Psyllid ID: psy876

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
Protein Sequence
MTILSSRKHTCINDEVLKAKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV
Secondary Structure (PSIPRED)
ccccccccccEEHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEccccccccccccccccccccccccccEEEEEcccHHHHHHHHHHcccEEEEEccccccHHHHHHHHccccccEEEccccccccccEEEEEccccEEEEEEEEcccccccEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cEEEcccccEEEcHHHHHcHHHHHHHHHHHHccccccccEEEccccccccHHHHHHccccccccHHHHcccccccccccccEEEEEEEEccHHHHHHHHHccccEEEEEccccccccHHHHHccccccEEEEcccEEcccEEEEEEEcccccccccccccccccHHHHHcccEEEEccc
Coil and Loop (DISEMBL)
mtilssrkhtcindEVLKAKENINDLCQELKEtegesnrwyrkdrtpmrgiepvvsqgphadeyqgesnrwyrkdrtpmsiKYTLHFWCLNSGLVFSDIRESARSVIltsgtlapvdsfqselgtqfpikleanhvidkdqvFIGVLGQGQKVFIGVlgqgpqniplqalykntlvgdv
Flexible Loop (DISEMBL)
mtilssrkhtcindevlkaKENINDLCQelketegesnrwyrkdrtpmrgiepvvsqgphadeyqgesnrwyrkdRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGqgpqniplqalykntlvgdv
Low Complexity Region (SEG)
MTILSSRKHTCINDEVLKAKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV
Disordered region (IsUnstruct)
**********CINDEVLK****IN*L********************************************WYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTL****
Disordered Region (DISOPRED)
*********TCINDEVLKAKENINDLCQEL*******************GIEPVVSQGP**********************KYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALY**TL****
Disordered Region (DISEMBL)
MTILSSRKHTCINDEVLKAKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV
Disordered Region (DISPRO)
MTILSSRKHTCINDEVLKAKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTILSSRKHTCIxxxxxxxxxxxxxxxxxxxxxxxxSNRWYRKDRTPMRGIEPVVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	179	2.2.26 [Sep-21-2011]
Q5SXJ3	1174	Fanconi anemia group J pr	yes	N/A	0.374	0.057	0.565	3e-18
Q3YK19	1252	Fanconi anemia group J pr	yes	N/A	0.435	0.062	0.493	7e-18
Q9BX63	1249	Fanconi anemia group J pr	yes	N/A	0.385	0.055	0.528	2e-17
Q5RE34	1302	Regulator of telomere elo	no	N/A	0.368	0.050	0.492	9e-13
Q9NZ71	1219	Regulator of telomere elo	no	N/A	0.368	0.054	0.477	5e-12
P0C928	1177	Regulator of telomere elo	no	N/A	0.368	0.056	0.417	1e-11
A4K436	1216	Regulator of telomere elo	no	N/A	0.368	0.054	0.432	2e-10
B0W9F4	978	Regulator of telomere elo	N/A	N/A	0.374	0.068	0.455	3e-10
Q5RJZ1	1274	Regulator of telomere elo	no	N/A	0.368	0.051	0.417	4e-10
Q7QEI1	991	Regulator of telomere elo	yes	N/A	0.463	0.083	0.357	9e-10

>sp|Q5SXJ3|FANCJ_MOUSE Fanconi anemia group J protein homolog OS=Mus musculus GN=Brip1 PE=2 SV=1

 Score = 91.7 bits (226), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 39/69 (56%), Positives = 51/69 (73%)

Query: 84  TLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVF 143
            L+FWCLN  + FSDI +  R+++LTSGTL+P+ SF SELG  F I+LEANHVI   QV+
Sbjct: 591 ALNFWCLNPAVAFSDINDKVRTIVLTSGTLSPLKSFSSELGVTFSIQLEANHVISNSQVW 650

Query: 144 IGVLGQGQK 152
           +G +G G K
Sbjct: 651 VGTVGSGPK 659

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the 'Fanconi anemia' pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q3YK19|FANCJ_CHICK Fanconi anemia group J protein homolog OS=Gallus gallus GN=BRIP1 PE=2 SV=1

 Score = 90.1 bits (222), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 39/79 (49%), Positives = 59/79 (74%), Gaps = 1/79 (1%)

Query: 72  YRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKL 131
           ++++    ++ + L+FWCLN  + FSD+ +  R+V+LTSGTL+P+DSF SELG +F I+L
Sbjct: 587 HKRNLRHKTVVHMLNFWCLNPAVAFSDLND-VRTVVLTSGTLSPMDSFSSELGVKFSIQL 645

Query: 132 EANHVIDKDQVFIGVLGQG 150
           EANHVI   QV++G +G G
Sbjct: 646 EANHVIRNSQVWVGTIGTG 664

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the 'Fanconi anemia' pathway of DNA repair, after FANCD2 ubiquitination. Probably not involved in the repair of DNA double-strand breaks by homologous recombination.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9BX63|FANCJ_HUMAN Fanconi anemia group J protein OS=Homo sapiens GN=BRIP1 PE=1 SV=1

 Score = 88.2 bits (217), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 51/70 (72%)

Query: 83  YTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQV 142
           + L+FWCLN  + FSDI    ++++LTSGTL+P+ SF SELG  F I+LEANH+I   QV
Sbjct: 587 HVLNFWCLNPAVAFSDINGKVQTIVLTSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQV 646

Query: 143 FIGVLGQGQK 152
           ++G +G G K
Sbjct: 647 WVGTIGSGPK 656

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the Fanconi anemia pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RE34|RTEL1_PONAB Regulator of telomere elongation helicase 1 OS=Pongo abelii GN=RTEL1 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 33/67 (49%), Positives = 47/67 (70%), Gaps = 1/67 (1%)

Query: 85  LHFWCLNSGLVFSD-IRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVF 143
           L +WC + GL   + +R+  RS+ILTSGTLAPV SF  E+   FP+ LE  H+IDK Q++
Sbjct: 454 LSYWCFSPGLSMRELVRQGVRSLILTSGTLAPVSSFALEMQIPFPVCLENPHIIDKHQIW 513

Query: 144 IGVLGQG 150
           +GV+ +G
Sbjct: 514 VGVVPRG 520

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates. Also required to regulate telomere length; probably due to its anti-recombinase function.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9NZ71|RTEL1_HUMAN Regulator of telomere elongation helicase 1 OS=Homo sapiens GN=RTEL1 PE=1 SV=2

 Score = 70.5 bits (171), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 32/67 (47%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 85  LHFWCLNSGLVFSD-IRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVF 143
           L +WC + G    + +R+  RS+ILTSGTLAPV SF  E+   FP+ LE  H+IDK Q++
Sbjct: 453 LSYWCFSPGHSMHELVRQGVRSLILTSGTLAPVSSFALEMQIPFPVCLENPHIIDKHQIW 512

Query: 144 IGVLGQG 150
           +GV+ +G
Sbjct: 513 VGVVPRG 519

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates. Also required to regulate telomere length; probably due to its anti-recombinase function.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P0C928|RTEL1_DANRE Regulator of telomere elongation helicase 1 OS=Danio rerio GN=rtel1 PE=3 SV=1

 Score = 69.3 bits (168), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 44/67 (65%), Gaps = 1/67 (1%)

Query: 85  LHFWCLNSGLVFSDI-RESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVF 143
           L +WC + G    ++ R+  R +ILTSGTL+P+ SF  E+   FP+ LE  HVI +DQ+F
Sbjct: 452 LSYWCFSPGFSMQELLRQEVRCIILTSGTLSPLSSFTCEMQIPFPVSLENPHVIQRDQIF 511

Query: 144 IGVLGQG 150
           + ++ +G
Sbjct: 512 VSIIEKG 518

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates. Also required to regulate telomere length; probably due to its anti-recombinase function.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|A4K436|RTEL1_BOVIN Regulator of telomere elongation helicase 1 OS=Bos taurus GN=RTEL1 PE=2 SV=1

 Score = 65.5 bits (158), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 85  LHFWCLNSGLVFSD-IRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVF 143
           L +WC + G    + +R+  R++ILTSGTLAP+ SF  E+   FP+ LE  HVI++ Q++
Sbjct: 451 LSYWCFSPGHSMRELVRQGVRTLILTSGTLAPMASFSLEMQIPFPVCLENPHVINQHQIW 510

Query: 144 IGVLGQG 150
           +GV+ +G
Sbjct: 511 VGVIPKG 517

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates. Also required to regulate telomere length; probably due to its anti-recombinase function.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|B0W9F4|RTEL1_CULQU Regulator of telomere elongation helicase 1 homolog OS=Culex quinquefasciatus GN=CPIJ003765 PE=3 SV=1

 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 84  TLHFWCLNSGLVFSDIR-ESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQV 142
            ++FWC N G     +   +ARS+ILTSGTLAP+    SEL     +KLE  H+ID  QV
Sbjct: 463 VINFWCFNPGFGMRQLLGRNARSIILTSGTLAPLKPLISELDIPIAVKLENPHIIDGSQV 522

Query: 143 FIGVLGQG 150
            + ++GQG
Sbjct: 523 CVKIVGQG 530

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates.

Culex quinquefasciatus (taxid: 7176)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q5RJZ1|RTEL1_RAT Regulator of telomere elongation helicase 1 OS=Rattus norvegicus GN=Rtel1 PE=2 SV=2

 Score = 64.3 bits (155), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 85  LHFWCLNSGLVFSD-IRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVF 143
           L +WC +      + +++  R++ILTSGTLAP+ SF  E+   FP+ LE  H+IDK+Q++
Sbjct: 453 LSYWCFSPSHSMRELVQQGVRTLILTSGTLAPLSSFALEMQIPFPVCLENPHIIDKNQLW 512

Query: 144 IGVLGQG 150
           +GV+ +G
Sbjct: 513 VGVIPRG 519

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates. Also required to regulate telomere length; probably due to its anti-recombinase function.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q7QEI1|RTEL1_ANOGA Regulator of telomere elongation helicase 1 homolog OS=Anopheles gambiae GN=AGAP000634 PE=3 SV=5

 Score = 63.2 bits (152), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 49/95 (51%), Gaps = 12/95 (12%)

Query: 80  SIKYTLHFWCLNSGLVFSDIRESA-RSVILTSGTLAPVDSFQSELGTQFPIKLEANHVID 138
           S    ++FWC N G     + +S  RS+ILTSGTLAP+  F SEL     + LE  H+I 
Sbjct: 450 STSKVINFWCFNPGFGMRQLVDSGTRSIILTSGTLAPLKPFISELSLPVAVSLENPHIIA 509

Query: 139 KDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKN 173
           + Q           V++ V+  GP  + L + +KN
Sbjct: 510 RSQ-----------VYVKVITHGPDRVELNSSFKN 533

ATP-dependent DNA helicase required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by promoting the disassembly of D loop recombination intermediates.

Anopheles gambiae (taxid: 7165)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	179
405960555	1410	Fanconi anemia group J protein [Crassost	0.603	0.076	0.433	2e-19
148232300	713	BRCA1 interacting protein C-terminal hel	0.480	0.120	0.505	2e-19
47204868	529	unnamed protein product [Tetraodon nigro	0.513	0.173	0.484	6e-19
47224934	862	unnamed protein product [Tetraodon nigro	0.513	0.106	0.484	7e-19
47214240	204	unnamed protein product [Tetraodon nigro	0.513	0.450	0.484	7e-19
160333450	1217	BRCA1 interacting protein C-terminal hel	0.508	0.074	0.489	9e-19
301608630	1229	PREDICTED: Fanconi anemia group J protei	0.368	0.053	0.6	9e-19
410928893	1109	PREDICTED: Fanconi anemia group J protei	0.513	0.082	0.494	3e-18
301094332	988	conserved hypothetical protein [Phytopht	0.424	0.076	0.523	4e-18
348687642	1025	hypothetical protein PHYSODRAFT_554000 [	0.430	0.075	0.517	4e-18

>gi|405960555|gb|EKC26471.1| Fanconi anemia group J protein [Crassostrea gigas]

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 52/120 (43%), Positives = 76/120 (63%), Gaps = 12/120 (10%)

Query: 54  VVSQGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTL 113
           V ++ P+ D+    S R         + + TL+FWC+N G+ FSD+    RSV+LTSGTL
Sbjct: 501 VYTRNPNTDDMWLNSKRRRGGQSMIPTTQLTLNFWCMNPGVAFSDL-SVCRSVVLTSGTL 559

Query: 114 APVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKN 173
           +P++SF+SELG  FPIKLEANHVI+  Q           V++G +GQGP+   L+A+Y++
Sbjct: 560 SPINSFESELGVPFPIKLEANHVIEDKQ-----------VWVGAVGQGPRGGTLEAVYRS 608

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|148232300|ref|NP_001083272.1| BRCA1 interacting protein C-terminal helicase 1 [Xenopus laevis] gi|37747678|gb|AAH60014.1| MGC68622 protein [Xenopus laevis]

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/91 (50%), Positives = 66/91 (72%), Gaps = 5/91 (5%)

Query: 67  ESNRWYRKDRTPMSIK-----YTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQS 121
           + N ++ + R+  SI+     YTL+FWCLN  + FSD+  +AR+++LTSGTL+P+ SF S
Sbjct: 571 DENGFFARPRSRRSIRQKIMVYTLNFWCLNPAVAFSDLSSNARTIVLTSGTLSPMGSFSS 630

Query: 122 ELGTQFPIKLEANHVIDKDQVFIGVLGQGQK 152
           ELG +F I+LEANHVI K QV++G +G G K
Sbjct: 631 ELGVKFSIQLEANHVIHKSQVWVGTVGAGPK 661

Source: Xenopus laevis

Species: Xenopus laevis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|47204868|emb|CAF94395.1| unnamed protein product [Tetraodon nigroviridis]

 Score = 99.0 bits (245), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/95 (48%), Positives = 67/95 (70%), Gaps = 3/95 (3%)

Query: 59  PHADEYQGESNRWYRKDRTPMSIK---YTLHFWCLNSGLVFSDIRESARSVILTSGTLAP 115
           P A + QG   R +++ R  + +K    T+ FWCLN  + FSD+ ++ RS++LTSGTL+P
Sbjct: 388 PDAPDAQGFFGRPHQRQRRSIRVKSEVLTVSFWCLNPAVAFSDLGDAVRSIVLTSGTLSP 447

Query: 116 VDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQG 150
           + SF SELG +F I+LEANHVI+K QV++G +G G
Sbjct: 448 MASFSSELGVKFSIQLEANHVINKSQVWVGTVGAG 482

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|47224934|emb|CAG06504.1| unnamed protein product [Tetraodon nigroviridis]

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 46/95 (48%), Positives = 67/95 (70%), Gaps = 3/95 (3%)

Query: 59  PHADEYQGESNRWYRKDRTPMSIK---YTLHFWCLNSGLVFSDIRESARSVILTSGTLAP 115
           P A + QG   R +++ R  + +K    T+ FWCLN  + FSD+ ++ RS++LTSGTL+P
Sbjct: 561 PDAPDAQGFFGRPHQRQRRSIRVKSEVLTVSFWCLNPAVAFSDLGDAVRSIVLTSGTLSP 620

Query: 116 VDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQG 150
           + SF SELG +F I+LEANHVI+K QV++G +G G
Sbjct: 621 MASFSSELGVKFSIQLEANHVINKSQVWVGTVGAG 655

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|47214240|emb|CAG12459.1| unnamed protein product [Tetraodon nigroviridis]

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 46/95 (48%), Positives = 67/95 (70%), Gaps = 3/95 (3%)

Query: 59  PHADEYQGESNRWYRKDRTPMSIK---YTLHFWCLNSGLVFSDIRESARSVILTSGTLAP 115
           P A + QG   R +++ R  + +K    T+ FWCLN  + FSD+ ++ RS++LTSGTL+P
Sbjct: 62  PDAPDAQGFFGRPHQRQRRSIRVKSEVLTVSFWCLNPAVAFSDLGDAVRSIVLTSGTLSP 121

Query: 116 VDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQG 150
           + SF SELG +F I+LEANHVI+K QV++G +G G
Sbjct: 122 MASFSSELGVKFSIQLEANHVINKSQVWVGTVGAG 156

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|160333450|ref|NP_001103766.1| BRCA1 interacting protein C-terminal helicase 1 [Danio rerio] gi|126843119|gb|ABO27623.1| Fanconi anemia J [Danio rerio]

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/92 (48%), Positives = 65/92 (70%), Gaps = 1/92 (1%)

Query: 59  PHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDS 118
           P A  +    +R  + +RT  ++ +TL FWCLN  + FSD+  + RS++LTSGTL+P+ S
Sbjct: 593 PDAQGFFARPHRRRQSNRT-KTLVHTLSFWCLNPAVAFSDLSSTVRSIVLTSGTLSPMGS 651

Query: 119 FQSELGTQFPIKLEANHVIDKDQVFIGVLGQG 150
           F SELG +F I+LEANHVI+K QV++G +G G
Sbjct: 652 FSSELGIKFSIQLEANHVINKSQVWVGTIGAG 683

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|301608630|ref|XP_002933884.1| PREDICTED: Fanconi anemia group J protein-like [Xenopus (Silurana) tropicalis]

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 42/70 (60%), Positives = 56/70 (80%)

Query: 83  YTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQV 142
           YTL+FWCLN  + FSD+  +AR+++LTSGTL+P+ SF SELG +F I+LEANHVI K QV
Sbjct: 592 YTLNFWCLNPAVAFSDLSSNARTIVLTSGTLSPMGSFSSELGVKFSIQLEANHVIHKSQV 651

Query: 143 FIGVLGQGQK 152
           ++G +G G K
Sbjct: 652 WVGTVGAGPK 661

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410928893|ref|XP_003977834.1| PREDICTED: Fanconi anemia group J protein homolog [Takifugu rubripes]

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/95 (49%), Positives = 65/95 (68%), Gaps = 3/95 (3%)

Query: 59  PHADEYQGESNRWYRKDRTPMSIK---YTLHFWCLNSGLVFSDIRESARSVILTSGTLAP 115
           P A + QG   R  ++ R  + +K    TL FWCLN  + FSD+  S +S++LTSGTL+P
Sbjct: 527 PDAPDAQGFFVRPRQRQRQSIRVKAEMLTLSFWCLNPAVAFSDLSNSLKSIVLTSGTLSP 586

Query: 116 VDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQG 150
           + SF SELG +F I+LEANHVI+K QV++G +G G
Sbjct: 587 MGSFSSELGVKFSIQLEANHVINKSQVWVGTVGAG 621

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|301094332|ref|XP_002896272.1| conserved hypothetical protein [Phytophthora infestans T30-4] gi|262109667|gb|EEY67719.1| conserved hypothetical protein [Phytophthora infestans T30-4]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/86 (52%), Positives = 58/86 (67%), Gaps = 10/86 (11%)

Query: 88  WCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVL 147
           WCLN+ + FSDI   ARSVILTSGTL+P++SF  ELG  FPI+LEANHV++         
Sbjct: 595 WCLNAAVAFSDIASQARSVILTSGTLSPMESFAGELGVDFPIRLEANHVVN--------- 645

Query: 148 GQGQKVFIGVLGQGPQNIPLQALYKN 173
              ++VFIG +  GP N+ LQ+ Y N
Sbjct: 646 -MRKQVFIGAVMHGPGNVDLQSTYNN 670

Source: Phytophthora infestans T30-4

Species: Phytophthora infestans

Genus: Phytophthora

Order: Peronosporales

Superkingdom: Eukaryota

>gi|348687642|gb|EGZ27456.1| hypothetical protein PHYSODRAFT_554000 [Phytophthora sojae]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/87 (51%), Positives = 58/87 (66%), Gaps = 10/87 (11%)

Query: 87  FWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGV 146
            WCLN+ + FSDI   ARSVILTSGTL+P++SF  ELG  FPI+LEANHV++        
Sbjct: 628 IWCLNAAVAFSDIASQARSVILTSGTLSPMESFAGELGVDFPIRLEANHVVN-------- 679

Query: 147 LGQGQKVFIGVLGQGPQNIPLQALYKN 173
               ++VFIG +  GP N+ LQ+ Y N
Sbjct: 680 --MRKQVFIGAVMHGPGNVDLQSTYNN 704

Source: Phytophthora sojae

Species: Phytophthora sojae

Genus: Phytophthora

Order: Peronosporales

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	179
ZFIN|ZDB-GENE-081107-11	1217	brip1 "BRCA1 interacting prote	0.508	0.074	0.489	1.7e-25
UNIPROTKB|E1C1X9	1249	BRIP1 "Fanconi anemia group J	0.435	0.062	0.493	6.1e-23
UNIPROTKB|Q3YK19	1252	BRIP1 "Fanconi anemia group J	0.435	0.062	0.493	6.1e-23
RGD|1307659	818	Brip1 "BRCA1 interacting prote	0.379	0.083	0.573	1.3e-22
UNIPROTKB|D4ACW5	1170	Brip1 "Protein Brip1" [Rattus	0.379	0.058	0.573	1.3e-22
UNIPROTKB|J3QSE8	994	BRIP1 "Fanconi anemia group J	0.441	0.079	0.475	2.3e-22
UNIPROTKB|Q9BX63	1249	BRIP1 "Fanconi anemia group J	0.441	0.063	0.475	4.2e-22
UNIPROTKB|J9NVZ8	1214	BRIP1 "Uncharacterized protein	0.452	0.066	0.476	5e-22
UNIPROTKB|E2RHN5	1244	BRIP1 "Uncharacterized protein	0.452	0.065	0.476	5.3e-22
MGI|MGI:2442836	1174	Brip1 "BRCA1 interacting prote	0.379	0.057	0.573	5.7e-22

ZFIN|ZDB-GENE-081107-11 brip1 "BRCA1 interacting protein C-terminal helicase 1" [Danio rerio (taxid:7955)]

 Score = 238 (88.8 bits), Expect = 1.7e-25, Sum P(2) = 1.7e-25
 Identities = 45/92 (48%), Positives = 65/92 (70%)

Query:    59 PHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDS 118
             P A  +    +R  + +RT  ++ +TL FWCLN  + FSD+  + RS++LTSGTL+P+ S
Sbjct:   593 PDAQGFFARPHRRRQSNRTK-TLVHTLSFWCLNPAVAFSDLSSTVRSIVLTSGTLSPMGS 651

Query:   119 FQSELGTQFPIKLEANHVIDKDQVFIGVLGQG 150
             F SELG +F I+LEANHVI+K QV++G +G G
Sbjct:   652 FSSELGIKFSIQLEANHVINKSQVWVGTIGAG 683

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

UNIPROTKB|E1C1X9 BRIP1 "Fanconi anemia group J protein homolog" [Gallus gallus (taxid:9031)]

 Score = 217 (81.4 bits), Expect = 6.1e-23, Sum P(2) = 6.1e-23
 Identities = 39/79 (49%), Positives = 59/79 (74%)

Query:    72 YRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKL 131
             ++++    ++ + L+FWCLN  + FSD+ +  R+V+LTSGTL+P+DSF SELG +F I+L
Sbjct:   587 HKRNLRHKTVVHMLNFWCLNPAVAFSDLND-VRTVVLTSGTLSPMDSFSSELGVKFSIQL 645

Query:   132 EANHVIDKDQVFIGVLGQG 150
             EANHVI   QV++G +G G
Sbjct:   646 EANHVIRNSQVWVGTIGTG 664

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q3YK19 BRIP1 "Fanconi anemia group J protein homolog" [Gallus gallus (taxid:9031)]

 Score = 217 (81.4 bits), Expect = 6.1e-23, Sum P(2) = 6.1e-23
 Identities = 39/79 (49%), Positives = 59/79 (74%)

Query:    72 YRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKL 131
             ++++    ++ + L+FWCLN  + FSD+ +  R+V+LTSGTL+P+DSF SELG +F I+L
Sbjct:   587 HKRNLRHKTVVHMLNFWCLNPAVAFSDLND-VRTVVLTSGTLSPMDSFSSELGVKFSIQL 645

Query:   132 EANHVIDKDQVFIGVLGQG 150
             EANHVI   QV++G +G G
Sbjct:   646 EANHVIRNSQVWVGTIGTG 664

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

RGD|1307659 Brip1 "BRCA1 interacting protein C-terminal helicase 1" [Rattus norvegicus (taxid:10116)]

 Score = 219 (82.2 bits), Expect = 1.3e-22, Sum P(2) = 1.3e-22
 Identities = 39/68 (57%), Positives = 51/68 (75%)

Query:    85 LHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFI 144
             L+FWCLN  + FSDI +  R+++LTSGTL+P+ SF SELG  F I+LEANHVI   QV++
Sbjct:   512 LNFWCLNPAVAFSDINDKVRTIVLTSGTLSPLKSFSSELGVTFNIQLEANHVISNSQVWV 571

Query:   145 GVLGQGQK 152
             G +G G K
Sbjct:   572 GTVGSGPK 579

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0008285 "negative regulation of cell proliferation" evidence=IDA

GO:0031965 "nuclear membrane" evidence=ISO

GO:0071295 "cellular response to vitamin" evidence=IEP

UNIPROTKB|D4ACW5 Brip1 "Protein Brip1" [Rattus norvegicus (taxid:10116)]

 Score = 219 (82.2 bits), Expect = 1.3e-22, Sum P(2) = 1.3e-22
 Identities = 39/68 (57%), Positives = 51/68 (75%)

Query:    85 LHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFI 144
             L+FWCLN  + FSDI +  R+++LTSGTL+P+ SF SELG  F I+LEANHVI   QV++
Sbjct:   590 LNFWCLNPAVAFSDINDKVRTIVLTSGTLSPLKSFSSELGVTFNIQLEANHVISNSQVWV 649

Query:   145 GVLGQGQK 152
             G +G G K
Sbjct:   650 GTVGSGPK 657

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|J3QSE8 BRIP1 "Fanconi anemia group J protein" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 2.3e-22, Sum P(2) = 2.3e-22
 Identities = 38/80 (47%), Positives = 56/80 (70%)

Query:    73 RKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLE 132
             ++ R   ++ + L+FWCLN  + FSDI    ++++LTSGTL+P+ SF SELG  F I+LE
Sbjct:   578 KRSRQKTAV-HVLNFWCLNPAVAFSDINGKVQTIVLTSGTLSPMKSFSSELGVTFTIQLE 636

Query:   133 ANHVIDKDQVFIGVLGQGQK 152
             ANH+I   QV++G +G G K
Sbjct:   637 ANHIIKNSQVWVGTIGSGPK 656

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q9BX63 BRIP1 "Fanconi anemia group J protein" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 4.2e-22, Sum P(2) = 4.2e-22
 Identities = 38/80 (47%), Positives = 56/80 (70%)

Query:    73 RKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLE 132
             ++ R   ++ + L+FWCLN  + FSDI    ++++LTSGTL+P+ SF SELG  F I+LE
Sbjct:   578 KRSRQKTAV-HVLNFWCLNPAVAFSDINGKVQTIVLTSGTLSPMKSFSSELGVTFTIQLE 636

Query:   133 ANHVIDKDQVFIGVLGQGQK 152
             ANH+I   QV++G +G G K
Sbjct:   637 ANHIIKNSQVWVGTIGSGPK 656

GO:0005524 "ATP binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0004003 "ATP-dependent DNA helicase activity" evidence=NAS

GO:0003677 "DNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0000077 "DNA damage checkpoint" evidence=NAS

GO:0006302 "double-strand break repair" evidence=NAS

GO:0005737 "cytoplasm" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0031965 "nuclear membrane" evidence=IDA

UNIPROTKB|J9NVZ8 BRIP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 214 (80.4 bits), Expect = 5.0e-22, Sum P(2) = 5.0e-22
 Identities = 40/84 (47%), Positives = 58/84 (69%)

Query:    69 NRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFP 128
             N+ + + +T + +   L+FWCLN  + FSDI     +++LTSGTL+P+ SF SELG  F 
Sbjct:   575 NKKHLRQKTAVHV---LNFWCLNPAVAFSDINGKVLTIVLTSGTLSPMKSFSSELGVTFT 631

Query:   129 IKLEANHVIDKDQVFIGVLGQGQK 152
             I+LEANHVI+  QV++G +G G K
Sbjct:   632 IQLEANHVINNSQVWVGTIGSGPK 655

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RHN5 BRIP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 214 (80.4 bits), Expect = 5.3e-22, Sum P(2) = 5.3e-22
 Identities = 40/84 (47%), Positives = 58/84 (69%)

Query:    69 NRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFP 128
             N+ + + +T + +   L+FWCLN  + FSDI     +++LTSGTL+P+ SF SELG  F 
Sbjct:   576 NKKHLRQKTAVHV---LNFWCLNPAVAFSDINGKVLTIVLTSGTLSPMKSFSSELGVTFT 632

Query:   129 IKLEANHVIDKDQVFIGVLGQGQK 152
             I+LEANHVI+  QV++G +G G K
Sbjct:   633 IQLEANHVINNSQVWVGTIGSGPK 656

GO:0031965 "nuclear membrane" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:2442836 Brip1 "BRCA1 interacting protein C-terminal helicase 1" [Mus musculus (taxid:10090)]

 Score = 220 (82.5 bits), Expect = 5.7e-22, Sum P(2) = 5.7e-22
 Identities = 39/68 (57%), Positives = 51/68 (75%)

Query:    85 LHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFI 144
             L+FWCLN  + FSDI +  R+++LTSGTL+P+ SF SELG  F I+LEANHVI   QV++
Sbjct:   592 LNFWCLNPAVAFSDINDKVRTIVLTSGTLSPLKSFSSELGVTFSIQLEANHVISNSQVWV 651

Query:   145 GVLGQGQK 152
             G +G G K
Sbjct:   652 GTVGSGPK 659

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	179
TIGR00604	705	TIGR00604, rad3, DNA repair helicase (rad3)	6e-11
pfam06733	168	pfam06733, DEAD_2, DEAD_2	5e-06
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	0.003

>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3)

 Score = 59.7 bits (145), Expect = 6e-11
 Identities = 21/69 (30%), Positives = 36/69 (52%)

Query: 82  KYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQ 141
              L F CL+  +    + E  RSVIL SGTL+P+D+F   LG     +    H++ ++ 
Sbjct: 420 NPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHILKREN 479

Query: 142 VFIGVLGQG 150
           +   ++ +G
Sbjct: 480 LLTLIVTRG 488

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 705

>gnl|CDD|219153 pfam06733, DEAD_2, DEAD_2

 Score = 44.3 bits (105), Expect = 5e-06
 Identities = 18/33 (54%), Positives = 23/33 (69%), Gaps = 2/33 (6%)

Query: 1  MTILSSRKHTCINDEVLKAK--ENINDLCQELK 31
            IL SRK+ CIN EV K +  E+IN+ C+ELK
Sbjct: 27 GVILGSRKNLCINPEVKKLRKGEDINEKCKELK 59

This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast. Length = 168

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 15/38 (39%), Positives = 21/38 (55%)

Query: 87  FWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELG 124
              L    +  ++     SV+LTS TL+P+DSF S LG
Sbjct: 387 LPLLVPSKLLEELFSKVASVVLTSATLSPLDSFSSLLG 424

Length = 654

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	179
KOG1133|consensus	821		99.81
KOG1132|consensus	945		99.71
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.7
KOG1131|consensus	755		99.43
KOG1132|consensus	945		98.46
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.34
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.32
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.24
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	96.75
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	96.73
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.72
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	95.7
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	93.04
KOG1133|consensus	821		92.1
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	91.91
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	91.91
KOG1131|consensus	755		82.28

>KOG1133|consensus

Probab=99.81  E-value=3.1e-20  Score=176.50  Aligned_cols=112  Identities=23%  Similarity=0.325  Sum_probs=102.3

Q ss_pred             cCCCChhhhhhhccccccccCCCC--CCCeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCC---CCCeE
Q psy876           56 SQGPHADEYQGESNRWYRKDRTPM--SIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGT---QFPIK  130 (179)
Q Consensus        56 ~~~~~~~~f~~~~~~~~~~~~~~~--~~~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~---~f~~~  130 (179)
                      ...+++.+|+..|+|...|||..-  ....+|+|++|+|+..|.+++.+||+|||++|||+|+++|.+.|+.   +....
T Consensus       496 s~l~~l~~FL~~LTn~~~dGri~~~k~~s~~lky~lL~pA~~f~evv~earavvLAGGTMeP~~e~~e~L~~~~~~~i~~  575 (821)
T KOG1133|consen  496 SPLFELSSFLGALTNNNEDGRIFYSKQGSGTLKYMLLNPAKHFAEVVLEARAVVLAGGTMEPVDELREQLFPGCPERISP  575 (821)
T ss_pred             chhHHHHHHHHHHhCCCCCCcEEEeccCCceEEEEecCcHHHHHHHHHHhheeeecCCccccHHHHHHHhcccchhhccc
Confidence            478899999999999999999753  2337899999999999999999999999999999999999999986   33477


Q ss_pred             EEeCCccCCCCceEEEeccccceeeeeeccCCCCcceEEEeccccCCC
Q psy876          131 LEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGD  178 (179)
Q Consensus       131 ls~~HVI~~enl~~~i~~~~~~~~~~vl~~G~~g~~L~~ty~~R~~~~  178 (179)
                      ++|.||||++|+++++           +.+||+|.+|.|||++|.++.
T Consensus       576 fsc~Hvip~e~il~~v-----------v~~gpsg~p~eftf~~R~s~~  612 (821)
T KOG1133|consen  576 FSCSHVIPPENILPLV-----------VSSGPSGQPLEFTFETRESPE  612 (821)
T ss_pred             eecccccChhheeeee-----------eccCCCCCceEEEeeccCChH
Confidence            9999999999999999           999999999999999999864

>KOG1132|consensus

Probab=99.71  E-value=9.8e-18  Score=162.45  Aligned_cols=85  Identities=46%  Similarity=0.882  Sum_probs=81.4

Q ss_pred             eEEEEEecChHHHHHHHHhh-cceeEEeccccCChHhHHHhhCCCCCeEEEeCCccCCCCceEEEeccccceeeeeeccC
Q psy876           83 YTLHFWCLNSGLVFSDIRES-ARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQG  161 (179)
Q Consensus        83 ~~L~~~cLdPs~~f~~I~~~-arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HVI~~enl~~~i~~~~~~~~~~vl~~G  161 (179)
                      +.++|||++|+..|.+++.+ +||||||||||+||+.|+.+||.+|+..++++|+|++.|+|+.+           +++|
T Consensus       459 ~vi~~wcf~p~~sf~d~~~k~vrsIiLtSGTLsP~~s~~~El~~~f~~~lEn~hii~~~qv~~~v-----------v~~G  527 (945)
T KOG1132|consen  459 PVINFWCFSPGYSFRDLLGKGVRSIILTSGTLSPMDSFASELGLEFKIQLENPHIINKSQVWVGV-----------VPKG  527 (945)
T ss_pred             cceeeeecCcchhHHHHhcccceeEEEecccccCchhHHHHhCCccceeeecchhccccceEEEe-----------eccC
Confidence            55899999999999999965 99999999999999999999999999999999999999999999           9999


Q ss_pred             CCCcceEEEeccccCCC
Q psy876          162 PQNIPLQALYKNTLVGD  178 (179)
Q Consensus       162 ~~g~~L~~ty~~R~~~~  178 (179)
                      |+|..|+.+|.||++++
T Consensus       528 p~~~ql~sty~nr~~~e  544 (945)
T KOG1132|consen  528 PDGAQLDSTYGNRFTPE  544 (945)
T ss_pred             CCccccccccccccCHH
Confidence            99999999999999874

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.70  E-value=1.6e-17  Score=158.51  Aligned_cols=107  Identities=22%  Similarity=0.392  Sum_probs=92.6

Q ss_pred             hhhhhhhccccccccCCC----CCCCeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCCCCCeEEEeCCc
Q psy876           61 ADEYQGESNRWYRKDRTP----MSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHV  136 (179)
Q Consensus        61 ~~~f~~~~~~~~~~~~~~----~~~~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HV  136 (179)
                      ...|+..+.+.+.+++..    ...+..|++|||||+..|+++++.+||||||||||+|+++|..+||++++..++.+|+
T Consensus       395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~ps~~~~~i~~~~~svil~SgTL~p~~~~~~~Lg~~~~~~~~~~~~  474 (705)
T TIGR00604       395 FATLVLTYTNGFLEGIEPYENKTVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHI  474 (705)
T ss_pred             HHHHHHHhccccccceeEeecCCCCCceEEEEecChHHHHHHHHHhcCEEEEecccCCcHHHHHHHhCCCCccceecCcc
Confidence            345566666655555432    2356889999999999999999999999999999999999999999988888899999


Q ss_pred             cCCCCceEEEeccccceeeeeeccCCCCcceEEEeccccCCC
Q psy876          137 IDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGD  178 (179)
Q Consensus       137 I~~enl~~~i~~~~~~~~~~vl~~G~~g~~L~~ty~~R~~~~  178 (179)
                      |+++|+++++           ++.|++|.+|+++|++|++++
T Consensus       475 ~~~~~~~~~i-----------~~~~~~~~~l~~~~~~r~~~~  505 (705)
T TIGR00604       475 LKRENLLTLI-----------VTRGSDQVPLSSTFEIRNDPS  505 (705)
T ss_pred             cchHHeEEEE-----------EeeCCCCCeeeeehhccCCHH
Confidence            9999999999           999999999999999998753

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG1131|consensus

Probab=99.43  E-value=3.5e-14  Score=132.93  Aligned_cols=110  Identities=19%  Similarity=0.314  Sum_probs=92.0

Q ss_pred             CCCChhhhhhhccccccccCCCCCCCeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCCCCCeEEEeCCc
Q psy876           57 QGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHV  136 (179)
Q Consensus        57 ~~~~~~~f~~~~~~~~~~~~~~~~~~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HV  136 (179)
                      ++....||....++.  |++++...++.|+|.|+|+|++++++++.++|||+|||||+|+++|..+|........+..-.
T Consensus       405 VstY~kGF~iIiEPf--d~~~~tv~npil~~sClDaSiAikPVf~RFqsViITSGTlspldmyPk~lnf~pv~~~s~~mt  482 (755)
T KOG1131|consen  405 VSTYSKGFSIIIEPF--DDRNPTVPNPILRFSCLDASIAIKPVFERFQSVIITSGTLSPLDMYPKILNFGPVVGASFTMT  482 (755)
T ss_pred             HHHHhcCcEEEEccc--ccCCCCCCCCeeEEeecccchhhhHHHHhhheEEEecCcccccccCchhhccCcccchhhhee
Confidence            345567888888886  888899999999999999999999999999999999999999999999998743333333333


Q ss_pred             cCCCCceEEEeccccceeeeeeccCCCCcceEEEeccccCCCC
Q psy876          137 IDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV  179 (179)
Q Consensus       137 I~~enl~~~i~~~~~~~~~~vl~~G~~g~~L~~ty~~R~~~~v  179 (179)
                      ...+-+++++           +++|.+...+...|+.|.++.|
T Consensus       483 LaR~c~~Pmi-----------itrG~Dqv~iss~fe~r~d~~V  514 (755)
T KOG1131|consen  483 LARNCLLPLI-----------ITRGNDQVAISSKFEARGDPSV  514 (755)
T ss_pred             ccccccccee-----------eecCCcchhhhhhhhhccChHH
Confidence            3334467788           9999999999999999999875

>KOG1132|consensus

Probab=98.46  E-value=6.7e-08  Score=94.94  Aligned_cols=63  Identities=25%  Similarity=0.319  Sum_probs=47.5

Q ss_pred             CceeccCCccccChhhhc--cccCHHHHHHHhhhccCccceEeccCCCCCCCCCccccCCCChhhhhh
Q psy876            1 MTILSSRKHTCINDEVLK--AKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQG   66 (179)
Q Consensus         1 mtil~sr~~tci~~~~~~--~~~~~~~~c~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~f~~   66 (179)
                      ||||+||||.||||+|.+  -+.+++.+|+++.  ++.+|.||+....++-.-.-+-+ -.++..+-.
T Consensus       139 mtVLgSReq~Cinpev~k~~~~~~~~~~C~k~~--~~~~C~f~~~~~~~sl~~~l~~~-i~DIEDLVk  203 (945)
T KOG1132|consen  139 MTVLGSREQLCINPEVKKLEGNALQNHVCKKLV--KSRSCHFYKIVEEKSLQPRLHDE-IFDIEDLVK  203 (945)
T ss_pred             eEEeecchhhccCHHHhhhhcchhhhhHHHhhc--ccccccccccccccccccccCCC-cccHHHHHH
Confidence            899999999999998887  3445689999987  78999999887777655443333 455555533

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=97.34  E-value=0.0004  Score=68.45  Aligned_cols=65  Identities=22%  Similarity=0.215  Sum_probs=50.8

Q ss_pred             CCeEEEEEecChHHHH-HHHHhhcceeEEeccccC---ChHhHHHhhCCCCC--eEEEeCCccC-CCCceEEE
Q psy876           81 IKYTLHFWCLNSGLVF-SDIRESARSVILTSGTLA---PVDSFQSELGTQFP--IKLEANHVID-KDQVFIGV  146 (179)
Q Consensus        81 ~~~~L~~~cLdPs~~f-~~I~~~arSVILtSGTLs---Pi~~f~~~Lg~~f~--~~ls~~HVI~-~enl~~~i  146 (179)
                      ....|+..++||+..+ +.++...+++|||||||+   |+++|.+.||.+-.  ..+. ++.++ ++|..+++
T Consensus       572 ~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~~~~lGl~~~~~~~~~-~spf~~~~~~~l~v  643 (850)
T TIGR01407       572 STIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLTDVHFNTIE-PTPLNYAENQRVLI  643 (850)
T ss_pred             ceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHHHHhcCCCccccceec-CCCCCHHHcCEEEe
Confidence            4567899999999777 556689999999999999   89999999998532  2333 66667 57777666

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.32  E-value=0.0006  Score=66.11  Aligned_cols=67  Identities=24%  Similarity=0.149  Sum_probs=49.8

Q ss_pred             CCCeEEEEEecChHHHHH-HHHhhcceeEEeccccCCh---HhHHHhhCCCC---CeEEEeCCccCCCCceEEE
Q psy876           80 SIKYTLHFWCLNSGLVFS-DIRESARSVILTSGTLAPV---DSFQSELGTQF---PIKLEANHVIDKDQVFIGV  146 (179)
Q Consensus        80 ~~~~~L~~~cLdPs~~f~-~I~~~arSVILtSGTLsPi---~~f~~~Lg~~f---~~~ls~~HVI~~enl~~~i  146 (179)
                      ..+..|+...+||+..+. .++..++++|||||||+|.   ++|...||++.   ...+..+..++.+|...++
T Consensus       432 ~~~~~l~~~Pl~~~~~l~~~l~~~~~~vIltSATL~~~~~f~~~~~~lGL~~~~~~~~~~~~SpF~~~~q~~l~  505 (697)
T PRK11747        432 QGDYLFHASPIRVGDQLERLLWSRAPGAVLTSATLRSLNSFDRFQEQSGLPEKDGDRFLALPSPFDYPNQGKLV  505 (697)
T ss_pred             CceEEEEEecCCHHHHHHHHHHhhCCEEEEEeeeCCCCCchHHHHHHcCCCCCCCceEEEcCCCCCHHHccEEE
Confidence            356778999999999996 5679999999999999975   67778899853   3445556666654433343

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=97.24  E-value=0.00025  Score=67.22  Aligned_cols=42  Identities=38%  Similarity=0.481  Sum_probs=39.6

Q ss_pred             EEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCC
Q psy876           84 TLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGT  125 (179)
Q Consensus        84 ~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~  125 (179)
                      .+..+|++|+...++++..++++|||||||+|+++|...++.
T Consensus       384 ~~~~~~~~~~~l~~~~~~~~~~~vl~SaTL~~~~~f~~~~~~  425 (654)
T COG1199         384 LLVLPLLVPSKLLEELFSKVASVVLTSATLSPLDSFSSLLGL  425 (654)
T ss_pred             eEEeecccHHHHHHHHHhhcCcEEEeeeeccCCCcHHHHHHH
Confidence            578999999999999999999999999999999999998876

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=96.75  E-value=0.00047  Score=54.98  Aligned_cols=44  Identities=36%  Similarity=0.710  Sum_probs=32.8

Q ss_pred             CceeccCCccccChhhhcc--ccCHHHHHHHhhhc--cCccceEeccC
Q psy876            1 MTILSSRKHTCINDEVLKA--KENINDLCQELKET--EGESNRWYRKD   44 (179)
Q Consensus         1 mtil~sr~~tci~~~~~~~--~~~~~~~c~~~~~~--~~~~c~~~~~~   44 (179)
                      |++|+||++.|+|+.+...  ..+.++.|.++.+.  ....|.||++.
T Consensus        31 ~~~l~gR~~~C~~~~v~~~~~~~~~~~~C~~l~~~~~~~~~C~~~~~~   78 (174)
T PF06733_consen   31 AVILKGRQNLCINSKVKRLANNEDINEFCRELRKSGKRKESCPYYNNF   78 (174)
T ss_dssp             EEEE--CCCC-TTCHHHTT-SHHHHHHHHHHHHHHHHCTCCSTTTTGG
T ss_pred             eeEeccccccccCchhhhhhhhhhHHHHHHHhhcccccccccchhHHH
Confidence            5799999999999998862  34678999998873  34589999876

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=96.73  E-value=0.0013  Score=63.47  Aligned_cols=45  Identities=31%  Similarity=0.462  Sum_probs=35.0

Q ss_pred             CceeccCCccccChhhhccc--cCHHHHHHHhhhc----------cCccceEeccCC
Q psy876            1 MTILSSRKHTCINDEVLKAK--ENINDLCQELKET----------EGESNRWYRKDR   45 (179)
Q Consensus         1 mtil~sr~~tci~~~~~~~~--~~~~~~c~~~~~~----------~~~~c~~~~~~~   45 (179)
                      +++|+||++.||||.|.+..  ...|+.|+++...          ++.+|.||++..
T Consensus        99 ~v~L~SR~~lCin~~v~~~~~~~~~~~~C~~l~~~~~~~~~~~~~~~~~C~yy~~~~  155 (705)
T TIGR00604        99 GLSLASRKNLCLHPEVSKERQGKVVNGKCIKLTVSKIKEQRTEKPNVESCEFYENFD  155 (705)
T ss_pred             EEEechHhhcccChHHHhhcchhhHHHHHHHHHhhhhcccccccCCCCCCCCCchhh
Confidence            35899999999999998632  2478899998652          246799998854

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=96.72  E-value=0.0043  Score=62.06  Aligned_cols=65  Identities=23%  Similarity=0.150  Sum_probs=48.9

Q ss_pred             CeEEEEEecChHHHHHHHH-hhcceeEEeccccC---ChHhHHHhhCCCC-C-eEEEeCCccCC-CCceEEE
Q psy876           82 KYTLHFWCLNSGLVFSDIR-ESARSVILTSGTLA---PVDSFQSELGTQF-P-IKLEANHVIDK-DQVFIGV  146 (179)
Q Consensus        82 ~~~L~~~cLdPs~~f~~I~-~~arSVILtSGTLs---Pi~~f~~~Lg~~f-~-~~ls~~HVI~~-enl~~~i  146 (179)
                      ...|+..++|++..+.+.+ ..++++|||||||+   ++++|...||.+. . ..+..+..++. +|..+++
T Consensus       650 ~~~l~~~pld~~~~l~~~l~~~~~~~iltSATL~~~~~f~~~~~~lGl~~~~~~~~~~~SpF~~~~q~~l~v  721 (928)
T PRK08074        650 ATRLYAQPVEVAERLADEFFAKKKSVILTSATLTVNGSFDYIIERLGLEDFYPRTLQIPSPFSYEEQAKLMI  721 (928)
T ss_pred             eEEEEEeeccHHHHHHHHHHhcCCcEEEEeeecccCCCcHHHHHhcCCCCCCccEEEeCCCCCHHHhcEEEe
Confidence            4678999999999998755 89999999999999   6777888999852 2 23444444453 5666655

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=95.70  E-value=0.022  Score=56.50  Aligned_cols=62  Identities=18%  Similarity=0.077  Sum_probs=46.2

Q ss_pred             eEEEEEecChHHHHHHHHhhcceeEEeccccC--ChHhHHHhhCCCCCeEEEeCCccCCCCceEEE
Q psy876           83 YTLHFWCLNSGLVFSDIRESARSVILTSGTLA--PVDSFQSELGTQFPIKLEANHVIDKDQVFIGV  146 (179)
Q Consensus        83 ~~L~~~cLdPs~~f~~I~~~arSVILtSGTLs--Pi~~f~~~Lg~~f~~~ls~~HVI~~enl~~~i  146 (179)
                      ..|+...++.+ .++.++...+++|||||||+  |..+|.+.||.+....++.++..+ +|...++
T Consensus       554 ~~l~~~pl~v~-~~~~~~~~~~~~i~tSATL~v~~~f~~~~~lGl~~~~~~~~~~~~~-~~~~~~i  617 (820)
T PRK07246        554 TYLNSASKAFT-HFSQLLPETCKTYFVSATLQISPRVSLADLLGFEEYLFHKIEKDKK-QDQLVVV  617 (820)
T ss_pred             eEEEeeeCcHH-HHHHHHhcCCeEEEEecccccCCCCcHHHHcCCCccceecCCCChH-HccEEEe
Confidence            46888889998 45889999999999999996  766799999986544555555433 4444443

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=93.04  E-value=0.29  Score=47.65  Aligned_cols=55  Identities=20%  Similarity=0.215  Sum_probs=44.1

Q ss_pred             eEEEEEecChHHHHHHHH-hhcceeEEeccccCC--------hHhHHHhhCCCCCeEEEeCCccC
Q psy876           83 YTLHFWCLNSGLVFSDIR-ESARSVILTSGTLAP--------VDSFQSELGTQFPIKLEANHVID  138 (179)
Q Consensus        83 ~~L~~~cLdPs~~f~~I~-~~arSVILtSGTLsP--------i~~f~~~Lg~~f~~~ls~~HVI~  138 (179)
                      +.|....+|.+..|+.++ +..+++||||+||+-        +++|+..||++.. .+.-+..++
T Consensus       350 ~~L~~~Pl~va~~l~~~~~~~~~~~I~TSATL~v~~~~~~~~F~~f~~~lGL~~~-~l~~~SPFd  413 (636)
T TIGR03117       350 PSLIVGREDLGKVMGGLWKDVTHGAIIVSATLYLPDRFGQMSCDYLKRVLSLPLS-RLDTPSPIV  413 (636)
T ss_pred             eEEEEecccHHHHHHHHHhcCCCeEEEEccccccCCcCCCcCcHHHHHhcCCCcc-ceeCCCCCC
Confidence            478888899999999887 577899999999998        7899999998543 444444445

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>KOG1133|consensus

Probab=92.10  E-value=0.081  Score=52.17  Aligned_cols=30  Identities=43%  Similarity=0.766  Sum_probs=25.9

Q ss_pred             eeccCCccccChhhhcc--ccCHHHHHHHhhh
Q psy876            3 ILSSRKHTCINDEVLKA--KENINDLCQELKE   32 (179)
Q Consensus         3 il~sr~~tci~~~~~~~--~~~~~~~c~~~~~   32 (179)
                      -|+||+.-|||+.|.++  ..-+||.|.++-.
T Consensus       224 sL~SRk~LCiNe~V~Klk~~~~iNE~Cldlq~  255 (821)
T KOG1133|consen  224 SLGSRKNLCINEDVKKLKSVDAINERCLDLQK  255 (821)
T ss_pred             eecchhhcccCHHhccccchhHHHHHHHHHHh
Confidence            48999999999999994  3469999999865

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=91.91  E-value=0.11  Score=45.30  Aligned_cols=44  Identities=27%  Similarity=0.500  Sum_probs=31.2

Q ss_pred             ceeccCCccccChhhhc--cccCHH-HHHHHhhh----------ccCccceEeccCC
Q psy876            2 TILSSRKHTCINDEVLK--AKENIN-DLCQELKE----------TEGESNRWYRKDR   45 (179)
Q Consensus         2 til~sr~~tci~~~~~~--~~~~~~-~~c~~~~~----------~~~~~c~~~~~~~   45 (179)
                      ++|.||+|.|||+.+.+  ...+.+ +.|.++..          .+..+|.||.+..
T Consensus       116 ~~l~sR~~lCin~~v~~~~~~~~~~~~~C~~l~~~~~~~~~~~~~~~~~c~~~~~~~  172 (289)
T smart00488      116 LSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLTASKARKYRYENPKVERCPFYENTE  172 (289)
T ss_pred             eEeechhhcCCChHHhhcccccchHHHHHHHHHhhccccccccccCCCCCCccchhh
Confidence            57999999999999974  122234 78998754          2345788887653

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=91.91  E-value=0.11  Score=45.30  Aligned_cols=44  Identities=27%  Similarity=0.500  Sum_probs=31.2

Q ss_pred             ceeccCCccccChhhhc--cccCHH-HHHHHhhh----------ccCccceEeccCC
Q psy876            2 TILSSRKHTCINDEVLK--AKENIN-DLCQELKE----------TEGESNRWYRKDR   45 (179)
Q Consensus         2 til~sr~~tci~~~~~~--~~~~~~-~~c~~~~~----------~~~~~c~~~~~~~   45 (179)
                      ++|.||+|.|||+.+.+  ...+.+ +.|.++..          .+..+|.||.+..
T Consensus       116 ~~l~sR~~lCin~~v~~~~~~~~~~~~~C~~l~~~~~~~~~~~~~~~~~c~~~~~~~  172 (289)
T smart00489      116 LSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLTASKARKYRYENPKVERCPFYENTE  172 (289)
T ss_pred             eEeechhhcCCChHHhhcccccchHHHHHHHHHhhccccccccccCCCCCCccchhh
Confidence            57999999999999974  122234 78998754          2345788887653

>KOG1131|consensus

Probab=82.28  E-value=0.67  Score=45.00  Aligned_cols=51  Identities=31%  Similarity=0.463  Sum_probs=39.1

Q ss_pred             eccCCccccChhhhccccC---HHHHHHHhhh----------ccCccceEeccCCCCCCCCCccc
Q psy876            4 LSSRKHTCINDEVLKAKEN---INDLCQELKE----------TEGESNRWYRKDRTPMRGIEPVV   55 (179)
Q Consensus         4 l~sr~~tci~~~~~~~~~~---~~~~c~~~~~----------~~~~~c~~~~~~~~~~~~~~~~~   55 (179)
                      |+||.--||||.|++ ..+   .+..|..+.-          .+...|.||.|=..+.+...+-+
T Consensus       109 lssRKNlCi~~~v~~-~r~g~~VD~~Cr~ltas~vr~~~~ed~~~~~C~f~en~~~~~~~lp~gv  172 (755)
T KOG1131|consen  109 LSSRKNLCIHPEVLK-ERNGNVVDAACRKLTASYVRAKLAEDPNVELCDFFENLEDKESLLPVGV  172 (755)
T ss_pred             eccccccccCHHHHH-HhcCCchhHHHHHHhHHHHHHHHhcCCCcchhhHHhhhhcccccCCccc
Confidence            899999999999998 335   7789988743          46678999999888655544333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	179
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	5e-15
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	2e-10
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	9e-09

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620

 Score = 70.9 bits (174), Expect = 5e-15
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 8/87 (9%)

Query: 61  ADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQ 120
           +D+ + +       +         +   CL+   +   ++E     I  SGTL P D + 
Sbjct: 340 SDQDEEKYAAILSPEDGG-----YMQAACLDPSGILEVLKE--SKTIHMSGTLDPFDFYS 392

Query: 121 SELGTQFPIKLEANHVIDKDQVFIGVL 147
              G + P   +   +   +  +I   
Sbjct: 393 DITGFEIPF-KKIGEIFPPENRYIAYY 418

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540

 Score = 57.7 bits (139), Expect = 2e-10
 Identities = 7/68 (10%), Positives = 16/68 (23%)

Query: 70  RWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPI 129
           ++        +   +L     +   +  D        +L SGTL    +  +        
Sbjct: 286 KFVEMKGDLYNCNGSLVKVPSDVNQLIEDALNVKTFKVLMSGTLPESLTLTNSYKIVVNE 345

Query: 130 KLEANHVI 137
                   
Sbjct: 346 SYGRGEYY 353

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551

 Score = 52.7 bits (126), Expect = 9e-09
 Identities = 18/95 (18%), Positives = 29/95 (30%), Gaps = 1/95 (1%)

Query: 60  HADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSF 119
           H        +        P S    L           + + ++  S+IL SGTL P +  
Sbjct: 272 HIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYLNLLNDNELSIILMSGTLPPREYM 331

Query: 120 QSELGTQFP-IKLEANHVIDKDQVFIGVLGQGQKV 153
           +   G +   + L+    I K          G  V
Sbjct: 332 EKVWGIKRNMLYLDVEREIQKRVSGSYECYIGVDV 366

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	179
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.98
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.74
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	86.84

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.98  E-value=5.5e-10  Score=104.12  Aligned_cols=62  Identities=18%  Similarity=0.263  Sum_probs=58.4

Q ss_pred             CeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCCCCCeEEEeCCccCCCCceEEE
Q psy876           82 KYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGV  146 (179)
Q Consensus        82 ~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HVI~~enl~~~i  146 (179)
                      +..|+++||||+..|+ ++ .+++||||||||+|+++|.++||++ ...++.+|+++.+|..+++
T Consensus       356 ~~~l~~~~l~~~~~l~-~~-~~~~~il~SaTL~p~~~~~~~lGl~-~~~~~~~spf~~~~~~~~~  417 (620)
T 4a15_A          356 GGYMQAACLDPSGILE-VL-KESKTIHMSGTLDPFDFYSDITGFE-IPFKKIGEIFPPENRYIAY  417 (620)
T ss_dssp             GCEEEEEECCTHHHHG-GG-GGSEEEEEESSCCSHHHHHHHHCCC-CCEEECCCCSCGGGEEEEE
T ss_pred             CcEEEEEECCHHHHHH-HH-hCCeEEEEccCCCcHHHHHHHhCCC-ceeeecCCCCCHHHeEEEE
Confidence            4789999999999999 99 9999999999999999999999998 7889999999999988776

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.74  E-value=5e-09  Score=95.50  Aligned_cols=61  Identities=18%  Similarity=0.193  Sum_probs=54.1

Q ss_pred             EEEEEecChHHHHHHHHhhc-ceeEEeccccCChHhHHHhhCCCCCe-----EEEeCCccCCCCceEEE
Q psy876           84 TLHFWCLNSGLVFSDIRESA-RSVILTSGTLAPVDSFQSELGTQFPI-----KLEANHVIDKDQVFIGV  146 (179)
Q Consensus        84 ~L~~~cLdPs~~f~~I~~~a-rSVILtSGTLsPi~~f~~~Lg~~f~~-----~ls~~HVI~~enl~~~i  146 (179)
                      .|+++||||+..|+ +++++ +++|||||||+|+++|.++||++++.     .++.+|++ ++|..+++
T Consensus       296 ~l~~~pl~~~~~l~-~~~~~~~svIltSaTL~~~~~~~~~lGl~~~~~~~~~~~~~~spf-~~~~~l~v  362 (551)
T 3crv_A          296 RLVIKNPEISYYLN-LLNDNELSIILMSGTLPPREYMEKVWGIKRNMLYLDVEREIQKRV-SGSYECYI  362 (551)
T ss_dssp             EEEEECCCTHHHHG-GGGCTTCEEEEEESSCCCHHHHHHTSCCCSCEEEEEHHHHTTSCC-SCEEEEEE
T ss_pred             EEEEEECCHHHHHH-HHhccCceEEEEeeCCCcHHHHHHHhCCCCccccccceeecCCcC-CCceEEEE
Confidence            89999999999999 88999 99999999999999999999997543     45678888 88887766

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=86.84  E-value=0.21  Score=45.13  Aligned_cols=26  Identities=35%  Similarity=0.245  Sum_probs=19.4

Q ss_pred             cChHHHHHHHHhhccee----EEeccccCCh
Q psy876           90 LNSGLVFSDIRESARSV----ILTSGTLAPV  116 (179)
Q Consensus        90 LdPs~~f~~I~~~arSV----ILtSGTLsPi  116 (179)
                      ++|+..+..+. +++++    |||||||+|+
T Consensus       303 ~~P~~~~~~l~-~~~~~~~~~IltSATL~p~  332 (540)
T 2vl7_A          303 KVPSDVNQLIE-DALNVKTFKVLMSGTLPES  332 (540)
T ss_dssp             EECSCHHHHHH-HHTCCSSCEEEEESSCCTT
T ss_pred             EehHHHHHHHH-HhcCccCCeEEEcccCCCC
Confidence            78877665444 44675    9999999994

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00