Psyllid ID: psy4496

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------23
Protein Sequence
MNWAVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLFPSIPGK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHccccccHHHHHccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHcccccccHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEcccccHHHccccccHccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHcccccccccHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHcHHHHHccccccccccccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccccccccccccccccEEEEEEcccccEEEEccccccc
Coil and Loop (DISEMBL)
mnwavfaltskpqvvqkvdmtkvkldiLKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFdlakkvpvckeigkgdlgLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYltckptkvsAQTATEAvsssseqpfpiptpdgadktyspkiTKLANDISSLTLLECADLSSLLKKqlnlpdapmmamGAFAQGRYLRTIFDATsceiklfpsipgk
Flexible Loop (DISEMBL)
mnwavfaltskpqvvqkvdmtkvkldilkpWITQKITQLLGMEDDVVVAFVYNQLEAEKVStifefdlakkvPVCKEIGKGDLGLMQVVTVVLAILMQevegrrkilrgrktitrtyyskiyltckptKVSAQTATEavsssseqpfpiptpdgadktYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEiklfpsipgk
Low Complexity Region (SEG)
MNWAVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLFPSIPGK
Disordered region (IsUnstruct)
**WAVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPT**********************************ITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLF******
Disordered Region (DISOPRED)
***AVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEG***********************************A*S************************KLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLFPSIP**
Disordered Region (DISEMBL)
MNWAVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPT******************FPIPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLFPSIPGK
Disordered Region (DISPRO)
MNWAVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAVSS**EQPFPIPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLFPSIP**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNWAVFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTIFEFDLAKKVPVCKEIGKGDLGLMQVVTVVLAILMQEVEGRRKILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQGRYLRTIFDATSCEIKLFPSIPGK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	228	2.2.26 [Sep-21-2011]
Q5R5Q2	917	Serine/arginine repetitiv	yes	N/A	0.179	0.044	0.609	7e-12
Q8IYB3	904	Serine/arginine repetitiv	yes	N/A	0.179	0.045	0.609	7e-12
Q52KI8	946	Serine/arginine repetitiv	yes	N/A	0.188	0.045	0.581	4e-09
Q5ZMJ9	888	Serine/arginine repetitiv	yes	N/A	0.188	0.048	0.581	5e-09
Q9USH5	301	PWI domain-containing pro	yes	N/A	0.175	0.132	0.55	8e-08
Q7YR75	198	39S ribosomal protein L12	no	N/A	0.232	0.267	0.528	1e-07
Q9DB15	201	39S ribosomal protein L12	no	N/A	0.232	0.263	0.528	1e-07
P52827	203	39S ribosomal protein L12	N/A	N/A	0.219	0.246	0.54	3e-07
P52815	198	39S ribosomal protein L12	no	N/A	0.232	0.267	0.509	6e-07

>sp|Q5R5Q2|SRRM1_PONAB Serine/arginine repetitive matrix protein 1 OS=Pongo abelii GN=SRRM1 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 38/41 (92%)

Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE
Sbjct: 36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLE 76

Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.
Pongo abelii (taxid: 9601)

>sp|Q8IYB3|SRRM1_HUMAN Serine/arginine repetitive matrix protein 1 OS=Homo sapiens GN=SRRM1 PE=1 SV=2

 Score = 70.9 bits (172), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 38/41 (92%)

Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE
Sbjct: 36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLE 76

Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.

Homo sapiens (taxid: 9606)

>sp|Q52KI8|SRRM1_MOUSE Serine/arginine repetitive matrix protein 1 OS=Mus musculus GN=Srrm1 PE=1 SV=2

 Score = 61.6 bits (148), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct: 36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.

Mus musculus (taxid: 10090)

>sp|Q5ZMJ9|SRRM1_CHICK Serine/arginine repetitive matrix protein 1 OS=Gallus gallus GN=SRRM1 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct: 36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

Involved in pre-mRNA splicing and processing events.

Gallus gallus (taxid: 9031)

>sp|Q9USH5|YJQ5_SCHPO PWI domain-containing protein C825.05c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC825.05c PE=1 SV=1

 Score = 57.4 bits (137), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 31/40 (77%)

Query: 17 KVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          KVDM KV +++LKPWI  ++ +L+G ED+VV+ FVY  LE
Sbjct: 36 KVDMKKVNIEVLKPWIATRLNELIGFEDEVVINFVYGMLE 75

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q7YR75|RM12_BOVIN 39S ribosomal protein L12, mitochondrial OS=Bos taurus GN=MRPL12 PE=1 SV=1

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 34/53 (64%)

Query: 153 DGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
           D A K Y PKI +L  DI+SLTLLE +DL+ LLKK L + D  +M MG    G
Sbjct: 54  DNAPKEYPPKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPG 106

Bos taurus (taxid: 9913)

>sp|Q9DB15|RM12_MOUSE 39S ribosomal protein L12, mitochondrial OS=Mus musculus GN=Mrpl12 PE=1 SV=2

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 34/53 (64%)

Query: 153 DGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
           D A K Y PKI +L  DI+SLTLLE +DL+ LLKK L + D  +M MG    G
Sbjct: 55  DNAPKEYPPKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPG 107

Mus musculus (taxid: 10090)

>sp|P52827|RM12_CRICR 39S ribosomal protein L12, mitochondrial OS=Cricetus cricetus GN=MRPL12 PE=2 SV=1

 Score = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 33/50 (66%)

Query: 153 DGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAF 202
           D A K Y PKI +L  DI+SLTLLE +DL+ LLKK L + D  +M MG  
Sbjct: 56  DNAPKEYPPKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGM 105

Cricetus cricetus (taxid: 10034)

>sp|P52815|RM12_HUMAN 39S ribosomal protein L12, mitochondrial OS=Homo sapiens GN=MRPL12 PE=1 SV=2

 Score = 54.3 bits (129), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 34/53 (64%)

Query: 153 DGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
           D A K Y PKI +L  DI+SLTLLE +DL+ LLKK L + D  ++ MG    G
Sbjct: 54  DNAPKEYPPKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLVPMGGVMSG 106

Homo sapiens (taxid: 9606)

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	228
380027196	1202	PREDICTED: uncharacterized protein LOC10	0.188	0.035	0.813	6e-14
350421089	1203	PREDICTED: hypothetical protein LOC10074	0.188	0.035	0.813	6e-14
332021163	845	Serine/arginine repetitive matrix protei	0.188	0.050	0.813	2e-13
383858194	429	PREDICTED: serine/arginine repetitive ma	0.188	0.100	0.790	8e-13
345480448	1321	PREDICTED: hypothetical protein LOC10011	0.188	0.032	0.790	2e-12
345480452	1315	PREDICTED: hypothetical protein LOC10011	0.188	0.032	0.790	2e-12
345480454	1336	PREDICTED: hypothetical protein LOC10011	0.188	0.032	0.790	2e-12
307201244	1153	Serine/arginine repetitive matrix protei	0.175	0.034	0.8	2e-12
328786765	77	PREDICTED: serine/arginine repetitive ma	0.188	0.558	0.813	3e-12
270483719	181	mitochondrial ribosomal protein L12 [Nas	0.241	0.303	0.636	3e-12

>gi|380027196|ref|XP_003697315.1| PREDICTED: uncharacterized protein LOC100871392 [Apis florea]

 Score = 83.6 bits (205), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 40/43 (93%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM+KVKLD++KPWIT KITQ+LGMEDDVVV FVYNQLE
Sbjct: 31 LTQKVDMSKVKLDVIKPWITTKITQILGMEDDVVVEFVYNQLE 73

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350421089|ref|XP_003492729.1| PREDICTED: hypothetical protein LOC100741990 [Bombus impatiens]

 Score = 83.6 bits (205), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 40/43 (93%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM+KVKLD++KPWIT KITQ+LGMEDDVVV FVYNQLE
Sbjct: 31 LTQKVDMSKVKLDVIKPWITTKITQILGMEDDVVVEFVYNQLE 73

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332021163|gb|EGI61548.1| Serine/arginine repetitive matrix protein 1 [Acromyrmex echinatior]

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 40/43 (93%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM+KVKLD++KPWIT KITQ+LGMEDDVVV FVYNQLE
Sbjct: 7  LTQKVDMSKVKLDVIKPWITTKITQILGMEDDVVVEFVYNQLE 49

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858194|ref|XP_003704587.1| PREDICTED: serine/arginine repetitive matrix protein 1-like [Megachile rotundata]

 Score = 79.7 bits (195), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 40/43 (93%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM+KVKLD++KPWIT KITQ+LGMEDDVV+ FVYNQLE
Sbjct: 31 LTQKVDMSKVKLDVIKPWITTKITQILGMEDDVVIEFVYNQLE 73

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480448|ref|XP_003424149.1| PREDICTED: hypothetical protein LOC100117836 isoform 2 [Nasonia vitripennis]

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 38/43 (88%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM KVKLD++KPWIT KITQ+LGMEDDVVV FV NQLE
Sbjct: 31 LTQKVDMQKVKLDVIKPWITTKITQILGMEDDVVVEFVINQLE 73

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480452|ref|XP_003424150.1| PREDICTED: hypothetical protein LOC100117836 isoform 3 [Nasonia vitripennis]

 Score = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 38/43 (88%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM KVKLD++KPWIT KITQ+LGMEDDVVV FV NQLE
Sbjct: 25 LTQKVDMQKVKLDVIKPWITTKITQILGMEDDVVVEFVINQLE 67

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480454|ref|XP_003424151.1| PREDICTED: hypothetical protein LOC100117836 isoform 4 [Nasonia vitripennis]

 Score = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 38/43 (88%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM KVKLD++KPWIT KITQ+LGMEDDVVV FV NQLE
Sbjct: 31 LTQKVDMQKVKLDVIKPWITTKITQILGMEDDVVVEFVINQLE 73

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307201244|gb|EFN81125.1| Serine/arginine repetitive matrix protein 1 [Harpegnathos saltator]

 Score = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/40 (80%), Positives = 37/40 (92%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYN 53
          + QKVDM+KVKLD++KPWIT KITQ+LGMEDDVVV FVYN
Sbjct: 27 LTQKVDMSKVKLDVIKPWITTKITQILGMEDDVVVEFVYN 66

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328786765|ref|XP_001120994.2| PREDICTED: serine/arginine repetitive matrix protein 1-like [Apis mellifera]

 Score = 78.2 bits (191), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 40/43 (93%)

Query: 14 VVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          + QKVDM+KVKLD++KPWIT KITQ+LGMEDDVVV FVYNQLE
Sbjct: 31 LTQKVDMSKVKLDVIKPWITTKITQILGMEDDVVVEFVYNQLE 73

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270483719|ref|NP_001162028.1| mitochondrial ribosomal protein L12 [Nasonia vitripennis]

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 35/55 (63%), Positives = 44/55 (80%)

Query: 149 IPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFA 203
           IP P+G DK  SPKI K+A +I+SL L+E A+LS LLKK+LNLPDAP+M +G FA
Sbjct: 40  IPVPEGVDKPVSPKIDKIAQEITSLNLIEVAELSDLLKKRLNLPDAPVMPVGGFA 94

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	228
ZFIN|ZDB-GENE-050417-187	412	mrpl12 "mitochondrial ribosoma	0.315	0.174	0.5	8.2e-12
FB|FBgn0036340	954	SRm160 "SRm160" [Drosophila me	0.192	0.046	0.704	2e-11
ZFIN|ZDB-GENE-040426-2789	929	srrm1 "serine/arginine repetit	0.188	0.046	0.681	2.4e-11
UNIPROTKB|E1BYZ6	643	E1BYZ6 "Uncharacterized protei	0.188	0.066	0.581	1.4e-10
MGI|MGI:1858303	946	Srrm1 "serine/arginine repetit	0.188	0.045	0.581	3.1e-10
FB|FBgn0011787	182	mRpL12 "mitochondrial ribosoma	0.381	0.478	0.395	4.1e-10
UNIPROTKB|E1BP16	901	SRRM1 "Uncharacterized protein	0.188	0.047	0.581	4.4e-10
UNIPROTKB|Q8IYB3	904	SRRM1 "Serine/arginine repetit	0.188	0.047	0.581	4.4e-10
UNIPROTKB|A9Z1X7	913	SRRM1 "Serine/arginine repetit	0.188	0.047	0.581	4.5e-10
UNIPROTKB|E9PCT1	916	SRRM1 "Serine/arginine repetit	0.188	0.046	0.581	4.5e-10

ZFIN|ZDB-GENE-050417-187 mrpl12 "mitochondrial ribosomal protein L12" [Danio rerio (taxid:7955)]

 Score = 167 (63.8 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 36/72 (50%), Positives = 46/72 (63%)

Query:   132 AQTATEAVSSSSEQPFPIPTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNL 191
             AQ   +  S S+      P  DG  K YSPKI +L NDI+SLTL+E +DL+ LLKK LN+
Sbjct:     1 AQRTLKTSSVSAVDAIATPHLDGTPKEYSPKIQQLVNDIASLTLIEVSDLNELLKKTLNI 60

Query:   192 PDAPMMAMGAFA 203
              D  MM+MG+ A
Sbjct:    61 QDVGMMSMGSMA 72

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

GO:0005622 "intracellular" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0006810 "transport" evidence=IEA

FB|FBgn0036340 SRm160 "SRm160" [Drosophila melanogaster (taxid:7227)]

 Score = 169 (64.5 bits), Expect = 2.0e-11, P = 2.0e-11
 Identities = 31/44 (70%), Positives = 40/44 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEK 59
             ++VDM+KVKLD+L+PWI++KIT +L +EDDVVV FVYNQLE EK
Sbjct:    33 KRVDMSKVKLDVLRPWISKKITDILHIEDDVVVEFVYNQLEEEK 76

GO:0035145 "exon-exon junction complex" evidence=TAS

GO:0006397 "mRNA processing" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0071011 "precatalytic spliceosome" evidence=IDA

ZFIN|ZDB-GENE-040426-2789 srrm1 "serine/arginine repetitive matrix 1" [Danio rerio (taxid:7955)]

 Score = 168 (64.2 bits), Expect = 2.4e-11, P = 2.4e-11
 Identities = 30/44 (68%), Positives = 40/44 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEK 59
             +KVDMTKV L+++KPWITQ++T++LG EDDVV+ FV+NQLE EK
Sbjct:    36 KKVDMTKVNLEVIKPWITQRVTEILGFEDDVVIEFVFNQLE-EK 78

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|E1BYZ6 E1BYZ6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 159 (61.0 bits), Expect = 1.4e-10, Sum P(2) = 1.4e-10
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
             +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct:    36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

GO:0006397 "mRNA processing" evidence=IEA

MGI|MGI:1858303 Srrm1 "serine/arginine repetitive matrix 1" [Mus musculus (taxid:10090)]

 Score = 159 (61.0 bits), Expect = 3.1e-10, Sum P(2) = 3.1e-10
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
             +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct:    36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

GO:0000375 "RNA splicing, via transesterification reactions" evidence=ISO

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016363 "nuclear matrix" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

FB|FBgn0011787 mRpL12 "mitochondrial ribosomal protein L12" [Drosophila melanogaster (taxid:7227)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 36/91 (39%), Positives = 55/91 (60%)

Query:   113 ITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPDGADKTYSPKITKLANDISS 172
             ITR    +I    +  ++ +  A  A  S +E+  P P P+GA K  +PK+  + N+I++
Sbjct:     3 ITRLALRQISRQVQLHRMYSAAAPAAAVSGAEKLVP-PAPEGAAKPPNPKLDSIVNNIAA 61

Query:   173 LTLLECADLSSLLKKQLNLPD---APMMAMG 200
             L LLE A+LS+LLK++LNLP+   AP  A G
Sbjct:    62 LNLLEVAELSTLLKQKLNLPETAFAPQFAAG 92

GO:0005762 "mitochondrial large ribosomal subunit" evidence=ISS

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

GO:0006412 "translation" evidence=ISS

GO:0005763 "mitochondrial small ribosomal subunit" evidence=ISS

GO:0016049 "cell growth" evidence=IMP

GO:0007005 "mitochondrion organization" evidence=IMP

GO:0005811 "lipid particle" evidence=IDA

GO:0003682 "chromatin binding" evidence=IGI

UNIPROTKB|E1BP16 SRRM1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 159 (61.0 bits), Expect = 4.4e-10, Sum P(2) = 4.4e-10
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
             +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct:    36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|Q8IYB3 SRRM1 "Serine/arginine repetitive matrix protein 1" [Homo sapiens (taxid:9606)]

 Score = 159 (61.0 bits), Expect = 4.4e-10, Sum P(2) = 4.4e-10
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
             +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct:    36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0000375 "RNA splicing, via transesterification reactions" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005634 "nucleus" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

UNIPROTKB|A9Z1X7 SRRM1 "Serine/arginine repetitive matrix protein 1" [Homo sapiens (taxid:9606)]

 Score = 159 (61.0 bits), Expect = 4.5e-10, Sum P(2) = 4.5e-10
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
             +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct:    36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|E9PCT1 SRRM1 "Serine/arginine repetitive matrix protein 1" [Homo sapiens (taxid:9606)]

 Score = 159 (61.0 bits), Expect = 4.5e-10, Sum P(2) = 4.5e-10
 Identities = 25/43 (58%), Positives = 39/43 (90%)

Query:    16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAE 58
             +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +
Sbjct:    36 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVK 78

GO:0006397 "mRNA processing" 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

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

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	228
pfam01480	74	pfam01480, PWI, PWI domain	8e-13
smart00311	74	smart00311, PWI, PWI, domain in splicing factors	6e-10
cd00387	127	cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L1	9e-07

>gnl|CDD|216523 pfam01480, PWI, PWI domain

 Score = 61.5 bits (150), Expect = 8e-13
 Identities = 16/39 (41%), Positives = 28/39 (71%)

Query: 25 LDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTI 63
          L+++KPWI +K+T++LG EDD+V+ ++ N LE +     
Sbjct: 1  LEVIKPWIEKKVTEILGFEDDIVIDYILNLLEDKHNPDP 39

Length = 74

>gnl|CDD|214609 smart00311, PWI, PWI, domain in splicing factors

 Score = 53.5 bits (129), Expect = 6e-10
 Identities = 18/41 (43%), Positives = 30/41 (73%)

Query: 20 MTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKV 60
          ++K+KLD +KPWIT+K+ + LG E+D +V F+ +Q+   K 
Sbjct: 1  LSKLKLDEIKPWITKKVIEFLGFEEDTLVEFILSQIRQHKG 41

Length = 74

>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12

 Score = 46.4 bits (111), Expect = 9e-07
 Identities = 12/45 (26%), Positives = 22/45 (48%)

Query: 161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
            K+ ++   +  LTLLE A+L   L+++  +  +   A  A A  
Sbjct: 1   LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAAAAP 45

Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors. In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homolog is found in some eukaryotes, in mitochondria and chloroplasts. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12. Length = 127

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	228
KOG2146|consensus	354		99.96
PF01480	77	PWI: PWI domain; InterPro: IPR002483 The PWI domai	99.72
smart00311	74	PWI PWI, domain in splicing factors.	99.68
KOG1715|consensus	187		99.42
CHL00083	131	rpl12 ribosomal protein L12	99.25
TIGR00855	126	L12 ribosomal protein L7/L12. THis model resembles	99.18
PRK00157	123	rplL 50S ribosomal protein L7/L12; Reviewed	99.15
COG0222	124	RplL Ribosomal protein L7/L12 [Translation, riboso	99.11
cd00387	127	Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosom	99.06
KOG2253|consensus	668		98.53

>KOG2146|consensus

Probab=99.96  E-value=8.1e-31  Score=238.63  Aligned_cols=86  Identities=36%  Similarity=0.578  Sum_probs=77.3

Q ss_pred             cccccCccccccccCccccCcchhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCcc-------chhcccccCchh-HHH
Q psy4496           5 VFALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVS-------TIFEFDLAKKVP-VCK   76 (228)
Q Consensus         5 ~~~~kfP~~f~~kVDm~KVnl~vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~p-------~I~gFL~~~~a~-F~~   76 (228)
                      ++.||||++|++||||+||||+||||||++||||||||||||||||||||||+..+|       +++|||....|. ||-
T Consensus        22 mkqmKF~~~lekkVDmsKvnleVlkPWItkrvneilgfEDdVViefvynqLee~k~ldpkkmQiNlTGFLngrnAreFmg  101 (354)
T KOG2146|consen   22 MKQMKFPACLEKKVDMSKVNLEVLKPWITKRVNEILGFEDDVVIEFVYNQLEEAKNLDPKKMQINLTGFLNGRNAREFMG  101 (354)
T ss_pred             HHhcccHHHHhhhcchhhcchhhhhHHHHHHHHHhhccccchhHHHHHHHHhhhcCCCchheeeeeehhcccccHHHHHH
Confidence            467999999999999999999999999999999999999999999999999996554       569999877765 999


Q ss_pred             HHhhhcc--------ChhHHHH
Q psy4496          77 EIGKGDL--------GLMQVVT   90 (228)
Q Consensus        77 eLWkLll--------gi~q~vl   90 (228)
                      |||.|||        |||.-+.
T Consensus       102 eLW~LliS~a~~s~~giP~s~~  123 (354)
T KOG2146|consen  102 ELWSLLISEASQSQYGIPASFI  123 (354)
T ss_pred             HHHHHHHhhccccccCCchHHH
Confidence            9999999        6776544

>PF01480 PWI: PWI domain; InterPro: IPR002483 The PWI domain, named after a highly conserved PWI tri-peptide located within its N-terminal region, is a ~80 amino acid module, which is found either at the N terminus or at the C terminus of eukaryotic proteins involved in pre-mRNA processing []

Probab=99.72  E-value=1.7e-18  Score=128.97  Aligned_cols=61  Identities=30%  Similarity=0.528  Sum_probs=51.8

Q ss_pred             cchhhhHHHHHHHHhcCCCchHHHHHHHHHhhccC---c--c-----chhcccccCchhHHHHHhhhccCh
Q psy4496          25 LDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEK---V--S-----TIFEFDLAKKVPVCKEIGKGDLGL   85 (228)
Q Consensus        25 l~vikpWI~~rItelLG~EDDVvieyi~~lLe~~~---~--p-----~I~gFL~~~~a~F~~eLWkLllgi   85 (228)
                      |++|||||.+||+++||+|||+|+|||+++|....   .  |     ++.+||+++++.||.+||++|+..
T Consensus         1 l~~lk~WI~~kl~e~lG~edd~lvdyI~~~l~~~~~~~~~~~~~l~~~L~~fL~~~a~~Fv~~Lw~~l~~~   71 (77)
T PF01480_consen    1 LEKLKPWISKKLEEILGFEDDVLVDYIVALLKSHKSSNEPDPKELQEQLEDFLDEEAEEFVDELWRLLISA   71 (77)
T ss_dssp             CHHHHHHHHHHHHHHHSS--CHHHHHHHHHCCTT--SSS--HHHHHHHHTTTTGHHCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccccccHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999643   2  2     678999988888999999998743

It is generally found in association with other domains such as RRM and RS. The PWI domain is a RNA/DNA-binding domain that has an equal preference for single- and double-stranded nucleic acids and is likely to have multiple important functions in pre-mRNA processing []. Proteins containing this domain include the SR-related nuclear matrix protein of 160kDa (SRm160) splicing and 3'-end cleavage-stimulatory factor, and the mammalian splicing factor PRP3. The PWI domain is a soluble, globular and independently folded domain which consists of a four-helix bundle, with structured N- and C-terminal elements [].; GO: 0006397 mRNA processing; PDB: 1MP1_A 1X4Q_A.

>smart00311 PWI PWI, domain in splicing factors

Probab=99.68  E-value=2e-17  Score=122.57  Aligned_cols=64  Identities=31%  Similarity=0.561  Sum_probs=55.3

Q ss_pred             ccccCcchhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCccc-----h--hcccccCchhHHHHHhhhccCh
Q psy4496          20 MTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVST-----I--FEFDLAKKVPVCKEIGKGDLGL   85 (228)
Q Consensus        20 m~KVnl~vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~p~-----I--~gFL~~~~a~F~~eLWkLllgi   85 (228)
                      ++|||++++||||+++|+++||++||+||+||++++++...|+     |  ++|+  ++..||.+||++++..
T Consensus         1 ~~kv~~~~lk~WI~~kv~e~LG~~d~~vvd~i~~~l~~~~~~~~l~~~L~~~~f~--da~~Fv~~Lw~~l~~~   71 (74)
T smart00311        1 LSKLKLDEIKPWITKKVIEFLGFEEDTLVEFILSQIRQHKGPQAKLLQINLTGFE--DAEEFVDKLWRLLIFE   71 (74)
T ss_pred             CchhHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCChHHHHHHHHhhcch--hHHHHHHHHHHHHHHh
Confidence            4799999999999999999999999999999999999876662     3  4565  4666999999998754

>KOG1715|consensus

Probab=99.42  E-value=3.1e-13  Score=116.94  Aligned_cols=86  Identities=40%  Similarity=0.496  Sum_probs=64.2

Q ss_pred             hhhhhhhhhccCCCCCCCC-CCCCCCCCCCChHHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCccccccc---cc---
Q psy4496         131 SAQTATEAVSSSSEQPFPI-PTPDGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGA---FA---  203 (228)
Q Consensus       131 ~~~~~~~~~~~~~~~~l~~-p~~~~~~~~~spKv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaaa---aA---  203 (228)
                      |...++.+++.++....+. +.+..+++++++||.+|||+|++||++|++||+++|++||||++.++||+++   ++   
T Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~~~g~~~~~~  106 (187)
T KOG1715|consen   27 IEYPHAFSSSKSSTLSHRATPLPPIAAVPPPPKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPDA  106 (187)
T ss_pred             ecchhhcCcccccccccccCCCCcccccCCCHHHHHHHHHHHhcCHHHHHHHHHHHHHHcCCCcccchhhccccCCCCCc
Confidence            3455666666665544444 4455588999999999999999999999999999999999999998776533   11   


Q ss_pred             ccc-----cccccccccc
Q psy4496         204 QGR-----YLRTIFDATS  216 (228)
Q Consensus       204 aaA-----aEkTeFdv~~  216 (228)
                      .++     .|+|.|||--
T Consensus       107 ~~a~ee~k~ekt~FdVkL  124 (187)
T KOG1715|consen  107 GGAEEEAKKEKTTFDVKL  124 (187)
T ss_pred             ccccccchhhcceEEEEE
Confidence            111     2677799864

>CHL00083 rpl12 ribosomal protein L12

Probab=99.25  E-value=5.5e-12  Score=104.03  Aligned_cols=59  Identities=27%  Similarity=0.306  Sum_probs=47.0

Q ss_pred             CChHHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCccccc--c---c-cc----ccccccccccccce
Q psy4496         159 YSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAM--G---A-FA----QGRYLRTIFDATSC  217 (228)
Q Consensus       159 ~spKv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aa--a---a-aA----aaAaEkTeFdv~~~  217 (228)
                      .|+++++|+|+|++||++|++||++.|+++|||++++++++  +   + ++    ++++|||+|||.--
T Consensus         1 ~s~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~~~~~~~a~~~~~~~~~~~EKT~F~V~L~   69 (131)
T CHL00083          1 MSTKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPAAAAAQAAEEVEEKTEFDVILE   69 (131)
T ss_pred             CCchHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhhhhccccCcccccccchhhhcceeeEEEe
Confidence            47899999999999999999999999999999999874333  1   1 11    12359999999743

>TIGR00855 L12 ribosomal protein L7/L12

Probab=99.18  E-value=2.2e-11  Score=99.94  Aligned_cols=56  Identities=23%  Similarity=0.310  Sum_probs=44.6

Q ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCccccccc---cc--ccccccccccccce
Q psy4496         162 KITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGA---FA--QGRYLRTIFDATSC  217 (228)
Q Consensus       162 Kv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaaa---aA--aaAaEkTeFdv~~~  217 (228)
                      ..++|+|+|++||++|++||++.|+++|||++++++++++   ++  ++++|||+|||.--
T Consensus         5 ~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~~a~~~a~~~~~~~~~eEKt~f~V~L~   65 (126)
T TIGR00855         5 SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAGAAGAAAAAAAAEEKTEFDVILK   65 (126)
T ss_pred             cHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccchhhhcccccccccccccccceeeEEEe
Confidence            3589999999999999999999999999999987543322   11  23359999999743

THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.

>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed

Probab=99.15  E-value=3.8e-11  Score=98.23  Aligned_cols=58  Identities=21%  Similarity=0.261  Sum_probs=46.1

Q ss_pred             ChHHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCccccccc-c--cccccccccccccce
Q psy4496         160 SPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGA-F--AQGRYLRTIFDATSC  217 (228)
Q Consensus       160 spKv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaaa-a--AaaAaEkTeFdv~~~  217 (228)
                      +-++++|+|+|++||++|++||++.|+++|||++++++++++ +  +++++|||+|||.--
T Consensus         2 ~~~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~~~~~~~~~~~~~~~eEkt~f~V~L~   62 (123)
T PRK00157          2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAAAAAAAAAAAEEKTEFDVVLK   62 (123)
T ss_pred             CccHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhccccccccccccccccceeEEEe
Confidence            345789999999999999999999999999999987543322 1  233469999999754

>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]

Probab=99.11  E-value=5.9e-11  Score=97.16  Aligned_cols=55  Identities=24%  Similarity=0.317  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCccccccc----ccccccccccccccc
Q psy4496         162 KITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGA----FAQGRYLRTIFDATS  216 (228)
Q Consensus       162 Kv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaaa----aAaaAaEkTeFdv~~  216 (228)
                      .+++|+++|++||++|++||++.++++|||++++++++++    ++++++|||+|||.-
T Consensus         4 ~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~a~~~a~a~~aaeEktefdVvL   62 (124)
T COG0222           4 TKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAAGAAAAEAAEEKTEFDVVL   62 (124)
T ss_pred             cHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccchhhhhccccccccccccccceeEEEe
Confidence            4689999999999999999999999999999998655432    223345999999964

>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12

Probab=99.06  E-value=1.5e-10  Score=94.88  Aligned_cols=57  Identities=26%  Similarity=0.338  Sum_probs=42.9

Q ss_pred             hHHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcccc--c-cc-ccc-c----ccccccccccce
Q psy4496         161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMA--M-GA-FAQ-G----RYLRTIFDATSC  217 (228)
Q Consensus       161 pKv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~a--a-aa-aAa-a----AaEkTeFdv~~~  217 (228)
                      +++++|+|+|++||++|++||++.|+++|||++.++++  + ++ +++ +    ++|||+|||.--
T Consensus         1 ~~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~~~~~a~~~~~~~~~~~~EKt~F~V~L~   66 (127)
T cd00387           1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAAAAPAAAAAAAAEAEEKTEFDVVLE   66 (127)
T ss_pred             CcHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCcccccccccccCcccccccccchhhcceEEEEEe
Confidence            36899999999999999999999999999999853221  1 11 111 1    138999999743

Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and

>KOG2253|consensus

Probab=98.53  E-value=4.4e-08  Score=97.68  Aligned_cols=73  Identities=16%  Similarity=0.297  Sum_probs=60.6

Q ss_pred             ccccccccCccccCcc----hhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCcc-ch----hcccccCchhHHHHHhhh
Q psy4496          11 KPQVVQKVDMTKVKLD----ILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVS-TI----FEFDLAKKVPVCKEIGKG   81 (228)
Q Consensus        11 P~~f~~kVDm~KVnl~----vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~p-~I----~gFL~~~~a~F~~eLWkL   81 (228)
                      +..|..++|-++||-.    .|+|||+++|+|+||.++|-+||||++.+.....| +|    ..-|+++...|+.++|+|
T Consensus       576 eeLf~~pidw~~ld~~lm~~rirpwV~KKIiEflGeeE~tLVdFI~s~i~~h~~~q~iL~dl~~ilDEdAE~FV~KmWRl  655 (668)
T KOG2253|consen  576 EELFAYPIDWDELDSILMNERIRPWVNKKIIEFLGEEEDTLVDFICSNIRQHSSPQQILDDLAMILDEDAEVFVVKMWRL  655 (668)
T ss_pred             HHHhhCcccHHHHhhHHHHHHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCHHHHHHHHHHHHhcchHHHHHHHHHH
Confidence            4568888888888865    68999999999999999999999999999988776 34    344544444599999999


Q ss_pred             cc
Q psy4496          82 DL   83 (228)
Q Consensus        82 ll   83 (228)
                      |+
T Consensus       656 Li  657 (668)
T KOG2253|consen  656 LI  657 (668)
T ss_pred             HH
Confidence            87

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	228
1mp1_A	111	Solution Structure Of The Pwi Motif From Srm160 Len		1e-11
2ftc_E	137	Structural Model For The Large Subunit Of The Mamma		9e-07

>pdb|1MP1|A Chain A, Solution Structure Of The Pwi Motif From Srm160 Length = 111

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 38/41 (92%)
Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLE 56
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE
Sbjct: 13 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLE 53

>pdb|2FTC|E Chain E, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 137

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 30/45 (66%)
Query: 161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
           PKI +L  DI+SLTLLE +DL+ LLKK L + D  +M MG    G
Sbjct: 1   PKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPG 45

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	228
1mp1_A	111	Ser/Arg-related nuclear matrix protein; four helix	7e-15
2ftc_E	137	L12MT, MRP-L12, 39S ribosomal protein L12, mitocho	1e-08

>1mp1_A Ser/Arg-related nuclear matrix protein; four helix bundle, RNA binding protein; NMR {Homo sapiens} SCOP: a.188.1.1 Length = 111

 Score = 67.3 bits (164), Expect = 7e-15
 Identities = 25/49 (51%), Positives = 40/49 (81%)

Query: 12 PQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKV 60
            + +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +  
Sbjct: 9  ECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNP 57

>2ftc_E L12MT, MRP-L12, 39S ribosomal protein L12, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} Length = 137

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 24/45 (53%), Positives = 30/45 (66%)

Query: 161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
           PKI +L  DI+SLTLLE +DL+ LLKK L + D  +M MG    G
Sbjct: 1   PKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPG 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	228
1mp1_A	111	Ser/Arg-related nuclear matrix protein; four helix	99.97
1x4q_A	92	U4/U6 small nuclear ribonucleoprotein PRP3; PWI do	99.87
3v53_A	119	RNA-binding protein 25; PWI, RNA-binding domain; 2	99.68
2ftc_E	137	L12MT, MRP-L12, 39S ribosomal protein L12, mitocho	99.3
2zjq_5	122	50S ribosomal protein L7/L12; ribosome, ribosomal	99.27
2j01_L	125	50S ribosomal protein L7; ribosome, tRNA, paromomy	99.24
3sgf_J	121	50S ribosomal protein L7/L12; typeii release facto	99.23
1dd3_A	128	50S ribosomal protein L7/L12; dimer formation, fle	99.11
1dd4_C	40	50S ribosomal protein L7/L12; dimer formation, fle	99.01
1zav_U	30	50S ribosomal protein L7/L12; ribosome structure a	98.33

>1mp1_A Ser/Arg-related nuclear matrix protein; four helix bundle, RNA binding protein; NMR {Homo sapiens} SCOP: a.188.1.1

Probab=99.97  E-value=7.7e-33  Score=220.18  Aligned_cols=85  Identities=35%  Similarity=0.582  Sum_probs=77.4

Q ss_pred             ccccCccccccccCccccCcchhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCcc------chhcccc-cCchhHHHHH
Q psy4496           6 FALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVS------TIFEFDL-AKKVPVCKEI   78 (228)
Q Consensus         6 ~~~kfP~~f~~kVDm~KVnl~vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~p------~I~gFL~-~~~a~F~~eL   78 (228)
                      +++|||++|++||||+|||+++|||||++||+++||+|||||||||||+|+++.++      ||+|||+ +++..||++|
T Consensus         3 ~~~kfp~~f~~kVD~~kV~l~~ikpWI~kki~e~LG~EDdvlid~i~~~L~~~~~dpk~lqi~L~gFL~~e~a~~Fv~eL   82 (111)
T 1mp1_A            3 MQLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGEL   82 (111)
T ss_dssp             CCCCCCSGGGGCCCTTTSCSGGGHHHHHHHHHHHHSSCCSHHHHHHHHHTTSSSCCHHHHHHHHTTTSCSHHHHHHHHHH
T ss_pred             ccccCCHHHhccccHHHhhHHHHHHHHHHHHHHHcCCccHHHHHHHHHHhhccCCCHHHHHHHHHHHhCcccHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999975432      6799998 4555699999


Q ss_pred             hhhcc-------ChhHHHH
Q psy4496          79 GKGDL-------GLMQVVT   90 (228)
Q Consensus        79 WkLll-------gi~q~vl   90 (228)
                      |+||+       |||++++
T Consensus        83 W~LLi~aq~~~~GIP~~~l  101 (111)
T 1mp1_A           83 WPLLLSAQENIAGIPSAFL  101 (111)
T ss_dssp             HHHHHHHTTSSSSCCHHHH
T ss_pred             HHHHHHhhcCCcCcCHHHH
Confidence            99998       9999877

>1x4q_A U4/U6 small nuclear ribonucleoprotein PRP3; PWI domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=5.9e-23  Score=158.06  Aligned_cols=71  Identities=20%  Similarity=0.276  Sum_probs=63.7

Q ss_pred             ccccCccccCcchhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCcc-----chhcccccCchhHHHHHhhhccCh
Q psy4496          15 VQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVS-----TIFEFDLAKKVPVCKEIGKGDLGL   85 (228)
Q Consensus        15 ~~kVDm~KVnl~vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~p-----~I~gFL~~~~a~F~~eLWkLllgi   85 (228)
                      +..|||+|||+++|||||+++|+|+||+|||+|||||+++|+....|     +|++||++++..||.+||++++..
T Consensus         5 ~~~~d~~kv~l~~lkpWI~kkv~e~LG~eD~~lVd~i~~~l~~~~dpk~l~~~L~~fLd~~a~~Fv~eLW~lL~~a   80 (92)
T 1x4q_A            5 SSGMALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAVEEG   80 (92)
T ss_dssp             SSCCCCCHHHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHTTCCHHHHHHHHTTTTGGGTHHHHHHHHHHHHHH
T ss_pred             CCCccchHHhHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence            45799999999999999999999999999999999999999965444     688999988666999999999743

>3v53_A RNA-binding protein 25; PWI, RNA-binding domain; 2.90A {Homo sapiens}

Probab=99.68  E-value=8.7e-18  Score=135.13  Aligned_cols=71  Identities=18%  Similarity=0.251  Sum_probs=60.9

Q ss_pred             ccccccCccccCcc----hhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCcc-----chhcccccCchhHHHHHhhhcc
Q psy4496          13 QVVQKVDMTKVKLD----ILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVS-----TIFEFDLAKKVPVCKEIGKGDL   83 (228)
Q Consensus        13 ~f~~kVDm~KVnl~----vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~p-----~I~gFL~~~~a~F~~eLWkLll   83 (228)
                      .|+.+||-+.||-.    +|||||+++|+|+||+|||+|||||+++|++...|     ++++||++++..||.+||++|+
T Consensus        28 Lf~~~i~W~~vd~~~i~~~lkPWI~kKI~E~LG~eEd~LVdfI~~~L~~~~~pk~l~~~L~~~LDeeA~~FV~kLWrlLI  107 (119)
T 3v53_A           28 LFAYPLDWSIVDSILMERRIRPWINKKIIEYIGEEEATLVDFVCSKVMAHSSPQSILDDVAMVLDEEAEVFIVKMWRLLI  107 (119)
T ss_dssp             HHHSCCCTTTSCHHHHHHTHHHHHHHHHHHHTC---CHHHHHHHHHHHTTCCHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HhcccCChhhhhHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            57888888888766    77999999999999999999999999999987766     6899998877789999999976

>2ftc_E L12MT, MRP-L12, 39S ribosomal protein L12, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus}

Probab=99.30  E-value=1.3e-12  Score=107.22  Aligned_cols=57  Identities=46%  Similarity=0.617  Sum_probs=44.8

Q ss_pred             hHHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcccccc----c---ccc--------c--ccccccccccce
Q psy4496         161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMG----A---FAQ--------G--RYLRTIFDATSC  217 (228)
Q Consensus       161 pKv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaa----a---aAa--------a--AaEkTeFdv~~~  217 (228)
                      ||+++|+|+|++||++|++||++.|+++|||+++++++++    +   +++        +  ++|||+|||.--
T Consensus         1 ~kv~~ive~i~~LtllE~~eLv~~leekfgv~aaa~~~~~~~~~~~~~~a~a~~~~~~~a~~~eEKteFdV~L~   74 (137)
T 2ftc_E            1 PKIQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPGAAPAPTAPEAAEEDVPKQKERTHFTVRLT   74 (137)
T ss_pred             CcHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcccccccccccccCCCCccccccccccccccccCCeeEEEee
Confidence            6899999999999999999999999999999987643322    1   111        1  247999999754

>2zjq_5 50S ribosomal protein L7/L12; ribosome, ribosomal subunit, thiopeptide antibiotics, complex, translational regulation, molecular switch; 3.30A {Deinococcus radiodurans} SCOP: d.45.1.1

Probab=99.27  E-value=3.1e-12  Score=103.35  Aligned_cols=57  Identities=28%  Similarity=0.296  Sum_probs=44.4

Q ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcccccc-ccc--cccccccccccccee
Q psy4496         162 KITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMG-AFA--QGRYLRTIFDATSCE  218 (228)
Q Consensus       162 Kv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaa-aaA--aaAaEkTeFdv~~~~  218 (228)
                      +.++|+|+|++||++|++||++.|+++|||+++++++++ +++  ++++|||+|||.--+
T Consensus         4 ~~~~i~e~i~~ltllE~~eLv~~lee~fgv~aaap~a~a~~~a~a~a~eEKteFdV~L~~   63 (122)
T 2zjq_5            4 DKQALIDQLGQLTIMELADLIDGLKETWGVTAAVAVSGGGAGAASPAAEEKTEFDVVLID   63 (122)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCCcccccccCCCcccccccccceeEEEEec
Confidence            358999999999999999999999999999987533222 212  233589999997543

>3sgf_J 50S ribosomal protein L7/L12; typeii release factor binding with ribosome, ribosome-antibi complex; 3.20A {Escherichia coli} PDB: 2xtg_L 2xux_L 3uos_J 1rqu_A 1rqv_A 2gya_3 2gyc_3 1rqt_A

Probab=99.23  E-value=8.1e-13  Score=106.61  Aligned_cols=56  Identities=14%  Similarity=0.277  Sum_probs=26.8

Q ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcccccccc-cccccccccccccce
Q psy4496         162 KITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAF-AQGRYLRTIFDATSC  217 (228)
Q Consensus       162 Kv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~aaaaa-AaaAaEkTeFdv~~~  217 (228)
                      .+++|+|+|++||++|++||++.|+++|||+++++++++++ +++++|||+|||.--
T Consensus         4 ~~~~ive~i~~ltllE~~eLv~~lee~fgVsaaa~~a~~a~~a~a~eEKteFdV~L~   60 (121)
T 3sgf_J            4 TKDQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAVAVAAGPVEAAEEKTEFDVILK   60 (121)
T ss_dssp             CHHHHHHGGGGCHHHHHHHHHTTTCSCC-----------------------------
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCccccccccccccccccccceeEEEEe
Confidence            46899999999999999999999999999998875433222 233469999998744

>1dd3_A 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge region, four-helix-bundl helix- bundle, alpha-beta structure; 2.00A {Thermotoga maritima} SCOP: a.108.1.1 d.45.1.1 PDB: 1dd4_A* 1giy_I 1yl3_I

Probab=99.11  E-value=5.5e-12  Score=102.62  Aligned_cols=55  Identities=25%  Similarity=0.274  Sum_probs=42.5

Q ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcccc-c-cc--cc---ccccccccccccce
Q psy4496         163 ITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMA-M-GA--FA---QGRYLRTIFDATSC  217 (228)
Q Consensus       163 v~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~a-a-aa--aA---aaAaEkTeFdv~~~  217 (228)
                      +++|+|+|++||++|++||++.|+++|||+++++++ + ++  ++   ++++|||+|||.--
T Consensus         3 ~~~ive~i~~ltllE~~eLv~~lee~fgv~aaapva~~~~~~~~~a~~~a~eEKteFdV~L~   64 (128)
T 1dd3_A            3 IDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLK   64 (128)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEE
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHhCCCCcchhhccccccccccccccccccceeeEEEe
Confidence            579999999999999999999999999999865322 1 11  11   12248999999754

>1dd4_C 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge region, four-helix- bundle, five-helix- bundle, alpha-beta structure; HET: TBR; 2.40A {Thermotoga maritima} SCOP: a.108.1.1

Probab=99.01  E-value=2.9e-10  Score=75.86  Aligned_cols=34  Identities=26%  Similarity=0.398  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCc
Q psy4496         162 KITKLANDISSLTLLECADLSSLLKKQLNLPDAP  195 (228)
Q Consensus       162 Kv~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa  195 (228)
                      ++++|+|+|++||++|++||++.||+||||++++
T Consensus         2 ~~~~iie~i~~lTvlE~~eLvk~leekfGVsaaa   35 (40)
T 1dd4_C            2 TIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAA   35 (40)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHTCCCSCC
T ss_pred             CHHHHHHHHHhCcHHHHHHHHHHHHHHHCCCccc
Confidence            3689999999999999999999999999999764

>1zav_U 50S ribosomal protein L7/L12; ribosome structure and function, L10-L12 complex structure, L10E structure, L7/12 ribosomal stalk; 1.90A {Thermotoga maritima} SCOP: a.108.1.1 PDB: 1zaw_U 1zax_U 1dd3_C

Probab=98.33  E-value=3.8e-07  Score=57.42  Aligned_cols=28  Identities=29%  Similarity=0.431  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHcC
Q psy4496         163 ITKLANDISSLTLLECADLSSLLKKQLN  190 (228)
Q Consensus       163 v~~IvdeIs~LTLlEvsELv~~LkeKlG  190 (228)
                      +++|+|+|++||++|++||++.|+++||
T Consensus         3 ~~~iie~i~~lTvlEl~eLvk~lEe~fG   30 (30)
T 1zav_U            3 IDEIIEAIEKLTVSELAELVKKLEDKFG   30 (30)
T ss_dssp             HHHHHHHHHHSBHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHhCcHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	228
d1mp1a_	111	a.188.1.1 (A:) Ser/Arg-related nuclear matrix prot	1e-15

>d1mp1a_ a.188.1.1 (A:) Ser/Arg-related nuclear matrix protein srm160 {Human (Homo sapiens) [TaxId: 9606]} Length = 111

class: All alpha proteins
fold: PWI domain
superfamily: PWI domain
family: PWI domain
domain: Ser/Arg-related nuclear matrix protein srm160
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.2 bits (167), Expect = 1e-15
 Identities = 25/46 (54%), Positives = 39/46 (84%)

Query: 16 QKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVS 61
          +KVDM+KV L+++KPWIT+++T++LG EDDVV+ F++NQLE +   
Sbjct: 13 KKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPD 58

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	228
d1mp1a_	111	Ser/Arg-related nuclear matrix protein srm160 {Hum	99.97
d1dd3a1	57	Ribosomal protein L7/12, oligomerisation (N-termin	98.9
d2gyc31	47	Ribosomal protein L7/12, oligomerisation (N-termin	98.63
d1zavu1	30	Ribosomal protein L7/12, oligomerisation (N-termin	97.88

>d1mp1a_ a.188.1.1 (A:) Ser/Arg-related nuclear matrix protein srm160 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PWI domain
superfamily: PWI domain
family: PWI domain
domain: Ser/Arg-related nuclear matrix protein srm160
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.9e-32  Score=215.19  Aligned_cols=84  Identities=38%  Similarity=0.602  Sum_probs=76.7

Q ss_pred             cccCccccccccCccccCcchhhhHHHHHHHHhcCCCchHHHHHHHHHhhccCc-c-----chhcccccC-chhHHHHHh
Q psy4496           7 ALTSKPQVVQKVDMTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKV-S-----TIFEFDLAK-KVPVCKEIG   79 (228)
Q Consensus         7 ~~kfP~~f~~kVDm~KVnl~vikpWI~~rItelLG~EDDVvieyi~~lLe~~~~-p-----~I~gFL~~~-~a~F~~eLW   79 (228)
                      .+|||++|++||||+|||+++|||||++||+|+||+|||||||||+|+|++... |     |++|||+++ +..||.+||
T Consensus         4 ~~kfp~~f~~kVD~~kV~l~~ikpWI~kkI~e~LG~EDdvvvd~i~~~L~~~~~dpk~l~i~L~gfLd~k~a~~Fv~eLW   83 (111)
T d1mp1a_           4 QLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEFIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELW   83 (111)
T ss_dssp             CCCCCSGGGGCCCTTTSCSGGGHHHHHHHHHHHHSSCCSHHHHHHHHHTTSSSCCHHHHHHHHTTTSCSHHHHHHHHHHH
T ss_pred             ccccCHHHccccCHHHcCHHHHHHHHHHHHHHHhCcchHHHHHHHHHHHHccCCCHHHHHHHHHHHhCcccHHHHHHHHH
Confidence            489999999999999999999999999999999999999999999999997653 3     689999865 455999999


Q ss_pred             hhcc-------ChhHHHH
Q psy4496          80 KGDL-------GLMQVVT   90 (228)
Q Consensus        80 kLll-------gi~q~vl   90 (228)
                      +||+       |||+.++
T Consensus        84 ~LLi~aq~s~~GIP~~~l  101 (111)
T d1mp1a_          84 PLLLSAQENIAGIPSAFL  101 (111)
T ss_dssp             HHHHHHTTSSSSCCHHHH
T ss_pred             HHHHHhhcCCcCCcHHHH
Confidence            9998       9999876

>d1dd3a1 a.108.1.1 (A:1-57) Ribosomal protein L7/12, oligomerisation (N-terminal) domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
domain: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.90  E-value=6.3e-11  Score=82.51  Aligned_cols=34  Identities=26%  Similarity=0.374  Sum_probs=32.0

Q ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcc
Q psy4496         163 ITKLANDISSLTLLECADLSSLLKKQLNLPDAPM  196 (228)
Q Consensus       163 v~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~  196 (228)
                      +++|++.|.+||++|++||++.|++||||+++++
T Consensus         3 ~e~iie~I~~~tv~El~ELvKalEekfGVsAaaP   36 (57)
T d1dd3a1           3 IDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAP   36 (57)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHHhCcccchh
Confidence            5899999999999999999999999999998873

>d2gyc31 a.108.1.1 (3:2-48) Ribosomal protein L7/12, oligomerisation (N-terminal) domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
domain: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
species: Escherichia coli [TaxId: 562]

Probab=98.63  E-value=8.2e-09  Score=69.21  Aligned_cols=35  Identities=11%  Similarity=0.420  Sum_probs=32.3

Q ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHcCCCCCcccc
Q psy4496         164 TKLANDISSLTLLECADLSSLLKKQLNLPDAPMMA  198 (228)
Q Consensus       164 ~~IvdeIs~LTLlEvsELv~~LkeKlGVs~aa~~a  198 (228)
                      ++|++.|++||++|+.||++.|++||||++++..+
T Consensus         4 e~Ileaia~MSVmdvveLi~amEEKFGVsaaa~va   38 (47)
T d2gyc31           4 DQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAVA   38 (47)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHTCTTTTHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHhCcchhcccc
Confidence            78999999999999999999999999999987444

>d1zavu1 a.108.1.1 (U:1-30) Ribosomal protein L7/12, oligomerisation (N-terminal) domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
domain: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.88  E-value=5.9e-06  Score=50.09  Aligned_cols=28  Identities=29%  Similarity=0.431  Sum_probs=27.1

Q ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHcC
Q psy4496         163 ITKLANDISSLTLLECADLSSLLKKQLN  190 (228)
Q Consensus       163 v~~IvdeIs~LTLlEvsELv~~LkeKlG  190 (228)
                      +++|++.|.+||+.|++||++.|++|||
T Consensus         3 ~eeiv~aiekltvaelaelvk~ledkfg   30 (30)
T d1zavu1           3 IDEIIEAIEKLTVSELAELVKKLEDKFG   30 (30)
T ss_dssp             HHHHHHHHHHSBHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHhhcC
Confidence            6899999999999999999999999998