Query psy4234
Match_columns 177
No_of_seqs 146 out of 922
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:14:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4234.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4234hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01018 rpsD_arch ribosomal 100.0 1.3E-47 2.9E-52 311.8 12.3 128 7-177 4-131 (162)
2 PLN00189 40S ribosomal protein 100.0 1.1E-47 2.3E-52 319.9 11.2 136 1-177 1-136 (194)
3 PTZ00155 40S ribosomal protein 100.0 2.7E-47 5.9E-52 314.5 11.8 132 5-177 3-134 (181)
4 PRK04051 rps4p 30S ribosomal p 100.0 2.5E-44 5.4E-49 295.9 12.1 127 7-177 4-130 (177)
5 KOG3301|consensus 100.0 5.6E-39 1.2E-43 263.0 7.6 124 11-177 1-124 (183)
6 KOG4655|consensus 99.9 6.2E-27 1.3E-31 192.3 5.9 121 15-177 14-134 (181)
7 COG0522 RpsD Ribosomal protein 99.9 1E-24 2.2E-29 183.1 8.5 115 7-177 5-121 (205)
8 CHL00113 rps4 ribosomal protei 99.2 4.6E-12 1E-16 106.3 2.6 78 80-177 39-116 (201)
9 TIGR01017 rpsD_bact ribosomal 99.0 3.3E-10 7.1E-15 94.5 2.9 78 80-177 40-117 (200)
10 PRK05327 rpsD 30S ribosomal pr 99.0 3.7E-10 8E-15 94.4 3.0 78 80-177 43-120 (203)
11 PF00163 Ribosomal_S4: Ribosom 98.6 4.1E-10 8.8E-15 82.9 -5.7 92 9-149 3-94 (94)
12 PF01479 S4: S4 domain; Inter 97.1 0.00029 6.4E-09 45.3 1.8 28 150-177 1-28 (48)
13 KOG3301|consensus 95.2 0.019 4.1E-07 48.2 3.4 64 36-127 52-115 (183)
14 PF00163 Ribosomal_S4: Ribosom 86.5 0.23 5.1E-06 36.3 0.2 46 59-108 49-94 (94)
15 cd00165 S4 S4/Hsp/ tRNA synthe 85.7 0.6 1.3E-05 29.7 1.9 27 151-177 2-28 (70)
16 smart00363 S4 S4 RNA-binding d 79.0 1.6 3.5E-05 26.9 1.9 28 150-177 1-28 (60)
17 TIGR02988 YaaA_near_RecF S4 do 70.3 3.8 8.3E-05 27.4 2.1 28 150-177 9-36 (59)
18 COG0522 RpsD Ribosomal protein 69.6 2.1 4.6E-05 36.5 0.9 73 35-124 37-109 (205)
19 PTZ00155 40S ribosomal protein 67.0 2.7 5.8E-05 35.4 1.0 25 99-123 97-121 (181)
20 TIGR01018 rpsD_arch ribosomal 44.2 11 0.00024 31.2 1.0 24 100-123 95-118 (162)
21 COG1188 Ribosome-associated he 39.6 13 0.00027 28.9 0.6 30 148-177 7-36 (100)
22 PF10862 FcoT: FcoT-like thioe 28.0 53 0.0012 27.4 2.5 37 113-156 61-97 (157)
23 TIGR03069 PS_II_S4 photosystem 26.7 32 0.00069 29.9 1.1 27 150-177 184-210 (257)
24 COG4994 Uncharacterized protei 26.6 31 0.00067 27.5 0.9 53 119-177 7-59 (120)
25 PRK04051 rps4p 30S ribosomal p 25.9 88 0.0019 26.2 3.5 31 101-131 95-132 (177)
26 PLN00189 40S ribosomal protein 25.0 99 0.0021 26.5 3.7 18 114-131 73-90 (194)
27 PRK13354 tyrosyl-tRNA syntheta 21.6 63 0.0014 30.0 2.0 28 150-177 343-370 (410)
28 PRK00117 recX recombination re 21.4 3E+02 0.0066 21.3 5.6 16 115-130 77-92 (157)
No 1
>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=1.3e-47 Score=311.77 Aligned_cols=128 Identities=66% Similarity=1.054 Sum_probs=123.7
Q ss_pred CCCCCccccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhc
Q psy4234 7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIG 86 (177)
Q Consensus 7 ~~~~~k~~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~G 86 (177)
|++++|+|+||+|||+++++++|+++|++|||+||+|||+|+++|++||++|+.|++++ ||++++++++|+++|++||
T Consensus 4 p~~~~k~~~~P~~pw~ker~~~E~~l~~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~--d~~r~~~~~~LL~kL~~~G 81 (162)
T TIGR01018 4 PRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD--DEQRLFEGNQLLRRLVRLG 81 (162)
T ss_pred CCCCCcccCCCCCChhhhhCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHcCC--cHHHHHHHHHHHHHHHHcC
Confidence 78999999999999999999999999999999999999999999999999999999999 8999999999999999999
Q ss_pred cccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCChH
Q psy4234 87 VLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIH 166 (177)
Q Consensus 87 ll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~si~ 166 (177)
+|++.+.+| |+|+++++++|||||||++||++|||+|++
T Consensus 82 ll~e~~~~L-----------------------------------------d~vl~Ltv~~~leRRL~~vv~r~g~a~s~~ 120 (162)
T TIGR01018 82 ILDEENAKL-----------------------------------------DDVLGLTVEDFLERRLQTQVFKKGLARTIH 120 (162)
T ss_pred CCccccCCH-----------------------------------------HHHHhccHHHHHHHhHhhHhhhccCcCCHH
Confidence 998545666 999999999999999999999999999999
Q ss_pred hhhhhhccCCC
Q psy4234 167 HARVLIRQRHI 177 (177)
Q Consensus 167 ~ArqlI~hGHI 177 (177)
||||||+||||
T Consensus 121 ~ArqlI~hgHI 131 (162)
T TIGR01018 121 QARQLIVHGHI 131 (162)
T ss_pred HHHHHhhCCCe
Confidence 99999999998
No 2
>PLN00189 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=1.1e-47 Score=319.94 Aligned_cols=136 Identities=71% Similarity=1.097 Sum_probs=131.6
Q ss_pred CCCCCCCCCCCccccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHH
Q psy4234 1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLR 80 (177)
Q Consensus 1 ~~~~~~~~~~~k~~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~ 80 (177)
||.+..+++++|+|+||+|||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||++++++++|++
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 88888899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcc
Q psy4234 81 RLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLG 160 (177)
Q Consensus 81 kL~~~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlg 160 (177)
+|+++|+|++.+.+| |+|++|++++|||||||++||++|
T Consensus 81 kL~~~GlL~~~~~~L-----------------------------------------d~vl~Ltvs~~leRRL~~vv~r~g 119 (194)
T PLN00189 81 RMNRYGLLDESQNKL-----------------------------------------DYVLALTVENFLERRLQTLVFKSG 119 (194)
T ss_pred HHHHhCCccccccCH-----------------------------------------HHHhhccHHHHHHhhhceeeeecC
Confidence 999999997645566 999999999999999999999999
Q ss_pred cCCChHhhhhhhccCCC
Q psy4234 161 LAKSIHHARVLIRQRHI 177 (177)
Q Consensus 161 lA~si~~ArqlI~hGHI 177 (177)
||+|+++|||||+||||
T Consensus 120 ~a~si~~ARqlI~hgHI 136 (194)
T PLN00189 120 MAKSIHHARVLIRQRHI 136 (194)
T ss_pred CcCCHHHHHHheeCCCE
Confidence 99999999999999998
No 3
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=100.00 E-value=2.7e-47 Score=314.50 Aligned_cols=132 Identities=77% Similarity=1.189 Sum_probs=127.9
Q ss_pred CCCCCCCccccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHH
Q psy4234 5 RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVR 84 (177)
Q Consensus 5 ~~~~~~~k~~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~ 84 (177)
+.|++++|+|+||+|||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||+++.++++||+||++
T Consensus 3 ~~~~~~~k~y~~P~~P~~k~rl~~E~~li~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~~~d~~r~~~~~~LL~kL~~ 82 (181)
T PTZ00155 3 RNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMHR 82 (181)
T ss_pred CCCCCCCcccCCCCCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCC
Q psy4234 85 IGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKS 164 (177)
Q Consensus 85 ~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~s 164 (177)
||++++++++| ++|+++++++|||||||++||++|||+|
T Consensus 83 ~Gi~~~~k~~l-----------------------------------------~~~~~l~~~~~leRRL~~iv~r~g~A~t 121 (181)
T PTZ00155 83 LGLLDEDERKL-----------------------------------------DYVLGLTVEKLLERRLQTKVFKLGLAKS 121 (181)
T ss_pred hCCcchhhccH-----------------------------------------HHHHCccHHHHHHHhhhhHHHhccCcCC
Confidence 99997778888 7888889999999999999999999999
Q ss_pred hHhhhhhhccCCC
Q psy4234 165 IHHARVLIRQRHI 177 (177)
Q Consensus 165 i~~ArqlI~hGHI 177 (177)
+++|||||+||||
T Consensus 122 i~~ARqlI~HGHI 134 (181)
T PTZ00155 122 IHHARVLIRQRHI 134 (181)
T ss_pred HHHhhhheeCCCE
Confidence 9999999999998
No 4
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=100.00 E-value=2.5e-44 Score=295.89 Aligned_cols=127 Identities=46% Similarity=0.752 Sum_probs=122.2
Q ss_pred CCCCCccccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhc
Q psy4234 7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIG 86 (177)
Q Consensus 7 ~~~~~k~~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~G 86 (177)
|++++|+|.||+|||+++++++|+++|++|||+||+|||+|+++|++||++|+.|++ ..|+++..++++|+++|++||
T Consensus 4 p~~~~k~~~~P~~pw~~~r~~~E~~l~~~YgLknk~E~wk~~~~~~~iR~~Ar~Ll~--~~~~~r~~~~~~Ll~kL~~~G 81 (177)
T PRK04051 4 PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLA--LPPEERAKEEEQLLGKLKRYG 81 (177)
T ss_pred CCCCCcCcCCCCCchhhhhcHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHHHHcC
Confidence 799999999999999999999999999999999999999999999999999999998 446899999999999999999
Q ss_pred cccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCChH
Q psy4234 87 VLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIH 166 (177)
Q Consensus 87 ll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~si~ 166 (177)
+|++ +.+| |+|++|++++|||||||++|+++|||+|++
T Consensus 82 il~~-~~~L-----------------------------------------~~vl~L~v~~~lerRLd~il~r~gla~S~~ 119 (177)
T PRK04051 82 ILKE-NATL-----------------------------------------DDVLSLTVEDILERRLQTIVYRKGLARTPK 119 (177)
T ss_pred CCCC-CCCH-----------------------------------------HHHHhccHHHHHHhHHHHHHHHccCcCCHH
Confidence 9987 6667 999999999999999999999999999999
Q ss_pred hhhhhhccCCC
Q psy4234 167 HARVLIRQRHI 177 (177)
Q Consensus 167 ~ArqlI~hGHI 177 (177)
+|+|||.||||
T Consensus 120 ~Ar~lI~hGhV 130 (177)
T PRK04051 120 QARQFIVHGHI 130 (177)
T ss_pred HHHHHHHcCCE
Confidence 99999999997
No 5
>KOG3301|consensus
Probab=100.00 E-value=5.6e-39 Score=263.01 Aligned_cols=124 Identities=81% Similarity=1.225 Sum_probs=115.5
Q ss_pred CccccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhccccc
Q psy4234 11 SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDE 90 (177)
Q Consensus 11 ~k~~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~Gll~~ 90 (177)
+|+|.||++||+++|+++|++++++|||+|++|+|++.+.++++|+.||.| ++++||.++|++.+|+++|.+||++++
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 689999999999999999999999999999999999999999999999999 789999999988888877777777766
Q ss_pred cccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCChHhhhh
Q psy4234 91 SRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARV 170 (177)
Q Consensus 91 ~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~si~~Arq 170 (177)
.++|| |+|+++++++||||||||+||++|||+||+|||+
T Consensus 79 ~~~Kl-----------------------------------------dyvl~l~ie~fLErRLqt~vFklGlAkSIhhARv 117 (183)
T KOG3301|consen 79 RKNKL-----------------------------------------DYVLALTVEDFLERRLQTIVFKLGLAKSIHHARV 117 (183)
T ss_pred cccch-----------------------------------------hHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHH
Confidence 55555 9999999999999999999999999999999999
Q ss_pred hhccCCC
Q psy4234 171 LIRQRHI 177 (177)
Q Consensus 171 lI~hGHI 177 (177)
+|.|+||
T Consensus 118 Li~~rhI 124 (183)
T KOG3301|consen 118 LIRQRHI 124 (183)
T ss_pred HhcCccE
Confidence 9999997
No 6
>KOG4655|consensus
Probab=99.93 E-value=6.2e-27 Score=192.30 Aligned_cols=121 Identities=26% Similarity=0.369 Sum_probs=114.8
Q ss_pred cCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhccccccccc
Q psy4234 15 VTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMK 94 (177)
Q Consensus 15 ~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~Gll~~~k~k 94 (177)
.+.+-.|+.+...+|+.++.+|+|++++||.+|+.+++++|++|..|..+++.||+|...+..||.|||.||++.. +.+
T Consensus 14 kVdFLnWkv~d~~re~~v~rrY~l~~REdY~kyn~l~~~~r~la~~l~~l~~sDpfR~~~t~~LL~kly~~GvipT-r~~ 92 (181)
T KOG4655|consen 14 KVDFLNWKVTDHHRELCVLRRYHLKKREDYTKYNRLAGKVRKLANRLALLDESDPFRLQYTLLLLEKLYAMGVIPT-RKS 92 (181)
T ss_pred hcccceeeecCchhhHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhhccccccceecc-hhh
Confidence 4678899999999999999999999999999999999999999999999999999999999999999999999988 444
Q ss_pred hhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCChHhhhhhhcc
Q psy4234 95 LDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQ 174 (177)
Q Consensus 95 l~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~si~~ArqlI~h 174 (177)
+ +.+...+++.||+||||+|+.+++||+|+++|..||+|
T Consensus 93 l-----------------------------------------~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEq 131 (181)
T KOG4655|consen 93 L-----------------------------------------ELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQ 131 (181)
T ss_pred h-----------------------------------------hhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHc
Confidence 4 67778999999999999999999999999999999999
Q ss_pred CCC
Q psy4234 175 RHI 177 (177)
Q Consensus 175 GHI 177 (177)
|||
T Consensus 132 GHV 134 (181)
T KOG4655|consen 132 GHV 134 (181)
T ss_pred Cce
Confidence 997
No 7
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1e-24 Score=183.10 Aligned_cols=115 Identities=32% Similarity=0.447 Sum_probs=91.7
Q ss_pred CCCCCcc--ccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHH
Q psy4234 7 PSVHSKT--YVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVR 84 (177)
Q Consensus 7 ~~~~~k~--~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~ 84 (177)
|+ ++++ |.+|.+||.+++...|.+.+..|| +|+.+.|.-.+.++..+..
T Consensus 5 ~~-~~~K~~rr~g~~~~~~~~~~~~~~~~~~pG-qhk~~~~~k~s~yg~qL~e--------------------------- 55 (205)
T COG0522 5 PG-PKKKLSRRLGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLRE--------------------------- 55 (205)
T ss_pred cC-cccceeeecCCChHHHHHHHHHhhcCCCcc-ccchhHHHHHHHHHHHHHH---------------------------
Confidence 55 5566 999999999999999999999999 9999988876555554444
Q ss_pred hccccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCC
Q psy4234 85 IGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKS 164 (177)
Q Consensus 85 ~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~s 164 (177)
+|+++++||+.++||. ++|.++|+++ +++++++++||||||||+|||+|||.|
T Consensus 56 -------kqkl~~~yg~~ekqf~-------------~~l~~a~~l~-------g~~~~~~~~~LErRLd~vVyR~GfA~T 108 (205)
T COG0522 56 -------KQKLRAFYGVLEKQFR-------------RYLKEAGRLK-------GVTGLNLLALLERRLDNVVYRLGFAKT 108 (205)
T ss_pred -------HHHhhhhccHHHHHHH-------------HHHHHHhccC-------ChHHHHHHHHHHHHHHHHHHHhccccc
Confidence 5555555565444443 3334444443 488999999999999999999999999
Q ss_pred hHhhhhhhccCCC
Q psy4234 165 IHHARVLIRQRHI 177 (177)
Q Consensus 165 i~~ArqlI~hGHI 177 (177)
+.||||||+||||
T Consensus 109 ~~qARQlV~HGHI 121 (205)
T COG0522 109 RRQARQLVSHGHI 121 (205)
T ss_pred HHHHHHHhhcceE
Confidence 9999999999997
No 8
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=99.22 E-value=4.6e-12 Score=106.31 Aligned_cols=78 Identities=28% Similarity=0.360 Sum_probs=67.9
Q ss_pred HHHHHhccccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhc
Q psy4234 80 RRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKL 159 (177)
Q Consensus 80 ~kL~~~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rl 159 (177)
.|+++||+...+|||++++||++|+|| ++++.+|-. ..++.+.++..+||.|||.+++++
T Consensus 39 ~k~S~y~~~L~eKqk~~~~Yg~~ekq~-----~~~~~~a~~---------------~~g~tg~~ll~~LE~RLD~~L~r~ 98 (201)
T CHL00113 39 GKKSQYRIRLEEKQKLRFNYGLTERQL-----LKYVRIARK---------------AKGSTGQVLLQLLEMRLDNILFRL 98 (201)
T ss_pred ccccHHHHHHHHHHHHHHHcCCCHHHH-----HHHHHHHHh---------------cCCcHHHHHHHHHHHHHHHHHHHc
Confidence 689999995555999999999977776 456666643 257889999999999999999999
Q ss_pred ccCCChHhhhhhhccCCC
Q psy4234 160 GLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 160 glA~si~~ArqlI~hGHI 177 (177)
|++.|..+|+|+|.||||
T Consensus 99 g~~~SR~~ArqlI~~G~V 116 (201)
T CHL00113 99 GMAPTIPAARQLVNHGHI 116 (201)
T ss_pred CCCCCHHHHHHHHHCCcE
Confidence 999999999999999997
No 9
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=98.96 E-value=3.3e-10 Score=94.49 Aligned_cols=78 Identities=27% Similarity=0.425 Sum_probs=63.5
Q ss_pred HHHHHhccccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhc
Q psy4234 80 RRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKL 159 (177)
Q Consensus 80 ~kL~~~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rl 159 (177)
.|+++||+...+|||+++.||+.++||. .++..|+-. .+..+.++.+++|.|||.+++++
T Consensus 40 ~k~S~y~~~l~eKQk~~~~Yg~~e~q~~-----~~~~~a~~~---------------~g~t~~~ll~~le~RLD~~L~~~ 99 (200)
T TIGR01017 40 KKLSDYGLQLQEKQKLKFMYGITEKQFR-----KYFKEAKKL---------------KGNTGENLLRLLESRLDNVVYRL 99 (200)
T ss_pred CcccHHHHHHHHHHHHHHHHhchHHHHH-----HHHHHHhcc---------------CCCchhHHHHHHHHHHHHHHHHc
Confidence 6899999955559999999998777764 455555321 23346667889999999999999
Q ss_pred ccCCChHhhhhhhccCCC
Q psy4234 160 GLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 160 glA~si~~ArqlI~hGHI 177 (177)
|++.|..+|+++|.||||
T Consensus 100 g~~~SR~~ArqlI~~G~V 117 (200)
T TIGR01017 100 GFAPTRFAARQLVSHGHI 117 (200)
T ss_pred CCCCCHHHHHHHHHCCCE
Confidence 999999999999999997
No 10
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.95 E-value=3.7e-10 Score=94.37 Aligned_cols=78 Identities=28% Similarity=0.428 Sum_probs=63.7
Q ss_pred HHHHHhccccccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhc
Q psy4234 80 RRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKL 159 (177)
Q Consensus 80 ~kL~~~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rl 159 (177)
.|+++||+...+|||++|.||+.++|| ..++..|+-. .+..+.++.+++|.|||+++++.
T Consensus 43 ~k~s~y~~~L~eKQk~~~~Y~~~e~q~-----~~~~~~a~~~---------------~g~t~~~ll~~lE~RLD~iL~~~ 102 (203)
T PRK05327 43 PKLSDYGLQLREKQKLRRIYGVLEKQF-----RRYFKEAARR---------------KGNTGENLLQLLESRLDNVVYRL 102 (203)
T ss_pred ccccHHHHHHHHHHHhHHHhcCcHHHH-----HHHHHHHHhc---------------cCCcHhHHHHHHHHHHHHHHHHc
Confidence 478999995555999999999977776 3455555331 24456677889999999999999
Q ss_pred ccCCChHhhhhhhccCCC
Q psy4234 160 GLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 160 glA~si~~ArqlI~hGHI 177 (177)
||+.|..+|+++|.||||
T Consensus 103 g~~~SR~~arqlI~~G~V 120 (203)
T PRK05327 103 GFAPTRRQARQLVSHGHI 120 (203)
T ss_pred CccCCHHHHHHHHHCCcE
Confidence 999999999999999997
No 11
>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=4.1e-10 Score=82.89 Aligned_cols=92 Identities=32% Similarity=0.430 Sum_probs=70.1
Q ss_pred CCCccccCCCCccchhhhhHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhccc
Q psy4234 9 VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVL 88 (177)
Q Consensus 9 ~~~k~~~~p~~p~~~~r~~~e~~~~~~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~Gll 88 (177)
...+++..|++||....+..|..+++.||+++..+.|+..+. +++++||+.
T Consensus 3 ~~~~~~k~~Rr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------rk~s~y~~q 53 (94)
T PF00163_consen 3 YRGPKCKLPRRLGEKLWLTEKAKLIRRYGLRPGQHGWRRKSR-----------------------------RKLSRYGLQ 53 (94)
T ss_dssp SHSCCCHHHHHCTSHCTCSCCCSHCCSSSSSSSSSTTSHHHH-----------------------------HCCHHHHHH
T ss_pred cCCCccccCCCCCCCccCCCcccccccccccccccccccccc-----------------------------ccchhhhcc
Confidence 456789999999999999999999999999999999988643 455556663
Q ss_pred cccccchhhhhchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccchhhhcchhhhhhh
Q psy4234 89 DESRMKLDYVLGLKIEDFLERRLQTQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLE 149 (177)
Q Consensus 89 ~~~k~kl~~~ygl~~~q~~~rr~~~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fle 149 (177)
..++|++++.||+.++|| +.++..| .++++++++++++|||
T Consensus 54 L~eKqk~r~~yg~lekql-----~~~~~~a---------------~k~~g~tg~~l~~lLE 94 (94)
T PF00163_consen 54 LREKQKLRFYYGILEKQL-----RRYGKIA---------------AKLKGVTGENLLQLLE 94 (94)
T ss_dssp HHHHHHHHHHHTHHHHHH-----HHHHHHH---------------HHSSSHHHHHHHHHHH
T ss_pred cccCCchhhhhhhHHHHH-----HHHHHHH---------------HhcCCCHHHHHHHHhC
Confidence 233777877787655544 3344333 3458999999999997
No 12
>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=97.09 E-value=0.00029 Score=45.31 Aligned_cols=28 Identities=43% Similarity=0.541 Sum_probs=26.7
Q ss_pred hhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 150 RRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
+||+.++.++|++.|..+|+++|.||+|
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V 28 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRV 28 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEE
Confidence 5899999999999999999999999996
No 13
>KOG3301|consensus
Probab=95.25 E-value=0.019 Score=48.21 Aligned_cols=64 Identities=28% Similarity=0.420 Sum_probs=43.7
Q ss_pred hCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhccccccccchhhhhchhhHHHHHHHHHHHH
Q psy4234 36 YGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQV 115 (177)
Q Consensus 36 Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~~ 115 (177)
...++++.+..++.+++.+-+... +++. .+++ +- . +|++++||+|+|++|++
T Consensus 52 l~~k~p~rlf~g~allrrLvr~g~----l~e~----------------~~Kl----dy-v---l~l~ie~fLErRLqt~v 103 (183)
T KOG3301|consen 52 LDEKDPKRLFEGNALLRRLVRYGV----LDER----------------KNKL----DY-V---LALTVEDFLERRLQTIV 103 (183)
T ss_pred hccccHHHHhcchHHHHHHHHHhh----hhcc----------------ccch----hH-H---HHHHHHHHHHHHHHHHH
Confidence 456788888888877766554431 1111 1111 11 2 36789999999999999
Q ss_pred HHHHHHHHHHhc
Q psy4234 116 SNALLRRLVRIG 127 (177)
Q Consensus 116 ~~a~~~rl~~~~ 127 (177)
++++++++|...
T Consensus 104 FklGlAkSIhhA 115 (183)
T KOG3301|consen 104 FKLGLAKSIHHA 115 (183)
T ss_pred HHHhhhhhhHHH
Confidence 999999998753
No 14
>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=86.49 E-value=0.23 Score=36.33 Aligned_cols=46 Identities=37% Similarity=0.486 Sum_probs=36.0
Q ss_pred HHHhcCCchhHHHHHhHHHHHHHHHHhccccccccchhhhhchhhHHHHH
Q psy4234 59 RELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLE 108 (177)
Q Consensus 59 ~~L~~l~~~d~~r~~~~~~Ll~kL~~~Gll~~~k~kl~~~ygl~~~q~~~ 108 (177)
+.++.|.++++.+...+ .+.++|++||++. .+++.+.|.+.-+|+|
T Consensus 49 ~y~~qL~eKqk~r~~yg-~lekql~~~~~~a---~k~~g~tg~~l~~lLE 94 (94)
T PF00163_consen 49 RYGLQLREKQKLRFYYG-ILEKQLRRYGKIA---AKLKGVTGENLLQLLE 94 (94)
T ss_dssp HHHHHHHHHHHHHHHHT-HHHHHHHHHHHHH---HHSSSHHHHHHHHHHH
T ss_pred hhhcccccCCchhhhhh-hHHHHHHHHHHHH---HhcCCCHHHHHHHHhC
Confidence 44567789999999888 8999999999986 4566677776666654
No 15
>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=85.73 E-value=0.6 Score=29.72 Aligned_cols=27 Identities=44% Similarity=0.642 Sum_probs=24.2
Q ss_pred hhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 151 RLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 151 RLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
||+.++...++..|..+|+++|.+|+|
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V 28 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHV 28 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCE
Confidence 778888888889999999999999986
No 16
>smart00363 S4 S4 RNA-binding domain.
Probab=78.99 E-value=1.6 Score=26.91 Aligned_cols=28 Identities=46% Similarity=0.600 Sum_probs=23.8
Q ss_pred hhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 150 RRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
+||+.++...++..|..+|+.+|.+|+|
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i 28 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRV 28 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCE
Confidence 3677888888888999999999999975
No 17
>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=70.26 E-value=3.8 Score=27.36 Aligned_cols=28 Identities=18% Similarity=0.280 Sum_probs=24.3
Q ss_pred hhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 150 RRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
.||+..+...+++.|...|+.+|..|+|
T Consensus 9 ~rLd~~L~~~~~~~SR~~~k~li~~G~V 36 (59)
T TIGR02988 9 ITLGQLLKELGIIDSGGQAKWFLQENEV 36 (59)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHHcCCE
Confidence 5788888888888899999999999986
No 18
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=69.57 E-value=2.1 Score=36.46 Aligned_cols=73 Identities=22% Similarity=0.184 Sum_probs=55.0
Q ss_pred HhCCCCchhHHHHHHHHHHHHHHHHHHhcCCchhHHHHHhHHHHHHHHHHhccccccccchhhhhchhhHHHHHHHHHHH
Q psy4234 35 EYGLRNKREVWRVKYALAKIRKAARELLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQ 114 (177)
Q Consensus 35 ~Ygl~nk~E~w~~~~~l~~irk~A~~L~~l~~~d~~r~~~~~~Ll~kL~~~Gll~~~k~kl~~~ygl~~~q~~~rr~~~~ 114 (177)
+-|=..+.-.-.|...++.-+++-. .+-..+.+|++.|.++|.+.+ +.|++..+++|+||.|.
T Consensus 37 qhk~~~~~k~s~yg~qL~ekqkl~~----------~yg~~ekqf~~~l~~a~~l~g-------~~~~~~~~~LErRLd~v 99 (205)
T COG0522 37 QHGQERWKKLSDYGLQLREKQKLRA----------FYGVLEKQFRRYLKEAGRLKG-------VTGLNLLALLERRLDNV 99 (205)
T ss_pred ccchhHHHHHHHHHHHHHHHHHhhh----------hccHHHHHHHHHHHHHhccCC-------hHHHHHHHHHHHHHHHH
Confidence 3343444556667777777777652 222578899999999999977 56889999999999999
Q ss_pred HHHHHHHHHH
Q psy4234 115 VSNALLRRLV 124 (177)
Q Consensus 115 ~~~a~~~rl~ 124 (177)
+..+++++.+
T Consensus 100 VyR~GfA~T~ 109 (205)
T COG0522 100 VYRLGFAKTR 109 (205)
T ss_pred HHHhcccccH
Confidence 9998775544
No 19
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=67.05 E-value=2.7 Score=35.37 Aligned_cols=25 Identities=52% Similarity=0.685 Sum_probs=20.0
Q ss_pred hchhhHHHHHHHHHHHHHHHHHHHH
Q psy4234 99 LGLKIEDFLERRLQTQVSNALLRRL 123 (177)
Q Consensus 99 ygl~~~q~~~rr~~~~~~~a~~~rl 123 (177)
|||++++|+||||.+.+..+.++..
T Consensus 97 ~~l~~~~~leRRL~~iv~r~g~A~t 121 (181)
T PTZ00155 97 LGLTVEKLLERRLQTKVFKLGLAKS 121 (181)
T ss_pred HCccHHHHHHHhhhhHHHhccCcCC
Confidence 3668889999999999988776443
No 20
>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=44.24 E-value=11 Score=31.18 Aligned_cols=24 Identities=67% Similarity=0.852 Sum_probs=19.0
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHH
Q psy4234 100 GLKIEDFLERRLQTQVSNALLRRL 123 (177)
Q Consensus 100 gl~~~q~~~rr~~~~~~~a~~~rl 123 (177)
+|+..+|+|||+.+.+.++.++..
T Consensus 95 ~Ltv~~~leRRL~~vv~r~g~a~s 118 (162)
T TIGR01018 95 GLTVEDFLERRLQTQVFKKGLART 118 (162)
T ss_pred hccHHHHHHHhHhhHhhhccCcCC
Confidence 457889999999999988665443
No 21
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=39.61 E-value=13 Score=28.87 Aligned_cols=30 Identities=17% Similarity=0.183 Sum_probs=27.8
Q ss_pred hhhhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 148 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 148 leRRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
-+.|||-.+.-..|.++..-|..+++.|||
T Consensus 7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV 36 (100)
T COG1188 7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRV 36 (100)
T ss_pred cceehHHHHHHHHHhhhHHHHHHHHHCCeE
Confidence 367999999999999999999999999997
No 22
>PF10862 FcoT: FcoT-like thioesterase domain; InterPro: IPR022598 Proteins in this family have a HotDog fold. This family was formerly known as DUF2662. The structure of Rv0098 from M. tuberculosis [] suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups []. The maximal Kcat was observed for palmitoyl-CoA, although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.; PDB: 2PFC_A 3B18_A.
Probab=28.03 E-value=53 Score=27.40 Aligned_cols=37 Identities=24% Similarity=0.446 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhh
Q psy4234 113 TQVSNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQV 156 (177)
Q Consensus 113 ~~~~~a~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv 156 (177)
++..=.+++..|.-+.++ ...+.+++||++|.|+.++
T Consensus 61 NQl~Y~~~A~~v~~~l~~-------~f~~Wt~ddf~~rQLsdil 97 (157)
T PF10862_consen 61 NQLAYYLIAKCVKNELIP-------AFAGWTLDDFWERQLSDIL 97 (157)
T ss_dssp HHHHHHHHHHHHHTT-SC-------CCTT--HHHHHHCHHHHEE
T ss_pred HHHHHHHHHHHHhhccch-------hhcccCHHHHHHhhcCcee
Confidence 344446778888888766 3568999999999999886
No 23
>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=26.73 E-value=32 Score=29.94 Aligned_cols=27 Identities=15% Similarity=0.159 Sum_probs=23.4
Q ss_pred hhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 150 RRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
.|||.++ ..++.-|...|.++|.+|+|
T Consensus 184 ~RLD~ll-s~~~~~SRs~a~~lI~~G~V 210 (257)
T TIGR03069 184 LRIDAIA-SAGFGLSRSKIVDQIKAGRL 210 (257)
T ss_pred ccHHHHH-HhhhhhhHHHHHHHHHCCeE
Confidence 5999655 78887799999999999986
No 24
>COG4994 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.59 E-value=31 Score=27.53 Aligned_cols=53 Identities=26% Similarity=0.253 Sum_probs=44.5
Q ss_pred HHHHHHHhcccccccccchhhhcchhhhhhhhhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 119 LLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 119 ~~~rl~~~~~~~e~~~~l~~vl~l~v~~fleRRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
-++||.-|..-+|-|...++...+...+|-| +...|...+.-....+-+|||+
T Consensus 7 ~~~kLe~i~l~pE~r~~~~~~~~~l~d~f~E------v~~SGy~~~yv~g~~~~~~~~l 59 (120)
T COG4994 7 ELRKLEPIFLRPEHRTRREDFERMLEDDFWE------VGASGYSRSYVLGVLDARHGHL 59 (120)
T ss_pred HHHhhhhhhcCchhcchHHHHHHHHhhhhhh------hccCceeeeeeeeeeccccCch
Confidence 4578999999999999999988888888887 6678888888777777788885
No 25
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=25.88 E-value=88 Score=26.20 Aligned_cols=31 Identities=42% Similarity=0.557 Sum_probs=22.2
Q ss_pred hhhHHHHHHHHHHHHHHH-------HHHHHHHhccccc
Q psy4234 101 LKIEDFLERRLQTQVSNA-------LLRRLVRIGVLDE 131 (177)
Q Consensus 101 l~~~q~~~rr~~~~~~~a-------~~~rl~~~~~~~e 131 (177)
|+..+|+|+|+.+.+... --+.||..|.+.-
T Consensus 95 L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV~V 132 (177)
T PRK04051 95 LTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAV 132 (177)
T ss_pred ccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCEEE
Confidence 477888898988888773 3366777776653
No 26
>PLN00189 40S ribosomal protein S9; Provisional
Probab=24.96 E-value=99 Score=26.46 Aligned_cols=18 Identities=56% Similarity=0.776 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHhccccc
Q psy4234 114 QVSNALLRRLVRIGVLDE 131 (177)
Q Consensus 114 ~~~~a~~~rl~~~~~~~e 131 (177)
...+++++||.+.|++++
T Consensus 73 ~~~~~LL~kL~~~GlL~~ 90 (194)
T PLN00189 73 FEGEALLRRMNRYGLLDE 90 (194)
T ss_pred HHHHHHHHHHHHhCCccc
Confidence 356899999999999874
No 27
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=21.58 E-value=63 Score=30.01 Aligned_cols=28 Identities=36% Similarity=0.464 Sum_probs=24.5
Q ss_pred hhhhhhhhhcccCCChHhhhhhhccCCC
Q psy4234 150 RRLQTQVFKLGLAKSIHHARVLIRQRHI 177 (177)
Q Consensus 150 RRLqtvv~rlglA~si~~ArqlI~hGHI 177 (177)
..+..++...|++.|-.+||.+|.+|=|
T Consensus 343 ~~~~~~l~~~~~~~S~~earrli~~ggv 370 (410)
T PRK13354 343 KNLVDLLVDLGLEPSKREARRLIQNGAI 370 (410)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHcCCE
Confidence 4677889999999999999999999843
No 28
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=21.43 E-value=3e+02 Score=21.32 Aligned_cols=16 Identities=19% Similarity=0.135 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHhcccc
Q psy4234 115 VSNALLRRLVRIGVLD 130 (177)
Q Consensus 115 ~~~a~~~rl~~~~~~~ 130 (177)
.-+.+...|..-|+=.
T Consensus 77 g~~~I~~~L~~kGi~~ 92 (157)
T PRK00117 77 GPRRIRQELRQKGVDR 92 (157)
T ss_pred hHHHHHHHHHHcCCCH
Confidence 3346667777777733
Done!