Citrus Sinensis ID: 032091

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------
Protein Sequence
MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRGK
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHccEEEEEcccHHHccccccccccccccccccHHHHHHHHHHHHccEEccccccccccccccccEEEccccccccccccccEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccHcccccHHHHHHHHHHHHHHcccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEcccccHHHHHHHHHHHccEEEcccccccccccHHccEEEEccccccccccccccEEEEEEEEEEcc
Coil and Loop (DISEMBL)
mpkllavpnIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRfpnieklrsraskddpielrspvtKEELVAEVARQLSIsiepenlhlpsplsafgeyevpmrlpkaiplpegkvqwtlnvkvrgk
Flexible Loop (DISEMBL)
MPKLLAVPNIEKFahlireqrricqpveeeevkvirksednmsREFEKAARrlenarlvlrrfpnieklrsraskddpielrspvtkeELVAEVARQLSisiepenlhlpsPLSAFGEYEVPMRLPkaiplpegkvqwtlnvkvrgk
Low Complexity Region (SEG)
MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRGK
Disordered region (IsUnstruct)
*****AVPNIEKFAHLIREQRRICQ********************************LVLR***************************************************LSAFGEYEVPMRLPKAIPLPEGKVQWTLNV*****
Disordered Region (DISOPRED)
*****AVPNIEKFAHLIREQRRIC***********************KAARRLENARLVLRRFPNIE************ELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVR**
Disordered Region (DISEMBL)
MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRGK
Disordered Region (DISPRO)
*PKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRGK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	147
356558761	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.662	0.626	5e-50
255634861	222	unknown [Glycine max]	1.0	0.662	0.633	9e-50
388493818	222	unknown [Lotus japonicus]	1.0	0.662	0.646	9e-50
356517474	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.662	0.633	1e-49
356571485	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.662	0.633	1e-49
255645711	150	unknown [Glycine max]	1.0	0.98	0.626	1e-49
224118314	219	predicted protein [Populus trichocarpa]	1.0	0.671	0.653	7e-46
224146953	219	predicted protein [Populus trichocarpa]	1.0	0.671	0.646	1e-45
224115542	219	predicted protein [Populus trichocarpa]	1.0	0.671	0.646	2e-45
357486623	222	50S ribosomal protein L9 [Medicago trunc	1.0	0.662	0.593	5e-45

>gi|356558761|ref|XP_003547671.1| PREDICTED: 50S ribosomal protein L9-like [Glycine max]

 Score =  202 bits (513), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 94/150 (62%), Positives = 126/150 (84%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEE---EVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLA PNI+KFAHL+ EQR+I QP EEE   +V ++++S+++M +E+EKAA RL+ A+
Sbjct: 73  MPKLLAFPNIDKFAHLLNEQRKIYQPTEEEKQEDVTLVKESKEDMMKEYEKAALRLDKAK 132

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  N++K +SR SKDDP+ELR PVTK+ LVAEV+RQ+ +++ P+NLHLPSPL+  G
Sbjct: 133 LVLRRLINVQKAKSRESKDDPLELRYPVTKDILVAEVSRQICVNVAPDNLHLPSPLATLG 192

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+RLP++IPLPEGKV W+L VK+R K
Sbjct: 193 EYEVPLRLPRSIPLPEGKVNWSLKVKIRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255634861|gb|ACU17789.1| unknown [Glycine max]

 Score =  201 bits (511), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 95/150 (63%), Positives = 126/150 (84%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEE---EVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLA PNI+KFA+L+ EQR+I QP EEE   +V ++++S+++M +E+EKAA RL+ A+
Sbjct: 73  MPKLLAFPNIDKFAYLLNEQRKIYQPTEEEKQEDVTLVKESKEDMMKEYEKAALRLDKAQ 132

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  N++K +SR SK+DP+ELR PVTK+ LVAEVARQL +++ P+NLHLPSPLS  G
Sbjct: 133 LVLRRLINVQKAKSRESKEDPLELRYPVTKDTLVAEVARQLCVNVAPDNLHLPSPLSTLG 192

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+R+P++IPLPEGKV W+L VKVR K
Sbjct: 193 EYEVPLRIPRSIPLPEGKVNWSLKVKVRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388493818|gb|AFK34975.1| unknown [Lotus japonicus]

 Score =  201 bits (511), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 97/150 (64%), Positives = 127/150 (84%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEE---EVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLAVPNI+KFA+L+ EQR+I QP EEE   +V V+++S++++ +E+E AA RL+ A+
Sbjct: 73  MPKLLAVPNIDKFAYLLTEQRKIYQPTEEEKQEDVTVVKESKEDLMKEYEAAALRLDKAK 132

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  +++K ++RASKD+P+E+R PVTKE LVAEVARQL ++I PENLHLPSPLS  G
Sbjct: 133 LVLRRLIDVKKAKARASKDEPLEIRLPVTKEVLVAEVARQLCVNIAPENLHLPSPLSTVG 192

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+RLP++IPLPEGKV W+L VKVR K
Sbjct: 193 EYEVPLRLPRSIPLPEGKVNWSLQVKVRSK 222

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517474|ref|XP_003527412.1| PREDICTED: 50S ribosomal protein L9-like isoform 1 [Glycine max] gi|356517476|ref|XP_003527413.1| PREDICTED: 50S ribosomal protein L9-like isoform 2 [Glycine max]

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 95/150 (63%), Positives = 126/150 (84%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEE---EVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLA PNI+KFA+L+ EQR+I QP EEE   +V ++++S+++M +E+EKAA RL+ A+
Sbjct: 73  MPKLLAFPNIDKFAYLLNEQRKIYQPTEEEKQEDVTLVKESKEDMMKEYEKAALRLDKAQ 132

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  N++K +SR SK+DP+ELR PVTK+ LVAEVARQL +++ P+NLHLPSPLS  G
Sbjct: 133 LVLRRLINVQKAKSRESKEDPLELRYPVTKDTLVAEVARQLCVNVAPDNLHLPSPLSTLG 192

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+R+P++IPLPEGKV W+L VKVR K
Sbjct: 193 EYEVPLRIPRSIPLPEGKVNWSLKVKVRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571485|ref|XP_003553907.1| PREDICTED: 50S ribosomal protein L9-like [Glycine max]

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 95/150 (63%), Positives = 126/150 (84%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEE---EVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLA PNI+KFA+L+ EQR+I QP EEE   +V ++++S+++M +E+EKAA RL+ A+
Sbjct: 73  MPKLLAFPNIDKFAYLLNEQRKIYQPTEEENQEDVTLVKESKEDMMKEYEKAALRLDKAK 132

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  N++K +SR SK+DP+ELR PVTK+ LVAEVARQL +++ P+NLHLPSPLS  G
Sbjct: 133 LVLRRLINVQKAKSRESKEDPLELRYPVTKDILVAEVARQLCVNVAPDNLHLPSPLSTLG 192

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+RLP++IPLPEGKV W+L VK+R K
Sbjct: 193 EYEVPLRLPRSIPLPEGKVNWSLKVKIRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645711|gb|ACU23349.1| unknown [Glycine max]

 Score =  200 bits (509), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 94/150 (62%), Positives = 126/150 (84%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEE---EVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLA PNI+KFAHL+ EQR+I QP EEE   +V ++++S+++M +E+EKAA RL+ A+
Sbjct: 1   MPKLLAFPNIDKFAHLLNEQRKIYQPTEEEKQEDVTLVKESKEDMMKEYEKAALRLDKAK 60

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  N++K +SR SKDDP+ELR PVTK+ LVAEV+RQ+ +++ P+NLHLPSPL+  G
Sbjct: 61  LVLRRLINVQKAKSRESKDDPLELRYPVTKDILVAEVSRQICVNVAPDNLHLPSPLATLG 120

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+RLP++IPLPEGKV W+L VK+R K
Sbjct: 121 EYEVPLRLPRSIPLPEGKVNWSLKVKIRSK 150

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118314|ref|XP_002317788.1| predicted protein [Populus trichocarpa] gi|222858461|gb|EEE96008.1| predicted protein [Populus trichocarpa]

 Score =  188 bits (477), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 96/147 (65%), Positives = 121/147 (82%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVL 60
           MPKLLAVPNIEKFAHLIREQR+I QP EEEEVKV++++ ++  +E+E AA+R   ARL  
Sbjct: 73  MPKLLAVPNIEKFAHLIREQRKIYQPEEEEEVKVVKETMEDKMKEYETAAKRFVKARLAF 132

Query: 61  RRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYE 120
           R   N  K RSR SKDDPIE+ SPVTK++++ EV RQ ++ IEP+N+HLPSPL+A GE+E
Sbjct: 133 RVGINTAKFRSRESKDDPIEILSPVTKDDILKEVTRQFNVQIEPDNVHLPSPLTALGEFE 192

Query: 121 VPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           VP+R PK+IPLPEGKV+WTL VK+RGK
Sbjct: 193 VPLRFPKSIPLPEGKVKWTLQVKIRGK 219

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146953|ref|XP_002336372.1| predicted protein [Populus trichocarpa] gi|222834835|gb|EEE73284.1| predicted protein [Populus trichocarpa]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 95/147 (64%), Positives = 122/147 (82%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVL 60
           MPKLLAVPNIEKFAHLIREQR+I QP EEEEVKV++++ ++  +E+E AA+RL  ARL  
Sbjct: 73  MPKLLAVPNIEKFAHLIREQRKIYQPEEEEEVKVVKETMEDKMKEYETAAKRLVKARLAF 132

Query: 61  RRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYE 120
           R   N  K R+R SKDDPIE+ SPVTK++++ EV RQ ++ IEP+N+HLPSPL+A GE+E
Sbjct: 133 RVGINTAKFRARESKDDPIEILSPVTKDDILKEVTRQFNVQIEPDNVHLPSPLTALGEFE 192

Query: 121 VPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           VP+R PK+IP+PEGKV+WTL VK+RGK
Sbjct: 193 VPLRFPKSIPMPEGKVKWTLKVKIRGK 219

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115542|ref|XP_002332160.1| predicted protein [Populus trichocarpa] gi|222875210|gb|EEF12341.1| predicted protein [Populus trichocarpa]

 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 95/147 (64%), Positives = 122/147 (82%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVL 60
           MPKLLAVPNIEKFAHLIREQR+I QP EEEEVKV++++ ++  +E+E AA+RL  A+L  
Sbjct: 73  MPKLLAVPNIEKFAHLIREQRKIYQPEEEEEVKVVKETMEDKMKEYETAAKRLVKAQLAF 132

Query: 61  RRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYE 120
           R   N  K R+R SKDDPIE+ SPVTK++++ EV RQ ++ IEP+N+HLPSPL+A GE+E
Sbjct: 133 RVGINTAKFRARESKDDPIEILSPVTKDDILKEVTRQFNVQIEPDNVHLPSPLTALGEFE 192

Query: 121 VPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           VP+R PK+IPLPEGKV+WTL VK+RGK
Sbjct: 193 VPLRFPKSIPLPEGKVKWTLKVKIRGK 219

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357486623|ref|XP_003613599.1| 50S ribosomal protein L9 [Medicago truncatula] gi|355514934|gb|AES96557.1| 50S ribosomal protein L9 [Medicago truncatula]

 Score =  185 bits (470), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 89/150 (59%), Positives = 122/150 (81%), Gaps = 3/150 (2%)

Query: 1   MPKLLAVPNIEKFAHLIREQRRICQPVEE---EEVKVIRKSEDNMSREFEKAARRLENAR 57
           MPKLLAVPNI+KFA+L+ EQR+I QP EE   E+V V+ +S++++ +E+E+AA  L+ A+
Sbjct: 73  MPKLLAVPNIDKFAYLLTEQRKIYQPTEEVKQEDVVVVTESKEDLMKEYERAALILDKAK 132

Query: 58  LVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG 117
           LVLRR  +++K ++R SKD+P+EL+ PV+K  LVAEVARQL ++I  ENLHLP+PLS  G
Sbjct: 133 LVLRRLIDVKKAKARESKDEPLELQIPVSKNALVAEVARQLCVNITAENLHLPTPLSTIG 192

Query: 118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK 147
           EYEVP+RLP++IPLPEGK+ W L VK+R K
Sbjct: 193 EYEVPLRLPRSIPLPEGKLNWALKVKIRSK 222

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	147
TAIR|locus:2168377	221	AT5G53070 [Arabidopsis thalian	0.993	0.660	0.585	3.5e-43

TAIR|locus:2168377 AT5G53070 [Arabidopsis thaliana (taxid:3702)]

 Score = 456 (165.6 bits), Expect = 3.5e-43, P = 3.5e-43
 Identities = 86/147 (58%), Positives = 119/147 (80%)

Query:     1 MPKLLAVPNIEKFAHLIREQRRICQPVE-EEEVKVIRKSEDNMSREFEKAARRLENARLV 59
             MPKLLAVPNI+K+A+LIREQR++    E +EEVKV+ K+ +  ++E+EKAA+RL NA LV
Sbjct:    74 MPKLLAVPNIDKYAYLIREQRKMYNHEEVKEEVKVVHKTSEVQTKEYEKAAKRLANANLV 133

Query:    60 LRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEY 119
             LR+  + EK ++R+SKDD  ++++P+TKEE+V+EVARQL + I+P+N+ L +PL  FGEY
Sbjct:   134 LRKLVDKEKFKNRSSKDDKPDVQTPITKEEIVSEVARQLCVKIDPDNVVLAAPLETFGEY 193

Query:   120 EVPMRLPKAIPLPEGKVQWTLNVKVRG 146
             EVP++ PK IPLP+G VQW L VKVRG
Sbjct:   194 EVPLKFPKTIPLPQGTVQWILKVKVRG 220


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.134   0.374    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      147       147   0.00091  103 3  11 22  0.49    31
                                                     30  0.50    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  566 (60 KB)
  Total size of DFA:  123 KB (2079 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.46u 0.06s 22.52t   Elapsed:  00:00:02
  Total cpu time:  22.46u 0.06s 22.52t   Elapsed:  00:00:02
  Start:  Fri May 10 15:08:25 2013   End:  Fri May 10 15:08:27 2013

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0042254 "ribosome biogenesis" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Your Input: grail3.0031018701 hypothetical protein (219 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	147
CHL00160	153	rpl9 ribosomal protein L9; Provisional	99.96
TIGR00158	148	L9 ribosomal protein L9. Ribosomal protein L9 appe	99.96
COG0359	148	RplI Ribosomal protein L9 [Translation, ribosomal	99.96
PRK00137	147	rplI 50S ribosomal protein L9; Reviewed	99.95
PF03948	87	Ribosomal_L9_C: Ribosomal protein L9, C-terminal d	99.94
PRK14538	838	putative bifunctional signaling protein/50S riboso	99.92
KOG4607	222	consensus Mitochondrial ribosomal protein L9 [Tran	97.88
PF01281	48	Ribosomal_L9_N: Ribosomal protein L9, N-terminal d	85.72

>CHL00160 rpl9 ribosomal protein L9; Provisional

Probab=99.96  E-value=1.7e-29  Score=197.10  Aligned_cols=116  Identities=16%  Similarity=0.296  Sum_probs=107.4

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccC-ceEEEEcccccccccccCCCCCC
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENA-RLVLRRFPNIEKLRSRASKDDPI   79 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~-~l~i~~~~g~~~~~~~~~~~~~g   79 (147)
                      ||+++|++||..|++.++.+++..+.           +.++.++++++++++|++. .+++.+++|++           |
T Consensus        36 iP~glA~~AT~~n~~~~e~~~~~~~~-----------~~~~~~~~a~~la~~l~~~~~~~i~~k~ge~-----------g   93 (153)
T CHL00160         36 IPNKMAKVATQGSLKQQKMYQKILDL-----------KLKEAKEKCLKVKQLLEEIQKFSVKKKVGEN-----------N   93 (153)
T ss_pred             cccCchhhCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCCceEEEEEEeCCC-----------C
Confidence            79999999999999999988876655           7778889999999999998 59999999865           5


Q ss_pred             ceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           80 ELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        80 kLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      +||||||++||+++|++++|++|||++|+||+ |+++|+|+|.|+||++|       +|+++|+|++
T Consensus        94 klfGSVt~~dIa~~l~~~~g~~idk~~I~l~~-Ik~~G~~~v~v~L~~~V-------~a~i~v~V~~  152 (153)
T CHL00160         94 QIFGSVTEKEISQIIKNKTNIDLEKQNIELPE-IKTIGIYNIEIKLTSDV-------KANINLQILP  152 (153)
T ss_pred             eEEcccCHHHHHHHHHHhhCCccccceeehhh-ccccEeEEEEEEecCCc-------EEEEEEEEEE
Confidence            99999999999999988889999999999988 99999999999999999       9999999986

>TIGR00158 L9 ribosomal protein L9

Probab=99.96  E-value=4.4e-29  Score=193.66  Aligned_cols=116  Identities=21%  Similarity=0.287  Sum_probs=107.4

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      +|++||++||..|++.++.+++..+.           +.++.++++++++++|++..+++.+++|++           |+
T Consensus        31 iP~g~A~~aT~~nl~~~e~~~~~~~~-----------~~~~~~~~a~~l~~~l~~~~~~i~~k~ge~-----------gk   88 (148)
T TIGR00158        31 IPKGLAVPATKKNIEFFEARRKKLEE-----------KLAANKAAAARLKEVLELGTLTISKKVGDE-----------GK   88 (148)
T ss_pred             cccCchhhCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCcEEEEEEEeCCC-----------Ce
Confidence            79999999999999999888877666           667888999999999999999999999866           59


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCc-cccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSP-LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~p-Ik~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||+++|+++ |++|||+.|.||+| ||++|+|.|.|+||++|       +++++|+|.+
T Consensus        89 lfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V-------~a~i~v~V~~  147 (148)
T TIGR00158        89 LFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLHEEV-------FAVLKVIVVP  147 (148)
T ss_pred             EEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEEEEEcCCc-------EEEEEEEEEE
Confidence            99999999999999876 99999999999986 99999999999999999       9999999975

Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.

>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=8.9e-29  Score=192.66  Aligned_cols=116  Identities=22%  Similarity=0.322  Sum_probs=108.4

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      +||+||++||+.|+..++.+++..+.           +....+++++++++.|++..+.+..++|++           |+
T Consensus        31 iPkglAv~At~~n~~~~e~~r~~~e~-----------~~~~~~~~a~~lk~~Le~~~~~i~~kag~~-----------Gk   88 (148)
T COG0359          31 IPKGLAVPATKGNLKLLEARRAKLEK-----------KAAEELAEAEALKEKLEGKTVEIAVKAGED-----------GK   88 (148)
T ss_pred             ccccchhhCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCceEEEEEEcCCC-----------Cc
Confidence            69999999999999999997776666           777888999999999999889999999966           59


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||++++.++ |++|||++|.||++|+++|+|+|+|+||++|       +++++|.|.+
T Consensus        89 lfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vkLh~eV-------~a~v~v~V~~  146 (148)
T COG0359          89 LFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVKLHEEV-------TATVKVNVVA  146 (148)
T ss_pred             eeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEEecCce-------EEEEEEEEEe
Confidence            99999999999999998 9999999999999999999999999999999       9999999976

>PRK00137 rplI 50S ribosomal protein L9; Reviewed

Probab=99.95  E-value=5.9e-28  Score=186.79  Aligned_cols=116  Identities=24%  Similarity=0.389  Sum_probs=107.9

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      +|++||++||..|+..++..++..+.           +.++.++++++++..|++..+++.+++|++           |+
T Consensus        31 iP~~lA~~aT~~~~~~~~~~~~~~~~-----------~~~~~~~~a~~l~~~l~~~~l~i~~k~g~~-----------gk   88 (147)
T PRK00137         31 IPQGKAVRATKGNLKQLEARRAELEA-----------KAAEELAEAEALAEKLEGLTVTIKAKAGED-----------GK   88 (147)
T ss_pred             ccCCceeeCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCCEEEEEEEcCCC-----------Ce
Confidence            79999999999999999988777655           677889999999999999999999999855           59


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||+++|.++ |++||++.|.||+||+++|+|.|+|+||++|       +|+++|+|.+
T Consensus        89 lfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i~L~~~v-------~a~l~v~V~~  146 (147)
T PRK00137         89 LFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPVKLHPEV-------TATIKVNVVA  146 (147)
T ss_pred             EEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEEEECCCc-------EEEEEEEEEE
Confidence            99999999999999887 9999999999999999999999999999999       9999999986

>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.94  E-value=2.4e-26  Score=164.01  Aligned_cols=86  Identities=27%  Similarity=0.462  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHhccCceEEEEcccccccccccCCCCCCceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEE
Q 032091           43 SREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVP  122 (147)
Q Consensus        43 ~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~  122 (147)
                      +++|++++++|++..+++.+++|++           |+||||||++||+++|++++|++|||++|.||+|||++|+|+|+
T Consensus         1 k~~A~~l~~~l~~~~l~i~~k~g~~-----------gklfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~   69 (87)
T PF03948_consen    1 KAEAQALAEKLEGITLTIKRKAGEN-----------GKLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVK   69 (87)
T ss_dssp             HHHHHHHHHHHCSSEEEEEECBSSC-----------SSBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEE
T ss_pred             CHHHHHHHHHhcCCEEEEEEEecCC-----------cceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEE
Confidence            4688999999999999999999865           59999999999999999988999999999999999999999999


Q ss_pred             EEcCCCCCCCCCceEEEEEEEEEc
Q 032091          123 MRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus       123 I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      |+||++|       +|+++|+|.+
T Consensus        70 v~L~~~V-------~a~i~v~V~~   86 (87)
T PF03948_consen   70 VKLHPEV-------SAKIKVNVVA   86 (87)
T ss_dssp             EEEETTE-------EEEEEEEEEE
T ss_pred             EEeCCCe-------EEEEEEEEEe
Confidence            9999999       9999999975

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....

>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional

Probab=99.92  E-value=5e-25  Score=207.44  Aligned_cols=117  Identities=17%  Similarity=0.214  Sum_probs=109.5

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      +|++||++||+.|++.++.+++..+.           +.++.+++|++++++|++.++++.+++|++           |+
T Consensus       718 iP~~~A~~aT~~nlk~~e~~~~~~~~-----------~~~~~~~~a~~l~~~l~~~~~~i~~k~ge~-----------gk  775 (838)
T PRK14538        718 IQNKKALLADKENLAKIKKKKILEQE-----------KKRNHELLMKKLKSEIDNKKITLDIQLGPK-----------GK  775 (838)
T ss_pred             ccCCchhhcCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCcEEEEEEEeCCC-----------Ce
Confidence            79999999999999999998877666           777888999999999999999999999966           49


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||+++|++++|++|||+.|.||+|||++|+|.|.|+||++|       +|+++|+|+.
T Consensus       776 lfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~~~V-------~a~i~v~V~~  834 (838)
T PRK14538        776 IYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDVFLTDQI-------KATFFLNVIE  834 (838)
T ss_pred             eeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEEEEcCCe-------EEEEEEEEEE
Confidence            9999999999999998889999999999999999999999999999999       9999999974

>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

Probab=97.88  E-value=2.4e-05  Score=64.78  Aligned_cols=113  Identities=19%  Similarity=0.172  Sum_probs=76.8

Q ss_pred             CCCcccccccHHHHHH--HHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCC
Q 032091            1 MPKLLAVPNIEKFAHL--IREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDP   78 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~--~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~   78 (147)
                      ||++||+.|+-.|...  +.++++.+...             .-..++..++ -|+...+.....-+...          
T Consensus        79 lp~glAvy~tp~~~~~~k~~~~e~~~~k~-------------~vk~e~k~V~-~lqt~v~~~~~~k~~kw----------  134 (222)
T KOG4607|consen   79 LPKGLAVYNTPLNLKKYKLREQEEEAEKI-------------RVKEEAKVVA-VLQTVVLFKVMNKGGKW----------  134 (222)
T ss_pred             ccccccccCChhhHHHHHHHHHHHHhhhh-------------ccHHHHHHHH-HHHhhhhhheeccCCce----------
Confidence            7999999999999433  33344333331             1222232333 45544433333333221          


Q ss_pred             CceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEE
Q 032091           79 IELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVR  145 (147)
Q Consensus        79 gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~  145 (147)
                      -=-|++|+++.....+.+++-+.+|++-|+.|. ++.-|+|.+.|+++++.       ++-+...|.
T Consensus       135 ~l~~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~-~k~e~~~~~~V~in~~~-------~vr~~~~v~  193 (222)
T KOG4607|consen  135 KLNPNLVKASLRKGVIVAELTIKLDKELVSGPI-TKEEGEYICEVKINPDV-------TVRVKIRVT  193 (222)
T ss_pred             eecHHHHHHHHhcceEeccccccCcccccCCCc-ccccceEEEEEEECCcc-------eEEeeeeee
Confidence            135899999998888877788999999999986 78888999999999999       888777664

>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=85.72  E-value=0.58  Score=30.26  Aligned_cols=18  Identities=22%  Similarity=0.217  Sum_probs=16.3

Q ss_pred             CCCcccccccHHHHHHHH
Q 032091            1 MPKLLAVPNIEKFAHLIR   18 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~   18 (147)
                      +|+++|+.||..+++.++
T Consensus        31 ~p~~~A~~at~~~~~~~e   48 (48)
T PF01281_consen   31 IPQGLAVYATPENLKQLE   48 (48)
T ss_dssp             TTTTSEEECSHHHHHHHH
T ss_pred             cCCCceeeCCHHHHHhcC
Confidence            699999999999998764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	147
1div_A	149	Ribosomal protein L9; rRNA-binding; 2.60A {Geobaci	99.97
1nkw_F	146	50S ribosomal protein L9; ribosome, large subunit,	99.97
3r8s_H	149	50S ribosomal protein L9; protein biosynthesis, RN	99.97
3v2d_I	148	50S ribosomal protein L9; ribosome associated inhi	99.97
3bbo_J	197	Ribosomal protein L9; large ribosomal subunit, spi	99.94
2hba_A	52	BL17, 50S ribosomal protein L9; NTL9, K12M, RNA bi	94.94

>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K

Probab=99.97  E-value=1e-31  Score=207.55  Aligned_cols=117  Identities=17%  Similarity=0.239  Sum_probs=110.3

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      ||++||++||..|++.++++++..+.           +.++.++++++++++|++..+++.+++|++|           +
T Consensus        31 iP~glA~~AT~~n~~~~e~~~~~~~~-----------~~~~~~~~A~~~a~~L~~~~v~i~~k~g~~g-----------k   88 (149)
T 1div_A           31 FKQGLAIEATPANLKALEAQKQKEQR-----------QAAEELANAKKLKEQLEKLTVTIPAKAGEGG-----------R   88 (149)
T ss_dssp             TTTTSEEECCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHTTCCEEEEECBCGGG-----------E
T ss_pred             ccCCceecCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHcCCeEEEEEEeCCCC-----------c
Confidence            79999999999999999988877665           7778999999999999999999999999765           9


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||+++|++++|++|||+.|.||+|||++|+|+|+|+||++|       +++|+|+|.+
T Consensus        89 lfGSVt~~dIa~al~~~~g~~idk~~I~l~~~Ik~~G~~~v~vkLh~~V-------~a~i~v~V~~  147 (149)
T 1div_A           89 LFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPVKLHPEV-------TATLKVHVTE  147 (149)
T ss_dssp             EEEEECHHHHHHHHHHHHCCCCCGGGBCCCSCEEESEEEEEEEEEETTE-------EEEEEEEEEE
T ss_pred             EEeecCHHHHHHHHHHhhCCeechheEECCCCccccEEEEEEEEECCCC-------EEEEEEEEEe
Confidence            9999999999999999889999999999999999999999999999999       9999999985

>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I

Probab=99.97  E-value=4e-31  Score=203.66  Aligned_cols=115  Identities=17%  Similarity=0.311  Sum_probs=108.4

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      ||++||++||..|++.++++++..+.           +.++.++++++++++|++..+++.+++| +|           +
T Consensus        30 iP~glA~~AT~~n~~~~e~~~~~~~~-----------~~~~~~~~A~~~a~~L~~~~v~i~~k~g-~g-----------k   86 (146)
T 1nkw_F           30 IPQGLAVSATRTNMKTLEAQLRSIEK-----------RQAQEKAVAEDLASRLNGVAVELSVRAG-EG-----------K   86 (146)
T ss_pred             ccCCceecCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCCEEEEEEEcC-CC-----------c
Confidence            79999999999999999998877665           7778999999999999999999999998 64           9


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||+++|+++ |++|||+.|.||+|||++|+|+|+|+||++|       +++|+|+|.+
T Consensus        87 lfGSVt~~dIa~al~~~-g~~idk~~I~l~~~Ik~~G~~~v~vkLh~~V-------~a~i~v~V~~  144 (146)
T 1nkw_F           87 IYGAVTHQDVANSLDQL-GFDVDRRKIDMPKTVKEVGEYDIAYRAHPEV-------TIPMKLVVHA  144 (146)
T ss_pred             eeeccCHHHHHHHHHHc-CCeechheEECCCcccccEEEEEEEEECCCC-------EEEEEEEEEe
Confidence            99999999999999998 9999999999999999999999999999999       9999999985

>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...

Probab=99.97  E-value=5.3e-31  Score=203.54  Aligned_cols=116  Identities=16%  Similarity=0.233  Sum_probs=107.8

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccC-ceEEEEcccccccccccCCCCCC
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENA-RLVLRRFPNIEKLRSRASKDDPI   79 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~-~l~i~~~~g~~~~~~~~~~~~~g   79 (147)
                      ||++||++||..|++.++++++..+.           +.++.++++++++++|++. .+++.+++|++           |
T Consensus        31 iP~glA~~AT~~n~k~~e~~~~~~~~-----------~~~~~~~~A~~~~~~L~~~~~v~i~~k~g~~-----------g   88 (149)
T 3r8s_H           31 VPQGKAVPATKKNIEFFEARRAELEA-----------KLAEVLAAANARAEKINALETVTIASKAGDE-----------G   88 (149)
T ss_dssp             SSSSSEECCCSHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHTTCCEEEEECBCTT-----------S
T ss_pred             ccCCceeeCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCCcEEEEEEEcCCC-----------C
Confidence            79999999999999999988776555           7778899999999999997 99999999865           5


Q ss_pred             ceeeccCHHHHHHHHHhhcCCccccccccCCC-ccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           80 ELRSPVTKEELVAEVARQLSISIEPENLHLPS-PLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        80 kLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~-pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      +||||||++||+++|+++ |++|||+.|.||+ |||++|+|+|+|+||++|       +++|+|+|++
T Consensus        89 klfGSVt~~dIa~al~~~-g~~idk~~I~l~~~pIk~~G~~~v~v~Lh~~V-------~a~i~v~V~~  148 (149)
T 3r8s_H           89 KLFGSIGTRDIADAVTAA-GVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEV-------FAKVIVNVVA  148 (149)
T ss_dssp             EEEEEECHHHHHHHHHTT-SCCCCTTSEECSSCCEEESEEEEEEECSSSSC-------CCCEEEEEEE
T ss_pred             ceEcccCHHHHHHHHHHc-CCceehheEEcCCccccceEEEEEEEEECCCC-------EEEEEEEEEE
Confidence            999999999999999887 9999999999997 999999999999999999       9999999985

>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ...

Probab=99.97  E-value=6.2e-31  Score=203.01  Aligned_cols=116  Identities=23%  Similarity=0.353  Sum_probs=108.3

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE   80 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk   80 (147)
                      ||+++|++||..|++.++++++..+.           +.++.++++++++++|++..+++.+++|           ++ +
T Consensus        31 iP~g~A~~AT~~n~k~~e~~~~~~~~-----------~~~~~~~~A~~~~~~L~~~~v~i~~kag-----------~~-k   87 (148)
T 3v2d_I           31 LPRGLAVLATESNLKALEARIRAQAK-----------RLAERKAEAERLKEILENLTLTIPVRAG-----------ET-K   87 (148)
T ss_dssp             GGGTSEEECCHHHHHHHHHHHHTHHH-----------HHHHHHHHHHHHHHHSSSCCEEEECCBS-----------SS-S
T ss_pred             cccCchhhcCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHcCCEEEEEEEcC-----------CC-c
Confidence            69999999999999999988776655           7788999999999999999999999987           55 9


Q ss_pred             eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      ||||||++||+++|++++|++|||+.|.||+|||++|+|+|+|+||++|       +++++|+|.+
T Consensus        88 LfGSVt~~dIa~al~~~~g~~idk~~I~l~~pIk~~G~~~v~v~Lh~~V-------~a~i~v~V~~  146 (148)
T 3v2d_I           88 IYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTYKPHPEV-------PIQLKVSVVA  146 (148)
T ss_dssp             BSSCBCHHHHHHHHTTTTCCCCCTTSSCCSSCBCSCEEEEEECCSBTTB-------CCEEEEEEEC
T ss_pred             cccccCHHHHHHHHHHhcCCCcchheEEcCchhhceEEEEEEEEECCCc-------EEEEEEEEEe
Confidence            9999999999999998889999999999999999999999999999999       9999999975

>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=99.94  E-value=3.1e-29  Score=201.50  Aligned_cols=116  Identities=16%  Similarity=0.220  Sum_probs=105.2

Q ss_pred             CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccC-ceEEEEcccccccccccCCCCCC
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENA-RLVLRRFPNIEKLRSRASKDDPI   79 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~-~l~i~~~~g~~~~~~~~~~~~~g   79 (147)
                      ||++||++||..|++.++++++..+.           +.++.++++++++++|++. .+++.+++|++           |
T Consensus        80 iP~glAv~AT~~nlk~~e~~~~~~e~-----------~~~~~~~~A~~la~~L~~~~~v~i~~kaGe~-----------G  137 (197)
T 3bbo_J           80 LPTGKAQLMTPLLLKELKMEDERIEA-----------EKQRVKEEAQQLAMVFQTVGAFKVKRKGGKG-----------K  137 (197)
T ss_dssp             TTTTCCCCCCHHHHHHHHTTTHHHHG-----------GGTTTTHHHHTHHHHSSSCCCCBCCCCBCTT-----------S
T ss_pred             ccCCceecCCHHHHHHHHHhHHHHHH-----------HHHHHHHHHHHHHHHhcCCceEEEEEEeCCC-----------C
Confidence            79999999999999999887776665           5567788999999999998 58888888755           5


Q ss_pred             ceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091           80 ELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus        80 kLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      +||||||++||+++|++++|++|||+.|.||+ ||++|+|+|+|+||++|       +++|+|+|.+
T Consensus       138 kLFGSVT~~dIa~al~~~~Gi~Idk~~I~L~~-IK~lG~y~V~VkLh~eV-------~a~i~V~V~~  196 (197)
T 3bbo_J          138 LIFGSVTAQDLVDIIKSQLQKDIDKRLVSLPE-IRETGEYIAELKLHPDV-------TARVKINVFA  196 (197)
T ss_dssp             SBSSCCSSHHHHGGGTSSSSCCCCSTTCCSCC-CSSSSCEEECCCCBTTB-------CCCEEEBCCC
T ss_pred             cEecccCHHHHHHHHHHhhCCeeeeeEEEecc-ccceEEEEEEEEECCCc-------EEEEEEEEEe
Confidence            99999999999999998889999999999985 99999999999999999       9999999875

>2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein; 1.25A {Geobacillus stearothermophilus} SCOP: d.100.1.1 PDB: 1cqu_A 2hbb_A 2hvf_A

Probab=94.94  E-value=0.012  Score=37.93  Aligned_cols=21  Identities=14%  Similarity=0.145  Sum_probs=19.7

Q ss_pred             CCCcccccccHHHHHHHHHHH
Q 032091            1 MPKLLAVPNIEKFAHLIREQR   21 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~   21 (147)
                      +|+++|++||..|++.+++++
T Consensus        31 iP~g~A~~AT~~n~~~~~~~~   51 (52)
T 2hba_A           31 FKQGLAIEATPANLKALEAQK   51 (52)
T ss_dssp             TTTTSEEECCHHHHHHHHHHH
T ss_pred             ccCCceeeCCHHHHHHHHHhh
Confidence            799999999999999999876

---

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	147
d1diva1	94	d.99.1.1 (A:56-149) Ribosomal protein L9 C-domain	6e-04

>d1diva1 d.99.1.1 (A:56-149) Ribosomal protein L9 C-domain {Bacillus stearothermophilus [TaxId: 1422]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 34.8 bits (80), Expect = 6e-04
 Identities = 15/79 (18%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 48  KAARRLENARLVLRRFPNIE-KLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPEN 106
           +AA  L NA+ +  +   +   + ++A +     L   +T +++   +  Q  + ++   
Sbjct: 2   QAAEELANAKKLKEQLEKLTVTIPAKAGEGG--RLFGSITSKQIAESLQAQHGLKLDKRK 59

Query: 107 LHLPSPLSAFGEYEVPMRL 125
           + L   + A G   VP++L
Sbjct: 60  IELADAIRALGYTNVPVKL 78

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	147
d1diva1	94	Ribosomal protein L9 C-domain {Bacillus stearother	99.94
d2j01i1	91	Ribosomal protein L9 C-domain {Thermus thermophilu	99.92
d2gycf1	91	Ribosomal protein L9 C-domain {Escherichia coli [T	99.92
d2hbaa1	52	Ribosomal protein L9 N-domain {Bacillus stearother	94.65
d2j01i2	55	Ribosomal protein L9 N-domain {Thermus thermophilu	93.66
d2gycf2	58	Ribosomal protein L9 N-domain {Escherichia coli [T	93.46

>d1diva1 d.99.1.1 (A:56-149) Ribosomal protein L9 C-domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.94  E-value=2e-27  Score=169.07  Aligned_cols=92  Identities=17%  Similarity=0.283  Sum_probs=86.5

Q ss_pred             hHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCceeeccCHHHHHHHHHhhcCCccccccccCCCccccce
Q 032091           38 SEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFG  117 (147)
Q Consensus        38 ~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG  117 (147)
                      +.++.++++++++++|++..++|.+++|++|           +||||||++||+++|..++|++|||++|.||+|||++|
T Consensus         2 k~~~~~~~A~~la~~L~~~~i~i~~k~ge~G-----------kLfGSVt~~dI~~~l~~~~g~~idk~~I~l~~~IK~~G   70 (94)
T d1diva1           2 QAAEELANAKKLKEQLEKLTVTIPAKAGEGG-----------RLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALG   70 (94)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEECBCGGG-----------EEEEEECHHHHHHHHHHHHCCCCCGGGBCCCSCEEESE
T ss_pred             hHHHHHHHHHHHHHHhhCCEEEEEEEECCCC-----------eeEecccHHHHHHHHHHccCceecHHHhhccCchhhcE
Confidence            5567888999999999999999999999775           99999999999999988889999999999999999999


Q ss_pred             eEEEEEEcCCCCCCCCCceEEEEEEEEEcC
Q 032091          118 EYEVPMRLPKAIPLPEGKVQWTLNVKVRGK  147 (147)
Q Consensus       118 ~~~V~I~L~~~V~~~~~~~~a~l~V~V~~~  147 (147)
                      +|+|.|+||++|       +++++|+|.+.
T Consensus        71 ~y~v~i~Lh~~V-------~a~i~v~V~~e   93 (94)
T d1diva1          71 YTNVPVKLHPEV-------TATLKVHVTEQ   93 (94)
T ss_dssp             EEEEEEEEETTE-------EEEEEEEEEEC
T ss_pred             eEEEEEEecCCe-------EEEEEEEEEeC
Confidence            999999999999       99999999863

>d2j01i1 d.99.1.1 (I:56-146) Ribosomal protein L9 C-domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=3.6e-27  Score=166.87  Aligned_cols=88  Identities=24%  Similarity=0.388  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeE
Q 032091           40 DNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEY  119 (147)
Q Consensus        40 ~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~  119 (147)
                      +++++++++++++|++..+++.+++|+            |+||||||++||+++|.+++|++|||++|.||.|||++|.|
T Consensus         4 ae~~~~A~~l~~~L~~~~i~i~~k~~e------------gkLfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~   71 (91)
T d2j01i1           4 AERKAEAERLKEILENLTLTIPVRAGE------------TKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEY   71 (91)
T ss_dssp             SSTTTTTHHHHHHHTTCBCCCCCCBCS------------SSBSSCCCHHHHHHHHHTTTCCCCCTTTTCCSSCCCSCEEE
T ss_pred             HHHHHHHHHHHHHhcCCEEEEEEEecC------------CceecccCHHHHHHHHHhccCceechHHhhccccccceEEE
Confidence            345667889999999999999888873            49999999999999999888999999999999999999999


Q ss_pred             EEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091          120 EVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus       120 ~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      .|.|+||++|       +++|+|+|++
T Consensus        72 ~v~i~L~~~V-------~a~i~v~VvA   91 (91)
T d2j01i1          72 VLTYKPHPEV-------PIQLKVSVVA   91 (91)
T ss_dssp             ECCCSSSSCC-------CCEEEECCC-
T ss_pred             EEEEEecCCE-------EEEEEEEEEC
Confidence            9999999999       9999999864

>d2gycf1 d.99.1.1 (F:59-149) Ribosomal protein L9 C-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Escherichia coli [TaxId: 562]

Probab=99.92  E-value=2.7e-25  Score=157.50  Aligned_cols=87  Identities=15%  Similarity=0.229  Sum_probs=80.9

Q ss_pred             HHHHHHHHHHHHhccC-ceEEEEcccccccccccCCCCCCceeeccCHHHHHHHHHhhcCCccccccccCCC-cccccee
Q 032091           41 NMSREFEKAARRLENA-RLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPS-PLSAFGE  118 (147)
Q Consensus        41 ~~~~eae~~a~~L~~~-~l~i~~~~g~~~~~~~~~~~~~gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~-pIk~lG~  118 (147)
                      +.+++|++++++|++. .++|.+++|++           |+||||||++||+++|.++ |++|||++|.||+ |||++|+
T Consensus         2 e~l~~A~~~a~kl~~~~~i~i~~kage~-----------GkLfGSVt~~dI~~~l~~~-g~~Idk~~I~l~~~~IK~lG~   69 (91)
T d2gycf1           2 EVLAAANARAEKINALETVTIASKAGDE-----------GKLFGSIGTRDIADAVTAA-GVEVAKSEVRLPNGVLRTTGE   69 (91)
T ss_dssp             HHHHHHHHHHHHHTTTCCCEEEECEEET-----------TEESSCCCHHHHHHHHTTT-TCCCCSTTSCCSSCCCCBSSE
T ss_pred             hHHHHHHHHHHHhcCCcEEEEEEEeCCC-----------CeeeeecCHHHHHHHHHHc-CCcccHHHEECCCccccccEE
Confidence            4678899999999997 59999999966           4999999999999999986 9999999999987 8999999


Q ss_pred             EEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091          119 YEVPMRLPKAIPLPEGKVQWTLNVKVRG  146 (147)
Q Consensus       119 ~~V~I~L~~~V~~~~~~~~a~l~V~V~~  146 (147)
                      |+|.|+||++|       +++++|+|.+
T Consensus        70 y~v~i~Lh~~V-------~~~i~v~Vv~   90 (91)
T d2gycf1          70 HEVSFQVHSEV-------FAKVIVNVVA   90 (91)
T ss_dssp             EEEEECSSSSC-------CEEEEEEEEE
T ss_pred             EEEEEEEcCCE-------EEEEEEEEEE
Confidence            99999999999       9999999986

>d2hbaa1 d.100.1.1 (A:1-52) Ribosomal protein L9 N-domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.65  E-value=0.0071  Score=37.37  Aligned_cols=22  Identities=14%  Similarity=0.161  Sum_probs=20.0

Q ss_pred             CCCcccccccHHHHHHHHHHHH
Q 032091            1 MPKLLAVPNIEKFAHLIREQRR   22 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~   22 (147)
                      +|+++|++||..|+..++++++
T Consensus        31 iP~g~A~~at~~n~~~~~~~k~   52 (52)
T d2hbaa1          31 FKQGLAIEATPANLKALEAQKQ   52 (52)
T ss_dssp             TTTTSEEECCHHHHHHHHHHHC
T ss_pred             ccCCchhhCCHHHHHHHHHhhC
Confidence            7999999999999999988764

>d2j01i2 d.100.1.1 (I:1-55) Ribosomal protein L9 N-domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.66  E-value=0.017  Score=36.03  Aligned_cols=23  Identities=26%  Similarity=0.296  Sum_probs=19.8

Q ss_pred             CCCcccccccHHHHHHHHHHHHh
Q 032091            1 MPKLLAVPNIEKFAHLIREQRRI   23 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~~   23 (147)
                      ||+++|++||..|+..++++++.
T Consensus        31 iP~~~A~~at~~nl~~~~~~~~~   53 (55)
T d2j01i2          31 LPRGLAVLATESNLKALEARIRA   53 (55)
T ss_dssp             TTTTSEEECCHHHHHHHHHHHHH
T ss_pred             cccCchhhcCHHHHHHHHHHHHh
Confidence            79999999999999998766543

>d2gycf2 d.100.1.1 (F:1-58) Ribosomal protein L9 N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: Ribosomal protein L9 N-domain
domain: Ribosomal protein L9 N-domain
species: Escherichia coli [TaxId: 562]

Probab=93.46  E-value=0.016  Score=36.33  Aligned_cols=22  Identities=27%  Similarity=0.404  Sum_probs=19.3

Q ss_pred             CCCcccccccHHHHHHHHHHHH
Q 032091            1 MPKLLAVPNIEKFAHLIREQRR   22 (147)
Q Consensus         1 ~p~~la~~a~~~~~~~~~~~~~   22 (147)
                      +|+++|++||..|++.++.++.
T Consensus        31 iP~glA~~at~~n~~~~~~~~~   52 (58)
T d2gycf2          31 VPQGKAVPATKKNIEFFEARRA   52 (58)
T ss_dssp             TTTTSEEECCCHHHHHHHHHHH
T ss_pred             ccCCceecCCHHHHHHHHHHHH
Confidence            7999999999999998876654