Psyllid ID: psy8661

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-
Protein Sequence
MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR
Secondary Structure (PSIPRED)
cccccccEEccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHcccEEEccEEEEcccccEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccEccccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHcccEEEccEEEccccccEEEEEc
Coil and Loop (DISEMBL)
mldklggvfaprpstgphklreslpLVIFLRNRLKYALTNQEVLKILMQRLIKVDgkvrtdtnypagfmvr
Flexible Loop (DISEMBL)
mldklggvfaprpstgphklresLPLVIFLRNRLKYALTNQEVLKILMQRLikvdgkvrtdtnypagfmvr
Low Complexity Region (SEG)
MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR
Disordered region (IsUnstruct)
**********************SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNY*******
Disordered Region (DISOPRED)
**DKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR
Disordered Region (DISEMBL)
MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR
Disordered Region (DISPRO)
*****GGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR
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	71	2.2.26 [Sep-21-2011]
Q4GXU6	261	40S ribosomal protein S4	N/A	N/A	0.971	0.264	0.913	5e-31
Q4PMB3	262	40S ribosomal protein S4	N/A	N/A	0.971	0.263	0.898	1e-29
Q5UAP0	263	40S ribosomal protein S4	N/A	N/A	0.971	0.262	0.884	4e-29
Q95V34	263	40S ribosomal protein S4	N/A	N/A	0.971	0.262	0.884	4e-29
Q56FH2	262	40S ribosomal protein S4	N/A	N/A	0.971	0.263	0.869	7e-29
P41042	261	40S ribosomal protein S4	yes	N/A	0.971	0.264	0.855	1e-28
Q90YS0	263	40S ribosomal protein S4	N/A	N/A	0.971	0.262	0.855	2e-28
O62738	263	40S ribosomal protein S4,	yes	N/A	0.971	0.262	0.840	3e-28
Q6PBC4	263	40S ribosomal protein S4	yes	N/A	0.971	0.262	0.840	4e-28
P49401	263	40S ribosomal protein S4	N/A	N/A	0.971	0.262	0.840	4e-28

>sp|Q4GXU6|RS4_CARGR 40S ribosomal protein S4 OS=Carabus granulatus GN=RpS4 PE=2 SV=1

 Score =  132 bits (332), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGV+APRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVYAPRPSTGPHKLRESLPLVIFLRNRLKYALTNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYP+GFM
Sbjct: 79 DPNYPSGFM 87

Carabus granulatus (taxid: 118799)

>sp|Q4PMB3|RS4_IXOSC 40S ribosomal protein S4 OS=Ixodes scapularis GN=RpS4 PE=2 SV=1

 Score =  128 bits (322), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 62/69 (89%), Positives = 64/69 (92%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPL+I LRNRLKYALT  EV KI+ QRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLIIMLRNRLKYALTGAEVKKIVKQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          DTNYPAGFM
Sbjct: 79 DTNYPAGFM 87

Ixodes scapularis (taxid: 6945)

>sp|Q5UAP0|RS4_BOMMO 40S ribosomal protein S4 OS=Bombyx mori GN=RpS4 PE=2 SV=1

 Score =  126 bits (317), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 61/69 (88%), Positives = 63/69 (91%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGV+APRPSTGPHKLRE LPLVIFLRNRLKYALT  EVLKI+ QRLIKVDGKVRT
Sbjct: 19 MLDKLGGVYAPRPSTGPHKLRECLPLVIFLRNRLKYALTGNEVLKIVKQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DPTYPAGFM 87

Bombyx mori (taxid: 7091)

>sp|Q95V34|RS4_SPOFR 40S ribosomal protein S4 OS=Spodoptera frugiperda GN=RpS4 PE=2 SV=1

 Score =  126 bits (317), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 61/69 (88%), Positives = 63/69 (91%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGV+APRPSTGPHKLRE LPLVIFLRNRLKYALT  EVLKI+ QRLIKVDGKVRT
Sbjct: 19 MLDKLGGVYAPRPSTGPHKLRECLPLVIFLRNRLKYALTGNEVLKIVKQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DPTYPAGFM 87

Spodoptera frugiperda (taxid: 7108)

>sp|Q56FH2|RS4_LYSTE 40S ribosomal protein S4 OS=Lysiphlebus testaceipes GN=RpS4 PE=2 SV=1

 Score =  125 bits (314), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 60/69 (86%), Positives = 63/69 (91%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          ML KLGGV+APRPSTGPHKLRE LPL+IFLRNRLKYALTN EV KI MQRLIKVDGKVRT
Sbjct: 19 MLGKLGGVYAPRPSTGPHKLRECLPLLIFLRNRLKYALTNCEVTKITMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D+NYP GFM
Sbjct: 79 DSNYPLGFM 87

Lysiphlebus testaceipes (taxid: 77504)

>sp|P41042|RS4_DROME 40S ribosomal protein S4 OS=Drosophila melanogaster GN=RpS4 PE=2 SV=2

 Score =  125 bits (313), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 63/69 (91%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPL+IFLRNRLKYAL   EV KI+MQRL+KVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAG+M
Sbjct: 79 DPTYPAGYM 87

Drosophila melanogaster (taxid: 7227)

>sp|Q90YS0|RS4_ICTPU 40S ribosomal protein S4 OS=Ictalurus punctatus GN=rps4 PE=2 SV=3

 Score =  124 bits (310), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 60/69 (86%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IKVDGKVRT
Sbjct: 19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DITYPAGFM 87

Ictalurus punctatus (taxid: 7998)

>sp|O62738|RS4X_MONDO 40S ribosomal protein S4, X isoform OS=Monodelphis domestica GN=RPS4X PE=2 SV=3

 Score =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct: 19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query: 61 DTNYPAGFM 69
          DT YP GFM
Sbjct: 79 DTTYPVGFM 87

Monodelphis domestica (taxid: 13616)

>sp|Q6PBC4|RS4_XENTR 40S ribosomal protein S4 OS=Xenopus tropicalis GN=rps4 PE=2 SV=3

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct: 19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DITYPAGFM 87

Xenopus tropicalis (taxid: 8364)

>sp|P49401|RS4_XENLA 40S ribosomal protein S4 OS=Xenopus laevis GN=rps4 PE=2 SV=4

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct: 19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DITYPAGFM 87

Xenopus laevis (taxid: 8355)

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	71
264667395	261	ribosomal protein S4 [Chrysomela tremula	0.971	0.264	0.942	2e-30
332376168	261	unknown [Dendroctonus ponderosae]	0.971	0.264	0.942	5e-30
70909487	261	ribosomal protein S4e [Mycetophagus quad	0.971	0.264	0.942	5e-30
91083095	261	PREDICTED: similar to ribosomal protein	0.971	0.264	0.942	5e-30
66517407	262	PREDICTED: 40S ribosomal protein S4-like	0.971	0.263	0.927	6e-30
70909479	261	ribosomal protein S4e [Biphyllus lunatus	0.971	0.264	0.942	7e-30
332017152	286	40S ribosomal protein S4 [Acromyrmex ech	0.971	0.241	0.913	1e-29
70909489	262	ribosomal protein S4e [Sphaerius sp. APV	0.971	0.263	0.942	1e-29
307191745	262	40S ribosomal protein S4 [Harpegnathos s	0.971	0.263	0.927	1e-29
321450822	244	hypothetical protein DAPPUDRAFT_300650 [	0.971	0.282	0.913	1e-29

>gi|264667395|gb|ACY71283.1| ribosomal protein S4 [Chrysomela tremula]

 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 67/69 (97%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D+NYPAGFM
Sbjct: 79 DSNYPAGFM 87

Source: Chrysomela tremula

Species: Chrysomela tremula

Genus: Chrysomela

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332376168|gb|AEE63224.1| unknown [Dendroctonus ponderosae]

 Score =  134 bits (338), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DPNYPAGFM 87

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909487|emb|CAJ17168.1| ribosomal protein S4e [Mycetophagus quadripustulatus]

 Score =  134 bits (338), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DPNYPAGFM 87

Source: Mycetophagus quadripustulatus

Species: Mycetophagus quadripustulatus

Genus: Mycetophagus

Family: Mycetophagidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91083095|ref|XP_969262.1| PREDICTED: similar to ribosomal protein S4e [Tribolium castaneum] gi|270006993|gb|EFA03441.1| hypothetical protein TcasGA2_TC013431 [Tribolium castaneum]

 Score =  134 bits (338), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DPNYPAGFM 87

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66517407|ref|XP_623050.1| PREDICTED: 40S ribosomal protein S4-like isoform 1 [Apis mellifera] gi|380027232|ref|XP_003697333.1| PREDICTED: 40S ribosomal protein S4-like [Apis florea]

 Score =  134 bits (337), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 64/69 (92%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGV+APRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVYAPRPSTGPHKLRESLPLVIFLRNRLKYALTNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DANYPAGFM 87

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909479|emb|CAJ17164.1| ribosomal protein S4e [Biphyllus lunatus]

 Score =  134 bits (337), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNCEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DPNYPAGFM 87

Source: Biphyllus lunatus

Species: Biphyllus lunatus

Genus: Biphyllus

Family: Biphyllidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332017152|gb|EGI57951.1| 40S ribosomal protein S4 [Acromyrmex echinatior]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 67/69 (97%)

Query: 1   MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
           MLDKLGGV+APRPSTGPHKLRESLPLVIFLRNRLKYALTN EV+KI+MQRLIKVDGK+RT
Sbjct: 43  MLDKLGGVYAPRPSTGPHKLRESLPLVIFLRNRLKYALTNCEVIKIVMQRLIKVDGKIRT 102

Query: 61  DTNYPAGFM 69
           D NYPAGFM
Sbjct: 103 DPNYPAGFM 111

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909489|emb|CAJ17169.1| ribosomal protein S4e [Sphaerius sp. APV-2005]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNCEVKKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DPNYPAGFM 87

Source: Sphaerius sp. APV-2005

Species: Sphaerius sp. APV-2005

Genus: Sphaerius

Family: Sphaeriusidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307191745|gb|EFN75187.1| 40S ribosomal protein S4 [Harpegnathos saltator]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 64/69 (92%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGV+APRPSTGPHKLRESLPLVIFLRNRLKYALTN EV KILMQRLIKVDGK+RT
Sbjct: 19 MLDKLGGVYAPRPSTGPHKLRESLPLVIFLRNRLKYALTNCEVTKILMQRLIKVDGKIRT 78

Query: 61 DTNYPAGFM 69
          D NYPAGFM
Sbjct: 79 DPNYPAGFM 87

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321450822|gb|EFX62690.1| hypothetical protein DAPPUDRAFT_300650 [Daphnia pulex]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 63/69 (91%), Positives = 66/69 (95%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGGVFAPRPSTGPHKLRESLPLV+FLRNRLKYAL N EV KI+MQRLIKVDGKVRT
Sbjct: 19 MLDKLGGVFAPRPSTGPHKLRESLPLVVFLRNRLKYALNNSEVTKIVMQRLIKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D+NYPAGFM
Sbjct: 79 DSNYPAGFM 87

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	71
FB|FBgn0011284	261	RpS4 "Ribosomal protein S4" [D	0.971	0.264	0.855	1.7e-27
UNIPROTKB|O62738	263	RPS4X "40S ribosomal protein S	0.971	0.262	0.840	9.4e-27
UNIPROTKB|A2VE06	263	RPS4Y1 "Ribosomal protein S4,	0.971	0.262	0.840	1.2e-26
UNIPROTKB|F1NFC6	229	RPS4X "Uncharacterized protein	0.971	0.301	0.840	1.5e-26
UNIPROTKB|F1P0F2	233	RPS4X "Uncharacterized protein	0.971	0.296	0.840	1.5e-26
UNIPROTKB|P47836	263	RPS4 "40S ribosomal protein S4	0.971	0.262	0.840	1.5e-26
UNIPROTKB|F1MJH2	263	F1MJH2 "Uncharacterized protei	0.971	0.262	0.840	1.5e-26
UNIPROTKB|P79103	263	RPS4 "40S ribosomal protein S4	0.971	0.262	0.840	1.5e-26
UNIPROTKB|F2Z4Q1	263	RPS4X "Uncharacterized protein	0.971	0.262	0.840	1.5e-26
UNIPROTKB|A6NH36	122	RPS4X "40S ribosomal protein S	0.971	0.565	0.840	1.5e-26

FB|FBgn0011284 RpS4 "Ribosomal protein S4" [Drosophila melanogaster (taxid:7227)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 59/69 (85%), Positives = 63/69 (91%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKLGGVFAPRPSTGPHKLRESLPL+IFLRNRLKYAL   EV KI+MQRL+KVDGKVRT
Sbjct:    19 MLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAG+M
Sbjct:    79 DPTYPAGYM 87

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;NAS

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

GO:0006412 "translation" evidence=ISS;NAS

GO:0005840 "ribosome" evidence=IDA;NAS

GO:0003723 "RNA binding" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0051297 "centrosome organization" evidence=IMP

GO:0051298 "centrosome duplication" evidence=IMP

UNIPROTKB|O62738 RPS4X "40S ribosomal protein S4, X isoform" [Monodelphis domestica (taxid:13616)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             DT YP GFM
Sbjct:    79 DTTYPVGFM 87

GO:0005840 "ribosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISS

UNIPROTKB|A2VE06 RPS4Y1 "Ribosomal protein S4, Y-linked 1" [Bos taurus (taxid:9913)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    79 DVTYPAGFM 87

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NFC6 RPS4X "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    18 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 77

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    78 DITYPAGFM 86

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|F1P0F2 RPS4X "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    23 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 82

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    83 DITYPAGFM 91

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|P47836 RPS4 "40S ribosomal protein S4" [Gallus gallus (taxid:9031)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    79 DITYPAGFM 87

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

UNIPROTKB|F1MJH2 F1MJH2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    79 DITYPAGFM 87

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P79103 RPS4 "40S ribosomal protein S4" [Bos taurus (taxid:9913)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    79 DITYPAGFM 87

GO:0019843 "rRNA binding" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|F2Z4Q1 RPS4X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    79 DITYPAGFM 87

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|A6NH36 RPS4X "40S ribosomal protein S4, X isoform" [Homo sapiens (taxid:9606)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 58/69 (84%), Positives = 60/69 (86%)

Query:     1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
             MLDKL GVFAPRPSTGPHKLRE LPL+IFLRNRLKYALT  EV KI MQR IK+DGKVRT
Sbjct:    19 MLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRT 78

Query:    61 DTNYPAGFM 69
             D  YPAGFM
Sbjct:    79 DITYPAGFM 87

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

---

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)
Q9N3X2	RS4_CAEEL	No assigned EC number	0.7246	0.9718	0.2664	yes	N/A
P47836	RS4_CHICK	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P49204	RS42_ARATH	No assigned EC number	0.7681	0.9718	0.2633	yes	N/A
Q8VYK6	RS43_ARATH	No assigned EC number	0.7681	0.9718	0.2633	yes	N/A
O59950	RS4_YARLI	No assigned EC number	0.7971	0.9718	0.2653	yes	N/A
Q9P4W9	RS4C_SCHPO	No assigned EC number	0.7246	0.9718	0.2633	yes	N/A
Q9USW5	RS4B_SCHPO	No assigned EC number	0.7101	0.9718	0.2633	yes	N/A
Q4GXU6	RS4_CARGR	No assigned EC number	0.9130	0.9718	0.2643	N/A	N/A
P79103	RS4_BOVIN	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P47961	RS4_CRIGR	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
A3MWZ7	RS4E_PYRCJ	No assigned EC number	0.5303	0.9295	0.2784	yes	N/A
O62739	RS4Y1_MONDO	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
O62738	RS4X_MONDO	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P87158	RS4A_SCHPO	No assigned EC number	0.7246	0.9718	0.2633	yes	N/A
Q93VH9	RS41_ARATH	No assigned EC number	0.7681	0.9718	0.2643	yes	N/A
P41042	RS4_DROME	No assigned EC number	0.8550	0.9718	0.2643	yes	N/A
P62701	RS4X_HUMAN	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P62703	RS4X_RAT	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P62702	RS4X_MOUSE	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P51405	RS4_DICDI	No assigned EC number	0.7971	0.9718	0.2584	yes	N/A
P0CX36	RS4B_YEAST	No assigned EC number	0.7826	0.9718	0.2643	yes	N/A
Q6PBC4	RS4_XENTR	No assigned EC number	0.8405	0.9718	0.2623	yes	N/A
P0CX35	RS4A_YEAST	No assigned EC number	0.7826	0.9718	0.2643	yes	N/A
Q642H9	RS4X_DANRE	No assigned EC number	0.8260	0.9718	0.2623	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	71
PLN00036	261	PLN00036, PLN00036, 40S ribosomal protein S4; Prov	3e-40
PTZ00118	262	PTZ00118, PTZ00118, 40S ribosomal protein S4; Prov	3e-32
COG1471	241	COG1471, RPS4A, Ribosomal protein S4E [Translation	2e-29
PTZ00223	273	PTZ00223, PTZ00223, 40S ribosomal protein S4; Prov	8e-26
PRK04313	237	PRK04313, PRK04313, 30S ribosomal protein S4e; Val	5e-21
pfam08071	38	pfam08071, RS4NT, RS4NT (NUC023) domain	1e-07
pfam01479	48	pfam01479, S4, S4 domain	0.004

>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional

 Score =  131 bits (332), Expect = 3e-40
 Identities = 53/69 (76%), Positives = 59/69 (85%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGG FAP+PS+GPHK RE LPL++ LRNRLKYALT +EV  ILMQR +KVDGKVRT
Sbjct: 19 MLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DKTYPAGFM 87

Length = 261

>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional

 Score =  111 bits (279), Expect = 3e-32
 Identities = 50/69 (72%), Positives = 57/69 (82%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGG +AP+ S GPHKLRE LPLVI LRNRLKYALT  EV  I++Q+++KVDGKVRT
Sbjct: 19 MLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YP GFM
Sbjct: 79 DCTYPVGFM 87

Length = 262

>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

 Score =  103 bits (260), Expect = 2e-29
 Identities = 33/69 (47%), Positives = 44/69 (63%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
           + +  G +A RPS GPHK  ESLPL++ +R+ LKYA   +E  KIL +  + VDGKVR 
Sbjct: 18 PIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRK 77

Query: 61 DTNYPAGFM 69
          D  +P G M
Sbjct: 78 DYKFPVGLM 86

Length = 241

>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional

 Score = 95.1 bits (236), Expect = 8e-26
 Identities = 47/69 (68%), Positives = 51/69 (73%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          ML KL GVFAPRP  GPHKLRE LPL+I +RNRLKYAL  +E   IL Q L+ VDGK R 
Sbjct: 16 MLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRK 75

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 76 DGKYPAGFM 84

Length = 273

>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated

 Score = 81.4 bits (202), Expect = 5e-21
 Identities = 27/63 (42%), Positives = 40/63 (63%)

Query: 7  GVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA 66
            +  +PS GPH + ES+PL++ LR+ L YA T +E  KI+ +  + VDG+VR D  +P 
Sbjct: 21 YKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPV 80

Query: 67 GFM 69
          G M
Sbjct: 81 GLM 83

Length = 237

>gnl|CDD|191938 pfam08071, RS4NT, RS4NT (NUC023) domain

 Score = 42.6 bits (101), Expect = 1e-07
 Identities = 15/22 (68%), Positives = 16/22 (72%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRE 22
           LDK GG FA +PS GPHK RE
Sbjct: 17 PLDKKGGKFAVKPSPGPHKKRE 38

This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains. Length = 38

>gnl|CDD|201819 pfam01479, S4, S4 domain

 Score = 31.7 bits (73), Expect = 0.004
 Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP 65
          + L   L  RL  A +  E  +++    ++V+GKV  D +Y 
Sbjct: 1  MRLDKVLA-RLGLASSRSEARQLIRHGHVRVNGKVVKDPSYR 41

The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Length = 48

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	71
PRK04313	237	30S ribosomal protein S4e; Validated	100.0
PLN00036	261	40S ribosomal protein S4; Provisional	100.0
PTZ00118	262	40S ribosomal protein S4; Provisional	100.0
PTZ00223	273	40S ribosomal protein S4; Provisional	100.0
COG1471	241	RPS4A Ribosomal protein S4E [Translation, ribosoma	100.0
KOG0378|consensus	263		99.97
PF08071	38	RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843	98.95
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	98.85
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	97.5
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	97.44
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	97.32
PTZ00155	181	40S ribosomal protein S9; Provisional	97.26
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	97.22
smart00363	60	S4 S4 RNA-binding domain.	97.16
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	97.11
PLN00189	194	40S ribosomal protein S9; Provisional	97.02
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	96.01
CHL00113	201	rps4 ribosomal protein S4; Reviewed	95.89
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	95.78
PRK11507	70	ribosome-associated protein; Provisional	95.49
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	95.09
PF13275	65	S4_2: S4 domain; PDB: 1P9K_A.	94.3
PRK05912	408	tyrosyl-tRNA synthetase; Validated	94.23
COG2501	73	S4-like RNA binding protein [Replication, recombin	94.23
PRK13354	410	tyrosyl-tRNA synthetase; Provisional	93.56
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	93.35
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	93.03
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	91.42
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	90.84
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	90.45
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	89.43
KOG4655|consensus	181		88.7
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	88.41
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	87.77
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	87.08
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	86.98
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	85.17
PF03417	225	AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl	83.86
COG0162	401	TyrS Tyrosyl-tRNA synthetase [Translation, ribosom	81.41

>PRK04313 30S ribosomal protein S4e; Validated

Probab=100.00  E-value=5.3e-39  Score=233.76  Aligned_cols=70  Identities=39%  Similarity=0.668  Sum_probs=69.3

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++||++||||||+++|||||+|||||+||||+|++||++||+||+|+|||+||||++|||||||
T Consensus        15 ~i~kk~~~~a~kpspGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmD   84 (237)
T PRK04313         15 PIPRKEYKWTVKPSPGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMD   84 (237)
T ss_pred             ccccccceeccCCCCCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCcee
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999

>PLN00036 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=7.9e-39  Score=235.48  Aligned_cols=70  Identities=76%  Similarity=1.200  Sum_probs=69.4

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+||||+|++||++||+|++|+|||+||||++|||||||
T Consensus        19 ~l~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mD   88 (261)
T PLN00036         19 MLDKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMD   88 (261)
T ss_pred             ccccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeE
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=1.2e-38  Score=234.59  Aligned_cols=70  Identities=71%  Similarity=1.155  Sum_probs=69.4

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+|+||+|++||++||+|++|+|||+||||++|||||||
T Consensus        19 ~i~kk~~~~a~rpspGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mD   88 (262)
T PTZ00118         19 MLDKLGGQYAPKTSPGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMD   88 (262)
T ss_pred             ccccccceeccCCCCCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeE
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=2e-38  Score=234.48  Aligned_cols=70  Identities=67%  Similarity=1.061  Sum_probs=69.4

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+|+||+|++||++||+|++|+|||+||||++|||||||
T Consensus        16 ~i~kk~~~~a~rpspGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMD   85 (273)
T PTZ00223         16 MLSKLTGVFAPRPRAGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMD   85 (273)
T ss_pred             ccccccceeccCCCCCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeE
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999

>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=9.7e-37  Score=222.45  Aligned_cols=70  Identities=47%  Similarity=0.758  Sum_probs=69.0

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      +++|++++|+++|+||||++++|+||++++||+|+||+|+|||++||++|.|+|||+||+|++|||||||
T Consensus        18 ~i~rK~~kw~~~P~pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmD   87 (241)
T COG1471          18 PIPRKTGKWAVRPSPGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMD   87 (241)
T ss_pred             EeccccceEeccCCCCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEE
Confidence            5789999999999999999999999999999999999999999999999999999999999999999998

>KOG0378|consensus

Probab=99.97  E-value=2.5e-32  Score=200.87  Aligned_cols=70  Identities=81%  Similarity=1.280  Sum_probs=69.6

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||||++|.|||+||+|||+++||+||++||||+|+||+|.+|+++||+|+.|+|||+||||.+||+||||
T Consensus        19 mldk~~G~fa~~ps~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gkvrt~~~yp~g~mD   88 (263)
T KOG0378|consen   19 MLDKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGKVRTDSTYPAGFMD   88 (263)
T ss_pred             eecccCcEEecCCCCCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccceeecccccccceeE
Confidence            8999999999999999999999999999999999999999999999999999999999999999999998

>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.95  E-value=2.6e-10  Score=63.51  Aligned_cols=22  Identities=77%  Similarity=1.271  Sum_probs=13.0

Q ss_pred             CccccccccccCCCCCCCCCcc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRE   22 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~   22 (71)
                      ||+|++++||++||||||+++|
T Consensus        17 ~i~kk~~~~a~rpspGPH~~~e   38 (38)
T PF08071_consen   17 MIDKKTGKFAPRPSPGPHKLRE   38 (38)
T ss_dssp             T--SSSSSB-----SSSS-CCC
T ss_pred             ccccccCccccCCCCCCccCCC
Confidence            6899999999999999999986

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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the N-terminal region of these proteins.; PDB: 2XZM_W 2XZN_W 3U5G_E 3U5C_E.

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.85  E-value=6.2e-09  Score=57.60  Aligned_cols=46  Identities=33%  Similarity=0.354  Sum_probs=41.3

Q ss_pred             hHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcccccC
Q psy8661          25 PLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMVR   71 (71)
Q Consensus        25 PL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md~   71 (71)
                      +|..|| ..++++.|..||++++.+|.|+|||++++|+.|++...|.
T Consensus         2 RLd~~L-~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~   47 (48)
T PF01479_consen    2 RLDKFL-SRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDV   47 (48)
T ss_dssp             BHHHHH-HHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEE
T ss_pred             CHHHHH-HHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCC
Confidence            567777 4589999999999999999999999999999999988763

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=97.50  E-value=9.6e-05  Score=53.15  Aligned_cols=34  Identities=26%  Similarity=0.359  Sum_probs=31.3

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ++|+|.|.++|++.+.+|.|.|||++++.+.|=|
T Consensus       102 R~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V  135 (205)
T COG0522         102 RLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLV  135 (205)
T ss_pred             HhcccccHHHHHHHhhcceEEECCEEeccCcEEe
Confidence            4799999999999999999999999999997744

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

Probab=97.44  E-value=0.00049  Score=37.72  Aligned_cols=42  Identities=24%  Similarity=0.257  Sum_probs=33.5

Q ss_pred             HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661          26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF   68 (71)
Q Consensus        26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~   68 (71)
                      |.-+|+.. +.+.+..++++++.+|.|+|||+..++..+++-.
T Consensus         3 l~~~l~~~-~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~   44 (70)
T cd00165           3 LDKILARL-GLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKP   44 (70)
T ss_pred             HHHHHHHh-ccccCHHHHHHHHHcCCEEECCEEccCCccCcCC
Confidence            44566543 3567899999999999999999999888887643

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

Probab=97.32  E-value=0.0002  Score=50.08  Aligned_cols=34  Identities=24%  Similarity=0.330  Sum_probs=31.7

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ++|+|.|..+|++.+.||.|.|||++++++.|-|
T Consensus       112 r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V  145 (162)
T TIGR01018       112 KKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIV  145 (162)
T ss_pred             hccCcCCHHHHHHHhhCCCeeECCEEeccCceEe
Confidence            4799999999999999999999999999998765

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=97.26  E-value=0.00023  Score=50.53  Aligned_cols=33  Identities=18%  Similarity=0.213  Sum_probs=30.7

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +|+|.|..+|++++.+|.|.|||++++++.|=|
T Consensus       116 ~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V  148 (181)
T PTZ00155        116 LGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLV  148 (181)
T ss_pred             ccCcCCHHHhhhheeCCCEEECCEEeccCceEe
Confidence            499999999999999999999999999997744

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=97.22  E-value=0.001  Score=38.27  Aligned_cols=42  Identities=12%  Similarity=0.128  Sum_probs=34.7

Q ss_pred             hhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        24 lPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .-|--||... .++.+...+++++.+|.|.|||++++...|.+
T Consensus         9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l   50 (59)
T TIGR02988         9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKL   50 (59)
T ss_pred             HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCC
Confidence            5566777777 77779999999999999999999997666543

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>smart00363 S4 S4 RNA-binding domain

Probab=97.16  E-value=0.0015  Score=34.83  Aligned_cols=42  Identities=29%  Similarity=0.294  Sum_probs=32.7

Q ss_pred             HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661          26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF   68 (71)
Q Consensus        26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~   68 (71)
                      +..+|... +.+.+..++++++.+|.|.|||++.++..+.+--
T Consensus         3 l~~~l~~~-~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~   44 (60)
T smart00363        3 LDKFLARL-GLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKP   44 (60)
T ss_pred             HHHHHHHc-CcccCHHHHHHHHHcCCEEECCEEecCCCeEeCC
Confidence            44556543 3457899999999999999999999888777643

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=97.11  E-value=0.00062  Score=48.11  Aligned_cols=33  Identities=21%  Similarity=0.294  Sum_probs=31.3

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +|+|.|..+|++.+.+|.|.|||++++++.|-|
T Consensus       112 ~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V  144 (177)
T PRK04051        112 KGLARTPKQARQFIVHGHIAVNGRRVTSPSYLV  144 (177)
T ss_pred             ccCcCCHHHHHHHHHcCCEEECCEEeCCCCeEC
Confidence            699999999999999999999999999998866

>PLN00189 40S ribosomal protein S9; Provisional

Probab=97.02  E-value=0.00043  Score=49.76  Aligned_cols=34  Identities=15%  Similarity=0.184  Sum_probs=31.4

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ++|+|.|..+|++++.+|.|.|||++++++.|-|
T Consensus       117 r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V  150 (194)
T PLN00189        117 KSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMV  150 (194)
T ss_pred             ecCCcCCHHHHHHheeCCCEeECCEEEecCcEEE
Confidence            4789999999999999999999999999998754

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=96.01  E-value=0.011  Score=41.94  Aligned_cols=34  Identities=24%  Similarity=0.263  Sum_probs=30.6

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      ++++.|..+|++.+.+|.|.|||+++++..|.+-
T Consensus        99 ~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~  132 (200)
T TIGR01017        99 LGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVR  132 (200)
T ss_pred             cCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCC
Confidence            4678899999999999999999999999888774

This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=95.89  E-value=0.012  Score=42.15  Aligned_cols=33  Identities=21%  Similarity=0.253  Sum_probs=30.2

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +++|.+..+|++++.+|.|.|||+++++..|.+
T Consensus        98 ~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~V  130 (201)
T CHL00113         98 LGMAPTIPAARQLVNHGHILVNGRIVDIPSYRC  130 (201)
T ss_pred             cCCCCCHHHHHHHHHCCcEEECCEEecCccccC
Confidence            578889999999999999999999999888776

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=95.78  E-value=0.015  Score=41.24  Aligned_cols=34  Identities=24%  Similarity=0.317  Sum_probs=30.6

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      ++++.+..+|++++.+|.|.|||++++...|++-
T Consensus       102 ~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~  135 (203)
T PRK05327        102 LGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVK  135 (203)
T ss_pred             cCccCCHHHHHHHHHCCcEEECCEEECCCCcCCC
Confidence            3778899999999999999999999998888774

>PRK11507 ribosome-associated protein; Provisional

Probab=95.49  E-value=0.019  Score=35.53  Aligned_cols=39  Identities=21%  Similarity=0.276  Sum_probs=31.4

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecC
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTD   61 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD   61 (71)
                      +-|-|.=||. ..+++.|+=|||..+.++.|+|||.+.+-
T Consensus        10 e~I~L~QlLK-~~~~v~SGG~AK~~I~eg~V~VNGeve~r   48 (70)
T PRK11507         10 PHVELCDLLK-LEGWSESGAQAKIAIAEGQVKVDGAVETR   48 (70)
T ss_pred             CeEEHHHHHh-hhCcccChHHHHHHHHcCceEECCEEecc
Confidence            3455666665 35788999999999999999999998653

>TIGR00478 tly hemolysin TlyA family protein

Probab=95.09  E-value=0.031  Score=40.31  Aligned_cols=37  Identities=11%  Similarity=0.200  Sum_probs=31.3

Q ss_pred             HHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          29 FLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        29 ~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +|.+ .+++.|.++|+.++++|.|.|||+++++..+.+
T Consensus         5 ~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V   41 (228)
T TIGR00478         5 LLVR-RGLFESREKAKRLILKGFVLVNGKKVDKPSALV   41 (228)
T ss_pred             HHHH-cCCccHHHHHHHHHHCCcEEECCEEeCCCCCCC
Confidence            3443 467889999999999999999999999887766

Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).

>PF13275 S4_2: S4 domain; PDB: 1P9K_A

Probab=94.30  E-value=0.0094  Score=36.20  Aligned_cols=40  Identities=23%  Similarity=0.292  Sum_probs=27.2

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCC
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDT   62 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~   62 (71)
                      +.|.|.=||.- .+++.|+-|||..+.++.|+|||.+.+..
T Consensus         6 e~I~L~qlLK~-~glv~sGGeAK~~I~~g~V~VNGe~e~rr   45 (65)
T PF13275_consen    6 EYITLGQLLKL-AGLVSSGGEAKALIQEGEVKVNGEVETRR   45 (65)
T ss_dssp             S---HHHHHHH-HTS-SSSSTTSHHHHHHHHEETTB----S
T ss_pred             CcEEHHHHHhH-cCCcccHHHHHHHHHcCceEECCEEcccc
Confidence            45666666664 57889999999999999999999998765

>PRK05912 tyrosyl-tRNA synthetase; Validated

Probab=94.23  E-value=0.092  Score=40.67  Aligned_cols=43  Identities=21%  Similarity=0.362  Sum_probs=37.2

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .++++-+|.+ .+.|.+..||++.+.||-|+|||..++|..+-+
T Consensus       342 ~~~~~~~l~~-~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~  384 (408)
T PRK05912        342 GIDLLALLVE-AGLVPSKSEARRLIKQGGVKINGEKVSDENYVL  384 (408)
T ss_pred             CCcHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEecCccccc
Confidence            4677777764 699999999999999999999999999987543

>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]

Probab=94.23  E-value=0.052  Score=33.89  Aligned_cols=37  Identities=19%  Similarity=0.242  Sum_probs=30.3

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEec
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT   60 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrt   60 (71)
                      -|-|.=||. .++.++|+-+||..+.++.|+|||++-|
T Consensus        11 ~I~L~qlLK-~~g~i~sGG~AK~~i~eg~V~vNGe~Et   47 (73)
T COG2501          11 FITLGQLLK-LAGLIESGGQAKAFIAEGEVKVNGEVET   47 (73)
T ss_pred             eEEHHHHHH-HhCcccCcHHHHHHHHCCeEEECCeeee
Confidence            445555655 4689999999999999999999999854

>PRK13354 tyrosyl-tRNA synthetase; Provisional

Probab=93.56  E-value=0.13  Score=39.94  Aligned_cols=42  Identities=24%  Similarity=0.328  Sum_probs=36.5

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCC
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYP   65 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~p   65 (71)
                      .++++-+|-. .|.|.+..||++.+.||-|.|||..++|..+-
T Consensus       342 ~~~~~~~l~~-~~~~~S~~earrli~~ggv~in~~~v~~~~~~  383 (410)
T PRK13354        342 TKNLVDLLVD-LGLEPSKREARRLIQNGAIKINGEKVTDVDAI  383 (410)
T ss_pred             CCCHHHHHHH-hCCCCCHHHHHHHHHcCCEEECCEEccCcccc
Confidence            4677777764 79999999999999999999999999998653

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=93.35  E-value=0.26  Score=35.63  Aligned_cols=45  Identities=24%  Similarity=0.351  Sum_probs=34.7

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      .+.-|.-||...+. ..+.+++++.+.+|.|.|||+++++..+.+-
T Consensus         4 ~g~rLd~~L~~~~~-~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~   48 (299)
T TIGR00005         4 AGQRLDDFLASLLP-DLSRSRIQKLIENGQVKVNGKVTANPKLKVK   48 (299)
T ss_pred             cchhHHHHHHHhcc-cCCHHHHHHHHHCCcEEECCEeccCcccCCC
Confidence            34667778877664 3568899999999999999987777666663

modifies uracil-65 in transfer RNAs to pseudouridine.

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]

Probab=93.03  E-value=0.11  Score=38.40  Aligned_cols=29  Identities=24%  Similarity=0.298  Sum_probs=24.7

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTN   63 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~   63 (71)
                      +++| +.+||+++|.+|.|.|||++.++..
T Consensus        12 ~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~   40 (248)
T COG1187          12 AGVG-SRREAEKLIEEGRVTVNGKVATLGG   40 (248)
T ss_pred             cCCC-CHHHHHHHHHcCCEEECCEEeccCC
Confidence            3555 5789999999999999999998864

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=91.42  E-value=0.42  Score=35.07  Aligned_cols=43  Identities=12%  Similarity=0.160  Sum_probs=34.7

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      |+=|-.++...+  ..+.+.|++.+.+|.|+|||+++++..+.+-
T Consensus       183 s~RLD~lls~~~--~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~  225 (257)
T TIGR03069       183 SLRIDAIASAGF--GLSRSKIVDQIKAGRLRLNWKTVTQPSRELK  225 (257)
T ss_pred             cccHHHHHHhhh--hhhHHHHHHHHHCCeEEECCEEcCCCCCcCC
Confidence            445666777654  4588999999999999999999998887664

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=90.84  E-value=0.55  Score=32.96  Aligned_cols=39  Identities=18%  Similarity=0.312  Sum_probs=29.3

Q ss_pred             HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      |.-||...+  ..+.+.+++++.+|.|.|||++.++..+.+
T Consensus         3 ld~~L~~~~--~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l   41 (232)
T PRK10839          3 LDKFISQQL--GVSRAIAGRELRANRVTVDGEIVKNGAFKL   41 (232)
T ss_pred             HHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeccCCcCc
Confidence            345666555  357899999999999999999987554433

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=90.45  E-value=0.64  Score=34.43  Aligned_cols=43  Identities=14%  Similarity=0.178  Sum_probs=33.5

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ...|.-+|+..+. ..+.+++++++.+|.|.|||+.++...+.+
T Consensus        17 g~RLd~~L~~~~~-~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v   59 (325)
T PRK11180         17 GQRLDQALAELFP-DYSRSRIKEWILDQRVLVNGKVINKPKEKV   59 (325)
T ss_pred             CccHHHHHHhhcc-ccCHHHHHHHHHCCCEEECCEEccCCCcCc
Confidence            4677788887654 357889999999999999999886554443

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

Probab=89.43  E-value=0.7  Score=34.31  Aligned_cols=43  Identities=21%  Similarity=0.301  Sum_probs=35.3

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF   68 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~   68 (71)
                      ..-+--||++ |.- .+..+..+++.+|.|.|||++++ ..|.+.-
T Consensus        12 g~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~   54 (289)
T COG0564          12 GQRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKP   54 (289)
T ss_pred             CCCHHHHHHH-ccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCC
Confidence            4567788888 665 67889999999999999999998 7776643

>KOG4655|consensus

Probab=88.70  E-value=0.36  Score=34.69  Aligned_cols=34  Identities=29%  Similarity=0.419  Sum_probs=31.1

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .|+.|.+-+||-+.+.||.|.|.-+++||+.|=|
T Consensus       115 ~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lv  148 (181)
T KOG4655|consen  115 RLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLV  148 (181)
T ss_pred             echhhhhHHHHHHHHHcCceeeCCeeccCchHHh
Confidence            4789999999999999999999999999997743

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=88.41  E-value=0.57  Score=34.98  Aligned_cols=31  Identities=10%  Similarity=0.138  Sum_probs=27.8

Q ss_pred             cccccHHHHHHHHHcCceEeCCeEecCCcCC
Q psy8661          35 KYALTNQEVLKILMQRLIKVDGKVRTDTNYP   65 (71)
Q Consensus        35 kyA~t~~EakkIl~~~~V~VdGkvrtD~~~p   65 (71)
                      |++.|..+|+..++.|+|+|||...+-+.+=
T Consensus        13 gl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~   43 (245)
T COG1189          13 GLFESREKAKELILAGNVLVNGEKVTKPSQL   43 (245)
T ss_pred             cchhhHHHHHHHHHcCeEEECCEEecCccee
Confidence            7899999999999999999999998876543

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=87.77  E-value=1.2  Score=33.20  Aligned_cols=42  Identities=14%  Similarity=0.150  Sum_probs=31.3

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +++-|.-||.+. ++ .+.+||++.+.+|.|+|||++. +..+.+
T Consensus         5 ~~~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V   46 (290)
T PRK10475          5 SSTRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQV   46 (290)
T ss_pred             hHHHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCc
Confidence            356677777653 43 4689999999999999999987 344444

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=87.08  E-value=2  Score=29.28  Aligned_cols=42  Identities=10%  Similarity=0.125  Sum_probs=34.5

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ++-|-.||.. .+++.|..-|+..|..|.|.|||.+ .-....|
T Consensus         8 ~~RlDk~L~~-~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V   49 (133)
T PRK10348          8 EVRLDKWLWA-ARFYKTRALAREMIEGGKVHYNGQR-SKPSKIV   49 (133)
T ss_pred             cccHHHHHHH-cCccccHHHHHHHHHCCCEEECCEE-CCCCCcc
Confidence            4677777775 5899999999999999999999998 5555544

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=86.98  E-value=0.78  Score=33.95  Aligned_cols=36  Identities=19%  Similarity=0.193  Sum_probs=26.3

Q ss_pred             HHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          28 IFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        28 i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      =||.+ +++ .+.++|++++.+|.|+|||++. +..+-|
T Consensus         7 k~La~-~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V   42 (289)
T PRK10700          7 KVLAR-AGH-GSRREIESIIEAGRVSVDGKIA-TLGDRV   42 (289)
T ss_pred             HHHHH-CCC-CCHHHHHHHHHcCCEEECCEec-cCCCEe
Confidence            34443 343 5789999999999999999986 444433

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=85.17  E-value=2.4  Score=31.32  Aligned_cols=42  Identities=24%  Similarity=0.377  Sum_probs=32.6

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ...|.-||.+.+. ..+.+.+++++.+|.|.|||++++ ..+.+
T Consensus        19 g~RLd~~L~~~~~-~~sr~~i~~li~~G~V~VNg~~v~-~~~~v   60 (317)
T PRK11025         19 GQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRIK-PEYKL   60 (317)
T ss_pred             CchHHHHHHHhcc-cCCHHHHHHHHHcCCEEECCEEcC-ccccc
Confidence            4567788887663 356889999999999999999874 45554

>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification

Probab=83.86  E-value=1.3  Score=30.42  Aligned_cols=29  Identities=28%  Similarity=0.394  Sum_probs=25.0

Q ss_pred             ccchhHHHHHHhhhcccccHHHHHHHHHcC
Q psy8661          21 RESLPLVIFLRNRLKYALTNQEVLKILMQR   50 (71)
Q Consensus        21 ~~slPL~i~LRd~LkyA~t~~EakkIl~~~   50 (71)
                      ...+|..+++|..|. |.|..||..+|.+-
T Consensus        69 ~~G~p~~~l~R~iLe-~~t~~eA~~~l~~~   97 (225)
T PF03417_consen   69 QPGLPRHFLVRKILE-CRTVEEAIAILRSA   97 (225)
T ss_dssp             TTSB-HHHHHHHHHC--SSHHHHHHCHHCC
T ss_pred             cCCChHHHHHHHHhc-CCCHHHHHHHHHhc
Confidence            669999999999999 99999999999875

; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.

>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=81.41  E-value=1.5  Score=34.43  Aligned_cols=33  Identities=24%  Similarity=0.352  Sum_probs=30.8

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .+++.+.+||++.+.++.|++||..+.|.+++.
T Consensus       345 ~~L~psr~earr~i~~g~v~in~~~v~d~~~~~  377 (401)
T COG0162         345 AGLAPSRSEARRLIQQGGVKINGEKVEDENYVL  377 (401)
T ss_pred             hCCcccHHHHHhhcccCCEEECCEeccccccch
Confidence            578999999999999999999999999998776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	71
3izb_D	261	Localization Of The Small Subunit Ribosomal Protein		2e-27
3iz6_D	265	Localization Of The Small Subunit Ribosomal Protein		1e-25
3zey_1	273	High-resolution Cryo-electron Microscopy Structure		9e-20
2xzm_W	260	Crystal Structure Of The Eukaryotic 40s Ribosomal S		5e-17
3j20_E	243	Promiscuous Behavior Of Proteins In Archaeal Riboso		1e-09

>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 261

Iteration: 1
 Score =  117 bits (293), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 54/69 (78%), Positives = 60/69 (86%)
Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          +LDKL G +APRPS GPHKLRESLPL++FLRNRLKYAL  +EV  ILMQR +KVDGKVRT
Sbjct: 19 LLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRT 78
Query: 61 DTNYPAGFM 69
          DT YPAGFM
Sbjct: 79 DTTYPAGFM 87

>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 265

Iteration: 1
 Score =  111 bits (278), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 59/69 (85%)
Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGG FAP+PS+GPHK RE LPL++ +RNRLKYALT +EV+ ILMQR + VDGKVRT
Sbjct: 19 MLDKLGGAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRT 78
Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DKTYPAGFM 87

>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 273

Iteration: 1
 Score = 91.7 bits (226), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 46/69 (66%), Positives = 49/69 (71%)
Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          ML KL GVFAPRP  GPHKLRE L L+I +RNRLKYAL   E   IL Q L+ VDGK R 
Sbjct: 16 MLSKLTGVFAPRPRAGPHKLRECLSLLIIIRNRLKYALNALEAQMILRQGLVCVDGKPRK 75
Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 76 DGKYPAGFM 84

>pdb|2XZM|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 260

Iteration: 1
 Score = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 51/71 (71%), Gaps = 2/71 (2%)
Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKIL--MQRLIKVDGKV 58
          ML+KLGG++A RPS GPHKLRESLPL + L+ RL YAL  ++V  IL   ++ + VDGKV
Sbjct: 19 MLNKLGGIWATRPSQGPHKLRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKV 78
Query: 59 RTDTNYPAGFM 69
          R D  YP G M
Sbjct: 79 RRDKGYPTGLM 89

>pdb|3J20|E Chain E, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 243

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 38/61 (62%)
Query: 9  FAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF 68
          +A RP  GPH +R S+PL+  +R+ L YA T +E  KIL +    VDG+VR D  +P G 
Sbjct: 28 WAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGI 87
Query: 69 M 69
          M
Sbjct: 88 M 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	71
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	2e-30
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	2e-30
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	4e-29
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	2e-22

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Length = 261

 Score =  106 bits (265), Expect = 2e-30
 Identities = 54/69 (78%), Positives = 60/69 (86%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          +LDKL G +APRPS GPHKLRESLPL++FLRNRLKYAL  +EV  ILMQR +KVDGKVRT
Sbjct: 19 LLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRT 78

Query: 61 DTNYPAGFM 69
          DT YPAGFM
Sbjct: 79 DTTYPAGFM 87

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 265

 Score =  105 bits (264), Expect = 2e-30
 Identities = 51/69 (73%), Positives = 59/69 (85%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRT 60
          MLDKLGG FAP+PS+GPHK RE LPL++ +RNRLKYALT +EV+ ILMQR + VDGKVRT
Sbjct: 19 MLDKLGGAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRT 78

Query: 61 DTNYPAGFM 69
          D  YPAGFM
Sbjct: 79 DKTYPAGFM 87

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Length = 260

 Score =  102 bits (256), Expect = 4e-29
 Identities = 41/71 (57%), Positives = 51/71 (71%), Gaps = 2/71 (2%)

Query: 1  MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKIL--MQRLIKVDGKV 58
          ML+KLGG++A RPS GPHKLRESLPL + L+ RL YAL  ++V  IL   ++ + VDGKV
Sbjct: 19 MLNKLGGIWATRPSQGPHKLRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKV 78

Query: 59 RTDTNYPAGFM 69
          R D  YP G M
Sbjct: 79 RRDKGYPTGLM 89

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Length = 213

 Score = 84.4 bits (208), Expect = 2e-22
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 18 HKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFM 69
          H   +S+ L+  +R+ LK +   +E  +IL   L+KVDGK   +  +  GFM
Sbjct: 2  HPKDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFM 53

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	71
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	100.0
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	100.0
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	100.0
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	100.0
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	99.94
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	97.69
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	97.4
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	97.01
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	96.95
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	96.92
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	96.83
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	96.45
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	96.39
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	96.06
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	95.7
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	95.49
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	95.42
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	94.76
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	94.39
2ktl_A	164	Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s	94.3
1h3f_A	432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	94.03
2jan_A	432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	93.76
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	93.43
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	93.22
1jil_A	420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	92.57
2ts1_A	419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	90.23
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	89.3

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E

Probab=100.00  E-value=6e-40  Score=240.35  Aligned_cols=70  Identities=77%  Similarity=1.242  Sum_probs=69.5

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+|+||+|++||++||+|++|+||||||||++|||||||
T Consensus        19 ~l~kk~~~fa~rps~GPH~l~eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~MD   88 (261)
T 3u5c_E           19 LLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMD   88 (261)
T ss_dssp             CCCSSSSSBCCCCCSSSSCGGGEEEHHHHHHHTTCCCSSSHHHHHHHTTTCEEETTBCCCCTTCEEETTC
T ss_pred             ccccccceeccCCCCCCCcchhheeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCceEE
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999

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

Probab=100.00  E-value=2.5e-39  Score=236.93  Aligned_cols=70  Identities=59%  Similarity=1.002  Sum_probs=69.4

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHc--CceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQ--RLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~--~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+||||+|++||++||+|  ++|+||||||+|++|||||||
T Consensus        19 ~l~kk~~~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~q~~~~VkVDGkvr~D~~~PvG~MD   90 (260)
T 2xzm_W           19 MLNKLGGIWATRPSQGPHKLRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKVRRDKGYPTGLMD   90 (260)
T ss_dssp             TCCSSSCSBCCCCCSSSSCSSSCEEHHHHHTTTTCSCCSHHHHHHHTTSTTCCEEETTEECCCTTCEECTTC
T ss_pred             eeccccceEccCCCCCCCccceeehhHhhhhhhhccccchhHHHHHHhccCCeEEECCEEeccCCCCCcEEE
Confidence            7999999999999999999999999999999999999999999999999  999999999999999999999

>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=100.00  E-value=6.6e-40  Score=240.54  Aligned_cols=70  Identities=73%  Similarity=1.198  Sum_probs=45.9

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+|+||+|++||++||+|++|+||||||||++|||||||
T Consensus        19 ~l~kk~~~fa~rpspGPHkl~eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~MD   88 (265)
T 3iz6_D           19 MLDKLGGAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFMD   88 (265)
T ss_dssp             ------------------------CHHHHHHHHHTTSSCSSSTHHHHHTTCCEETTEECCCTTCCCCTTC
T ss_pred             ccccccceeccCCCCCCCcchhheeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCcEEE
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999

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

Probab=100.00  E-value=1.5e-38  Score=230.89  Aligned_cols=70  Identities=40%  Similarity=0.690  Sum_probs=69.5

Q ss_pred             CccccccccccCCCCCCCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661           1 MLDKLGGVFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus         1 ~l~K~~~~~a~~pspGPH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ||+|++++|||+||||||+++|||||+|||||+||||+|.+||++||+|++|+||||+|+|++|||||||
T Consensus        20 ~l~kk~~~~a~rps~GPH~~~~~lPL~i~LRdrLgyA~t~rEar~Iv~~~~I~VdGKvr~d~~ypvG~mD   89 (243)
T 3j20_E           20 YIERKAYKWAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMD   89 (243)
T ss_dssp             CCCTTSSSCBCCCCSCSSCSTTCEEHHHHHHTTSCCCSSHHHHHHHHHHCSCEETTEECCCSSCEECTTC
T ss_pred             ccccccceeccCCCCCCCccccceeehhhhhhhhccccCHHHHHHHHHCCcEEECCEEeccccCCcccce
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}

Probab=99.94  E-value=1.1e-27  Score=171.35  Aligned_cols=54  Identities=33%  Similarity=0.546  Sum_probs=50.8

Q ss_pred             CCCCccchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661          17 PHKLRESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus        17 PH~~~~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      .|+++|||||++||||+||||+|.+||++||+||+|+||||+|+|++|||||||
T Consensus         1 ~Hkl~eslPL~i~LRdrLgyA~t~rEarkIv~~~~I~VDGKvr~d~~ypvG~mD   54 (213)
T 3kbg_A            1 MHPKDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFMD   54 (213)
T ss_dssp             ---CCSCEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTC
T ss_pred             CCcchhceeeHHHHhhhhcccccHHHHHHHHHCCCEEECCEEecccCCCcccee
Confidence            399999999999999999999999999999999999999999999999999999

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.69  E-value=2.8e-05  Score=46.21  Aligned_cols=35  Identities=23%  Similarity=0.286  Sum_probs=31.9

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      ++++|.|.++|+..+++|.|.|||++++.+.|.|-
T Consensus        16 ~~gla~SR~~A~~lI~~G~V~Vng~~v~kps~~V~   50 (71)
T 2cqj_A           16 KLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVT   50 (71)
T ss_dssp             HTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEE
T ss_pred             HhCCcCCHHHHHHHHHCCcEEECCEEECCCCCCCC
Confidence            37999999999999999999999999999987763

>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6

Probab=97.40  E-value=3.6e-05  Score=45.62  Aligned_cols=42  Identities=19%  Similarity=0.269  Sum_probs=36.7

Q ss_pred             hhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        24 lPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +-|--+|.+. +++.+.+||++.+.+|.|.|||+++++..+.+
T Consensus        21 ~RLdk~L~~~-g~~~SR~~a~~lI~~G~V~VNG~~v~~~~~~v   62 (79)
T 1p9k_A           21 VELCDLLKLE-GWSESGAQAKIAIAEGQVKVDGAVETRKRCKI   62 (79)
T ss_dssp             CCHHHHHHHH-TSCSSSSTTSHHHHHHHHEETTBCCCCSSCCC
T ss_pred             chHHHHHHHC-CCCCCHHHHHHHHHCCEEEECCEEecCCCCCC
Confidence            5677888875 88889999999999999999999998887765

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=97.01  E-value=0.00041  Score=48.04  Aligned_cols=35  Identities=17%  Similarity=0.232  Sum_probs=32.2

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF   68 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~   68 (71)
                      +++|.|..+|++.+.+|.|.|||++++++.|.|-.
T Consensus       112 ~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~  146 (180)
T 3j20_D          112 KGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLK  146 (180)
T ss_dssp             HTSSSSHHHHHHHHHHTCCEESSSBCCCSSCCCCT
T ss_pred             CcccCcHHHHHHHHHcCCeEECCEEeCCCCcccCC
Confidence            68999999999999999999999999999887753

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D

Probab=96.95  E-value=0.00037  Score=48.12  Aligned_cols=35  Identities=20%  Similarity=0.214  Sum_probs=32.4

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      .+++|.|.++|+..+.+|.|.|||++++++.|.|-
T Consensus       115 ~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~  149 (181)
T 2xzm_D          115 KLNLANSIHHSRVLIRQRHIKVGKNLVNVPSFMVR  149 (181)
T ss_dssp             HTTCSSSTTHHHHHTTTTCCEETTEECCCSCCBCC
T ss_pred             hccccCCHHHHHHHHHCCEEEECCEEECCCCcCCC
Confidence            36899999999999999999999999999988874

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*

Probab=96.92  E-value=0.00046  Score=48.57  Aligned_cols=35  Identities=17%  Similarity=0.207  Sum_probs=32.1

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      ++++|.|..+|++.+.+|.|.|||++++++.|-|-
T Consensus       115 r~G~a~Sr~~ArqLI~~GhV~VNG~~V~~Ps~~V~  149 (197)
T 3u5c_J          115 KLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVR  149 (197)
T ss_dssp             HSSTTSSHHHHHHHHHTSCCBSSSCBCCCTTCCCC
T ss_pred             HccccCCHHHHHHHHHcCCEEECCEEeCCCccccC
Confidence            37899999999999999999999999999988764

>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C

Probab=96.83  E-value=0.0012  Score=44.04  Aligned_cols=41  Identities=22%  Similarity=0.227  Sum_probs=32.9

Q ss_pred             HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      |--+|.. +++|.+.++|++++.+|.|.|||+++++..|.+-
T Consensus        53 LD~~L~~-~g~~~SR~~ar~lI~~G~V~VNG~~v~~ps~~V~   93 (159)
T 1c05_A           53 LDNLVYR-LGLARTRRQARQLVTHGHILVDGSRVNIPSYRVK   93 (159)
T ss_dssp             HHHHHHH-TTSCSSHHHHHHHHHTTCEEETTEECCCSSCBCC
T ss_pred             HHHHHHH-cCCcCCHHHHHHHHHCCCEEECCEEeCcCCcEeC
Confidence            3334442 4678899999999999999999999988877653

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=96.45  E-value=0.002  Score=45.10  Aligned_cols=34  Identities=24%  Similarity=0.283  Sum_probs=30.4

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      +++|.|..+|++.+.+|.|.|||+++++..|.+-
T Consensus        98 ~g~a~SR~~ArqLI~~G~V~VNG~~V~~pS~~V~  131 (201)
T 3bbn_D           98 LGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCK  131 (201)
T ss_dssp             TTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCC
T ss_pred             cCCcCCHHHHHHHHhCCcEEeCCEEEeecceecC
Confidence            4678899999999999999999999998887764

>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...

Probab=96.39  E-value=0.0034  Score=43.74  Aligned_cols=33  Identities=18%  Similarity=0.373  Sum_probs=29.6

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +++|.|.++|++++.+|.|.|||+++++..|.+
T Consensus       108 ~g~~~SR~~arqLI~~G~V~VNG~~v~~ps~~V  140 (209)
T 2vqe_D          108 LGFAVSRRQARQLVRHGHITVNGRRVDLPSYRV  140 (209)
T ss_dssp             TTSSSSHHHHHHHHHTTCEEETTEECCCTTCBC
T ss_pred             hcCcCCHHHHHHHHHCCCEEECCEEeCcCCcCc
Confidence            467889999999999999999999998877765

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=95.70  E-value=0.00045  Score=48.54  Aligned_cols=34  Identities=15%  Similarity=0.149  Sum_probs=31.6

Q ss_pred             hcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          34 LKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        34 LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      +++|.|..+|++++.+|.|.|||++++++.|.|-
T Consensus       118 ~G~a~SR~~ArqlI~~GhV~VNG~~V~~Ps~~V~  151 (195)
T 3iz6_C          118 AGMAKSIHHARVLIRQRHIRVGRQIVNIPSFMVR  151 (195)
T ss_dssp             CCCHHHHSCTTSHHHHHSTTTSCCCCCCCCCCCS
T ss_pred             ccccCCHHHHHHHHHcCCEEECCEEeCCCCcCcC
Confidence            6899999999999999999999999999988774

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*

Probab=95.49  E-value=0.018  Score=39.30  Aligned_cols=42  Identities=14%  Similarity=0.295  Sum_probs=33.9

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ++-|--||....  ..+.+++++++.+|.|+|||+++++..+.+
T Consensus         3 ~~RLd~~L~~~~--~~SR~~~~~li~~G~V~VNG~~v~~~~~~v   44 (234)
T 1ksk_A            3 HMRLDKFIAQQL--GVSRAIAGREIRGNRVTVDGEIVRNAAFKL   44 (234)
T ss_dssp             CEEHHHHHHHHH--TCCHHHHHHHHHTTCEEETTEECCCTTCEE
T ss_pred             cccHHHHHHHcC--CCCHHHHHHHHHcCeEEECCEEeCCCCCCC
Confidence            455667787763  568899999999999999999998766655

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5

Probab=95.42  E-value=0.019  Score=39.56  Aligned_cols=41  Identities=22%  Similarity=0.374  Sum_probs=33.0

Q ss_pred             hhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        24 lPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +-|--||.+..  ..+.+++++.+.+|.|+|||+++++..+.+
T Consensus         3 ~RLd~~L~~~~--~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v   43 (243)
T 1vio_A            3 LRLDKFIAENV--GLTRSQATKAIRQSAVKINGEIVKSGSVQI   43 (243)
T ss_dssp             EEHHHHHHHHH--TCCHHHHHHHHHTTCEEETTEECCCTTCEE
T ss_pred             ccHHHHHHHcC--CCCHHHHHHHHHcCcEEECCEEeCCCCCCc
Confidence            34666777763  578899999999999999999998766655

>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A

Probab=94.76  E-value=0.06  Score=34.80  Aligned_cols=43  Identities=9%  Similarity=0.061  Sum_probs=33.4

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +++-|--||.... +..+...|+++|.+|.|.|||+++ ...+.|
T Consensus         7 ~~~RLDk~L~~~~-~~~SRs~a~~li~~G~V~VNG~~v-k~s~~V   49 (133)
T 1dm9_A            7 VEVRLDKWLWAAR-FYKTRALAREMIEGGKVHYNGQRS-KPSKIV   49 (133)
T ss_dssp             TCCBHHHHHHHTT-SSSSHHHHHHHHHTTCEEETTEEC-CTTCBC
T ss_pred             cchhHHHHHHHCC-CCCCHHHHHHHHHCCcEEECCEEc-CCCCEe
Confidence            4567778887642 345889999999999999999986 555655

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}

Probab=94.39  E-value=0.045  Score=39.46  Aligned_cols=42  Identities=14%  Similarity=0.181  Sum_probs=34.3

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +++-|--||.+. +++ +.++|++++.+|.|.|||+++ +..+.+
T Consensus         5 ~g~RLdk~La~~-g~~-SR~~a~~lI~~G~V~VNG~~v-~~~~~V   46 (290)
T 3dh3_A            5 SSVRLNKYISES-GIC-SRREADRYIEQGNVFLNGKRA-TIGDQV   46 (290)
T ss_dssp             CCEEHHHHHHTT-TSS-CHHHHHHHHHTTCEEETTEEC-CTTCEE
T ss_pred             cchHHHHHHHhC-CCC-CHHHHHHHHHCCCEEECCEEc-cCCcCc
Confidence            456788888886 554 889999999999999999998 666654

>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4}

Probab=94.30  E-value=0.024  Score=38.80  Aligned_cols=44  Identities=18%  Similarity=0.149  Sum_probs=33.1

Q ss_pred             hHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcccc
Q psy8661          25 PLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFM   69 (71)
Q Consensus        25 PL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~m   69 (71)
                      +++=+|- ..++|.+..||++.+.||-|+|||....|..-+.|+|
T Consensus        51 ~ivdlLv-~aGLa~SKsEARRlI~qGGv~VNg~kv~~~~~~~~i~   94 (164)
T 2ktl_A           51 TFSKVLW-SAGLVASKSEGQRIINNNGAYVGSRPGVKKNEPGGGM   94 (164)
T ss_dssp             SHHHHHH-HHTSCSTHHHHHHHHHHTCEEEEECCSCCCCCCCSSS
T ss_pred             cHHHHHH-HhCcccCHHHHHHHHHhCCEEECCEeccccccccccc
Confidence            4554454 4699999999999999999999998876632344443

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*

Probab=94.03  E-value=0.059  Score=40.97  Aligned_cols=43  Identities=19%  Similarity=0.278  Sum_probs=36.9

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .++++=+|. ..+++.+..||++.+.||-|+|||..++|..+-+
T Consensus       368 ~~~~~~~l~-~~~l~~S~~earr~i~~ggv~vn~~~v~d~~~~~  410 (432)
T 1h3f_A          368 RIWVARLFT-LAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQV  410 (432)
T ss_dssp             EEEHHHHHH-HTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEE
T ss_pred             cCcHHHHHH-HhCCcccHHHHHHHHHhCCEEECCEEecCcccee
Confidence            456666666 4699999999999999999999999999998754

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}

Probab=93.76  E-value=0.08  Score=40.41  Aligned_cols=42  Identities=7%  Similarity=0.063  Sum_probs=36.1

Q ss_pred             hHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          25 PLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        25 PL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      +++=+|. ..|+|.+..||++.+.||-|+|||..++|..+-+.
T Consensus       357 ~~~~ll~-~~gl~~S~~earr~i~~ggv~in~~~v~d~~~~~~  398 (432)
T 2jan_A          357 GIVDLLV-ASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQ  398 (432)
T ss_dssp             SHHHHHH-HHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCC
T ss_pred             hHHHHHH-HhCCcccHHHHHHHHHhCCEEECCEEccChhcccC
Confidence            4565665 47999999999999999999999999999987654

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}

Probab=93.43  E-value=0.052  Score=39.16  Aligned_cols=41  Identities=7%  Similarity=-0.093  Sum_probs=32.3

Q ss_pred             hHHHHHHhhhcccccHHHHHHHHHcCceEeCC-e-EecCCcCCc
Q psy8661          25 PLVIFLRNRLKYALTNQEVLKILMQRLIKVDG-K-VRTDTNYPA   66 (71)
Q Consensus        25 PL~i~LRd~LkyA~t~~EakkIl~~~~V~VdG-k-vrtD~~~pv   66 (71)
                      -|-.+|-. .+++.+..+|++.+++|.|.||| + +.++..+.|
T Consensus         8 RLD~~L~~-~g~~~SR~~a~~lI~~G~V~Vng~~~~v~kp~~~V   50 (291)
T 3hp7_A            8 RVDVLAYK-QGLFETREQAKRGVMAGLVVNVINGERYDKPGEKI   50 (291)
T ss_dssp             EHHHHHHH-TTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEE
T ss_pred             hHHHHHHH-cCCcccHHHHHHHHHCCeEEECCeEEEEccCCCCC
Confidence            35556544 46888999999999999999999 8 777776554

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}

Probab=93.22  E-value=0.01  Score=35.43  Aligned_cols=37  Identities=8%  Similarity=0.087  Sum_probs=25.9

Q ss_pred             HHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          28 IFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        28 i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      -||.. .+++.+...+++++.+|.|+|||+++ +..+.+
T Consensus         5 ~~L~~-~~~~~sR~~~~~li~~G~V~VNg~~~-~~~~~v   41 (92)
T 2k6p_A            5 KFLQS-VGLVKRRVLATDMCNVGAVWLNGSCA-KASKEV   41 (92)
T ss_dssp             HHSTT-TTSCCCCCSSCCHHHHTCCEETTEEC-CTTCBC
T ss_pred             HHHHH-CCCCCCHHHHHHHHHCCcEEECCEEc-CCCCCc
Confidence            34444 23444555589999999999999987 555554

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*

Probab=92.57  E-value=0.022  Score=43.08  Aligned_cols=43  Identities=16%  Similarity=0.230  Sum_probs=0.0

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .++|.=+|. ..++|.+..|||+.+.||-|+|||.+++|..+-+
T Consensus       352 ~i~l~~lL~-~agl~~SksEARRlI~~GgV~VNgekv~d~~~~l  394 (420)
T 1jil_A          352 TTNIVEVLI-ETGISPSKRQAREDVNNGAIYINGERQQDVNYAL  394 (420)
T ss_dssp             --------------------------------------------
T ss_pred             cccHHHHHH-HcCCccCHHHHHHHHHhCCEEECCEEeccccccc
Confidence            345666665 4689999999999999999999999999987654

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A

Probab=90.23  E-value=0.054  Score=41.11  Aligned_cols=42  Identities=19%  Similarity=0.200  Sum_probs=0.0

Q ss_pred             hhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        24 lPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      ++++=+|. ..++|.+..||++.+.||-|+|||..++|..+-+
T Consensus       352 ~~~~~~l~-~~gl~~S~~earr~i~~ggv~in~~~v~d~~~~~  393 (419)
T 2ts1_A          352 VPLVELLV-SAGISPSKRQAREDIQNGAIYVNGERLQDVGAIL  393 (419)
T ss_dssp             -------------------------------------------
T ss_pred             ccHHHHHH-HhCCCCCHHHHHHHHHhCCEEECCEEecCccccc
Confidence            45555555 4699999999999999999999999999987754

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A

Probab=89.30  E-value=0.07  Score=38.25  Aligned_cols=44  Identities=14%  Similarity=0.135  Sum_probs=0.0

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      +++-|--||...+ ...+.+++++++.+|.|+|||+++++..+.+
T Consensus        15 ~g~RLd~~L~~~~-~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v   58 (325)
T 1v9f_A           15 LGQRLDQALAEMF-PDYSRSRIKEWILDQRVLVNGKVCDKPKEKV   58 (325)
T ss_dssp             ---------------------------------------------
T ss_pred             CCchHHHHHHhhc-cccCHHHHHHHHHCCCEEECCEEccCCCCEe
Confidence            3456777777654 2457789999999999999999866665554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	71
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	97.58
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	97.55
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	97.5
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	97.48
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	97.19
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	97.1
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	96.81
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	96.54
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	95.33

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.58  E-value=5.2e-05  Score=44.43  Aligned_cols=43  Identities=19%  Similarity=0.271  Sum_probs=38.7

Q ss_pred             chhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCc
Q psy8661          23 SLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPA   66 (71)
Q Consensus        23 slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pv   66 (71)
                      .++|.=+|.. .++|.+..||++.+.||-|+|||...+|..|-+
T Consensus        17 ~i~l~~ll~~-~gl~~S~searRlI~~g~V~iN~~ki~d~~~~l   59 (81)
T d1h3fa2          17 RIWVARLFTL-AGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQV   59 (81)
T ss_dssp             EEEHHHHHHH-TTSSSSHHHHHHHHHTTCEEETTEECCCTTCEE
T ss_pred             cccHHHHHHH-cCCCcCHHHHHHHHHcCCEEECCEEecCcccee
Confidence            4788888886 799999999999999999999999999998754

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.55  E-value=6.8e-05  Score=41.41  Aligned_cols=39  Identities=13%  Similarity=0.179  Sum_probs=31.8

Q ss_pred             HHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          27 VIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        27 ~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      --||-+.+ +. +.+||++.+.+|.|.|||+++++..|-|-
T Consensus         4 dk~l~~~~-~~-SR~~a~~lI~~g~V~Vng~~v~~~~~~V~   42 (59)
T d1kska3           4 DKFIAQQL-GV-SRAIAGREIRGNRVTVDGEIVRNAAFKLL   42 (59)
T ss_dssp             HHHHHHHH-TC-CHHHHHHHHHTTCEEETTEECCCTTCEEC
T ss_pred             HHHHHHcC-CC-CHHHHHHHHHcCcEEECCEEeecCCcCcC
Confidence            34565554 44 89999999999999999999999988653

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.50  E-value=9.3e-05  Score=40.78  Aligned_cols=43  Identities=16%  Similarity=0.203  Sum_probs=33.7

Q ss_pred             HHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661          26 LVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus        26 L~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      |--+|-+.. +. +.+||++.+.+|.|.|||+++++..|-+--.|
T Consensus         4 LD~~Ls~~~-~~-SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d   46 (58)
T d1vioa2           4 LDKFIAENV-GL-TRSQATKAIRQSAVKINGEIVKSGSVQISQED   46 (58)
T ss_dssp             HHHHHHHHH-TC-CHHHHHHHHHTTCEEETTEECCCTTCEECTTS
T ss_pred             HHHHHHHcC-CC-CHHHHHHHHHcCeEEECCEEeCCCCCCCCCCC
Confidence            445666554 33 88999999999999999999999988765443

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.48  E-value=0.00011  Score=44.29  Aligned_cols=46  Identities=17%  Similarity=0.156  Sum_probs=39.8

Q ss_pred             cchhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661          22 ESLPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF   68 (71)
Q Consensus        22 ~slPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~   68 (71)
                      +.+++.=+|. ..+.|.+..|||+.+.||-|+|||..++|..|-+..
T Consensus        30 ~~~~l~~ll~-~~~l~~S~seaRrlI~~ggv~iN~~kv~d~~~~l~~   75 (99)
T d1jh3a_          30 GDVPLVELLV-SAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTA   75 (99)
T ss_dssp             SCCCHHHHHH-HHTSCCSHHHHHHHHHSTTEEETTEECCSTTTCCSS
T ss_pred             CCCCHHHHHH-HcCCCcCHHHHHHHHHcCCEEECCEEecCcccccCH
Confidence            4677777776 469999999999999999999999999999887653

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.19  E-value=0.0002  Score=47.06  Aligned_cols=38  Identities=24%  Similarity=0.204  Sum_probs=33.6

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCccccc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGFMV   70 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~md   70 (71)
                      ++|+|.|..+|++++..|.|.|||+.++=+.|-+---|
T Consensus        59 r~gfa~t~~~arQ~v~Hghi~vNgk~v~iPSy~vk~GD   96 (159)
T d1c06a_          59 RLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQ   96 (159)
T ss_dssp             HHTSSSSHHHHHHHHHTSCEEETTEECCCSSCCCCSSC
T ss_pred             cCcccCCHHHHHHHHHhcceEccceEEEecceeecCCc
Confidence            48999999999999999999999999988888765433

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=97.10  E-value=1.7e-05  Score=46.64  Aligned_cols=43  Identities=19%  Similarity=0.213  Sum_probs=37.2

Q ss_pred             hhHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          24 LPLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        24 lPL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      +-|.=||.. .+++.+..||++.+.+|.|.|||++.++..+.+-
T Consensus        21 irL~k~L~~-~gl~~Sr~eAk~lI~~G~V~VNG~~~~~p~~~V~   63 (79)
T d1p9ka_          21 VELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIV   63 (79)
T ss_dssp             CCHHHHHHH-HTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCC
T ss_pred             EEHHHHHHH-CCCccCHHHHHHHHHhCCcccCCEEeccccccCC
Confidence            566667765 5889999999999999999999999999988764

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=96.81  E-value=0.00063  Score=46.43  Aligned_cols=35  Identities=20%  Similarity=0.387  Sum_probs=32.0

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      ++++|.|..+|++++..|.|.|||+.++=+.|-+-
T Consensus       106 r~g~a~t~~~ARQ~v~Hg~i~vNg~~v~ips~~~~  140 (208)
T d2uubd1         106 RLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVR  140 (208)
T ss_dssp             HTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCC
T ss_pred             hccccccHHHHHHHHHhcCeecCCeEEEeccEEec
Confidence            58999999999999999999999999988877654

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=96.54  E-value=0.00094  Score=45.33  Aligned_cols=35  Identities=23%  Similarity=0.453  Sum_probs=31.0

Q ss_pred             hhcccccHHHHHHHHHcCceEeCCeEecCCcCCcc
Q psy8661          33 RLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAG   67 (71)
Q Consensus        33 ~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG   67 (71)
                      +||+|.|..+|+++++.|+|.||||.+.=+.|=+-
T Consensus       102 R~gfa~t~~~ARQ~v~Hghi~VNgk~VnIPSy~vk  136 (204)
T d2gy9d1         102 RMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVS  136 (204)
T ss_dssp             HHTSSSSHHHHHHHHHTTCEEESSSBCCCTTCBCC
T ss_pred             hccccccHHHHHHHHHhcceecCCEEEEeccEeec
Confidence            48999999999999999999999999877766543

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=95.33  E-value=0.011  Score=35.88  Aligned_cols=42  Identities=10%  Similarity=0.100  Sum_probs=33.1

Q ss_pred             hHHHHHHhhhcccccHHHHHHHHHcCceEeCCeEecCCcCCccc
Q psy8661          25 PLVIFLRNRLKYALTNQEVLKILMQRLIKVDGKVRTDTNYPAGF   68 (71)
Q Consensus        25 PL~i~LRd~LkyA~t~~EakkIl~~~~V~VdGkvrtD~~~pvG~   68 (71)
                      =|--||. ..+++.|...|.++|.+|.|.|||++.+ ..|.|-.
T Consensus         6 RlD~~L~-~~r~~ktR~~A~~~i~~G~V~vNg~~vK-ps~~vk~   47 (104)
T d1dm9a_           6 RLDKWLW-AARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVEL   47 (104)
T ss_dssp             BHHHHHH-HTTSSSSHHHHHHHHHTTCEEETTEECC-TTCBCCT
T ss_pred             eHHHHHH-HhhhHhhHHHHHHHHHcCCeeeCCeecc-ccccCCC
Confidence            3445554 3688899999999999999999999875 6676644