Psyllid ID: psy2180

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATRGSTSWAAFTSTGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCRKFSAEQTGKRPNQSVG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEccccccEEEcccccEEEccccccHHHHHHHHHHHHccccHHHHHHEHEEccccccEccccccEcccHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
maqsgalfgcsaaghsginqlggvyvngrplpdstRQKIVELAhsgarpcdisrtcsavrrpatrgstswaaftstgapyrtqrdrrswnwrtlardpvisrascrsptdvcrkfsaeqtgkrpnqsvg
Flexible Loop (DISEMBL)
MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAhsgarpcdisrtcsavrrpatrgstswaaftstgapyrtqrdrrswnwrtlardpvisrascrsptdvcrkfsaeqtgkrpnqsvg
Low Complexity Region (SEG)
MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATRGSTSWAAFTSTGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCRKFSAEQTGKRPNQSVG
Disordered region (IsUnstruct)
******LFGCSAAGHSGINQLGGVYVNGRP********IVELAHSGARPCDISRTCSAV*********SWAAFTSTGAPYRTQRDRRSWNWRTLARDPVIS****************************
Disordered Region (DISOPRED)
********************LGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRR*******SW**********************************CRSPTDV******************
Disordered Region (DISEMBL)
MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATRGSTSWAAFTSTGAPYRTQRDRRSWNWRTLARDPVISRAS*************************
Disordered Region (DISPRO)
****GALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATRGSTSWAAFTSTGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCRKFSAEQTG********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATRGSTSWAAFTSTGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCRKFSAEQTGKRPNQSVG
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	129	2.2.26 [Sep-21-2011]
O73917	437	Paired box protein Pax-6	N/A	N/A	0.325	0.096	0.904	4e-17
P63016	422	Paired box protein Pax-6	yes	N/A	0.325	0.099	0.904	4e-17
P26630	437	Paired box protein Pax-6	yes	N/A	0.325	0.096	0.904	4e-17
P63015	422	Paired box protein Pax-6	yes	N/A	0.325	0.099	0.904	4e-17
P26367	422	Paired box protein Pax-6	yes	N/A	0.325	0.099	0.904	4e-17
Q1LZF1	422	Paired box protein Pax-6	yes	N/A	0.325	0.099	0.904	4e-17
P55864	422	Paired box protein Pax-6	N/A	N/A	0.325	0.099	0.904	4e-17
P47238	416	Paired box protein Pax-6	N/A	N/A	0.325	0.100	0.904	4e-17
O18381	857	Paired box protein Pax-6	no	N/A	0.310	0.046	0.925	3e-16
Q02962	417	Paired box protein Pax-2	no	N/A	0.364	0.112	0.723	4e-15

>sp|O73917|PAX6_ORYLA Paired box protein Pax-6 OS=Oryzias latipes GN=pax6 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 24 HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 65

May be a transcription factor with important functions in eye and nasal development.
Oryzias latipes (taxid: 8090)

>sp|P63016|PAX6_RAT Paired box protein Pax-6 OS=Rattus norvegicus GN=Pax6 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 5  HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 46

Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells. Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters (By similarity). Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains.

Rattus norvegicus (taxid: 10116)

>sp|P26630|PAX6_DANRE Paired box protein Pax-6 OS=Danio rerio GN=pax6a PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 24 HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 65

Transcription factor expressed in spatially restricted regions of the neural tube during embryonic development.

Danio rerio (taxid: 7955)

>sp|P63015|PAX6_MOUSE Paired box protein Pax-6 OS=Mus musculus GN=Pax6 PE=1 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 5  HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 46

Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells. Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains.

Mus musculus (taxid: 10090)

>sp|P26367|PAX6_HUMAN Paired box protein Pax-6 OS=Homo sapiens GN=PAX6 PE=1 SV=2

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 5  HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 46

Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells (By similarity). Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains (By similarity). Isoform 5a appears to function as a molecular switch that specifies target genes.

Homo sapiens (taxid: 9606)

>sp|Q1LZF1|PAX6_BOVIN Paired box protein Pax-6 OS=Bos taurus GN=PAX6 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 5  HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 46

Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells. Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains.

Bos taurus (taxid: 9913)

>sp|P55864|PAX6_XENLA Paired box protein Pax-6 OS=Xenopus laevis GN=pax6 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 5  HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 46

May be a transcription factor with important functions in eye and nasal development.

Xenopus laevis (taxid: 8355)

>sp|P47238|PAX6_COTJA Paired box protein Pax-6 OS=Coturnix coturnix japonica GN=PAX6 PE=2 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/42 (90%), Positives = 40/42 (95%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 5  HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRIL 46

May be a transcription factor with important functions in eye and nasal development.

Coturnix coturnix japonica (taxid: 93934)

>sp|O18381|PAX6_DROME Paired box protein Pax-6 OS=Drosophila melanogaster GN=ey PE=2 SV=3

 Score = 83.6 bits (205), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/40 (92%), Positives = 39/40 (97%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          HSG+NQLGGV+V GRPLPDSTRQKIVELAHSGARPCDISR
Sbjct: 57 HSGVNQLGGVFVGGRPLPDSTRQKIVELAHSGARPCDISR 96

Involved in eye morphogenesis.

Drosophila melanogaster (taxid: 7227)

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

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 37/47 (78%)

Query: 8  FGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          F     GH G+NQLGGV+VNGRPLPD  RQ+IVELAH G RPCDISR
Sbjct: 10 FSAMHPGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISR 56

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)

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	129
242006165	509	Paired box protein Pax-6, putative [Pedi	0.434	0.110	0.857	1e-21
328716918	571	PREDICTED: paired box protein Pax-6-like	0.410	0.092	0.943	2e-21
195450696	552	GK13683 [Drosophila willistoni] gi|19416	0.426	0.099	0.910	2e-21
195064095	545	GH23963 [Drosophila grimshawi] gi|193892	0.426	0.100	0.910	2e-21
328716920	622	PREDICTED: paired box protein Pax-6-like	0.410	0.085	0.943	3e-21
357616883	133	hypothetical protein KGM_02181 [Danaus p	0.395	0.383	0.960	4e-21
195175466	546	GL17563 [Drosophila persimilis] gi|19846	0.395	0.093	0.941	5e-21
195134022	569	GI14042 [Drosophila mojavensis] gi|19391	0.395	0.089	0.941	6e-21
340715062	514	PREDICTED: paired box protein Pax-6-like	0.434	0.108	0.839	7e-21
195402191	549	GJ13300 [Drosophila virilis] gi|19415590	0.395	0.092	0.941	7e-21

>gi|242006165|ref|XP_002423925.1| Paired box protein Pax-6, putative [Pediculus humanus corporis] gi|212507188|gb|EEB11187.1| Paired box protein Pax-6, putative [Pediculus humanus corporis]

 Score =  107 bits (267), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/56 (85%), Positives = 51/56 (91%)

Query: 1   MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
           +A +  +FGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 61  LAHTSTIFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 116

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328716918|ref|XP_003246075.1| PREDICTED: paired box protein Pax-6-like isoform 2 [Acyrthosiphon pisum]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 50/53 (94%)

Query: 4  SGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          S ALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 23 SAALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 75

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195450696|ref|XP_002072593.1| GK13683 [Drosophila willistoni] gi|194168678|gb|EDW83579.1| GK13683 [Drosophila willistoni]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 51/56 (91%), Gaps = 1/56 (1%)

Query: 1  MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          M QS ALFGCS AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 18 MGQS-ALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 72

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195064095|ref|XP_001996496.1| GH23963 [Drosophila grimshawi] gi|193892042|gb|EDV90908.1| GH23963 [Drosophila grimshawi]

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 51/56 (91%), Gaps = 1/56 (1%)

Query: 1  MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          M QS ALFGCS AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 21 MGQS-ALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 75

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328716920|ref|XP_001944246.2| PREDICTED: paired box protein Pax-6-like isoform 1 [Acyrthosiphon pisum]

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 50/53 (94%), Positives = 50/53 (94%)

Query: 4   SGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
           S ALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 74  SAALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 126

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357616883|gb|EHJ70462.1| hypothetical protein KGM_02181 [Danaus plexippus]

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/51 (96%), Positives = 50/51 (98%)

Query: 5  GALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRT 55
          GALFGCS+AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 
Sbjct: 4  GALFGCSSAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRI 54

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195175466|ref|XP_002028472.1| GL17563 [Drosophila persimilis] gi|198462201|ref|XP_002135664.1| GA27636 [Drosophila pseudoobscura pseudoobscura] gi|194103225|gb|EDW25268.1| GL17563 [Drosophila persimilis] gi|198139762|gb|EDY70832.1| GA27636 [Drosophila pseudoobscura pseudoobscura]

 Score =  105 bits (262), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 48/51 (94%), Positives = 48/51 (94%)

Query: 6  ALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          ALFGCS AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 22 ALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 72

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195134022|ref|XP_002011437.1| GI14042 [Drosophila mojavensis] gi|193912060|gb|EDW10927.1| GI14042 [Drosophila mojavensis]

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 48/51 (94%), Positives = 48/51 (94%)

Query: 6  ALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          ALFGCS AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 26 ALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 76

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715062|ref|XP_003396039.1| PREDICTED: paired box protein Pax-6-like [Bombus terrestris] gi|350414727|ref|XP_003490400.1| PREDICTED: paired box protein Pax-6-like [Bombus impatiens]

 Score =  105 bits (261), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 47/56 (83%), Positives = 50/56 (89%)

Query: 1  MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          M    ++FGCSAAGHSG+NQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 21 MVGQNSIFGCSAAGHSGVNQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 76

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195402191|ref|XP_002059690.1| GJ13300 [Drosophila virilis] gi|194155904|gb|EDW71088.1| GJ13300 [Drosophila virilis] gi|263359635|gb|ACY70471.1| hypothetical protein DVIR88_6g0008 [Drosophila virilis]

 Score =  105 bits (261), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 48/51 (94%), Positives = 48/51 (94%)

Query: 6  ALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTC 56
          ALFGCS AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR  
Sbjct: 25 ALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRIL 75

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	129
FB|FBgn0019650	543	toy "twin of eyeless" [Drosoph	0.410	0.097	0.907	8.8e-21
UNIPROTKB|F1M5I1	305	Pax6 "Paired box protein Pax-6	0.387	0.163	0.86	1.7e-18
UNIPROTKB|F1M368	146	Pax6 "Paired box protein Pax-6	0.372	0.328	0.812	9.5e-18
UNIPROTKB|F1NF66	422	PAX6 "Paired box protein Pax-6	0.325	0.099	0.952	2.8e-17
UNIPROTKB|F1NXF3	436	PAX6 "Paired box protein Pax-6	0.325	0.096	0.952	3.2e-17
UNIPROTKB|F1NXF7	186	PAX6 "Paired box protein Pax-6	0.310	0.215	0.95	8.6e-17
UNIPROTKB|B1B1I9	66	PAX6 "Paired box protein Pax-6	0.310	0.606	0.95	8.6e-17
UNIPROTKB|B1B1J0	124	PAX6 "Paired box protein Pax-6	0.310	0.322	0.95	8.6e-17
UNIPROTKB|E9PKM0	58	PAX6 "Paired box protein Pax-6	0.310	0.689	0.95	8.6e-17
ZFIN|ZDB-GENE-990415-200	461	pax6a "paired box gene 6a" [Da	0.317	0.088	0.951	1e-16

FB|FBgn0019650 toy "twin of eyeless" [Drosophila melanogaster (taxid:7227)]

 Score = 252 (93.8 bits), Expect = 8.8e-21, P = 8.8e-21
 Identities = 49/54 (90%), Positives = 50/54 (92%)

Query:     1 MAQSGALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             + QS  LFGCS AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:    17 VGQS-TLFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 69

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

GO:0005634 "nucleus" evidence=IEA;NAS

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

GO:0035214 "eye-antennal disc development" evidence=IMP

GO:0048749 "compound eye development" evidence=TAS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0016319 "mushroom body development" evidence=IMP

GO:0048854 "brain morphogenesis" evidence=IMP

GO:0010628 "positive regulation of gene expression" evidence=IMP

GO:0008056 "ocellus development" evidence=IGI;IMP

UNIPROTKB|F1M5I1 Pax6 "Paired box protein Pax-6" [Rattus norvegicus (taxid:10116)]

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 43/50 (86%), Positives = 45/50 (90%)

Query:     5 GALFGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             G L    AAGHSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:    46 GLLSRHGAAGHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 95

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|F1M368 Pax6 "Paired box protein Pax-6" [Rattus norvegicus (taxid:10116)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 39/48 (81%), Positives = 44/48 (91%)

Query:    12 AAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAV 59
             ++GHSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR    +
Sbjct:     2 SSGHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRILQVI 49

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" 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

UNIPROTKB|F1NF66 PAX6 "Paired box protein Pax-6" [Gallus gallus (taxid:9031)]

 Score = 217 (81.4 bits), Expect = 2.8e-17, P = 2.8e-17
 Identities = 40/42 (95%), Positives = 42/42 (100%)

Query:    13 AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             AGHSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:     3 AGHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 44

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1NXF3 PAX6 "Paired box protein Pax-6" [Gallus gallus (taxid:9031)]

 Score = 217 (81.4 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 40/42 (95%), Positives = 42/42 (100%)

Query:    13 AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             AGHSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:     3 AGHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 44

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000979 "RNA polymerase II core promoter sequence-specific DNA binding" evidence=IEA

GO:0000981 "sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0001709 "cell fate determination" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0002052 "positive regulation of neuroblast proliferation" evidence=IEA

GO:0002088 "lens development in camera-type eye" evidence=IEA

GO:0003322 "pancreatic A cell development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0007435 "salivary gland morphogenesis" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0009611 "response to wounding" evidence=IEA

GO:0009950 "dorsal/ventral axis specification" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0021778 "oligodendrocyte cell fate specification" evidence=IEA

GO:0021796 "cerebral cortex regionalization" evidence=IEA

GO:0021797 "forebrain anterior/posterior pattern specification" evidence=IEA

GO:0021798 "forebrain dorsal/ventral pattern formation" evidence=IEA

GO:0021902 "commitment of neuronal cell to specific neuron type in forebrain" evidence=IEA

GO:0021905 "forebrain-midbrain boundary formation" evidence=IEA

GO:0021912 "regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification" evidence=IEA

GO:0021913 "regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification" evidence=IEA

GO:0021918 "regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment" evidence=IEA

GO:0021983 "pituitary gland development" evidence=IEA

GO:0023019 "signal transduction involved in regulation of gene expression" evidence=IEA

GO:0030216 "keratinocyte differentiation" evidence=IEA

GO:0030334 "regulation of cell migration" evidence=IEA

GO:0030858 "positive regulation of epithelial cell differentiation" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0032808 "lacrimal gland development" evidence=IEA

GO:0033365 "protein localization to organelle" evidence=IEA

GO:0035035 "histone acetyltransferase binding" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0042593 "glucose homeostasis" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

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

GO:0048505 "regulation of timing of cell differentiation" evidence=IEA

GO:0048596 "embryonic camera-type eye morphogenesis" evidence=IEA

GO:0048708 "astrocyte differentiation" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0061072 "iris morphogenesis" evidence=IEA

GO:0061303 "cornea development in camera-type eye" evidence=IEA

GO:0070410 "co-SMAD binding" evidence=IEA

GO:0070412 "R-SMAD binding" evidence=IEA

GO:0071837 "HMG box domain binding" evidence=IEA

UNIPROTKB|F1NXF7 PAX6 "Paired box protein Pax-6" [Gallus gallus (taxid:9031)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 38/40 (95%), Positives = 40/40 (100%)

Query:    15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:     1 HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 40

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|B1B1I9 PAX6 "Paired box protein Pax-6" [Homo sapiens (taxid:9606)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 38/40 (95%), Positives = 40/40 (100%)

Query:    15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:     5 HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 44

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000979 "RNA polymerase II core promoter sequence-specific DNA binding" evidence=IEA

GO:0000981 "sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0001709 "cell fate determination" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0002052 "positive regulation of neuroblast proliferation" evidence=IEA

GO:0002088 "lens development in camera-type eye" evidence=IEA

GO:0003322 "pancreatic A cell development" evidence=IEA

GO:0003680 "AT DNA binding" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IEA

GO:0007224 "smoothened signaling pathway" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0007435 "salivary gland morphogenesis" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0009950 "dorsal/ventral axis specification" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0021778 "oligodendrocyte cell fate specification" evidence=IEA

GO:0021796 "cerebral cortex regionalization" evidence=IEA

GO:0021797 "forebrain anterior/posterior pattern specification" evidence=IEA

GO:0021798 "forebrain dorsal/ventral pattern formation" evidence=IEA

GO:0021902 "commitment of neuronal cell to specific neuron type in forebrain" evidence=IEA

GO:0021905 "forebrain-midbrain boundary formation" evidence=IEA

GO:0021912 "regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification" evidence=IEA

GO:0021913 "regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification" evidence=IEA

GO:0021918 "regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment" evidence=IEA

GO:0021983 "pituitary gland development" evidence=IEA

GO:0023019 "signal transduction involved in regulation of gene expression" evidence=IEA

GO:0030216 "keratinocyte differentiation" evidence=IEA

GO:0030334 "regulation of cell migration" evidence=IEA

GO:0030858 "positive regulation of epithelial cell differentiation" evidence=IEA

GO:0030902 "hindbrain development" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0032808 "lacrimal gland development" evidence=IEA

GO:0033365 "protein localization to organelle" evidence=IEA

GO:0035035 "histone acetyltransferase binding" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0042660 "positive regulation of cell fate specification" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

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

GO:0048505 "regulation of timing of cell differentiation" evidence=IEA

GO:0048596 "embryonic camera-type eye morphogenesis" evidence=IEA

GO:0048708 "astrocyte differentiation" evidence=IEA

GO:0050680 "negative regulation of epithelial cell proliferation" evidence=IEA

GO:0070410 "co-SMAD binding" evidence=IEA

GO:0070412 "R-SMAD binding" evidence=IEA

GO:0071837 "HMG box domain binding" evidence=IEA

UNIPROTKB|B1B1J0 PAX6 "Paired box protein Pax-6" [Homo sapiens (taxid:9606)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 38/40 (95%), Positives = 40/40 (100%)

Query:    15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:     5 HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 44

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|E9PKM0 PAX6 "Paired box protein Pax-6" [Homo sapiens (taxid:9606)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 38/40 (95%), Positives = 40/40 (100%)

Query:    15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             HSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:     5 HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 44

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

ZFIN|ZDB-GENE-990415-200 pax6a "paired box gene 6a" [Danio rerio (taxid:7955)]

 Score = 213 (80.0 bits), Expect = 1.0e-16, P = 1.0e-16
 Identities = 39/41 (95%), Positives = 41/41 (100%)

Query:    14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
             GHSG+NQLGGV+VNGRPLPDSTRQKIVELAHSGARPCDISR
Sbjct:    33 GHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISR 73

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IMP

GO:0030902 "hindbrain development" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

GO:0030900 "forebrain development" evidence=IGI

GO:0001071 "nucleic acid binding transcription factor activity" evidence=IDA

GO:2001141 "regulation of RNA biosynthetic process" evidence=IDA

---

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	129
cd00131	128	cd00131, PAX, Paired Box domain	1e-21
smart00351	125	smart00351, PAX, Paired Box domain	3e-21
pfam00292	125	pfam00292, PAX, 'Paired box' domain	1e-20

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

 Score = 82.9 bits (205), Expect = 1e-21
 Identities = 33/41 (80%), Positives = 36/41 (87%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G  G+NQLGGV+VNGRPLPDS RQ+IVELA SG RPCDISR
Sbjct: 1  GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISR 41

Length = 128

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

 Score = 82.0 bits (203), Expect = 3e-21
 Identities = 32/41 (78%), Positives = 36/41 (87%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          GH G+NQLGGV+VNGRPLPD  RQ+IVELA +G RPCDISR
Sbjct: 1  GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISR 41

Length = 125

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

 Score = 80.2 bits (198), Expect = 1e-20
 Identities = 32/41 (78%), Positives = 35/41 (85%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G   +NQLGGV+VNGRPLP+  RQKIVELAHSG RPCDISR
Sbjct: 1  GQGRVNQLGGVFVNGRPLPNHIRQKIVELAHSGVRPCDISR 41

Length = 125

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	129
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	100.0
KOG3517|consensus	334		100.0
KOG3862|consensus	327		100.0
KOG0849|consensus	354		99.91
cd00131	128	PAX Paired Box domain	99.79
smart00351	125	PAX Paired Box domain.	99.69
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	93.47
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	89.21
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	88.42
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	84.56
PF13551	112	HTH_29: Winged helix-turn helix	83.76

>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=100.00  E-value=8e-41  Score=250.98  Aligned_cols=94  Identities=39%  Similarity=0.725  Sum_probs=75.9

Q ss_pred             CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc-----------
Q psy2180          14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT-----------   74 (129)
Q Consensus        14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~-----------   74 (129)
                      |++++|||||+|+||||||.++|++||||+++|+|||||||+|+        ||.||++|||+.|++++           
T Consensus         1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v   80 (125)
T PF00292_consen    1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEV   80 (125)
T ss_dssp             S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCH
T ss_pred             CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHH
Confidence            68999999999999999999999999999999999999999998        89999999999999885           


Q ss_pred             -ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180          75 -STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD  110 (129)
Q Consensus        75 -s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~  110 (129)
                       .+|++| |++||+||+||  |||+|++|++|+.+++
T Consensus        81 ~~~I~~~-k~enP~ifawE--iR~~L~~~gvc~~~~~  114 (125)
T PF00292_consen   81 VEKIEQY-KRENPTIFAWE--IRDRLIADGVCDRSNV  114 (125)
T ss_dssp             HHHHHHH-HHH-TTS-HHH--HHHHHHHTTSS-TTTS
T ss_pred             HHHHHHH-HhcCCCcchHH--HHHHHHHcCCCCCCCC
Confidence             248999 99999999999  9999999999999885

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.

>KOG3517|consensus

Probab=100.00  E-value=8.3e-38  Score=261.36  Aligned_cols=94  Identities=41%  Similarity=0.656  Sum_probs=88.2

Q ss_pred             CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCcccccccc-c--------
Q psy2180          14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFTS-T--------   76 (129)
Q Consensus        14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~s-~--------   76 (129)
                      ..+.||||||+|+||||||.+.|-|||||++.|+|||||||||+        ||.||.|||||-|+|++. +        
T Consensus         4 ~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~V   83 (334)
T KOG3517|consen    4 SYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKV   83 (334)
T ss_pred             cccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhH
Confidence            45799999999999999999999999999999999999999999        899999999999999962 1        


Q ss_pred             ---ccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180          77 ---GAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD  110 (129)
Q Consensus        77 ---Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~  110 (129)
                         |++| ||++|.|||||  |||||++||+||..|.
T Consensus        84 V~~IR~~-Kq~DPGIFAWE--IRDRLlsdgiCDk~Nv  117 (334)
T KOG3517|consen   84 VKYIRSL-KQRDPGIFAWE--IRDRLLSDGICDKYNV  117 (334)
T ss_pred             HHHHHHh-hccCCceeeeh--hhhhhhhcccccccCC
Confidence               8888 99999999999  9999999999999883

>KOG3862|consensus

Probab=100.00  E-value=2.5e-36  Score=253.39  Aligned_cols=100  Identities=42%  Similarity=0.731  Sum_probs=92.9

Q ss_pred             eeeecCCCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc-----
Q psy2180           8 FGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT-----   74 (129)
Q Consensus         8 ~~~~~~~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~-----   74 (129)
                      +.+...||++||||||+|+||||||+..|++||||+++|+|||||||||+        ||-||+|||||.|+.++     
T Consensus         3 ~~s~~~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~K   82 (327)
T KOG3862|consen    3 HNSIHSGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPK   82 (327)
T ss_pred             ccCCCCCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccc
Confidence            45567899999999999999999999999999999999999999999998        89999999999888875     


Q ss_pred             -------ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180          75 -------STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD  110 (129)
Q Consensus        75 -------s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~  110 (129)
                             .+|+.| |++||+|||||  |||+|+.|++|++|+.
T Consensus        83 vAtp~Vvk~i~~~-k~~n~~mfawe--iR~~l~~~~ic~~d~v  122 (327)
T KOG3862|consen   83 VATPKVVKKIALY-KRQNPTMFAWE--IRDRLLAEPICDNDTV  122 (327)
T ss_pred             cccchHHHHHHHH-hhcCcchhhhh--hhhhhhcccccCCCCC
Confidence                   348899 99999999999  9999999999999983

>KOG0849|consensus

Probab=99.91  E-value=6.5e-26  Score=191.39  Aligned_cols=92  Identities=40%  Similarity=0.708  Sum_probs=86.8

Q ss_pred             CCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc-------------
Q psy2180          16 SGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT-------------   74 (129)
Q Consensus        16 ~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~-------------   74 (129)
                      +.+|||||+|+||+|||.+.|++|+||++.|+|||+||++|.        ||+||++|||+.|..++             
T Consensus         1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~   80 (354)
T KOG0849|consen    1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVE   80 (354)
T ss_pred             CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhH
Confidence            479999999999999999999999999999999999999998        89999999999999885             


Q ss_pred             ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180          75 STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD  110 (129)
Q Consensus        75 s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~  110 (129)
                      ..|++| |++||.+|+||  |||+|+.+++|+++|.
T Consensus        81 ~~i~~~-k~~~P~~~~~~--ir~~l~~~~~~~~~t~  113 (354)
T KOG0849|consen   81 AKIEQY-KRENPAMFAWE--IRDQLLHEGLCTQATL  113 (354)
T ss_pred             HHHHHH-HhcCCcccchh--hhhcccCcccccCCCC
Confidence            348889 99999999999  9999999999999863

>cd00131 PAX Paired Box domain

Probab=99.79  E-value=4.1e-20  Score=136.45  Aligned_cols=98  Identities=44%  Similarity=0.726  Sum_probs=86.1

Q ss_pred             CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc----cc-----
Q psy2180          14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT----ST-----   76 (129)
Q Consensus        14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~----s~-----   76 (129)
                      |++++|||||+|.+|+||+.++|++||+|++.|+.+.+||++++        ++.||.++|++.|+..+    .+     
T Consensus         1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~   80 (128)
T cd00131           1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEV   80 (128)
T ss_pred             CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHH
Confidence            57899999999999999999999999999999999999999998        79999999999988653    11     


Q ss_pred             ---ccccccccCCcchhhhhhhhhhhhhcccCCCCchhhhh
Q psy2180          77 ---GAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCRK  114 (129)
Q Consensus        77 ---Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~v~~~  114 (129)
                         |..+ .++||.++.||  |+|.|..+|+|.+++.|+.+
T Consensus        81 ~~~i~~~-v~~~p~~Tl~E--l~~~L~~~gv~~~~~~~s~s  118 (128)
T cd00131          81 VKKIEIY-KQENPGMFAWE--IRDRLLQEGVCDKSNVPSVS  118 (128)
T ss_pred             HHHHHHH-HHHCCCCCHHH--HHHHHHHcCCcccCCCCCHH
Confidence               4444 67899999999  99999999999976666553

>smart00351 PAX Paired Box domain

Probab=99.69  E-value=1.2e-17  Score=122.40  Aligned_cols=93  Identities=47%  Similarity=0.813  Sum_probs=82.6

Q ss_pred             CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc----c------
Q psy2180          14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT----S------   75 (129)
Q Consensus        14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~----s------   75 (129)
                      +++++|||||+|++|+|++.+.|.+||.++..|....+||++++        ++.||.++|++.|+..+    .      
T Consensus         1 ~~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~   80 (125)
T smart00351        1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKV   80 (125)
T ss_pred             CCCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHH
Confidence            47899999999999999999999999999999999999999998        69999999999886443    1      


Q ss_pred             --cccccccccCCcchhhhhhhhhhhhhcccCCCCc
Q psy2180          76 --TGAPYRTQRDRRSWNWRTLARDPVISRASCRSPT  109 (129)
Q Consensus        76 --~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~  109 (129)
                        .|..+ .++||.++.||  |++.|..+|+|..++
T Consensus        81 ~~~I~~~-~~~~p~~t~~e--l~~~L~~~gv~~~~~  113 (125)
T smart00351       81 VKKIADY-KQENPGIFAWE--IRDRLLSEGVCDKDN  113 (125)
T ss_pred             HHHHHHH-HHHCCCCCHHH--HHHHHHHcCCCcCCC
Confidence              25556 78899999999  999999999999544

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=93.47  E-value=0.025  Score=34.39  Aligned_cols=34  Identities=21%  Similarity=0.365  Sum_probs=19.1

Q ss_pred             hHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccC
Q psy2180          33 DSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRG   66 (129)
Q Consensus        33 ~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tG   66 (129)
                      ...|..||+|..+|...-+||+.|+        +++||.+.|
T Consensus         4 ~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G   45 (50)
T PF13384_consen    4 EERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEG   45 (50)
T ss_dssp             ------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred             hhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence            4578999999999999999999998        689998877

>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA

Probab=89.21  E-value=0.3  Score=31.80  Aligned_cols=25  Identities=28%  Similarity=0.433  Sum_probs=22.7

Q ss_pred             hHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180          33 DSTRQKIVELAHSGARPCDISRTCS   57 (129)
Q Consensus        33 ~~~R~kIVELa~~GvRPcdISR~L~   57 (129)
                      +...++||||+..|+---|+||-|.
T Consensus         8 pgikeqIvema~nG~GiRdtaRvL~   32 (46)
T PF12759_consen    8 PGIKEQIVEMAFNGSGIRDTARVLK   32 (46)
T ss_pred             ccHHHHHHHHHhcCCcchhhHhHhc
Confidence            3578899999999999999999998

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=88.42  E-value=0.16  Score=33.22  Aligned_cols=36  Identities=28%  Similarity=0.431  Sum_probs=26.2

Q ss_pred             CCCCCChHHHHHHHHHHhcCCCCCchhhhhh----cccCC
Q psy2180          27 NGRPLPDSTRQKIVELAHSGARPCDISRTCS----AVRRP   62 (129)
Q Consensus        27 nGrPLp~~~R~kIVELa~~GvRPcdISR~L~----IL~Ry   62 (129)
                      .|.+|.+.+|.+|.-|.+.|+.-.+||+++.    .+++|
T Consensus         1 RG~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~y   40 (50)
T PF11427_consen    1 RGKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRY   40 (50)
T ss_dssp             -S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHH
Confidence            3789999999999999999999999999997    56655

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=84.56  E-value=0.67  Score=33.51  Aligned_cols=64  Identities=6%  Similarity=0.035  Sum_probs=49.8

Q ss_pred             ChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCcccccccc-c-----ccccccccCCcchhhhhhhhh
Q psy2180          32 PDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFTS-T-----GAPYRTQRDRRSWNWRTLARD   97 (129)
Q Consensus        32 p~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~s-~-----Ia~y~K~~np~~faWE~~IRd   97 (129)
                      +.+.|++||+....|....++|+...        -+. ..++|++.+..-+. +     +..+ =++||.+..+|  |.+
T Consensus         4 S~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid~~~L~~~-v~~~pd~tl~E--la~   79 (119)
T PF01710_consen    4 SLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKIDRDELKAL-VEENPDATLRE--LAE   79 (119)
T ss_pred             CHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hcccccccccccccccccHHHHHHH-HHHCCCcCHHH--HHH
Confidence            67899999999999999999999988        255 56788887766543 3     3344 35579999999  877


Q ss_pred             hh
Q psy2180          98 PV   99 (129)
Q Consensus        98 ~L   99 (129)
                      +|
T Consensus        80 ~l   81 (119)
T PF01710_consen   80 RL   81 (119)
T ss_pred             Hc
Confidence            76

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PF13551 HTH_29: Winged helix-turn helix

Probab=83.76  E-value=0.28  Score=33.07  Aligned_cols=31  Identities=26%  Similarity=0.369  Sum_probs=27.8

Q ss_pred             HHHHHHHHhcCCC-CCchhhhhh--------cccCCCccC
Q psy2180          36 RQKIVELAHSGAR-PCDISRTCS--------AVRRPATRG   66 (129)
Q Consensus        36 R~kIVELa~~GvR-PcdISR~L~--------IL~Ry~~tG   66 (129)
                      |.+||.|+.+|+. +.+||+.++        .+++|.++|
T Consensus         1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G   40 (112)
T PF13551_consen    1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG   40 (112)
T ss_pred             CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence            6789999999995 999999998        588888888

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	129
6pax_A	133	Crystal Structure Of The Human Pax-6 Paired Domain-		1e-17
1k78_A	149	Pax5(1-149)+ets-1(331-440)+dna Length = 149		5e-16
2k27_A	159	Solution Structure Of Human Pax8 Paired Box Domain		5e-14
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		2e-10

>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 = 84.3 bits (207), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 37/41 (90%), Positives = 40/41 (97%)
Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRT 55
          HSG+NQLGGV+VNGRPLPDSTRQ+IVELAHSGARPCDISR 
Sbjct: 2  HSGVNQLGGVFVNGRPLPDSTRQRIVELAHSGARPCDISRI 42

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 34/44 (77%), Positives = 37/44 (84%)
Query: 11 SAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          S  GH G+NQLGGV+VNGRPLPD  RQ+IVELAH G RPCDISR
Sbjct: 13 SRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISR 56

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 36/42 (85%)
Query: 13 AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          +GH G+NQLGG +VNGRPLP+  RQ+IV+LAH G RPCDISR
Sbjct: 8  SGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISR 49

>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 = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 32/41 (78%)
Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G   +NQLGGV++NGRPLP++ R KIVE+A  G RPC ISR
Sbjct: 1  GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISR 41

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	129
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	2e-19
2k27_A	159	Paired box protein PAX-8; paired domain, solution	5e-19
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	1e-18

>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 = 77.0 bits (189), Expect = 2e-19
 Identities = 26/41 (63%), Positives = 32/41 (78%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G   +NQLGGV++NGRPLP++ R KIVE+A  G RPC ISR
Sbjct: 1  GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISR 41

>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 = 76.8 bits (188), Expect = 5e-19
 Identities = 32/76 (42%), Positives = 44/76 (57%), Gaps = 4/76 (5%)

Query: 13 AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR----TCSAVRRPATRGST 68
          +GH G+NQLGG +VNGRPLP+  RQ+IV+LAH G RPCDISR    +   V +   R   
Sbjct: 8  SGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYE 67

Query: 69 SWAAFTSTGAPYRTQR 84
          + +         + + 
Sbjct: 68 TGSIRPGVIGGSKPKV 83

>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 = 75.6 bits (185), Expect = 1e-18
 Identities = 36/78 (46%), Positives = 45/78 (57%), Gaps = 4/78 (5%)

Query: 11 SAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR----TCSAVRRPATRG 66
          S  GH G+NQLGGV+VNGRPLPD  RQ+IVELAH G RPCDISR    +   V +   R 
Sbjct: 13 SRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRY 72

Query: 67 STSWAAFTSTGAPYRTQR 84
            + +         + + 
Sbjct: 73 YETGSIKPGVIGGSKPKV 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	129
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.15
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.06
2k27_A	159	Paired box protein PAX-8; paired domain, solution	98.61
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.47
1u78_A	141	TC3 transposase, transposable element TC3 transpos	93.9
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	92.61
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	84.51

>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=99.15  E-value=1.1e-11  Score=87.85  Aligned_cols=116  Identities=40%  Similarity=0.682  Sum_probs=76.7

Q ss_pred             eeeecCCCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccc-------
Q psy2180           8 FGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAA-------   72 (129)
Q Consensus         8 ~~~~~~~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a-------   72 (129)
                      -+.+++|++++|+|||+|..++.++.+.|.+||+|+..|....+||+.++        .+++|.++|...+..       
T Consensus        10 ~~~~~~~~~~~~~~gg~~~~~~~~s~e~r~~iv~~~~~G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~   89 (149)
T 1k78_A           10 PRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPK   89 (149)
T ss_dssp             ---------CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCS
T ss_pred             CccccCCCCCccCCCceecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCC
Confidence            35788999999999999999999999999999999999999999999998        467777666543321       


Q ss_pred             --cc---ccccccccccCCcchhhhhhhhhhhhhcccCCCC----chhhhhhhhhHhCCCCCC
Q psy2180          73 --FT---STGAPYRTQRDRRSWNWRTLARDPVISRASCRSP----TDVCRKFSAEQTGKRPNQ  126 (129)
Q Consensus        73 --~~---s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~----~~v~~~~~~~~~~~~~~~  126 (129)
                        +.   ..|.++ .+++|....||  |.+.|..+.+|...    ....+++.....+..|||
T Consensus        90 ~~~~~~~~~I~~~-~~~~~~~s~~~--i~~~l~~~~~~~~g~~~S~sTV~r~L~~~~~~~~~~  149 (149)
T 1k78_A           90 VATPKVVEKIAEY-KRQNPTMFAWE--IRDRLLAERVCDNDTVPSVSSINRIIRTKVQQPPNQ  149 (149)
T ss_dssp             SSCHHHHHHHHHH-HHHCTTCCHHH--HHHHHHHTTSSCTTTSCCHHHHHHHHHCC-------
T ss_pred             CCCHHHHHHHHHH-HHhCcchhHHH--HHHHHHHhcccccCCCcCHHHHHHHHHHHhcCCCCC
Confidence              11   235556 45679999999  99999988766432    233345666677777876

>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=99.06  E-value=4.6e-11  Score=80.16  Aligned_cols=89  Identities=38%  Similarity=0.706  Sum_probs=70.9

Q ss_pred             CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccc--------c-c--
Q psy2180          14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAA--------F-T--   74 (129)
Q Consensus        14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a--------~-~--   74 (129)
                      |++.+|++||+|..++.++.+.|.+|++|+..|....+||+.+.        .+++|..+|...+..        . +  
T Consensus         1 ~~~~~~~~gg~~~m~~~~s~~~r~~i~~~~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~   80 (128)
T 1pdn_C            1 GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEI   80 (128)
T ss_dssp             -CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTH
T ss_pred             CCchHhhhcccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHH
Confidence            67899999999999999999999999999999999999999998        467776666543211        1 1  


Q ss_pred             -ccccccccccCCcchhhhhhhhhhhhhcccC
Q psy2180          75 -STGAPYRTQRDRRSWNWRTLARDPVISRASC  105 (129)
Q Consensus        75 -s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C  105 (129)
                       ..|.++ .+++|....||  |.+.|..+|++
T Consensus        81 ~~~i~~~-~~~~~~~s~~~--i~~~l~~~g~~  109 (128)
T 1pdn_C           81 ENRIEEY-KRSSPGMFSWE--IREKLIREGVC  109 (128)
T ss_dssp             HHHHHHT-TTTCTTCCHHH--HHHHHHHTSSS
T ss_pred             HHHHHHH-HHhCcchHHHH--HHHHHHHcCCc
Confidence             125555 56689999999  99999888875

>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=98.61  E-value=6e-08  Score=69.61  Aligned_cols=93  Identities=41%  Similarity=0.794  Sum_probs=75.7

Q ss_pred             cCCCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCcccccc----c-----
Q psy2180          12 AAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAF----T-----   74 (129)
Q Consensus        12 ~~~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~----~-----   74 (129)
                      ++|..+++++|+.|..++.++.+.|.+||+|...|....+||+.|.        .+++|.++|...+..-    +     
T Consensus         7 ~~~~~~~~~~g~~~~~~~~~s~e~r~~ii~l~~~G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~   86 (159)
T 2k27_A            7 RSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATP   86 (159)
T ss_dssp             CCSCSSCCCCCCTTSSSCSSCHHHHHHHHHHHHHTCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCT
T ss_pred             hhcchhhhhcCCcCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCH
Confidence            5788999999999999999999999999999999999999999998        5889988886544221    1     


Q ss_pred             ---ccccccccccCCcchhhhhhhhhhhhhcccCCC
Q psy2180          75 ---STGAPYRTQRDRRSWNWRTLARDPVISRASCRS  107 (129)
Q Consensus        75 ---s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~  107 (129)
                         ..|.++ .+++|....||  |.+.|..+++|..
T Consensus        87 ~~~~~I~~~-~~~~~~~s~~~--i~~~l~~~~~~~~  119 (159)
T 2k27_A           87 KVVEKIGDY-KRQNPTMFAWE--IRDRLLAEGVCDN  119 (159)
T ss_dssp             THHHHHHHH-HHHCSSSCHHH--HHHHHHHHTCSCT
T ss_pred             HHHHHHHHH-HHHCccchHHH--HHHHHHHhccccc
Confidence               124455 45579999999  9999998886643

>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=96.47  E-value=0.0021  Score=35.95  Aligned_cols=38  Identities=21%  Similarity=0.358  Sum_probs=32.3

Q ss_pred             CCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCC
Q psy2180          30 PLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGS   67 (129)
Q Consensus        30 PLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS   67 (129)
                      .|++..+..|+.|...|+...+||+.|.        .+.+|...|.
T Consensus         5 ~l~~~~~~~i~~~~~~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g~   50 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT   50 (51)
T ss_dssp             CCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCSTTTTC
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhhHHhcCC
Confidence            3788999999999999999999999998        4677776664

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=93.90  E-value=0.042  Score=37.12  Aligned_cols=79  Identities=15%  Similarity=0.178  Sum_probs=51.4

Q ss_pred             CCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccccc--------ccccccccCCcchhh
Q psy2180          28 GRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFTST--------GAPYRTQRDRRSWNW   91 (129)
Q Consensus        28 GrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~s~--------Ia~y~K~~np~~faW   91 (129)
                      +..+..+.|.+|++|...|....+||+.|+        .+.+|...|...+..-+.+        |..+  .++|..-.-
T Consensus         4 ~~~~s~~~r~~i~~~~~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~~gr~~~l~~~~~~~i~~~--~~~~~~s~~   81 (141)
T 1u78_A            4 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKRAPRRKALSVRDERNVIRA--ASNSCKTAR   81 (141)
T ss_dssp             SCCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCCCCCCCSSCHHHHHHHHHH--HHHCCCCHH
T ss_pred             cccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHcccccCCcCCCCCCCcCCHHHHHHHHHH--HhCCCCCHH
Confidence            356889999999999999999999999998        5788877775432111111        3333  334655455


Q ss_pred             hhhhhhhhhhcccCCCCchhhh
Q psy2180          92 RTLARDPVISRASCRSPTDVCR  113 (129)
Q Consensus        92 E~~IRd~Li~e~~C~~~~~v~~  113 (129)
                      |  |.+.|   ++.-+...|.+
T Consensus        82 ~--i~~~l---g~~~s~~tV~r   98 (141)
T 1u78_A           82 D--IRNEL---QLSASKRTILN   98 (141)
T ss_dssp             H--HHHHT---TCCSCHHHHHH
T ss_pred             H--HHHHH---CCCccHHHHHH
Confidence            5  66666   44334444544

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=92.61  E-value=0.019  Score=44.56  Aligned_cols=30  Identities=7%  Similarity=-0.101  Sum_probs=27.4

Q ss_pred             ccccccccccCCcchhhhhhhhhhhhhcccCCC
Q psy2180          75 STGAPYRTQRDRRSWNWRTLARDPVISRASCRS  107 (129)
Q Consensus        75 s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~  107 (129)
                      .+|++| +++||.+|+||  |++.|+..|+|..
T Consensus        18 ~~ie~~-~~e~p~~l~~~--Ik~~l~~~gitQ~   47 (194)
T 1ic8_A           18 AVVETL-LQEDPWRVAKM--VKSYLQQHNIPQR   47 (194)
T ss_dssp             HHHHHH-TTSCHHHHHHH--HHHHHHHTTCCHH
T ss_pred             HHHHHH-HccCHHHHHHH--HHHHHHHcCCCHH
Confidence            679999 99999999999  9999999998754

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=84.51  E-value=0.34  Score=27.14  Aligned_cols=27  Identities=11%  Similarity=0.206  Sum_probs=23.1

Q ss_pred             CChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180          31 LPDSTRQKIVELAHSGARPCDISRTCS   57 (129)
Q Consensus        31 Lp~~~R~kIVELa~~GvRPcdISR~L~   57 (129)
                      +.++.+..|++|...|....+||+.+.
T Consensus         6 ~~~~~~~~i~~l~~~g~s~~~ia~~lg   32 (52)
T 1jko_C            6 INKHEQEQISRLLEKGHPRQQLAIIFG   32 (52)
T ss_dssp             SCTTHHHHHHHHHHTTCCHHHHHHTTS
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHC
Confidence            456677899999999998999999987

---

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	129
d1k78a1	63	a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax	3e-16
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	6e-15

>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 = 65.4 bits (160), Expect = 3e-16
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 17 GINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G+NQLGGV+VNGRPLPD  RQ+IVELAH G RPCDISR
Sbjct: 1  GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISR 38

>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 = 64.2 bits (156), Expect = 6e-15
 Identities = 25/43 (58%), Positives = 31/43 (72%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS 57
             +NQLGGV++NGRPLP++ R KIVE+A  G RPC ISR   
Sbjct: 1  QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLR 43

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	129
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	99.93
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1k78a2	61	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.76
d6paxa2	65	Pax-6 {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	91.18
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	84.96

>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=99.93  E-value=5.2e-28  Score=174.37  Aligned_cols=96  Identities=35%  Similarity=0.634  Sum_probs=86.0

Q ss_pred             CCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc------------
Q psy2180          15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT------------   74 (129)
Q Consensus        15 ~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~------------   74 (129)
                      ++++|||||+|+||||||.++|++||+|+.+|+++|+||++++        ++.||.++|++.|+..+            
T Consensus         1 ~~~~n~~gg~~~~GrpLs~dlR~rIv~~~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~   80 (123)
T d1pdnc_           1 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIE   80 (123)
T ss_dssp             CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHH
T ss_pred             CcCcccCCCcccCCcCCCHHHHHHHHHHHHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHH
Confidence            4789999999999999999999999999999999999999998        79999999999877653            


Q ss_pred             ccccccccccCCcchhhhhhhhhhhhhcccCCCCchhhh
Q psy2180          75 STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCR  113 (129)
Q Consensus        75 s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~v~~  113 (129)
                      ..|..| +++||.+++||  |+|+|+.||+|+.+++.+.
T Consensus        81 ~~I~~~-~~~~P~~t~~E--l~~~L~~egv~~~~~~pSv  116 (123)
T d1pdnc_          81 NRIEEY-KRSSPGMFSWE--IREKLIREGVCDRSTAPSV  116 (123)
T ss_dssp             HHHHHT-TTTCTTCCHHH--HHHHHHHTSSSCSTTCCCH
T ss_pred             HHHHHH-HHhCCCccHHH--HHHHHHHcCCCCCCCCCCh
Confidence            126667 88899999999  9999999999999885543

>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=99.79  E-value=7.3e-21  Score=126.17  Aligned_cols=55  Identities=62%  Similarity=0.995  Sum_probs=53.1

Q ss_pred             CCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCcccc
Q psy2180          17 GINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWA   71 (129)
Q Consensus        17 ~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~   71 (129)
                      ++|||||+|+||||||.++|+|||+++.+|+++|+||++++        ++.||++||++.|+
T Consensus         1 ~~n~~gg~~~~GrPls~DLR~Riv~~~~~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i~PG   63 (63)
T d1k78a1           1 GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPG   63 (63)
T ss_dssp             CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCC
T ss_pred             CcCCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCC
Confidence            58999999999999999999999999999999999999999        79999999999985

>d1k78a2 a.4.1.5 (A:82-142) 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=99.76  E-value=2.6e-20  Score=123.67  Aligned_cols=44  Identities=23%  Similarity=0.410  Sum_probs=41.4

Q ss_pred             ccCCccccccc---ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180          64 TRGSTSWAAFT---STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD  110 (129)
Q Consensus        64 ~tGS~~p~a~~---s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~  110 (129)
                      ++||+|++||+   .+|++| |++||+|||||  |||+||+||+|+++|+
T Consensus         2 IGGSKPrvaTP~V~~kI~~y-K~enP~iFaWE--IRd~Li~egiC~~~nv   48 (61)
T d1k78a2           2 IGGSKPKVATPKVVEKIAEY-KRQNPTMFAWE--IRDRLLAERVCDNDTV   48 (61)
T ss_dssp             CCCCCCSSSCHHHHHHHHHH-HHHCTTCCHHH--HHHHHHHTTSSCTTTS
T ss_pred             CCCCCCCcCCHHHHHHHHHH-HhcCCcccHHH--HHHHHHHcCCCCCCCC
Confidence            68999999998   569999 99999999999  9999999999999985

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.8e-20  Score=124.18  Aligned_cols=52  Identities=29%  Similarity=0.445  Sum_probs=45.5

Q ss_pred             cCCccccccc---ccccccccccCCcchhhhhhhhhhhhhcccCCCCch--------hhhhhhhhH
Q psy2180          65 RGSTSWAAFT---STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD--------VCRKFSAEQ  119 (129)
Q Consensus        65 tGS~~p~a~~---s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~--------v~~~~~~~~  119 (129)
                      +||+|++||+   .+|++| |++||+|||||  |||+||+||+|+.+|+        ++|+..+|+
T Consensus         1 GGSKPrvaTP~V~~kI~~y-K~enP~iFaWE--IRd~Li~egiC~~~~vPSvSsInRilR~~~~~~   63 (65)
T d6paxa2           1 GGSKPRVATPEVVSKIAQY-KQECPSIFAWE--IRDRLLSEGVCTNDNIPSVSSINRVLRNLASEK   63 (65)
T ss_dssp             SCCCCSSSCHHHHHHHHHH-HHHCTTCCHHH--HHHHHHHTTSSCTTTCCCHHHHHHHHHHHHHHT
T ss_pred             CCCCcCcCCHHHHHHHHHH-HHhCCccchHH--HHHHHHHcCCCCCCCCCchHHHHHHHHHhhhhh
Confidence            6999999998   569999 99999999999  9999999999999984        455666654

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=91.18  E-value=0.027  Score=33.73  Aligned_cols=27  Identities=19%  Similarity=0.313  Sum_probs=23.9

Q ss_pred             ChHHHHHHHHHHhcCCCCCchhhhhhc
Q psy2180          32 PDSTRQKIVELAHSGARPCDISRTCSA   58 (129)
Q Consensus        32 p~~~R~kIVELa~~GvRPcdISR~L~I   58 (129)
                      +.-+|.+|.+|..+|+-|..||++|.|
T Consensus         4 ~~Id~~~V~~L~~~G~gat~IAk~lgI   30 (43)
T d1gdta1           4 RKIDRDAVLNMWQQGLGASHISKTMNI   30 (43)
T ss_dssp             CCSCHHHHHHHHHTTCCHHHHHHHHTC
T ss_pred             CccCHHHHHHHHHcCCCHHHHHHHHCC
Confidence            445689999999999999999999984

>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=84.96  E-value=0.1  Score=32.05  Aligned_cols=33  Identities=18%  Similarity=0.408  Sum_probs=27.7

Q ss_pred             CcCCCC----CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180          25 YVNGRP----LPDSTRQKIVELAHS-GARPCDISRTCS   57 (129)
Q Consensus        25 f~nGrP----Lp~~~R~kIVELa~~-GvRPcdISR~L~   57 (129)
                      +.||+|    +++++|++|.+.+.+ |-+|..+|+.|+
T Consensus        20 vLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~~Ar~Lr   57 (59)
T d1uxda_          20 VINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVAAGLR   57 (59)
T ss_dssp             HHHTCGGGTTCTTTTHHHHHHHHHHHTCCCCSCCSCSS
T ss_pred             HHcCCCCcCcCCHHHHHHHHHHHHHHCCCcCHHHHHhc
Confidence            345665    799999999999887 999999998875