Query psy13908
Match_columns 149
No_of_seqs 171 out of 1071
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 23:33:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4655|consensus 100.0 3.2E-57 6.9E-62 354.5 9.2 146 2-147 1-146 (181)
2 TIGR01018 rpsD_arch ribosomal 100.0 8.4E-52 1.8E-56 324.2 10.6 131 14-147 11-143 (162)
3 PLN00189 40S ribosomal protein 100.0 2.1E-50 4.6E-55 323.7 11.5 133 14-147 14-148 (194)
4 PTZ00155 40S ribosomal protein 100.0 2.5E-49 5.3E-54 314.9 9.6 133 14-147 12-146 (181)
5 PRK04051 rps4p 30S ribosomal p 100.0 2.7E-48 5.8E-53 308.1 10.5 131 14-147 11-142 (177)
6 KOG3301|consensus 100.0 9.6E-39 2.1E-43 250.1 4.9 131 14-147 4-136 (183)
7 COG0522 RpsD Ribosomal protein 100.0 1.2E-34 2.7E-39 234.4 6.8 132 1-147 1-133 (205)
8 PF01479 S4: S4 domain; Inter 99.2 2.2E-11 4.9E-16 76.4 3.0 41 108-148 1-41 (48)
9 CHL00113 rps4 ribosomal protei 99.0 7.7E-11 1.7E-15 95.5 2.4 48 100-147 81-128 (201)
10 TIGR01017 rpsD_bact ribosomal 99.0 3E-10 6.4E-15 91.6 2.7 46 103-148 85-130 (200)
11 PRK05327 rpsD 30S ribosomal pr 98.9 4.1E-10 8.9E-15 91.0 2.4 46 103-148 88-133 (203)
12 PF00163 Ribosomal_S4: Ribosom 98.8 8.1E-11 1.8E-15 83.9 -6.5 91 5-107 3-94 (94)
13 cd00165 S4 S4/Hsp/ tRNA synthe 98.0 4.9E-06 1.1E-10 52.9 2.5 40 108-147 1-40 (70)
14 TIGR02988 YaaA_near_RecF S4 do 97.9 7.7E-06 1.7E-10 53.5 2.4 40 108-147 9-48 (59)
15 PRK10348 ribosome-associated h 97.9 7.9E-06 1.7E-10 62.7 2.6 41 107-148 8-48 (133)
16 smart00363 S4 S4 RNA-binding d 97.8 1.3E-05 2.8E-10 49.5 2.6 40 108-147 1-40 (60)
17 COG1188 Ribosome-associated he 97.0 0.00028 6.2E-09 51.9 1.5 40 107-147 8-47 (100)
18 TIGR03069 PS_II_S4 photosystem 96.9 0.00041 8.9E-09 58.0 1.8 39 108-147 184-222 (257)
19 COG2302 Uncharacterized conser 96.8 0.00046 1E-08 58.1 0.9 48 97-148 173-220 (257)
20 PLN00051 RNA-binding S4 domain 96.5 0.0017 3.6E-08 54.9 2.3 40 108-148 192-231 (267)
21 PRK13354 tyrosyl-tRNA syntheta 95.6 0.016 3.4E-07 51.5 4.5 69 74-147 314-382 (410)
22 PRK04313 30S ribosomal protein 95.2 0.016 3.5E-07 48.4 3.0 33 116-148 47-79 (237)
23 PRK05912 tyrosyl-tRNA syntheta 95.1 0.044 9.6E-07 48.6 5.7 68 73-147 315-382 (408)
24 PTZ00118 40S ribosomal protein 94.9 0.026 5.6E-07 47.9 3.2 33 116-148 51-83 (262)
25 PLN00036 40S ribosomal protein 94.8 0.027 5.9E-07 47.7 3.3 33 116-148 51-83 (261)
26 PTZ00223 40S ribosomal protein 94.6 0.031 6.8E-07 47.6 3.1 33 116-148 48-80 (273)
27 COG0162 TyrS Tyrosyl-tRNA synt 94.5 0.094 2E-06 46.8 6.1 106 27-146 269-374 (401)
28 PRK11180 rluD 23S rRNA pseudou 94.3 0.031 6.8E-07 47.6 2.4 42 106-147 16-57 (325)
29 PRK11507 ribosome-associated p 94.0 0.042 9.1E-07 38.0 2.2 36 109-144 13-48 (70)
30 COG1471 RPS4A Ribosomal protei 92.9 0.094 2E-06 43.9 2.9 33 116-148 50-82 (241)
31 PF13275 S4_2: S4 domain; PDB: 91.8 0.017 3.8E-07 39.2 -2.2 37 110-146 10-46 (65)
32 COG0564 RluA Pseudouridylate s 88.9 0.3 6.6E-06 41.4 2.4 39 107-147 12-50 (289)
33 PRK11025 23S rRNA pseudouridyl 87.0 0.44 9.5E-06 40.6 2.2 40 107-147 19-58 (317)
34 TIGR00234 tyrS tyrosyl-tRNA sy 86.4 1.4 3.1E-05 38.7 5.2 39 109-147 331-369 (377)
35 COG2501 S4-like RNA binding pr 86.1 0.47 1E-05 33.1 1.6 31 114-144 18-48 (73)
36 KOG2623|consensus 84.3 1.7 3.7E-05 39.4 4.6 121 10-146 307-437 (467)
37 PF09079 Cdc6_C: CDC6, C termi 45.1 38 0.00081 22.9 3.7 40 40-90 18-57 (85)
38 cd08768 Cdc6_C Winged-helix do 40.8 55 0.0012 21.8 3.9 41 39-90 24-64 (87)
39 KOG0378|consensus 39.5 14 0.00031 31.4 0.9 42 100-148 42-83 (263)
40 PF13471 Transglut_core3: Tran 37.9 16 0.00035 26.3 0.9 46 96-145 57-105 (117)
41 COG4911 Uncharacterized conser 34.4 88 0.0019 23.7 4.4 40 50-89 19-67 (123)
42 TIGR02757 conserved hypothetic 33.9 63 0.0014 26.9 3.9 50 16-73 159-219 (229)
43 PF11609 DUF3248: Protein of u 30.7 45 0.00098 22.6 2.1 27 111-137 19-59 (63)
44 PF06417 DUF1077: Protein of u 29.4 34 0.00074 26.0 1.5 15 78-92 99-113 (124)
45 PF08260 Kinin: Insect kinin p 28.7 28 0.0006 14.6 0.5 6 144-149 1-6 (8)
46 PRK06015 keto-hydroxyglutarate 27.3 94 0.002 25.2 3.8 62 73-134 16-77 (201)
47 PF06014 DUF910: Bacterial pro 25.4 2.2E+02 0.0047 19.2 4.8 45 7-51 5-55 (62)
48 PF04614 Pex19: Pex19 protein 24.7 2.3E+02 0.0049 23.5 5.8 51 40-90 164-216 (248)
49 PF09674 DUF2400: Protein of u 24.2 1.6E+02 0.0035 24.4 4.8 50 16-73 162-222 (232)
50 PF14066 DUF4256: Protein of u 20.8 67 0.0015 25.8 1.7 53 77-129 110-167 (173)
51 COG4483 Uncharacterized protei 20.7 2.7E+02 0.0058 19.2 4.4 46 7-52 5-56 (68)
52 PF09851 SHOCT: Short C-termin 20.5 57 0.0012 18.6 1.0 14 77-90 6-19 (31)
53 PRK05718 keto-hydroxyglutarate 20.2 1.5E+02 0.0032 24.1 3.7 63 72-134 26-88 (212)
54 COG3629 DnrI DNA-binding trans 20.2 97 0.0021 26.6 2.7 41 50-90 165-205 (280)
No 1
>KOG4655|consensus
Probab=100.00 E-value=3.2e-57 Score=354.46 Aligned_cols=146 Identities=52% Similarity=0.864 Sum_probs=145.0
Q ss_pred cccchhhhhhhcccCCCCcccccccHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHH
Q psy13908 2 VRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEK 81 (149)
Q Consensus 2 ~r~lk~he~kLlkkv~f~~w~~~~~~~E~~l~~~YgLkkrE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~k 81 (149)
|||||||||||||||||.+|+.+.+.+|..++++|||++||+|.+||.+|+++|++|+.|..|++.||||...+..||+|
T Consensus 1 vRKLK~HEQKLLKkVdFLnWkv~d~~re~~v~rrY~l~~REdY~kyn~l~~~~r~la~~l~~l~~sDpfR~~~t~~LL~k 80 (181)
T KOG4655|consen 1 VRKLKFHEQKLLKKVDFLNWKVTDHHRELCVLRRYHLKKREDYTKYNRLAGKVRKLANRLALLDESDPFRLQYTLLLLEK 80 (181)
T ss_pred CchhhHHHHHHHHhcccceeeecCchhhHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhhcc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccCCcccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 82 LYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 82 L~~~Gll~~~~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
||.||++++.++++++.++|+++||+|||++|+.+++||+|+++|..||+||||+||+++|++|||
T Consensus 81 ly~~GvipTr~~l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~ 146 (181)
T KOG4655|consen 81 LYAMGVIPTRKSLELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAF 146 (181)
T ss_pred ccccceecchhhhhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchH
Confidence 999999999999999999999999999999999999999999999999999999999999999998
No 2
>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=8.4e-52 Score=324.15 Aligned_cols=131 Identities=21% Similarity=0.356 Sum_probs=126.0
Q ss_pred ccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccC-Cc
Q psy13908 14 KKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIR-TK 91 (149)
Q Consensus 14 kkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~-~~ 91 (149)
-++|.+||++|++++|.++|++|||+ ++|.|+ |+++|++||++|+.|++++ ||+|+.++++||+|||+||||+ ++
T Consensus 11 ~~~P~~pw~ker~~~E~~l~~kYgLknk~E~wk-~~~~~~kiR~~Ar~L~~l~--d~~r~~~~~~LL~kL~~~Gll~e~~ 87 (162)
T TIGR01018 11 YETPRHPWIKERLDRELKLVGKYGLRNKKEVWK-AETTLRKYRRAARELLGLD--DEQRLFEGNQLLRRLVRLGILDEEN 87 (162)
T ss_pred cCCCCCChhhhhCHHHHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHHHHHcCC--cHHHHHHHHHHHHHHHHcCCCcccc
Confidence 58999999999999999999999999 566666 9999999999999999999 9999999999999999999998 57
Q ss_pred ccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 92 WDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 92 ~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
++||+|++||+++|||||||++||++|||+|++||||||+||||+|||++|++|||
T Consensus 88 ~~Ld~vl~Ltv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~ 143 (162)
T TIGR01018 88 AKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSY 143 (162)
T ss_pred CCHHHHHhccHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCce
Confidence 89999999999999999999999999999999999999999999999999999998
No 3
>PLN00189 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=2.1e-50 Score=323.65 Aligned_cols=133 Identities=25% Similarity=0.380 Sum_probs=127.6
Q ss_pred ccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccC-Cc
Q psy13908 14 KKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIR-TK 91 (149)
Q Consensus 14 kkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~-~~ 91 (149)
-++|.+||+++|+.+|.++|++|||+ ++|.|+ |+++|++||++|+.|++++++||+|++++++||+|||+||||+ ++
T Consensus 14 y~tP~~P~ek~Rl~~E~kli~kYgLknK~E~wk-y~~ll~kiRk~Ar~Ll~l~~~d~~r~~~~~~LL~kL~~~GlL~~~~ 92 (194)
T PLN00189 14 FKKPRRPYEKERLDAELKLVGEYGLRNKRELWR-VQYALSRIRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGLLDESQ 92 (194)
T ss_pred cCCCCCchhhHHHHHHHHHHHHhCCCcHHHHHH-HHHHHHHHHHHHHHHHccCCCccHhHHHHHHHHHHHHHhCCccccc
Confidence 47999999999999999999999999 555566 9999999999999999999999999999999999999999995 47
Q ss_pred ccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 92 WDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 92 ~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
++||+|++|++++|||||||++||++|||+|+++|||||+||||+|||++||+|||
T Consensus 93 ~~Ld~vl~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~ 148 (194)
T PLN00189 93 NKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSF 148 (194)
T ss_pred cCHHHHhhccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcE
Confidence 89999999999999999999999999999999999999999999999999999998
No 4
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=2.5e-49 Score=314.88 Aligned_cols=133 Identities=24% Similarity=0.352 Sum_probs=127.3
Q ss_pred ccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccC-Cc
Q psy13908 14 KKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIR-TK 91 (149)
Q Consensus 14 kkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~-~~ 91 (149)
-.+|.+||+++++++|.++|++|||+ ++|.|+ |+++|++||++|+.|++++++||||+.++++||+|||+||++. ++
T Consensus 12 y~~P~~P~~k~rl~~E~~li~kYgLknk~E~wk-~~~~~~kiR~~Ar~L~~l~~~d~~r~~~~~~LL~kL~~~Gi~~~~k 90 (181)
T PTZ00155 12 YKTPRRPFEKERLDAELKLCGEYGLKNKREIWR-VQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHRLGLLDEDE 90 (181)
T ss_pred cCCCCCchhHHHHHHHHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHhCCcchhh
Confidence 47999999999999999999999999 555555 9999999999999999999999999999999999999999995 46
Q ss_pred ccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 92 WDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 92 ~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.+|++|++|++++|||||||++||++|||+|+++|||||+||||+|||++||+|||
T Consensus 91 ~~l~~~~~l~~~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~ 146 (181)
T PTZ00155 91 RKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146 (181)
T ss_pred ccHHHHHCccHHHHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCce
Confidence 89999999999999999999999999999999999999999999999999999998
No 5
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=100.00 E-value=2.7e-48 Score=308.07 Aligned_cols=131 Identities=21% Similarity=0.345 Sum_probs=125.5
Q ss_pred ccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccCCcc
Q psy13908 14 KKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIRTKW 92 (149)
Q Consensus 14 kkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~~~~ 92 (149)
-++|.+||++|++.+|.++|++|||+ ++|.|+ |+++|++||++|+.|++ ++||+|..++++||+|||+||||++++
T Consensus 11 ~~~P~~pw~~~r~~~E~~l~~~YgLknk~E~wk-~~~~~~~iR~~Ar~Ll~--~~~~~r~~~~~~Ll~kL~~~Gil~~~~ 87 (177)
T PRK04051 11 YETPNHPWQKERIAEERELLGKYGLRNKRELWK-AQSILRKYRRQARSLLA--LPPEERAKEEEQLLGKLKRYGILKENA 87 (177)
T ss_pred cCCCCCchhhhhcHHHHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHHHHcCCCCCCC
Confidence 37899999999999999999999999 666666 99999999999999998 456899999999999999999999999
Q ss_pred cccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 93 DLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 93 ~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
+||+|++||+++|||||||++||++|||+|+++|+|||.||||+|||++|++|||
T Consensus 88 ~L~~vl~L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~ 142 (177)
T PRK04051 88 TLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142 (177)
T ss_pred CHHHHHhccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCe
Confidence 9999999999999999999999999999999999999999999999999999998
No 6
>KOG3301|consensus
Probab=100.00 E-value=9.6e-39 Score=250.12 Aligned_cols=131 Identities=27% Similarity=0.412 Sum_probs=126.6
Q ss_pred ccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccCC-c
Q psy13908 14 KKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIRT-K 91 (149)
Q Consensus 14 kkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~~-~ 91 (149)
.++|..||+++|.+.|+++++.|||+ |+|+|+...+++ ++|..||.| |+++||.|.+++.+|+++|.++|++++ .
T Consensus 4 y~~PRrpfek~Rld~elkl~g~yglknk~elwr~~~~l~-K~r~aaR~l--l~~k~p~rlf~g~allrrLvr~g~l~e~~ 80 (183)
T KOG3301|consen 4 YKTPRRPFEKERLDAELKLVGEYGLKNKRELWRVSRSLS-KIRYAAREL--LDEKDPKRLFEGNALLRRLVRYGVLDERK 80 (183)
T ss_pred cCCCCChHHHHHHHhhhccccccccccchHHHHHHHHHH-HHHHHHHHH--hccccHHHHhcchHHHHHHHHHhhhhccc
Confidence 37899999999999999999999999 999999888888 999999999 789999999999999999999999987 5
Q ss_pred ccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 92 WDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 92 ~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.+||.|+++++++|||||||++||++|||.||++||++|.|+||+||+++|++|||
T Consensus 81 ~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf 136 (183)
T KOG3301|consen 81 NKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSF 136 (183)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccce
Confidence 88999999999999999999999999999999999999999999999999999998
No 7
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-34 Score=234.41 Aligned_cols=132 Identities=20% Similarity=0.216 Sum_probs=123.5
Q ss_pred CcccchhhhhhhcccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHH
Q psy13908 1 MVRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLL 79 (149)
Q Consensus 1 m~r~lk~he~kLlkkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL 79 (149)
|+|..+ |.+|+++.+|+.||.+++...|.+.+..|| + ++|.|.+ .+..+..++.+++|+.... ..+++|.
T Consensus 1 M~r~~~-~~~K~~rr~g~~~~~~~~~~~~~~~~~~pG-qhk~~~~~k-~s~yg~qL~ekqkl~~~yg------~~ekqf~ 71 (205)
T COG0522 1 MARYPG-PKKKLSRRLGFNPWLKERLCKERKLPYKPG-QHGQERWKK-LSDYGLQLREKQKLRAFYG------VLEKQFR 71 (205)
T ss_pred CCCCcC-cccceeeecCCChHHHHHHHHHhhcCCCcc-ccchhHHHH-HHHHHHHHHHHHHhhhhcc------HHHHHHH
Confidence 899999 999999999999999999999999999999 8 8899996 5566689999999887654 7899999
Q ss_pred HHHHHhcccCCcccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 80 EKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 80 ~kL~~~Gll~~~~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
++|+++|++++ ++++|+.++||||||++|||+|||+|+.||||||+||||.|||++||+|||
T Consensus 72 ~~l~~a~~l~g------~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy 133 (205)
T COG0522 72 RYLKEAGRLKG------VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSY 133 (205)
T ss_pred HHHHHHhccCC------hHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcE
Confidence 99999999976 789999999999999999999999999999999999999999999999998
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=99.16 E-value=2.2e-11 Score=76.39 Aligned_cols=41 Identities=22% Similarity=0.169 Sum_probs=39.4
Q ss_pred ccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 108 rRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
+|||.++.+.|++.|..+|+++|.||+|+|||++|++|+|.
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~ 41 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYI 41 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSB
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCC
Confidence 59999999999999999999999999999999999999983
No 9
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=99.05 E-value=7.7e-11 Score=95.48 Aligned_cols=48 Identities=17% Similarity=0.211 Sum_probs=45.2
Q ss_pred chhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 100 VTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 100 l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
-++.++||.|||.++++.|++.|+.+|+|+|.||||.|||++|++|||
T Consensus 81 ~~ll~~LE~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~ 128 (201)
T CHL00113 81 QVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSY 128 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccc
Confidence 346788999999999999999999999999999999999999999997
No 10
>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=98.96 E-value=3e-10 Score=91.65 Aligned_cols=46 Identities=20% Similarity=0.146 Sum_probs=43.4
Q ss_pred hhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 103 SSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 103 ~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
.+++|.|||.++++.||+.|+.+|+|+|.||||.|||++|++|||-
T Consensus 85 l~~le~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~ 130 (200)
T TIGR01017 85 LRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQ 130 (200)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCC
Confidence 5678899999999999999999999999999999999999999973
No 11
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.93 E-value=4.1e-10 Score=91.03 Aligned_cols=46 Identities=22% Similarity=0.205 Sum_probs=43.6
Q ss_pred hhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 103 SSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 103 ~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
.+++|.|||+++++.||+.|+.+|+|+|.||||.|||++|++|||-
T Consensus 88 l~~lE~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~ 133 (203)
T PRK05327 88 LQLLESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYR 133 (203)
T ss_pred HHHHHHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcC
Confidence 5688999999999999999999999999999999999999999973
No 12
>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=98.75 E-value=8.1e-11 Score=83.91 Aligned_cols=91 Identities=21% Similarity=0.311 Sum_probs=81.7
Q ss_pred chhhhhhhcccCCCCcccccccHHHHHHHHHhcCC-CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHH
Q psy13908 5 LKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLY 83 (149)
Q Consensus 5 lk~he~kLlkkv~f~~w~~~~~~~E~~l~~~YgLk-krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~ 83 (149)
+++|+.|+.+++.+.+|..+. ..++++||+. +++.|.. . ++ |+.++.+..|++++|+|...+ .++++|+
T Consensus 3 ~~~~~~k~~Rr~g~~~~~~~~----~~~~~~~~~~~~~~~~~~-~--~~--rk~s~y~~qL~eKqk~r~~yg-~lekql~ 72 (94)
T PF00163_consen 3 YRGPKCKLPRRLGEKLWLTEK----AKLIRRYGLRPGQHGWRR-K--SR--RKLSRYGLQLREKQKLRFYYG-ILEKQLR 72 (94)
T ss_dssp SHSCCCHHHHHCTSHCTCSCC----CSHCCSSSSSSSSSTTSH-H--HH--HCCHHHHHHHHHHHHHHHHHT-HHHHHHH
T ss_pred cCCCccccCCCCCCCccCCCc----cccccccccccccccccc-c--cc--ccchhhhcccccCCchhhhhh-hHHHHHH
Confidence 789999999999999997664 8899999999 9999884 2 22 899999999999999999999 9999999
Q ss_pred HhcccCCcccccccccchhhhhhc
Q psy13908 84 LMGLIRTKWDLENCNKVTASSFCK 107 (149)
Q Consensus 84 ~~Gll~~~~~L~~vl~l~~~~~le 107 (149)
++|++. ..++.+.+.+++++||
T Consensus 73 ~~~~~a--~k~~g~tg~~l~~lLE 94 (94)
T PF00163_consen 73 RYGKIA--AKLKGVTGENLLQLLE 94 (94)
T ss_dssp HHHHHH--HHSSSHHHHHHHHHHH
T ss_pred HHHHHH--HhcCCCHHHHHHHHhC
Confidence 999996 6788899999999997
No 13
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.98 E-value=4.9e-06 Score=52.86 Aligned_cols=40 Identities=23% Similarity=0.197 Sum_probs=35.9
Q ss_pred ccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 108 rRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.||+.++...+++.|..+|+++|.+|+|.|||+.++.|++
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~ 40 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSY 40 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCcc
Confidence 3778888888889999999999999999999999988875
No 14
>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=97.90 E-value=7.7e-06 Score=53.50 Aligned_cols=40 Identities=20% Similarity=0.165 Sum_probs=36.4
Q ss_pred ccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 108 rRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.|||..+-..+++.|...|+.+|..|+|+|||++++.|++
T Consensus 9 ~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~ 48 (59)
T TIGR02988 9 ITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGK 48 (59)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCC
Confidence 6888888888888899999999999999999999998886
No 15
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.89 E-value=7.9e-06 Score=62.72 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=38.3
Q ss_pred cccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 107 KRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 107 erRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
..|||..|+..+|++|...|.++|..|+|+|||++ ..||..
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~ 48 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKI 48 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCc
Confidence 36999999999999999999999999999999999 889863
No 16
>smart00363 S4 S4 RNA-binding domain.
Probab=97.84 E-value=1.3e-05 Score=49.53 Aligned_cols=40 Identities=25% Similarity=0.221 Sum_probs=35.3
Q ss_pred ccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 108 rRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
+|||..+...+++.|..+|+++|.+|.|.|||+.+++|++
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~ 40 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSY 40 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCe
Confidence 3678888777788999999999999999999999977864
No 17
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.04 E-value=0.00028 Score=51.85 Aligned_cols=40 Identities=20% Similarity=0.347 Sum_probs=38.0
Q ss_pred cccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 107 KRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 107 erRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
+.|||--++-+.|.++...|..+|..|+|.|||+.+ .||.
T Consensus 8 ~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~ 47 (100)
T COG1188 8 RMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSK 47 (100)
T ss_pred ceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-cccc
Confidence 789999999999999999999999999999999998 6875
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=96.94 E-value=0.00041 Score=58.03 Aligned_cols=39 Identities=8% Similarity=-0.022 Sum_probs=35.6
Q ss_pred ccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 108 rRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.|||. +...++.-|+.+|+++|.+|+|.|||++|++|++
T Consensus 184 ~RLD~-lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~ 222 (257)
T TIGR03069 184 LRIDA-IASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSR 222 (257)
T ss_pred ccHHH-HHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCC
Confidence 69996 4588998899999999999999999999999986
No 19
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=96.77 E-value=0.00046 Score=58.08 Aligned_cols=48 Identities=29% Similarity=0.207 Sum_probs=43.2
Q ss_pred cccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 97 CNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 97 vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
.+.+++++ -|||+++ ..+|-.|+..|.|+|+.|.|.||.++|+.|||.
T Consensus 173 e~~~~vsS---lRLD~vi-s~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~ 220 (257)
T COG2302 173 ELDVTVSS---LRLDVVI-SEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYE 220 (257)
T ss_pred EEeeeeeh---hhHHHHH-HHHHhhhHHHHHHHHHcCceEEeeEEeccccce
Confidence 45677777 5999988 889999999999999999999999999999984
No 20
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=96.47 E-value=0.0017 Score=54.85 Aligned_cols=40 Identities=15% Similarity=0.009 Sum_probs=36.5
Q ss_pred ccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 108 rRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
-|||.++ ..++--|+..|.++|..|+|.||+..|+.||+-
T Consensus 192 ~RLD~vl-a~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~ 231 (267)
T PLN00051 192 LRLDALA-SAGFRMSRSKLVDLISSGDVRVNWREVTKNGTT 231 (267)
T ss_pred ccHHHHH-HHHhccCHHHHHHHHHcCcEEECCEEcCCCCCC
Confidence 6999977 568899999999999999999999999999973
No 21
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=95.64 E-value=0.016 Score=51.53 Aligned_cols=69 Identities=14% Similarity=0.185 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHhcccCCcccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 74 SSAKLLEKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 74 ~~~~LL~kL~~~Gll~~~~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.....-+.||.-+..+.. ++-.+.+.. -...+-.++...|++.|-.+||.+|.+|-|+|||++|++|.+
T Consensus 314 ~a~~~~~~~f~~~~~~~~----~~p~~~~~~-~~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~ 382 (410)
T PRK13354 314 EAEKIFKALFSGDVKPLK----DIPTFEVSA-ETKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDA 382 (410)
T ss_pred HHHHHHHHHhCCCCCCcC----CCCeEEecC-CCCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCccc
Confidence 444555667765544331 222222211 124566678899999999999999999999999999998854
No 22
>PRK04313 30S ribosomal protein S4e; Validated
Probab=95.25 E-value=0.016 Score=48.45 Aligned_cols=33 Identities=18% Similarity=0.099 Sum_probs=31.3
Q ss_pred eccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 116 RNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 116 r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
++|+|.|.++|+..+.+|.|.|||++.+++.|+
T Consensus 47 ~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~P 79 (237)
T PRK04313 47 VLGYADTAREAKKIINEGKVLVDGRVRKDYKFP 79 (237)
T ss_pred HhhhhccHHHHHHHHhCCcEEECCEEEcccccC
Confidence 579999999999999999999999999999986
No 23
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=95.14 E-value=0.044 Score=48.61 Aligned_cols=68 Identities=19% Similarity=0.193 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHhcccCCcccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 73 ESSAKLLEKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 73 ~~~~~LL~kL~~~Gll~~~~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
......-+.||.-|-++++ +..+.+.. .-.+-.++...|+++|-.+||.+|.+|-|+|||++|+++.+
T Consensus 315 ~~a~~~~~~~f~~~~~~~~-----~~~~~~~~--~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~ 382 (408)
T PRK05912 315 EAAEEAFEALFGSGELPDD-----LPEVELEL--GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENY 382 (408)
T ss_pred HHHHHHHHHHhcCCCCccC-----CCeEEecC--CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccc
Confidence 3445556777766654432 11111210 12445567899999999999999999999999999988753
No 24
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=94.86 E-value=0.026 Score=47.88 Aligned_cols=33 Identities=18% Similarity=0.097 Sum_probs=31.3
Q ss_pred eccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 116 RNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 116 r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
++|+|.|.++|+..+.+|.|.|||++.+++.|+
T Consensus 51 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fP 83 (262)
T PTZ00118 51 RLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYP 83 (262)
T ss_pred hhhhhccHHHHHHHHHCCcEEECCEEEccCCCC
Confidence 568999999999999999999999999999886
No 25
>PLN00036 40S ribosomal protein S4; Provisional
Probab=94.83 E-value=0.027 Score=47.70 Aligned_cols=33 Identities=24% Similarity=0.240 Sum_probs=31.3
Q ss_pred eccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 116 RNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 116 r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
++|+|.|.++|+..+.+|.|.|||++.+++.|+
T Consensus 51 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fP 83 (261)
T PLN00036 51 RLKYALTYREVQAILMQRHVKVDGKVRTDKTYP 83 (261)
T ss_pred HhhhhccHHHHHHHHhCCeEEECCEEeccCCCC
Confidence 568999999999999999999999999999986
No 26
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=94.58 E-value=0.031 Score=47.61 Aligned_cols=33 Identities=24% Similarity=0.079 Sum_probs=31.3
Q ss_pred eccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 116 RNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 116 r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
++|+|.|.++|+..+.+|.|.|||++.+++.|+
T Consensus 48 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~P 80 (273)
T PTZ00223 48 RLKYALNAREAQMILRQGLVCVDGKPRKDGKYP 80 (273)
T ss_pred HhhhhccHHHHHHHHhCCeEEECCEEEccCCCC
Confidence 579999999999999999999999999999986
No 27
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=94.54 E-value=0.094 Score=46.81 Aligned_cols=106 Identities=15% Similarity=0.225 Sum_probs=64.5
Q ss_pred HHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccCCcccccccccchhhhhh
Q psy13908 27 LHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIRTKWDLENCNKVTASSFC 106 (149)
Q Consensus 27 ~~E~~l~~~YgLkkrE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~~~~~L~~vl~l~~~~~l 106 (149)
..|..-+.+|.+..++.-.+...|+.-++...+ ..+ -...+..-.+++|.-| .+++-.-.++-. .+
T Consensus 269 ~~eI~~i~~~~~~~~~~r~~k~~LA~e~~~~~h------G~~--~a~~a~~~~~~~F~~g-~~~~l~~~dlk~-----~~ 334 (401)
T COG0162 269 LEEIEEIEKYVLKGPEPREAKKLLAKEVTKLVH------GEE--AAEAAEEEFEKLFSEG-LPENLPPADLKQ-----KL 334 (401)
T ss_pred hHHHHHHHHHhhcCCChHHHHHHHHHHhhHhhc------CHH--HHHHHHHHHHHHHhcC-CcccCCHHHHhh-----hh
Confidence 366666677776644332222223322222211 111 3345667789999999 544222111111 11
Q ss_pred cccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCC
Q psy13908 107 KRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMI 146 (149)
Q Consensus 107 erRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps 146 (149)
+..+-..+...|+++|..+||.+|.+|-|+|||++|.++.
T Consensus 335 ~~~~~~~lv~~~L~psr~earr~i~~g~v~in~~~v~d~~ 374 (401)
T COG0162 335 EDGLVDLLVDAGLAPSRSEARRLIQQGGVKINGEKVEDEN 374 (401)
T ss_pred HHHHHHHHHHhCCcccHHHHHhhcccCCEEECCEeccccc
Confidence 2245556789999999999999999999999999999985
No 28
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=94.26 E-value=0.031 Score=47.63 Aligned_cols=42 Identities=14% Similarity=-0.001 Sum_probs=36.2
Q ss_pred hcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 106 CKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 106 lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
..+|||.++.......|...++++|..|.|+|||..++.|++
T Consensus 16 ~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~ 57 (325)
T PRK11180 16 LGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKE 57 (325)
T ss_pred CCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCc
Confidence 457999888766556799999999999999999999988875
No 29
>PRK11507 ribosome-associated protein; Provisional
Probab=93.97 E-value=0.042 Score=38.01 Aligned_cols=36 Identities=17% Similarity=0.090 Sum_probs=31.1
Q ss_pred cccceeeeccCCCChHHHHhhHhcCcEEECCeeeCC
Q psy13908 109 RLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGD 144 (149)
Q Consensus 109 RL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~ 144 (149)
+|+-.+--.|++.|=-+|..+|..|.|.|||++.+-
T Consensus 13 ~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~r 48 (70)
T PRK11507 13 ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETR 48 (70)
T ss_pred EHHHHHhhhCcccChHHHHHHHHcCceEECCEEecc
Confidence 455556788999999999999999999999998764
No 30
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=92.88 E-value=0.094 Score=43.95 Aligned_cols=33 Identities=18% Similarity=0.137 Sum_probs=30.3
Q ss_pred eccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 116 RNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 116 r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
.+++|.+.++|+..|..|+|.|||.+.++.-|+
T Consensus 50 ~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfP 82 (241)
T COG1471 50 YLKYADNAREARKILSEGKVLVDGKVRKDYKFP 82 (241)
T ss_pred HHHhccchHHHHHHHhcCcEEECCEEeccccCC
Confidence 468999999999999999999999999988774
No 31
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=91.78 E-value=0.017 Score=39.25 Aligned_cols=37 Identities=22% Similarity=0.187 Sum_probs=27.1
Q ss_pred ccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCC
Q psy13908 110 LPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMI 146 (149)
Q Consensus 110 L~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps 146 (149)
|+-.+--.|++.|=-+|..+|..|.|.|||++.+..+
T Consensus 10 L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg 46 (65)
T PF13275_consen 10 LGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRG 46 (65)
T ss_dssp HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS
T ss_pred HHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccC
Confidence 3444567899999999999999999999999987654
No 32
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=88.87 E-value=0.3 Score=41.45 Aligned_cols=39 Identities=15% Similarity=0.049 Sum_probs=33.5
Q ss_pred cccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 107 KRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 107 erRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
..|||..+..+.- -|..+...+|..|.|+|||++|+ |++
T Consensus 12 g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~ 50 (289)
T COG0564 12 GQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSY 50 (289)
T ss_pred CCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCe
Confidence 4788888877444 68999999999999999999999 876
No 33
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=87.02 E-value=0.44 Score=40.55 Aligned_cols=40 Identities=10% Similarity=0.025 Sum_probs=32.5
Q ss_pred cccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 107 KRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 107 erRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
..|||..+....-.-|...++.+|.+|.|+|||.+++ |++
T Consensus 19 g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~-~~~ 58 (317)
T PRK11025 19 GQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIK-PEY 58 (317)
T ss_pred CchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcC-ccc
Confidence 4688887765555668999999999999999999984 654
No 34
>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=86.40 E-value=1.4 Score=38.69 Aligned_cols=39 Identities=18% Similarity=0.110 Sum_probs=33.7
Q ss_pred cccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCC
Q psy13908 109 RLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIE 147 (149)
Q Consensus 109 RL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~ 147 (149)
.+..++...|++.|-.+||.+|.+|-|+||+.+|+++.+
T Consensus 331 ~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~ 369 (377)
T TIGR00234 331 TLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEP 369 (377)
T ss_pred CHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchh
Confidence 344556678999999999999999999999999998753
No 35
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=86.05 E-value=0.47 Score=33.11 Aligned_cols=31 Identities=23% Similarity=0.321 Sum_probs=27.3
Q ss_pred eeeccCCCChHHHHhhHhcCcEEECCeeeCC
Q psy13908 114 MYRNKMVQQLRLATQFIEQAHVRVGPELEGD 144 (149)
Q Consensus 114 v~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~ 144 (149)
+--.|+++|=-+|.++|.-|.|.|||++-|-
T Consensus 18 LK~~g~i~sGG~AK~~i~eg~V~vNGe~EtR 48 (73)
T COG2501 18 LKLAGLIESGGQAKAFIAEGEVKVNGEVETR 48 (73)
T ss_pred HHHhCcccCcHHHHHHHHCCeEEECCeeeec
Confidence 4467999999999999999999999988653
No 36
>KOG2623|consensus
Probab=84.32 E-value=1.7 Score=39.39 Aligned_cols=121 Identities=16% Similarity=0.171 Sum_probs=73.3
Q ss_pred hhhcccCCCCcccccccHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHh---c
Q psy13908 10 QKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLM---G 86 (149)
Q Consensus 10 ~kLlkkv~f~~w~~~~~~~E~~l~~~YgLkkrE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~---G 86 (149)
.|+||=.-|.|- .|++-|-+-|.++-|.|.....|+..+.++.+--..|+ .++..-+-||.- |
T Consensus 307 ~k~LklfTfl~l------~eI~~I~~~H~k~P~~r~aQ~~LA~eVTr~VHG~egL~--------~A~r~T~al~g~~~~~ 372 (467)
T KOG2623|consen 307 EKFLKLFTFLPL------EEIKQILEEHRKEPSQRIAQKLLAAEVTRMVHGKEGLE--------VAERCTKALFGAKKAG 372 (467)
T ss_pred HHHHHHHhcCCH------HHHHHHHHHHhcChhhhhHHHHHHHHHHHHHcccchHH--------HHHHHHHHhhcccccc
Confidence 356666677664 57776677889988999998889988888877544432 222222223322 1
Q ss_pred ccCCcccccccc----cchhhhhhcc-ccc--ceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCC
Q psy13908 87 LIRTKWDLENCN----KVTASSFCKR-RLP--VVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMI 146 (149)
Q Consensus 87 ll~~~~~L~~vl----~l~~~~~ler-RL~--~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps 146 (149)
+- .-++..+. +.+..++.-+ =.+ -.+..++..+|-.+|+.+|.+|-|.||++.|++|+
T Consensus 373 ~~--~ls~~ei~~lfk~a~~~~l~~~~~~s~~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es 437 (467)
T KOG2623|consen 373 LS--GLSLSEILQLFKDATFIDLKDEPGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDES 437 (467)
T ss_pred cc--cCCHHHHHHHHhcCCceecccCCCCcHHHHHHHhhcCCCcHHHHHHHHccceeecCccccCch
Confidence 11 01111110 1111111111 000 12457788899999999999999999999999975
No 37
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=45.13 E-value=38 Score=22.90 Aligned_cols=40 Identities=25% Similarity=0.429 Sum_probs=27.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccCC
Q psy13908 40 KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIRT 90 (149)
Q Consensus 40 krE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~~ 90 (149)
-.|.|..|..+|.. -.-||.-...-..+|..|-.+|||+.
T Consensus 18 ~~~vy~~Y~~lc~~-----------~~~~pls~~r~~~~l~eL~~~gli~~ 57 (85)
T PF09079_consen 18 TGEVYEVYEELCES-----------LGVDPLSYRRFSDYLSELEMLGLIES 57 (85)
T ss_dssp HHHHHHHHHHHHHH-----------TTS----HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHHH-----------cCCCCCCHHHHHHHHHHHHhCCCeEE
Confidence 57899999988841 22355555666788999999999965
No 38
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=40.85 E-value=55 Score=21.79 Aligned_cols=41 Identities=27% Similarity=0.451 Sum_probs=30.8
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccCC
Q psy13908 39 QKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIRT 90 (149)
Q Consensus 39 kkrE~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~~ 90 (149)
.-.|.|..|..+|.. ..-+|-....-..+|..|-.+|||..
T Consensus 24 ~~~~vy~~Y~~~c~~-----------~~~~~l~~~~~~~~l~~L~~~gli~~ 64 (87)
T cd08768 24 TTGEVYEVYEELCEE-----------IGVDPLTQRRISDLLSELEMLGLLET 64 (87)
T ss_pred cHHHHHHHHHHHHHH-----------cCCCCCcHHHHHHHHHHHHHcCCeEE
Confidence 356788888888731 13456677788889999999999975
No 39
>KOG0378|consensus
Probab=39.50 E-value=14 Score=31.42 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=35.6
Q ss_pred chhhhhhcccccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCCCCC
Q psy13908 100 VTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDMIEG 148 (149)
Q Consensus 100 l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~Ps~~ 148 (149)
+++.-|++.|| ..|.+-+++.+...+.+|.|+|.+-++++|.
T Consensus 42 lpl~~~~~~~L-------kya~~~~e~~~I~~qr~i~v~gkvrt~~~yp 83 (263)
T KOG0378|consen 42 LPLIVFLRNRL-------KYALNGKEVKKILMQREIKVDGKVRTDSTYP 83 (263)
T ss_pred eeEEEEeehhh-------hhhhcccHHHHHHHHhhhhccceeecccccc
Confidence 55666777765 5678999999999999999999999999885
No 40
>PF13471 Transglut_core3: Transglutaminase-like superfamily
Probab=37.93 E-value=16 Score=26.27 Aligned_cols=46 Identities=17% Similarity=0.300 Sum_probs=33.9
Q ss_pred ccc--cchhhhhhccc-ccceeeeccCCCChHHHHhhHhcCcEEECCeeeCCC
Q psy13908 96 NCN--KVTASSFCKRR-LPVVMYRNKMVQQLRLATQFIEQAHVRVGPELEGDM 145 (149)
Q Consensus 96 ~vl--~l~~~~~lerR-L~~vv~r~~~a~s~~~ArqlI~hGhV~V~~~~V~~P 145 (149)
.|+ ++.+..+|+++ ++..+ ..|+...-. .|-.|--|.+||.+|+..
T Consensus 57 ~CL~~ala~~~~L~~~gi~~~l-~iGv~~~~~---~~~aHAWve~~g~~v~~~ 105 (117)
T PF13471_consen 57 KCLPRALALQRLLRRRGIPATL-VIGVRKDDD---PFAAHAWVECGGRVVTGG 105 (117)
T ss_pred ChHHHHHHHHHHHHhcCCCcEE-EEEEeeCCC---CceEEEEEEECCEEEcCC
Confidence 565 67777788766 66555 678777654 777888889999999875
No 41
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=34.35 E-value=88 Score=23.67 Aligned_cols=40 Identities=25% Similarity=0.354 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhc-----CCCCCchhHH----HHHHHHHHHHHhcccC
Q psy13908 50 LSRLIRTLAQKIKD-----LDPKDPFRVE----SSAKLLEKLYLMGLIR 89 (149)
Q Consensus 50 l~~~irk~Ar~L~~-----l~~~dp~r~~----~~~~LL~kL~~~Gll~ 89 (149)
+++.++..+++|.. +++.|.++++ +++.+|+..-.+|+|=
T Consensus 19 ~l~d~~~~~r~~~n~~e~L~~qedk~~l~e~e~q~k~~l~~i~e~G~ii 67 (123)
T COG4911 19 WLRDRLIQLRKIKNEIELLLVQEDKYALQEYESQTKKILDEIIEKGIII 67 (123)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHcCcee
Confidence 44445555554443 4677877777 6678899999999883
No 42
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=33.93 E-value=63 Score=26.93 Aligned_cols=50 Identities=26% Similarity=0.598 Sum_probs=37.1
Q ss_pred CCCCcccccccH---------HHHHHHHHhcCCCch--HHHHHHHHHHHHHHHHHHHhcCCCCCchhHH
Q psy13908 16 VDFISWEADNNL---------HEVKIMRRFGIQKRQ--DYTTYNKLSRLIRTLAQKIKDLDPKDPFRVE 73 (149)
Q Consensus 16 v~f~~w~~~~~~---------~E~~l~~~YgLkkrE--~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~ 73 (149)
|||--|+.= .- +=.++-++-||-+|. +|+ ..++++..|..++|+||.+-.
T Consensus 159 VD~GlW~~i-~ps~LiiPLDtH~~rvar~LgL~~Rk~~d~k-------aa~ElT~~Lr~~dp~DPvKYD 219 (229)
T TIGR02757 159 VDLGIWESF-KPSDLILPLDTHVFRIAKKLKLLKRKSYDLK-------AAIEITEALRELNPEDPIKYD 219 (229)
T ss_pred CCCcCCCCC-CHHHceeechHhHHHHHHHhCCcccCchhHH-------HHHHHHHHHHhcCCCCCcchh
Confidence 999999852 22 336777899999554 556 466778888999999998754
No 43
>PF11609 DUF3248: Protein of unknown function (DUF3248); InterPro: IPR021650 This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known function. ; PDB: 2E6X_A.
Probab=30.69 E-value=45 Score=22.58 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=18.3
Q ss_pred cceeeeccCCCChHHH--------------HhhHhcCcEEE
Q psy13908 111 PVVMYRNKMVQQLRLA--------------TQFIEQAHVRV 137 (149)
Q Consensus 111 ~~vv~r~~~a~s~~~A--------------rqlI~hGhV~V 137 (149)
|.+++|.|+|++...- .+++..|.|+|
T Consensus 19 ~~vvVRvG~AsatprF~~LpRLrnv~daeie~~~~~G~vrv 59 (63)
T PF11609_consen 19 EVVVVRVGLASATPRFAHLPRLRNVSDAEIEAAVQEGRVRV 59 (63)
T ss_dssp SSEEEEEEEGGGHHHHHHS---B---HHHHHHHHHCT-EEE
T ss_pred CeEEEEEeccccCchhhhchhhccCCHHHHHHHHHcCcEEE
Confidence 4578899999865543 56677777776
No 44
>PF06417 DUF1077: Protein of unknown function (DUF1077); InterPro: IPR009445 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=29.42 E-value=34 Score=25.99 Aligned_cols=15 Identities=40% Similarity=0.250 Sum_probs=12.5
Q ss_pred HHHHHHHhcccCCcc
Q psy13908 78 LLEKLYLMGLIRTKW 92 (149)
Q Consensus 78 LL~kL~~~Gll~~~~ 92 (149)
-+.||+.|||||+..
T Consensus 99 gl~K~~~MGLLPt~~ 113 (124)
T PF06417_consen 99 GLYKCNSMGLLPTTS 113 (124)
T ss_pred HHHHHhHccCCCCCc
Confidence 478999999998753
No 45
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=28.70 E-value=28 Score=14.63 Aligned_cols=6 Identities=33% Similarity=0.013 Sum_probs=4.3
Q ss_pred CCCCCC
Q psy13908 144 DMIEGS 149 (149)
Q Consensus 144 ~Ps~~~ 149 (149)
+|+|.|
T Consensus 1 ~pafns 6 (8)
T PF08260_consen 1 DPAFNS 6 (8)
T ss_pred Cccccc
Confidence 588875
No 46
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=27.26 E-value=94 Score=25.22 Aligned_cols=62 Identities=11% Similarity=0.041 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHhcccCCcccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCc
Q psy13908 73 ESSAKLLEKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAH 134 (149)
Q Consensus 73 ~~~~~LL~kL~~~Gll~~~~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGh 134 (149)
.....+.+-|++-|+=-=+-++..-..+.+...+..+.+.++.-.|-+-|..+|++.|..|-
T Consensus 16 ~~a~~ia~al~~gGi~~iEit~~tp~a~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA 77 (201)
T PRK06015 16 EHAVPLARALAAGGLPAIEITLRTPAALDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGS 77 (201)
T ss_pred HHHHHHHHHHHHCCCCEEEEeCCCccHHHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCC
Confidence 46668899999999864333444433445555566667889999999999999999999874
No 47
>PF06014 DUF910: Bacterial protein of unknown function (DUF910); InterPro: IPR009256 This family consists of several short bacterial proteins of unknown function.; PDB: 2NN4_A.
Probab=25.40 E-value=2.2e+02 Score=19.19 Aligned_cols=45 Identities=29% Similarity=0.415 Sum_probs=30.2
Q ss_pred hhhhhhcccCCCCccccccc------HHHHHHHHHhcCCCchHHHHHHHHH
Q psy13908 7 YHEQKLLKKVDFISWEADNN------LHEVKIMRRFGIQKRQDYTTYNKLS 51 (149)
Q Consensus 7 ~he~kLlkkv~f~~w~~~~~------~~E~~l~~~YgLkkrE~~~~y~~l~ 51 (149)
|.-|-|||+....-|=++|. ..|++-+-++||=++++|..+..+.
T Consensus 5 yDVqQLLK~fG~~IY~gdr~~DielM~~El~~Ly~~~lidk~~y~~A~liL 55 (62)
T PF06014_consen 5 YDVQQLLKKFGIIIYVGDRLWDIELMEIELKELYKSGLIDKKEYLTAKLIL 55 (62)
T ss_dssp HHHHHHHHTTS-----S-HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHH
T ss_pred HHHHHHHHHCCEEEEeCChHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 66789999999988877764 4678888899999999999765444
No 48
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=24.69 E-value=2.3e+02 Score=23.54 Aligned_cols=51 Identities=22% Similarity=0.365 Sum_probs=35.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHHhcCCCCC--chhHHHHHHHHHHHHHhcccCC
Q psy13908 40 KRQDYTTYNKLSRLIRTLAQKIKDLDPKD--PFRVESSAKLLEKLYLMGLIRT 90 (149)
Q Consensus 40 krE~~~~y~~l~~~irk~Ar~L~~l~~~d--p~r~~~~~~LL~kL~~~Gll~~ 90 (149)
..|+|..|.+...-|+++....=.-+.+| |.+...--.|+.+|-..|=-|+
T Consensus 164 ~~ed~~rY~~Q~~~v~~I~~~fE~~~~~d~~~~~~~~i~~lmqemQ~~G~PP~ 216 (248)
T PF04614_consen 164 SAEDYERYEKQYELVKEICAIFEKPPYDDEDPERREKIMELMQEMQELGQPPE 216 (248)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHH--TT--HHHHHHHHHHHHHHHHHT----G
T ss_pred CHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHHHHHHHHHcCCCcH
Confidence 57888889888888888888877766666 6666667779999999998764
No 49
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=24.21 E-value=1.6e+02 Score=24.44 Aligned_cols=50 Identities=32% Similarity=0.743 Sum_probs=36.7
Q ss_pred CCCCcccccccH---------HHHHHHHHhcCCCc--hHHHHHHHHHHHHHHHHHHHhcCCCCCchhHH
Q psy13908 16 VDFISWEADNNL---------HEVKIMRRFGIQKR--QDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVE 73 (149)
Q Consensus 16 v~f~~w~~~~~~---------~E~~l~~~YgLkkr--E~~~~y~~l~~~irk~Ar~L~~l~~~dp~r~~ 73 (149)
|||--|+.= .- +=.++-++-||-+| .+|+ ..++++..|...+|+||.+-.
T Consensus 162 VD~GlW~~i-~ps~LiiPLDtHv~~var~LGL~~rk~~d~k-------~A~elT~~lr~~~p~DPvKYD 222 (232)
T PF09674_consen 162 VDFGLWSSI-DPSDLIIPLDTHVFRVARKLGLLKRKSADWK-------AARELTEALREFDPDDPVKYD 222 (232)
T ss_pred CCCcCCCCC-CHHHccccchHhHHHHHHHcCCccCCCccHH-------HHHHHHHHHHhcCCCCCcchh
Confidence 888888861 22 23677889999944 4676 356777888999999998754
No 50
>PF14066 DUF4256: Protein of unknown function (DUF4256)
Probab=20.79 E-value=67 Score=25.82 Aligned_cols=53 Identities=21% Similarity=0.293 Sum_probs=42.8
Q ss_pred HHHHHHHHhcccCCc-----ccccccccchhhhhhcccccceeeeccCCCChHHHHhh
Q psy13908 77 KLLEKLYLMGLIRTK-----WDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQF 129 (149)
Q Consensus 77 ~LL~kL~~~Gll~~~-----~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~Arql 129 (149)
.--+.|..+|-.+.+ .|-++|=+|.-.-||.||-++|..--.=|.|...||-|
T Consensus 110 eqYr~LQ~lg~FD~KTSSWi~TP~~IR~lGGAiF~DrRY~~VFvYHNGA~SYYaaRGF 167 (173)
T PF14066_consen 110 EQYRELQKLGEFDLKTSSWIKTPDDIRKLGGAIFCDRRYGTVFVYHNGADSYYAARGF 167 (173)
T ss_pred HHHHHHHHhCCCccccchhhcCcHHHHHhcCceeccccCCeEEEEeCChHHHHhhccc
Confidence 345678888888764 33566777888899999999998888889999999977
No 51
>COG4483 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.69 E-value=2.7e+02 Score=19.18 Aligned_cols=46 Identities=26% Similarity=0.361 Sum_probs=35.8
Q ss_pred hhhhhhcccCCCCccccccc------HHHHHHHHHhcCCCchHHHHHHHHHH
Q psy13908 7 YHEQKLLKKVDFISWEADNN------LHEVKIMRRFGIQKRQDYTTYNKLSR 52 (149)
Q Consensus 7 ~he~kLlkkv~f~~w~~~~~------~~E~~l~~~YgLkkrE~~~~y~~l~~ 52 (149)
|--|-|||+.-+..|=++|. ..|+.-+=.+||=++|+|-.+..+.+
T Consensus 5 YDVqQlLK~~G~ivyfg~r~~~iemm~~El~~ly~~~ll~Ke~yl~a~~IL~ 56 (68)
T COG4483 5 YDVQQLLKKFGIIVYFGKRLYDIEMMQIELSELYDSGLLDKEDYLRARLILR 56 (68)
T ss_pred HHHHHHHHHCCeeeecCCHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence 55688999999988877764 45677777899999999997665543
No 52
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=20.49 E-value=57 Score=18.55 Aligned_cols=14 Identities=36% Similarity=0.463 Sum_probs=11.8
Q ss_pred HHHHHHHHhcccCC
Q psy13908 77 KLLEKLYLMGLIRT 90 (149)
Q Consensus 77 ~LL~kL~~~Gll~~ 90 (149)
.-|..||+.|+|++
T Consensus 6 ~~L~~l~~~G~Ise 19 (31)
T PF09851_consen 6 EKLKELYDKGEISE 19 (31)
T ss_pred HHHHHHHHcCCCCH
Confidence 45889999999975
No 53
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=20.24 E-value=1.5e+02 Score=24.12 Aligned_cols=63 Identities=19% Similarity=0.166 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHhcccCCcccccccccchhhhhhcccccceeeeccCCCChHHHHhhHhcCc
Q psy13908 72 VESSAKLLEKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAH 134 (149)
Q Consensus 72 ~~~~~~LL~kL~~~Gll~~~~~L~~vl~l~~~~~lerRL~~vv~r~~~a~s~~~ArqlI~hGh 134 (149)
......+.+.|++-|+=-=+-++..-..+.+...++...+.++.-.|.+-+..+|++.+..|-
T Consensus 26 ~~~a~~i~~al~~~Gi~~iEitl~~~~~~~~I~~l~~~~p~~~IGAGTVl~~~~a~~a~~aGA 88 (212)
T PRK05718 26 LEDAVPLAKALVAGGLPVLEVTLRTPAALEAIRLIAKEVPEALIGAGTVLNPEQLAQAIEAGA 88 (212)
T ss_pred HHHHHHHHHHHHHcCCCEEEEecCCccHHHHHHHHHHHCCCCEEEEeeccCHHHHHHHHHcCC
Confidence 346677889999988742223333333445555566677889999999999999999998774
No 54
>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]
Probab=20.19 E-value=97 Score=26.55 Aligned_cols=41 Identities=15% Similarity=0.227 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHhcccCC
Q psy13908 50 LSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGLIRT 90 (149)
Q Consensus 50 l~~~irk~Ar~L~~l~~~dp~r~~~~~~LL~kL~~~Gll~~ 90 (149)
.++.++.....|..|.+.|||....-.+|++-.+.+|=.+.
T Consensus 165 ~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ 205 (280)
T COG3629 165 ACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSA 205 (280)
T ss_pred hcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchH
Confidence 55667788888889999999999999999999999998765
Done!