Psyllid ID: psy6808

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130--
Protein Sequence
MLTSPTHWCNSTVHFWPFTSPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCTEWD
Secondary Structure (PSIPRED)
ccccccccccccEEEEcccccHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHcccccccccccccccHHHHHHHHccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEccccccccHHHHccccHHHHHHHcccccccEHHHcccccHHHHHHHHHccccEHccccccccccHHHHEEEEcccccccccEEEEHHccHHcccccccccccccccccEcccccccc
Coil and Loop (DISEMBL)
mltspthwcnstvhfwpftsptqelakmstsqkhqnfvsepmgekpvtelaGVGDVLGkrleskgfdksinpqmfpdpdieEKVLlfknpnslpipigvevlgytkiknnksrypyldygcteihntctewd
Flexible Loop (DISEMBL)
mltspthwcnstvhFWPFTSPTQELAKMSTSQKHQNFvsepmgekpvtELAGVGDVLGKRLEskgfdksinpqmfPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIknnksrypyldygCTEIHNTCTEWD
Low Complexity Region (SEG)
MLTSPTHWCNSTVHFWPFTSPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCTEWD
Disordered region (IsUnstruct)
******HWCNSTVHFWPFT************************************************************IEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCT***
Disordered Region (DISOPRED)
***S*THWCNSTVHFWPF*******************VSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCTEW*
Disordered Region (DISEMBL)
MLTSPTHWCNSTVHFWPFTSPTQ*****************PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCTEWD
Disordered Region (DISPRO)
****PTHWCNSTVHFWPFTSPTQ*********KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCT***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLTSPTHWCNSTVHFWPFTSPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIHNTCTEWD
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	132	2.2.26 [Sep-21-2011]
Q9R1T1	89	Barrier-to-autointegratio	yes	N/A	0.318	0.471	0.738	5e-13
O54962	89	Barrier-to-autointegratio	yes	N/A	0.318	0.471	0.738	1e-12
Q5RBU9	89	Barrier-to-autointegratio	yes	N/A	0.318	0.471	0.714	2e-12
O75531	89	Barrier-to-autointegratio	yes	N/A	0.318	0.471	0.714	2e-12
P61283	89	Barrier-to-autointegratio	no	N/A	0.318	0.471	0.714	2e-12
Q6P026	90	Barrier-to-autointegratio	yes	N/A	0.310	0.455	0.756	4e-12
Q66KV4	90	Barrier-to-autointegratio	N/A	N/A	0.310	0.455	0.731	1e-11
Q5HZM3	91	Barrier-to-autointegratio	N/A	N/A	0.303	0.439	0.7	3e-11
Q6NTS2	90	Barrier-to-autointegratio	N/A	N/A	0.310	0.455	0.707	9e-11
Q9VLU0	90	Barrier-to-autointegratio	yes	N/A	0.295	0.433	0.692	8e-10

>sp|Q9R1T1|BAF_RAT Barrier-to-autointegration factor OS=Rattus norvegicus GN=Banf1 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          M+TSQKH++FV+EPMGEKPV  LAG+GD LGKRLE +GFDK+
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGDALGKRLEERGFDKA 42

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 nons-pecific dsDNA-binding sites which may promote DNA cross-bridging.
Rattus norvegicus (taxid: 10116)

>sp|O54962|BAF_MOUSE Barrier-to-autointegration factor OS=Mus musculus GN=Banf1 PE=1 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          M+TSQKH++FV+EPMGEKPV  LAG+GDVL KRLE +GFDK+
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGDVLSKRLEERGFDKA 42

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging.

Mus musculus (taxid: 10090)

>sp|Q5RBU9|BAF_PONAB Barrier-to-autointegration factor OS=Pongo abelii GN=BANF1 PE=3 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 39/42 (92%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging.

Pongo abelii (taxid: 9601)

>sp|O75531|BAF_HUMAN Barrier-to-autointegration factor OS=Homo sapiens GN=BANF1 PE=1 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 39/42 (92%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging. Exploited by retroviruses for inhibiting self-destructing autointegration of retroviral DNA, thereby promoting integration of viral DNA into the host chromosome. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD.

Homo sapiens (taxid: 9606)

>sp|P61283|BAF_BOVIN Barrier-to-autointegration factor OS=Bos taurus GN=BANF1 PE=3 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 39/42 (92%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging.

Bos taurus (taxid: 9913)

>sp|Q6P026|BAF_DANRE Barrier-to-autointegration factor OS=Danio rerio GN=banf1 PE=1 SV=1

 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 31/41 (75%), Positives = 37/41 (90%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH++FV+EPMGEK V  LAG+G+VLGKRLE KGFDK+
Sbjct: 3  STSQKHKDFVAEPMGEKSVMALAGIGEVLGKRLEEKGFDKA 43

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging.

Danio rerio (taxid: 7955)

>sp|Q66KV4|BAFB_XENLA Barrier-to-autointegration factor B OS=Xenopus laevis GN=banf1-b PE=3 SV=1

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/41 (73%), Positives = 36/41 (87%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH++FV+EPMGEK V  LAG+GD LG+RLE KGFDK+
Sbjct: 3  STSQKHRDFVAEPMGEKSVQCLAGIGDTLGRRLEEKGFDKA 43

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging.

Xenopus laevis (taxid: 8355)

>sp|Q5HZM3|BAFL_XENLA Barrier-to-autointegration factor-like protein OS=Xenopus laevis GN=banf2 PE=3 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 28/40 (70%), Positives = 37/40 (92%)

Query: 30 TSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          TSQKH++FVSEPMG+KP+T LAG+G+VLG +LE +GFDK+
Sbjct: 4  TSQKHRDFVSEPMGDKPITALAGIGEVLGGKLEEQGFDKA 43

Xenopus laevis (taxid: 8355)

>sp|Q6NTS2|BAFA_XENLA Barrier-to-autointegration factor A OS=Xenopus laevis GN=banf1-a PE=1 SV=1

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 35/41 (85%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH++FV+EPMGEK V  LAG+G+ LG RLE KGFDK+
Sbjct: 3  STSQKHRDFVAEPMGEKSVQCLAGIGEALGHRLEEKGFDKA 43

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging.

Xenopus laevis (taxid: 8355)

>sp|Q9VLU0|BAF_DROME Barrier-to-autointegration factor OS=Drosophila melanogaster GN=baf PE=3 SV=1

 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 27/39 (69%), Positives = 32/39 (82%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFD 67
           TSQKH+NFV+EPMG K VTELAG+G+ LG RL+  GFD
Sbjct: 3  GTSQKHRNFVAEPMGNKSVTELAGIGETLGGRLKDAGFD 41

Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Functions are required in both M phase and interphase of the cell cycle.

Drosophila melanogaster (taxid: 7227)

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	132
312380000	97	hypothetical protein AND_26343 [Anophele	0.310	0.422	0.853	5e-13
31211799	90	AGAP008753-PA [Anopheles gambiae str. PE	0.310	0.455	0.829	1e-12
346466001	120	hypothetical protein [Amblyomma maculatu	0.378	0.416	0.7	3e-12
156547257	90	PREDICTED: barrier-to-autointegration fa	0.310	0.455	0.829	4e-12
157119560	90	barrier-to-autointegration factor, putat	0.310	0.455	0.804	4e-12
322784997	109	hypothetical protein SINV_15557 [Solenop	0.325	0.394	0.818	4e-12
170033210	90	barrier-to-autointegration factor B [Cul	0.310	0.455	0.804	4e-12
442748555	90	Putative dna-bridging protein baf [Ixode	0.310	0.455	0.829	5e-12
307182778	90	Barrier-to-autointegration factor [Campo	0.310	0.455	0.804	5e-12
307204003	90	Barrier-to-autointegration factor [Harpe	0.310	0.455	0.780	9e-12

>gi|312380000|gb|EFR26120.1| hypothetical protein AND_26343 [Anopheles darlingi]

 Score = 79.3 bits (194), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/41 (85%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH+NFV+EPMGEKPVTELAGVGDVLGKRLE+ GFD++
Sbjct: 3  STSQKHRNFVAEPMGEKPVTELAGVGDVLGKRLEAAGFDRA 43

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|31211799|ref|XP_314872.1| AGAP008753-PA [Anopheles gambiae str. PEST] gi|21298149|gb|EAA10294.1| AGAP008753-PA [Anopheles gambiae str. PEST]

 Score = 77.8 bits (190), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/41 (82%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH+NFV+EPMGEKPVT+LAGVGDVLGKRLE+ GFD++
Sbjct: 3  STSQKHRNFVAEPMGEKPVTDLAGVGDVLGKRLEAAGFDRA 43

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346466001|gb|AEO32845.1| hypothetical protein [Amblyomma maculatum]

 Score = 76.6 bits (187), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 35/50 (70%), Positives = 44/50 (88%)

Query: 20 SPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          +P ++ A  STSQKH+NF+SEPMGEK VT+LAG+GDVLGKRL+ KGFDK+
Sbjct: 24 TPVEKPAMSSTSQKHRNFISEPMGEKDVTDLAGIGDVLGKRLKDKGFDKA 73

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156547257|ref|XP_001601780.1| PREDICTED: barrier-to-autointegration factor-like isoform 1 [Nasonia vitripennis] gi|345484674|ref|XP_003425099.1| PREDICTED: barrier-to-autointegration factor-like isoform 2 [Nasonia vitripennis]

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 34/41 (82%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH+NFV+EPMGEKPVT+LAGVG+VLGKRLE+ GFDK+
Sbjct: 3  STSQKHKNFVAEPMGEKPVTDLAGVGEVLGKRLEAAGFDKA 43

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157119560|ref|XP_001659424.1| barrier-to-autointegration factor, putative [Aedes aegypti] gi|94468590|gb|ABF18144.1| DNA-bridging protein BAF [Aedes aegypti] gi|108875292|gb|EAT39517.1| AAEL008692-PA [Aedes aegypti]

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/41 (80%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH+NFV+EPMG+KPVT+LAGVGDVLGKRL++ GFDK+
Sbjct: 3  STSQKHRNFVAEPMGDKPVTDLAGVGDVLGKRLDAAGFDKA 43

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322784997|gb|EFZ11768.1| hypothetical protein SINV_15557 [Solenopsis invicta]

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 36/44 (81%), Positives = 41/44 (93%), Gaps = 1/44 (2%)

Query: 26 AKMST-SQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDK 68
           KMST SQKH+NFV+EPMG+KPVTELAGVG+VLGKRLES GFD+
Sbjct: 5  VKMSTTSQKHRNFVAEPMGDKPVTELAGVGEVLGKRLESAGFDR 48

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170033210|ref|XP_001844471.1| barrier-to-autointegration factor B [Culex quinquefasciatus] gi|167873878|gb|EDS37261.1| barrier-to-autointegration factor B [Culex quinquefasciatus]

 Score = 76.3 bits (186), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/41 (80%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH+NFV+EPMG+KPVT+LAGVGDVLGKRL++ GFDK+
Sbjct: 3  STSQKHRNFVAEPMGDKPVTDLAGVGDVLGKRLDAAGFDKA 43

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442748555|gb|JAA66437.1| Putative dna-bridging protein baf [Ixodes ricinus]

 Score = 75.9 bits (185), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/41 (82%), Positives = 39/41 (95%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          STSQKH+NFVSEPMGEK VT+LAG+G+VLGKRLE KGFDK+
Sbjct: 3  STSQKHRNFVSEPMGEKAVTDLAGIGEVLGKRLEQKGFDKA 43

Source: Ixodes ricinus

Species: Ixodes ricinus

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307182778|gb|EFN69901.1| Barrier-to-autointegration factor [Camponotus floridanus] gi|332017164|gb|EGI57963.1| Barrier-to-autointegration factor [Acromyrmex echinatior]

 Score = 75.9 bits (185), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 33/41 (80%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          +TSQKH+NFV+EPMG+KPVTELAGVG+VLGKRLE+ GFDK+
Sbjct: 3  TTSQKHRNFVAEPMGDKPVTELAGVGEVLGKRLEAAGFDKA 43

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307204003|gb|EFN82907.1| Barrier-to-autointegration factor [Harpegnathos saltator]

 Score = 75.1 bits (183), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/41 (78%), Positives = 40/41 (97%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          +TSQKH+NFV+EPMG+KPVTELAGVG+VLGKRLE+ GFD++
Sbjct: 3  TTSQKHRNFVAEPMGDKPVTELAGVGEVLGKRLEAAGFDRA 43

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

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	132
UNIPROTKB|F1RU33	89	LOC100622671 "Uncharacterized	0.318	0.471	0.738	3.4e-13
RGD|620662	89	Banf1 "barrier to autointegrat	0.318	0.471	0.738	4.4e-13
MGI|MGI:1346330	89	Banf1 "barrier to autointegrat	0.318	0.471	0.738	7.1e-13
UNIPROTKB|P61283	89	BANF1 "Barrier-to-autointegrat	0.318	0.471	0.714	9.1e-13
UNIPROTKB|E2RGE0	89	BANF1 "Uncharacterized protein	0.318	0.471	0.714	9.1e-13
UNIPROTKB|O75531	89	BANF1 "Barrier-to-autointegrat	0.318	0.471	0.714	9.1e-13
ZFIN|ZDB-GENE-030131-6657	90	banf1 "barrier to autointegrat	0.310	0.455	0.756	2.4e-12
FB|FBgn0031977	90	baf "barrier to autointegratio	0.287	0.422	0.710	2.5e-10
WB|WBGene00000235	89	baf-1 [Caenorhabditis elegans	0.318	0.471	0.571	3.3e-08
UNIPROTKB|Q03565	89	baf-1 "Barrier-to-autointegrat	0.318	0.471	0.571	3.3e-08

UNIPROTKB|F1RU33 LOC100622671 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 31/42 (73%), Positives = 39/42 (92%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             M+TSQKH++FV+EPMGEKPV  LAG+GDVLGK+LE +GFDK+
Sbjct:     1 MTTSQKHRDFVAEPMGEKPVGSLAGIGDVLGKKLEERGFDKA 42

GO:0003677 "DNA binding" evidence=IEA

RGD|620662 Banf1 "barrier to autointegration factor 1" [Rattus norvegicus (taxid:10116)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             M+TSQKH++FV+EPMGEKPV  LAG+GD LGKRLE +GFDK+
Sbjct:     1 MTTSQKHRDFVAEPMGEKPVGSLAGIGDALGKRLEERGFDKA 42

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0015074 "DNA integration" evidence=IEA;ISO

GO:0050792 "regulation of viral reproduction" evidence=TAS

MGI|MGI:1346330 Banf1 "barrier to autointegration factor 1" [Mus musculus (taxid:10090)]

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             M+TSQKH++FV+EPMGEKPV  LAG+GDVL KRLE +GFDK+
Sbjct:     1 MTTSQKHRDFVAEPMGEKPVGSLAGIGDVLSKRLEERGFDKA 42

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

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0015074 "DNA integration" evidence=IDA

GO:0075713 "establishment of integrated proviral latency" evidence=TAS

UNIPROTKB|P61283 BANF1 "Barrier-to-autointegration factor" [Bos taurus (taxid:9913)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 30/42 (71%), Positives = 39/42 (92%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct:     1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

GO:0005737 "cytoplasm" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0015074 "DNA integration" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RGE0 BANF1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 30/42 (71%), Positives = 39/42 (92%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct:     1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

GO:0015074 "DNA integration" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|O75531 BANF1 "Barrier-to-autointegration factor" [Homo sapiens (taxid:9606)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 30/42 (71%), Positives = 39/42 (92%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct:     1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

GO:0003677 "DNA binding" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0015074 "DNA integration" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009615 "response to virus" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

ZFIN|ZDB-GENE-030131-6657 banf1 "barrier to autointegration factor 1" [Danio rerio (taxid:7955)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 31/41 (75%), Positives = 37/41 (90%)

Query:    29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             STSQKH++FV+EPMGEK V  LAG+G+VLGKRLE KGFDK+
Sbjct:     3 STSQKHKDFVAEPMGEKSVMALAGIGEVLGKRLEEKGFDKA 43

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

FB|FBgn0031977 baf "barrier to autointegration factor" [Drosophila melanogaster (taxid:7227)]

 Score = 146 (56.5 bits), Expect = 2.5e-10, P = 2.5e-10
 Identities = 27/38 (71%), Positives = 32/38 (84%)

Query:    30 TSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFD 67
             TSQKH+NFV+EPMG K VTELAG+G+ LG RL+  GFD
Sbjct:     4 TSQKHRNFVAEPMGNKSVTELAGIGETLGGRLKDAGFD 41

GO:0003677 "DNA binding" evidence=IEA;NAS

GO:0005634 "nucleus" evidence=NAS

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005635 "nuclear envelope" evidence=IDA

GO:0030717 "karyosome formation" evidence=IMP

WB|WBGene00000235 baf-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 24/42 (57%), Positives = 30/42 (71%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             MSTS KH+ FV EPMG+K VT +AG+G   G +L   GFDK+
Sbjct:     1 MSTSVKHREFVGEPMGDKEVTCIAGIGPTYGTKLTDAGFDKA 42

GO:0003677 "DNA binding" evidence=IEA

GO:0010171 "body morphogenesis" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IGI;IMP

GO:0006997 "nucleus organization" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0007059 "chromosome segregation" evidence=IMP

GO:0051276 "chromosome organization" evidence=IMP

GO:0005635 "nuclear envelope" evidence=IDA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0000793 "condensed chromosome" evidence=IDA

GO:0000779 "condensed chromosome, centromeric region" evidence=IDA

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

GO:0042802 "identical protein binding" evidence=ISS

GO:0010165 "response to X-ray" evidence=IGI;IMP

UNIPROTKB|Q03565 baf-1 "Barrier-to-autointegration factor 1" [Caenorhabditis elegans (taxid:6239)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 24/42 (57%), Positives = 30/42 (71%)

Query:    28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
             MSTS KH+ FV EPMG+K VT +AG+G   G +L   GFDK+
Sbjct:     1 MSTSVKHREFVGEPMGDKEVTCIAGIGPTYGTKLTDAGFDKA 42

GO:0005515 "protein binding" evidence=IPI

---

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)
Q5RBU9	BAF_PONAB	No assigned EC number	0.7142	0.3181	0.4719	yes	N/A
O54962	BAF_MOUSE	No assigned EC number	0.7380	0.3181	0.4719	yes	N/A
O75531	BAF_HUMAN	No assigned EC number	0.7142	0.3181	0.4719	yes	N/A
Q9VLU0	BAF_DROME	No assigned EC number	0.6923	0.2954	0.4333	yes	N/A
Q6P026	BAF_DANRE	No assigned EC number	0.7560	0.3106	0.4555	yes	N/A
Q9R1T1	BAF_RAT	No assigned EC number	0.7380	0.3181	0.4719	yes	N/A
Q03565	BAF1_CAEEL	No assigned EC number	0.5714	0.3181	0.4719	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	132
smart01023	87	smart01023, BAF, Barrier to autointegration factor	1e-21
pfam02961	89	pfam02961, BAF, Barrier to autointegration factor	2e-21

>gnl|CDD|198091 smart01023, BAF, Barrier to autointegration factor

 Score = 81.6 bits (202), Expect = 1e-21
 Identities = 32/41 (78%), Positives = 38/41 (92%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          +TSQKH+NFV EPMGEKPVT LAG+G+VLG RLE+KGFDK+
Sbjct: 1  TTSQKHRNFVGEPMGEKPVTALAGIGEVLGGRLETKGFDKA 41

Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organization, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA. Length = 87

>gnl|CDD|111809 pfam02961, BAF, Barrier to autointegration factor

 Score = 81.3 bits (201), Expect = 2e-21
 Identities = 32/41 (78%), Positives = 38/41 (92%)

Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          +TSQKH+NFVSEPMG+KPVT LAG+G+VLG RLE KGFDK+
Sbjct: 3  TTSQKHRNFVSEPMGDKPVTALAGIGEVLGGRLEDKGFDKA 43

The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration. Length = 89

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	132
PF02961	89	BAF: Barrier to autointegration factor; InterPro:	99.96
KOG4233|consensus	90		99.92
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.33
PF11798	32	IMS_HHH: IMS family HHH motif; InterPro: IPR024728	96.03
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	91.89
TIGR02236	310	recomb_radA DNA repair and recombination protein R	90.58
cd00424	343	PolY Y-family of DNA polymerases. Y-family DNA pol	88.73
PRK02406	343	DNA polymerase IV; Validated	88.55
cd01703	379	PolY_Pol_iota DNA Polymerase iota. Pol iota, also	87.85
PRK03352	346	DNA polymerase IV; Validated	87.82
COG3743	133	Uncharacterized conserved protein [Function unknow	87.65
cd01701	404	PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesi	85.91
PRK03858	396	DNA polymerase IV; Validated	85.53
cd01700	344	PolY_Pol_V_umuC umuC subunit of DNA Polymerase V.	85.33
cd03586	334	PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV,	84.22
PRK03609	422	umuC DNA polymerase V subunit UmuC; Reviewed	82.37
PRK03103	409	DNA polymerase IV; Reviewed	80.77
PRK12311	326	rpsB 30S ribosomal protein S2/unknown domain fusio	80.18
PRK02794	419	DNA polymerase IV; Provisional	80.08

>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []

Probab=99.96  E-value=2.4e-30  Score=185.87  Aligned_cols=47  Identities=74%  Similarity=1.066  Sum_probs=35.5

Q ss_pred             cccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceee
Q psy6808          27 KMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQ   73 (132)
Q Consensus        27 MstTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl   73 (132)
                      ||+|||||||||+||||||+|++|||||++||+||+++|||||||||
T Consensus         1 MsttSqKhr~Fv~EPMGeK~V~~laGIG~~lg~~L~~~GfdKAy~vL   47 (89)
T PF02961_consen    1 MSTTSQKHRNFVSEPMGEKPVTELAGIGPVLGKRLEEKGFDKAYVVL   47 (89)
T ss_dssp             ---S-HHHHHHTTS--TT-BGGGSTT--HHHHHHHHHTT--BHHHHH
T ss_pred             CCccCHHHHHHhcCccCCCCccccCCcCHHHHHHHHHCCCcHHHHHh
Confidence            89999999999999999999999999999999999999999999996

BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.

>KOG4233|consensus

Probab=99.92  E-value=2.6e-26  Score=166.23  Aligned_cols=47  Identities=55%  Similarity=0.793  Sum_probs=45.8

Q ss_pred             cccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceee
Q psy6808          27 KMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQ   73 (132)
Q Consensus        27 MstTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl   73 (132)
                      |+.||||||+||+||||||+|++|||||++||.+|.++||||||+|+
T Consensus         1 Ms~tS~khR~FvaEPmGeK~V~~laGIg~~lg~~L~~~GfdkAYvll   47 (90)
T KOG4233|consen    1 MSNTSQKHRAFVAEPMGEKDVTWLAGIGETLGIKLVDAGFDKAYVLL   47 (90)
T ss_pred             CCccCHHHHHHhcCccCCCcceeeccccHHhhhhHHhccccHHHHHH
Confidence            78899999999999999999999999999999999999999999986

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.33  E-value=0.0013  Score=52.41  Aligned_cols=43  Identities=28%  Similarity=0.479  Sum_probs=37.4

Q ss_pred             CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808          40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEE   82 (132)
Q Consensus        40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~   82 (132)
                      |-|+..++.++||||++++++|.+.||..+-.++.....++++
T Consensus         1 ~~~~~~~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~   43 (317)
T PRK04301          1 EKMKEKDLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSE   43 (317)
T ss_pred             CCcccccHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHH
Confidence            5699999999999999999999999999999998875545433

>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []

Probab=96.03  E-value=0.0043  Score=36.52  Aligned_cols=23  Identities=26%  Similarity=0.554  Sum_probs=19.1

Q ss_pred             CCCccccCCCchHHHHhHHhcCC
Q psy6808          44 EKPVTELAGVGDVLGKRLESKGF   66 (132)
Q Consensus        44 EK~Vt~LAGIGpvLGkrLeekGF   66 (132)
                      +-+|++++|||+..+++|++.|.
T Consensus        10 ~lpi~~~~GIG~kt~~kL~~~GI   32 (32)
T PF11798_consen   10 PLPIRKFWGIGKKTAKKLNKLGI   32 (32)
T ss_dssp             CSBGGGSTTS-HHHHHHHHCTT-
T ss_pred             cCCHHhhCCccHHHHHHHHHccC
Confidence            34999999999999999999873

This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=91.89  E-value=0.092  Score=33.11  Aligned_cols=28  Identities=14%  Similarity=0.262  Sum_probs=23.2

Q ss_pred             ccccCCCchHHHHhHHhcCCCccceeee
Q psy6808          47 VTELAGVGDVLGKRLESKGFDKSINPQM   74 (132)
Q Consensus        47 Vt~LAGIGpvLGkrLeekGFDKAYvVl~   74 (132)
                      ...++|||+..+.+|.+.||.....+..
T Consensus         7 L~~I~Gig~~~a~~L~~~G~~t~~~l~~   34 (60)
T PF14520_consen    7 LLSIPGIGPKRAEKLYEAGIKTLEDLAN   34 (60)
T ss_dssp             HHTSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred             hccCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence            3578999999999999999987655543

...

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=90.58  E-value=0.098  Score=41.19  Aligned_cols=36  Identities=22%  Similarity=0.442  Sum_probs=30.6

Q ss_pred             ccccCCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808          47 VTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEE   82 (132)
Q Consensus        47 Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~   82 (132)
                      +.+++|||+..+++|.+.||.....++.....++.+
T Consensus         1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~   36 (310)
T TIGR02236         1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSE   36 (310)
T ss_pred             CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHh
Confidence            467999999999999999999999988876666544

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>cd00424 PolY Y-family of DNA polymerases

Probab=88.73  E-value=0.24  Score=39.84  Aligned_cols=36  Identities=31%  Similarity=0.459  Sum_probs=32.5

Q ss_pred             CCCCCCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808          41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFP   76 (132)
Q Consensus        41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~   76 (132)
                      =+..-||.+|+|||+.+.++|++.|.....+++-.+
T Consensus       169 ~L~~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~~~  204 (343)
T cd00424         169 FLSKLPLTDLPGIGAVTAKRLEAVGINPIGDLLAAS  204 (343)
T ss_pred             HHhcCChhhcCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence            356679999999999999999999999999998776

Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord

>PRK02406 DNA polymerase IV; Validated

Probab=88.55  E-value=0.13  Score=41.20  Aligned_cols=41  Identities=22%  Similarity=0.395  Sum_probs=34.8

Q ss_pred             CCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808          41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE   81 (132)
Q Consensus        41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~   81 (132)
                      -+..-||++|+|||+.++++|+..|+.....+.-.+...+.
T Consensus       164 ~L~~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~  204 (343)
T PRK02406        164 FLATLPVEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELI  204 (343)
T ss_pred             HHHcCCcchhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHH
Confidence            44567999999999999999999999999999887654443

>cd01703 PolY_Pol_iota DNA Polymerase iota

Probab=87.85  E-value=0.3  Score=41.08  Aligned_cols=35  Identities=23%  Similarity=0.409  Sum_probs=31.1

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFP   76 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~   76 (132)
                      |..-+|.+|+|||+.++++|.+.|.....++.-.+
T Consensus       169 l~~lpv~~l~GiG~~~~~kL~~~GI~tigdl~~~~  203 (379)
T cd01703         169 MDLHDLRKIPGIGYKTAAKLEAHGISSVRDLQEFS  203 (379)
T ss_pred             hccCCccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence            45678999999999999999999999988887665

Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.

>PRK03352 DNA polymerase IV; Validated

Probab=87.82  E-value=0.24  Score=39.74  Aligned_cols=39  Identities=28%  Similarity=0.476  Sum_probs=33.4

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      +.+.||.+|+|||+....+|++.|+.+..+++--+...+
T Consensus       174 L~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L  212 (346)
T PRK03352        174 MGDRPTDALWGVGPKTAKRLAALGITTVADLAAADPAEL  212 (346)
T ss_pred             HhcCCHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHH
Confidence            457899999999999999999999999999887654433

>COG3743 Uncharacterized conserved protein [Function unknown]

Probab=87.65  E-value=0.42  Score=37.07  Aligned_cols=46  Identities=24%  Similarity=0.316  Sum_probs=35.6

Q ss_pred             HhhhcCCCCCC-CccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          35 QNFVSEPMGEK-PVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        35 RnFVsEPMGEK-~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      ..++--|-+.| +.+.+-||||++.+.|.+.|.-.--|+--.-.-||
T Consensus        56 p~~~~~~~~~~DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAwt~~di  102 (133)
T COG3743          56 PAGADAPAAPKDDLTRISGIGPKLEKVLNELGIFTFAQIAAWTRADI  102 (133)
T ss_pred             cccccCCCCCcccchhhcccCHHHHHHHHHcCCccHHHHHhcCHHHH
Confidence            46788888885 99999999999999999999866555544443333

>cd01701 PolY_Rev1 DNA polymerase Rev1

Probab=85.91  E-value=0.38  Score=40.15  Aligned_cols=37  Identities=24%  Similarity=0.233  Sum_probs=33.1

Q ss_pred             CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808          40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFP   76 (132)
Q Consensus        40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~   76 (132)
                      +-|..-||++|+|||+.++++|...|+....++.-.+
T Consensus       217 ~~L~~lPv~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~  253 (404)
T cd01701         217 EFLSQLKVGDLPGVGSSLAEKLVKLFGDTCGGLELRS  253 (404)
T ss_pred             HHhhcCCHhHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence            3467779999999999999999999999999888776

Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.

>PRK03858 DNA polymerase IV; Validated

Probab=85.53  E-value=0.38  Score=39.16  Aligned_cols=36  Identities=28%  Similarity=0.464  Sum_probs=31.5

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecCC
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPD   77 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~   77 (132)
                      |..-||++|+|||+.+.++|++.|+....++.-.+.
T Consensus       170 L~~lpl~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~  205 (396)
T PRK03858        170 LHPLPVRRLWGVGPVTAAKLRAHGITTVGDVAELPE  205 (396)
T ss_pred             HhcCChhhcCCCCHHHHHHHHHhCCCcHHHHhcCCH
Confidence            456699999999999999999999999999876543

>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V

Probab=85.33  E-value=0.54  Score=37.71  Aligned_cols=41  Identities=17%  Similarity=0.230  Sum_probs=35.0

Q ss_pred             CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      +-|..-|+..|+|||+.+.++|+..|+....+++-.+..++
T Consensus       171 ~~l~~lpl~~l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L  211 (344)
T cd01700         171 KLLKILPVGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLL  211 (344)
T ss_pred             HHhccCChhhcCccCHHHHHHHHHcCCCcHHHHhcCCHHHH
Confidence            45688899999999999999999999999999887754333

umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.

>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa

Probab=84.22  E-value=0.56  Score=36.80  Aligned_cols=39  Identities=21%  Similarity=0.340  Sum_probs=33.1

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      |..-||++|+|||+.++.+|...|+.+..++.-.+...+
T Consensus       168 L~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L  206 (334)
T cd03586         168 LAPLPVRKIPGVGKVTAEKLKELGIKTIGDLAKLDVELL  206 (334)
T ss_pred             HhcCCchhhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHH
Confidence            345699999999999999999999999999887765444

Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a

>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed

Probab=82.37  E-value=0.76  Score=38.28  Aligned_cols=36  Identities=25%  Similarity=0.413  Sum_probs=31.7

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecCC
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPD   77 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~   77 (132)
                      +..-||.+|+|||+...++|+..|+....++.-.+.
T Consensus       176 L~~lPv~~l~GiG~~~~~~L~~lGi~TigdL~~~~~  211 (422)
T PRK03609        176 LSLQPVEEVWGVGRRISKKLNAMGIKTALDLADTNI  211 (422)
T ss_pred             hhcCChhhcCCccHHHHHHHHHcCCCcHHHHhcCCH
Confidence            355699999999999999999999999999887653

>PRK03103 DNA polymerase IV; Reviewed

Probab=80.77  E-value=0.51  Score=38.82  Aligned_cols=39  Identities=26%  Similarity=0.279  Sum_probs=33.0

Q ss_pred             CCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808          43 GEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE   81 (132)
Q Consensus        43 GEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~   81 (132)
                      ..-||++|+|||+.+.++|+..|+....++.-.+...+.
T Consensus       179 ~~lpi~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~  217 (409)
T PRK03103        179 WPLPVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLK  217 (409)
T ss_pred             HcCCHhhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHH
Confidence            445999999999999999999999999998877654443

>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional

Probab=80.18  E-value=0.88  Score=38.78  Aligned_cols=37  Identities=19%  Similarity=0.236  Sum_probs=33.1

Q ss_pred             CCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808          45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE   81 (132)
Q Consensus        45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~   81 (132)
                      .+.+.+.||||.+.++|.+.|+..-.|+--+.+-|++
T Consensus       263 DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~~t~~~~a  299 (326)
T PRK12311        263 DDLKKLTGVSPQIEKKLNDLGIFHFWQLAELDPDDAA  299 (326)
T ss_pred             hhhhhhccCChhhhhhhhhcCCCCHHHhhCCChhhhh
Confidence            5678899999999999999999999999888888765

>PRK02794 DNA polymerase IV; Provisional

Probab=80.08  E-value=0.86  Score=37.96  Aligned_cols=38  Identities=26%  Similarity=0.303  Sum_probs=32.5

Q ss_pred             CCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCC
Q psy6808          41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDP   78 (132)
Q Consensus        41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~   78 (132)
                      -|.+-||++|+|||+...++|+..|+....++.-.+..
T Consensus       205 ~L~~lPl~~L~GiG~~~~~~L~~~GI~tigdL~~l~~~  242 (419)
T PRK02794        205 FLAPKPVGIIWGVGPATAARLARDGIRTIGDLQRADEA  242 (419)
T ss_pred             HHhcCChhhhCCCCHHHHHHHHHhccchHHHHhhCCHH
Confidence            45566999999999999999999999999988766533

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	132
2ezz_A	89	Solution Structure Of Human Barrier-To-Autointegrat		2e-13
1ci4_A	89	The Crystal Structure Of Human Barrier-To-Autointeg		7e-12

>pdb|2EZZ|A Chain A, Solution Structure Of Human Barrier-To-Autointegration Factor Baf Nmr, Ensemble Of 20 Simulated Annealing Structures Length = 89

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 39/42 (92%)
Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKA 42

>pdb|1CI4|A Chain A, The Crystal Structure Of Human Barrier-To-Autointegration Factor (Baf) Length = 89

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 28/41 (68%), Positives = 37/41 (90%)
Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
          +TSQKH++FV+EP GEKPV  LAG+G+VLGK+LE +GFDK+
Sbjct: 2  TTSQKHRDFVAEPXGEKPVGSLAGIGEVLGKKLEERGFDKA 42

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	132
1ci4_A	89	Protein (barrier-TO-autointegration factor (BAF) )	4e-23

>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A Length = 89

 Score = 85.3 bits (211), Expect = 4e-23
 Identities = 30/41 (73%), Positives = 38/41 (92%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDK 68
          M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDK 41

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	132
1ci4_A	89	Protein (barrier-TO-autointegration factor (BAF) )	99.93
1im4_A	221	DBH; DNA polymerase PALM, thumb, fingers, helix-ha	93.32
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	92.01
4dez_A	356	POL IV 1, DNA polymerase IV 1; Y-family, transfera	91.93
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	91.09
1jx4_A	352	DNA polymerase IV (family Y); protein-DNA complex,	90.81
3bq0_A	354	POL IV, DBH, DNA polymerase IV; Y-family, lesion b	90.41
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	90.13
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	89.72
2z43_A	324	DNA repair and recombination protein RADA; archaea	89.5
4f4y_A	362	POL IV, DNA polymerase IV; Y-family polymerase, tr	87.94
3osn_A	420	DNA polymerase IOTA; hoogsteen base PAIR, protein-	87.15
3bqs_A	93	Uncharacterized protein; 10114F, NYSGXRC, PSI-2, s	87.09
2aq4_A	434	DNA repair protein REV1; polymerase, PAD, N-digit,	86.85
3gqc_A	504	DNA repair protein REV1; protein-DNA complex, DNA	84.01
1t94_A	459	Polymerase (DNA directed) kappa; replication, DNA	83.59
3pzp_A	517	DNA polymerase kappa; DNA nucleotidyltransferase,	82.25
4ecq_A	435	DNA polymerase ETA; transferase-DNA complex; HET:	80.44

>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A

Probab=99.93  E-value=6.4e-27  Score=166.92  Aligned_cols=46  Identities=65%  Similarity=1.076  Sum_probs=45.0

Q ss_pred             ccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceee
Q psy6808          28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQ   73 (132)
Q Consensus        28 stTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl   73 (132)
                      |+|||||||||+||||||+|++|||||+++|+||+++|||||||||
T Consensus         1 ~~ts~Kh~~Fv~EPmgeK~V~evpGIG~~~~~~L~~~Gf~kAy~lL   46 (89)
T 1ci4_A            1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVL   46 (89)
T ss_dssp             CCSCHHHHHHHTSCCTTCCGGGSTTCCHHHHHHHHHTTCCSHHHHH
T ss_pred             CcccHHHHHHHhCCCCCCCcccCCCcCHHHHHHHHHcCccHHHHHH
Confidence            6899999999999999999999999999999999999999999997

>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7

Probab=93.32  E-value=0.044  Score=41.29  Aligned_cols=36  Identities=28%  Similarity=0.411  Sum_probs=26.4

Q ss_pred             CCCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808          44 EKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD   79 (132)
Q Consensus        44 EK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~   79 (132)
                      .-||++|+|||+.++++|++.|+....+++-.+...
T Consensus       183 ~lpv~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~  218 (221)
T 1im4_A          183 ELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNE  218 (221)
T ss_dssp             TCBGGGSTTCCHHHHHHHHHTTCCBTTC--------
T ss_pred             hCCcccccCCCHHHHHHHHHcCCCcHHHHHCCCHHH
Confidence            358999999999999999999999999998776543

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=92.01  E-value=0.069  Score=37.97  Aligned_cols=35  Identities=29%  Similarity=0.502  Sum_probs=30.7

Q ss_pred             CCCCCccccC--CCchHHHHhHHhcCCCccceeeecC
Q psy6808          42 MGEKPVTELA--GVGDVLGKRLESKGFDKSINPQMFP   76 (132)
Q Consensus        42 MGEK~Vt~LA--GIGpvLGkrLeekGFDKAYvVl~f~   76 (132)
                      =|..+|.+|+  |||+...++|.++||...-.|.+.+
T Consensus        20 ~~~~~I~~L~~~GIg~~~i~kL~eAG~~Tve~va~a~   56 (114)
T 1b22_A           20 FGPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAP   56 (114)
T ss_dssp             SSCCCHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSB
T ss_pred             cCCccHHHHHhcCCCHHHHHHHHHcCcCcHHHHHhCC
Confidence            3445899999  9999999999999999999888776

>4dez_A POL IV 1, DNA polymerase IV 1; Y-family, transferase; HET: DNA; 2.60A {Mycobacterium smegmatis}

Probab=91.93  E-value=0.056  Score=42.33  Aligned_cols=39  Identities=26%  Similarity=0.410  Sum_probs=33.1

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      |..-||.+|+|||+.++++|++.|...+.++.-.+...+
T Consensus       175 L~~lpv~~l~GiG~~~~~~L~~~GI~Ti~dL~~~~~~~L  213 (356)
T 4dez_A          175 MGDRPPDALWGVGPKTTKKLAAMGITTVADLAVTDPSVL  213 (356)
T ss_dssp             HTTSCGGGSTTCCHHHHHHHHHTTCCSHHHHHTSCHHHH
T ss_pred             hhcCcHHHHcCCchhHHHHHHHcCCCeecccccCCHHHH
Confidence            446799999999999999999999999999876654443

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=91.09  E-value=0.061  Score=35.10  Aligned_cols=35  Identities=20%  Similarity=0.157  Sum_probs=28.2

Q ss_pred             CCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808          45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD   79 (132)
Q Consensus        45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~   79 (132)
                      .++.+|+|||+..+.+|.++||...-.|.+....+
T Consensus         7 ~~l~~L~Gi~~~~~~kL~e~Gi~TvedlA~~~~~e   41 (70)
T 1wcn_A            7 DDLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDD   41 (70)
T ss_dssp             HHHHSSTTCCHHHHHHHHTTTCCSHHHHHTSCHHH
T ss_pred             hHHHHcCCCCHHHHHHHHHcCCCcHHHHHcCCHHH
Confidence            35778999999999999999998877766654333

>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase-D complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB: 1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A* 1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A* 2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...

Probab=90.81  E-value=0.13  Score=40.16  Aligned_cols=44  Identities=14%  Similarity=0.418  Sum_probs=35.2

Q ss_pred             HHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          33 KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        33 KHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      .-+.|+.    .-||++|+|||+.++++|++.|+....++.-.+...+
T Consensus       170 ~~~~~L~----~lpv~~l~GiG~~~~~~L~~~Gi~t~~dL~~~~~~~L  213 (352)
T 1jx4_A          170 EVKRLIR----ELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKL  213 (352)
T ss_dssp             HHHHHHH----HSBGGGSTTCCHHHHHHHHTTTCCBGGGGGSSCHHHH
T ss_pred             HHHHHHH----hCCCCcccccCHHHHHHHHHcCCchHHHHHCCCHHHH
Confidence            4455554    3589999999999999999999999999987654333

>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1 e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A

Probab=90.41  E-value=0.13  Score=40.25  Aligned_cols=43  Identities=28%  Similarity=0.451  Sum_probs=34.5

Q ss_pred             HHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808          33 KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD   79 (132)
Q Consensus        33 KHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~   79 (132)
                      .-+.|+.    .-||++|+|||+.++++|++.|+....++.-.+...
T Consensus       171 ~~~~~L~----~lpv~~l~GiG~~~~~~L~~~Gi~t~~dL~~~~~~~  213 (354)
T 3bq0_A          171 EVQDFLN----ELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNE  213 (354)
T ss_dssp             GHHHHHH----HCBSTTSTTCCHHHHHHHTTTTCCBGGGGGGSCHHH
T ss_pred             HHHHHHH----hCCcccccCcCHHHHHHHHHcCCccHHHHhcCCHHH
Confidence            3445554    348999999999999999999999999998765433

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=90.13  E-value=0.11  Score=40.86  Aligned_cols=38  Identities=18%  Similarity=0.313  Sum_probs=31.6

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD   79 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~   79 (132)
                      |+..++.+||||++...++|+++||...-.+++..-.+
T Consensus        32 ~~~~~l~~l~Gi~~~~~~kL~~ag~~t~~~~~~~~~~~   69 (349)
T 1pzn_A           32 KIIRSIEDLPGVGPATAEKLREAGYDTLEAIAVASPIE   69 (349)
T ss_dssp             ---CCSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHH
T ss_pred             cccccHHHcCCCCHHHHHHHHHcCCCcHHHHHhCCHHH
Confidence            66678999999999999999999999999888876544

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=89.72  E-value=0.058  Score=40.57  Aligned_cols=35  Identities=20%  Similarity=0.309  Sum_probs=29.1

Q ss_pred             CCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808          45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD   79 (132)
Q Consensus        45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~   79 (132)
                      .++.+|+||++.++++|+++||..+-.++..+-++
T Consensus         3 ~~~~~l~gi~~~~~~kL~~~gi~t~~~~~~~~~~~   37 (322)
T 2i1q_A            3 DNLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGE   37 (322)
T ss_dssp             --CTTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHH
T ss_pred             ccHhhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHH
Confidence            47889999999999999999999998888766443

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=89.50  E-value=0.066  Score=40.91  Aligned_cols=43  Identities=14%  Similarity=0.284  Sum_probs=0.0

Q ss_pred             cCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808          39 SEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE   81 (132)
Q Consensus        39 sEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~   81 (132)
                      +++=+..++.+|+||++...++|+++||..+-.+++.+-+++-
T Consensus         6 ~~~~~~~~~~~l~g~~~~~~~~l~~~g~~t~~~~~~~~~~~l~   48 (324)
T 2z43_A            6 EQKKNIKTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLS   48 (324)
T ss_dssp             -------------------------------------------
T ss_pred             cCCCCCccHHHcCCCCHHHHHHHHHcCCCcHHHHHcCCHHHHH
Confidence            3445566899999999999999999999999999988866643

>4f4y_A POL IV, DNA polymerase IV; Y-family polymerase, transferase-DNA complex; HET: DNA DCP; 2.34A {Sulfolobus acidocaldarius} PDB: 3bq0_A* 3bq1_A* 3bq2_A* 4hyk_A* 1k1q_A 1k1s_A

Probab=87.94  E-value=0.19  Score=40.05  Aligned_cols=44  Identities=30%  Similarity=0.480  Sum_probs=35.4

Q ss_pred             HHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808          34 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE   81 (132)
Q Consensus        34 HRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~   81 (132)
                      -+.|+.    .-||++|+|||+.++++|++.|+....++.-.+...+.
T Consensus       172 ~~~~L~----~lpv~~l~GiG~~~~~~L~~~GI~Ti~dL~~~~~~~L~  215 (362)
T 4f4y_A          172 VQDFLN----ELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELE  215 (362)
T ss_dssp             HHHHHH----TCBSTTSTTCCSTTHHHHHHTTCCBGGGGTTSCHHHHH
T ss_pred             HHHHHH----hCChhhccCCCHHHHHHHHHcCCChHHHHhcCCHHHHH
Confidence            345554    34899999999999999999999999998876644443

>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 4ebc_A* 4ebd_A* ...

Probab=87.15  E-value=0.22  Score=40.80  Aligned_cols=35  Identities=26%  Similarity=0.392  Sum_probs=30.9

Q ss_pred             CccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          46 PVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        46 ~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      +|++|+|||+.++++|++.|.....+|.-++...+
T Consensus       235 pv~~l~GIG~~t~~~L~~lGI~TigdLa~~~~~~L  269 (420)
T 3osn_A          235 HIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKIL  269 (420)
T ss_dssp             SGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCHHHH
T ss_pred             cHHHccCCCHHHHHHHHHhCCCcHHHHhhCCHHHH
Confidence            59999999999999999999999999988765444

>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* 3osp_A*

Probab=86.85  E-value=0.23  Score=40.45  Aligned_cols=34  Identities=24%  Similarity=0.187  Sum_probs=30.5

Q ss_pred             CCCCCccccCCCchHHHHhHHh--cCCCccceeeec
Q psy6808          42 MGEKPVTELAGVGDVLGKRLES--KGFDKSINPQMF   75 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLee--kGFDKAYvVl~f   75 (132)
                      |..-||++|+|||+.++++|++  .|+..+.++.-.
T Consensus       238 l~~lpv~~l~GiG~~~~~~L~~~~~GI~ti~dL~~~  273 (434)
T 2aq4_A          238 WSSFKLDDLPGVGHSTLSRLESTFDSPHSLNDLRKR  273 (434)
T ss_dssp             HTTCCGGGSTTCCHHHHHHHHHHTTCCCSHHHHHHH
T ss_pred             hhcCCcccccCcCHHHHHHHHHhcCCceEHHHHHhc
Confidence            4567999999999999999999  999999888766

>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA repair, DNA synthesis, binding, magnesium, metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens}

Probab=84.01  E-value=0.41  Score=40.81  Aligned_cols=43  Identities=26%  Similarity=0.419  Sum_probs=34.7

Q ss_pred             HHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          34 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        34 HRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      -+.|+.    .-||.+|+|||+.++++|++.|+..+.+|.-.+...+
T Consensus       308 ~~~~L~----~LPV~~l~GIG~~t~~kL~~lGI~TigDLa~~~~~~L  350 (504)
T 3gqc_A          308 VDDFIR----GQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKL  350 (504)
T ss_dssp             HHHHHH----HSBGGGSTTCCHHHHHHHHHTTCCBHHHHTTSCHHHH
T ss_pred             HHHHHh----cCChhHhhCcCHHHHHHHHHcCCCcHHHHHhccHHHH
Confidence            345554    3599999999999999999999999998887654444

>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*

Probab=83.59  E-value=0.4  Score=39.17  Aligned_cols=34  Identities=21%  Similarity=0.365  Sum_probs=29.6

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeeec
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMF   75 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f   75 (132)
                      |..-||++|+|||+.++++|++.|......+.-.
T Consensus       279 L~~lpv~~l~GiG~~~~~~L~~lGI~T~gdL~~~  312 (459)
T 1t94_A          279 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQ  312 (459)
T ss_dssp             HTTCBGGGCTTSCHHHHHHHHHTTCCBHHHHHHT
T ss_pred             HHcCCHHhcCCcCHHHHHHHHHcCCCcHHHHHhh
Confidence            5566899999999999999999999998877654

>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding nucleotide binding M binding, nucleus; HET: DNA TTD DTP; 3.34A {Homo sapiens}

Probab=82.25  E-value=0.48  Score=40.09  Aligned_cols=33  Identities=21%  Similarity=0.402  Sum_probs=28.9

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeee
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQM   74 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~   74 (132)
                      |..-||++|+|||+...++|++.|...+..|.-
T Consensus       335 L~~LPV~kl~GIG~~t~~~L~~lGI~TigDL~~  367 (517)
T 3pzp_A          335 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQ  367 (517)
T ss_dssp             HTTCBGGGSTTCCHHHHHHHHHTTCCBHHHHHH
T ss_pred             HhcCChhhhccccHHHHHHHHHhCCCcHHHHHh
Confidence            345689999999999999999999999888764

>4ecq_A DNA polymerase ETA; transferase-DNA complex; HET: DNA DTP; 1.50A {Homo sapiens} PDB: 3mr2_A* 3mr4_A* 3mr5_A* 3si8_A* 4dl2_A* 4dl3_A* 4dl4_A* 4dl5_A* 4dl6_A* 4dl7_A* 3mr3_A* 4ecr_A* 4ecs_A* 4ect_A* 4ecu_A* 4ecv_A* 4ecw_A* 4ecx_A* 4ecy_A* 4ecz_A* ...

Probab=80.44  E-value=0.83  Score=37.36  Aligned_cols=38  Identities=18%  Similarity=0.434  Sum_probs=32.1

Q ss_pred             CCCccccCCCchHHHHh-HHhcCCCccceeeecCCCChh
Q psy6808          44 EKPVTELAGVGDVLGKR-LESKGFDKSINPQMFPDPDIE   81 (132)
Q Consensus        44 EK~Vt~LAGIGpvLGkr-LeekGFDKAYvVl~f~~~~~~   81 (132)
                      .-||++|+|||+.++++ |+..|+..+.++.-.+...+.
T Consensus       252 ~lpv~~l~GiG~~~~~~lL~~lGI~TigdLa~~~~~~L~  290 (435)
T 4ecq_A          252 QMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQ  290 (435)
T ss_dssp             TCBGGGSTTCSSHHHHHHHHHHTCCBGGGGGGSCHHHHH
T ss_pred             hCCHHHhcCCCHHHHHHHHHHcCCCcHHHHhhCCHHHHH
Confidence            45999999999999877 899999999999887655554

---

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	132
d1ci4a_	89	a.60.5.1 (A:) Barrier-to-autointegration factor, B	1e-24

>d1ci4a_ a.60.5.1 (A:) Barrier-to-autointegration factor, BAF {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: All alpha proteins
fold: SAM domain-like
superfamily: Barrier-to-autointegration factor, BAF
family: Barrier-to-autointegration factor, BAF
domain: Barrier-to-autointegration factor, BAF
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 88.2 bits (219), Expect = 1e-24
 Identities = 30/41 (73%), Positives = 38/41 (92%)

Query: 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDK 68
          M+TSQKH++FV+EPMGEKPV  LAG+G+VLGK+LE +GFDK
Sbjct: 1  MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDK 41

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	132
d1ci4a_	89	Barrier-to-autointegration factor, BAF {Human (Hom	99.95
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	96.0
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	95.85
d1gm5a2	180	RecG "wedge" domain {Thermotoga maritima [TaxId: 2	95.49
d1jx4a2	240	DinB homolog (DBH) {Archaeon Sulfolobus solfataric	93.96
d1zeta2	273	DNA polymerase iota {Human (Homo sapiens) [TaxId:	93.8
d1im4a_	209	DinB homolog (DBH) {Archaeon Sulfolobus solfataric	93.6
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	90.56
d1t94a2	333	DNA polymerase kappa {Human (Homo sapiens) [TaxId:	90.45
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	83.58

>d1ci4a_ a.60.5.1 (A:) Barrier-to-autointegration factor, BAF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Barrier-to-autointegration factor, BAF
family: Barrier-to-autointegration factor, BAF
domain: Barrier-to-autointegration factor, BAF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=7e-30  Score=181.26  Aligned_cols=46  Identities=65%  Similarity=1.076  Sum_probs=45.1

Q ss_pred             ccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceee
Q psy6808          28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQ   73 (132)
Q Consensus        28 stTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl   73 (132)
                      ||||||||||||||||||+|++|||||++||+||+++||||||+||
T Consensus         1 mtTSqKhr~FvsEPMG~K~V~~l~GIG~~lg~~L~~kGfdKAy~vL   46 (89)
T d1ci4a_           1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVL   46 (89)
T ss_dssp             CCSCHHHHHHHTSCCTTCCGGGSTTCCHHHHHHHHHTTCCSHHHHH
T ss_pred             CcccHHHHHHhcCCCCCCcccccCCccHHHHHHHHHcCccHHHHHH
Confidence            6899999999999999999999999999999999999999999997

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.00  E-value=0.0017  Score=39.69  Aligned_cols=28  Identities=25%  Similarity=0.539  Sum_probs=23.5

Q ss_pred             CCccccCCCchHHHHhHHhcCCCcccee
Q psy6808          45 KPVTELAGVGDVLGKRLESKGFDKSINP   72 (132)
Q Consensus        45 K~Vt~LAGIGpvLGkrLeekGFDKAYvV   72 (132)
                      |...++||||+..+++|.++||.-.-.|
T Consensus         1 ~~L~~i~GIG~~~a~~L~~~g~~sv~~l   28 (61)
T d1pzna1           1 RSIEDLPGVGPATAEKLREAGYDTLEAI   28 (61)
T ss_dssp             CCSSCCTTCCHHHHHHHHTTTCCSHHHH
T ss_pred             CccccCCCCCHHHHHHHHHhcCCCHHHH
Confidence            4678999999999999999999765443

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.85  E-value=0.0019  Score=39.58  Aligned_cols=26  Identities=27%  Similarity=0.456  Sum_probs=22.1

Q ss_pred             cccCCCchHHHHhHHhcCCCccceee
Q psy6808          48 TELAGVGDVLGKRLESKGFDKSINPQ   73 (132)
Q Consensus        48 t~LAGIGpvLGkrLeekGFDKAYvVl   73 (132)
                      +++||||+..+++|.++||.-.-.|.
T Consensus         2 ~~IpGIG~~~a~~L~~~G~~tv~~l~   27 (60)
T d2i1qa1           2 TDLPGVGPSTAEKLVEAGYIDFMKIA   27 (60)
T ss_dssp             TTSTTCCHHHHHHHHHHTCCSHHHHH
T ss_pred             CCCCCCCHHHHHHHHHccCCCHHHHH
Confidence            68999999999999999997655443

>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RecG "wedge" domain
domain: RecG "wedge" domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.49  E-value=0.0036  Score=42.99  Aligned_cols=39  Identities=23%  Similarity=0.275  Sum_probs=34.0

Q ss_pred             CCCccccCCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808          44 EKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEE   82 (132)
Q Consensus        44 EK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~   82 (132)
                      +.+++.|.||||..+++|++.|......+|+++--..+.
T Consensus         9 ~~~i~~lkGvGpk~~~~L~klgI~ti~DLL~~~P~~Y~D   47 (180)
T d1gm5a2           9 STDIQYAKGVGPNRKKKLKKLGIETLRDLLEFFPRDYED   47 (180)
T ss_dssp             CCCSSSSSSCCHHHHHHHHTTTCCSSGGGTSCCCSEEEC
T ss_pred             CCChhhcCCcCHHHHHHHHHhCCCcHHHHHHhCccceee
Confidence            568999999999999999999999999999988554443

>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DinB homolog (DBH)
species: Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]

Probab=93.96  E-value=0.006  Score=44.12  Aligned_cols=45  Identities=13%  Similarity=0.421  Sum_probs=36.0

Q ss_pred             HHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          32 QKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        32 qKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      +..+.|+.    +-|+.+|+|||+.++++|+..|+..+.+++-.+...+
T Consensus       169 ~~~~~~L~----~lpl~~l~GiG~~~~~~L~~~Gi~t~gdl~~~~~~~L  213 (240)
T d1jx4a2         169 EEVKRLIR----ELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKL  213 (240)
T ss_dssp             HHHHHHHH----HSBGGGSTTCCHHHHHHHHTTTCCBGGGGGSSCHHHH
T ss_pred             cccccccc----ccchhhcCCCCHHHHHHHHHhCCCcHHHHHcCCHHHH
Confidence            34566665    4689999999999999999999999999876654333

>d1zeta2 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DNA polymerase iota
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.80  E-value=0.0052  Score=45.11  Aligned_cols=46  Identities=22%  Similarity=0.353  Sum_probs=35.5

Q ss_pred             HHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808          32 QKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI   80 (132)
Q Consensus        32 qKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~   80 (132)
                      ..-++|+..   -++|++|+|||+.++++|++.|..++.+++-.+...+
T Consensus       198 ~~~~~~l~~---l~pv~~l~GiG~~~~~~L~~~GI~ti~dl~~~~~~~L  243 (273)
T d1zeta2         198 ESCQHLIHS---LNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKIL  243 (273)
T ss_dssp             GGHHHHHTT---CSSGGGSTTCCHHHHHHHHTTTCCSHHHHHHSCHHHH
T ss_pred             hhHHHHHhc---CcchHHhcCCCHHHHHHHHHhCCCcHHHHhcCCHHHH
Confidence            344566653   1489999999999999999999999998876644333

>d1im4a_ e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DinB homolog (DBH)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.60  E-value=0.017  Score=41.37  Aligned_cols=33  Identities=33%  Similarity=0.657  Sum_probs=27.3

Q ss_pred             HHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCcc
Q psy6808          33 KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS   69 (132)
Q Consensus        33 KHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKA   69 (132)
                      ..++|+. |   -+|++|+|||+.++++|++.|...+
T Consensus       175 ~~~~~L~-~---lpi~~i~GIG~~~~~~L~~~Gi~Ti  207 (209)
T d1im4a_         175 EVQDFLN-E---LDIDEIPGIGSVLARRLNELGIQKL  207 (209)
T ss_dssp             GHHHHHH-T---CBGGGSTTCCHHHHHHHHHTTCCBT
T ss_pred             HHHHHHh-C---CCceeeCCchHHHHHHHHHcCCccc
Confidence            4556665 3   4899999999999999999998765

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.56  E-value=0.03  Score=34.80  Aligned_cols=30  Identities=20%  Similarity=0.275  Sum_probs=24.2

Q ss_pred             cCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808          50 LAGVGDVLGKRLESKGFDKSINPQMFPDPD   79 (132)
Q Consensus        50 LAGIGpvLGkrLeekGFDKAYvVl~f~~~~   79 (132)
                      ++|||+...++|.++||+..-.+.+..--|
T Consensus         8 ~~Gig~~~~~kL~~aG~~Tve~ia~~t~~~   37 (64)
T d1szpa1           8 VNGITMADVKKLRESGLHTAEAVAYAPRKD   37 (64)
T ss_dssp             CTTCCHHHHHHHHTTSCCSHHHHHHSCSHH
T ss_pred             HCCCCHHHHHHHHHcCCCcHHHHHhCCHHH
Confidence            369999999999999999877776654433

>d1t94a2 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DNA polymerase kappa
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.45  E-value=0.044  Score=42.02  Aligned_cols=33  Identities=21%  Similarity=0.402  Sum_probs=28.9

Q ss_pred             CCCCCccccCCCchHHHHhHHhcCCCccceeee
Q psy6808          42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQM   74 (132)
Q Consensus        42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~   74 (132)
                      |.+-+|++|+|||+.++++|++.|+.+...|.-
T Consensus       272 l~~lpi~~i~GiG~~~~~~L~~~gi~ti~dl~~  304 (333)
T d1t94a2         272 IKDLPIRKVSGIGKVTEKMLKALGIITCTELYQ  304 (333)
T ss_dssp             HTTCBGGGCTTSCHHHHHHHHHTTCCBHHHHHH
T ss_pred             HhCCCccccCCcCHHHHHHHHHcCCcCHHHHhc
Confidence            455689999999999999999999999888653

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.58  E-value=0.25  Score=30.95  Aligned_cols=34  Identities=29%  Similarity=0.506  Sum_probs=26.7

Q ss_pred             CCCCcccc--CCCchHHHHhHHhcCCCccceeeecC
Q psy6808          43 GEKPVTEL--AGVGDVLGKRLESKGFDKSINPQMFP   76 (132)
Q Consensus        43 GEK~Vt~L--AGIGpvLGkrLeekGFDKAYvVl~f~   76 (132)
                      |.-++..|  +|||+.-.++|.++||+-.-.++...
T Consensus         6 gp~~i~~L~~~Gig~~~i~kL~~aG~~Tv~~i~~at   41 (70)
T d1b22a_           6 GPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAP   41 (70)
T ss_dssp             SCCCHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSB
T ss_pred             CCccHHHHhhCCCCHHHHHHHHHcCcchHHHHHhCC
Confidence            34455554  69999999999999999887776653