Query psy7990
Match_columns 76
No_of_seqs 125 out of 661
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 23:59:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7990.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7990hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00189 40S ribosomal protein 100.0 1E-28 2.2E-33 179.4 6.0 73 1-73 120-192 (194)
2 PTZ00155 40S ribosomal protein 99.9 2.1E-25 4.6E-30 160.3 5.2 63 1-63 118-180 (181)
3 KOG3301|consensus 99.9 6.9E-25 1.5E-29 158.2 4.6 76 1-76 108-183 (183)
4 COG0522 RpsD Ribosomal protein 99.8 6E-21 1.3E-25 139.0 3.1 54 1-54 105-159 (205)
5 TIGR01018 rpsD_arch ribosomal 99.8 2.1E-20 4.6E-25 132.6 4.7 48 1-48 115-162 (162)
6 PRK04051 rps4p 30S ribosomal p 99.7 8E-18 1.7E-22 120.6 5.3 57 1-57 114-171 (177)
7 CHL00113 rps4 ribosomal protei 99.0 3.6E-10 7.7E-15 82.2 3.7 43 1-45 100-142 (201)
8 PF01479 S4: S4 domain; Inter 98.9 7.6E-10 1.6E-14 62.3 2.8 36 1-36 12-47 (48)
9 TIGR01017 rpsD_bact ribosomal 98.9 2E-09 4.3E-14 77.5 4.1 43 1-45 101-143 (200)
10 PRK05327 rpsD 30S ribosomal pr 98.9 1.8E-09 3.9E-14 77.9 3.5 41 2-44 105-145 (203)
11 cd00165 S4 S4/Hsp/ tRNA synthe 98.1 3.6E-06 7.8E-11 47.0 3.7 40 2-43 13-52 (70)
12 TIGR02988 YaaA_near_RecF S4 do 98.0 4.7E-06 1E-10 49.0 2.4 35 3-37 22-56 (59)
13 smart00363 S4 S4 RNA-binding d 97.8 2E-05 4.4E-10 42.9 3.0 40 2-43 13-52 (60)
14 PRK10348 ribosome-associated h 97.6 5.4E-05 1.2E-09 52.6 3.0 41 1-42 20-60 (133)
15 KOG4655|consensus 97.6 1.4E-05 3E-10 58.4 -0.2 46 1-46 118-163 (181)
16 TIGR00478 tly hemolysin TlyA f 97.4 0.00017 3.7E-09 53.0 3.2 41 2-44 12-52 (228)
17 COG1188 Ribosome-associated he 97.4 0.00014 3E-09 48.9 2.5 39 4-43 23-61 (100)
18 TIGR03069 PS_II_S4 photosystem 97.1 0.00035 7.6E-09 52.1 2.4 38 3-42 196-233 (257)
19 PLN00051 RNA-binding S4 domain 96.3 0.0034 7.3E-08 47.4 2.6 38 3-40 204-241 (267)
20 COG1189 Predicted rRNA methyla 96.2 0.0046 1E-07 47.0 3.0 45 2-48 15-60 (245)
21 PRK10839 16S rRNA pseudouridyl 96.1 0.0057 1.2E-07 43.7 3.0 37 4-42 14-50 (232)
22 PRK10700 23S rRNA pseudouridyl 95.8 0.011 2.4E-07 44.5 3.5 39 3-42 15-53 (289)
23 COG2302 Uncharacterized conser 95.3 0.013 2.8E-07 44.9 2.4 36 4-39 194-229 (257)
24 PRK11180 rluD 23S rRNA pseudou 95.3 0.017 3.6E-07 43.6 2.9 38 3-42 31-68 (325)
25 TIGR00005 rluA_subfam pseudour 95.0 0.018 3.9E-07 42.3 2.4 37 4-42 20-56 (299)
26 PRK10475 23S rRNA pseudouridin 94.8 0.022 4.7E-07 43.2 2.5 37 3-42 19-55 (290)
27 PRK11507 ribosome-associated p 94.1 0.061 1.3E-06 34.0 2.8 36 1-36 23-58 (70)
28 PRK11025 23S rRNA pseudouridyl 93.2 0.068 1.5E-06 40.2 2.4 36 4-42 34-69 (317)
29 COG0564 RluA Pseudouridylate s 92.9 0.1 2.2E-06 39.5 2.8 39 4-43 26-64 (289)
30 PRK13354 tyrosyl-tRNA syntheta 92.9 0.086 1.9E-06 41.8 2.5 34 1-34 354-387 (410)
31 COG1187 RsuA 16S rRNA uridine- 92.5 0.17 3.8E-06 38.1 3.7 33 3-35 15-47 (248)
32 PF13275 S4_2: S4 domain; PDB: 91.8 0.043 9.3E-07 34.0 -0.3 35 2-36 20-54 (65)
33 PRK05912 tyrosyl-tRNA syntheta 91.0 0.21 4.6E-06 39.4 2.8 33 1-33 354-386 (408)
34 COG1471 RPS4A Ribosomal protei 90.7 0.29 6.2E-06 37.4 3.2 61 3-63 55-133 (241)
35 PF14451 Ub-Mut7C: Mut7-C ubiq 83.3 0.77 1.7E-05 29.2 1.5 26 15-43 50-75 (81)
36 PLN02799 Molybdopterin synthas 82.6 2.4 5.1E-05 25.7 3.5 30 16-50 53-82 (82)
37 cd00754 MoaD Ubiquitin domain 79.5 3.1 6.8E-05 24.4 3.2 33 13-50 48-80 (80)
38 PRK01777 hypothetical protein; 77.9 5.3 0.00012 26.0 4.1 42 13-60 48-89 (95)
39 PRK04313 30S ribosomal protein 74.2 2.4 5.2E-05 32.1 2.0 34 3-36 52-85 (237)
40 PF11736 DUF3299: Protein of u 73.3 3.1 6.7E-05 29.1 2.2 24 18-41 52-77 (146)
41 COG2501 S4-like RNA binding pr 72.8 5.1 0.00011 25.5 3.0 33 3-35 25-57 (73)
42 PLN00036 40S ribosomal protein 70.0 3.1 6.7E-05 32.0 1.8 33 3-35 56-88 (261)
43 TIGR01682 moaD molybdopterin c 68.3 8.7 0.00019 23.1 3.2 31 15-50 50-80 (80)
44 PTZ00118 40S ribosomal protein 67.5 3.8 8.3E-05 31.5 1.8 34 3-36 56-89 (262)
45 PF02597 ThiS: ThiS family; I 67.2 6.3 0.00014 22.9 2.4 34 13-50 42-77 (77)
46 TIGR01687 moaD_arch MoaD famil 65.1 9.3 0.0002 23.2 2.9 35 13-50 54-88 (88)
47 TIGR00234 tyrS tyrosyl-tRNA sy 65.0 5.4 0.00012 31.3 2.3 33 1-33 341-373 (377)
48 PTZ00223 40S ribosomal protein 64.4 4.7 0.0001 31.2 1.8 34 3-36 53-86 (273)
49 cd01764 Urm1 Urm1-like ubuitin 61.2 11 0.00024 24.1 2.9 35 14-50 59-94 (94)
50 COG0162 TyrS Tyrosyl-tRNA synt 57.0 8.3 0.00018 31.0 2.1 30 1-30 347-376 (401)
51 KOG2623|consensus 56.5 7.6 0.00016 32.2 1.8 29 2-30 411-439 (467)
52 PF01324 Diphtheria_R: Diphthe 53.3 16 0.00034 26.0 2.7 32 13-47 66-97 (154)
53 PRK11130 moaD molybdopterin sy 51.4 34 0.00073 20.8 3.8 30 16-50 52-81 (81)
54 PRK06944 sulfur carrier protei 45.1 40 0.00087 19.2 3.3 32 15-50 31-65 (65)
55 PRK06437 hypothetical protein; 43.9 20 0.00044 21.4 1.9 25 16-43 38-62 (67)
56 PRK09273 hypothetical protein; 43.6 6 0.00013 29.6 -0.6 57 2-62 92-154 (211)
57 PHA01635 hypothetical protein 42.3 13 0.00027 28.4 1.0 20 13-32 61-80 (231)
58 PF04571 Lipin_N: lipin, N-ter 38.6 41 0.0009 22.9 2.9 26 16-44 63-88 (110)
59 PF07908 D-aminoacyl_C: D-amin 38.1 21 0.00045 20.3 1.2 10 16-25 22-31 (48)
60 PF14478 DUF4430: Domain of un 36.9 39 0.00085 19.9 2.4 28 15-42 41-68 (68)
61 PRK08364 sulfur carrier protei 34.8 64 0.0014 19.2 3.1 30 15-49 40-69 (70)
62 PF14259 RRM_6: RNA recognitio 34.1 24 0.00052 19.7 1.1 24 2-25 46-70 (70)
63 PF13893 RRM_5: RNA recognitio 34.0 38 0.00082 18.4 1.9 23 3-26 29-53 (56)
64 TIGR01683 thiS thiamine biosyn 33.6 28 0.00061 20.2 1.3 12 17-28 1-12 (64)
65 PF05949 DUF881: Bacterial pro 32.9 22 0.00047 24.4 0.9 27 16-42 60-86 (149)
66 COG1351 THY1 Predicted alterna 32.8 18 0.0004 27.5 0.5 34 4-41 87-120 (273)
67 PRK12268 methionyl-tRNA synthe 32.6 23 0.0005 28.3 1.1 19 9-27 320-338 (556)
68 TIGR02170 thyX thymidylate syn 32.4 18 0.00039 25.7 0.5 17 3-19 64-80 (209)
69 PF00498 FHA: FHA domain; Int 31.4 74 0.0016 17.8 2.9 24 15-39 42-65 (68)
70 PF13810 DUF4185: Domain of un 31.1 33 0.00071 26.3 1.7 40 5-45 75-115 (316)
71 PRK15200 fimbrial protein FimI 30.8 36 0.00078 23.6 1.7 38 3-41 15-53 (177)
72 PRK08053 sulfur carrier protei 30.1 74 0.0016 18.6 2.8 27 17-43 34-61 (66)
73 PRK05659 sulfur carrier protei 29.5 39 0.00085 19.4 1.5 13 16-28 2-14 (66)
74 PRK12267 methionyl-tRNA synthe 29.4 23 0.0005 29.2 0.6 42 8-49 284-334 (648)
75 COG3395 Uncharacterized protei 27.7 28 0.00061 28.4 0.8 28 1-28 111-138 (413)
76 PRK00847 thyX FAD-dependent th 26.6 31 0.00066 24.8 0.8 18 3-20 71-88 (217)
77 PRK12300 leuS leucyl-tRNA synt 26.0 25 0.00054 30.5 0.2 17 9-25 563-579 (897)
78 COG3243 PhaC Poly(3-hydroxyalk 25.8 60 0.0013 27.0 2.4 28 11-40 312-344 (445)
79 cd00565 ThiS ThiaminS ubiquiti 25.5 54 0.0012 18.9 1.6 11 17-27 2-12 (65)
80 PF02511 Thy1: Thymidylate syn 24.9 32 0.0007 23.9 0.6 17 4-20 61-77 (190)
81 PRK14129 heat shock protein Hs 24.8 24 0.00053 24.0 -0.0 30 1-30 1-31 (105)
82 PF09334 tRNA-synt_1g: tRNA sy 24.7 22 0.00048 27.8 -0.3 18 8-25 312-329 (391)
83 COG2301 CitE Citrate lyase bet 24.6 34 0.00073 26.4 0.7 17 13-29 247-265 (283)
84 PF13991 BssS: BssS protein fa 24.1 33 0.00071 21.9 0.5 12 2-13 41-52 (73)
85 cd06880 PX_SNX22 The phosphoin 23.5 61 0.0013 20.9 1.7 21 23-43 2-24 (110)
86 PTZ00198 60S ribosomal protein 22.8 73 0.0016 22.2 2.0 39 13-51 43-81 (122)
87 smart00216 VWD von Willebrand 22.7 59 0.0013 21.2 1.6 16 14-29 82-97 (162)
88 PF05965 FYRC: F/Y rich C-term 22.5 40 0.00086 20.6 0.6 23 26-48 3-25 (86)
89 KOG0436|consensus 21.5 31 0.00067 29.3 -0.0 38 5-42 326-370 (578)
90 PRK06488 sulfur carrier protei 21.4 71 0.0015 18.4 1.6 30 16-49 32-64 (65)
91 TIGR00395 leuS_arch leucyl-tRN 20.4 36 0.00078 29.7 0.2 18 8-25 605-622 (938)
92 TIGR00398 metG methionyl-tRNA 20.2 44 0.00095 26.6 0.6 19 8-26 312-330 (530)
93 PF14541 TAXi_C: Xylanase inhi 20.0 1.3E+02 0.0029 19.9 2.8 33 16-48 8-41 (161)
No 1
>PLN00189 40S ribosomal protein S9; Provisional
Probab=99.95 E-value=1e-28 Score=179.38 Aligned_cols=73 Identities=48% Similarity=0.756 Sum_probs=67.2
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhhhccCCCCCCc
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEE 73 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~~~~~~~~~~e 73 (76)
||+|+.+|||||+||||.|||++||+|||+|++++|++|+|+.+|||+++.|||+|||+++++++++++|+|+
T Consensus 120 ~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~~Sp~~~~~p~r~~~k~~~~~~~~~~~~~~~ 192 (194)
T PLN00189 120 MAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQKAASGGGDGDEED 192 (194)
T ss_pred CcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEecCCcccCCChhHHHHHHHHhccCCCCccccc
Confidence 7999999999999999999999999999999999999999999999999789999999999997765554443
No 2
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=99.91 E-value=2.1e-25 Score=160.28 Aligned_cols=63 Identities=46% Similarity=0.741 Sum_probs=60.1
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhh
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKA 63 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~ 63 (76)
||+|+.+|||||+||||.|||++||+|||+|++++|++|+|+.+|||+++.|+|++||+++++
T Consensus 118 ~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~~~~~~r~~~~~~~~~ 180 (181)
T PTZ00155 118 LAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAA 180 (181)
T ss_pred CcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceeeecCCCccCCChHHHHHHhhhhc
Confidence 799999999999999999999999999999999999999999999999877999999888754
No 3
>KOG3301|consensus
Probab=99.91 E-value=6.9e-25 Score=158.18 Aligned_cols=76 Identities=50% Similarity=0.738 Sum_probs=67.1
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhhhccCCCCCCcccC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~~~~~~~~~~e~~~ 76 (76)
|.-|+.+|||||+|+||.|++|+||||||+|+.+++++|||+.+|||++++|||+|+|++++..++.++.+++||+
T Consensus 108 lAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrldsqk~iD~s~~s~~g~~~pg~~krk~~~k~~~~~g~~~~~Ee~ 183 (183)
T KOG3301|consen 108 LAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLDSQKHIDFSLPSPYGGARPGRVKRKNNQKADAKGGGLDENEEE 183 (183)
T ss_pred hhhhhHHHHHHhcCccEEecCeEeeccceeEeechhhhccccccccCCCCCcchhhhhhhhhhhcccCCccccccC
Confidence 4568999999999999999999999999999999999999999999999999999999877776555555555543
No 4
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=6e-21 Score=138.96 Aligned_cols=54 Identities=20% Similarity=0.133 Sum_probs=50.2
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC-cch
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-TGR 54 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~-pgR 54 (76)
|.+|+++|||||+||||+|||++||||||+|+++|+..|.+..+|++.... +.+
T Consensus 105 fA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~~~ 159 (205)
T COG0522 105 FAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALEL 159 (205)
T ss_pred ccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchhhhhhhhhh
Confidence 578999999999999999999999999999999999999999999999766 443
No 5
>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=99.81 E-value=2.1e-20 Score=132.57 Aligned_cols=48 Identities=31% Similarity=0.509 Sum_probs=46.9
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFG 48 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~ 48 (76)
||+|+.+|||||+||||.|||++||+|||+|++++|++|+|+.+|||+
T Consensus 115 ~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~ 162 (162)
T TIGR01018 115 LARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSSPFK 162 (162)
T ss_pred CcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeecCCCCC
Confidence 789999999999999999999999999999999999999999999985
No 6
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=99.72 E-value=8e-18 Score=120.60 Aligned_cols=57 Identities=21% Similarity=0.318 Sum_probs=53.1
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC-cchhhh
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-TGRVKR 57 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~-pgR~kr 57 (76)
||.|+.+|||||.||||.|||++|++|||+|+.++|++|+|+.+||+.... |+|..-
T Consensus 114 la~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~i~~~~~~~r~~~ 171 (177)
T PRK04051 114 LARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLADELHPERAEA 171 (177)
T ss_pred CcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCCCCCCCCcchhhh
Confidence 689999999999999999999999999999999999999999999999855 887543
No 7
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.99 E-value=3.6e-10 Score=82.15 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=37.8
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS 45 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S 45 (76)
+|+|+.+|||||.||||.|||++|++|||.|+.| +.|.+...|
T Consensus 100 ~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~G--D~I~V~~~~ 142 (201)
T CHL00113 100 MAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPK--DIITVKDKQ 142 (201)
T ss_pred CCCCHHHHHHHHHCCcEEECCEEecCccccCCCC--CEEEEcccc
Confidence 3789999999999999999999999999999998 467776533
No 8
>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=98.93 E-value=7.6e-10 Score=62.30 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=33.7
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ 36 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de 36 (76)
.|+|+.+|++||.||+|.|||++|+-|+|.|+.+|+
T Consensus 12 ~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~ 47 (48)
T PF01479_consen 12 LASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDV 47 (48)
T ss_dssp SSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEE
T ss_pred CcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCC
Confidence 478999999999999999999999999999998874
No 9
>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=98.88 E-value=2e-09 Score=77.52 Aligned_cols=43 Identities=28% Similarity=0.311 Sum_probs=37.9
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS 45 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S 45 (76)
+|+|+.+|||||.||||.|||++|++|||.|+.|| .|.+...+
T Consensus 101 ~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD--~I~V~~~~ 143 (200)
T TIGR01017 101 FAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGD--IISIKEKS 143 (200)
T ss_pred CCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCC--EEEEeeCc
Confidence 36899999999999999999999999999999995 67776543
No 10
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.86 E-value=1.8e-09 Score=77.93 Aligned_cols=41 Identities=24% Similarity=0.216 Sum_probs=37.3
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeC
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLN 44 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~ 44 (76)
++|+.+|||||.||||.|||++|++|||.|+.||. |++...
T Consensus 105 ~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~--I~v~~~ 145 (203)
T PRK05327 105 APTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDV--IEVREK 145 (203)
T ss_pred cCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCE--EEECCc
Confidence 67999999999999999999999999999999965 777755
No 11
>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=98.14 E-value=3.6e-06 Score=47.03 Aligned_cols=40 Identities=23% Similarity=0.189 Sum_probs=35.2
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL 43 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~ 43 (76)
+.|..+|++++.+|+|.|||++++.|++.|..++ .|.+..
T Consensus 13 ~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d--~i~i~~ 52 (70)
T cd00165 13 APSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGD--VIEVDG 52 (70)
T ss_pred ccCHHHHHHHHHcCCEEECCEEccCCccCcCCCC--EEEEcC
Confidence 4688999999999999999999988999999985 477765
No 12
>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=97.99 E-value=4.7e-06 Score=49.00 Aligned_cols=35 Identities=6% Similarity=-0.150 Sum_probs=32.3
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQK 37 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~ 37 (76)
+|.-.++++|..|+|.|||+.++-|+|.|+.||.=
T Consensus 22 ~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v 56 (59)
T TIGR02988 22 DSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVI 56 (59)
T ss_pred cCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEE
Confidence 57889999999999999999999999999999863
No 13
>smart00363 S4 S4 RNA-binding domain.
Probab=97.83 E-value=2e-05 Score=42.88 Aligned_cols=40 Identities=18% Similarity=0.177 Sum_probs=33.9
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL 43 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~ 43 (76)
+.|..+|++++.+|+|.|||+.++-|++.|..+|. |.+..
T Consensus 13 ~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~--i~~~~ 52 (60)
T smart00363 13 APSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDV--ISVRG 52 (60)
T ss_pred ccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCE--EEEcc
Confidence 36788999999999999999999779999988864 66544
No 14
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.61 E-value=5.4e-05 Score=52.59 Aligned_cols=41 Identities=17% Similarity=0.124 Sum_probs=36.7
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
++.|+..|.+||..|+|.|||++ ..||..|+++|+=.|.|.
T Consensus 20 l~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~ 60 (133)
T PRK10348 20 FYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQG 60 (133)
T ss_pred ccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEEC
Confidence 46799999999999999999999 789999999998777654
No 15
>KOG4655|consensus
Probab=97.58 E-value=1.4e-05 Score=58.36 Aligned_cols=46 Identities=20% Similarity=0.271 Sum_probs=43.5
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSP 46 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP 46 (76)
||+++-+|-.||.|||+.|+-.+|+=|+|+|....|+.|.+..+|.
T Consensus 118 m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SK 163 (181)
T KOG4655|consen 118 MAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSK 163 (181)
T ss_pred hhhhHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhhhhhhHH
Confidence 8999999999999999999999999999999999999999887764
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=97.37 E-value=0.00017 Score=52.95 Aligned_cols=41 Identities=20% Similarity=0.105 Sum_probs=36.0
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeC
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLN 44 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~ 44 (76)
++|+.+|++||.+|.|.|||++++.|++.|..+ +.|.+...
T Consensus 12 ~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~--d~I~v~~~ 52 (228)
T TIGR00478 12 FESREKAKRLILKGFVLVNGKKVDKPSALVDFD--AKIELLQN 52 (228)
T ss_pred ccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCC--CEEeccCc
Confidence 578999999999999999999999999999887 46777644
No 17
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.36 E-value=0.00014 Score=48.86 Aligned_cols=39 Identities=23% Similarity=0.129 Sum_probs=35.4
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL 43 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~ 43 (76)
|+..|.-++.-|+|.|||+++ .||+.|++||+=.|.|..
T Consensus 23 rRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 23 RRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGN 61 (100)
T ss_pred hHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCC
Confidence 677899999999999999998 699999999998888863
No 18
>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=97.09 E-value=0.00035 Score=52.10 Aligned_cols=38 Identities=8% Similarity=0.024 Sum_probs=33.6
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
-|+..|++||..|+|.|||+.|+.||+.|+.|| .|.+.
T Consensus 196 ~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD--~Isvr 233 (257)
T TIGR03069 196 LSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGD--RLQLR 233 (257)
T ss_pred hhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCC--EEEEc
Confidence 478899999999999999999999999999986 55554
No 19
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=96.26 E-value=0.0034 Score=47.42 Aligned_cols=38 Identities=5% Similarity=-0.095 Sum_probs=33.4
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCcee
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHID 40 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~ 40 (76)
-|+..|.+||..|+|.||++.|+-|||.|+.||.=.|.
T Consensus 204 ~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiR 241 (267)
T PLN00051 204 MSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVS 241 (267)
T ss_pred cCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence 46788999999999999999999999999999864443
No 20
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=96.18 E-value=0.0046 Score=46.97 Aligned_cols=45 Identities=18% Similarity=0.178 Sum_probs=36.8
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee-eCCCCC
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS-LNSPFG 48 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~-~~SP~~ 48 (76)
|.|+..|+-+|.-|.|.|||++|+.||+.|..+++ |+.. +..||-
T Consensus 15 ~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~--i~v~~~~~~yV 60 (245)
T COG1189 15 FESREKAKELILAGNVLVNGEKVTKPSQLVDIDDE--IEVKGEEQPYV 60 (245)
T ss_pred hhhHHHHHHHHHcCeEEECCEEecCcceecCCCce--EEEcccCcCcc
Confidence 78999999999999999999999999999995554 5554 444443
No 21
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=96.11 E-value=0.0057 Score=43.73 Aligned_cols=37 Identities=8% Similarity=0.146 Sum_probs=32.4
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
|...+++++..|.|.|||++++.|++.|+.+|. |.++
T Consensus 14 Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~--I~l~ 50 (232)
T PRK10839 14 SRAIAGRELRANRVTVDGEIVKNGAFKLLPEHD--VAYD 50 (232)
T ss_pred CHHHHHHHHHcCeEEECCEEeccCCcCcCCCCE--EEEC
Confidence 577899999999999999999889999999875 5554
No 22
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=95.80 E-value=0.011 Score=44.55 Aligned_cols=39 Identities=10% Similarity=-0.032 Sum_probs=33.8
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
.|+-+|++||..|.|.|||++++ |++.|.+++.+.|.+.
T Consensus 15 ~SRr~a~~lI~~G~V~VNG~~~~-~g~~V~~~~~d~I~v~ 53 (289)
T PRK10700 15 GSRREIESIIEAGRVSVDGKIAT-LGDRVEVTPGLKIRID 53 (289)
T ss_pred CCHHHHHHHHHcCCEEECCEecc-CCCEeCCCCCeEEEEC
Confidence 36788999999999999999985 9999998877777665
No 23
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=95.32 E-value=0.013 Score=44.93 Aligned_cols=36 Identities=22% Similarity=0.121 Sum_probs=32.0
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCce
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHI 39 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I 39 (76)
|+..|-|||.-|-+.||.+.|+-|||.|+.||-=.|
T Consensus 194 SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSi 229 (257)
T COG2302 194 SRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISI 229 (257)
T ss_pred hHHHHHHHHHcCceEEeeEEeccccceeccCCEEEE
Confidence 577899999999999999999999999999875333
No 24
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=95.28 E-value=0.017 Score=43.56 Aligned_cols=38 Identities=18% Similarity=0.054 Sum_probs=33.0
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
.|+..++++|..|.|.|||++|+.|++.|+.+|. |.++
T Consensus 31 ~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~--I~v~ 68 (325)
T PRK11180 31 YSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQ--VAID 68 (325)
T ss_pred cCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCE--EEEe
Confidence 4788899999999999999999889999998875 4444
No 25
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=95.04 E-value=0.018 Score=42.30 Aligned_cols=37 Identities=16% Similarity=0.112 Sum_probs=31.2
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
|...++++|..|.|.|||+++.-|++.|+.+|. |.++
T Consensus 20 Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~--I~i~ 56 (299)
T TIGR00005 20 SRSRIQKLIENGQVKVNGKVTANPKLKVKDGDR--ITVR 56 (299)
T ss_pred CHHHHHHHHHCCcEEECCEeccCcccCCCCCCE--EEEe
Confidence 678899999999999999877679999999864 5543
No 26
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=94.84 E-value=0.022 Score=43.21 Aligned_cols=37 Identities=8% Similarity=0.017 Sum_probs=30.9
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
.|+.+|++||..|.|.|||++++ |++.|..+|. |.++
T Consensus 19 ~SRr~a~~lI~~G~V~VNGk~v~-~~~~V~~gD~--V~v~ 55 (290)
T PRK10475 19 CSRREADRYIEQGNVFINGKRAT-IGDQVKAGDV--VKVN 55 (290)
T ss_pred CCHHHHHHHHHCCcEEECCEEcc-CCCCcCCCCE--EEEC
Confidence 36889999999999999999985 9999988754 5554
No 27
>PRK11507 ribosome-associated protein; Provisional
Probab=94.06 E-value=0.061 Score=34.01 Aligned_cols=36 Identities=6% Similarity=-0.171 Sum_probs=32.5
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ 36 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de 36 (76)
.|+|=-+|.+||.-|.|.|||.+-+.-+-.+++||.
T Consensus 23 ~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~ 58 (70)
T PRK11507 23 WSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQT 58 (70)
T ss_pred cccChHHHHHHHHcCceEECCEEecccCCCCCCCCE
Confidence 367888999999999999999999999988888875
No 28
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=93.24 E-value=0.068 Score=40.23 Aligned_cols=36 Identities=8% Similarity=0.187 Sum_probs=31.0
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
+...+++++..|.|.|||++++ |++.|+.+|+ |.+.
T Consensus 34 sr~~i~~li~~G~V~VNg~~v~-~~~~v~~GD~--I~i~ 69 (317)
T PRK11025 34 PKSMIYRILRKGEVRVNKKRIK-PEYKLEAGDE--VRIP 69 (317)
T ss_pred CHHHHHHHHHcCCEEECCEEcC-cccccCCCCE--EEeC
Confidence 6778899999999999999996 9999999964 6553
No 29
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=92.87 E-value=0.1 Score=39.49 Aligned_cols=39 Identities=13% Similarity=0.095 Sum_probs=33.9
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL 43 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~ 43 (76)
+.-+...++..|.|.|||++|+ |+|.|..||.=.|.+..
T Consensus 26 sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~ 64 (289)
T COG0564 26 SRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPE 64 (289)
T ss_pred CHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEeccc
Confidence 3456678899999999999999 99999999998888765
No 30
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=92.85 E-value=0.086 Score=41.77 Aligned_cols=34 Identities=3% Similarity=-0.015 Sum_probs=30.3
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeecC
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLD 34 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~ 34 (76)
+|+|--+||.||..|-|.|||.+|+-|.+.+..+
T Consensus 354 ~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~ 387 (410)
T PRK13354 354 LEPSKREARRLIQNGAIKINGEKVTDVDAIINPE 387 (410)
T ss_pred CCCCHHHHHHHHHcCCEEECCEEccCcccccChh
Confidence 5899999999999999999999998887777654
No 31
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=92.54 E-value=0.17 Score=38.11 Aligned_cols=33 Identities=18% Similarity=0.126 Sum_probs=30.6
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDS 35 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~d 35 (76)
-|+.+|.+||.-|.|.|||+++..+...|..++
T Consensus 15 ~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~ 47 (248)
T COG1187 15 GSRREAEKLIEEGRVTVNGKVATLGGVVVDPDD 47 (248)
T ss_pred CCHHHHHHHHHcCCEEECCEEeccCCeEeCCCC
Confidence 478899999999999999999999999998886
No 32
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=91.79 E-value=0.043 Score=34.01 Aligned_cols=35 Identities=11% Similarity=-0.100 Sum_probs=23.7
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ 36 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de 36 (76)
++|=-+|..||.-|.|.|||.+.+-.+-.+++||.
T Consensus 20 v~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~ 54 (65)
T PF13275_consen 20 VSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDV 54 (65)
T ss_dssp -SSSSTTSHHHHHHHHEETTB----SS----SSEE
T ss_pred cccHHHHHHHHHcCceEECCEEccccCCcCCCCCE
Confidence 56778999999999999999999999998888875
No 33
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=90.96 E-value=0.21 Score=39.45 Aligned_cols=33 Identities=9% Similarity=0.148 Sum_probs=29.0
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeec
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRL 33 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~ 33 (76)
+|+|--+||.||..|-|.|||.+|.-+.+.+..
T Consensus 354 ~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 354 LVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 489999999999999999999999877766654
No 34
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=90.74 E-value=0.29 Score=37.40 Aligned_cols=61 Identities=18% Similarity=0.117 Sum_probs=49.3
Q ss_pred ccchhhhhhhhcCCeEECCEE-------------eCcc----ceeeecCCCCceeeeeCCCCCCC-Ccchhhhhhhhhh
Q psy7990 3 SALFLSTQYWEHQGPGVRKQV-------------VNIP----SFVVRLDSQKHIDFSLNSPFGGG-GTGRVKRKNLRKA 63 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~-------------VniP----Sy~Vk~~de~~I~~~~~SP~~~~-~pgR~krk~~~~~ 63 (76)
.+..+||-+++-|+|.|||++ |.|| +|+|=.++.....+.+-|-=... .+-|+++|..-++
T Consensus 55 d~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkg 133 (241)
T COG1471 55 DNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKG 133 (241)
T ss_pred cchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecC
Confidence 466799999999999999985 6688 89999999999999987744444 4888888776433
No 35
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=83.30 E-value=0.77 Score=29.18 Aligned_cols=26 Identities=8% Similarity=-0.052 Sum_probs=20.4
Q ss_pred CCeEECCEEeCccceeeecCCCCceeeee
Q psy7990 15 QGPGVRKQVVNIPSFVVRLDSQKHIDFSL 43 (76)
Q Consensus 15 gHI~Vng~~VniPSy~Vk~~de~~I~~~~ 43 (76)
+-|+|||+.|+ ++|+++.|| .|.+++
T Consensus 50 ~~i~vNG~~v~-~~~~~~~Gd--~v~V~P 75 (81)
T PF14451_consen 50 GLILVNGRPVD-FDYRLKDGD--RVAVYP 75 (81)
T ss_pred EEEEECCEECC-CcccCCCCC--EEEEEe
Confidence 56899999999 799988776 455554
No 36
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=82.55 E-value=2.4 Score=25.68 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=21.7
Q ss_pred CeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990 16 GPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 16 HI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
-|.||++.|+ .++.|+ |-+.|.|.+ |++|+
T Consensus 53 ~vavN~~~v~-~~~~l~--dgDeVai~P--pvsGG 82 (82)
T PLN02799 53 VLALNEEYTT-ESAALK--DGDELAIIP--PISGG 82 (82)
T ss_pred EEEECCEEcC-CCcCcC--CCCEEEEeC--CCCCC
Confidence 4899999987 776654 455677776 76664
No 37
>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=79.49 E-value=3.1 Score=24.44 Aligned_cols=33 Identities=15% Similarity=0.234 Sum_probs=22.8
Q ss_pred hcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990 13 EHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 13 ~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
..-.|.|||+.|. .++.|+ +.+.|.|.+ |++|+
T Consensus 48 ~~~~v~vNg~~v~-~~~~l~--~gD~v~i~p--pv~GG 80 (80)
T cd00754 48 ARVRIAVNGEYVR-LDTPLK--DGDEVAIIP--PVSGG 80 (80)
T ss_pred hcEEEEECCeEcC-CCcccC--CCCEEEEeC--CCCCC
Confidence 3456899999998 666554 445677766 66654
No 38
>PRK01777 hypothetical protein; Validated
Probab=77.86 E-value=5.3 Score=26.00 Aligned_cols=42 Identities=14% Similarity=0.226 Sum_probs=28.1
Q ss_pred hcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhh
Q psy7990 13 EHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNL 60 (76)
Q Consensus 13 ~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~ 60 (76)
+++.+.|||+.|+ +...++.| +.|++++ |+.-. |-..+|++.
T Consensus 48 ~~~~vgI~Gk~v~-~d~~L~dG--DRVeIyr--PL~~D-Pk~~Rr~ra 89 (95)
T PRK01777 48 AKNKVGIYSRPAK-LTDVLRDG--DRVEIYR--PLLAD-PKELRRKRA 89 (95)
T ss_pred ccceEEEeCeECC-CCCcCCCC--CEEEEec--CCCCC-HHHHHHHHH
Confidence 4578999999998 66666555 5788888 66633 433334333
No 39
>PRK04313 30S ribosomal protein S4e; Validated
Probab=74.18 E-value=2.4 Score=32.10 Aligned_cols=34 Identities=15% Similarity=-0.060 Sum_probs=26.8
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ 36 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de 36 (76)
-|..+|++++..|.|.|||++.+=+.|-|-.=|.
T Consensus 52 ~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDV 85 (237)
T PRK04313 52 DTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDV 85 (237)
T ss_pred ccHHHHHHHHhCCcEEECCEEEcccccCcCceeE
Confidence 4778999999999999999988766665444333
No 40
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=73.27 E-value=3.1 Score=29.06 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=19.6
Q ss_pred EECCEEeCccceeeecCCCC-ce-ee
Q psy7990 18 GVRKQVVNIPSFVVRLDSQK-HI-DF 41 (76)
Q Consensus 18 ~Vng~~VniPSy~Vk~~de~-~I-~~ 41 (76)
.+||+.|.||+|+|-.+.+. .| +|
T Consensus 52 ~L~Gk~V~i~Gf~vPle~~~~~v~eF 77 (146)
T PF11736_consen 52 ALDGKQVRIPGFMVPLEQEEGKVTEF 77 (146)
T ss_pred HhCCCEEEEeeEEEeeccCCCcEEEE
Confidence 47999999999999998764 45 44
No 41
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=72.81 E-value=5.1 Score=25.54 Aligned_cols=33 Identities=9% Similarity=-0.082 Sum_probs=27.8
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDS 35 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~d 35 (76)
+|=-+|.+++.-+-|.|||.+=|--.--++.+|
T Consensus 25 ~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd 57 (73)
T COG2501 25 ESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGD 57 (73)
T ss_pred cCcHHHHHHHHCCeEEECCeeeeccCCEeecCC
Confidence 456789999999999999999888886666665
No 42
>PLN00036 40S ribosomal protein S4; Provisional
Probab=69.99 E-value=3.1 Score=31.99 Aligned_cols=33 Identities=6% Similarity=-0.091 Sum_probs=25.9
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDS 35 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~d 35 (76)
-|..+|++++..|.|.|||++.+=+.|-|-.=|
T Consensus 56 ~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mD 88 (261)
T PLN00036 56 LTYREVQAILMQRHVKVDGKVRTDKTYPAGFMD 88 (261)
T ss_pred ccHHHHHHHHhCCeEEECCEEeccCCCCCceeE
Confidence 467899999999999999998776665544433
No 43
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=68.32 E-value=8.7 Score=23.11 Aligned_cols=31 Identities=23% Similarity=0.385 Sum_probs=21.8
Q ss_pred CCeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990 15 QGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 15 gHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
-.|.||++.++ .+.. +.+.+.|.|.+ |++|+
T Consensus 50 ~~v~vn~~~v~-~~~~--l~dgDevai~P--pvsGG 80 (80)
T TIGR01682 50 VMVAVNEEYVT-DDAL--LNEGDEVAFIP--PVSGG 80 (80)
T ss_pred eEEEECCEEcC-CCcC--cCCCCEEEEeC--CCCCC
Confidence 35899999998 4544 45556677777 77664
No 44
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=67.53 E-value=3.8 Score=31.49 Aligned_cols=34 Identities=9% Similarity=-0.176 Sum_probs=26.1
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ 36 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de 36 (76)
-|..+|+.++..|.|.|||++.+=+.|-|-.=|.
T Consensus 56 ~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDV 89 (262)
T PTZ00118 56 LTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDV 89 (262)
T ss_pred ccHHHHHHHHHCCcEEECCEEEccCCCCCceeEE
Confidence 4677999999999999999987766554444333
No 45
>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=67.25 E-value=6.3 Score=22.87 Aligned_cols=34 Identities=15% Similarity=0.221 Sum_probs=22.6
Q ss_pred hcCCeEECCEEeCc--cceeeecCCCCceeeeeCCCCCCC
Q psy7990 13 EHQGPGVRKQVVNI--PSFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 13 ~HgHI~Vng~~Vni--PSy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
..--|.|||+.|+- ..+.|+. .+.|.|-+ |++|+
T Consensus 42 ~~~~v~vN~~~v~~~~~~~~l~~--gD~V~i~p--pvsGG 77 (77)
T PF02597_consen 42 DRVAVAVNGEIVPDDGLDTPLKD--GDEVAILP--PVSGG 77 (77)
T ss_dssp TTEEEEETTEEEGGGTTTSBEET--TEEEEEEE--STSTS
T ss_pred ccEEEEECCEEcCCccCCcCcCC--CCEEEEEC--CCCCC
Confidence 44568999999986 3555554 45566666 66654
No 46
>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=65.09 E-value=9.3 Score=23.18 Aligned_cols=35 Identities=17% Similarity=0.149 Sum_probs=22.5
Q ss_pred hcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990 13 EHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 13 ~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
.|--|.|||+.|+- .--....|-+.|.|.+ |++|+
T Consensus 54 ~~~~v~vN~~~v~~-~~~~~l~dgdev~i~P--pvsGG 88 (88)
T TIGR01687 54 PNVIILVNGRNVDW-GLGTELKDGDVVAIFP--PVSGG 88 (88)
T ss_pred ccEEEEECCEecCc-cCCCCCCCCCEEEEeC--CCcCC
Confidence 45568999999863 2213455666777776 77664
No 47
>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=64.98 E-value=5.4 Score=31.28 Aligned_cols=33 Identities=6% Similarity=-0.065 Sum_probs=28.6
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccceeeec
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRL 33 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~ 33 (76)
+|+|--+||++|..|-|.||+.+|+.+.+.+..
T Consensus 341 ~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~~ 373 (377)
T TIGR00234 341 LFPSKSEARRDIKQGGVYINGEKVTDLEPIRKE 373 (377)
T ss_pred CCcChHHHHHHHHhCCEEECCEeccCchhhhcc
Confidence 478888999999999999999999988776543
No 48
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=64.40 E-value=4.7 Score=31.19 Aligned_cols=34 Identities=3% Similarity=-0.221 Sum_probs=27.2
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ 36 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de 36 (76)
-|..+|++++.-|.|.|||++.+=+.|-|-.=|.
T Consensus 53 ~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDV 86 (273)
T PTZ00223 53 LNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDV 86 (273)
T ss_pred ccHHHHHHHHhCCeEEECCEEEccCCCCCceeEE
Confidence 4778999999999999999998777665544443
No 49
>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=61.23 E-value=11 Score=24.07 Aligned_cols=35 Identities=14% Similarity=0.056 Sum_probs=22.5
Q ss_pred cCCeEECCEEeCcc-ceeeecCCCCceeeeeCCCCCCC
Q psy7990 14 HQGPGVRKQVVNIP-SFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 14 HgHI~Vng~~VniP-Sy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
+--|+|||+.+..- ..--.+.+.+.|.|.+ |++|+
T Consensus 59 ~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P--~v~GG 94 (94)
T cd01764 59 GIIVLINDTDWELLGEEDYILEDGDHVVFIS--TLHGG 94 (94)
T ss_pred CEEEEECCccccccCCcccCCCCcCEEEEEC--CCCCC
Confidence 55789999998644 3334445555677776 66654
No 50
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=56.96 E-value=8.3 Score=31.02 Aligned_cols=30 Identities=10% Similarity=0.168 Sum_probs=25.2
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCcccee
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFV 30 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~ 30 (76)
.||+.-+||.+|.-|-+.|||.+|.=+.+.
T Consensus 347 L~psr~earr~i~~g~v~in~~~v~d~~~~ 376 (401)
T COG0162 347 LAPSRSEARRLIQQGGVKINGEKVEDENYV 376 (401)
T ss_pred CcccHHHHHhhcccCCEEECCEeccccccc
Confidence 489999999999999999999976644433
No 51
>KOG2623|consensus
Probab=56.48 E-value=7.6 Score=32.23 Aligned_cols=29 Identities=10% Similarity=0.015 Sum_probs=26.2
Q ss_pred CccchhhhhhhhcCCeEECCEEeCcccee
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSFV 30 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~ 30 (76)
||+-.+||.+|..|-+.||+++|..+|-.
T Consensus 411 ~~s~~~a~r~i~qG~vslnh~~v~~es~~ 439 (467)
T KOG2623|consen 411 FPSGKEARRMIQQGGVSLNHEKVRDESVS 439 (467)
T ss_pred CCCcHHHHHHHHccceeecCccccCchhh
Confidence 78888999999999999999999987743
No 52
>PF01324 Diphtheria_R: Diphtheria toxin, R domain; InterPro: IPR022404 This entry represents the C-terminal receptor-binding domain, also known as the R domain. This domain has a beta-sandwich fold consisiting of nine strands in two sheet with greek-key topology; it is a subclass of immunoglobin-like fold []. The R domain binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis [, ]. Diphtheria toxin (2.4.2.36 from EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis []. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows: NAD+ + peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution []. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology []. The TM- and receptor binding-domains together constitute fragment B.; PDB: 1MDT_B 1SGK_A 1F0L_B 1DDT_A 1TOX_B 4AE0_A 1XDT_T 4AE1_A.
Probab=53.30 E-value=16 Score=25.96 Aligned_cols=32 Identities=13% Similarity=0.067 Sum_probs=21.3
Q ss_pred hcCCeEECCEEeCccceeeecCCCCceeeeeCCCC
Q psy7990 13 EHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPF 47 (76)
Q Consensus 13 ~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~ 47 (76)
+--||.|||+++. ++++.=|.+..--.+.||.
T Consensus 66 skthisvngrkir---mrcraid~~~tfcrpk~pv 97 (154)
T PF01324_consen 66 SKTHISVNGRKIR---MRCRAIDDDTTFCRPKSPV 97 (154)
T ss_dssp TT-EEEETTEEEE---EEEEEETTTEEEEEESS-E
T ss_pred cceeEEEcCeEEE---EEEEEecCceeeecCCCCE
Confidence 3469999999986 5677766665555566664
No 53
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=51.44 E-value=34 Score=20.75 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=20.2
Q ss_pred CeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990 16 GPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 16 HI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
.|.||+..+. +... +.|-+.|.|.+ |.+|+
T Consensus 52 ~~aVN~~~~~-~~~~--l~dgDeVai~P--PVsGG 81 (81)
T PRK11130 52 LAAVNQTLVS-FDHP--LTDGDEVAFFP--PVTGG 81 (81)
T ss_pred EEEECCEEcC-CCCC--CCCCCEEEEeC--CCCCC
Confidence 3789998875 5554 44555688887 66654
No 54
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=45.09 E-value=40 Score=19.20 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=18.7
Q ss_pred CCeEECCEEeCcc---ceeeecCCCCceeeeeCCCCCCC
Q psy7990 15 QGPGVRKQVVNIP---SFVVRLDSQKHIDFSLNSPFGGG 50 (76)
Q Consensus 15 gHI~Vng~~VniP---Sy~Vk~~de~~I~~~~~SP~~~~ 50 (76)
-.|.|||..|.-. ... ..+-+.|++.+ |++|+
T Consensus 31 ~~v~vN~~~v~~~~~~~~~--L~~gD~vei~~--~v~GG 65 (65)
T PRK06944 31 FAVAVNGDFVARTQHAARA--LAAGDRLDLVQ--PVAGG 65 (65)
T ss_pred eEEEECCEEcCchhccccc--CCCCCEEEEEe--eccCC
Confidence 3467888887533 333 44555677765 55543
No 55
>PRK06437 hypothetical protein; Provisional
Probab=43.87 E-value=20 Score=21.41 Aligned_cols=25 Identities=12% Similarity=-0.100 Sum_probs=18.0
Q ss_pred CeEECCEEeCccceeeecCCCCceeeee
Q psy7990 16 GPGVRKQVVNIPSFVVRLDSQKHIDFSL 43 (76)
Q Consensus 16 HI~Vng~~VniPSy~Vk~~de~~I~~~~ 43 (76)
.|.|||+.|. +.+.|+.+ +.|++..
T Consensus 38 aV~vNg~iv~-~~~~L~dg--D~Veiv~ 62 (67)
T PRK06437 38 VVIVNGSPVL-EDHNVKKE--DDVLILE 62 (67)
T ss_pred EEEECCEECC-CceEcCCC--CEEEEEe
Confidence 4669999998 88877754 4566554
No 56
>PRK09273 hypothetical protein; Provisional
Probab=43.60 E-value=6 Score=29.60 Aligned_cols=57 Identities=9% Similarity=0.040 Sum_probs=40.0
Q ss_pred CccchhhhhhhhcCCeEECCEEeCccce----eeec-CCCCceeeeeCCCCCCCC-cchhhhhhhhh
Q psy7990 2 CSALFLSTQYWEHQGPGVRKQVVNIPSF----VVRL-DSQKHIDFSLNSPFGGGG-TGRVKRKNLRK 62 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy----~Vk~-~de~~I~~~~~SP~~~~~-pgR~krk~~~~ 62 (76)
|..++.|+.+..|- |+.++.+|+- .+-. .-..-++-..+++|+++. ++|+.++.+.+
T Consensus 92 c~d~~sA~lar~hN----naNVL~Lg~r~~~g~~g~~~a~~Ive~fl~tef~gGyp~er~~~~~~n~ 154 (211)
T PRK09273 92 CIDPTDAYLFAQIN----NGNALSLPFAKGFGWGAELNLRYIFEKLFTGERGEGYPKERAEPQQRNA 154 (211)
T ss_pred eCCHHHHHHHHHhc----CCcEEEEcCCcCCCcccHHHHHHHHHHHHcCCccCCCChHHhhHHHhhH
Confidence 78889999999986 7888888885 2222 112334456889999988 78877765444
No 57
>PHA01635 hypothetical protein
Probab=42.26 E-value=13 Score=28.41 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=16.0
Q ss_pred hcCCeEECCEEeCccceeee
Q psy7990 13 EHQGPGVRKQVVNIPSFVVR 32 (76)
Q Consensus 13 ~HgHI~Vng~~VniPSy~Vk 32 (76)
.-.-|.+|||.|+||+|+.-
T Consensus 61 RGA~l~ingq~v~vP~YiFG 80 (231)
T PHA01635 61 RGAELNINGQQVTVPDYIFG 80 (231)
T ss_pred eccEEEEcCcEeeccceecc
Confidence 33458899999999999753
No 58
>PF04571 Lipin_N: lipin, N-terminal conserved region; InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=38.60 E-value=41 Score=22.93 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=19.4
Q ss_pred CeEECCEEeCccceeeecCCCCceeeeeC
Q psy7990 16 GPGVRKQVVNIPSFVVRLDSQKHIDFSLN 44 (76)
Q Consensus 16 HI~Vng~~VniPSy~Vk~~de~~I~~~~~ 44 (76)
+|.|||+.++ +..++++...--|...
T Consensus 63 ~I~VNG~~~~---~~MkLg~~GeAfFv~e 88 (110)
T PF04571_consen 63 DIEVNGKPVD---FHMKLGENGEAFFVEE 88 (110)
T ss_pred EEEECCEEcc---eEEEECCCcEEEEEEe
Confidence 6899999986 4777777776666543
No 59
>PF07908 D-aminoacyl_C: D-aminoacylase, C-terminal region; InterPro: IPR012855 D-aminoacylase (Q9AGH8 from SWISSPROT, 3.5.1.81 from EC) hydrolyses a wide variety of N-acyl derivatives of neutral D-amino acids, in a zinc-dependent manner. The enzyme is composed of a small beta-barrel domain and a larger catalytic alpha/beta-barrel that contains a short alpha/beta insert. The overall structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well []. The C-terminal region featured in this entry forms part of the beta-barrel domain, together with a short N-terminal segment. This domain does not seem to contribute to the substrate-binding site or to be involved in the catalytic process.; GO: 0008270 zinc ion binding, 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; PDB: 3GIQ_B 3GIP_B 1V4Y_A 1M7J_A 1RK5_A 1RJP_A 1RJR_A 1RJQ_A 1RK6_A 1V51_A.
Probab=38.15 E-value=21 Score=20.32 Aligned_cols=10 Identities=30% Similarity=-0.044 Sum_probs=7.9
Q ss_pred CeEECCEEeC
Q psy7990 16 GPGVRKQVVN 25 (76)
Q Consensus 16 HI~Vng~~Vn 25 (76)
|+.|||+.|=
T Consensus 22 ~V~VNG~~vv 31 (48)
T PF07908_consen 22 YVFVNGQIVV 31 (48)
T ss_dssp EEEETTEEEE
T ss_pred EEEECCEEEE
Confidence 6889998863
No 60
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=36.86 E-value=39 Score=19.88 Aligned_cols=28 Identities=14% Similarity=0.035 Sum_probs=17.5
Q ss_pred CCeEECCEEeCccceeeecCCCCceeee
Q psy7990 15 QGPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 15 gHI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
-.+.|||+..+.-.-.+++.+-+.|.|.
T Consensus 41 W~~~vNG~~~~~ga~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 41 WMYYVNGESANVGAGSYKLKDGDKITWY 68 (68)
T ss_dssp EEEEETTEE-SS-CCC-B--TTEEEEE-
T ss_pred eEEEECCEEhhcCcceeEeCCCCEEEeC
Confidence 3578999998887777777788888773
No 61
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=34.79 E-value=64 Score=19.16 Aligned_cols=30 Identities=13% Similarity=0.007 Sum_probs=19.4
Q ss_pred CCeEECCEEeCccceeeecCCCCceeeeeCCCCCC
Q psy7990 15 QGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGG 49 (76)
Q Consensus 15 gHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~ 49 (76)
.-|.|||+.|. +.+.++.+| .|++.+ |.+|
T Consensus 40 v~v~vNg~iv~-~~~~l~~gD--~Veii~--~V~G 69 (70)
T PRK08364 40 AIAKVNGKVAL-EDDPVKDGD--YVEVIP--VVSG 69 (70)
T ss_pred EEEEECCEECC-CCcCcCCCC--EEEEEc--cccC
Confidence 35679999995 666655554 666665 4444
No 62
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=34.13 E-value=24 Score=19.70 Aligned_cols=24 Identities=8% Similarity=-0.076 Sum_probs=17.9
Q ss_pred CccchhhhhhhhcCC-eEECCEEeC
Q psy7990 2 CSALFLSTQYWEHQG-PGVRKQVVN 25 (76)
Q Consensus 2 ~~t~~~ARQ~V~HgH-I~Vng~~Vn 25 (76)
++|...|.+++..-| ..++|+.|+
T Consensus 46 f~~~~~a~~al~~~~~~~~~g~~l~ 70 (70)
T PF14259_consen 46 FSSEEDAKRALELLNGKEIDGRKLR 70 (70)
T ss_dssp ESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred eCCHHHHHHHHHHCCCcEECCEEcC
Confidence 356777888777666 999999873
No 63
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=33.98 E-value=38 Score=18.43 Aligned_cols=23 Identities=4% Similarity=0.031 Sum_probs=16.9
Q ss_pred ccchhhhhhhh--cCCeEECCEEeCc
Q psy7990 3 SALFLSTQYWE--HQGPGVRKQVVNI 26 (76)
Q Consensus 3 ~t~~~ARQ~V~--HgHI~Vng~~Vni 26 (76)
.++.+|+..+. ||.. ++|+.+.|
T Consensus 29 ~~~~~A~~a~~~l~~~~-~~g~~l~V 53 (56)
T PF13893_consen 29 ASVEDAQKAIEQLNGRQ-FNGRPLKV 53 (56)
T ss_dssp SSHHHHHHHHHHHTTSE-ETTEEEEE
T ss_pred CCHHHHHHHHHHhCCCE-ECCcEEEE
Confidence 36778888887 7776 68887764
No 64
>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=33.64 E-value=28 Score=20.18 Aligned_cols=12 Identities=17% Similarity=0.174 Sum_probs=6.1
Q ss_pred eEECCEEeCccc
Q psy7990 17 PGVRKQVVNIPS 28 (76)
Q Consensus 17 I~Vng~~VniPS 28 (76)
|.|||+.+++|.
T Consensus 1 i~iNg~~~~~~~ 12 (64)
T TIGR01683 1 ITVNGEPVEVED 12 (64)
T ss_pred CEECCeEEEcCC
Confidence 345555555543
No 65
>PF05949 DUF881: Bacterial protein of unknown function (DUF881); InterPro: IPR010273 This family consists of a series of hypothetical bacterial proteins. One of the family members Q45543 from SWISSPROT from Bacillus subtilis is thought to be involved in cell division and sporulation [].; PDB: 3GMG_B.
Probab=32.90 E-value=22 Score=24.44 Aligned_cols=27 Identities=7% Similarity=-0.053 Sum_probs=12.1
Q ss_pred CeEECCEEeCccceeeecCCCCceeee
Q psy7990 16 GPGVRKQVVNIPSFVVRLDSQKHIDFS 42 (76)
Q Consensus 16 HI~Vng~~VniPSy~Vk~~de~~I~~~ 42 (76)
.|.|||++|.--|+..-.+..-.|+..
T Consensus 60 AIsINg~Ri~~~S~Ir~~g~~i~Vng~ 86 (149)
T PF05949_consen 60 AISINGQRIVATSAIRCAGGTILVNGR 86 (149)
T ss_dssp EEEEE-EE--TT--EEEETTEEEETTE
T ss_pred EEEECCEEEcCcEEEEEeCCEEEECCE
Confidence 466666666655655555554444443
No 66
>COG1351 THY1 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]
Probab=32.81 E-value=18 Score=27.54 Aligned_cols=34 Identities=12% Similarity=0.160 Sum_probs=21.2
Q ss_pred cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceee
Q psy7990 4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDF 41 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~ 41 (76)
|++.|+||+.|+|-..+-+- --|.. .+++.++.+
T Consensus 87 Sr~~~~Ql~RHR~aSy~e~S---~RYv~-~~~e~~~~~ 120 (273)
T COG1351 87 SRVAAHQLIRHRIASYSEKS---QRYVL-DGDEFYVPF 120 (273)
T ss_pred CHHHHHHHHhccccCccccc---eeeec-CCCceeecc
Confidence 68899999999998544221 11222 456666653
No 67
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=32.60 E-value=23 Score=28.35 Aligned_cols=19 Identities=0% Similarity=-0.165 Sum_probs=16.1
Q ss_pred hhhhhcCCeEECCEEeCcc
Q psy7990 9 TQYWEHQGPGVRKQVVNIP 27 (76)
Q Consensus 9 RQ~V~HgHI~Vng~~VniP 27 (76)
+.+++|||+.++|++....
T Consensus 320 ~~v~~~G~v~~~G~KMSKS 338 (556)
T PRK12268 320 DEIVSSEYLTLEGGKFSKS 338 (556)
T ss_pred CEeeccCCEEECCeeeccC
Confidence 4889999999999987643
No 68
>TIGR02170 thyX thymidylate synthase, flavin-dependent. Two forms of microbial thymidylate synthase are known: ThyA (2.1.1.45) and ThyX (2.1.1.148). This model describes ThyX, a homotetrameric flavoprotein. Both enzymes convert dUMP to dTMP. Under oxygen-limiting conditions, thyX can complement a thyA mutation.
Probab=32.45 E-value=18 Score=25.72 Aligned_cols=17 Identities=12% Similarity=0.059 Sum_probs=13.8
Q ss_pred ccchhhhhhhhcCCeEE
Q psy7990 3 SALFLSTQYWEHQGPGV 19 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~V 19 (76)
-+++.++||+.|++...
T Consensus 64 ~sr~~~~ql~RHR~~s~ 80 (209)
T TIGR02170 64 ASRSVAAQLTRHRIASY 80 (209)
T ss_pred ecHHHHHHHHHHhcCce
Confidence 46889999999998643
No 69
>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=31.39 E-value=74 Score=17.80 Aligned_cols=24 Identities=29% Similarity=0.263 Sum_probs=11.5
Q ss_pred CCeEECCEEeCccceeeecCCCCce
Q psy7990 15 QGPGVRKQVVNIPSFVVRLDSQKHI 39 (76)
Q Consensus 15 gHI~Vng~~VniPSy~Vk~~de~~I 39 (76)
.-+.|||+++. |...+...+.+.|
T Consensus 42 ngt~vng~~l~-~~~~~~L~~gd~i 65 (68)
T PF00498_consen 42 NGTFVNGQRLG-PGEPVPLKDGDII 65 (68)
T ss_dssp S-EEETTEEES-STSEEEE-TTEEE
T ss_pred CcEEECCEEcC-CCCEEECCCCCEE
Confidence 34567777776 4333333333333
No 70
>PF13810 DUF4185: Domain of unknown function (DUF4185)
Probab=31.08 E-value=33 Score=26.35 Aligned_cols=40 Identities=10% Similarity=0.061 Sum_probs=30.8
Q ss_pred chhhhhhhh-cCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990 5 LFLSTQYWE-HQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS 45 (76)
Q Consensus 5 ~~~ARQ~V~-HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S 45 (76)
.-.|||||. |..+. ++..--||+-.|.+++.-+|.|-..-
T Consensus 75 ~~~a~ql~~~~~~~~-~~e~t~iPt~~I~v~~~~Yl~~msv~ 115 (316)
T PF13810_consen 75 PGRARQLIPPHDKVN-GGETTVIPTDGISVGGRQYLHYMSVR 115 (316)
T ss_pred CCcccccccCCCCCC-CCceEEcccceEEECCcEEEEEEEEc
Confidence 347999996 55553 45566789999999999999997553
No 71
>PRK15200 fimbrial protein FimI; Provisional
Probab=30.77 E-value=36 Score=23.58 Aligned_cols=38 Identities=24% Similarity=0.191 Sum_probs=24.4
Q ss_pred ccchhhhhhhhcCCeEECCEEeCccceeeecCCCC-ceee
Q psy7990 3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQK-HIDF 41 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~-~I~~ 41 (76)
++.|++-....+|-|.++|.+|+- .-.|..+++. .|+|
T Consensus 15 ~~~~A~~~~~~~G~I~f~G~Iv~~-~C~V~~~s~~~~V~L 53 (177)
T PRK15200 15 SPVIAQPVMVESGRVHLRGQLVNG-GCAVATESQDLRVLM 53 (177)
T ss_pred hhhhhcccccCCcEEEEEEEEEcc-cceEcCCCCceEEEC
Confidence 334444445679999999999985 4455555533 3554
No 72
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=30.14 E-value=74 Score=18.56 Aligned_cols=27 Identities=7% Similarity=0.122 Sum_probs=14.1
Q ss_pred eEECCEEeCccceee-ecCCCCceeeee
Q psy7990 17 PGVRKQVVNIPSFVV-RLDSQKHIDFSL 43 (76)
Q Consensus 17 I~Vng~~VniPSy~V-k~~de~~I~~~~ 43 (76)
|.||+..|.-..|.= ...+.+.|++-.
T Consensus 34 VavN~~iv~r~~w~~~~L~~gD~Ieii~ 61 (66)
T PRK08053 34 LAINQQIIPREQWAQHIVQDGDQILLFQ 61 (66)
T ss_pred EEECCEEeChHHcCccccCCCCEEEEEE
Confidence 567888876332221 244455565544
No 73
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=29.54 E-value=39 Score=19.37 Aligned_cols=13 Identities=8% Similarity=0.194 Sum_probs=10.1
Q ss_pred CeEECCEEeCccc
Q psy7990 16 GPGVRKQVVNIPS 28 (76)
Q Consensus 16 HI~Vng~~VniPS 28 (76)
.|.|||+.+++|.
T Consensus 2 ~i~vNG~~~~~~~ 14 (66)
T PRK05659 2 NIQLNGEPRELPD 14 (66)
T ss_pred EEEECCeEEEcCC
Confidence 4788999888764
No 74
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=29.43 E-value=23 Score=29.21 Aligned_cols=42 Identities=14% Similarity=0.199 Sum_probs=26.8
Q ss_pred hhhhhhcCCeEECCEEeCcc-------ceeeecCCCCceeeee--CCCCCC
Q psy7990 8 STQYWEHQGPGVRKQVVNIP-------SFVVRLDSQKHIDFSL--NSPFGG 49 (76)
Q Consensus 8 ARQ~V~HgHI~Vng~~VniP-------Sy~Vk~~de~~I~~~~--~SP~~~ 49 (76)
-+++++|||++++|++.... .-+++.-.-+.+.|+. ++|++.
T Consensus 284 p~~v~~hg~l~~eg~KMSKS~GN~i~p~d~l~~ygaD~lR~~L~~~~~~~~ 334 (648)
T PRK12267 284 PKKVFAHGWWLMKDGKMSKSKGNVVDPEELVDRYGLDALRYYLLREVPFGS 334 (648)
T ss_pred CcEEEecceEEECCceecccCCcccCHHHHHHHcCCcHHHHHHHhcCCCCC
Confidence 47899999999999886532 2223333456666654 345554
No 75
>COG3395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.69 E-value=28 Score=28.42 Aligned_cols=28 Identities=18% Similarity=-0.066 Sum_probs=24.9
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCccc
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNIPS 28 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPS 28 (76)
.||.++..+.-|.+||..|||..|+-+.
T Consensus 111 v~PA~P~~gRtv~~gyl~v~Gvlv~es~ 138 (413)
T COG3395 111 VVPALPLNGRTVFGGYLFVNGVLVDESG 138 (413)
T ss_pred EecCccCCCeeEEeeEEEEcCEEcccCc
Confidence 3899999999999999999999988554
No 76
>PRK00847 thyX FAD-dependent thymidylate synthase; Reviewed
Probab=26.60 E-value=31 Score=24.77 Aligned_cols=18 Identities=17% Similarity=0.180 Sum_probs=14.3
Q ss_pred ccchhhhhhhhcCCeEEC
Q psy7990 3 SALFLSTQYWEHQGPGVR 20 (76)
Q Consensus 3 ~t~~~ARQ~V~HgHI~Vn 20 (76)
-+++.+|||+.|++...+
T Consensus 71 ~sr~~~~ql~RHR~~s~~ 88 (217)
T PRK00847 71 ISRFVAHQLVRHRIASYS 88 (217)
T ss_pred ecHHHHHHHHHhccceee
Confidence 367899999999987443
No 77
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=25.97 E-value=25 Score=30.54 Aligned_cols=17 Identities=0% Similarity=-0.275 Sum_probs=15.4
Q ss_pred hhhhhcCCeEECCEEeC
Q psy7990 9 TQYWEHQGPGVRKQVVN 25 (76)
Q Consensus 9 RQ~V~HgHI~Vng~~Vn 25 (76)
++++.|||++.+|++..
T Consensus 563 k~v~~hG~vl~~G~KMS 579 (897)
T PRK12300 563 RGIVVNGFVLLEGKKMS 579 (897)
T ss_pred cEEEEcceEEECCcccc
Confidence 89999999999998765
No 78
>COG3243 PhaC Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]
Probab=25.85 E-value=60 Score=26.96 Aligned_cols=28 Identities=21% Similarity=0.360 Sum_probs=20.9
Q ss_pred hhhcCCeEECCEEe-----CccceeeecCCCCcee
Q psy7990 11 YWEHQGPGVRKQVV-----NIPSFVVRLDSQKHID 40 (76)
Q Consensus 11 ~V~HgHI~Vng~~V-----niPSy~Vk~~de~~I~ 40 (76)
|++ |-..|+|++| ++|+|.+- +.++||.
T Consensus 312 l~~-g~~~v~G~~VdL~~It~pvy~~a-~~~DhI~ 344 (445)
T COG3243 312 LIR-GGLEVSGTMVDLGDITCPVYNLA-AEEDHIA 344 (445)
T ss_pred hhc-cceEECCEEechhhcccceEEEe-ecccccC
Confidence 455 8899999976 58999884 5566664
No 79
>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=25.50 E-value=54 Score=18.94 Aligned_cols=11 Identities=9% Similarity=0.012 Sum_probs=5.5
Q ss_pred eEECCEEeCcc
Q psy7990 17 PGVRKQVVNIP 27 (76)
Q Consensus 17 I~Vng~~VniP 27 (76)
|.|||+...+|
T Consensus 2 i~iNg~~~~~~ 12 (65)
T cd00565 2 ITVNGEPREVE 12 (65)
T ss_pred EEECCeEEEcC
Confidence 44555555444
No 80
>PF02511 Thy1: Thymidylate synthase complementing protein; InterPro: IPR003669 All cellular organisms need thymidylate (dTMP) for the replication of their chromosomes, as dTMP is required for the biosynthesis of dTTP, a building block of DNA. Cells can produce thymidylate either de novo from dUMP or incorporate thymidine using thymidine kinase. The de novo pathway of dTMP synthesis requires a specific enzyme, thymidylate synthase, which methylates dUMP at position 5 of the pyrimidine ring. There are two pathways for thymidylate synthesis, each utilising a different thymidylate synthase enzyme: ThyA (2.1.1.45 from EC) and ThyX (2.1.1.148 from EC) []. Both enzymes convert dUMP to dTMP, but there is no sequence identity between the two enzymes, and their mechanisms of action differ []. Only ThyX uses FAD as cofactor. The well studied thyA proteins catalyse the reductive methylation reaction of dUMP, with methylenetetrahydrofolate (CH(2)H(4)folate) serving as one-carbon donor and as source of reductive power. On the other hand the thyX family of thymidylate synthases contains FAD that is tightly bound by a novel fold. FAD mediates hydride transfer from NADPH during catalysis. Consequently, in the reaction catalysed by thyX, CH(2)H(4)folate serves only as a carbon donor and tetrahydrofolate (and not dihydrofolate as in the case of thyA) is produced [, ]. The thyX domain consists of a central alpha/beta domain and two alpha-helices located away from the central domain. The central domain is made up of a five-stranded antiparallel beta-sheet, flanked by six alpha-helices on one side of the sheet [, , ]. Sequence alignments reveal a specific sequence motif R-H-R-X(7)-S (thyX motif) common to this family of proteins []. This entry represents the flavin-dependent enzyme ThyX, which is a homotetramer bound to four FAD molecules. Under oxygen-limiting conditions, thyX can complement a thyA mutation [].; GO: 0050660 flavin adenine dinucleotide binding, 0050797 thymidylate synthase (FAD) activity, 0006231 dTMP biosynthetic process; PDB: 3N3Y_A 3GE9_A 3FNN_A 3AH5_E 3GWC_B 2AF6_D 2GQ2_B 3HZG_B 2CFA_A 3N0B_B ....
Probab=24.89 E-value=32 Score=23.87 Aligned_cols=17 Identities=18% Similarity=0.100 Sum_probs=13.9
Q ss_pred cchhhhhhhhcCCeEEC
Q psy7990 4 ALFLSTQYWEHQGPGVR 20 (76)
Q Consensus 4 t~~~ARQ~V~HgHI~Vn 20 (76)
+++.++||+.|++...+
T Consensus 61 sr~~~~ql~RHR~~s~~ 77 (190)
T PF02511_consen 61 SRAVSRQLVRHRIASFN 77 (190)
T ss_dssp EHHHHHHHTTSTTSEEE
T ss_pred CHHHHHHHHHCCCCccc
Confidence 57889999999996553
No 81
>PRK14129 heat shock protein HspQ; Provisional
Probab=24.77 E-value=24 Score=23.99 Aligned_cols=30 Identities=30% Similarity=0.300 Sum_probs=25.2
Q ss_pred CCccchhhhhhhhcCCeEECCEEeCc-ccee
Q psy7990 1 MCSALFLSTQYWEHQGPGVRKQVVNI-PSFV 30 (76)
Q Consensus 1 ~~~t~~~ARQ~V~HgHI~Vng~~Vni-PSy~ 30 (76)
|..+.|.-=|+|.|+.+--.|.+++| |.|.
T Consensus 1 mi~akF~IGQ~VrHrl~~yrGVV~DVDP~fs 31 (105)
T PRK14129 1 MIASKFGIGQQVRHSLLGYLGVVVDIDPEYS 31 (105)
T ss_pred CccccccCCcEEEEeecCCCeEEEeeCCCcC
Confidence 66778888899999999999999987 5554
No 82
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=24.69 E-value=22 Score=27.82 Aligned_cols=18 Identities=6% Similarity=-0.075 Sum_probs=13.3
Q ss_pred hhhhhhcCCeEECCEEeC
Q psy7990 8 STQYWEHQGPGVRKQVVN 25 (76)
Q Consensus 8 ARQ~V~HgHI~Vng~~Vn 25 (76)
=+++++|+|++++|++..
T Consensus 312 P~~i~~~~~~~~~g~K~S 329 (391)
T PF09334_consen 312 PRRIVVHGFLTLDGEKMS 329 (391)
T ss_dssp -SEEEEE--EEETTCCEE
T ss_pred CCEEEeeeeEEECCeecc
Confidence 378999999999999864
No 83
>COG2301 CitE Citrate lyase beta subunit [Carbohydrate transport and metabolism]
Probab=24.56 E-value=34 Score=26.44 Aligned_cols=17 Identities=12% Similarity=0.206 Sum_probs=14.9
Q ss_pred hcC--CeEECCEEeCccce
Q psy7990 13 EHQ--GPGVRKQVVNIPSF 29 (76)
Q Consensus 13 ~Hg--HI~Vng~~VniPSy 29 (76)
++| -|.+||+.|+.|.+
T Consensus 247 ~~G~gv~~~~GkMvd~~~l 265 (283)
T COG2301 247 SKGAGVISLDGKMVDAPIL 265 (283)
T ss_pred cCCCceEeeCCeeehhHHH
Confidence 477 99999999999874
No 84
>PF13991 BssS: BssS protein family
Probab=24.09 E-value=33 Score=21.85 Aligned_cols=12 Identities=8% Similarity=-0.078 Sum_probs=9.7
Q ss_pred Cccchhhhhhhh
Q psy7990 2 CSALFLSTQYWE 13 (76)
Q Consensus 2 ~~t~~~ARQ~V~ 13 (76)
|=|+.+|||||+
T Consensus 41 ~lT~e~Ar~Li~ 52 (73)
T PF13991_consen 41 WLTTEMARQLIS 52 (73)
T ss_pred EecHHHHHHHHH
Confidence 447889999986
No 85
>cd06880 PX_SNX22 The phosphoinositide binding Phox Homology domain of Sorting Nexin 22. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX22 may be involved in recruiting other proteins to the membrane via protein-protein and protein-ligand interaction. The biological function of SNX22 is not yet known.
Probab=23.48 E-value=61 Score=20.91 Aligned_cols=21 Identities=29% Similarity=0.551 Sum_probs=15.4
Q ss_pred EeCccceeeecCC--CCceeeee
Q psy7990 23 VVNIPSFVVRLDS--QKHIDFSL 43 (76)
Q Consensus 23 ~VniPSy~Vk~~d--e~~I~~~~ 43 (76)
.|+||||.+..+. ..++.|..
T Consensus 2 ~V~Ip~~~~~~~~~~~~y~~Y~I 24 (110)
T cd06880 2 EVSIPSYRLEVDESEKPYTVFTI 24 (110)
T ss_pred EEEeCcEEEeeCCCCCCeEEEEE
Confidence 4789999988875 46666653
No 86
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=22.79 E-value=73 Score=22.18 Aligned_cols=39 Identities=15% Similarity=0.083 Sum_probs=29.3
Q ss_pred hcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC
Q psy7990 13 EHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG 51 (76)
Q Consensus 13 ~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~ 51 (76)
-|-||.|||+.=|.-.-..=..+...|....+.||..-.
T Consensus 43 L~erIKV~GK~gnLg~~V~v~~~k~ki~V~s~~~FSKRY 81 (122)
T PTZ00198 43 LQDRIKVDGKTGNLGNKVRVSREKNKITVTTTIPFSKRY 81 (122)
T ss_pred HHHhEEECCCcCccCCcEEEEEECCEEEEEecccccHHH
Confidence 367999999998876654444456778888999998753
No 87
>smart00216 VWD von Willebrand factor (vWF) type D domain. Von Willebrand factor contains several type D domains: D1 and D2 are present within the N-terminal propeptide whereas the remaining D domains are required for multimerisation.
Probab=22.73 E-value=59 Score=21.22 Aligned_cols=16 Identities=25% Similarity=0.200 Sum_probs=13.7
Q ss_pred cCCeEECCEEeCccce
Q psy7990 14 HQGPGVRKQVVNIPSF 29 (76)
Q Consensus 14 HgHI~Vng~~VniPSy 29 (76)
...|+|||+.|.+|-.
T Consensus 82 ~~~v~vng~~v~~p~~ 97 (162)
T smart00216 82 NGTVTVNGQQVSLPYK 97 (162)
T ss_pred CCEEEECCEEeeCCcC
Confidence 5789999999999864
No 88
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=22.49 E-value=40 Score=20.65 Aligned_cols=23 Identities=26% Similarity=0.208 Sum_probs=17.9
Q ss_pred ccceeeecCCCCceeeeeCCCCC
Q psy7990 26 IPSFVVRLDSQKHIDFSLNSPFG 48 (76)
Q Consensus 26 iPSy~Vk~~de~~I~~~~~SP~~ 48 (76)
-|-|.|..+|...+.|..+||-.
T Consensus 3 ~P~F~Vt~~d~p~~~~~g~s~~~ 25 (86)
T PF05965_consen 3 GPLFEVTSEDDPGEVFEGSSPTE 25 (86)
T ss_dssp SEEEEEEETT-GGG-EEESSHHH
T ss_pred CCEEEEEECCCCCCEEEeCCHHH
Confidence 48899999998889999988865
No 89
>KOG0436|consensus
Probab=21.55 E-value=31 Score=29.31 Aligned_cols=38 Identities=13% Similarity=0.036 Sum_probs=27.7
Q ss_pred chhhhhhhhcCCeEECCEEeCc-------cceeeecCCCCceeee
Q psy7990 5 LFLSTQYWEHQGPGVRKQVVNI-------PSFVVRLDSQKHIDFS 42 (76)
Q Consensus 5 ~~~ARQ~V~HgHI~Vng~~Vni-------PSy~Vk~~de~~I~~~ 42 (76)
+..-+|++.|||-++||++... |--+|+.--.+.|.|+
T Consensus 326 lplP~~I~vHghwt~ngmKMsKSLGNvvdP~~l~~kygvD~vRyf 370 (578)
T KOG0436|consen 326 LPLPKMIFVHGHWTKNGMKMSKSLGNVVDPFELVQKYGVDAVRYF 370 (578)
T ss_pred CCCccEEEEeeeeeecceecchhhccccCHHHHHHHhCccceeeE
Confidence 4456899999999999987532 5556666666777766
No 90
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=21.44 E-value=71 Score=18.42 Aligned_cols=30 Identities=23% Similarity=0.461 Sum_probs=19.2
Q ss_pred CeEECCEEeCc---cceeeecCCCCceeeeeCCCCCC
Q psy7990 16 GPGVRKQVVNI---PSFVVRLDSQKHIDFSLNSPFGG 49 (76)
Q Consensus 16 HI~Vng~~Vni---PSy~Vk~~de~~I~~~~~SP~~~ 49 (76)
.|.||+..|.- +++.+ .|.+.|++.+ |.+|
T Consensus 32 avavN~~iv~~~~~~~~~L--~dgD~Ieiv~--~V~G 64 (65)
T PRK06488 32 ATAVNGELVHKEARAQFVL--HEGDRIEILS--PMQG 64 (65)
T ss_pred EEEECCEEcCHHHcCcccc--CCCCEEEEEE--eccC
Confidence 37999999984 25444 4555677665 4444
No 91
>TIGR00395 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.
Probab=20.44 E-value=36 Score=29.73 Aligned_cols=18 Identities=0% Similarity=-0.213 Sum_probs=16.2
Q ss_pred hhhhhhcCCeEECCEEeC
Q psy7990 8 STQYWEHQGPGVRKQVVN 25 (76)
Q Consensus 8 ARQ~V~HgHI~Vng~~Vn 25 (76)
.|+++.||||+++|++..
T Consensus 605 Pk~i~~~G~vl~~G~KMS 622 (938)
T TIGR00395 605 PRGIVVNGYVMLEGKKMS 622 (938)
T ss_pred CcEEEEeceEEeCCcccc
Confidence 489999999999999866
No 92
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=20.23 E-value=44 Score=26.60 Aligned_cols=19 Identities=21% Similarity=0.113 Sum_probs=16.2
Q ss_pred hhhhhhcCCeEECCEEeCc
Q psy7990 8 STQYWEHQGPGVRKQVVNI 26 (76)
Q Consensus 8 ARQ~V~HgHI~Vng~~Vni 26 (76)
-++++.|||+.++|++...
T Consensus 312 ~~~~~~~g~v~~~g~KmSK 330 (530)
T TIGR00398 312 PTQVFSHGYLTVEGGKMSK 330 (530)
T ss_pred CCEEEeeccEEECCceecc
Confidence 5789999999999988653
No 93
>PF14541 TAXi_C: Xylanase inhibitor C-terminal; PDB: 3AUP_D 3HD8_A 1T6G_A 1T6E_X 2B42_A 3VLB_A 3VLA_A.
Probab=20.04 E-value=1.3e+02 Score=19.88 Aligned_cols=33 Identities=18% Similarity=0.224 Sum_probs=19.4
Q ss_pred CeEECCEEeCccceeee-cCCCCceeeeeCCCCC
Q psy7990 16 GPGVRKQVVNIPSFVVR-LDSQKHIDFSLNSPFG 48 (76)
Q Consensus 16 HI~Vng~~VniPSy~Vk-~~de~~I~~~~~SP~~ 48 (76)
-|.|+|+++.+|+.... .+....+-++..++|+
T Consensus 8 ~Isvg~~~l~~~~~~~~~~~~~g~~iiDSGT~~T 41 (161)
T PF14541_consen 8 GISVGGKRLPIPPSVFQLSDGSGGTIIDSGTTYT 41 (161)
T ss_dssp EEEETTEEE---TTCSCETTSTCSEEE-SSSSSE
T ss_pred EEEECCEEecCChHHhhccCCCCCEEEECCCCcc
Confidence 38999999999985421 4445566666666665
Done!