Psyllid ID: psy10746

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------6
Protein Sequence
MRKYTNVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYSHVI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccEEEccccccHHHHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEcccccccccccccEEEcccccEEEccccccHHHHHHHHHHHHcccEEEEEEcccc
Coil and Loop (DISEMBL)
mrkytnvtSKNIIkwshggvnqlggvfvngrplpdVVRQRIVELAHnggllsakYSHVI
Flexible Loop (DISEMBL)
mrkytnvtskniikwshggvnqLGGVFVNGRPLPDVVRQRIVELahnggllsakyshvi
Low Complexity Region (SEG)
MRKYTNVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYSHVI
Disordered region (IsUnstruct)
******VTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA******
Disordered Region (DISOPRED)
*********************QLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYSHV*
Disordered Region (DISEMBL)
********SKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYSHVI
Disordered Region (DISPRO)
*************KWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYS***
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MRKYTNVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSAKYSHVI
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	59	2.2.26 [Sep-21-2011]
Q02650	391	Paired box protein Pax-5	yes	N/A	0.728	0.109	0.767	8e-13
O57682	494	Paired box protein Pax-2-	N/A	N/A	0.542	0.064	0.968	2e-12
O57685	497	Paired box protein Pax-2-	N/A	N/A	0.542	0.064	0.968	3e-12
Q02548	391	Paired box protein Pax-5	no	N/A	0.728	0.109	0.744	4e-12
Q9YH95	388	Paired box protein Pax-5	N/A	N/A	0.542	0.082	0.968	8e-12
Q90268	410	Paired box protein Pax-2a	no	N/A	0.542	0.078	0.968	1e-11
P32114	414	Paired box protein Pax-2	no	N/A	0.542	0.077	0.968	1e-11
Q02962	417	Paired box protein Pax-2	no	N/A	0.542	0.076	0.968	1e-11
Q5R9M8	457	Paired box protein Pax-8	no	N/A	0.644	0.083	0.763	3e-11
Q06710	450	Paired box protein Pax-8	no	N/A	0.644	0.084	0.763	3e-11

>sp|Q02650|PAX5_MOUSE Paired box protein Pax-5 OS=Mus musculus GN=Pax5 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 33/43 (76%), Positives = 35/43 (81%)

Query: 6  NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N  +   I+  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 6  NYPTPRTIRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

May play an important role in B-cell differentiation as well as neural development and spermatogenesis. Involved in the regulation of the CD19 gene, a B-lymphoid-specific target gene.
Mus musculus (taxid: 10090)

>sp|O57682|PAX2B_XENLA Paired box protein Pax-2-B OS=Xenopus laevis GN=pax2-b PE=2 SV=2

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 16 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 47

Probable transcription factor. Involved in kidney development, acting synergistically with lhx1/lim-1 in pronephric morphogenesis during the tailbud stages.

Xenopus laevis (taxid: 8355)

>sp|O57685|PAX2A_XENLA Paired box protein Pax-2-A OS=Xenopus laevis GN=pax2-a PE=2 SV=2

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

Probable transcription factor. Involved in kidney development, acting synergistically with lhx1/lim-1 in pronephric morphogenesis during the tailbud stages.

Xenopus laevis (taxid: 8355)

>sp|Q02548|PAX5_HUMAN Paired box protein Pax-5 OS=Homo sapiens GN=PAX5 PE=1 SV=1

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/43 (74%), Positives = 34/43 (79%)

Query: 6  NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 6  NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

May play an important role in B-cell differentiation as well as neural development and spermatogenesis. Involved in the regulation of the CD19 gene, a B-lymphoid-specific target gene.

Homo sapiens (taxid: 9606)

>sp|Q9YH95|PAX5_XENLA Paired box protein Pax-5 OS=Xenopus laevis GN=pax5 PE=2 SV=1

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 16 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 47

Probable transcription factor.

Xenopus laevis (taxid: 8355)

>sp|Q90268|PAX2A_DANRE Paired box protein Pax-2a OS=Danio rerio GN=pax2a PE=2 SV=2

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 20 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 51

Probable transcription factor involved in the development of the midbrain/hindbrain boundary (MHB) organizer and specification of neuronal cell fates. Required for establishment of eng2 and eng3 gene expression in the midbrain and MHB primordium during late gastrulation.

Danio rerio (taxid: 7955)

>sp|P32114|PAX2_MOUSE Paired box protein Pax-2 OS=Mus musculus GN=Pax2 PE=1 SV=2

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 16 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 47

Probable transcription factor that may have a role in kidney cell differentiation.

Mus musculus (taxid: 10090)

>sp|Q02962|PAX2_HUMAN Paired box protein Pax-2 OS=Homo sapiens GN=PAX2 PE=1 SV=4

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

Probable transcription factor that may have a role in kidney cell differentiation. Has a critical role in the development of the urogenital tract, the eyes, and the CNS.

Homo sapiens (taxid: 9606)

>sp|Q5R9M8|PAX8_PONAB Paired box protein Pax-8 OS=Pongo abelii GN=PAX8 PE=2 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 29/38 (76%), Positives = 33/38 (86%)

Query: 11 NIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N I+  HGG+NQLGG FVNGRPLP+VVRQRIV+LAH G
Sbjct: 4  NSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQG 41

Thought to encode a transcription factor. It may have a role in kidney cell differentiation. May play a regulatory role in mammalian development.

Pongo abelii (taxid: 9601)

>sp|Q06710|PAX8_HUMAN Paired box protein Pax-8 OS=Homo sapiens GN=PAX8 PE=1 SV=2

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 29/38 (76%), Positives = 33/38 (86%)

Query: 11 NIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N I+  HGG+NQLGG FVNGRPLP+VVRQRIV+LAH G
Sbjct: 4  NSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQG 41

Transcription factor for the thyroid-specific expression of the genes exclusively expressed in the thyroid cell type, maintaining the functional differentiation of such cells.

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	59
350417103	557	PREDICTED: hypothetical protein LOC10074	0.627	0.066	0.891	2e-11
157128230	593	paired box protein pax-6 [Aedes aegypti]	0.542	0.053	0.968	2e-11
340713172	558	PREDICTED: hypothetical protein LOC10064	0.627	0.066	0.891	2e-11
157824085	391	paired box protein Pax-5 [Rattus norvegi	0.728	0.109	0.767	3e-11
6679213	391	paired box protein Pax-5 [Mus musculus]	0.728	0.109	0.767	3e-11
312379688	601	hypothetical protein AND_08376 [Anophele	0.542	0.053	0.968	4e-11
198462147	807	sparkling shaven [Drosophila pseudoobscu	0.542	0.039	1.0	4e-11
113201774	1541	PAX5/ZNF521 fusion protein [Homo sapiens	0.542	0.020	0.968	4e-11
347963077	551	AGAP000057-PA [Anopheles gambiae str. PE	0.542	0.058	0.968	4e-11
270004886	472	shaven [Tribolium castaneum]	0.593	0.074	0.942	5e-11

>gi|350417103|ref|XP_003491258.1| PREDICTED: hypothetical protein LOC100744373 [Bombus impatiens]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 33/37 (89%), Positives = 36/37 (97%)

Query: 12 IIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          I+ +SHGGVNQLGGVFVNGRPLPDVVRQRIVELAH+G
Sbjct: 30 ILFYSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHSG 66

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157128230|ref|XP_001661355.1| paired box protein pax-6 [Aedes aegypti] gi|108882242|gb|EAT46467.1| AAEL002348-PA [Aedes aegypti]

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 31/32 (96%), Positives = 32/32 (100%)

Query: 17  HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           HGGVNQLGGVFVNGRPLPD+VRQRIVELAHNG
Sbjct: 97  HGGVNQLGGVFVNGRPLPDLVRQRIVELAHNG 128

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340713172|ref|XP_003395121.1| PREDICTED: hypothetical protein LOC100647018 [Bombus terrestris]

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/37 (89%), Positives = 36/37 (97%)

Query: 12 IIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          I+ +SHGGVNQLGGVFVNGRPLPDVVRQRIVELAH+G
Sbjct: 30 ILCYSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHSG 66

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157824085|ref|NP_001102731.1| paired box protein Pax-5 [Rattus norvegicus] gi|149045794|gb|EDL98794.1| similar to transcription factor (predicted) [Rattus norvegicus]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/43 (76%), Positives = 35/43 (81%)

Query: 6  NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N  +   I+  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 6  NYPTPRTIRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|6679213|ref|NP_032808.1| paired box protein Pax-5 [Mus musculus] gi|400733|sp|Q02650.1|PAX5_MOUSE RecName: Full=Paired box protein Pax-5; AltName: Full=B-cell-specific transcription factor; Short=BSAP gi|192242|gb|AAA37325.1| transcription factor [Mus musculus] gi|148670473|gb|EDL02420.1| paired box gene 5 [Mus musculus] gi|162318416|gb|AAI57082.1| Paired box gene 5 [synthetic construct] gi|162318892|gb|AAI56135.1| Paired box gene 5 [synthetic construct]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/43 (76%), Positives = 35/43 (81%)

Query: 6  NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N  +   I+  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 6  NYPTPRTIRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|312379688|gb|EFR25884.1| hypothetical protein AND_08376 [Anopheles darlingi]

 Score = 72.4 bits (176), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/32 (96%), Positives = 32/32 (100%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPD+VRQRIVELAHNG
Sbjct: 15 HGGVNQLGGVFVNGRPLPDLVRQRIVELAHNG 46

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198462147|ref|XP_002135676.1| sparkling shaven [Drosophila pseudoobscura pseudoobscura] gi|198142524|gb|EDY71260.1| sparkling shaven [Drosophila pseudoobscura pseudoobscura]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/32 (100%), Positives = 32/32 (100%)

Query: 17  HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG
Sbjct: 184 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 215

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|113201774|gb|ABI33104.1| PAX5/ZNF521 fusion protein [Homo sapiens]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|347963077|ref|XP_311100.5| AGAP000057-PA [Anopheles gambiae str. PEST] gi|333467371|gb|EAA06142.5| AGAP000057-PA [Anopheles gambiae str. PEST]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/32 (96%), Positives = 32/32 (100%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          HGGVNQLGGVFVNGRPLPD+VRQRIVELAHNG
Sbjct: 25 HGGVNQLGGVFVNGRPLPDLVRQRIVELAHNG 56

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270004886|gb|EFA01334.1| shaven [Tribolium castaneum]

 Score = 72.0 bits (175), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 33/35 (94%), Positives = 33/35 (94%)

Query: 14 KWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          K  HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG
Sbjct: 34 KKRHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 68

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

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	59
UNIPROTKB|F1ST83	260	PAX5 "Uncharacterized protein"	0.728	0.165	0.790	9.1e-13
MGI|MGI:97489	391	Pax5 "paired box gene 5" [Mus	0.728	0.109	0.767	2.7e-12
UNIPROTKB|Q5SZP1	214	PAX2 "Paired box protein Pax-2	0.542	0.149	0.968	3.1e-12
UNIPROTKB|F1MWQ4	261	PAX5 "Uncharacterized protein"	0.542	0.122	0.968	3.5e-12
UNIPROTKB|C0KTF9	291	PAX5 "B cell specific activato	0.728	0.147	0.744	4.9e-12
UNIPROTKB|E7ERW5	295	PAX5 "Paired box protein Pax-5	0.728	0.145	0.744	5.1e-12
UNIPROTKB|J9P1P0	288	PAX5 "Uncharacterized protein"	0.542	0.111	0.968	6e-12
UNIPROTKB|C0KTG0	307	PAX5 "B cell specific activato	0.728	0.140	0.744	6e-12
UNIPROTKB|C0KTF8	319	PAX5 "B cell specific activato	0.728	0.134	0.744	6.9e-12
UNIPROTKB|E7EQT0	324	PAX5 "Paired box protein Pax-5	0.728	0.132	0.744	7.2e-12

UNIPROTKB|F1ST83 PAX5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 34/43 (79%), Positives = 34/43 (79%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N T   I    HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NFTYSEISVSGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0005634 "nucleus" evidence=IEA

GO:0051573 "negative regulation of histone H3-K9 methylation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

MGI|MGI:97489 Pax5 "paired box gene 5" [Mus musculus (taxid:10090)]

 Score = 171 (65.3 bits), Expect = 2.7e-12, P = 2.7e-12
 Identities = 33/43 (76%), Positives = 35/43 (81%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N  +   I+  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NYPTPRTIRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA

GO:0003677 "DNA binding" evidence=IMP;IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IDA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0007399 "nervous system development" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=TAS

GO:0030154 "cell differentiation" evidence=IEA

GO:0035914 "skeletal muscle cell differentiation" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=TAS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=TAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IGI

GO:0051573 "negative regulation of histone H3-K9 methylation" evidence=IMP

UNIPROTKB|Q5SZP1 PAX2 "Paired box protein Pax-2" [Homo sapiens (taxid:9606)]

 Score = 164 (62.8 bits), Expect = 3.1e-12, P = 3.1e-12
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query:    17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:    17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000987 "core promoter proximal region sequence-specific DNA binding" evidence=IEA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IEA

GO:0001709 "cell fate determination" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0002072 "optic cup morphogenesis involved in camera-type eye development" evidence=IEA

GO:0003337 "mesenchymal to epithelial transition involved in metanephros morphogenesis" evidence=IEA

GO:0003406 "retinal pigment epithelium development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005764 "lysosome" evidence=IEA

GO:0007501 "mesodermal cell fate specification" evidence=IEA

GO:0007568 "aging" evidence=IEA

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

GO:0010001 "glial cell differentiation" evidence=IEA

GO:0016175 "superoxide-generating NADPH oxidase activity" evidence=IEA

GO:0021633 "optic nerve structural organization" evidence=IEA

GO:0021650 "vestibulocochlear nerve formation" evidence=IEA

GO:0031016 "pancreas development" evidence=IEA

GO:0031667 "response to nutrient levels" evidence=IEA

GO:0032993 "protein-DNA complex" evidence=IEA

GO:0035566 "regulation of metanephros size" evidence=IEA

GO:0035799 "ureter maturation" evidence=IEA

GO:0039003 "pronephric field specification" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0043491 "protein kinase B signaling cascade" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0048854 "brain morphogenesis" evidence=IEA

GO:0048863 "stem cell differentiation" evidence=IEA

GO:0061205 "paramesonephric duct development" evidence=IEA

GO:0061360 "optic chiasma development" evidence=IEA

GO:0070301 "cellular response to hydrogen peroxide" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0071260 "cellular response to mechanical stimulus" evidence=IEA

GO:0071300 "cellular response to retinoic acid" evidence=IEA

GO:0071333 "cellular response to glucose stimulus" evidence=IEA

GO:0071364 "cellular response to epidermal growth factor stimulus" evidence=IEA

GO:0072108 "positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis" evidence=IEA

GO:0072162 "metanephric mesenchymal cell differentiation" evidence=IEA

GO:0072172 "mesonephric tubule formation" evidence=IEA

GO:0072177 "mesonephric duct development" evidence=IEA

GO:0072179 "nephric duct formation" evidence=IEA

GO:0072197 "ureter morphogenesis" evidence=IEA

GO:0072205 "metanephric collecting duct development" evidence=IEA

GO:0072221 "metanephric distal convoluted tubule development" evidence=IEA

GO:0072289 "metanephric nephron tubule formation" evidence=IEA

GO:0072300 "positive regulation of metanephric glomerulus development" evidence=IEA

GO:0072305 "negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis" evidence=IEA

GO:0072307 "regulation of metanephric nephron tubule epithelial cell differentiation" evidence=IEA

GO:0072593 "reactive oxygen species metabolic process" evidence=IEA

GO:0090103 "cochlea morphogenesis" evidence=IEA

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=IEA

GO:1900215 "negative regulation of apoptotic process involved in metanephric collecting duct development" evidence=IEA

GO:1900218 "negative regulation of apoptotic process involved in metanephric nephron tubule development" evidence=IEA

GO:2000594 "positive regulation of metanephric DCT cell differentiation" evidence=IEA

GO:2000597 "positive regulation of optic nerve formation" evidence=IEA

UNIPROTKB|F1MWQ4 PAX5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 164 (62.8 bits), Expect = 3.5e-12, P = 3.5e-12
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query:    17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:    18 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 49

GO:0005634 "nucleus" evidence=IEA

GO:0051573 "negative regulation of histone H3-K9 methylation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|C0KTF9 PAX5 "B cell specific activator protein variant A delta 3/8" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 4.9e-12, P = 4.9e-12
 Identities = 32/43 (74%), Positives = 34/43 (79%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E7ERW5 PAX5 "Paired box protein Pax-5" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 5.1e-12, P = 5.1e-12
 Identities = 32/43 (74%), Positives = 34/43 (79%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|J9P1P0 PAX5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 164 (62.8 bits), Expect = 6.0e-12, P = 6.0e-12
 Identities = 31/32 (96%), Positives = 31/32 (96%)

Query:    17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:    17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|C0KTG0 PAX5 "B cell specific activator protein variant A delta 7 insert 6/7" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 6.0e-12, P = 6.0e-12
 Identities = 32/43 (74%), Positives = 34/43 (79%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|C0KTF8 PAX5 "B cell specific activator protein variant A delta 5/9" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 6.9e-12, P = 6.9e-12
 Identities = 32/43 (74%), Positives = 34/43 (79%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E7EQT0 PAX5 "Paired box protein Pax-5" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 7.2e-12, P = 7.2e-12
 Identities = 32/43 (74%), Positives = 34/43 (79%)

Query:     6 NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
             N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct:     6 NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" 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)
Q02650	PAX5_MOUSE	No assigned EC number	0.7674	0.7288	0.1099	yes	N/A
P32114	PAX2_MOUSE	No assigned EC number	0.9687	0.5423	0.0772	no	N/A
Q02962	PAX2_HUMAN	No assigned EC number	0.9687	0.5423	0.0767	no	N/A
Q90268	PAX2A_DANRE	No assigned EC number	0.9687	0.5423	0.0780	no	N/A
O57685	PAX2A_XENLA	No assigned EC number	0.9687	0.5423	0.0643	N/A	N/A
Q9YH95	PAX5_XENLA	No assigned EC number	0.9687	0.5423	0.0824	N/A	N/A
O57682	PAX2B_XENLA	No assigned EC number	0.9687	0.5423	0.0647	N/A	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	59
smart00351	125	smart00351, PAX, Paired Box domain	2e-17
cd00131	128	cd00131, PAX, Paired Box domain	1e-16
pfam00292	125	pfam00292, PAX, 'Paired box' domain	3e-16

>gnl|CDD|128645 smart00351, PAX, Paired Box domain

 Score = 69.3 bits (170), Expect = 2e-17
 Identities = 29/33 (87%), Positives = 29/33 (87%)

Query: 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           HGGVNQLGGVFVNGRPLPD  RQRIVELA NG
Sbjct: 1  GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNG 33

Length = 125

>gnl|CDD|238076 cd00131, PAX, Paired Box domain

 Score = 67.4 bits (165), Expect = 1e-16
 Identities = 27/32 (84%), Positives = 29/32 (90%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           GGVNQLGGVFVNGRPLPD +RQRIVELA +G
Sbjct: 2  QGGVNQLGGVFVNGRPLPDSIRQRIVELAQSG 33

Length = 128

>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain

 Score = 66.4 bits (162), Expect = 3e-16
 Identities = 25/33 (75%), Positives = 29/33 (87%)

Query: 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
            G VNQLGGVFVNGRPLP+ +RQ+IVELAH+G
Sbjct: 1  GQGRVNQLGGVFVNGRPLPNHIRQKIVELAHSG 33

Length = 125

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	59
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	99.8
KOG3862|consensus	327		99.79
KOG3517|consensus	334		99.71
KOG0849|consensus	354		99.15
cd00131	128	PAX Paired Box domain	99.14
smart00351	125	PAX Paired Box domain.	98.87
PLN00061	150	photosystem II protein Psb27; Provisional	88.73
cd03482	123	MutL_Trans_MutL MutL_Trans_MutL: transducer domain	87.21
PF08069	60	Ribosomal_S13_N: Ribosomal S13/S15 N-terminal doma	83.63
TIGR03044	135	PS_II_psb27 photosystem II protein Psb27. Members	83.24
PF01119	119	DNA_mis_repair: DNA mismatch repair protein, C-ter	83.15
PF13326	145	PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF	82.21
cd00782	122	MutL_Trans MutL_Trans: transducer domain, having a	81.98

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]

Probab=99.80  E-value=1.6e-20  Score=124.40  Aligned_cols=38  Identities=63%  Similarity=0.997  Sum_probs=31.1

Q ss_pred             CCcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746         16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~   53 (59)
                      ||++||||||+|+||||||+++|++|||||++|+|||+
T Consensus         1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~   38 (125)
T PF00292_consen    1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCD   38 (125)
T ss_dssp             S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHH
T ss_pred             CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHH
Confidence            78999999999999999999999999999999999986

Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.

>KOG3862|consensus

Probab=99.79  E-value=2.9e-20  Score=139.45  Aligned_cols=43  Identities=77%  Similarity=1.105  Sum_probs=40.2

Q ss_pred             chhccCCcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746         11 NIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        11 ~~~~~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~   53 (59)
                      +.+..||+|||||||||||||||||.+|++|||||++|||||.
T Consensus         4 ~s~~~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcd   46 (327)
T KOG3862|consen    4 NSIHSGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCD   46 (327)
T ss_pred             cCCCCCccchhhccceeecCccCchHHHHHHHHHHHcCCcchh
Confidence            3456799999999999999999999999999999999999995

>KOG3517|consensus

Probab=99.71  E-value=3.4e-18  Score=128.35  Aligned_cols=40  Identities=63%  Similarity=0.856  Sum_probs=37.4

Q ss_pred             ccCCcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746         14 KWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        14 ~~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~   53 (59)
                      .+..+.|||||||||||||||+.+|.||||||+.|+|||.
T Consensus         2 ~~~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCD   41 (334)
T KOG3517|consen    2 EPSYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCD   41 (334)
T ss_pred             CccccchhhccceeEcCccCcchhhhhHHHHHHcCCCccc
Confidence            3456899999999999999999999999999999999996

>KOG0849|consensus

Probab=99.15  E-value=7.4e-12  Score=92.08  Aligned_cols=36  Identities=64%  Similarity=1.032  Sum_probs=34.6

Q ss_pred             cceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746         18 GGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        18 ~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~   53 (59)
                      +++|||||+|+||||||+++|++|++||+.|+|||.
T Consensus         1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~   36 (354)
T KOG0849|consen    1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCV   36 (354)
T ss_pred             CCcccCCcccccCCCCCCchhhccccccccccCccc
Confidence            579999999999999999999999999999999985

>cd00131 PAX Paired Box domain

Probab=99.14  E-value=2.7e-11  Score=77.89  Aligned_cols=37  Identities=73%  Similarity=1.135  Sum_probs=34.2

Q ss_pred             CCcceecccccccCCCCCChHHHHHHHHHHHcCCCCC
Q psy10746         16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLS   52 (59)
Q Consensus        16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps   52 (59)
                      |++++|||||+|+||+||+.++|.+||+|++.|..+.
T Consensus         1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~   37 (128)
T cd00131           1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPC   37 (128)
T ss_pred             CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHH
Confidence            6789999999999999999999999999999997543

>smart00351 PAX Paired Box domain

Probab=98.87  E-value=1.6e-09  Score=69.03  Aligned_cols=36  Identities=81%  Similarity=1.193  Sum_probs=33.0

Q ss_pred             CCcceecccccccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746         16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLL   51 (59)
Q Consensus        16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRp   51 (59)
                      +++++|||||.|++|+||+.+.|.+||+|++.|...
T Consensus         1 ~~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~   36 (125)
T smart00351        1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRP   36 (125)
T ss_pred             CCCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCH
Confidence            478999999999999999999999999999988643

>PLN00061 photosystem II protein Psb27; Provisional

Probab=88.73  E-value=0.16  Score=35.50  Aligned_cols=28  Identities=21%  Similarity=0.517  Sum_probs=23.9

Q ss_pred             CcceecccccccCC---CCCChHHHHHHHHH
Q psy10746         17 HGGVNQLGGVFVNG---RPLPDVVRQRIVEL   44 (59)
Q Consensus        17 ~~~vNQLGG~FvNG---RPLP~~~R~kIveL   44 (59)
                      +.-+|.|+|-|.+=   ||||+.+|.+|.+-
T Consensus       115 qtALnsLAghYssyGpnrPLPe~lK~Rll~E  145 (150)
T PLN00061        115 EKAIRSLASFYSKAGPSAPLPEDVKSEILDD  145 (150)
T ss_pred             HHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence            46789999998765   99999999999863

>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL

Probab=87.21  E-value=0.38  Score=30.30  Aligned_cols=31  Identities=26%  Similarity=0.262  Sum_probs=23.7

Q ss_pred             ccccCCCCCChHHHHHHHHHHHcCCCCCccc
Q psy10746         25 GVFVNGRPLPDVVRQRIVELAHNGGLLSAKY   55 (59)
Q Consensus        25 G~FvNGRPLP~~~R~kIveLA~~GvRps~~~   55 (59)
                      =.||||||.-+..=.+.|+-|-++.-|..+|
T Consensus        47 ~ifVN~R~V~~~~l~~ai~~~y~~~~~~~~~   77 (123)
T cd03482          47 YFYVNGRMVRDKLISHAVRQAYSDVLHGGRH   77 (123)
T ss_pred             EEEEcCcEECChHHHHHHHHHHHHhccCCCC
Confidence            3799999999888888888777666655443

EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.

>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=83.63  E-value=0.28  Score=29.50  Aligned_cols=20  Identities=40%  Similarity=0.479  Sum_probs=18.3

Q ss_pred             ChHHHHHHHHHHHcCCCCCc
Q psy10746         34 PDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        34 P~~~R~kIveLA~~GvRps~   53 (59)
                      |+++-..|++||.+|.-||.
T Consensus        30 ~~eVe~~I~klakkG~tpSq   49 (60)
T PF08069_consen   30 PEEVEELIVKLAKKGLTPSQ   49 (60)
T ss_dssp             HHHHHHHHHHHCCTTHCHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHH
Confidence            68999999999999999874

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 [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.

>TIGR03044 PS_II_psb27 photosystem II protein Psb27

Probab=83.24  E-value=0.59  Score=32.03  Aligned_cols=27  Identities=30%  Similarity=0.717  Sum_probs=22.6

Q ss_pred             CcceecccccccC--CCCCChHHHHHHHH
Q psy10746         17 HGGVNQLGGVFVN--GRPLPDVVRQRIVE   43 (59)
Q Consensus        17 ~~~vNQLGG~FvN--GRPLP~~~R~kIve   43 (59)
                      +.-+|.|.|-|.+  -||||+..+.+|.+
T Consensus        95 ~TALNsLAGHY~sy~~rPlPeklk~Rl~~  123 (135)
T TIGR03044        95 QTALNSLAGHYKSYANRPLPEKLKERLEK  123 (135)
T ss_pred             HHHHHHHHHHhccCCCCCCCHHHHHHHHH
Confidence            5678999997665  59999999999964

Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.

>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL

Probab=83.15  E-value=0.86  Score=28.12  Aligned_cols=30  Identities=30%  Similarity=0.564  Sum_probs=19.9

Q ss_pred             cccCCCCCChHHHHHHHHHHHcCCCCCccc
Q psy10746         26 VFVNGRPLPDVVRQRIVELAHNGGLLSAKY   55 (59)
Q Consensus        26 ~FvNGRPLP~~~R~kIveLA~~GvRps~~~   55 (59)
                      +||||||.-+..=.+.|+-+-++.-|..+|
T Consensus        44 ifVN~R~V~~~~l~~~I~~~y~~~~~~~~~   73 (119)
T PF01119_consen   44 IFVNGRPVENKALSKAINEAYRERLPKGRY   73 (119)
T ss_dssp             EEETTEEE--HHHHHHHHHHHHCTTCTTSB
T ss_pred             EEeCCCeEeChHHHHHHHHHHhhcccCCCC
Confidence            799999998876666666666555555554

This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....

>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A

Probab=82.21  E-value=0.39  Score=32.29  Aligned_cols=27  Identities=30%  Similarity=0.725  Sum_probs=20.3

Q ss_pred             CcceecccccccC--CC-CCChHHHHHHHH
Q psy10746         17 HGGVNQLGGVFVN--GR-PLPDVVRQRIVE   43 (59)
Q Consensus        17 ~~~vNQLGG~FvN--GR-PLP~~~R~kIve   43 (59)
                      ..-+|.|+|-|..  =| |||+..|.+|.+
T Consensus       107 ~tAln~LaghY~s~g~raPlP~k~k~rll~  136 (145)
T PF13326_consen  107 YTALNALAGHYSSYGNRAPLPEKLKERLLK  136 (145)
T ss_dssp             HHHHHHHHHHCHHHTTS-S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence            3679999998764  36 999999999975

>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family

Probab=81.98  E-value=0.91  Score=27.51  Aligned_cols=26  Identities=35%  Similarity=0.517  Sum_probs=18.1

Q ss_pred             cccCCCCCChHHHHHHHHHHHcCCCC
Q psy10746         26 VFVNGRPLPDVVRQRIVELAHNGGLL   51 (59)
Q Consensus        26 ~FvNGRPLP~~~R~kIveLA~~GvRp   51 (59)
                      .||||||+-+..=.+.|.-+-++.-+
T Consensus        48 ~fVN~R~v~~~~l~~ai~~~y~~~~~   73 (122)
T cd00782          48 LFVNGRPVRDKLLSKAINEAYRSYLP   73 (122)
T ss_pred             EEECCeEecCHHHHHHHHHHHHHhCc
Confidence            79999999876666666655544443

This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	59
1k78_A	149	Pax5(1-149)+ets-1(331-440)+dna Length = 149		9e-13
2k27_A	159	Solution Structure Of Human Pax8 Paired Box Domain		1e-11
6pax_A	133	Crystal Structure Of The Human Pax-6 Paired Domain-		3e-11
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		8e-07

>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149

Iteration: 1
 Score = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 32/43 (74%), Positives = 34/43 (79%)
Query: 6  NVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 6  NYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 33/38 (86%)
Query: 11 NIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          N I+  HGG+NQLGG FVNGRPLP+VVRQRIV+LAH G
Sbjct: 4  NSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQG 41

>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions Length = 133

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 28/33 (84%), Positives = 29/33 (87%)
Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGG 49
          H GVNQLGGVFVNGRPLPD  RQRIVELAH+G 
Sbjct: 2  HSGVNQLGGVFVNGRPLPDSTRQRIVELAHSGA 34

>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations Length = 128

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 27/32 (84%)
Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           G VNQLGGVF+NGRPLP+ +R +IVE+A +G
Sbjct: 2  QGRVNQLGGVFINGRPLPNNIRLKIVEMAADG 33

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	59
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	2e-16
2k27_A	159	Paired box protein PAX-8; paired domain, solution	1e-15
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	2e-15

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Length = 149

 Score = 66.7 bits (162), Expect = 2e-16
 Identities = 33/48 (68%), Positives = 35/48 (72%)

Query: 1  MRKYTNVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          M    N  +    +  HGGVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 1  MDLEKNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQG 48

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159

 Score = 65.2 bits (158), Expect = 1e-15
 Identities = 27/33 (81%), Positives = 30/33 (90%)

Query: 16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           HGG+NQLGG FVNGRPLP+VVRQRIV+LAH G
Sbjct: 9  GHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQG 41

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Length = 128

 Score = 64.0 bits (155), Expect = 2e-15
 Identities = 21/32 (65%), Positives = 27/32 (84%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           G VNQLGGVF+NGRPLP+ +R +IVE+A +G
Sbjct: 2  QGRVNQLGGVFINGRPLPNNIRLKIVEMAADG 33

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	59
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	98.56
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	98.41
2k27_A	159	Paired box protein PAX-8; paired domain, solution	97.48
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	92.36
2y6x_A	113	PSB27, photosystem II 11 KD protein; photosynthesi	86.58
2kmf_A	115	Photosystem II 11 kDa protein; PSB27, structure, h	85.29
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	80.47

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=98.56  E-value=4.3e-08  Score=56.02  Aligned_cols=35  Identities=60%  Similarity=1.032  Sum_probs=32.1

Q ss_pred             CCcceecccccccCCCCCChHHHHHHHHHHHcCCC
Q psy10746         16 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGL   50 (59)
Q Consensus        16 g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvR   50 (59)
                      |+|++||+||+|+++++++.+.|.+|++|...|..
T Consensus         1 ~~~~~~~~gg~~~m~~~~s~~~r~~i~~~~~~g~s   35 (128)
T 1pdn_C            1 GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIR   35 (128)
T ss_dssp             -CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCC
T ss_pred             CCchHhhhcccccCCCcCCHHHHHHHHHHHHcCCC
Confidence            68999999999999999999999999999988864

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=98.41  E-value=2.2e-07  Score=56.34  Aligned_cols=46  Identities=70%  Similarity=1.046  Sum_probs=30.4

Q ss_pred             ccccccchhccCCcceecccccccCCCCCChHHHHHHHHHHHcCCC
Q psy10746          5 TNVTSKNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGL   50 (59)
Q Consensus         5 tn~~~~~~~~~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvR   50 (59)
                      .|......+++|++++|+|||+|.+++.++.+.|.+|++|...|..
T Consensus         5 ~~~~~~~~~~~~~~~~~~~gg~~~~~~~~s~e~r~~iv~~~~~G~s   50 (149)
T 1k78_A            5 KNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVR   50 (149)
T ss_dssp             --------------CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCC
T ss_pred             ccCCCCccccCCCCCccCCCceecCCCCCCHHHHHHHHHHHHcCCC
Confidence            4677788899999999999999999999999999999999988864

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=97.48  E-value=0.00011  Score=45.03  Aligned_cols=41  Identities=71%  Similarity=1.151  Sum_probs=37.2

Q ss_pred             cchhccCCcceecccccccCCCCCChHHHHHHHHHHHcCCC
Q psy10746         10 KNIIKWSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGL   50 (59)
Q Consensus        10 ~~~~~~g~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvR   50 (59)
                      .+.+++|..+++++|+.|..++.++.+.|.+|++|...|..
T Consensus         3 ~~~~~~~~~~~~~~g~~~~~~~~~s~e~r~~ii~l~~~G~s   43 (159)
T 2k27_A            3 HNSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVR   43 (159)
T ss_dssp             CSCCCCSCSSCCCCCCTTSSSCSSCHHHHHHHHHHHHHTCC
T ss_pred             cchhhhcchhhhhcCCcCCCCCCCCHHHHHHHHHHHHcCCC
Confidence            45678999999999999999999999999999999988853

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=92.36  E-value=0.16  Score=24.02  Aligned_cols=20  Identities=20%  Similarity=0.124  Sum_probs=17.2

Q ss_pred             CCC--CChHHHHHHHHHHHcCC
Q psy10746         30 GRP--LPDVVRQRIVELAHNGG   49 (59)
Q Consensus        30 GRP--LP~~~R~kIveLA~~Gv   49 (59)
                      |||  |+++.|.+|++|...|.
T Consensus         1 GR~~~l~~~~~~~i~~~~~~g~   22 (51)
T 1tc3_C            1 PRGSALSDTERAQLDVMKLLNV   22 (51)
T ss_dssp             CCSCCCCHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCHHHHHHHHHHHHcCC
Confidence            565  89999999999988886

>2y6x_A PSB27, photosystem II 11 KD protein; photosynthesis; 1.60A {Thermosynechococcus elongatus}

Probab=86.58  E-value=0.17  Score=32.55  Aligned_cols=27  Identities=30%  Similarity=0.687  Sum_probs=23.4

Q ss_pred             Ccceeccccccc--CCCCCChHHHHHHHH
Q psy10746         17 HGGVNQLGGVFV--NGRPLPDVVRQRIVE   43 (59)
Q Consensus        17 ~~~vNQLGG~Fv--NGRPLP~~~R~kIve   43 (59)
                      ..-+|+|+|-|.  .-||||+..+.+|.+
T Consensus        70 ~tAlNaLAGHY~s~g~~PlPek~k~Rl~~   98 (113)
T 2y6x_A           70 QTALNSLAGHYSSYPNRPLPEKLKARLEQ   98 (113)
T ss_dssp             HHHHHHHHHHHHHCTTSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Confidence            467999999887  689999999999974

>2kmf_A Photosystem II 11 kDa protein; PSB27, structure, helical bundle, cyanobacteria, photosynthesis; NMR {Synechocystis SP} PDB: 2knd_A

Probab=85.29  E-value=0.2  Score=32.17  Aligned_cols=27  Identities=26%  Similarity=0.683  Sum_probs=23.6

Q ss_pred             Ccceeccccccc--CCCCCChHHHHHHHH
Q psy10746         17 HGGVNQLGGVFV--NGRPLPDVVRQRIVE   43 (59)
Q Consensus        17 ~~~vNQLGG~Fv--NGRPLP~~~R~kIve   43 (59)
                      ..-+|+|+|-|.  .-||||+..+.+|.+
T Consensus        74 ~tAlNaLAGHY~s~g~~PlPek~k~Rl~~  102 (115)
T 2kmf_A           74 QTALNSLAGYYTSYGARPIPEKLKKRLQL  102 (115)
T ss_dssp             HHHHHHHHHHHHHHSSCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Confidence            467999999887  689999999999974

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=80.47  E-value=0.87  Score=25.37  Aligned_cols=27  Identities=15%  Similarity=0.348  Sum_probs=20.9

Q ss_pred             ccCCCC----CChHHHHHHHHHHH-cCCCCCc
Q psy10746         27 FVNGRP----LPDVVRQRIVELAH-NGGLLSA   53 (59)
Q Consensus        27 FvNGRP----LP~~~R~kIveLA~-~GvRps~   53 (59)
                      ++||++    +.+++|.+|.+.|. .|-+|..
T Consensus        20 vLng~~~~~~vs~et~~rI~~aa~~lgY~pn~   51 (65)
T 1uxc_A           20 VINGKAKQYRVSDKTVEKVMAVVREHNYHPNA   51 (65)
T ss_dssp             HHHTCTTTTTCTTHHHHHHHHHHHHHTCCCC-
T ss_pred             HHcCCCCCCCCCHHHHHHHHHHHHHhCCCccH
Confidence            456664    89999999999874 7888764

---

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	59
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	7e-15
d1k78a1	63	a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax	2e-14

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 61.1 bits (148), Expect = 7e-15
 Identities = 21/32 (65%), Positives = 27/32 (84%)

Query: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
           G VNQLGGVF+NGRPLP+ +R +IVE+A +G
Sbjct: 1  QGRVNQLGGVFINGRPLPNNIRLKIVEMAADG 32

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (141), Expect = 2e-14
 Identities = 29/30 (96%), Positives = 29/30 (96%)

Query: 19 GVNQLGGVFVNGRPLPDVVRQRIVELAHNG 48
          GVNQLGGVFVNGRPLPDVVRQRIVELAH G
Sbjct: 1  GVNQLGGVFVNGRPLPDVVRQRIVELAHQG 30

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	59
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	99.64
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	81.82

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.2e-17  Score=96.02  Aligned_cols=35  Identities=83%  Similarity=1.218  Sum_probs=33.4

Q ss_pred             ceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746         19 GVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        19 ~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~   53 (59)
                      |+|||||.|+||||||.++|+|||+++..|+++++
T Consensus         1 ~~n~~gg~~~~GrPls~DLR~Riv~~~~~G~s~r~   35 (63)
T d1k78a1           1 GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCD   35 (63)
T ss_dssp             CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHH
T ss_pred             CcCCCCccccCCCcCCHHHHHHHHHHHHcCCCHHH
Confidence            68999999999999999999999999999998875

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.64  E-value=2.7e-17  Score=102.47  Aligned_cols=37  Identities=57%  Similarity=0.954  Sum_probs=34.6

Q ss_pred             CcceecccccccCCCCCChHHHHHHHHHHHcCCCCCc
Q psy10746         17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGGLLSA   53 (59)
Q Consensus        17 ~~~vNQLGG~FvNGRPLP~~~R~kIveLA~~GvRps~   53 (59)
                      ++++|||||+|+||||||.++|++||+|+..|+++++
T Consensus         1 ~~~~n~~gg~~~~GrpLs~dlR~rIv~~~~~G~s~r~   37 (123)
T d1pdnc_           1 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCV   37 (123)
T ss_dssp             CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHH
T ss_pred             CcCcccCCCcccCCcCCCHHHHHHHHHHHHhcCCHHH
Confidence            5899999999999999999999999999999997764

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.82  E-value=0.19  Score=27.05  Aligned_cols=27  Identities=15%  Similarity=0.346  Sum_probs=21.7

Q ss_pred             ccCCCC----CChHHHHHHHHHH-HcCCCCCc
Q psy10746         27 FVNGRP----LPDVVRQRIVELA-HNGGLLSA   53 (59)
Q Consensus        27 FvNGRP----LP~~~R~kIveLA-~~GvRps~   53 (59)
                      ++||+|    +++++|++|.+.| ..|-+|..
T Consensus        20 vLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~   51 (59)
T d1uxda_          20 VINGKAKQYRVSDKTVEKVMAVVREHNYHPNA   51 (59)
T ss_dssp             HHHTCGGGTTCTTTTHHHHHHHHHHHTCCCCS
T ss_pred             HHcCCCCcCcCCHHHHHHHHHHHHHHCCCcCH
Confidence            568877    7999999999998 56777654