Citrus Sinensis ID: 034338

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKIRSNYDVEIHVCGFR
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHccEEEEEEHHHHHHHHHHHHHHHHHccEEEEEEEEEcEEEccccccccccccccEEEEEEEEEEEcccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEEEEEcccccccccccHHHHEEEEHEEEEEHccccEEEEEcccc
Coil and Loop (DISEMBL)
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVdireetggrpvqkakvNTLNIIHYkirsnydvEIHVCGFR
Flexible Loop (DISEMBL)
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILknnglavekkittstvdireetggrpvqkakvntlniihykirsnydvEIHVCGFR
Low Complexity Region (SEG)
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKIRSNYDVEIHVCGFR
Disordered region (IsUnstruct)
****LVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKIRSNYDVEIHVCGF*
Disordered Region (DISOPRED)
*FDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITT*******************NTLNIIHYKIRSNYDVEIHVCGFR
Disordered Region (DISEMBL)
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKIRSNYDVEIHVCGFR
Disordered Region (DISPRO)
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKIRSNYDVEIHVCGFR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFDDLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKIRSNYDVEIHVCGFR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	97	2.2.26 [Sep-21-2011]
O22969	130	Uncharacterized protein A	yes	no	0.670	0.5	0.757	2e-22

>sp|O22969|Y2416_ARATH Uncharacterized protein At2g34160 OS=Arabidopsis thaliana GN=At2g34160 PE=1 SV=1

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 60/66 (90%), Gaps = 1/66 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQ+N+VELSALGMAIATVVT+ EILKNNG AVEKKI TSTVDI+++  GRP
Sbjct: 35  YVNLAKRYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSTVDIKDDARGRP 94

Query: 68  VQKAKV 73
           VQKAK+
Sbjct: 95  VQKAKI 100

Arabidopsis thaliana (taxid: 3702)

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	97
224141887	133	predicted protein [Populus trichocarpa]	0.701	0.511	0.869	2e-25
118484649	133	unknown [Populus trichocarpa]	0.701	0.511	0.869	2e-25
224089211	136	predicted protein [Populus trichocarpa]	0.701	0.5	0.855	9e-25
255548958	128	conserved hypothetical protein [Ricinus	0.701	0.531	0.826	3e-24
225443021	129	PREDICTED: uncharacterized protein At2g3	0.701	0.527	0.826	5e-24
356522351	159	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.742	0.452	0.763	2e-23
225430245	130	PREDICTED: uncharacterized protein At2g3	0.701	0.523	0.797	3e-23
225445462	130	PREDICTED: uncharacterized protein At2g3	0.701	0.523	0.797	4e-23
116781647	132	unknown [Picea sitchensis]	0.670	0.492	0.803	1e-22
388505602	136	unknown [Lotus japonicus]	0.670	0.477	0.818	1e-22

>gi|224141887|ref|XP_002324292.1| predicted protein [Populus trichocarpa] gi|222865726|gb|EEF02857.1| predicted protein [Populus trichocarpa]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/69 (86%), Positives = 65/69 (94%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVD+REETGGRP
Sbjct: 39  YVNLAKRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDMREETGGRP 98

Query: 68  VQKAKVNTL 76
           V KAK+  L
Sbjct: 99  VPKAKIEIL 107

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118484649|gb|ABK94195.1| unknown [Populus trichocarpa]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/69 (86%), Positives = 65/69 (94%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVD+REETGGRP
Sbjct: 39  YVNLAKRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDMREETGGRP 98

Query: 68  VQKAKVNTL 76
           V KAK+  L
Sbjct: 99  VPKAKIEIL 107

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224089211|ref|XP_002308658.1| predicted protein [Populus trichocarpa] gi|118487145|gb|ABK95401.1| unknown [Populus trichocarpa] gi|222854634|gb|EEE92181.1| predicted protein [Populus trichocarpa]

 Score =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 64/69 (92%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKI TSTVD+REETGGRP
Sbjct: 42  YVNLAKRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKIMTSTVDMREETGGRP 101

Query: 68  VQKAKVNTL 76
           V KAK+  L
Sbjct: 102 VPKAKIEIL 110

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548958|ref|XP_002515535.1| conserved hypothetical protein [Ricinus communis] gi|223545479|gb|EEF46984.1| conserved hypothetical protein [Ricinus communis]

 Score =  115 bits (289), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 64/69 (92%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVTIAEILKNNGLA+EKKI TSTVD+RE+TGGRP
Sbjct: 35  YVNLAKRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAIEKKIMTSTVDMREDTGGRP 94

Query: 68  VQKAKVNTL 76
           V KAK+  L
Sbjct: 95  VPKAKIEIL 103

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443021|ref|XP_002270136.1| PREDICTED: uncharacterized protein At2g34160 [Vitis vinifera] gi|297743423|emb|CBI36290.3| unnamed protein product [Vitis vinifera]

 Score =  114 bits (286), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 65/69 (94%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVD+++E+ GRP
Sbjct: 34  YVNLAKRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDMKDESRGRP 93

Query: 68  VQKAKVNTL 76
           VQKAK+  L
Sbjct: 94  VQKAKIEIL 102

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522351|ref|XP_003529810.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein At2g34160-like [Glycine max]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 64/72 (88%)

Query: 5   LVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETG 64
           L +  +S +RYMQQHNEVELSALGMAIATVVT+AEILKNN LAVEKKITTSTVDI++++ 
Sbjct: 56  LFSTSISPKRYMQQHNEVELSALGMAIATVVTVAEILKNNELAVEKKITTSTVDIKDDSR 115

Query: 65  GRPVQKAKVNTL 76
           GRPVQKAK+  L
Sbjct: 116 GRPVQKAKIEIL 127

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430245|ref|XP_002285046.1| PREDICTED: uncharacterized protein At2g34160 [Vitis vinifera] gi|296082016|emb|CBI21021.3| unnamed protein product [Vitis vinifera]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 55/69 (79%), Positives = 65/69 (94%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +R+MQQ+N+VELSALGMAIATVVTIAEILKNNGLAVEK+ITTSTVDIR+E GGRP
Sbjct: 35  YVNLAKRFMQQYNDVELSALGMAIATVVTIAEILKNNGLAVEKRITTSTVDIRDEFGGRP 94

Query: 68  VQKAKVNTL 76
           +QKAK+  L
Sbjct: 95  LQKAKIEIL 103

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225445462|ref|XP_002285115.1| PREDICTED: uncharacterized protein At2g34160 [Vitis vinifera] gi|297738936|emb|CBI28181.3| unnamed protein product [Vitis vinifera]

 Score =  112 bits (279), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 55/69 (79%), Positives = 64/69 (92%), Gaps = 1/69 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKI TSTVD+++E+ GRP
Sbjct: 34  YVNLAKRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKIMTSTVDMKDESRGRP 93

Query: 68  VQKAKVNTL 76
           +QKAK+  L
Sbjct: 94  IQKAKIEIL 102

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116781647|gb|ABK22189.1| unknown [Picea sitchensis]

 Score =  110 bits (275), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 63/66 (95%), Gaps = 1/66 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQH EVELSALGMAIATVVT+AEILKNNGLAVEKKI+TST+D+R+E+ GRP
Sbjct: 36  YVNLAKRYMQQHEEVELSALGMAIATVVTVAEILKNNGLAVEKKISTSTIDMRDESRGRP 95

Query: 68  VQKAKV 73
           +QKAKV
Sbjct: 96  IQKAKV 101

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505602|gb|AFK40867.1| unknown [Lotus japonicus]

 Score =  110 bits (274), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 54/66 (81%), Positives = 63/66 (95%), Gaps = 1/66 (1%)

Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RYMQQHNEVELSALGMAIATVVT+AEILKNNGLAVEKKI TSTVDI++++ GRP
Sbjct: 38  YVNLAKRYMQQHNEVELSALGMAIATVVTVAEILKNNGLAVEKKILTSTVDIKDDSRGRP 97

Query: 68  VQKAKV 73
           VQKAK+
Sbjct: 98  VQKAKI 103

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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	97
TAIR|locus:2055516	130	AT2G34160 [Arabidopsis thalian	0.670	0.5	0.757	3e-21
TAIR|locus:2029949	130	AT1G29250 [Arabidopsis thalian	0.670	0.5	0.757	3.9e-21
TAIR|locus:2084873	164	DAN1 "D NUCLDUO1-ACTIVATEEIC A	0.670	0.396	0.727	5.7e-20

TAIR|locus:2055516 AT2G34160 [Arabidopsis thaliana (taxid:3702)]

 Score = 249 (92.7 bits), Expect = 3.0e-21, P = 3.0e-21
 Identities = 50/66 (75%), Positives = 60/66 (90%)

Query:     9 YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
             Y++L +RYMQQ+N+VELSALGMAIATVVT+ EILKNNG AVEKKI TSTVDI+++  GRP
Sbjct:    35 YVNLAKRYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSTVDIKDDARGRP 94

Query:    68 VQKAKV 73
             VQKAK+
Sbjct:    95 VQKAKI 100

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IDA

GO:0009062 "fatty acid catabolic process" evidence=RCA

TAIR|locus:2029949 AT1G29250 [Arabidopsis thaliana (taxid:3702)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 50/66 (75%), Positives = 61/66 (92%)

Query:     9 YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
             Y++L +RYMQQ+ +VELSALGMAIATVVT+AEILKNNG AVEKKI TSTVDI++++ GRP
Sbjct:    35 YVNLAKRYMQQYTDVELSALGMAIATVVTVAEILKNNGFAVEKKIMTSTVDIKDDSRGRP 94

Query:    68 VQKAKV 73
             VQKAK+
Sbjct:    95 VQKAKI 100

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008150 "biological_process" evidence=ND

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2084873 DAN1 "D NUCLDUO1-ACTIVATEEIC ACID BINDING PROTEIN 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 48/66 (72%), Positives = 59/66 (89%)

Query:     9 YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
             Y++L +RY+QQHNEVELSALGMAI TVVTI+EILKNNGLA EKK+ TSTV +++ET G+ 
Sbjct:    52 YVNLAKRYIQQHNEVELSALGMAITTVVTISEILKNNGLATEKKVLTSTVGMKDETKGKM 111

Query:    68 VQKAKV 73
             VQKAK+
Sbjct:   112 VQKAKI 117


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.134   0.366    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       97        97   0.00091  102 3  11 22  0.50    29
                                                     29  0.44    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  503 (54 KB)
  Total size of DFA:  94 KB (2068 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.97u 0.16s 12.13t   Elapsed:  00:00:01
  Total cpu time:  11.97u 0.16s 12.13t   Elapsed:  00:00:01
  Start:  Fri May 10 21:22:48 2013   End:  Fri May 10 21:22:49 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0048235 "pollen sperm cell differentiation" evidence=IEP

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

GO:0010332 "response to gamma radiation" evidence=RCA

---

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)
O22969	Y2416_ARATH	No assigned EC number	0.7575	0.6701	0.5	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	97
pfam01918	67	pfam01918, Alba, Alba	3e-05

>gnl|CDD|216785 pfam01918, Alba, Alba

 Score = 38.0 bits (89), Expect = 3e-05
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 17 QQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTST 56
             +EV L  LG AI+  V++AEILK   L    ++   T
Sbjct: 25 GGADEVVLKGLGRAISKAVSVAEILKRRFLKGLHQVNVIT 64

Alba is a novel chromosomal protein that coats archaeal DNA without compacting it. Length = 67

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	97
COG1581	91	Ssh10b Archaeal DNA-binding protein [Transcription	99.91
TIGR00285	87	DNA-binding protein Alba. This protein appears so	99.89
PRK04015	91	DNA/RNA-binding protein albA; Provisional	99.88
PF01918	70	Alba: Alba; InterPro: IPR002775 Members of this fa	99.19
KOG2567	179	consensus Uncharacterized conserved protein [Funct	97.53
PF12328	144	Rpp20: Rpp20 subunit of nuclear RNase MRP and P; P	97.21

>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]

Probab=99.91  E-value=4.3e-24  Score=147.88  Aligned_cols=69  Identities=26%  Similarity=0.353  Sum_probs=65.7

Q ss_pred             HHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338           10 LSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus        10 ~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ..-+|||+|.+||.|||||+|||+|||||||+||||+  +.+|+|+++|++++.++ |+..++|.|||+|.|
T Consensus        20 Avlt~fn~g~~eViiKARGraIskAVDvaeivRnrf~p~v~ik~Iki~se~~~~~~-gr~~~VS~IeI~L~k   90 (91)
T COG1581          20 AVLTQFNEGADEVIIKARGRAISKAVDVAEIVRNRFIPDVQIKDIKIGTEELEGED-GRTRNVSTIEIVLAK   90 (91)
T ss_pred             HHHHHHHcCCCEEEEEecchhhHhhHhHHHHHHHhcCCCceEEEEEecceeeecCC-CceeeEEEEEEEEec
Confidence            3458999999999999999999999999999999999  99999999999999996 898899999999986

>TIGR00285 DNA-binding protein Alba

Probab=99.89  E-value=4.2e-23  Score=141.51  Aligned_cols=71  Identities=30%  Similarity=0.362  Sum_probs=66.0

Q ss_pred             HHHHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            8 AYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         8 ~~~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ....-+|||+|.+||.|||||+|||+|||||||+|||++  +.+++|.++|+++.+++ |+..++|+|||+|.|
T Consensus        15 Vlavlt~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~v~v~~I~i~te~~~~~~-G~~~~VStIEI~l~~   87 (87)
T TIGR00285        15 VLAVLTQLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPDIKIKKIKIGTEEIKSEQ-GREVNVSTIEIVLAK   87 (87)
T ss_pred             HHHHHHHHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCCceEEEEEeccEEeecCC-CceeeEEEEEEEEeC
Confidence            345678999999999999999999999999999999999  77999999999999986 998899999999975

This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.

>PRK04015 DNA/RNA-binding protein albA; Provisional

Probab=99.88  E-value=9.5e-23  Score=140.45  Aligned_cols=71  Identities=28%  Similarity=0.348  Sum_probs=65.6

Q ss_pred             HHHHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            8 AYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         8 ~~~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ....-+||+++.+||.|||+|+|||+|||||||||||++  +.+++|.+||+.+++++ |+..++|+|||+|+|
T Consensus        18 V~~~~~~l~~g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v~v~~I~i~se~i~~~~-g~~~~VS~IEI~l~k   90 (91)
T PRK04015         18 VLAVLTQFNQGAKEVVIKARGRAISKAVDVAEIVRNRFLPDVEIKEIKIGTEEVTSED-GRESNVSTIEIVLEK   90 (91)
T ss_pred             HHHHHHHHhCCCCeEEEEEeccccchhhhHHHHHHHhccCCeEEEEEEeccEEeecCC-CcEEEEEEEEEEEec
Confidence            345567899999999999999999999999999999999  99999999999999986 888889999999987

>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function

Probab=99.19  E-value=7.3e-11  Score=74.32  Aligned_cols=51  Identities=29%  Similarity=0.352  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHHh-----ccCCeEEEeecchhhhHHHHHHHHHhhCC---eEEEEEEee
Q 034338            4 DLVAAYLSLQRYM-----QQHNEVELSALGMAIATVVTIAEILKNNG---LAVEKKITT   54 (97)
Q Consensus         4 ~~~~~~~lakqf~-----~~~~EVeLsAlG~AIS~aV~VAEILKn~~---la~~KkI~T   54 (97)
                      ....|..-+..++     +++++|.|+|+|+||++||++|||+|+++   +..+.++..
T Consensus        10 ~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv~~~t~   68 (70)
T PF01918_consen   10 PIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQVNKITS   68 (70)
T ss_dssp             -HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEEEEEEE
T ss_pred             CHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEEEEEec
Confidence            4567777788888     88999999999999999999999999994   566666543

The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....

>KOG2567 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.53  E-value=4.8e-05  Score=58.41  Aligned_cols=74  Identities=27%  Similarity=0.278  Sum_probs=49.9

Q ss_pred             HHHHHHHHhcc--CCeEEEeecchhhhHHHHHHHHHhhC--CeEEEEEEee-eeeeec--cCCC----CcccccceEEEE
Q 034338            8 AYLSLQRYMQQ--HNEVELSALGMAIATVVTIAEILKNN--GLAVEKKITT-STVDIR--EETG----GRPVQKAKVNTL   76 (97)
Q Consensus         8 ~~~lakqf~~~--~~EVeLsAlG~AIS~aV~VAEILKn~--~la~~KkI~T-sT~~i~--~e~r----g~~v~kskIEIv   76 (97)
                      |-.+|+-.+++  +.+|.+||.|+||++.|++||||||+  ||=.+.+|.- |+++.=  .+++    --..+++.|-|+
T Consensus        32 ~i~~A~~~L~~~~~r~VVfsg~Grai~KTVscaEilKrRipgLhQ~t~l~~~sv~d~W~p~~eGl~pl~vtRhVp~l~Il  111 (179)
T KOG2567|consen   32 LIEFATELLQKGSHRCVVFSGSGRAIVKTVSCAEILKRRIPGLHQVTRLRYTSVEDVWEPTEEGLEPLEVTRHVPMLHIL  111 (179)
T ss_pred             HHHHHHHHhhCCCeeEEEEecCCcceeeeeeHHHHHhhhCcchhhhceeeeeehhhcccccccCccceEEeeccceEEEE
Confidence            45567777775  89999999999999999999999987  5533334432 222110  1110    113367899999


Q ss_pred             Eeeec
Q 034338           77 NIIHY   81 (97)
Q Consensus        77 L~k~~   81 (97)
                      |++..
T Consensus       112 LS~de  116 (179)
T KOG2567|consen  112 LSLDE  116 (179)
T ss_pred             Eeccc
Confidence            98864

>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B

Probab=97.21  E-value=0.00083  Score=49.15  Aligned_cols=41  Identities=22%  Similarity=0.379  Sum_probs=32.8

Q ss_pred             CeEEEeecchhhhHHHHHHHHHhhCCeEEEEEEeeeeeeecc
Q 034338           20 NEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIRE   61 (97)
Q Consensus        20 ~EVeLsAlG~AIS~aV~VAEILKn~~la~~KkI~TsT~~i~~   61 (97)
                      .+|.|+|+|+||.+|+.+|--++++. --.-.|+|+|+++-|
T Consensus        62 ~~V~v~gtGkAIeKal~la~~Fq~~~-~~~V~V~TgTV~vvD  102 (144)
T PF12328_consen   62 EEVTVKGTGKAIEKALSLALWFQRKK-GYKVEVRTGTVEVVD  102 (144)
T ss_dssp             SEEEEEEEGGGHHHHHHHHHHHHHTT----EEEEEEEEEEEE
T ss_pred             cEEEEEeccHHHHHHHHHHHHHhhcC-CeEEEEEeceEEEEE
Confidence            79999999999999999999999885 223467888876543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
1vm0_A	130	X-Ray Structure Of Gene Product From Arabidopsis Th		3e-21

>pdb|1VM0|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis Thaliana At2g34160 Length = 130

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/66 (71%), Positives = 57/66 (86%), Gaps = 1/66 (1%)
Query: 9   YLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRP 67
           Y++L +RY QQ+N+VELSALG AIATVVT+ EILKNNG AVEKKI TS VDI+++  GRP
Sbjct: 35  YVNLAKRYXQQYNDVELSALGXAIATVVTVTEILKNNGFAVEKKIXTSIVDIKDDARGRP 94
Query: 68  VQKAKV 73
           VQKAK+
Sbjct: 95  VQKAKI 100

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
1vm0_A	130	Unknown protein; structural genomics, protein stru	1e-23

>1vm0_A Unknown protein; structural genomics, protein structure initiative, CESG, AT2 unknown function, nitrate; 1.80A {Arabidopsis thaliana} SCOP: d.68.6.2 PDB: 2q3v_A Length = 130

 Score = 86.5 bits (213), Expect = 1e-23
 Identities = 47/61 (77%), Positives = 55/61 (90%)

Query: 13  QRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAK 72
           +RYMQQ+N+VELSALGMAIATVVT+ EILKNNG AVEKKI TS VDI+++  GRPVQKAK
Sbjct: 40  KRYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSIVDIKDDARGRPVQKAK 99

Query: 73  V 73
           +
Sbjct: 100 I 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	97
1vm0_A	130	Unknown protein; structural genomics, protein stru	99.97
1nfj_A	89	ALBA, conserved hypothetical protein AF1956; SIR2,	99.9
1nh9_A	87	MJA10B, DNA-binding protein ALBA; 2.00A {Methanoca	99.89
2bky_A	97	DNA/RNA-binding protein ALBA 1; archaeal DNA bindi	99.88
3toe_A	91	MTH10B, DNA/RNA-binding protein ALBA; SAC10B famil	99.86
2h9u_A	102	DNA/RNA-binding protein ALBA 2; archaea, DNA bindi	99.86
2bky_X	89	DNA/RNA-binding protein ALBA 2; archaeal DNA bindi	99.83
3iab_B	140	Ribonucleases P/MRP protein subunit POP7; RNAse P,	97.5

>1vm0_A Unknown protein; structural genomics, protein structure initiative, CESG, AT2 unknown function, nitrate; 1.80A {Arabidopsis thaliana} SCOP: d.68.6.2 PDB: 2q3v_A

Probab=99.97  E-value=2.3e-32  Score=196.84  Aligned_cols=85  Identities=58%  Similarity=0.706  Sum_probs=76.4

Q ss_pred             hHHHHHHHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCeEEEEEEeeeeeeeccCCCCcccccceEEEEEeeeccc
Q 034338            4 DLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKI   83 (97)
Q Consensus         4 ~~~~~~~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~la~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k~~~~   83 (97)
                      .+|.|+++|++|+++++||+|||||+|||+||+||||||||||+++|+|.|||++++++.+||++|+|||||+|.|+++|
T Consensus        31 P~~nYV~~a~~~l~g~~eV~LkA~G~AIskAV~VAEiLkrr~l~~ikkI~t~t~~i~~~~~~r~v~~skIEI~L~k~~~f  110 (130)
T 1vm0_A           31 PLFFYVNLAKRYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSIVDIKDDARGRPVQKAKIEITLVKSEKF  110 (130)
T ss_dssp             CHHHHHHHHHHHHHHHSEEEEEEEGGGHHHHHHHHHHHHHTTSEEEEEEEEEEEEEC------CEEEEEEEEEEEECTTH
T ss_pred             CceeHHHHHHHHHcCCCEEEEEechHHHHHHHHHHHHHHhcCcceEEEEEeeeEEeccCCCCcccccceEEEEEEecCcH
Confidence            46899999999999999999999999999999999999999999999999999999999889999999999999999999


Q ss_pred             cccee
Q 034338           84 RSNYD   88 (97)
Q Consensus        84 ~~~~~   88 (97)
                      ++.|.
T Consensus       111 d~~~~  115 (130)
T 1vm0_A          111 DELMA  115 (130)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99873

>1nfj_A ALBA, conserved hypothetical protein AF1956; SIR2, HDAC, gene regulation, transcription; 2.00A {Archaeoglobus fulgidus} SCOP: d.68.6.1 PDB: 1nfh_A 2z7c_A*

Probab=99.90  E-value=1.9e-23  Score=140.57  Aligned_cols=74  Identities=24%  Similarity=0.327  Sum_probs=67.1

Q ss_pred             HHHHHHHH-HHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            5 LVAAYLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         5 ~~~~~~la-kqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ++.|...| ++|+++++||.|||+|+|||+||+||||||||++  +.+++|+|||+++++++ |++.++|+|||+|.|
T Consensus        13 v~~yV~~~~~~l~~g~~eV~ika~G~AIskAV~vaeilk~r~~~gl~i~~i~i~s~~i~~e~-g~~r~vs~IeI~L~k   89 (89)
T 1nfj_A           13 VMNYVLATLTQLNEGADEVVIKARGRAISRAVDVAEIVRNRFMPGVKVKEIKIDTEELESEQ-GRRSNVSTIEIVLAK   89 (89)
T ss_dssp             HHHHHHHHHHHHHTTCSEEEEEEETTHHHHHHHHHHHHHHHTCTTCEEEEEEEEEEECCCBT-TBCCEEEEEEEEEEC
T ss_pred             HHHHHHHHHHHHhCCCCEEEEEEecHHHHHHHHHHHHHHHhccCCcEEEEEEEeEEEEEcCC-CcEEEeeEEEEEEEC
Confidence            56777777 5666779999999999999999999999999998  78899999999999986 888899999999985

>1nh9_A MJA10B, DNA-binding protein ALBA; 2.00A {Methanocaldococcus jannaschii} SCOP: d.68.6.1

Probab=99.89  E-value=5e-23  Score=138.04  Aligned_cols=73  Identities=23%  Similarity=0.342  Sum_probs=59.9

Q ss_pred             HHHHHHHH-HHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            5 LVAAYLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         5 ~~~~~~la-kqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ++.|...| ++|+++ +||.|||+|+|||+||+||||||||++  +.+++|+|||+++.+++ |++.++|+|||+|.|
T Consensus        12 v~~YV~~~~~~l~~g-~eV~ikA~G~AIskAV~vaeilk~r~~~~l~v~~i~i~s~~i~~e~-g~~r~vS~IeI~L~k   87 (87)
T 1nh9_A           12 VMNYVVAVLTQLTSN-DEVIIKARGKAINKAVDVAEMIRNRFIKDIKIKKIEIGTDKVKNPD-GREVNVSTIEIVLAK   87 (87)
T ss_dssp             HHHHHHHHHHHHHHC-SEEEEEEEGGGHHHHHHHHHHHHHHTCTTCEEEEEEEEEEC--------CCCEEEEEEEEEC
T ss_pred             hHHHHHHHHHHhcCC-CEEEEEEechHHHHHHHHHHHHHHhccCCeEEEEEEEeEEEEEcCC-CcEEEeeEEEEEEEC
Confidence            56677766 677777 999999999999999999999999998  78899999999999986 888899999999975

>2bky_A DNA/RNA-binding protein ALBA 1; archaeal DNA binding protein, DNA condensation, DNA-binding, DNA binding protein; 1.70A {Sulfolobus solfataricus} SCOP: d.68.6.1 PDB: 1h0x_A* 1h0y_A* 1y9x_A

Probab=99.88  E-value=9.2e-23  Score=139.38  Aligned_cols=74  Identities=22%  Similarity=0.224  Sum_probs=66.9

Q ss_pred             HHHHHHHH-HHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe---EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            5 LVAAYLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGL---AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         5 ~~~~~~la-kqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l---a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ++.|...| ++|+++++||.|||+|+|||+||+||||||||++   +.+++|.|||+++.+|+ |++.++|.|||+|.|
T Consensus        19 v~~YV~~a~~ll~~g~~eV~ikA~G~AIskAV~vaeilk~r~~~~~l~~~~i~i~s~~i~~e~-G~~r~vS~IeI~L~k   96 (97)
T 2bky_A           19 VMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQD-GRQSRVSTIEIAIRK   96 (97)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEEETTHHHHHHHHHHHHHHHTSTTTEEEEEEEEEEEEEEETT-SCEEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHhCCCCEEEEEEechHHHHHHHHHHHHHHhccCCceEEEEEEeeeEEEecCC-CcEEEeeEEEEEEEc
Confidence            56777777 6777779999999999999999999999999998   66899999999999986 888899999999986

>3toe_A MTH10B, DNA/RNA-binding protein ALBA; SAC10B family, alpha/beta mixed, homodimer, unknown function; 2.20A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=99.86  E-value=1.3e-21  Score=133.58  Aligned_cols=70  Identities=23%  Similarity=0.247  Sum_probs=64.3

Q ss_pred             HHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEeee
Q 034338           10 LSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNIIH   80 (97)
Q Consensus        10 ~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k~   80 (97)
                      ..-++|++|++||.|||+|+|||+|||||||+|+|++  +.+++|.++|+.+++++ |+..++|.|||+|+|.
T Consensus        20 ~~i~~~n~g~~eV~ikA~G~aIskAVdvaei~k~R~~~~v~v~~I~I~se~~~~e~-G~~r~VS~IeI~L~k~   91 (91)
T 3toe_A           20 AVVTQMNGGTSEVILKARGIAISRAVDVAEIVRNRFIPDIQIENIDICTEEIIGNE-GTATNVSAIEIQLRKD   91 (91)
T ss_dssp             HHHHHHHTTCCEEEEEEETTHHHHHHHHHHHHHHHTCTTCEEEEEEEEEEEEECTT-SSEEEEEEEEEEEEC-
T ss_pred             HHHHHHhCCCCEEEEEEehhHHHHHHHHHHHHHHhccCCcEEEEEEeeeEEeecCC-CceeEeeEEEEEEECC
Confidence            3457888899999999999999999999999999999  99999999999999886 8888999999999873

>2h9u_A DNA/RNA-binding protein ALBA 2; archaea, DNA binding protein, structural G NPPSFA, national project on protein structural and function analyses; 2.00A {Aeropyrum pernix} PDB: 3u6y_A*

Probab=99.86  E-value=1.3e-21  Score=134.78  Aligned_cols=77  Identities=18%  Similarity=0.168  Sum_probs=68.6

Q ss_pred             HHHHHHHH--HHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccC--CCCc--ccccceEEEE
Q 034338            5 LVAAYLSL--QRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREE--TGGR--PVQKAKVNTL   76 (97)
Q Consensus         5 ~~~~~~la--kqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e--~rg~--~v~kskIEIv   76 (97)
                      .+.|...+  ++|+++++||.|||+|+|||+||+||||||||++  +.+++|++||+++.++  + |+  ..++|+|||+
T Consensus        16 ~~nyV~~a~~~ll~~g~~eV~ikA~G~AIskAV~vaEilk~r~~~gl~~q~i~i~s~~i~d~~e~-g~~~~r~vS~IeI~   94 (102)
T 2h9u_A           16 VMNYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFAKNIEIKDIKIDSQEIEVQTPE-GQTRTRRVSSIEIC   94 (102)
T ss_dssp             HHHHHHHHHHHHTSTTCCEEEEEEETTHHHHHHHHHHHHHHHTTTTEEEEEEEEEEEEEEEECTT-SCEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHhCCCCEEEEEEechhhhHHHHHHHHHHHhccCCceEEEEEEeeEEEeccccC-CccceeEeeeEEEE
Confidence            36677766  4777889999999999999999999999999998  8889999999999987  5 76  6789999999


Q ss_pred             Eeeecc
Q 034338           77 NIIHYK   82 (97)
Q Consensus        77 L~k~~~   82 (97)
                      |.|.|+
T Consensus        95 Lsk~~~  100 (102)
T 2h9u_A           95 LEKAGE  100 (102)
T ss_dssp             EEECSS
T ss_pred             EEccCC
Confidence            999875

>2bky_X DNA/RNA-binding protein ALBA 2; archaeal DNA binding protein, DNA condensation, DNA-binding, DNA binding protein; 1.70A {Sulfolobus solfataricus} SCOP: d.68.6.1 PDB: 2a2y_A 1udv_A

Probab=99.83  E-value=1.9e-20  Score=126.54  Aligned_cols=71  Identities=17%  Similarity=0.067  Sum_probs=61.5

Q ss_pred             HHHHHHHH-HHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEeeec
Q 034338            5 LVAAYLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHY   81 (97)
Q Consensus         5 ~~~~~~la-kqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k~~   81 (97)
                      +..|..-+ ++|+++.+||.|||+|+|||+|||||||+|+|++  +.+++|.++|++      |+..++|.|||+|.|.|
T Consensus        16 v~nYV~~~~~~ln~g~~eV~ikA~G~aIskAVdvaeilk~R~~~~~~i~~i~i~se~------~~~r~VS~IeI~L~k~~   89 (89)
T 2bky_X           16 VEDHVLDVIVLFNQGIDEVILKGTGREISKAVDVYNSLKDRLGDGVQLVNVQTGSEV------RDRRRISYILLRLKRVY   89 (89)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEEETTHHHHHHHHHHHHHHHHGGGEEEEEEEEEEEE------ETTEEEEEEEEEEEECC
T ss_pred             HHHHHHHHHHHHhCCCCEEEEEEechHHHHHHHHHHHHHHhccCceEEEEEEecccc------CcceEeeeEEEEEEecC
Confidence            34555555 8999999999999999999999999999999999  999999999986      33446889999999864

>3iab_B Ribonucleases P/MRP protein subunit POP7; RNAse P, ribonuclease P, ribonuclease MRP, POP6, POP6P, POP7, POP7P, NME1, yeast, tRNA; 2.70A {Saccharomyces cerevisiae}

Probab=97.50  E-value=0.00017  Score=52.43  Aligned_cols=44  Identities=14%  Similarity=0.249  Sum_probs=36.2

Q ss_pred             cCCeEEEeecchhhhHHHHHHHHHhhCCeEEEEEEeeeeeeeccC
Q 034338           18 QHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREE   62 (97)
Q Consensus        18 ~~~EVeLsAlG~AIS~aV~VAEILKn~~la~~KkI~TsT~~i~~e   62 (97)
                      +..||.|+|+|+||.+|+.+|=-++.++=..+ .|+|||+++-||
T Consensus        59 ~~~eV~v~GmGkAIeKal~lAl~fq~~~~~~V-~V~T~TV~vvDd  102 (140)
T 3iab_B           59 GSSYVAVLGMGKAVEKTLALGCHFQDQKNKKI-EVYTKTIEVLDE  102 (140)
T ss_dssp             TCSEEEEEEEGGGHHHHHHHHHHHHHTTCCCE-EEEEEEEEEEEE
T ss_pred             CCcEEEEEechHHHHHHHHHHHHHhhcCCEEE-EEEeceEEEEEe
Confidence            68999999999999999999999999754222 488998766543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	97
d1vm0a_	99	d.68.6.2 (A:) Hypothetical protein At2g34160 {Thal	5e-19
d1nh9a_	87	d.68.6.1 (A:) DNA-binding protein AlbA {Archaeon M	7e-10
d1nfja_	87	d.68.6.1 (A:) DNA-binding protein AlbA {Archaeon A	4e-07
d2bkya1	89	d.68.6.1 (A:9-97) DNA-binding protein AlbA {Archae	0.002

>d1vm0a_ d.68.6.2 (A:) Hypothetical protein At2g34160 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 99

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: Hypothetical protein At2g34160
domain: Hypothetical protein At2g34160
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 72.6 bits (178), Expect = 5e-19
 Identities = 47/60 (78%), Positives = 54/60 (90%)

Query: 14 RYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKV 73
          RYMQQ+N+VELSALGMAIATVVT+ EILKNNG AVEKKI TS VDI+++  GRPVQKAK+
Sbjct: 23 RYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSIVDIKDDARGRPVQKAKI 82

>d1nh9a_ d.68.6.1 (A:) DNA-binding protein AlbA {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 87

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 49.0 bits (117), Expect = 7e-10
 Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 14 RYMQQHNEVELSALGMAIATVVTIAEILKN---NGLAVEKKITTSTVDIREETGGRPV 68
            +  ++EV + A G AI   V +AE+++N     + ++K    +      +     V
Sbjct: 21 TQLTSNDEVIIKARGKAINKAVDVAEMIRNRFIKDIKIKKIEIGTDKVKNPDGREVNV 78

>d1nfja_ d.68.6.1 (A:) DNA-binding protein AlbA {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 87

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 42.0 bits (99), Expect = 4e-07
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 17 QQHNEVELSALGMAIATVVTIAEILKN---NGLAVEKKITTSTVDIREETGGRPV 68
          +  +EV + A G AI+  V +AEI++N    G+ V++    +     E+     V
Sbjct: 24 EGADEVVIKARGRAISRAVDVAEIVRNRFMPGVKVKEIKIDTEELESEQGRRSNV 78

>d2bkya1 d.68.6.1 (A:9-97) DNA-binding protein AlbA {Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287]} Length = 89

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287]

 Score = 32.0 bits (73), Expect = 0.002
 Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 7/66 (10%)

Query: 17 QQHNEVELSALGMAIATVVTIAEILKNNGLAVE---KKITTSTVDIREETGGRPVQKAKV 73
          Q  +E+ + A G AI+  V   EI++N  L  +   K+I   +  +  + G    ++++V
Sbjct: 24 QGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDG----RQSRV 79

Query: 74 NTLNII 79
          +T+ I 
Sbjct: 80 STIEIA 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	97
d1vm0a_	99	Hypothetical protein At2g34160 {Thale cress (Arabi	99.97
d1nh9a_	87	DNA-binding protein AlbA {Archaeon Methanococcus j	99.88
d1nfja_	87	DNA-binding protein AlbA {Archaeon Archaeoglobus f	99.87
d2bkya1	89	DNA-binding protein AlbA {Archaeon Sulfolobus solf	99.85
d2bkyx1	86	DNA-binding protein AlbA {Archaeon Sulfolobus solf	99.81

>d1vm0a_ d.68.6.2 (A:) Hypothetical protein At2g34160 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: Hypothetical protein At2g34160
domain: Hypothetical protein At2g34160
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.97  E-value=1.4e-31  Score=183.47  Aligned_cols=86  Identities=57%  Similarity=0.698  Sum_probs=77.3

Q ss_pred             hHHHHHHHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCeEEEEEEeeeeeeeccCCCCcccccceEEEEEeeeccc
Q 034338            4 DLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHYKI   83 (97)
Q Consensus         4 ~~~~~~~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~la~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k~~~~   83 (97)
                      .+|.|+++|+.++++++||.|||||+||++||+||||||++|++++++|+|||++++++.+|++.++|+|||+|.|||+|
T Consensus        13 P~~~YV~~a~~~l~~~~eV~l~a~G~AI~~aV~vaeil~~r~~~~i~~I~t~s~~~~~~~~gr~~~vs~IEI~L~K~~~F   92 (99)
T d1vm0a_          13 PLFFYVNLAKRYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSIVDIKDDARGRPVQKAKIEITLVKSEKF   92 (99)
T ss_dssp             CHHHHHHHHHHHHHHHSEEEEEEEGGGHHHHHHHHHHHHHTTSEEEEEEEEEEEEEC------CEEEEEEEEEEEECTTH
T ss_pred             cHHHHHHHHHHHhccCCeEEEEecHHHHHHHHHHHHHHHhcCceEEEEEEeeeEEeecCCCCcccccceEEEEEeeCccH
Confidence            37899999999999999999999999999999999999999999999999999999988889999999999999999999


Q ss_pred             ccceee
Q 034338           84 RSNYDV   89 (97)
Q Consensus        84 ~~~~~~   89 (97)
                      |+.|+.
T Consensus        93 ~~~~~~   98 (99)
T d1vm0a_          93 DELMAA   98 (99)
T ss_dssp             HHHHHH
T ss_pred             HHHhhc
Confidence            999863

>d1nh9a_ d.68.6.1 (A:) DNA-binding protein AlbA {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.88  E-value=6.7e-23  Score=137.21  Aligned_cols=75  Identities=23%  Similarity=0.325  Sum_probs=59.6

Q ss_pred             hHHHHHHHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            4 DLVAAYLSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         4 ~~~~~~~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      .++.|+..+..++++.+||.|||||+|||+|||||||+|||++  +.+++|.++++++++++ |+..++|.|||+|.|
T Consensus        11 P~m~YV~~~~~~~~~~~eV~lKArG~aIsrAVdVaEiik~R~~~~~~i~~i~i~se~~~~~~-g~~r~VS~IeI~L~k   87 (87)
T d1nh9a_          11 PVMNYVVAVLTQLTSNDEVIIKARGKAINKAVDVAEMIRNRFIKDIKIKKIEIGTDKVKNPD-GREVNVSTIEIVLAK   87 (87)
T ss_dssp             CHHHHHHHHHHHHHHCSEEEEEEEGGGHHHHHHHHHHHHHHTCTTCEEEEEEEEEEC--------CCCEEEEEEEEEC
T ss_pred             CHHHHHHHHHHHhccCCeEEEEEcchhhhHHHHHHHHHHHhccCCeEEEEEEecceEEecCC-CceeEEEEEEEEEeC
Confidence            4677887765444444999999999999999999999999887  89999999999998886 788889999999986

>d1nfja_ d.68.6.1 (A:) DNA-binding protein AlbA {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.87  E-value=2.3e-22  Score=134.20  Aligned_cols=75  Identities=24%  Similarity=0.320  Sum_probs=66.1

Q ss_pred             hHHHHHHHH-HHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338            4 DLVAAYLSL-QRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus         4 ~~~~~~~la-kqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      .++.|+..+ +||+++.+||.|||||+|||+|||||||+|||++  +.+++|.++|+.+++++ |+..++|+|||+|.|
T Consensus        10 p~~~YV~~~~~~l~~g~~eV~ikArG~aIs~AVdVaEi~k~r~~~~~~i~~i~i~se~~~~e~-g~~r~VS~IeI~L~K   87 (87)
T d1nfja_          10 PVMNYVLATLTQLNEGADEVVIKARGRAISRAVDVAEIVRNRFMPGVKVKEIKIDTEELESEQ-GRRSNVSTIEIVLAK   87 (87)
T ss_dssp             CHHHHHHHHHHHHHTTCSEEEEEEETTHHHHHHHHHHHHHHHTCTTCEEEEEEEEEEECCCBT-TBCCEEEEEEEEEEC
T ss_pred             cHHHHHHHHHHHHhCCCCEEEEEEehhHHHHHHHHHHHHHHhccCCcEEEEEEEccEEEecCC-CceeEEEEEEEEEeC
Confidence            356777666 4566689999999999999999999999999988  99999999999998886 777789999999986

>d2bkya1 d.68.6.1 (A:9-97) DNA-binding protein AlbA {Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287]

Probab=99.85  E-value=2.2e-21  Score=130.36  Aligned_cols=69  Identities=23%  Similarity=0.241  Sum_probs=63.8

Q ss_pred             HHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe---EEEEEEeeeeeeeccCCCCcccccceEEEEEee
Q 034338           10 LSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL---AVEKKITTSTVDIREETGGRPVQKAKVNTLNII   79 (97)
Q Consensus        10 ~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l---a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k   79 (97)
                      ..-+||+++.++|.|||||+|||+||||||++|+|||   ..+++|.++++++++++ |+..++|.|||.|.|
T Consensus        17 a~~~~l~~g~~~V~iKArG~aIskAVdVaEiik~R~l~~~~~i~~i~I~se~~~~~~-G~~r~VS~IeI~L~k   88 (89)
T d2bkya1          17 AALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQD-GRQSRVSTIEIAIRK   88 (89)
T ss_dssp             HHHHHHHTTCCEEEEEEETTHHHHHHHHHHHHHHHTSTTTEEEEEEEEEEEEEEETT-SCEEEEEEEEEEEEE
T ss_pred             HHHHHHhCCCCeEEEEEehhhhHHHHHHHHHHHHhcccCceEEEEEEeccEEeecCC-CcEEEEEEEEEEEEc
Confidence            3457888899999999999999999999999999998   89999999999999886 888889999999987

>d2bkyx1 d.68.6.1 (X:4-89) DNA-binding protein AlbA {Archaeon Sulfolobus solfataricus, Sso10b2 [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b2 [TaxId: 2287]

Probab=99.81  E-value=3.9e-20  Score=123.93  Aligned_cols=66  Identities=17%  Similarity=0.040  Sum_probs=58.6

Q ss_pred             HHHHHHhccCCeEEEeecchhhhHHHHHHHHHhhCCe--EEEEEEeeeeeeeccCCCCcccccceEEEEEeeec
Q 034338           10 LSLQRYMQQHNEVELSALGMAIATVVTIAEILKNNGL--AVEKKITTSTVDIREETGGRPVQKAKVNTLNIIHY   81 (97)
Q Consensus        10 ~lakqf~~~~~EVeLsAlG~AIS~aV~VAEILKn~~l--a~~KkI~TsT~~i~~e~rg~~v~kskIEIvL~k~~   81 (97)
                      ..-+||++|.+||.|+|+|+|||+|||||||+||+++  +.+++|.++|++      |+..++|.|||.|.|-|
T Consensus        19 a~i~~f~~g~~eV~iKArG~aIskAVdVaEiir~R~~~~v~i~~I~i~sE~------~~~r~VS~IeI~l~k~~   86 (86)
T d2bkyx1          19 DVIVLFNQGIDEVILKGTGREISKAVDVYNSLKDRLGDGVQLVNVQTGSEV------RDRRRISYILLRLKRVY   86 (86)
T ss_dssp             HHHHHHHTTCCEEEEEEETTHHHHHHHHHHHHHHHHGGGEEEEEEEEEEEE------ETTEEEEEEEEEEEECC
T ss_pred             HHHHHHHCCCCEEEEEEechhhHHHHHHHHHHHHhccCCeEEEEEEecccc------CCceEEEEEEEEEEecC
Confidence            3458999999999999999999999999999999998  999999999983      34447899999999864