Citrus Sinensis ID: 032704

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-----
Protein Sequence
MAAMAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFIH
Secondary Structure (PSIPRED)
cHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEEEEHHHHHcccccccccccEEEEcccEEEEEEccccccEEEEEEEEcccccEEEEcccEEEEccccccccccccEEEEcccccEEcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEccHHHHHccccccccEEEEEEEcccEEEEEEEcccccEEEEEEEEccccEEEEEEEEEEEEccccccccccccEEEEEccEEEEEc
Coil and Loop (DISEMBL)
MAAMAALQSSMtslsissnsffgqrlsfpslspitvkptdkpclIVVRLKRwerkeckpnslpvlhkmhvkagDTVKVIAgcdkgkigeitKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFIH
Flexible Loop (DISEMBL)
MAAMAALQSSMTSLSISSNSFFGQRLSFPslspitvkptdkPCLIVVRLkrwerkeckpnslpvlhkmhvkaGDTVKVIAGCdkgkigeitkvfrhnstvmvkdinlktkhvkkreeeeqgqiikvySLICYFIH
Low Complexity Region (SEG)
MAAMAALQssmtslsissnsFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFIH
Disordered region (IsUnstruct)
************************RLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL****************************
Disordered Region (DISOPRED)
**************SISSNSFFGQRLS******************VV********************MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLK*******************SLICYFIH
Disordered Region (DISEMBL)
**************SISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTK*********QGQIIKVYSLICYFIH
Disordered Region (DISPRO)
*************************LSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFIH
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAMAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFIH
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	135	2.2.26 [Sep-21-2011]
Q02764	187	50S ribosomal protein L24	N/A	no	0.918	0.663	0.677	6e-44
P92959	198	50S ribosomal protein L24	yes	no	0.8	0.545	0.690	6e-39
P11893	194	50S ribosomal protein L24	N/A	no	0.948	0.659	0.728	3e-38
P27683	191	50S ribosomal protein L24	N/A	no	0.792	0.560	0.678	2e-36
Q8DMM1	117	50S ribosomal protein L24	yes	no	0.496	0.572	0.611	2e-16
B1XJS8	116	50S ribosomal protein L24	yes	no	0.488	0.568	0.575	9e-16
O24700	113	50S ribosomal protein L24	yes	no	0.459	0.548	0.612	2e-15
Q31L18	113	50S ribosomal protein L24	yes	no	0.459	0.548	0.612	2e-15
Q3MFB0	117	50S ribosomal protein L24	yes	no	0.503	0.581	0.544	1e-14
B2ITP4	117	50S ribosomal protein L24	yes	no	0.503	0.581	0.573	2e-14

>sp|Q02764|RK24_TOBAC 50S ribosomal protein L24, chloroplastic OS=Nicotiana tabacum GN=RPL24 PE=1 SV=1

 Score =  175 bits (444), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 86/127 (67%), Positives = 100/127 (78%), Gaps = 3/127 (2%)

Query: 4   MAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLP 63
           MAALQSS   LS    SFFGQR S P   P  VK T+ PCLI  +LKRWERKECKPNSLP
Sbjct: 1   MAALQSSFAGLS---TSFFGQRFSPPLSLPPLVKSTEGPCLIQAKLKRWERKECKPNSLP 57

Query: 64  VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQI 123
           VLHKMHVK GDTVK+I+G DKGK+GEIT++ +HNS V+VKD+NLKTKHVK R E+E GQI
Sbjct: 58  VLHKMHVKLGDTVKIISGHDKGKVGEITEIIKHNSKVVVKDVNLKTKHVKSRSEDEPGQI 117

Query: 124 IKVYSLI 130
           +K+ + I
Sbjct: 118 VKIEAPI 124

One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
Nicotiana tabacum (taxid: 4097)

>sp|P92959|RK24_ARATH 50S ribosomal protein L24, chloroplastic OS=Arabidopsis thaliana GN=RPL24 PE=2 SV=2

 Score =  159 bits (401), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 76/110 (69%), Positives = 93/110 (84%), Gaps = 2/110 (1%)

Query: 23  GQRLSFP-SLSPIT-VKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIA 80
           GQRL  P SLS  + VKP + PCL++ +LKRWERKECKPNSLP+LHKMHVK GDTVKVI+
Sbjct: 24  GQRLISPISLSVTSPVKPAENPCLVLAKLKRWERKECKPNSLPILHKMHVKFGDTVKVIS 83

Query: 81  GCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLI 130
           G DKGKIGE+TK+F HNST+++KD+NLKTKH+K REE E GQI+K+ + I
Sbjct: 84  GRDKGKIGEVTKIFTHNSTIVIKDVNLKTKHMKSREEGEPGQIVKIEAPI 133

One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.

Arabidopsis thaliana (taxid: 3702)

>sp|P11893|RK24_PEA 50S ribosomal protein L24, chloroplastic OS=Pisum sativum GN=RPL24 PE=2 SV=1

 Score =  156 bits (395), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 94/129 (72%), Positives = 112/129 (86%), Gaps = 1/129 (0%)

Query: 3   AMAALQSSMTSLSISSNSFFGQRLSFPSLSP-ITVKPTDKPCLIVVRLKRWERKECKPNS 61
           AMA+LQSSM+SLS+SSNSF GQ LS  +LSP +  KPT+K CLIV++LKRWERKECKPNS
Sbjct: 5   AMASLQSSMSSLSLSSNSFLGQPLSPITLSPFLQGKPTEKKCLIVMKLKRWERKECKPNS 64

Query: 62  LPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQG 121
           LPVLHK+HVK GDTVKVI+G +KG+IGEITK+F+HNS+V+VKDINLKTKHVK  +E E G
Sbjct: 65  LPVLHKLHVKVGDTVKVISGHEKGQIGEITKIFKHNSSVIVKDINLKTKHVKSNQEGEPG 124

Query: 122 QIIKVYSLI 130
           QI KV + I
Sbjct: 125 QINKVEAPI 133

One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.

Pisum sativum (taxid: 3888)

>sp|P27683|RK24_SPIOL 50S ribosomal protein L24, chloroplastic OS=Spinacia oleracea GN=RPL24 PE=1 SV=1

 Score =  150 bits (380), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 74/109 (67%), Positives = 90/109 (82%), Gaps = 2/109 (1%)

Query: 23  GQRLSFPSLSPITVKPTD-KPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAG 81
           GQRL FPS + + VK     PCLIV+R+KRWERK+CKPNSLP LHK HVK GDTVKVI+G
Sbjct: 22  GQRL-FPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPNSLPKLHKRHVKVGDTVKVISG 80

Query: 82  CDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLI 130
            +KGKIGEI+K+ +HNSTV++KD+N KTKHVK +EE EQGQIIK+ + I
Sbjct: 81  GEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEAAI 129

One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). Located at the polypeptide exit tunnel on the outside of the subunit.

Spinacia oleracea (taxid: 3562)

>sp|Q8DMM1|RL24_THEEB 50S ribosomal protein L24 OS=Thermosynechococcus elongatus (strain BP-1) GN=rplX PE=3 SV=1

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/67 (61%), Positives = 50/67 (74%)

Query: 58  KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 117
           K N  PV ++MHVK GDTV+VIAG DK K+GE+  VF   S V+VK +NLKTKH+K R+E
Sbjct: 5   KANKKPVRYRMHVKKGDTVQVIAGSDKAKVGEVLAVFPKTSQVIVKGVNLKTKHLKPRQE 64

Query: 118 EEQGQII 124
            E GQII
Sbjct: 65  GESGQII 71

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.

Thermosynechococcus elongatus (strain BP-1) (taxid: 197221)

>sp|B1XJS8|RL24_SYNP2 50S ribosomal protein L24 OS=Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) GN=rplX PE=3 SV=1

 Score = 82.0 bits (201), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 38/66 (57%), Positives = 51/66 (77%)

Query: 58  KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 117
           + +S P  HKMHVK GDTV+VI+G DKGK+GE+ K    +S V+VKD+N++TKHVK ++E
Sbjct: 4   RKSSTPTRHKMHVKTGDTVQVISGRDKGKVGEVIKTLPKSSKVVVKDVNIRTKHVKPQQE 63

Query: 118 EEQGQI 123
            E GQI
Sbjct: 64  GESGQI 69

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.

Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) (taxid: 32049)

>sp|O24700|RL24_SYNP6 50S ribosomal protein L24 OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=rplX PE=3 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 48/62 (77%)

Query: 63  PVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQ 122
           PV H +HVK GDTV+VIAG DKG +GE+ +VF   S V+VK +NL+TKHVK R+E E GQ
Sbjct: 6   PVRHSVHVKKGDTVQVIAGKDKGTVGEVLQVFPKTSRVLVKGVNLRTKHVKPRQEGESGQ 65

Query: 123 II 124
           I+
Sbjct: 66  IV 67

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (taxid: 269084)

>sp|Q31L18|RL24_SYNE7 50S ribosomal protein L24 OS=Synechococcus elongatus (strain PCC 7942) GN=rplX PE=3 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 48/62 (77%)

Query: 63  PVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQ 122
           PV H +HVK GDTV+VIAG DKG +GE+ +VF   S V+VK +NL+TKHVK R+E E GQ
Sbjct: 6   PVRHSVHVKKGDTVQVIAGKDKGTVGEVLQVFPKTSRVLVKGVNLRTKHVKPRQEGESGQ 65

Query: 123 II 124
           I+
Sbjct: 66  IV 67

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|Q3MFB0|RL24_ANAVT 50S ribosomal protein L24 OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rplX PE=3 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/68 (54%), Positives = 50/68 (73%)

Query: 57  CKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKRE 116
            K ++ P  HK+HVK GDTV+VIAG DKGK+GE+ K     S V+VK +N+KTKHVK ++
Sbjct: 3   SKKDTTPKFHKLHVKTGDTVQVIAGKDKGKVGEVIKALPQLSKVIVKGVNIKTKHVKPQQ 62

Query: 117 EEEQGQII 124
           E E G+I+
Sbjct: 63  EGESGRIV 70

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|B2ITP4|RL24_NOSP7 50S ribosomal protein L24 OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=rplX PE=3 SV=1

 Score = 78.2 bits (191), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 39/68 (57%), Positives = 49/68 (72%)

Query: 57  CKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKRE 116
            K  +  V HKMHVK GDTV+VIAG DKGKIGEI +     S V+VK +N+KTKHVK ++
Sbjct: 3   TKQGTPKVFHKMHVKTGDTVQVIAGKDKGKIGEIVQALPQLSKVIVKGVNIKTKHVKPQQ 62

Query: 117 EEEQGQII 124
           E E G+I+
Sbjct: 63  EGESGRIV 70

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.

Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (taxid: 63737)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	135
449463166	191	PREDICTED: 50S ribosomal protein L24, ch	0.948	0.670	0.772	4e-51
449523692	191	PREDICTED: LOW QUALITY PROTEIN: 50S ribo	0.948	0.670	0.772	4e-51
255563629	193	mitochondrial ribosomal protein L24, put	0.962	0.673	0.748	1e-50
351723593	194	uncharacterized protein LOC100306643 [Gl	0.918	0.639	0.744	3e-47
224124188	194	predicted protein [Populus trichocarpa]	0.962	0.670	0.778	8e-46
351725277	193	uncharacterized protein LOC100500009 [Gl	0.948	0.663	0.706	3e-45
400989	187	RecName: Full=50S ribosomal protein L24,	0.918	0.663	0.677	4e-42
302143191	236	unnamed protein product [Vitis vinifera]	0.955	0.546	0.746	4e-39
225461164	191	PREDICTED: 50S ribosomal protein L24, ch	0.955	0.675	0.746	4e-39
357452635	194	50S ribosomal protein L24 [Medicago trun	0.948	0.659	0.736	2e-38

>gi|449463166|ref|XP_004149305.1| PREDICTED: 50S ribosomal protein L24, chloroplastic-like [Cucumis sativus]

 Score =  205 bits (522), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 102/132 (77%), Positives = 117/132 (88%), Gaps = 4/132 (3%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRLSFPSL--SPITVKPTDKPCLIVVRLKRWERKECK 58
           MAAMAALQSSMT+LS+SSNSF GQRL  P++  +PIT K  +KPCLIV++LKRWERKECK
Sbjct: 1   MAAMAALQSSMTALSLSSNSFLGQRLPPPTIYAAPITSK--EKPCLIVMKLKRWERKECK 58

Query: 59  PNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEE 118
           PNSLPV+HKMHVK GDTVKVIAG DKGKIGEITK+F+HNS V+V +INLKTKHVK REEE
Sbjct: 59  PNSLPVVHKMHVKIGDTVKVIAGRDKGKIGEITKIFKHNSKVVVNEINLKTKHVKSREEE 118

Query: 119 EQGQIIKVYSLI 130
           EQGQIIK+ + I
Sbjct: 119 EQGQIIKIEAPI 130

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449523692|ref|XP_004168857.1| PREDICTED: LOW QUALITY PROTEIN: 50S ribosomal protein L24, chloroplastic-like [Cucumis sativus]

 Score =  205 bits (522), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 102/132 (77%), Positives = 117/132 (88%), Gaps = 4/132 (3%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRLSFPSL--SPITVKPTDKPCLIVVRLKRWERKECK 58
           MAAMAALQSSMT+LS+SSNSF GQRL  P++  +PIT K  +KPCLIV++LKRWERKECK
Sbjct: 1   MAAMAALQSSMTALSLSSNSFLGQRLPPPTIYAAPITSK--EKPCLIVMKLKRWERKECK 58

Query: 59  PNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEE 118
           PNSLPV+HKMHVK GDTVKVIAG DKGKIGEITK+F+HNS V+V +INLKTKHVK REEE
Sbjct: 59  PNSLPVVHKMHVKIGDTVKVIAGRDKGKIGEITKIFKHNSKVVVNEINLKTKHVKSREEE 118

Query: 119 EQGQIIKVYSLI 130
           EQGQIIK+ + I
Sbjct: 119 EQGQIIKIEAPI 130

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563629|ref|XP_002522816.1| mitochondrial ribosomal protein L24, putative [Ricinus communis] gi|223537900|gb|EEF39514.1| mitochondrial ribosomal protein L24, putative [Ricinus communis]

 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 98/131 (74%), Positives = 113/131 (86%), Gaps = 1/131 (0%)

Query: 1   MAAMAALQSSMTSLSISSN-SFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKP 59
           MAAMAALQS+MTSLSISSN +FFGQRLSFPS +   VK  D  CLIV R+KRWERK+CKP
Sbjct: 1   MAAMAALQSAMTSLSISSNNTFFGQRLSFPSFTSTQVKRPDNSCLIVARIKRWERKKCKP 60

Query: 60  NSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE 119
           NSLP+LHKMHVK GDTVKVIAG DKGK+GE+TK+FRHNS+V++ +INLKTKHVK REE E
Sbjct: 61  NSLPILHKMHVKLGDTVKVIAGDDKGKVGEVTKIFRHNSSVVINEINLKTKHVKSREEGE 120

Query: 120 QGQIIKVYSLI 130
            GQIIK+ + I
Sbjct: 121 PGQIIKIEAPI 131

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723593|ref|NP_001238052.1| uncharacterized protein LOC100306643 [Glycine max] gi|255629161|gb|ACU14925.1| unknown [Glycine max]

 Score =  192 bits (489), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 96/129 (74%), Positives = 110/129 (85%), Gaps = 5/129 (3%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRLS---FPSLSPITVKPTDKPCLIVVRLKRWERKEC 57
           MAAMAALQSSM  LS+SSNSF GQRLS    PSL P   K T+K C IV+RLKRWERKEC
Sbjct: 1   MAAMAALQSSMVGLSLSSNSFLGQRLSPITLPSLLP--GKSTEKQCPIVMRLKRWERKEC 58

Query: 58  KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 117
           KPNSLP+LHKMHVK GDTV+VI+G ++GK+GEITK+F+HNSTV+VKD+NLKTKHVK REE
Sbjct: 59  KPNSLPILHKMHVKLGDTVQVISGRERGKVGEITKIFKHNSTVIVKDLNLKTKHVKSREE 118

Query: 118 EEQGQIIKV 126
            E GQIIK+
Sbjct: 119 GEPGQIIKI 127

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124188|ref|XP_002319267.1| predicted protein [Populus trichocarpa] gi|118484624|gb|ABK94184.1| unknown [Populus trichocarpa] gi|222857643|gb|EEE95190.1| predicted protein [Populus trichocarpa]

 Score =  187 bits (476), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 102/131 (77%), Positives = 112/131 (85%), Gaps = 1/131 (0%)

Query: 1   MAAMAALQSSM-TSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKP 59
           MAAMAALQSSM T    SSNSFFGQRLS PSLS   VK  +KPCLIVV++KRWERKECK 
Sbjct: 1   MAAMAALQSSMATLSLSSSNSFFGQRLSLPSLSFPQVKSPEKPCLIVVKIKRWERKECKE 60

Query: 60  NSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE 119
           NSLPVLHKMHVK GDT++VIAG DKGKIGEITK+FRHNSTV+VK+INLKTKHVK REE E
Sbjct: 61  NSLPVLHKMHVKVGDTIQVIAGDDKGKIGEITKIFRHNSTVVVKEINLKTKHVKSREEGE 120

Query: 120 QGQIIKVYSLI 130
            GQIIK+ + I
Sbjct: 121 PGQIIKIEAPI 131

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725277|ref|NP_001235551.1| uncharacterized protein LOC100500009 [Glycine max] gi|255628481|gb|ACU14585.1| unknown [Glycine max]

 Score =  186 bits (471), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 94/133 (70%), Positives = 109/133 (81%), Gaps = 5/133 (3%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRL---SFPSLSPITVKPTDKPCLIVVRLKRWERKEC 57
           MAAMAALQSSM  LS+SS SF GQ L   + PSL P   K T+K C IV+RLKRWERKEC
Sbjct: 1   MAAMAALQSSMAGLSLSSKSFLGQLLPPITLPSLLP--GKSTEKQCPIVMRLKRWERKEC 58

Query: 58  KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 117
           KPNSLP+LHKMHVK GDTV+VI+G ++GK+GEITK+F+HNSTV+VKD+NLKTKHVK REE
Sbjct: 59  KPNSLPILHKMHVKLGDTVQVISGRERGKVGEITKIFKHNSTVIVKDLNLKTKHVKSREE 118

Query: 118 EEQGQIIKVYSLI 130
            E GQIIK+   I
Sbjct: 119 GEPGQIIKIEGPI 131

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|400989|sp|Q02764.1|RK24_TOBAC RecName: Full=50S ribosomal protein L24, chloroplastic; AltName: Full=CL24; Flags: Precursor gi|170273|gb|AAA34086.1| ribosomal protein L24 [Nicotiana tabacum] gi|170324|gb|AAA34114.1| ribosomal protein L24 [Nicotiana tabacum]

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 86/127 (67%), Positives = 100/127 (78%), Gaps = 3/127 (2%)

Query: 4   MAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLP 63
           MAALQSS   LS    SFFGQR S P   P  VK T+ PCLI  +LKRWERKECKPNSLP
Sbjct: 1   MAALQSSFAGLS---TSFFGQRFSPPLSLPPLVKSTEGPCLIQAKLKRWERKECKPNSLP 57

Query: 64  VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQI 123
           VLHKMHVK GDTVK+I+G DKGK+GEIT++ +HNS V+VKD+NLKTKHVK R E+E GQI
Sbjct: 58  VLHKMHVKLGDTVKIISGHDKGKVGEITEIIKHNSKVVVKDVNLKTKHVKSRSEDEPGQI 117

Query: 124 IKVYSLI 130
           +K+ + I
Sbjct: 118 VKIEAPI 124

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143191|emb|CBI20486.3| unnamed protein product [Vitis vinifera]

 Score =  166 bits (419), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 97/130 (74%), Positives = 110/130 (84%), Gaps = 1/130 (0%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPN 60
           MAAMAALQSS TSLS+SSNSF GQ  S P L P   K T+KPC IV+RLKRWERKECKPN
Sbjct: 46  MAAMAALQSSFTSLSLSSNSFLGQPFS-PLLYPSLAKSTEKPCPIVMRLKRWERKECKPN 104

Query: 61  SLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQ 120
           SLPVLHKMHVK GDTVK+I+G +KG+ GEI+K+FRHNSTV+VKDINLKTKHVK R E+E 
Sbjct: 105 SLPVLHKMHVKVGDTVKIISGREKGRTGEISKIFRHNSTVVVKDINLKTKHVKGRGEDEP 164

Query: 121 GQIIKVYSLI 130
           GQIIK+ + I
Sbjct: 165 GQIIKIEAPI 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461164|ref|XP_002282889.1| PREDICTED: 50S ribosomal protein L24, chloroplastic isoform 1 [Vitis vinifera] gi|359493940|ref|XP_003634697.1| PREDICTED: 50S ribosomal protein L24, chloroplastic isoform 2 [Vitis vinifera] gi|359493942|ref|XP_003634698.1| PREDICTED: 50S ribosomal protein L24, chloroplastic isoform 3 [Vitis vinifera] gi|147860928|emb|CAN78749.1| hypothetical protein VITISV_002445 [Vitis vinifera]

 Score =  166 bits (419), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 97/130 (74%), Positives = 110/130 (84%), Gaps = 1/130 (0%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPN 60
           MAAMAALQSS TSLS+SSNSF GQ  S P L P   K T+KPC IV+RLKRWERKECKPN
Sbjct: 1   MAAMAALQSSFTSLSLSSNSFLGQPFS-PLLYPSLAKSTEKPCPIVMRLKRWERKECKPN 59

Query: 61  SLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQ 120
           SLPVLHKMHVK GDTVK+I+G +KG+ GEI+K+FRHNSTV+VKDINLKTKHVK R E+E 
Sbjct: 60  SLPVLHKMHVKVGDTVKIISGREKGRTGEISKIFRHNSTVVVKDINLKTKHVKGRGEDEP 119

Query: 121 GQIIKVYSLI 130
           GQIIK+ + I
Sbjct: 120 GQIIKIEAPI 129

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357452635|ref|XP_003596594.1| 50S ribosomal protein L24 [Medicago truncatula] gi|355485642|gb|AES66845.1| 50S ribosomal protein L24 [Medicago truncatula] gi|388513937|gb|AFK45030.1| unknown [Medicago truncatula]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/129 (73%), Positives = 112/129 (86%), Gaps = 1/129 (0%)

Query: 3   AMAALQSSMTSLSISSNSFFGQRLSFPSLSPITV-KPTDKPCLIVVRLKRWERKECKPNS 61
           AMA+LQSSMTSLS+SSNSFFGQ LS  +LSP+   KPTDK C IV++LKRWERKECKPNS
Sbjct: 5   AMASLQSSMTSLSLSSNSFFGQPLSPITLSPLLPGKPTDKQCRIVMKLKRWERKECKPNS 64

Query: 62  LPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQG 121
           LPVLHK+HVK GDTVKVI+G +KG+IGE+TK+F+HNST++VKDINLKTKHVK R+E E G
Sbjct: 65  LPVLHKLHVKVGDTVKVISGHEKGQIGEVTKIFKHNSTIIVKDINLKTKHVKSRQEGEPG 124

Query: 122 QIIKVYSLI 130
           QI K+   I
Sbjct: 125 QINKIEGPI 133

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	135
TAIR|locus:2172154	198	RPL24 "plastid ribosomal prote	0.933	0.636	0.635	2e-40
TIGR_CMR|BA_0121	103	BA_0121 "ribosomal protein L24	0.422	0.553	0.473	1.1e-07
TIGR_CMR|GSU_2846	108	GSU_2846 "ribosomal protein L2	0.437	0.546	0.355	6.1e-07
TIGR_CMR|CBU_0249	107	CBU_0249 "ribosomal protein L2	0.407	0.514	0.473	7.8e-07
TIGR_CMR|CHY_2298	107	CHY_2298 "ribosomal protein L2	0.437	0.551	0.389	2.6e-06
TIGR_CMR|DET_0485	103	DET_0485 "ribosomal protein L2	0.429	0.563	0.379	3.4e-06
TIGR_CMR|CJE_1864	77	CJE_1864 "ribosomal protein L2	0.429	0.753	0.379	4.3e-06
TAIR|locus:504954880	159	AT5G23535 [Arabidopsis thalian	0.362	0.308	0.428	3e-05
GENEDB_PFALCIPARUM|PFF0245w	194	PFF0245w "50S ribosomal subuni	0.437	0.304	0.377	5.6e-05
UNIPROTKB|C6KSP8	194	PFF0245w "Mitochondrial riboso	0.437	0.304	0.377	5.6e-05

TAIR|locus:2172154 RPL24 "plastid ribosomal protein L24" [Arabidopsis thaliana (taxid:3702)]

 Score = 430 (156.4 bits), Expect = 2.0e-40, P = 2.0e-40
 Identities = 82/129 (63%), Positives = 99/129 (76%)

Query:     1 MAAMAALQXXXXXXXXX-XXXFFGQRLSFP-SLSPIT-VKPTDKPCLIVVRLKRWERKEC 57
             MA M+ALQ             F GQRL  P SLS  + VKP + PCL++ +LKRWERKEC
Sbjct:     1 MATMSALQSSFTSLSLSPSSSFLGQRLISPISLSVTSPVKPAENPCLVLAKLKRWERKEC 60

Query:    58 KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 117
             KPNSLP+LHKMHVK GDTVKVI+G DKGKIGE+TK+F HNST+++KD+NLKTKH+K REE
Sbjct:    61 KPNSLPILHKMHVKFGDTVKVISGRDKGKIGEVTKIFTHNSTIVIKDVNLKTKHMKSREE 120

Query:   118 EEQGQIIKV 126
              E GQI+K+
Sbjct:   121 GEPGQIVKI 129

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0015934 "large ribosomal subunit" evidence=ISS

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0032544 "plastid translation" evidence=IMP

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

TIGR_CMR|BA_0121 BA_0121 "ribosomal protein L24" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 27/57 (47%), Positives = 34/57 (59%)

Query:    68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
             MHVK GD V+VI G DKGK G I   F   + V+V+ +N+  KH K  +   QG II
Sbjct:     1 MHVKKGDKVQVITGKDKGKQGVILVAFPKQNRVIVEGVNIVKKHSKPSQLNPQGGII 57

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TIGR_CMR|GSU_2846 GSU_2846 "ribosomal protein L24" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 114 (45.2 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query:    67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
             K H+K GDTV V+ G DK K G + ++      V+V+ +N+  +H + R  E  G + K
Sbjct:     5 KFHIKKGDTVSVVTGKDKSKTGTVLRILPKRDGVLVEGLNIVKRHTRARGNEPGGIVEK 63

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|CBU_0249 CBU_0249 "ribosomal protein L24" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 113 (44.8 bits), Expect = 7.8e-07, P = 7.8e-07
 Identities = 27/57 (47%), Positives = 37/57 (64%)

Query:    70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKR-EEEEQGQIIK 125
             +K  DTV VI G DKG+ G++ KV   NS ++V+ INL  KHVK    + EQG I++
Sbjct:     6 IKKDDTVIVITGRDKGRQGKVLKVLP-NSRLLVEGINLVKKHVKPNPNKNEQGGILE 61

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CHY_2298 CHY_2298 "ribosomal protein L24" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 108 (43.1 bits), Expect = 2.6e-06, P = 2.6e-06
 Identities = 23/59 (38%), Positives = 36/59 (61%)

Query:    67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
             K+ VK GD V VIAG DK K G+I +V    + V+V+ +N+  +H +   +  QG I++
Sbjct:     3 KLKVKKGDMVLVIAGKDKDKKGKIVQVLPKENRVVVEGVNIVKRHTRPNPKLPQGGIVE 61

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TIGR_CMR|DET_0485 DET_0485 "ribosomal protein L24" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 107 (42.7 bits), Expect = 3.4e-06, P = 3.4e-06
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query:    68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
             M +K  D V VIAG DKGK G++   F     V+V+ +N+  +H + R + +Q  II+
Sbjct:     1 MRLKKNDNVLVIAGKDKGKTGKVRYAFPRTDRVLVEGVNMIKRHSRARGQAKQAGIIE 58

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

TIGR_CMR|CJE_1864 CJE_1864 "ribosomal protein L24" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 106 (42.4 bits), Expect = 4.3e-06, P = 4.3e-06
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query:    67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
             K+ +K GD+VKVI G DKGK G++  V+     V+V+   +  K +K  E+   G  I
Sbjct:     4 KLKIKKGDSVKVITGDDKGKTGKVLAVYPKTLKVVVEGCKIAKKAIKPSEKNPNGGFI 61

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TAIR|locus:504954880 AT5G23535 [Arabidopsis thaliana (taxid:3702)]

 Score = 98 (39.6 bits), Expect = 3.0e-05, P = 3.0e-05
 Identities = 21/49 (42%), Positives = 29/49 (59%)

Query:    73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQG 121
             GD V +I G DKG+ G I +V R  + V+V+  NL  KH+K   + E G
Sbjct:    18 GDNVMIIRGKDKGETGTIKRVIRSQNRVIVEGKNLIKKHIKGGPDHEGG 66

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

GENEDB_PFALCIPARUM|PFF0245w PFF0245w "50S ribosomal subunit L24, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 98 (39.6 bits), Expect = 5.6e-05, P = 5.6e-05
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query:    55 KECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 114
             K  KP ++  + K  ++ GD VKVI+G DKGKIGE+    +  + V VK  N++   V  
Sbjct:    33 KIIKPRNIIKMWK--IRKGDEVKVISGKDKGKIGEVLSCDKFRNMVKVKGCNMRKLFVDN 90

Query:   115 R 115
             +
Sbjct:    91 K 91

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISS

UNIPROTKB|C6KSP8 PFF0245w "Mitochondrial ribosomal protein L24, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 98 (39.6 bits), Expect = 5.6e-05, P = 5.6e-05
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query:    55 KECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 114
             K  KP ++  + K  ++ GD VKVI+G DKGKIGE+    +  + V VK  N++   V  
Sbjct:    33 KIIKPRNIIKMWK--IRKGDEVKVISGKDKGKIGEVLSCDKFRNMVKVKGCNMRKLFVDN 90

Query:   115 R 115
             +
Sbjct:    91 K 91

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P11893	RK24_PEA	No assigned EC number	0.7286	0.9481	0.6597	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	135
PRK00004	105	PRK00004, rplX, 50S ribosomal protein L24; Reviewe	3e-20
CHL00141	83	CHL00141, rpl24, ribosomal protein L24; Validated	5e-20
TIGR01079	104	TIGR01079, rplX_bact, ribosomal protein L24, bacte	2e-18
cd06089	65	cd06089, KOW_RPL26, KOW motif of Ribosomal Protein	7e-18
COG0198	104	COG0198, RplX, Ribosomal protein L24 [Translation,	6e-14
PRK12281	76	PRK12281, rplX, 50S ribosomal protein L24; Reviewe	8e-14
pfam00467	32	pfam00467, KOW, KOW motif	2e-06
smart00739	28	smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) m	3e-04
cd00380	49	cd00380, KOW, KOW: an acronym for the authors' sur	3e-04
PRK01191	120	PRK01191, rpl24p, 50S ribosomal protein L24P; Vali	4e-04

>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed

 Score = 79.0 bits (196), Expect = 3e-20
 Identities = 28/60 (46%), Positives = 38/60 (63%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKV 126
            M +K GDTV VIAG DKGK G++ KV    + V+V+ +N+  KH K  +E  QG II+ 
Sbjct: 2   MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEK 61

Length = 105

>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated

 Score = 77.8 bits (192), Expect = 5e-20
 Identities = 33/59 (55%), Positives = 46/59 (77%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
           KMHVK GDTVK+I+G DKGKIGE+ K+ + ++ V+VK IN+K KH+K  +E E G+I +
Sbjct: 6   KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQ 64

Length = 83

>gnl|CDD|233263 TIGR01079, rplX_bact, ribosomal protein L24, bacterial/organelle

 Score = 74.2 bits (183), Expect = 2e-18
 Identities = 29/60 (48%), Positives = 40/60 (66%), Gaps = 1/60 (1%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE-EEQGQIIK 125
           KM +K GDTVKVI+G DKGK G++ KV    + V+V+ +N+  KHVK +     QG II+
Sbjct: 1   KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIE 60

This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 104

>gnl|CDD|240513 cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26

 Score = 71.8 bits (177), Expect = 7e-18
 Identities = 28/60 (46%), Positives = 39/60 (65%)

Query: 73  GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY 132
           GD V+VI G DKGK G++ KV R  + V+V+ +N+  KHVK  +E  QG II+V + I  
Sbjct: 1   GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIHI 60

RPL26 and its bacterial paralogs RPL24 have a KOW motif at their N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage. Length = 65

>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]

 Score = 62.7 bits (153), Expect = 6e-14
 Identities = 30/59 (50%), Positives = 39/59 (66%), Gaps = 2/59 (3%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
           KM VK GDTVKVIAG DKGK G++ KV      V+V+ +N+  KH+K  +E  +G II 
Sbjct: 2   KMKVKKGDTVKVIAGKDKGKEGKVLKVLPK--KVVVEGVNVVKKHIKPSQENPEGGIIN 58

Length = 104

>gnl|CDD|183399 PRK12281, rplX, 50S ribosomal protein L24; Reviewed

 Score = 61.6 bits (150), Expect = 8e-14
 Identities = 23/58 (39%), Positives = 34/58 (58%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
           K+ VK GD VKVIAG DKGK G++  V    + V+V+ + +  K +K  ++   G  I
Sbjct: 4   KLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFI 61

Length = 76

>gnl|CDD|144165 pfam00467, KOW, KOW motif

 Score = 41.3 bits (98), Expect = 2e-06
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 73  GDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103
           GD V+VI+G  KGK G++ +V    + V V+
Sbjct: 2   GDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32

This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG. Length = 32

>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif

 Score = 35.4 bits (83), Expect = 3e-04
 Identities = 13/28 (46%), Positives = 19/28 (67%)

Query: 69 HVKAGDTVKVIAGCDKGKIGEITKVFRH 96
            + GDTV+VIAG  KGK+G++ +V   
Sbjct: 1  KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28

Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54. Length = 28

>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese)

 Score = 36.0 bits (84), Expect = 3e-04
 Identities = 12/42 (28%), Positives = 17/42 (40%)

Query: 73  GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 114
           GD V+V+ G  KG+ G +  +      V VK          K
Sbjct: 1   GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGAELK 42

KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues. Length = 49

>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 6/56 (10%)

Query: 54  RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKT 109
           R++    SLPV      + GDTVKV+ G  KG+ G++ +V      + V+ + +K 
Sbjct: 36  REKYGIRSLPV------RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKK 85

Length = 120

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	135
KOG1708	236	consensus Mitochondrial/chloroplast ribosomal prot	99.97
PRK12281	76	rplX 50S ribosomal protein L24; Reviewed	99.93
CHL00141	83	rpl24 ribosomal protein L24; Validated	99.91
PRK00004	105	rplX 50S ribosomal protein L24; Reviewed	99.9
TIGR01079	104	rplX_bact ribosomal protein L24, bacterial/organel	99.9
COG0198	104	RplX Ribosomal protein L24 [Translation, ribosomal	99.89
PRK01191	120	rpl24p 50S ribosomal protein L24P; Validated	99.72
PTZ00194	143	60S ribosomal protein L26; Provisional	99.71
TIGR01080	114	rplX_A_E ribosomal protein L24p/L26e, archaeal/euk	99.68
PF00467	32	KOW: KOW motif; InterPro: IPR005824 Ribosomes are	98.89
smart00739	28	KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif i	98.01
KOG3401	145	consensus 60S ribosomal protein L26 [Translation,	97.78
TIGR00405	145	L26e_arch ribosomal protein L24p/L26e, archaeal. T	97.37
PRK05609	181	nusG transcription antitermination protein NusG; V	97.34
TIGR00922	172	nusG transcription termination/antitermination fac	97.28
PRK08559	153	nusG transcription antitermination protein NusG; V	97.25
COG0250	178	NusG Transcription antiterminator [Transcription]	97.06
TIGR01955	159	RfaH transcriptional activator RfaH. This model re	96.75
PRK09014	162	rfaH transcriptional activator RfaH; Provisional	96.61
TIGR01956	258	NusG_myco NusG family protein. This model represen	96.35
PRK04333	84	50S ribosomal protein L14e; Validated	94.69
KOG1999	1024	consensus RNA polymerase II transcription elongati	91.45
PTZ00065	130	60S ribosomal protein L14; Provisional	90.93
PRK04313	237	30S ribosomal protein S4e; Validated	87.86
KOG1999	1024	consensus RNA polymerase II transcription elongati	86.45
PTZ00471	134	60S ribosomal protein L27; Provisional	85.9
COG2163	125	RPL14A Ribosomal protein L14E/L6E/L27E [Translatio	84.8
COG5164	607	SPT5 Transcription elongation factor [Transcriptio	84.12
PF09953	57	DUF2187: Uncharacterized protein conserved in bact	83.28
PRK06531	113	yajC preprotein translocase subunit YajC; Validate	82.21
PF03144	74	GTP_EFTU_D2: Elongation factor Tu domain 2; InterP	80.48

>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=3.2e-31  Score=215.23  Aligned_cols=134  Identities=42%  Similarity=0.543  Sum_probs=124.4

Q ss_pred             Chhhhhhhhhcceeeecc-ccccCccc-CCCCCCC-ccccCCCCceeeeeeeeeeeeeecCCCCCcccccceeeeCCEEE
Q 032704            1 MAAMAALQSSMTSLSISS-NSFFGQRL-SFPSLSP-ITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVK   77 (135)
Q Consensus         1 ~~~~~~~~~~~~~l~~~~-~~f~g~~l-~~~~~~~-~~~~~~~~~~~~~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~   77 (135)
                      |+.|+||||++++||++- ..|.+|.+ +|.++.+ .+.+..+++|+.....++|+|+.|.++..+...+|+++.||+|+
T Consensus         1 M~ts~aL~s~l~s~s~lPs~y~er~y~isP~~~~~~~pr~~adk~~~~~qk~~~w~rrr~~~~e~i~d~dw~ff~GDtVe   80 (236)
T KOG1708|consen    1 MRTSSALASSLTSLSLLPSSYFERQYLISPISLSVTSPRKVADKRCLVLQKNKPWERRRCVPVEPIIDEDWHFFFGDTVE   80 (236)
T ss_pred             CchHHHHHHHhhhhhcCCHHHhhceeeeccccccccCCCChhhhhhhHHhhcCccccccCCCCCCccccceeEecCCEEE
Confidence            889999999999999865 66778888 5767774 44788899999999999999999999999999999999999999


Q ss_pred             EEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEEe
Q 032704           78 VIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFI  134 (135)
Q Consensus        78 VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S~  134 (135)
                      ||.|+||||+|+|++|++++|+|+|+|+|.+.+|++...++.+|.|+..|+|||+|-
T Consensus        81 VlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk  137 (236)
T KOG1708|consen   81 VLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSK  137 (236)
T ss_pred             EEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecc
Confidence            999999999999999999999999999999999999998999999999999999984

>PRK12281 rplX 50S ribosomal protein L24; Reviewed

Probab=99.93  E-value=3.8e-26  Score=159.21  Aligned_cols=68  Identities=35%  Similarity=0.520  Sum_probs=65.8

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      .+|+|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||++++++|+|+++|+|||+|
T Consensus         3 ~~~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~S   70 (76)
T PRK12281          3 VKLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHIS   70 (76)
T ss_pred             ccccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHH
Confidence            56899999999999999999999999999999999999999999999999888899999999999997

>CHL00141 rpl24 ribosomal protein L24; Validated

Probab=99.91  E-value=2.3e-24  Score=152.29  Aligned_cols=68  Identities=50%  Similarity=0.757  Sum_probs=65.3

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      .+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+|++++++.|+++++|+|||+|
T Consensus         5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~S   72 (83)
T CHL00141          5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSS   72 (83)
T ss_pred             eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHH
Confidence            46789999999999999999999999999999999999999999999999888899999999999987

>PRK00004 rplX 50S ribosomal protein L24; Reviewed

Probab=99.90  E-value=4.1e-24  Score=156.23  Aligned_cols=67  Identities=43%  Similarity=0.594  Sum_probs=65.3

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      +|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+|+++++++|+|++.|+|||||
T Consensus         2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~S   68 (105)
T PRK00004          2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHIS   68 (105)
T ss_pred             CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHH
Confidence            6899999999999999999999999999999999999999999999999888999999999999997

>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle

Probab=99.90  E-value=7.5e-24  Score=155.01  Aligned_cols=67  Identities=45%  Similarity=0.650  Sum_probs=64.1

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccC-CceEEEEeeeeeEE
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE-QGQIIKVYSLICYF  133 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~-~GgIi~~E~PIh~S  133 (135)
                      +++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||+++++ +|+|+++|+|||||
T Consensus         1 ~~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~S   68 (104)
T TIGR01079         1 KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHIS   68 (104)
T ss_pred             CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHH
Confidence            35899999999999999999999999999999999999999999999998777 89999999999997

This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.

>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=1.8e-23  Score=153.91  Aligned_cols=65  Identities=48%  Similarity=0.661  Sum_probs=62.6

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      +++|++||+|.||+|+|||++|+|++|++++  |+|||||+.++|.||+++++.|||+++|+|||+|
T Consensus         2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~S   66 (104)
T COG0198           2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHIS   66 (104)
T ss_pred             CcceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHH
Confidence            5789999999999999999999999999998  9999999999999988888889999999999997

>PRK01191 rpl24p 50S ribosomal protein L24P; Validated

Probab=99.72  E-value=5.7e-18  Score=127.47  Aligned_cols=64  Identities=30%  Similarity=0.373  Sum_probs=56.2

Q ss_pred             eeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704           53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY  132 (135)
Q Consensus        53 er~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~  132 (135)
                      .|++|+.+.      |+|++||+|+||+|+|||++|+|++|++++++|+|||||+.+.         +|  +++|+|||+
T Consensus        35 Lr~~y~ir~------~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~---------~G--~~~e~pIh~   97 (120)
T PRK01191         35 LREKYGIRS------LPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA---------DG--TEVPRPIHP   97 (120)
T ss_pred             HHHHhCCcc------ceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC---------CC--eEEEcccch
Confidence            466776554      5699999999999999999999999999999999999999872         35  689999999


Q ss_pred             E
Q 032704          133 F  133 (135)
Q Consensus       133 S  133 (135)
                      |
T Consensus        98 S   98 (120)
T PRK01191         98 S   98 (120)
T ss_pred             h
Confidence            7

>PTZ00194 60S ribosomal protein L26; Provisional

Probab=99.71  E-value=6.6e-18  Score=130.36  Aligned_cols=64  Identities=27%  Similarity=0.380  Sum_probs=58.5

Q ss_pred             eeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704           53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY  132 (135)
Q Consensus        53 er~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~  132 (135)
                      .|.+|+.++++      |++||+|+||+|+|||++|+|++|++++++|+|||||+.++|.++           .|+|||+
T Consensus        36 Lr~k~~~Rs~~------IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~-----------~e~PIh~   98 (143)
T PTZ00194         36 LRAKYNVRSMP------VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP-----------VQIGIHP   98 (143)
T ss_pred             HHHHhCCccce------eecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE-----------eecCcCc
Confidence            46778877764      899999999999999999999999999999999999999999875           6999998


Q ss_pred             E
Q 032704          133 F  133 (135)
Q Consensus       133 S  133 (135)
                      |
T Consensus        99 S   99 (143)
T PTZ00194         99 S   99 (143)
T ss_pred             h
Confidence            7

>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic

Probab=99.68  E-value=4.4e-17  Score=121.51  Aligned_cols=71  Identities=24%  Similarity=0.297  Sum_probs=62.0

Q ss_pred             eeeeeeeeeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEE
Q 032704           46 VVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK  125 (135)
Q Consensus        46 ~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~  125 (135)
                      ...+-+|.|++|+++..      +|++||+|+||+|+|||++|+|++|++++++|+|||||+.+    ++     |  ++
T Consensus        24 ~a~ls~elr~~y~~r~~------~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~~-----G--~~   86 (114)
T TIGR01080        24 SAPLSKELREKYGKRAL------PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----VN-----G--TE   86 (114)
T ss_pred             ecccCHHHHHHcCcccc------eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----CC-----C--eE
Confidence            34566788999986665      58999999999999999999999999999999999999987    22     4  78


Q ss_pred             EeeeeeEE
Q 032704          126 VYSLICYF  133 (135)
Q Consensus       126 ~E~PIh~S  133 (135)
                      .|+|||+|
T Consensus        87 ~e~pIh~S   94 (114)
T TIGR01080        87 VPVPIHPS   94 (114)
T ss_pred             EEeeechH
Confidence            99999987

This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.

>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.89  E-value=3e-09  Score=62.63  Aligned_cols=32  Identities=53%  Similarity=0.709  Sum_probs=30.8

Q ss_pred             eCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        72 kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      +||.|+|++|+++|++|+|++|++++++|+||
T Consensus         1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve   32 (32)
T PF00467_consen    1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE   32 (32)
T ss_dssp             TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred             CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence            59999999999999999999999999999986

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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....

>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif

Probab=98.01  E-value=9.4e-06  Score=44.87  Aligned_cols=26  Identities=50%  Similarity=0.704  Sum_probs=24.4

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEc
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFR   95 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r   95 (135)
                      +.+||.|+|+.|+++|++|+|.+++.
T Consensus         2 ~~~G~~V~I~~G~~~g~~g~i~~i~~   27 (28)
T smart00739        2 FEVGDTVRVIAGPFKGKVGKVLEVDG   27 (28)
T ss_pred             CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence            57999999999999999999999975

Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.

>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]

Probab=97.78  E-value=1.6e-05  Score=62.06  Aligned_cols=48  Identities=27%  Similarity=0.632  Sum_probs=42.7

Q ss_pred             eeecCCCCCcccccceeeeCCEEEEEecCCCC-eEeEEEEEEccCCEEEEeccce
Q 032704           54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVKDINL  107 (135)
Q Consensus        54 r~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKG-K~G~V~~V~r~~~~ViVegvN~  107 (135)
                      |.+++-.++|      |+.+|+|.|..|.++| ++|+|++|++++..+++|.|..
T Consensus        39 R~~y~vrs~p------ir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~   87 (145)
T KOG3401|consen   39 RQKYNVRSMP------IRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQR   87 (145)
T ss_pred             HHHhCccccc------eeeccEEEEEeccccccccceehhhhhhhheeeeEeEEE
Confidence            6667766665      8999999999999999 9999999999999999998765

>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal

Probab=97.37  E-value=0.00036  Score=52.17  Aligned_cols=38  Identities=29%  Similarity=0.434  Sum_probs=34.7

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccce
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL  107 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~  107 (135)
                      +.+||.|.|++|+++|..|+|.+++.++..|.|+-.+.
T Consensus        87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~  124 (145)
T TIGR00405        87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEA  124 (145)
T ss_pred             cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEc
Confidence            78999999999999999999999999888998886553

This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.

>PRK05609 nusG transcription antitermination protein NusG; Validated

Probab=97.34  E-value=0.00038  Score=53.15  Aligned_cols=36  Identities=25%  Similarity=0.288  Sum_probs=32.5

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..+++||+|.|++|+++|.+|+|.+++++++++.|.
T Consensus       125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~  160 (181)
T PRK05609        125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL  160 (181)
T ss_pred             cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE
Confidence            447899999999999999999999999888888765

>TIGR00922 nusG transcription termination/antitermination factor NusG

Probab=97.28  E-value=0.00047  Score=52.46  Aligned_cols=36  Identities=22%  Similarity=0.282  Sum_probs=32.2

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..+++||+|.|+.|+++|.+|+|.+++++++++.|.
T Consensus       118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~  153 (172)
T TIGR00922       118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS  153 (172)
T ss_pred             cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence            347899999999999999999999999888887765

Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).

>PRK08559 nusG transcription antitermination protein NusG; Validated

Probab=97.25  E-value=0.00053  Score=52.44  Aligned_cols=42  Identities=29%  Similarity=0.381  Sum_probs=38.0

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEE
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTK  110 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kk  110 (135)
                      .+.+||.|.|++|+++|..|.|.+++.+++++.|+-++...+
T Consensus        94 ~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~  135 (153)
T PRK08559         94 GIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVP  135 (153)
T ss_pred             CCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcce
Confidence            479999999999999999999999999999999997776544

>COG0250 NusG Transcription antiterminator [Transcription]

Probab=97.06  E-value=0.00094  Score=52.96  Aligned_cols=38  Identities=24%  Similarity=0.366  Sum_probs=34.9

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      .+..+.+||.|.|++|+++|-.|+|.+|+.+++++.|+
T Consensus       120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~  157 (178)
T COG0250         120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVE  157 (178)
T ss_pred             ccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEE
Confidence            45678999999999999999999999999999988776

>TIGR01955 RfaH transcriptional activator RfaH

Probab=96.75  E-value=0.0024  Score=47.84  Aligned_cols=35  Identities=17%  Similarity=0.102  Sum_probs=29.6

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..+.+||+|.|+.|+++|-.|.|.+++ .++++.|.
T Consensus       107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~-~~~r~~v~  141 (159)
T TIGR01955       107 TLPYKGDKVRITDGAFAGFEAIFLEPD-GEKRSMLL  141 (159)
T ss_pred             cCCCCCCEEEEeccCCCCcEEEEEEEC-CCceEEEE
Confidence            447899999999999999999999998 45576553

This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.

>PRK09014 rfaH transcriptional activator RfaH; Provisional

Probab=96.61  E-value=0.0032  Score=47.64  Aligned_cols=33  Identities=21%  Similarity=0.198  Sum_probs=28.4

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      +.+||+|.|+.|+++|.+|+|.+++ .++++.|.
T Consensus       110 ~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~  142 (162)
T PRK09014        110 PKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL  142 (162)
T ss_pred             CCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence            6899999999999999999999998 55565543

>TIGR01956 NusG_myco NusG family protein

Probab=96.35  E-value=0.0069  Score=51.11  Aligned_cols=36  Identities=28%  Similarity=0.508  Sum_probs=32.5

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..+.+||.|.|+.|+++|..|+|.+++.+++++.|.
T Consensus       204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl  239 (258)
T TIGR01956       204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE  239 (258)
T ss_pred             cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence            457899999999999999999999999888888775

This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.

>PRK04333 50S ribosomal protein L14e; Validated

Probab=94.69  E-value=0.074  Score=37.84  Aligned_cols=36  Identities=19%  Similarity=0.310  Sum_probs=32.2

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecc
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI  105 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegv  105 (135)
                      .+..|-.|.+..|+|+|+...|+.+.. .++|+|+|-
T Consensus         3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~   38 (84)
T PRK04333          3 AIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGP   38 (84)
T ss_pred             cccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECC
Confidence            478899999999999999999999875 589999887

>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]

Probab=91.45  E-value=0.21  Score=48.97  Aligned_cols=29  Identities=38%  Similarity=0.505  Sum_probs=26.9

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH   96 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~   96 (135)
                      -.|+.||-|+||+|+++|..|.|++|.+.
T Consensus       458 KyF~~GDhVKVi~G~~eG~tGlVvrVe~~  486 (1024)
T KOG1999|consen  458 KYFEPGDHVKVIAGRYEGDTGLVVRVEQG  486 (1024)
T ss_pred             hhccCCCeEEEEeccccCCcceEEEEeCC
Confidence            46899999999999999999999999984

>PTZ00065 60S ribosomal protein L14; Provisional

Probab=90.93  E-value=0.59  Score=36.03  Aligned_cols=35  Identities=26%  Similarity=0.369  Sum_probs=31.9

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecc
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI  105 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegv  105 (135)
                      +-.|=.|.|..|+++||...|..|.- .|+|+|+|=
T Consensus         8 VEiGRVvli~~Gp~~GKL~vIVDIID-~nRvLVDGP   42 (130)
T PTZ00065          8 VEPGRLCLIQYGPDAGKLCFIVDIVT-PTRVLVDGA   42 (130)
T ss_pred             eeeceEEEEecCCCCCCEEEEEEEEc-CCeEEEeCC
Confidence            67888899999999999999999986 579999997

>PRK04313 30S ribosomal protein S4e; Validated

Probab=87.86  E-value=0.94  Score=37.94  Aligned_cols=41  Identities=20%  Similarity=0.393  Sum_probs=34.8

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccC----CEEEEeccc
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKDIN  106 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~----~~ViVegvN  106 (135)
                      .-.++..|-.|.|+.|++-|.+|+|.++.+..    +.|.|++-+
T Consensus       168 ~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~  212 (237)
T PRK04313        168 DHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKD  212 (237)
T ss_pred             EEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCC
Confidence            45678899999999999999999999998655    678888644

>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]

Probab=86.45  E-value=1.9  Score=42.58  Aligned_cols=60  Identities=30%  Similarity=0.402  Sum_probs=41.6

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe----ccc---------ee--------EEEecCCCccCCceEEEEe
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK----DIN---------LK--------TKHVKKREEEEQGQIIKVY  127 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe----gvN---------~~--------kkhvK~~~e~~~GgIi~~E  127 (135)
                      .|.+||.|.|+.|..+|-.|+|..|+-.  .|++.    +++         ++        -|-+...-|+..|-|++.|
T Consensus       407 ~F~~GD~VeV~~Gel~glkG~ve~vdg~--~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe  484 (1024)
T KOG1999|consen  407 LFSPGDAVEVIVGELKGLKGKVESVDGT--IVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVE  484 (1024)
T ss_pred             ccCCCCeEEEeeeeeccceeEEEeccCc--eEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEe
Confidence            3899999999999999999999999854  33322    111         11        1223334567889998888


Q ss_pred             eee
Q 032704          128 SLI  130 (135)
Q Consensus       128 ~PI  130 (135)
                      .-+
T Consensus       485 ~~~  487 (1024)
T KOG1999|consen  485 QGD  487 (1024)
T ss_pred             CCe
Confidence            743

>PTZ00471 60S ribosomal protein L27; Provisional

Probab=85.90  E-value=1.4  Score=34.17  Aligned_cols=41  Identities=27%  Similarity=0.359  Sum_probs=35.4

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccC------CEEEEeccceeEE
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKTK  110 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~------~~ViVegvN~~kk  110 (135)
                      +++|-.|.|++|++.|+...|++.+.++      +.++|-||....+
T Consensus         5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~   51 (134)
T PTZ00471          5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPK   51 (134)
T ss_pred             ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccch
Confidence            6789999999999999999999988776      6899999776443

>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]

Probab=84.80  E-value=1.7  Score=33.23  Aligned_cols=34  Identities=32%  Similarity=0.401  Sum_probs=31.2

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD  104 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg  104 (135)
                      +.+|=.|.|.+|++.|+...|+++.-++ .+++.|
T Consensus         5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~g   38 (125)
T COG2163           5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITG   38 (125)
T ss_pred             ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeC
Confidence            6789999999999999999999999877 888887

>COG5164 SPT5 Transcription elongation factor [Transcription]

Probab=84.12  E-value=0.82  Score=42.35  Aligned_cols=29  Identities=31%  Similarity=0.444  Sum_probs=26.4

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN   97 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~   97 (135)
                      .+++||.|+||.|.+++.+|.|..|+.++
T Consensus       139 ~f~~gD~vkVI~g~~~~d~g~V~rI~~~~  167 (607)
T COG5164         139 GFYKGDLVKVIEGGEMVDIGTVPRIDGEK  167 (607)
T ss_pred             ccccCCeEEEeccccccccceEEEecCce
Confidence            47899999999999999999999998763

>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function

Probab=83.28  E-value=2.7  Score=28.36  Aligned_cols=27  Identities=33%  Similarity=0.665  Sum_probs=22.9

Q ss_pred             eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..||.+..    .+|-+|+|.+|+  .|+|+|+
T Consensus         5 ~vGdiIef----k~g~~G~V~kv~--eNSVIVd   31 (57)
T PF09953_consen    5 KVGDIIEF----KDGFTGIVEKVY--ENSVIVD   31 (57)
T ss_pred             ccCcEEEE----cCCcEEEEEEEe--cCcEEEE
Confidence            57999986    358999999999  7889987

It includes the uncharacterised YkvS protein from Bacillus subtilis.

>PRK06531 yajC preprotein translocase subunit YajC; Validated

Probab=82.21  E-value=3.9  Score=30.68  Aligned_cols=31  Identities=26%  Similarity=0.472  Sum_probs=26.3

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      .+++||+|.-+.    |-.|+|.+|..+.+.|.++
T Consensus        36 sLk~GD~VvT~G----Gi~G~V~~I~~~~~~v~le   66 (113)
T PRK06531         36 AIQKGDEVVTIG----GLYGTVDEVDTEAKTIVLD   66 (113)
T ss_pred             hcCCCCEEEECC----CcEEEEEEEecCCCEEEEE
Confidence            579999998765    5689999999888889886

>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]

Probab=80.48  E-value=3.3  Score=26.68  Aligned_cols=31  Identities=32%  Similarity=0.490  Sum_probs=25.4

Q ss_pred             ceeeeCCEEEEEecCCCCeE---eEEEEEEccCCE
Q 032704           68 MHVKAGDTVKVIAGCDKGKI---GEITKVFRHNST   99 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~---G~V~~V~r~~~~   99 (135)
                      =.|++||+|.++. .+.++.   .+|.+++...+.
T Consensus        11 G~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~   44 (74)
T PF03144_consen   11 GTLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGD   44 (74)
T ss_dssp             SEEETTEEEEEES-TTTTEECEEEEEEEEEETTEE
T ss_pred             eEEcCCCEEEECc-cCCcceeeeeecccccccccC
Confidence            3689999999998 666555   999999998764

EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	135
3bbo_W	191	Homology Model For The Spinach Chloroplast 50s Subu		3e-37
3pyo_U	100	Crystal Structure Of A Complex Containing Domain 3		7e-05
3fin_Y	101	T. Thermophilus 70s Ribosome In Complex With Mrna,		8e-05
3tve_U	102	Crystal Structure Analysis Of Ribosomal Decoding. T		8e-05
2j01_Y	110	Structure Of The Thermus Thermophilus 70s Ribosome		1e-04
3mrz_U	109	Recognition Of The Amber Stop Codon By Release Fact		1e-04

>pdb|3BBO|W Chain W, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 191

Iteration: 1
 Score =  150 bits (378), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 74/109 (67%), Positives = 90/109 (82%), Gaps = 2/109 (1%)
Query: 23  GQRLSFPSLSPITVKPTD-KPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAG 81
           GQRL FPS + + VK     PCLIV+R+KRWERK+CKPNSLP LHK HVK GDTVKVI+G
Sbjct: 22  GQRL-FPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPNSLPKLHKRHVKVGDTVKVISG 80
Query: 82  CDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLI 130
            +KGKIGEI+K+ +HNSTV++KD+N KTKHVK +EE EQGQIIK+ + I
Sbjct: 81  GEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEAAI 129

>pdb|3PYO|U Chain U, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 100

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
           KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I
Sbjct: 3   KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFI 60

>pdb|3FIN|Y Chain Y, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit Length = 101

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
           KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I
Sbjct: 3   KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFI 60

>pdb|3TVE|U Chain U, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
           KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I
Sbjct: 3   KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFI 60

>pdb|2J01|Y Chain Y, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 110

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
           KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I
Sbjct: 4   KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFI 61

>pdb|3MRZ|U Chain U, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
           KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I
Sbjct: 3   KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFI 60

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	135
3bbo_W	191	Ribosomal protein L24; large ribosomal subunit, sp	9e-46
3v2d_Y	110	50S ribosomal protein L24; ribosome associated inh	6e-20
2zjr_R	115	50S ribosomal protein L24; ribosome, large ribosom	7e-20
2ftc_N	96	Mitochondrial ribosomal protein L24; mitochondrial	4e-16
3r8s_U	102	50S ribosomal protein L24; protein biosynthesis, R	2e-12
1vq8_T	120	50S ribosomal protein L24P; ribosome 50S, protein-	9e-08
3iz5_Y	150	60S ribosomal protein L26 (L24P); eukaryotic ribos	5e-05
4a17_S	135	RPL26, 60S ribosomal protein L21; eukaryotic ribos	2e-04
3u5e_Y	127	L33, YL33, 60S ribosomal protein L26-A; translatio	2e-04

>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 191

 Score =  146 bits (369), Expect = 9e-46
 Identities = 85/125 (68%), Positives = 99/125 (79%), Gaps = 1/125 (0%)

Query: 1   MAAMAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPN 60
           MAAM  LQSS TSLS+SSNSF GQRL     +         PCLIV+R+KRWERK+CKPN
Sbjct: 1   MAAMV-LQSSFTSLSLSSNSFLGQRLFPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPN 59

Query: 61  SLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQ 120
           SLP LHK HVK GDTVKVI+G +KGKIGEI+K+ +HNSTV++KD+N KTKHVK +EE EQ
Sbjct: 60  SLPKLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQ 119

Query: 121 GQIIK 125
           GQIIK
Sbjct: 120 GQIIK 124

>3v2d_Y 50S ribosomal protein L24; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y 2jl8_Y 2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y 2wh4_Y 2wrj_Y 2wrl_Y 2wro_Y 2wrr_Y ... Length = 110

 Score = 77.6 bits (192), Expect = 6e-20
 Identities = 23/60 (38%), Positives = 36/60 (60%)

Query: 66  HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
            KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I+
Sbjct: 3   VKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIE 62

>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S* 1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R* 3pio_R* 3pip_R* 1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V Length = 115

 Score = 77.6 bits (192), Expect = 7e-20
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 58  KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 117
                    K+H K GDTV V++G  KG+ G++      +  V+V+ +N+ TK+VK    
Sbjct: 4   PSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMT 63

Query: 118 EEQGQIIK 125
             QG   +
Sbjct: 64  NPQGGQEQ 71

>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_N Length = 96

 Score = 67.6 bits (166), Expect = 4e-16
 Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 73  GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
           GDTV+++ G D GK G++ +V R  + V+V  +N   +++ K   + +G +I 
Sbjct: 1   GDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKT-MDYRGTMIP 52

>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2j28_U* 3fik_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U 3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U 3i20_U ... Length = 102

 Score = 58.3 bits (142), Expect = 2e-12
 Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 68  MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVK-KREEEEQGQIIK 125
             ++  D V V+ G DKGK G++  V      V+V+ INL  KH K      + G I++
Sbjct: 2   AKIRRDDEVIVLTGKDKGKRGKVKNVLSSG-KVIVEGINLVKKHQKPVPALNQPGGIVE 59

>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ... Length = 120

 Score = 46.4 bits (110), Expect = 9e-08
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 44  LIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103
            +   L    R+E    +      + V AGDTV+V+ G   G+ GE+  V    + + V+
Sbjct: 23  QVRATLSADLREEYGQRN------VRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE 76

Query: 104 DINLKTKHVKKRE 116
           D+ L+    ++  
Sbjct: 77  DVTLEKTDGEEVP 89

>4a17_S RPL26, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_S 4a1c_S 4a1e_S Length = 135

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 13/51 (25%), Positives = 25/51 (49%)

Query: 66  HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKRE 116
             M V+  D V ++ G  KG  G++T+V+R    + V+ I+    +    +
Sbjct: 45  RSMPVRKDDEVLIVRGKFKGNKGKVTQVYRKKWAIHVEKISKNKLNGAPYQ 95

>3u5e_Y L33, YL33, 60S ribosomal protein L26-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_L 2ww9_L 2wwb_L 3o5h_X 3o58_X 3u5i_Y 1s1i_U 3izc_Y 3izs_Y 3jyw_U Length = 127

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 66  HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKRE 116
             + ++  D V V+ G  KG+ G+I+ V+R    V V  +  +  +     
Sbjct: 46  KALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVP 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	135
3bbo_W	191	Ribosomal protein L24; large ribosomal subunit, sp	100.0
3v2d_Y	110	50S ribosomal protein L24; ribosome associated inh	99.92
2zjr_R	115	50S ribosomal protein L24; ribosome, large ribosom	99.91
3r8s_U	102	50S ribosomal protein L24; protein biosynthesis, R	99.91
2ftc_N	96	Mitochondrial ribosomal protein L24; mitochondrial	99.88
1vq8_T	120	50S ribosomal protein L24P; ribosome 50S, protein-	99.74
3j21_U	121	50S ribosomal protein L24P; archaea, archaeal, KIN	99.72
3u5e_Y	127	L33, YL33, 60S ribosomal protein L26-A; translatio	99.69
4a17_S	135	RPL26, 60S ribosomal protein L21; eukaryotic ribos	99.68
3iz5_Y	150	60S ribosomal protein L26 (L24P); eukaryotic ribos	99.67
2zkr_t	145	60S ribosomal protein L26; protein-RNA complex, 60	99.66
1nz9_A	58	Transcription antitermination protein NUSG; transc	98.27
2e6z_A	59	Transcription elongation factor SPT5; KOW motif, s	97.53
3p8b_B	152	Transcription antitermination protein NUSG; transc	97.52
2jvv_A	181	Transcription antitermination protein NUSG; transc	97.51
2do3_A	69	Transcription elongation factor SPT5; KOW motif, s	97.26
2ckk_A	127	KIN17; beta barrel, ribosomal protein, ribonucleop	96.86
2xhc_A	352	Transcription antitermination protein NUSG; 2.45A	96.42
1m1h_A	248	Transcription antitermination protein NUSG; transc	96.18
4a18_F	126	RPL14; ribosome, eukaryotic initiation factor 6, E	93.22
3iz5_N	134	60S ribosomal protein L14 (L14E); eukaryotic ribos	93.12
2joy_A	96	50S ribosomal protein L14E; protein solution struc	92.47
3izc_N	138	60S ribosomal protein RPL14 (L14E); eukaryotic rib	91.56
4a18_N	144	RPL27, ribosomal protein L22; ribosome, eukaryotic	91.19
3j21_5	83	50S ribosomal protein L14E; archaea, archaeal, KIN	90.76
2e70_A	71	Transcription elongation factor SPT5; KOW motif, s	90.27
1qp2_A	70	Protein (PSAE protein); mainly beta, roll, pleckst	88.19
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	83.98
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	83.68
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	82.59
2oug_A	162	Transcriptional activator RFAH; transcription fact	80.04

>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=1.2e-52  Score=333.83  Aligned_cols=132  Identities=65%  Similarity=0.951  Sum_probs=68.6

Q ss_pred             ChhhhhhhhhcceeeeccccccCcccCCCCCCCccccCCCCceeeeeeeeeeeeeecCCCCCcccccceeeeCCEEEEEe
Q 032704            1 MAAMAALQSSMTSLSISSNSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIA   80 (135)
Q Consensus         1 ~~~~~~~~~~~~~l~~~~~~f~g~~l~~~~~~~~~~~~~~~~~~~~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~VI~   80 (135)
                      |||| ||||||++|||||||||||||+|+++++.+++++++||++++++++|+|++|+++++|+..+|+|++||+|+||+
T Consensus         1 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lr~k~~~rslP~~~kmkIkKGD~V~VIa   79 (191)
T 3bbo_W            1 MAAM-VLQSSFTSLSLSSNSFLGQRLFPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPNSLPKLHKRHVKVGDTVKVIS   79 (191)
T ss_dssp             ---------------------------------------------------------------CTTSCCSCCSSCEEECS
T ss_pred             Ccch-hhhhhhhccccccccccCcccCCCccccCcccccCCceeeEecccHHHHHHhCCCCCCccccCeeecCCEEEEee
Confidence            8999 999999999999999999999988876667999999999999999999999999999998999999999999999


Q ss_pred             cCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           81 GCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        81 GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      |+||||+|+|++|++++|+|+|||+|+.++|+||++++++|||+++|+|||+|
T Consensus        80 GkDKGK~GkVl~V~~k~~rViVEGVN~vkKH~Kp~~~~~~GgIv~kEaPIhiS  132 (191)
T 3bbo_W           80 GGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEAAIHSS  132 (191)
T ss_dssp             SSSTTCCCSCCCCCSSSCCCCCSSCCCCCCBCCSCCSSSCCBSSCCCCCCCGG
T ss_pred             cCCCCceEEEEEEECCCCEEEEeCCEEEEEecCCcccCCCCCEEEEecCcCHH
Confidence            99999999999999999999999999999999999889999999999999987

>3v2d_Y 50S ribosomal protein L24; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y 2jl8_Y 2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y 2wh4_Y 2wrj_Y 2wrl_Y 2wro_Y 2wrr_Y ...

Probab=99.92  E-value=8.4e-26  Score=166.18  Aligned_cols=68  Identities=34%  Similarity=0.482  Sum_probs=66.1

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      .+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+||++++++|||+++|+|||+|
T Consensus         3 ~k~~IkkGD~V~Vi~GkdKGk~GkV~~V~~~~~~ViVEGvN~~kkh~kp~~~~~~Ggi~~~E~PIh~S   70 (110)
T 3v2d_Y            3 VKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEAPLHAS   70 (110)
T ss_dssp             CCCSCCTTSEEEECSSTTTTCEEEEEEEEGGGTEEEETTSSEEEEECCSSSSSTTCCEEEEECCEEGG
T ss_pred             cccccCCCCEEEEeEcCCCCeEeEEEEEECCCCEEEEeCEEEEEEEeCCCccCCCCCEEEEECCcCHH
Confidence            47899999999999999999999999999999999999999999999999988999999999999997

>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S* 1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R* 3pio_R* 3pip_R* 1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V

Probab=99.91  E-value=1.8e-25  Score=165.17  Aligned_cols=71  Identities=30%  Similarity=0.374  Sum_probs=67.6

Q ss_pred             cccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           63 PVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        63 p~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      +...+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+||++++++|||+++|+|||+|
T Consensus         9 ~~~rkm~IkkGD~V~Vi~GkdKGk~GkV~~V~~~~~~V~VEGvN~~kkh~kp~~~~~~Ggiv~~e~PIh~S   79 (115)
T 2zjr_R            9 HHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHAS   79 (115)
T ss_dssp             TTTSCCSSCTTSEEECCSSSSTTCEEEEEEEETTTTEEEESSSCBCCCCCCTTSSSCCCCCCCBCCCBCSS
T ss_pred             ccceeCcccCCCEEEEeEcCCCCcEEEEEEEECCCCEEEEeCcEeEEEecCCCcCCCCCCEEEEEcccCHH
Confidence            44567899999999999999999999999999999999999999999999999888999999999999997

>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2j28_U* 3fik_U 3j19_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U 3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U ...

Probab=99.91  E-value=1.5e-24  Score=157.64  Aligned_cols=65  Identities=32%  Similarity=0.475  Sum_probs=62.6

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCc-cCCceEEEEeeeeeEE
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE-EEQGQIIKVYSLICYF  133 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e-~~~GgIi~~E~PIh~S  133 (135)
                      .+|++||+|+||+|+||||+|+|++|+++ ++|+|||+|+.++|.||+++ +++|||+++|+|||+|
T Consensus         2 ~~IkkGD~V~Vi~GkdKGk~GkV~~V~~~-~~ViVeGvN~~kkh~kp~~~~~~~Ggi~~~E~PIh~S   67 (102)
T 3r8s_U            2 AKIRRDDEVIVLTGKDKGKRGKVKNVLSS-GKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVS   67 (102)
T ss_dssp             CSSCSSCEEEECSSSSTTCEEEEEEEETT-TEEEETTCSEEEEEECCCSSSSCSCEEEEEECCEEGG
T ss_pred             CCccCCCEEEEeEcCCCCeeeEEEEEEeC-CEEEEeCeEEEEeccccCcccCCCCCEEEEECCcCHH
Confidence            47999999999999999999999999999 99999999999999999986 8999999999999997

>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_N

Probab=99.88  E-value=4.9e-23  Score=148.14  Aligned_cols=60  Identities=28%  Similarity=0.449  Sum_probs=58.5

Q ss_pred             CCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        73 GD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      ||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||++ +++|+|+++|+|||+|
T Consensus         1 GD~V~Vi~GkdKGk~GkV~~V~~~~~~ViVeGvN~~kkh~kp~~-~~~Ggiv~~e~pIh~S   60 (96)
T 2ftc_N            1 GDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKTM-DYRGTMIPSEAPLLHR   60 (96)
T ss_pred             CCEEEEeEcCCCCcEEEEEEEECCCCEEEEeCCEEEEEEcCCCC-CCCCCEEEEecCcCHH
Confidence            89999999999999999999999999999999999999999997 7899999999999987

>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...

Probab=99.74  E-value=1.2e-18  Score=129.83  Aligned_cols=57  Identities=32%  Similarity=0.441  Sum_probs=52.1

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      .+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+ +|   +     +||  +.|+|||+|
T Consensus        39 r~~~IkkGD~V~Vi~G~dKGk~GkV~~V~~k~~~V~VEgvn~-kK---~-----~Gg--~~e~pIh~S   95 (120)
T 1vq8_T           39 RNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTL-EK---T-----DGE--EVPRPLDTS   95 (120)
T ss_dssp             SEEECCTTCEEEECSSTTTTCEEEEEEEETTTTEEEETTCEE-EC---S-----SSC--EEECCBCGG
T ss_pred             ccccccCCCEEEEEecCCCCCEEEEEEEECCCCEEEEeCeEe-Ec---C-----CCC--EEEeeechH
Confidence            467899999999999999999999999999999999999999 55   2     467  899999987

>3j21_U 50S ribosomal protein L24P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.72  E-value=2.3e-18  Score=128.41  Aligned_cols=63  Identities=25%  Similarity=0.420  Sum_probs=54.9

Q ss_pred             eeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        54 r~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      |.+|+.+      +|+|++||+|+||+|+|||++|+|++|++++++|+|||||+.++|         |  .+.|+|||+|
T Consensus        36 R~ky~~r------~~~IkkGD~V~Vi~GkdKGk~GkV~~V~~k~~~V~VEgvn~~k~~---------G--~~~e~pIh~S   98 (121)
T 3j21_U           36 REKYKVR------NLPVRVGDKVRIMRGDYKGHEGKVVEVDLKRYRIYVEGATLRKTN---------G--TEVFYPIHPS   98 (121)
T ss_dssp             HHHTCCS------EEECCSSSEEEECSSSCSSEEEEEEEEETTTTEEEETTCEEECSS---------S--CEEECCBCGG
T ss_pred             HHHhCCc------ccccccCCEEEEeecCCCCcEeEEEEEEecCCEEEEeCeEEEecC---------C--cEEEcccCHH
Confidence            5666643      566999999999999999999999999999999999999998742         3  3889999987

>3u5e_Y L33, YL33, 60S ribosomal protein L26-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_L 2ww9_L 2wwb_L 3o5h_X 3o58_X 3u5i_Y 4b6a_Y 1s1i_U 3izc_Y 3izs_Y 3jyw_U

Probab=99.69  E-value=7.1e-18  Score=126.84  Aligned_cols=64  Identities=27%  Similarity=0.389  Sum_probs=55.3

Q ss_pred             eeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704           53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY  132 (135)
Q Consensus        53 er~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~  132 (135)
                      .|.+|+.+++|      |++||+|+||+|+|||++|+|++|++++++|+|||||+.+    ++     |+  +.|+|||+
T Consensus        39 Lr~ky~vrs~~------IkkgD~V~Vi~GkdKGk~GkV~~V~~kk~~V~VEgVn~~K----~~-----G~--~~e~pIh~  101 (127)
T 3u5e_Y           39 LRAQYGIKALP------IRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEK----VN-----GA--SVPINLHP  101 (127)
T ss_dssp             HHHHHTCCEEE------CCTTCEEEECSSTTTTCEEEEEEEEGGGTEEEEETCEEEC----SS-----SC--EEECCBCG
T ss_pred             HHHHhCcCccc------ccCCCEEEEeecCCCCccceEEEEECCCCEEEEeCeEEEC----CC-----Cc--EEEcccch
Confidence            36777766655      8999999999999999999999999999999999999974    22     43  78999998


Q ss_pred             E
Q 032704          133 F  133 (135)
Q Consensus       133 S  133 (135)
                      |
T Consensus       102 S  102 (127)
T 3u5e_Y          102 S  102 (127)
T ss_dssp             G
T ss_pred             H
Confidence            7

>4a17_S RPL26, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_S 4a1c_S 4a1e_S

Probab=99.68  E-value=1.4e-17  Score=126.33  Aligned_cols=64  Identities=25%  Similarity=0.379  Sum_probs=55.6

Q ss_pred             eeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704           53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY  132 (135)
Q Consensus        53 er~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~  132 (135)
                      .|.+|+.+++|      |++||+|+||+|+|||++|+|++|++++++|+|||||+.+    +     .|+  +.|+|||+
T Consensus        38 Lr~ky~vRs~~------IkkgD~V~Vi~GkdKGk~GkV~~V~~kk~~V~VEgVn~~K----~-----~G~--~~e~pIh~  100 (135)
T 4a17_S           38 LRSKYNVRSMP------VRKDDEVLIVRGKFKGNKGKVTQVYRKKWAIHVEKISKNK----L-----NGA--PYQIPLSA  100 (135)
T ss_dssp             HHHHHTCSEEE------CCTTCEEEECSSTTTTCEEEEEEEETTTTEEEETTCCEEE----T-----TTE--EECCCBCG
T ss_pred             HHHHhCCCccc------ccCCCEEEEeecCCCCceeeEEEEEcCCCEEEEeCeEEEc----C-----CCC--EEEcccch
Confidence            36777766655      8999999999999999999999999999999999999975    2     243  88999998


Q ss_pred             E
Q 032704          133 F  133 (135)
Q Consensus       133 S  133 (135)
                      |
T Consensus       101 S  101 (135)
T 4a17_S          101 S  101 (135)
T ss_dssp             G
T ss_pred             H
Confidence            7

>2zkr_t 60S ribosomal protein L26; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=99.66  E-value=3.4e-17  Score=125.36  Aligned_cols=56  Identities=25%  Similarity=0.415  Sum_probs=51.3

Q ss_pred             cceeeeCCEEEEEecCCCCeE-eEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           67 KMHVKAGDTVKVIAGCDKGKI-GEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~-G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      +|+|++||+|+||+|+|||++ |+|++|++++++|+|||||+    .||+     |  ++.|+|||+|
T Consensus        46 ~~~IkkGD~V~Vi~GkdKGk~~GkV~~V~~k~~~V~VEgvn~----~Kp~-----G--~~~e~PIh~S  102 (145)
T 2zkr_t           46 SMPIRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQR----EKAN-----G--TTVHVGIHPS  102 (145)
T ss_dssp             CCBCCTTCEEEECSSTTTTCCSEEEEEEETTTTEEEETTCEE----ECSS-----C--CEEECCBCGG
T ss_pred             ccccCCCCEEEEeecCCCCcceeEEEEEECCCCEEEEeeeEe----EcCC-----C--ceEEeccCHH
Confidence            467999999999999999999 99999999999999999999    4554     4  8999999987

>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4

Probab=98.27  E-value=7.5e-07  Score=56.96  Aligned_cols=36  Identities=25%  Similarity=0.381  Sum_probs=32.9

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..+.+||+|.|++|+++|..|+|.++++++.++.|.
T Consensus         3 ~~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~k~~v~V~   38 (58)
T 1nz9_A            3 VAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVM   38 (58)
T ss_dssp             CSCCTTCEEEECSGGGTTCEEEEEEEETTTTEEEEE
T ss_pred             cccCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence            347899999999999999999999999999888775

>2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.53  E-value=2.7e-05  Score=50.54  Aligned_cols=37  Identities=30%  Similarity=0.288  Sum_probs=30.0

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      +..+.+||.|.|+.|+++|-.|+|.+|+.++=+|.|+
T Consensus         5 ~~~f~~GD~V~V~~Gpf~g~~G~V~evd~e~v~V~v~   41 (59)
T 2e6z_A            5 SSGFQPGDNVEVCEGELINLQGKILSVDGNKITIMPK   41 (59)
T ss_dssp             CSSCCTTSEEEECSSTTTTCEEEECCCBTTEEEEEEC
T ss_pred             cccCCCCCEEEEeecCCCCCEEEEEEEeCCEEEEEEE
Confidence            4457999999999999999999999999763333443

>3p8b_B Transcription antitermination protein NUSG; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus} PDB: 3qqc_D

Probab=97.52  E-value=9.3e-05  Score=54.78  Aligned_cols=36  Identities=33%  Similarity=0.473  Sum_probs=33.5

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..+.+||.|.|++|+++|..|+|.+|+.+++++.|+
T Consensus        90 ~~~~~Gd~VrI~~Gpf~g~~g~V~~vd~~k~~v~V~  125 (152)
T 3p8b_B           90 SGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQ  125 (152)
T ss_dssp             TTCCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEE
T ss_pred             ccCCCCCEEEEeeecCCCCEEEEEEEeCCCCEEEEE
Confidence            457999999999999999999999999999998877

>2jvv_A Transcription antitermination protein NUSG; transcription factor, transcription regulation, transcription termination; NMR {Escherichia coli} PDB: 2k06_A 2kvq_G

Probab=97.51  E-value=8.9e-05  Score=56.10  Aligned_cols=37  Identities=24%  Similarity=0.210  Sum_probs=32.8

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      +..+.+||+|.|+.|+++|..|+|.+|+.+++++.|.
T Consensus       125 ~~~~~~Gd~V~V~~GPf~g~~G~v~~v~~~k~r~~V~  161 (181)
T 2jvv_A          125 KTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVS  161 (181)
T ss_dssp             CCCCCTTEEEEECSSTTTTEEEEEEEEETTTTEEEEE
T ss_pred             cccCCCCCEEEEeccCCCCcEEEEEEEeCCCCEEEEE
Confidence            4467899999999999999999999999988887553

>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5

Probab=97.26  E-value=0.00046  Score=46.93  Aligned_cols=45  Identities=33%  Similarity=0.451  Sum_probs=35.3

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecC
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK  114 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~  114 (135)
                      +++.||-|+||.|++.|..|.|.+|..+ --+++-+.++..-.+-+
T Consensus        17 ~F~~GDHVkVi~G~~~getGlVV~v~~d-~v~v~SD~t~~Ei~V~~   61 (69)
T 2do3_A           17 YFKMGDHVKVIAGRFEGDTGLIVRVEEN-FVILFSDLTMHELKVLP   61 (69)
T ss_dssp             SCCTTCEEEESSSTTTTCEEEEEEECSS-CEEEEESSSCSEEEECT
T ss_pred             eccCCCeEEEeccEEcCceEEEEEEeCC-EEEEEeCCCCCEEEEEh
Confidence            5899999999999999999999999843 34566777765544443

>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens}

Probab=96.86  E-value=0.0012  Score=48.77  Aligned_cols=33  Identities=15%  Similarity=0.338  Sum_probs=31.0

Q ss_pred             eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ++||+|+|+.|+++|..|++.+++.++..++|+
T Consensus        72 ~~g~~V~Iv~G~~rG~~g~L~~id~~~~~~~V~  104 (127)
T 2ckk_A           72 APGKRILVLNGGYRGNEGTLESINEKTFSATIV  104 (127)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEEGGGTEEEEE
T ss_pred             CCCCEEEEEecccCCcEEEEEEEeCCCcEEEEE
Confidence            689999999999999999999999998888777

>2xhc_A Transcription antitermination protein NUSG; 2.45A {Thermotoga maritima}

Probab=96.42  E-value=0.0031  Score=53.42  Aligned_cols=37  Identities=27%  Similarity=0.369  Sum_probs=32.7

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ...+.+||+|.|+.|+++|..|+|.+++.+++++.|.
T Consensus       296 ~~~f~~Gd~VrV~~GPF~G~~G~V~evd~ek~rv~V~  332 (352)
T 2xhc_A          296 ELGFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVN  332 (352)
T ss_dssp             -CCCCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEE
T ss_pred             cccCCCCCEEEEeccCCCCcEEEEEEEcCCCCEEEEE
Confidence            4457899999999999999999999999999888764

>1m1h_A Transcription antitermination protein NUSG; transcription termination, RNP motif, immunoglobulin fold, nucleic acid interaction; 1.95A {Aquifex aeolicus} SCOP: b.114.1.1 d.58.42.1 PDB: 1m1g_A 1npp_A 1npr_A

Probab=96.18  E-value=0.00082  Score=54.47  Aligned_cols=37  Identities=27%  Similarity=0.383  Sum_probs=0.0

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      +..+.+||+|.|++|+++|-.|+|.+|+.+++++.|.
T Consensus       192 ~~~~~~Gd~V~I~~Gpf~g~~G~v~ev~~~k~~~~V~  228 (248)
T 1m1h_A          192 KVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVM  228 (248)
T ss_dssp             -------------------------------------
T ss_pred             cccCCCCCEEEEeccCCCCcEEEEEEEeCCCCEEEEE
Confidence            4567899999999999999999999999998877664

>4a18_F RPL14; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_F 4a1b_F 4a1d_F 4adx_7

Probab=93.22  E-value=0.16  Score=37.81  Aligned_cols=41  Identities=24%  Similarity=0.499  Sum_probs=34.8

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEe
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHV  112 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhv  112 (135)
                      +..|=.|.|..|++.|+...|+.|.-+ |+|+|+|-. ..++.
T Consensus         7 vevGRVv~i~~G~~aGklavIVdIID~-nrvLVdGp~-V~Rq~   47 (126)
T 4a18_F            7 VQVGRVVYINYGADKGKLAVIVNIINQ-NRILIDGEH-IVRQV   47 (126)
T ss_dssp             EETTEEEEECSSTTTTEEEEEEEEETT-TEEEEEETT-EEEEE
T ss_pred             eecceEEEEccCCccCCEEEEEEEecC-CeEEEeCCC-cccce
Confidence            678888999999999999999999875 799999987 34433

>2joy_A 50S ribosomal protein L14E; protein solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: b.34.5.7 PDB: 2kds_A

Probab=92.47  E-value=0.067  Score=37.55  Aligned_cols=36  Identities=17%  Similarity=0.323  Sum_probs=31.7

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccc
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN  106 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN  106 (135)
                      +.+|-.|.+.+|+|+|+.-.|+++. +++.|+|.|..
T Consensus         4 v~~GrVv~~~~Gr~~Gk~~VIv~~i-D~~~vLV~gp~   39 (96)
T 2joy_A            4 IEVGRICVKVKGREAGSKCVIVDII-DDNFVLVTGPK   39 (96)
T ss_dssp             SSTTEEEECSSSSTTCCEEEEEEEC-SSSCEEEECCT
T ss_pred             cccCEEEEEeecCCCCCEEEEEEEe-CCCEEEEECCc
Confidence            6789999999999999999999997 46799998864

>4a18_N RPL27, ribosomal protein L22; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_N 4a1b_N 4a1d_N

Probab=91.19  E-value=0.23  Score=37.79  Aligned_cols=41  Identities=27%  Similarity=0.325  Sum_probs=35.8

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccC------CEEEEeccceeEE
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKTK  110 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~------~~ViVegvN~~kk  110 (135)
                      +.+|-.|.|++|++.|+...|+++..++      +.++|.||....+
T Consensus         5 ~kpGrVvivl~Gr~aGkkaVIvk~iD~gt~d~~y~~aLVaGIdryP~   51 (144)
T 4a18_N            5 LKYGRVVILLQGRFAGKKAVIVKSSEDGTKDRKFGHVLVAGVERSPK   51 (144)
T ss_dssp             CCTTEEEEECSSTTTTCEEEEEEEESSCCSSCCSCEEEEEEEEECCC
T ss_pred             ccCCeEEEEecCCcCCCEEEEEEecCCCccCCccceEEEEecccCCc
Confidence            6788899999999999999999999775      8999999765443

>3j21_5 50S ribosomal protein L14E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=90.76  E-value=0.11  Score=35.72  Aligned_cols=36  Identities=22%  Similarity=0.355  Sum_probs=31.4

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccc
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN  106 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN  106 (135)
                      +..|-.|.+.+|+|+|+...|+++.-+ ++|+|.|..
T Consensus         4 ~~~Grvv~~~~Gr~~Gk~~vIv~iiD~-~~vlV~g~~   39 (83)
T 3j21_5            4 IDVGRIAVVIAGRRAGQKVVVVDIIDK-NFVLVTGAG   39 (83)
T ss_dssp             CCTTEEEECSSSSSSCCCEEEEEECSS-SCEEEECCT
T ss_pred             cccCEEEEEeecCCCCCEEEEEEEcCC-CEEEEECCc
Confidence            678999999999999999999998754 689998864

>2e70_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.27  E-value=0.31  Score=33.02  Aligned_cols=31  Identities=32%  Similarity=0.417  Sum_probs=25.3

Q ss_pred             eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      ..|-+|.|..|++||..|.|..+...  .+.||
T Consensus        19 liGktV~I~kGpyKG~~GiVkd~t~~--~~RVE   49 (71)
T 2e70_A           19 LIGQTVRISQGPYKGYIGVVKDATES--TARVE   49 (71)
T ss_dssp             STTSEEEECSSTTTTCEEEEEEECSS--CEEEE
T ss_pred             cCCCEEEEeccCCCCeEEEEEECCCC--eEEEE
Confidence            35779999999999999999888765  45555

>1qp2_A Protein (PSAE protein); mainly beta, roll, pleckstrin topology, SH3-like, electron T; NMR {Nostoc SP} SCOP: b.34.4.2 PDB: 1qp3_A

Probab=88.19  E-value=0.39  Score=32.69  Aligned_cols=38  Identities=18%  Similarity=0.283  Sum_probs=31.5

Q ss_pred             eeeCCEEEEEecC--CCCeEeEEEEEEccC----CEEEEeccce
Q 032704           70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN----STVMVKDINL  107 (135)
Q Consensus        70 I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~----~~ViVegvN~  107 (135)
                      |.+|++|.|++=.  .-+.+|+|.+|+..+    =.|..|++|-
T Consensus         2 i~rGs~VrIlr~eSywy~~vG~V~~Vd~~~~~ypV~VrFekvNy   45 (70)
T 1qp2_A            2 VQRGSKVRILRPESYWFQDVGTVASVDQSGIKYPVIVRFEKVNY   45 (70)
T ss_dssp             CCTTCEEEECCTTSTTTTCEEEEEEECCSSCSCSEEEECSSCCS
T ss_pred             cCCCCEEEEcCccceeecceeEEEEEeCCCcEeeEEEEeccccc
Confidence            6899999999986  679999999999975    2466777775

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=83.98  E-value=1.1  Score=36.93  Aligned_cols=41  Identities=27%  Similarity=0.467  Sum_probs=33.4

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEeccc
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKDIN  106 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~---~~ViVegvN  106 (135)
                      .-.++..|-.|.|+.|++-|.+|+|..+.++.   +.|.|++-+
T Consensus       171 d~ikfe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~  214 (265)
T 3iz6_D          171 DFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDAL  214 (265)
T ss_dssp             EEECCSTTCEEEECSSSSCSCEEEEEEEECCSSSCCEEEECCCS
T ss_pred             eEEEccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECC
Confidence            34567778899999999999999999999864   478887643

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.68  E-value=0.94  Score=36.86  Aligned_cols=41  Identities=22%  Similarity=0.327  Sum_probs=34.2

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccC----CEEEEeccc
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKDIN  106 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~----~~ViVegvN  106 (135)
                      .-.++..|-.|.|+.|++-|.+|+|..+.++.    +.|.|++-+
T Consensus       175 d~ikf~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~~V~v~d~~  219 (243)
T 3j20_E          175 EVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEE  219 (243)
T ss_dssp             EEEECCTTCEEEECSSSSTTCEEEEEECCCCCSSSCCEEEEEESS
T ss_pred             eEEeccCCCEEEEECCccceEEEEEEEEEEecCCCceEEEEEcCC
Confidence            34677789999999999999999999998753    668888754

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W

Probab=82.59  E-value=1.8  Score=35.55  Aligned_cols=39  Identities=26%  Similarity=0.491  Sum_probs=32.8

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEecc
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKDI  105 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~---~~ViVegv  105 (135)
                      -.++..|-.|.|+.|++-|.+|+|.++.++.   +.|.|++-
T Consensus       174 ~ikfe~G~l~mvtgG~n~GriG~I~~~e~~~gs~~iV~vkd~  215 (260)
T 2xzm_W          174 FAHLESGNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDA  215 (260)
T ss_dssp             CCBCCSSCEEEECSSTTTTCEEEEEEEECCCSSCCEEEEECT
T ss_pred             EEEecCCCEEEEECCccceeEEEEEEEEecCCCCcEEEEEeC
Confidence            3567889999999999999999999987663   67888864

>2oug_A Transcriptional activator RFAH; transcription factor, virulence, transcription pausing, transcription elongation; 2.10A {Escherichia coli}

Probab=80.04  E-value=0.0036  Score=46.11  Aligned_cols=30  Identities=20%  Similarity=0.125  Sum_probs=21.5

Q ss_pred             ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704           68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN   97 (135)
Q Consensus        68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~   97 (135)
                      ..+.+||+|.|+.|+++|..|+|.+++.++
T Consensus       108 ~~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~k  137 (162)
T 2oug_A          108 ATPYPGDKVIITEGAFEGFQAIFTEPDGEA  137 (162)
T ss_dssp             -------CTTHHHHHHHHHHHHTTCSSHHH
T ss_pred             CCCCCCCEEEEcccCCCCcEEEEEEECCCC
Confidence            457899999999999999999999998764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	135
d2j01y1	101	b.34.5.1 (Y:2-102) Ribosomal proteins L24 (L24p) {	1e-16
d2zjrr1	110	b.34.5.1 (R:4-113) Ribosomal proteins L24 (L24p) {	6e-16
d1vqot1	119	b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {	2e-14
d2gycs1	99	b.34.5.1 (S:3-101) Ribosomal proteins L24 (L24p) {	6e-13

>d2j01y1 b.34.5.1 (Y:2-102) Ribosomal proteins L24 (L24p) {Thermus thermophilus [TaxId: 274]} Length = 101

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Thermus thermophilus [TaxId: 274]

 Score = 67.8 bits (166), Expect = 1e-16
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKV 126
           KMHVK GDTV V +G  KG++G++ +V      V+V+ +N+  K V+   +  QG  I+ 
Sbjct: 3   KMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEK 62

Query: 127 YSLICY 132
            + +  
Sbjct: 63  EAPLHA 68

>d2zjrr1 b.34.5.1 (R:4-113) Ribosomal proteins L24 (L24p) {Deinococcus radiodurans [TaxId: 1299]} Length = 110

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 66.3 bits (162), Expect = 6e-16
 Identities = 21/66 (31%), Positives = 35/66 (53%)

Query: 67  KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKV 126
           K+H K GDTV V++G  KG+ G++      +  V+V+ +N+ TK+VK      QG   + 
Sbjct: 10  KLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQR 69

Query: 127 YSLICY 132
              +  
Sbjct: 70  ELALHA 75

>d1vqot1 b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 119

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 62.4 bits (152), Expect = 2e-14
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 44  LIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103
            +   L    R+E    +      + V AGDTV+V+ G   G+ GE+  V    + + V+
Sbjct: 22  QVRATLSADLREEYGQRN------VRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE 75

Query: 104 DINLKTKHVKKRE 116
           D+ L+    ++  
Sbjct: 76  DVTLEKTDGEEVP 88

>d2gycs1 b.34.5.1 (S:3-101) Ribosomal proteins L24 (L24p) {Escherichia coli [TaxId: 562]} Length = 99

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Escherichia coli [TaxId: 562]

 Score = 58.1 bits (141), Expect = 6e-13
 Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 70  VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKR-EEEEQGQIIKVYS 128
           ++  D V V+ G DKGK G++  V      V+V+ INL  KH K      + G I++  +
Sbjct: 2   IRRDDEVIVLTGKDKGKRGKVKNVLSSG-KVIVEGINLVKKHQKPVPALNQPGGIVEKEA 60

Query: 129 LICY 132
            I  
Sbjct: 61  AIQV 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	135
d2zjrr1	110	Ribosomal proteins L24 (L24p) {Deinococcus radiodu	99.92
d2j01y1	101	Ribosomal proteins L24 (L24p) {Thermus thermophilu	99.9
d2gycs1	99	Ribosomal proteins L24 (L24p) {Escherichia coli [T	99.88
d1vqot1	119	Ribosomal proteins L24 (L24p) {Archaeon Haloarcula	99.76
d1nppa2	58	N-utilization substance G protein NusG, C-terminal	98.15
d1nz9a_	58	N-utilization substance G protein NusG, C-terminal	98.08
d2do3a1	62	Transcription elongation factor SPT5 {Human (Homo	97.21
d2joya1	96	Ribosomal protein L14e {Sulfolobus solfataricus [T	88.92
d1nxza1	72	Hypothetical protein HI0303 {Haemophilus influenza	85.27
d1vhka1	72	Hypothetical protein YqeU {Bacillus subtilis [TaxI	85.25

>d2zjrr1 b.34.5.1 (R:4-113) Ribosomal proteins L24 (L24p) {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.92  E-value=7.4e-27  Score=170.04  Aligned_cols=70  Identities=30%  Similarity=0.384  Sum_probs=67.6

Q ss_pred             ccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           64 VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        64 ~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      ...||+|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||++++++|||+++|+|||+|
T Consensus         7 ~~~K~kikkGD~V~VisGkdKGk~G~Vl~V~~~~~~ViVeGvN~~kkh~Kp~~~~~~Ggiv~~E~PIhiS   76 (110)
T d2zjrr1           7 HNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHAS   76 (110)
T ss_dssp             TTSCCSSCTTSEEECCSSSSTTCEEEEEEEETTTTEEEESSSCBCCCCCCTTSSSCCCCCCCBCCCBCSS
T ss_pred             ccceeeeeCCCEEEEeecCCCCcceEEEEEECCCCEEEEeCcEEEEEEecccccCCCCCeEeeeeeEEhh
Confidence            4478999999999999999999999999999999999999999999999999999999999999999997

>d2j01y1 b.34.5.1 (Y:2-102) Ribosomal proteins L24 (L24p) {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Thermus thermophilus [TaxId: 274]

Probab=99.90  E-value=7.4e-27  Score=167.77  Aligned_cols=68  Identities=34%  Similarity=0.482  Sum_probs=66.1

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S  133 (135)
                      -||+|++||+|+||+|+|||++|+|++|++++|+|+|||+|+.++|+||++++++|||+++|+|||||
T Consensus         2 ~K~kIkkGD~V~VisGkdKGk~G~Vl~V~~~~~~ViVeGvN~~kkh~k~~~~~~~Ggi~~~E~pIh~S   69 (101)
T d2j01y1           2 VKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEAPLHAS   69 (101)
T ss_dssp             CCCCSCCSSCEECCSSTTSSCCBSCCCCCCTTCBCCTTSCCCCCCCCCSCCCSSCCCSSCCCCCCBGG
T ss_pred             cccEEECCCEEEEeeCCCCCCeEEEEEEECCCCEEEEEcceEEEEeecCCCCCCccceEEEEccccHH
Confidence            47899999999999999999999999999999999999999999999999988999999999999998

>d2gycs1 b.34.5.1 (S:3-101) Ribosomal proteins L24 (L24p) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Escherichia coli [TaxId: 562]

Probab=99.88  E-value=1.8e-24  Score=154.88  Aligned_cols=64  Identities=33%  Similarity=0.480  Sum_probs=59.9

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCC-CccCCceEEEEeeeeeEE
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKR-EEEEQGQIIKVYSLICYF  133 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~-~e~~~GgIi~~E~PIh~S  133 (135)
                      +|++||+|+||+|+||||+|+|++|++ +++|+|||+|+.++|+||+ +.+++|||+++|+|||+|
T Consensus         1 KikkGD~V~VisGkdKGK~G~V~~V~~-~~~viVeGvN~~kkh~Kp~~~~~~~Ggiv~~E~pIh~S   65 (99)
T d2gycs1           1 KIRRDDEVIVLTGKDKGKRGKVKNVLS-SGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVS   65 (99)
T ss_dssp             CCCTTSEEECSSSTTTTCEEEEEEECT-TSEEEETTCCEECTTCCEECCCSCCCSSCCCSCCEETT
T ss_pred             CccCCCEEEEeeCCCCCCceEEEEEEC-CCeEEEeCeEEEEEEeCCCCCcCCCCCEEEEEeeEEhh
Confidence            479999999999999999999999987 5899999999999999996 557899999999999997

>d1vqot1 b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.76  E-value=4.8e-20  Score=135.46  Aligned_cols=72  Identities=26%  Similarity=0.304  Sum_probs=64.6

Q ss_pred             eeeeeeeeeeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEE
Q 032704           45 IVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII  124 (135)
Q Consensus        45 ~~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi  124 (135)
                      ....+.+|.|++|+.++++      |++||+|+||+|+|||++|+|++|++++++|+|||||+.++|.++          
T Consensus        23 m~a~LskeLr~k~~~r~~~------IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~V~Vegin~~k~~~k~----------   86 (119)
T d1vqot1          23 VRATLSADLREEYGQRNVR------VNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEE----------   86 (119)
T ss_dssp             GEEEECHHHHHHHTCSEEE------CCTTCEEEECSSTTTTCEEEEEEEETTTTEEEETTCEEECTTSCE----------
T ss_pred             eeCccChhhHHHhCCcccc------eeCCCEEEEeecCCCCCcceEEEEECCCCEEEEeCcEEEecCCce----------
Confidence            4467888999999977655      899999999999999999999999999999999999998888763          


Q ss_pred             EEeeeeeEE
Q 032704          125 KVYSLICYF  133 (135)
Q Consensus       125 ~~E~PIh~S  133 (135)
                       .|+|||+|
T Consensus        87 -~~~pIh~S   94 (119)
T d1vqot1          87 -VPRPLDTS   94 (119)
T ss_dssp             -EECCBCGG
T ss_pred             -eeccCchH
Confidence             68999987

>d1nppa2 b.34.5.4 (A:191-248) N-utilization substance G protein NusG, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.15  E-value=1e-06  Score=55.86  Aligned_cols=37  Identities=27%  Similarity=0.383  Sum_probs=33.4

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      |..+.+||+|.|++|++.|.+|+|.+++.+++++.|.
T Consensus         2 kvdf~~Gd~V~I~~GpF~g~~g~V~~i~~~~~rv~V~   38 (58)
T d1nppa2           2 KVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVM   38 (58)
T ss_dssp             SCSCCTTCEEEECSSTTTTCEEEEEEEEGGGTEEEEE
T ss_pred             cccccCCCEEEEcccCCCCCEEEEEEEcCCCCEEEEE
Confidence            4457899999999999999999999999998888765

>d1nz9a_ b.34.5.4 (A:) N-utilization substance G protein NusG, C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=98.08  E-value=1.5e-06  Score=55.13  Aligned_cols=37  Identities=24%  Similarity=0.384  Sum_probs=33.4

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      +..+.+||+|.|++|++.|.+|+|.+++.++++|.|.
T Consensus         2 ~v~F~~Gd~V~I~~GpF~g~~g~V~~i~~~k~rv~V~   38 (58)
T d1nz9a_           2 QVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVM   38 (58)
T ss_dssp             CCSCCTTCEEEECSGGGTTCEEEEEEEETTTTEEEEE
T ss_pred             cccccCCCEEEEeccCCCCCEEEEEEEcCCCCEEEEE
Confidence            3457999999999999999999999999999988775

>d2do3a1 b.34.5.5 (A:462-523) Transcription elongation factor SPT5 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: SPT5 KOW domain-like
domain: Transcription elongation factor SPT5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.21  E-value=0.00031  Score=45.38  Aligned_cols=45  Identities=36%  Similarity=0.471  Sum_probs=35.0

Q ss_pred             eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecC
Q 032704           69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK  114 (135)
Q Consensus        69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~  114 (135)
                      .++.||-|+||+|++.|..|.|++|.. +.-+++-+.++..-.+-+
T Consensus        10 ~F~~GDhVkVi~G~~~g~tGlVV~v~~-~~v~~~SD~t~~Ei~V~~   54 (62)
T d2do3a1          10 YFKMGDHVKVIAGRFEGDTGLIVRVEE-NFVILFSDLTMHELKVLP   54 (62)
T ss_dssp             SCCTTCEEEESSSTTTTCEEEEEEECS-SCEEEEESSSCSEEEECT
T ss_pred             ccCCCCeEEEeccEEcCccEEEEEEeC-CEEEEEeCCCCCEEEEeh
Confidence            589999999999999999999999853 334566777766555544

>d2joya1 b.34.5.7 (A:1-96) Ribosomal protein L14e {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal protein L14e
domain: Ribosomal protein L14e
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=88.92  E-value=0.1  Score=35.32  Aligned_cols=34  Identities=18%  Similarity=0.335  Sum_probs=30.6

Q ss_pred             eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704           70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD  104 (135)
Q Consensus        70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg  104 (135)
                      |..|=.|.+..|+|+||...|+++..+ |++.|+|
T Consensus         4 VevGrV~ii~~G~~~GK~~vIvdiid~-~rvLVdG   37 (96)
T d2joya1           4 IEVGRICVKVKGREAGSKCVIVDIIDD-NFVLVTG   37 (96)
T ss_dssp             SSTTEEEECSSSSTTCCEEEEEEECSS-SCEEEEC
T ss_pred             eeccEEEEEeecCCCCCEEEEEEEecC-CeEEEec
Confidence            567888999999999999999998864 7999999

>d1nxza1 b.122.1.2 (A:2-73) Hypothetical protein HI0303 {Haemophilus influenzae [TaxId: 727]}

class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: YggJ N-terminal domain-like
domain: Hypothetical protein HI0303
species: Haemophilus influenzae [TaxId: 727]

Probab=85.27  E-value=0.37  Score=29.62  Aligned_cols=38  Identities=11%  Similarity=0.239  Sum_probs=31.0

Q ss_pred             ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704           66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK  103 (135)
Q Consensus        66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe  103 (135)
                      .-+.+++||.|.+..|...--.++|+++.++.-.+.|.
T Consensus        29 ~VLR~k~Gd~v~l~dg~g~~~~~~I~~i~k~~~~~~i~   66 (72)
T d1nxza1          29 RVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEIL   66 (72)
T ss_dssp             TTSCCCTTCEEEEECSSSEEEEEEEEEEETTEEEEEEC
T ss_pred             heeCCCCCCEEEEEeCCCCEEEEEEEEEeCCEEEEEEE
Confidence            34678999999999999989999999998775444443

>d1vhka1 b.122.1.2 (A:2-73) Hypothetical protein YqeU {Bacillus subtilis [TaxId: 1423]}

class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: YggJ N-terminal domain-like
domain: Hypothetical protein YqeU
species: Bacillus subtilis [TaxId: 1423]

Probab=85.25  E-value=0.41  Score=29.53  Aligned_cols=36  Identities=17%  Similarity=0.214  Sum_probs=29.8

Q ss_pred             cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704           67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV  102 (135)
Q Consensus        67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV  102 (135)
                      -+.++.||.|.+..|...--.++|.+|.++.-.+.|
T Consensus        31 VLR~k~Gd~i~l~dg~g~~~~~~I~~i~k~~v~~~i   66 (72)
T d1vhka1          31 VMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLV   66 (72)
T ss_dssp             TTCCCTTCEEEEECTTSCEEEEEEEEECSSEEEEEE
T ss_pred             eeccCCCCEEEEEECCCCEEEEEEEEEECCEEEEEE
Confidence            467899999999999988889999999987544433