Query 046291
Match_columns 197
No_of_seqs 243 out of 1460
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 10:33:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046291hhsearch_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 1.2E-64 2.6E-69 422.9 17.0 184 1-185 1-184 (194)
2 PTZ00155 40S ribosomal protein 100.0 9.2E-60 2E-64 390.6 15.8 179 4-183 2-180 (181)
3 TIGR01018 rpsD_arch ribosomal 100.0 5.6E-57 1.2E-61 368.2 16.1 161 5-167 2-162 (162)
4 PRK04051 rps4p 30S ribosomal p 100.0 6.3E-56 1.4E-60 366.7 17.2 170 5-177 2-171 (177)
5 KOG3301 Ribosomal protein S4 [ 100.0 3.1E-50 6.7E-55 326.2 12.5 182 11-195 1-182 (183)
6 KOG4655 U3 small nucleolar rib 100.0 1.3E-36 2.7E-41 247.3 4.3 151 16-167 15-165 (181)
7 COG0522 RpsD Ribosomal protein 100.0 6E-32 1.3E-36 228.4 12.5 151 10-174 7-159 (205)
8 CHL00113 rps4 ribosomal protei 99.6 2E-15 4.3E-20 127.6 6.9 102 31-162 39-140 (201)
9 TIGR01017 rpsD_bact ribosomal 99.5 8E-15 1.7E-19 123.6 6.0 113 18-158 27-139 (200)
10 PF01479 S4: S4 domain; Inter 99.5 7.2E-14 1.6E-18 91.7 5.0 47 109-155 1-47 (48)
11 PRK05327 rpsD 30S ribosomal pr 99.5 8.4E-14 1.8E-18 117.6 6.3 113 21-163 31-145 (203)
12 COG1189 Predicted rRNA methyla 99.2 9.4E-12 2E-16 107.7 5.2 62 108-170 2-63 (245)
13 PRK10348 ribosome-associated h 99.2 2.5E-11 5.4E-16 96.8 5.5 52 108-160 8-59 (133)
14 COG1188 Ribosome-associated he 99.1 8.5E-11 1.9E-15 89.4 4.6 56 107-163 7-62 (100)
15 TIGR02988 YaaA_near_RecF S4 do 98.9 1.6E-09 3.5E-14 74.2 5.3 50 109-158 9-58 (59)
16 TIGR00478 tly hemolysin TlyA f 98.9 1.5E-09 3.3E-14 93.2 5.0 59 110-170 1-59 (228)
17 cd00165 S4 S4/Hsp/ tRNA synthe 98.7 2.7E-08 5.9E-13 66.6 5.2 49 109-157 1-49 (70)
18 smart00363 S4 S4 RNA-binding d 98.7 3.5E-08 7.6E-13 64.3 5.6 50 109-158 1-50 (60)
19 PF00163 Ribosomal_S4: Ribosom 98.6 4.4E-10 9.6E-15 83.8 -5.6 93 8-108 2-94 (94)
20 TIGR03069 PS_II_S4 photosystem 98.2 1.3E-06 2.8E-11 76.5 4.7 51 107-158 182-232 (257)
21 COG1187 RsuA 16S rRNA uridine- 98.2 1.9E-06 4.1E-11 75.3 5.5 46 108-154 2-47 (248)
22 PLN00051 RNA-binding S4 domain 98.2 2.3E-06 4.9E-11 75.4 4.9 52 107-159 190-241 (267)
23 PRK10700 23S rRNA pseudouridyl 98.0 7.8E-06 1.7E-10 72.5 5.6 50 109-160 3-52 (289)
24 PRK10475 23S rRNA pseudouridin 97.9 1.5E-05 3.3E-10 70.8 5.3 49 109-159 7-55 (290)
25 COG2302 Uncharacterized conser 97.8 2.3E-05 4.9E-10 68.6 4.8 51 107-158 179-229 (257)
26 PRK10839 16S rRNA pseudouridyl 97.6 0.00011 2.4E-09 62.4 5.2 50 109-159 1-50 (232)
27 PRK11507 ribosome-associated p 97.6 0.00015 3.3E-09 52.1 4.9 50 109-160 12-61 (70)
28 PRK11180 rluD 23S rRNA pseudou 97.5 0.00013 2.9E-09 65.2 5.5 55 106-160 15-69 (325)
29 TIGR00005 rluA_subfam pseudour 97.4 0.00031 6.8E-09 61.6 5.4 54 107-160 4-57 (299)
30 PF13275 S4_2: S4 domain; PDB: 97.3 4.4E-05 9.6E-10 54.1 -0.4 50 109-160 8-57 (65)
31 COG0564 RluA Pseudouridylate s 97.1 0.00099 2.1E-08 59.2 5.9 54 106-161 10-63 (289)
32 PRK11025 23S rRNA pseudouridyl 96.9 0.0014 2.9E-08 58.6 5.2 51 107-158 18-68 (317)
33 COG2501 S4-like RNA binding pr 96.7 0.0041 9E-08 45.0 5.0 48 111-160 14-61 (73)
34 PRK13354 tyrosyl-tRNA syntheta 96.4 0.0036 7.8E-08 58.3 4.1 46 109-154 343-388 (410)
35 PRK05912 tyrosyl-tRNA syntheta 96.1 0.011 2.5E-07 54.9 5.7 44 109-152 343-386 (408)
36 PRK04313 30S ribosomal protein 95.3 0.03 6.5E-07 48.9 5.0 43 118-162 48-90 (237)
37 PTZ00118 40S ribosomal protein 94.5 0.064 1.4E-06 47.5 5.0 43 118-162 52-94 (262)
38 PTZ00223 40S ribosomal protein 94.4 0.066 1.4E-06 47.6 4.9 43 118-162 49-91 (273)
39 PLN00036 40S ribosomal protein 94.4 0.068 1.5E-06 47.3 4.9 43 118-162 52-94 (261)
40 COG1471 RPS4A Ribosomal protei 93.6 0.078 1.7E-06 46.2 3.6 42 118-161 51-92 (241)
41 COG0162 TyrS Tyrosyl-tRNA synt 93.3 0.21 4.5E-06 46.7 6.2 71 73-150 307-377 (401)
42 TIGR00234 tyrS tyrosyl-tRNA sy 87.5 0.63 1.4E-05 42.9 3.7 42 109-150 330-371 (377)
43 KOG2623 Tyrosyl-tRNA synthetas 87.2 1.7 3.8E-05 40.9 6.4 39 113-151 403-441 (467)
44 PRK06437 hypothetical protein; 58.0 15 0.00032 25.6 3.3 22 136-158 39-60 (67)
45 PF14451 Ub-Mut7C: Mut7-C ubiq 53.9 11 0.00024 27.5 2.2 25 133-158 49-73 (81)
46 cd00754 MoaD Ubiquitin domain 47.3 19 0.0004 24.9 2.4 25 133-158 49-73 (80)
47 PF02597 ThiS: ThiS family; I 42.3 32 0.00069 23.4 3.0 25 134-158 44-70 (77)
48 cd00565 ThiS ThiaminS ubiquiti 38.9 34 0.00073 23.2 2.6 24 135-158 32-58 (65)
49 PRK08364 sulfur carrier protei 38.5 43 0.00094 23.2 3.2 23 135-158 41-63 (70)
50 PF06777 DUF1227: Protein of u 37.5 92 0.002 25.4 5.3 71 41-122 53-123 (146)
51 PRK01777 hypothetical protein; 37.2 55 0.0012 24.5 3.8 27 133-162 49-75 (95)
52 PF06353 DUF1062: Protein of u 36.5 44 0.00095 27.0 3.3 41 101-142 95-135 (142)
53 PRK06488 sulfur carrier protei 33.0 44 0.00095 22.6 2.5 23 136-158 33-58 (65)
54 PRK02967 nickel responsive reg 28.3 45 0.00098 26.7 2.2 27 100-127 5-31 (139)
55 TIGR01683 thiS thiamine biosyn 27.8 70 0.0015 21.5 2.8 24 135-158 31-57 (64)
56 PLN02799 Molybdopterin synthas 27.6 1.1E+02 0.0024 21.3 3.9 23 135-158 53-75 (82)
57 COG4332 Uncharacterized protei 27.5 44 0.00095 28.5 2.0 60 100-160 130-189 (203)
58 PRK12901 secA preprotein trans 27.5 1.7E+02 0.0036 31.3 6.5 94 36-132 9-122 (1112)
59 KOG1919 RNA pseudouridylate sy 25.6 1.5E+02 0.0032 27.7 5.2 48 111-160 47-94 (371)
60 TIGR01682 moaD molybdopterin c 25.4 70 0.0015 22.3 2.5 23 135-158 51-73 (80)
61 TIGR02793 nikR nickel-responsi 25.0 58 0.0013 25.7 2.2 27 100-127 4-30 (129)
62 KOG4217 Nuclear receptors of t 24.8 1.4E+02 0.003 29.2 5.0 71 31-106 518-588 (605)
63 PRK06944 sulfur carrier protei 21.7 91 0.002 20.7 2.4 24 135-158 32-58 (65)
64 KOG0378 40S ribosomal protein 20.2 68 0.0015 28.5 1.8 44 101-151 42-85 (263)
65 PRK08053 sulfur carrier protei 20.1 1.2E+02 0.0025 20.6 2.7 23 136-158 34-59 (66)
No 1
>PLN00189 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=1.2e-64 Score=422.92 Aligned_cols=184 Identities=83% Similarity=1.268 Sum_probs=179.2
Q ss_pred CcccCCcccccccccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHH
Q 046291 1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLR 80 (197)
Q Consensus 1 ~~~~~~~~~~~k~~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~ 80 (197)
||++.+|++++|+|+||+|||+++++.+|.+++++|||+||+|||+|+++|++||++|+.|++++++|+++++++++||+
T Consensus 1 ~~~~~~~~~~~K~y~tP~~P~ek~Rl~~E~kli~kYgLknK~E~wky~~ll~kiRk~Ar~Ll~l~~~d~~r~~~~~~LL~ 80 (194)
T PLN00189 1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR 80 (194)
T ss_pred CCcccCCCCCCcccCCCCCchhhHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHccCCCccHhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcchhhhhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 81 RMFRYGLLEATQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 81 kL~~~Gli~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
+||+||||++++.+|++|++|++++|||+|||++|+++|||+|+++|++||.||||+|||++|++|||+|++++|++|+|
T Consensus 81 kL~~~GlL~~~~~~Ld~vl~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw 160 (194)
T PLN00189 81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDF 160 (194)
T ss_pred HHHHhCCccccccCHHHHhhccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEE
Confidence 99999999767789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcccCCCchhhhhhhhHHHhh
Q 046291 161 SLTSSLTQTGRPGRVKRKAQKAAAK 185 (197)
Q Consensus 161 ~~~s~~vs~~~~~r~~~~~~~~~~~ 185 (197)
.++|+|. +++|+|++||+++++++
T Consensus 161 ~~~Sp~~-~~~p~r~~~k~~~~~~~ 184 (194)
T PLN00189 161 SLTSPLG-GGRPGRVKRKNQKAASG 184 (194)
T ss_pred ecCCccc-CCChhHHHHHHHHhccC
Confidence 9999999 59999999999987643
No 2
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=9.2e-60 Score=390.56 Aligned_cols=179 Identities=71% Similarity=1.119 Sum_probs=173.7
Q ss_pred cCCcccccccccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHH
Q 046291 4 VSFYRNYGKTFKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMF 83 (197)
Q Consensus 4 ~~~~~~~~k~~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~ 83 (197)
..+|++++|+|+||+|||+++++++|.+++++|||+||+|||+|+++|++||++|+.|++++++|++++.++++||++|+
T Consensus 2 ~~~~~~~~k~y~~P~~P~~k~rl~~E~~li~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~~~d~~r~~~~~~LL~kL~ 81 (181)
T PTZ00155 2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMH 81 (181)
T ss_pred CCCCCCCCcccCCCCCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcchhhhhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccC
Q 046291 84 RYGLLEATQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLT 163 (197)
Q Consensus 84 ~~Gli~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~ 163 (197)
+||++.+++++|++|++|++++|||+|||++|+++|||+|+++|++||.||||+|||++|++|||+|++++|++|+|.++
T Consensus 82 ~~Gi~~~~k~~l~~~~~l~~~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~ 161 (181)
T PTZ00155 82 RLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADT 161 (181)
T ss_pred HhCCcchhhccHHHHHCccHHHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceeeecC
Confidence 99999878899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCchhhhhhhhHHH
Q 046291 164 SSLTQTGRPGRVKRKAQKAA 183 (197)
Q Consensus 164 s~~vs~~~~~r~~~~~~~~~ 183 (197)
|+|. +++|+|+++++.+++
T Consensus 162 S~~~-~~~~~r~~~~~~~~~ 180 (181)
T PTZ00155 162 SPFG-NGRPGRVKRKAAKAA 180 (181)
T ss_pred CCcc-CCChHHHHHHhhhhc
Confidence 9999 599999998887753
No 3
>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=100.00 E-value=5.6e-57 Score=368.24 Aligned_cols=161 Identities=50% Similarity=0.818 Sum_probs=157.1
Q ss_pred CCcccccccccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHH
Q 046291 5 SFYRNYGKTFKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFR 84 (197)
Q Consensus 5 ~~~~~~~k~~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~ 84 (197)
++|++++|+|+||+|||+++++++|.+++++|||+||+|||+|+++|++||++|+.|++++ |++++.++++||++||+
T Consensus 2 g~p~~~~k~~~~P~~pw~ker~~~E~~l~~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~--d~~r~~~~~~LL~kL~~ 79 (162)
T TIGR01018 2 GDPRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD--DEQRLFEGNQLLRRLVR 79 (162)
T ss_pred CCCCCCCcccCCCCCChhhhhCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHcCC--cHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999999999999999999999999999999999999999998 89999999999999999
Q ss_pred hcchhhhhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCC
Q 046291 85 YGLLEATQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTS 164 (197)
Q Consensus 85 ~Gli~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s 164 (197)
||||++++.+|++|++|++++|||||||++|+++|||+|+++|++||.||||+|||++|++|||+|++++|++|+|.++|
T Consensus 80 ~Gll~e~~~~Ld~vl~Ltv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S 159 (162)
T TIGR01018 80 LGILDEENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSS 159 (162)
T ss_pred cCCCccccCCHHHHHhccHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeecCC
Confidence 99998667899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ccc
Q 046291 165 SLT 167 (197)
Q Consensus 165 ~~v 167 (197)
+|.
T Consensus 160 ~~~ 162 (162)
T TIGR01018 160 PFK 162 (162)
T ss_pred CCC
Confidence 874
No 4
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=100.00 E-value=6.3e-56 Score=366.74 Aligned_cols=170 Identities=40% Similarity=0.635 Sum_probs=163.8
Q ss_pred CCcccccccccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHH
Q 046291 5 SFYRNYGKTFKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFR 84 (197)
Q Consensus 5 ~~~~~~~k~~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~ 84 (197)
++|++++|+|.+|+|||+++++.+|.+++++|||+||+|||+|+++|++||+.|+.|++ ..|++++.++++||++||+
T Consensus 2 g~p~~~~k~~~~P~~pw~~~r~~~E~~l~~~YgLknk~E~wk~~~~~~~iR~~Ar~Ll~--~~~~~r~~~~~~Ll~kL~~ 79 (177)
T PRK04051 2 GDPKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLA--LPPEERAKEEEQLLGKLKR 79 (177)
T ss_pred CCCCCCCcCcCCCCCchhhhhcHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999998 4468899999999999999
Q ss_pred hcchhhhhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCC
Q 046291 85 YGLLEATQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTS 164 (197)
Q Consensus 85 ~Gli~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s 164 (197)
||||++ +.+|++|++|++++|||+|||++|+++|||.|+++|++||.||||+|||++|++|||+|++++|++|+|.++|
T Consensus 80 ~Gil~~-~~~L~~vl~L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S 158 (177)
T PRK04051 80 YGILKE-NATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTS 158 (177)
T ss_pred cCCCCC-CCCHHHHHhccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCC
Confidence 999984 8899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCCchhhhh
Q 046291 165 SLTQTGRPGRVKR 177 (197)
Q Consensus 165 ~~vs~~~~~r~~~ 177 (197)
++.+.+||+|..-
T Consensus 159 ~i~~~~~~~r~~~ 171 (177)
T PRK04051 159 PLADELHPERAEA 171 (177)
T ss_pred CCCCCCCcchhhh
Confidence 9997799998754
No 5
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-50 Score=326.22 Aligned_cols=182 Identities=68% Similarity=1.102 Sum_probs=171.5
Q ss_pred cccccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhh
Q 046291 11 GKTFKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEA 90 (197)
Q Consensus 11 ~k~~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~ 90 (197)
+|+|.+|++||+++|+..|+++++.|||+||+|+|++.+.++++|..||.| |+++||.+++++.+|+++|.++|++++
T Consensus 1 ~k~y~~PRrpfek~Rld~elkl~g~yglknk~elwr~~~~l~K~r~aaR~l--l~~k~p~rlf~g~allrrLvr~g~l~e 78 (183)
T KOG3301|consen 1 SKTYKTPRRPFEKERLDAELKLVGEYGLKNKRELWRVSRSLSKIRYAAREL--LDEKDPKRLFEGNALLRRLVRYGVLDE 78 (183)
T ss_pred CCccCCCCChHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHHHHH--hccccHHHHhcchHHHHHHHHHhhhhc
Confidence 589999999999999999999999999999999999999999999999999 789999999999999999999999999
Q ss_pred hhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCCCcccCC
Q 046291 91 TQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTSSLTQTG 170 (197)
Q Consensus 91 ~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s~~vs~~ 170 (197)
.+.+|+++++|++++|||||||++|+++|||+|+++|+.||.|+||+|++++|++|||+|..+.+.+|+++..|+|. ++
T Consensus 79 ~~~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrldsqk~iD~s~~s~~g-~~ 157 (183)
T KOG3301|consen 79 RKNKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLDSQKHIDFSLPSPYG-GA 157 (183)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEeechhhhccccccccCC-CC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999 99
Q ss_pred CchhhhhhhhHHHhhhcCCCCCCCc
Q 046291 171 RPGRVKRKAQKAAAKKSAGGADEDD 195 (197)
Q Consensus 171 ~~~r~~~~~~~~~~~~~~~~~~~~~ 195 (197)
.|||+++++++++.++.|+++++|+
T Consensus 158 ~pg~~krk~~~k~~~~~g~~~~~Ee 182 (183)
T KOG3301|consen 158 RPGRVKRKNNQKADAKGGGLDENEE 182 (183)
T ss_pred CcchhhhhhhhhhhcccCCcccccc
Confidence 9999999997666544444444443
No 6
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=100.00 E-value=1.3e-36 Score=247.28 Aligned_cols=151 Identities=26% Similarity=0.402 Sum_probs=146.4
Q ss_pred CCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhhhhcch
Q 046291 16 KPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEATQNKL 95 (197)
Q Consensus 16 ~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~~~~~L 95 (197)
+.+.-|+.+.+.+|..++++|+|++++||.+|+.+++++|++|..|..|++.||||...+..||.|||.||+++ +..++
T Consensus 15 VdFLnWkv~d~~re~~v~rrY~l~~REdY~kyn~l~~~~r~la~~l~~l~~sDpfR~~~t~~LL~kly~~Gvip-Tr~~l 93 (181)
T KOG4655|consen 15 VDFLNWKVTDHHRELCVLRRYHLKKREDYTKYNRLAGKVRKLANRLALLDESDPFRLQYTLLLLEKLYAMGVIP-TRKSL 93 (181)
T ss_pred cccceeeecCchhhHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhhccccccceec-chhhh
Confidence 77889999999999999999999999999999999999999999999999999999999999999999999999 67889
Q ss_pred hHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCCCcc
Q 046291 96 DYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTSSLT 167 (197)
Q Consensus 96 ~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s~~v 167 (197)
+.+..+++++||+|||++++.+.+||+|.+.|..||+||||+||..+|++|+|+|+.++||+|+|.++|+..
T Consensus 94 ~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SKIK 165 (181)
T KOG4655|consen 94 ELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSKIK 165 (181)
T ss_pred hhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhhhhhhHHHH
Confidence 998899999999999999999999999999999999999999999999999999999999999999988765
No 7
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=6e-32 Score=228.39 Aligned_cols=151 Identities=28% Similarity=0.321 Sum_probs=138.4
Q ss_pred cccc--ccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcc
Q 046291 10 YGKT--FKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGL 87 (197)
Q Consensus 10 ~~k~--~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gl 87 (197)
++++ +.+|.+||..++...|.+.+..|| +++.+.|...+.++..++.++.|..+-. ..+.+|++.|+.+|+
T Consensus 7 ~~~K~~rr~g~~~~~~~~~~~~~~~~~~pG-qhk~~~~~k~s~yg~qL~ekqkl~~~yg------~~ekqf~~~l~~a~~ 79 (205)
T COG0522 7 PKKKLSRRLGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLREKQKLRAFYG------VLEKQFRRYLKEAGR 79 (205)
T ss_pred cccceeeecCCChHHHHHHHHHhhcCCCcc-ccchhHHHHHHHHHHHHHHHHHhhhhcc------HHHHHHHHHHHHHhc
Confidence 6666 999999999999999999999999 9999999999999999999999987654 577889999999999
Q ss_pred hhhhhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCCCcc
Q 046291 88 LEATQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTSSLT 167 (197)
Q Consensus 88 i~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s~~v 167 (197)
+.+ ++++++.++||+|||++|+++|||.|+.+|||||.||||.|||++|++|||+|+++|++.|.+.+.|++.
T Consensus 80 l~g-------~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~ 152 (205)
T COG0522 80 LKG-------VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIK 152 (205)
T ss_pred cCC-------hHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchhh
Confidence 873 7889999999999999999999999999999999999999999999999999999999999998888877
Q ss_pred cCCCchh
Q 046291 168 QTGRPGR 174 (197)
Q Consensus 168 s~~~~~r 174 (197)
...++.+
T Consensus 153 ~~~~~~~ 159 (205)
T COG0522 153 IKEALEL 159 (205)
T ss_pred hhhhhhh
Confidence 5545444
No 8
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=99.59 E-value=2e-15 Score=127.58 Aligned_cols=102 Identities=25% Similarity=0.335 Sum_probs=83.9
Q ss_pred HHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhhhhcchhHHhhhhhHHHHHhh
Q 046291 31 RLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEATQNKLDYVLALTVESFLERR 110 (197)
Q Consensus 31 ~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~~~~~L~~~~~l~~~~~lerR 110 (197)
..+..||++-.+ ++.++.++++.|+++.+.+..+. ...|..+ -++..+||+|
T Consensus 39 ~k~S~y~~~L~e------------Kqk~~~~Yg~~ekq~~~~~~~a~-----~~~g~tg-----------~~ll~~LE~R 90 (201)
T CHL00113 39 GKKSQYRIRLEE------------KQKLRFNYGLTERQLLKYVRIAR-----KAKGSTG-----------QVLLQLLEMR 90 (201)
T ss_pred ccccHHHHHHHH------------HHHHHHHcCCCHHHHHHHHHHHH-----hcCCcHH-----------HHHHHHHHHH
Confidence 567888887544 56788999999999877776665 2345544 2366899999
Q ss_pred hhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEecc
Q 046291 111 LQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSL 162 (197)
Q Consensus 111 LD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~ 162 (197)
||.+|++.||+.|+.+|+++|.||||+|||++|++||+.|.++|+ |++..
T Consensus 91 LD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~--I~V~~ 140 (201)
T CHL00113 91 LDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDI--ITVKD 140 (201)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCE--EEEcc
Confidence 999999999999999999999999999999999999999999975 45443
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=99.54 E-value=8e-15 Score=123.63 Aligned_cols=113 Identities=26% Similarity=0.400 Sum_probs=86.7
Q ss_pred CCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhhhhcchhH
Q 046291 18 RRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEATQNKLDY 97 (197)
Q Consensus 18 ~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~~~~~L~~ 97 (197)
++|+.+..+..-.+.+..||++-++ ++.++..+++.+++....+..+. ...|..+
T Consensus 27 ~~~~~pg~hg~~~~k~S~y~~~l~e------------KQk~~~~Yg~~e~q~~~~~~~a~-----~~~g~t~-------- 81 (200)
T TIGR01017 27 KRKYPPGQHGQRRKKLSDYGLQLQE------------KQKLKFMYGITEKQFRKYFKEAK-----KLKGNTG-------- 81 (200)
T ss_pred ccCCCCCCCCcCCCcccHHHHHHHH------------HHHHHHHHhchHHHHHHHHHHHh-----ccCCCch--------
Confidence 5666666665434578889987544 56777888888887666544443 4455433
Q ss_pred HhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeE
Q 046291 98 VLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 98 ~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
.++..++++|||.+|++.||+.||.+|+++|.||||.|||++|++||+.|.+||.+.|
T Consensus 82 ---~~ll~~le~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V 139 (200)
T TIGR01017 82 ---ENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISI 139 (200)
T ss_pred ---hHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEE
Confidence 1234688999999999999999999999999999999999999999999999975443
No 10
>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=99.47 E-value=7.2e-14 Score=91.65 Aligned_cols=47 Identities=36% Similarity=0.526 Sum_probs=45.4
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCe
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQ 155 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de 155 (197)
||||.+|++.|++.|+++|+++|.+|+|+|||+++++|++.|.++|+
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~ 47 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDV 47 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCC
Confidence 69999999999999999999999999999999999999999999874
No 11
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=99.46 E-value=8.4e-14 Score=117.65 Aligned_cols=113 Identities=29% Similarity=0.435 Sum_probs=85.0
Q ss_pred CccccchHH--HHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhhhhcchhHH
Q 046291 21 YEKERLDAE--LRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEATQNKLDYV 98 (197)
Q Consensus 21 w~~~~~~~E--~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~~~~~L~~~ 98 (197)
+.+..+.+. ...+..||++-.+ ++.++..+++.+++....+..+. ...|..+.
T Consensus 31 ~~pg~hg~~~~~~k~s~y~~~L~e------------KQk~~~~Y~~~e~q~~~~~~~a~-----~~~g~t~~-------- 85 (203)
T PRK05327 31 YPPGQHGQRRRKPKLSDYGLQLRE------------KQKLRRIYGVLEKQFRRYFKEAA-----RRKGNTGE-------- 85 (203)
T ss_pred CCCCCCCcccCCccccHHHHHHHH------------HHHhHHHhcCcHHHHHHHHHHHH-----hccCCcHh--------
Confidence 445555432 2357889887544 56778888888887655544433 44555431
Q ss_pred hhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccC
Q 046291 99 LALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLT 163 (197)
Q Consensus 99 ~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~ 163 (197)
++..++|+|||.+|++.||+.|+.+|+++|.||||.|||++|++||+.|.++|. |++...
T Consensus 86 ---~ll~~lE~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~--I~v~~~ 145 (203)
T PRK05327 86 ---NLLQLLESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDV--IEVREK 145 (203)
T ss_pred ---HHHHHHHHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCE--EEECCc
Confidence 235688999999999999999999999999999999999999999999999975 555443
No 12
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=99.23 E-value=9.4e-12 Score=107.68 Aligned_cols=62 Identities=27% Similarity=0.339 Sum_probs=55.8
Q ss_pred HhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCCCcccCC
Q 046291 108 ERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTSSLTQTG 170 (197)
Q Consensus 108 erRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s~~vs~~ 170 (197)
++|||.+|+++|+++||++|+.+|++|.|.|||..|++||+.|..++++.|.- +..+|||+|
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~-~~~~yVSRG 63 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG-EEQPYVSRG 63 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcc-cCcCccccH
Confidence 58999999999999999999999999999999999999999999887654432 678999975
No 13
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=99.19 E-value=2.5e-11 Score=96.81 Aligned_cols=52 Identities=25% Similarity=0.276 Sum_probs=48.8
Q ss_pred HhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 108 ERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 108 erRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
.+|||.|||..||++||+.|+++|.+|+|+|||++ ++||..|.++|++.|.+
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQ 59 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEE
Confidence 36999999999999999999999999999999999 89999999999877765
No 14
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=99.10 E-value=8.5e-11 Score=89.42 Aligned_cols=56 Identities=21% Similarity=0.192 Sum_probs=51.7
Q ss_pred HHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccC
Q 046291 107 LERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLT 163 (197)
Q Consensus 107 lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~ 163 (197)
.++|||.||+..+|+++|+.|+.+|..|+|.|||+.+ +||..|+.||++.|.+...
T Consensus 7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNK 62 (100)
T ss_pred cceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCc
Confidence 4789999999999999999999999999999999998 9999999999888876443
No 15
>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=98.94 E-value=1.6e-09 Score=74.20 Aligned_cols=50 Identities=12% Similarity=0.122 Sum_probs=46.4
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeE
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
.|||.+|.+.+++.|+..|+.+|..|+|+|||+++++|++.|..||.+.|
T Consensus 9 ~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 9 ITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 69999999998888999999999999999999999999999999986543
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=98.90 E-value=1.5e-09 Score=93.23 Aligned_cols=59 Identities=29% Similarity=0.403 Sum_probs=52.5
Q ss_pred hhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEeccCCCcccCC
Q 046291 110 RLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSLTSSLTQTG 170 (197)
Q Consensus 110 RLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~~s~~vs~~ 170 (197)
|||.+|+..|++.||++|+++|.+|+|+|||+++++|++.|..++ .|++.....|||++
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d--~I~v~~~~~~vsr~ 59 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDA--KIELLQNPLFVSRG 59 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCC--EEeccCccchhhhh
Confidence 899999999999999999999999999999999999999999886 45555555699764
No 17
>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=98.71 E-value=2.7e-08 Score=66.64 Aligned_cols=49 Identities=35% Similarity=0.480 Sum_probs=44.7
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeee
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNH 157 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~ 157 (197)
+|||.+|.+.+++.|+++|+++|.+|+|+|||+.++.|++.|.+++.+.
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~ 49 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIE 49 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEE
Confidence 4899999999888899999999999999999999999999999987533
No 18
>smart00363 S4 S4 RNA-binding domain.
Probab=98.71 E-value=3.5e-08 Score=64.33 Aligned_cols=50 Identities=36% Similarity=0.507 Sum_probs=45.1
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeE
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
+|||.+|...+++.|+.+|+.+|.+|.|.|||++++.|++.+..+|.+.+
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~ 50 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISV 50 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEE
Confidence 48999999998888999999999999999999999889999999875443
No 19
>PF00163 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal domain; InterPro: IPR001912 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 [, ]. Ribosomal protein S4 is one of the proteins from the small ribosomal subunit. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within domain 1 and displays some structural homology with the ETS DNA binding domain []. This entry represents the domain found at the N terminus of small ribosomal subunits S4 and S9. ; GO: 0019843 rRNA binding, 0005622 intracellular; PDB: 3BBN_D 2WWL_D 3OR9_D 3OFA_D 2QBB_D 3OFP_D 4A2I_D 2QB9_D 3OFO_D 2QBF_D ....
Probab=98.65 E-value=4.4e-10 Score=83.76 Aligned_cols=93 Identities=34% Similarity=0.467 Sum_probs=84.6
Q ss_pred ccccccccCCCCCCccccchHHHHHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcc
Q 046291 8 RNYGKTFKKPRRPYEKERLDAELRLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGL 87 (197)
Q Consensus 8 ~~~~k~~~~p~~pw~~~~~~~E~~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gl 87 (197)
+...++|+.|++||....+..+..++++||+.++.+.|+.... |+.++.+.+|.|+|+.+...+ .++++|+++|+
T Consensus 2 R~~~~~~k~~Rr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----rk~s~y~~qL~eKqk~r~~yg-~lekql~~~~~ 76 (94)
T PF00163_consen 2 RYRGPKCKLPRRLGEKLWLTEKAKLIRRYGLRPGQHGWRRKSR----RKLSRYGLQLREKQKLRFYYG-ILEKQLRRYGK 76 (94)
T ss_dssp CSHSCCCHHHHHCTSHCTCSCCCSHCCSSSSSSSSSTTSHHHH----HCCHHHHHHHHHHHHHHHHHT-HHHHHHHHHHH
T ss_pred CcCCCccccCCCCCCCccCCCcccccccccccccccccccccc----ccchhhhcccccCCchhhhhh-hHHHHHHHHHH
Confidence 4456788999999999999999999999999999999988755 899999999999999999888 89999999999
Q ss_pred hhhhhcchhHHhhhhhHHHHH
Q 046291 88 LEATQNKLDYVLALTVESFLE 108 (197)
Q Consensus 88 i~~~~~~L~~~~~l~~~~~le 108 (197)
+. .+++.++++++.++||
T Consensus 77 ~a---~k~~g~tg~~l~~lLE 94 (94)
T PF00163_consen 77 IA---AKLKGVTGENLLQLLE 94 (94)
T ss_dssp HH---HHSSSHHHHHHHHHHH
T ss_pred HH---HhcCCCHHHHHHHHhC
Confidence 86 5788999999999997
No 20
>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=98.23 E-value=1.3e-06 Score=76.47 Aligned_cols=51 Identities=22% Similarity=0.260 Sum_probs=44.1
Q ss_pred HHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeE
Q 046291 107 LERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 107 lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
-.+|||. +...++.-||++|+++|.+|+|.|||++|++|++.|.++|.+.|
T Consensus 182 ~s~RLD~-lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isv 232 (257)
T TIGR03069 182 ASLRIDA-IASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQL 232 (257)
T ss_pred ccccHHH-HHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEE
Confidence 3479995 55778877999999999999999999999999999999975433
No 21
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=98.22 E-value=1.9e-06 Score=75.26 Aligned_cols=46 Identities=24% Similarity=0.382 Sum_probs=44.0
Q ss_pred HhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCC
Q 046291 108 ERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDA 154 (197)
Q Consensus 108 erRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~d 154 (197)
.+|||.+|.++|++ ||.+|.++|.+|.|.|||++++.++..|.+++
T Consensus 2 ~~RL~K~La~~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~ 47 (248)
T COG1187 2 SMRLNKFLAEAGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDD 47 (248)
T ss_pred ccchHHHHHHcCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCC
Confidence 57999999999999 99999999999999999999999999999885
No 22
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.17 E-value=2.3e-06 Score=75.43 Aligned_cols=52 Identities=19% Similarity=0.161 Sum_probs=45.9
Q ss_pred HHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEE
Q 046291 107 LERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVG 159 (197)
Q Consensus 107 lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~ 159 (197)
...|||.++.. ++--||++|.++|.+|+|+||+.++++|++.|.+||.+.|.
T Consensus 190 as~RLD~vla~-~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiR 241 (267)
T PLN00051 190 ASLRLDALASA-GFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVS 241 (267)
T ss_pred CcccHHHHHHH-HhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence 34799998776 56889999999999999999999999999999999865553
No 23
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=98.03 E-value=7.8e-06 Score=72.49 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=44.2
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
+|||.+|.+.|++ ||++|..+|.+|.|+|||+++ .|++.|.+++.+.|.+
T Consensus 3 ~RL~k~La~~g~~-SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v 52 (289)
T PRK10700 3 EKLQKVLARAGHG-SRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRI 52 (289)
T ss_pred hhHHHHHHHCCCC-CHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEE
Confidence 7999999999987 999999999999999999988 6999998775555554
No 24
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=97.91 E-value=1.5e-05 Score=70.82 Aligned_cols=49 Identities=18% Similarity=0.199 Sum_probs=43.6
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEE
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVG 159 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~ 159 (197)
+|||.+|...|++ ||.+|..+|.+|.|+|||+++ .|++.|.++|.+.|.
T Consensus 7 ~RL~k~La~~g~~-SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~ 55 (290)
T PRK10475 7 TRLNKYISESGIC-SRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVN 55 (290)
T ss_pred HHHHHHHHhCCCC-CHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEEC
Confidence 5999999999977 999999999999999999988 599999988765543
No 25
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.83 E-value=2.3e-05 Score=68.57 Aligned_cols=51 Identities=24% Similarity=0.340 Sum_probs=44.8
Q ss_pred HHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeE
Q 046291 107 LERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 107 lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
...|||.++.. +|-.||++|.++|..|.|.||.++|++|||.|..||.+.|
T Consensus 179 sSlRLD~vis~-~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSi 229 (257)
T COG2302 179 SSLRLDVVISE-GFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISI 229 (257)
T ss_pred ehhhHHHHHHH-HHhhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEE
Confidence 34699997765 5788999999999999999999999999999999985544
No 26
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=97.57 E-value=0.00011 Score=62.45 Aligned_cols=50 Identities=16% Similarity=0.120 Sum_probs=43.7
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEE
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVG 159 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~ 159 (197)
+|||.+|.+.+ .-|++.++++|.+|.|+|||+++++|++.|..+|.+.|.
T Consensus 1 ~rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~ 50 (232)
T PRK10839 1 MRLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYD 50 (232)
T ss_pred CcHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEEC
Confidence 48999999886 459999999999999999999998899999999865543
No 27
>PRK11507 ribosome-associated protein; Provisional
Probab=97.56 E-value=0.00015 Score=52.10 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=46.1
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
.+|+++|--.|++.|=-+|..+|..|.|.|||++.+.-+..+.+||. |++
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~--V~~ 61 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQT--VSF 61 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCE--EEE
Confidence 47899999999999999999999999999999999999999999974 554
No 28
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=97.54 E-value=0.00013 Score=65.24 Aligned_cols=55 Identities=18% Similarity=0.133 Sum_probs=47.8
Q ss_pred HHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 106 FLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 106 ~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
...+|||.+|......-|++.++++|.+|.|+|||..+++|++.|..+|.+.|..
T Consensus 15 ~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~ 69 (325)
T PRK11180 15 QLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDA 69 (325)
T ss_pred cCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEee
Confidence 3458999999988656699999999999999999999999999999998766643
No 29
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=97.36 E-value=0.00031 Score=61.62 Aligned_cols=54 Identities=19% Similarity=0.203 Sum_probs=46.0
Q ss_pred HHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 107 LERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 107 lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
..+|||.+|......-|++.++.+|.+|.|+|||+++..|++.|..+|.+.|.+
T Consensus 4 ~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~ 57 (299)
T TIGR00005 4 AGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRV 57 (299)
T ss_pred cchhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEec
Confidence 357999999887654599999999999999999987788999999998766643
No 30
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.31 E-value=4.4e-05 Score=54.06 Aligned_cols=50 Identities=22% Similarity=0.246 Sum_probs=35.9
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
..|+.+|-..|++.|=-+|..+|..|.|+|||++.+..+..+.++|. |++
T Consensus 8 I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~--V~~ 57 (65)
T PF13275_consen 8 ITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDV--VEI 57 (65)
T ss_dssp --HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEE--EEE
T ss_pred EEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCE--EEE
Confidence 36889999999999999999999999999999999999999999974 554
No 31
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=97.10 E-value=0.00099 Score=59.23 Aligned_cols=54 Identities=20% Similarity=0.243 Sum_probs=47.3
Q ss_pred HHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEec
Q 046291 106 FLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVS 161 (197)
Q Consensus 106 ~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~ 161 (197)
.-.+|||.+|..+.. -|+++...+|..|.|+|||+++. |++.|..||.+.+.+.
T Consensus 10 ~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~ 63 (289)
T COG0564 10 EAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLP 63 (289)
T ss_pred hcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecc
Confidence 345799999999444 69999999999999999999999 9999999998877764
No 32
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=96.93 E-value=0.0014 Score=58.61 Aligned_cols=51 Identities=8% Similarity=0.205 Sum_probs=43.7
Q ss_pred HHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeE
Q 046291 107 LERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 107 lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
-.+|||.+|......-|++.++.+|.+|.|+|||+++ +|++.|..+|.+.|
T Consensus 18 ~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i 68 (317)
T PRK11025 18 AGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRI 68 (317)
T ss_pred CCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEe
Confidence 3579999999765556999999999999999999998 59999999976544
No 33
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.66 E-value=0.0041 Score=45.04 Aligned_cols=48 Identities=21% Similarity=0.246 Sum_probs=43.3
Q ss_pred hhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 111 LQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 111 LD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
|+.+|--.|++.|=-+|..+|..|.|.|||++-|.-+..+..+|. |++
T Consensus 14 L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~--V~i 61 (73)
T COG2501 14 LGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDV--VEI 61 (73)
T ss_pred HHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCE--EEE
Confidence 667788899999999999999999999999999999999999974 554
No 34
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=96.38 E-value=0.0036 Score=58.29 Aligned_cols=46 Identities=22% Similarity=0.328 Sum_probs=41.3
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCC
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDA 154 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~d 154 (197)
..|-.+|+..|++.|..+||++|.+|-|+|||+.|+.|.+.+.+++
T Consensus 343 ~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~ 388 (410)
T PRK13354 343 KNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPED 388 (410)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhh
Confidence 4566789999999999999999999999999999999988887654
No 35
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=96.08 E-value=0.011 Score=54.88 Aligned_cols=44 Identities=27% Similarity=0.394 Sum_probs=39.3
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeec
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRV 152 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~ 152 (197)
..+-.+|+..|++.|.++||++|.+|-|+|||+.|+.+.+.+..
T Consensus 343 ~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 343 IDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 35556889999999999999999999999999999988887765
No 36
>PRK04313 30S ribosomal protein S4e; Validated
Probab=95.29 E-value=0.03 Score=48.86 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=36.9
Q ss_pred hccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEecc
Q 046291 118 AGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSL 162 (197)
Q Consensus 118 ~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~ 162 (197)
+++|.|..+|+..+.+|.|.|||.+.+++.|.|.-- |.|++..
T Consensus 48 L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlm--DVIsI~~ 90 (237)
T PRK04313 48 LGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLM--DVISIPE 90 (237)
T ss_pred hhhhccHHHHHHHHhCCcEEECCEEEcccccCcCce--eEEEEcc
Confidence 689999999999999999999999999999988554 4555543
No 37
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=94.52 E-value=0.064 Score=47.48 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=36.6
Q ss_pred hccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEecc
Q 046291 118 AGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSL 162 (197)
Q Consensus 118 ~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~ 162 (197)
+++|.|..+|+..+.+|.|.|||.+.+++.|.|.-- |.|++..
T Consensus 52 LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~m--DVIsI~k 94 (262)
T PTZ00118 52 LKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFM--DVVSLTK 94 (262)
T ss_pred hhhhccHHHHHHHHHCCcEEECCEEEccCCCCCcee--EEEEEcC
Confidence 589999999999999999999999999999988544 4555533
No 38
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=94.42 E-value=0.066 Score=47.63 Aligned_cols=43 Identities=12% Similarity=0.092 Sum_probs=36.7
Q ss_pred hccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEecc
Q 046291 118 AGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSL 162 (197)
Q Consensus 118 ~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~ 162 (197)
+++|.|..+|+..+.+|.|.|||.+.+++.|.|.-- |.|++..
T Consensus 49 LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlM--DVIsI~k 91 (273)
T PTZ00223 49 LKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFM--DVVEIPK 91 (273)
T ss_pred hhhhccHHHHHHHHhCCeEEECCEEEccCCCCCcee--EEEEEcC
Confidence 689999999999999999999999999999988544 4555533
No 39
>PLN00036 40S ribosomal protein S4; Provisional
Probab=94.42 E-value=0.068 Score=47.29 Aligned_cols=43 Identities=9% Similarity=0.232 Sum_probs=36.5
Q ss_pred hccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEecc
Q 046291 118 AGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVSL 162 (197)
Q Consensus 118 ~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~~ 162 (197)
+++|.|..+|+..+.+|.|.|||.+.+++.|.|.-- |.|++..
T Consensus 52 LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~m--DVIsI~k 94 (261)
T PLN00036 52 LKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFM--DVISIPK 94 (261)
T ss_pred hhhhccHHHHHHHHhCCeEEECCEEeccCCCCCcee--EEEEEcC
Confidence 589999999999999999999999999999988544 4555533
No 40
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=93.60 E-value=0.078 Score=46.24 Aligned_cols=42 Identities=14% Similarity=0.218 Sum_probs=35.7
Q ss_pred hccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEec
Q 046291 118 AGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGVS 161 (197)
Q Consensus 118 ~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~~ 161 (197)
+++|.+-.+|+..|..|+|.|||.+.+..-|.| |.-|.|++.
T Consensus 51 LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPV--GlmDVisip 92 (241)
T COG1471 51 LKYADNAREARKILSEGKVLVDGKVRKDYKFPV--GLMDVISIP 92 (241)
T ss_pred HHhccchHHHHHHHhcCcEEECCEEeccccCCc--ceEEEEEEC
Confidence 478999999999999999999999999999887 444556654
No 41
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=93.29 E-value=0.21 Score=46.73 Aligned_cols=71 Identities=25% Similarity=0.323 Sum_probs=50.2
Q ss_pred hhHHHHHHHHHHhcchhhhhcchhHHhhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceee
Q 046291 73 FEGQALLRRMFRYGLLEATQNKLDYVLALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLV 150 (197)
Q Consensus 73 ~~~~~Ll~kL~~~Gli~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V 150 (197)
+....-.+++|.-| ..+. ....+ |.. .+...+-..++..|+++|+.+|+++|.+|-|++||+.|.++.+.+
T Consensus 307 ~~a~~~~~~~F~~g-~~~~-l~~~d---lk~--~~~~~~~~~lv~~~L~psr~earr~i~~g~v~in~~~v~d~~~~~ 377 (401)
T COG0162 307 EAAEEEFEKLFSEG-LPEN-LPPAD---LKQ--KLEDGLVDLLVDAGLAPSRSEARRLIQQGGVKINGEKVEDENYVL 377 (401)
T ss_pred HHHHHHHHHHHhcC-Cccc-CCHHH---Hhh--hhHHHHHHHHHHhCCcccHHHHHhhcccCCEEECCEeccccccch
Confidence 34455667788888 3211 11111 111 223367778999999999999999999999999999999887655
No 42
>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=87.54 E-value=0.63 Score=42.95 Aligned_cols=42 Identities=24% Similarity=0.151 Sum_probs=37.0
Q ss_pred hhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceee
Q 046291 109 RRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLV 150 (197)
Q Consensus 109 rRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V 150 (197)
..+..++...|++.|..+|+++|.+|-|+||+.+++.+...+
T Consensus 330 ~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~ 371 (377)
T TIGR00234 330 ITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEPIR 371 (377)
T ss_pred cCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchhhh
Confidence 456677888999999999999999999999999999877654
No 43
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=87.24 E-value=1.7 Score=40.90 Aligned_cols=39 Identities=23% Similarity=0.181 Sum_probs=34.1
Q ss_pred hhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeee
Q 046291 113 TVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVR 151 (197)
Q Consensus 113 ~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~ 151 (197)
.++..++.+.|.++|+++|.+|-|.||++.|+.++..+.
T Consensus 403 ~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es~~~~ 441 (467)
T KOG2623|consen 403 DLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSIA 441 (467)
T ss_pred HHHHHhhcCCCcHHHHHHHHccceeecCccccCchhhcc
Confidence 356788899999999999999999999999999776553
No 44
>PRK06437 hypothetical protein; Provisional
Probab=57.99 E-value=15 Score=25.56 Aligned_cols=22 Identities=14% Similarity=0.080 Sum_probs=18.1
Q ss_pred eeeCCEEeccCceeeecCCeeeE
Q 046291 136 IRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 136 V~Vng~~V~kPs~~V~~~de~~I 158 (197)
|.+||.++. +.+.++++|.+.|
T Consensus 39 V~vNg~iv~-~~~~L~dgD~Vei 60 (67)
T PRK06437 39 VIVNGSPVL-EDHNVKKEDDVLI 60 (67)
T ss_pred EEECCEECC-CceEcCCCCEEEE
Confidence 779999997 9999999875444
No 45
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=53.88 E-value=11 Score=27.49 Aligned_cols=25 Identities=16% Similarity=0.102 Sum_probs=20.3
Q ss_pred cCCeeeCCEEeccCceeeecCCeeeE
Q 046291 133 QKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 133 ~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
=|.|.|||+.+. +++.+.+||.+.|
T Consensus 49 V~~i~vNG~~v~-~~~~~~~Gd~v~V 73 (81)
T PF14451_consen 49 VGLILVNGRPVD-FDYRLKDGDRVAV 73 (81)
T ss_pred eEEEEECCEECC-CcccCCCCCEEEE
Confidence 367999999985 8999999985444
No 46
>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=47.27 E-value=19 Score=24.86 Aligned_cols=25 Identities=12% Similarity=0.111 Sum_probs=20.2
Q ss_pred cCCeeeCCEEeccCceeeecCCeeeE
Q 046291 133 QKHIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 133 ~G~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
.-.|.|||+.|. ..+.+..+|++.|
T Consensus 49 ~~~v~vNg~~v~-~~~~l~~gD~v~i 73 (80)
T cd00754 49 RVRIAVNGEYVR-LDTPLKDGDEVAI 73 (80)
T ss_pred cEEEEECCeEcC-CCcccCCCCEEEE
Confidence 346999999998 8889999986554
No 47
>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=42.29 E-value=32 Score=23.41 Aligned_cols=25 Identities=12% Similarity=0.057 Sum_probs=19.6
Q ss_pred CCeeeCCEEecc--CceeeecCCeeeE
Q 046291 134 KHIRVGRQIVNI--PSFLVRVDAQNHV 158 (197)
Q Consensus 134 G~V~Vng~~V~k--Ps~~V~~~de~~I 158 (197)
-.|.|||+.+.. ..+.+..+|++.|
T Consensus 44 ~~v~vN~~~v~~~~~~~~l~~gD~V~i 70 (77)
T PF02597_consen 44 VAVAVNGEIVPDDGLDTPLKDGDEVAI 70 (77)
T ss_dssp EEEEETTEEEGGGTTTSBEETTEEEEE
T ss_pred EEEEECCEEcCCccCCcCcCCCCEEEE
Confidence 358899999986 5888889886544
No 48
>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=38.88 E-value=34 Score=23.16 Aligned_cols=24 Identities=8% Similarity=0.102 Sum_probs=17.3
Q ss_pred CeeeCCEEeccCc---eeeecCCeeeE
Q 046291 135 HIRVGRQIVNIPS---FLVRVDAQNHV 158 (197)
Q Consensus 135 ~V~Vng~~V~kPs---~~V~~~de~~I 158 (197)
.|.|||++|.... +.+..+|++.|
T Consensus 32 ~V~vNg~~v~~~~~~~~~L~~gD~V~i 58 (65)
T cd00565 32 AVALNGEIVPRSEWASTPLQDGDRIEI 58 (65)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEE
Confidence 3779999997542 78888876544
No 49
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=38.53 E-value=43 Score=23.19 Aligned_cols=23 Identities=13% Similarity=0.007 Sum_probs=18.0
Q ss_pred CeeeCCEEeccCceeeecCCeeeE
Q 046291 135 HIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 135 ~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
.|.+||++|. +.+.+..+|++.|
T Consensus 41 ~v~vNg~iv~-~~~~l~~gD~Vei 63 (70)
T PRK08364 41 IAKVNGKVAL-EDDPVKDGDYVEV 63 (70)
T ss_pred EEEECCEECC-CCcCcCCCCEEEE
Confidence 5789999994 7888988875443
No 50
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=37.47 E-value=92 Score=25.39 Aligned_cols=71 Identities=10% Similarity=0.062 Sum_probs=48.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhhhhcchhHHhhhhhHHHHHhhhhhhHhhhcc
Q 046291 41 KRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEATQNKLDYVLALTVESFLERRLQTVVFKAGL 120 (197)
Q Consensus 41 K~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~~~~~L~~~~~l~~~~~lerRLD~~L~~~gl 120 (197)
.-.++++.-.++-+|+.+..|..--.-.-........+|..++....|+. +...||..||-.+|.-+++
T Consensus 53 PGnIR~AeHFv~flkR~veylk~rlrv~~v~~e~P~sFL~~~~~~~~id~-----------k~LrFc~eRL~sLl~TLei 121 (146)
T PF06777_consen 53 PGNIRRAEHFVAFLKRFVEYLKTRLRVQHVISESPLSFLQHLKDETFIDR-----------KPLRFCSERLSSLLRTLEI 121 (146)
T ss_pred CchHHhHHHHHHHHHHHHHHHHHHhhhcceeecCHHHHHHHHHHHhCCCc-----------HHHHHHHHHHHHHHHHHCC
Confidence 45677888888888888888765222222233355677777777666642 2458999999999999987
Q ss_pred cc
Q 046291 121 AK 122 (197)
Q Consensus 121 a~ 122 (197)
..
T Consensus 122 ~d 123 (146)
T PF06777_consen 122 TD 123 (146)
T ss_pred Cc
Confidence 74
No 51
>PRK01777 hypothetical protein; Validated
Probab=37.19 E-value=55 Score=24.53 Aligned_cols=27 Identities=7% Similarity=0.085 Sum_probs=21.2
Q ss_pred cCCeeeCCEEeccCceeeecCCeeeEEecc
Q 046291 133 QKHIRVGRQIVNIPSFLVRVDAQNHVGVSL 162 (197)
Q Consensus 133 ~G~V~Vng~~V~kPs~~V~~~de~~I~~~~ 162 (197)
.+.|.|||+.++ +...+..||. |++..
T Consensus 49 ~~~vgI~Gk~v~-~d~~L~dGDR--VeIyr 75 (95)
T PRK01777 49 KNKVGIYSRPAK-LTDVLRDGDR--VEIYR 75 (95)
T ss_pred cceEEEeCeECC-CCCcCCCCCE--EEEec
Confidence 478999999995 8899999975 55433
No 52
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=36.53 E-value=44 Score=27.00 Aligned_cols=41 Identities=22% Similarity=0.203 Sum_probs=32.6
Q ss_pred hhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEE
Q 046291 101 LTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQI 142 (197)
Q Consensus 101 l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~ 142 (197)
|.+..-+..|||.+|.+. |.-|+++-++||..|.|+.....
T Consensus 95 i~~~~~~~~Rld~lLa~~-L~lSrs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 95 IRFPFPFPLRLDRLLARQ-LGLSRSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred EEeCCCCCccHHHHHHHH-hCcCHHHHHHHHHCCCEEecCcc
Confidence 445566778999988654 77799999999999999977543
No 53
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=32.97 E-value=44 Score=22.58 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=18.5
Q ss_pred eeeCCEEecc---CceeeecCCeeeE
Q 046291 136 IRVGRQIVNI---PSFLVRVDAQNHV 158 (197)
Q Consensus 136 V~Vng~~V~k---Ps~~V~~~de~~I 158 (197)
|-||+++|.+ +++.+..+|++.|
T Consensus 33 vavN~~iv~~~~~~~~~L~dgD~Iei 58 (65)
T PRK06488 33 TAVNGELVHKEARAQFVLHEGDRIEI 58 (65)
T ss_pred EEECCEEcCHHHcCccccCCCCEEEE
Confidence 8999999986 4788888886544
No 54
>PRK02967 nickel responsive regulator; Provisional
Probab=28.34 E-value=45 Score=26.71 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=22.3
Q ss_pred hhhhHHHHHhhhhhhHhhhccccCHHHH
Q 046291 100 ALTVESFLERRLQTVVFKAGLAKSIHHA 127 (197)
Q Consensus 100 ~l~~~~~lerRLD~~L~~~gla~Sr~~A 127 (197)
++++..-+-..||.++.+.||. ||++|
T Consensus 5 svslp~~ll~~lD~~~~~~gy~-sRSea 31 (139)
T PRK02967 5 TITLDDDLLETLDSLIARRGYQ-NRSEA 31 (139)
T ss_pred EEEcCHHHHHHHHHHHHHcCCC-CHhHH
Confidence 4556677778899999999986 99998
No 55
>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=27.80 E-value=70 Score=21.53 Aligned_cols=24 Identities=13% Similarity=0.214 Sum_probs=17.7
Q ss_pred CeeeCCEEecc---CceeeecCCeeeE
Q 046291 135 HIRVGRQIVNI---PSFLVRVDAQNHV 158 (197)
Q Consensus 135 ~V~Vng~~V~k---Ps~~V~~~de~~I 158 (197)
.|.||+++|.+ +.+.+..+|++.|
T Consensus 31 ~v~vN~~iv~~~~~~~~~L~~gD~vei 57 (64)
T TIGR01683 31 AVAVNGEIVPRSEWDDTILKEGDRIEI 57 (64)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEE
Confidence 47899999973 4467888876544
No 56
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=27.55 E-value=1.1e+02 Score=21.34 Aligned_cols=23 Identities=4% Similarity=0.073 Sum_probs=18.4
Q ss_pred CeeeCCEEeccCceeeecCCeeeE
Q 046291 135 HIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 135 ~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
.|.||++.+. .++.+..+|++.|
T Consensus 53 ~vavN~~~v~-~~~~l~dgDeVai 75 (82)
T PLN02799 53 VLALNEEYTT-ESAALKDGDELAI 75 (82)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEE
Confidence 4889999985 8889999986544
No 57
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.49 E-value=44 Score=28.51 Aligned_cols=60 Identities=18% Similarity=0.193 Sum_probs=42.3
Q ss_pred hhhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 100 ALTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 100 ~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
.|+++.-..-|||.+|... +--|++.-+.+|..|.|++.......---....+..+.|+.
T Consensus 130 ~l~~~~p~qlrl~~Ll~se-L~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~ 189 (203)
T COG4332 130 SLRISRPFQLRLDRLLASE-LGLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDV 189 (203)
T ss_pred EEcccCcchhHHHHHHHHH-hCcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEc
Confidence 4555556667999988765 45589999999999999998875544444445565555553
No 58
>PRK12901 secA preprotein translocase subunit SecA; Reviewed
Probab=27.49 E-value=1.7e+02 Score=31.25 Aligned_cols=94 Identities=19% Similarity=0.257 Sum_probs=59.6
Q ss_pred hcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHh-cchh----h------hhcchhHH------
Q 046291 36 FGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRY-GLLE----A------TQNKLDYV------ 98 (197)
Q Consensus 36 YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~-Gli~----~------~~~~L~~~------ 98 (197)
||-+|.+++-+++.++.+|...-..+..|+..+... .+..+-.+|.+. .-+. + +...++..
T Consensus 9 fg~~~~r~lk~~~~~v~kIn~le~~~~~LSDeeLr~--kT~efk~rl~~~~~~~~~~~~~l~~~~~~~~~~~~~e~~~~~ 86 (1112)
T PRK12901 9 FGDKSERDLKEIQPIVEKIKAEYPELEALSNDELRA--KTDEFKQYIKEAVADIDAKIEELKAEAIESLDIDEREDIYAQ 86 (1112)
T ss_pred cCCccHHHHHHHHHHHHHHHHhHHHHHhCCHHHHHH--HHHHHHHHHHHhhhhhhhHHHHHHhhhccccchhhhhHHHHH
Confidence 788999999999999999999999999998765332 444444444430 0000 0 00011110
Q ss_pred ---hhhhhHHHHHhhhhhhHhhhccccCHHHHHHHHH
Q 046291 99 ---LALTVESFLERRLQTVVFKAGLAKSIHHARVLIK 132 (197)
Q Consensus 99 ---~~l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~ 132 (197)
+.-.....+..=||.+|.++ ||--+..|++++.
T Consensus 87 id~~~~~~~~~~~~~Ld~iLpEA-FAvvREaarR~lg 122 (1112)
T PRK12901 87 IDKLEKEAYEILEKVLDEILPEA-FAIVKETARRFAE 122 (1112)
T ss_pred HHHHHHHHHHHHHhHHHHhHHHH-HHHHHHHHHHHhc
Confidence 11112244556699999988 8888888888874
No 59
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=25.64 E-value=1.5e+02 Score=27.71 Aligned_cols=48 Identities=17% Similarity=0.081 Sum_probs=35.3
Q ss_pred hhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeeecCCeeeEEe
Q 046291 111 LQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVRVDAQNHVGV 160 (197)
Q Consensus 111 LD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~~~de~~I~~ 160 (197)
+|.++.+.. ...+.-.+..|..|.|.|||+.+. .++.++.++.+..++
T Consensus 47 ~~~~~~ef~-~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~v 94 (371)
T KOG1919|consen 47 VDVFVSEFR-LRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHTV 94 (371)
T ss_pred HHHHHHHHh-cCchHhhhhhhhcCceEECcEeee-eEEEeccCCEEEEee
Confidence 444444443 445556788999999999999987 888888887665544
No 60
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=25.35 E-value=70 Score=22.33 Aligned_cols=23 Identities=13% Similarity=0.156 Sum_probs=18.5
Q ss_pred CeeeCCEEeccCceeeecCCeeeE
Q 046291 135 HIRVGRQIVNIPSFLVRVDAQNHV 158 (197)
Q Consensus 135 ~V~Vng~~V~kPs~~V~~~de~~I 158 (197)
.|.||++.+. .+..+..+|++.|
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai 73 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAF 73 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEE
Confidence 4889999987 5889999986544
No 61
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=24.99 E-value=58 Score=25.73 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=22.0
Q ss_pred hhhhHHHHHhhhhhhHhhhccccCHHHH
Q 046291 100 ALTVESFLERRLQTVVFKAGLAKSIHHA 127 (197)
Q Consensus 100 ~l~~~~~lerRLD~~L~~~gla~Sr~~A 127 (197)
++++..-|-..||.++.+.|+. ||++|
T Consensus 4 svslp~~ll~~lD~~~~~~g~~-~RSe~ 30 (129)
T TIGR02793 4 TITLDDDLLETLDRLIARRGYQ-NRSEA 30 (129)
T ss_pred EEEcCHHHHHHHHHHHHHcCCC-CHHHH
Confidence 3456667778899999999985 99998
No 62
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=24.75 E-value=1.4e+02 Score=29.20 Aligned_cols=71 Identities=20% Similarity=0.213 Sum_probs=47.6
Q ss_pred HHhhhhcCCchhHHHHHHHHHHHHHHHHHHHhcCCCCCchhhhhHHHHHHHHHHhcchhhhhcchhHHhhhhhHHH
Q 046291 31 RLVGSFGLRCKRELWRVQYALSRIRNAARDLLTLDEKDPRRIFEGQALLRRMFRYGLLEATQNKLDYVLALTVESF 106 (197)
Q Consensus 31 ~~~~~YgLknK~E~~r~~~~l~kiR~~ar~L~~l~~~d~~r~~~~~~Ll~kL~~~Gli~~~~~~L~~~~~l~~~~~ 106 (197)
-+..+.||++++ ++..+..+|-.-.+.-.+-......++.-...||.+|..++.+- .+.|..++-|..+++
T Consensus 518 ~iTErhGL~epk---rVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~--tqgLqrifyLklEdl 588 (605)
T KOG4217|consen 518 LITERHGLKEPK---RVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLC--TQGLQRIFYLKLEDL 588 (605)
T ss_pred hhhhhhcCCCcc---hHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHH--HHhhhhhhcccHhhc
Confidence 456678999876 44444555555555555445555566655667899999999985 466777777777654
No 63
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=21.67 E-value=91 Score=20.72 Aligned_cols=24 Identities=8% Similarity=0.081 Sum_probs=17.7
Q ss_pred CeeeCCEEeccC---ceeeecCCeeeE
Q 046291 135 HIRVGRQIVNIP---SFLVRVDAQNHV 158 (197)
Q Consensus 135 ~V~Vng~~V~kP---s~~V~~~de~~I 158 (197)
.|.|||..+.+. .+.+..+|++.|
T Consensus 32 ~v~vN~~~v~~~~~~~~~L~~gD~vei 58 (65)
T PRK06944 32 AVAVNGDFVARTQHAARALAAGDRLDL 58 (65)
T ss_pred EEEECCEEcCchhcccccCCCCCEEEE
Confidence 378999998654 677888875444
No 64
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=20.22 E-value=68 Score=28.52 Aligned_cols=44 Identities=20% Similarity=0.344 Sum_probs=35.2
Q ss_pred hhhHHHHHhhhhhhHhhhccccCHHHHHHHHHcCCeeeCCEEeccCceeee
Q 046291 101 LTVESFLERRLQTVVFKAGLAKSIHHARVLIKQKHIRVGRQIVNIPSFLVR 151 (197)
Q Consensus 101 l~~~~~lerRLD~~L~~~gla~Sr~~Ar~lI~~G~V~Vng~~V~kPs~~V~ 151 (197)
|.+.-|++.||. +|.+-.++.+..++.+|.|+|.+-+.++|.+.
T Consensus 42 lpl~~~~~~~Lk-------ya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g 85 (263)
T KOG0378|consen 42 LPLIVFLRNRLK-------YALNGKEVKKILMQREIKVDGKVRTDSTYPAG 85 (263)
T ss_pred eeEEEEeehhhh-------hhhcccHHHHHHHHhhhhccceeecccccccc
Confidence 455567777765 45566788888899999999999999998765
No 65
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=20.13 E-value=1.2e+02 Score=20.64 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=16.8
Q ss_pred eeeCCEEecc---CceeeecCCeeeE
Q 046291 136 IRVGRQIVNI---PSFLVRVDAQNHV 158 (197)
Q Consensus 136 V~Vng~~V~k---Ps~~V~~~de~~I 158 (197)
|-||+++|.+ +.+.+..+|++.|
T Consensus 34 VavN~~iv~r~~w~~~~L~~gD~Iei 59 (66)
T PRK08053 34 LAINQQIIPREQWAQHIVQDGDQILL 59 (66)
T ss_pred EEECCEEeChHHcCccccCCCCEEEE
Confidence 7899999984 4556778875444
Done!