Citrus Sinensis ID: 037283

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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
MLFSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Secondary Structure (PSIPRED)
ccHHHHHHHHHHcHHcccccccHHHHHHHcccccEEcccccccHHHHHcccccccEEcccccccccEEEEEccccccccccccEEEcccccccccEEEHHHHHHHccccccccEEEccccHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHccEEEEcccEEEEEcccEEEccccccEEEEEcccccccccccccccccccEEEEEccccccccccEEEEEccccccccEEHHHHHHHccccccccEEEEEcccccHHHHHHHHcccccc
Coil and Loop (DISEMBL)
MLFSTYYKTLSLLIRSNLNiffskqadvSIWTSSLlcrkqpgiaigrlcekcdgkcvicdsyvrpctlvrvcdecnygsfqgrcvicggvgisdayyckectqqekdrdgcpkivnlgsaktdLFYERKKYGFKKR
Flexible Loop (DISEMBL)
MLFSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTqqekdrdgcpkivnlgsaktdlfyerkkygfkkr
Low Complexity Region (SEG)
MLFSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Disordered region (IsUnstruct)
**FSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERK*******
Disordered Region (DISOPRED)
***STY*KTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYER*K******
Disordered Region (DISEMBL)
MLFSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Disordered Region (DISPRO)
MLFSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYG****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLFSTYYKTLSLLIRSNLNIFFSKQADVSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
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	136	2.2.26 [Sep-21-2011]
Q0WMV8	110	PHD finger-like domain-co	yes	no	0.75	0.927	0.970	3e-53
P0DI19	110	PHD finger-like domain-co	yes	no	0.75	0.927	0.970	3e-53
P83871	110	PHD finger-like domain-co	yes	no	0.75	0.927	0.901	2e-49
P83870	110	PHD finger-like domain-co	yes	no	0.75	0.927	0.901	2e-49
Q7RTV0	110	PHD finger-like domain-co	yes	no	0.75	0.927	0.901	2e-49
Q9VMC8	111	Uncharacterized protein C	yes	no	0.742	0.909	0.881	1e-47
Q9UTB8	117	Pre-mRNA-splicing factor	yes	no	0.713	0.829	0.680	6e-37
Q06835	107	Pre-mRNA-splicing factor	yes	no	0.705	0.897	0.567	5e-26

>sp|Q0WMV8|PHF5B_ARATH PHD finger-like domain-containing protein 5B OS=Arabidopsis thaliana GN=At1g07170 PE=2 SV=1

 Score =  206 bits (525), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Arabidopsis thaliana (taxid: 3702)

>sp|P0DI19|PHF5A_ARATH PHD finger-like domain-containing protein 5A OS=Arabidopsis thaliana GN=At2g30000 PE=2 SV=1

 Score =  206 bits (525), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Arabidopsis thaliana (taxid: 3702)

>sp|P83871|PHF5A_RAT PHD finger-like domain-containing protein 5A OS=Rattus norvegicus GN=Phf5a PE=2 SV=1

 Score =  194 bits (492), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct: 9   IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha. Also involved in pre-mRNA splicing.

Rattus norvegicus (taxid: 10116)

>sp|P83870|PHF5A_MOUSE PHD finger-like domain-containing protein 5A OS=Mus musculus GN=Phf5a PE=1 SV=1

 Score =  194 bits (492), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct: 9   IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha. Also involved in pre-mRNA splicing.

Mus musculus (taxid: 10090)

>sp|Q7RTV0|PHF5A_HUMAN PHD finger-like domain-containing protein 5A OS=Homo sapiens GN=PHF5A PE=1 SV=1

 Score =  194 bits (492), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct: 9   IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha. Also involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

>sp|Q9VMC8|PHF5_DROME Uncharacterized protein CG9548 OS=Drosophila melanogaster GN=CG9548 PE=3 SV=2

 Score =  188 bits (477), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 89/101 (88%), Positives = 96/101 (95%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           + CRKQPG+AIGRLCEK DGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct: 9   IFCRKQPGVAIGRLCEKDDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKK 135
           AYYCK CT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFK+
Sbjct: 69  AYYCKSCTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKQ 109

Drosophila melanogaster (taxid: 7227)

>sp|Q9UTB8|INI1_SCHPO Pre-mRNA-splicing factor ini1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ini1 PE=3 SV=1

 Score =  152 bits (384), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 66/97 (68%), Positives = 83/97 (85%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           +LCR+QPGI +G+LCE+CD KC ICDS+VRP TLVR+CDEC +GS Q RC+ICG  G+SD
Sbjct: 9   VLCRRQPGITVGKLCERCDEKCPICDSHVRPTTLVRICDECAFGSSQDRCIICGAPGVSD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKY 131
            YYC ECT+ E DRDGCP+++NLGS++TD FYERKK+
Sbjct: 69  CYYCSECTRMEYDRDGCPRVINLGSSRTDWFYERKKF 105

Required for pre-mRNA splicing.

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

>sp|Q06835|RDS3_YEAST Pre-mRNA-splicing factor RDS3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RDS3 PE=1 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 55/97 (56%), Positives = 72/97 (74%), Gaps = 1/97 (1%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGIS 93
           ++C KQPG+  G LCEKCDGKC ICDSYVRP   VRVC+ C++G     C+IC   VG++
Sbjct: 9   IMCLKQPGVQTGLLCEKCDGKCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVN 68

Query: 94  DAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKK 130
           DA+YC EC +  KD+DGCP+I+NLGS + D  +E+KK
Sbjct: 69  DAFYCWECCRLGKDKDGCPRILNLGSNRLDRHFEKKK 105

Required for pre-mRNA splicing. Involved in regulation of drug sensitivity and may play a role in multidrug resistance.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	136
115461126	110	Os04g0663300 [Oryza sativa Japonica Grou	0.75	0.927	0.980	1e-51
226494093	110	PHD finger-like domain-containing protei	0.75	0.927	0.970	2e-51
18390735	110	PHF5-like protein [Arabidopsis thaliana]	0.75	0.927	0.970	2e-51
255569387	110	Pre-mRNA-splicing factor ini1 [Ricinus c	0.75	0.927	0.970	3e-51
357438293	110	PHD finger-like domain-containing protei	0.75	0.927	0.970	6e-51
302794063	110	hypothetical protein SELMODRAFT_228566 [	0.75	0.927	0.960	7e-51
195618516	101	PHD finger-like domain-containing protei	0.742	1.0	0.980	7e-51
168031973	110	predicted protein [Physcomitrella patens	0.75	0.927	0.950	2e-50
195618288	110	PHD finger-like domain-containing protei	0.75	0.927	0.960	2e-50
255569385	110	Pre-mRNA-splicing factor ini1 [Ricinus c	0.75	0.927	0.960	3e-50

>gi|115461126|ref|NP_001054163.1| Os04g0663300 [Oryza sativa Japonica Group] gi|115463469|ref|NP_001055334.1| Os05g0367000 [Oryza sativa Japonica Group] gi|351720989|ref|NP_001235659.1| uncharacterized protein LOC100305969 [Glycine max] gi|224059768|ref|XP_002299987.1| predicted protein [Populus trichocarpa] gi|224103931|ref|XP_002313249.1| predicted protein [Populus trichocarpa] gi|242047572|ref|XP_002461532.1| hypothetical protein SORBIDRAFT_02g004290 [Sorghum bicolor] gi|242077540|ref|XP_002448706.1| hypothetical protein SORBIDRAFT_06g031860 [Sorghum bicolor] gi|255582664|ref|XP_002532111.1| Pre-mRNA-splicing factor ini1 [Ricinus communis] gi|356566078|ref|XP_003551262.1| PREDICTED: uncharacterized protein At1g07170/At2g30000-like isoform 1 [Glycine max] gi|356566080|ref|XP_003551263.1| PREDICTED: uncharacterized protein At1g07170/At2g30000-like isoform 2 [Glycine max] gi|356566082|ref|XP_003551264.1| PREDICTED: uncharacterized protein At1g07170/At2g30000-like isoform 3 [Glycine max] gi|357123892|ref|XP_003563641.1| PREDICTED: uncharacterized protein At1g07170/At2g30000-like [Brachypodium distachyon] gi|357166580|ref|XP_003580757.1| PREDICTED: uncharacterized protein At1g07170/At2g30000-like [Brachypodium distachyon] gi|449455024|ref|XP_004145253.1| PREDICTED: PHD finger-like domain-containing protein 5B-like [Cucumis sativus] gi|449475086|ref|XP_004154370.1| PREDICTED: PHD finger-like domain-containing protein 5B-like [Cucumis sativus] gi|449525868|ref|XP_004169938.1| PREDICTED: PHD finger-like domain-containing protein 5B-like [Cucumis sativus] gi|38346076|emb|CAE04844.2| OSJNBa0084K01.16 [Oryza sativa Japonica Group] gi|47777378|gb|AAT38012.1| unknown protein [Oryza sativa Japonica Group] gi|113565734|dbj|BAF16077.1| Os04g0663300 [Oryza sativa Japonica Group] gi|113578885|dbj|BAF17248.1| Os05g0367000 [Oryza sativa Japonica Group] gi|116309854|emb|CAH66889.1| OSIGBa0099L20.4 [Oryza sativa Indica Group] gi|118482169|gb|ABK93014.1| unknown [Populus trichocarpa] gi|118484477|gb|ABK94114.1| unknown [Populus trichocarpa] gi|125550107|gb|EAY95929.1| hypothetical protein OsI_17797 [Oryza sativa Indica Group] gi|125552053|gb|EAY97762.1| hypothetical protein OsI_19674 [Oryza sativa Indica Group] gi|125591958|gb|EAZ32308.1| hypothetical protein OsJ_16517 [Oryza sativa Japonica Group] gi|147789122|emb|CAN64656.1| hypothetical protein VITISV_003384 [Vitis vinifera] gi|215737191|dbj|BAG96120.1| unnamed protein product [Oryza sativa Japonica Group] gi|215768987|dbj|BAH01216.1| unnamed protein product [Oryza sativa Japonica Group] gi|222631322|gb|EEE63454.1| hypothetical protein OsJ_18267 [Oryza sativa Japonica Group] gi|222847245|gb|EEE84792.1| predicted protein [Populus trichocarpa] gi|222849657|gb|EEE87204.1| predicted protein [Populus trichocarpa] gi|223528214|gb|EEF30273.1| Pre-mRNA-splicing factor ini1 [Ricinus communis] gi|241924909|gb|EER98053.1| hypothetical protein SORBIDRAFT_02g004290 [Sorghum bicolor] gi|241939889|gb|EES13034.1| hypothetical protein SORBIDRAFT_06g031860 [Sorghum bicolor] gi|255627145|gb|ACU13917.1| unknown [Glycine max] gi|326530700|dbj|BAK01148.1| predicted protein [Hordeum vulgare subsp. vulgare] gi|388514489|gb|AFK45306.1| unknown [Lotus japonicus]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 100/102 (98%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226494093|ref|NP_001152699.1| PHD finger-like domain-containing protein 5A [Zea mays] gi|226499812|ref|NP_001148557.1| PHD finger-like domain-containing protein 5A [Zea mays] gi|195620406|gb|ACG32033.1| PHD finger-like domain-containing protein 5A [Zea mays] gi|195636738|gb|ACG37837.1| PHD finger-like domain-containing protein 5A [Zea mays] gi|195659129|gb|ACG49032.1| PHD finger-like domain-containing protein 5A [Zea mays] gi|223946749|gb|ACN27458.1| unknown [Zea mays] gi|414584947|tpg|DAA35518.1| TPA: PHD finger-like domain-containing protein 5A isoform 1 [Zea mays] gi|414584948|tpg|DAA35519.1| TPA: PHD finger-like domain-containing protein 5A isoform 2 [Zea mays] gi|414584949|tpg|DAA35520.1| TPA: PHD finger-like domain-containing protein 5A isoform 3 [Zea mays]

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCV+CDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVVCDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18390735|ref|NP_563782.1| PHF5-like protein [Arabidopsis thaliana] gi|18402218|ref|NP_565691.1| PHD finger-like domain-containing protein 5A [Arabidopsis thaliana] gi|145323768|ref|NP_001077473.1| PHF5-like protein [Arabidopsis thaliana] gi|334182358|ref|NP_001184928.1| PHF5-like protein [Arabidopsis thaliana] gi|297826397|ref|XP_002881081.1| hypothetical protein ARALYDRAFT_901975 [Arabidopsis lyrata subsp. lyrata] gi|122223686|sp|Q0WMV8.1|PHF5B_ARATH RecName: Full=PHD finger-like domain-containing protein 5B gi|387935355|sp|P0DI19.1|PHF5A_ARATH RecName: Full=PHD finger-like domain-containing protein 5A gi|3420051|gb|AAC31852.1| expressed protein [Arabidopsis thaliana] gi|21593073|gb|AAM65022.1| unknown [Arabidopsis thaliana] gi|21618034|gb|AAM67084.1| unknown [Arabidopsis thaliana] gi|26451992|dbj|BAC43086.1| unknown protein [Arabidopsis thaliana] gi|28416819|gb|AAO42940.1| At2g30000 [Arabidopsis thaliana] gi|30793845|gb|AAP40375.1| unknown protein [Arabidopsis thaliana] gi|30794025|gb|AAP40459.1| unknown protein [Arabidopsis thaliana] gi|110739257|dbj|BAF01542.1| hypothetical protein [Arabidopsis thaliana] gi|297326920|gb|EFH57340.1| hypothetical protein ARALYDRAFT_901975 [Arabidopsis lyrata subsp. lyrata] gi|330253240|gb|AEC08334.1| PHD finger-like domain-containing protein 5A [Arabidopsis thaliana] gi|332189964|gb|AEE28085.1| PHF5-like protein [Arabidopsis thaliana] gi|332189965|gb|AEE28086.1| PHF5-like protein [Arabidopsis thaliana] gi|332189966|gb|AEE28087.1| PHF5-like protein [Arabidopsis thaliana]

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569387|ref|XP_002525661.1| Pre-mRNA-splicing factor ini1 [Ricinus communis] gi|223535097|gb|EEF36779.1| Pre-mRNA-splicing factor ini1 [Ricinus communis]

 Score =  206 bits (523), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRK+PGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKEPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357438293|ref|XP_003589422.1| PHD finger-like domain-containing protein 5A [Medicago truncatula] gi|357469465|ref|XP_003605017.1| PHD finger-like domain-containing protein 5A [Medicago truncatula] gi|217075230|gb|ACJ85975.1| unknown [Medicago truncatula] gi|355478470|gb|AES59673.1| PHD finger-like domain-containing protein 5A [Medicago truncatula] gi|355506072|gb|AES87214.1| PHD finger-like domain-containing protein 5A [Medicago truncatula] gi|388511423|gb|AFK43773.1| unknown [Medicago truncatula]

 Score =  205 bits (521), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 99/102 (97%), Positives = 101/102 (99%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRK PGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKTPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302794063|ref|XP_002978796.1| hypothetical protein SELMODRAFT_228566 [Selaginella moellendorffii] gi|302805917|ref|XP_002984709.1| hypothetical protein SELMODRAFT_156788 [Selaginella moellendorffii] gi|116778758|gb|ABK20981.1| unknown [Picea sitchensis] gi|300147691|gb|EFJ14354.1| hypothetical protein SELMODRAFT_156788 [Selaginella moellendorffii] gi|300153605|gb|EFJ20243.1| hypothetical protein SELMODRAFT_228566 [Selaginella moellendorffii]

 Score =  204 bits (520), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 102/102 (100%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGS+QGRCVICGG+GISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSYQGRCVICGGLGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195618516|gb|ACG31088.1| PHD finger-like domain-containing protein 5A [Zea mays]

 Score =  204 bits (520), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 99/101 (98%), Positives = 101/101 (100%)

Query: 36  LCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDA 95
           +CRKQPGIAIGRLCEKCDGKCV+CDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDA
Sbjct: 1   MCRKQPGIAIGRLCEKCDGKCVVCDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDA 60

Query: 96  YYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           YYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 61  YYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 101

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168031973|ref|XP_001768494.1| predicted protein [Physcomitrella patens subsp. patens] gi|162680207|gb|EDQ66645.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 97/102 (95%), Positives = 101/102 (99%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVR CDECNYGS+QGRCVICGG+GISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRTCDECNYGSYQGRCVICGGLGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195618288|gb|ACG30974.1| PHD finger-like domain-containing protein 5A [Zea mays]

 Score =  203 bits (516), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 101/102 (99%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEKCDGKCV+ DSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKCDGKCVVFDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569385|ref|XP_002525660.1| Pre-mRNA-splicing factor ini1 [Ricinus communis] gi|223535096|gb|EEF36778.1| Pre-mRNA-splicing factor ini1 [Ricinus communis]

 Score =  202 bits (515), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 98/102 (96%), Positives = 101/102 (99%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++CRKQPGIAIGRLCEK DGKCVICDSYVRPCTLVR+CDECNYGSFQGRCVICGGVGISD
Sbjct: 9   IMCRKQPGIAIGRLCEKDDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGVGISD 68

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
           AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct: 69  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

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	136
TAIR|locus:2007432	110	AT1G07170 "AT1G07170" [Arabido	0.75	0.927	0.970	1.8e-55
TAIR|locus:2045698	110	AT2G30000 [Arabidopsis thalian	0.75	0.927	0.970	1.8e-55
UNIPROTKB|E1BV20	110	PHF5A "Uncharacterized protein	0.75	0.927	0.901	4.4e-52
UNIPROTKB|A4FV59	110	PHF5A "PHF5A protein" [Bos tau	0.75	0.927	0.901	4.4e-52
UNIPROTKB|Q7RTV0	110	PHF5A "PHD finger-like domain-	0.75	0.927	0.901	4.4e-52
MGI|MGI:2156864	110	Phf5a "PHD finger protein 5A"	0.75	0.927	0.901	4.4e-52
RGD|621555	110	Phf5a "PHD finger protein 5A"	0.75	0.927	0.901	4.4e-52
FB|FBgn0031822	111	CG9548 [Drosophila melanogaste	0.742	0.909	0.881	3.6e-50
WB|WBGene00004016	110	phf-5 [Caenorhabditis elegans	0.742	0.918	0.871	9.5e-50
DICTYBASE|DDB_G0284403	110	phf5a "PHD finger-like domain-	0.75	0.927	0.813	1.6e-47

TAIR|locus:2007432 AT1G07170 "AT1G07170" [Arabidopsis thaliana (taxid:3702)]

 Score = 572 (206.4 bits), Expect = 1.8e-55, P = 1.8e-55
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGSFQGRCVICGGVGISD
Sbjct:     9 IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGVGISD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

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

GO:0005689 "U12-type spliceosomal complex" evidence=ISS

TAIR|locus:2045698 AT2G30000 [Arabidopsis thaliana (taxid:3702)]

 Score = 572 (206.4 bits), Expect = 1.8e-55, P = 1.8e-55
 Identities = 99/102 (97%), Positives = 102/102 (100%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             ++CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGSFQGRCVICGGVGISD
Sbjct:     9 IMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGVGISD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 110

GO:0005634 "nucleus" evidence=ISM

UNIPROTKB|E1BV20 PHF5A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 540 (195.1 bits), Expect = 4.4e-52, P = 4.4e-52
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

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

GO:0005686 "U2 snRNP" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|A4FV59 PHF5A "PHF5A protein" [Bos taurus (taxid:9913)]

 Score = 540 (195.1 bits), Expect = 4.4e-52, P = 4.4e-52
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

GO:0016607 "nuclear speck" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0005686 "U2 snRNP" evidence=IEA

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

UNIPROTKB|Q7RTV0 PHF5A "PHD finger-like domain-containing protein 5A" [Homo sapiens (taxid:9606)]

 Score = 540 (195.1 bits), Expect = 4.4e-52, P = 4.4e-52
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

GO:0003677 "DNA binding" evidence=IEA

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

GO:0016363 "nuclear matrix" evidence=IEA

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

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

GO:0005686 "U2 snRNP" evidence=IDA

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

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0016607 "nuclear speck" evidence=ISS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

MGI|MGI:2156864 Phf5a "PHD finger protein 5A" [Mus musculus (taxid:10090)]

 Score = 540 (195.1 bits), Expect = 4.4e-52, P = 4.4e-52
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005686 "U2 snRNP" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

GO:0005730 "nucleolus" evidence=IDA

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IDA

GO:0016607 "nuclear speck" evidence=IDA

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

RGD|621555 Phf5a "PHD finger protein 5A" [Rattus norvegicus (taxid:10116)]

 Score = 540 (195.1 bits), Expect = 4.4e-52, P = 4.4e-52
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQ G+AIGRLCEKCDGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYCKECT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFKKR
Sbjct:    69 AYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR 110

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005686 "U2 snRNP" evidence=ISO;ISS

GO:0005689 "U12-type spliceosomal complex" evidence=IEA;ISO

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

GO:0016363 "nuclear matrix" evidence=IEA;ISO

GO:0016607 "nuclear speck" evidence=ISO;ISS

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

GO:0005730 "nucleolus" evidence=ISO

FB|FBgn0031822 CG9548 [Drosophila melanogaster (taxid:7227)]

 Score = 522 (188.8 bits), Expect = 3.6e-50, P = 3.6e-50
 Identities = 89/101 (88%), Positives = 96/101 (95%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQPG+AIGRLCEK DGKCVICDSYVRPCTLVR+CDECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQPGVAIGRLCEKDDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKK 135
             AYYCK CT QEKDRDGCPKIVNLGS+KTDLFYERKKYGFK+
Sbjct:    69 AYYCKSCTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKQ 109

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

WB|WBGene00004016 phf-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 518 (187.4 bits), Expect = 9.5e-50, P = 9.5e-50
 Identities = 88/101 (87%), Positives = 96/101 (95%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             + CRKQPGIAIGRLCEKCDG+CVICDS+VRPCTLVR+C+ECNYGS+QGRCVICGG G+SD
Sbjct:     9 IFCRKQPGIAIGRLCEKCDGRCVICDSHVRPCTLVRICEECNYGSYQGRCVICGGAGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKK 135
             AYYCKECT  EKDRDGCPKIVNLGSAKTDLFYERKK+G KK
Sbjct:    69 AYYCKECTILEKDRDGCPKIVNLGSAKTDLFYERKKFGSKK 109

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

GO:0002119 "nematode larval development" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

DICTYBASE|DDB_G0284403 phf5a "PHD finger-like domain-containing protein 5A" [Dictyostelium discoideum (taxid:44689)]

 Score = 497 (180.0 bits), Expect = 1.6e-47, P = 1.6e-47
 Identities = 83/102 (81%), Positives = 95/102 (93%)

Query:    35 LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
             ++C+KQ GIAIGR+C+KCDGKCVICDSYVRP TLVR+CDECNYGSFQG+CVICGG G+SD
Sbjct:     9 IMCKKQTGIAIGRVCDKCDGKCVICDSYVRPTTLVRICDECNYGSFQGKCVICGGQGVSD 68

Query:    95 AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYGFKKR 136
             AYYC  C+++EKDRDGCPKIVNLG +K DLFYERKKYGFKKR
Sbjct:    69 AYYCFACSREEKDRDGCPKIVNLGGSKIDLFYERKKYGFKKR 110

GO:0003674 "molecular_function" evidence=ND

GO:0005686 "U2 snRNP" evidence=ISS

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

---

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)
P83870	PHF5A_MOUSE	No assigned EC number	0.9019	0.75	0.9272	yes	no
P83871	PHF5A_RAT	No assigned EC number	0.9019	0.75	0.9272	yes	no
P0DI19	PHF5A_ARATH	No assigned EC number	0.9705	0.75	0.9272	yes	no
Q0WMV8	PHF5B_ARATH	No assigned EC number	0.9705	0.75	0.9272	yes	no
Q9UTB8	INI1_SCHPO	No assigned EC number	0.6804	0.7132	0.8290	yes	no
Q9VMC8	PHF5_DROME	No assigned EC number	0.8811	0.7426	0.9099	yes	no
Q06835	RDS3_YEAST	No assigned EC number	0.5670	0.7058	0.8971	yes	no
Q7RTV0	PHF5A_HUMAN	No assigned EC number	0.9019	0.75	0.9272	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	136
pfam03660	105	pfam03660, PHF5, PHF5-like protein	1e-54
COG1107	715	COG1107, COG1107, Archaea-specific RecJ-like exonu	7e-04

>gnl|CDD|146345 pfam03660, PHF5, PHF5-like protein

 Score =  166 bits (422), Expect = 1e-54
 Identities = 69/98 (70%), Positives = 82/98 (83%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISD 94
           ++C KQPG AIGRLCEKCDGKC ICDSYVRP T VR+CDEC++GS   +C+ICG  G+SD
Sbjct: 8   IMCMKQPGTAIGRLCEKCDGKCPICDSYVRPTTKVRICDECSFGSLGNKCIICGSPGVSD 67

Query: 95  AYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKYG 132
           AYYC EC + EKDRDGCP+I+N+GS +TD FYERKK G
Sbjct: 68  AYYCWECVRLEKDRDGCPRIINVGSNRTDRFYERKKAG 105

This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse, may act as a chromatin-associated protein. The S. pombe ini1 gene is essential, required for splicing. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1. Length = 105

>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 9/62 (14%)

Query: 46  GRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGV-GISDAYYCKECTQQ 104
              C KC GK  +        T+   C EC        C ICG +    +   C EC ++
Sbjct: 53  EIPCPKCRGKGTV--------TVYDTCPECGGTGKVLTCDICGDIIVPWEEGLCPECRRK 104

Query: 105 EK 106
            K
Sbjct: 105 PK 106

Length = 715

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	136
KOG1705	110	consensus Uncharacterized conserved protein, conta	100.0
PF03660	106	PHF5: PHF5-like protein; InterPro: IPR005345 Phf5	100.0
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	91.18
PRK11595	227	DNA utilization protein GntX; Provisional	87.95
PF12773	50	DZR: Double zinc ribbon	87.37
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	85.16
PRK04023	1121	DNA polymerase II large subunit; Validated	84.27
PRK14559	645	putative protein serine/threonine phosphatase; Pro	82.55
PF03833	900	PolC_DP2: DNA polymerase II large subunit DP2; Int	81.03
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	80.69

>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]

Probab=100.00  E-value=4.8e-67  Score=388.89  Aligned_cols=108  Identities=88%  Similarity=1.656  Sum_probs=105.9

Q ss_pred             ccCcceeeeccCCCcccccccccCCCceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCccceeeehhhhhhhccC
Q 037283           29 SIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDR  108 (136)
Q Consensus        29 ~~~~DLi~C~KqpG~~iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~lEKDR  108 (136)
                      +||||||||+||||++||+||||||||||||||||||+|+||||++|+||+++++|||||++|++||||||||+++||||
T Consensus         3 kHhpDLi~CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~~gV~d~~yc~ectr~ekdr   82 (110)
T KOG1705|consen    3 KHHPDLIMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGVGVSDAYYCKECTRQEKDR   82 (110)
T ss_pred             CcCCcEEEEecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCccccCceEEecCCcccchHHHHHHHhhcccc
Confidence            45999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcceeccCCchhHHHHHHhhhcccCC
Q 037283          109 DGCPKIVNLGSAKTDLFYERKKYGFKKR  136 (136)
Q Consensus       109 DGCPrIiN~Gs~ktD~~yekkk~~~kk~  136 (136)
                      ||||||+|+||+|+|+||||||++|+++
T Consensus        83 dgCpri~nlgS~r~d~~~erkk~~~~~~  110 (110)
T KOG1705|consen   83 DGCPKIVNLGSSKTDLFYERKKYGFKKR  110 (110)
T ss_pred             ccChhhhhcccccchHHHHHHhhccccC
Confidence            9999999999999999999999999875

>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins

Probab=100.00  E-value=1e-67  Score=392.22  Aligned_cols=103  Identities=71%  Similarity=1.436  Sum_probs=66.3

Q ss_pred             ccCcceeeeccCCCcccccccccCCCceecccCCCCCceeeEecCCCCCCCcCCeeEEec-CCCccceeeehhhhhhhcc
Q 037283           29 SIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGISDAYYCKECTQQEKD  107 (136)
Q Consensus        29 ~~~~DLi~C~KqpG~~iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg-~~g~sdAYYC~EC~~lEKD  107 (136)
                      +|||||||||||||++||+||++||||||||||||||+++|||||+||||++++|||||| ++|+++|||||||++||||
T Consensus         3 rH~~DLvmC~KqpG~~iG~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC~~lEKd   82 (106)
T PF03660_consen    3 RHQPDLVMCRKQPGTAIGRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWECVRLEKD   82 (106)
T ss_dssp             S--TT--B----EEEEE-EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHHHHHTST
T ss_pred             ccChhHhhhccCCcchhhhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhhHhhhcc
Confidence            459999999999999999999999999999999999999999999999999999999999 8999999999999999999


Q ss_pred             CCCCcceeccCCchhHHHHHHhhh
Q 037283          108 RDGCPKIVNLGSAKTDLFYERKKY  131 (136)
Q Consensus       108 RDGCPrIiN~Gs~ktD~~yekkk~  131 (136)
                      |||||||||+||+|+|+|||+||.
T Consensus        83 RDGCPriiN~Gs~r~d~~~~~kk~  106 (106)
T PF03660_consen   83 RDGCPRIINVGSSRTDRFYEKKKK  106 (106)
T ss_dssp             TS----B-S-SS-SSTT---SSTT
T ss_pred             ccCCceeEeccchhhhHHHHhhcC
Confidence            999999999999999999999874

At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=91.18  E-value=0.06  Score=44.05  Aligned_cols=79  Identities=25%  Similarity=0.490  Sum_probs=47.8

Q ss_pred             CceecccCC-----CCCc----eeeEecCCCCCCC--cCCeeEEecCCC-------------ccceeeehhhhh------
Q 037283           54 GKCVICDSY-----VRPC----TLVRVCDECNYGS--FQGRCVICGGVG-------------ISDAYYCKECTQ------  103 (136)
Q Consensus        54 GkCpICDS~-----Vrp~----~~VrICdeCs~G~--~~~rCIiCg~~g-------------~sdAYYC~EC~~------  103 (136)
                      |.||+|.|.     |++.    .+.-.|..|++.-  .+.+|..||+.+             ..-++-|.+|..      
T Consensus       173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd  252 (290)
T PF04216_consen  173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD  252 (290)
T ss_dssp             SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred             CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence            899999996     4443    5888999999754  467899999755             233778999943      


Q ss_pred             hhccCCCCcceeccCCchhHHHHHHhhhc
Q 037283          104 QEKDRDGCPKIVNLGSAKTDLFYERKKYG  132 (136)
Q Consensus       104 lEKDRDGCPrIiN~Gs~ktD~~yekkk~~  132 (136)
                      +|+|.+-=|-+-+++|-.-|+..+.+-+.
T Consensus       253 ~~~~~~~~~~~dDl~tl~LD~~a~e~Gy~  281 (290)
T PF04216_consen  253 REKDPELDPVADDLATLHLDLLAQEEGYR  281 (290)
T ss_dssp             TTT-TT--HHHHHHTTHHHHHHHHHTT-E
T ss_pred             hhhCcccchhhHHhhhhhHHHHHHhCCCC
Confidence            57777776777799999999988766543

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PRK11595 DNA utilization protein GntX; Provisional

Probab=87.95  E-value=0.26  Score=39.04  Aligned_cols=49  Identities=22%  Similarity=0.551  Sum_probs=33.5

Q ss_pred             CceecccCCCCCceeeEecCCCCCC--CcCCeeEEecCCCccceeeehhhhh
Q 037283           54 GKCVICDSYVRPCTLVRVCDECNYG--SFQGRCVICGGVGISDAYYCKECTQ  103 (136)
Q Consensus        54 GkCpICDS~Vrp~~~VrICdeCs~G--~~~~rCIiCg~~g~sdAYYC~EC~~  103 (136)
                      .+|++|+-.+.+. ...||+.|.-.  .....|..||.+.....+.|.+|..
T Consensus         6 ~~C~~C~~~~~~~-~~~lC~~C~~~l~~~~~~C~~Cg~~~~~~~~~C~~C~~   56 (227)
T PRK11595          6 GLCWLCRMPLALS-HWGICSVCSRALRTLKTCCPQCGLPATHPHLPCGRCLQ   56 (227)
T ss_pred             CcCccCCCccCCC-CCcccHHHHhhCCcccCcCccCCCcCCCCCCCcHHHHc
Confidence            5799999776432 23489999522  2346899999875544567999954

>PF12773 DZR: Double zinc ribbon

Probab=87.37  E-value=0.3  Score=30.13  Aligned_cols=44  Identities=23%  Similarity=0.590  Sum_probs=27.4

Q ss_pred             eecccCCCCCceeeEecCCCCCCCc-----CCeeEEecCCCccceeeehhh
Q 037283           56 CVICDSYVRPCTLVRVCDECNYGSF-----QGRCVICGGVGISDAYYCKEC  101 (136)
Q Consensus        56 CpICDS~Vrp~~~VrICdeCs~G~~-----~~rCIiCg~~g~sdAYYC~EC  101 (136)
                      ||.|...+.+.  ++.|..|+.--.     ...|..||.+...+|-||..|
T Consensus         1 Cp~Cg~~~~~~--~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C   49 (50)
T PF12773_consen    1 CPHCGTPNPDD--AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC   49 (50)
T ss_pred             CCCcCCcCCcc--ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence            45555554443  456666654332     346888888777778888776

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=85.16  E-value=0.97  Score=30.59  Aligned_cols=38  Identities=29%  Similarity=0.590  Sum_probs=31.7

Q ss_pred             CceecccCCCCCceeeEecCCCCCCC------cCCeeEE--ecCCC
Q 037283           54 GKCVICDSYVRPCTLVRVCDECNYGS------FQGRCVI--CGGVG   91 (136)
Q Consensus        54 GkCpICDS~Vrp~~~VrICdeCs~G~------~~~rCIi--Cg~~g   91 (136)
                      ++|++|...++|..-+-+|.+|+--.      ..+.|++  ||.+-
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence            68999999999999999999999542      3578999  87643

>PRK04023 DNA polymerase II large subunit; Validated

Probab=84.27  E-value=0.58  Score=46.71  Aligned_cols=44  Identities=32%  Similarity=0.736  Sum_probs=33.8

Q ss_pred             eeEecCCCCCCCcCCeeEEecCCCccceeeehhhhhhhccCCCCcc
Q 037283           68 LVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPK  113 (136)
Q Consensus        68 ~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~lEKDRDGCPr  113 (136)
                      -.|.|.+|+......+|..||.. +..+|.|.+|..+.. .+-||+
T Consensus       625 g~RfCpsCG~~t~~frCP~CG~~-Te~i~fCP~CG~~~~-~y~CPK  668 (1121)
T PRK04023        625 GRRKCPSCGKETFYRRCPFCGTH-TEPVYRCPRCGIEVE-EDECEK  668 (1121)
T ss_pred             cCccCCCCCCcCCcccCCCCCCC-CCcceeCccccCcCC-CCcCCC
Confidence            45788888888888999999987 467899999966543 355775

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=82.55  E-value=0.82  Score=42.72  Aligned_cols=48  Identities=23%  Similarity=0.452  Sum_probs=38.6

Q ss_pred             CceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCccceeeehhhhh
Q 037283           54 GKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQ  103 (136)
Q Consensus        54 GkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~  103 (136)
                      .+||-|...+.+..  +-|.+|+..-....|.-||.+-..+|-+|.+|..
T Consensus         2 ~~Cp~Cg~~n~~~a--kFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~   49 (645)
T PRK14559          2 LICPQCQFENPNNN--RFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGA   49 (645)
T ss_pred             CcCCCCCCcCCCCC--ccccccCCCCCCCcCCCCCCCCCcccccccccCC
Confidence            36899988876554  5899997765557899999988888999999954

>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus

Probab=81.03  E-value=0.49  Score=46.28  Aligned_cols=43  Identities=37%  Similarity=0.896  Sum_probs=0.0

Q ss_pred             eEecCCCCCCCcCCeeEEecCCCccceeeehhhhhhhccCCCCcc
Q 037283           69 VRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPK  113 (136)
Q Consensus        69 VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~lEKDRDGCPr  113 (136)
                      -|.|..|+.-+...+|-.||+.. ..-|+|..|.. +-+.+-||+
T Consensus       655 ~r~Cp~Cg~~t~~~~Cp~CG~~T-~~~~~Cp~C~~-~~~~~~C~~  697 (900)
T PF03833_consen  655 RRRCPKCGKETFYNRCPECGSHT-EPVYVCPDCGI-EVEEDECPK  697 (900)
T ss_dssp             ---------------------------------------------
T ss_pred             cccCcccCCcchhhcCcccCCcc-ccceecccccc-ccCcccccc
Confidence            47888888888888998898743 44788888854 444557875

The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=80.69  E-value=2.2  Score=36.82  Aligned_cols=77  Identities=26%  Similarity=0.386  Sum_probs=57.9

Q ss_pred             CCceecccCC-----CC----CceeeEecCCCCCCC--cCCeeEEecCCC------------ccceeeehhhh------h
Q 037283           53 DGKCVICDSY-----VR----PCTLVRVCDECNYGS--FQGRCVICGGVG------------ISDAYYCKECT------Q  103 (136)
Q Consensus        53 dGkCpICDS~-----Vr----p~~~VrICdeCs~G~--~~~rCIiCg~~g------------~sdAYYC~EC~------~  103 (136)
                      .|.||+|.|.     |+    ...+.-.|..|+..-  .+.+|..||..+            ..-++-|.+|.      -
T Consensus       187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~  266 (309)
T PRK03564        187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILY  266 (309)
T ss_pred             CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccccceecc
Confidence            6899999996     32    234677899999754  477899999754            12357788884      3


Q ss_pred             hhccCCCCcceeccCCchhHHHHHHh
Q 037283          104 QEKDRDGCPKIVNLGSAKTDLFYERK  129 (136)
Q Consensus       104 lEKDRDGCPrIiN~Gs~ktD~~yekk  129 (136)
                      +|||...=|..-++.|---|+..+.+
T Consensus       267 ~~~d~~~~p~adDlatL~LDl~a~e~  292 (309)
T PRK03564        267 QEKDPKVEAVADDLASLVLDARMEQE  292 (309)
T ss_pred             cccCCCCCcchhHHhhhHhHHHHHhc
Confidence            67887767877899999999988665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	136
2k0a_A	109	1h, 15n And 13c Chemical Shift Assignments For Rds3		6e-27

>pdb|2K0A|A Chain A, 1h, 15n And 13c Chemical Shift Assignments For Rds3 Protein Length = 109

Iteration: 1
 Score =  115 bits (289), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 55/97 (56%), Positives = 72/97 (74%), Gaps = 1/97 (1%)
Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGIS 93
           ++C KQPG+  G LCEKCDGKC ICDSYVRP   VRVC+ C++G     C+IC   VG++
Sbjct: 11  IMCLKQPGVQTGLLCEKCDGKCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVN 70
Query: 94  DAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKK 130
           DA+YC EC +  KD+DGCP+I+NLGS + D  +E+KK
Sbjct: 71  DAFYCWECCRLGKDKDGCPRILNLGSNRLDRHFEKKK 107

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	136
2k0a_A	109	PRE-mRNA-splicing factor RDS3; zinc finger, topolo	3e-48

>2k0a_A PRE-mRNA-splicing factor RDS3; zinc finger, topological knot, mRNA processing, nucleus, spliceosome, RNA binding protein; NMR {Saccharomyces cerevisiae} Length = 109

 Score =  149 bits (378), Expect = 3e-48
 Identities = 55/98 (56%), Positives = 72/98 (73%), Gaps = 1/98 (1%)

Query: 35  LLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGIS 93
           ++C KQPG+  G LCEKCDGKC ICDSYVRP   VRVC+ C++G     C+IC   VG++
Sbjct: 11  IMCLKQPGVQTGLLCEKCDGKCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVN 70

Query: 94  DAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFYERKKY 131
           DA+YC EC +  KD+DGCP+I+NLGS + D  +E+KK 
Sbjct: 71  DAFYCWECCRLGKDKDGCPRILNLGSNRLDRHFEKKKK 108

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	136
2k0a_A	109	PRE-mRNA-splicing factor RDS3; zinc finger, topolo	100.0
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	83.52

>2k0a_A PRE-mRNA-splicing factor RDS3; zinc finger, topological knot, mRNA processing, nucleus, spliceosome, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.7e-68  Score=395.70  Aligned_cols=104  Identities=53%  Similarity=1.120  Sum_probs=101.1

Q ss_pred             cccCcceeeeccCCCcccccccccCCCceecccCCCCCceeeEecCCCCCCCcCCeeEEec-CCCccceeeehhhhhhhc
Q 037283           28 VSIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGISDAYYCKECTQQEK  106 (136)
Q Consensus        28 ~~~~~DLi~C~KqpG~~iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg-~~g~sdAYYC~EC~~lEK  106 (136)
                      .+|||||||||||||++||+||++||||||||||||||.++||||||||||++++|||||| ++|++||||||||++|||
T Consensus         4 srH~~DLimC~KqpG~~iG~lCekcdGkC~iCDs~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~~dAYYC~eC~~lEK   83 (109)
T 2k0a_A            4 SRHQFDLIMCLKQPGVQTGLLCEKCDGKCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVNDAFYCWECCRLGK   83 (109)
T ss_dssp             SSCCTTCCBCCCCEEEEECEECGGGTTCCTTTCCCCCCCEECEEEHHHHTSSTTSBCTTTSSSBCCEECEECHHHHHHTS
T ss_pred             cccCchhhhccCCCcchhhhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCCceEEcCCCCCcccceehHhhhhhhc
Confidence            3569999999999999999999999999999999999999999999999999999999999 899999999999999999


Q ss_pred             cCCCCcceeccCCchhHHHHHHhhh
Q 037283          107 DRDGCPKIVNLGSAKTDLFYERKKY  131 (136)
Q Consensus       107 DRDGCPrIiN~Gs~ktD~~yekkk~  131 (136)
                      ||||||||||+||+|||+|||+||+
T Consensus        84 DRDGCPriiN~Gs~ktD~~y~~kk~  108 (109)
T 2k0a_A           84 DKDGCPRILNLGSNRLDRHFEKKKK  108 (109)
T ss_dssp             TTSCCCCBCSCSSCSSTTCCCSSTT
T ss_pred             cccCCCeeEecCcchhhHHhHhhcc
Confidence            9999999999999999999998874

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=83.52  E-value=0.61  Score=38.47  Aligned_cols=79  Identities=23%  Similarity=0.355  Sum_probs=58.2

Q ss_pred             CCceecccCC-----CCC-----ceeeEecCCCCCCC--cCCeeEEecCCC-----------------ccceeeehhhhh
Q 037283           53 DGKCVICDSY-----VRP-----CTLVRVCDECNYGS--FQGRCVICGGVG-----------------ISDAYYCKECTQ  103 (136)
Q Consensus        53 dGkCpICDS~-----Vrp-----~~~VrICdeCs~G~--~~~rCIiCg~~g-----------------~sdAYYC~EC~~  103 (136)
                      .|.||+|.|.     |+.     -.+.-.|..|++.-  ...+|..||..+                 ..-++-|..|..
T Consensus       182 ~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~  261 (309)
T 2fiy_A          182 RTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQG  261 (309)
T ss_dssp             CSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTE
T ss_pred             CCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeecCcCCcCCCCCCCeeEEEecCccccCCCcceEEEEcccccc
Confidence            7999999986     442     33577899999744  477999999743                 123788999953


Q ss_pred             ------hhccCCCCcceeccCCchhHHHHHHhhh
Q 037283          104 ------QEKDRDGCPKIVNLGSAKTDLFYERKKY  131 (136)
Q Consensus       104 ------lEKDRDGCPrIiN~Gs~ktD~~yekkk~  131 (136)
                            +|||.+-=|-.-+++|---|+..+.+-+
T Consensus       262 YlK~~~~~~d~~~dp~adDlatL~LDl~a~e~Gy  295 (309)
T 2fiy_A          262 YLKQFYLEFDRHADALADDLASLALDMRLAEDGY  295 (309)
T ss_dssp             EEEEEETTTCTTCCHHHHHHTTHHHHHHHHHTTC
T ss_pred             hHhhhhhccCCCCCcchhHHHHHHHHHHHHhcCC
Confidence                  5777665566668999999998887644

---

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

ID	Length	Definition	Probability
Query	136
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	85.86

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.86  E-value=0.19  Score=39.24  Aligned_cols=79  Identities=23%  Similarity=0.330  Sum_probs=60.2

Q ss_pred             CCceecccCC-----CCC-----ceeeEecCCCCCCC--cCCeeEEecCCCc-----------------cceeeehhhh-
Q 037283           53 DGKCVICDSY-----VRP-----CTLVRVCDECNYGS--FQGRCVICGGVGI-----------------SDAYYCKECT-  102 (136)
Q Consensus        53 dGkCpICDS~-----Vrp-----~~~VrICdeCs~G~--~~~rCIiCg~~g~-----------------sdAYYC~EC~-  102 (136)
                      .|.||+|.|.     ++.     -.+.-.|..|++.-  .+-+|..||+...                 .-++.|.+|- 
T Consensus       164 ~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~~R~~C~~Cg~~~~~~~~~~~~~~~~~~~~~~r~e~C~~C~~  243 (290)
T d2fiya1         164 RTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQG  243 (290)
T ss_dssp             CSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTE
T ss_pred             CCcCCCCCCcchhheeeccCCCCCceEEECCCCCCccccccccCCCCCCCCCcceEEEecCCCcccccceEEEEcCCcCC
Confidence            6889999996     332     23566899999754  4779999997541                 2367899993 


Q ss_pred             -----hhhccCCCCcceeccCCchhHHHHHHhhh
Q 037283          103 -----QQEKDRDGCPKIVNLGSAKTDLFYERKKY  131 (136)
Q Consensus       103 -----~lEKDRDGCPrIiN~Gs~ktD~~yekkk~  131 (136)
                           -+|||...=|..-+++|-.-|+..+.+-+
T Consensus       244 Y~K~~~~~~~~~~~p~~dDlasl~LD~~a~e~Gy  277 (290)
T d2fiya1         244 YLKQFYLEFDRHADALADDLASLALDMRLAEDGY  277 (290)
T ss_dssp             EEEEEETTTCTTCCHHHHHHTTHHHHHHHHHTTC
T ss_pred             eEEEeecccCCccCccHHHhhhhHhhHHHHhCCC
Confidence                 46888888888889999999998887754