Sum_probs=36.7
Q ss_pred ccHHHHHHHhCCC--cCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 246 SLRVDALASAGFK--LSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 246 S~RLD~~Ls~~~~--~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
|+-|--++...++ -.-++|+..|.+|.|+|||.+.++..+.|--=|+|+|..
T Consensus 40 slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~ 93 (241)
T COG1471 40 SLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK 93 (241)
T ss_pred cccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECC
Confidence 3444444444443 334689999999999999999876666665459999973
No 44
>PRK01777 hypothetical protein; Validated
Probab=83.37 E-value=1.9 Score=35.00 Aligned_cols=57 Identities=19% Similarity=0.145 Sum_probs=38.4
Q ss_pred CceeEeeccc-ccHHHHHHHhCCCcCHH--HHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 020729 236 RTKSFKTIEA-SLRVDALASAGFKLSRS--KLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 296 (322)
Q Consensus 236 ~~k~~~~~va-S~RLD~~Ls~~~~~SRs--~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVr 296 (322)
+++.....+. +.++-..+.+ .++... .+ -+..+.|.|||+.+ +.++.|++||.|+|-
T Consensus 15 ~~~~~~l~vp~GtTv~dal~~-sgi~~~~pei--~~~~~~vgI~Gk~v-~~d~~L~dGDRVeIy 74 (95)
T PRK01777 15 RQYLQRLTLQEGATVEEAIRA-SGLLELRTDI--DLAKNKVGIYSRPA-KLTDVLRDGDRVEIY 74 (95)
T ss_pred ceEEEEEEcCCCCcHHHHHHH-cCCCccCccc--ccccceEEEeCeEC-CCCCcCCCCCEEEEe
Confidence 4444555443 6666666655 244433 22 23468999999998 799999999999873
No 45
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=79.23 E-value=15 Score=27.75 Aligned_cols=51 Identities=12% Similarity=0.049 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCC
Q 020729 78 IEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGG 128 (322)
Q Consensus 78 ~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GG 128 (322)
..+.....++++++..++.+..-+=+|++|..++..++++.+++...+.|-
T Consensus 6 ~~L~~~A~~~a~~v~~tg~~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G~ 56 (67)
T cd02644 6 ETLIRLAERAAEKVRRTGKPVKLEPMNAYERRIIHDALANDEDVETESEGE 56 (67)
T ss_pred HHHHHHHHHHHHHHHHHCCeeEeCCCCHHHHHHHHHHHHhCCCceEEeecC
Confidence 355667778889999999999999999999999999999988898887764
No 46
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=73.25 E-value=3.6 Score=36.81 Aligned_cols=44 Identities=20% Similarity=0.191 Sum_probs=38.0
Q ss_pred ccHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCC
Q 020729 246 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRT 289 (322)
Q Consensus 246 S~RLD~~Ls-~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~ 289 (322)
-+||+..+- .++-.|=..|..+|.++.|.||++++.-||+.|+.
T Consensus 96 ErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 96 ERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 478988864 45578888999999999999999999999999984
No 47
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=72.58 E-value=7.5 Score=39.43 Aligned_cols=40 Identities=38% Similarity=0.474 Sum_probs=35.5
Q ss_pred HHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCccc
Q 020729 248 RVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTL 287 (322)
Q Consensus 248 RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~V 287 (322)
-+|.++...+.-||+.++++|.+|.|++||..+.+.++.+
T Consensus 338 ~~~~lv~~~L~psr~earr~i~~g~v~in~~~v~d~~~~~ 377 (401)
T COG0162 338 LVDLLVDAGLAPSRSEARRLIQQGGVKINGEKVEDENYVL 377 (401)
T ss_pred HHHHHHHhCCcccHHHHHhhcccCCEEECCEeccccccch
Confidence 4677788889999999999999999999999998887665
No 48
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=72.42 E-value=2.6 Score=34.35 Aligned_cols=49 Identities=16% Similarity=0.221 Sum_probs=37.3
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 249 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 249 LD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
|-..+++..++|+..+...++. ..+.....|..||.|+++|+|.|++.+
T Consensus 7 li~~ia~~~~l~k~~a~~~v~~--------~~~~i~~aL~~G~~V~l~gFG~F~v~~ 55 (94)
T COG0776 7 LIDAIAEKAGLSKKDAEEAVDA--------FLEEITEALAKGERVELRGFGTFEVRE 55 (94)
T ss_pred HHHHHHHHcCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEeeeeeeEeec
Confidence 3445666678999999998864 233345678889999999999999965
No 49
>PRK06437 hypothetical protein; Provisional
Probab=69.95 E-value=5.6 Score=29.95 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=31.5
Q ss_pred cccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 020729 245 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 296 (322)
Q Consensus 245 aS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVr 296 (322)
.+..+-.+|.. ++++.+.+ .|.+||+.+ ..++.|++||.|.|-
T Consensus 19 ~~~tv~dLL~~-Lgi~~~~v-------aV~vNg~iv-~~~~~L~dgD~Veiv 61 (67)
T PRK06437 19 HELTVNDIIKD-LGLDEEEY-------VVIVNGSPV-LEDHNVKKEDDVLIL 61 (67)
T ss_pred CCCcHHHHHHH-cCCCCccE-------EEEECCEEC-CCceEcCCCCEEEEE
Confidence 34567777776 45553222 577999999 589999999999873
No 50
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=69.69 E-value=7.9 Score=41.30 Aligned_cols=61 Identities=13% Similarity=0.214 Sum_probs=51.5
Q ss_pred cCCCchhhHHHHHc-CCCCCCCcccEEEecCCeEEEEechhHHHHHHhccce--eeceEEEEEEe
Q 020729 164 QPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEK--VGNVSVSCTRI 225 (322)
Q Consensus 164 ~~lsHrD~LGaLm~-LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~k--Vg~~~V~~~~i 225 (322)
+.++.+|++|+|-+ .||.+..||+|=+.+ +...|=+.+++++-+...|.+ |..-+|.++..
T Consensus 497 ~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~-~~s~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 (629)
T PRK11634 497 DGVEVRHIVGAIANEGDISSRYIGNIKLFA-SHSTIELPKGMPGEVLQHFTRTRILNKPMNMQLL 560 (629)
T ss_pred cCCCHHHHHHHHHhhcCCChhhCCcEEEeC-CceEEEcChhhHHHHHHHhccccccCCceEEEEC
Confidence 56799999999999 999999999998855 588899999999999999976 44566666544
No 51
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=67.50 E-value=21 Score=33.13 Aligned_cols=54 Identities=19% Similarity=0.106 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccce
Q 020729 80 EVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAER 134 (322)
Q Consensus 80 ~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AER 134 (322)
++.=....|++|.++++++..+=|+|+|++++...++..+++.-.+ -|.+..-|
T Consensus 149 L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~~~~~V~T~S-eG~ep~R~ 202 (208)
T COG1847 149 LIKLAERAAERVLETGRSVELEPMPPFERKIVHTALSANPGVETYS-EGEEPNRR 202 (208)
T ss_pred HHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHHhcCCcceee-cCCCCceE
Confidence 3444455678899999999999999999999999999999997765 55555544
No 52
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=66.19 E-value=7.1 Score=29.37 Aligned_cols=28 Identities=32% Similarity=0.442 Sum_probs=23.3
Q ss_pred HHHCCcEEECCEEecCCCcccCCCCEEEE
Q 020729 267 LISNGDVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 267 lI~~G~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
....-.|.|||+.+ ..+..|++||.|.+
T Consensus 46 ~~~~~~v~vNg~~v-~~~~~l~~gD~v~i 73 (80)
T cd00754 46 LLARVRIAVNGEYV-RLDTPLKDGDEVAI 73 (80)
T ss_pred hhhcEEEEECCeEc-CCCcccCCCCEEEE
Confidence 33455799999999 48999999999987
No 53
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=65.40 E-value=12 Score=31.08 Aligned_cols=42 Identities=17% Similarity=0.428 Sum_probs=33.1
Q ss_pred HHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEE
Q 020729 262 SKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG 304 (322)
Q Consensus 262 s~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ 304 (322)
..--++|++|+=+|-++........+++||.|...| +++++.
T Consensus 9 eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~-~~l~v~ 50 (111)
T COG4043 9 EEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG-DKLKVE 50 (111)
T ss_pred HHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC-CeeEEE
Confidence 344578999998888888766778999999999986 555543
No 54
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=65.14 E-value=8.2 Score=29.11 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=32.3
Q ss_pred cccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 020729 245 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 245 aS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
+++.+..+|... +++. +.-.|.+|++.+ ..++.+++||.|.+
T Consensus 22 ~~~tv~~ll~~l-~~~~-------~~v~v~vNg~iv-~~~~~l~~gD~Vei 63 (70)
T PRK08364 22 KGMKVADILRAV-GFNT-------ESAIAKVNGKVA-LEDDPVKDGDYVEV 63 (70)
T ss_pred CCCcHHHHHHHc-CCCC-------ccEEEEECCEEC-CCCcCcCCCCEEEE
Confidence 356688888764 4543 445789999999 68999999999887
No 55
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=64.07 E-value=6.9 Score=28.87 Aligned_cols=41 Identities=22% Similarity=0.236 Sum_probs=28.2
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCC----cccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNG----TTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s----~~Vk~GD~IsV 295 (322)
++.+..++... +++. ..=.|.|||+.+ ..+ +.+++||.|.+
T Consensus 14 ~~tv~~ll~~l-~~~~-------~~i~V~vNg~~v-~~~~~~~~~L~~gD~V~i 58 (65)
T cd00565 14 GATLAELLEEL-GLDP-------RGVAVALNGEIV-PRSEWASTPLQDGDRIEI 58 (65)
T ss_pred CCCHHHHHHHc-CCCC-------CcEEEEECCEEc-CHHHcCceecCCCCEEEE
Confidence 45577777663 4432 111478999998 445 89999999987
No 56
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=61.31 E-value=24 Score=27.00 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=21.6
Q ss_pred CCcEEECCEEecCCCcccCCCCEEEE
Q 020729 270 NGDVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 270 ~G~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
.=.|.||++.+ ..++.|+.||.|.+
T Consensus 51 ~~~vavN~~~v-~~~~~l~dgDeVai 75 (82)
T PLN02799 51 CCVLALNEEYT-TESAALKDGDELAI 75 (82)
T ss_pred CcEEEECCEEc-CCCcCcCCCCEEEE
Confidence 33689999998 68999999999987
No 57
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=58.03 E-value=13 Score=27.27 Aligned_cols=42 Identities=29% Similarity=0.355 Sum_probs=29.0
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec---CCCcccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT---KNGTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~---~~s~~Vk~GD~IsV 295 (322)
++.+-.+|.. +++.. +.-.|.+|++.+. ..++.++.||.|.|
T Consensus 13 ~~tv~~ll~~-l~~~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~vei 57 (64)
T TIGR01683 13 GLTLAALLES-LGLDP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEI 57 (64)
T ss_pred CCcHHHHHHH-cCCCC-------CeEEEEECCEEcCHHHcCceecCCCCEEEE
Confidence 4557777776 34332 3346889999985 33478999999887
No 58
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=56.56 E-value=17 Score=36.57 Aligned_cols=48 Identities=25% Similarity=0.245 Sum_probs=40.5
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729 249 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 297 (322)
Q Consensus 249 LD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg 297 (322)
+|.+.+.-....|..-+..|+.|.|.+||..+ ..++.++.||.+...-
T Consensus 47 ~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~-~v~~i~k~~d~l~~~v 94 (371)
T KOG1919|consen 47 VDVFVSEFRLRERAYYESAIKLGRVTVNGEQV-RVSLIVKNGDVLCHTV 94 (371)
T ss_pred HHHHHHHHhcCchHhhhhhhhcCceEECcEee-eeEEEeccCCEEEEee
Confidence 55556665588888999999999999999998 6999999999998643
No 59
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=56.20 E-value=12 Score=27.48 Aligned_cols=24 Identities=29% Similarity=0.382 Sum_probs=20.1
Q ss_pred CcEEECCEEecCCCcccCCCCEEEE
Q 020729 271 GDVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 271 G~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
-...|||+.+ ..++.++.||+|.|
T Consensus 35 ~~A~Vng~~v-dl~~~L~~~d~v~i 58 (60)
T PF02824_consen 35 VAAKVNGQLV-DLDHPLEDGDVVEI 58 (60)
T ss_dssp EEEEETTEEE-ETTSBB-SSEEEEE
T ss_pred eEEEEcCEEC-CCCCCcCCCCEEEE
Confidence 3577999998 89999999999987
No 60
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=56.17 E-value=13 Score=27.31 Aligned_cols=41 Identities=20% Similarity=0.119 Sum_probs=27.7
Q ss_pred cHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecC---CCcccCCCCEEEE
Q 020729 247 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTK---NGTTLRTGDIVSV 295 (322)
Q Consensus 247 ~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~---~s~~Vk~GD~IsV 295 (322)
..|..++... ++..+ .=.|.+|++.+.+ .++.|++||.|.|
T Consensus 15 ~tl~~Ll~~l-~~~~~-------~vavavN~~iv~~~~~~~~~L~dgD~Iei 58 (65)
T PRK06488 15 TTLALLLAEL-DYEGN-------WLATAVNGELVHKEARAQFVLHEGDRIEI 58 (65)
T ss_pred CcHHHHHHHc-CCCCC-------eEEEEECCEEcCHHHcCccccCCCCEEEE
Confidence 4577777653 33211 1138999999843 3789999999987
No 61
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=55.93 E-value=22 Score=27.40 Aligned_cols=23 Identities=35% Similarity=0.270 Sum_probs=20.1
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 020729 272 DVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
.+.||++.+ ..++.|++||.|.+
T Consensus 52 ~~aVN~~~~-~~~~~l~dgDeVai 74 (81)
T PRK11130 52 LAAVNQTLV-SFDHPLTDGDEVAF 74 (81)
T ss_pred EEEECCEEc-CCCCCCCCCCEEEE
Confidence 488999887 67899999999987
No 62
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=55.86 E-value=9.9 Score=28.26 Aligned_cols=49 Identities=27% Similarity=0.211 Sum_probs=31.2
Q ss_pred ccccHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecC--CCcccCCCCEEEE
Q 020729 244 EASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTK--NGTTLRTGDIVSV 295 (322)
Q Consensus 244 vaS~RLD~~Ls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~--~s~~Vk~GD~IsV 295 (322)
..+..+..++.... ...+-. ....=.|.|||+.+.+ .+..|++||.|.+
T Consensus 19 ~~~~tv~~ll~~l~~~~p~~~---~~~~~~v~vN~~~v~~~~~~~~l~~gD~V~i 70 (77)
T PF02597_consen 19 PEGSTVRDLLEALAERYPELA---LRDRVAVAVNGEIVPDDGLDTPLKDGDEVAI 70 (77)
T ss_dssp SSTSBHHHHHHHHCHHTGGGH---TTTTEEEEETTEEEGGGTTTSBEETTEEEEE
T ss_pred CCCCcHHHHHHHHHhhccccc---cCccEEEEECCEEcCCccCCcCcCCCCEEEE
Confidence 34455666655432 121111 3345579999999954 3899999999987
No 63
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=55.14 E-value=15 Score=28.07 Aligned_cols=23 Identities=35% Similarity=0.338 Sum_probs=20.6
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 020729 272 DVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
.|.||++.+ ..+..|+.||.|.+
T Consensus 51 ~v~vn~~~v-~~~~~l~dgDevai 73 (80)
T TIGR01682 51 MVAVNEEYV-TDDALLNEGDEVAF 73 (80)
T ss_pred EEEECCEEc-CCCcCcCCCCEEEE
Confidence 699999998 46999999999987
No 64
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=53.38 E-value=21 Score=27.54 Aligned_cols=24 Identities=33% Similarity=0.439 Sum_probs=19.4
Q ss_pred CcEEECCEEecCCCc--ccCCCCEEEE
Q 020729 271 GDVRVNWTTVTKNGT--TLRTGDIVSV 295 (322)
Q Consensus 271 G~V~VNg~~v~~~s~--~Vk~GD~IsV 295 (322)
=.|.||++.+ +.+. .++.||.|.+
T Consensus 56 ~~v~vN~~~v-~~~~~~~l~dgdev~i 81 (88)
T TIGR01687 56 VIILVNGRNV-DWGLGTELKDGDVVAI 81 (88)
T ss_pred EEEEECCEec-CccCCCCCCCCCEEEE
Confidence 3589999998 4455 8999999986
No 65
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=53.16 E-value=17 Score=26.51 Aligned_cols=41 Identities=22% Similarity=0.148 Sum_probs=27.8
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCC---CcccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKN---GTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~---s~~Vk~GD~IsV 295 (322)
+..+..++... ++.. .-.|.+|++.+.+. +..|++||.|.|
T Consensus 15 ~~tl~~ll~~l-~~~~--------~~~v~vN~~~v~~~~~~~~~L~~gD~vei 58 (65)
T PRK06944 15 GATVADALAAY-GARP--------PFAVAVNGDFVARTQHAARALAAGDRLDL 58 (65)
T ss_pred CCcHHHHHHhh-CCCC--------CeEEEECCEEcCchhcccccCCCCCEEEE
Confidence 34566777653 3321 13689999998433 678999999987
No 66
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=52.35 E-value=16 Score=27.90 Aligned_cols=41 Identities=29% Similarity=0.293 Sum_probs=28.8
Q ss_pred cHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecC---CCcccCCCCEEEE
Q 020729 247 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTK---NGTTLRTGDIVSV 295 (322)
Q Consensus 247 ~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~---~s~~Vk~GD~IsV 295 (322)
+++-.+|.+. +++- +.=-|.+||.++-+ .++.++.||.|.|
T Consensus 18 ~tv~dLL~~l-~~~~-------~~vav~vNg~iVpr~~~~~~~l~~gD~iev 61 (68)
T COG2104 18 TTVADLLAQL-GLNP-------EGVAVAVNGEIVPRSQWADTILKEGDRIEV 61 (68)
T ss_pred CcHHHHHHHh-CCCC-------ceEEEEECCEEccchhhhhccccCCCEEEE
Confidence 6677777663 2221 12248899999943 7899999999887
No 67
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=51.91 E-value=19 Score=26.32 Aligned_cols=42 Identities=33% Similarity=0.419 Sum_probs=27.7
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec---CCCcccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT---KNGTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~---~~s~~Vk~GD~IsV 295 (322)
++.|-.+|.. +++..+.+ .|.+|+..+. ..++.|++||.|.|
T Consensus 15 ~~tl~~lL~~-l~~~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei 59 (66)
T PRK05659 15 GESVAALLAR-EGLAGRRV-------AVEVNGEIVPRSQHASTALREGDVVEI 59 (66)
T ss_pred CCCHHHHHHh-cCCCCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEE
Confidence 4456666655 33333222 2889998773 36789999999987
No 68
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=51.71 E-value=38 Score=31.17 Aligned_cols=86 Identities=19% Similarity=0.238 Sum_probs=54.7
Q ss_pred cccchhhHHHHHh------hCchHHhhc----------c--CCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHH--H
Q 020729 49 HTASGIRHLIQAV------KGNFDDLLK----------G--VGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPV--L 108 (322)
Q Consensus 49 ~~~~~~~~~~~~~------~~~~~~ll~----------~--~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e--~ 108 (322)
+..+|-+..|.|+ +|-.-.+|. + +.++|-.+-+.|+-+.|..-.+.+-++.+.|.+|+- .
T Consensus 31 LSGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR~gL~~dLgFs~edR~eniRRvaevAkll~daG~iviva~ISP~r~~R 110 (197)
T COG0529 31 LSGSGKSTIANALEEKLFAKGYHVYLLDGDNVRHGLNRDLGFSREDRIENIRRVAEVAKLLADAGLIVIVAFISPYREDR 110 (197)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCeEEEecChhHhhcccCCCCCChHHHHHHHHHHHHHHHHHHHCCeEEEEEeeCccHHHH
Confidence 4678888888887 222112222 1 344454566999999999999999999999999984 3
Q ss_pred HHHHHHhhccCCeEEEEcCCCcccce
Q 020729 109 KESMMALEKLADVKAVAQGGYPQAER 134 (322)
Q Consensus 109 ~~~~~~l~~~~~i~~~~~GGy~~AER 134 (322)
..+..++++-.-+.++..--.+.+|+
T Consensus 111 ~~aR~~~~~~~FiEVyV~~pl~vce~ 136 (197)
T COG0529 111 QMARELLGEGEFIEVYVDTPLEVCER 136 (197)
T ss_pred HHHHHHhCcCceEEEEeCCCHHHHHh
Confidence 34444555433455555444444443
No 69
>PRK07440 hypothetical protein; Provisional
Probab=49.26 E-value=22 Score=26.91 Aligned_cols=42 Identities=14% Similarity=0.096 Sum_probs=28.0
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec---CCCcccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT---KNGTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~---~~s~~Vk~GD~IsV 295 (322)
++.|..+|... +++.+ .=.|.+|++.+. ..++.|++||.|.|
T Consensus 19 ~~tl~~lL~~l-~~~~~-------~vav~~N~~iv~r~~w~~~~L~~gD~IEI 63 (70)
T PRK07440 19 GTSLPDLLQQL-GFNPR-------LVAVEYNGEILHRQFWEQTQVQPGDRLEI 63 (70)
T ss_pred CCCHHHHHHHc-CCCCC-------eEEEEECCEEeCHHHcCceecCCCCEEEE
Confidence 44577777652 33211 125889999983 16789999999887
No 70
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=48.83 E-value=24 Score=26.17 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=19.5
Q ss_pred cEEECCEEec---CCCcccCCCCEEEE
Q 020729 272 DVRVNWTTVT---KNGTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~---~~s~~Vk~GD~IsV 295 (322)
.|.+|++.+. ..++.|++||.|.|
T Consensus 33 aVavN~~iv~r~~w~~~~L~~gD~Iei 59 (66)
T PRK08053 33 ALAINQQIIPREQWAQHIVQDGDQILL 59 (66)
T ss_pred EEEECCEEeChHHcCccccCCCCEEEE
Confidence 4789999985 34568999999987
No 71
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=47.67 E-value=14 Score=29.47 Aligned_cols=47 Identities=21% Similarity=0.340 Sum_probs=35.3
Q ss_pred HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 251 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 251 ~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
..++...++|+..+...++. ........|..|+.|+++|+|.|++.+
T Consensus 8 ~~ia~~~~~s~~~~~~~v~~--------~~~~i~~~L~~~~~v~l~gfG~F~v~~ 54 (90)
T PRK10664 8 DKIAAGADISKAAAGRALDA--------IIASVTESLKEGDDVALVGFGTFAVKE 54 (90)
T ss_pred HHHHHHhCCCHHHHHHHHHH--------HHHHHHHHHhCCCEEEECCcEEEEEEE
Confidence 34556678999999888763 222334578889999999999999964
No 72
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=46.07 E-value=11 Score=31.98 Aligned_cols=39 Identities=28% Similarity=0.509 Sum_probs=34.2
Q ss_pred CcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEEE
Q 020729 184 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCT 223 (322)
Q Consensus 184 kiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~ 223 (322)
+-|+|++ ||++.-++-++...|||+-=++.|-.+.+++.
T Consensus 23 ~yGkimi-GDkaFEFyn~~n~~dyIQIPW~eI~~V~a~V~ 61 (118)
T PF06115_consen 23 KYGKIMI-GDKAFEFYNDRNVEDYIQIPWEEIDYVIASVS 61 (118)
T ss_pred ccCeEEE-cccceEeecCCChhhcEEeChhheeEEEEEEE
Confidence 7899998 77788888889999999999999988877775
No 73
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=44.35 E-value=15 Score=29.12 Aligned_cols=46 Identities=22% Similarity=0.380 Sum_probs=34.9
Q ss_pred HHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 252 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 252 ~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
.++...++|+..++..++. ........|..|+.|.++|+|.|++..
T Consensus 9 ~ia~~~~~s~~~~~~~v~~--------~~~~i~~~L~~g~~V~i~gfG~F~v~~ 54 (90)
T PRK10753 9 VIADKAELSKTQAKAALES--------TLAAITESLKEGDAVQLVGFGTFKVNH 54 (90)
T ss_pred HHHHHhCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEcCCEEEEEee
Confidence 3455578999999888763 222345678889999999999999964
No 74
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=43.25 E-value=20 Score=28.35 Aligned_cols=48 Identities=21% Similarity=0.334 Sum_probs=34.8
Q ss_pred HHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 250 DALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 250 D~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
+.+.+...++|+..+...++. ........|..|+.|.+.|+|.|.+..
T Consensus 8 ~~ia~~~~~~s~~~~~~vv~~--------~~~~i~~~L~~g~~V~l~gfG~F~~~~ 55 (94)
T PRK00199 8 ERLAARNPHLSAKDVENAVKE--------ILEEMSDALARGDRIEIRGFGSFSLHY 55 (94)
T ss_pred HHHHHHcCCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEcCCEEEEEEE
Confidence 333334458899999888763 222345678889999999999999865
No 75
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=42.53 E-value=34 Score=25.41 Aligned_cols=28 Identities=32% Similarity=0.297 Sum_probs=22.4
Q ss_pred CcEEECCEEecCCCcccCCCCEEEEeecC
Q 020729 271 GDVRVNWTTVTKNGTTLRTGDIVSVSGKG 299 (322)
Q Consensus 271 G~V~VNg~~v~~~s~~Vk~GD~IsVrg~G 299 (322)
.-+-+||-++ +.+..+++||.|.+=.+|
T Consensus 30 DI~I~NGF~~-~~d~~L~e~D~v~~IkkG 57 (57)
T PF14453_consen 30 DIVILNGFPT-KEDIELKEGDEVFLIKKG 57 (57)
T ss_pred CEEEEcCccc-CCccccCCCCEEEEEeCC
Confidence 3466799987 789999999999875544
No 76
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=42.28 E-value=79 Score=23.94 Aligned_cols=41 Identities=15% Similarity=-0.049 Sum_probs=33.3
Q ss_pred HHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcC
Q 020729 87 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQG 127 (322)
Q Consensus 87 ~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~G 127 (322)
..-...+.+++..-+=++|+|.+++...+++..++...+.|
T Consensus 10 ~f~~~~~~~r~v~LePM~~~ERkIIH~~Lq~~~~v~T~S~G 50 (62)
T cd02638 10 IFLLSFQRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVG 50 (62)
T ss_pred HHHHhcccCCeEecCCCChHHHHHHHHHHhcCCCceEEEcc
Confidence 34444557789999999999999999999999998777655
No 77
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=42.25 E-value=24 Score=25.54 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=18.8
Q ss_pred CCcEEECCEEecC-CCcccCCCCEEEE
Q 020729 270 NGDVRVNWTTVTK-NGTTLRTGDIVSV 295 (322)
Q Consensus 270 ~G~V~VNg~~v~~-~s~~Vk~GD~IsV 295 (322)
..-++|||+++.. ..+.|+.||+|.+
T Consensus 41 ~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 41 TNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp SS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 4678999999843 2588999999875
No 78
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=40.95 E-value=29 Score=26.02 Aligned_cols=24 Identities=25% Similarity=0.339 Sum_probs=18.9
Q ss_pred cEEECCEEecCC---CcccCCCCEEEE
Q 020729 272 DVRVNWTTVTKN---GTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~~~---s~~Vk~GD~IsV 295 (322)
-|.+|++.+.+. ++.|+.||.|.|
T Consensus 34 av~vN~~iv~r~~w~~~~L~~gD~iEI 60 (67)
T PRK07696 34 VVERNKDILQKDDHTDTSVFDGDQIEI 60 (67)
T ss_pred EEEECCEEeCHHHcCceecCCCCEEEE
Confidence 488999998332 288999999887
No 79
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=40.65 E-value=28 Score=28.00 Aligned_cols=24 Identities=29% Similarity=0.205 Sum_probs=20.2
Q ss_pred cEEECCEEec---CCCcccCCCCEEEE
Q 020729 272 DVRVNWTTVT---KNGTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~---~~s~~Vk~GD~IsV 295 (322)
.|.||++.+. ..++.|+.||.|++
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i 87 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVF 87 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEE
Confidence 6899998863 46799999999987
No 80
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=40.29 E-value=1.4e+02 Score=21.48 Aligned_cols=39 Identities=13% Similarity=0.035 Sum_probs=26.8
Q ss_pred CeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEE
Q 020729 96 EVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS 138 (322)
Q Consensus 96 ~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~ 138 (322)
...+-+ +|+++...+..+.. ..++.-...| ++..|..++
T Consensus 22 ~~~f~p-m~~~~R~~iH~~a~-~~gL~s~S~g--~~~~R~vvv 60 (63)
T PF01424_consen 22 SLEFPP-MNSFERKLIHELAE-YYGLKSKSEG--EGPNRRVVV 60 (63)
T ss_dssp EEEEEC---SHHHHHHHHHHH-HCTEEEEEES--SSSSSEEEE
T ss_pred EEEECC-CCHHHHHHHHHHHH-HCCCEEEEec--CCCCeEEEE
Confidence 555666 99999998887777 6788888876 555665444
No 81
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=36.60 E-value=39 Score=35.54 Aligned_cols=149 Identities=15% Similarity=0.205 Sum_probs=86.2
Q ss_pred EecCCChHHHHHHHHHhhccCCeEEEEcCCCcccce-------eEEEecCCCCCCCCcCceEEEEEecCC-CCcCCCchh
Q 020729 99 HSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAER-------CRLSVGHPEALTSDPDIVAALSITGNF-GFQPCSHGD 170 (322)
Q Consensus 99 ~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AER-------kr~~i~~~~~~~~~~~~i~~l~i~~~~-kF~~lsHrD 170 (322)
.-.||-.-...++...+.+..++.....- |.-.. ..+.+-.|..+++. ..+. +|.-++ +-.=++..+
T Consensus 344 RcGFLGlLHmeiiqERLeREf~ldlI~Ta--PsV~Y~v~~~~g~~~~i~NPs~~P~~-~~I~--~i~EP~v~~~ii~P~e 418 (603)
T COG0481 344 RCGFLGLLHMEIIQERLEREFDLDLITTA--PSVVYKVELTDGEEIEVDNPSDLPDP-NKIE--EIEEPYVKATIITPQE 418 (603)
T ss_pred eehhhhHHHHHHHHHHHHHhhCcceEecC--CceEEEEEEcCCcEEEecChHhCCCh-hhhh--eeeCceeEEEEeCcHH
Confidence 45799998888777777665554443221 11111 12233344433211 1111 121111 112347899
Q ss_pred hHHHHHcCCC-CCCCcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEEEEecCccccCCCCCceeEeecccccHH
Q 020729 171 FLGSILGTGI-AREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRV 249 (322)
Q Consensus 171 ~LGaLm~LGI-~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~i~~~~l~~~~~~~k~~~~~vaS~RL 249 (322)
|||++|.|=. +|....|+-.-+++.+.+...=.+++.+.+=+++.+.++==.-..+.+...+.+.......+-+.+..+
T Consensus 419 ylG~vm~Lcq~kRG~~~~m~yl~~~rv~l~Y~lPl~Eiv~DFfDkLKS~skGYAS~DYe~~~y~~~~lVK~dIlvNge~V 498 (603)
T COG0481 419 YLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPLAEIVFDFFDKLKSISKGYASFDYEFIGYRESDLVKVDILVNGEKV 498 (603)
T ss_pred HHHHHHHHHHHhcCceecceEecCceEEEEEecchHHHHHHHhHhhhccccceeeeccccccccccceEEEEEEecCccc
Confidence 9999999655 677778875556568888888777777766666655443333333444444555566668888899999
Q ss_pred HHH
Q 020729 250 DAL 252 (322)
Q Consensus 250 D~~ 252 (322)
|++
T Consensus 499 DAL 501 (603)
T COG0481 499 DAL 501 (603)
T ss_pred cce
Confidence 987
No 82
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=34.46 E-value=56 Score=22.69 Aligned_cols=23 Identities=39% Similarity=0.527 Sum_probs=19.2
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 020729 272 DVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
.+.+||+.+ +.+..+..||.|.+
T Consensus 36 a~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEE
Confidence 467999998 68899999998765
No 83
>PF07550 DUF1533: Protein of unknown function (DUF1533); InterPro: IPR011432 This domain is found duplicated in proteins of unknown function. The proteins typically also contain leucine-rich repeats.
Probab=34.35 E-value=85 Score=23.26 Aligned_cols=46 Identities=26% Similarity=0.339 Sum_probs=28.1
Q ss_pred CcEEECCEEecCCCcccCCCCEEEEeecCeEEEEEeecccccceEEEEE
Q 020729 271 GDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI 319 (322)
Q Consensus 271 G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei~~TKKgR~~i~l~ 319 (322)
..|.|||... +..++..+...+...|.+.+..-.-.+-|.+.|+|+
T Consensus 9 ~~V~VNg~~y---~~~~~~~~~y~~~~~~~l~i~~~~f~~~G~~~I~I~ 54 (65)
T PF07550_consen 9 TSVTVNGKEY---NKSLKGNDKYSISSKGSLKIKASAFNKDGENTIVIK 54 (65)
T ss_pred CEEEECCEEe---eccccccccEEeccCCcEEEcHHHcCcCCceEEEEE
Confidence 4699999987 333444455666666665554333455666666654
No 84
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=34.31 E-value=34 Score=26.94 Aligned_cols=46 Identities=15% Similarity=0.309 Sum_probs=33.5
Q ss_pred HHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 252 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 252 ~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
+.+...++|+..+...++. ..+.....|..|+.|.+.|+|.|.+..
T Consensus 10 i~~~~~~~s~~~v~~vv~~--------~~~~i~~~L~~g~~V~l~gfG~F~~~~ 55 (94)
T TIGR00988 10 IATQQSHLPAKDVEDAVKT--------MLEHMASALAQGDRIEIRGFGSFSLHY 55 (94)
T ss_pred HHHHcCCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEcCcEEEEEEE
Confidence 3333457899988888763 222345677889999999999999864
No 85
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=33.01 E-value=64 Score=32.33 Aligned_cols=41 Identities=24% Similarity=0.212 Sum_probs=32.6
Q ss_pred cHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCccc
Q 020729 247 LRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTL 287 (322)
Q Consensus 247 ~RLD~~L-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~V 287 (322)
..+..++ ......|++.++.+|++|.|+||+..++..+...
T Consensus 330 ~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~ 371 (377)
T TIGR00234 330 ITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEPIR 371 (377)
T ss_pred cCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchhhh
Confidence 5565565 4556999999999999999999999987665444
No 86
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=29.66 E-value=37 Score=22.39 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=17.4
Q ss_pred HHhCCCcCHHHHHHHHHCCcE
Q 020729 253 ASAGFKLSRSKLVNLISNGDV 273 (322)
Q Consensus 253 Ls~~~~~SRs~a~~lI~~G~V 273 (322)
+++.+++|++.+.+++++|.+
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCC
Confidence 345579999999999999963
No 87
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=29.57 E-value=45 Score=30.08 Aligned_cols=38 Identities=26% Similarity=0.281 Sum_probs=30.9
Q ss_pred CcCHHHHHHHHHCCcEEECCEEecCCCcccCC--CCEEEE
Q 020729 258 KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRT--GDIVSV 295 (322)
Q Consensus 258 ~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~--GD~IsV 295 (322)
--|-+.|..+|++|.|+|.-..+++|++.|.- .|-|+-
T Consensus 119 ~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtW 158 (181)
T KOG4655|consen 119 AESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTW 158 (181)
T ss_pred hhhHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhhh
Confidence 44567899999999999999999999999864 355543
No 88
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=27.77 E-value=41 Score=26.77 Aligned_cols=46 Identities=20% Similarity=0.289 Sum_probs=34.9
Q ss_pred HHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 252 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 252 ~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
.++...++|+..++..+.. ........|..|+.|.+.|+|.|++..
T Consensus 10 ~ia~~~~~s~~~v~~vv~~--------~~~~i~~~L~~g~~V~l~gfG~F~~~~ 55 (96)
T TIGR00987 10 YLFDELGLSKREAKELVEL--------FFEEIRRALENGEQVKLSGFGNFDLRD 55 (96)
T ss_pred HHHHHhCcCHHHHHHHHHH--------HHHHHHHHHHcCCeEEecCCEEEEEEE
Confidence 3556678999999888763 222335578889999999999999865
No 89
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=27.70 E-value=42 Score=25.66 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=35.2
Q ss_pred HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEE
Q 020729 251 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 305 (322)
Q Consensus 251 ~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~e 305 (322)
..++...++|+..++..+.. ........|..|+.|.+.|.|.|.+..
T Consensus 7 ~~ia~~~~~~~~~v~~vl~~--------~~~~i~~~L~~g~~V~l~~~G~F~~~~ 53 (87)
T cd00591 7 EAIAEKTGLSKKDAEAAVDA--------FLDVITEALAKGEKVELPGFGTFEVRE 53 (87)
T ss_pred HHHHHHhCcCHHHHHHHHHH--------HHHHHHHHHhCCCeEEEeCCEEEEEEE
Confidence 44666678999999988653 222344577889999999999999864
No 90
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=27.62 E-value=71 Score=25.27 Aligned_cols=42 Identities=21% Similarity=0.310 Sum_probs=27.5
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecC---CCcccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTK---NGTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~---~s~~Vk~GD~IsV 295 (322)
++.|..+|.. +++..+.+ .|.+|++.+.+ .++.|++||.|.|
T Consensus 33 ~~tl~~LL~~-l~~~~~~v-------AVevNg~iVpr~~w~~t~L~egD~IEI 77 (84)
T PRK06083 33 SSSLAQIIAQ-LSLPELGC-------VFAINNQVVPRSEWQSTVLSSGDAISL 77 (84)
T ss_pred CCcHHHHHHH-cCCCCceE-------EEEECCEEeCHHHcCcccCCCCCEEEE
Confidence 4557777765 33322111 57899999833 3478999999887
No 91
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=27.53 E-value=87 Score=20.83 Aligned_cols=22 Identities=41% Similarity=0.404 Sum_probs=18.3
Q ss_pred EEECCEEecCCCcccCCCCEEEE
Q 020729 273 VRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 273 V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
+.+||+.+ +.++.+..||.|.+
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 56999987 68899999998765
No 92
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=27.28 E-value=43 Score=29.33 Aligned_cols=109 Identities=17% Similarity=0.170 Sum_probs=62.6
Q ss_pred cEEEecCCeEEEEechhHHHHHHhccceeeceEEEE------EEecCcc--ccCCCCCceeEeeccc-ccHHHHHHHhCC
Q 020729 187 DIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSC------TRIPLLA--LEYEPPRTKSFKTIEA-SLRVDALASAGF 257 (322)
Q Consensus 187 DI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~------~~i~~~~--l~~~~~~~k~~~~~va-S~RLD~~Ls~~~ 257 (322)
|+++.....|-++++++-+..+..-+.++...+-.- ..-||.. .....+.|+...+++. +.+|- -..
T Consensus 5 d~ivv~t~DaiLV~~k~~~q~vK~~v~~lk~~~~~E~~~~~~~~rpWG~~~~l~~~~~~~vkri~V~pG~~lS----lq~ 80 (151)
T PF01050_consen 5 DLIVVDTPDAILVADKDRSQDVKEVVEQLKQKGRYEAKEHRRVYRPWGSYEVLDEGEGYKVKRITVNPGKRLS----LQY 80 (151)
T ss_pred CEEEEECCCEEEEECcHHhhhhHHHHHhhhcccccccccceeEecCCcEEEEEEccCCEEEEEEEEcCCCccc----eee
Confidence 666666678999999888887776666654432211 1123321 1123446666666553 45543 333
Q ss_pred CcCHHHHHHHHH-CCcEEECCEEecCCCcccCCCCEEEEeecCeEEEE
Q 020729 258 KLSRSKLVNLIS-NGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG 304 (322)
Q Consensus 258 ~~SRs~a~~lI~-~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ 304 (322)
+.-|+..=-.++ .|.|.+|++.. .+.+||.+.|.-.-+-++.
T Consensus 81 H~~R~E~W~Vv~G~a~v~~~~~~~-----~~~~g~sv~Ip~g~~H~i~ 123 (151)
T PF01050_consen 81 HHHRSEHWTVVSGTAEVTLDDEEF-----TLKEGDSVYIPRGAKHRIE 123 (151)
T ss_pred ecccccEEEEEeCeEEEEECCEEE-----EEcCCCEEEECCCCEEEEE
Confidence 444443333334 56788887764 6888888888665555543
No 93
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=26.85 E-value=2.8e+02 Score=21.00 Aligned_cols=48 Identities=19% Similarity=0.084 Sum_probs=32.4
Q ss_pred HHHHhc-CCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEEe
Q 020729 88 ARRASS-RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSV 139 (322)
Q Consensus 88 ~~~a~~-~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~i 139 (322)
++.+.. .....+.+ ||+++...+..++..+ ++.....|- +..|..++.
T Consensus 29 ~~~v~~~~~~~~~~p-m~~~~R~~iH~~a~~~-~l~s~S~g~--g~~R~vvv~ 77 (79)
T smart00393 29 ARFVKSTKESVELPP-MNSYERKIVHELAEKY-GLESESFGE--GPKRRVVIS 77 (79)
T ss_pred HHHHhccCCeEEcCC-CCHHHHHHHHHHHHHc-CCEEEEEcC--CCCcEEEEE
Confidence 333443 44566666 9999999998888887 888887665 334654443
No 94
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=26.20 E-value=2.8e+02 Score=20.65 Aligned_cols=57 Identities=23% Similarity=0.335 Sum_probs=38.4
Q ss_pred CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEEeecccccceEEE
Q 020729 258 KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVE 317 (322)
Q Consensus 258 ~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei~~TKKgR~~i~ 317 (322)
.++|..|.+++++.. +|.-+-..|..-...=+|+++..++++=-.|..+..|+|.+.
T Consensus 7 ~i~r~~Ae~lL~~~~---~G~FLvR~s~~~~~~~~Lsv~~~~~~~h~~I~~~~~~~~~l~ 63 (84)
T smart00252 7 FISREEAEKLLKNEG---DGDFLVRDSESEPGDYVLSVRVKGKVKHYRIRRNEDGKFYLD 63 (84)
T ss_pred cCCHHHHHHHHhcCC---CcEEEEEcCCCCCCCEEEEEEECCEEEEEEEEECCCCcEEEC
Confidence 789999999998754 666543444332223478999888877666655554777764
No 95
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=26.20 E-value=77 Score=32.48 Aligned_cols=41 Identities=22% Similarity=0.272 Sum_probs=30.9
Q ss_pred ccH-HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcc
Q 020729 246 SLR-VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTT 286 (322)
Q Consensus 246 S~R-LD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~ 286 (322)
++- +|-...+...-|++++..+|.+|.|.+|++.+++.|..
T Consensus 398 ~~s~~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es~~ 439 (467)
T KOG2623|consen 398 GVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVS 439 (467)
T ss_pred CCcHHHHHHHhhcCCCcHHHHHHHHccceeecCccccCchhh
Confidence 444 44445555677888999999999999999999764533
No 96
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=26.14 E-value=52 Score=25.48 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=19.8
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 020729 272 DVRVNWTTVTKNGTTLRTGDIVSV 295 (322)
Q Consensus 272 ~V~VNg~~v~~~s~~Vk~GD~IsV 295 (322)
.+..||+.+ ..++.|+.||+|+|
T Consensus 51 s~~~~gq~V-gl~~~L~d~DvVeI 73 (75)
T cd01666 51 SVKHSPQRV-GLDHVLEDEDVVQI 73 (75)
T ss_pred CCcCCCeEC-CCCCEecCCCEEEE
Confidence 345699998 79999999999987
No 97
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=25.31 E-value=49 Score=24.48 Aligned_cols=42 Identities=26% Similarity=0.471 Sum_probs=26.8
Q ss_pred ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEe--cCCCcccCCCCEEEE
Q 020729 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTV--TKNGTTLRTGDIVSV 295 (322)
Q Consensus 246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v--~~~s~~Vk~GD~IsV 295 (322)
++.|-.+|.. +++....+ .|.+|+..+ .+.+..|++||.|.|
T Consensus 15 ~~tl~~ll~~-l~~~~~~v-------av~~N~~iv~r~~~~~~L~~gD~ieI 58 (65)
T PRK05863 15 QTTVAALLDS-LGFPEKGI-------AVAVDWSVLPRSDWATKLRDGARLEV 58 (65)
T ss_pred CCcHHHHHHH-cCCCCCcE-------EEEECCcCcChhHhhhhcCCCCEEEE
Confidence 4557777766 34432222 578899854 334456999999987
No 98
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=25.00 E-value=2e+02 Score=21.36 Aligned_cols=41 Identities=15% Similarity=0.101 Sum_probs=30.2
Q ss_pred cCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeE
Q 020729 93 SRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCR 136 (322)
Q Consensus 93 ~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr 136 (322)
......+.+-||+.|.+.+..+..+ .+++....|- +.+|..
T Consensus 16 ~~~~l~f~p~lt~~eR~~vH~~a~~-~gL~s~S~G~--g~~R~v 56 (60)
T cd02640 16 DIRDMVFSPEFSKEERALIHQIAQK-YGLKSRSYGS--GNDRYL 56 (60)
T ss_pred ccceEEcCCCCCHHHHHHHHHHHHH-cCCceeeEeC--CCCeEE
Confidence 3668889999999999998877766 4677776664 335643
No 99
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=24.98 E-value=1.6e+02 Score=21.98 Aligned_cols=35 Identities=20% Similarity=0.419 Sum_probs=19.4
Q ss_pred cCCCCEEEEee----------cCeEEEEEeecccccceEEEEEEe
Q 020729 287 LRTGDIVSVSG----------KGRIKIGEINSTRKGKFAVELIQY 321 (322)
Q Consensus 287 Vk~GD~IsVrg----------~GR~~i~ei~~TKKgR~~i~l~ry 321 (322)
+++||+|.+.. .|+-.+..--.+..|++.|++.+.
T Consensus 29 L~~Gdvi~l~~~~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~ 73 (77)
T PF01052_consen 29 LKVGDVIPLDKPADEPVELRVNGQPIFRGELGRVNGRLAVRITEL 73 (77)
T ss_dssp --TT-EEEECCESSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE
T ss_pred CCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 45555555544 455444332247788999988765
No 100
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=24.69 E-value=46 Score=34.90 Aligned_cols=67 Identities=21% Similarity=0.207 Sum_probs=53.4
Q ss_pred ccccHHHHHHHhCCCcCHHHHHHHHH---CCcEEECCEEecCCCcccCCCCEEEEeec--CeEEEEEeeccc
Q 020729 244 EASLRVDALASAGFKLSRSKLVNLIS---NGDVRVNWTTVTKNGTTLRTGDIVSVSGK--GRIKIGEINSTR 310 (322)
Q Consensus 244 vaS~RLD~~Ls~~~~~SRs~a~~lI~---~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~--GR~~i~ei~~TK 310 (322)
+.+.-||-+|.+---+|-+.|+..|. +-.+.+|....---.|-++||.++-+.|. |-++|...|.+|
T Consensus 550 ceGNDLDFYLKQhklmSEKEARSIiMQiVnAL~YLNEikpPIIHYDLKPgNILLv~GtacGeIKITDFGLSK 621 (775)
T KOG1151|consen 550 CEGNDLDFYLKQHKLMSEKEARSIIMQIVNALKYLNEIKPPIIHYDLKPGNILLVNGTACGEIKITDFGLSK 621 (775)
T ss_pred cCCCchhHHHHhhhhhhHHHHHHHHHHHHHHHHHHhccCCCeeeeccCCccEEEecCcccceeEeeecchhh
Confidence 56788999999988899999888876 56788886543345799999999999886 888887776544
No 101
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=24.55 E-value=59 Score=25.03 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=35.5
Q ss_pred HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEEe
Q 020729 251 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 306 (322)
Q Consensus 251 ~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei 306 (322)
..+++..++|+..+...++. ..+.....|..|..|.+.|.|.|.+..-
T Consensus 8 ~~ia~~~~~~~~~v~~vl~~--------l~~~i~~~L~~g~~V~i~g~G~F~~~~~ 55 (90)
T smart00411 8 DAIAEKAGLSKKDAKAAVDA--------FLEIITEALKKGEKVELRGFGTFEVRER 55 (90)
T ss_pred HHHHHHhCCCHHHHHHHHHH--------HHHHHHHHHhCCCeEEEeCcEEEEEEee
Confidence 34566678999999888763 2223455777899999999999998643
No 102
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=24.17 E-value=1.5e+02 Score=22.02 Aligned_cols=36 Identities=19% Similarity=0.272 Sum_probs=27.1
Q ss_pred CCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCc
Q 020729 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYP 130 (322)
Q Consensus 94 ~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~ 130 (322)
.+...+..-|+|.|..++..+..++ ++...+.|+.+
T Consensus 17 ~~eL~Fp~~ls~~eRriih~la~~l-GL~~~s~G~g~ 52 (60)
T cd02639 17 RDELAFPSSLSPAERRIVHLLASRL-GLNHVSDGTGE 52 (60)
T ss_pred ceEEEcCCCCCHHHHHHHHHHHHHc-CCceEEeCCCc
Confidence 4577788889999999877666665 66677778753
No 103
>KOG4469 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.98 E-value=14 Score=35.03 Aligned_cols=44 Identities=25% Similarity=0.385 Sum_probs=32.7
Q ss_pred cCCCCcccccCCCCcccccccccccCcccccccchhhHHHHHhhC
Q 020729 19 FSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKG 63 (322)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (322)
....|.+|--.+.||.|+|.+.+++|.|+. ..+|.|.+...+|-
T Consensus 279 psvshvtharhqesclhttrtsfslpipls-stpgfctaivslkw 322 (391)
T KOG4469|consen 279 PSVSHVTHARHQESCLHTTRTSFSLPIPLS-STPGFCTAIVSLKW 322 (391)
T ss_pred CcchhhhhhhhhhhhhhcccceeeeccccC-CCCccEeeEeeeee
Confidence 344455555668899999999999998863 45788988776654
No 104
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=23.09 E-value=3.2e+02 Score=20.24 Aligned_cols=50 Identities=8% Similarity=0.028 Sum_probs=37.2
Q ss_pred HHHHHHHHHhcCC-CeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCccccee
Q 020729 83 HILEMARRASSRR-EVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERC 135 (322)
Q Consensus 83 ~l~d~~~~a~~~~-~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERk 135 (322)
.....++++...+ .++--.=++|++.+++..++++. ++.....|- +..|.
T Consensus 5 ea~~aa~~V~~~~~~~veL~Pm~~~eRri~H~~v~~~-~l~s~S~G~--ep~Rr 55 (60)
T cd02645 5 EARLAIEQVVIPKGEPVELLPRSAYIRRLQHDLVERY-QLRSESFGS--EPNRR 55 (60)
T ss_pred HHHHHHHHHHhcCCceEEcCCCCHHHHHHHHHHHHHC-CCeEEEecC--CCCcE
Confidence 3445666777777 88888999999999999988874 787777663 34453
No 105
>PRK08433 flagellar motor switch protein; Validated
Probab=22.59 E-value=2e+02 Score=24.11 Aligned_cols=32 Identities=19% Similarity=0.167 Sum_probs=20.4
Q ss_pred CCEEEEeecCeEEEEEeecccccceEEEEEEe
Q 020729 290 GDIVSVSGKGRIKIGEINSTRKGKFAVELIQY 321 (322)
Q Consensus 290 GD~IsVrg~GR~~i~ei~~TKKgR~~i~l~ry 321 (322)
+|-+.+.-.|+-++...-.+.+|++.|.+...
T Consensus 66 ~e~v~v~V~g~~~f~G~~G~~~~k~AVrI~e~ 97 (111)
T PRK08433 66 GESVELYINGRIIGKGEVMVYEKNLAIRINEI 97 (111)
T ss_pred CCCEEEEECCEEEEEEEEEEECCEEEEEEEEe
Confidence 34455555677776544345578999888764
No 106
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=22.56 E-value=2.6e+02 Score=20.64 Aligned_cols=41 Identities=17% Similarity=0.028 Sum_probs=30.1
Q ss_pred CCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEE
Q 020729 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (322)
Q Consensus 94 ~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~ 137 (322)
.....+.+=||+.|.+.+..+..+ .++.....|- +.+|..+
T Consensus 16 ~~~l~Fpp~ls~~eR~~vH~~a~~-~gL~s~S~G~--g~~R~v~ 56 (59)
T cd06007 16 NEEYEFPSSLTNHERAVIHRLCRK-LGLKSKSKGK--GSNRRLS 56 (59)
T ss_pred ccEEEcCCCCCHHHHHHHHHHHHH-cCCCceeecC--CCCeEEE
Confidence 667888889999999988877766 4677776665 3366443
No 107
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=22.44 E-value=1.6e+02 Score=24.42 Aligned_cols=36 Identities=19% Similarity=0.206 Sum_probs=29.8
Q ss_pred cEEECCEEecCCCcccCCCCEEEEeecCeEEEEEee
Q 020729 272 DVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEIN 307 (322)
Q Consensus 272 ~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei~ 307 (322)
+|.|||....+-.+.+...++-.|.-.|-+.+..+.
T Consensus 91 ~i~vng~~~~~f~~R~~~~~i~~l~v~Gdv~l~~v~ 126 (128)
T smart00276 91 QIFVNGVHITTFPHRLPLESIDYLSINGDVQLTSVS 126 (128)
T ss_pred EEEECCEeEEEecCCCCcccEeEEEEeCCEEEEEEE
Confidence 599999998888888888777788888888887764
No 108
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=20.70 E-value=74 Score=25.30 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=34.7
Q ss_pred HHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEEEe
Q 020729 253 ASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 306 (322)
Q Consensus 253 Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~ei 306 (322)
++...++|+..+...++. ........|..|+.|.+.|+|.|++..-
T Consensus 12 ia~~~~~s~~~v~~vl~~--------~~~~i~~~L~~g~~V~l~gfG~F~~~~~ 57 (99)
T PRK00285 12 LFEKVGLSKREAKELVEL--------FFEEIRDALENGEQVKLSGFGNFQLRDK 57 (99)
T ss_pred HHHHhCcCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEcCCEEEEEEEE
Confidence 445578999988887763 2233456788999999999999998643
Done!