Query 026574
Match_columns 236
No_of_seqs 253 out of 1633
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 09:47:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026574.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026574hhsearch_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 5.9E-74 1.3E-78 507.2 24.6 236 1-236 32-267 (267)
2 TIGR03069 PS_II_S4 photosystem 100.0 5.1E-71 1.1E-75 487.1 23.8 234 1-234 22-257 (257)
3 COG2302 Uncharacterized conser 100.0 7E-70 1.5E-74 468.8 22.0 232 2-236 23-257 (257)
4 KOG4837 Uncharacterized conser 99.8 2.2E-21 4.8E-26 163.1 -0.9 213 1-233 35-247 (248)
5 TIGR01017 rpsD_bact ribosomal 99.3 1.5E-12 3.3E-17 111.3 5.2 86 109-213 57-143 (200)
6 PRK05327 rpsD 30S ribosomal pr 99.3 2.4E-12 5.1E-17 110.4 3.9 87 109-214 60-147 (203)
7 PF01479 S4: S4 domain; Inter 99.2 3.8E-11 8.3E-16 79.4 5.9 47 161-207 1-48 (48)
8 TIGR02988 YaaA_near_RecF S4 do 99.1 1.6E-10 3.5E-15 79.9 6.9 51 158-209 6-58 (59)
9 COG1188 Ribosome-associated he 99.0 2.3E-09 5E-14 81.5 7.2 61 159-220 7-68 (100)
10 PRK10348 ribosome-associated h 98.8 2.1E-08 4.5E-13 80.4 8.8 67 159-226 7-76 (133)
11 CHL00113 rps4 ribosomal protei 98.6 7.5E-08 1.6E-12 82.5 6.8 55 160-214 88-143 (201)
12 smart00363 S4 S4 RNA-binding d 98.6 1.1E-07 2.3E-12 63.6 6.3 51 161-211 1-52 (60)
13 cd00165 S4 S4/Hsp/ tRNA synthe 98.6 1.2E-07 2.7E-12 65.1 6.2 52 161-212 1-53 (70)
14 COG0522 RpsD Ribosomal protein 98.4 3.4E-07 7.5E-12 78.6 6.1 59 159-217 92-151 (205)
15 PRK10475 23S rRNA pseudouridin 98.3 1.5E-06 3.2E-11 78.4 6.5 54 157-211 3-56 (290)
16 TIGR00478 tly hemolysin TlyA f 98.3 1.2E-06 2.7E-11 76.4 5.8 52 162-213 1-53 (228)
17 PRK10839 16S rRNA pseudouridyl 98.3 1.6E-06 3.4E-11 75.4 6.3 51 161-211 1-51 (232)
18 TIGR00005 rluA_subfam pseudour 98.2 3.7E-06 8.1E-11 75.5 6.7 55 158-212 3-58 (299)
19 PRK11180 rluD 23S rRNA pseudou 98.1 5.7E-06 1.2E-10 75.5 6.9 56 157-212 14-70 (325)
20 COG1187 RsuA 16S rRNA uridine- 98.0 8.5E-06 1.8E-10 71.9 6.1 53 160-212 2-55 (248)
21 PRK11025 23S rRNA pseudouridyl 98.0 1.9E-05 4E-10 72.0 7.1 54 157-211 16-70 (317)
22 COG1189 Predicted rRNA methyla 98.0 1.4E-05 3E-10 70.0 5.8 52 160-211 2-54 (245)
23 COG0564 RluA Pseudouridylate s 97.9 1.7E-05 3.8E-10 71.5 6.3 55 157-212 9-63 (289)
24 PRK10700 23S rRNA pseudouridyl 97.9 3.1E-05 6.7E-10 69.8 6.3 51 160-211 2-54 (289)
25 PRK11507 ribosome-associated p 97.8 6.6E-05 1.4E-09 53.8 5.7 52 161-212 12-64 (70)
26 PRK04051 rps4p 30S ribosomal p 97.8 6.2E-05 1.3E-09 63.3 6.5 53 160-212 102-157 (177)
27 PF03880 DbpA: DbpA RNA bindin 97.8 4.5E-05 9.7E-10 55.0 4.6 62 76-138 9-73 (74)
28 PF13275 S4_2: S4 domain; PDB: 97.6 2.2E-05 4.9E-10 55.5 0.5 58 159-217 6-64 (65)
29 TIGR01018 rpsD_arch ribosomal 97.4 0.00027 5.8E-09 58.7 5.5 51 160-210 103-156 (162)
30 PLN00189 40S ribosomal protein 97.2 0.00023 5E-09 60.6 3.0 54 160-213 108-162 (194)
31 PTZ00155 40S ribosomal protein 97.0 0.00066 1.4E-08 57.3 3.7 51 160-210 106-157 (181)
32 COG2501 S4-like RNA binding pr 96.7 0.0066 1.4E-07 43.8 6.0 53 161-213 12-65 (73)
33 COG4332 Uncharacterized protei 95.9 0.013 2.9E-07 49.2 5.0 96 116-211 85-189 (203)
34 PF06353 DUF1062: Protein of u 95.8 0.015 3.3E-07 47.3 4.7 33 160-192 102-134 (142)
35 KOG4837 Uncharacterized conser 95.5 0.021 4.6E-07 49.0 4.5 86 150-235 129-226 (248)
36 PRK13354 tyrosyl-tRNA syntheta 94.0 0.16 3.5E-06 48.1 6.9 45 163-207 346-390 (410)
37 PRK04313 30S ribosomal protein 93.7 0.2 4.3E-06 44.1 6.3 62 159-220 36-110 (237)
38 PTZ00223 40S ribosomal protein 93.0 0.26 5.7E-06 44.2 6.2 62 159-220 37-111 (273)
39 PLN00036 40S ribosomal protein 93.0 0.28 6.1E-06 43.7 6.3 62 159-220 40-114 (261)
40 PTZ00118 40S ribosomal protein 93.0 0.28 6E-06 43.8 6.2 62 159-220 40-114 (262)
41 PRK05912 tyrosyl-tRNA syntheta 92.7 0.45 9.8E-06 45.0 7.7 42 163-204 346-387 (408)
42 PF14451 Ub-Mut7C: Mut7-C ubiq 91.5 0.21 4.5E-06 36.8 3.1 44 160-211 32-75 (81)
43 COG1471 RPS4A Ribosomal protei 90.1 0.88 1.9E-05 39.9 6.1 52 160-211 40-93 (241)
44 PRK01777 hypothetical protein; 88.3 1.1 2.3E-05 34.0 4.8 59 150-210 15-74 (95)
45 COG0776 HimA Bacterial nucleoi 84.9 0.59 1.3E-05 35.4 1.8 47 165-219 9-55 (94)
46 KOG3301 Ribosomal protein S4 [ 82.3 1.6 3.5E-05 36.3 3.4 44 160-203 96-140 (183)
47 COG4043 Preprotein translocase 78.3 3.3 7.1E-05 31.8 3.7 41 176-217 9-49 (111)
48 COG0162 TyrS Tyrosyl-tRNA synt 78.2 6.6 0.00014 37.3 6.5 40 162-201 338-377 (401)
49 PRK06437 hypothetical protein; 76.9 3.3 7.2E-05 29.0 3.2 43 159-210 19-61 (67)
50 PRK11634 ATP-dependent RNA hel 76.3 4.8 0.0001 40.3 5.3 72 66-139 486-560 (629)
51 cd00754 MoaD Ubiquitin domain 74.7 3.9 8.5E-05 28.8 3.2 27 182-209 47-73 (80)
52 PRK08364 sulfur carrier protei 73.5 4.7 0.0001 28.3 3.3 41 160-209 23-63 (70)
53 PRK10664 transcriptional regul 72.6 2.5 5.5E-05 31.4 1.8 46 166-219 9-54 (90)
54 cd00565 ThiS ThiaminS ubiquiti 72.3 4 8.6E-05 28.1 2.7 42 160-210 14-59 (65)
55 cd02644 R3H_jag R3H domain fou 71.3 14 0.0003 26.0 5.3 42 1-42 15-56 (67)
56 PRK10753 transcriptional regul 69.1 3.1 6.8E-05 30.9 1.6 45 167-219 10-54 (90)
57 PRK11130 moaD molybdopterin sy 68.2 12 0.00026 26.9 4.5 23 186-209 52-74 (81)
58 PLN02799 Molybdopterin synthas 67.9 17 0.00037 25.9 5.4 25 184-209 51-75 (82)
59 TIGR01687 moaD_arch MoaD famil 66.6 12 0.00026 27.1 4.3 24 185-209 56-81 (88)
60 PF02597 ThiS: ThiS family; I 66.3 5.1 0.00011 27.9 2.3 49 158-209 19-70 (77)
61 TIGR01683 thiS thiamine biosyn 66.1 8.5 0.00018 26.4 3.3 42 160-209 13-57 (64)
62 PRK06488 sulfur carrier protei 65.3 8 0.00017 26.5 3.0 25 186-210 32-59 (65)
63 TIGR01682 moaD molybdopterin c 65.2 8.6 0.00019 27.4 3.3 23 186-209 51-73 (80)
64 PRK00199 ihfB integration host 64.7 5.4 0.00012 29.6 2.2 48 164-219 8-55 (94)
65 PRK06944 sulfur carrier protei 62.5 10 0.00022 25.8 3.2 41 160-209 15-58 (65)
66 KOG1919 RNA pseudouridylate sy 61.9 13 0.00028 34.9 4.6 48 163-211 47-94 (371)
67 PF04225 OapA: Opacity-associa 60.7 39 0.00084 24.8 6.1 54 159-220 9-64 (85)
68 PF02824 TGS: TGS domain; Int 60.6 9.8 0.00021 25.9 2.7 34 172-209 25-58 (60)
69 COG2104 ThiS Sulfur transfer p 60.0 11 0.00024 26.7 2.9 41 161-209 18-61 (68)
70 PRK05659 sulfur carrier protei 59.6 13 0.00029 25.3 3.3 43 160-210 15-60 (66)
71 PF14453 ThiS-like: ThiS-like 57.1 16 0.00035 25.1 3.3 28 185-213 30-57 (57)
72 PRK08053 sulfur carrier protei 56.9 16 0.00035 25.2 3.4 24 186-209 33-59 (66)
73 PRK07440 hypothetical protein; 56.3 16 0.00035 25.7 3.3 42 160-209 19-63 (70)
74 TIGR00988 hip integration host 54.9 10 0.00022 28.0 2.2 48 164-219 8-55 (94)
75 PRK00285 ihfA integration host 54.7 8.1 0.00018 28.9 1.6 46 167-220 12-57 (99)
76 PF00498 FHA: FHA domain; Int 54.4 12 0.00026 25.3 2.4 26 184-209 41-67 (68)
77 TIGR00987 himA integration hos 51.7 9.7 0.00021 28.4 1.7 46 166-219 10-55 (96)
78 cd01764 Urm1 Urm1-like ubuitin 50.8 17 0.00036 27.3 2.8 24 186-209 61-87 (94)
79 cd00591 HU_IHF Integration hos 49.3 12 0.00027 26.8 1.9 47 165-219 7-53 (87)
80 PRK07696 sulfur carrier protei 46.6 22 0.00049 24.7 2.8 23 186-209 34-60 (67)
81 smart00411 BHL bacterial (prok 46.5 14 0.00031 26.7 1.8 47 166-220 9-55 (90)
82 PF06115 DUF956: Domain of unk 44.2 12 0.00027 29.4 1.2 39 98-137 23-61 (118)
83 PRK10377 PTS system glucitol/s 42.8 38 0.00083 26.7 3.8 43 98-143 53-95 (120)
84 TIGR01764 excise DNA binding d 42.8 18 0.00038 22.4 1.6 21 167-187 7-27 (49)
85 TIGR00234 tyrS tyrosyl-tRNA sy 42.4 40 0.00086 31.6 4.5 41 161-201 330-371 (377)
86 TIGR00849 gutA PTS system, glu 42.1 40 0.00087 26.6 3.8 41 98-141 53-93 (121)
87 cd01668 TGS_RelA_SpoT TGS_RelA 41.2 42 0.0009 21.8 3.4 23 186-209 36-58 (60)
88 PF07550 DUF1533: Protein of u 40.3 70 0.0015 22.0 4.5 46 185-233 9-54 (65)
89 TIGR01201 HU_rel DNA-binding p 39.0 29 0.00063 28.0 2.7 61 150-218 20-83 (145)
90 KOG2623 Tyrosyl-tRNA synthetas 38.4 39 0.00084 32.3 3.7 39 163-201 402-440 (467)
91 cd02638 R3H_unknown_1 R3H doma 36.9 84 0.0018 22.0 4.3 35 7-41 16-50 (62)
92 PF00216 Bac_DNA_binding: Bact 35.5 10 0.00023 27.3 -0.4 48 165-220 8-55 (90)
93 cd02639 R3H_RRM R3H domain of 35.0 97 0.0021 21.3 4.4 36 8-44 17-52 (60)
94 COG0481 LepA Membrane GTPase L 34.7 48 0.001 32.6 3.8 84 80-166 414-501 (603)
95 cd01666 TGS_DRG_C TGS_DRG_C: 34.3 33 0.00072 24.7 2.1 23 186-209 51-73 (75)
96 PF12728 HTH_17: Helix-turn-he 33.2 30 0.00066 22.1 1.6 21 167-187 7-27 (51)
97 cd04762 HTH_MerR-trunc Helix-T 30.5 36 0.00078 20.7 1.6 22 167-188 6-27 (49)
98 PF01050 MannoseP_isomer: Mann 29.0 57 0.0012 26.6 2.9 109 101-218 5-123 (151)
99 KOG4655 U3 small nucleolar rib 29.0 48 0.001 27.8 2.4 32 172-203 119-150 (181)
100 cd01616 TGS The TGS domain, na 28.9 87 0.0019 19.4 3.3 22 187-209 37-58 (60)
101 PF02563 Poly_export: Polysacc 28.0 45 0.00097 23.9 1.9 22 196-217 8-29 (82)
102 PRK05863 sulfur carrier protei 27.9 42 0.00092 23.0 1.7 42 160-209 15-58 (65)
103 cd06555 ASCH_PF0470_like ASC-1 27.8 1.3E+02 0.0029 23.2 4.6 34 179-212 10-43 (109)
104 KOG1151 Tousled-like protein k 27.5 38 0.00083 33.1 1.8 75 150-224 542-621 (775)
105 cd04867 TGS_YchF_C TGS_YchF_C: 27.1 41 0.00089 24.9 1.6 39 161-210 44-82 (83)
106 cd02645 R3H_AAA R3H domain of 26.9 1.5E+02 0.0033 20.3 4.3 40 2-42 10-50 (60)
107 PRK11092 bifunctional (p)ppGpp 26.8 62 0.0013 33.0 3.3 24 186-210 423-446 (702)
108 PRK06083 sulfur carrier protei 26.3 53 0.0012 24.1 2.1 42 160-209 33-77 (84)
109 PF01424 R3H: R3H domain; Int 24.7 2.1E+02 0.0044 19.1 4.7 39 10-52 22-60 (63)
110 PF01052 SpoA: Surface present 23.6 2.1E+02 0.0045 19.9 4.7 31 205-235 43-73 (77)
111 cd01669 TGS_Ygr210_C TGS_Ygr21 23.2 86 0.0019 22.5 2.6 19 190-209 56-74 (76)
112 smart00393 R3H Putative single 22.9 2.7E+02 0.0059 19.6 5.3 41 8-52 36-76 (79)
113 PF14478 DUF4430: Domain of un 22.4 99 0.0022 21.3 2.8 25 186-210 42-68 (68)
114 PF03829 PTSIIA_gutA: PTS syst 22.2 49 0.0011 25.9 1.2 40 98-140 53-92 (117)
115 smart00276 GLECT Galectin. Gal 21.8 1.9E+02 0.004 22.3 4.5 36 186-221 91-126 (128)
116 cd06919 Asp_decarbox Aspartate 21.7 67 0.0015 25.1 1.9 29 184-216 65-93 (111)
117 PF01356 A_amylase_inhib: Alph 21.6 38 0.00083 24.0 0.5 22 190-213 35-56 (68)
118 cd04487 RecJ_OBF2_like RecJ_OB 21.4 1.7E+02 0.0036 20.7 3.8 30 197-234 40-69 (73)
119 smart00252 SH2 Src homology 2 20.7 3E+02 0.0065 19.0 7.1 57 172-231 7-63 (84)
120 cd00060 FHA Forkhead associate 20.1 1.8E+02 0.0039 20.5 3.9 27 185-211 66-93 (102)
No 1
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=100.00 E-value=5.9e-74 Score=507.25 Aligned_cols=236 Identities=74% Similarity=1.162 Sum_probs=221.9
Q ss_pred ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCCCccceEEEEeecCCCccCC
Q 026574 1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPC 80 (236)
Q Consensus 1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~~~~~i~~l~i~~~~kf~~l 80 (236)
++++|+++|.+++|+||||+++.++.+++++++++++.++|||++|||+|++|+|+++.+.+.+|+++++|++++||.+|
T Consensus 32 ~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~~p~~~~~~~~f~i~~l~i~~~~kF~~l 111 (267)
T PLN00051 32 MAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEVLTSQPDIVAALSVSGNFMFDPA 111 (267)
T ss_pred HHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEEechHhccccCCcEEEEEEEcccCCCCC
Confidence 47899999999999999999999999999888899999999999999999999855444233369999999999999999
Q ss_pred CccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccc
Q 026574 81 SHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEAS 160 (236)
Q Consensus 81 ~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s 160 (236)
+|||||||||||||+|+++|||++.++++||++|+++|++||++||+|||+++|++++++++++.+|+++|++++.+++|
T Consensus 112 ~HrD~LGaLm~LGIkRe~iGDIlv~~~~~~~v~v~~~i~~fi~~nl~kIg~~~V~~~~~~~~~~~~~~~~~~e~~~~vas 191 (267)
T PLN00051 112 SHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVPVECRAIPLSALEVEPPRVESFKSVEAS 191 (267)
T ss_pred CHHHHHHHHHHcCCcHhhcCCEEEcCCCcEEEEEcHHHHHHHHHHhhhccceeEEEEEecHHHcCCCccceEEccCCcCc
Confidence 99999999999999999999999855546999999999999999999999999999999999988888899999999999
Q ss_pred hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEEEeC
Q 026574 161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236 (236)
Q Consensus 161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~r~~ 236 (236)
+|||++++..+++||++++++|++|+|+|||+.+++|++.|++||+|||||+|||++.+++.|||||++|++++|+
T Consensus 192 ~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~GR~~i~~~~~TKKgr~~i~i~ky~ 267 (267)
T PLN00051 192 LRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGRLEVGEINTTKKGKFAVELIRYL 267 (267)
T ss_pred ccHHHHHHHHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeCCEEEEEEEecccCCcEEEEEEecC
Confidence 9999999999999999999999999999999999999999999999999999999999988999999999999985
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=5.1e-71 Score=487.13 Aligned_cols=234 Identities=47% Similarity=0.759 Sum_probs=216.8
Q ss_pred ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCCC-ccceEEEEeecCCCccC
Q 026574 1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSD-PDIVAALSITGNFGFQP 79 (236)
Q Consensus 1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~~-~~~i~~l~i~~~~kf~~ 79 (236)
++++|+++|.+.+|+||||+|+.++.+++++.+++++.+||||++|||+|++|+|+++.+.. ++|+++++|+|++||.+
T Consensus 22 ~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~~~~~~~df~i~~l~i~~~~kF~~ 101 (257)
T TIGR03069 22 LAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSDNPLDPDIIPIQGLLIEGNFLFDP 101 (257)
T ss_pred HHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEecccccCCcccCceEEEEEEcccccCC
Confidence 47899999999999999999999999999888899999999999999999999744443222 35999999999999999
Q ss_pred CCccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCc-eEEeeec
Q 026574 80 CSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRT-KSFKTIE 158 (236)
Q Consensus 80 l~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~-~~~~~~v 158 (236)
|+|||||||||||||+|+++|||++.++++||++|+++|++||++||+|||+++|++++++++++..|+++| +++..++
T Consensus 102 l~Hrd~LGalm~lGi~R~~iGDI~v~~~~~~~v~v~~~i~~~i~~~l~kIg~~~V~~~~~~~~~~~~~~~~~~~~~~~~v 181 (257)
T TIGR03069 102 ASHEDFRGALLGTGIVREKIGDIWVLGDRGAQALCTPELAEFLQEKLGQVRDVEVKCKAIPLEELQIPAPRTPKELTTVE 181 (257)
T ss_pred CCHHHHHHHHHHcCCcHhhcCCEEEecCCcEEEEECHHHHHHHHHHhhhccceeEEEEEeCHHHcCCCCcccceEecCCC
Confidence 999999999999999999999998876656999999999999999999999999999999999876666656 9999999
Q ss_pred cchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEEE
Q 026574 159 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQ 234 (236)
Q Consensus 159 ~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~r 234 (236)
+|+|||.+++..+++||++++++|++|+|+|||+.+++|++.|++||+|+++|+|||++.+++.|||||++|++.|
T Consensus 182 ~s~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~Gr~~i~~~~~TKKgr~~i~i~~ 257 (257)
T TIGR03069 182 ASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGRLEILELEITKKERWRVELLR 257 (257)
T ss_pred ccccHHHHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCCceEEEEEeecCcCCcEEEEEeC
Confidence 9999999999999999999999999999999999998999999999999999999999999899999999999874
No 3
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=100.00 E-value=7e-70 Score=468.77 Aligned_cols=232 Identities=38% Similarity=0.590 Sum_probs=219.7
Q ss_pred hhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCC--CCccceEEEEeecCCCccC
Q 026574 2 ARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT--SDPDIVAALSITGNFGFQP 79 (236)
Q Consensus 2 ~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~--~~~~~i~~l~i~~~~kf~~ 79 (236)
+++|+++|.+.+||||||+|+.+...+++ +.++++.+|||||+|||+|++++ |+|++ ..++++++++|.|++||.+
T Consensus 23 ~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l~-P~y~~~~~~df~l~l~eI~y~~kF~~ 100 (257)
T COG2302 23 IKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLILY-PAYYPLEESDFELTLLEISYASKFVS 100 (257)
T ss_pred HHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEEc-ccccChhhcccceEEEEEEccccccc
Confidence 57899999999999999999988877777 88999999999999999999997 66655 2234899999999999999
Q ss_pred CCccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeecc
Q 026574 80 CSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEA 159 (236)
Q Consensus 80 l~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~ 159 (236)
++|+||||+||||||+|+++|||++.+ ++||++|.+++++|+..+|++||+++|++++++++++..+.++|++.+.+++
T Consensus 101 l~H~~~LGtll~lGikRe~~GDIiv~~-~~aQliv~~~~~~f~~~~Ltkig~~~V~l~ei~~~~l~~~~~~~~e~~~~vs 179 (257)
T COG2302 101 LTHRDILGTLLSLGIKREKFGDIIVEG-EGAQLIVATELADFFLLHLTKIGKAPVKLEEIDLEELKESTEKWKELDVTVS 179 (257)
T ss_pred ccHHHHHHHHHhccCcHHhhccEEEeC-CeeEEEEehhHHHHHHHHHHhhcCcceEEEEcCHHHcccCccceeEEeeeee
Confidence 999999999999999999999999976 5899999999999999999999999999999999999988889999999999
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe-eccccccEEEEEEEeC
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI-NSTRKGKFAVELIQYL 236 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~-~~TKKgr~~i~~~r~~ 236 (236)
|+|||.+++.++++||++++++|.+|+|+|||++++++++.|++||.||+||+||+++.++ |.|||||+||++.+|+
T Consensus 180 SlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR~~i~~i~g~TKKdK~ri~l~~~~ 257 (257)
T COG2302 180 SLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGRLKILEINGVTKKDKFRITLRRYK 257 (257)
T ss_pred hhhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEeccccEEEEeecCccccccEEEEEEEcC
Confidence 9999999999999999999999999999999999999999999999999999999999999 5999999999999985
No 4
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.81 E-value=2.2e-21 Score=163.13 Aligned_cols=213 Identities=61% Similarity=0.953 Sum_probs=178.3
Q ss_pred ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCCCccceEEEEeecCCCccCC
Q 026574 1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPC 80 (236)
Q Consensus 1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~~~~~i~~l~i~~~~kf~~l 80 (236)
||.++.......+|+||.|. +.-.++++....-+||+.||+|++-|..|+-...+.+..+.+++..++.|++-
T Consensus 35 m~~~~~~~r~f~~t~~l~ps-------l~t~F~~v~s~~lpgl~~a~ec~~pi~~~~~~ts~k~~kksl~~td~~dsd~e 107 (248)
T KOG4837|consen 35 MARRASSKREFLHTDFLTPS-------LLTKFADVKSVALPGLPEAEECRIPIGHPDVLTSDKDIKKSLSITDNFDSDPE 107 (248)
T ss_pred HHHHHHhhHHHHhhhhhCch-------hhhccccchhhhcCCCCCChheEeeccCccccccchhHHHHhhhccccCCCcc
Confidence 45667677778899999994 34456788888899999999999999988776666665688899999999999
Q ss_pred CccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccc
Q 026574 81 SHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEAS 160 (236)
Q Consensus 81 ~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s 160 (236)
+|-||||+++ ||+.|||.+..+ ++...+++.+|-.+-|.|+| ..|....+++.-.... ++.-.....-.|
T Consensus 108 sh~Df~~e~~-----~e~~~D~~Vvk~---~~~i~~~v~sfr~d~llK~G-lgv~rnKVel~fye~e-~R~N~~Kl~kkS 177 (248)
T KOG4837|consen 108 SHGDFLGEIL-----REKLGDILVVKE---KVLIVPEVVSFRVDALLKVG-LGVTRNKVELLFYEYE-PRTNSFKLVKKS 177 (248)
T ss_pred cchhHHHHHH-----HHhcCCceeeeh---hhhhhhHHHHHHHHHHHHhc-cccccchhhHhhhhcc-cccCcccccccc
Confidence 9999999998 999999998754 47788999999999999999 8888877775433322 344444556679
Q ss_pred hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEE
Q 026574 161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI 233 (236)
Q Consensus 161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~ 233 (236)
.|+|.--+..+.++|+ ..++.+..+.|||..+.+.+..++.||++..||++ +++.++..|||||+.+++.
T Consensus 178 ~~i~vgds~d~~ig~~--~~~~s~~~~rV~~~tV~~~~t~~e~~~Vvlrr~Ks-Lki~~~r~tk~~k~a~~i~ 247 (248)
T KOG4837|consen 178 LRIDVGDSADFKIGRS--VDLISSKDVRVNWATVTKNGTIVETGDVVLRRGKS-LKIGEIRETKKGKFAVEII 247 (248)
T ss_pred eeeecccccceeeecc--cccCCcceEEEeeeeecccceEeecceEEEEeccc-cccccccccccccchhhhc
Confidence 9999877777778887 77889999999999999999999999999999999 9999999999999988764
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=99.32 E-value=1.5e-12 Score=111.33 Aligned_cols=86 Identities=26% Similarity=0.335 Sum_probs=76.3
Q ss_pred eEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccchHHHHHHH-hCCCcCHHHHHHHHHCCcE
Q 026574 109 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALAS-AGFKLSRSKLVNLISNGDV 187 (236)
Q Consensus 109 ~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~ils-~~~~~SR~~a~~lI~~G~V 187 (236)
.+|.++.+++.+|+..++.++|++.+.+ +.+.+ +|||.++. ..+..||+.|+++|.+|+|
T Consensus 57 ~~Yg~~e~q~~~~~~~a~~~~g~t~~~l--l~~le-----------------~RLD~~L~~~g~~~SR~~ArqlI~~G~V 117 (200)
T TIGR01017 57 FMYGITEKQFRKYFKEAKKLKGNTGENL--LRLLE-----------------SRLDNVVYRLGFAPTRFAARQLVSHGHI 117 (200)
T ss_pred HHHhchHHHHHHHHHHHhccCCCchhHH--HHHHH-----------------HHHHHHHHHcCCCCCHHHHHHHHHCCCE
Confidence 6899999999999999999999999877 22111 89999995 5568899999999999999
Q ss_pred EECCEEecCCCcccCCCCEEEEeeCC
Q 026574 188 RVNWTTVTKNGTTLRTGDIVSVSGKG 213 (236)
Q Consensus 188 ~VNg~~~~~~~~~v~~GD~Isvrg~G 213 (236)
.|||+.++.|++.|++||.|+|+|.-
T Consensus 118 ~VNgk~v~~ps~~V~~GD~I~V~~~~ 143 (200)
T TIGR01017 118 LVNGKKVDIPSYQVRPGDIISIKEKS 143 (200)
T ss_pred EECCEEeCCCCCCCCCCCEEEEeeCc
Confidence 99999999999999999999999864
No 6
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=99.27 E-value=2.4e-12 Score=110.36 Aligned_cols=87 Identities=23% Similarity=0.385 Sum_probs=76.7
Q ss_pred eEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccchHHHHHH-HhCCCcCHHHHHHHHHCCcE
Q 026574 109 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLISNGDV 187 (236)
Q Consensus 109 ~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~il-s~~~~~SR~~a~~lI~~G~V 187 (236)
.+|.++.+++.+|+..+++++|++++.+ +.+.| +|||.++ +..+..||++|+++|.+|.|
T Consensus 60 ~~Y~~~e~q~~~~~~~a~~~~g~t~~~l--l~~lE-----------------~RLD~iL~~~g~~~SR~~arqlI~~G~V 120 (203)
T PRK05327 60 RIYGVLEKQFRRYFKEAARRKGNTGENL--LQLLE-----------------SRLDNVVYRLGFAPTRRQARQLVSHGHI 120 (203)
T ss_pred HHhcCcHHHHHHHHHHHHhccCCcHhHH--HHHHH-----------------HHHHHHHHHcCccCCHHHHHHHHHCCcE
Confidence 6899999999999999999999998876 22211 8999998 45668999999999999999
Q ss_pred EECCEEecCCCcccCCCCEEEEeeCCe
Q 026574 188 RVNWTTVTKNGTTLRTGDIVSVSGKGR 214 (236)
Q Consensus 188 ~VNg~~~~~~~~~v~~GD~Isvrg~Gr 214 (236)
.|||+.++.|++.|++||.|+|++.-|
T Consensus 121 ~VNgk~v~~ps~~v~~GD~I~v~~~sr 147 (203)
T PRK05327 121 LVNGKKVNIPSYRVKPGDVIEVREKSK 147 (203)
T ss_pred EECCEEECCCCcCCCCCCEEEECCcCc
Confidence 999999988999999999999998643
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=99.20 E-value=3.8e-11 Score=79.44 Aligned_cols=47 Identities=34% Similarity=0.543 Sum_probs=44.0
Q ss_pred hHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 026574 161 LRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV 207 (236)
Q Consensus 161 ~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~I 207 (236)
||||.+|+ ..+..||+.|+++|++|.|+|||+.+++|++.|++||+|
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 69999998 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=99.14 E-value=1.6e-10 Score=79.95 Aligned_cols=51 Identities=18% Similarity=0.280 Sum_probs=47.2
Q ss_pred ccchHHHHHHHhCCCc--CHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574 158 EASLRVDALASAGFKL--SRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 158 v~s~RLD~ils~~~~~--SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.+.+|||.+|+.. ++ ||+.++.+|++|.|+|||+.+++|++.|++||.|.|
T Consensus 6 ~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 6 TEYITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred chHHHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 3669999999987 67 999999999999999999999889999999999986
No 9
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.96 E-value=2.3e-09 Score=81.50 Aligned_cols=61 Identities=25% Similarity=0.316 Sum_probs=54.2
Q ss_pred cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574 159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 220 (236)
Q Consensus 159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~ 220 (236)
..||||.||. ..+--+|+.|++++++|+|.|||..+ +|++.|++||+|.|+-..+.....|
T Consensus 7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~~~v~V 68 (100)
T COG1188 7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKEFTVKV 68 (100)
T ss_pred cceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcEEEEEE
Confidence 5799999986 44788999999999999999999999 7999999999999998887765555
No 10
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.83 E-value=2.1e-08 Score=80.44 Aligned_cols=67 Identities=15% Similarity=0.199 Sum_probs=57.4
Q ss_pred cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe-e-ccccc
Q 026574 159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI-N-STRKG 226 (236)
Q Consensus 159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~-~-~TKKg 226 (236)
.++|||.+|. ..+--||+.|+++|.+|+|.|||+. .+|+..|++||.|.|+-.++.....| . ..+.|
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 4689999975 6678999999999999999999999 58999999999999988887777666 3 45444
No 11
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.63 E-value=7.5e-08 Score=82.46 Aligned_cols=55 Identities=20% Similarity=0.265 Sum_probs=50.0
Q ss_pred chHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCe
Q 026574 160 SLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR 214 (236)
Q Consensus 160 s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr 214 (236)
.+|||.+|... +..||+.|+++|.+|.|.|||+.++.|++.|++||.|+|++..+
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 48999999654 57899999999999999999999999999999999999998654
No 12
>smart00363 S4 S4 RNA-binding domain.
Probab=98.63 E-value=1.1e-07 Score=63.56 Aligned_cols=51 Identities=37% Similarity=0.510 Sum_probs=46.6
Q ss_pred hHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 161 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 161 ~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
+|||.++... +..||+.++.++++|.|+|||+.+.+++..+++||.|++.+
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 47999999999999999999999977999999999999876
No 13
>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=98.60 E-value=1.2e-07 Score=65.08 Aligned_cols=52 Identities=37% Similarity=0.526 Sum_probs=47.2
Q ss_pred hHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574 161 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212 (236)
Q Consensus 161 ~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~ 212 (236)
+|||.++++. +..||+.+++++++|.|+|||+.++++++.+++||.|++.+.
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 5899999876 578999999999999999999999789999999999998764
No 14
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.45 E-value=3.4e-07 Score=78.57 Aligned_cols=59 Identities=29% Similarity=0.386 Sum_probs=52.5
Q ss_pred cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEE
Q 026574 159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI 217 (236)
Q Consensus 159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~ 217 (236)
-..|||+++- .+|..||.+|+++|.+|.|.|||+.++.|++.|++||.++|+-+-+-.+
T Consensus 92 LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~ 151 (205)
T COG0522 92 LERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPI 151 (205)
T ss_pred HHHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchh
Confidence 3579999985 5679999999999999999999999999999999999999997765443
No 15
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=98.29 E-value=1.5e-06 Score=78.44 Aligned_cols=54 Identities=28% Similarity=0.397 Sum_probs=49.6
Q ss_pred eccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 157 IEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 157 ~v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
+.+++|||.+|+....+||+.+.++|.+|+|+|||+.+ .+++.|.+||.|.|.|
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 45789999999987678999999999999999999998 6999999999999986
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=98.28 E-value=1.2e-06 Score=76.36 Aligned_cols=52 Identities=27% Similarity=0.202 Sum_probs=47.2
Q ss_pred HHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574 162 RVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG 213 (236)
Q Consensus 162 RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~G 213 (236)
|||.+|... +..||++|+++|++|+|+|||+.+++|++.|.+||.|++.+.-
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~~~ 53 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQNP 53 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccCcc
Confidence 899998765 4789999999999999999999999999999999999998753
No 17
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=98.28 E-value=1.6e-06 Score=75.41 Aligned_cols=51 Identities=22% Similarity=0.232 Sum_probs=47.5
Q ss_pred hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
+|||.+++..+.+||+.+++++++|+|+|||+.+.++++.|++||.|++.+
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 589999998889999999999999999999999866999999999999975
No 18
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=98.18 E-value=3.7e-06 Score=75.53 Aligned_cols=55 Identities=31% Similarity=0.462 Sum_probs=49.4
Q ss_pred ccchHHHHHHHhCCC-cCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574 158 EASLRVDALASAGFK-LSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212 (236)
Q Consensus 158 v~s~RLD~ils~~~~-~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~ 212 (236)
.+++|||.+++..+. +||+.++++|++|.|+|||+.+.++++.|++||.|++.+.
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 368999999998885 9999999999999999999766679999999999999654
No 19
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=98.13 E-value=5.7e-06 Score=75.53 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=50.5
Q ss_pred eccchHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574 157 IEASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212 (236)
Q Consensus 157 ~v~s~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~ 212 (236)
..+++|||.+++..+ ..||+.++++|++|+|+|||+.+.++++.|++||.|++.+.
T Consensus 14 ~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~ 70 (325)
T PRK11180 14 SQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE 70 (325)
T ss_pred ccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeec
Confidence 346799999999876 68999999999999999999998779999999999999863
No 20
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=98.05 E-value=8.5e-06 Score=71.93 Aligned_cols=53 Identities=32% Similarity=0.417 Sum_probs=48.8
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC-CEEEEeeC
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG-DIVSVSGK 212 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G-D~Isvrg~ 212 (236)
++||++++|+.-..||+.|.++|.+|+|+|||+++..+...+.++ |.|.+.|.
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 689999999988999999999999999999999999999999998 47777765
No 21
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=97.97 E-value=1.9e-05 Score=71.96 Aligned_cols=54 Identities=28% Similarity=0.438 Sum_probs=48.6
Q ss_pred eccchHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 157 IEASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 157 ~v~s~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
..+++|||.+|+..+ ++||+.++.++++|.|+|||+.+ ++++.|++||.|.+..
T Consensus 16 ~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~ 70 (317)
T PRK11025 16 DEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPP 70 (317)
T ss_pred ccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCC
Confidence 346899999999766 78999999999999999999998 6999999999999854
No 22
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.96 E-value=1.4e-05 Score=69.96 Aligned_cols=52 Identities=38% Similarity=0.460 Sum_probs=47.9
Q ss_pred chHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 160 SLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 160 s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
-||||.+|.+ .+.-||++|+.+|.+|.|.|||+.+.+|+..|..++.|.|.+
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 4899999764 578999999999999999999999999999999999999984
No 23
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=97.94 E-value=1.7e-05 Score=71.48 Aligned_cols=55 Identities=35% Similarity=0.477 Sum_probs=49.1
Q ss_pred eccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574 157 IEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212 (236)
Q Consensus 157 ~v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~ 212 (236)
..+++|||.+++..+.+||+.+++++++|.|+|||+.+. +++.|++||+|++.-.
T Consensus 9 ~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~ 63 (289)
T COG0564 9 EEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLP 63 (289)
T ss_pred hhcCCCHHHHHHHccCcCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecc
Confidence 457899999999833399999999999999999999996 9999999999998653
No 24
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=97.85 E-value=3.1e-05 Score=69.83 Aligned_cols=51 Identities=18% Similarity=0.235 Sum_probs=44.4
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEee
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSG 211 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvrg 211 (236)
++|||.+|+....+||+.+.++|++|+|+|||+.+ .+.+.|.++ |.|.+.|
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 58999999986569999999999999999999988 699999887 5566654
No 25
>PRK11507 ribosome-associated protein; Provisional
Probab=97.78 E-value=6.6e-05 Score=53.77 Aligned_cols=52 Identities=23% Similarity=0.344 Sum_probs=46.6
Q ss_pred hHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574 161 LRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212 (236)
Q Consensus 161 ~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~ 212 (236)
.+||.+|+. .+--|=..|+.+|.+|.|+|||.+.+.-..++.+||+|++.|.
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g~ 64 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH 64 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECCE
Confidence 579999974 3466888999999999999999999999999999999999885
No 26
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.78 E-value=6.2e-05 Score=63.30 Aligned_cols=53 Identities=17% Similarity=0.267 Sum_probs=45.8
Q ss_pred chHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEeeC
Q 026574 160 SLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSGK 212 (236)
Q Consensus 160 s~RLD~il-s~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvrg~ 212 (236)
..|||.++ ...+.-||++|+++|.+|.|.|||+.+++|++.|.++ |.|+....
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 46999986 4667899999999999999999999999999999998 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=97.76 E-value=4.5e-05 Score=55.01 Aligned_cols=62 Identities=24% Similarity=0.305 Sum_probs=43.9
Q ss_pred CccCCCccchHHHHHc-CCCCccccccEEEecCCeEEEEechhhHHHHHhccc--eecceEEEEEE
Q 026574 76 GFQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLE--KVGNVSVSCTR 138 (236)
Q Consensus 76 kf~~l~Hrd~LGalm~-lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~--kI~~~~V~~~~ 138 (236)
+-+.++++|++|+|.+ .||+++.||+|-+.+ +.++|-|.++.++-+.+.|. ++++-+|+++.
T Consensus 9 r~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-~~S~vev~~~~a~~v~~~l~~~~~~gk~v~ve~ 73 (74)
T PF03880_consen 9 RKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD-NFSFVEVPEEVAEKVLEALNGKKIKGKKVRVER 73 (74)
T ss_dssp GGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S-S-EEEEE-TT-HHHHHHHHTT--SSS----EEE
T ss_pred cccCCCHHHHHHHHHhccCCCHHhEEEEEEee-eEEEEEECHHHHHHHHHHhcCCCCCCeeEEEEE
Confidence 3367899999999999 599999999998865 48999999999999999998 77777887764
No 28
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.55 E-value=2.2e-05 Score=55.49 Aligned_cols=58 Identities=28% Similarity=0.461 Sum_probs=38.1
Q ss_pred cchHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEE
Q 026574 159 ASLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI 217 (236)
Q Consensus 159 ~s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~ 217 (236)
...+|+.+|.. .+--|=..|+.+|.+|.|+|||...+..+..+.+||+|++ ..+.+++
T Consensus 6 e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~-~~~~~~V 64 (65)
T PF13275_consen 6 EYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI-DGEEYRV 64 (65)
T ss_dssp S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE-TTEEEEE
T ss_pred CcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE-CCEEEEE
Confidence 45779999974 3455777999999999999999999999999999999999 4445554
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=97.43 E-value=0.00027 Score=58.65 Aligned_cols=51 Identities=18% Similarity=0.236 Sum_probs=45.1
Q ss_pred chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEe
Q 026574 160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVS 210 (236)
Q Consensus 160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvr 210 (236)
..|||.++- ..+.-|..+|+++|.+|.|.||++.++.|++.|..| |.|+.-
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 479999975 567899999999999999999999999999999998 666653
No 30
>PLN00189 40S ribosomal protein S9; Provisional
Probab=97.23 E-value=0.00023 Score=60.57 Aligned_cols=54 Identities=19% Similarity=0.129 Sum_probs=47.7
Q ss_pred chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574 160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG 213 (236)
Q Consensus 160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~G 213 (236)
..|||.++. ..+.-|..+|+++|.+|.|.||++.++.|++.|..||...|....
T Consensus 108 eRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 108 ERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred HhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 479999875 567889999999999999999999999999999999888876543
No 31
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=97.01 E-value=0.00066 Score=57.31 Aligned_cols=51 Identities=18% Similarity=0.131 Sum_probs=44.1
Q ss_pred chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 026574 160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 210 (236)
Q Consensus 160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr 210 (236)
..|||.++. ..+.-|...|+++|.+|.|.|||+.++.|++.|..||.=.|.
T Consensus 106 eRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~ 157 (181)
T PTZ00155 106 ERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHID 157 (181)
T ss_pred HHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCcee
Confidence 579999975 457889999999999999999999999999999998654333
No 32
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.66 E-value=0.0066 Score=43.83 Aligned_cols=53 Identities=28% Similarity=0.490 Sum_probs=46.1
Q ss_pred hHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574 161 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG 213 (236)
Q Consensus 161 ~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~G 213 (236)
..|+.+|... .--|=.+|+.++.+|.|+|||++.+.-...+..||+|.+.+..
T Consensus 12 I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~ 65 (73)
T COG2501 12 ITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQR 65 (73)
T ss_pred EEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECCEE
Confidence 4588888753 4567789999999999999999999999999999999998874
No 33
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.95 E-value=0.013 Score=49.16 Aligned_cols=96 Identities=22% Similarity=0.240 Sum_probs=67.3
Q ss_pred hhhHHHHHhccceecceEEEEEEecCcccc----cCCCCceEEe--eec---cchHHHHHHHhCCCcCHHHHHHHHHCCc
Q 026574 116 PELADYLITSLEKVGNVSVSCTRIPLLALE----YEPPRTKSFK--TIE---ASLRVDALASAGFKLSRSKLVNLISNGD 186 (236)
Q Consensus 116 ~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~----~~~~~~~~~~--~~v---~s~RLD~ils~~~~~SR~~a~~lI~~G~ 186 (236)
++.+.+..-|+.-+++.+-++++.|.-.++ -...++...+ ..+ +++|||+++++.+++||+..+.++..|.
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 567777777888888877777776653322 1222343322 222 4799999999999999999999999999
Q ss_pred EEECCEEecCCCcccCCCCEEEEee
Q 026574 187 VRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 187 V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
+..+-.........+..|-.|.+.-
T Consensus 165 Irgdtd~~~l~rkrlr~~~~i~Id~ 189 (203)
T COG4332 165 IRGDTDKMLLLRKRLRAGYDIQIDV 189 (203)
T ss_pred eeecchHHHHhhhhhhcCcEEEEEc
Confidence 9987665434556777777766643
No 34
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=95.82 E-value=0.015 Score=47.28 Aligned_cols=33 Identities=39% Similarity=0.527 Sum_probs=30.5
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWT 192 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~ 192 (236)
+.|||++|++.+++||+.+++++.+|.+..+-.
T Consensus 102 ~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~~ 134 (142)
T PF06353_consen 102 PLRLDRLLARQLGLSRSRLKRLIEQGLIRSDPD 134 (142)
T ss_pred CccHHHHHHHHhCcCHHHHHHHHHCCCEEecCc
Confidence 799999999999999999999999999987643
No 35
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.48 E-value=0.021 Score=49.03 Aligned_cols=86 Identities=24% Similarity=0.255 Sum_probs=67.7
Q ss_pred CceEEeeeccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe-eC---------CeEEEEE
Q 026574 150 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS-GK---------GRIKIGE 219 (236)
Q Consensus 150 ~~~~~~~~v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr-g~---------Gr~~~~~ 219 (236)
+++.+...+.|.|.|.++..++++.|+++.-+.-.+..++|+....+.+.++..||.+-+. |. -|+-...
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 4555666788999999999999999999999999999999999998999999999998874 31 1444444
Q ss_pred e--eccccccEEEEEEEe
Q 026574 220 I--NSTRKGKFAVELIQY 235 (236)
Q Consensus 220 ~--~~TKKgr~~i~~~r~ 235 (236)
+ +.|.-..+.|.+.||
T Consensus 209 V~~~~t~~e~~~Vvlrr~ 226 (248)
T KOG4837|consen 209 VTKNGTIVETGDVVLRRG 226 (248)
T ss_pred ecccceEeecceEEEEec
Confidence 4 245555666666665
No 36
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=94.02 E-value=0.16 Score=48.14 Aligned_cols=45 Identities=29% Similarity=0.434 Sum_probs=38.6
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 026574 163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV 207 (236)
Q Consensus 163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~I 207 (236)
+|.+++..+.-|++.|+++|++|.|+|||..+.++.+.+.++|.+
T Consensus 346 ~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~l 390 (410)
T PRK13354 346 VDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDAF 390 (410)
T ss_pred HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhhc
Confidence 455556778899999999999999999999998898888887753
No 37
>PRK04313 30S ribosomal protein S4e; Validated
Probab=93.66 E-value=0.2 Score=44.11 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=50.3
Q ss_pred cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574 159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 220 (236)
Q Consensus 159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~ 220 (236)
.|+-|--+|...+ ..+++.|+..+.+|.|+|||++.+++.+.+---|+||+.. .|||.+.++
T Consensus 36 ~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I 110 (237)
T PRK04313 36 ESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPI 110 (237)
T ss_pred cccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCCCeEEEEECCCCcEEEEEC
Confidence 4566777777655 5788999999999999999999999999998889999943 567766555
No 38
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=93.02 E-value=0.26 Score=44.17 Aligned_cols=62 Identities=16% Similarity=0.192 Sum_probs=50.3
Q ss_pred cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574 159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 220 (236)
Q Consensus 159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~ 220 (236)
.|+-|--+|...+ -.+.+.|+..+.+|.|+|||++.+++.+.+---|+|+|.. .|||.+.++
T Consensus 37 esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I 111 (273)
T PTZ00223 37 ECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKV 111 (273)
T ss_pred cccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEc
Confidence 4566777777655 4677899999999999999999998988888889999954 677777666
No 39
>PLN00036 40S ribosomal protein S4; Provisional
Probab=92.96 E-value=0.28 Score=43.70 Aligned_cols=62 Identities=18% Similarity=0.264 Sum_probs=49.9
Q ss_pred cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574 159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 220 (236)
Q Consensus 159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~ 220 (236)
.|+-|--+|...+ -.+.+.|+..+.+|.|+|||++.+++.+.+---|+|++.. .|||.+.++
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 4566777777655 5677899999999999999999998888888789999954 667766655
No 40
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=92.96 E-value=0.28 Score=43.80 Aligned_cols=62 Identities=21% Similarity=0.198 Sum_probs=49.8
Q ss_pred cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574 159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI 220 (236)
Q Consensus 159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~ 220 (236)
.|+-|--+|...+ ..+.+.|+..+.+|.|+|||++.++..+.+---|+|++.. .|||.+.++
T Consensus 40 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I 114 (262)
T PTZ00118 40 ECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKI 114 (262)
T ss_pred cccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEc
Confidence 4566667777655 5677899999999999999999998888888889999953 667666555
No 41
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=92.70 E-value=0.45 Score=45.05 Aligned_cols=42 Identities=29% Similarity=0.404 Sum_probs=35.6
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC
Q 026574 163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG 204 (236)
Q Consensus 163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G 204 (236)
+|.++...+.-|++.|+++|++|.|+||++.+.+++..+.+.
T Consensus 346 ~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~~ 387 (408)
T PRK05912 346 LALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTAD 387 (408)
T ss_pred HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCcccccccc
Confidence 455566677899999999999999999999998888777763
No 42
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=91.54 E-value=0.21 Score=36.77 Aligned_cols=44 Identities=23% Similarity=0.293 Sum_probs=34.5
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
...+..++.+ +|+.-+.+ |.|.|||+.+ .+++.+++||.|+|.-
T Consensus 32 ~~tvkd~IEs-LGVP~tEV------~~i~vNG~~v-~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 32 GATVKDVIES-LGVPHTEV------GLILVNGRPV-DFDYRLKDGDRVAVYP 75 (81)
T ss_pred CCcHHHHHHH-cCCChHHe------EEEEECCEEC-CCcccCCCCCEEEEEe
Confidence 3456666654 67777654 8899999999 6999999999999853
No 43
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=90.09 E-value=0.88 Score=39.89 Aligned_cols=52 Identities=15% Similarity=0.139 Sum_probs=37.0
Q ss_pred chHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 160 SLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 160 s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
|+-|-.++...+ --.-+.|+..|.+|.|+|||++.++..+.|--=|+|++.-
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 344444444433 2345688999999999999999876666665559999973
No 44
>PRK01777 hypothetical protein; Validated
Probab=88.35 E-value=1.1 Score=34.00 Aligned_cols=59 Identities=19% Similarity=0.098 Sum_probs=38.8
Q ss_pred CceEEeeecc-chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 026574 150 RTKSFKTIEA-SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 210 (236)
Q Consensus 150 ~~~~~~~~v~-s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr 210 (236)
++......++ +.++-.++.+ .++....-.--+..+.|-|||+.+ ..++.|++||.|+|-
T Consensus 15 ~~~~~~l~vp~GtTv~dal~~-sgi~~~~pei~~~~~~vgI~Gk~v-~~d~~L~dGDRVeIy 74 (95)
T PRK01777 15 RQYLQRLTLQEGATVEEAIRA-SGLLELRTDIDLAKNKVGIYSRPA-KLTDVLRDGDRVEIY 74 (95)
T ss_pred ceEEEEEEcCCCCcHHHHHHH-cCCCccCcccccccceEEEeCeEC-CCCCcCCCCCEEEEe
Confidence 3444555444 6666666654 355444111123468899999999 599999999999873
No 45
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=84.92 E-value=0.59 Score=35.42 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=35.8
Q ss_pred HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 165 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 165 ~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
..++...++|+..+..++.. ....-...|..||.|+++|+|.|++.+
T Consensus 9 ~~ia~~~~l~k~~a~~~v~~--------~~~~i~~aL~~G~~V~l~gFG~F~v~~ 55 (94)
T COG0776 9 DAIAEKAGLSKKDAEEAVDA--------FLEEITEALAKGERVELRGFGTFEVRE 55 (94)
T ss_pred HHHHHHcCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEeeeeeeEeec
Confidence 34555568999999998775 222334578899999999999999864
No 46
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=82.30 E-value=1.6 Score=36.32 Aligned_cols=44 Identities=20% Similarity=0.191 Sum_probs=38.2
Q ss_pred chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCC
Q 026574 160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRT 203 (236)
Q Consensus 160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~ 203 (236)
.+||+..+- ..+..|=..|+.+|.++.|.||++.+.-|++.|+.
T Consensus 96 ErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 96 ERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 589998864 45677888999999999999999999999999974
No 47
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=78.30 E-value=3.3 Score=31.85 Aligned_cols=41 Identities=17% Similarity=0.445 Sum_probs=33.0
Q ss_pred HHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEE
Q 026574 176 SKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI 217 (236)
Q Consensus 176 ~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~ 217 (236)
..--++|++|+=+|-++........+++||.|...| +++++
T Consensus 9 eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~-~~l~v 49 (111)
T COG4043 9 EEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG-DKLKV 49 (111)
T ss_pred HHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC-CeeEE
Confidence 344578999999999998876778999999999986 55554
No 48
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=78.16 E-value=6.6 Score=37.26 Aligned_cols=40 Identities=38% Similarity=0.474 Sum_probs=34.8
Q ss_pred HHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCccc
Q 026574 162 RVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTL 201 (236)
Q Consensus 162 RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v 201 (236)
-+|.++...+.-||+.|++++.+|.|++||..+.+.+..+
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 4667777888999999999999999999999998777555
No 49
>PRK06437 hypothetical protein; Provisional
Probab=76.85 E-value=3.3 Score=29.03 Aligned_cols=43 Identities=21% Similarity=0.209 Sum_probs=31.1
Q ss_pred cchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 026574 159 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 210 (236)
Q Consensus 159 ~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr 210 (236)
.+.++-.+|+. ++++... =.|.+||+.+. +++.|++||.|.+-
T Consensus 19 ~~~tv~dLL~~-Lgi~~~~-------vaV~vNg~iv~-~~~~L~dgD~Veiv 61 (67)
T PRK06437 19 HELTVNDIIKD-LGLDEEE-------YVVIVNGSPVL-EDHNVKKEDDVLIL 61 (67)
T ss_pred CCCcHHHHHHH-cCCCCcc-------EEEEECCEECC-CceEcCCCCEEEEE
Confidence 34567777765 4664322 15679999995 99999999999874
No 50
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=76.27 E-value=4.8 Score=40.27 Aligned_cols=72 Identities=13% Similarity=0.136 Sum_probs=55.8
Q ss_pred eEEEEeecCCCccCCCccchHHHHHc-CCCCccccccEEEecCCeEEEEechhhHHHHHhccce--ecceEEEEEEe
Q 026574 66 VAALSITGNFGFQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEK--VGNVSVSCTRI 139 (236)
Q Consensus 66 i~~l~i~~~~kf~~l~Hrd~LGalm~-lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~k--I~~~~V~~~~~ 139 (236)
..-+.|+- .+=+.++.++++|+|-+ .||++..||+|=+.++ ...|=+.+++++-+...|.+ |.+-+|.++..
T Consensus 486 ~~~~~~~~-g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~-~s~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 (629)
T PRK11634 486 MQLYRIEV-GRDDGVEVRHIVGAIANEGDISSRYIGNIKLFAS-HSTIELPKGMPGEVLQHFTRTRILNKPMNMQLL 560 (629)
T ss_pred CEEEEEec-ccccCCCHHHHHHHHHhhcCCChhhCCcEEEeCC-ceEEEcChhhHHHHHHHhccccccCCceEEEEC
Confidence 33455543 22356899999999999 9999999999977554 78888999999999999976 44667776644
No 51
>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=74.68 E-value=3.9 Score=28.82 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=23.1
Q ss_pred HHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574 182 ISNGDVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 182 I~~G~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
...-.|.|||+.+. .+..|++||.|.+
T Consensus 47 ~~~~~v~vNg~~v~-~~~~l~~gD~v~i 73 (80)
T cd00754 47 LARVRIAVNGEYVR-LDTPLKDGDEVAI 73 (80)
T ss_pred hhcEEEEECCeEcC-CCcccCCCCEEEE
Confidence 34557999999995 8999999999987
No 52
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=73.48 E-value=4.7 Score=28.34 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=31.3
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
++.+..++.. ++++. +.-.|.+|++.+ .+++.+++||.|.+
T Consensus 23 ~~tv~~ll~~-l~~~~-------~~v~v~vNg~iv-~~~~~l~~gD~Vei 63 (70)
T PRK08364 23 GMKVADILRA-VGFNT-------ESAIAKVNGKVA-LEDDPVKDGDYVEV 63 (70)
T ss_pred CCcHHHHHHH-cCCCC-------ccEEEEECCEEC-CCCcCcCCCCEEEE
Confidence 4667777765 45543 345788999999 58999999999887
No 53
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=72.63 E-value=2.5 Score=31.40 Aligned_cols=46 Identities=22% Similarity=0.349 Sum_probs=35.2
Q ss_pred HHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 166 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 166 ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
.++...++|+..+...+.. ....-...|..|+.|+++|+|.|++..
T Consensus 9 ~ia~~~~~s~~~~~~~v~~--------~~~~i~~~L~~~~~v~l~gfG~F~v~~ 54 (90)
T PRK10664 9 KIAAGADISKAAAGRALDA--------IIASVTESLKEGDDVALVGFGTFAVKE 54 (90)
T ss_pred HHHHHhCCCHHHHHHHHHH--------HHHHHHHHHhCCCEEEECCcEEEEEEE
Confidence 3556679999999988765 222234568899999999999999864
No 54
>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=72.31 E-value=4 Score=28.12 Aligned_cols=42 Identities=21% Similarity=0.279 Sum_probs=28.6
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCC----cccCCCCEEEEe
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNG----TTLRTGDIVSVS 210 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~----~~v~~GD~Isvr 210 (236)
++.+..++.. ++++. ..=.|.+||+.+. .+ +.|++||.|.+-
T Consensus 14 ~~tv~~ll~~-l~~~~-------~~i~V~vNg~~v~-~~~~~~~~L~~gD~V~ii 59 (65)
T cd00565 14 GATLAELLEE-LGLDP-------RGVAVALNGEIVP-RSEWASTPLQDGDRIEIV 59 (65)
T ss_pred CCCHHHHHHH-cCCCC-------CcEEEEECCEEcC-HHHcCceecCCCCEEEEE
Confidence 4557777765 34432 1124779999984 56 899999999873
No 55
>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=71.26 E-value=14 Score=25.99 Aligned_cols=42 Identities=14% Similarity=0.097 Sum_probs=37.0
Q ss_pred ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCC
Q 026574 1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGG 42 (236)
Q Consensus 1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GG 42 (236)
+|++|..++.+..-+=||+.+..+++.++++++++.....|-
T Consensus 15 ~a~~v~~tg~~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G~ 56 (67)
T cd02644 15 AAEKVRRTGKPVKLEPMNAYERRIIHDALANDEDVETESEGE 56 (67)
T ss_pred HHHHHHHHCCeeEeCCCCHHHHHHHHHHHHhCCCceEEeecC
Confidence 367888999999999999999999999999999898887764
No 56
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=69.08 E-value=3.1 Score=30.86 Aligned_cols=45 Identities=22% Similarity=0.375 Sum_probs=34.6
Q ss_pred HHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 167 ASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 167 ls~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
++...++|+..++..+.. ....-...|..|+.|.++|+|.|++..
T Consensus 10 ia~~~~~s~~~~~~~v~~--------~~~~i~~~L~~g~~V~i~gfG~F~v~~ 54 (90)
T PRK10753 10 IADKAELSKTQAKAALES--------TLAAITESLKEGDAVQLVGFGTFKVNH 54 (90)
T ss_pred HHHHhCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEcCCEEEEEee
Confidence 455678999999988765 222234578999999999999999854
No 57
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=68.22 E-value=12 Score=26.93 Aligned_cols=23 Identities=35% Similarity=0.270 Sum_probs=20.1
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 026574 186 DVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.+.||++.+ ..+..|++||.|.+
T Consensus 52 ~~aVN~~~~-~~~~~l~dgDeVai 74 (81)
T PRK11130 52 LAAVNQTLV-SFDHPLTDGDEVAF 74 (81)
T ss_pred EEEECCEEc-CCCCCCCCCCEEEE
Confidence 478999987 58899999999987
No 58
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=67.91 E-value=17 Score=25.93 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=21.4
Q ss_pred CCcEEECCEEecCCCcccCCCCEEEE
Q 026574 184 NGDVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 184 ~G~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.=.|.||++.+ ..++.|++||.|.+
T Consensus 51 ~~~vavN~~~v-~~~~~l~dgDeVai 75 (82)
T PLN02799 51 CCVLALNEEYT-TESAALKDGDELAI 75 (82)
T ss_pred CcEEEECCEEc-CCCcCcCCCCEEEE
Confidence 33688999998 58999999999987
No 59
>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=66.55 E-value=12 Score=27.05 Aligned_cols=24 Identities=33% Similarity=0.432 Sum_probs=19.6
Q ss_pred CcEEECCEEecCCCc--ccCCCCEEEE
Q 026574 185 GDVRVNWTTVTKNGT--TLRTGDIVSV 209 (236)
Q Consensus 185 G~V~VNg~~~~~~~~--~v~~GD~Isv 209 (236)
=.|.||++.+. .+. .++.||.|.+
T Consensus 56 ~~v~vN~~~v~-~~~~~~l~dgdev~i 81 (88)
T TIGR01687 56 VIILVNGRNVD-WGLGTELKDGDVVAI 81 (88)
T ss_pred EEEEECCEecC-ccCCCCCCCCCEEEE
Confidence 35889999984 555 8999999987
No 60
>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=66.32 E-value=5.1 Score=27.91 Aligned_cols=49 Identities=27% Similarity=0.211 Sum_probs=31.0
Q ss_pred ccchHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecC--CCcccCCCCEEEE
Q 026574 158 EASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTK--NGTTLRTGDIVSV 209 (236)
Q Consensus 158 v~s~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~--~~~~v~~GD~Isv 209 (236)
.++..+..++.... ...+-. ....=.|.|||+.+.. .+..|++||.|.+
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 34555666655432 111111 3345578899999963 2899999999987
No 61
>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=66.08 E-value=8.5 Score=26.36 Aligned_cols=42 Identities=29% Similarity=0.355 Sum_probs=28.5
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec---CCCcccCCCCEEEE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT---KNGTTLRTGDIVSV 209 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~---~~~~~v~~GD~Isv 209 (236)
++.+-.++.. +++.. ..-.|.+|++.+. ..++.|++||.|.+
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 4556666665 34432 3346789999985 23468999999987
No 62
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=65.29 E-value=8 Score=26.55 Aligned_cols=25 Identities=28% Similarity=0.287 Sum_probs=20.3
Q ss_pred cEEECCEEecC---CCcccCCCCEEEEe
Q 026574 186 DVRVNWTTVTK---NGTTLRTGDIVSVS 210 (236)
Q Consensus 186 ~V~VNg~~~~~---~~~~v~~GD~Isvr 210 (236)
.|.+|++.+.+ ++..|++||.|.+-
T Consensus 32 avavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 32 ATAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred EEEECCEEcCHHHcCccccCCCCEEEEE
Confidence 38899999853 27899999999873
No 63
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=65.22 E-value=8.6 Score=27.44 Aligned_cols=23 Identities=39% Similarity=0.372 Sum_probs=20.7
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 026574 186 DVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.|.||++.+. .+..|+.||.|.+
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai 73 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAF 73 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEE
Confidence 5889999985 7999999999987
No 64
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=64.68 E-value=5.4 Score=29.58 Aligned_cols=48 Identities=21% Similarity=0.334 Sum_probs=35.0
Q ss_pred HHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 164 DALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 164 D~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
+.+-+...++|+..+...+.. ....-...|..|+.|.+.|+|.|.+..
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 333334468999999988765 222234568999999999999999864
No 65
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=62.53 E-value=10 Score=25.78 Aligned_cols=41 Identities=22% Similarity=0.222 Sum_probs=27.3
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCC---CcccCCCCEEEE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKN---GTTLRTGDIVSV 209 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~---~~~v~~GD~Isv 209 (236)
+..+-.++.. +++.. .-.|.+|++.+.+. +..|++||.|.|
T Consensus 15 ~~tl~~ll~~-l~~~~--------~~~v~vN~~~v~~~~~~~~~L~~gD~vei 58 (65)
T PRK06944 15 GATVADALAA-YGARP--------PFAVAVNGDFVARTQHAARALAAGDRLDL 58 (65)
T ss_pred CCcHHHHHHh-hCCCC--------CeEEEECCEEcCchhcccccCCCCCEEEE
Confidence 3456666654 33321 13588999998533 678999999987
No 66
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=61.93 E-value=13 Score=34.93 Aligned_cols=48 Identities=25% Similarity=0.225 Sum_probs=40.5
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574 163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG 211 (236)
Q Consensus 163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg 211 (236)
+|.+.++.....|..-...|+.|.|.+||..+. .++.++.||.+...-
T Consensus 47 ~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~v 94 (371)
T KOG1919|consen 47 VDVFVSEFRLRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHTV 94 (371)
T ss_pred HHHHHHHHhcCchHhhhhhhhcCceEECcEeee-eEEEeccCCEEEEee
Confidence 666666655778888899999999999999994 999999999998643
No 67
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=60.69 E-value=39 Score=24.79 Aligned_cols=54 Identities=15% Similarity=0.195 Sum_probs=32.1
Q ss_pred cchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee--CCeEEEEEe
Q 026574 159 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG--KGRIKIGEI 220 (236)
Q Consensus 159 ~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg--~Gr~~~~~~ 220 (236)
++..|-.++.+ .++|-+.+.++++... +++.. ..++|||.|++.- .|++.-..+
T Consensus 9 ~GDtLs~iF~~-~gls~~dl~~v~~~~~---~~k~L----~~L~pGq~l~f~~d~~g~L~~L~~ 64 (85)
T PF04225_consen 9 SGDTLSTIFRR-AGLSASDLYAVLEADG---EAKPL----TRLKPGQTLEFQLDEDGQLTALRY 64 (85)
T ss_dssp TT--HHHHHHH-TT--HHHHHHHHHHGG---GT--G----GG--TT-EEEEEE-TTS-EEEEEE
T ss_pred CCCcHHHHHHH-cCCCHHHHHHHHhccC---ccchH----hhCCCCCEEEEEECCCCCEEEEEE
Confidence 67888888887 5999999999998643 33444 3799999999854 676654443
No 68
>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=60.56 E-value=9.8 Score=25.93 Aligned_cols=34 Identities=24% Similarity=0.259 Sum_probs=25.2
Q ss_pred CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574 172 KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 172 ~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.++.+.+++. -...|||+.+ ..++.|+.||.|.+
T Consensus 25 ~I~~~l~~~~---~~A~Vng~~v-dl~~~L~~~d~v~i 58 (60)
T PF02824_consen 25 SIHSSLAKRA---VAAKVNGQLV-DLDHPLEDGDVVEI 58 (60)
T ss_dssp HHSHHHHHCE---EEEEETTEEE-ETTSBB-SSEEEEE
T ss_pred HHCHHHHhhe---eEEEEcCEEC-CCCCCcCCCCEEEE
Confidence 4566655533 3567999998 69999999999987
No 69
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=60.01 E-value=11 Score=26.72 Aligned_cols=41 Identities=29% Similarity=0.345 Sum_probs=28.4
Q ss_pred hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecC---CCcccCCCCEEEE
Q 026574 161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTK---NGTTLRTGDIVSV 209 (236)
Q Consensus 161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~---~~~~v~~GD~Isv 209 (236)
+++-.+|++ ++++- +.=-|.+||..+.+ .++.++.||.|.|
T Consensus 18 ~tv~dLL~~-l~~~~-------~~vav~vNg~iVpr~~~~~~~l~~gD~iev 61 (68)
T COG2104 18 TTVADLLAQ-LGLNP-------EGVAVAVNGEIVPRSQWADTILKEGDRIEV 61 (68)
T ss_pred CcHHHHHHH-hCCCC-------ceEEEEECCEEccchhhhhccccCCCEEEE
Confidence 667777765 33321 11247799999954 7899999999887
No 70
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=59.65 E-value=13 Score=25.34 Aligned_cols=43 Identities=33% Similarity=0.401 Sum_probs=27.2
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec---CCCcccCCCCEEEEe
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT---KNGTTLRTGDIVSVS 210 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~---~~~~~v~~GD~Isvr 210 (236)
++.+-.+|.. +++....+ .|.+|+..+. .+++.|++||.|.|-
T Consensus 15 ~~tl~~lL~~-l~~~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 15 GESVAALLAR-EGLAGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred CCCHHHHHHh-cCCCCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 4456666654 34332221 2889997763 267899999999873
No 71
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=57.09 E-value=16 Score=25.10 Aligned_cols=28 Identities=32% Similarity=0.297 Sum_probs=22.4
Q ss_pred CcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574 185 GDVRVNWTTVTKNGTTLRTGDIVSVSGKG 213 (236)
Q Consensus 185 G~V~VNg~~~~~~~~~v~~GD~Isvrg~G 213 (236)
.-+-+||-++ +.+..|++||.|.+--+|
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 3455799998 689999999999875544
No 72
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=56.91 E-value=16 Score=25.18 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=19.3
Q ss_pred cEEECCEEec---CCCcccCCCCEEEE
Q 026574 186 DVRVNWTTVT---KNGTTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~---~~~~~v~~GD~Isv 209 (236)
.|.+|++.+. ..++.|++||.|.+
T Consensus 33 aVavN~~iv~r~~w~~~~L~~gD~Iei 59 (66)
T PRK08053 33 ALAINQQIIPREQWAQHIVQDGDQILL 59 (66)
T ss_pred EEEECCEEeChHHcCccccCCCCEEEE
Confidence 4779999985 24568999999987
No 73
>PRK07440 hypothetical protein; Provisional
Probab=56.28 E-value=16 Score=25.73 Aligned_cols=42 Identities=14% Similarity=0.196 Sum_probs=27.6
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecC---CCcccCCCCEEEE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTK---NGTTLRTGDIVSV 209 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~---~~~~v~~GD~Isv 209 (236)
++.+..+|.. ++++. +.=.|.+|++.+.+ ++..|++||.|.|
T Consensus 19 ~~tl~~lL~~-l~~~~-------~~vav~~N~~iv~r~~w~~~~L~~gD~IEI 63 (70)
T PRK07440 19 GTSLPDLLQQ-LGFNP-------RLVAVEYNGEILHRQFWEQTQVQPGDRLEI 63 (70)
T ss_pred CCCHHHHHHH-cCCCC-------CeEEEEECCEEeCHHHcCceecCCCCEEEE
Confidence 4556666654 34321 11257799999831 6789999999887
No 74
>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=54.87 E-value=10 Score=28.00 Aligned_cols=48 Identities=15% Similarity=0.311 Sum_probs=34.3
Q ss_pred HHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 164 DALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 164 D~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
+.+.+...++|+..+...+.. ....-...|..|+.|.+.|+|.|++..
T Consensus 8 ~~i~~~~~~~s~~~v~~vv~~--------~~~~i~~~L~~g~~V~l~gfG~F~~~~ 55 (94)
T TIGR00988 8 ERIATQQSHLPAKDVEDAVKT--------MLEHMASALAQGDRIEIRGFGSFSLHY 55 (94)
T ss_pred HHHHHHcCCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEcCcEEEEEEE
Confidence 333333457899999888765 222334568889999999999999864
No 75
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=54.68 E-value=8.1 Score=28.90 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=34.7
Q ss_pred HHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574 167 ASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 220 (236)
Q Consensus 167 ls~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~ 220 (236)
++...++|+..+...+.. ....-...|..|+.|.+.|+|.|.+..-
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 445578999999888765 2223345789999999999999998643
No 76
>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=54.43 E-value=12 Score=25.33 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=18.9
Q ss_pred CCcEEECCEEecC-CCcccCCCCEEEE
Q 026574 184 NGDVRVNWTTVTK-NGTTLRTGDIVSV 209 (236)
Q Consensus 184 ~G~V~VNg~~~~~-~~~~v~~GD~Isv 209 (236)
...++|||+.+.. ..+.|+.||+|.+
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 4678999999853 2589999999875
No 77
>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=51.68 E-value=9.7 Score=28.36 Aligned_cols=46 Identities=20% Similarity=0.289 Sum_probs=34.9
Q ss_pred HHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 166 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 166 ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
.++...++|+..++..+.+ ...--...|..|+.|.+.|+|.|++..
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 3456678999999988765 222234568899999999999999865
No 78
>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=50.75 E-value=17 Score=27.25 Aligned_cols=24 Identities=29% Similarity=0.205 Sum_probs=20.2
Q ss_pred cEEECCEEec---CCCcccCCCCEEEE
Q 026574 186 DVRVNWTTVT---KNGTTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~---~~~~~v~~GD~Isv 209 (236)
.|.||++.+. ..++.|++||.|++
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 6889999864 35799999999987
No 79
>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=49.29 E-value=12 Score=26.76 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=35.3
Q ss_pred HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574 165 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219 (236)
Q Consensus 165 ~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~ 219 (236)
..++...++|+..++..+.. ....-...|..|+.|.+.|+|.|.+..
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 34566678999999988764 122234578899999999999999863
No 80
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=46.56 E-value=22 Score=24.71 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=19.0
Q ss_pred cEEECCEEecCCC----cccCCCCEEEE
Q 026574 186 DVRVNWTTVTKNG----TTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~~~~----~~v~~GD~Isv 209 (236)
.|.+|+..+. .+ +.|++||.|.|
T Consensus 34 av~vN~~iv~-r~~w~~~~L~~gD~iEI 60 (67)
T PRK07696 34 VVERNKDILQ-KDDHTDTSVFDGDQIEI 60 (67)
T ss_pred EEEECCEEeC-HHHcCceecCCCCEEEE
Confidence 4779999984 45 88999999887
No 81
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=46.51 E-value=14 Score=26.69 Aligned_cols=47 Identities=17% Similarity=0.224 Sum_probs=35.1
Q ss_pred HHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574 166 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 220 (236)
Q Consensus 166 ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~ 220 (236)
.+++..++|+..+...+.+ ...--...|..|..|.+.|.|.|.+...
T Consensus 9 ~ia~~~~~~~~~v~~vl~~--------l~~~i~~~L~~g~~V~i~g~G~F~~~~~ 55 (90)
T smart00411 9 AIAEKAGLSKKDAKAAVDA--------FLEIITEALKKGEKVELRGFGTFEVRER 55 (90)
T ss_pred HHHHHhCCCHHHHHHHHHH--------HHHHHHHHHhCCCeEEEeCcEEEEEEee
Confidence 3566678999999988765 1222345688899999999999998643
No 82
>PF06115 DUF956: Domain of unknown function (DUF956); InterPro: IPR010360 This is a family of bacterial sequences with undetermined function.
Probab=44.19 E-value=12 Score=29.43 Aligned_cols=39 Identities=28% Similarity=0.509 Sum_probs=32.2
Q ss_pred ccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEE
Q 026574 98 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCT 137 (236)
Q Consensus 98 ~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~ 137 (236)
+-|+|++ +|.+.-++-++...|||+-=++.|-.+.+++.
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 8899998 66677888889999999988888887766664
No 83
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=42.81 E-value=38 Score=26.67 Aligned_cols=43 Identities=12% Similarity=0.122 Sum_probs=32.4
Q ss_pred ccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcc
Q 026574 98 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLA 143 (236)
Q Consensus 98 ~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~ 143 (236)
+.||.+.-++ ..|.+.. +-+-..+||..+||+.+.+...+..+
T Consensus 53 ~~Gd~l~i~~-~~Y~Ita--VG~~a~~NL~~LGHiTi~F~g~~~~~ 95 (120)
T PRK10377 53 QPGLQFELGQ-HRYPVTA--VGSVAEDNLRELGHVTLRFDGLNEAE 95 (120)
T ss_pred CCCCEEEECC-EEEEEEE--EhHHHHHHHHhcCCEEEEECCCCCcc
Confidence 7899988765 4555544 67777899999999999997655433
No 84
>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=42.77 E-value=18 Score=22.37 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=17.6
Q ss_pred HHhCCCcCHHHHHHHHHCCcE
Q 026574 167 ASAGFKLSRSKLVNLISNGDV 187 (236)
Q Consensus 167 ls~~~~~SR~~a~~lI~~G~V 187 (236)
+++.+++|++.+.+++++|.+
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCC
Confidence 456679999999999999864
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=42.38 E-value=40 Score=31.63 Aligned_cols=41 Identities=24% Similarity=0.221 Sum_probs=32.1
Q ss_pred hHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCccc
Q 026574 161 LRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTL 201 (236)
Q Consensus 161 ~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v 201 (236)
..+..++. .....|++.++++|++|.|+||+..+..++...
T Consensus 330 ~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~ 371 (377)
T TIGR00234 330 ITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEPIR 371 (377)
T ss_pred cCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchhhh
Confidence 45655543 456889999999999999999999987665444
No 86
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=42.08 E-value=40 Score=26.63 Aligned_cols=41 Identities=20% Similarity=0.289 Sum_probs=31.6
Q ss_pred ccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecC
Q 026574 98 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPL 141 (236)
Q Consensus 98 ~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~ 141 (236)
+.||.+.-++ ..|.+.. +-+-..+||..+||+.+.+...+.
T Consensus 53 ~~Gd~l~i~~-~~Y~Ita--VG~~a~~NL~~LGHiTi~F~g~~~ 93 (121)
T TIGR00849 53 KPGQVFMIGG-IAYPVTA--VGDVAEKNLRSLGHITVRFDGSNV 93 (121)
T ss_pred CCCCEEEECC-EEEEEEE--EhHHHHHHHHhcCCEEEEECCCCC
Confidence 7799988765 4555544 677778999999999999976543
No 87
>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=41.19 E-value=42 Score=21.77 Aligned_cols=23 Identities=39% Similarity=0.527 Sum_probs=19.1
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 026574 186 DVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.+.+||+.+ +.++.+..||.|.+
T Consensus 36 a~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEE
Confidence 466999998 58899999998775
No 88
>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=40.30 E-value=70 Score=22.00 Aligned_cols=46 Identities=26% Similarity=0.339 Sum_probs=28.4
Q ss_pred CcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEE
Q 026574 185 GDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI 233 (236)
Q Consensus 185 G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~ 233 (236)
-.|.|||... ...++..+.-.+...|.+.+..-...+-|.+.|+++
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 223445556666666665554433556666666653
No 89
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=39.02 E-value=29 Score=28.00 Aligned_cols=61 Identities=11% Similarity=0.136 Sum_probs=41.4
Q ss_pred CceEEeeeccchHHHHH---HHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEE
Q 026574 150 RTKSFKTIEASLRVDAL---ASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG 218 (236)
Q Consensus 150 ~~~~~~~~v~s~RLD~i---ls~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~ 218 (236)
.|-........+..+.+ +++..++|+..+...+.+ ...--...|..|..|.+.|+|.|++.
T Consensus 20 ~~ya~~~~~~~mt~~el~~~Ia~~s~~s~~dv~~vl~~--------l~~~i~~~L~~G~~V~L~gfGtF~~~ 83 (145)
T TIGR01201 20 MWYPQTVKSGVIDFEEIAELIAEESSLSPGDVKGIIDR--------LAYVLRRELANGKTVRLGEIGTFRLS 83 (145)
T ss_pred eEEEEEeeCCCcCHHHHHHHHHHHhCCCHHHHHHHHHH--------HHHHHHHHHhCCCeEEeCCCEEEEEE
Confidence 34333333334555554 455578999999988775 22233457899999999999999985
No 90
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=38.43 E-value=39 Score=32.25 Aligned_cols=39 Identities=23% Similarity=0.293 Sum_probs=29.2
Q ss_pred HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCccc
Q 026574 163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTL 201 (236)
Q Consensus 163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v 201 (236)
+|-......--|++.|.++|.+|.|.+|++.+.+++..+
T Consensus 402 ~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es~~~ 440 (467)
T KOG2623|consen 402 LDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSI 440 (467)
T ss_pred HHHHHHhhcCCCcHHHHHHHHccceeecCccccCchhhc
Confidence 344444445668889999999999999999997655333
No 91
>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=36.94 E-value=84 Score=21.99 Aligned_cols=35 Identities=17% Similarity=-0.001 Sum_probs=29.6
Q ss_pred cCCceEEecCCChHHHHHHHHHhcccCCeeEEEeC
Q 026574 7 SRREVLHSDFLTPPVLKESMMALEKLADVKAVAQG 41 (236)
Q Consensus 7 ~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~G 41 (236)
+.+++..-+=|+|+|..++++.+++.+++.....|
T Consensus 16 ~~~r~v~LePM~~~ERkIIH~~Lq~~~~v~T~S~G 50 (62)
T cd02638 16 QRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVG 50 (62)
T ss_pred ccCCeEecCCCChHHHHHHHHHHhcCCCceEEEcc
Confidence 45678888889999999999999999998776655
No 92
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=35.53 E-value=10 Score=27.32 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=33.9
Q ss_pred HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574 165 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI 220 (236)
Q Consensus 165 ~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~ 220 (236)
..++...++|+..+...+.. ....-...|..|+.|.+.|.|.|.+..-
T Consensus 8 ~~ia~~~~~s~~~v~~vl~~--------~~~~i~~~L~~g~~V~l~g~G~F~~~~~ 55 (90)
T PF00216_consen 8 KRIAEKTGLSKKDVEAVLDA--------LFDVIKEALKEGESVKLPGFGTFSVKER 55 (90)
T ss_dssp HHHHHHHTSSHHHHHHHHHH--------HHHHHHHHHHTT-EEEETTTEEEEEEEE
T ss_pred HHHHHhcCCCHHHHHHHHHH--------HHHHHHHHHhcCCeEEeeceeEEEEecc
Confidence 34555567899988888764 1222334688999999999999998653
No 93
>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=35.05 E-value=97 Score=21.34 Aligned_cols=36 Identities=19% Similarity=0.272 Sum_probs=27.5
Q ss_pred CCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCc
Q 026574 8 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYP 44 (236)
Q Consensus 8 ~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~ 44 (236)
.+...+.+-|+|.|...+..+..++ ++...+.|+.+
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 5667788889999998887766665 67777888853
No 94
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=34.71 E-value=48 Score=32.60 Aligned_cols=84 Identities=15% Similarity=0.179 Sum_probs=53.7
Q ss_pred CCccchHHHHHcCCC-CccccccEEEecCCeEEEEechhhHHHHH---hccceecceEEEEEEecCcccccCCCCceEEe
Q 026574 80 CSHGDFLGSILGTGI-AREKIGDIILQGEKGAQFLVVPELADYLI---TSLEKVGNVSVSCTRIPLLALEYEPPRTKSFK 155 (236)
Q Consensus 80 l~Hrd~LGalm~lGi-~Re~iGDI~~~~~~~~~~~v~~~i~~~i~---~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~ 155 (236)
++..+|||++|.|=. +|....|+-..+.+++.+...-.+++.+. +.|.++.+---++ +.+.....+.+--.+.
T Consensus 414 i~P~eylG~vm~Lcq~kRG~~~~m~yl~~~rv~l~Y~lPl~Eiv~DFfDkLKS~skGYAS~---DYe~~~y~~~~lVK~d 490 (603)
T COG0481 414 ITPQEYLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPLAEIVFDFFDKLKSISKGYASF---DYEFIGYRESDLVKVD 490 (603)
T ss_pred eCcHHHHHHHHHHHHHhcCceecceEecCceEEEEEecchHHHHHHHhHhhhccccceeee---ccccccccccceEEEE
Confidence 577899999999654 67777787555555777776655555444 4555555544433 2222333344455677
Q ss_pred eeccchHHHHH
Q 026574 156 TIEASLRVDAL 166 (236)
Q Consensus 156 ~~v~s~RLD~i 166 (236)
+-+.+..+|++
T Consensus 491 IlvNge~VDAL 501 (603)
T COG0481 491 ILVNGEKVDAL 501 (603)
T ss_pred EEecCccccce
Confidence 78889999975
No 95
>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=34.30 E-value=33 Score=24.66 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=19.7
Q ss_pred cEEECCEEecCCCcccCCCCEEEE
Q 026574 186 DVRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 186 ~V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
.+..||+.+ ..++.|+.||+|+|
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 445799998 59999999999987
No 96
>PF12728 HTH_17: Helix-turn-helix domain
Probab=33.23 E-value=30 Score=22.12 Aligned_cols=21 Identities=29% Similarity=0.430 Sum_probs=17.7
Q ss_pred HHhCCCcCHHHHHHHHHCCcE
Q 026574 167 ASAGFKLSRSKLVNLISNGDV 187 (236)
Q Consensus 167 ls~~~~~SR~~a~~lI~~G~V 187 (236)
+++.+++|++.+.+++++|.+
T Consensus 7 ~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 7 AAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHCcCHHHHHHHHHcCCC
Confidence 455679999999999999865
No 97
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=30.45 E-value=36 Score=20.71 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=18.5
Q ss_pred HHhCCCcCHHHHHHHHHCCcEE
Q 026574 167 ASAGFKLSRSKLVNLISNGDVR 188 (236)
Q Consensus 167 ls~~~~~SR~~a~~lI~~G~V~ 188 (236)
+++.+++|++.+..++++|.+.
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCCC
Confidence 4566899999999999998763
No 98
>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=29.03 E-value=57 Score=26.61 Aligned_cols=109 Identities=17% Similarity=0.167 Sum_probs=60.8
Q ss_pred cEEEecCCeEEEEechhhHHHHHhccceecceEEEE------EEecCc--ccccCCCCceEEeeecc-chHHHHHHHhCC
Q 026574 101 DIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSC------TRIPLL--ALEYEPPRTKSFKTIEA-SLRVDALASAGF 171 (236)
Q Consensus 101 DI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~------~~~~~~--~~~~~~~~~~~~~~~v~-s~RLD~ils~~~ 171 (236)
|+++.+...|-++|+++-++.+..-+.++...+-.- ..-|+. +.....+.|+....++. +.+|. -..
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 665555567999999988888776666554432211 112332 11123345666665554 55543 233
Q ss_pred CcCHHHHHHHHH-CCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEE
Q 026574 172 KLSRSKLVNLIS-NGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG 218 (236)
Q Consensus 172 ~~SR~~a~~lI~-~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~ 218 (236)
+.-|+..=-.+. .|.|.+|++.. .+.+||.+.|.-.-+-++.
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 444443222122 45788888775 4889999888655444443
No 99
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=28.98 E-value=48 Score=27.78 Aligned_cols=32 Identities=25% Similarity=0.259 Sum_probs=27.6
Q ss_pred CcCHHHHHHHHHCCcEEECCEEecCCCcccCC
Q 026574 172 KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRT 203 (236)
Q Consensus 172 ~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~ 203 (236)
.-|=+.|..++++|.|+|.-+.+++|++.|.-
T Consensus 119 ~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr 150 (181)
T KOG4655|consen 119 AESVKEAVRFVEQGHVRVGPKVVTDPAFLVTR 150 (181)
T ss_pred hhhHHHHHHHHHcCceeeCCeeccCchHHhhh
Confidence 34567889999999999999999999998854
No 100
>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=28.91 E-value=87 Score=19.43 Aligned_cols=22 Identities=41% Similarity=0.404 Sum_probs=18.1
Q ss_pred EEECCEEecCCCcccCCCCEEEE
Q 026574 187 VRVNWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 187 V~VNg~~~~~~~~~v~~GD~Isv 209 (236)
+.+||+.+ ..++.+..||.|.+
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 56999987 58889999998765
No 101
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=28.01 E-value=45 Score=23.90 Aligned_cols=22 Identities=23% Similarity=0.302 Sum_probs=10.9
Q ss_pred CCCcccCCCCEEEEeeCCeEEE
Q 026574 196 KNGTTLRTGDIVSVSGKGRIKI 217 (236)
Q Consensus 196 ~~~~~v~~GD~Isvrg~Gr~~~ 217 (236)
.+.+.+.+||.|.|.-+|.-.+
T Consensus 8 ~~~y~l~pGD~l~i~v~~~~~l 29 (82)
T PF02563_consen 8 PPEYRLGPGDVLRISVFGWPEL 29 (82)
T ss_dssp T------TT-EEEEEETT-HHH
T ss_pred CCCCEECCCCEEEEEEecCCCc
Confidence 4789999999999998775443
No 102
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=27.87 E-value=42 Score=23.03 Aligned_cols=42 Identities=26% Similarity=0.402 Sum_probs=25.5
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec--CCCcccCCCCEEEE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT--KNGTTLRTGDIVSV 209 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~--~~~~~v~~GD~Isv 209 (236)
++.+-.+|.. +++.... =.|.+|+..+. ..+..|++||.|.|
T Consensus 15 ~~tl~~ll~~-l~~~~~~-------vav~~N~~iv~r~~~~~~L~~gD~ieI 58 (65)
T PRK05863 15 QTTVAALLDS-LGFPEKG-------IAVAVDWSVLPRSDWATKLRDGARLEV 58 (65)
T ss_pred CCcHHHHHHH-cCCCCCc-------EEEEECCcCcChhHhhhhcCCCCEEEE
Confidence 4556666655 3443221 14678998443 23356999999887
No 103
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=27.84 E-value=1.3e+02 Score=23.20 Aligned_cols=34 Identities=15% Similarity=0.290 Sum_probs=23.8
Q ss_pred HHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574 179 VNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212 (236)
Q Consensus 179 ~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~ 212 (236)
-++|++|.=.+-.+........+++||.|.+...
T Consensus 10 F~~I~~G~KtiEiRlnD~kr~~ikvGD~I~f~~~ 43 (109)
T cd06555 10 FELIKSGKKTIEIRLNDEKRQQIKVGDKILFNDL 43 (109)
T ss_pred HHHHHcCCCEEEEEecccchhcCCCCCEEEEEEc
Confidence 4568888755555554434457999999999764
No 104
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=27.50 E-value=38 Score=33.14 Aligned_cols=75 Identities=19% Similarity=0.144 Sum_probs=56.8
Q ss_pred CceEEeeeccchHHHHHHHhCCCcCHHHHHHHHH---CCcEEECCEEecCCCcccCCCCEEEEee--CCeEEEEEeeccc
Q 026574 150 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLIS---NGDVRVNWTTVTKNGTTLRTGDIVSVSG--KGRIKIGEINSTR 224 (236)
Q Consensus 150 ~~~~~~~~v~s~RLD~ils~~~~~SR~~a~~lI~---~G~V~VNg~~~~~~~~~v~~GD~Isvrg--~Gr~~~~~~~~TK 224 (236)
.|=.+-.-+.+.-||-+|.+.--+|-..|+..|. +-.+.+|-....--.|-++||.++-+.| .|-++|...|.+|
T Consensus 542 sFCTVLEYceGNDLDFYLKQhklmSEKEARSIiMQiVnAL~YLNEikpPIIHYDLKPgNILLv~GtacGeIKITDFGLSK 621 (775)
T KOG1151|consen 542 SFCTVLEYCEGNDLDFYLKQHKLMSEKEARSIIMQIVNALKYLNEIKPPIIHYDLKPGNILLVNGTACGEIKITDFGLSK 621 (775)
T ss_pred cceeeeeecCCCchhHHHHhhhhhhHHHHHHHHHHHHHHHHHHhccCCCeeeeccCCccEEEecCcccceeEeeecchhh
Confidence 3434444567889999999887899988888865 5677888766544568999999999987 5788887776554
No 105
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. 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=27.12 E-value=41 Score=24.89 Aligned_cols=39 Identities=21% Similarity=0.343 Sum_probs=27.3
Q ss_pred hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 026574 161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 210 (236)
Q Consensus 161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr 210 (236)
...|.++... |-. .+.++|++++-|+ +|.|+.||++.++
T Consensus 44 i~~~d~i~~g---~~~---~ak~~Gkir~eGK-----~Yiv~DGDi~~f~ 82 (83)
T cd04867 44 MKYEDLVELG---SEA---AAKEAGKYRQEGK-----DYVVQDGDIIFFK 82 (83)
T ss_pred EcHHHHHHcC---CHH---HHHHcChhhhhCC-----ceEeeCCeEEEEE
Confidence 3466666542 333 3446899988886 6789999999875
No 106
>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=26.92 E-value=1.5e+02 Score=20.31 Aligned_cols=40 Identities=8% Similarity=0.040 Sum_probs=32.2
Q ss_pred hhhhhcCC-ceEEecCCChHHHHHHHHHhcccCCeeEEEeCC
Q 026574 2 ARRASSRR-EVLHSDFLTPPVLKESMMALEKLADVKAVAQGG 42 (236)
Q Consensus 2 ~~~~~~~~-~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GG 42 (236)
|+++...+ .++--.=++|++..+++.+++++ ++.....|-
T Consensus 10 a~~V~~~~~~~veL~Pm~~~eRri~H~~v~~~-~l~s~S~G~ 50 (60)
T cd02645 10 IEQVVIPKGEPVELLPRSAYIRRLQHDLVERY-QLRSESFGS 50 (60)
T ss_pred HHHHHhcCCceEEcCCCCHHHHHHHHHHHHHC-CCeEEEecC
Confidence 56777777 88888889999999999999874 887777663
No 107
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=26.76 E-value=62 Score=33.01 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=21.5
Q ss_pred cEEECCEEecCCCcccCCCCEEEEe
Q 026574 186 DVRVNWTTVTKNGTTLRTGDIVSVS 210 (236)
Q Consensus 186 ~V~VNg~~~~~~~~~v~~GD~Isvr 210 (236)
..+|||+.+ ..++.|+.||+|.|-
T Consensus 423 gAkVNg~~v-pL~~~L~~Gd~VeIi 446 (702)
T PRK11092 423 GARVDRQPY-PLSQPLTSGQTVEII 446 (702)
T ss_pred EEEECCEEC-CCCccCCCCCEEEEE
Confidence 468999999 599999999999984
No 108
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=26.33 E-value=53 Score=24.11 Aligned_cols=42 Identities=21% Similarity=0.310 Sum_probs=26.9
Q ss_pred chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecC---CCcccCCCCEEEE
Q 026574 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTK---NGTTLRTGDIVSV 209 (236)
Q Consensus 160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~---~~~~v~~GD~Isv 209 (236)
++.|..+|.. +++....+ .|.+|+..+.+ .+..|++||.|.|
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 4557777764 34322111 46799999843 3478999999887
No 109
>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=24.71 E-value=2.1e+02 Score=19.06 Aligned_cols=39 Identities=13% Similarity=0.035 Sum_probs=26.4
Q ss_pred ceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEE
Q 026574 10 EVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS 52 (236)
Q Consensus 10 ~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~ 52 (236)
...+-+ ||+.+...++.++. ..++.....| ++..|..++
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 99999998888776 6789888876 445564443
No 110
>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=23.58 E-value=2.1e+02 Score=19.88 Aligned_cols=31 Identities=16% Similarity=0.218 Sum_probs=18.0
Q ss_pred CEEEEeeCCeEEEEEeeccccccEEEEEEEe
Q 026574 205 DIVSVSGKGRIKIGEINSTRKGKFAVELIQY 235 (236)
Q Consensus 205 D~Isvrg~Gr~~~~~~~~TKKgr~~i~~~r~ 235 (236)
+.+.+.-.|+-.+...-.+..|++-+.+.+.
T Consensus 43 ~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~ 73 (77)
T PF01052_consen 43 EPVELRVNGQPIFRGELGRVNGRLAVRITEL 73 (77)
T ss_dssp TEEEEEETTEEEEEEEEEEETTEEEEEEEEE
T ss_pred CCEEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 3444444555555433246778888887664
No 111
>cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. 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=23.17 E-value=86 Score=22.50 Aligned_cols=19 Identities=16% Similarity=0.298 Sum_probs=17.1
Q ss_pred CCEEecCCCcccCCCCEEEE
Q 026574 190 NWTTVTKNGTTLRTGDIVSV 209 (236)
Q Consensus 190 Ng~~~~~~~~~v~~GD~Isv 209 (236)
|++.+ ..++.|+.||+|.|
T Consensus 56 ~~~~v-g~~~~L~dgDvV~I 74 (76)
T cd01669 56 TGRRV-GEDYELKHRDVIKI 74 (76)
T ss_pred CCEEe-CCCcEecCCCEEEE
Confidence 88888 58999999999987
No 112
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=22.92 E-value=2.7e+02 Score=19.57 Aligned_cols=41 Identities=15% Similarity=0.054 Sum_probs=29.2
Q ss_pred CCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEE
Q 026574 8 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS 52 (236)
Q Consensus 8 ~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~ 52 (236)
.....+.+ ||+.+...++.++.++ ++.....|- +..|..++
T Consensus 36 ~~~~~~~p-m~~~~R~~iH~~a~~~-~l~s~S~g~--g~~R~vvv 76 (79)
T smart00393 36 KESVELPP-MNSYERKIVHELAEKY-GLESESFGE--GPKRRVVI 76 (79)
T ss_pred CCeEEcCC-CCHHHHHHHHHHHHHc-CCEEEEEcC--CCCcEEEE
Confidence 44556666 9999999999988887 888887665 23354444
No 113
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=22.35 E-value=99 Score=21.26 Aligned_cols=25 Identities=20% Similarity=0.170 Sum_probs=14.6
Q ss_pred cEEECCEEecC--CCcccCCCCEEEEe
Q 026574 186 DVRVNWTTVTK--NGTTLRTGDIVSVS 210 (236)
Q Consensus 186 ~V~VNg~~~~~--~~~~v~~GD~Isvr 210 (236)
...|||+.... .++.|+.||.|..+
T Consensus 42 ~~~vNG~~~~~ga~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 42 MYYVNGESANVGAGSYKLKDGDKITWY 68 (68)
T ss_dssp EEEETTEE-SS-CCC-B--TTEEEEE-
T ss_pred EEEECCEEhhcCcceeEeCCCCEEEeC
Confidence 46789998643 24788999998753
No 114
>PF03829 PTSIIA_gutA: PTS system glucitol/sorbitol-specific IIA component; InterPro: IPR004716 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2F9H_A.
Probab=22.17 E-value=49 Score=25.93 Aligned_cols=40 Identities=15% Similarity=0.292 Sum_probs=25.1
Q ss_pred ccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEec
Q 026574 98 KIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIP 140 (236)
Q Consensus 98 ~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~ 140 (236)
+.||.+.-++ ..|.+.. +-+-..+||..+||+.+.+...+
T Consensus 53 ~~Gd~l~i~~-~~y~Ita--VG~~an~NL~~LGH~Tl~F~g~~ 92 (117)
T PF03829_consen 53 KPGDTLIIGG-QEYTITA--VGSVANQNLRELGHITLVFDGAE 92 (117)
T ss_dssp -TT-EEEETT-EEEEEEE--E-TTHHHHHHHHS-EEEE-S-SG
T ss_pred CCCCEEEECC-eEEEEEE--EhHHHHHHHHhcCcEEEEECCCC
Confidence 5699888776 4555544 55556799999999999997643
No 115
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=21.80 E-value=1.9e+02 Score=22.34 Aligned_cols=36 Identities=19% Similarity=0.206 Sum_probs=28.9
Q ss_pred cEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEee
Q 026574 186 DVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEIN 221 (236)
Q Consensus 186 ~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~ 221 (236)
.|.|||....+-.+++...++-.+.-.|-+.+..+.
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 488999998888888888777777777878877653
No 116
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=21.65 E-value=67 Score=25.08 Aligned_cols=29 Identities=17% Similarity=0.186 Sum_probs=23.8
Q ss_pred CCcEEECCEEecCCCcccCCCCEEEEeeCCeEE
Q 026574 184 NGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIK 216 (236)
Q Consensus 184 ~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~ 216 (236)
+|.|.+||..+ ..+++||.|-|--|+-+.
T Consensus 65 Sg~I~lNGAAA----r~~~~GD~vII~sy~~~~ 93 (111)
T cd06919 65 SGVICLNGAAA----RLGQPGDRVIIMAYALMD 93 (111)
T ss_pred CCEEEeCCHHH----hcCCCCCEEEEEECccCC
Confidence 68999999755 479999999998887544
No 117
>PF01356 A_amylase_inhib: Alpha amylase inhibitor; InterPro: IPR000833 Alpha-amylase inhibitor inhibits mammalian alpha-amylases specifically, by forming a tight stoichiometric 1:1 complex with alpha-amylase. The inhibitor has no action on plant and microbial alpha amylases. A crystal structure has been determined for tendamistat, the 74-amino acid inhibitor produced by Streptomyces tendae that targets a wide range of mammalian alpha-amylases []. The binding of tendamistat to alpha-amylase leads to the steric blockage of the active site of the enzyme. The crystal structure of tendamistat revealed an immunoglobulin-like fold that could potentially adopt multiple conformations. Such molecular flexibility could enable an induced-fit type of binding that would both optimise binding and allow broad target specificity. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0015066 alpha-amylase inhibitor activity; PDB: 2KER_A 3AIT_A 1BVN_T 1HOE_A 4AIT_A 2AIT_A 1OK0_A.
Probab=21.56 E-value=38 Score=23.96 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=16.0
Q ss_pred CCEEecCCCcccCCCCEEEEeeCC
Q 026574 190 NWTTVTKNGTTLRTGDIVSVSGKG 213 (236)
Q Consensus 190 Ng~~~~~~~~~v~~GD~Isvrg~G 213 (236)
||+.+ |-..+.|||++++-|+|
T Consensus 35 dG~~~--PCrv~~PG~~~Tf~Gyg 56 (68)
T PF01356_consen 35 DGQEV--PCRVIPPGDIATFPGYG 56 (68)
T ss_dssp TS-CE--EEEEE-TTEEEEEE-TT
T ss_pred CCCcc--eeEEeCCCCEEEecccc
Confidence 66655 67789999999999998
No 118
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=21.41 E-value=1.7e+02 Score=20.67 Aligned_cols=30 Identities=30% Similarity=0.610 Sum_probs=21.3
Q ss_pred CCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEEE
Q 026574 197 NGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQ 234 (236)
Q Consensus 197 ~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~r 234 (236)
....+++||.|.+.|. +. . ++|++.+.+..
T Consensus 40 ~~~~l~~Gd~V~v~G~--v~-----~-~~G~~ql~v~~ 69 (73)
T cd04487 40 AYPEVEVGDIVRVTGE--VE-----P-RDGQLQIEVES 69 (73)
T ss_pred CcCCCCCCCEEEEEEE--Ee-----c-CCeEEEEEEee
Confidence 4567899999888877 21 2 78888776643
No 119
>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=20.72 E-value=3e+02 Score=19.03 Aligned_cols=57 Identities=23% Similarity=0.335 Sum_probs=36.9
Q ss_pred CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEE
Q 026574 172 KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVE 231 (236)
Q Consensus 172 ~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~ 231 (236)
.++|..|.+++.+.. +|.-+-..+..-...=.||++-.++++=-.|..+..|++.+.
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 589999999988743 555443344332222378888888877666654444777664
No 120
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=20.06 E-value=1.8e+02 Score=20.46 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=21.0
Q ss_pred CcEEECCEEecC-CCcccCCCCEEEEee
Q 026574 185 GDVRVNWTTVTK-NGTTLRTGDIVSVSG 211 (236)
Q Consensus 185 G~V~VNg~~~~~-~~~~v~~GD~Isvrg 211 (236)
..+.||++.+.. ....+..||.|.+-.
T Consensus 66 ~g~~vn~~~~~~~~~~~l~~gd~i~ig~ 93 (102)
T cd00060 66 NGTFVNGQRVSPGEPVRLRDGDVIRLGN 93 (102)
T ss_pred CCeEECCEECCCCCcEECCCCCEEEECC
Confidence 367899999853 457889999999864
Done!